PARADIGM pathway analysis of mRNASeq expression data
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1MG7N91
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1MG7N91
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 50 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
FOXM1 transcription factor network 191
Aurora B signaling 159
Signaling events regulated by Ret tyrosine kinase 119
HIF-1-alpha transcription factor network 117
Angiopoietin receptor Tie2-mediated signaling 105
Endothelins 102
PDGFR-alpha signaling pathway 96
Signaling events mediated by the Hedgehog family 91
p75(NTR)-mediated signaling 83
Integrins in angiogenesis 73
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 527 . 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 ( 527 ).

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
FOXM1 transcription factor network 0.3624 191 9755 51 -0.97 0.011 1000 -1000 -0.13 -1000
Aurora B signaling 0.3017 159 10682 67 -0.52 0.011 1000 -1000 -0.036 -1000
Signaling events regulated by Ret tyrosine kinase 0.2258 119 9827 82 -0.19 0.011 1000 -1000 -0.04 -1000
HIF-1-alpha transcription factor network 0.2220 117 8898 76 -0.49 0.017 1000 -1000 -0.07 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1992 105 9293 88 -0.32 0.043 1000 -1000 -0.072 -1000
Endothelins 0.1935 102 9813 96 -0.33 0.011 1000 -1000 -0.046 -1000
PDGFR-alpha signaling pathway 0.1822 96 4251 44 -0.29 0.025 1000 -1000 -0.03 -1000
Signaling events mediated by the Hedgehog family 0.1727 91 4753 52 -0.26 0.15 1000 -1000 -0.015 -1000
p75(NTR)-mediated signaling 0.1575 83 10436 125 -0.2 0.03 1000 -1000 -0.056 -1000
Integrins in angiogenesis 0.1385 73 6180 84 -0.29 0.024 1000 -1000 -0.052 -1000
Cellular roles of Anthrax toxin 0.1290 68 2663 39 -0.13 0.019 1000 -1000 -0.014 -1000
Nongenotropic Androgen signaling 0.1271 67 3496 52 -0.21 0.1 1000 -1000 -0.032 -1000
Aurora C signaling 0.1252 66 468 7 -0.29 0.01 1000 -1000 -0.021 -1000
Fc-epsilon receptor I signaling in mast cells 0.1252 66 6438 97 -0.12 0.028 1000 -1000 -0.043 -1000
S1P3 pathway 0.1233 65 2749 42 -0.41 0.016 1000 -1000 -0.02 -1000
Wnt signaling 0.1120 59 418 7 -0.089 -0.003 1000 -1000 -0.013 -1000
Signaling mediated by p38-alpha and p38-beta 0.1082 57 2519 44 -0.08 0.011 1000 -1000 -0.034 -1000
Reelin signaling pathway 0.1063 56 3146 56 -0.16 0.03 1000 -1000 -0.045 -1000
PLK1 signaling events 0.1044 55 4704 85 -0.3 0.044 1000 -1000 -0.032 -1000
Effects of Botulinum toxin 0.1025 54 1428 26 -0.11 0.018 1000 -1000 -0.036 -1000
Glypican 1 network 0.1006 53 2570 48 -0.22 0.022 1000 -1000 -0.018 -1000
LPA4-mediated signaling events 0.0987 52 635 12 -0.12 0.015 1000 -1000 -0.01 -1000
IGF1 pathway 0.0968 51 2953 57 -0.077 0.022 1000 -1000 -0.044 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0930 49 3850 78 -0.1 0.044 1000 -1000 -0.035 -1000
Aurora A signaling 0.0911 48 2934 60 -0.25 0.022 1000 -1000 -0.015 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0911 48 5787 120 -0.19 0.14 1000 -1000 -0.042 -1000
S1P5 pathway 0.0854 45 781 17 -0.099 0.032 1000 -1000 -0.012 -1000
Noncanonical Wnt signaling pathway 0.0835 44 1164 26 -0.14 0.011 1000 -1000 -0.023 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0835 44 3032 68 -0.2 0.081 1000 -1000 -0.076 -1000
TCGA08_retinoblastoma 0.0835 44 353 8 -0.13 0.024 1000 -1000 -0.01 -1000
Thromboxane A2 receptor signaling 0.0816 43 4615 105 -0.18 0.031 1000 -1000 -0.038 -1000
Plasma membrane estrogen receptor signaling 0.0778 41 3601 86 -0.15 0.066 1000 -1000 -0.045 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0759 40 1373 34 -0.039 0.011 1000 -1000 -0.015 -1000
Syndecan-1-mediated signaling events 0.0759 40 1382 34 -0.17 0.011 1000 -1000 -0.021 -1000
amb2 Integrin signaling 0.0759 40 3345 82 -0.15 0.022 1000 -1000 -0.043 -1000
BMP receptor signaling 0.0740 39 3193 81 -0.28 0.038 1000 -1000 -0.056 -1000
FOXA2 and FOXA3 transcription factor networks 0.0721 38 1793 46 -0.22 0.015 1000 -1000 -0.055 -1000
Ras signaling in the CD4+ TCR pathway 0.0683 36 615 17 -0.075 0.016 1000 -1000 -0.015 -1000
Osteopontin-mediated events 0.0664 35 1332 38 -0.12 0.014 1000 -1000 -0.054 -1000
Ephrin A reverse signaling 0.0664 35 251 7 -0.021 0 1000 -1000 -0.007 -1000
IL4-mediated signaling events 0.0664 35 3205 91 -0.52 0.26 1000 -1000 -0.12 -1000
LPA receptor mediated events 0.0626 33 3453 102 -0.14 0.029 1000 -1000 -0.049 -1000
Ephrin B reverse signaling 0.0607 32 1553 48 -0.094 0.015 1000 -1000 -0.037 -1000
TCGA08_p53 0.0588 31 222 7 -0.089 0.047 1000 -1000 -0.009 -1000
FAS signaling pathway (CD95) 0.0588 31 1457 47 -0.074 0.037 1000 -1000 -0.021 -1000
EGFR-dependent Endothelin signaling events 0.0588 31 654 21 -0.12 0.019 1000 -1000 -0.036 -1000
S1P1 pathway 0.0550 29 1046 36 -0.12 0.011 1000 -1000 -0.036 -1000
Glypican 2 network 0.0550 29 117 4 -0.014 -0.001 1000 -1000 -0.013 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0531 28 1516 54 -0.14 0.022 1000 -1000 -0.052 -1000
Visual signal transduction: Rods 0.0512 27 1437 52 -0.11 0.011 1000 -1000 -0.046 -1000
Arf6 signaling events 0.0493 26 1665 62 -0.085 0.027 1000 -1000 -0.036 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0493 26 1364 52 -0.079 0.023 1000 -1000 -0.036 -1000
TCGA08_rtk_signaling 0.0493 26 677 26 -0.15 0.023 1000 -1000 -0.01 -1000
Coregulation of Androgen receptor activity 0.0474 25 1936 76 -0.13 0.022 1000 -1000 -0.025 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0474 25 2200 85 -0.21 0.012 1000 -1000 -0.041 -1000
Syndecan-4-mediated signaling events 0.0474 25 1711 67 -0.26 0.016 1000 -1000 -0.048 -1000
Visual signal transduction: Cones 0.0455 24 917 38 -0.081 0.011 1000 -1000 -0.031 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0436 23 2890 125 -0.065 0.029 1000 -1000 -0.053 -1000
Glucocorticoid receptor regulatory network 0.0417 22 2577 114 -0.24 0.045 1000 -1000 -0.046 -1000
Calcium signaling in the CD4+ TCR pathway 0.0417 22 697 31 -0.12 0.015 1000 -1000 -0.045 -1000
IL2 signaling events mediated by STAT5 0.0417 22 485 22 -0.1 0.056 1000 -1000 -0.022 -1000
BCR signaling pathway 0.0417 22 2178 99 -0.06 0.047 1000 -1000 -0.048 -1000
S1P4 pathway 0.0417 22 561 25 -0.099 0.024 1000 -1000 -0.017 -1000
Syndecan-2-mediated signaling events 0.0398 21 1508 69 -0.1 0.028 1000 -1000 -0.014 -1000
Hedgehog signaling events mediated by Gli proteins 0.0398 21 1425 65 -0.099 0.038 1000 -1000 -0.035 -1000
Presenilin action in Notch and Wnt signaling 0.0398 21 1291 61 -0.12 0.03 1000 -1000 -0.04 -1000
Insulin Pathway 0.0398 21 1573 74 -0.13 0.03 1000 -1000 -0.047 -1000
Regulation of Androgen receptor activity 0.0398 21 1487 70 -0.22 0.023 1000 -1000 -0.055 -1000
IL6-mediated signaling events 0.0380 20 1532 75 -0.12 0.061 1000 -1000 -0.04 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0361 19 649 33 -0.16 0.034 1000 -1000 -0.021 -1000
Rapid glucocorticoid signaling 0.0342 18 363 20 -0.051 0.011 1000 -1000 -0.006 -1000
Regulation of nuclear SMAD2/3 signaling 0.0323 17 2434 136 -0.16 0.053 1000 -1000 -0.037 -1000
Signaling events mediated by PTP1B 0.0323 17 1355 76 -0.12 0.024 1000 -1000 -0.046 -1000
Nectin adhesion pathway 0.0323 17 1084 63 -0.065 0.021 1000 -1000 -0.047 -1000
Retinoic acid receptors-mediated signaling 0.0323 17 987 58 -0.052 0.022 1000 -1000 -0.043 -1000
Canonical Wnt signaling pathway 0.0323 17 879 51 -0.097 0.05 1000 -1000 -0.027 -1000
BARD1 signaling events 0.0304 16 965 57 -0.13 0.028 1000 -1000 -0.034 -1000
Class I PI3K signaling events mediated by Akt 0.0304 16 1117 68 -0.24 0.04 1000 -1000 -0.021 -1000
Regulation of p38-alpha and p38-beta 0.0304 16 917 54 -0.18 0.044 1000 -1000 -0.039 -1000
Signaling mediated by p38-gamma and p38-delta 0.0285 15 229 15 -0.017 0.021 1000 -1000 -0.012 -1000
Regulation of Telomerase 0.0285 15 1579 102 -0.3 0.038 1000 -1000 -0.068 -1000
IL12-mediated signaling events 0.0266 14 1289 87 -0.3 0.044 1000 -1000 -0.093 -1000
IL1-mediated signaling events 0.0266 14 891 62 -0.039 0.041 1000 -1000 -0.052 -1000
TCR signaling in naïve CD8+ T cells 0.0266 14 1331 93 -0.043 0.04 1000 -1000 -0.045 -1000
JNK signaling in the CD4+ TCR pathway 0.0247 13 228 17 -0.015 0.034 1000 -1000 -0.017 -1000
IFN-gamma pathway 0.0247 13 899 68 -0.22 0.048 1000 -1000 -0.05 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0247 13 1114 83 -0.24 0.044 1000 -1000 -0.042 -1000
FoxO family signaling 0.0247 13 886 64 -0.24 0.043 1000 -1000 -0.04 -1000
EPHB forward signaling 0.0247 13 1136 85 -0.034 0.03 1000 -1000 -0.051 -1000
PDGFR-beta signaling pathway 0.0247 13 1297 97 -0.021 0.039 1000 -1000 -0.045 -1000
Signaling events mediated by PRL 0.0247 13 473 34 -0.13 0.018 1000 -1000 -0.017 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0228 12 352 28 -0.099 0.032 1000 -1000 -0.02 -1000
Insulin-mediated glucose transport 0.0228 12 400 32 -0.24 0.025 1000 -1000 -0.033 -1000
Signaling events mediated by HDAC Class III 0.0228 12 499 40 -0.077 0.016 1000 -1000 -0.019 -1000
IL2 signaling events mediated by PI3K 0.0228 12 726 58 -0.11 0.042 1000 -1000 -0.046 -1000
ErbB4 signaling events 0.0209 11 810 69 -0.074 0.031 1000 -1000 -0.057 -1000
mTOR signaling pathway 0.0209 11 628 53 -0.026 0.018 1000 -1000 -0.033 -1000
HIF-2-alpha transcription factor network 0.0209 11 488 43 -0.14 0.022 1000 -1000 -0.042 -1000
Syndecan-3-mediated signaling events 0.0209 11 419 35 -0.09 0.03 1000 -1000 -0.021 -1000
Class IB PI3K non-lipid kinase events 0.0209 11 33 3 -0.003 0.003 1000 -1000 -0.005 -1000
ErbB2/ErbB3 signaling events 0.0190 10 689 65 -0.12 0.022 1000 -1000 -0.038 -1000
EPO signaling pathway 0.0152 8 469 55 -0.026 0.035 1000 -1000 -0.047 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0152 8 322 37 -0.021 0.027 1000 -1000 -0.025 -1000
IL27-mediated signaling events 0.0152 8 427 51 -0.053 0.014 1000 -1000 -0.044 -1000
Signaling events mediated by HDAC Class II 0.0133 7 536 75 -0.053 0.029 1000 -1000 -0.025 -1000
Ceramide signaling pathway 0.0133 7 599 76 -0.069 0.036 1000 -1000 -0.018 -1000
ceramide signaling pathway 0.0133 7 353 49 -0.032 0.038 1000 -1000 -0.018 -1000
IL23-mediated signaling events 0.0133 7 479 60 -0.048 0.042 1000 -1000 -0.11 -1000
p38 MAPK signaling pathway 0.0133 7 321 44 -0.046 0.028 1000 -1000 -0.037 -1000
Caspase cascade in apoptosis 0.0114 6 480 74 -0.032 0.035 1000 -1000 -0.021 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0114 6 292 45 -0.032 0.056 1000 -1000 -0.05 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0095 5 413 74 -0.074 0.062 1000 -1000 -0.047 -1000
Canonical NF-kappaB pathway 0.0076 4 170 39 -0.032 0.059 1000 -1000 -0.043 -1000
PLK2 and PLK4 events 0.0076 4 12 3 0.008 0.015 1000 -1000 -0.009 -1000
TRAIL signaling pathway 0.0076 4 197 48 -0.001 0.038 1000 -1000 -0.034 -1000
Class I PI3K signaling events 0.0076 4 344 73 -0.015 0.053 1000 -1000 -0.031 -1000
Arf6 trafficking events 0.0076 4 343 71 -0.19 0.035 1000 -1000 -0.039 -1000
Signaling events mediated by HDAC Class I 0.0057 3 354 104 -0.032 0.044 1000 -1000 -0.032 -1000
Paxillin-dependent events mediated by a4b1 0.0057 3 141 36 -0.031 0.032 1000 -1000 -0.034 -1000
a4b1 and a4b7 Integrin signaling 0.0038 2 11 5 0.009 0.015 1000 -1000 -0.01 -1000
VEGFR1 specific signals 0.0038 2 141 56 -0.063 0.052 1000 -1000 -0.022 -1000
E-cadherin signaling in keratinocytes 0.0038 2 118 43 -0.034 0.036 1000 -1000 -0.034 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0019 1 45 23 -0.004 0.036 1000 -1000 -0.027 -1000
Arf6 downstream pathway 0.0019 1 50 43 -0.023 0.023 1000 -1000 -0.023 -1000
Atypical NF-kappaB pathway 0.0019 1 37 31 0 0.04 1000 -1000 -0.016 -1000
E-cadherin signaling in the nascent adherens junction 0.0019 1 97 76 -0.003 0.048 1000 -1000 -0.047 -1000
E-cadherin signaling events 0.0019 1 7 5 0.009 0.021 1000 -1000 -0.009 -1000
Circadian rhythm pathway 0.0000 0 15 22 -0.011 0.04 1000 -1000 -0.018 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.028 1000 -1000 -0.03 -1000
Arf1 pathway 0.0000 0 8 54 0 0.028 1000 -1000 -0.021 -1000
Alternative NF-kappaB pathway 0.0000 0 2 13 0 0.033 1000 -1000 -0.01 -1000
Total NA 3914 234739 7203 -17 4.3 131000 -131000 -4.7 -131000
FOXM1 transcription factor network

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
NFATC3 -0.63 0.36 -9999 0 -0.95 232 232
PLK1 -0.15 0.087 -9999 0 -10000 0 0
BIRC5 -0.16 0.081 -9999 0 -10000 0 0
HSPA1B -0.63 0.36 -9999 0 -0.93 256 256
MAP2K1 -0.022 0.016 -9999 0 -10000 0 0
BRCA2 -0.63 0.36 -9999 0 -0.95 234 234
FOXM1 -0.76 0.48 -9999 0 -1.1 298 298
XRCC1 -0.63 0.36 -9999 0 -0.93 254 254
FOXM1B/p19 -0.68 0.4 -9999 0 -0.94 312 312
Cyclin D1/CDK4 -0.58 0.32 -9999 0 -0.86 242 242
CDC2 -0.67 0.38 -9999 0 -0.94 294 294
TGFA -0.57 0.31 -9999 0 -0.83 254 254
SKP2 -0.63 0.36 -9999 0 -0.91 273 273
CCNE1 -0.14 0.17 -9999 0 -0.34 214 214
CKS1B -0.63 0.36 -9999 0 -0.91 273 273
RB1 -0.24 0.12 -9999 0 -0.67 6 6
FOXM1C/SP1 -0.7 0.42 -9999 0 -1 291 291
AURKB -0.18 0.067 -9999 0 -10000 0 0
CENPF -0.67 0.37 -9999 0 -0.97 271 271
CDK4 -0.001 0.005 -9999 0 -10000 0 0
MYC -0.56 0.32 -9999 0 -0.81 275 275
CHEK2 -0.022 0.016 -9999 0 -10000 0 0
ONECUT1 -0.62 0.35 -9999 0 -0.88 279 279
CDKN2A -0.13 0.17 -9999 0 -0.32 219 219
LAMA4 -0.66 0.4 -9999 0 -1 252 252
FOXM1B/HNF6 -0.7 0.42 -9999 0 -1 279 279
FOS -0.77 0.48 -9999 0 -1.1 280 280
SP1 0.011 0.001 -9999 0 -10000 0 0
CDC25B -0.63 0.36 -9999 0 -0.95 236 236
response to radiation -0.03 0.014 -9999 0 -10000 0 0
CENPB -0.63 0.36 -9999 0 -0.91 273 273
CENPA -0.69 0.38 -9999 0 -0.96 293 293
NEK2 -0.69 0.37 -9999 0 -0.98 277 277
HIST1H2BA -0.64 0.36 -9999 0 -0.97 223 223
CCNA2 -0.07 0.14 -9999 0 -0.34 111 111
EP300 0.011 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.72 0.43 -9999 0 -1.1 273 273
CCNB2 -0.69 0.38 -9999 0 -0.96 292 292
CCNB1 -0.67 0.39 -9999 0 -0.98 269 269
ETV5 -0.63 0.36 -9999 0 -0.96 232 232
ESR1 -0.68 0.41 -9999 0 -1 250 250
CCND1 -0.59 0.33 -9999 0 -0.88 242 242
GSK3A -0.014 0.013 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.12 0.14 -9999 0 -0.25 257 257
CDK2 0.003 0.004 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.038 0.017 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.68 0.38 -9999 0 -0.92 324 324
GAS1 -0.97 0.48 -9999 0 -1.2 387 387
MMP2 -0.65 0.38 -9999 0 -0.94 268 268
RB1/FOXM1C -0.63 0.36 -9999 0 -0.92 258 258
CREBBP 0.009 0.026 -9999 0 -0.41 2 2
Aurora B 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
Condensin I complex -0.12 0.064 -9999 0 -0.16 62 62
STMN1 -0.18 0.076 -9999 0 -0.21 464 464
Aurora B/RasGAP/Survivin -0.28 0.12 -9999 0 -0.32 429 429
Chromosomal passenger complex/Cul3 protein complex -0.12 0.092 -9999 0 -0.29 91 91
BIRC5 -0.26 0.14 -9999 0 -0.33 410 410
DES -0.52 0.24 -9999 0 -0.63 442 442
Aurora C/Aurora B/INCENP -0.13 0.06 -9999 0 -0.22 5 5
Aurora B/TACC1 -0.19 0.11 -9999 0 -0.22 473 473
Aurora B/PP2A -0.18 0.076 -9999 0 -0.21 464 464
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.024 0.014 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition -0.004 0.003 -9999 0 -10000 0 0
NDC80 -0.2 0.095 -9999 0 -0.23 465 465
Cul3 protein complex -0.026 0.1 -9999 0 -0.23 102 102
KIF2C -0.068 0.035 -9999 0 -10000 0 0
PEBP1 0.002 0.004 -9999 0 -10000 0 0
KIF20A -0.3 0.1 -9999 0 -0.33 477 477
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.18 0.081 -9999 0 -0.21 464 464
SEPT1 0.01 0.018 -9999 0 -0.41 1 1
SMC2 0.01 0.015 -9999 0 -0.33 1 1
SMC4 0.011 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.01 0.015 -9999 0 -10000 0 0
PSMA3 0.011 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.004 0.001 -9999 0 -10000 0 0
H3F3B -0.074 0.034 -9999 0 -10000 0 0
AURKB -0.29 0.11 -9999 0 -0.33 464 464
AURKC 0.01 0.021 -9999 0 -0.33 2 2
CDCA8 -0.19 0.17 -9999 0 -0.34 307 307
cytokinesis -0.15 0.068 -9999 0 -0.25 20 20
Aurora B/Septin1 -0.13 0.079 -9999 0 -0.24 18 18
AURKA -0.091 0.16 -9999 0 -0.33 155 155
INCENP 0.004 0.004 -9999 0 -10000 0 0
KLHL13 -0.071 0.17 -9999 0 -0.41 102 102
BUB1 -0.26 0.14 -9999 0 -0.33 413 413
hSgo1/Aurora B/Survivin -0.37 0.15 -9999 0 -0.42 466 466
EVI5 0.011 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.11 0.064 -9999 0 -0.28 21 21
SGOL1 -0.25 0.14 -9999 0 -0.33 408 408
CENPA -0.1 0.05 -9999 0 -0.15 149 149
NCAPG -0.22 0.16 -9999 0 -0.33 350 350
Aurora B/HC8 Proteasome -0.18 0.076 -9999 0 -0.21 464 464
NCAPD2 0.011 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.18 0.076 -9999 0 -0.21 464 464
RHOA 0.011 0 -9999 0 -10000 0 0
NCAPH -0.25 0.14 -9999 0 -0.33 409 409
NPM1 -0.041 0.018 -9999 0 -10000 0 0
RASA1 0.007 0.041 -9999 0 -0.41 5 5
KLHL9 0.01 0.018 -9999 0 -0.41 1 1
mitotic prometaphase -0.009 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.18 0.076 -9999 0 -0.21 464 464
PPP1CC 0.011 0 -9999 0 -10000 0 0
Centraspindlin -0.13 0.071 -9999 0 -0.23 63 63
RhoA/GDP 0.008 0 -9999 0 -10000 0 0
NSUN2 -0.041 0.018 -9999 0 -10000 0 0
MYLK -0.24 0.15 -9999 0 -0.37 304 304
KIF23 -0.005 0.067 -9999 0 -0.34 21 21
VIM -0.19 0.083 -9999 0 -0.22 464 464
RACGAP1 0.007 0.021 -9999 0 -0.34 2 2
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.041 0.018 -9999 0 -10000 0 0
Chromosomal passenger complex -0.14 0.067 -9999 0 -0.18 289 289
Chromosomal passenger complex/EVI5 -0.26 0.19 -9999 0 -0.36 411 411
TACC1 -0.066 0.16 -9999 0 -0.41 96 96
PPP2R5D 0.011 0 -9999 0 -10000 0 0
CUL3 0.011 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.032 0.034 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.13 0.13 -9999 0 -0.25 258 258
JUN -0.078 0.13 -9999 0 -0.39 36 36
HRAS 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.1 0.13 -9999 0 -0.23 256 256
RAP1A 0.011 0 -9999 0 -10000 0 0
FRS2 0.011 0 -9999 0 -10000 0 0
RAP1A/GDP 0.008 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.1 0.13 -9999 0 -0.23 255 255
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.09 0.11 -9999 0 -0.21 250 250
RHOA 0.011 0 -9999 0 -10000 0 0
RAP1A/GTP -0.099 0.11 -9999 0 -0.21 169 169
GRB7 -0.011 0.084 -9999 0 -0.34 33 33
RET51/GFRalpha1/GDNF -0.1 0.13 -9999 0 -0.22 261 261
MAPKKK cascade -0.099 0.11 -9999 0 -0.37 32 32
BCAR1 0.011 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.11 0.14 -9999 0 -0.24 265 265
lamellipodium assembly -0.13 0.13 -9999 0 -0.24 258 258
RET51/GFRalpha1/GDNF/SHC -0.1 0.13 -9999 0 -0.23 255 255
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
RET9/GFRalpha1/GDNF/SHC -0.09 0.11 -9999 0 -0.21 250 250
RET9/GFRalpha1/GDNF/Shank3 -0.09 0.11 -9999 0 -0.21 250 250
MAPK3 -0.076 0.11 -9999 0 -0.34 30 30
DOK1 0.011 0 -9999 0 -10000 0 0
DOK6 -0.072 0.17 -9999 0 -0.41 104 104
PXN 0.011 0 -9999 0 -10000 0 0
neurite development -0.083 0.12 -9999 0 -0.27 94 94
DOK5 -0.03 0.12 -9999 0 -0.41 51 51
GFRA1 -0.19 0.21 -9999 0 -0.41 250 250
MAPK8 -0.085 0.13 -9999 0 -0.39 34 34
HRAS/GTP -0.11 0.12 -9999 0 -0.23 255 255
tube development -0.079 0.11 -9999 0 -0.19 249 249
MAPK1 -0.076 0.11 -9999 0 -0.34 30 30
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.082 0.11 -9999 0 -0.2 248 248
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
PDLIM7 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.13 0.16 -9999 0 -0.26 287 287
SHC1 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.1 0.13 -9999 0 -0.23 255 255
RET51/GFRalpha1/GDNF/Dok5 -0.12 0.16 -9999 0 -0.26 267 267
PRKCA -0.016 0.1 -9999 0 -0.41 34 34
HRAS/GDP 0.008 0 -9999 0 -10000 0 0
CREB1 -0.1 0.14 -9999 0 -0.25 248 248
PIK3R1 0.007 0.041 -9999 0 -0.41 5 5
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.084 0.12 -9999 0 -0.2 248 248
RET51/GFRalpha1/GDNF/Grb7 -0.11 0.14 -9999 0 -0.24 258 258
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.025 0.11 -9999 0 -0.37 49 49
DOK4 0.011 0 -9999 0 -10000 0 0
JNK cascade -0.076 0.13 -9999 0 -0.38 36 36
RET9/GFRalpha1/GDNF/FRS2 -0.09 0.11 -9999 0 -0.21 250 250
SHANK3 0.011 0 -9999 0 -10000 0 0
RASA1 0.007 0.041 -9999 0 -0.41 5 5
NCK1 0.009 0.026 -9999 0 -0.41 2 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.083 0.11 -9999 0 -0.2 248 248
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.091 0.13 -9999 0 -0.21 255 255
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.095 0.14 -9999 0 -0.22 256 256
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.095 0.14 -9999 0 -0.22 255 255
PI3K -0.17 0.21 -9999 0 -0.36 258 258
SOS1 0.011 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.079 0.11 -9999 0 -0.19 249 249
GRB10 0.01 0.018 -9999 0 -0.41 1 1
activation of MAPKK activity -0.083 0.11 -9999 0 -0.2 249 249
RET51/GFRalpha1/GDNF/FRS2 -0.1 0.13 -9999 0 -0.23 255 255
GAB1 0.008 0.037 -9999 0 -0.41 4 4
IRS1 -0.031 0.13 -9999 0 -0.41 53 53
IRS2 -0.045 0.14 -9999 0 -0.41 70 70
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.098 0.14 -9999 0 -0.23 255 255
RET51/GFRalpha1/GDNF/PKC alpha -0.12 0.15 -9999 0 -0.24 265 265
GRB2 0.011 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GDNF 0.003 0.026 -9999 0 -0.33 3 3
RAC1 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.12 0.16 -9999 0 -0.25 275 275
Rac1/GTP -0.15 0.15 -9999 0 -0.29 258 258
RET9/GFRalpha1/GDNF -0.11 0.13 -9999 0 -0.24 250 250
GFRalpha1/GDNF -0.13 0.15 -9999 0 -0.29 250 250
HIF-1-alpha transcription factor network

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
PKM2 -0.36 0.41 -9999 0 -0.85 158 158
HDAC7 0.012 0.001 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.3 0.36 -9999 0 -0.76 139 139
SMAD4 0.011 0.018 -9999 0 -0.41 1 1
ID2 -0.36 0.41 -9999 0 -0.84 164 164
AP1 -0.075 0.14 -9999 0 -0.29 160 160
ABCG2 -0.47 0.47 -9999 0 -0.92 220 220
HIF1A -0.048 0.062 -9999 0 -10000 0 0
TFF3 -0.42 0.44 -9999 0 -0.89 194 194
GATA2 -0.028 0.12 -9999 0 -0.41 50 50
AKT1 -0.061 0.084 -9999 0 -0.22 21 21
response to hypoxia -0.078 0.087 -9999 0 -0.21 75 75
MCL1 -0.36 0.41 -9999 0 -0.85 156 156
NDRG1 -0.36 0.41 -9999 0 -0.84 164 164
SERPINE1 -0.36 0.41 -9999 0 -0.85 159 159
FECH -0.36 0.41 -9999 0 -0.84 164 164
FURIN -0.36 0.41 -9999 0 -0.84 162 162
NCOA2 -0.003 0.077 -9999 0 -0.41 18 18
EP300 -0.073 0.13 -9999 0 -0.34 73 73
HMOX1 -0.36 0.41 -9999 0 -0.85 158 158
BHLHE40 -0.36 0.41 -9999 0 -0.85 158 158
BHLHE41 -0.38 0.43 -9999 0 -0.89 165 165
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.041 0.083 -9999 0 -0.3 5 5
ENG -0.025 0.085 -9999 0 -0.28 4 4
JUN 0.006 0.049 -9999 0 -0.41 7 7
RORA -0.37 0.42 -9999 0 -0.87 162 162
ABCB1 -0.35 0.5 -9999 0 -1.2 136 136
TFRC -0.36 0.41 -9999 0 -0.84 164 164
CXCR4 -0.36 0.41 -9999 0 -0.85 156 156
TF -0.37 0.42 -9999 0 -0.87 159 159
CITED2 -0.37 0.41 -9999 0 -0.85 165 165
HIF1A/ARNT -0.4 0.47 -9999 0 -0.93 171 171
LDHA -0.053 0.048 -9999 0 -10000 0 0
ETS1 -0.36 0.41 -9999 0 -0.84 163 163
PGK1 -0.36 0.41 -9999 0 -0.84 163 163
NOS2 -0.37 0.41 -9999 0 -0.85 165 165
ITGB2 -0.36 0.41 -9999 0 -0.85 156 156
ALDOA -0.36 0.41 -9999 0 -0.84 163 163
Cbp/p300/CITED2 -0.39 0.46 -9999 0 -0.95 154 154
FOS -0.12 0.19 -9999 0 -0.41 159 159
HK2 -0.37 0.41 -9999 0 -0.86 163 163
SP1 0.01 0.022 -9999 0 -10000 0 0
GCK -0.23 0.47 -9999 0 -1.4 74 74
HK1 -0.36 0.41 -9999 0 -0.84 164 164
NPM1 -0.36 0.41 -9999 0 -0.85 158 158
EGLN1 -0.36 0.41 -9999 0 -0.84 164 164
CREB1 0.017 0 -9999 0 -10000 0 0
PGM1 -0.36 0.41 -9999 0 -0.84 163 163
SMAD3 0.009 0.036 -9999 0 -0.41 4 4
EDN1 -0.14 0.24 -9999 0 -0.68 50 50
IGFBP1 -0.4 0.43 -9999 0 -0.88 175 175
VEGFA -0.25 0.32 -9999 0 -0.7 107 107
HIF1A/JAB1 -0.023 0.036 -9999 0 -10000 0 0
CP -0.4 0.43 -9999 0 -0.88 179 179
CXCL12 -0.49 0.46 -9999 0 -0.93 221 221
COPS5 0.011 0.003 -9999 0 -10000 0 0
SMAD3/SMAD4 0.015 0.029 -9999 0 -0.28 5 5
BNIP3 -0.36 0.41 -9999 0 -0.84 164 164
EGLN3 -0.36 0.41 -9999 0 -0.85 157 157
CA9 -0.44 0.44 -9999 0 -0.87 212 212
TERT -0.41 0.43 -9999 0 -0.89 182 182
ENO1 -0.36 0.41 -9999 0 -0.85 157 157
PFKL -0.36 0.41 -9999 0 -0.84 164 164
NCOA1 0.01 0.018 -9999 0 -0.41 1 1
ADM -0.37 0.41 -9999 0 -0.85 166 166
ARNT -0.048 0.062 -9999 0 -10000 0 0
HNF4A -0.049 0.12 -9999 0 -0.34 77 77
ADFP -0.37 0.4 -9999 0 -0.83 171 171
SLC2A1 -0.25 0.32 -9999 0 -0.69 109 109
LEP -0.37 0.41 -9999 0 -0.84 164 164
HIF1A/ARNT/Cbp/p300 -0.32 0.37 -9999 0 -0.78 148 148
EPO -0.22 0.29 -9999 0 -0.78 48 48
CREBBP -0.075 0.14 -9999 0 -0.34 74 74
HIF1A/ARNT/Cbp/p300/HDAC7 -0.3 0.36 -9999 0 -0.77 132 132
PFKFB3 -0.36 0.41 -9999 0 -0.85 156 156
NT5E -0.4 0.43 -9999 0 -0.88 178 178
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 -0.2 0.44 -10000 0 -0.83 165 165
NCK1/PAK1/Dok-R -0.12 0.19 -10000 0 -0.4 165 165
NCK1/Dok-R -0.27 0.51 -10000 0 -0.99 165 165
PIK3CA 0.011 0.018 -10000 0 -0.41 1 1
mol:beta2-estradiol 0.043 0.095 0.23 106 -10000 0 106
RELA 0.011 0 -10000 0 -10000 0 0
SHC1 0.011 0.002 -10000 0 -10000 0 0
Rac/GDP 0.008 0 -10000 0 -10000 0 0
F2 0.025 0.14 0.25 106 -0.34 39 145
TNIP2 0.011 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.29 0.44 -10000 0 -0.92 165 165
FN1 0.007 0.041 -10000 0 -0.41 5 5
PLD2 -0.28 0.53 -10000 0 -1 165 165
PTPN11 0.011 0 -10000 0 -10000 0 0
GRB14 -0.11 0.16 -10000 0 -0.33 191 191
ELK1 -0.24 0.47 -10000 0 -0.93 165 165
GRB7 -0.011 0.084 -10000 0 -0.34 33 33
PAK1 0.011 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.3 0.47 -10000 0 -0.97 165 165
CDKN1A -0.11 0.3 -10000 0 -0.59 124 124
ITGA5 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.27 0.51 -10000 0 -0.99 165 165
CRK 0.011 0 -10000 0 -10000 0 0
mol:NO -0.13 0.33 -10000 0 -0.62 165 165
PLG -0.3 0.53 -10000 0 -1 165 165
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.22 0.4 -10000 0 -0.8 165 165
GRB2 0.011 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
ANGPT2 -0.06 0.2 -10000 0 -0.51 48 48
BMX -0.3 0.54 -10000 0 -1.1 165 165
ANGPT1 -0.23 0.48 -10000 0 -1.2 106 106
tube development -0.13 0.34 -10000 0 -0.61 164 164
ANGPT4 0.001 0.042 -10000 0 -0.38 6 6
response to hypoxia -0.018 0.032 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.32 0.56 -10000 0 -1.1 165 165
alpha5/beta1 Integrin 0.016 0 -10000 0 -10000 0 0
FGF2 -0.22 0.21 -10000 0 -0.41 284 284
STAT5A (dimer) -0.15 0.38 -10000 0 -0.69 162 162
mol:L-citrulline -0.13 0.33 -10000 0 -0.62 165 165
AGTR1 -0.083 0.17 -10000 0 -0.41 116 116
MAPK14 -0.28 0.54 -10000 0 -1 165 165
Tie2/SHP2 -0.21 0.4 -10000 0 -1.1 91 91
TEK -0.21 0.46 -10000 0 -1.2 91 91
RPS6KB1 -0.19 0.42 -10000 0 -0.8 165 165
Angiotensin II/AT1 -0.056 0.12 -10000 0 -0.28 116 116
Tie2/Ang1/GRB2 -0.29 0.55 -10000 0 -1.1 165 165
MAPK3 -0.25 0.48 -10000 0 -0.94 165 165
MAPK1 -0.25 0.48 -10000 0 -0.94 165 165
Tie2/Ang1/GRB7 -0.3 0.55 -10000 0 -1.1 165 165
NFKB1 0.01 0.018 -10000 0 -0.41 1 1
MAPK8 -0.28 0.53 -10000 0 -1 165 165
PI3K -0.24 0.5 -10000 0 -0.96 165 165
FES -0.28 0.54 -10000 0 -1 165 165
Crk/Dok-R -0.27 0.51 -10000 0 -0.99 165 165
Tie2/Ang1/ABIN2 -0.29 0.55 -10000 0 -1.1 165 165
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.17 0.39 -10000 0 -0.74 165 165
STAT5A 0.01 0.018 -10000 0 -0.41 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.19 0.42 -10000 0 -0.8 165 165
Tie2/Ang2 -0.2 0.45 -10000 0 -0.82 164 164
Tie2/Ang1 -0.31 0.58 -10000 0 -1.1 165 165
FOXO1 -0.17 0.4 -10000 0 -0.75 165 165
ELF1 -0.005 0.051 -10000 0 -0.43 3 3
ELF2 -0.28 0.53 -10000 0 -1 165 165
mol:Choline -0.27 0.5 -10000 0 -0.98 165 165
cell migration -0.071 0.1 -10000 0 -0.22 165 165
FYN -0.16 0.38 -10000 0 -0.69 164 164
DOK2 0.008 0.031 -10000 0 -0.35 4 4
negative regulation of cell cycle -0.096 0.28 -10000 0 -0.54 124 124
ETS1 -0.031 0.095 -10000 0 -0.22 104 104
PXN -0.15 0.35 -10000 0 -0.66 165 165
ITGB1 0.011 0 -10000 0 -10000 0 0
NOS3 -0.16 0.37 -10000 0 -0.7 165 165
RAC1 0.011 0 -10000 0 -10000 0 0
TNF -0.074 0.15 -10000 0 -0.28 162 162
MAPKKK cascade -0.27 0.5 -10000 0 -0.98 165 165
RASA1 0.007 0.041 -10000 0 -0.41 5 5
Tie2/Ang1/Shc -0.29 0.55 -10000 0 -1.1 165 165
NCK1 0.009 0.026 -10000 0 -0.41 2 2
vasculogenesis -0.11 0.3 -10000 0 -0.55 165 165
mol:Phosphatidic acid -0.27 0.5 -10000 0 -0.98 165 165
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.13 0.33 -10000 0 -0.62 165 165
Rac1/GTP -0.23 0.35 -10000 0 -0.75 165 165
MMP2 -0.29 0.54 -10000 0 -1 165 165
Endothelins

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
AKT1 -0.091 0.2 -10000 0 -0.39 113 113
PTK2B 0.011 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.12 0.31 -10000 0 -0.8 78 78
EDN1 -0.002 0.09 -10000 0 -0.39 11 11
EDN3 -0.098 0.17 -10000 0 -0.36 153 153
EDN2 -0.044 0.12 -10000 0 -0.33 84 84
HRAS/GDP -0.12 0.21 -10000 0 -0.41 135 135
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.085 0.18 -10000 0 -0.36 123 123
ADCY4 -0.11 0.2 -10000 0 -0.39 135 135
ADCY5 -0.14 0.2 -10000 0 -0.4 156 156
ADCY6 -0.11 0.18 -10000 0 -0.37 131 131
ADCY7 -0.11 0.18 -10000 0 -0.37 131 131
ADCY1 -0.12 0.2 -10000 0 -0.39 139 139
ADCY2 -0.22 0.23 -10000 0 -0.46 202 202
ADCY3 -0.11 0.19 -10000 0 -0.37 131 131
ADCY8 -0.11 0.18 -10000 0 -0.38 131 131
ADCY9 -0.13 0.22 -10000 0 -0.42 153 153
arachidonic acid secretion -0.17 0.28 -10000 0 -0.46 209 209
ETB receptor/Endothelin-1/Gq/GTP -0.068 0.15 -10000 0 -0.32 110 110
GNAO1 -0.099 0.18 -10000 0 -0.41 138 138
HRAS 0.009 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.059 0.21 -10000 0 -0.36 113 113
ETA receptor/Endothelin-1/Gs/GTP -0.089 0.22 -10000 0 -0.4 131 131
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.099 0.22 -10000 0 -0.49 83 83
EDNRB -0.085 0.18 -10000 0 -0.41 122 122
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.13 0.26 -10000 0 -0.56 114 114
CYSLTR1 -0.096 0.21 -10000 0 -0.44 101 101
SLC9A1 -0.059 0.11 -10000 0 -0.23 114 114
mol:GDP -0.13 0.23 -10000 0 -0.44 137 137
SLC9A3 -0.14 0.31 -10000 0 -0.62 131 131
RAF1 -0.16 0.24 -10000 0 -0.42 197 197
JUN -0.1 0.26 -10000 0 -0.67 73 73
JAK2 -0.095 0.2 -10000 0 -0.4 118 118
mol:IP3 -0.09 0.18 -10000 0 -0.4 94 94
ETA receptor/Endothelin-1 -0.087 0.26 -10000 0 -0.43 140 140
PLCB1 0.006 0.032 -10000 0 -0.41 3 3
PLCB2 0.008 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.16 0.19 -10000 0 -0.33 274 274
FOS -0.28 0.42 -10000 0 -0.87 172 172
Gai/GDP -0.18 0.34 -10000 0 -0.73 139 139
CRK 0.011 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.14 0.25 -10000 0 -0.48 145 145
BCAR1 0.011 0 -10000 0 -10000 0 0
PRKCB1 -0.091 0.17 -10000 0 -0.38 100 100
GNAQ 0.007 0.027 -10000 0 -0.41 2 2
GNAZ -0.001 0.07 -10000 0 -0.41 15 15
GNAL -0.051 0.15 -10000 0 -0.41 77 77
Gs family/GDP -0.16 0.2 -10000 0 -0.42 163 163
ETA receptor/Endothelin-1/Gq/GTP -0.098 0.21 -10000 0 -0.43 111 111
MAPK14 -0.051 0.13 -10000 0 -0.31 73 73
TRPC6 -0.14 0.34 -10000 0 -0.86 78 78
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 0.005 0.052 -10000 0 -0.41 8 8
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.06 0.14 -10000 0 -0.3 93 93
ETB receptor/Endothelin-2 -0.086 0.15 -10000 0 -0.29 180 180
ETB receptor/Endothelin-3 -0.12 0.16 -10000 0 -0.28 246 246
ETB receptor/Endothelin-1 -0.057 0.15 -10000 0 -0.3 129 129
MAPK3 -0.25 0.38 -10000 0 -0.74 183 183
MAPK1 -0.25 0.38 -10000 0 -0.74 182 182
Rac1/GDP -0.12 0.21 -10000 0 -0.41 134 134
cAMP biosynthetic process -0.19 0.24 -10000 0 -0.44 212 212
MAPK8 -0.13 0.3 -10000 0 -0.73 82 82
SRC 0.011 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.087 0.17 -10000 0 -0.34 119 119
p130Cas/CRK/Src/PYK2 -0.11 0.23 -10000 0 -0.53 96 96
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.12 0.21 -10000 0 -0.41 134 134
COL1A2 -0.13 0.25 -10000 0 -0.52 120 120
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.13 0.18 -10000 0 -0.32 219 219
mol:DAG -0.09 0.18 -10000 0 -0.4 94 94
MAP2K2 -0.2 0.3 -10000 0 -0.56 190 190
MAP2K1 -0.2 0.3 -10000 0 -0.55 191 191
EDNRA -0.13 0.24 -10000 0 -0.47 162 162
positive regulation of muscle contraction -0.072 0.17 -10000 0 -0.34 113 113
Gq family/GDP -0.13 0.19 -10000 0 -0.44 107 107
HRAS/GTP -0.12 0.21 -10000 0 -0.42 132 132
PRKCH -0.086 0.18 -10000 0 -0.42 80 80
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCA -0.098 0.19 -10000 0 -0.43 94 94
PRKCB -0.097 0.19 -10000 0 -0.43 92 92
PRKCE -0.084 0.17 -10000 0 -0.41 78 78
PRKCD -0.086 0.17 -10000 0 -0.42 79 79
PRKCG -0.11 0.18 -10000 0 -0.41 102 102
regulation of vascular smooth muscle contraction -0.33 0.5 -10000 0 -1 171 171
PRKCQ -0.1 0.18 -10000 0 -0.4 108 108
PLA2G4A -0.19 0.31 -10000 0 -0.51 209 209
GNA14 -0.034 0.13 -10000 0 -0.41 53 53
GNA15 0.004 0.04 -10000 0 -0.34 7 7
GNA12 0.011 0 -10000 0 -10000 0 0
GNA11 0 0.061 -10000 0 -0.41 11 11
Rac1/GTP -0.059 0.21 -10000 0 -0.36 113 113
MMP1 -0.05 0.15 0.27 7 -10000 0 7
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 -0.12 0.19 -9999 0 -0.43 145 145
PDGF/PDGFRA/CRKL -0.07 0.13 -9999 0 -0.28 145 145
positive regulation of JUN kinase activity -0.037 0.099 -9999 0 -0.2 145 145
CRKL 0.011 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.077 0.13 -9999 0 -0.29 146 146
AP1 -0.29 0.39 -9999 0 -0.87 159 159
mol:IP3 -0.08 0.14 -9999 0 -0.3 145 145
PLCG1 -0.08 0.14 -9999 0 -0.3 145 145
PDGF/PDGFRA/alphaV Integrin -0.07 0.13 -9999 0 -0.28 145 145
RAPGEF1 0.011 0 -9999 0 -10000 0 0
CRK 0.011 0 -9999 0 -10000 0 0
mol:Ca2+ -0.08 0.14 -9999 0 -0.3 145 145
CAV3 0.002 0.015 -9999 0 -0.33 1 1
CAV1 -0.063 0.16 -9999 0 -0.41 93 93
SHC/Grb2/SOS1 -0.036 0.099 -9999 0 -0.2 145 145
PDGF/PDGFRA/Shf -0.073 0.14 -9999 0 -0.29 147 147
FOS -0.27 0.4 -9999 0 -0.86 159 159
JUN -0.025 0.045 -9999 0 -0.34 7 7
oligodendrocyte development -0.07 0.13 -9999 0 -0.28 145 145
GRB2 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.041 -9999 0 -0.41 5 5
mol:DAG -0.08 0.14 -9999 0 -0.3 145 145
PDGF/PDGFRA -0.12 0.19 -9999 0 -0.43 145 145
actin cytoskeleton reorganization -0.07 0.13 -9999 0 -0.28 145 145
SRF 0.025 0.011 -9999 0 -10000 0 0
SHC1 0.011 0 -9999 0 -10000 0 0
PI3K -0.052 0.11 -9999 0 -0.23 148 148
PDGF/PDGFRA/Crk/C3G -0.049 0.11 -9999 0 -0.23 145 145
JAK1 -0.069 0.14 -9999 0 -0.29 145 145
ELK1/SRF -0.042 0.11 -9999 0 -0.22 145 145
SHB 0.011 0 -9999 0 -10000 0 0
SHF 0.005 0.048 -9999 0 -0.41 7 7
CSNK2A1 0.021 0.024 -9999 0 -10000 0 0
GO:0007205 -0.09 0.16 -9999 0 -0.34 145 145
SOS1 0.011 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.037 0.099 -9999 0 -0.2 145 145
PDGF/PDGFRA/SHB -0.07 0.13 -9999 0 -0.28 145 145
PDGF/PDGFRA/Caveolin-1 -0.12 0.19 -9999 0 -0.36 186 186
ITGAV 0.011 0 -9999 0 -10000 0 0
ELK1 -0.081 0.14 -9999 0 -0.3 145 145
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
PDGF/PDGFRA/Crk -0.07 0.13 -9999 0 -0.28 145 145
JAK-STAT cascade -0.069 0.14 -9999 0 -0.29 145 145
cell proliferation -0.073 0.14 -9999 0 -0.29 147 147
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.056 0.18 -10000 0 -0.59 37 37
IHH -0.13 0.2 -10000 0 -0.39 184 184
SHH Np/Cholesterol/GAS1 -0.15 0.13 -10000 0 -0.23 349 349
LRPAP1 0.011 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.15 0.13 0.23 349 -10000 0 349
SMO/beta Arrestin2 -0.052 0.16 -10000 0 -0.3 132 132
SMO -0.061 0.16 -10000 0 -0.32 133 133
AKT1 -0.018 0.096 -10000 0 -0.44 7 7
ARRB2 0.011 0 -10000 0 -10000 0 0
BOC -0.003 0.077 -10000 0 -0.41 18 18
ADRBK1 0.011 0 -10000 0 -10000 0 0
heart looping -0.06 0.16 -10000 0 -0.32 133 133
STIL -0.049 0.12 -10000 0 -0.34 33 33
DHH N/PTCH2 -0.023 0.1 -10000 0 -0.3 66 66
DHH N/PTCH1 -0.06 0.14 -10000 0 -0.35 52 52
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
DHH -0.023 0.11 -10000 0 -0.41 41 41
PTHLH -0.07 0.21 -10000 0 -0.65 37 37
determination of left/right symmetry -0.06 0.16 -10000 0 -0.32 133 133
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
skeletal system development -0.07 0.21 -10000 0 -0.64 37 37
IHH N/Hhip -0.08 0.13 -10000 0 -0.26 154 154
DHH N/Hhip -0.024 0.098 -10000 0 -0.26 74 74
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.06 0.16 -10000 0 -0.32 133 133
pancreas development -0.013 0.088 -10000 0 -0.34 35 35
HHAT 0.008 0.037 -10000 0 -0.41 4 4
PI3K 0.013 0.031 -10000 0 -0.28 6 6
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.26 0.2 -10000 0 -0.41 338 338
somite specification -0.06 0.16 -10000 0 -0.32 133 133
SHH Np/Cholesterol/PTCH1 -0.052 0.12 -10000 0 -0.34 30 30
SHH Np/Cholesterol/PTCH2 -0.017 0.08 -10000 0 -0.18 96 96
SHH Np/Cholesterol/Megalin -0.068 0.1 -10000 0 -0.18 232 232
SHH -0.015 0.082 -10000 0 -0.22 71 71
catabolic process -0.055 0.14 -10000 0 -0.26 148 148
SMO/Vitamin D3 -0.049 0.14 -10000 0 -0.4 28 28
SHH Np/Cholesterol/Hhip -0.018 0.075 -10000 0 -0.17 102 102
LRP2 -0.11 0.16 -10000 0 -0.33 188 188
receptor-mediated endocytosis -0.076 0.14 -10000 0 -0.32 78 78
SHH Np/Cholesterol/BOC -0.012 0.074 -10000 0 -0.17 86 86
SHH Np/Cholesterol/CDO -0.03 0.097 -10000 0 -0.2 117 117
mesenchymal cell differentiation 0.018 0.075 0.17 102 -10000 0 102
mol:Vitamin D3 -0.042 0.12 -10000 0 -0.34 30 30
IHH N/PTCH2 -0.079 0.14 -10000 0 -0.28 143 143
CDON -0.036 0.13 -10000 0 -0.41 59 59
IHH N/PTCH1 -0.035 0.15 -10000 0 -0.26 148 148
Megalin/LRPAP1 -0.068 0.11 -10000 0 -0.22 188 188
PTCH2 -0.012 0.096 -10000 0 -0.41 29 29
SHH Np/Cholesterol -0.012 0.061 -10000 0 -0.16 71 71
PTCH1 -0.055 0.14 -10000 0 -0.26 148 148
HHIP -0.013 0.089 -10000 0 -0.34 35 35
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.016 0 -10000 0 -10000 0 0
Necdin/E2F1 -0.17 0.18 -10000 0 -0.31 294 294
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.085 0.15 -10000 0 -0.38 64 64
NGF (dimer)/p75(NTR)/BEX1 -0.16 0.2 -10000 0 -0.33 271 271
NT-4/5 (dimer)/p75(NTR) -0.094 0.14 -10000 0 -0.28 195 195
IKBKB 0.011 0 -10000 0 -10000 0 0
AKT1 -0.085 0.14 -10000 0 -0.38 64 64
IKBKG 0.011 0 -10000 0 -10000 0 0
BDNF -0.043 0.12 -10000 0 -0.33 83 83
MGDIs/NGR/p75(NTR)/LINGO1 -0.064 0.12 -10000 0 -0.23 176 176
FURIN 0.011 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.091 0.12 -10000 0 -0.24 175 175
LINGO1 0.006 0.04 -10000 0 -0.34 7 7
Sortilin/TRAF6/NRIF -0.002 0.017 -10000 0 -10000 0 0
proBDNF (dimer) -0.043 0.12 -10000 0 -0.33 83 83
NTRK1 0.001 0.059 -10000 0 -0.37 13 13
RTN4R 0.01 0.018 -10000 0 -0.41 1 1
neuron apoptosis -0.092 0.14 -10000 0 -0.35 69 69
IRAK1 0.011 0 -10000 0 -10000 0 0
SHC1 -0.11 0.17 -10000 0 -0.29 227 227
ARHGDIA 0.011 0 -10000 0 -10000 0 0
RhoA/GTP 0.008 0 -10000 0 -10000 0 0
Gamma Secretase 0.03 0.024 -10000 0 -0.18 7 7
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.15 0.19 -10000 0 -0.29 287 287
MAGEH1 -0.092 0.18 -10000 0 -0.41 129 129
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.2 0.2 -10000 0 -0.32 347 347
Mammalian IAPs/DIABLO 0.024 0.03 -10000 0 -0.2 8 8
proNGF (dimer) -0.08 0.17 -10000 0 -0.41 114 114
MAGED1 0.009 0.026 -10000 0 -0.41 2 2
APP 0.011 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.006 0.07 -10000 0 -0.33 23 23
ZNF274 0.011 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.089 0.14 -10000 0 -0.24 227 227
NGF -0.08 0.17 -10000 0 -0.41 114 114
cell cycle arrest -0.079 0.13 0.14 41 -0.36 62 103
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.09 0.15 -10000 0 -0.37 71 71
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.071 0.12 -10000 0 -0.23 176 176
NCSTN 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.12 0.17 -10000 0 -0.29 231 231
PSENEN 0.011 0 -10000 0 -10000 0 0
mol:ceramide -0.095 0.15 -10000 0 -0.38 71 71
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.071 0.13 -10000 0 -0.34 62 62
p75(NTR)/beta APP -0.083 0.14 -10000 0 -0.28 176 176
BEX1 -0.074 0.17 -10000 0 -0.41 107 107
mol:GDP -0.12 0.17 -10000 0 -0.29 228 228
NGF (dimer) -0.077 0.14 -10000 0 -0.25 170 170
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.05 0.11 -10000 0 -0.2 176 176
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
RAC1/GTP -0.095 0.14 -10000 0 -0.25 227 227
MYD88 0.011 0 -10000 0 -10000 0 0
CHUK 0.011 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.12 0.17 -10000 0 -0.29 231 231
RHOB 0.009 0.026 -10000 0 -0.41 2 2
RHOA 0.011 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.028 0.092 -10000 0 -0.22 100 100
NT3 (dimer) -0.017 0.1 -10000 0 -0.4 36 36
TP53 -0.056 0.1 -10000 0 -0.31 11 11
PRDM4 -0.095 0.15 -10000 0 -0.26 227 227
BDNF (dimer) -0.087 0.14 -10000 0 -0.3 109 109
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
SORT1 0.011 0 -10000 0 -10000 0 0
activation of caspase activity -0.1 0.13 -10000 0 -0.38 64 64
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.095 0.15 -10000 0 -0.26 227 227
RHOC 0.011 0 -10000 0 -10000 0 0
XIAP 0.011 0 -10000 0 -10000 0 0
MAPK10 -0.13 0.18 -10000 0 -0.4 125 125
DIABLO 0.011 0 -10000 0 -10000 0 0
SMPD2 -0.095 0.15 -10000 0 -0.38 71 71
APH1B 0.005 0.048 -10000 0 -0.41 7 7
APH1A 0.011 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.11 0.17 -10000 0 -0.29 227 227
PSEN1 0.011 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.016 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.1 0.16 -10000 0 -0.3 198 198
MAPK8 -0.094 0.15 -10000 0 -0.36 76 76
MAPK9 -0.092 0.15 -10000 0 -0.36 74 74
APAF1 0.011 0 -10000 0 -10000 0 0
NTF3 -0.017 0.1 -10000 0 -0.4 36 36
NTF4 -0.006 0.07 -10000 0 -0.33 23 23
NDN -0.19 0.21 -10000 0 -0.41 257 257
RAC1/GDP 0.008 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.094 0.12 -10000 0 -0.35 64 64
p75 CTF/Sortilin/TRAF6/NRIF 0.028 0 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.11 0.17 -10000 0 -0.29 231 231
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.064 0.11 -10000 0 -0.34 11 11
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.075 0.11 -10000 0 -0.21 175 175
PRKACB 0.006 0.045 -10000 0 -0.41 6 6
proBDNF (dimer)/p75 ECD -0.021 0.085 -10000 0 -0.22 83 83
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.003 0.055 -10000 0 -0.39 10 10
BIRC2 0.011 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.19 0.2 0.15 18 -0.36 255 273
BAD -0.11 0.16 -10000 0 -0.37 101 101
RIPK2 0.011 0 -10000 0 -10000 0 0
NGFR -0.13 0.2 -10000 0 -0.41 176 176
CYCS -0.084 0.14 -10000 0 -0.38 62 62
ADAM17 0.011 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.095 0.15 -10000 0 -0.26 227 227
BCL2L11 -0.11 0.16 -10000 0 -0.35 118 118
BDNF (dimer)/p75(NTR) -0.12 0.15 -10000 0 -0.27 248 248
PI3K -0.097 0.15 -10000 0 -0.26 231 231
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.095 0.15 -10000 0 -0.41 62 62
NDNL2 0.011 0 -10000 0 -10000 0 0
YWHAE 0.011 0 -10000 0 -10000 0 0
PRKCI 0.011 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.14 0.19 -10000 0 -0.35 228 228
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.095 0.15 -10000 0 -0.26 229 229
TRAF6 0.011 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.024 -10000 0 -0.37 2 2
PLG -0.03 0.12 -10000 0 -0.4 50 50
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.12 0.16 -10000 0 -0.3 180 180
SQSTM1 0.011 0 -10000 0 -10000 0 0
NGFRAP1 0.006 0.045 -10000 0 -0.41 6 6
CASP3 -0.1 0.16 -10000 0 -0.33 118 118
E2F1 -0.054 0.13 -10000 0 -0.33 100 100
CASP9 0.011 0 -10000 0 -10000 0 0
IKK complex -0.094 0.13 -10000 0 -0.3 120 120
NGF (dimer)/TRKA -0.055 0.13 -10000 0 -0.28 125 125
MMP7 -0.057 0.14 -10000 0 -0.36 96 96
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.083 0.14 -10000 0 -0.38 62 62
MMP3 -0.051 0.13 -10000 0 -0.33 94 94
APAF-1/Caspase 9 -0.072 0.094 -10000 0 -0.28 63 63
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 -0.001 0.07 -9999 0 -0.28 31 31
alphaV beta3 Integrin -0.15 0.16 -9999 0 -0.28 309 309
PTK2 -0.13 0.19 -9999 0 -0.41 127 127
IGF1R -0.006 0.082 -9999 0 -0.41 21 21
PI4KB 0.011 0 -9999 0 -10000 0 0
MFGE8 0.009 0.026 -9999 0 -0.41 2 2
SRC 0.011 0 -9999 0 -10000 0 0
CDKN1B -0.14 0.21 -9999 0 -0.58 86 86
VEGFA 0.011 0 -9999 0 -10000 0 0
ILK -0.12 0.18 -9999 0 -0.55 69 69
ROCK1 0.011 0 -9999 0 -10000 0 0
AKT1 -0.1 0.17 -9999 0 -0.51 69 69
PTK2B -0.019 0.1 -9999 0 -0.38 16 16
alphaV/beta3 Integrin/JAM-A -0.15 0.16 -9999 0 -0.36 140 140
CBL 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.027 0.097 -9999 0 -0.23 97 97
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.045 0.14 -9999 0 -0.26 134 134
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.038 0.11 -9999 0 -0.36 29 29
alphaV/beta3 Integrin/Syndecan-1 -0.078 0.12 -9999 0 -0.25 95 95
PI4KA 0.011 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.18 0.18 -9999 0 -0.42 151 151
PI4 Kinase 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
alphaV/beta3 Integrin/Osteopontin -0.077 0.12 -9999 0 -0.25 95 95
RPS6KB1 -0.15 0.18 -9999 0 -0.39 151 151
TLN1 0.011 0 -9999 0 -10000 0 0
MAPK3 -0.29 0.28 -9999 0 -0.5 308 308
GPR124 -0.09 0.18 -9999 0 -0.41 126 126
MAPK1 -0.29 0.28 -9999 0 -0.5 308 308
PXN 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.041 -9999 0 -0.41 5 5
alphaV/beta3 Integrin/Tumstatin -0.051 0.12 -9999 0 -0.24 144 144
cell adhesion -0.032 0.094 -9999 0 -0.23 94 94
ANGPTL3 0.004 0.021 -9999 0 -0.33 2 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.008 0.059 -9999 0 -0.23 31 31
IGF-1R heterotetramer -0.006 0.082 -9999 0 -0.41 21 21
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
TGFBR2 0.001 0.065 -9999 0 -0.41 13 13
ITGB3 -0.065 0.16 -9999 0 -0.41 96 96
IGF1 -0.069 0.16 -9999 0 -0.41 100 100
RAC1 0.011 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.081 0.15 -9999 0 -0.27 182 182
apoptosis 0.011 0 -9999 0 -10000 0 0
CD47 0.011 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.023 0.096 -9999 0 -0.23 94 94
VCL 0.011 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.07 0.15 -9999 0 -0.28 161 161
CSF1 0.003 0.057 -9999 0 -0.41 10 10
PIK3C2A -0.12 0.18 -9999 0 -0.55 69 69
PI4 Kinase/Pyk2 -0.14 0.14 -9999 0 -0.35 125 125
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.026 0.11 -9999 0 -0.23 110 110
FAK1/Vinculin -0.097 0.15 -9999 0 -0.34 115 115
alphaV beta3/Integrin/ppsTEM5 -0.081 0.15 -9999 0 -0.28 182 182
RHOA 0.011 0 -9999 0 -10000 0 0
VTN -0.047 0.14 -9999 0 -0.41 72 72
BCAR1 0.011 0 -9999 0 -10000 0 0
FGF2 -0.22 0.21 -9999 0 -0.41 284 284
F11R -0.14 0.15 -9999 0 -0.28 285 285
alphaV/beta3 Integrin/Lactadherin -0.024 0.099 -9999 0 -0.23 94 94
alphaV/beta3 Integrin/TGFBR2 -0.029 0.11 -9999 0 -0.25 99 99
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.024 0.031 -9999 0 -0.2 10 10
HSP90AA1 0.011 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.02 0.087 -9999 0 -0.2 94 94
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.007 0.041 -9999 0 -0.41 5 5
alphaV/beta3 Integrin/Pyk2 -0.018 0.1 -9999 0 -0.38 16 16
SDC1 -0.086 0.15 -9999 0 -0.33 150 150
VAV3 -0.012 0.074 -9999 0 -0.34 1 1
PTPN11 0.011 0 -9999 0 -10000 0 0
IRS1 -0.031 0.13 -9999 0 -0.41 53 53
FAK1/Paxillin -0.097 0.15 -9999 0 -0.34 115 115
cell migration -0.084 0.14 -9999 0 -0.31 114 114
ITGAV 0.011 0 -9999 0 -10000 0 0
PI3K -0.14 0.14 -9999 0 -0.36 116 116
SPP1 -0.085 0.15 -9999 0 -0.33 148 148
KDR -0.014 0.099 -9999 0 -0.41 31 31
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.011 0 -9999 0 -10000 0 0
COL4A3 -0.038 0.13 -9999 0 -0.39 63 63
angiogenesis -0.29 0.28 -9999 0 -0.5 309 309
Rac1/GTP -0.005 0.068 -9999 0 -0.3 1 1
EDIL3 -0.071 0.17 -9999 0 -0.41 102 102
cell proliferation -0.029 0.11 -9999 0 -0.25 99 99
Cellular roles of Anthrax toxin

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
ANTXR1 -0.004 0.079 -10000 0 -0.41 19 19
ANTXR2 -0.13 0.2 -10000 0 -0.41 173 173
negative regulation of myeloid dendritic cell antigen processing and presentation -0.019 0.028 -10000 0 -0.058 177 177
monocyte activation -0.029 0.11 -10000 0 -0.41 41 41
MAP2K2 -0.007 0.011 -10000 0 -10000 0 0
MAP2K1 -0.016 0.023 -10000 0 -10000 0 0
MAP2K7 -0.016 0.023 -10000 0 -10000 0 0
MAP2K6 -0.035 0.054 -10000 0 -0.17 66 66
CYAA -0.064 0.11 -10000 0 -0.21 177 177
MAP2K4 -0.016 0.025 -10000 0 -0.25 1 1
IL1B -0.011 0.042 -10000 0 -0.16 22 22
Channel -0.067 0.12 -10000 0 -0.23 177 177
NLRP1 -0.026 0.053 -10000 0 -0.24 25 25
CALM1 0.011 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.021 0.03 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.019 0.028 0.058 177 -10000 0 177
MAPK3 -0.016 0.023 -10000 0 -10000 0 0
MAPK1 -0.016 0.023 -10000 0 -10000 0 0
PGR -0.078 0.1 -10000 0 -0.22 164 164
PA/Cellular Receptors -0.075 0.13 -10000 0 -0.25 177 177
apoptosis -0.019 0.028 -10000 0 -0.058 177 177
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.064 0.11 -10000 0 -0.22 177 177
macrophage activation -0.003 0.026 -10000 0 -10000 0 0
TNF -0.032 0.11 -10000 0 -0.33 66 66
VCAM1 -0.029 0.11 -10000 0 -0.41 41 41
platelet activation -0.021 0.03 -10000 0 -10000 0 0
MAPKKK cascade 0.013 0.031 0.085 31 -10000 0 31
IL18 -0.012 0.042 -10000 0 -0.15 27 27
negative regulation of macrophage activation -0.019 0.028 -10000 0 -0.058 177 177
LEF -0.019 0.028 -10000 0 -0.058 177 177
CASP1 -0.021 0.036 -10000 0 -0.12 40 40
mol:cAMP -0.021 0.03 -10000 0 -10000 0 0
necrosis -0.019 0.028 -10000 0 -0.058 177 177
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.063 0.11 -10000 0 -0.21 177 177
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 0.009 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.023 0.09 -10000 0 -0.21 98 98
regulation of S phase of mitotic cell cycle -0.018 0.088 -10000 0 -0.2 93 93
GNAO1 -0.1 0.18 -10000 0 -0.41 138 138
HRAS 0.01 0.002 -10000 0 -10000 0 0
SHBG/T-DHT 0.005 0.024 -10000 0 -0.24 5 5
PELP1 0.01 0.002 -10000 0 -10000 0 0
AKT1 0.009 0.001 -10000 0 -10000 0 0
MAP2K1 -0.031 0.092 -10000 0 -0.27 31 31
T-DHT/AR -0.044 0.11 -10000 0 -0.29 90 90
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 159 159
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 0.004 0.051 -10000 0 -0.41 8 8
mol:GDP -0.059 0.14 -10000 0 -0.35 91 91
cell proliferation -0.1 0.2 -10000 0 -0.38 159 159
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
FOS -0.21 0.37 -10000 0 -0.77 159 159
mol:Ca2+ -0.024 0.03 -10000 0 -0.061 168 168
MAPK3 -0.069 0.14 -10000 0 -0.26 159 159
MAPK1 -0.049 0.1 -10000 0 -0.2 159 159
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
mol:IP3 -0.001 0.002 -10000 0 -0.004 159 159
cAMP biosynthetic process 0.008 0.031 0.094 5 -0.2 5 10
GNG2 0.003 0.056 -10000 0 -0.4 10 10
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 159 159
HRAS/GTP -0.041 0.072 -10000 0 -0.19 90 90
actin cytoskeleton reorganization -0.002 0.019 -10000 0 -0.18 6 6
SRC 0.01 0.002 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 159 159
PI3K 0.012 0.026 -10000 0 -0.23 6 6
apoptosis 0.1 0.2 0.4 159 -10000 0 159
T-DHT/AR/PELP1 -0.031 0.095 -10000 0 -0.24 90 90
HRAS/GDP -0.056 0.13 -10000 0 -0.33 90 90
CREB1 -0.11 0.21 -10000 0 -0.43 159 159
RAC1-CDC42/GTP -0.002 0.019 -10000 0 -0.18 6 6
AR -0.062 0.16 -10000 0 -0.41 90 90
GNB1 0.011 0 -10000 0 -10000 0 0
RAF1 -0.028 0.085 -10000 0 -0.25 31 31
RAC1-CDC42/GDP -0.049 0.12 -10000 0 -0.31 90 90
T-DHT/AR/PELP1/Src -0.024 0.086 -10000 0 -0.21 90 90
MAP2K2 -0.031 0.092 -10000 0 -0.27 31 31
T-DHT/AR/PELP1/Src/PI3K -0.018 0.089 -10000 0 -0.21 93 93
GNAZ -0.001 0.07 -10000 0 -0.41 15 15
SHBG 0.007 0.041 -10000 0 -0.41 5 5
Gi family/GNB1/GNG2/GDP -0.072 0.16 -10000 0 -0.32 141 141
mol:T-DHT -0.001 0.001 -10000 0 -0.003 128 128
RAC1 0.011 0 -10000 0 -10000 0 0
GNRH1 0.005 0.032 -10000 0 -0.29 6 6
Gi family/GTP -0.058 0.12 -10000 0 -0.21 150 150
CDC42 0.011 0 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.011 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.13 0.058 -9999 0 -0.32 2 2
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.038 0.014 -9999 0 -10000 0 0
AURKB -0.29 0.11 -9999 0 -0.33 464 464
AURKC 0.01 0.021 -9999 0 -0.33 2 2
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.009 0.032 -9999 0 -0.41 3 3
LAT2 -0.065 0.13 -9999 0 -0.23 163 163
AP1 -0.12 0.14 -9999 0 -0.36 98 98
mol:PIP3 -0.066 0.15 -9999 0 -0.26 165 165
IKBKB -0.035 0.097 -9999 0 -0.22 51 51
AKT1 -0.03 0.1 -9999 0 -0.28 37 37
IKBKG -0.035 0.097 -9999 0 -0.22 51 51
MS4A2 -0.12 0.19 -9999 0 -0.4 162 162
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
MAP3K1 -0.041 0.12 -9999 0 -0.31 34 34
mol:Ca2+ -0.049 0.12 -9999 0 -0.2 165 165
LYN 0.01 0.003 -9999 0 -10000 0 0
CBLB -0.064 0.12 -9999 0 -0.23 163 163
SHC1 0.011 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.036 0.1 -9999 0 -0.21 130 130
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.01 0.018 -9999 0 -0.41 1 1
PLD2 -0.056 0.11 -9999 0 -0.24 84 84
PTPN13 -0.09 0.15 -9999 0 -0.38 62 62
PTPN11 0.01 0.005 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.029 0.11 -9999 0 -0.26 37 37
SYK 0.01 0.015 -9999 0 -0.33 1 1
GRB2 0.011 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.097 0.13 -9999 0 -0.26 165 165
LAT -0.064 0.12 -9999 0 -0.23 163 163
PAK2 -0.051 0.13 -9999 0 -0.34 34 34
NFATC2 -0.081 0.16 -9999 0 -0.52 54 54
HRAS -0.061 0.14 -9999 0 -0.24 162 162
GAB2 0.008 0.037 -9999 0 -0.41 4 4
PLA2G1B 0.028 0.015 -9999 0 -10000 0 0
Fc epsilon R1 -0.1 0.13 -9999 0 -0.25 215 215
Antigen/IgE/Fc epsilon R1 -0.089 0.12 -9999 0 -0.22 215 215
mol:GDP -0.069 0.14 -9999 0 -0.25 163 163
JUN 0.005 0.048 -9999 0 -0.41 7 7
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.006 0.041 -9999 0 -0.41 5 5
FOS -0.12 0.19 -9999 0 -0.41 159 159
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.074 0.13 -9999 0 -0.24 165 165
CHUK -0.035 0.097 -9999 0 -0.22 51 51
KLRG1 -0.055 0.11 -9999 0 -0.19 165 165
VAV1 -0.066 0.13 -9999 0 -0.23 164 164
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.064 0.12 -9999 0 -0.23 163 163
negative regulation of mast cell degranulation -0.046 0.1 -9999 0 -0.3 34 34
BTK -0.074 0.14 -9999 0 -0.4 35 35
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.075 0.15 -9999 0 -0.23 217 217
GAB2/PI3K/SHP2 -0.063 0.088 -9999 0 -0.31 37 37
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.063 0.12 -9999 0 -0.26 86 86
RAF1 0.019 0.018 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.08 0.11 -9999 0 -0.26 87 87
FCER1G 0.016 0.024 -9999 0 -0.34 2 2
FCER1A -0.059 0.16 -9999 0 -0.42 84 84
Antigen/IgE/Fc epsilon R1/Fyn -0.08 0.11 -9999 0 -0.2 214 214
MAPK3 0.027 0.015 -9999 0 -10000 0 0
MAPK1 0.027 0.015 -9999 0 -10000 0 0
NFKB1 0.01 0.018 -9999 0 -0.41 1 1
MAPK8 -0.01 0.075 -9999 0 -0.56 6 6
DUSP1 -0.092 0.18 -9999 0 -0.41 129 129
NF-kappa-B/RelA -0.036 0.046 -9999 0 -0.18 6 6
actin cytoskeleton reorganization -0.075 0.14 -9999 0 -0.35 46 46
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.08 0.11 -9999 0 -0.34 37 37
FER -0.064 0.12 -9999 0 -0.23 163 163
RELA 0.011 0 -9999 0 -10000 0 0
ITK -0.032 0.062 -9999 0 -0.36 14 14
SOS1 0.011 0 -9999 0 -10000 0 0
PLCG1 -0.066 0.14 -9999 0 -0.25 163 163
cytokine secretion -0.027 0.034 -9999 0 -0.14 2 2
SPHK1 -0.065 0.13 -9999 0 -0.23 163 163
PTK2 -0.078 0.15 -9999 0 -0.4 34 34
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.1 0.13 -9999 0 -0.27 165 165
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.063 0.15 -9999 0 -0.25 165 165
MAP2K2 0.023 0.015 -9999 0 -10000 0 0
MAP2K1 0.023 0.015 -9999 0 -10000 0 0
MAP2K7 0.011 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.057 0.086 -9999 0 -0.28 35 35
MAP2K4 0.012 0.038 -9999 0 -0.84 1 1
Fc epsilon R1/FcgammaRIIB -0.089 0.12 -9999 0 -0.22 214 214
mol:Choline -0.056 0.11 -9999 0 -0.24 84 84
SHC/Grb2/SOS1 -0.068 0.11 -9999 0 -0.33 32 32
FYN 0.011 0 -9999 0 -10000 0 0
DOK1 0.011 0 -9999 0 -10000 0 0
PXN -0.068 0.14 -9999 0 -0.37 34 34
HCLS1 -0.064 0.13 -9999 0 -0.23 164 164
PRKCB -0.056 0.13 -9999 0 -0.21 171 171
FCGR2B 0.008 0.035 -9999 0 -0.39 4 4
IGHE -0.001 0.004 -9999 0 -10000 0 0
KLRG1/SHIP -0.047 0.11 -9999 0 -0.3 34 34
LCP2 0.01 0.015 -9999 0 -0.33 1 1
PLA2G4A -0.075 0.14 -9999 0 -0.24 172 172
RASA1 0.007 0.041 -9999 0 -0.41 5 5
mol:Phosphatidic acid -0.056 0.11 -9999 0 -0.24 84 84
IKK complex -0.016 0.078 -9999 0 -0.16 49 49
WIPF1 0.009 0.026 -9999 0 -0.41 2 2
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 -0.007 0.084 -9999 0 -0.41 22 22
mol:S1P -0.009 0.014 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.072 0.12 -9999 0 -0.24 150 150
GNAO1 -0.11 0.19 -9999 0 -0.42 138 138
S1P/S1P3/G12/G13 0.003 0.046 -9999 0 -0.22 19 19
AKT1 -0.063 0.16 -9999 0 -0.66 25 25
AKT3 -0.41 0.55 -9999 0 -1.1 199 199
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.007 0.084 -9999 0 -0.41 22 22
GNAI2 0.002 0.014 -9999 0 -10000 0 0
GNAI3 0.004 0.011 -9999 0 -10000 0 0
GNAI1 -0.002 0.053 -9999 0 -0.42 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.014 0.081 -9999 0 -0.42 19 19
S1PR2 0.011 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.2 -9999 0 -0.34 205 205
MAPK3 -0.12 0.19 -9999 0 -0.32 205 205
MAPK1 -0.12 0.19 -9999 0 -0.32 205 205
JAK2 -0.12 0.2 -9999 0 -0.33 205 205
CXCR4 -0.12 0.19 -9999 0 -0.32 205 205
FLT1 0.003 0.016 -9999 0 -10000 0 0
RhoA/GDP 0.008 0 -9999 0 -10000 0 0
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
SRC -0.12 0.19 -9999 0 -0.32 205 205
S1P/S1P3/Gi -0.13 0.2 -9999 0 -0.34 205 205
RAC1 0.011 0 -9999 0 -10000 0 0
RhoA/GTP -0.12 0.18 -9999 0 -0.31 205 205
VEGFA 0.003 0.016 -9999 0 -10000 0 0
S1P/S1P2/Gi -0.084 0.14 -9999 0 -0.27 142 142
VEGFR1 homodimer/VEGFA homodimer -0.001 0.031 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.021 0.1 -9999 0 -0.26 72 72
GNAQ 0.009 0.026 -9999 0 -0.41 2 2
GNAZ -0.008 0.07 -9999 0 -0.41 15 15
G12/G13 0.016 0 -9999 0 -10000 0 0
GNA14 -0.031 0.13 -9999 0 -0.41 53 53
GNA15 0.006 0.039 -9999 0 -0.33 7 7
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.011 0 -9999 0 -10000 0 0
GNA11 0.002 0.06 -9999 0 -0.41 11 11
Rac1/GTP -0.12 0.18 -9999 0 -0.31 205 205
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.063 0.15 -9999 0 -0.25 158 158
FZD6 0.01 0.018 -9999 0 -0.41 1 1
WNT6 -0.031 0.12 -9999 0 -0.38 57 57
WNT4 -0.089 0.18 -9999 0 -0.41 125 125
FZD3 0.011 0 -9999 0 -10000 0 0
WNT5A -0.003 0.074 -9999 0 -0.41 17 17
WNT11 -0.03 0.12 -9999 0 -0.35 60 60
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.08 0.31 -9999 0 -0.95 58 58
MKNK1 0.011 0 -9999 0 -10000 0 0
MAPK14 -0.014 0.097 -9999 0 -0.27 65 65
ATF2/c-Jun -0.004 0.11 -9999 0 -0.51 10 10
MAPK11 -0.015 0.1 -9999 0 -0.27 67 67
MITF -0.041 0.16 -9999 0 -0.34 108 108
MAPKAPK5 -0.01 0.12 -9999 0 -0.32 67 67
KRT8 -0.026 0.13 -9999 0 -0.34 69 69
MAPKAPK3 0.011 0 -9999 0 -10000 0 0
MAPKAPK2 0.011 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.021 0.14 -9999 0 -0.39 67 67
CEBPB -0.01 0.12 -9999 0 -0.32 67 67
SLC9A1 -0.01 0.12 -9999 0 -0.32 67 67
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.008 0.12 -9999 0 -0.31 70 70
p38alpha-beta/MNK1 -0.006 0.11 -9999 0 -0.3 65 65
JUN -0.004 0.1 -9999 0 -0.5 10 10
PPARGC1A -0.072 0.18 -9999 0 -0.32 157 157
USF1 -0.01 0.12 -9999 0 -0.32 67 67
RAB5/GDP/GDI1 -0.029 0.074 -9999 0 -0.22 65 65
NOS2 -0.019 0.16 -9999 0 -0.66 15 15
DDIT3 -0.01 0.12 -9999 0 -0.32 67 67
RAB5A 0.011 0 -9999 0 -10000 0 0
HSPB1 -0.001 0.097 -9999 0 -0.25 65 65
p38alpha-beta/HBP1 -0.006 0.11 -9999 0 -0.3 65 65
CREB1 -0.011 0.13 -9999 0 -0.34 67 67
RAB5/GDP 0.008 0 -9999 0 -10000 0 0
EIF4E -0.001 0.099 -9999 0 -0.26 65 65
RPS6KA4 -0.01 0.12 -9999 0 -0.32 67 67
PLA2G4A -0.013 0.12 -9999 0 -0.31 66 66
GDI1 -0.01 0.12 -9999 0 -0.32 67 67
TP53 -0.017 0.14 -9999 0 -0.39 67 67
RPS6KA5 -0.013 0.12 -9999 0 -0.32 72 72
ESR1 -0.045 0.17 -9999 0 -0.35 111 111
HBP1 0.011 0 -9999 0 -10000 0 0
MEF2C -0.04 0.16 -9999 0 -0.34 106 106
MEF2A -0.014 0.13 -9999 0 -0.33 71 71
EIF4EBP1 -0.011 0.13 -9999 0 -0.34 67 67
KRT19 -0.014 0.12 -9999 0 -0.32 71 71
ELK4 -0.01 0.12 -9999 0 -0.32 67 67
ATF6 -0.01 0.12 -9999 0 -0.32 67 67
ATF1 -0.011 0.13 -9999 0 -0.34 67 67
p38alpha-beta/MAPKAPK2 -0.006 0.11 -9999 0 -0.3 65 65
p38alpha-beta/MAPKAPK3 -0.006 0.11 -9999 0 -0.3 65 65
Reelin signaling pathway

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
CDK5R1/CDK5 0.016 0.01 -9999 0 -0.22 1 1
VLDLR 0.009 0.026 -9999 0 -0.41 2 2
CRKL 0.011 0 -9999 0 -10000 0 0
LRPAP1 0.011 0 -9999 0 -10000 0 0
FYN 0.011 0 -9999 0 -10000 0 0
ITGA3 0.01 0.018 -9999 0 -0.41 1 1
RELN/VLDLR/Fyn -0.069 0.12 -9999 0 -0.23 186 186
MAPK8IP1/MKK7/MAP3K11/JNK1 0.03 0.024 -9999 0 -0.18 6 6
AKT1 -0.051 0.1 -9999 0 -0.18 192 192
MAP2K7 0.011 0 -9999 0 -10000 0 0
RAPGEF1 0.011 0 -9999 0 -10000 0 0
DAB1 -0.001 0.053 -9999 0 -0.33 13 13
RELN/LRP8/DAB1 -0.069 0.11 -9999 0 -0.2 205 205
LRPAP1/LRP8 0.014 0.023 -9999 0 -0.22 5 5
RELN/LRP8/DAB1/Fyn -0.058 0.1 -9999 0 -0.19 187 187
DAB1/alpha3/beta1 Integrin -0.062 0.08 -9999 0 -0.33 5 5
long-term memory -0.13 0.15 -9999 0 -0.36 103 103
DAB1/LIS1 -0.065 0.083 -9999 0 -0.31 5 5
DAB1/CRLK/C3G -0.061 0.078 -9999 0 -0.3 5 5
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
DAB1/NCK2 -0.066 0.084 -9999 0 -0.31 5 5
ARHGEF2 0.011 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.16 0.2 -9999 0 -0.41 207 207
CDK5R1 0.01 0.015 -9999 0 -0.33 1 1
RELN -0.14 0.2 -9999 0 -0.41 191 191
PIK3R1 0.007 0.041 -9999 0 -0.41 5 5
RELN/LRP8/Fyn -0.07 0.12 -9999 0 -0.23 186 186
GRIN2A/RELN/LRP8/DAB1/Fyn -0.13 0.15 -9999 0 -0.28 193 193
MAPK8 0.007 0.041 -9999 0 -0.41 5 5
RELN/VLDLR/DAB1 -0.068 0.11 -9999 0 -0.2 204 204
ITGB1 0.011 0 -9999 0 -10000 0 0
MAP1B -0.068 0.12 -9999 0 -0.2 197 197
RELN/LRP8 -0.07 0.12 -9999 0 -0.23 193 193
GRIN2B/RELN/LRP8/DAB1/Fyn -0.061 0.11 -9999 0 -0.2 130 130
PI3K 0.013 0.031 -9999 0 -0.28 6 6
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.016 0.013 -9999 0 -0.28 1 1
RAP1A -0.031 0.092 -9999 0 -0.28 5 5
PAFAH1B1 0.011 0 -9999 0 -10000 0 0
MAPK8IP1 0.01 0.024 -9999 0 -0.37 2 2
CRLK/C3G 0.016 0 -9999 0 -10000 0 0
GRIN2B -0.008 0.066 -9999 0 -0.33 21 21
NCK2 0.011 0 -9999 0 -10000 0 0
neuron differentiation -0.03 0.083 -9999 0 -0.25 3 3
neuron adhesion -0.02 0.091 -9999 0 -0.33 3 3
LRP8 0.008 0.033 -9999 0 -0.33 5 5
GSK3B -0.043 0.096 -9999 0 -0.36 1 1
RELN/VLDLR/DAB1/Fyn -0.058 0.1 -9999 0 -0.19 187 187
MAP3K11 0.011 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.061 0.11 -9999 0 -0.2 192 192
CDK5 0.011 0 -9999 0 -10000 0 0
MAPT 0.002 0.077 -9999 0 -0.37 20 20
neuron migration -0.05 0.13 -9999 0 -0.23 76 76
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.03 0.083 -9999 0 -0.25 3 3
RELN/VLDLR -0.056 0.11 -9999 0 -0.2 187 187
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.044 0.028 0.071 70 -10000 0 70
BUB1B -0.061 0.051 -10000 0 -0.11 164 164
PLK1 -0.013 0.023 -10000 0 -10000 0 0
PLK1S1 -0.003 0.017 -10000 0 -0.26 1 1
KIF2A -0.005 0.02 -10000 0 -10000 0 0
regulation of mitotic centrosome separation -0.013 0.023 -10000 0 -10000 0 0
GOLGA2 0.011 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.11 0.1 -10000 0 -0.18 334 334
WEE1 -0.008 0.023 -10000 0 -10000 0 0
cytokinesis -0.079 0.042 -10000 0 -0.22 13 13
PP2A-alpha B56 0.037 0.005 -10000 0 -10000 0 0
AURKA -0.005 0.014 -10000 0 -10000 0 0
PICH/PLK1 -0.079 0.11 -10000 0 -0.23 131 131
CENPE -0.055 0.089 -10000 0 -0.19 156 156
RhoA/GTP 0.008 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.005 0.02 -10000 0 -10000 0 0
PPP2CA 0.011 0 -10000 0 -10000 0 0
FZR1 0.011 0 -10000 0 -10000 0 0
TPX2 -0.016 0.015 -10000 0 -10000 0 0
PAK1 0.01 0.001 -10000 0 -10000 0 0
SPC24 -0.2 0.17 -10000 0 -0.33 324 324
FBXW11 0.011 0 -10000 0 -10000 0 0
CLSPN -0.014 0.019 -10000 0 -10000 0 0
GORASP1 0.011 0 -10000 0 -10000 0 0
metaphase 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.008 0.013 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle -0.001 0.002 -10000 0 -10000 0 0
STAG2 0.011 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.012 0.007 -10000 0 -10000 0 0
spindle elongation -0.013 0.023 -10000 0 -10000 0 0
ODF2 0.01 0.001 -10000 0 -10000 0 0
BUB1 0.023 0.011 -10000 0 -10000 0 0
TPT1 -0.003 0.013 -10000 0 -10000 0 0
CDC25C -0.018 0.014 -10000 0 -10000 0 0
CDC25B 0.01 0.001 -10000 0 -10000 0 0
SGOL1 -0.044 0.028 -10000 0 -0.071 70 70
RHOA 0.011 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.018 0.048 -10000 0 -10000 0 0
CDC14B 0.008 0.013 -10000 0 -0.3 1 1
CDC20 -0.29 0.11 -10000 0 -0.33 467 467
PLK1/PBIP1 -0.016 0.045 -10000 0 -0.18 32 32
mitosis -0.004 0.007 -10000 0 -0.016 70 70
FBXO5 -0.005 0.02 -10000 0 -10000 0 0
CDC2 -0.001 0.002 -10000 0 -10000 0 0
NDC80 -0.013 0.087 -10000 0 -0.33 37 37
metaphase plate congression -0.006 0.015 -10000 0 -10000 0 0
ERCC6L -0.069 0.1 -10000 0 -0.26 68 68
NLP/gamma Tubulin -0.005 0.012 -10000 0 -10000 0 0
microtubule cytoskeleton organization -0.003 0.013 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.001 -10000 0 -10000 0 0
PPP1R12A 0.01 0.018 -10000 0 -0.41 1 1
interphase -0.001 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.15 0.068 -10000 0 -0.17 477 477
GRASP65/GM130/RAB1/GTP/PLK1 0.008 0.018 -10000 0 -10000 0 0
RAB1A 0.011 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.006 0.022 -10000 0 -10000 0 0
mitotic prometaphase -0.002 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.013 0.018 -10000 0 -10000 0 0
microtubule-based process -0.16 0.059 -10000 0 -0.18 477 477
Golgi organization -0.013 0.023 -10000 0 -10000 0 0
Cohesin/SA2 -0.013 0.014 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.015 0.013 -10000 0 -0.28 1 1
KIF20A -0.3 0.1 -10000 0 -0.33 477 477
APC/C/CDC20 -0.16 0.065 -10000 0 -0.18 467 467
PPP2R1A 0.011 0 -10000 0 -10000 0 0
chromosome segregation -0.019 0.042 -10000 0 -0.18 32 32
PRC1 -0.003 0.068 -10000 0 -0.33 22 22
ECT2 -0.016 0.05 -10000 0 -0.19 33 33
C13orf34 -0.005 0.02 -10000 0 -10000 0 0
NUDC -0.006 0.015 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.06 0.05 -10000 0 -0.11 164 164
spindle assembly -0.008 0.018 -10000 0 -10000 0 0
spindle stabilization -0.003 0.017 -10000 0 -0.26 1 1
APC/C/HCDH1 0.014 0.011 -10000 0 -0.24 1 1
MKLP2/PLK1 -0.16 0.06 -10000 0 -0.18 477 477
CCNB1 -0.048 0.13 -10000 0 -0.33 91 91
PPP1CB 0.011 0.001 -10000 0 -10000 0 0
BTRC 0.011 0 -10000 0 -10000 0 0
ROCK2 -0.009 0.064 -10000 0 -0.4 13 13
TUBG1 -0.003 0.013 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.026 0.043 -10000 0 -10000 0 0
MLF1IP -0.011 0.056 -10000 0 -0.23 32 32
INCENP 0.01 0.001 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.009 0.01 -9999 0 -0.23 1 1
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.011 0.023 -9999 0 -0.22 5 5
STXBP1 -0.017 0.1 -9999 0 -0.41 35 35
ACh/CHRNA1 -0.099 0.1 -9999 0 -0.23 189 189
RAB3GAP2/RIMS1/UNC13B 0.018 0.019 -9999 0 -0.17 5 5
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0.003 0.033 -9999 0 -0.33 5 5
mol:ACh -0.044 0.056 -9999 0 -0.1 242 242
RAB3GAP2 0.011 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.063 0.075 -9999 0 -0.28 28 28
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.098 0.1 -9999 0 -0.23 189 189
UNC13B 0.011 0 -9999 0 -10000 0 0
CHRNA1 -0.11 0.16 -9999 0 -0.33 189 189
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.082 0.12 -9999 0 -0.3 117 117
SNAP25 -0.11 0.13 -9999 0 -0.25 242 242
VAMP2 0.005 0 -9999 0 -10000 0 0
SYT1 -0.083 0.18 -9999 0 -0.41 117 117
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.002 0.063 -9999 0 -0.23 36 36
STX1A/SNAP25 fragment 1/VAMP2 -0.063 0.075 -9999 0 -0.28 28 28
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.11 0.12 -9999 0 -0.23 284 284
fibroblast growth factor receptor signaling pathway -0.11 0.12 -9999 0 -0.23 284 284
LAMA1 -0.1 0.16 -9999 0 -0.33 175 175
PRNP -0.047 0.15 -9999 0 -0.41 73 73
GPC1/SLIT2 -0.023 0.1 -9999 0 -0.28 69 69
SMAD2 0.021 0.035 -9999 0 -0.2 13 13
GPC1/PrPc/Cu2+ -0.02 0.086 -9999 0 -0.23 73 73
GPC1/Laminin alpha1 -0.062 0.11 -9999 0 -0.22 175 175
TDGF1 -0.02 0.11 -9999 0 -0.38 42 42
CRIPTO/GPC1 -0.005 0.074 -9999 0 -0.26 42 42
APP/GPC1 0.016 0 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 0.004 0.062 -9999 0 -0.2 42 42
FLT1 0.011 0 -9999 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.016 0.039 -9999 0 -0.23 13 13
SERPINC1 0.004 0.039 -9999 0 -0.33 7 7
FYN 0.004 0.062 -9999 0 -0.2 42 42
FGR -0.001 0.073 -9999 0 -0.22 51 51
positive regulation of MAPKKK cascade 0.014 0.074 -9999 0 -0.27 26 26
SLIT2 -0.044 0.14 -9999 0 -0.41 69 69
GPC1/NRG 0.005 0.055 -9999 0 -0.28 19 19
NRG1 -0.005 0.078 -9999 0 -0.41 19 19
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.022 0 -9999 0 -10000 0 0
LYN 0.004 0.062 -9999 0 -0.2 42 42
mol:Spermine 0.009 0 -9999 0 -10000 0 0
cell growth -0.11 0.12 -9999 0 -0.23 284 284
BMP signaling pathway -0.011 0 -9999 0 -10000 0 0
SRC 0.004 0.062 -9999 0 -0.2 42 42
TGFBR1 0.011 0 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.031 0.12 -9999 0 -0.39 51 51
GPC1 0.011 0 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.011 0 -9999 0 -10000 0 0
VEGFA 0.011 0 -9999 0 -10000 0 0
BLK -0.011 0.078 -9999 0 -0.2 77 77
HCK 0.001 0.065 -9999 0 -0.2 49 49
FGF2 -0.22 0.21 -9999 0 -0.41 284 284
FGFR1 0.01 0.018 -9999 0 -0.41 1 1
VEGFR1 homodimer 0.011 0 -9999 0 -10000 0 0
TGFBR2 0.001 0.065 -9999 0 -0.41 13 13
cell death 0.016 0 -9999 0 -10000 0 0
ATIII/GPC1 0.012 0.027 -9999 0 -0.22 7 7
PLA2G2A/GPC1 -0.013 0.084 -9999 0 -0.27 51 51
LCK 0.002 0.066 -9999 0 -0.21 46 46
neuron differentiation 0.005 0.055 -9999 0 -0.28 19 19
PrPc/Cu2+ -0.033 0.1 -9999 0 -0.29 73 73
APP 0.011 0 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.001 0.065 -9999 0 -0.41 13 13
LPA4-mediated signaling events

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
ADCY4 0.005 0.05 -9999 0 -0.24 22 22
ADCY5 -0.031 0.097 -9999 0 -0.24 97 97
ADCY6 0.015 0 -9999 0 -10000 0 0
ADCY7 0.015 0 -9999 0 -10000 0 0
ADCY1 0.002 0.053 -9999 0 -0.22 29 29
ADCY2 -0.12 0.12 -9999 0 -0.24 289 289
ADCY3 0.014 0.015 -9999 0 -0.24 2 2
ADCY8 0.008 0.017 -9999 0 -0.18 4 4
PRKCE 0.009 0 -9999 0 -10000 0 0
ADCY9 -0.017 0.084 -9999 0 -0.24 69 69
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.06 0.079 -9999 0 -0.17 123 123
IGF1 pathway

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
NCK2 0.011 0 -10000 0 -10000 0 0
PTK2 0.011 0 -10000 0 -10000 0 0
CRKL -0.042 0.12 -10000 0 -0.25 110 110
GRB2/SOS1/SHC 0.022 0 -10000 0 -10000 0 0
HRAS 0.011 0 -10000 0 -10000 0 0
IRS1/Crk -0.042 0.12 -10000 0 -0.26 110 110
IGF-1R heterotetramer/IGF1/PTP1B -0.036 0.12 -10000 0 -0.25 110 110
AKT1 -0.022 0.11 -10000 0 -0.32 38 38
BAD -0.015 0.1 -10000 0 -0.3 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.042 0.12 -10000 0 -0.25 110 110
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.042 0.12 -10000 0 -0.26 110 110
RAF1 -0.01 0.1 -10000 0 -0.28 38 38
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.033 0.12 -10000 0 -0.24 110 110
YWHAZ 0.011 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.053 0.13 -10000 0 -0.26 134 134
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
RPS6KB1 -0.022 0.11 -10000 0 -0.32 38 38
GNB2L1 0.011 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.01 0.088 -10000 0 -0.25 38 38
PXN 0.011 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
HRAS/GTP -0.047 0.092 -10000 0 -0.32 37 37
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.013 0.092 -10000 0 -0.24 37 37
IGF-1R heterotetramer -0.02 0.094 -10000 0 -0.46 21 21
IGF-1R heterotetramer/IGF1/IRS/Nck -0.041 0.12 -10000 0 -0.26 110 110
Crk/p130 Cas/Paxillin -0.026 0.11 -10000 0 -0.22 110 110
IGF1R -0.02 0.094 -10000 0 -0.47 21 21
IGF1 -0.077 0.18 -10000 0 -0.44 100 100
IRS2/Crk -0.061 0.14 -10000 0 -0.25 161 161
PI3K -0.035 0.12 -10000 0 -0.24 113 113
apoptosis 0.007 0.092 0.26 38 -10000 0 38
HRAS/GDP 0.008 0 -10000 0 -10000 0 0
PRKCD -0.048 0.16 -10000 0 -0.34 110 110
RAF1/14-3-3 E -0.002 0.09 -10000 0 -0.28 13 13
BAD/14-3-3 -0.008 0.097 -10000 0 -0.28 38 38
PRKCZ -0.022 0.11 -10000 0 -0.32 38 38
Crk/p130 Cas/Paxillin/FAK1 -0.038 0.078 -10000 0 -0.27 38 38
PTPN1 0.011 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.056 0.16 -10000 0 -0.36 110 110
BCAR1 0.011 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.023 0.1 -10000 0 -0.21 111 111
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.011 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.042 0.12 -10000 0 -0.25 110 110
GRB10 0.01 0.018 -10000 0 -0.41 1 1
PTPN11 -0.042 0.12 -10000 0 -0.25 110 110
IRS1 -0.047 0.13 -10000 0 -0.28 110 110
IRS2 -0.07 0.15 -10000 0 -0.27 161 161
IGF-1R heterotetramer/IGF1 -0.061 0.15 -10000 0 -0.34 110 110
GRB2 0.011 0 -10000 0 -10000 0 0
PDPK1 -0.029 0.11 -10000 0 -0.33 41 41
YWHAE 0.011 0 -10000 0 -10000 0 0
PRKD1 -0.061 0.17 -10000 0 -0.36 114 114
SHC1 0.011 0 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.03 0.15 -10000 0 -0.41 51 51
CRKL -0.034 0.15 -10000 0 -0.35 78 78
HRAS -0.014 0.14 -10000 0 -0.38 45 45
mol:PIP3 -0.04 0.14 0.19 2 -0.33 80 82
SPRED1 0.011 0 -10000 0 -10000 0 0
SPRED2 0.01 0.018 -10000 0 -0.41 1 1
GAB1 -0.042 0.16 -10000 0 -0.36 82 82
FOXO3 -0.026 0.14 -10000 0 -0.39 48 48
AKT1 -0.034 0.15 -10000 0 -0.42 50 50
BAD -0.026 0.14 -10000 0 -0.39 48 48
megakaryocyte differentiation -0.044 0.16 -10000 0 -0.36 83 83
GSK3B -0.026 0.14 -10000 0 -0.39 48 48
RAF1 -0.003 0.11 -10000 0 -0.3 45 45
SHC1 0.011 0 -10000 0 -10000 0 0
STAT3 -0.041 0.16 -10000 0 -0.36 82 82
STAT1 -0.1 0.34 -10000 0 -0.84 81 81
HRAS/SPRED1 -0.005 0.11 -10000 0 -0.3 45 45
cell proliferation -0.041 0.16 -10000 0 -0.36 82 82
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
TEC 0.01 0.015 -10000 0 -0.33 1 1
RPS6KB1 -0.042 0.16 -10000 0 -0.33 106 106
HRAS/SPRED2 -0.005 0.11 -10000 0 -0.31 45 45
LYN/TEC/p62DOK -0.028 0.15 -10000 0 -0.42 49 49
MAPK3 0.009 0.086 -10000 0 -0.21 45 45
STAP1 -0.043 0.16 -10000 0 -0.35 87 87
GRAP2 -0.003 0.074 -10000 0 -0.41 17 17
JAK2 -0.089 0.3 -10000 0 -0.72 81 81
STAT1 (dimer) -0.099 0.34 -10000 0 -0.82 81 81
mol:Gleevec 0 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.03 0.15 -10000 0 -0.42 51 51
actin filament polymerization -0.04 0.15 -10000 0 -0.35 82 82
LYN 0.011 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.054 0.21 -10000 0 -0.51 81 81
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
CBL/CRKL/GRB2 -0.02 0.14 -10000 0 -0.39 48 48
PI3K -0.032 0.16 -10000 0 -0.44 53 53
PTEN 0.006 0.045 -10000 0 -0.41 6 6
SCF/KIT/EPO/EPOR -0.1 0.37 -10000 0 -1.2 47 47
MAPK8 -0.043 0.16 -10000 0 -0.37 82 82
STAT3 (dimer) -0.04 0.15 -10000 0 -0.35 82 82
positive regulation of transcription 0.011 0.073 -10000 0 -0.18 45 45
mol:GDP -0.018 0.14 -10000 0 -0.37 51 51
PIK3C2B -0.041 0.16 -10000 0 -0.36 82 82
CBL/CRKL -0.026 0.14 -10000 0 -0.41 48 48
FER -0.041 0.16 -10000 0 -0.36 81 81
SH2B3 -0.041 0.16 -10000 0 -0.36 82 82
PDPK1 -0.032 0.13 -10000 0 -0.36 53 53
SNAI2 -0.067 0.18 -10000 0 -0.41 92 92
positive regulation of cell proliferation -0.071 0.26 -10000 0 -0.62 81 81
KITLG -0.03 0.13 -10000 0 -0.43 50 50
cell motility -0.071 0.26 -10000 0 -0.62 81 81
PTPN6 0.011 0.017 -10000 0 -0.33 1 1
EPOR -0.011 0.12 -10000 0 -0.71 2 2
STAT5A (dimer) -0.057 0.22 -10000 0 -0.52 81 81
SOCS1 0.01 0.018 -10000 0 -0.41 1 1
cell migration 0.044 0.16 0.32 108 -10000 0 108
SOS1 0.011 0 -10000 0 -10000 0 0
EPO -0.005 0.073 -10000 0 -0.41 16 16
VAV1 0.007 0.038 -10000 0 -0.34 6 6
GRB10 -0.041 0.16 -10000 0 -0.36 83 83
PTPN11 0.012 0.006 -10000 0 -10000 0 0
SCF/KIT -0.049 0.16 -10000 0 -0.34 108 108
GO:0007205 0.001 0.008 -10000 0 -10000 0 0
MAP2K1 0.006 0.093 -10000 0 -0.24 45 45
CBL 0.011 0 -10000 0 -10000 0 0
KIT -0.081 0.35 -10000 0 -1.2 40 40
MAP2K2 0.006 0.093 -10000 0 -0.24 45 45
SHC/Grb2/SOS1 -0.028 0.15 -10000 0 -0.41 51 51
STAT5A -0.06 0.22 -10000 0 -0.53 81 81
GRB2 0.011 0 -10000 0 -10000 0 0
response to radiation -0.065 0.18 -10000 0 -0.4 92 92
SHC/GRAP2 0.007 0.052 -10000 0 -0.28 17 17
PTPRO -0.045 0.16 -10000 0 -0.37 83 83
SH2B2 -0.041 0.16 -10000 0 -0.36 82 82
DOK1 0.011 0 -10000 0 -10000 0 0
MATK -0.046 0.16 -10000 0 -0.32 108 108
CREBBP 0.016 0.045 -10000 0 -0.43 2 2
BCL2 -0.1 0.38 -10000 0 -1.2 51 51
Aurora A 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
Aurora A/GADD45A -0.012 0.043 -9999 0 -10000 0 0
BIRC5 -0.25 0.14 -9999 0 -0.33 410 410
NFKBIA -0.013 0.042 -9999 0 -10000 0 0
CPEB1 -0.17 0.21 -9999 0 -0.41 229 229
AKT1 -0.013 0.042 -9999 0 -10000 0 0
NDEL1 0.011 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.011 0.038 -9999 0 -10000 0 0
NDEL1/TACC3 -0.04 0.09 -9999 0 -0.22 82 82
GADD45A 0.011 0 -9999 0 -10000 0 0
GSK3B 0.007 0.001 -9999 0 -10000 0 0
PAK1/Aurora A -0.012 0.043 -9999 0 -10000 0 0
MDM2 0.011 0 -9999 0 -10000 0 0
JUB 0.011 0 -9999 0 -10000 0 0
TPX2 -0.17 0.093 -9999 0 -0.22 427 427
TP53 0 0.029 -9999 0 -0.28 1 1
DLG7 -0.02 0.042 -9999 0 -10000 0 0
AURKAIP1 0.011 0 -9999 0 -10000 0 0
ARHGEF7 0.011 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.043 0.096 -9999 0 -0.23 82 82
G2/M transition of mitotic cell cycle -0.011 0.038 -9999 0 -10000 0 0
AURKA -0.024 0.053 -9999 0 -10000 0 0
AURKB -0.014 0.013 -9999 0 -10000 0 0
CDC25B -0.005 0.032 -9999 0 -10000 0 0
G2/M transition checkpoint -0.011 0.038 -9999 0 -10000 0 0
mRNA polyadenylation -0.11 0.12 -9999 0 -0.23 229 229
Aurora A/CPEB -0.11 0.12 -9999 0 -0.23 229 229
Aurora A/TACC1/TRAP/chTOG -0.034 0.091 -9999 0 -0.21 96 96
BRCA1 0.011 0 -9999 0 -10000 0 0
centrosome duplication -0.012 0.043 -9999 0 -10000 0 0
regulation of centrosome cycle -0.04 0.089 -9999 0 -0.22 82 82
spindle assembly -0.035 0.09 -9999 0 -0.21 96 96
TDRD7 0.011 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.12 0.086 -9999 0 -0.21 160 160
CENPA -0.003 0.016 -9999 0 -10000 0 0
Aurora A/PP2A -0.012 0.043 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.003 0.028 -9999 0 -10000 0 0
negative regulation of DNA binding 0 0.029 -9999 0 -0.28 1 1
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.016 0 -9999 0 -10000 0 0
RASA1 0.007 0.041 -9999 0 -0.41 5 5
Ajuba/Aurora A -0.011 0.038 -9999 0 -10000 0 0
mitotic prometaphase -0.02 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.024 0.053 -9999 0 -10000 0 0
TACC1 -0.066 0.16 -9999 0 -0.41 96 96
TACC3 -0.068 0.14 -9999 0 -0.33 122 122
Aurora A/Antizyme1 -0.003 0.038 -9999 0 -10000 0 0
Aurora A/RasGAP -0.014 0.048 -9999 0 -0.24 5 5
OAZ1 0.011 0 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.007 0.001 -9999 0 -10000 0 0
GIT1 0.011 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.022 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.17 0.092 -9999 0 -0.22 427 427
PPP2R5D 0.011 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.15 0.088 -9999 0 -0.23 155 155
PAK1 0.011 0 -9999 0 -10000 0 0
CKAP5 0.011 0 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.011 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.054 0.09 -10000 0 -0.25 37 37
NT3 (dimer)/TRKC -0.14 0.17 -10000 0 -0.3 260 260
NT3 (dimer)/TRKB -0.11 0.16 -10000 0 -0.28 227 227
SHC/Grb2/SOS1/GAB1/PI3K 0.026 0.03 -10000 0 -0.19 10 10
RAPGEF1 0.011 0 -10000 0 -10000 0 0
BDNF -0.043 0.12 -10000 0 -0.33 83 83
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
DYNLT1 0.011 0 -10000 0 -10000 0 0
NTRK1 0.001 0.059 -10000 0 -0.37 13 13
NTRK2 -0.041 0.14 -10000 0 -0.4 67 67
NTRK3 -0.19 0.21 -10000 0 -0.41 249 249
NT-4/5 (dimer)/TRKB -0.1 0.15 -10000 0 -0.26 228 228
neuron apoptosis 0.14 0.19 0.39 153 -0.17 1 154
SHC 2-3/Grb2 -0.15 0.21 -10000 0 -0.42 153 153
SHC1 0.011 0 -10000 0 -10000 0 0
SHC2 -0.18 0.24 0.17 1 -0.53 140 141
SHC3 -0.12 0.16 0.17 1 -0.38 105 106
STAT3 (dimer) 0.017 0.009 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.083 0.14 -10000 0 -0.25 204 204
RIN/GDP -0.044 0.08 -10000 0 -0.18 48 48
GIPC1 0.011 0 -10000 0 -10000 0 0
KRAS 0.01 0.015 -10000 0 -0.33 1 1
DNAJA3 -0.13 0.16 0.2 2 -0.32 177 179
RIN/GTP 0.002 0.003 -10000 0 -10000 0 0
CCND1 0.024 0.015 -10000 0 -10000 0 0
MAGED1 0.009 0.026 -10000 0 -0.41 2 2
PTPN11 0.011 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.006 0.07 -10000 0 -0.33 23 23
SHC/GRB2/SOS1 0.022 0 -10000 0 -10000 0 0
GRB2 0.011 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.043 0.11 -10000 0 -0.24 134 134
TRKA/NEDD4-2 0.009 0.043 -10000 0 -0.25 14 14
ELMO1 0.008 0.037 -10000 0 -0.41 4 4
RhoG/GTP/ELMO1/DOCK1 0.01 0.037 -10000 0 -0.26 9 9
NGF -0.08 0.17 -10000 0 -0.41 114 114
HRAS 0.011 0 -10000 0 -10000 0 0
DOCK1 0.006 0.045 -10000 0 -0.41 6 6
GAB2 0.008 0.037 -10000 0 -0.41 4 4
RIT2 0.002 0.004 -10000 0 -10000 0 0
RIT1 0.011 0 -10000 0 -10000 0 0
FRS2 0.011 0 -10000 0 -10000 0 0
DNM1 0.006 0.045 -10000 0 -0.41 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.011 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.12 0.16 0.19 2 -0.31 178 180
mol:GDP -0.064 0.11 -10000 0 -0.24 72 72
NGF (dimer) -0.08 0.17 -10000 0 -0.41 114 114
RhoG/GDP 0.006 0.026 -10000 0 -0.29 4 4
RIT1/GDP -0.04 0.081 -10000 0 -0.18 47 47
TIAM1 0 0.068 -10000 0 -0.41 14 14
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
BDNF (dimer)/TRKB -0.039 0.1 -10000 0 -0.2 146 146
KIDINS220/CRKL/C3G 0.016 0 -10000 0 -10000 0 0
SHC/RasGAP 0.014 0.029 -10000 0 -0.28 5 5
FRS2 family/SHP2 0.022 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.027 0.02 -10000 0 -0.2 4 4
RIT1/GTP 0.008 0 -10000 0 -10000 0 0
NT3 (dimer) -0.017 0.1 -10000 0 -0.4 36 36
RAP1/GDP -0.048 0.053 -10000 0 -0.16 27 27
KIDINS220/CRKL 0.011 0 -10000 0 -10000 0 0
BDNF (dimer) -0.043 0.12 -10000 0 -0.33 83 83
ubiquitin-dependent protein catabolic process -0.038 0.11 -10000 0 -0.23 121 121
Schwann cell development -0.037 0.03 -10000 0 -10000 0 0
EHD4 0.011 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.028 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.031 0.017 -10000 0 -10000 0 0
RAP1B 0.011 0 -10000 0 -10000 0 0
RAP1A 0.011 0 -10000 0 -10000 0 0
CDC42/GTP -0.12 0.12 -10000 0 -0.34 101 101
ABL1 0.009 0.026 -10000 0 -0.41 2 2
SH2B family/GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
Rap1/GTP 0.015 0.046 -10000 0 -0.22 1 1
STAT3 0.017 0.009 -10000 0 -10000 0 0
axon guidance -0.12 0.12 -10000 0 -0.32 101 101
MAPK3 -0.033 0.1 -10000 0 -0.21 128 128
MAPK1 -0.033 0.1 -10000 0 -0.21 128 128
CDC42/GDP -0.04 0.081 -10000 0 -0.19 31 31
NTF3 -0.017 0.1 -10000 0 -0.4 36 36
NTF4 -0.006 0.07 -10000 0 -0.33 23 23
NGF (dimer)/TRKA/FAIM -0.038 0.11 -10000 0 -0.23 126 126
PI3K 0.013 0.031 -10000 0 -0.28 6 6
FRS3 0.011 0 -10000 0 -10000 0 0
FAIM 0.01 0.018 -10000 0 -0.41 1 1
GAB1 0.008 0.037 -10000 0 -0.41 4 4
RASGRF1 -0.15 0.17 0.2 2 -0.35 183 185
SOS1 0.011 0 -10000 0 -10000 0 0
MCF2L -0.11 0.14 -10000 0 -0.25 261 261
RGS19 0.011 0 -10000 0 -10000 0 0
CDC42 0.011 0 -10000 0 -10000 0 0
RAS family/GTP -0.017 0.07 -10000 0 -10000 0 0
Rac1/GDP -0.04 0.081 -10000 0 -0.18 47 47
NGF (dimer)/TRKA/GRIT -0.045 0.11 -10000 0 -0.24 125 125
neuron projection morphogenesis -0.11 0.17 -10000 0 -0.43 67 67
NGF (dimer)/TRKA/NEDD4-2 -0.038 0.11 -10000 0 -0.23 121 121
MAP2K1 0.029 0.018 -10000 0 -0.18 4 4
NGFR -0.13 0.2 -10000 0 -0.41 176 176
NGF (dimer)/TRKA/GIPC/GAIP -0.024 0.096 -10000 0 -0.2 124 124
RAS family/GTP/PI3K 0.022 0.024 -10000 0 -0.2 6 6
FRS2 family/SHP2/GRB2/SOS1 0.033 0 -10000 0 -10000 0 0
NRAS 0.011 0 -10000 0 -10000 0 0
GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
PRKCI 0.011 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.024 -10000 0 -0.37 2 2
MAPKKK cascade -0.15 0.25 -10000 0 -0.6 121 121
RASA1 0.007 0.041 -10000 0 -0.41 5 5
TRKA/c-Abl 0.008 0.045 -10000 0 -0.25 15 15
SQSTM1 0.011 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.028 0.093 -10000 0 -0.21 59 59
NGF (dimer)/TRKA/p62/Atypical PKCs -0.019 0.092 -10000 0 -0.21 13 13
MATK 0.001 0.064 -10000 0 -0.4 13 13
NEDD4L 0.01 0.018 -10000 0 -0.41 1 1
RAS family/GDP -0.044 0.05 -10000 0 -0.16 22 22
NGF (dimer)/TRKA -0.14 0.17 0.21 2 -0.31 230 232
Rac1/GTP -0.11 0.11 -10000 0 -0.26 165 165
FRS2 family/SHP2/CRK family 0.033 0 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.032 0.1 0.18 141 -10000 0 141
GNAI2 0.011 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.008 0.037 -10000 0 -0.19 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.099 0.18 -10000 0 -0.41 138 138
RhoA/GTP -0.033 0.1 -10000 0 -0.19 141 141
negative regulation of cAMP metabolic process -0.042 0.11 -10000 0 -0.21 152 152
GNAZ -0.001 0.07 -10000 0 -0.41 15 15
GNAI3 0.011 0 -10000 0 -10000 0 0
GNA12 0.011 0 -10000 0 -10000 0 0
S1PR5 -0.001 0.064 -10000 0 -0.35 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.042 0.11 -10000 0 -0.21 152 152
RhoA/GDP 0.008 0 -10000 0 -10000 0 0
RHOA 0.011 0 -10000 0 -10000 0 0
GNAI1 0.005 0.052 -10000 0 -0.41 8 8
Noncanonical Wnt signaling pathway

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
NFATC2 -0.032 0.13 -9999 0 -0.41 53 53
GNB1/GNG2 -0.049 0.14 -9999 0 -0.41 39 39
mol:DAG -0.04 0.13 -9999 0 -0.37 39 39
PLCG1 -0.041 0.13 -9999 0 -0.39 39 39
YES1 -0.054 0.14 -9999 0 -0.44 36 36
FZD3 0.011 0 -9999 0 -10000 0 0
FZD6 0.01 0.018 -9999 0 -0.41 1 1
G protein -0.041 0.13 -9999 0 -0.39 39 39
MAP3K7 -0.12 0.14 -9999 0 -0.33 120 120
mol:Ca2+ -0.039 0.12 -9999 0 -0.36 39 39
mol:IP3 -0.04 0.13 -9999 0 -0.37 39 39
NLK -0.005 0.009 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
CAMK2A -0.14 0.15 -9999 0 -0.34 138 138
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.063 0.15 -9999 0 -0.25 158 158
CSNK1A1 0.011 0 -9999 0 -10000 0 0
GNAS -0.054 0.14 -9999 0 -0.44 36 36
GO:0007205 -0.04 0.13 -9999 0 -0.37 39 39
WNT6 -0.031 0.12 -9999 0 -0.38 57 57
WNT4 -0.089 0.18 -9999 0 -0.41 125 125
NFAT1/CK1 alpha -0.051 0.14 -9999 0 -0.41 44 44
GNG2 0.003 0.056 -9999 0 -0.4 10 10
WNT5A -0.003 0.074 -9999 0 -0.41 17 17
WNT11 -0.03 0.12 -9999 0 -0.35 60 60
CDC42 -0.045 0.14 -9999 0 -0.41 36 36
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.035 0.13 -10000 0 -0.38 62 62
NFATC2 -0.023 0.18 -10000 0 -0.52 41 41
NFATC3 -0.015 0.083 -10000 0 -0.26 26 26
CD40LG -0.17 0.33 -10000 0 -0.86 77 77
ITCH 0.027 0.036 -10000 0 -10000 0 0
CBLB 0.027 0.036 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.14 0.25 -10000 0 -0.71 54 54
JUNB 0.007 0.041 -10000 0 -0.41 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.01 0.035 -10000 0 -10000 0 0
T cell anergy 0.015 0.058 -10000 0 -10000 0 0
TLE4 -0.032 0.21 -10000 0 -0.61 56 56
Jun/NFAT1-c-4/p21SNFT -0.095 0.33 -10000 0 -0.82 79 79
AP-1/NFAT1-c-4 -0.17 0.39 -10000 0 -0.99 76 76
IKZF1 0.002 0.13 -10000 0 -0.48 17 17
T-helper 2 cell differentiation -0.083 0.23 -10000 0 -0.74 36 36
AP-1/NFAT1 -0.081 0.18 -10000 0 -0.38 92 92
CALM1 0.015 0.025 -10000 0 -10000 0 0
EGR2 -0.11 0.41 -10000 0 -1.2 51 51
EGR3 -0.14 0.46 -10000 0 -1.2 77 77
NFAT1/FOXP3 -0.044 0.16 -10000 0 -0.39 55 55
EGR1 -0.045 0.14 -10000 0 -0.41 68 68
JUN 0 0.05 -10000 0 -0.41 7 7
EGR4 -0.003 0.059 -10000 0 -0.34 15 15
mol:Ca2+ 0.004 0.027 -10000 0 -10000 0 0
GBP3 -0.001 0.14 -10000 0 -0.49 24 24
FOSL1 -0.015 0.09 -10000 0 -0.33 40 40
NFAT1-c-4/MAF/IRF4 -0.13 0.35 -10000 0 -0.86 84 84
DGKA 0.004 0.13 -10000 0 -0.42 22 22
CREM 0.011 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.11 0.34 -10000 0 -0.83 84 84
CTLA4 -0.042 0.16 -10000 0 -0.42 47 47
NFAT1-c-4 (dimer)/EGR1 -0.12 0.36 -10000 0 -0.88 84 84
NFAT1-c-4 (dimer)/EGR4 -0.1 0.34 -10000 0 -0.82 84 84
FOS -0.12 0.19 -10000 0 -0.41 159 159
IFNG -0.077 0.19 -10000 0 -0.63 33 33
T cell activation -0.084 0.21 -10000 0 -0.62 45 45
MAF -0.067 0.16 -10000 0 -0.41 98 98
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.081 0.3 0.78 67 -10000 0 67
TNF -0.13 0.33 -10000 0 -0.8 86 86
FASLG -0.17 0.48 -10000 0 -1.2 82 82
TBX21 0.002 0.062 -10000 0 -0.4 12 12
BATF3 0.01 0.015 -10000 0 -0.33 1 1
PRKCQ -0.024 0.12 -10000 0 -0.41 47 47
PTPN1 0.004 0.13 -10000 0 -0.41 24 24
NFAT1-c-4/ICER1 -0.097 0.33 -10000 0 -0.82 84 84
GATA3 -0.002 0.07 -10000 0 -0.35 20 20
T-helper 1 cell differentiation -0.064 0.2 -10000 0 -0.61 34 34
IL2RA -0.13 0.25 -10000 0 -0.68 61 61
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.004 0.13 -10000 0 -0.41 24 24
E2F1 -0.048 0.13 -10000 0 -0.32 100 100
PPARG -0.012 0.096 -10000 0 -0.41 29 29
SLC3A2 0.004 0.13 -10000 0 -0.4 26 26
IRF4 -0.003 0.072 -10000 0 -0.37 19 19
PTGS2 -0.19 0.35 -10000 0 -0.88 82 82
CSF2 -0.17 0.33 -10000 0 -0.85 77 77
JunB/Fra1/NFAT1-c-4 -0.096 0.33 -10000 0 -0.79 84 84
IL4 -0.087 0.24 -10000 0 -0.8 34 34
IL5 -0.17 0.33 -10000 0 -0.85 76 76
IL2 -0.086 0.21 -10000 0 -0.64 44 44
IL3 -0.037 0.048 -10000 0 -10000 0 0
RNF128 0.013 0.076 -10000 0 -0.25 40 40
NFATC1 -0.082 0.31 -10000 0 -0.78 67 67
CDK4 0.042 0.18 0.56 20 -10000 0 20
PTPRK 0.003 0.13 -10000 0 -0.46 17 17
IL8 -0.2 0.34 -10000 0 -0.88 77 77
POU2F1 0.011 0 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0.001 0.049 -10000 0 -0.35 9 9
CDKN2C 0.021 0.056 -10000 0 -0.38 9 9
CDKN2A -0.13 0.17 -10000 0 -0.34 219 219
CCND2 0.005 0.049 0.16 10 -0.11 37 47
RB1 -0.006 0.048 0.13 5 -0.17 12 17
CDK4 0.024 0.037 0.17 12 -10000 0 12
CDK6 0.016 0.045 0.17 12 -0.18 11 23
G1/S progression 0.006 0.048 0.16 12 -0.13 5 17
Thromboxane A2 receptor signaling

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
TGM2 -0.032 0.13 -10000 0 -0.41 53 53
GNB1/GNG2 -0.041 0.072 -10000 0 -0.19 93 93
AKT1 -0.016 0.098 -10000 0 -0.2 91 91
EGF -0.005 0.071 -10000 0 -0.34 23 23
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.017 0.054 -10000 0 -0.3 1 1
mol:Ca2+ -0.046 0.14 -10000 0 -0.3 115 115
LYN 0.021 0.047 -10000 0 -10000 0 0
RhoA/GTP -0.029 0.05 -10000 0 -0.13 94 94
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.045 0.16 -10000 0 -0.33 106 106
GNG2 0.003 0.057 -10000 0 -0.4 10 10
ARRB2 0.011 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.005 0.071 -10000 0 -0.33 14 14
G beta5/gamma2 -0.054 0.097 -10000 0 -0.25 93 93
PRKCH -0.053 0.16 -10000 0 -0.35 106 106
DNM1 0.006 0.045 -10000 0 -0.41 6 6
TXA2/TP beta/beta Arrestin3 -0.005 0.021 -10000 0 -0.21 1 1
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.027 0.12 -10000 0 -0.41 47 47
G12 family/GTP -0.07 0.12 -10000 0 -0.3 107 107
ADRBK1 0.011 0 -10000 0 -10000 0 0
ADRBK2 0.01 0.018 -10000 0 -0.41 1 1
RhoA/GTP/ROCK1 0.012 0.006 -10000 0 -10000 0 0
mol:GDP 0.022 0.094 0.23 41 -10000 0 41
mol:NADP 0.009 0.024 -10000 0 -0.37 2 2
RAB11A 0.011 0 -10000 0 -10000 0 0
PRKG1 -0.18 0.21 -10000 0 -0.41 232 232
mol:IP3 -0.061 0.18 -10000 0 -0.38 115 115
cell morphogenesis 0.012 0.006 -10000 0 -10000 0 0
PLCB2 -0.09 0.24 -10000 0 -0.51 115 115
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.007 0.057 -10000 0 -0.25 2 2
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.019 0.05 -10000 0 -0.26 1 1
RHOA 0.011 0 -10000 0 -10000 0 0
PTGIR 0.01 0.018 -10000 0 -0.41 1 1
PRKCB1 -0.058 0.17 -10000 0 -0.37 108 108
GNAQ 0.009 0.026 -10000 0 -0.41 2 2
mol:L-citrulline 0.009 0.024 -10000 0 -0.37 2 2
TXA2/TXA2-R family -0.084 0.23 -10000 0 -0.52 106 106
LCK 0.019 0.049 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.015 0.046 -10000 0 -0.16 18 18
TXA2-R family/G12 family/GDP/G beta/gamma 0.018 0.028 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.014 0.045 -10000 0 -10000 0 0
MAPK14 -0.022 0.11 -10000 0 -0.23 96 96
TGM2/GTP -0.079 0.21 -10000 0 -0.45 118 118
MAPK11 -0.023 0.11 -10000 0 -0.23 97 97
ARHGEF1 -0.018 0.085 -10000 0 -0.18 95 95
GNAI2 0.011 0 -10000 0 -10000 0 0
JNK cascade -0.057 0.18 -10000 0 -0.38 107 107
RAB11/GDP 0.011 0.001 -10000 0 -10000 0 0
ICAM1 -0.035 0.13 -10000 0 -0.28 94 94
cAMP biosynthetic process -0.063 0.17 -10000 0 -0.36 118 118
Gq family/GTP/EBP50 -0.001 0.068 -10000 0 -0.27 12 12
actin cytoskeleton reorganization 0.012 0.006 -10000 0 -10000 0 0
SRC 0.021 0.047 -10000 0 -10000 0 0
GNB5 0.011 0 -10000 0 -10000 0 0
GNB1 0.011 0 -10000 0 -10000 0 0
EGF/EGFR 0.031 0.047 -10000 0 -0.21 3 3
VCAM1 -0.044 0.15 -10000 0 -0.33 95 95
TP beta/Gq family/GDP/G beta5/gamma2 0.005 0.071 -10000 0 -0.33 14 14
platelet activation -0.032 0.14 -10000 0 -0.3 106 106
PGI2/IP 0.008 0.013 -10000 0 -0.29 1 1
PRKACA -0.003 0.064 -10000 0 -0.21 48 48
Gq family/GDP/G beta5/gamma2 0.003 0.07 -10000 0 -0.31 14 14
TXA2/TP beta/beta Arrestin2 -0.006 0.047 -10000 0 -0.44 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.003 0.06 -10000 0 -0.19 48 48
mol:DAG -0.068 0.19 -10000 0 -0.42 108 108
EGFR 0 0.067 -10000 0 -0.4 14 14
TXA2/TP alpha -0.089 0.23 -10000 0 -0.49 118 118
Gq family/GTP -0.023 0.071 -10000 0 -0.21 62 62
YES1 0.021 0.047 -10000 0 -10000 0 0
GNAI2/GTP -0.013 0.042 -10000 0 -10000 0 0
PGD2/DP -0.019 0.084 -10000 0 -0.29 47 47
SLC9A3R1 0.009 0.026 -10000 0 -0.33 3 3
FYN 0.021 0.047 -10000 0 -10000 0 0
mol:NO 0.009 0.024 -10000 0 -0.37 2 2
GNA15 0.006 0.039 -10000 0 -0.33 7 7
PGK/cGMP -0.096 0.12 -10000 0 -0.24 233 233
RhoA/GDP 0.011 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.002 0.091 -10000 0 -0.34 17 17
NOS3 0.009 0.024 -10000 0 -0.37 2 2
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCA -0.059 0.17 -10000 0 -0.36 106 106
PRKCB -0.059 0.17 -10000 0 -0.37 105 105
PRKCE -0.051 0.16 -10000 0 -0.35 100 100
PRKCD -0.056 0.17 -10000 0 -0.38 101 101
PRKCG -0.066 0.18 -10000 0 -0.4 107 107
muscle contraction -0.077 0.22 -10000 0 -0.48 107 107
PRKCZ -0.045 0.16 -10000 0 -0.34 106 106
ARR3 0.003 0.015 -10000 0 -0.33 1 1
TXA2/TP beta 0.01 0.056 -10000 0 -0.17 16 16
PRKCQ -0.062 0.17 -10000 0 -0.37 108 108
MAPKKK cascade -0.077 0.21 -10000 0 -0.46 108 108
SELE -0.048 0.16 -10000 0 -0.35 98 98
TP beta/GNAI2/GDP/G beta/gamma 0.016 0.061 -10000 0 -0.33 2 2
ROCK1 0.011 0 -10000 0 -10000 0 0
GNA14 -0.031 0.13 -10000 0 -0.41 53 53
chemotaxis -0.093 0.26 -10000 0 -0.6 95 95
GNA12 0.011 0 -10000 0 -10000 0 0
GNA13 0.011 0 -10000 0 -10000 0 0
GNA11 0.002 0.06 -10000 0 -0.41 11 11
Rac1/GTP 0.006 0.004 -10000 0 -10000 0 0
Plasma membrane estrogen 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
GNB1/GNG2 -0.002 0.073 -10000 0 -0.19 69 69
ER alpha/Gai/GDP/Gbeta gamma -0.087 0.19 -10000 0 -0.32 178 178
AKT1 -0.07 0.25 -10000 0 -0.75 61 61
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.075 0.25 -10000 0 -0.76 61 61
mol:Ca2+ -0.015 0.12 -10000 0 -0.34 56 56
IGF1R -0.006 0.082 -10000 0 -0.41 21 21
E2/ER alpha (dimer)/Striatin -0.014 0.08 -10000 0 -0.23 62 62
SHC1 0.011 0 -10000 0 -10000 0 0
apoptosis 0.066 0.24 0.71 61 -10000 0 61
RhoA/GTP -0.018 0.051 -10000 0 -0.3 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.087 0.14 -10000 0 -0.4 72 72
regulation of stress fiber formation -0.017 0.058 0.26 3 -10000 0 3
E2/ERA-ERB (dimer) -0.014 0.079 -10000 0 -0.23 61 61
KRAS 0.01 0.015 -10000 0 -0.33 1 1
G13/GTP -0.011 0.071 -10000 0 -0.21 60 60
pseudopodium formation 0.017 0.058 -10000 0 -0.26 3 3
E2/ER alpha (dimer)/PELP1 -0.013 0.079 -10000 0 -0.23 60 60
GRB2 0.011 0 -10000 0 -10000 0 0
GNG2 0.003 0.056 -10000 0 -0.4 10 10
GNAO1 -0.099 0.18 -10000 0 -0.41 138 138
HRAS 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.056 0.18 -10000 0 -0.5 62 62
E2/ER beta (dimer) 0.008 0.01 -10000 0 -0.23 1 1
mol:GDP -0.035 0.098 -10000 0 -0.31 60 60
mol:NADP -0.056 0.18 -10000 0 -0.5 62 62
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
mol:IP3 -0.016 0.13 -10000 0 -0.36 56 56
IGF-1R heterotetramer -0.006 0.082 -10000 0 -0.41 21 21
PLCB1 -0.022 0.13 -10000 0 -0.37 56 56
PLCB2 -0.021 0.13 -10000 0 -0.37 55 55
IGF1 -0.069 0.16 -10000 0 -0.41 100 100
mol:L-citrulline -0.056 0.18 -10000 0 -0.5 62 62
RHOA 0.011 0 -10000 0 -10000 0 0
Gai/GDP -0.15 0.29 -10000 0 -0.63 139 139
JNK cascade 0.008 0.01 -10000 0 -0.22 1 1
BCAR1 0.011 0 -10000 0 -10000 0 0
ESR2 0.01 0.015 -10000 0 -0.33 1 1
GNAQ 0.009 0.026 -10000 0 -0.41 2 2
ESR1 -0.037 0.13 -10000 0 -0.41 60 60
Gq family/GDP/Gbeta gamma -0.002 0.094 -10000 0 -0.4 15 15
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.009 0.082 -10000 0 -0.26 21 21
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.087 0.14 -10000 0 -0.4 72 72
GNAZ -0.001 0.07 -10000 0 -0.41 15 15
E2/ER alpha (dimer) -0.026 0.094 -10000 0 -0.29 60 60
STRN 0.009 0.026 -10000 0 -0.41 2 2
GNAL -0.051 0.15 -10000 0 -0.41 77 77
PELP1 0.011 0 -10000 0 -10000 0 0
MAPK11 0.014 0.018 -10000 0 -0.22 3 3
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 0.005 0.052 -10000 0 -0.41 8 8
HBEGF -0.1 0.18 -10000 0 -0.37 116 116
cAMP biosynthetic process -0.047 0.09 -10000 0 -0.2 124 124
SRC -0.077 0.18 -10000 0 -0.3 178 178
PI3K 0.013 0.031 -10000 0 -0.28 6 6
GNB1 0.011 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.033 0.085 -10000 0 -0.26 60 60
SOS1 0.011 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.1 0.15 -10000 0 -0.36 108 108
Gs family/GTP -0.048 0.091 -10000 0 -0.2 124 124
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.021 0.008 -10000 0 -0.16 1 1
vasodilation -0.053 0.17 -10000 0 -0.47 62 62
mol:DAG -0.016 0.13 -10000 0 -0.36 56 56
Gs family/GDP/Gbeta gamma -0.052 0.1 -10000 0 -0.29 64 64
MSN 0.017 0.062 -10000 0 -0.28 3 3
Gq family/GTP -0.029 0.13 -10000 0 -0.39 55 55
mol:PI-3-4-5-P3 -0.071 0.24 -10000 0 -0.73 61 61
NRAS 0.011 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.053 0.17 0.47 62 -10000 0 62
GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
RhoA/GDP -0.033 0.091 -10000 0 -0.29 60 60
NOS3 -0.059 0.19 -10000 0 -0.52 62 62
GNA11 0.002 0.06 -10000 0 -0.41 11 11
MAPKKK cascade -0.05 0.19 -10000 0 -0.54 62 62
E2/ER alpha (dimer)/PELP1/Src -0.092 0.15 -10000 0 -0.42 72 72
ruffle organization 0.017 0.058 -10000 0 -0.26 3 3
ROCK2 0.012 0.065 -10000 0 -0.31 3 3
GNA14 -0.031 0.13 -10000 0 -0.41 53 53
GNA15 0.006 0.039 -10000 0 -0.33 7 7
GNA13 0.011 0 -10000 0 -10000 0 0
MMP9 -0.13 0.18 -10000 0 -0.4 114 114
MMP2 -0.076 0.18 -10000 0 -0.41 79 79
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 0.028 0.1 0.28 75 -10000 0 75
KIRREL -0.039 0.14 -10000 0 -0.41 62 62
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.028 0.1 -10000 0 -0.28 75 75
PLCG1 0.011 0 -10000 0 -10000 0 0
ARRB2 0.011 0 -10000 0 -10000 0 0
WASL 0.011 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.011 0.076 -10000 0 -0.2 63 63
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.005 0.077 -10000 0 -0.21 62 62
FYN -0.013 0.072 -10000 0 -0.2 63 63
mol:Ca2+ -0.014 0.074 -10000 0 -0.2 63 63
mol:DAG -0.011 0.075 -10000 0 -0.2 63 63
NPHS2 -0.004 0.029 -10000 0 -0.33 3 3
mol:IP3 -0.011 0.075 -10000 0 -0.2 63 63
regulation of endocytosis -0.005 0.068 -10000 0 -0.18 63 63
Nephrin/NEPH1/podocin/Cholesterol -0.018 0.076 -10000 0 -0.21 63 63
establishment of cell polarity -0.028 0.1 -10000 0 -0.28 75 75
Nephrin/NEPH1/podocin/NCK1-2 -0.003 0.072 -10000 0 -0.2 32 32
Nephrin/NEPH1/beta Arrestin2 -0.005 0.069 -10000 0 -0.18 63 63
NPHS1 -0.005 0.055 -10000 0 -0.33 14 14
Nephrin/NEPH1/podocin -0.013 0.072 -10000 0 -0.2 63 63
TJP1 0.01 0.018 -10000 0 -0.41 1 1
NCK1 0.009 0.026 -10000 0 -0.41 2 2
NCK2 0.011 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.011 0.076 -10000 0 -0.2 63 63
CD2AP 0.011 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.011 0.076 -10000 0 -0.2 63 63
GRB2 0.011 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.026 0.096 -10000 0 -0.22 91 91
cytoskeleton organization -0.001 0.08 -10000 0 -0.21 62 62
Nephrin/NEPH1 -0.017 0.071 -10000 0 -0.2 63 63
Nephrin/NEPH1/ZO-1 -0.013 0.083 -10000 0 -0.22 63 63
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.01 0.018 -9999 0 -0.41 1 1
CCL5 0.003 0.054 -9999 0 -0.37 11 11
SDCBP 0.011 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.07 0.07 -9999 0 -0.26 28 28
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.061 0.066 -9999 0 -0.24 29 29
Syndecan-1/Syntenin -0.061 0.066 -9999 0 -0.24 28 28
MAPK3 -0.045 0.062 -9999 0 -0.25 14 14
HGF/MET -0.047 0.12 -9999 0 -0.28 111 111
TGFB1/TGF beta receptor Type II 0.01 0.018 -9999 0 -0.41 1 1
BSG 0.011 0 -9999 0 -10000 0 0
keratinocyte migration -0.06 0.066 -9999 0 -0.24 29 29
Syndecan-1/RANTES -0.064 0.073 -9999 0 -0.26 36 36
Syndecan-1/CD147 -0.053 0.065 -9999 0 -0.24 28 28
Syndecan-1/Syntenin/PIP2 -0.058 0.064 -9999 0 -0.24 28 28
LAMA5 0.01 0.015 -9999 0 -0.33 1 1
positive regulation of cell-cell adhesion -0.058 0.062 -9999 0 -0.23 28 28
MMP7 -0.057 0.14 -9999 0 -0.36 96 96
HGF -0.074 0.17 -9999 0 -0.41 106 106
Syndecan-1/CASK -0.067 0.066 -9999 0 -0.25 28 28
Syndecan-1/HGF/MET -0.094 0.11 -9999 0 -0.27 119 119
regulation of cell adhesion -0.038 0.061 -9999 0 -0.24 14 14
HPSE 0.002 0.058 -9999 0 -0.4 11 11
positive regulation of cell migration -0.07 0.07 -9999 0 -0.26 28 28
SDC1 -0.071 0.07 -9999 0 -0.26 28 28
Syndecan-1/Collagen -0.07 0.07 -9999 0 -0.26 28 28
PPIB 0.01 0.015 -9999 0 -0.33 1 1
MET 0.005 0.047 -9999 0 -0.37 8 8
PRKACA 0.011 0 -9999 0 -10000 0 0
MMP9 -0.13 0.17 -9999 0 -0.33 215 215
MAPK1 -0.045 0.062 -9999 0 -0.25 14 14
homophilic cell adhesion -0.07 0.069 -9999 0 -0.26 28 28
MMP1 -0.17 0.17 -9999 0 -0.33 285 285
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 0.005 0.068 -9999 0 -0.24 34 34
alphaM/beta2 Integrin/GPIbA 0.014 0.041 -9999 0 -0.27 7 7
alphaM/beta2 Integrin/proMMP-9 -0.062 0.1 -9999 0 -0.18 218 218
PLAUR 0.01 0.021 -9999 0 -0.33 2 2
HMGB1 0.009 0.011 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.017 0.034 -9999 0 -0.21 9 9
AGER 0.008 0.021 -9999 0 -0.4 1 1
RAP1A 0.011 0 -9999 0 -10000 0 0
SELPLG 0.01 0.021 -9999 0 -0.33 2 2
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.018 0.057 -9999 0 -0.27 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.17 -9999 0 -0.33 215 215
CYR61 -0.026 0.12 -9999 0 -0.41 46 46
TLN1 0.011 0 -9999 0 -10000 0 0
Rap1/GTP -0.029 0.061 -9999 0 -0.26 15 15
RHOA 0.011 0 -9999 0 -10000 0 0
P-selectin oligomer -0.15 0.2 -9999 0 -0.41 201 201
MYH2 -0.03 0.11 -9999 0 -0.31 35 35
MST1R -0.022 0.1 -9999 0 -0.33 51 51
leukocyte activation during inflammatory response -0.015 0.05 -9999 0 -0.21 16 16
APOB 0 0.049 -9999 0 -0.39 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.011 0.093 -9999 0 -0.41 27 27
JAM3 -0.1 0.19 -9999 0 -0.41 142 142
GP1BA 0.008 0.03 -9999 0 -0.38 3 3
alphaM/beta2 Integrin/CTGF 0.011 0.052 -9999 0 -0.23 21 21
alphaM/beta2 Integrin -0.022 0.085 -9999 0 -0.25 30 30
JAM3 homodimer -0.1 0.19 -9999 0 -0.41 142 142
ICAM2 0.011 0 -9999 0 -10000 0 0
ICAM1 0.008 0.03 -9999 0 -0.33 4 4
phagocytosis triggered by activation of immune response cell surface activating receptor -0.022 0.085 -9999 0 -0.25 30 30
cell adhesion 0.014 0.041 -9999 0 -0.27 7 7
NFKB1 0.018 0.087 -9999 0 -0.28 26 26
THY1 0.011 0 -9999 0 -10000 0 0
RhoA/GDP 0.008 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.005 0.055 -9999 0 -0.2 39 39
alphaM/beta2 Integrin/LRP/tPA -0.001 0.081 -9999 0 -0.21 60 60
IL6 0.011 0.13 -9999 0 -0.53 23 23
ITGB2 0.006 0.035 -9999 0 -0.33 5 5
elevation of cytosolic calcium ion concentration 0.021 0.035 -9999 0 -0.19 9 9
alphaM/beta2 Integrin/JAM2/JAM3 -0.11 0.17 -9999 0 -0.28 238 238
JAM2 -0.14 0.2 -9999 0 -0.41 185 185
alphaM/beta2 Integrin/ICAM1 0.009 0.063 -9999 0 -0.36 3 3
alphaM/beta2 Integrin/uPA/Plg 0.001 0.075 -9999 0 -0.21 49 49
RhoA/GTP -0.034 0.11 -9999 0 -0.32 39 39
positive regulation of phagocytosis -0.02 0.055 -9999 0 -0.26 7 7
Ron/MSP -0.009 0.073 -9999 0 -0.22 57 57
alphaM/beta2 Integrin/uPAR/uPA 0.022 0.036 -9999 0 -0.19 9 9
alphaM/beta2 Integrin/uPAR 0.017 0.036 -9999 0 -0.2 11 11
PLAU 0.009 0.026 -9999 0 -0.33 3 3
PLAT -0.035 0.13 -9999 0 -0.41 57 57
actin filament polymerization -0.029 0.1 -9999 0 -0.3 35 35
MST1 0.007 0.036 -9999 0 -0.33 6 6
alphaM/beta2 Integrin/lipoprotein(a) 0.004 0.057 -9999 0 -0.21 16 16
TNF 0.01 0.11 -9999 0 -0.31 25 25
RAP1B 0.011 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.016 0.037 -9999 0 -0.21 12 12
fibrinolysis 0 0.074 -9999 0 -0.21 49 49
HCK 0.006 0.039 -9999 0 -0.33 7 7
dendritic cell antigen processing and presentation -0.022 0.085 -9999 0 -0.25 30 30
VTN -0.047 0.14 -9999 0 -0.41 72 72
alphaM/beta2 Integrin/CYR61 -0.004 0.079 -9999 0 -0.24 49 49
LPA -0.013 0.081 -9999 0 -0.33 32 32
LRP1 0.009 0.026 -9999 0 -0.41 2 2
cell migration -0.06 0.1 -9999 0 -0.21 78 78
FN1 0.007 0.041 -9999 0 -0.41 5 5
alphaM/beta2 Integrin/Thy1 0.017 0.034 -9999 0 -0.24 5 5
MPO 0.005 0.042 -9999 0 -0.33 8 8
KNG1 -0.01 0.07 -9999 0 -0.33 24 24
RAP1/GDP 0.015 0 -9999 0 -10000 0 0
ROCK1 -0.026 0.11 -9999 0 -0.31 35 35
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.03 0.12 -9999 0 -0.4 50 50
CTGF 0.001 0.065 -9999 0 -0.41 13 13
alphaM/beta2 Integrin/Hck 0.015 0.045 -9999 0 -0.22 14 14
ITGAM 0.005 0.039 -9999 0 -0.37 5 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.063 0.12 -9999 0 -0.2 205 205
HP -0.1 0.17 -9999 0 -0.35 160 160
leukocyte adhesion -0.11 0.13 -9999 0 -0.32 118 118
SELP -0.15 0.2 -9999 0 -0.41 201 201
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.03 0.11 -9999 0 -0.34 26 26
SMAD6-7/SMURF1 0.021 0.019 -9999 0 -0.23 3 3
NOG -0.018 0.095 -9999 0 -0.33 44 44
SMAD9 -0.058 0.17 -9999 0 -0.51 57 57
SMAD4 0.01 0.018 -9999 0 -0.41 1 1
SMAD5 -0.018 0.095 -9999 0 -0.3 30 30
BMP7/USAG1 -0.049 0.12 -9999 0 -0.27 121 121
SMAD5/SKI -0.012 0.091 -9999 0 -0.3 23 23
SMAD1 0.033 0.014 -9999 0 -10000 0 0
BMP2 -0.025 0.12 -9999 0 -0.41 45 45
SMAD1/SMAD1/SMAD4 -0.001 0.012 -9999 0 -10000 0 0
BMPR1A 0.011 0 -9999 0 -10000 0 0
BMPR1B -0.016 0.1 -9999 0 -0.41 34 34
BMPR1A-1B/BAMBI -0.004 0.081 -9999 0 -0.24 54 54
AHSG 0.001 0.046 -9999 0 -0.33 10 10
CER1 0.004 0.005 -9999 0 -10000 0 0
BMP2-4/CER1 -0.018 0.093 -9999 0 -0.24 73 73
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.037 0.12 -9999 0 -0.36 35 35
BMP2-4 (homodimer) -0.026 0.11 -9999 0 -0.29 73 73
RGMB 0.01 0.018 -9999 0 -0.41 1 1
BMP6/BMPR2/BMPR1A-1B 0.009 0.064 -9999 0 -0.2 43 43
RGMA -0.08 0.17 -9999 0 -0.41 114 114
SMURF1 0.011 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.042 0.12 -9999 0 -0.34 41 41
BMP2-4/USAG1 -0.043 0.12 -9999 0 -0.24 133 133
SMAD6/SMURF1/SMAD5 -0.012 0.091 -9999 0 -0.3 23 23
SOSTDC1 -0.04 0.13 -9999 0 -0.36 71 71
BMP7/BMPR2/BMPR1A-1B -0.009 0.088 -9999 0 -0.22 59 59
SKI 0.011 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.002 0.06 -9999 0 -0.41 11 11
HFE2 0.003 0.021 -9999 0 -0.33 2 2
ZFYVE16 0.011 0 -9999 0 -10000 0 0
MAP3K7 0.011 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.056 0.14 -9999 0 -0.26 145 145
SMAD5/SMAD5/SMAD4 -0.012 0.093 -9999 0 -0.31 23 23
MAPK1 0.011 0 -9999 0 -10000 0 0
TAK1/TAB family -0.051 0.087 -9999 0 -0.3 36 36
BMP7 (homodimer) -0.032 0.12 -9999 0 -0.37 60 60
NUP214 0.011 0 -9999 0 -10000 0 0
BMP6/FETUA 0.003 0.052 -9999 0 -0.25 21 21
SMAD1/SKI 0.038 0.014 -9999 0 -10000 0 0
SMAD6 0.01 0.018 -9999 0 -0.41 1 1
CTDSP2 0.011 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.02 0.097 -9999 0 -0.24 81 81
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.095 0.18 -9999 0 -0.41 132 132
BMPR2 (homodimer) 0.011 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.022 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.003 0.072 -9999 0 -0.28 34 34
CHRDL1 -0.28 0.2 -9999 0 -0.41 359 359
ENDOFIN/SMAD1 0.038 0.014 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0 0.012 -9999 0 -10000 0 0
SMAD6/SMURF1 0.011 0 -9999 0 -10000 0 0
BAMBI -0.007 0.083 -9999 0 -0.38 24 24
SMURF2 0.011 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.18 0.15 -9999 0 -0.26 377 377
BMP2-4/GREM1 -0.075 0.14 -9999 0 -0.26 181 181
SMAD7 0.009 0.026 -9999 0 -0.41 2 2
SMAD8A/SMAD8A/SMAD4 -0.049 0.16 -9999 0 -0.47 58 58
SMAD1/SMAD6 0.038 0.014 -9999 0 -10000 0 0
TAK1/SMAD6 0.016 0 -9999 0 -10000 0 0
BMP7 -0.032 0.12 -9999 0 -0.37 60 60
BMP6 0.002 0.06 -9999 0 -0.41 11 11
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.037 0.12 -9999 0 -0.34 38 38
PPM1A 0.011 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.038 0.014 -9999 0 -10000 0 0
SMAD7/SMURF1 0.015 0.018 -9999 0 -0.28 2 2
CTDSPL 0.011 0 -9999 0 -10000 0 0
PPP1CA 0.011 0 -9999 0 -10000 0 0
XIAP 0.011 0 -9999 0 -10000 0 0
CTDSP1 0.011 0 -9999 0 -10000 0 0
PPP1R15A 0.011 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.076 0.16 -9999 0 -0.42 67 67
CHRD -0.063 0.16 -9999 0 -0.41 92 92
BMPR2 0.011 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.05 0.13 -9999 0 -0.37 41 41
BMP4 -0.015 0.098 -9999 0 -0.39 34 34
FST -0.044 0.14 -9999 0 -0.4 69 69
BMP2-4/NOG -0.03 0.11 -9999 0 -0.23 110 110
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.002 0.083 -9999 0 -0.36 8 8
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.099 0.25 -10000 0 -0.67 38 38
PCK1 -0.12 0.32 -10000 0 -1.2 34 34
HNF4A -0.16 0.34 -10000 0 -0.83 72 72
KCNJ11 -0.088 0.26 -10000 0 -0.71 32 32
AKT1 -0.048 0.14 -10000 0 -0.36 18 18
response to starvation -0.01 0.032 -10000 0 -10000 0 0
DLK1 -0.15 0.34 -10000 0 -0.8 78 78
NKX2-1 -0.019 0.15 -10000 0 -10000 0 0
ACADM -0.1 0.26 -10000 0 -0.67 47 47
TAT -0.098 0.2 -10000 0 -0.57 31 31
CEBPB 0.013 0.002 -10000 0 -10000 0 0
CEBPA 0.01 0.038 -10000 0 -0.38 5 5
TTR -0.037 0.13 -10000 0 -0.58 9 9
PKLR -0.11 0.25 -10000 0 -0.69 37 37
APOA1 -0.21 0.44 -10000 0 -1.1 74 74
CPT1C -0.1 0.26 -10000 0 -0.74 39 39
ALAS1 -0.042 0.16 -10000 0 -10000 0 0
TFRC -0.056 0.19 -10000 0 -0.62 8 8
FOXF1 0.008 0.046 -10000 0 -0.4 6 6
NF1 0.015 0.026 -10000 0 -0.41 2 2
HNF1A (dimer) 0.003 0.047 -10000 0 -0.35 8 8
CPT1A -0.099 0.25 -10000 0 -0.67 38 38
HMGCS1 -0.099 0.25 -10000 0 -0.66 43 43
NR3C1 -0.069 0.16 -10000 0 -0.38 98 98
CPT1B -0.1 0.25 -10000 0 -0.68 36 36
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.007 0.016 -10000 0 -10000 0 0
GCK -0.17 0.35 -10000 0 -0.79 95 95
CREB1 0.004 0.041 -10000 0 -0.18 13 13
IGFBP1 -0.22 0.44 -10000 0 -1.1 88 88
PDX1 -0.052 0.15 -10000 0 -0.47 7 7
UCP2 -0.1 0.25 -10000 0 -0.69 35 35
ALDOB -0.09 0.26 -10000 0 -0.7 31 31
AFP -0.056 0.072 -10000 0 -0.4 10 10
BDH1 -0.099 0.25 -10000 0 -0.68 35 35
HADH -0.087 0.26 -10000 0 -0.7 31 31
F2 -0.14 0.31 -10000 0 -0.87 40 40
HNF1A 0.003 0.047 -10000 0 -0.35 8 8
G6PC 0.008 0.066 -10000 0 -10000 0 0
SLC2A2 -0.055 0.17 -10000 0 -10000 0 0
INS 0.015 0.058 0.2 21 -10000 0 21
FOXA1 -0.21 0.16 -10000 0 -0.32 353 353
FOXA3 -0.056 0.15 -10000 0 -0.33 114 114
FOXA2 -0.11 0.3 -10000 0 -0.75 43 43
ABCC8 -0.18 0.38 -10000 0 -0.85 106 106
ALB -0.063 0.14 -10000 0 -0.96 10 10
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.075 0.17 -9999 0 -0.31 161 161
MAP3K8 0.006 0.032 -9999 0 -0.41 3 3
FOS -0.043 0.12 -9999 0 -0.38 24 24
PRKCA -0.019 0.1 -9999 0 -0.41 34 34
PTPN7 0.005 0.038 -9999 0 -0.34 6 6
HRAS 0.01 0.001 -9999 0 -10000 0 0
PRKCB -0.017 0.1 -9999 0 -0.41 32 32
NRAS 0.01 0.001 -9999 0 -10000 0 0
RAS family/GTP 0.016 0.013 -9999 0 -0.15 1 1
MAPK3 -0.016 0.068 -9999 0 -0.27 3 3
MAP2K1 -0.038 0.14 -9999 0 -0.4 62 62
ELK1 0.005 0.01 -9999 0 -10000 0 0
BRAF -0.034 0.14 -9999 0 -0.38 62 62
mol:GTP -0.001 0.002 -9999 0 -0.005 159 159
MAPK1 -0.016 0.068 -9999 0 -0.25 5 5
RAF1 -0.034 0.14 -9999 0 -0.38 62 62
KRAS 0.01 0.015 -9999 0 -0.33 1 1
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.038 0.1 -9999 0 -0.32 14 14
NF kappa B1 p50/RelA/I kappa B alpha -0.012 0.091 -9999 0 -0.28 13 13
alphaV/beta3 Integrin/Osteopontin/Src -0.042 0.1 -9999 0 -0.21 148 148
AP1 -0.079 0.15 -9999 0 -0.34 92 92
ILK -0.049 0.11 -9999 0 -0.33 16 16
bone resorption -0.027 0.1 -9999 0 -0.3 28 28
PTK2B 0.011 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.033 0.097 -9999 0 -0.3 15 15
ITGAV 0.014 0.001 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.005 0.057 -9999 0 -0.28 20 20
alphaV/beta3 Integrin/Osteopontin -0.064 0.12 -9999 0 -0.24 95 95
MAP3K1 -0.05 0.11 -9999 0 -0.32 18 18
JUN 0.006 0.048 -9999 0 -0.41 7 7
MAPK3 -0.035 0.1 -9999 0 -0.32 14 14
MAPK1 -0.035 0.1 -9999 0 -0.32 14 14
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
NFKB1 0.01 0.018 -9999 0 -0.41 1 1
MAPK8 -0.041 0.1 -9999 0 -0.32 20 20
ITGB3 -0.062 0.16 -9999 0 -0.4 96 96
NFKBIA -0.024 0.098 -9999 0 -0.3 14 14
FOS -0.12 0.19 -9999 0 -0.41 159 159
CD44 0.005 0.048 -9999 0 -0.41 7 7
CHUK 0.011 0 -9999 0 -10000 0 0
PLAU -0.02 0.095 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.045 0.059 -9999 0 -0.26 13 13
BCAR1 0.011 0 -9999 0 -10000 0 0
RELA 0.011 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.031 0.11 -9999 0 -0.27 96 96
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.051 0.11 -9999 0 -0.23 54 54
VAV3 -0.079 0.12 -9999 0 -0.3 65 65
MAP3K14 -0.048 0.11 -9999 0 -0.32 17 17
ROCK2 0.001 0.065 -9999 0 -0.41 13 13
SPP1 -0.081 0.15 -9999 0 -0.32 148 148
RAC1 0.011 0 -9999 0 -10000 0 0
Rac1/GTP -0.067 0.11 -9999 0 -0.27 65 65
MMP2 -0.071 0.15 -9999 0 -0.37 70 70
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.013 0.073 -9999 0 -0.24 50 50
EFNA5 -0.003 0.075 -9999 0 -0.4 18 18
FYN -0.005 0.066 -9999 0 -0.21 50 50
neuron projection morphogenesis -0.013 0.073 -9999 0 -0.24 50 50
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.013 0.074 -9999 0 -0.24 50 50
EPHA5 -0.021 0.1 -9999 0 -0.41 33 33
IL4-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
BCL2L1 -0.24 0.38 -10000 0 -1 59 59
STAT6 (cleaved dimer) -0.27 0.34 -10000 0 -0.91 86 86
IGHG1 -0.085 0.14 -10000 0 -0.35 29 29
IGHG3 -0.24 0.36 -10000 0 -0.9 81 81
AKT1 -0.1 0.2 -10000 0 -0.58 24 24
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.064 0.16 -10000 0 -0.58 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.12 0.23 -10000 0 -0.62 43 43
THY1 -0.24 0.38 -10000 0 -1 59 59
MYB -0.02 0.098 -10000 0 -0.33 48 48
HMGA1 -0.035 0.12 -10000 0 -0.33 71 71
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.14 0.23 -10000 0 -0.58 49 49
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.1 0.2 -10000 0 -0.58 23 23
SP1 0.017 0.002 -10000 0 -10000 0 0
INPP5D 0.01 0.018 -10000 0 -0.41 1 1
SOCS5 0.017 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.22 0.37 -10000 0 -0.95 71 71
SOCS1 -0.14 0.26 -10000 0 -0.69 48 48
SOCS3 -0.1 0.21 -10000 0 -0.8 9 9
FCER2 -0.18 0.3 -10000 0 -0.81 48 48
PARP14 0.012 0.002 -10000 0 -10000 0 0
CCL17 -0.24 0.38 -10000 0 -1 60 60
GRB2 0.011 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.08 0.17 -10000 0 -0.52 11 11
T cell proliferation -0.24 0.38 -10000 0 -1 64 64
IL4R/JAK1 -0.24 0.38 -10000 0 -1 60 60
EGR2 -0.27 0.46 -10000 0 -1.3 64 64
JAK2 -0.01 0.061 -10000 0 -0.43 9 9
JAK3 0.012 0.031 -10000 0 -0.34 4 4
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
JAK1 0.007 0.028 -10000 0 -0.4 2 2
COL1A2 -0.079 0.18 -10000 0 -1.4 5 5
CCL26 -0.24 0.38 -10000 0 -1 59 59
IL4R -0.25 0.4 -10000 0 -1.1 59 59
PTPN6 0.017 0.018 -10000 0 -0.31 1 1
IL13RA2 -0.24 0.38 -10000 0 -1 61 61
IL13RA1 -0.002 0.027 -10000 0 -10000 0 0
IRF4 -0.061 0.22 -10000 0 -1.1 18 18
ARG1 -0.054 0.11 -10000 0 -10000 0 0
CBL -0.12 0.22 -10000 0 -0.55 46 46
GTF3A 0.018 0.001 -10000 0 -10000 0 0
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
IL13RA1/JAK2 -0.008 0.051 -10000 0 -0.28 9 9
IRF4/BCL6 -0.054 0.21 -10000 0 -1 18 18
CD40LG 0.007 0.063 -10000 0 -0.42 11 11
MAPK14 -0.12 0.22 -10000 0 -0.57 39 39
mitosis -0.097 0.2 -10000 0 -0.55 24 24
STAT6 -0.27 0.42 -10000 0 -1.1 80 80
SPI1 0.011 0.026 -10000 0 -0.33 3 3
RPS6KB1 -0.089 0.19 -10000 0 -0.55 19 19
STAT6 (dimer) -0.27 0.42 -10000 0 -1.1 80 80
STAT6 (dimer)/PARP14 -0.25 0.39 -10000 0 -0.98 80 80
mast cell activation 0.006 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.096 0.19 -10000 0 -0.55 20 20
FRAP1 -0.1 0.2 -10000 0 -0.58 24 24
LTA -0.24 0.38 -10000 0 -1 62 62
FES 0.01 0.018 -10000 0 -0.41 1 1
T-helper 1 cell differentiation 0.26 0.42 1 80 -10000 0 80
CCL11 -0.25 0.39 -10000 0 -1 71 71
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.095 0.19 -10000 0 -0.56 19 19
IL2RG 0.009 0.049 -10000 0 -0.36 9 9
IL10 -0.24 0.37 -10000 0 -1 58 58
IRS1 -0.031 0.13 -10000 0 -0.41 53 53
IRS2 -0.045 0.14 -10000 0 -0.41 70 70
IL4 -0.058 0.1 -10000 0 -10000 0 0
IL5 -0.24 0.37 -10000 0 -1 60 60
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.21 0.32 -10000 0 -0.82 66 66
COL1A1 -0.075 0.16 -10000 0 -1.5 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.24 0.38 -10000 0 -1.1 56 56
IL2R gamma/JAK3 0.015 0.046 -10000 0 -0.3 10 10
TFF3 -0.3 0.43 -10000 0 -1.1 76 76
ALOX15 -0.25 0.38 -10000 0 -1 63 63
MYBL1 0.011 0 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.21 0.32 -10000 0 -0.82 68 68
SHC1 0.011 0 -10000 0 -10000 0 0
CEBPB 0.013 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.12 0.21 -10000 0 -0.56 37 37
mol:PI-3-4-5-P3 -0.1 0.2 -10000 0 -0.58 24 24
PI3K -0.11 0.22 -10000 0 -0.62 24 24
DOK2 0.008 0.031 -10000 0 -0.35 4 4
ETS1 0.017 0.02 -10000 0 -0.38 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.072 0.16 -10000 0 -0.56 7 7
ITGB3 -0.36 0.56 -10000 0 -1.3 112 112
PIGR -0.33 0.47 -10000 0 -1.2 87 87
IGHE 0.019 0.033 -10000 0 -10000 0 0
MAPKKK cascade -0.071 0.16 -10000 0 -0.54 7 7
BCL6 0.01 0.018 -10000 0 -0.41 1 1
OPRM1 -0.24 0.38 -10000 0 -1 59 59
RETNLB -0.24 0.38 -10000 0 -1 57 57
SELP -0.52 0.66 -10000 0 -1.3 208 208
AICDA -0.23 0.36 -10000 0 -0.99 59 59
LPA receptor mediated events

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
GNB1/GNG2 0.005 0.075 -9999 0 -0.23 44 44
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.068 -9999 0 -0.26 5 5
AP1 -0.08 0.11 -9999 0 -0.35 49 49
mol:PIP3 -0.03 0.069 -9999 0 -0.32 15 15
AKT1 0.029 0.057 -9999 0 -0.27 8 8
PTK2B 0.006 0.059 -9999 0 -0.21 26 26
RHOA 0.018 0.03 -9999 0 -10000 0 0
PIK3CB 0.011 0 -9999 0 -10000 0 0
mol:Ca2+ 0.005 0.063 -9999 0 -0.23 6 6
MAGI3 0.011 0 -9999 0 -10000 0 0
RELA 0.011 0 -9999 0 -10000 0 0
apoptosis -0.011 0.085 -9999 0 -0.23 61 61
HRAS/GDP 0.008 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.009 0.066 -9999 0 -0.23 17 17
NF kappa B1 p50/RelA -0.026 0.068 -9999 0 -0.33 10 10
endothelial cell migration -0.011 0.13 -9999 0 -0.44 38 38
ADCY4 -0.044 0.14 -9999 0 -0.37 54 54
ADCY5 -0.071 0.16 -9999 0 -0.38 76 76
ADCY6 -0.035 0.13 -9999 0 -0.34 46 46
ADCY7 -0.035 0.13 -9999 0 -0.34 46 46
ADCY1 -0.044 0.14 -9999 0 -0.38 55 55
ADCY2 -0.14 0.19 -9999 0 -0.4 137 137
ADCY3 -0.036 0.13 -9999 0 -0.35 48 48
ADCY8 -0.038 0.13 -9999 0 -0.35 46 46
ADCY9 -0.063 0.16 -9999 0 -0.38 82 82
GSK3B 0.011 0.057 -9999 0 -0.2 26 26
arachidonic acid secretion -0.04 0.13 -9999 0 -0.34 48 48
GNG2 0.003 0.056 -9999 0 -0.4 10 10
TRIP6 0.014 0.038 -9999 0 -0.35 5 5
GNAO1 -0.061 0.14 -9999 0 -0.26 158 158
HRAS 0.011 0 -9999 0 -10000 0 0
NFKBIA 0.009 0.076 -9999 0 -0.23 30 30
GAB1 0.008 0.037 -9999 0 -0.41 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.002 0.14 -9999 0 -0.86 14 14
JUN 0.005 0.048 -9999 0 -0.41 7 7
LPA/LPA2/NHERF2 0.012 0.023 -9999 0 -0.18 3 3
TIAM1 -0.025 0.16 -9999 0 -1 14 14
PIK3R1 0.007 0.041 -9999 0 -0.41 5 5
mol:IP3 0.004 0.064 -9999 0 -0.24 6 6
PLCB3 0.018 0.02 -9999 0 -0.15 3 3
FOS -0.12 0.19 -9999 0 -0.41 159 159
positive regulation of mitosis -0.04 0.13 -9999 0 -0.34 48 48
LPA/LPA1-2-3 -0.013 0.089 -9999 0 -0.22 61 61
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.011 0 -9999 0 -10000 0 0
stress fiber formation 0.007 0.068 -9999 0 -0.26 14 14
GNAZ -0.004 0.085 -9999 0 -0.25 51 51
EGFR/PI3K-beta/Gab1 -0.031 0.071 -9999 0 -0.33 15 15
positive regulation of dendritic cell cytokine production -0.017 0.087 -9999 0 -0.22 61 61
LPA/LPA2/MAGI-3 0.012 0.023 -9999 0 -0.18 3 3
ARHGEF1 0.015 0.061 -9999 0 -0.37 5 5
GNAI2 0.003 0.073 -9999 0 -0.25 38 38
GNAI3 0.003 0.073 -9999 0 -0.25 38 38
GNAI1 -0.001 0.079 -9999 0 -0.25 45 45
LPA/LPA3 -0.02 0.081 -9999 0 -0.26 50 50
LPA/LPA2 0.004 0.028 -9999 0 -0.22 3 3
LPA/LPA1 -0.007 0.085 -9999 0 -0.3 38 38
HB-EGF/EGFR -0.064 0.1 -9999 0 -0.18 221 221
HBEGF -0.078 0.12 -9999 0 -0.22 215 215
mol:DAG 0.004 0.064 -9999 0 -0.24 6 6
cAMP biosynthetic process -0.067 0.15 -9999 0 -0.28 142 142
NFKB1 0.01 0.018 -9999 0 -0.41 1 1
SRC 0.011 0 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
LYN 0.009 0.076 -9999 0 -0.27 9 9
GNAQ -0.003 0.06 -9999 0 -0.22 28 28
LPAR2 0.009 0.026 -9999 0 -0.33 3 3
LPAR3 -0.026 0.11 -9999 0 -0.37 50 50
LPAR1 -0.006 0.085 -9999 0 -0.45 16 16
IL8 -0.072 0.11 -9999 0 -0.33 42 42
PTK2 -0.004 0.083 -9999 0 -0.22 42 42
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
CASP3 -0.011 0.086 -9999 0 -0.23 61 61
EGFR 0 0.067 -9999 0 -0.4 14 14
PLCG1 -0.009 0.075 -9999 0 -0.22 45 45
PLD2 -0.005 0.084 -9999 0 -0.22 43 43
G12/G13 0.01 0.066 -9999 0 -0.22 38 38
PI3K-beta -0.014 0.05 -9999 0 -0.3 9 9
cell migration -0.014 0.049 -9999 0 -0.23 19 19
SLC9A3R2 0.011 0 -9999 0 -10000 0 0
PXN 0.007 0.069 -9999 0 -0.27 14 14
HRAS/GTP -0.041 0.14 -9999 0 -0.35 48 48
RAC1 0.011 0 -9999 0 -10000 0 0
MMP9 -0.13 0.17 -9999 0 -0.33 215 215
PRKCE 0.011 0.002 -9999 0 -10000 0 0
PRKCD 0.01 0.061 -9999 0 -0.23 5 5
Gi(beta/gamma) -0.034 0.12 -9999 0 -0.33 48 48
mol:LPA -0.004 0.034 -9999 0 -0.16 22 22
TRIP6/p130 Cas/FAK1/Paxillin -0.023 0.072 -9999 0 -0.39 9 9
MAPKKK cascade -0.04 0.13 -9999 0 -0.34 48 48
contractile ring contraction involved in cytokinesis 0.018 0.03 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.025 0.095 -9999 0 -0.24 77 77
GNA15 -0.003 0.06 -9999 0 -0.22 26 26
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.011 0 -9999 0 -10000 0 0
MAPT 0.009 0.067 -9999 0 -0.23 17 17
GNA11 -0.007 0.066 -9999 0 -0.22 37 37
Rac1/GTP -0.003 0.15 -9999 0 -0.91 14 14
MMP2 -0.011 0.13 -9999 0 -0.44 38 38
Ephrin B 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
EFNB2 0.009 0.032 -10000 0 -0.41 3 3
EPHB2 0.01 0.026 -10000 0 -0.33 3 3
EFNB1 0.015 0.037 -10000 0 -0.32 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.009 0.071 -10000 0 -0.35 4 4
Ephrin B2/EPHB1-2 -0.001 0.068 -10000 0 -0.2 53 53
neuron projection morphogenesis -0.021 0.056 -10000 0 -0.33 4 4
Ephrin B1/EPHB1-2/Tiam1 0.006 0.076 -10000 0 -0.38 4 4
DNM1 0.007 0.044 -10000 0 -0.41 6 6
cell-cell signaling 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.047 0.18 -10000 0 -0.52 65 65
YES1 -0.092 0.25 -10000 0 -0.76 65 65
Ephrin B1/EPHB1-2/NCK2 0.011 0.067 -10000 0 -0.38 1 1
PI3K -0.048 0.18 -10000 0 -0.53 65 65
mol:GDP 0.005 0.075 -10000 0 -0.37 4 4
ITGA2B 0.006 0.047 -10000 0 -0.4 7 7
endothelial cell proliferation 0.014 0.022 -10000 0 -0.23 4 4
FYN -0.092 0.25 -10000 0 -0.76 65 65
MAP3K7 -0.055 0.19 -10000 0 -0.56 65 65
FGR -0.094 0.25 -10000 0 -0.76 65 65
TIAM1 0 0.068 -10000 0 -0.41 14 14
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
RGS3 0.011 0 -10000 0 -10000 0 0
cell adhesion -0.07 0.2 -10000 0 -0.56 65 65
LYN -0.092 0.25 -10000 0 -0.76 65 65
Ephrin B1/EPHB1-2/Src Family Kinases -0.086 0.23 -10000 0 -0.7 65 65
Ephrin B1/EPHB1-2 -0.075 0.2 -10000 0 -0.6 65 65
SRC -0.091 0.25 -10000 0 -0.75 65 65
ITGB3 -0.065 0.16 -10000 0 -0.41 96 96
EPHB1 -0.029 0.12 -10000 0 -0.41 51 51
EPHB4 0.01 0.018 -10000 0 -0.41 1 1
RAC1 0.011 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.014 0.022 -10000 0 -0.23 4 4
alphaIIb/beta3 Integrin -0.041 0.12 -10000 0 -0.28 103 103
BLK -0.092 0.25 -10000 0 -0.75 65 65
HCK -0.091 0.25 -10000 0 -0.75 65 65
regulation of stress fiber formation -0.01 0.066 0.37 1 -10000 0 1
MAPK8 -0.041 0.17 -10000 0 -0.5 65 65
Ephrin B1/EPHB1-2/RGS3 0.011 0.067 -10000 0 -0.38 1 1
endothelial cell migration -0.054 0.16 -10000 0 -0.46 66 66
NCK2 0.011 0 -10000 0 -10000 0 0
PTPN13 -0.057 0.18 -10000 0 -0.52 65 65
regulation of focal adhesion formation -0.01 0.066 0.37 1 -10000 0 1
chemotaxis -0.01 0.066 0.37 1 -10000 0 1
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
Rac1/GTP -0.022 0.057 -10000 0 -0.34 4 4
angiogenesis -0.074 0.2 -10000 0 -0.6 65 65
LCK -0.091 0.25 -10000 0 -0.75 65 65
TCGA08_p53

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
CDKN2A -0.089 0.12 -9999 0 -0.23 219 219
TP53 -0.023 0.03 -9999 0 -0.34 1 1
Senescence -0.023 0.03 -9999 0 -0.34 1 1
Apoptosis -0.023 0.03 -9999 0 -0.34 1 1
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.047 0.055 -9999 0 -10000 0 0
MDM4 0.011 0 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.02 0.059 0.2 52 -10000 0 52
RFC1 0.02 0.059 0.2 52 -10000 0 52
PRKDC 0.02 0.059 0.2 52 -10000 0 52
RIPK1 0.011 0.002 -10000 0 -10000 0 0
CASP7 -0.002 0.016 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 0.018 0.064 0.19 57 -0.21 5 62
MAP2K4 0.036 0.057 -10000 0 -0.23 18 18
mol:ceramide 0.027 0.046 -10000 0 -0.24 4 4
GSN 0.017 0.063 0.2 51 -0.22 5 56
FASLG/FAS/FADD/FAF1/Caspase 8 0.037 0.055 0.17 56 -0.2 5 61
FAS 0.007 0.041 -10000 0 -0.41 5 5
BID 0.001 0.017 0.27 2 -10000 0 2
MAP3K1 0.034 0.038 -10000 0 -10000 0 0
MAP3K7 0.011 0.002 -10000 0 -10000 0 0
RB1 0.018 0.061 0.2 51 -0.22 2 53
CFLAR 0.011 0.002 -10000 0 -10000 0 0
HGF/MET -0.061 0.13 -10000 0 -0.26 158 158
ARHGDIB 0.02 0.059 0.2 52 -10000 0 52
FADD 0.011 0.003 -10000 0 -10000 0 0
actin filament polymerization -0.017 0.063 0.22 5 -0.2 51 56
NFKB1 -0.009 0.044 -10000 0 -0.65 1 1
MAPK8 0.036 0.087 -10000 0 -0.41 16 16
DFFA 0.02 0.059 0.2 52 -10000 0 52
DNA fragmentation during apoptosis 0.02 0.059 0.2 52 -10000 0 52
FAS/FADD/MET 0.017 0.037 -10000 0 -0.21 13 13
CFLAR/RIP1 0.015 0.003 -10000 0 -10000 0 0
FAIM3 0.009 0.03 -10000 0 -0.38 3 3
FAF1 0.011 0.004 -10000 0 -10000 0 0
PARP1 0.02 0.059 0.2 52 -10000 0 52
DFFB 0.02 0.059 0.2 52 -10000 0 52
CHUK -0.008 0.04 -10000 0 -0.6 1 1
FASLG 0.003 0.055 -10000 0 -0.36 12 12
FAS/FADD 0.014 0.029 -10000 0 -0.28 5 5
HGF -0.074 0.17 -10000 0 -0.41 106 106
LMNA 0.018 0.055 0.18 52 -10000 0 52
CASP6 0.02 0.059 0.2 52 -10000 0 52
CASP10 0.01 0.026 -10000 0 -0.41 2 2
CASP3 0.023 0.069 0.23 52 -10000 0 52
PTPN13 -0.041 0.14 -10000 0 -0.41 65 65
CASP8 0.001 0.021 0.33 2 -10000 0 2
IL6 -0.007 0.21 -10000 0 -1.2 16 16
MET 0.005 0.047 -10000 0 -0.37 8 8
ICAD/CAD 0.018 0.055 0.18 52 -10000 0 52
FASLG/FAS/FADD/FAF1/Caspase 10 0.028 0.046 -10000 0 -0.24 4 4
activation of caspase activity by cytochrome c 0.001 0.017 0.27 2 -10000 0 2
PAK2 0.02 0.059 0.2 52 -10000 0 52
BCL2 -0.029 0.12 -10000 0 -0.41 50 50
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.011 0 -9999 0 -10000 0 0
EGFR 0 0.067 -9999 0 -0.4 14 14
EGF/EGFR -0.067 0.1 -9999 0 -0.2 169 169
EGF/EGFR dimer/SHC/GRB2/SOS1 0.019 0.049 -9999 0 -0.19 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.12 0.19 -9999 0 -0.41 159 159
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.005 0.071 -9999 0 -0.34 23 23
EGF/EGFR dimer/SHC 0.007 0.058 -9999 0 -0.2 36 36
mol:GDP -0.011 0.041 -9999 0 -0.19 15 15
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.005 0.048 -9999 0 -0.41 7 7
GRB2/SOS1 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.009 0.036 -9999 0 -0.3 1 1
SHC1 0.011 0 -9999 0 -10000 0 0
HRAS/GDP -0.01 0.037 -9999 0 -0.31 1 1
FRAP1 0.016 0.046 -9999 0 -0.18 15 15
EGF/EGFR dimer -0.002 0.068 -9999 0 -0.25 36 36
SOS1 0.011 0 -9999 0 -10000 0 0
GRB2 0.011 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.077 0.14 -9999 0 -0.28 163 163
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.002 0.071 -9999 0 -0.28 31 31
PDGFRB -0.008 0.085 -9999 0 -0.42 22 22
SPHK1 -0.013 0.023 -9999 0 -10000 0 0
mol:S1P -0.016 0.03 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.079 0.19 -9999 0 -0.42 85 85
GNAO1 -0.1 0.19 -9999 0 -0.41 138 138
PDGFB-D/PDGFRB/PLCgamma1 -0.064 0.17 -9999 0 -0.38 89 89
PLCG1 -0.068 0.18 -9999 0 -0.39 86 86
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.008 0.085 -9999 0 -0.42 22 22
GNAI2 0.011 0.004 -9999 0 -10000 0 0
GNAI3 0.01 0.004 -9999 0 -10000 0 0
GNAI1 0.004 0.052 -9999 0 -0.42 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.001 0.06 -9999 0 -0.24 31 31
S1P1/S1P -0.023 0.065 -9999 0 -0.27 15 15
negative regulation of cAMP metabolic process -0.076 0.18 -9999 0 -0.41 85 85
MAPK3 -0.088 0.22 -9999 0 -0.55 80 80
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
RhoA/GDP 0.008 0 -9999 0 -10000 0 0
KDR -0.014 0.1 -9999 0 -0.41 31 31
PLCB2 0.004 0.068 -9999 0 -0.24 14 14
RAC1 0.011 0 -9999 0 -10000 0 0
RhoA/GTP -0.019 0.055 -9999 0 -0.23 14 14
receptor internalization -0.022 0.061 -9999 0 -0.25 15 15
PTGS2 -0.12 0.33 -9999 0 -0.98 60 60
Rac1/GTP -0.019 0.055 -9999 0 -0.23 14 14
RHOA 0.011 0 -9999 0 -10000 0 0
VEGFA 0.011 0.002 -9999 0 -10000 0 0
negative regulation of T cell proliferation -0.076 0.18 -9999 0 -0.41 85 85
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.002 0.071 -9999 0 -0.42 15 15
MAPK1 -0.088 0.22 -9999 0 -0.55 80 80
S1P1/S1P/PDGFB-D/PDGFRB -0.005 0.098 -9999 0 -0.32 26 26
ABCC1 0.01 0.002 -9999 0 -10000 0 0
Glypican 2 network

Figure S48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.01 0.015 -9999 0 -0.33 1 1
GPC2 -0.014 0.088 -9999 0 -0.33 38 38
GPC2/Midkine -0.001 0.061 -9999 0 -0.22 39 39
neuron projection morphogenesis -0.001 0.061 -9999 0 -0.22 39 39
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.011 0 -9999 0 -10000 0 0
VLDLR 0.009 0.026 -9999 0 -0.41 2 2
LRPAP1 0.011 0 -9999 0 -10000 0 0
NUDC 0.011 0 -9999 0 -10000 0 0
RELN/LRP8 -0.07 0.12 -9999 0 -0.23 193 193
CaM/Ca2+ 0.008 0 -9999 0 -10000 0 0
KATNA1 0.011 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.057 0.11 -9999 0 -0.2 188 188
IQGAP1/CaM 0.016 0 -9999 0 -10000 0 0
DAB1 -0.001 0.053 -9999 0 -0.33 13 13
IQGAP1 0.011 0 -9999 0 -10000 0 0
PLA2G7 0.006 0.043 -9999 0 -0.4 6 6
CALM1 0.011 0 -9999 0 -10000 0 0
DYNLT1 0.011 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.014 0.023 -9999 0 -0.22 5 5
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.011 0 -9999 0 -10000 0 0
CDK5R1 0.01 0.015 -9999 0 -0.33 1 1
LIS1/Poliovirus Protein 3A 0.013 0 -9999 0 -10000 0 0
CDK5R2 -0.028 0.1 -9999 0 -0.33 55 55
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.076 0.12 -9999 0 -0.23 204 204
YWHAE 0.011 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.032 0.091 -9999 0 -0.26 3 3
MAP1B -0.013 0.056 -9999 0 -0.25 27 27
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.039 0.097 -9999 0 -0.3 3 3
RELN -0.14 0.2 -9999 0 -0.41 191 191
PAFAH/LIS1 0.019 0.026 -9999 0 -0.22 6 6
LIS1/CLIP170 0.022 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.039 0.054 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.05 0.1 -9999 0 -0.19 187 187
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.04 0.095 -9999 0 -0.24 17 17
LIS1/IQGAP1 0.022 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.018 0 -9999 0 -10000 0 0
PAFAH1B3 0.005 0.044 -9999 0 -0.33 9 9
PAFAH1B2 0.01 0.018 -9999 0 -0.41 1 1
MAP1B/LIS1/Dynein heavy chain 0.012 0.037 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.026 0.088 -9999 0 -0.26 2 2
LRP8 0.008 0.033 -9999 0 -0.33 5 5
NDEL1/Katanin 60 -0.032 0.091 -9999 0 -0.26 3 3
P39/CDK5 -0.057 0.1 -9999 0 -0.31 18 18
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.022 0 -9999 0 -10000 0 0
CDK5 -0.047 0.1 -9999 0 -0.32 3 3
PPP2R5D 0.011 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.019 0 -9999 0 -10000 0 0
CSNK2A1 0.011 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.051 0.1 -9999 0 -0.18 187 187
RELN/VLDLR -0.056 0.11 -9999 0 -0.2 187 187
CDC42 0 0 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.011 0 -9999 0 -10000 0 0
GNAT1/GTP 0.002 0.025 -9999 0 -0.23 6 6
Metarhodopsin II/Arrestin 0.006 0.015 -9999 0 -0.18 3 3
PDE6G/GNAT1/GTP -0.007 0.059 -9999 0 -0.19 50 50
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.002 0.036 -9999 0 -0.33 6 6
GRK1 0.002 0.015 -9999 0 -0.33 1 1
CNG Channel -0.029 0.064 -9999 0 -0.29 13 13
mol:Na + -0.018 0.053 -9999 0 -0.34 6 6
mol:ADP 0.002 0.015 -9999 0 -0.33 1 1
RGS9-1/Gbeta5/R9AP -0.042 0.11 -9999 0 -0.23 115 115
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.018 0.054 -9999 0 -0.34 6 6
CNGB1 -0.006 0.072 -9999 0 -0.33 25 25
RDH5 0.009 0.026 -9999 0 -0.33 3 3
SAG 0.005 0.005 -9999 0 -10000 0 0
mol:Ca2+ 0.011 0.06 -9999 0 -0.32 6 6
Na + (4 Units) -0.016 0.049 -9999 0 -0.31 6 6
RGS9 -0.081 0.17 -9999 0 -0.41 115 115
GNB1/GNGT1 -0.067 0.11 -9999 0 -0.22 186 186
GNAT1/GDP -0.033 0.094 -9999 0 -0.2 116 116
GUCY2D 0.001 0.049 -9999 0 -0.33 11 11
GNGT1 -0.11 0.16 -9999 0 -0.33 186 186
GUCY2F 0.005 0.005 -9999 0 -10000 0 0
GNB5 0.011 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.003 0.067 -9999 0 -0.21 23 23
mol:11-cis-retinal 0.009 0.026 -9999 0 -0.33 3 3
mol:cGMP 0.007 0.045 -9999 0 -0.22 9 9
GNB1 0.011 0 -9999 0 -10000 0 0
Rhodopsin 0.009 0.025 -9999 0 -0.22 6 6
SLC24A1 0.011 0 -9999 0 -10000 0 0
CNGA1 0.002 0.055 -9999 0 -0.33 14 14
Metarhodopsin II 0.004 0.015 -9999 0 -0.16 4 4
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.005 0.048 -9999 0 -0.23 9 9
RGS9BP -0.006 0.071 -9999 0 -0.33 24 24
Metarhodopsin II/Transducin -0.014 0.038 -9999 0 -0.13 2 2
GCAP Family/Ca ++ 0.003 0.04 -9999 0 -0.18 24 24
PDE6A/B 0.001 0.063 -9999 0 -0.26 28 28
mol:Pi -0.042 0.11 -9999 0 -0.23 115 115
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.046 0.087 -9999 0 -0.16 187 187
PDE6B -0.008 0.086 -9999 0 -0.4 24 24
PDE6A 0.008 0.03 -9999 0 -0.33 4 4
PDE6G -0.018 0.096 -9999 0 -0.33 45 45
RHO 0.003 0.026 -9999 0 -0.33 3 3
PDE6 -0.062 0.09 -9999 0 -0.33 21 21
GUCA1A -0.004 0.06 -9999 0 -0.33 17 17
GC2/GCAP Family 0.006 0.04 -9999 0 -0.21 7 7
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.005 0.048 -9999 0 -0.41 7 7
Arf6 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
CENTA1/KIF3B 0.015 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.02 0.068 -9999 0 -0.33 1 1
EGFR 0 0.067 -9999 0 -0.4 14 14
EPHA2 0.011 0 -9999 0 -10000 0 0
USP6 0.011 0 -9999 0 -10000 0 0
IQSEC1 0.01 0.018 -9999 0 -0.41 1 1
EGFR/EGFR/EGF/EGF -0.002 0.068 -9999 0 -0.25 36 36
ARRB2 0.008 0.002 -9999 0 -10000 0 0
mol:GTP 0.015 0.011 -9999 0 -0.14 1 1
ARRB1 0.009 0.026 -9999 0 -0.41 2 2
FBXO8 0.011 0 -9999 0 -10000 0 0
TSHR -0.006 0.071 -9999 0 -0.34 22 22
EGF -0.005 0.071 -9999 0 -0.34 23 23
somatostatin receptor activity 0 0 -9999 0 -0.001 59 59
ARAP2 0.009 0.032 -9999 0 -0.41 3 3
mol:GDP -0.045 0.09 -9999 0 -0.22 70 70
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 40 40
ITGA2B 0.005 0.047 -9999 0 -0.4 7 7
ARF6 0.011 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.027 0.018 -9999 0 -0.2 2 2
ADAP1 0.011 0 -9999 0 -10000 0 0
KIF13B 0.011 0 -9999 0 -10000 0 0
HGF/MET -0.047 0.12 -9999 0 -0.28 111 111
PXN 0.011 0 -9999 0 -10000 0 0
ARF6/GTP -0.04 0.095 -9999 0 -0.23 58 58
EGFR/EGFR/EGF/EGF/ARFGEP100 0.006 0.058 -9999 0 -0.2 37 37
ADRB2 -0.063 0.16 -9999 0 -0.41 92 92
receptor agonist activity 0 0 -9999 0 0 67 67
actin filament binding 0 0 -9999 0 0 64 64
SRC 0.011 0 -9999 0 -10000 0 0
ITGB3 -0.065 0.16 -9999 0 -0.41 96 96
GNAQ 0.009 0.026 -9999 0 -0.41 2 2
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 56 56
ARF6/GDP 0.018 0.048 -9999 0 -0.28 5 5
ARF6/GDP/GULP/ACAP1 -0.046 0.11 -9999 0 -0.29 61 61
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.016 0.09 -9999 0 -0.2 100 100
ACAP1 0.007 0.036 -9999 0 -0.36 5 5
ACAP2 0.01 0.018 -9999 0 -0.41 1 1
LHCGR/beta Arrestin2 0.001 0.004 -9999 0 -10000 0 0
EFNA1 0.01 0.021 -9999 0 -0.33 2 2
HGF -0.074 0.17 -9999 0 -0.41 106 106
CYTH3 0.009 0 -9999 0 -10000 0 0
CYTH2 0.007 0.002 -9999 0 -10000 0 0
NCK1 0.009 0.026 -9999 0 -0.41 2 2
fibronectin binding 0 0 -9999 0 0 53 53
endosomal lumen acidification 0 0 0 1 0 44 45
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.035 0.13 -9999 0 -0.41 58 58
GNAQ/ARNO 0.012 0.013 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 8 8
MET 0.005 0.047 -9999 0 -0.37 8 8
GNA14 -0.031 0.13 -9999 0 -0.41 53 53
GNA15 0.006 0.039 -9999 0 -0.33 7 7
GIT1 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 56 56
GNA11 0.002 0.06 -9999 0 -0.41 11 11
LHCGR 0.001 0.003 -9999 0 -10000 0 0
AGTR1 -0.085 0.17 -9999 0 -0.41 116 116
desensitization of G-protein coupled receptor protein signaling pathway 0.001 0.004 -9999 0 -10000 0 0
IPCEF1/ARNO 0.006 0.044 -9999 0 -0.31 1 1
alphaIIb/beta3 Integrin -0.041 0.12 -9999 0 -0.28 103 103
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.007 0.05 -10000 0 -1.1 1 1
VDR 0.003 0.053 -10000 0 -0.33 13 13
FAM120B 0.011 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.011 0.086 -10000 0 -0.26 21 21
RXRs/LXRs/DNA/Oxysterols 0.017 0.086 -10000 0 -0.28 21 21
MED1 0.011 0 -10000 0 -10000 0 0
mol:9cRA 0.003 0.007 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.026 0.11 -10000 0 -0.21 125 125
RXRs/NUR77 -0.01 0.1 -10000 0 -0.21 92 92
RXRs/PPAR -0.006 0.091 -10000 0 -0.23 34 34
NCOR2 0.011 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.002 0.036 -10000 0 -0.23 13 13
RARs/VDR/DNA/Vit D3 0.018 0.039 -10000 0 -0.19 11 11
RARA 0.011 0 -10000 0 -10000 0 0
NCOA1 0.01 0.018 -10000 0 -0.41 1 1
VDR/VDR/DNA 0.003 0.053 -10000 0 -0.33 13 13
RARs/RARs/DNA/9cRA 0.017 0.031 -10000 0 -0.19 11 11
RARG 0.011 0 -10000 0 -10000 0 0
RPS6KB1 0.012 0.031 -10000 0 -0.4 1 1
RARs/THRs/DNA/SMRT -0.026 0.1 -10000 0 -0.46 7 7
THRA 0.003 0.057 -10000 0 -0.41 10 10
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.002 0.036 -10000 0 -0.23 13 13
RXRs/PPAR/9cRA/PGJ2/DNA 0 0.084 0.28 1 -0.21 67 68
NR1H4 -0.009 0.062 -10000 0 -0.33 19 19
RXRs/LXRs/DNA 0.018 0.083 -10000 0 -0.23 20 20
NR1H2 0.014 0.006 -10000 0 -10000 0 0
NR1H3 0.014 0.016 -10000 0 -0.32 1 1
RXRs/VDR/DNA/Vit D3 0 0.082 -10000 0 -0.2 66 66
NR4A1 -0.015 0.1 -10000 0 -0.41 33 33
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.003 0.071 -10000 0 -0.18 66 66
RXRG -0.045 0.14 -10000 0 -0.4 75 75
RXR alpha/CCPG 0.018 0.007 -10000 0 -10000 0 0
RXRA 0.014 0.006 -10000 0 -10000 0 0
RXRB 0.015 0.005 -10000 0 -10000 0 0
THRB -0.079 0.17 -10000 0 -0.41 112 112
PPARG -0.012 0.095 -10000 0 -0.41 29 29
PPARD 0.011 0 -10000 0 -10000 0 0
TNF 0.011 0.11 -10000 0 -0.37 21 21
mol:Oxysterols 0.003 0.006 -10000 0 -10000 0 0
cholesterol transport 0.017 0.086 -10000 0 -0.27 21 21
PPARA 0.011 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.002 0.06 -10000 0 -0.41 11 11
RXRs/NUR77/BCL2 -0.039 0.13 -10000 0 -0.25 123 123
SREBF1 0.023 0.08 -10000 0 -0.5 1 1
RXRs/RXRs/DNA/9cRA 0.001 0.084 0.27 1 -0.21 67 68
ABCA1 0.023 0.08 -10000 0 -0.5 1 1
RARs/THRs -0.021 0.1 -10000 0 -0.19 125 125
RXRs/FXR -0.007 0.091 -10000 0 -0.22 67 67
BCL2 -0.029 0.12 -10000 0 -0.41 50 50
TCGA08_rtk_signaling

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
PDGFRA -0.1 0.19 -10000 0 -0.41 145 145
HRAS 0.011 0 -10000 0 -10000 0 0
EGFR 0 0.067 -10000 0 -0.4 14 14
AKT -0.069 0.13 -10000 0 -0.23 196 196
FOXO3 0.011 0 -10000 0 -10000 0 0
AKT1 0.011 0 -10000 0 -10000 0 0
FOXO1 0.009 0.032 -10000 0 -0.41 3 3
AKT3 -0.15 0.2 -10000 0 -0.41 199 199
FOXO4 0.009 0.026 -10000 0 -0.41 2 2
MET 0.005 0.047 -10000 0 -0.37 8 8
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
PIK3CB 0.011 0 -10000 0 -10000 0 0
NRAS 0.011 0 -10000 0 -10000 0 0
PIK3CG -0.002 0.071 -10000 0 -0.4 16 16
PIK3R3 0.01 0.015 -10000 0 -0.33 1 1
PIK3R2 0.011 0 -10000 0 -10000 0 0
NF1 0.009 0.026 -10000 0 -0.41 2 2
RAS -0.023 0.074 0.18 1 -0.26 14 15
ERBB2 0.002 0.055 -10000 0 -0.33 14 14
proliferation/survival/translation 0.011 0.066 0.22 20 -10000 0 20
PI3K -0.014 0.074 0.15 2 -0.21 27 29
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
KRAS 0.01 0.015 -10000 0 -0.33 1 1
FOXO 0.023 0.022 -10000 0 -10000 0 0
AKT2 0.011 0 -10000 0 -10000 0 0
PTEN 0.006 0.045 -10000 0 -0.41 6 6
Coregulation of Androgen receptor activity

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
NRIP1 0.009 0.032 -9999 0 -0.41 3 3
SVIL -0.036 0.13 -9999 0 -0.41 59 59
ZNF318 0.01 0.005 -9999 0 -10000 0 0
JMJD2C -0.003 0.03 -9999 0 -0.11 34 34
T-DHT/AR/Ubc9 -0.026 0.1 -9999 0 -0.24 90 90
CARM1 0.011 0 -9999 0 -10000 0 0
PRDX1 0.011 0 -9999 0 -10000 0 0
PELP1 0.011 0.001 -9999 0 -10000 0 0
CTNNB1 0.011 0.002 -9999 0 -10000 0 0
AKT1 0.011 0.001 -9999 0 -10000 0 0
PTK2B 0.011 0.002 -9999 0 -10000 0 0
MED1 0.011 0.001 -9999 0 -10000 0 0
MAK -0.011 0.082 -9999 0 -0.33 32 32
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.007 0.041 -9999 0 -0.41 5 5
GSN 0.007 0.045 -9999 0 -0.41 6 6
NCOA2 -0.003 0.076 -9999 0 -0.41 18 18
NCOA6 0.011 0.002 -9999 0 -10000 0 0
DNA-PK 0.022 0.005 -9999 0 -10000 0 0
NCOA4 0.011 0 -9999 0 -10000 0 0
PIAS3 0.011 0.002 -9999 0 -10000 0 0
cell proliferation -0.012 0.024 -9999 0 -10000 0 0
XRCC5 0.011 0.001 -9999 0 -10000 0 0
UBE3A 0.012 0.002 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.046 0.12 -9999 0 -0.25 127 127
FHL2 0.001 0.11 -9999 0 -0.98 5 5
RANBP9 0.011 0.002 -9999 0 -10000 0 0
JMJD1A 0.005 0.03 -9999 0 -0.13 23 23
CDK6 0.001 0.065 -9999 0 -0.41 13 13
TGFB1I1 -0.12 0.2 -9999 0 -0.41 171 171
T-DHT/AR/CyclinD1 -0.026 0.11 -9999 0 -0.25 91 91
XRCC6 0.011 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.021 0.12 -9999 0 -0.26 97 97
CTDSP1 0.011 0.001 -9999 0 -10000 0 0
CTDSP2 0.01 0.003 -9999 0 -10000 0 0
BRCA1 0.011 0.002 -9999 0 -10000 0 0
TCF4 -0.005 0.08 -9999 0 -0.41 20 20
CDKN2A -0.13 0.17 -9999 0 -0.33 219 219
SRF 0.016 0.011 -9999 0 -10000 0 0
NKX3-1 -0.024 0.17 -9999 0 -0.81 20 20
KLK3 -0.006 0.043 -9999 0 -10000 0 0
TMF1 0.011 0.001 -9999 0 -10000 0 0
HNRNPA1 0.011 0.002 -9999 0 -10000 0 0
AOF2 0 0.002 -9999 0 -10000 0 0
APPL1 0.018 0.003 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.026 0.1 -9999 0 -0.24 90 90
AR -0.062 0.16 -9999 0 -0.42 90 90
UBA3 0.011 0.001 -9999 0 -10000 0 0
PATZ1 0.011 0.002 -9999 0 -10000 0 0
PAWR 0.011 0.001 -9999 0 -10000 0 0
PRKDC 0.011 0.001 -9999 0 -10000 0 0
PA2G4 0.011 0.002 -9999 0 -10000 0 0
UBE2I 0.011 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.022 0.094 -9999 0 -0.22 90 90
RPS6KA3 0.011 0.018 -9999 0 -0.41 1 1
T-DHT/AR/ARA70 -0.025 0.1 -9999 0 -0.24 90 90
LATS2 0.009 0.026 -9999 0 -0.41 2 2
T-DHT/AR/PRX1 -0.022 0.094 -9999 0 -0.22 90 90
Cyclin D3/CDK11 p58 0.008 0 -9999 0 -10000 0 0
VAV3 -0.07 0.14 -9999 0 -0.33 126 126
KLK2 -0.065 0.19 -9999 0 -0.87 27 27
CASP8 0.011 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.023 0.11 -9999 0 -0.23 102 102
TMPRSS2 -0.018 0.14 -9999 0 -0.88 10 10
CCND1 0.01 0.021 -9999 0 -0.33 2 2
PIAS1 0.012 0.002 -9999 0 -10000 0 0
mol:T-DHT -0.001 0.02 -9999 0 -0.066 35 35
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.012 0.004 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.032 0.11 -9999 0 -0.25 102 102
CMTM2 0.008 0.026 -9999 0 -0.33 3 3
SNURF -0.024 0.11 -9999 0 -0.41 40 40
ZMIZ1 0.008 0.037 -9999 0 -0.42 3 3
CCND3 0.011 0 -9999 0 -10000 0 0
TGIF1 0.011 0.002 -9999 0 -10000 0 0
FKBP4 0.011 0.002 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.012 0.033 -10000 0 -0.25 8 8
CRKL -0.013 0.096 -10000 0 -0.41 10 10
mol:PIP3 -0.009 0.043 0.38 6 -10000 0 6
AKT1 0.005 0.03 0.28 6 -10000 0 6
PTK2B 0.011 0 -10000 0 -10000 0 0
RAPGEF1 -0.007 0.091 -10000 0 -0.46 7 7
RANBP10 0.011 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
HGF/MET/SHIP2 -0.031 0.1 -10000 0 -0.23 111 111
MAP3K5 0.001 0.09 -10000 0 -0.39 10 10
HGF/MET/CIN85/CBL/ENDOPHILINS -0.02 0.096 -10000 0 -0.2 107 107
AP1 -0.066 0.12 -10000 0 -0.25 160 160
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.011 0 -10000 0 -10000 0 0
apoptosis -0.21 0.34 -10000 0 -0.72 160 160
STAT3 (dimer) -0.015 0.097 -10000 0 -0.2 110 110
GAB1/CRKL/SHP2/PI3K -0.034 0.076 -10000 0 -0.4 11 11
INPP5D 0.01 0.018 -10000 0 -0.41 1 1
CBL/CRK -0.006 0.092 -10000 0 -0.46 7 7
PTPN11 0.011 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.011 0 -10000 0 -10000 0 0
PTEN 0.006 0.045 -10000 0 -0.41 6 6
ELK1 -0.003 0.019 -10000 0 -0.14 8 8
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.025 0.052 -10000 0 -0.26 5 5
PAK1 0.01 0.028 0.27 6 -10000 0 6
HGF/MET/RANBP10 -0.031 0.1 -10000 0 -0.23 107 107
HRAS -0.024 0.12 -10000 0 -0.55 6 6
DOCK1 -0.009 0.097 -10000 0 -0.43 11 11
GAB1 -0.02 0.1 -10000 0 -0.44 10 10
CRK -0.013 0.096 -10000 0 -0.43 9 9
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.086 0.17 -10000 0 -0.42 107 107
JUN 0.005 0.048 -10000 0 -0.41 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.025 0.074 -10000 0 -0.17 107 107
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
cell morphogenesis 0 0.11 -10000 0 -0.4 10 10
GRB2/SHC -0.009 0.067 -10000 0 -0.29 4 4
FOS -0.12 0.19 -10000 0 -0.41 159 159
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.003 0.019 -10000 0 -0.14 8 8
HGF/MET/MUC20 -0.039 0.1 -10000 0 -0.24 111 111
cell migration -0.009 0.066 -10000 0 -0.29 4 4
GRB2 0.011 0 -10000 0 -10000 0 0
CBL 0.011 0 -10000 0 -10000 0 0
MET/RANBP10 0.012 0.033 -10000 0 -0.25 8 8
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.019 0.096 -10000 0 -0.2 110 110
MET/MUC20 0.004 0.033 -10000 0 -0.26 8 8
RAP1B 0 0.087 -10000 0 -0.43 7 7
RAP1A 0 0.087 -10000 0 -0.43 7 7
HGF/MET/RANBP9 -0.031 0.1 -10000 0 -0.23 111 111
RAF1 -0.017 0.11 -10000 0 -0.63 4 4
STAT3 -0.015 0.097 -10000 0 -0.2 110 110
cell proliferation -0.023 0.13 -10000 0 -0.28 107 107
RPS6KB1 -0.003 0.029 -10000 0 -0.14 3 3
MAPK3 -0.007 0.017 -10000 0 -10000 0 0
MAPK1 -0.007 0.017 -10000 0 -10000 0 0
RANBP9 0.011 0 -10000 0 -10000 0 0
MAPK8 0.012 0.095 -10000 0 -0.45 10 10
SRC -0.011 0.09 -10000 0 -0.37 5 5
PI3K -0.011 0.072 -10000 0 -0.3 9 9
MET/Glomulin 0.007 0.028 -10000 0 -0.22 8 8
SOS1 0.011 0 -10000 0 -10000 0 0
MAP2K1 -0.01 0.1 -10000 0 -0.58 4 4
MET 0.005 0.047 -10000 0 -0.37 8 8
MAP4K1 -0.005 0.092 -10000 0 -0.46 7 7
PTK2 0.011 0 -10000 0 -10000 0 0
MAP2K2 -0.01 0.1 -10000 0 -0.58 4 4
BAD 0.01 0.028 0.27 6 -10000 0 6
MAP2K4 0.006 0.084 -10000 0 -0.36 10 10
SHP2/GRB2/SOS1/GAB1 -0.033 0.075 -10000 0 -0.44 8 8
INPPL1 0.011 0 -10000 0 -10000 0 0
PXN 0.011 0 -10000 0 -10000 0 0
SH3KBP1 0.011 0 -10000 0 -10000 0 0
HGS -0.017 0.069 -10000 0 -0.31 4 4
PLCgamma1/PKC 0.008 0 -10000 0 -10000 0 0
HGF -0.074 0.17 -10000 0 -0.41 106 106
RASA1 0.007 0.041 -10000 0 -0.41 5 5
NCK1 0.009 0.026 -10000 0 -0.41 2 2
PTPRJ 0.011 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.012 0.076 -10000 0 -0.29 6 6
PDPK1 -0.001 0.034 0.31 6 -10000 0 6
HGF/MET/SHIP -0.032 0.1 -10000 0 -0.23 112 112
Syndecan-4-mediated signaling events

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
PTK2 0.014 0.043 -9999 0 -0.41 5 5
Syndecan-4/Syndesmos -0.011 0.068 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.12 0.11 -9999 0 -0.35 33 33
Syndecan-4/ADAM12 -0.014 0.071 -9999 0 -10000 0 0
CCL5 0.003 0.054 -9999 0 -0.37 11 11
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
DNM2 0.011 0 -9999 0 -10000 0 0
ITGA5 0.011 0 -9999 0 -10000 0 0
SDCBP 0.011 0 -9999 0 -10000 0 0
PLG -0.026 0.12 -9999 0 -0.38 50 50
ADAM12 0.003 0.051 -9999 0 -0.33 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.039 0.042 -9999 0 -0.12 24 24
Syndecan-4/Laminin alpha1 -0.06 0.095 -9999 0 -0.34 16 16
Syndecan-4/CXCL12/CXCR4 -0.12 0.11 -9999 0 -0.37 33 33
Syndecan-4/Laminin alpha3 -0.016 0.074 -9999 0 -10000 0 0
MDK 0.01 0.015 -9999 0 -0.33 1 1
Syndecan-4/FZD7 -0.041 0.098 -9999 0 -0.37 8 8
Syndecan-4/Midkine -0.011 0.068 -9999 0 -10000 0 0
FZD7 -0.055 0.15 -9999 0 -0.41 83 83
Syndecan-4/FGFR1/FGF -0.11 0.1 -9999 0 -0.36 29 29
THBS1 -0.046 0.14 -9999 0 -0.41 71 71
integrin-mediated signaling pathway -0.015 0.073 -9999 0 -0.37 2 2
positive regulation of MAPKKK cascade -0.12 0.11 -9999 0 -0.35 33 33
Syndecan-4/TACI -0.017 0.074 -9999 0 -0.34 2 2
CXCR4 0.011 0 -9999 0 -10000 0 0
cell adhesion 0.013 0.051 -9999 0 -0.26 5 5
Syndecan-4/Dynamin -0.011 0.068 -9999 0 -10000 0 0
Syndecan-4/TSP1 -0.037 0.093 -9999 0 -0.37 8 8
Syndecan-4/GIPC -0.011 0.068 -9999 0 -10000 0 0
Syndecan-4/RANTES -0.014 0.073 -9999 0 -0.36 2 2
ITGB1 0.011 0 -9999 0 -10000 0 0
LAMA1 -0.1 0.16 -9999 0 -0.33 175 175
LAMA3 0 0.068 -9999 0 -0.41 14 14
RAC1 0.011 0 -9999 0 -10000 0 0
PRKCA -0.007 0.099 -9999 0 -0.37 34 34
Syndecan-4/alpha-Actinin -0.011 0.068 -9999 0 -10000 0 0
TFPI -0.038 0.14 -9999 0 -0.41 61 61
F2 -0.024 0.095 -9999 0 -0.33 46 46
alpha5/beta1 Integrin 0.016 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.058 0.096 -9999 0 -0.32 20 20
ACTN1 0.011 0 -9999 0 -10000 0 0
TNC 0.002 0.062 -9999 0 -0.4 12 12
Syndecan-4/CXCL12 -0.13 0.12 -9999 0 -0.36 41 41
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
CXCL12 -0.26 0.2 -9999 0 -0.41 334 334
TNFRSF13B -0.002 0.058 -9999 0 -0.33 16 16
FGF2 -0.22 0.21 -9999 0 -0.41 284 284
FGFR1 0.01 0.018 -9999 0 -0.41 1 1
Syndecan-4/PI-4-5-P2 -0.018 0.067 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.011 0.04 -9999 0 -0.39 5 5
cell migration -0.017 0.019 -9999 0 -10000 0 0
PRKCD 0.015 0.008 -9999 0 -10000 0 0
vasculogenesis -0.036 0.091 -9999 0 -0.36 8 8
SDC4 -0.018 0.071 -9999 0 -10000 0 0
Syndecan-4/Tenascin C -0.015 0.075 -9999 0 -0.38 2 2
Syndecan-4/PI-4-5-P2/PKC alpha -0.031 0.034 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.011 0.068 -9999 0 -10000 0 0
MMP9 -0.13 0.17 -9999 0 -0.33 215 215
Rac1/GTP 0.013 0.052 -9999 0 -0.26 5 5
cytoskeleton organization -0.011 0.067 -9999 0 -10000 0 0
GIPC1 0.011 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.033 0.095 -9999 0 -0.36 10 10
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.004 0.056 -9999 0 -0.2 36 36
RGS9BP -0.006 0.071 -9999 0 -0.33 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.002 0.015 -9999 0 -0.33 1 1
mol:Na + -0.004 0.053 -9999 0 -0.23 27 27
mol:ADP 0.007 0.015 -9999 0 -0.22 2 2
GNAT2 0.007 0.026 -9999 0 -0.33 3 3
RGS9-1/Gbeta5/R9AP -0.042 0.11 -9999 0 -0.23 115 115
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.007 0.015 -9999 0 -0.19 3 3
GRK7 0.006 0.016 -9999 0 -0.33 1 1
CNGB3 -0.013 0.087 -9999 0 -0.41 24 24
Cone Metarhodopsin II/X-Arrestin 0.002 0.011 -9999 0 -0.23 1 1
mol:Ca2+ -0.002 0.048 -9999 0 -0.21 26 26
Cone PDE6 -0.031 0.092 -9999 0 -0.19 111 111
Cone Metarhodopsin II 0.006 0.011 -9999 0 -0.16 2 2
Na + (4 Units) -0.001 0.048 -9999 0 -0.21 26 26
GNAT2/GDP -0.03 0.093 -9999 0 -0.19 115 115
GNB5 0.011 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.008 0.016 -9999 0 -0.16 4 4
Cone Transducin 0.004 0.06 -9999 0 -0.21 36 36
SLC24A2 0.004 0.015 -9999 0 -0.33 1 1
GNB3/GNGT2 -0.003 0.075 -9999 0 -0.29 34 34
GNB3 -0.015 0.1 -9999 0 -0.41 32 32
GNAT2/GTP 0.006 0.018 -9999 0 -0.23 3 3
CNGA3 0.005 0.026 -9999 0 -0.33 3 3
ARR3 0.003 0.015 -9999 0 -0.33 1 1
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.004 0.053 -9999 0 -0.23 27 27
mol:Pi -0.042 0.11 -9999 0 -0.23 115 115
Cone CNG Channel -0.01 0.041 -9999 0 -0.18 24 24
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.004 0.015 -9999 0 -0.33 1 1
RGS9 -0.081 0.17 -9999 0 -0.41 115 115
PDE6C 0.003 0.015 -9999 0 -0.33 1 1
GNGT2 0.009 0.032 -9999 0 -0.41 3 3
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.002 0.004 -9999 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.037 0.11 -9999 0 -0.28 96 96
AKT1 0.022 0.15 -9999 0 -0.51 33 33
PTK2B -0.02 0.15 -9999 0 -0.55 31 31
VEGFR2 homodimer/Frs2 -0.005 0.14 -9999 0 -0.56 31 31
CAV1 -0.063 0.16 -9999 0 -0.41 93 93
CALM1 0.011 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.005 0.13 -9999 0 -0.52 31 31
endothelial cell proliferation 0.018 0.15 -9999 0 -0.45 39 39
mol:Ca2+ 0 0.14 -9999 0 -0.54 31 31
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.011 0.12 -9999 0 -0.49 31 31
RP11-342D11.1 -0.007 0.14 -9999 0 -0.55 31 31
CDH5 0.005 0.048 -9999 0 -0.41 7 7
VEGFA homodimer 0.029 0.01 -9999 0 -0.2 1 1
SHC1 0.011 0 -9999 0 -10000 0 0
SHC2 -0.049 0.15 -9999 0 -0.41 75 75
HRAS/GDP -0.034 0.11 -9999 0 -0.47 31 31
SH2D2A -0.002 0.065 -9999 0 -0.33 20 20
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.034 0.11 -9999 0 -0.46 31 31
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.002 0.14 -9999 0 -0.53 31 31
VEGFR1 homodimer 0.011 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.037 0.12 -9999 0 -0.51 31 31
GRB10 0 0.15 -9999 0 -0.55 31 31
PTPN11 0.011 0 -9999 0 -10000 0 0
GRB2 0.011 0 -9999 0 -10000 0 0
PAK1 0.011 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.013 0.13 -9999 0 -0.5 31 31
HRAS 0.011 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.012 0.12 -9999 0 -0.38 31 31
HIF1A 0.011 0 -9999 0 -10000 0 0
FRS2 0.011 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.01 0.12 -9999 0 -0.48 31 31
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.006 0.082 -9999 0 -0.41 21 21
Nck/Pak 0.015 0.018 -9999 0 -0.28 2 2
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.005 0.13 -9999 0 -0.52 31 31
mol:GDP -0.036 0.12 -9999 0 -0.5 31 31
mol:NADP 0.025 0.12 -9999 0 -0.4 31 31
eNOS/Hsp90 0.029 0.11 -9999 0 -0.38 31 31
PIK3R1 0.007 0.041 -9999 0 -0.41 5 5
mol:IP3 -0.001 0.15 -9999 0 -0.55 31 31
HIF1A/ARNT 0.016 0 -9999 0 -10000 0 0
SHB 0.011 0 -9999 0 -10000 0 0
VEGFA 0.013 0.001 -9999 0 -10000 0 0
VEGFC 0.004 0.055 -9999 0 -0.41 9 9
FAK1/Vinculin -0.008 0.16 -9999 0 -0.6 31 31
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.026 0.16 -9999 0 -0.58 31 31
PTPN6 0.01 0.015 -9999 0 -0.33 1 1
EPAS1 -0.001 0.084 -9999 0 -0.33 31 31
mol:L-citrulline 0.025 0.12 -9999 0 -0.4 31 31
ITGAV 0.011 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.011 0.12 -9999 0 -0.49 31 31
VEGFR2 homodimer/VEGFA homodimer -0.007 0.16 -9999 0 -0.6 31 31
VEGFR2/3 heterodimer -0.015 0.15 -9999 0 -0.58 31 31
VEGFB 0.011 0 -9999 0 -10000 0 0
MAPK11 -0.002 0.15 -9999 0 -0.56 32 32
VEGFR2 homodimer -0.011 0.16 -9999 0 -0.65 31 31
FLT1 0.011 0 -9999 0 -10000 0 0
NEDD4 -0.019 0.11 -9999 0 -0.41 40 40
MAPK3 -0.005 0.14 -9999 0 -0.51 32 32
MAPK1 -0.005 0.14 -9999 0 -0.51 32 32
VEGFA145/NRP2 0.004 0.063 -9999 0 -0.28 25 25
VEGFR1/2 heterodimer -0.005 0.14 -9999 0 -0.56 31 31
KDR -0.011 0.16 -9999 0 -0.65 31 31
VEGFA165/NRP1/VEGFR2 homodimer -0.009 0.16 -9999 0 -0.56 33 33
SRC 0.011 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.005 0.15 -9999 0 -0.52 32 32
PI3K 0.012 0.16 -9999 0 -0.57 33 33
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.004 0.13 -9999 0 -0.52 31 31
FES -0.001 0.15 -9999 0 -0.55 32 32
GAB1 -0.039 0.14 -9999 0 -0.59 31 31
VEGFR2 homodimer/VEGFA homodimer/Src 0.005 0.13 -9999 0 -0.52 31 31
CTNNB1 0.011 0 -9999 0 -10000 0 0
SOS1 0.011 0 -9999 0 -10000 0 0
ARNT 0.011 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.014 0.13 -9999 0 -0.41 40 40
VEGFR2 homodimer/VEGFA homodimer/Yes 0.005 0.13 -9999 0 -0.52 31 31
PI3K/GAB1 0.022 0.15 -9999 0 -0.53 33 33
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.015 0.12 -9999 0 -0.47 31 31
PRKACA 0.011 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.01 0.15 -9999 0 -0.57 31 31
HSP90AA1 0.011 0 -9999 0 -10000 0 0
CDC42 -0.001 0.15 -9999 0 -0.56 31 31
actin cytoskeleton reorganization -0.002 0.13 -9999 0 -0.52 31 31
PTK2 -0.015 0.17 -9999 0 -0.65 31 31
EDG1 -0.007 0.14 -9999 0 -0.55 31 31
mol:DAG -0.001 0.15 -9999 0 -0.55 31 31
CaM/Ca2+ 0.004 0.14 -9999 0 -0.5 31 31
MAP2K3 0.004 0.14 -9999 0 -0.53 31 31
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0 0.15 -9999 0 -0.57 31 31
PLCG1 -0.001 0.15 -9999 0 -0.56 31 31
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.011 0.12 -9999 0 -0.49 31 31
IQGAP1 0.011 0 -9999 0 -10000 0 0
YES1 0.011 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.005 0.13 -9999 0 -0.52 31 31
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.004 0.13 -9999 0 -0.52 31 31
cell migration 0.014 0.15 -9999 0 -0.53 31 31
mol:PI-3-4-5-P3 0.013 0.15 -9999 0 -0.52 33 33
FYN 0.011 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.001 0.14 -9999 0 -0.52 31 31
mol:NO 0.025 0.12 -9999 0 -0.4 31 31
PXN 0.011 0 -9999 0 -10000 0 0
HRAS/GTP -0.034 0.11 -9999 0 -0.46 31 31
VEGFR2 homodimer/VEGFA homodimer/GRB10 0 0.15 -9999 0 -0.57 31 31
VHL 0.01 0.018 -9999 0 -0.41 1 1
ITGB3 -0.065 0.16 -9999 0 -0.41 96 96
NOS3 0.023 0.13 -9999 0 -0.45 31 31
VEGFR2 homodimer/VEGFA homodimer/Sck -0.027 0.15 -9999 0 -0.55 31 31
RAC1 0.011 0 -9999 0 -10000 0 0
PRKCA -0.007 0.15 -9999 0 -0.51 36 36
PRKCB -0.006 0.15 -9999 0 -0.52 34 34
VCL 0.011 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.006 0.14 -9999 0 -0.55 31 31
VEGFR1/2 heterodimer/VEGFA homodimer 0.005 0.13 -9999 0 -0.52 31 31
VEGFA165/NRP2 0.004 0.063 -9999 0 -0.28 25 25
MAPKKK cascade 0.021 0.13 -9999 0 -0.47 31 31
NRP2 -0.009 0.09 -9999 0 -0.41 25 25
VEGFC homodimer 0.004 0.054 -9999 0 -0.41 9 9
NCK1 0.009 0.026 -9999 0 -0.41 2 2
ROCK1 0.011 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.008 0.16 -9999 0 -0.6 31 31
MAP3K13 -0.002 0.15 -9999 0 -0.56 31 31
PDPK1 0.02 0.14 -9999 0 -0.46 33 33
Glucocorticoid receptor regulatory network

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
PCK2 -0.01 0.04 -10000 0 -10000 0 0
SMARCC2 0.012 0.002 -10000 0 -10000 0 0
SMARCC1 0.012 0.003 -10000 0 -10000 0 0
TBX21 0.007 0.12 -10000 0 -0.6 12 12
SUMO2 0.01 0.005 -10000 0 -10000 0 0
STAT1 (dimer) 0.017 0.015 -10000 0 -0.32 1 1
FKBP4 0.011 0 -10000 0 -10000 0 0
FKBP5 0.005 0.052 -10000 0 -0.41 8 8
GR alpha/HSP90/FKBP51/HSP90 0 0.1 0.21 13 -0.26 47 60
PRL -0.025 0.24 -10000 0 -1.2 18 18
cortisol/GR alpha (dimer)/TIF2 0.025 0.16 0.42 24 -0.43 8 32
RELA -0.016 0.062 -10000 0 -0.24 7 7
FGG 0.003 0.14 0.37 15 -0.45 5 20
GR beta/TIF2 -0.016 0.13 0.22 13 -0.31 65 78
IFNG -0.092 0.14 -10000 0 -0.44 24 24
apoptosis -0.077 0.19 0.47 8 -0.5 50 58
CREB1 0.008 0.023 -10000 0 -10000 0 0
histone acetylation 0.039 0.075 0.24 10 -0.24 9 19
BGLAP 0.025 0.065 -10000 0 -10000 0 0
GR/PKAc 0.004 0.093 0.2 11 -0.23 41 52
NF kappa B1 p50/RelA -0.025 0.11 -10000 0 -0.33 28 28
SMARCD1 0.012 0.003 -10000 0 -10000 0 0
MDM2 0.022 0.041 0.18 15 -10000 0 15
GATA3 0.001 0.07 -10000 0 -0.35 20 20
AKT1 0.005 0.002 -10000 0 -10000 0 0
CSF2 0.018 0.067 -10000 0 -0.32 1 1
GSK3B 0.01 0.005 -10000 0 -10000 0 0
NR1I3 -0.055 0.17 0.45 8 -0.55 22 30
CSN2 0.002 0.11 0.31 13 -0.39 3 16
BRG1/BAF155/BAF170/BAF60A 0.035 0.009 -10000 0 -10000 0 0
NFATC1 0.001 0.07 -10000 0 -0.41 15 15
POU2F1 0.008 0.042 -10000 0 -0.23 14 14
CDKN1A 0.032 0.061 -10000 0 -1.3 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.006 -10000 0 -10000 0 0
SFN -0.24 0.15 -10000 0 -0.33 388 388
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.11 0.14 0.22 16 -0.34 77 93
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.11 0.29 0.43 8 -0.8 69 77
JUN -0.039 0.1 -10000 0 -0.36 15 15
IL4 0.007 0.081 -10000 0 -0.56 1 1
CDK5R1 0.01 0.015 -10000 0 -0.33 1 1
PRKACA 0.011 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.18 0.17 -10000 0 -0.37 177 177
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.007 0.096 0.21 11 -0.24 35 46
cortisol/GR alpha (monomer) 0.027 0.18 0.48 25 -0.47 4 29
NCOA2 -0.003 0.077 -10000 0 -0.41 18 18
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.15 0.2 -10000 0 -0.44 159 159
AP-1/NFAT1-c-4 -0.16 0.18 -10000 0 -0.47 68 68
AFP -0.015 0.079 -10000 0 -0.44 2 2
SUV420H1 0.011 0 -10000 0 -10000 0 0
IRF1 0.025 0.089 0.31 4 -10000 0 4
TP53 0.027 0.028 -10000 0 -0.42 2 2
PPP5C 0.011 0 -10000 0 -10000 0 0
KRT17 -0.12 0.19 -10000 0 -0.6 28 28
KRT14 -0.051 0.11 0.43 1 -10000 0 1
TBP 0.019 0 -10000 0 -10000 0 0
CREBBP 0.031 0.046 -10000 0 -0.32 4 4
HDAC1 0.01 0.003 -10000 0 -10000 0 0
HDAC2 0.01 0.002 -10000 0 -10000 0 0
AP-1 -0.16 0.18 -10000 0 -0.47 69 69
MAPK14 0.01 0.005 -10000 0 -10000 0 0
MAPK10 -0.079 0.17 -10000 0 -0.41 111 111
MAPK11 0.008 0.026 -10000 0 -0.41 2 2
KRT5 -0.14 0.21 -10000 0 -0.68 31 31
interleukin-1 receptor activity -0.001 0.002 -10000 0 -10000 0 0
NCOA1 0.012 0.018 -10000 0 -0.41 1 1
STAT1 0.017 0.015 -10000 0 -0.32 1 1
CGA 0.006 0.083 -10000 0 -0.35 4 4
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.008 0.099 0.26 8 -0.41 3 11
MAPK3 0.01 0.006 -10000 0 -10000 0 0
MAPK1 0.01 0.005 -10000 0 -10000 0 0
ICAM1 -0.014 0.11 -10000 0 -0.44 4 4
NFKB1 -0.017 0.065 -10000 0 -0.24 10 10
MAPK8 -0.015 0.097 0.26 1 -0.31 16 17
MAPK9 0.01 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.084 0.2 0.47 8 -0.52 54 62
BAX 0.034 0.025 -10000 0 -10000 0 0
POMC -0.018 0.21 -10000 0 -1.3 10 10
EP300 0.032 0.038 -10000 0 -0.23 2 2
cortisol/GR alpha (dimer)/p53 0.044 0.16 0.44 25 -0.46 2 27
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.033 0.14 6 -10000 0 6
SGK1 0.045 0.094 -10000 0 -1.3 2 2
IL13 -0.057 0.11 -10000 0 -0.56 4 4
IL6 -0.037 0.19 -10000 0 -0.77 23 23
PRKACG 0.003 0.005 -10000 0 -10000 0 0
IL5 -0.055 0.098 -10000 0 -0.54 3 3
IL2 -0.087 0.13 -10000 0 -0.48 12 12
CDK5 0.01 0.003 -10000 0 -10000 0 0
PRKACB 0.006 0.045 -10000 0 -0.41 6 6
HSP90AA1 0.011 0 -10000 0 -10000 0 0
IL8 -0.051 0.14 -10000 0 -0.42 15 15
CDK5R1/CDK5 0.014 0.013 -10000 0 -0.22 1 1
NF kappa B1 p50/RelA/PKAc -0.002 0.085 -10000 0 -0.3 12 12
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.041 0.14 0.4 25 -0.42 2 27
SMARCA4 0.012 0.002 -10000 0 -10000 0 0
chromatin remodeling 0.025 0.11 0.29 15 -0.43 4 19
NF kappa B1 p50/RelA/Cbp 0.021 0.1 -10000 0 -0.34 9 9
JUN (dimer) -0.039 0.1 -10000 0 -0.36 15 15
YWHAH 0.011 0 -10000 0 -10000 0 0
VIPR1 0.013 0.09 -10000 0 -0.47 5 5
NR3C1 -0.017 0.16 0.31 15 -0.4 65 80
NR4A1 -0.022 0.12 -10000 0 -0.43 42 42
TIF2/SUV420H1 0.006 0.054 -10000 0 -0.28 18 18
MAPKKK cascade -0.077 0.19 0.47 8 -0.5 50 58
cortisol/GR alpha (dimer)/Src-1 0.038 0.15 0.43 25 -0.4 4 29
PBX1 -0.009 0.095 -10000 0 -0.35 35 35
POU1F1 -0.002 0.047 -10000 0 -0.25 18 18
SELE -0.098 0.32 -10000 0 -0.92 64 64
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.025 0.11 0.29 15 -0.43 4 19
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.041 0.14 0.4 25 -0.42 2 27
mol:cortisol 0.023 0.076 0.26 24 -10000 0 24
MMP1 -0.12 0.11 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.008 0.046 -9999 0 -0.24 15 15
NFATC2 -0.01 0.079 -9999 0 -0.24 53 53
NFATC3 0.015 0.018 -9999 0 -10000 0 0
CD40LG -0.054 0.18 -9999 0 -0.52 36 36
PTGS2 -0.074 0.21 -9999 0 -0.51 65 65
JUNB 0.007 0.041 -9999 0 -0.41 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.007 -9999 0 -10000 0 0
CaM/Ca2+ -0.001 0.007 -9999 0 -10000 0 0
CALM1 0.011 0.005 -9999 0 -10000 0 0
JUN 0.006 0.049 -9999 0 -0.41 7 7
mol:Ca2+ -0.002 0.007 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.004 0.004 -9999 0 -10000 0 0
FOSL1 -0.015 0.09 -9999 0 -0.33 40 40
CREM 0.011 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.036 0.082 -9999 0 -0.33 19 19
FOS -0.12 0.19 -9999 0 -0.41 159 159
IFNG -0.066 0.19 -9999 0 -0.48 56 56
AP-1/NFAT1-c-4 -0.062 0.2 -9999 0 -0.53 43 43
FASLG -0.053 0.18 -9999 0 -0.51 38 38
NFAT1-c-4/ICER1 -0.01 0.082 -9999 0 -0.27 23 23
IL2RA -0.055 0.18 -9999 0 -0.51 40 40
FKBP12/FK506 0.008 0 -9999 0 -10000 0 0
CSF2 -0.054 0.18 -9999 0 -0.48 38 38
JunB/Fra1/NFAT1-c-4 -0.022 0.084 -9999 0 -0.27 25 25
IL4 -0.054 0.17 -9999 0 -0.49 34 34
IL2 -0.009 0.03 -9999 0 -10000 0 0
IL3 -0.011 0.015 -9999 0 -10000 0 0
FKBP1A 0.011 0 -9999 0 -10000 0 0
BATF3 0.01 0.015 -9999 0 -0.33 1 1
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.011 0 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.008 0.037 -9999 0 -0.41 4 4
ELF1 0.01 0.043 -9999 0 -0.38 4 4
CCNA2 -0.061 0.14 -9999 0 -0.33 111 111
PIK3CA 0.011 0.018 -9999 0 -0.41 1 1
JAK3 0.009 0.03 -9999 0 -0.33 4 4
PIK3R1 0.008 0.041 -9999 0 -0.41 5 5
JAK1 0.01 0.026 -9999 0 -0.41 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.053 0.045 -9999 0 -0.33 3 3
SHC1 0.012 0 -9999 0 -10000 0 0
SP1 -0.043 0.13 -9999 0 -0.3 100 100
IL2RA 0.013 0.059 -9999 0 -0.36 4 4
IL2RB 0.011 0.018 -9999 0 -0.41 1 1
SOS1 0.012 0 -9999 0 -10000 0 0
IL2RG 0.005 0.048 -9999 0 -0.36 9 9
G1/S transition of mitotic cell cycle -0.1 0.27 -9999 0 -0.64 101 101
PTPN11 0.012 0 -9999 0 -10000 0 0
CCND2 -0.1 0.26 -9999 0 -0.65 100 100
LCK 0.008 0.035 -9999 0 -0.34 5 5
GRB2 0.012 0 -9999 0 -10000 0 0
IL2 -0.006 0.059 -9999 0 -0.33 17 17
CDK6 0.001 0.065 -9999 0 -0.41 13 13
CCND3 0.056 0.041 -9999 0 -0.43 1 1
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.015 0.086 -10000 0 -0.3 29 29
IKBKB 0.027 0.048 0.16 1 -0.17 3 4
AKT1 0.004 0.066 0.19 4 -0.2 28 32
IKBKG 0.029 0.049 0.16 1 -0.18 2 3
CALM1 0.02 0.08 0.18 6 -0.25 20 26
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
MAP3K1 0.004 0.11 -10000 0 -0.43 26 26
MAP3K7 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ 0.015 0.083 0.18 65 -0.27 20 85
DOK1 0.011 0 -10000 0 -10000 0 0
AP-1 0 0.077 0.14 40 -0.19 30 70
LYN 0.011 0 -10000 0 -10000 0 0
BLNK 0.009 0.03 -10000 0 -0.38 3 3
SHC1 0.011 0 -10000 0 -10000 0 0
BCR complex -0.024 0.096 -10000 0 -0.24 81 81
CD22 -0.06 0.13 -10000 0 -0.52 31 31
CAMK2G 0.025 0.076 0.18 4 -0.23 20 24
CSNK2A1 0.011 0 -10000 0 -10000 0 0
INPP5D 0.01 0.018 -10000 0 -0.41 1 1
SHC/GRB2/SOS1 -0.02 0.048 -10000 0 -0.3 3 3
GO:0007205 0.015 0.084 0.18 65 -0.27 20 85
SYK 0.01 0.015 -10000 0 -0.33 1 1
ELK1 0.02 0.08 0.17 60 -0.25 20 80
NFATC1 0.004 0.1 0.18 1 -0.36 27 28
B-cell antigen/BCR complex -0.024 0.096 -10000 0 -0.24 81 81
PAG1/CSK 0.015 0.022 -10000 0 -0.28 3 3
NFKBIB 0.019 0.021 0.083 1 -0.12 1 2
HRAS 0.02 0.072 0.19 1 -0.23 20 21
NFKBIA 0.019 0.021 0.083 1 -0.12 1 2
NF-kappa-B/RelA/I kappa B beta 0.022 0.02 0.084 1 -0.14 1 2
RasGAP/Csk 0 0.074 -10000 0 -0.36 4 4
mol:GDP 0.014 0.08 0.18 6 -0.26 20 26
PTEN 0.006 0.045 -10000 0 -0.41 6 6
CD79B -0.009 0.089 -10000 0 -0.41 25 25
NF-kappa-B/RelA/I kappa B alpha 0.022 0.02 0.084 1 -0.14 1 2
GRB2 0.011 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.008 0.12 -10000 0 -0.44 28 28
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
mol:IP3 0.015 0.084 0.18 65 -0.27 20 85
CSK 0.011 0 -10000 0 -10000 0 0
FOS -0.03 0.12 0.17 45 -0.25 43 88
CHUK 0.029 0.049 0.16 1 -0.18 2 3
IBTK 0.011 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.013 0.047 -10000 0 -0.3 5 5
PTPN6 -0.034 0.14 -10000 0 -0.49 30 30
RELA 0.011 0 -10000 0 -10000 0 0
BCL2A1 0.019 0.016 -10000 0 -10000 0 0
VAV2 -0.009 0.12 -10000 0 -0.45 25 25
ubiquitin-dependent protein catabolic process 0.022 0.021 0.086 1 -0.12 1 2
BTK -0.005 0.066 -10000 0 -1.1 2 2
CD19 -0.041 0.11 -10000 0 -0.45 26 26
MAP4K1 0.003 0.053 -10000 0 -0.33 13 13
CD72 0.009 0.026 -10000 0 -0.33 3 3
PAG1 0.009 0.032 -10000 0 -0.41 3 3
MAPK14 0.011 0.097 -10000 0 -0.37 26 26
SH3BP5 -0.051 0.15 -10000 0 -0.41 77 77
PIK3AP1 0.022 0.093 0.2 62 -0.3 20 82
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.013 0.055 -10000 0 -0.34 5 5
RAF1 0.025 0.069 0.19 1 -0.31 3 4
RasGAP/p62DOK/SHIP -0.025 0.058 -10000 0 -0.34 4 4
CD79A -0.027 0.11 -10000 0 -0.34 58 58
re-entry into mitotic cell cycle 0 0.076 0.14 40 -0.19 30 70
RASA1 0.007 0.041 -10000 0 -0.41 5 5
MAPK3 0.034 0.062 0.18 1 -0.26 3 4
MAPK1 0.034 0.062 0.18 1 -0.26 3 4
CD72/SHP1 -0.026 0.13 -10000 0 -0.47 29 29
NFKB1 0.01 0.018 -10000 0 -0.41 1 1
MAPK8 0.01 0.1 -10000 0 -0.36 29 29
actin cytoskeleton organization 0 0.1 -10000 0 -0.39 25 25
NF-kappa-B/RelA 0.047 0.038 0.16 1 -0.18 1 2
Calcineurin -0.011 0.045 -10000 0 -0.31 5 5
PI3K -0.047 0.094 -10000 0 -0.36 32 32
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.019 0.095 0.2 64 -0.31 20 84
SOS1 0.011 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.025 0.17 -10000 0 -0.64 34 34
DAPP1 -0.05 0.18 -10000 0 -0.72 34 34
cytokine secretion 0.005 0.097 0.18 3 -0.33 27 30
mol:DAG 0.015 0.084 0.18 65 -0.27 20 85
PLCG2 0.009 0.024 -10000 0 -0.37 2 2
MAP2K1 0.029 0.066 0.19 1 -0.29 3 4
B-cell antigen/BCR complex/FcgammaRIIB -0.013 0.085 -10000 0 -0.2 83 83
mol:PI-3-4-5-P3 -0.034 0.073 0.21 5 -0.27 30 35
ETS1 0.029 0.072 0.2 1 -0.3 3 4
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.002 0.071 -10000 0 -0.35 3 3
B-cell antigen/BCR complex/LYN -0.033 0.11 -10000 0 -0.47 26 26
MALT1 0.011 0 -10000 0 -10000 0 0
TRAF6 0.011 0 -10000 0 -10000 0 0
RAC1 -0.001 0.11 -10000 0 -0.42 25 25
B-cell antigen/BCR complex/LYN/SYK -0.055 0.12 -10000 0 -0.48 27 27
CARD11 0.016 0.085 0.17 62 -0.26 21 83
FCGR2B 0.008 0.035 -10000 0 -0.39 4 4
PPP3CA 0.011 0 -10000 0 -10000 0 0
BCL10 0.011 0 -10000 0 -10000 0 0
IKK complex 0.02 0.025 0.11 1 -10000 0 1
PTPRC 0.003 0.056 -10000 0 -0.4 10 10
PDPK1 -0.001 0.062 0.17 4 -0.19 28 32
PPP3CB 0.011 0 -10000 0 -10000 0 0
PPP3CC 0.008 0.037 -10000 0 -0.41 4 4
POU2F2 0.02 0.015 -10000 0 -0.1 1 1
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.099 0.18 -9999 0 -0.41 138 138
CDC42/GTP -0.03 0.1 -9999 0 -0.35 13 13
PLCG1 -0.031 0.1 -9999 0 -0.35 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.011 0 -9999 0 -10000 0 0
GNAI3 0.011 0 -9999 0 -10000 0 0
G12/G13 0.016 0 -9999 0 -10000 0 0
cell migration -0.03 0.099 -9999 0 -0.34 13 13
S1PR5 -0.001 0.064 -9999 0 -0.35 17 17
S1PR4 0.009 0.03 -9999 0 -0.38 3 3
MAPK3 -0.031 0.1 -9999 0 -0.36 13 13
MAPK1 -0.031 0.1 -9999 0 -0.36 13 13
S1P/S1P5/Gi -0.042 0.11 -9999 0 -0.21 152 152
GNAI1 0.005 0.052 -9999 0 -0.41 8 8
CDC42/GDP 0.008 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0.008 0.037 -9999 0 -0.19 17 17
RHOA 0.024 0.015 -9999 0 -0.18 2 2
S1P/S1P4/Gi -0.039 0.11 -9999 0 -0.21 140 140
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.001 0.07 -9999 0 -0.41 15 15
S1P/S1P4/G12/G13 0.02 0.016 -9999 0 -0.19 3 3
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.011 0 -9999 0 -10000 0 0
CDC42 0.011 0 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.012 0.045 -9999 0 -0.23 18 18
EPHB2 0.009 0.026 -9999 0 -0.33 3 3
Syndecan-2/TACI 0.006 0.051 -9999 0 -0.21 28 28
LAMA1 -0.1 0.16 -9999 0 -0.33 175 175
Syndecan-2/alpha2 ITGB1 0.016 0.061 -9999 0 -0.2 35 35
HRAS 0.011 0 -9999 0 -10000 0 0
Syndecan-2/CASK 0.006 0.038 -9999 0 -0.23 13 13
ITGA5 0.011 0 -9999 0 -10000 0 0
BAX 0.024 0.04 -9999 0 -10000 0 0
EPB41 0.01 0.018 -9999 0 -0.41 1 1
positive regulation of cell-cell adhesion 0.013 0.034 -9999 0 -0.2 13 13
LAMA3 0 0.068 -9999 0 -0.41 14 14
EZR 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.025 0.12 -9999 0 -0.41 45 45
Syndecan-2/MMP2 0.001 0.069 -9999 0 -0.24 38 38
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.01 0.044 -9999 0 -0.28 12 12
dendrite morphogenesis 0.013 0.041 -9999 0 -0.22 16 16
Syndecan-2/GM-CSF 0.008 0.046 -9999 0 -0.22 20 20
determination of left/right symmetry 0.009 0.046 -9999 0 -0.28 13 13
Syndecan-2/PKC delta 0.014 0.038 -9999 0 -0.23 13 13
GNB2L1 0.011 0 -9999 0 -10000 0 0
MAPK3 0.015 0.042 -9999 0 -0.21 13 13
MAPK1 0.015 0.042 -9999 0 -0.21 13 13
Syndecan-2/RACK1 0.019 0.033 -9999 0 -0.18 13 13
NF1 0.009 0.026 -9999 0 -0.41 2 2
FGFR/FGF/Syndecan-2 0.009 0.046 -9999 0 -0.28 13 13
ITGA2 0.001 0.063 -9999 0 -0.41 12 12
MAPK8 0.018 0.045 -9999 0 -0.22 18 18
Syndecan-2/alpha2/beta1 Integrin -0.033 0.089 -9999 0 -0.22 28 28
Syndecan-2/Kininogen 0.001 0.054 -9999 0 -0.19 37 37
ITGB1 0.011 0 -9999 0 -10000 0 0
SRC 0.024 0.031 -9999 0 -0.17 13 13
Syndecan-2/CASK/Protein 4.1 0.012 0.036 -9999 0 -0.2 14 14
extracellular matrix organization 0.013 0.04 -9999 0 -0.23 14 14
actin cytoskeleton reorganization 0.012 0.045 -9999 0 -0.23 18 18
Syndecan-2/Caveolin-2/Ras 0.001 0.073 -9999 0 -0.21 56 56
Syndecan-2/Laminin alpha3 0.007 0.056 -9999 0 -0.24 26 26
Syndecan-2/RasGAP 0.022 0.037 -9999 0 -0.17 18 18
alpha5/beta1 Integrin 0.016 0 -9999 0 -10000 0 0
PRKCD 0.011 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.013 0.041 -9999 0 -0.22 16 16
GO:0007205 0.003 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.028 0.036 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
SDCBP 0.011 0 -9999 0 -10000 0 0
TNFRSF13B -0.002 0.058 -9999 0 -0.33 16 16
RASA1 0.007 0.041 -9999 0 -0.41 5 5
alpha2/beta1 Integrin 0.01 0.044 -9999 0 -0.28 12 12
Syndecan-2/Synbindin 0.014 0.038 -9999 0 -0.23 13 13
TGFB1 0.01 0.018 -9999 0 -0.41 1 1
CASP3 0.02 0.035 -9999 0 -0.2 13 13
FN1 0.007 0.041 -9999 0 -0.41 5 5
Syndecan-2/IL8 -0.043 0.094 -9999 0 -0.18 168 168
SDC2 0.009 0.046 -9999 0 -0.28 13 13
KNG1 -0.01 0.07 -9999 0 -0.33 24 24
Syndecan-2/Neurofibromin 0.013 0.041 -9999 0 -0.23 15 15
TRAPPC4 0.011 0 -9999 0 -10000 0 0
CSF2 0.001 0.041 -9999 0 -0.33 8 8
Syndecan-2/TGFB1 0.014 0.04 -9999 0 -0.23 14 14
Syndecan-2/Syntenin/PI-4-5-P2 0.013 0.035 -9999 0 -0.2 13 13
Syndecan-2/Ezrin 0.02 0.035 -9999 0 -0.2 13 13
PRKACA 0.019 0.037 -9999 0 -0.2 15 15
angiogenesis -0.043 0.093 -9999 0 -0.18 168 168
MMP2 -0.011 0.093 -9999 0 -0.41 27 27
IL8 -0.09 0.16 -9999 0 -0.33 156 156
calcineurin-NFAT signaling pathway 0.006 0.051 -9999 0 -0.2 28 28
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.011 0 -9999 0 -10000 0 0
HDAC2 0.011 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0.014 0.041 -9999 0 -0.22 15 15
forebrain development -0.066 0.2 -9999 0 -0.44 100 100
GNAO1 -0.099 0.18 -9999 0 -0.41 138 138
SMO/beta Arrestin2 0.015 0.029 -9999 0 -0.28 5 5
SMO 0.007 0.041 -9999 0 -0.41 5 5
ARRB2 0.011 0.003 -9999 0 -10000 0 0
GLI3/SPOP -0.03 0.11 -9999 0 -0.46 4 4
mol:GTP 0 0.001 -9999 0 -10000 0 0
GSK3B 0.011 0 -9999 0 -10000 0 0
GNAI2 0.011 0.002 -9999 0 -10000 0 0
SIN3/HDAC complex 0.028 0.002 -9999 0 -10000 0 0
GNAI1 0.005 0.052 -9999 0 -0.41 8 8
XPO1 0.012 0.004 -9999 0 -10000 0 0
GLI1/Su(fu) -0.065 0.13 -9999 0 -0.44 30 30
SAP30 0.011 0.001 -9999 0 -10000 0 0
mol:GDP 0.007 0.041 -9999 0 -0.41 5 5
MIM/GLI2A 0.014 0.017 -9999 0 -10000 0 0
IFT88 0.011 0 -9999 0 -10000 0 0
GNAI3 0.011 0.002 -9999 0 -10000 0 0
GLI2 -0.012 0.078 -9999 0 -10000 0 0
GLI3 -0.037 0.12 -9999 0 -0.22 136 136
CSNK1D 0.011 0 -9999 0 -10000 0 0
CSNK1E 0.011 0 -9999 0 -10000 0 0
SAP18 0.011 0 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.011 0 -9999 0 -10000 0 0
GNG2 0.003 0.056 -9999 0 -0.4 10 10
Gi family/GTP -0.039 0.11 -9999 0 -0.21 144 144
SIN3B 0.011 0.001 -9999 0 -10000 0 0
SIN3A 0.011 0 -9999 0 -10000 0 0
GLI3/Su(fu) -0.004 0.087 -9999 0 -0.39 3 3
GLI2/Su(fu) 0.004 0.07 -9999 0 -0.23 3 3
FOXA2 -0.095 0.3 -9999 0 -1.1 45 45
neural tube patterning -0.066 0.2 -9999 0 -0.44 100 100
SPOP 0.011 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.025 0.016 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
CSNK1G2 0.011 0 -9999 0 -10000 0 0
CSNK1G3 0.011 0 -9999 0 -10000 0 0
MTSS1 0.014 0.017 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.066 0.2 -9999 0 -0.44 100 100
SUFU 0.021 0.018 -9999 0 -10000 0 0
LGALS3 0.009 0.026 -9999 0 -0.41 2 2
catabolic process -0.036 0.13 -9999 0 -0.28 75 75
GLI3A/CBP -0.043 0.13 -9999 0 -0.31 99 99
KIF3A 0.01 0.018 -9999 0 -0.41 1 1
GLI1 -0.068 0.2 -9999 0 -0.45 100 100
RAB23 0.007 0.041 -9999 0 -0.41 5 5
CSNK1A1 0.011 0 -9999 0 -10000 0 0
IFT172 0.011 0 -9999 0 -10000 0 0
RBBP7 0.011 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.024 0.021 -9999 0 -10000 0 0
GNAZ -0.001 0.07 -9999 0 -0.41 15 15
RBBP4 0.009 0.032 -9999 0 -0.41 3 3
CSNK1G1 0.011 0 -9999 0 -10000 0 0
PIAS1 0.011 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GLI2/SPOP -0.006 0.073 -9999 0 -10000 0 0
STK36 0.012 0.004 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.03 0.1 -9999 0 -0.32 22 22
PTCH1 -0.053 0.18 -9999 0 -0.52 33 33
MIM/GLI1 -0.072 0.23 -9999 0 -0.46 120 120
CREBBP -0.043 0.13 -9999 0 -0.31 99 99
Su(fu)/SIN3/HDAC complex 0.038 0.016 -9999 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.01 0.064 -10000 0 -0.65 4 4
HDAC1 0.008 0.005 -10000 0 -10000 0 0
AES 0.01 0.001 -10000 0 -10000 0 0
FBXW11 0.011 0 -10000 0 -10000 0 0
DTX1 0.006 0.045 -10000 0 -0.41 6 6
LRP6/FZD1 0.015 0.022 -10000 0 -0.28 3 3
TLE1 0.01 0.018 -10000 0 -0.41 1 1
AP1 -0.063 0.12 -10000 0 -0.24 164 164
NCSTN 0.011 0 -10000 0 -10000 0 0
ADAM10 0.008 0.037 -10000 0 -0.41 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.03 0.053 -10000 0 -0.56 2 2
NICD/RBPSUH 0.023 0.046 -10000 0 -0.5 4 4
WIF1 -0.097 0.16 -10000 0 -0.35 158 158
NOTCH1 -0.004 0.046 -10000 0 -0.53 4 4
PSENEN 0.011 0 -10000 0 -10000 0 0
KREMEN2 -0.021 0.1 -10000 0 -0.33 50 50
DKK1 -0.063 0.14 -10000 0 -0.33 112 112
beta catenin/beta TrCP1 0.026 0.027 -10000 0 -10000 0 0
APH1B 0.005 0.048 -10000 0 -0.41 7 7
APH1A 0.011 0 -10000 0 -10000 0 0
AXIN1 0.001 0.019 -10000 0 -0.18 4 4
CtBP/CBP/TCF1/TLE1/AES 0.017 0.027 -10000 0 -0.21 3 3
PSEN1 0.011 0 -10000 0 -10000 0 0
FOS -0.12 0.19 -10000 0 -0.41 159 159
JUN 0.005 0.048 -10000 0 -0.41 7 7
MAP3K7 0.01 0.002 -10000 0 -10000 0 0
CTNNB1 0.02 0.029 -10000 0 -10000 0 0
MAPK3 0.011 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.012 0.084 -10000 0 -0.21 79 79
HNF1A 0.005 0.042 -10000 0 -0.33 8 8
CTBP1 0.01 0.001 -10000 0 -10000 0 0
MYC -0.004 0.18 -10000 0 -1.3 10 10
NKD1 -0.02 0.1 -10000 0 -0.34 46 46
FZD1 0.009 0.032 -10000 0 -0.41 3 3
NOTCH1 precursor/Deltex homolog 1 0.021 0.051 -10000 0 -0.5 4 4
apoptosis -0.063 0.12 -10000 0 -0.24 164 164
Delta 1/NOTCHprecursor 0.017 0.067 -10000 0 -0.64 4 4
DLL1 -0.003 0.074 -10000 0 -0.41 17 17
PPARD 0.018 0.013 -10000 0 -10000 0 0
Gamma Secretase 0.03 0.025 -10000 0 -0.18 7 7
APC 0.001 0.019 -10000 0 -0.18 4 4
DVL1 0 0.015 -10000 0 -10000 0 0
CSNK2A1 0.011 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.038 0.096 -10000 0 -0.18 155 155
LRP6 0.011 0 -10000 0 -10000 0 0
CSNK1A1 0.011 0.001 -10000 0 -10000 0 0
NLK 0.011 0.006 -10000 0 -10000 0 0
CCND1 0.018 0.017 -10000 0 -10000 0 0
WNT1 0.004 0.042 -10000 0 -0.33 8 8
Axin1/APC/beta catenin 0.029 0.025 -10000 0 -10000 0 0
DKK2 -0.016 0.1 -10000 0 -0.4 34 34
NOTCH1 precursor/DVL1 0 0.041 -10000 0 -0.46 4 4
GSK3B 0.011 0 -10000 0 -10000 0 0
FRAT1 0.01 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.006 0.048 -10000 0 -0.51 4 4
PPP2R5D 0.012 0.046 0.23 8 -10000 0 8
MAPK1 0.011 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.033 0.089 -10000 0 -0.21 38 38
RBPJ 0.011 0 -10000 0 -10000 0 0
CREBBP 0.012 0.026 -10000 0 -0.41 2 2
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.076 0.11 -9999 0 -0.36 37 37
TC10/GTP -0.055 0.076 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.001 0.07 -9999 0 -0.21 53 53
HRAS 0.011 0 -9999 0 -10000 0 0
APS homodimer 0.011 0 -9999 0 -10000 0 0
GRB14 -0.11 0.16 -9999 0 -0.33 191 191
FOXO3 -0.01 0.037 -9999 0 -0.57 2 2
AKT1 -0.032 0.092 -9999 0 -0.28 28 28
INSR 0.012 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.03 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.01 0.018 -9999 0 -0.41 1 1
SORBS1 -0.13 0.2 -9999 0 -0.41 182 182
CRK 0.011 0 -9999 0 -10000 0 0
PTPN1 0.027 0.001 -9999 0 -10000 0 0
CAV1 -0.037 0.11 -9999 0 -0.23 124 124
CBL/APS/CAP/Crk-II/C3G -0.041 0.1 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.001 0.07 -9999 0 -0.21 53 53
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.02 0.058 -9999 0 -0.18 57 57
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.013 0.055 -9999 0 -10000 0 0
RPS6KB1 -0.024 0.086 -9999 0 -0.25 28 28
PARD6A 0.011 0 -9999 0 -10000 0 0
CBL 0.011 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.003 -9999 0 -10000 0 0
PIK3R1 0.007 0.041 -9999 0 -0.41 5 5
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.047 0.067 -9999 0 -0.26 28 28
HRAS/GTP -0.015 0.043 -9999 0 -10000 0 0
Insulin Receptor 0.012 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.007 0.065 -9999 0 -0.19 53 53
PRKCI -0.012 0.018 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.06 0.081 -9999 0 -0.3 28 28
SHC1 0.011 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade -0.002 0.028 -9999 0 -0.39 2 2
PI3K -0.02 0.058 -9999 0 -0.18 57 57
NCK2 0.011 0 -9999 0 -10000 0 0
RHOQ 0.011 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP 0.008 0 -9999 0 -10000 0 0
AKT2 -0.032 0.092 -9999 0 -0.28 28 28
PRKCZ -0.013 0.029 -9999 0 -0.52 1 1
SH2B2 0.011 0 -9999 0 -10000 0 0
SHC/SHIP 0.007 0.062 -9999 0 -0.18 54 54
F2RL2 -0.017 0.1 -9999 0 -0.4 35 35
TRIP10 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.017 0.002 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.029 0.001 -9999 0 -10000 0 0
RAPGEF1 0.011 0 -9999 0 -10000 0 0
RASA1 0.007 0.041 -9999 0 -0.41 5 5
NCK1 0.009 0.026 -9999 0 -0.41 2 2
CBL/APS/CAP/Crk-II -0.05 0.11 -9999 0 -0.2 182 182
TC10/GDP 0.008 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.024 0.01 -9999 0 -0.21 1 1
INPP5D 0 0.065 -9999 0 -0.19 54 54
SOS1 0.011 0 -9999 0 -10000 0 0
SGK1 -0.006 0.05 -9999 0 -0.82 2 2
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.011 0 -9999 0 -10000 0 0
IRS1 -0.031 0.13 -9999 0 -0.41 53 53
p62DOK/RasGAP -0.002 0.028 -9999 0 -0.4 2 2
INS 0.003 0.002 -9999 0 -10000 0 0
mol:PI-3-4-P2 0 0.064 -9999 0 -0.19 54 54
GRB2 0.011 0 -9999 0 -10000 0 0
EIF4EBP1 -0.027 0.09 -9999 0 -0.26 32 32
PTPRA 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
TC10/GTP/CIP4 0.015 0 -9999 0 -10000 0 0
PDPK1 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.006 0.065 -9999 0 -0.19 53 53
Insulin Receptor/Insulin/IRS1 -0.006 0.07 -9999 0 -0.21 53 53
Insulin Receptor/Insulin/IRS3 0.012 0.002 -9999 0 -10000 0 0
Par3/Par6 0.012 0.052 -9999 0 -0.19 32 32
Regulation of Androgen receptor activity

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
HDAC1 0.018 0.001 -9999 0 -10000 0 0
SMARCC1 0.006 0.016 -9999 0 -10000 0 0
REL 0.011 0.001 -9999 0 -10000 0 0
HDAC7 0.021 0.066 -9999 0 -0.38 1 1
JUN 0.006 0.048 -9999 0 -0.41 7 7
EP300 0.011 0 -9999 0 -10000 0 0
KAT2B 0.004 0.055 -9999 0 -0.41 9 9
KAT5 0.011 0 -9999 0 -10000 0 0
MAPK14 -0.009 0.078 -9999 0 -0.21 66 66
FOXO1 0.009 0.032 -9999 0 -0.41 3 3
T-DHT/AR 0.019 0.071 -9999 0 -0.33 2 2
MAP2K6 -0.031 0.11 -9999 0 -0.33 66 66
BRM/BAF57 0.008 0.051 -9999 0 -0.28 16 16
MAP2K4 0.011 0.019 -9999 0 -0.41 1 1
SMARCA2 -0.002 0.072 -9999 0 -0.41 16 16
PDE9A -0.02 0.1 -9999 0 -0.96 4 4
NCOA2 -0.004 0.077 -9999 0 -0.41 18 18
CEBPA 0.007 0.038 -9999 0 -0.38 5 5
EHMT2 0.011 0.001 -9999 0 -10000 0 0
cell proliferation 0.012 0.12 -9999 0 -0.4 15 15
NR0B1 -0.014 0.076 -9999 0 -0.33 29 29
EGR1 -0.043 0.14 -9999 0 -0.41 68 68
RXRs/9cRA -0.01 0.077 -9999 0 -0.2 75 75
AR/RACK1/Src 0.009 0.069 -9999 0 -0.29 5 5
AR/GR -0.049 0.12 -9999 0 -0.25 97 97
GNB2L1 0.011 0.002 -9999 0 -10000 0 0
PKN1 0.011 0 -9999 0 -10000 0 0
RCHY1 0.011 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.016 0.032 -9999 0 -0.28 6 6
T-DHT/AR/TIF2/CARM1 0.005 0.082 -9999 0 -0.34 10 10
SRC 0.012 0.06 -9999 0 -0.36 1 1
NR3C1 -0.053 0.15 -9999 0 -0.41 80 80
KLK3 -0.048 0.092 -9999 0 -0.45 3 3
APPBP2 0.012 0.002 -9999 0 -10000 0 0
TRIM24 0.011 0.002 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.005 0.062 -9999 0 -0.36 2 2
TMPRSS2 -0.031 0.14 -9999 0 -1 8 8
RXRG -0.048 0.14 -9999 0 -0.4 75 75
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.011 0 -9999 0 -10000 0 0
RXRB 0.011 0 -9999 0 -10000 0 0
CARM1 0.011 0.002 -9999 0 -10000 0 0
NR2C2 0.003 0.057 -9999 0 -0.41 10 10
KLK2 -0.01 0.15 -9999 0 -0.57 31 31
AR -0.022 0.099 -9999 0 -0.22 90 90
SENP1 0.011 0 -9999 0 -10000 0 0
HSP90AA1 0.011 0 -9999 0 -10000 0 0
MDM2 0.011 0.002 -9999 0 -10000 0 0
SRY 0 0.002 -9999 0 -10000 0 0
GATA2 -0.029 0.12 -9999 0 -0.41 50 50
MYST2 0.011 0 -9999 0 -10000 0 0
HOXB13 -0.22 0.16 -9999 0 -0.33 354 354
T-DHT/AR/RACK1/Src 0.01 0.064 -9999 0 -0.36 2 2
positive regulation of transcription -0.029 0.12 -9999 0 -0.41 50 50
DNAJA1 0.012 0.002 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.001 -9999 0 -10000 0 0
NCOA1 0.013 0.02 -9999 0 -0.44 1 1
SPDEF -0.11 0.17 -9999 0 -0.34 182 182
T-DHT/AR/TIF2 0.011 0.072 -9999 0 -0.29 15 15
T-DHT/AR/Hsp90 0.005 0.062 -9999 0 -0.36 2 2
GSK3B 0.012 0.002 -9999 0 -10000 0 0
NR2C1 0.011 0 -9999 0 -10000 0 0
mol:T-DHT 0.007 0.064 -9999 0 -0.26 3 3
SIRT1 0.009 0.026 -9999 0 -0.41 2 2
ZMIZ2 0.011 0.002 -9999 0 -10000 0 0
POU2F1 0.021 0.011 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.008 0.071 -9999 0 -0.31 5 5
CREBBP 0.009 0.026 -9999 0 -0.41 2 2
SMARCE1 0.011 0.001 -9999 0 -10000 0 0
IL6-mediated signaling events

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.032 0.13 -9999 0 -0.55 3 3
CRP 0.027 0.13 -9999 0 -0.57 3 3
cell cycle arrest 0.026 0.14 -9999 0 -0.53 10 10
TIMP1 0.028 0.12 -9999 0 -0.57 4 4
IL6ST -0.049 0.15 -9999 0 -0.41 80 80
Rac1/GDP -0.001 0.12 -9999 0 -0.36 36 36
AP1 -0.02 0.12 -9999 0 -0.46 14 14
GAB2 0.009 0.037 -9999 0 -0.41 4 4
TNFSF11 0.013 0.14 -9999 0 -0.56 4 4
HSP90B1 0.032 0.03 -9999 0 -10000 0 0
GAB1 0.008 0.037 -9999 0 -0.41 4 4
MAPK14 -0.026 0.13 -9999 0 -0.38 39 39
AKT1 0.042 0.04 -9999 0 -0.39 2 2
FOXO1 0.045 0.041 -9999 0 -0.37 2 2
MAP2K6 -0.031 0.14 -9999 0 -0.38 44 44
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 0.015 0.12 -9999 0 -0.39 20 20
MITF -0.03 0.15 -9999 0 -0.4 54 54
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.011 0 -9999 0 -10000 0 0
A2M 0.012 0.079 -9999 0 -1.3 2 2
CEBPB 0.017 0.002 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.013 0.086 -9999 0 -0.57 6 6
STAT3 0.028 0.14 -9999 0 -0.56 10 10
STAT1 0.002 0.014 -9999 0 -10000 0 0
CEBPD 0.031 0.13 -9999 0 -0.67 4 4
PIK3CA 0.012 0.018 -9999 0 -0.41 1 1
PI3K 0.015 0.032 -9999 0 -0.28 6 6
JUN 0.005 0.048 -9999 0 -0.41 7 7
PIAS3/MITF -0.024 0.14 -9999 0 -0.37 54 54
MAPK11 -0.026 0.13 -9999 0 -0.38 39 39
STAT3 (dimer)/FOXO1 0.061 0.13 -9999 0 -0.47 6 6
GRB2/SOS1/GAB family -0.042 0.1 -9999 0 -0.37 33 33
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.02 0.13 -9999 0 -0.33 52 52
GRB2 0.012 0.001 -9999 0 -10000 0 0
JAK2 0.004 0.055 -9999 0 -0.41 9 9
LBP 0.019 0.12 -9999 0 -0.52 2 2
PIK3R1 0.008 0.041 -9999 0 -0.41 5 5
JAK1 0.012 0.026 -9999 0 -0.4 2 2
MYC 0.021 0.18 -9999 0 -0.89 12 12
FGG 0.026 0.13 -9999 0 -0.57 3 3
macrophage differentiation 0.026 0.14 -9999 0 -0.53 10 10
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.041 0.12 -9999 0 -0.39 36 36
JUNB 0.025 0.15 -9999 0 -0.76 8 8
FOS -0.12 0.19 -9999 0 -0.41 159 159
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.017 0.13 -9999 0 -0.4 38 38
STAT1/PIAS1 0.002 0.12 -9999 0 -0.33 35 35
GRB2/SOS1/GAB family/SHP2/PI3K 0.033 0.042 -9999 0 -0.3 5 5
STAT3 (dimer) 0.029 0.14 -9999 0 -0.55 10 10
PRKCD 0.03 0.12 -9999 0 -0.46 10 10
IL6R -0.023 0.12 -9999 0 -0.41 45 45
SOCS3 -0.026 0.14 -9999 0 -0.61 11 11
gp130 (dimer)/JAK1/JAK1/LMO4 -0.007 0.092 -9999 0 -0.22 82 82
Rac1/GTP 0.003 0.12 -9999 0 -0.35 36 36
HCK 0.006 0.039 -9999 0 -0.33 7 7
MAPKKK cascade 0.026 0.082 -9999 0 -0.77 4 4
bone resorption 0.014 0.13 -9999 0 -0.54 4 4
IRF1 0.032 0.13 -9999 0 -0.55 3 3
mol:GDP -0.009 0.13 -9999 0 -0.37 37 37
SOS1 0.011 0.001 -9999 0 -10000 0 0
VAV1 -0.01 0.13 -9999 0 -0.38 37 37
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.038 0.16 -9999 0 -0.47 48 48
PTPN11 0.002 0.014 -9999 0 -10000 0 0
IL6/IL6RA -0.016 0.11 -9999 0 -0.29 64 64
gp130 (dimer)/TYK2/TYK2/LMO4 -0.01 0.091 -9999 0 -0.22 80 80
gp130 (dimer)/JAK2/JAK2/LMO4 -0.014 0.097 -9999 0 -0.23 87 87
IL6 -0.004 0.084 -9999 0 -0.38 25 25
PIAS3 0.011 0 -9999 0 -10000 0 0
PTPRE 0.003 0.024 -9999 0 -0.37 2 2
PIAS1 0.011 0 -9999 0 -10000 0 0
RAC1 0.011 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.029 0.13 -9999 0 -0.31 63 63
LMO4 0.015 0.005 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.019 0.14 -9999 0 -0.54 10 10
MCL1 0.046 0.037 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.16 0.21 -9999 0 -0.41 210 210
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.011 0 -9999 0 -10000 0 0
TCEB1 0.011 0 -9999 0 -10000 0 0
HIF1A/p53 0.025 0.01 -9999 0 -10000 0 0
HIF1A 0.02 0.005 -9999 0 -10000 0 0
COPS5 0.011 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.032 0.009 -9999 0 -0.18 1 1
FIH (dimer) 0.011 0 -9999 0 -10000 0 0
CDKN2A -0.13 0.17 -9999 0 -0.33 219 219
ARNT/IPAS -0.1 0.14 -9999 0 -0.28 210 210
HIF1AN 0.011 0 -9999 0 -10000 0 0
GNB2L1 0.011 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.026 0.005 -9999 0 -10000 0 0
CUL2 0.011 0 -9999 0 -10000 0 0
OS9 0.011 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.022 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.026 0.005 -9999 0 -10000 0 0
PHD1-3/OS9 0.027 0.017 -9999 0 -0.2 1 1
HIF1A/RACK1/Elongin B/Elongin C 0.034 0.005 -9999 0 -10000 0 0
VHL 0.01 0.018 -9999 0 -0.41 1 1
HSP90AA1 0.011 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.026 0.005 -9999 0 -10000 0 0
EGLN3 0.008 0.031 -9999 0 -0.35 4 4
EGLN2 0.011 0 -9999 0 -10000 0 0
EGLN1 0.011 0 -9999 0 -10000 0 0
TP53 0.01 0.018 -9999 0 -0.41 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.03 0.023 -9999 0 -0.5 1 1
ARNT 0.011 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.011 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.037 0.074 -9999 0 -0.19 1 1
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.015 0.082 -10000 0 -0.2 83 83
MAPK9 0.007 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.003 0.033 -10000 0 -0.23 11 11
GNB1/GNG2 0.01 0.033 -10000 0 -0.23 10 10
GNB1 0.011 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0 -10000 0 -10000 0 0
Gs family/GTP -0.026 0.079 -10000 0 -0.22 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 0.009 0.021 0.061 77 -10000 0 77
GNAL -0.051 0.15 -10000 0 -0.41 77 77
GNG2 0.003 0.056 -10000 0 -0.4 10 10
CRH -0.005 0.048 -10000 0 -0.33 11 11
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.028 -10000 0 -0.28 5 5
MAPK11 0.006 0.018 -10000 0 -0.28 2 2
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.012 0.005 -10000 0 -10000 0 0
HSPA8 0.011 0.001 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.03 0.089 0.15 3 -0.26 63 66
AKT1 0.013 0.002 -10000 0 -10000 0 0
GSC -0.029 0.077 -10000 0 -10000 0 0
NKX2-5 -0.049 0.12 -10000 0 -0.34 80 80
muscle cell differentiation 0.044 0.098 0.36 23 -10000 0 23
SMAD2-3/SMAD4/SP1 0.038 0.052 -10000 0 -0.26 3 3
SMAD4 0.007 0.036 -10000 0 -0.42 1 1
CBFB 0.011 0 -10000 0 -10000 0 0
SAP18 0.011 0 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.016 0.045 -10000 0 -0.19 21 21
SMAD3/SMAD4/VDR 0.004 0.041 -10000 0 -0.22 4 4
MYC 0.001 0.058 -10000 0 -0.41 10 10
CDKN2B 0.025 0.032 -10000 0 -10000 0 0
AP1 -0.024 0.12 -10000 0 -0.36 22 22
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.044 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.011 0.045 -10000 0 -0.34 3 3
SP3 0.013 0 -10000 0 -10000 0 0
CREB1 0.011 0 -10000 0 -10000 0 0
FOXH1 -0.08 0.15 -10000 0 -0.34 130 130
SMAD3/SMAD4/GR -0.038 0.098 -10000 0 -0.25 83 83
GATA3 -0.004 0.072 -10000 0 -0.35 20 20
SKI/SIN3/HDAC complex/NCoR1 0.036 0.013 -10000 0 -10000 0 0
MEF2C/TIF2 -0.07 0.18 -10000 0 -0.44 71 71
endothelial cell migration -0.015 0.12 1.2 4 -10000 0 4
MAX 0.01 0.004 -10000 0 -10000 0 0
RBBP7 0.011 0 -10000 0 -10000 0 0
RBBP4 0.008 0.032 -10000 0 -0.41 3 3
RUNX2 0.001 0.058 -10000 0 -0.34 15 15
RUNX3 0.002 0.055 -10000 0 -0.33 14 14
RUNX1 0.011 0 -10000 0 -10000 0 0
CTBP1 0.011 0 -10000 0 -10000 0 0
NR3C1 -0.054 0.15 -10000 0 -0.41 80 80
VDR 0.003 0.053 -10000 0 -0.33 13 13
CDKN1A 0.053 0.067 -10000 0 -1.2 1 1
KAT2B 0.004 0.054 -10000 0 -0.41 9 9
SMAD2/SMAD2/SMAD4/FOXH1 -0.036 0.1 -10000 0 -0.25 46 46
DCP1A 0.011 0 -10000 0 -10000 0 0
SKI 0.011 0 -10000 0 -10000 0 0
SERPINE1 0.015 0.12 -10000 0 -1.3 4 4
SMAD3/SMAD4/ATF2 0.011 0.048 -10000 0 -0.31 6 6
SMAD3/SMAD4/ATF3 -0.011 0.09 -10000 0 -0.27 51 51
SAP30 0.011 0 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.026 0.019 -10000 0 -0.22 2 2
JUN -0.024 0.12 -10000 0 -0.4 17 17
SMAD3/SMAD4/IRF7 0.006 0.055 -10000 0 -0.29 8 8
TFE3 0.016 0.005 -10000 0 -10000 0 0
COL1A2 0.008 0.087 -10000 0 -0.79 5 5
mesenchymal cell differentiation -0.005 0.059 0.27 17 -10000 0 17
DLX1 -0.032 0.11 -10000 0 -0.33 61 61
TCF3 0.011 0 -10000 0 -10000 0 0
FOS -0.11 0.2 -10000 0 -0.41 159 159
SMAD3/SMAD4/Max 0.001 0.036 -10000 0 -0.26 5 5
Cbp/p300/SNIP1 0.023 0.016 -10000 0 -0.23 2 2
ZBTB17 0.009 0.002 -10000 0 -10000 0 0
LAMC1 0.033 0.036 -10000 0 -0.26 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.012 0.041 -10000 0 -0.25 5 5
IRF7 0.004 0.051 -10000 0 -0.35 10 10
ESR1 -0.038 0.13 -10000 0 -0.41 60 60
HNF4A -0.041 0.12 -10000 0 -0.33 77 77
MEF2C -0.074 0.17 -10000 0 -0.43 77 77
SMAD2-3/SMAD4 0.017 0.048 -10000 0 -0.28 4 4
Cbp/p300/Src-1 0.023 0.02 -10000 0 -0.22 3 3
IGHV3OR16-13 -0.001 0.008 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.011 0 -10000 0 -10000 0 0
CREBBP 0.01 0.026 -10000 0 -0.41 2 2
SKIL 0.011 0 -10000 0 -10000 0 0
HDAC1 0.011 0 -10000 0 -10000 0 0
HDAC2 0.011 0 -10000 0 -10000 0 0
SNIP1 0.011 0.001 -10000 0 -10000 0 0
GCN5L2 0.001 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.03 0.045 -10000 0 -0.26 4 4
MSG1/HSC70 0.004 0.047 -10000 0 -0.23 20 20
SMAD2 0.008 0.018 -10000 0 -10000 0 0
SMAD3 0.009 0.047 -10000 0 -0.45 4 4
SMAD3/E2F4-5/DP1/p107/SMAD4 0.026 0.033 -10000 0 -0.22 5 5
SMAD2/SMAD2/SMAD4 0.002 0.043 -10000 0 -0.28 10 10
NCOR1 0.011 0 -10000 0 -10000 0 0
NCOA2 -0.003 0.077 -10000 0 -0.41 18 18
NCOA1 0.01 0.018 -10000 0 -0.41 1 1
MYOD/E2A -0.01 0.067 -10000 0 -0.22 50 50
SMAD2-3/SMAD4/SP1/MIZ-1 0.044 0.049 -10000 0 -0.25 2 2
IFNB1 0.013 0.064 -10000 0 -0.31 12 12
SMAD3/SMAD4/MEF2C -0.065 0.17 -10000 0 -0.44 66 66
CITED1 -0.003 0.068 -10000 0 -0.34 20 20
SMAD2-3/SMAD4/ARC105 0.024 0.044 -10000 0 -0.28 2 2
RBL1 0.011 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.041 0.037 -10000 0 -0.34 2 2
RUNX1-3/PEBPB2 0.017 0.031 -10000 0 -0.17 14 14
SMAD7 0.001 0.13 -10000 0 -0.49 11 11
MYC/MIZ-1 0.007 0.041 -10000 0 -0.28 10 10
SMAD3/SMAD4 0.012 0.056 -10000 0 -0.4 4 4
IL10 0.009 0.092 -10000 0 -0.29 32 32
PIASy/HDAC complex 0.01 0.003 -10000 0 -10000 0 0
PIAS3 0.011 0.002 -10000 0 -10000 0 0
CDK2 0.012 0.003 -10000 0 -10000 0 0
IL5 0.011 0.065 -10000 0 -0.4 2 2
CDK4 0.012 0.003 -10000 0 -10000 0 0
PIAS4 0.01 0.003 -10000 0 -10000 0 0
ATF3 -0.027 0.12 -10000 0 -0.41 47 47
SMAD3/SMAD4/SP1 0.033 0.049 -10000 0 -0.25 5 5
FOXG1 -0.16 0.17 -10000 0 -0.33 252 252
FOXO3 0.022 0.003 -10000 0 -10000 0 0
FOXO1 0.02 0.023 -10000 0 -0.28 3 3
FOXO4 0.021 0.019 -10000 0 -0.28 2 2
heart looping -0.073 0.17 -10000 0 -0.43 77 77
CEBPB 0.012 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.012 0.081 -10000 0 -0.25 35 35
MYOD1 -0.028 0.098 -10000 0 -0.33 50 50
SMAD3/SMAD4/HNF4 -0.017 0.08 -10000 0 -0.22 32 32
SMAD3/SMAD4/GATA3 0 0.071 -10000 0 -0.31 8 8
SnoN/SIN3/HDAC complex/NCoR1 0.011 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.027 0.046 -10000 0 -0.21 5 5
SMAD3/SMAD4/SP1-3 0.041 0.046 -10000 0 -0.25 2 2
MED15 0.011 0 -10000 0 -10000 0 0
SP1 0.018 0.013 -10000 0 -10000 0 0
SIN3B 0.011 0 -10000 0 -10000 0 0
SIN3A 0.011 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.061 0.14 -10000 0 -0.36 58 58
ITGB5 0.043 0.036 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.037 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.032 0.11 -10000 0 -0.26 92 92
AR -0.061 0.16 -10000 0 -0.41 90 90
negative regulation of cell growth 0.019 0.062 -10000 0 -0.3 5 5
SMAD3/SMAD4/MYOD -0.009 0.069 -10000 0 -0.22 25 25
E2F5 0.011 0 -10000 0 -10000 0 0
E2F4 0.011 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.016 0.085 -10000 0 -0.25 13 13
SMAD2-3/SMAD4/FOXO1-3a-4 0.038 0.038 -10000 0 -0.35 2 2
TFDP1 0.011 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.018 0.12 -10000 0 -0.36 23 23
SMAD3/SMAD4/RUNX2 0.007 0.06 -10000 0 -0.27 17 17
TGIF2 0.011 0 -10000 0 -10000 0 0
TGIF1 0.011 0 -10000 0 -10000 0 0
ATF2 0.009 0.032 -10000 0 -0.41 3 3
Signaling events mediated by PTP1B

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
PDGFRB -0.007 0.084 -10000 0 -0.41 22 22
Jak2/Leptin Receptor -0.098 0.14 -10000 0 -0.36 78 78
PTP1B/AKT1 0.017 0.04 -10000 0 -0.21 4 4
FYN 0.011 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.013 0.044 -10000 0 -0.23 5 5
EGFR 0 0.068 -10000 0 -0.41 14 14
EGF/EGFR -0.016 0.05 -10000 0 -0.25 16 16
CSF1 0.003 0.057 -10000 0 -0.41 10 10
AKT1 0.011 0.001 -10000 0 -10000 0 0
INSR 0.011 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.013 0.089 -10000 0 -0.28 25 25
Insulin Receptor/Insulin -0.008 0.023 -10000 0 -10000 0 0
HCK 0.006 0.039 -10000 0 -0.33 7 7
CRK 0.011 0 -10000 0 -10000 0 0
TYK2 0.018 0.042 -10000 0 -0.22 5 5
EGF -0.004 0.071 -10000 0 -0.33 23 23
YES1 0.011 0 -10000 0 -10000 0 0
CAV1 -0.002 0.078 -10000 0 -0.32 11 11
TXN 0.011 0.002 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.004 0.079 -10000 0 -0.24 31 31
cell migration -0.013 0.044 0.23 5 -10000 0 5
STAT3 0.011 0.001 -10000 0 -10000 0 0
PRLR -0.074 0.17 -10000 0 -0.41 106 106
ITGA2B 0.005 0.047 -10000 0 -0.4 7 7
CSF1R 0.008 0.035 -10000 0 -0.39 4 4
Prolactin Receptor/Prolactin -0.057 0.13 -10000 0 -0.3 119 119
FGR 0.002 0.06 -10000 0 -0.41 11 11
PTP1B/p130 Cas 0.018 0.041 -10000 0 -0.22 5 5
Crk/p130 Cas 0.024 0.04 -10000 0 -0.2 5 5
DOK1 0.015 0.06 -10000 0 -0.25 14 14
JAK2 -0.037 0.13 -10000 0 -0.32 51 51
Jak2/Leptin Receptor/Leptin -0.014 0.052 -10000 0 -0.38 7 7
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
PTPN1 0.013 0.044 -10000 0 -0.23 5 5
LYN 0.011 0 -10000 0 -10000 0 0
CDH2 -0.053 0.15 -10000 0 -0.41 80 80
SRC 0.019 0.019 -10000 0 -10000 0 0
ITGB3 -0.066 0.16 -10000 0 -0.41 96 96
CAT1/PTP1B 0.018 0.072 -10000 0 -0.31 7 7
CAPN1 0.012 0.001 -10000 0 -10000 0 0
CSK 0.011 0 -10000 0 -10000 0 0
PI3K -0.007 0.025 -10000 0 -0.23 2 2
mol:H2O2 0 0.001 -10000 0 -10000 0 0
STAT3 (dimer) -0.012 0.048 -10000 0 -0.35 7 7
negative regulation of transcription -0.036 0.12 -10000 0 -0.32 51 51
FCGR2A 0.01 0.015 -10000 0 -0.33 1 1
FER 0.011 0.002 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.042 0.12 -10000 0 -0.28 103 103
BLK -0.015 0.087 -10000 0 -0.33 37 37
Insulin Receptor/Insulin/Shc 0.016 0.002 -10000 0 -10000 0 0
RHOA 0.012 0.001 -10000 0 -10000 0 0
LEPR -0.12 0.19 -10000 0 -0.41 160 160
BCAR1 0.011 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.011 0 -10000 0 -10000 0 0
mol:NADPH 0.001 0.001 -10000 0 -10000 0 0
TRPV6 0.013 0.067 -10000 0 -0.33 7 7
PRL -0.008 0.079 -10000 0 -0.4 21 21
SOCS3 0.005 0.076 -10000 0 -1.2 2 2
SPRY2 0.006 0.045 -10000 0 -0.42 6 6
Insulin Receptor/Insulin/IRS1 -0.009 0.076 -10000 0 -0.24 53 53
CSF1/CSF1R 0.019 0.057 -10000 0 -0.26 12 12
Ras protein signal transduction 0.007 0.014 -10000 0 -10000 0 0
IRS1 -0.031 0.13 -10000 0 -0.41 53 53
INS 0.001 0.003 -10000 0 -10000 0 0
LEP 0.005 0.026 -10000 0 -0.33 3 3
STAT5B -0.003 0.065 -10000 0 -0.24 16 16
STAT5A -0.003 0.065 -10000 0 -0.25 14 14
GRB2 0.011 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.064 -10000 0 -0.26 17 17
CSN2 -0.03 0.061 -10000 0 -10000 0 0
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
LAT 0.019 0.019 -10000 0 -10000 0 0
YBX1 0.017 0.018 -10000 0 -0.4 1 1
LCK 0.008 0.035 -10000 0 -0.35 5 5
SHC1 0.011 0 -10000 0 -10000 0 0
NOX4 0.007 0.04 -10000 0 -0.4 5 5
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.007 0.084 -9999 0 -0.41 22 22
alphaV beta3 Integrin -0.037 0.11 -9999 0 -0.28 96 96
PTK2 -0.036 0.086 -9999 0 -0.38 22 22
positive regulation of JNK cascade -0.014 0.057 -9999 0 -0.28 22 22
CDC42/GDP 0.019 0.087 -9999 0 -0.38 22 22
Rac1/GDP 0.02 0.087 -9999 0 -0.38 22 22
RAP1B 0.011 0 -9999 0 -10000 0 0
RAP1A 0.011 0 -9999 0 -10000 0 0
CTNNB1 0.011 0 -9999 0 -10000 0 0
CDC42/GTP -0.017 0.07 -9999 0 -0.35 22 22
nectin-3/I-afadin 0.004 0.059 -9999 0 -0.28 22 22
RAPGEF1 0.013 0.094 -9999 0 -0.42 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.007 0.11 -9999 0 -0.48 22 22
PDGFB-D/PDGFRB -0.007 0.084 -9999 0 -0.41 22 22
TLN1 0.001 0.076 -9999 0 -0.26 34 34
Rap1/GTP -0.014 0.06 -9999 0 -0.3 22 22
IQGAP1 0.011 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.021 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.004 0.059 -9999 0 -0.28 22 22
PVR 0.011 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.011 0 -9999 0 -10000 0 0
mol:GDP 0.015 0.1 -9999 0 -0.46 22 22
MLLT4 0.011 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
PI3K 0.013 0.069 -9999 0 -0.33 8 8
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.015 0.014 -9999 0 -0.22 2 2
positive regulation of lamellipodium assembly -0.015 0.06 -9999 0 -0.3 22 22
PVRL1 0.01 0.021 -9999 0 -0.33 2 2
PVRL3 -0.007 0.084 -9999 0 -0.41 22 22
PVRL2 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.041 -9999 0 -0.41 5 5
CDH1 0.009 0.026 -9999 0 -0.41 2 2
CLDN1 -0.043 0.14 -9999 0 -0.41 68 68
JAM-A/CLDN1 -0.011 0.091 -9999 0 -0.21 86 86
SRC 0 0.12 -9999 0 -0.53 22 22
ITGB3 -0.065 0.16 -9999 0 -0.41 96 96
nectin-1(dimer)/I-afadin/I-afadin 0.015 0.014 -9999 0 -0.22 2 2
FARP2 0.01 0.1 -9999 0 -0.46 22 22
RAC1 0.011 0 -9999 0 -10000 0 0
CTNNA1 0.011 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.012 0.05 -9999 0 -0.23 22 22
nectin-1/I-afadin 0.015 0.014 -9999 0 -0.22 2 2
nectin-2/I-afadin 0.016 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.015 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.011 0.054 -9999 0 -0.24 22 22
CDC42/GTP/IQGAP1/filamentous actin 0.015 0 -9999 0 -10000 0 0
F11R 0.01 0.018 -9999 0 -0.41 1 1
positive regulation of filopodium formation -0.014 0.057 -9999 0 -0.28 22 22
alphaV/beta3 Integrin/Talin -0.022 0.11 -9999 0 -0.31 40 40
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.016 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.016 0 -9999 0 -10000 0 0
PIP5K1C -0.005 0.081 -9999 0 -0.29 34 34
VAV2 0.01 0.1 -9999 0 -0.46 22 22
RAP1/GDP -0.016 0.07 -9999 0 -0.35 22 22
ITGAV 0.011 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.012 0.05 -9999 0 -0.23 22 22
nectin-3(dimer)/I-afadin/I-afadin 0.004 0.059 -9999 0 -0.28 22 22
Rac1/GTP -0.018 0.073 -9999 0 -0.36 22 22
PTPRM -0.013 0.089 -9999 0 -0.26 55 55
E-cadherin/beta catenin/alpha catenin -0.001 0.013 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.011 0 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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 0.011 0 -10000 0 -10000 0 0
HDAC3 0.011 0 -10000 0 -10000 0 0
VDR 0.003 0.053 -10000 0 -0.33 13 13
Cbp/p300/PCAF 0.017 0.036 -10000 0 -0.23 11 11
EP300 0.011 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.02 0.051 -10000 0 -0.28 7 7
KAT2B 0.004 0.055 -10000 0 -0.41 9 9
MAPK14 0.011 0 -10000 0 -10000 0 0
AKT1 0.012 0.06 0.19 20 -0.24 12 32
RAR alpha/9cRA/Cyclin H -0.02 0.064 -10000 0 -0.24 34 34
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.017 0.056 -10000 0 -0.26 12 12
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.004 0.066 -10000 0 -0.32 10 10
NCOR2 0.011 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.002 0.036 -10000 0 -0.23 13 13
RXRs/RARs/NRIP1/9cRA -0.002 0.13 -10000 0 -0.4 42 42
NCOA2 -0.003 0.077 -10000 0 -0.41 18 18
NCOA3 0.01 0.015 -10000 0 -0.33 1 1
NCOA1 0.01 0.018 -10000 0 -0.41 1 1
VDR/VDR/DNA 0.003 0.053 -10000 0 -0.33 13 13
RARG 0.012 0.001 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.015 0.001 -10000 0 -10000 0 0
MAPK3 0.012 0.001 -10000 0 -10000 0 0
MAPK1 0.011 0 -10000 0 -10000 0 0
MAPK8 0.008 0.041 -10000 0 -0.41 5 5
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.011 0.12 -10000 0 -0.38 42 42
RARA -0.004 0.072 -10000 0 -0.23 44 44
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.01 0.07 -10000 0 -0.3 16 16
PRKCA -0.014 0.1 -10000 0 -0.41 34 34
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.012 0.14 -10000 0 -0.42 43 43
RXRG -0.052 0.13 -10000 0 -0.3 100 100
RXRA 0.003 0.067 -10000 0 -0.21 37 37
RXRB -0.013 0.087 -10000 0 -0.28 40 40
VDR/Vit D3/DNA 0.002 0.036 -10000 0 -0.23 13 13
RBP1 -0.007 0.084 -10000 0 -0.41 22 22
CRBP1/9-cic-RA -0.004 0.059 -10000 0 -0.29 22 22
RARB 0.004 0.061 -10000 0 -0.41 11 11
PRKCG -0.036 0.12 -10000 0 -0.34 73 73
MNAT1 0.011 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.002 0.14 -10000 0 -0.42 42 42
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.003 0.11 -10000 0 -0.34 41 41
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.069 -10000 0 -0.35 8 8
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.012 0.14 -10000 0 -0.42 43 43
positive regulation of DNA binding -0.019 0.061 -10000 0 -0.23 34 34
NRIP1 -0.012 0.15 -10000 0 -0.78 10 10
RXRs/RARs -0.017 0.14 -10000 0 -0.41 45 45
RXRs/RXRs/DNA/9cRA -0.017 0.12 -10000 0 -0.4 42 42
PRKACA 0.011 0 -10000 0 -10000 0 0
CDK7 0.011 0 -10000 0 -10000 0 0
TFIIH 0.022 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.01 0.039 -10000 0 -0.33 2 2
CCNH 0.011 0 -10000 0 -10000 0 0
CREBBP 0.009 0.026 -10000 0 -0.41 2 2
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.011 0.02 0.18 1 -10000 0 1
AES 0.011 0.017 -10000 0 -10000 0 0
FBXW11 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.014 0.023 -10000 0 -0.28 3 3
SMAD4 0.01 0.018 -10000 0 -0.41 1 1
DKK2 -0.016 0.1 -10000 0 -0.4 34 34
TLE1 0.011 0.025 0.16 1 -0.41 1 2
MACF1 0.011 0 -10000 0 -10000 0 0
CTNNB1 0.04 0.048 0.21 6 -10000 0 6
WIF1 -0.097 0.16 -10000 0 -0.35 158 158
beta catenin/RanBP3 0.02 0.091 0.36 33 -10000 0 33
KREMEN2 -0.021 0.1 -10000 0 -0.33 50 50
DKK1 -0.063 0.14 -10000 0 -0.33 112 112
beta catenin/beta TrCP1 0.045 0.045 0.2 6 -10000 0 6
FZD1 0.009 0.032 -10000 0 -0.41 3 3
AXIN2 -0.052 0.28 -10000 0 -1.3 26 26
AXIN1 0.011 0 -10000 0 -10000 0 0
RAN 0.011 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.014 0.023 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.05 0.056 0.22 1 -0.32 5 6
Axin1/APC/GSK3 0.018 0.031 0.18 2 -10000 0 2
Axin1/APC/GSK3/beta catenin/Macf1 0.043 0.028 -10000 0 -10000 0 0
HNF1A 0.006 0.046 0.16 1 -0.34 8 9
CTBP1 0.011 0.017 0.17 1 -10000 0 1
MYC -0.017 0.19 -10000 0 -1.3 10 10
RANBP3 0.011 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.012 0.084 -10000 0 -0.21 79 79
NKD1 -0.02 0.1 -10000 0 -0.34 46 46
TCF4 -0.005 0.081 0.16 1 -0.4 20 21
TCF3 0.011 0.017 0.16 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.024 0.028 -10000 0 -0.2 3 3
Ran/GTP 0.008 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.019 0.11 0.41 34 -0.4 2 36
LEF1 0.007 0.045 0.16 1 -0.38 6 7
DVL1 0.03 0.019 -10000 0 -10000 0 0
CSNK2A1 0.011 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.047 0.077 -10000 0 -0.34 9 9
DKK1/LRP6/Kremen 2 -0.038 0.096 -10000 0 -0.18 155 155
LRP6 0.011 0 -10000 0 -10000 0 0
CSNK1A1 0.012 0.02 0.18 1 -10000 0 1
NLK 0.011 0.003 -10000 0 -10000 0 0
CCND1 0.003 0.056 -10000 0 -0.51 1 1
WNT1 0.004 0.042 -10000 0 -0.33 8 8
GSK3A 0.011 0 -10000 0 -10000 0 0
GSK3B 0.011 0 -10000 0 -10000 0 0
FRAT1 0.011 0 -10000 0 -10000 0 0
PPP2R5D 0.031 0.047 0.25 8 -10000 0 8
APC 0.027 0.025 -10000 0 -0.18 3 3
WNT1/LRP6/FZD1 0.037 0.059 0.2 32 -0.19 3 35
CREBBP 0.01 0.03 0.16 1 -0.39 2 3
BARD1 signaling events

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
BARD1/CSTF1 0.01 0.042 -10000 0 -0.28 11 11
ATM 0.011 0 -10000 0 -10000 0 0
UBE2D3 0.011 0 -10000 0 -10000 0 0
PRKDC 0.011 0 -10000 0 -10000 0 0
ATR 0.011 0 -10000 0 -10000 0 0
UBE2L3 0.011 0 -10000 0 -10000 0 0
FANCD2 0.02 0.007 -10000 0 -10000 0 0
protein ubiquitination -0.057 0.07 -10000 0 -0.25 11 11
XRCC5 0.011 0 -10000 0 -10000 0 0
XRCC6 0.011 0 -10000 0 -10000 0 0
M/R/N Complex 0.022 0 -10000 0 -10000 0 0
MRE11A 0.011 0 -10000 0 -10000 0 0
DNA-PK 0.022 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.019 0.029 -10000 0 -10000 0 0
FANCF 0.009 0.026 -10000 0 -0.41 2 2
BRCA1 0.011 0 -10000 0 -10000 0 0
CCNE1 -0.13 0.17 -10000 0 -0.33 214 214
CDK2/Cyclin E1 -0.079 0.12 -10000 0 -0.22 214 214
FANCG 0.011 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.01 0.042 -10000 0 -0.28 11 11
FANCE 0.011 0 -10000 0 -10000 0 0
FANCC 0.011 0 -10000 0 -10000 0 0
NBN 0.011 0 -10000 0 -10000 0 0
FANCA -0.071 0.14 -10000 0 -0.33 126 126
DNA repair -0.015 0.087 -10000 0 -0.31 7 7
BRCA1/BARD1/ubiquitin 0.01 0.042 -10000 0 -0.28 11 11
BARD1/DNA-PK 0.024 0.032 -10000 0 -0.2 11 11
FANCL 0.011 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.01 0.042 0.28 11 -10000 0 11
BRCA1/BARD1/CTIP/M/R/N Complex 0.028 0.031 -10000 0 -0.18 11 11
BRCA1/BACH1/BARD1/TopBP1 0.017 0.036 -10000 0 -0.23 11 11
BRCA1/BARD1/P53 0.023 0.034 -10000 0 -0.2 12 12
BARD1/CSTF1/BRCA1 0.017 0.036 -10000 0 -0.23 11 11
BRCA1/BACH1 0.011 0 -10000 0 -10000 0 0
BARD1 0.002 0.06 -10000 0 -0.41 11 11
PCNA 0.011 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.017 0.036 -10000 0 -0.23 11 11
BRCA1/BARD1/UbcH7 0.017 0.036 -10000 0 -0.23 11 11
BRCA1/BARD1/RAD51/PCNA -0.028 0.089 -10000 0 -0.29 11 11
BARD1/DNA-PK/P53 0.028 0.032 -10000 0 -0.18 12 12
BRCA1/BARD1/Ubiquitin 0.01 0.042 -10000 0 -0.28 11 11
BRCA1/BARD1/CTIP 0.022 0.032 -10000 0 -0.2 11 11
FA complex 0.013 0.036 -10000 0 -0.24 1 1
BARD1/EWS 0.01 0.042 -10000 0 -0.28 11 11
RBBP8 0.018 0 -10000 0 -10000 0 0
TP53 0.01 0.018 -10000 0 -0.41 1 1
TOPBP1 0.011 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.022 0.034 0.2 12 -10000 0 12
BRCA1/BARD1 -0.039 0.087 -10000 0 -0.25 11 11
CSTF1 0.011 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.002 0.042 -10000 0 -0.29 11 11
CDK2 0.011 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.089 0.16 -10000 0 -0.33 155 155
RAD50 0.011 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.01 0.042 -10000 0 -0.28 11 11
EWSR1 0.011 0 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.018 0.01 -9999 0 -0.22 1 1
BAD/BCL-XL/YWHAZ 0.027 0.008 -9999 0 -10000 0 0
CDKN1B 0.021 0.041 -9999 0 -0.23 1 1
CDKN1A 0.029 0.009 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.011 0 -9999 0 -10000 0 0
FOXO3 0.029 0.004 -9999 0 -10000 0 0
AKT1 0 0.002 -9999 0 -10000 0 0
BAD 0.011 0 -9999 0 -10000 0 0
AKT3 -0.096 0.14 -9999 0 -0.28 199 199
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.029 0.013 -9999 0 -10000 0 0
AKT1/ASK1 0.027 0.015 -9999 0 -10000 0 0
BAD/YWHAZ 0.022 0 -9999 0 -10000 0 0
RICTOR 0.009 0.026 -9999 0 -0.41 2 2
RAF1 0.011 0 -9999 0 -10000 0 0
JNK cascade -0.026 0.015 -9999 0 -10000 0 0
TSC1 0.029 0.009 -9999 0 -10000 0 0
YWHAZ 0.011 0 -9999 0 -10000 0 0
AKT1/RAF1 0.03 0.004 -9999 0 -10000 0 0
EP300 0.011 0 -9999 0 -10000 0 0
mol:GDP 0.024 0.004 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.029 0.004 -9999 0 -10000 0 0
YWHAQ 0.011 0 -9999 0 -10000 0 0
TBC1D4 0.017 0.021 -9999 0 -0.22 4 4
MAP3K5 0.009 0.032 -9999 0 -0.41 3 3
MAPKAP1 0.011 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.01 0.015 -9999 0 -10000 0 0
YWHAH 0.011 0 -9999 0 -10000 0 0
AKT1S1 0.029 0.004 -9999 0 -10000 0 0
CASP9 0.029 0.004 -9999 0 -10000 0 0
YWHAB 0.011 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.026 0.04 -9999 0 -0.21 1 1
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0.022 0 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
AKT2/p21CIP1 0.033 0.009 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.015 0.002 -9999 0 -10000 0 0
CHUK 0.029 0.004 -9999 0 -10000 0 0
BAD/BCL-XL 0.04 0.007 -9999 0 -10000 0 0
mTORC2 0.013 0.014 -9999 0 -0.21 2 2
AKT2 0.014 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.022 0.018 -9999 0 -10000 0 0
PDPK1 0.011 0 -9999 0 -10000 0 0
MDM2 0.029 0.004 -9999 0 -10000 0 0
MAPKKK cascade -0.029 0.004 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.039 0.012 -9999 0 -10000 0 0
TSC1/TSC2 0.034 0.009 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.012 -9999 0 -10000 0 0
glucose import -0.085 0.11 -9999 0 -0.2 257 257
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.025 0.004 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.085 0.11 -9999 0 -0.2 257 257
GSK3A 0.029 0.004 -9999 0 -10000 0 0
FOXO1 0.028 0.015 -9999 0 -10000 0 0
GSK3B 0.029 0.004 -9999 0 -10000 0 0
SFN -0.24 0.15 -9999 0 -0.33 388 388
G1/S transition of mitotic cell cycle 0.034 0.003 -9999 0 -10000 0 0
p27Kip1/14-3-3 family -0.002 0.025 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
KPNA1 0.011 0 -9999 0 -10000 0 0
HSP90AA1 0.011 0 -9999 0 -10000 0 0
YWHAG 0.011 0 -9999 0 -10000 0 0
RHEB 0.011 0 -9999 0 -10000 0 0
CREBBP 0.009 0.026 -9999 0 -0.41 2 2
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 0.015 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.011 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.032 0.11 -9999 0 -0.33 66 66
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.01 0.018 -9999 0 -0.41 1 1
RAC1-CDC42/GTP/PAK family -0.007 0.068 -9999 0 -0.17 74 74
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.011 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.011 0 -9999 0 -10000 0 0
FYN 0.011 0 -9999 0 -10000 0 0
MAP3K12 0.008 0.037 -9999 0 -0.41 4 4
FGR 0.002 0.06 -9999 0 -0.41 11 11
p38 alpha/TAB1 -0.003 0.016 -9999 0 -0.21 1 1
PRKG1 -0.18 0.21 -9999 0 -0.41 232 232
DUSP8 0.007 0.041 -9999 0 -0.41 5 5
PGK/cGMP/p38 alpha -0.066 0.076 -9999 0 -0.22 24 24
apoptosis -0.003 0.015 -9999 0 -0.2 1 1
RAL/GTP 0.015 0 -9999 0 -10000 0 0
LYN 0.011 0 -9999 0 -10000 0 0
DUSP1 -0.092 0.18 -9999 0 -0.41 129 129
PAK1 0.011 0 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.028 0 -9999 0 -10000 0 0
TRAF6 0.011 0 -9999 0 -10000 0 0
RAC1 0.011 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.011 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.015 0 -9999 0 -10000 0 0
MAPK11 0.032 0.036 -9999 0 -10000 0 0
BLK -0.015 0.087 -9999 0 -0.33 37 37
HCK 0.006 0.039 -9999 0 -0.33 7 7
MAP2K3 0.011 0 -9999 0 -10000 0 0
DUSP16 0.011 0 -9999 0 -10000 0 0
DUSP10 0.011 0 -9999 0 -10000 0 0
TRAF6/MEKK3 0.014 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.035 0.028 -9999 0 -0.23 1 1
positive regulation of innate immune response 0.039 0.04 -9999 0 -0.22 1 1
LCK 0.008 0.035 -9999 0 -0.35 5 5
p38alpha-beta/MKP7 0.044 0.038 -9999 0 -10000 0 0
p38alpha-beta/MKP5 0.044 0.038 -9999 0 -10000 0 0
PGK/cGMP -0.12 0.15 -9999 0 -0.29 232 232
PAK2 0.011 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.018 0.074 -9999 0 -0.26 12 12
CDC42 0.011 0 -9999 0 -10000 0 0
RALB 0.011 0 -9999 0 -10000 0 0
RALA 0.011 0 -9999 0 -10000 0 0
PAK3 -0.052 0.14 -9999 0 -0.41 74 74
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.021 0.021 -9999 0 -10000 0 0
SNTA1 0.011 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.021 0.021 -9999 0 -10000 0 0
MAPK12 -0.01 0.073 -9999 0 -0.21 28 28
CCND1 0.003 0.033 -9999 0 -10000 0 0
p38 gamma/SNTA1 -0.003 0.069 -9999 0 -0.19 28 28
MAP2K3 0.011 0 -9999 0 -10000 0 0
PKN1 0.011 0 -9999 0 -10000 0 0
G2/M transition checkpoint -0.01 0.073 -9999 0 -0.21 28 28
MAP2K6 -0.017 0.081 -9999 0 -0.19 92 92
MAPT 0.001 0.062 -9999 0 -0.27 20 20
MAPK13 0.015 0.025 -9999 0 -0.22 6 6
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK -0.001 0.064 -9999 0 -0.28 27 27
Regulation of Telomerase

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
Telomerase catalytic core complex -0.13 0.12 -9999 0 -0.47 2 2
RAD9A 0.011 0 -9999 0 -10000 0 0
AP1 -0.08 0.14 -9999 0 -0.29 160 160
IFNAR2 0.007 0.019 -9999 0 -0.41 1 1
AKT1 -0.012 0.058 -9999 0 -0.18 23 23
ER alpha/Oestrogen -0.028 0.094 -9999 0 -0.29 60 60
NFX1/SIN3/HDAC complex 0.032 0.016 -9999 0 -10000 0 0
EGF -0.005 0.071 -9999 0 -0.34 23 23
SMG5 0.011 0 -9999 0 -10000 0 0
SMG6 0.011 0 -9999 0 -10000 0 0
SP3/HDAC2 0.012 0.009 -9999 0 -10000 0 0
TERT/c-Abl -0.12 0.11 -9999 0 -0.46 4 4
SAP18 0.011 0.001 -9999 0 -10000 0 0
MRN complex 0.022 0 -9999 0 -10000 0 0
WT1 -0.3 0.18 -9999 0 -0.41 391 391
WRN 0.011 0 -9999 0 -10000 0 0
SP1 0.009 0.007 -9999 0 -10000 0 0
SP3 0.01 0.002 -9999 0 -10000 0 0
TERF2IP 0.011 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.1 0.09 -9999 0 -0.4 2 2
Mad/Max 0.012 0.009 -9999 0 -10000 0 0
TERT -0.13 0.12 -9999 0 -0.48 2 2
CCND1 -0.11 0.11 -9999 0 -10000 0 0
MAX 0.01 0.002 -9999 0 -10000 0 0
RBBP7 0.011 0.001 -9999 0 -10000 0 0
RBBP4 0.008 0.032 -9999 0 -0.41 3 3
TERF2 0.01 0 -9999 0 -10000 0 0
PTGES3 0.011 0 -9999 0 -10000 0 0
SIN3A 0.011 0.001 -9999 0 -10000 0 0
Telomerase/911 0.009 0.021 -9999 0 -10000 0 0
CDKN1B -0.016 0.12 -9999 0 -0.5 23 23
RAD1 0.011 0 -9999 0 -10000 0 0
XRCC5 0.011 0 -9999 0 -10000 0 0
XRCC6 0.011 0 -9999 0 -10000 0 0
SAP30 0.011 0.001 -9999 0 -10000 0 0
TRF2/PARP2 0.016 0 -9999 0 -10000 0 0
UBE3A 0.01 0.002 -9999 0 -10000 0 0
JUN 0.005 0.048 -9999 0 -0.41 7 7
E6 -0.001 0.002 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.006 0.005 -9999 0 -10000 0 0
FOS -0.12 0.19 -9999 0 -0.41 159 159
IFN-gamma/IRF1 -0.02 0.086 -9999 0 -0.22 80 80
PARP2 0.011 0 -9999 0 -10000 0 0
BLM -0.027 0.11 -9999 0 -0.33 59 59
Telomerase -0.013 0.036 -9999 0 -10000 0 0
IRF1 0.007 0.033 -9999 0 -10000 0 0
ESR1 -0.037 0.13 -9999 0 -0.41 60 60
KU/TER 0.016 0 -9999 0 -10000 0 0
ATM/TRF2 0.017 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.037 0.015 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.038 0.015 -9999 0 -10000 0 0
HDAC1 0.011 0.001 -9999 0 -10000 0 0
HDAC2 0.008 0.006 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.016 0.029 -9999 0 -0.28 5 5
ABL1 0.009 0.026 -9999 0 -0.41 2 2
MXD1 0.01 0.002 -9999 0 -10000 0 0
MRE11A 0.011 0 -9999 0 -10000 0 0
HUS1 0.011 0 -9999 0 -10000 0 0
RPS6KB1 0.011 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.097 0.096 -9999 0 -10000 0 0
NR2F2 -0.008 0.09 -9999 0 -0.41 25 25
MAPK3 0.003 0.041 -9999 0 -0.22 17 17
MAPK1 0.003 0.041 -9999 0 -0.22 17 17
TGFB1/TGF beta receptor Type II 0.01 0.018 -9999 0 -0.41 1 1
NFKB1 0.01 0.018 -9999 0 -0.41 1 1
HNRNPC 0.011 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.011 0 -9999 0 -10000 0 0
EGFR -0.001 0.067 -9999 0 -0.41 14 14
mol:Oestrogen -0.001 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.006 0.068 -9999 0 -0.25 36 36
MYC 0.002 0.058 -9999 0 -0.41 10 10
IL2 -0.008 0.059 -9999 0 -0.33 17 17
KU 0.016 0 -9999 0 -10000 0 0
RAD50 0.011 0 -9999 0 -10000 0 0
HSP90AA1 0.011 0 -9999 0 -10000 0 0
TGFB1 0.011 0.018 -9999 0 -0.41 1 1
TRF2/BLM -0.008 0.068 -9999 0 -0.2 59 59
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.11 0.11 -9999 0 -0.44 2 2
SP1/HDAC2 0.014 0.01 -9999 0 -10000 0 0
PINX1 0.011 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.1 0.09 -9999 0 -0.41 1 1
Smad3/Myc 0.015 0.044 -9999 0 -0.24 14 14
911 complex 0.022 0 -9999 0 -10000 0 0
IFNG -0.032 0.11 -9999 0 -0.31 62 62
Telomerase/PinX1 -0.1 0.09 -9999 0 -0.41 1 1
Telomerase/AKT1/mTOR/p70S6K -0.015 0.041 -9999 0 -10000 0 0
SIN3B 0.011 0.001 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.1 0.09 -9999 0 -0.41 1 1
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.032 0 -9999 0 -10000 0 0
TRF2/WRN 0.016 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.1 0.09 -9999 0 -0.4 2 2
E2F1 -0.056 0.13 -9999 0 -0.33 100 100
ZNFX1 0.011 0.001 -9999 0 -10000 0 0
PIF1 -0.074 0.15 -9999 0 -0.33 132 132
NCL 0.011 0 -9999 0 -10000 0 0
DKC1 0.011 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.023 0.076 -10000 0 -0.33 8 8
TBX21 0.004 0.25 -10000 0 -0.96 21 21
B2M 0.012 0.005 -10000 0 -10000 0 0
TYK2 0.014 0.016 -10000 0 -10000 0 0
IL12RB1 0.002 0.072 -10000 0 -0.37 18 18
GADD45B 0.038 0.17 -10000 0 -0.85 6 6
IL12RB2 -0.005 0.082 -10000 0 -0.33 30 30
GADD45G 0.015 0.25 -10000 0 -0.97 23 23
natural killer cell activation 0.003 0.016 -10000 0 -10000 0 0
RELB 0.011 0 -10000 0 -10000 0 0
RELA 0.011 0 -10000 0 -10000 0 0
IL18 0.01 0.042 -10000 0 -0.33 8 8
IL2RA -0.003 0.068 -10000 0 -0.33 21 21
IFNG -0.028 0.1 -10000 0 -0.33 57 57
STAT3 (dimer) 0.028 0.19 -10000 0 -0.62 21 21
HLA-DRB5 -0.005 0.068 -10000 0 -0.38 16 16
FASLG 0.009 0.23 -10000 0 -0.95 16 16
NF kappa B2 p52/RelB -0.064 0.17 -10000 0 -0.69 25 25
CD4 0.006 0.017 -10000 0 -0.35 1 1
SOCS1 0.01 0.018 -10000 0 -0.41 1 1
EntrezGene:6955 -0.006 0.014 -10000 0 -10000 0 0
CD3D -0.008 0.074 -10000 0 -0.37 21 21
CD3E -0.002 0.065 -10000 0 -0.39 14 14
CD3G 0 0.048 -10000 0 -0.35 9 9
IL12Rbeta2/JAK2 0.005 0.074 -10000 0 -0.24 39 39
CCL3 0.013 0.22 -10000 0 -0.89 14 14
CCL4 0.009 0.24 -10000 0 -0.97 16 16
HLA-A 0.011 0.016 -10000 0 -0.33 1 1
IL18/IL18R 0.043 0.054 -10000 0 -0.24 12 12
NOS2 0.018 0.23 -10000 0 -0.86 22 22
IL12/IL12R/TYK2/JAK2/SPHK2 0.023 0.074 -10000 0 -0.3 8 8
IL1R1 0.003 0.26 -10000 0 -1.1 18 18
IL4 0.001 0.017 -10000 0 -10000 0 0
JAK2 0.007 0.058 -10000 0 -0.42 9 9
EntrezGene:6957 -0.005 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.002 0.12 -10000 0 -0.56 18 18
RAB7A 0.044 0.18 -10000 0 -0.66 12 12
lysosomal transport 0.044 0.17 -10000 0 -0.63 12 12
FOS -0.3 0.56 -10000 0 -1.1 162 162
STAT4 (dimer) 0.04 0.2 -10000 0 -0.66 20 20
STAT5A (dimer) -0.074 0.18 -10000 0 -0.69 29 29
GZMA -0.004 0.27 -10000 0 -1 22 22
GZMB 0.003 0.23 -10000 0 -0.99 14 14
HLX 0.011 0 -10000 0 -10000 0 0
LCK 0.02 0.23 -10000 0 -0.77 25 25
TCR/CD3/MHC II/CD4 -0.042 0.12 -10000 0 -0.21 139 139
IL2/IL2R 0.008 0.063 -10000 0 -0.3 14 14
MAPK14 0.036 0.2 -10000 0 -0.7 21 21
CCR5 0.03 0.2 -10000 0 -0.84 14 14
IL1B 0.011 0.042 -10000 0 -0.44 4 4
STAT6 0.024 0.078 -10000 0 -0.31 5 5
STAT4 0.01 0.018 -10000 0 -0.41 1 1
STAT3 0.011 0 -10000 0 -10000 0 0
STAT1 0.01 0.015 -10000 0 -0.33 1 1
NFKB1 0.01 0.018 -10000 0 -0.41 1 1
NFKB2 0.011 0 -10000 0 -10000 0 0
IL12B 0.01 0.021 -10000 0 -0.31 1 1
CD8A 0 0.068 -10000 0 -0.39 15 15
CD8B -0.011 0.088 -10000 0 -0.35 33 33
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.023 0.076 0.33 8 -10000 0 8
IL2RB 0.01 0.018 -10000 0 -0.41 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.041 0.19 -10000 0 -0.61 20 20
IL2RG 0.005 0.048 -10000 0 -0.36 9 9
IL12 0.014 0.05 -10000 0 -0.23 16 16
STAT5A 0.01 0.018 -10000 0 -0.41 1 1
CD247 0.006 0.031 -10000 0 -0.38 3 3
IL2 -0.007 0.059 -10000 0 -0.33 17 17
SPHK2 0.011 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.003 0.062 -10000 0 -0.35 15 15
IL12/IL12R/TYK2/JAK2 0.019 0.24 -10000 0 -0.81 25 25
MAP2K3 0.031 0.2 -10000 0 -0.71 19 19
RIPK2 0.011 0 -10000 0 -10000 0 0
MAP2K6 0.033 0.2 -10000 0 -0.71 19 19
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.004 0.028 -10000 0 -0.42 2 2
IL18RAP 0.01 0.046 -10000 0 -0.38 7 7
IL12Rbeta1/TYK2 0.012 0.056 -10000 0 -0.26 18 18
EOMES -0.01 0.14 -10000 0 -1.2 7 7
STAT1 (dimer) 0.03 0.18 -10000 0 -0.63 19 19
T cell proliferation 0.038 0.16 -10000 0 -0.51 20 20
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.012 0.038 -10000 0 -0.41 4 4
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.039 0.13 -10000 0 -0.55 21 21
ATF2 0.039 0.19 -10000 0 -0.66 20 20
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A -0.007 0.07 -10000 0 -0.28 32 32
PRKCZ 0.01 0.024 -10000 0 -0.37 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.011 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.003 0.023 -10000 0 -0.23 4 4
IRAK/TOLLIP 0.01 0.053 -10000 0 -0.2 32 32
IKBKB 0.011 0 -10000 0 -10000 0 0
IKBKG 0.011 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.015 0.086 -10000 0 -0.24 64 64
IL1A -0.012 0.084 -10000 0 -0.33 34 34
IL1B 0.015 0.035 -10000 0 -0.33 5 5
IRAK/TRAF6/p62/Atypical PKCs 0.011 0.047 -10000 0 -0.34 1 1
IL1R2 -0.013 0.089 -10000 0 -0.34 36 36
IL1R1 0.004 0.055 -10000 0 -0.41 9 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.026 0.057 0.18 23 -0.26 10 33
TOLLIP 0.011 0 -10000 0 -10000 0 0
TICAM2 0.004 0.051 -10000 0 -0.41 8 8
MAP3K3 0.011 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.007 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.041 0.042 -10000 0 -10000 0 0
JUN 0.002 0.069 -10000 0 -0.28 9 9
MAP3K7 0.011 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.028 0.05 -10000 0 -0.42 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88 0.011 0.057 -10000 0 -0.23 11 11
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.017 0.053 -10000 0 -0.36 2 2
IL1 beta fragment/IL1R1/IL1RAP 0.02 0.045 -10000 0 -0.22 16 16
NFKB1 0.01 0.018 -10000 0 -0.41 1 1
MAPK8 -0.001 0.068 -10000 0 -0.29 7 7
IRAK1 0.003 0.059 -10000 0 -0.23 32 32
IL1RN/IL1R1 -0.023 0.092 -10000 0 -0.23 85 85
IRAK4 0.011 0 -10000 0 -10000 0 0
PRKCI 0.011 0 -10000 0 -10000 0 0
TRAF6 0.011 0 -10000 0 -10000 0 0
PI3K 0.013 0.031 -10000 0 -0.28 6 6
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.026 0.04 -10000 0 -0.28 4 4
CHUK 0.011 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.02 0.045 -10000 0 -0.22 16 16
IL1 beta/IL1R2 0.005 0.058 -10000 0 -0.25 9 9
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.01 0.039 -10000 0 -0.16 32 32
NF kappa B1 p50/RelA -0.007 0.039 -10000 0 -0.38 3 3
IRAK3 -0.008 0.088 -10000 0 -0.41 24 24
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.027 0.049 -10000 0 -0.36 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.02 0.04 -10000 0 -0.22 11 11
IL1 alpha/IL1R1/IL1RAP 0.004 0.062 -10000 0 -0.2 44 44
RELA 0.011 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.011 0 -10000 0 -10000 0 0
MYD88 0.011 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.016 0.05 -10000 0 -0.18 32 32
IL1RAP 0.009 0.032 -10000 0 -0.41 3 3
UBE2N 0.011 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.015 0.047 -10000 0 -0.3 6 6
CASP1 0.009 0.026 -10000 0 -0.41 2 2
IL1RN/IL1R2 -0.034 0.1 -10000 0 -0.24 105 105
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.026 0.042 -10000 0 -0.38 2 2
TMEM189-UBE2V1 -0.021 0.099 -10000 0 -0.41 32 32
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.018 0.058 -10000 0 -0.34 9 9
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
IL1RN -0.039 0.12 -10000 0 -0.33 78 78
TRAF6/TAK1/TAB1/TAB2 -0.011 0.042 -10000 0 -0.18 32 32
MAP2K6 -0.005 0.069 -10000 0 -0.31 6 6
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.012 0.068 -10000 0 -0.35 15 15
FYN 0.033 0.1 -10000 0 -0.44 16 16
LAT/GRAP2/SLP76 -0.013 0.082 -10000 0 -0.39 18 18
IKBKB 0.011 0 -10000 0 -10000 0 0
AKT1 0.038 0.078 -10000 0 -0.32 17 17
B2M 0.012 0.002 -10000 0 -10000 0 0
IKBKG -0.004 0.019 -10000 0 -0.12 9 9
MAP3K8 0.009 0.032 -10000 0 -0.41 3 3
mol:Ca2+ -0.006 0.017 -10000 0 -0.082 19 19
integrin-mediated signaling pathway 0.015 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.037 0.11 -10000 0 -0.44 18 18
TRPV6 -0.043 0.12 -10000 0 -0.4 57 57
CD28 0.01 0.021 -10000 0 -0.33 2 2
SHC1 0.032 0.097 -10000 0 -0.43 16 16
receptor internalization 0.027 0.09 -10000 0 -0.43 15 15
PRF1 0.021 0.14 -10000 0 -0.99 7 7
KRAS 0.01 0.015 -10000 0 -0.33 1 1
GRB2 0.011 0 -10000 0 -10000 0 0
COT/AKT1 0.039 0.065 -10000 0 -0.27 15 15
LAT 0.032 0.097 -10000 0 -0.43 16 16
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D -0.002 0.073 -10000 0 -0.36 21 21
CD3E 0.002 0.065 -10000 0 -0.39 14 14
CD3G 0.005 0.047 -10000 0 -0.35 9 9
RASGRP2 -0.011 0.059 -10000 0 -0.16 73 73
RASGRP1 0.04 0.085 -10000 0 -0.36 16 16
HLA-A 0.012 0.015 -10000 0 -0.33 1 1
RASSF5 0.011 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.015 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.035 -10000 0 -0.11 12 12
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.008 0.032 -10000 0 -0.18 13 13
PRKCA -0.006 0.047 -10000 0 -0.21 16 16
GRAP2 -0.003 0.074 -10000 0 -0.41 17 17
mol:IP3 0.003 0.081 0.18 48 -0.33 14 62
EntrezGene:6957 0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.018 0.084 -10000 0 -0.41 14 14
ORAI1 0.027 0.074 0.24 57 -10000 0 57
CSK 0.031 0.099 -10000 0 -0.43 16 16
B7 family/CD28 0.032 0.098 -10000 0 -0.43 16 16
CHUK 0.011 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.027 0.11 -10000 0 -0.47 17 17
PTPN6 0.029 0.098 -10000 0 -0.43 16 16
VAV1 0.031 0.1 -10000 0 -0.45 16 16
Monovalent TCR/CD3 0.012 0.064 -10000 0 -0.29 19 19
CBL 0.011 0 -10000 0 -10000 0 0
LCK 0.03 0.1 -10000 0 -0.46 16 16
PAG1 0.03 0.1 -10000 0 -0.43 18 18
RAP1A 0.011 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.027 0.11 -10000 0 -0.48 16 16
CD80 -0.008 0.079 -10000 0 -0.33 30 30
CD86 0.01 0.021 -10000 0 -0.34 2 2
PDK1/CARD11/BCL10/MALT1 -0.01 0.039 -10000 0 -0.21 14 14
HRAS 0.011 0 -10000 0 -10000 0 0
GO:0035030 0.029 0.086 -10000 0 -0.37 16 16
CD8A 0.001 0.068 -10000 0 -0.39 15 15
CD8B -0.01 0.088 -10000 0 -0.35 33 33
PTPRC 0.003 0.057 -10000 0 -0.4 10 10
PDK1/PKC theta 0.039 0.097 -10000 0 -0.38 19 19
CSK/PAG1 0.033 0.099 -10000 0 -0.41 18 18
SOS1 0.011 0 -10000 0 -10000 0 0
peptide-MHC class I 0.018 0.011 -10000 0 -0.22 1 1
GRAP2/SLP76 -0.015 0.095 -10000 0 -0.45 18 18
STIM1 0.013 0.036 -10000 0 -10000 0 0
RAS family/GTP 0.039 0.036 -10000 0 -0.15 8 8
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.027 0.094 -10000 0 -0.45 15 15
mol:DAG -0.006 0.059 -10000 0 -0.29 15 15
RAP1A/GDP 0.012 0.015 -10000 0 -0.057 6 6
PLCG1 0.011 0 -10000 0 -10000 0 0
CD247 0.01 0.03 -10000 0 -0.39 3 3
cytotoxic T cell degranulation 0.022 0.13 -10000 0 -0.92 7 7
RAP1A/GTP -0.008 0.02 -10000 0 -0.057 73 73
mol:PI-3-4-5-P3 0.037 0.09 -10000 0 -0.37 18 18
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0 0.096 0.19 46 -0.42 14 60
NRAS 0.011 0 -10000 0 -10000 0 0
ZAP70 -0.001 0.064 -10000 0 -0.34 18 18
GRB2/SOS1 0.016 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.012 0.081 -10000 0 -0.39 17 17
MALT1 0.011 0 -10000 0 -10000 0 0
TRAF6 0.011 0 -10000 0 -10000 0 0
CD8 heterodimer -0.004 0.081 -10000 0 -0.26 44 44
CARD11 0.001 0.058 -10000 0 -0.35 14 14
PRKCB -0.008 0.058 -10000 0 -0.27 20 20
PRKCE -0.004 0.042 -10000 0 -0.21 14 14
PRKCQ 0.034 0.11 -10000 0 -0.42 20 20
LCP2 0.01 0.015 -10000 0 -0.33 1 1
BCL10 0.011 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.037 0.069 -10000 0 -0.28 17 17
IKK complex 0.03 0.037 -10000 0 -0.095 16 16
RAS family/GDP -0.001 0.005 -10000 0 -10000 0 0
MAP3K14 0.038 0.052 -10000 0 -0.21 13 13
PDPK1 0.039 0.075 -10000 0 -0.31 16 16
TCR/CD3/MHC I/CD8/Fyn 0.02 0.12 -10000 0 -0.48 21 21
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.016 0.051 -9999 0 -0.21 18 18
MAP4K1 0.003 0.053 -9999 0 -0.33 13 13
MAP3K8 0.009 0.032 -9999 0 -0.41 3 3
PRKCB -0.015 0.1 -9999 0 -0.41 32 32
DBNL 0.011 0 -9999 0 -10000 0 0
CRKL 0.011 0 -9999 0 -10000 0 0
MAP3K1 0.029 0.038 -9999 0 -0.17 17 17
JUN -0.01 0.14 -9999 0 -0.52 37 37
MAP3K7 0.029 0.038 -9999 0 -0.17 17 17
GRAP2 -0.003 0.074 -9999 0 -0.41 17 17
CRK 0.011 0 -9999 0 -10000 0 0
MAP2K4 0.034 0.04 -9999 0 -0.22 1 1
LAT 0.011 0 -9999 0 -10000 0 0
LCP2 0.01 0.015 -9999 0 -0.33 1 1
MAPK8 -0.014 0.15 -9999 0 -0.55 37 37
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.024 0.041 -9999 0 -0.19 17 17
LAT/GRAP2/SLP76/HPK1/HIP-55 0.022 0.048 -9999 0 -0.2 18 18
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.014 0.051 -10000 0 -0.17 11 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.011 0 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.037 0.047 -10000 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.015 0.037 -10000 0 -0.23 11 11
antigen processing and presentation of peptide antigen via MHC class I -0.031 0.043 -10000 0 -0.26 4 4
CaM/Ca2+ -0.013 0.036 -10000 0 -10000 0 0
RAP1A 0.011 0 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.019 0.049 -10000 0 -0.24 1 1
AKT1 0.024 0.049 -10000 0 -0.28 2 2
MAP2K1 0.024 0.046 -10000 0 -10000 0 0
MAP3K11 0.018 0.048 -10000 0 -10000 0 0
IFNGR1 0.011 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.18 0.16 -10000 0 -0.33 292 292
Rap1/GTP -0.009 0.023 -10000 0 -10000 0 0
CRKL/C3G 0.016 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.013 0.055 -10000 0 -10000 0 0
CEBPB 0.048 0.048 -10000 0 -0.38 2 2
STAT3 0.011 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.018 0.068 -10000 0 -1 1 1
STAT1 0.018 0.049 -10000 0 -0.24 1 1
CALM1 0.011 0 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.027 0.1 -10000 0 -0.32 57 57
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
STAT1 (dimer)/PIAS1 0.023 0.047 -10000 0 -0.23 1 1
CEBPB/PTGES2/Cbp/p300 -0.003 0.018 -10000 0 -0.24 2 2
mol:Ca2+ 0.012 0.05 -10000 0 -0.17 11 11
MAPK3 0.033 0.042 -10000 0 -10000 0 0
STAT1 (dimer) -0.038 0.057 -10000 0 -0.36 4 4
MAPK1 0.033 0.042 -10000 0 -10000 0 0
JAK2 0.004 0.054 -10000 0 -0.41 9 9
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
JAK1 0.009 0.026 -10000 0 -0.41 2 2
CAMK2D 0.009 0.026 -10000 0 -0.41 2 2
DAPK1 0.046 0.05 -10000 0 -0.58 2 2
SMAD7 0.001 0.041 -10000 0 -0.29 2 2
CBL/CRKL/C3G 0.027 0.044 -10000 0 -10000 0 0
PI3K -0.014 0.039 -10000 0 -0.31 2 2
IFNG -0.027 0.1 -10000 0 -0.32 57 57
apoptosis 0.027 0.04 -10000 0 -0.43 2 2
CAMK2G 0.011 0 -10000 0 -10000 0 0
STAT3 (dimer) 0.011 0 -10000 0 -10000 0 0
CAMK2A -0.22 0.21 -10000 0 -0.41 292 292
CAMK2B -0.046 0.13 -10000 0 -0.33 88 88
FRAP1 0.023 0.046 -10000 0 -0.27 2 2
PRKCD 0.026 0.05 -10000 0 -0.28 2 2
RAP1B 0.011 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.031 0.043 -10000 0 -0.26 4 4
PTPN2 0.011 0 -10000 0 -10000 0 0
EP300 0.011 0 -10000 0 -10000 0 0
IRF1 0.044 0.042 -10000 0 -0.25 1 1
STAT1 (dimer)/PIASy 0.021 0.047 0.18 1 -0.23 1 2
SOCS1 0.001 0.056 -10000 0 -1.3 1 1
mol:GDP -0.011 0.029 -10000 0 -10000 0 0
CASP1 0.001 0.041 -10000 0 -0.21 3 3
PTGES2 0.01 0.018 -10000 0 -0.41 1 1
IRF9 0.04 0.019 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.014 0.038 -10000 0 -0.3 2 2
RAP1/GDP -0.009 0.024 -10000 0 -10000 0 0
CBL 0.017 0.048 -10000 0 -10000 0 0
MAP3K1 0.018 0.048 -10000 0 -10000 0 0
PIAS1 0.011 0 -10000 0 -10000 0 0
PIAS4 0.011 0 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.031 0.043 -10000 0 -0.26 4 4
PTPN11 0.011 0.05 -10000 0 -0.17 11 11
CREBBP 0.01 0.026 -10000 0 -0.41 2 2
RAPGEF1 0.011 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.01 0.015 -10000 0 -0.33 1 1
NFATC1 0.034 0.051 -10000 0 -0.25 15 15
NFATC2 0.015 0.048 -10000 0 -0.21 8 8
NFATC3 0.018 0.016 -10000 0 -0.31 1 1
YWHAE 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.017 0.1 -10000 0 -0.34 30 30
Exportin 1/Ran/NUP214 0.021 0.006 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.032 0.081 -10000 0 -0.35 22 22
BCL2/BAX -0.012 0.087 -10000 0 -0.28 50 50
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.004 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.004 -10000 0 -10000 0 0
BAX 0.011 0 -10000 0 -10000 0 0
MAPK14 0.011 0.003 -10000 0 -10000 0 0
BAD 0.011 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.011 0.1 -10000 0 -0.38 21 21
Calcineurin A alpha-beta B1/BCL2 -0.029 0.12 -10000 0 -0.41 50 50
FKBP8 0.011 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.01 0.099 0.38 21 -10000 0 21
KPNB1 0.011 0 -10000 0 -10000 0 0
KPNA2 -0.004 0.07 -10000 0 -0.33 23 23
XPO1 0.011 0 -10000 0 -10000 0 0
SFN -0.24 0.15 -10000 0 -0.33 388 388
MAP3K8 0.008 0.032 -10000 0 -0.41 3 3
NFAT4/CK1 alpha 0.026 0.012 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.026 0.076 -10000 0 -0.23 34 34
CABIN1 -0.017 0.11 -10000 0 -0.34 30 30
CALM1 0.011 0.002 -10000 0 -10000 0 0
RAN 0.011 0 -10000 0 -10000 0 0
MAP3K1 0.011 0 -10000 0 -10000 0 0
CAMK4 0.003 0.051 -10000 0 -0.36 10 10
mol:Ca2+ 0 0.004 -10000 0 -10000 0 0
MAPK3 0.011 0 -10000 0 -10000 0 0
YWHAH 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.014 0.023 -10000 0 -0.28 3 3
YWHAB 0.011 0 -10000 0 -10000 0 0
MAPK8 0.007 0.041 -10000 0 -0.41 5 5
MAPK9 0.011 0 -10000 0 -10000 0 0
YWHAG 0.011 0 -10000 0 -10000 0 0
FKBP1A 0.011 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.044 0.049 -10000 0 -0.27 1 1
PRKCH 0.009 0.032 -10000 0 -0.41 3 3
CABIN1/Cbp/p300 0.015 0.019 -10000 0 -0.28 2 2
CASP3 0.011 0.003 -10000 0 -10000 0 0
PIM1 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.008 0.002 -10000 0 -10000 0 0
apoptosis -0.008 0.023 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.001 0.02 -10000 0 -10000 0 0
PRKCB -0.015 0.1 -10000 0 -0.41 32 32
PRKCE 0.011 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.022 0.014 -10000 0 -0.28 1 1
BAD/BCL-XL 0.016 0.01 -10000 0 -0.22 1 1
PRKCD 0.011 0 -10000 0 -10000 0 0
NUP214 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.009 0.024 -10000 0 -0.37 2 2
PRKCA -0.016 0.1 -10000 0 -0.41 34 34
PRKCG -0.038 0.12 -10000 0 -0.34 73 73
PRKCQ -0.026 0.12 -10000 0 -0.41 47 47
FKBP38/BCL2 -0.012 0.087 -10000 0 -0.28 50 50
EP300 0.011 0.003 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.011 0 -10000 0 -10000 0 0
NFATc/JNK1 0.036 0.053 -10000 0 -0.29 2 2
CaM/Ca2+/FKBP38 0.015 0.004 -10000 0 -10000 0 0
FKBP12/FK506 0.008 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.011 0.03 -10000 0 -0.2 10 10
NFATc/ERK1 0.039 0.048 -10000 0 -0.28 2 2
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.032 0.081 -10000 0 -0.35 22 22
NR4A1 0.016 0.12 -10000 0 -0.4 34 34
GSK3B 0.011 0.003 -10000 0 -10000 0 0
positive T cell selection 0.018 0.016 -10000 0 -0.31 1 1
NFAT1/CK1 alpha -0.01 0.029 -10000 0 -0.25 2 2
RCH1/ KPNB1 0.006 0.048 -10000 0 -0.22 23 23
YWHAQ 0.011 0 -10000 0 -10000 0 0
PRKACA 0.011 0.003 -10000 0 -10000 0 0
AKAP5 0.009 0.032 -10000 0 -0.41 3 3
MEF2D 0.011 0.003 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.011 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.038 0.049 -10000 0 -0.29 2 2
CREBBP 0.009 0.026 -10000 0 -0.41 2 2
BCL2 -0.029 0.12 -10000 0 -0.41 50 50
FoxO family signaling

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
G6PC 0.027 0.026 -9999 0 -10000 0 0
PLK1 -0.089 0.18 -9999 0 -0.53 54 54
CDKN1B 0.001 0.14 -9999 0 -0.44 28 28
FOXO3 -0.05 0.18 -9999 0 -0.5 56 56
KAT2B -0.002 0.057 -9999 0 -0.42 9 9
FOXO1/SIRT1 0.022 0.03 -9999 0 -10000 0 0
CAT -0.04 0.17 -9999 0 -0.55 20 20
CTNNB1 0.011 0 -9999 0 -10000 0 0
AKT1 0.007 0.016 -9999 0 -10000 0 0
FOXO1 0.026 0.026 -9999 0 -0.22 5 5
MAPK10 -0.019 0.089 -9999 0 -0.19 111 111
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.038 0.076 -9999 0 -0.29 5 5
response to oxidative stress -0.005 0.018 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.074 0.15 -9999 0 -0.47 57 57
XPO1 0.012 0 -9999 0 -10000 0 0
EP300 0.012 0.001 -9999 0 -10000 0 0
BCL2L11 0.011 0.025 -9999 0 -10000 0 0
FOXO1/SKP2 0.029 0.024 -9999 0 -0.2 3 3
mol:GDP -0.005 0.018 -9999 0 -10000 0 0
RAN 0.012 0 -9999 0 -10000 0 0
GADD45A 0.012 0.096 -9999 0 -0.42 2 2
YWHAQ 0.011 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.033 0.017 -9999 0 -10000 0 0
MST1 0.001 0.04 -9999 0 -0.34 6 6
CSNK1D 0.011 0 -9999 0 -10000 0 0
CSNK1E 0.011 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.011 0.021 -9999 0 -10000 0 0
YWHAB 0.011 0 -9999 0 -10000 0 0
MAPK8 0.024 0.023 -9999 0 -0.2 5 5
MAPK9 0.026 0.008 -9999 0 -10000 0 0
YWHAG 0.011 0 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
YWHAZ 0.011 0 -9999 0 -10000 0 0
SIRT1 0.009 0.026 -9999 0 -0.41 2 2
SOD2 0.019 0.12 -9999 0 -0.39 8 8
RBL2 -0.014 0.15 -9999 0 -0.7 7 7
RAL/GDP 0.016 0.012 -9999 0 -10000 0 0
CHUK 0.005 0.016 -9999 0 -10000 0 0
Ran/GTP 0.011 0.001 -9999 0 -10000 0 0
CSNK1G2 0.011 0 -9999 0 -10000 0 0
RAL/GTP 0.022 0.012 -9999 0 -10000 0 0
CSNK1G1 0.011 0 -9999 0 -10000 0 0
FASLG -0.001 0.12 -9999 0 -1.3 4 4
SKP2 0.011 0 -9999 0 -10000 0 0
USP7 0.012 0 -9999 0 -10000 0 0
IKBKB 0.005 0.016 -9999 0 -10000 0 0
CCNB1 -0.052 0.18 -9999 0 -0.61 21 21
FOXO1-3a-4/beta catenin 0.033 0.11 -9999 0 -0.37 7 7
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.024 -9999 0 -0.2 3 3
CSNK1A1 0.011 0 -9999 0 -10000 0 0
SGK1 0.003 0.032 -9999 0 -0.44 2 2
CSNK1G3 0.011 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.02 0.002 -9999 0 -10000 0 0
ZFAND5 0.043 0.067 -9999 0 -10000 0 0
SFN -0.24 0.15 -9999 0 -0.33 388 388
CDK2 0.013 0.002 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.003 0.035 -9999 0 -10000 0 0
CREBBP 0.011 0.026 -9999 0 -0.41 2 2
FBXO32 -0.14 0.41 -9999 0 -1.2 68 68
BCL6 -0.013 0.14 -9999 0 -0.5 13 13
RALB 0.012 0 -9999 0 -10000 0 0
RALA 0.012 0 -9999 0 -10000 0 0
YWHAH 0.011 0 -9999 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 0.006 0.046 -10000 0 -0.22 21 21
cell-cell adhesion 0.03 0.063 0.3 9 -10000 0 9
Ephrin B/EPHB2/RasGAP 0.008 0.069 -10000 0 -0.38 1 1
ITSN1 0.011 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
SHC1 0.011 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.006 0.045 -10000 0 -0.21 21 21
Ephrin B1/EPHB1 -0.01 0.074 -10000 0 -0.23 52 52
HRAS/GDP -0.03 0.067 -10000 0 -0.3 10 10
Ephrin B/EPHB1/GRB7 -0.02 0.098 -10000 0 -0.37 11 11
Endophilin/SYNJ1 0.008 0.062 -10000 0 -0.36 1 1
KRAS 0.01 0.015 -10000 0 -0.33 1 1
Ephrin B/EPHB1/Src -0.009 0.092 -10000 0 -0.38 8 8
endothelial cell migration -0.003 0.025 -10000 0 -0.18 10 10
GRB2 0.011 0 -10000 0 -10000 0 0
GRB7 -0.011 0.084 -10000 0 -0.34 33 33
PAK1 0.012 0.067 -10000 0 -0.36 3 3
HRAS 0.011 0 -10000 0 -10000 0 0
RRAS 0.008 0.063 -10000 0 -0.36 1 1
DNM1 0.006 0.045 -10000 0 -0.41 6 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.01 0.087 -10000 0 -0.36 8 8
lamellipodium assembly -0.03 0.063 -10000 0 -0.3 9 9
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.009 0.09 -10000 0 -0.37 8 8
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
EPHB2 0.009 0.026 -10000 0 -0.33 3 3
EPHB3 -0.004 0.072 -10000 0 -0.35 21 21
EPHB1 -0.03 0.12 -10000 0 -0.41 51 51
EPHB4 0.01 0.018 -10000 0 -0.41 1 1
mol:GDP -0.001 0.084 -10000 0 -0.22 44 44
Ephrin B/EPHB2 0.004 0.066 -10000 0 -0.19 53 53
Ephrin B/EPHB3 -0.002 0.082 -10000 0 -0.22 56 56
JNK cascade 0.009 0.065 -10000 0 -0.37 1 1
Ephrin B/EPHB1 -0.016 0.092 -10000 0 -0.2 96 96
RAP1/GDP 0.01 0.076 -10000 0 -0.28 10 10
EFNB2 0.009 0.032 -10000 0 -0.41 3 3
EFNB3 -0.029 0.12 -10000 0 -0.41 50 50
EFNB1 0.01 0.018 -10000 0 -0.41 1 1
Ephrin B2/EPHB1-2 -0.003 0.069 -10000 0 -0.2 53 53
RAP1B 0.011 0 -10000 0 -10000 0 0
RAP1A 0.011 0 -10000 0 -10000 0 0
CDC42/GTP -0.034 0.073 -10000 0 -0.35 9 9
Rap1/GTP -0.029 0.062 -10000 0 -0.31 9 9
axon guidance 0.005 0.046 -10000 0 -0.22 21 21
MAPK3 0.004 0.081 -10000 0 -0.32 8 8
MAPK1 0.004 0.081 -10000 0 -0.32 8 8
Rac1/GDP 0.006 0.079 -10000 0 -0.29 10 10
actin cytoskeleton reorganization -0.023 0.051 -10000 0 -0.25 9 9
CDC42/GDP 0.006 0.079 -10000 0 -0.29 10 10
PI3K 0.022 0.029 -10000 0 -0.19 10 10
EFNA5 -0.003 0.075 -10000 0 -0.4 18 18
Ephrin B2/EPHB4 0.013 0.022 -10000 0 -0.23 4 4
Ephrin B/EPHB2/Intersectin/N-WASP 0.007 0.068 -10000 0 -0.2 53 53
CDC42 0.011 0 -10000 0 -10000 0 0
RAS family/GTP -0.028 0.061 -10000 0 -0.3 9 9
PTK2 0.006 0.018 -10000 0 -10000 0 0
MAP4K4 0.009 0.065 -10000 0 -0.38 1 1
SRC 0.011 0 -10000 0 -10000 0 0
KALRN 0.007 0.041 -10000 0 -0.41 5 5
Intersectin/N-WASP 0.016 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.018 0.081 -10000 0 -0.28 11 11
MAP2K1 -0.002 0.085 -10000 0 -0.35 8 8
WASL 0.011 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.004 0.071 -10000 0 -0.2 52 52
cell migration -0.003 0.099 -10000 0 -0.4 8 8
NRAS 0.011 0 -10000 0 -10000 0 0
SYNJ1 0.008 0.063 -10000 0 -0.36 1 1
PXN 0.011 0 -10000 0 -10000 0 0
TF 0.005 0.072 -10000 0 -0.32 5 5
HRAS/GTP -0.032 0.068 -10000 0 -0.33 9 9
Ephrin B1/EPHB1-2 -0.002 0.068 -10000 0 -0.2 51 51
cell adhesion mediated by integrin 0.017 0.067 0.2 53 -10000 0 53
RAC1 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.007 0.087 -10000 0 -0.35 9 9
RAC1-CDC42/GTP -0.034 0.072 -10000 0 -0.3 19 19
RASA1 0.007 0.041 -10000 0 -0.41 5 5
RAC1-CDC42/GDP 0.01 0.076 -10000 0 -0.29 8 8
ruffle organization 0.009 0.081 -10000 0 -0.31 9 9
NCK1 0.009 0.026 -10000 0 -0.41 2 2
receptor internalization 0.012 0.067 -10000 0 -0.35 5 5
Ephrin B/EPHB2/KALRN 0.008 0.071 -10000 0 -0.38 3 3
ROCK1 0.012 0.04 -10000 0 -0.24 6 6
RAS family/GDP -0.023 0.05 -10000 0 -0.24 9 9
Rac1/GTP -0.031 0.066 -10000 0 -0.32 9 9
Ephrin B/EPHB1/Src/Paxillin -0.013 0.095 -10000 0 -0.4 8 8
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.016 0.084 -9999 0 -0.38 22 22
PDGFB-D/PDGFRB/SLAP 0.004 0.06 -9999 0 -0.28 23 23
PDGFB-D/PDGFRB/APS/CBL 0.012 0.05 -9999 0 -0.23 22 22
AKT1 0.035 0.047 -9999 0 -0.3 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.016 0.091 -9999 0 -0.41 22 22
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
FGR -0.021 0.1 -9999 0 -0.38 30 30
mol:Ca2+ 0.011 0.096 -9999 0 -0.44 22 22
MYC 0.021 0.13 -9999 0 -0.6 16 16
SHC1 0.011 0 -9999 0 -10000 0 0
HRAS/GDP 0.02 0.047 -9999 0 -0.18 26 26
LRP1/PDGFRB/PDGFB 0.011 0.054 -9999 0 -0.24 23 23
GRB10 0.01 0.018 -9999 0 -0.41 1 1
PTPN11 0.011 0 -9999 0 -10000 0 0
GO:0007205 0.011 0.097 -9999 0 -0.45 22 22
PTEN 0.006 0.045 -9999 0 -0.41 6 6
GRB2 0.011 0 -9999 0 -10000 0 0
GRB7 -0.011 0.084 -9999 0 -0.34 33 33
PDGFB-D/PDGFRB/SHP2 0.004 0.059 -9999 0 -0.28 22 22
PDGFB-D/PDGFRB/GRB10 0.004 0.061 -9999 0 -0.28 23 23
cell cycle arrest 0.004 0.06 -9999 0 -0.28 23 23
HRAS 0.011 0 -9999 0 -10000 0 0
HIF1A 0.039 0.043 -9999 0 -0.26 2 2
GAB1 0.014 0.093 -9999 0 -0.41 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.018 0.086 -9999 0 -0.37 22 22
PDGFB-D/PDGFRB 0.013 0.052 -9999 0 -0.23 22 22
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.004 0.059 -9999 0 -0.28 22 22
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.015 0.072 -9999 0 -0.34 22 22
positive regulation of MAPKKK cascade 0.004 0.059 -9999 0 -0.28 22 22
PIK3R1 0.007 0.041 -9999 0 -0.41 5 5
mol:IP3 0.011 0.098 -9999 0 -0.45 22 22
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.01 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.01 0.084 -9999 0 -0.26 52 52
SHB 0.011 0 -9999 0 -10000 0 0
BLK -0.011 0.053 -9999 0 -0.26 22 22
PTPN2 0.011 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.004 0.059 -9999 0 -0.28 22 22
BCAR1 0.011 0 -9999 0 -10000 0 0
VAV2 0.017 0.096 -9999 0 -0.39 23 23
CBL 0.011 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.004 0.059 -9999 0 -0.28 22 22
LCK -0.011 0.066 -9999 0 -0.29 22 22
PDGFRB -0.006 0.085 -9999 0 -0.41 22 22
ACP1 0.011 0 -9999 0 -10000 0 0
HCK -0.01 0.053 -9999 0 -0.26 22 22
ABL1 0.016 0.079 -9999 0 -0.34 22 22
PDGFB-D/PDGFRB/CBL 0.012 0.1 -9999 0 -0.47 22 22
PTPN1 0.011 0.002 -9999 0 -10000 0 0
SNX15 0.011 0 -9999 0 -10000 0 0
STAT3 0.011 0 -9999 0 -10000 0 0
STAT1 0.01 0.015 -9999 0 -0.33 1 1
cell proliferation 0.023 0.11 -9999 0 -0.38 32 32
SLA 0.01 0.015 -9999 0 -0.33 1 1
actin cytoskeleton reorganization 0.032 0.043 -9999 0 -0.35 1 1
SRC -0.01 0.053 -9999 0 -0.26 22 22
PI3K -0.01 0.039 -9999 0 -0.33 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0 0.071 -9999 0 -0.21 52 52
SH2B2 0.011 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 0.016 0.093 -9999 0 -0.42 22 22
LYN -0.01 0.053 -9999 0 -0.26 22 22
LRP1 0.009 0.026 -9999 0 -0.41 2 2
SOS1 0.011 0 -9999 0 -10000 0 0
STAT5B 0.009 0.026 -9999 0 -0.41 2 2
STAT5A 0.01 0.018 -9999 0 -0.41 1 1
NCK1-2/p130 Cas -0.004 0.039 -9999 0 -0.37 1 1
SPHK1 0.01 0.021 -9999 0 -0.33 2 2
EDG1 0.001 0.002 -9999 0 -10000 0 0
mol:DAG 0.011 0.098 -9999 0 -0.45 22 22
PLCG1 0.01 0.1 -9999 0 -0.46 22 22
NHERF/PDGFRB 0.011 0.052 -9999 0 -0.22 25 25
YES1 -0.011 0.052 -9999 0 -0.26 22 22
cell migration 0.011 0.051 -9999 0 -0.22 25 25
SHC/Grb2/SOS1 -0.003 0.036 -9999 0 -10000 0 0
SLC9A3R2 0.011 0 -9999 0 -10000 0 0
SLC9A3R1 0.009 0.026 -9999 0 -0.33 3 3
NHERF1-2/PDGFRB/PTEN 0.016 0.054 -9999 0 -0.2 27 27
FYN -0.01 0.053 -9999 0 -0.26 22 22
DOK1 0.017 0.046 -9999 0 -0.2 22 22
HRAS/GTP 0.008 0 -9999 0 -10000 0 0
PDGFB 0.011 0 -9999 0 -10000 0 0
RAC1 0.023 0.1 -9999 0 -0.37 32 32
PRKCD 0.018 0.046 -9999 0 -0.2 22 22
FER 0.018 0.046 -9999 0 -0.2 22 22
MAPKKK cascade -0.006 0.034 -9999 0 -10000 0 0
RASA1 0.016 0.052 -9999 0 -0.21 26 26
NCK1 0.009 0.026 -9999 0 -0.41 2 2
NCK2 0.011 0 -9999 0 -10000 0 0
p62DOK/Csk 0.022 0.042 -9999 0 -0.18 22 22
PDGFB-D/PDGFRB/SHB 0.004 0.059 -9999 0 -0.28 22 22
chemotaxis 0.016 0.077 -9999 0 -0.34 22 22
STAT1-3-5/STAT1-3-5 -0.008 0.036 -9999 0 -0.35 1 1
Bovine Papilomavirus E5/PDGFRB -0.003 0.06 -9999 0 -0.29 22 22
PTPRJ 0.011 0 -9999 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 -0.13 0.17 -9999 0 -0.33 214 214
mol:Halofuginone 0.004 0 -9999 0 -10000 0 0
ITGA1 0.009 0.032 -9999 0 -0.41 3 3
CDKN1A 0.012 0.04 -9999 0 -0.36 1 1
PRL-3/alpha Tubulin 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ -0.044 0.1 -9999 0 -0.29 80 80
AGT -0.052 0.15 -9999 0 -0.4 80 80
CCNA2 -0.028 0.098 -9999 0 -0.33 18 18
TUBA1B 0.011 0 -9999 0 -10000 0 0
EGR1 -0.019 0.099 -9999 0 -0.28 68 68
CDK2/Cyclin E1 -0.041 0.088 -9999 0 -0.46 1 1
MAPK3 0.018 0 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.016 0 -9999 0 -10000 0 0
MAPK1 0.018 0 -9999 0 -10000 0 0
PTP4A1 0 0.075 -9999 0 -10000 0 0
PTP4A3 0.011 0 -9999 0 -10000 0 0
PTP4A2 0.011 0 -9999 0 -10000 0 0
ITGB1 0.018 0 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
RAC1 0.013 0.036 -9999 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.016 0 -9999 0 -10000 0 0
PRL-1/ATF-5 0.005 0.071 -9999 0 -0.33 1 1
RABGGTA 0.011 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
RHOC 0.013 0.036 -9999 0 -10000 0 0
RHOA 0.013 0.036 -9999 0 -10000 0 0
cell motility 0.016 0.039 -9999 0 -10000 0 0
PRL-1/alpha Tubulin 0.006 0.069 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin 0.015 0.022 -9999 0 -0.28 3 3
ROCK1 0.016 0.039 -9999 0 -10000 0 0
RABGGTB 0.011 0 -9999 0 -10000 0 0
CDK2 0.011 0 -9999 0 -10000 0 0
mitosis 0 0.074 -9999 0 -10000 0 0
ATF5 0.008 0.03 -9999 0 -0.33 4 4
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.011 0 -9999 0 -10000 0 0
SPHK1 0.01 0.021 -9999 0 -0.33 2 2
GNAI2 0.011 0 -9999 0 -10000 0 0
mol:S1P 0.018 0.005 -9999 0 -10000 0 0
GNAO1 -0.099 0.18 -9999 0 -0.41 138 138
mol:Sphinganine-1-P 0.017 0.014 -9999 0 -0.22 2 2
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.032 0.004 -9999 0 -10000 0 0
GNAI3 0.011 0 -9999 0 -10000 0 0
G12/G13 0.016 0 -9999 0 -10000 0 0
S1PR3 -0.004 0.079 -9999 0 -0.41 19 19
S1PR2 0.011 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0 0.003 -9999 0 -10000 0 0
S1PR5 -0.001 0.064 -9999 0 -0.35 17 17
S1PR4 0.009 0.03 -9999 0 -0.38 3 3
GNAI1 0.005 0.052 -9999 0 -0.41 8 8
S1P/S1P5/G12 0.02 0.033 -9999 0 -0.19 4 4
S1P/S1P3/Gq -0.008 0.11 -9999 0 -0.27 57 57
S1P/S1P4/Gi -0.031 0.11 -9999 0 -0.37 14 14
GNAQ 0.009 0.026 -9999 0 -0.41 2 2
GNAZ -0.001 0.07 -9999 0 -0.41 15 15
GNA14 -0.031 0.13 -9999 0 -0.41 53 53
GNA15 0.006 0.039 -9999 0 -0.33 7 7
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.011 0 -9999 0 -10000 0 0
GNA11 0.002 0.06 -9999 0 -0.41 11 11
ABCC1 0.011 0 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.069 0.088 -9999 0 -0.28 1 1
CaM/Ca2+ 0.008 0 -9999 0 -10000 0 0
AKT1 0.011 0 -9999 0 -10000 0 0
AKT2 0.011 0 -9999 0 -10000 0 0
STXBP4 0.01 0.018 -9999 0 -0.41 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.073 0.1 -9999 0 -0.31 1 1
YWHAZ 0.011 0 -9999 0 -10000 0 0
CALM1 0.011 0 -9999 0 -10000 0 0
YWHAQ 0.011 0 -9999 0 -10000 0 0
TBC1D4 0.016 0.026 -9999 0 -0.28 4 4
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.011 0 -9999 0 -10000 0 0
YWHAB 0.011 0 -9999 0 -10000 0 0
SNARE/Synip 0.022 0.011 -9999 0 -0.23 1 1
YWHAG 0.011 0 -9999 0 -10000 0 0
ASIP 0.007 0.016 -9999 0 -0.33 1 1
PRKCI 0.011 0 -9999 0 -10000 0 0
AS160/CaM/Ca2+ 0.008 0 -9999 0 -10000 0 0
RHOQ 0.011 0 -9999 0 -10000 0 0
GYS1 0.025 0 -9999 0 -10000 0 0
PRKCZ 0.01 0.024 -9999 0 -0.37 2 2
TRIP10 0.011 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.015 0 -9999 0 -10000 0 0
AS160/14-3-3 -0.006 0.029 -9999 0 -10000 0 0
VAMP2 0.011 0 -9999 0 -10000 0 0
SLC2A4 -0.08 0.11 -9999 0 -0.34 1 1
STX4 0.011 0 -9999 0 -10000 0 0
GSK3B 0.021 0 -9999 0 -10000 0 0
SFN -0.24 0.15 -9999 0 -0.33 388 388
LNPEP 0.011 0 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.011 0 -10000 0 -10000 0 0
HDAC4 0.011 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.011 0.033 0.23 9 -10000 0 9
CDKN1A -0.001 0.028 -10000 0 -0.61 1 1
KAT2B 0.004 0.055 -10000 0 -0.41 9 9
BAX 0.011 0 -10000 0 -10000 0 0
FOXO3 0 0.006 -10000 0 -10000 0 0
FOXO1 0.009 0.032 -10000 0 -0.41 3 3
FOXO4 0.016 0.022 -10000 0 -0.24 4 4
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.011 0 -10000 0 -10000 0 0
TAT 0.007 0.016 -10000 0 -0.33 1 1
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.014 0.078 -10000 0 -0.23 58 58
PPARGC1A -0.077 0.17 -10000 0 -0.41 110 110
FHL2 0.007 0.041 -10000 0 -0.41 5 5
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 -0.001 0.018 0.14 1 -0.28 2 3
HIST2H4A 0.011 0.033 -10000 0 -0.23 9 9
SIRT1/FOXO3a -0.001 0.015 0.13 1 -0.23 2 3
SIRT1 0.006 0.027 0.18 1 -0.41 2 3
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 -0.001 0.015 0.13 1 -0.23 2 3
SIRT1/Histone H1b 0.013 0.026 -10000 0 -0.22 4 4
apoptosis 0.001 0.015 0.23 2 -0.13 1 3
SIRT1/PGC1A -0.05 0.097 0.12 1 -0.24 111 112
p53/SIRT1 -0.001 0.026 0.36 1 -0.28 3 4
SIRT1/FOXO4 0.016 0.024 0.14 1 -0.2 6 7
FOXO1/FHL2/SIRT1 0.015 0.031 -10000 0 -0.21 10 10
HIST1H1E 0.012 0.025 -10000 0 -0.24 2 2
SIRT1/p300 -0.001 0.018 0.14 1 -0.28 2 3
muscle cell differentiation 0.014 0.065 0.19 59 -0.14 1 60
TP53 0.006 0.02 0.18 1 -0.41 1 2
KU70/SIRT1/BAX -0.001 0.015 0.13 1 -0.23 2 3
CREBBP 0.009 0.026 -10000 0 -0.41 2 2
MEF2D 0.011 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.001 0.021 0.14 1 -0.26 3 4
ACSS2 0.015 0.019 -10000 0 -0.28 2 2
SIRT1/PCAF/MYOD -0.014 0.065 0.14 1 -0.19 59 60
IL2 signaling events mediated by PI3K

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 0.039 0.042 -9999 0 -0.54 1 1
UGCG 0.004 0.092 -9999 0 -0.64 10 10
AKT1/mTOR/p70S6K/Hsp90/TERT 0.022 0.1 -9999 0 -0.24 60 60
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucosylceramide 0.006 0.091 -9999 0 -0.63 10 10
mol:DAG 0 0.001 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.04 0.11 -9999 0 -0.34 60 60
FRAP1 0.017 0.15 -9999 0 -0.39 60 60
FOXO3 0.038 0.1 -9999 0 -0.36 17 17
AKT1 0.033 0.1 -9999 0 -0.38 17 17
GAB2 0.007 0.037 -9999 0 -0.41 4 4
SMPD1 0.017 0.02 -9999 0 -10000 0 0
SGMS1 0.017 0.02 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
mol:GDP 0.013 0.027 -9999 0 -0.24 6 6
CALM1 0.011 0 -9999 0 -10000 0 0
cell proliferation 0.02 0.074 -9999 0 -0.29 20 20
EIF3A 0.011 0 -9999 0 -10000 0 0
PI3K 0.016 0.033 -9999 0 -0.28 6 6
RPS6KB1 0.014 0.023 -9999 0 -10000 0 0
mol:sphingomyelin 0 0.001 -9999 0 -10000 0 0
natural killer cell activation 0 0.003 -9999 0 -0.012 10 10
JAK3 0.01 0.03 -9999 0 -0.33 4 4
PIK3R1 0.008 0.041 -9999 0 -0.41 5 5
JAK1 0.011 0.026 -9999 0 -0.41 2 2
NFKB1 0.01 0.018 -9999 0 -0.41 1 1
MYC 0.028 0.15 -9999 0 -0.82 12 12
MYB 0.013 0.046 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.039 0.072 -9999 0 -0.29 9 9
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.025 0.021 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.039 0.071 -9999 0 -0.28 9 9
Rac1/GDP 0.018 0.025 -9999 0 -0.21 6 6
T cell proliferation 0.042 0.069 -9999 0 -0.26 10 10
SHC1 0.011 0.004 -9999 0 -10000 0 0
RAC1 0.011 0 -9999 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.007 -9999 0 -10000 0 0
PRKCZ 0.042 0.07 -9999 0 -0.27 10 10
NF kappa B1 p50/RelA -0.034 0.11 -9999 0 -0.34 60 60
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.034 0.045 -9999 0 -0.44 2 2
HSP90AA1 0.011 0 -9999 0 -10000 0 0
RELA 0.011 0 -9999 0 -10000 0 0
IL2RA -0.003 0.067 -9999 0 -0.33 21 21
IL2RB 0.012 0.019 -9999 0 -0.41 1 1
TERT -0.11 0.16 -9999 0 -0.33 193 193
E2F1 0.014 0.031 -9999 0 -10000 0 0
SOS1 0.011 0.004 -9999 0 -10000 0 0
RPS6 0.011 0 -9999 0 -10000 0 0
mol:cAMP -0.001 0.003 -9999 0 -10000 0 0
PTPN11 0.011 0.004 -9999 0 -10000 0 0
IL2RG 0.006 0.048 -9999 0 -0.36 9 9
actin cytoskeleton organization 0.042 0.069 -9999 0 -0.26 10 10
GRB2 0.011 0.004 -9999 0 -10000 0 0
IL2 -0.005 0.059 -9999 0 -0.33 17 17
PIK3CA 0.011 0.019 -9999 0 -0.41 1 1
Rac1/GTP 0.024 0.025 -9999 0 -0.19 6 6
LCK 0.009 0.035 -9999 0 -0.35 5 5
BCL2 -0.021 0.26 -9999 0 -0.8 52 52
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.008 0.044 -9999 0 -10000 0 0
epithelial cell differentiation -0.04 0.077 -9999 0 -0.34 10 10
ITCH 0.017 0.011 -9999 0 -10000 0 0
WWP1 0.007 0.041 -9999 0 -10000 0 0
FYN 0.011 0 -9999 0 -10000 0 0
EGFR 0 0.067 -9999 0 -0.4 14 14
PRL -0.008 0.079 -9999 0 -0.4 21 21
neuron projection morphogenesis 0.031 0.048 -9999 0 -10000 0 0
PTPRZ1 -0.013 0.078 -9999 0 -0.33 30 30
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.022 0.051 -9999 0 -0.27 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.006 0.057 -9999 0 -0.3 5 5
ADAM17 0.017 0.011 -9999 0 -10000 0 0
ErbB4/ErbB4 0.003 0.053 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.008 0.057 -9999 0 -0.28 2 2
NCOR1 0.011 0 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.012 0.053 -9999 0 -0.28 5 5
GRIN2B 0.008 0.061 -9999 0 -0.37 2 2
ErbB4/ErbB2/betacellulin 0.007 0.057 -9999 0 -0.29 3 3
STAT1 0.01 0.015 -9999 0 -0.33 1 1
HBEGF 0.011 0 -9999 0 -10000 0 0
PRLR -0.074 0.17 -9999 0 -0.41 106 106
E4ICDs/ETO2 -0.026 0.095 -9999 0 -0.35 10 10
axon guidance 0.014 0.036 -9999 0 -10000 0 0
NEDD4 -0.018 0.11 -9999 0 -0.41 40 40
Prolactin receptor/Prolactin receptor/Prolactin -0.056 0.13 -9999 0 -0.3 119 119
CBFA2T3 -0.049 0.15 -9999 0 -0.41 75 75
ErbB4/ErbB2/HBEGF 0.015 0.042 -9999 0 -10000 0 0
MAPK3 0.026 0.049 -9999 0 -10000 0 0
STAT1 (dimer) 0.007 0.046 -9999 0 -0.28 1 1
MAPK1 0.026 0.049 -9999 0 -10000 0 0
JAK2 0.004 0.055 -9999 0 -0.41 9 9
ErbB4/ErbB2/neuregulin 1 beta 0.007 0.06 -9999 0 -0.29 6 6
NRG1 0.01 0.056 -9999 0 -0.28 19 19
NRG3 -0.008 0.069 -9999 0 -0.33 23 23
NRG2 -0.049 0.15 -9999 0 -0.41 74 74
NRG4 -0.02 0.097 -9999 0 -0.33 47 47
heart development 0.014 0.036 -9999 0 -10000 0 0
neural crest cell migration 0.007 0.059 -9999 0 -0.28 6 6
ERBB2 0.015 0.039 -9999 0 -0.22 14 14
WWOX/E4ICDs 0.008 0.044 -9999 0 -10000 0 0
SHC1 0.011 0 -9999 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.006 0.077 -9999 0 -0.34 8 8
apoptosis 0.007 0.037 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.026 0.093 -9999 0 -0.34 10 10
ErbB4/ErbB2/epiregulin -0.009 0.069 -9999 0 -0.3 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.001 0.062 -9999 0 -0.36 3 3
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.031 0.11 -9999 0 -0.37 17 17
MDM2 0.009 0.045 -9999 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.007 0.044 -9999 0 -0.26 5 5
STAT5A 0.019 0.036 -9999 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta 0.007 0.066 -9999 0 -0.32 9 9
DLG4 0.009 0.032 -9999 0 -0.41 3 3
GRB2/SHC 0.016 0 -9999 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.011 0.032 -9999 0 -10000 0 0
STAT5A (dimer) -0.043 0.081 -9999 0 -0.37 9 9
MAP3K7IP2 0 0 -9999 0 -10000 0 0
STAT5B (dimer) 0.018 0.038 -9999 0 -0.32 1 1
LRIG1 0.009 0.032 -9999 0 -0.41 3 3
EREG -0.035 0.12 -9999 0 -0.33 69 69
BTC -0.004 0.076 -9999 0 -0.41 18 18
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.017 0.034 -9999 0 -10000 0 0
ERBB4 0.003 0.053 -9999 0 -10000 0 0
STAT5B 0.009 0.026 -9999 0 -0.41 2 2
YAP1 -0.001 0.024 -9999 0 -0.52 1 1
GRB2 0.011 0 -9999 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0 0.067 -9999 0 -0.3 5 5
glial cell differentiation 0.011 0.032 -9999 0 -10000 0 0
WWOX 0.011 0 -9999 0 -10000 0 0
cell proliferation 0.01 0.069 -9999 0 -0.3 1 1
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.011 0 -10000 0 -10000 0 0
mol:PIP3 -0.024 0.081 0.23 5 -0.25 56 61
FRAP1 0.008 0.019 -10000 0 -10000 0 0
AKT1 0 0.073 0.2 5 -0.2 56 61
INSR 0.011 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.008 0.002 -10000 0 -10000 0 0
mol:GTP -0.017 0.049 -10000 0 -0.31 2 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.005 0.014 -10000 0 -10000 0 0
TSC2 0.011 0 -10000 0 -10000 0 0
RHEB/GDP -0.014 0.041 -10000 0 -0.27 2 2
TSC1 0.01 0.018 -10000 0 -0.41 1 1
Insulin Receptor/IRS1 -0.018 0.094 -10000 0 -0.3 53 53
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.006 0.017 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.011 0 -10000 0 -10000 0 0
RPS6KB1 0.011 0.041 0.16 5 -0.21 2 7
MAP3K5 0.007 0.025 -10000 0 -0.32 3 3
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
apoptosis 0.007 0.025 -10000 0 -0.32 3 3
mol:LY294002 0 0 -10000 0 -0.001 53 53
EIF4B 0.016 0.038 0.16 5 -0.19 2 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.018 0.034 -10000 0 -0.17 2 2
eIF4E/eIF4G1/eIF4A1 -0.001 0.004 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.01 0.091 -10000 0 -0.27 57 57
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.029 0.15 5 -0.14 3 8
FKBP1A 0.011 0 -10000 0 -10000 0 0
RHEB/GTP -0.014 0.041 -10000 0 -0.27 2 2
mol:Amino Acids 0 0 -10000 0 -0.001 53 53
FKBP12/Rapamycin 0.008 0.001 -10000 0 -10000 0 0
PDPK1 -0.022 0.073 0.21 5 -0.22 56 61
EIF4E 0.011 0 -10000 0 -10000 0 0
ASK1/PP5C 0.012 0.047 -10000 0 -0.58 3 3
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.014 0.002 -10000 0 -10000 0 0
TSC1/TSC2 0.01 0.062 -10000 0 -0.33 2 2
tumor necrosis factor receptor activity 0 0 0.001 53 -10000 0 53
RPS6 0.011 0 -10000 0 -10000 0 0
PPP5C 0.011 0 -10000 0 -10000 0 0
EIF4G1 0.011 0 -10000 0 -10000 0 0
IRS1 -0.026 0.1 -10000 0 -0.32 53 53
INS 0.001 0.003 -10000 0 -10000 0 0
PTEN 0.006 0.044 -10000 0 -0.41 6 6
PDK2 -0.022 0.073 0.21 5 -0.22 56 61
EIF4EBP1 0.012 0.007 -10000 0 -10000 0 0
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
PPP2R5D 0.013 0.018 -10000 0 -10000 0 0
peptide biosynthetic process 0.014 0.001 -10000 0 -10000 0 0
RHEB 0.011 0 -10000 0 -10000 0 0
EIF4A1 0.011 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.003 6 -0.002 2 8
EEF2 0.014 0.001 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.017 0.005 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.007 0.049 -10000 0 -1.1 1 1
oxygen homeostasis -0.002 0.014 -10000 0 -10000 0 0
TCEB2 0.011 0 -10000 0 -10000 0 0
TCEB1 0.011 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.017 0.04 -10000 0 -0.29 4 4
EPO -0.022 0.21 -10000 0 -0.53 26 26
FIH (dimer) 0.009 0.013 -10000 0 -10000 0 0
APEX1 0.007 0.015 -10000 0 -10000 0 0
SERPINE1 -0.014 0.2 -10000 0 -0.54 16 16
FLT1 -0.012 0.062 -10000 0 -1.1 1 1
ADORA2A -0.013 0.19 -10000 0 -0.49 15 15
germ cell development -0.021 0.21 -10000 0 -0.52 26 26
SLC11A2 -0.013 0.2 -10000 0 -0.51 14 14
BHLHE40 -0.013 0.2 -10000 0 -0.5 15 15
HIF1AN 0.009 0.013 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.005 0.12 -10000 0 -0.35 7 7
ETS1 0.021 0.02 -10000 0 -0.42 1 1
CITED2 -0.037 0.18 -10000 0 -1 17 17
KDR -0.065 0.26 -10000 0 -1.1 31 31
PGK1 -0.013 0.2 -10000 0 -0.49 16 16
SIRT1 0.009 0.026 -10000 0 -0.41 2 2
response to hypoxia 0 0.002 -10000 0 -10000 0 0
HIF2A/ARNT -0.017 0.22 -10000 0 -0.55 18 18
EPAS1 0.011 0.089 -10000 0 -0.37 3 3
SP1 0.017 0.001 -10000 0 -10000 0 0
ABCG2 -0.14 0.3 -10000 0 -0.54 100 100
EFNA1 -0.013 0.2 -10000 0 -0.5 16 16
FXN -0.013 0.19 -10000 0 -0.49 15 15
POU5F1 -0.023 0.21 -10000 0 -0.54 26 26
neuron apoptosis 0.017 0.22 0.54 18 -10000 0 18
EP300 0.011 0 -10000 0 -10000 0 0
EGLN3 0.006 0.034 -10000 0 -0.35 4 4
EGLN2 0.009 0.013 -10000 0 -10000 0 0
EGLN1 0.009 0.013 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.022 0.011 -10000 0 -0.23 1 1
VHL 0.01 0.018 -10000 0 -0.41 1 1
ARNT 0.007 0.015 -10000 0 -10000 0 0
SLC2A1 -0.013 0.19 -10000 0 -0.48 17 17
TWIST1 -0.04 0.24 -10000 0 -0.54 57 57
ELK1 0.016 0.01 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.001 0.12 -10000 0 -0.43 3 3
VEGFA -0.013 0.2 -10000 0 -0.5 15 15
CREBBP 0.009 0.026 -10000 0 -0.41 2 2
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.011 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.014 0.082 -9999 0 -10000 0 0
Syndecan-3/Neurocan 0.007 0.028 -9999 0 -10000 0 0
POMC -0.011 0.087 -9999 0 -0.36 31 31
EGFR 0 0.067 -9999 0 -0.4 14 14
Syndecan-3/EGFR 0.015 0.033 -9999 0 -10000 0 0
AGRP 0.006 0.016 -9999 0 -0.33 1 1
NCSTN 0.011 0 -9999 0 -10000 0 0
PSENEN 0.011 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.005 0.048 -9999 0 -0.41 7 7
APH1A 0.011 0 -9999 0 -10000 0 0
NCAN -0.004 0.058 -9999 0 -0.33 16 16
long-term memory 0.026 0.006 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.026 0.072 -9999 0 -10000 0 0
PSEN1 0.011 0 -9999 0 -10000 0 0
Src/Cortactin 0.016 0 -9999 0 -10000 0 0
FYN 0.011 0 -9999 0 -10000 0 0
limb bud formation -0.001 0.005 -9999 0 -10000 0 0
MC4R -0.004 0.056 -9999 0 -0.33 15 15
SRC 0.011 0 -9999 0 -10000 0 0
PTN -0.089 0.18 -9999 0 -0.41 125 125
FGFR/FGF/Syndecan-3 -0.001 0.005 -9999 0 -10000 0 0
neuron projection morphogenesis -0.025 0.078 -9999 0 -0.29 3 3
Syndecan-3/AgRP 0.011 0.013 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R 0.004 0.027 -9999 0 -10000 0 0
Fyn/Cortactin 0.016 0 -9999 0 -10000 0 0
SDC3 -0.001 0.005 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.026 0.071 -9999 0 -10000 0 0
IL8 -0.09 0.16 -9999 0 -0.33 156 156
Syndecan-3/Fyn/Cortactin 0.026 0.006 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.004 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.009 0.072 -9999 0 -0.24 44 44
Gamma Secretase 0.03 0.024 -9999 0 -0.18 7 7
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.003 0.053 0.36 11 -10000 0 11
PI3K Class IB/PDE3B 0.003 0.053 -10000 0 -0.36 11 11
PDE3B 0.003 0.053 -10000 0 -0.36 11 11
ErbB2/ErbB3 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
USP8 0.015 0.002 -9999 0 -10000 0 0
RAS family/GTP 0.009 0.049 -9999 0 -0.23 10 10
NFATC4 0.015 0.046 -9999 0 -0.33 2 2
ERBB2IP 0.011 0.001 -9999 0 -10000 0 0
HSP90 (dimer) 0.011 0 -9999 0 -10000 0 0
mammary gland morphogenesis 0.004 0.048 -9999 0 -0.22 10 10
JUN -0.005 0.069 -9999 0 -0.34 4 4
HRAS 0.01 0.001 -9999 0 -10000 0 0
DOCK7 0.014 0.048 -9999 0 -0.32 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.003 0.052 -9999 0 -0.21 20 20
AKT1 0.009 0.001 -9999 0 -10000 0 0
BAD 0.015 0.001 -9999 0 -10000 0 0
MAPK10 -0.008 0.067 -9999 0 -0.22 11 11
mol:GTP -0.001 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.004 0.051 -9999 0 -0.23 10 10
RAF1 0.012 0.055 -9999 0 -0.28 5 5
ErbB2/ErbB3/neuregulin 2 -0.026 0.085 -9999 0 -0.22 76 76
STAT3 0.001 0.003 -9999 0 -10000 0 0
cell migration 0.002 0.061 -9999 0 -0.2 16 16
mol:PI-3-4-5-P3 0 0.001 -9999 0 -10000 0 0
cell proliferation -0.076 0.18 -9999 0 -0.42 63 63
FOS -0.12 0.24 -9999 0 -0.47 160 160
NRAS 0.01 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.004 0.048 -9999 0 -0.22 10 10
MAPK3 -0.042 0.13 -9999 0 -0.48 10 10
MAPK1 -0.042 0.13 -9999 0 -0.48 10 10
JAK2 0.011 0.052 -9999 0 -0.32 2 2
NF2 0 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.011 0.051 -9999 0 -0.23 20 20
NRG1 -0.005 0.078 -9999 0 -0.41 19 19
GRB2/SOS1 0.016 0.001 -9999 0 -10000 0 0
MAPK8 0.005 0.056 -9999 0 -0.22 25 25
MAPK9 0.022 0.028 -9999 0 -0.16 2 2
ERBB2 -0.006 0.037 -9999 0 -0.23 14 14
ERBB3 0.008 0.032 -9999 0 -0.41 3 3
SHC1 0.01 0.001 -9999 0 -10000 0 0
RAC1 0.011 0 -9999 0 -10000 0 0
apoptosis 0.001 0.006 -9999 0 -10000 0 0
STAT3 (dimer) 0.017 0.003 -9999 0 -10000 0 0
RNF41 0.02 0.003 -9999 0 -10000 0 0
FRAP1 0.008 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.007 0.028 -9999 0 -0.23 2 2
ErbB2/ErbB2/HSP90 (dimer) -0.005 0.029 -9999 0 -0.18 14 14
CHRNA1 -0.051 0.13 -9999 0 -0.37 10 10
myelination 0.02 0.044 -9999 0 -0.31 2 2
PPP3CB 0.006 0.044 -9999 0 -0.3 2 2
KRAS 0.01 0.015 -9999 0 -0.33 1 1
RAC1-CDC42/GDP 0.022 0.045 -9999 0 -0.26 4 4
NRG2 -0.049 0.15 -9999 0 -0.41 74 74
mol:GDP 0.011 0.051 -9999 0 -0.23 20 20
SOS1 0.011 0.001 -9999 0 -10000 0 0
MAP2K2 0.011 0.061 -9999 0 -0.3 5 5
SRC 0.011 0 -9999 0 -10000 0 0
mol:cAMP 0 0.001 -9999 0 -10000 0 0
PTPN11 0.014 0.047 -9999 0 -0.31 2 2
MAP2K1 -0.046 0.13 -9999 0 -0.43 15 15
heart morphogenesis 0.004 0.048 -9999 0 -0.22 10 10
RAS family/GDP 0.017 0.047 -9999 0 -0.22 10 10
GRB2 0.011 0.001 -9999 0 -10000 0 0
PRKACA -0.001 0.003 -9999 0 -10000 0 0
CHRNE 0.006 0.023 -9999 0 -0.18 4 4
HSP90AA1 0.011 0 -9999 0 -10000 0 0
activation of caspase activity -0.009 0.001 -9999 0 -10000 0 0
nervous system development 0.004 0.048 -9999 0 -0.22 10 10
CDC42 0.011 0 -9999 0 -10000 0 0
EPO signaling 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
BCL2L1 0.02 0.12 -10000 0 -0.44 6 6
CRKL 0.019 0.054 -10000 0 -0.24 6 6
mol:DAG 0.019 0.066 -10000 0 -0.24 18 18
HRAS 0.035 0.05 -10000 0 -10000 0 0
MAPK8 0.016 0.047 -10000 0 -0.21 8 8
RAP1A 0.019 0.054 -10000 0 -0.24 6 6
GAB1 0.017 0.057 -10000 0 -0.24 8 8
MAPK14 0.018 0.041 -10000 0 -0.21 3 3
EPO -0.003 0.072 -10000 0 -0.4 16 16
PLCG1 0.019 0.067 -10000 0 -0.24 18 18
EPOR/TRPC2/IP3 Receptors 0.007 0.039 -10000 0 -0.32 7 7
RAPGEF1 0.011 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.012 0.048 -10000 0 -0.22 17 17
GAB1/SHC/GRB2/SOS1 -0.012 0.036 -10000 0 -0.22 2 2
EPO/EPOR (dimer) 0.005 0.057 -10000 0 -0.26 23 23
IRS2 -0.008 0.086 -10000 0 -0.26 19 19
STAT1 0.018 0.089 -10000 0 -0.37 6 6
STAT5B 0.017 0.08 -10000 0 -0.34 6 6
cell proliferation 0.021 0.044 -10000 0 -0.21 2 2
GAB1/SHIP/PIK3R1/SHP2/SHC -0.013 0.04 -10000 0 -0.23 7 7
TEC 0.018 0.054 -10000 0 -0.24 6 6
SOCS3 0.009 0.026 -10000 0 -0.41 2 2
STAT1 (dimer) 0.018 0.087 -10000 0 -0.37 6 6
JAK2 0.004 0.055 -10000 0 -0.41 9 9
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
EPO/EPOR (dimer)/JAK2 0.023 0.06 -10000 0 -0.26 6 6
EPO/EPOR 0.005 0.057 -10000 0 -0.26 23 23
LYN 0.011 0.004 -10000 0 -10000 0 0
TEC/VAV2 0.025 0.053 -10000 0 -0.22 6 6
elevation of cytosolic calcium ion concentration 0.007 0.039 -10000 0 -0.32 7 7
SHC1 0.011 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.017 0.048 -10000 0 -0.22 15 15
mol:IP3 0.019 0.066 -10000 0 -0.24 18 18
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.001 0.086 -10000 0 -0.25 22 22
SH2B3 0.01 0.019 -10000 0 -0.41 1 1
NFKB1 0.018 0.042 -10000 0 -0.19 16 16
EPO/EPOR (dimer)/JAK2/SOCS3 -0.01 0.049 0.23 1 -0.22 26 27
PTPN6 0.013 0.056 -10000 0 -0.25 6 6
TEC/VAV2/GRB2 0.029 0.052 -10000 0 -0.21 6 6
EPOR 0.007 0.039 -10000 0 -0.32 7 7
INPP5D 0.01 0.018 -10000 0 -0.41 1 1
mol:GDP -0.012 0.036 -10000 0 -0.21 5 5
SOS1 0.011 0 -10000 0 -10000 0 0
PLCG2 0.01 0.024 -10000 0 -0.37 2 2
CRKL/CBL/C3G 0.03 0.051 -10000 0 -0.21 6 6
VAV2 0.019 0.054 -10000 0 -0.24 6 6
CBL 0.019 0.054 -10000 0 -0.24 6 6
SHC/Grb2/SOS1 -0.012 0.036 -10000 0 -0.21 6 6
STAT5A 0.018 0.079 -10000 0 -0.34 6 6
GRB2 0.011 0 -10000 0 -10000 0 0
STAT5 (dimer) 0.023 0.11 -10000 0 -0.4 7 7
LYN/PLCgamma2 0.015 0.017 -10000 0 -0.25 2 2
PTPN11 0.011 0 -10000 0 -10000 0 0
BTK 0.017 0.057 -10000 0 -0.27 6 6
BCL2 -0.026 0.25 -10000 0 -0.79 50 50
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.023 0.021 -9999 0 -0.28 2 2
CRKL 0.011 0 -9999 0 -10000 0 0
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
DOCK1 0.006 0.045 -9999 0 -0.41 6 6
ITGA4 0.009 0.03 -9999 0 -0.38 3 3
alpha4/beta7 Integrin/MAdCAM1 0.013 0.05 -9999 0 -0.2 2 2
EPO -0.004 0.071 -9999 0 -0.4 16 16
alpha4/beta7 Integrin 0.014 0.023 -9999 0 -0.25 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.015 0.021 -9999 0 -0.26 3 3
EPO/EPOR (dimer) 0.003 0.056 -9999 0 -0.26 23 23
lamellipodium assembly 0.025 0.029 -9999 0 -0.24 6 6
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
PI3K 0.013 0.031 -9999 0 -0.28 6 6
ARF6 0.011 0 -9999 0 -10000 0 0
JAK2 0.013 0.056 -9999 0 -0.22 26 26
PXN 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.007 0.041 -9999 0 -0.41 5 5
MADCAM1 -0.016 0.09 -9999 0 -0.33 40 40
cell adhesion 0.012 0.049 -9999 0 -0.2 2 2
CRKL/CBL 0.016 0 -9999 0 -10000 0 0
ITGB1 0.011 0 -9999 0 -10000 0 0
SRC 0.008 0.064 -9999 0 -0.21 40 40
ITGB7 0.01 0.015 -9999 0 -0.33 1 1
RAC1 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.002 0.071 -9999 0 -0.24 41 41
p130Cas/Crk/Dock1 0.023 0.061 -9999 0 -0.43 2 2
VCAM1 -0.021 0.11 -9999 0 -0.41 40 40
RHOA 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.027 0.016 -9999 0 -0.2 2 2
BCAR1 0.014 0.06 -9999 0 -0.19 40 40
EPOR 0.006 0.039 -9999 0 -0.33 7 7
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.011 0 -9999 0 -10000 0 0
GIT1 0.011 0 -9999 0 -10000 0 0
Rac1/GTP -0.002 0.026 -9999 0 -0.26 4 4
IL27-mediated signaling events

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
TGFB1 0.011 0.019 -10000 0 -0.4 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.011 0.096 0.46 5 -10000 0 5
IL27/IL27R/JAK1 -0.016 0.11 -10000 0 -0.84 3 3
TBX21 0.001 0.12 -10000 0 -0.44 12 12
IL12B 0.006 0.016 -10000 0 -0.33 1 1
IL12A 0.001 0.042 -10000 0 -0.24 15 15
IL6ST -0.053 0.15 -10000 0 -0.42 80 80
IL27RA/JAK1 0.012 0.072 -10000 0 -1.1 2 2
IL27 0.001 0.051 -10000 0 -0.33 12 12
TYK2 0.012 0.005 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.001 0.048 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.011 0.096 0.46 5 -10000 0 5
T cell proliferation during immune response 0.011 0.096 0.46 5 -10000 0 5
MAPKKK cascade -0.011 0.096 -10000 0 -0.46 5 5
STAT3 0.011 0 -10000 0 -10000 0 0
STAT2 0.011 0 -10000 0 -10000 0 0
STAT1 0.011 0.015 -10000 0 -0.34 1 1
IL12RB1 -0.001 0.067 -10000 0 -0.35 18 18
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.002 0.12 -10000 0 -0.45 12 12
IL27/IL27R/JAK2/TYK2 -0.011 0.097 -10000 0 -0.47 5 5
positive regulation of T cell mediated cytotoxicity -0.011 0.096 -10000 0 -0.46 5 5
STAT1 (dimer) -0.04 0.12 0.47 4 -0.78 4 8
JAK2 0.003 0.055 -10000 0 -0.41 9 9
JAK1 0.01 0.026 -10000 0 -0.41 2 2
STAT2 (dimer) -0.004 0.092 -10000 0 -0.44 5 5
T cell proliferation -0.012 0.1 -10000 0 -0.41 12 12
IL12/IL12R/TYK2/JAK2 0.014 0.053 -10000 0 -0.52 1 1
IL17A -0.002 0.047 -10000 0 -10000 0 0
mast cell activation 0.011 0.096 0.46 5 -10000 0 5
IFNG 0 0.022 -10000 0 -0.073 5 5
T cell differentiation -0.002 0.004 -10000 0 -0.015 17 17
STAT3 (dimer) -0.004 0.092 -10000 0 -0.44 5 5
STAT5A (dimer) -0.005 0.093 -10000 0 -0.44 5 5
STAT4 (dimer) -0.005 0.092 -10000 0 -0.44 5 5
STAT4 0.01 0.018 -10000 0 -0.41 1 1
T cell activation -0.007 0.009 0.12 2 -10000 0 2
IL27R/JAK2/TYK2 -0.014 0.11 -10000 0 -0.71 4 4
GATA3 -0.012 0.13 -10000 0 -1.2 6 6
IL18 0.005 0.029 -10000 0 -0.23 8 8
positive regulation of mast cell cytokine production -0.004 0.091 -10000 0 -0.44 5 5
IL27/EBI3 0.004 0.056 -10000 0 -0.25 22 22
IL27RA 0.004 0.076 -10000 0 -1.2 2 2
IL6 -0.007 0.084 -10000 0 -0.38 25 25
STAT5A 0.01 0.018 -10000 0 -0.41 1 1
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.001 0.036 0.46 2 -10000 0 2
IL1B 0.007 0.026 -10000 0 -0.29 4 4
EBI3 0.002 0.054 -10000 0 -0.34 13 13
TNF -0.021 0.078 -10000 0 -0.23 66 66
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.024 0.03 -9999 0 -0.2 9 9
HDAC3 0.011 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 0.013 0.004 -9999 0 -10000 0 0
GATA1/HDAC5 0.013 0.004 -9999 0 -10000 0 0
GATA2/HDAC5 -0.012 0.087 -9999 0 -0.28 50 50
HDAC5/BCL6/BCoR 0.022 0.011 -9999 0 -0.23 1 1
HDAC9 0.003 0.057 -9999 0 -0.41 10 10
Glucocorticoid receptor/Hsp90/HDAC6 -0.015 0.09 -9999 0 -0.23 80 80
HDAC4/ANKRA2 0.016 0.013 -9999 0 -0.28 1 1
HDAC5/YWHAB 0.016 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0 -9999 0 -10000 0 0
GATA2 -0.029 0.12 -9999 0 -0.41 50 50
HDAC4/RFXANK 0.015 0.018 -9999 0 -0.22 3 3
BCOR 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.011 0 -9999 0 -10000 0 0
HDAC5 0.011 0 -9999 0 -10000 0 0
GNB1/GNG2 0.011 0.04 -9999 0 -0.27 10 10
Histones 0.029 0.027 -9999 0 -10000 0 0
ADRBK1 0.011 0 -9999 0 -10000 0 0
HDAC4 0.011 0 -9999 0 -10000 0 0
XPO1 0.011 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.016 0.013 -9999 0 -0.28 1 1
HDAC4/Ubc9 0.016 0 -9999 0 -10000 0 0
HDAC7 0.011 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.016 0 -9999 0 -10000 0 0
TUBA1B 0.011 0 -9999 0 -10000 0 0
HDAC6 0.011 0 -9999 0 -10000 0 0
HDAC5/RFXANK 0.015 0.018 -9999 0 -0.22 3 3
CAMK4 0.003 0.051 -9999 0 -0.36 10 10
Tubulin/HDAC6 0.02 0.024 -9999 0 -0.19 7 7
SUMO1 0.011 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.011 0 -9999 0 -10000 0 0
GATA1 0.006 0.005 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
NR3C1 -0.053 0.15 -9999 0 -0.41 80 80
SUMO1/HDAC4 0.025 0 -9999 0 -10000 0 0
SRF 0.011 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0.016 0 -9999 0 -10000 0 0
Tubulin 0.013 0.029 -9999 0 -0.24 7 7
HDAC4/14-3-3 E 0.016 0 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
RANGAP1 0.011 0 -9999 0 -10000 0 0
BCL6/BCoR 0.016 0.013 -9999 0 -0.28 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.022 0 -9999 0 -10000 0 0
HDAC4/SRF 0.018 0.03 -9999 0 -0.2 10 10
HDAC4/ER alpha -0.017 0.094 -9999 0 -0.28 60 60
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.029 0.027 -9999 0 -10000 0 0
cell motility 0.019 0.024 -9999 0 -0.19 7 7
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.011 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0.016 0 -9999 0 -10000 0 0
BCL6 0.01 0.018 -9999 0 -0.41 1 1
HDAC4/CaMK II delta B 0.011 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0.016 0 -9999 0 -10000 0 0
ESR1 -0.037 0.13 -9999 0 -0.41 60 60
HDAC6/HDAC11 0.016 0.01 -9999 0 -0.22 1 1
Ran/GTP/Exportin 1 0.027 0 -9999 0 -10000 0 0
NPC 0.007 0 -9999 0 -10000 0 0
MEF2C -0.031 0.13 -9999 0 -0.41 52 52
RAN 0.011 0 -9999 0 -10000 0 0
HDAC4/MEF2C 0.012 0.063 -9999 0 -10000 0 0
GNG2 0.003 0.056 -9999 0 -0.4 10 10
NCOR2 0.011 0 -9999 0 -10000 0 0
TUBB2A 0.006 0.042 -9999 0 -0.35 7 7
HDAC11 0.01 0.015 -9999 0 -0.33 1 1
HSP90AA1 0.011 0 -9999 0 -10000 0 0
RANBP2 0.011 0 -9999 0 -10000 0 0
ANKRA2 0.01 0.018 -9999 0 -0.41 1 1
RFXANK 0.009 0.026 -9999 0 -0.33 3 3
nuclear import -0.024 0 -9999 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.017 0.018 -10000 0 -0.28 2 2
MAP4K4 0.028 0.034 -10000 0 -0.4 1 1
BAG4 0.009 0.032 -10000 0 -0.41 3 3
PKC zeta/ceramide -0.001 0.016 0.12 2 -0.18 2 4
NFKBIA 0.011 0 -10000 0 -10000 0 0
BIRC3 0.003 0.055 -10000 0 -0.39 10 10
BAX 0.002 0.006 -10000 0 -10000 0 0
RIPK1 0.011 0 -10000 0 -10000 0 0
AKT1 0.014 0.002 -10000 0 -10000 0 0
BAD -0.002 0.012 0.13 2 -10000 0 2
SMPD1 0.015 0.025 -10000 0 -0.17 2 2
RB1 -0.003 0.02 0.13 2 -0.22 3 5
FADD/Caspase 8 0.036 0.033 -10000 0 -0.39 1 1
MAP2K4 0.003 0.014 0.14 1 -0.19 1 2
NSMAF 0.011 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.003 0.017 0.14 1 -0.19 2 3
EGF -0.005 0.071 -10000 0 -0.34 23 23
mol:ceramide -0.009 0.013 0.13 2 -10000 0 2
MADD 0.011 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.017 0.018 -10000 0 -0.28 2 2
ASAH1 0.011 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.003 0.02 0.13 2 -0.22 3 5
cell proliferation -0.012 0.07 -10000 0 -0.2 8 8
BID 0.024 0.025 -10000 0 -0.29 1 1
MAP3K1 -0.002 0.012 0.13 2 -10000 0 2
EIF2A 0.009 0.011 0.14 1 -10000 0 1
TRADD 0.011 0 -10000 0 -10000 0 0
CRADD 0.011 0 -10000 0 -10000 0 0
MAPK3 0.012 0.016 0.14 1 -0.17 2 3
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.012 0.016 0.14 1 -0.17 2 3
Cathepsin D/ceramide -0.001 0.014 0.12 2 -0.16 1 3
FADD 0.028 0.034 -10000 0 -0.4 1 1
KSR1 -0.003 0.017 0.13 2 -0.21 2 4
MAPK8 0.005 0.027 0.14 1 -0.22 6 7
PRKRA -0.002 0.012 0.13 2 -10000 0 2
PDGFA 0.009 0.026 -10000 0 -0.41 2 2
TRAF2 0.011 0 -10000 0 -10000 0 0
IGF1 -0.069 0.16 -10000 0 -0.41 100 100
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.009 0.013 0.13 2 -10000 0 2
CTSD 0.01 0.015 -10000 0 -0.33 1 1
regulation of nitric oxide biosynthetic process 0.016 0.013 -10000 0 -0.28 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.012 0.074 -10000 0 -0.21 8 8
PRKCD 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.024 -10000 0 -0.37 2 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.017 0.018 -10000 0 -0.28 2 2
RelA/NF kappa B1 0.016 0.013 -10000 0 -0.28 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.011 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.024 0.036 -10000 0 -0.43 1 1
TNFR1A/BAG4/TNF-alpha -0.004 0.067 -10000 0 -0.18 69 69
mol:Sphingosine-1-phosphate 0.017 0.018 -10000 0 -0.28 2 2
MAP2K1 0.008 0.016 0.14 1 -0.18 2 3
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.011 0 -10000 0 -10000 0 0
CYCS 0.014 0.041 0.14 51 -10000 0 51
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
NFKB1 0.01 0.018 -10000 0 -0.41 1 1
TNFR1A/BAG4 0.015 0.022 -10000 0 -0.28 3 3
EIF2AK2 0.004 0.011 0.13 2 -10000 0 2
TNF-alpha/TNFR1A/FAN -0.002 0.065 -10000 0 -0.18 66 66
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.03 0.023 -10000 0 -0.22 1 1
MAP2K2 0.008 0.016 0.14 1 -0.18 2 3
SMPD3 0.016 0.033 -10000 0 -0.25 4 4
TNF -0.032 0.11 -10000 0 -0.33 66 66
PKC zeta/PAR4 0.015 0.016 -10000 0 -0.25 2 2
mol:PHOSPHOCHOLINE -0.004 0.021 0.16 3 -10000 0 3
NF kappa B1/RelA/I kappa B alpha 0.032 0.015 -10000 0 -10000 0 0
AIFM1 0.014 0.041 0.14 51 -10000 0 51
BCL2 -0.029 0.12 -10000 0 -0.41 50 50
ceramide signaling pathway

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
MAP4K4 0.032 0.039 -10000 0 -0.24 8 8
BAG4 0.009 0.032 -10000 0 -0.41 3 3
BAD 0.023 0.014 -10000 0 -0.12 1 1
NFKBIA 0.011 0 -10000 0 -10000 0 0
BIRC3 0.003 0.055 -10000 0 -0.39 10 10
BAX 0.023 0.014 -10000 0 -0.12 1 1
EnzymeConsortium:3.1.4.12 0.01 0.011 -10000 0 -0.092 1 1
IKBKB 0.036 0.037 -10000 0 -0.36 1 1
MAP2K2 0.031 0.018 -10000 0 -0.16 1 1
MAP2K1 0.031 0.018 -10000 0 -0.16 1 1
SMPD1 0.015 0.011 -10000 0 -0.087 1 1
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.038 0.037 -10000 0 -0.37 1 1
MAP2K4 0.027 0.016 -10000 0 -0.15 1 1
protein ubiquitination 0.038 0.037 -10000 0 -0.36 1 1
EnzymeConsortium:2.7.1.37 0.035 0.019 -10000 0 -0.16 1 1
response to UV 0 0 -10000 0 -0.002 1 1
RAF1 0.027 0.018 -10000 0 -0.16 2 2
CRADD 0.011 0 -10000 0 -10000 0 0
mol:ceramide 0.018 0.015 -10000 0 -0.13 1 1
I-kappa-B-alpha/RELA/p50/ubiquitin 0.015 0 -10000 0 -10000 0 0
MADD 0.011 0 -10000 0 -10000 0 0
MAP3K1 0.023 0.014 -10000 0 -0.12 1 1
TRADD 0.011 0 -10000 0 -10000 0 0
RELA/p50 0.011 0 -10000 0 -10000 0 0
MAPK3 0.033 0.017 -10000 0 -0.16 1 1
MAPK1 0.033 0.017 -10000 0 -0.16 1 1
p50/RELA/I-kappa-B-alpha 0.016 0 -10000 0 -10000 0 0
FADD 0.032 0.039 -10000 0 -0.24 8 8
KSR1 0.023 0.019 -10000 0 -0.16 3 3
MAPK8 0.03 0.023 -10000 0 -10000 0 0
TRAF2 0.011 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.036 0.037 -10000 0 -0.36 1 1
TNF R/SODD 0.015 0.022 -10000 0 -0.28 3 3
TNF -0.032 0.11 -10000 0 -0.33 66 66
CYCS 0.033 0.03 0.12 47 -0.11 1 48
IKBKG 0.036 0.037 -10000 0 -0.36 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.027 0.041 -10000 0 -0.25 8 8
RELA 0.011 0 -10000 0 -10000 0 0
RIPK1 0.011 0 -10000 0 -10000 0 0
AIFM1 0.033 0.03 0.12 47 -0.11 1 48
TNF/TNF R/SODD -0.003 0.067 -10000 0 -0.18 69 69
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.023 0.011 -10000 0 -10000 0 0
NSMAF 0.032 0.038 -10000 0 -0.23 8 8
response to hydrogen peroxide 0 0 -10000 0 -0.002 1 1
BCL2 -0.029 0.12 -10000 0 -0.41 50 50
IL23-mediated signaling events

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
CCL2 0.017 0.23 -9999 0 -1.1 12 12
IL23A 0.018 0.22 -9999 0 -0.99 11 11
NF kappa B1 p50/RelA/I kappa B alpha -0.044 0.16 -9999 0 -0.95 10 10
positive regulation of T cell mediated cytotoxicity 0.018 0.22 -9999 0 -1 11 11
ITGA3 0.022 0.2 -9999 0 -1 8 8
IL17F 0.032 0.16 -9999 0 -0.63 10 10
IL12B 0.015 0.025 -9999 0 -0.32 1 1
STAT1 (dimer) 0.018 0.21 -9999 0 -1 10 10
CD4 0.024 0.2 -9999 0 -0.95 9 9
IL23 0.014 0.21 -9999 0 -0.96 11 11
IL23R 0.021 0.053 -9999 0 -10000 0 0
IL1B 0.016 0.22 -9999 0 -1.1 11 11
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 0.019 0.2 -9999 0 -0.96 9 9
TYK2 0.015 0.013 -9999 0 -10000 0 0
STAT4 0.01 0.018 -9999 0 -0.41 1 1
STAT3 0.011 0 -9999 0 -10000 0 0
IL18RAP 0.005 0.045 -9999 0 -0.38 7 7
IL12RB1 0.003 0.071 -9999 0 -0.36 18 18
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
IL12Rbeta1/TYK2 0.011 0.053 -9999 0 -0.25 18 18
IL23R/JAK2 0.028 0.076 -9999 0 -10000 0 0
positive regulation of chronic inflammatory response 0.018 0.22 -9999 0 -1 11 11
natural killer cell activation -0.001 0.005 -9999 0 -10000 0 0
JAK2 0.012 0.06 -9999 0 -0.42 9 9
PIK3R1 0.007 0.041 -9999 0 -0.41 5 5
NFKB1 0.011 0.018 -9999 0 -0.41 1 1
RELA 0.012 0.002 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.015 0.2 -9999 0 -0.91 11 11
ALOX12B 0.019 0.2 -9999 0 -0.96 9 9
CXCL1 -0.004 0.25 -9999 0 -1.1 15 15
T cell proliferation 0.018 0.22 -9999 0 -1 11 11
NFKBIA 0.012 0.002 -9999 0 -10000 0 0
IL17A 0.042 0.13 -9999 0 -0.51 8 8
PI3K -0.027 0.18 -9999 0 -0.93 11 11
IFNG 0.003 0.019 -9999 0 -10000 0 0
STAT3 (dimer) -0.048 0.16 -9999 0 -0.92 10 10
IL18R1 0.007 0.036 -9999 0 -0.41 4 4
IL23/IL23R/JAK2/TYK2/SOCS3 0.029 0.14 -9999 0 -0.6 9 9
IL18/IL18R 0.014 0.045 -9999 0 -0.22 16 16
macrophage activation -0.003 0.01 -9999 0 -0.041 12 12
TNF 0.014 0.22 -9999 0 -1 10 10
STAT3/STAT4 -0.026 0.18 -9999 0 -0.93 11 11
STAT4 (dimer) 0.018 0.21 -9999 0 -1 10 10
IL18 0.005 0.042 -9999 0 -0.34 8 8
IL19 0.005 0.21 -9999 0 -1 8 8
STAT5A (dimer) 0.018 0.21 -9999 0 -0.98 11 11
STAT1 0.01 0.015 -9999 0 -0.33 1 1
SOCS3 0.009 0.026 -9999 0 -0.41 2 2
CXCL9 0.005 0.23 -9999 0 -1.2 9 9
MPO 0.023 0.2 -9999 0 -0.95 9 9
positive regulation of humoral immune response 0.018 0.22 -9999 0 -1 11 11
IL23/IL23R/JAK2/TYK2 0.017 0.23 -9999 0 -1 11 11
IL6 0.001 0.27 -9999 0 -1.1 20 20
STAT5A 0.01 0.018 -9999 0 -0.41 1 1
IL2 -0.007 0.06 -9999 0 -0.33 17 17
positive regulation of tyrosine phosphorylation of STAT protein -0.001 0.005 -9999 0 -10000 0 0
CD3E 0.013 0.24 -9999 0 -1.1 14 14
keratinocyte proliferation 0.018 0.22 -9999 0 -1 11 11
NOS2 0.013 0.23 -9999 0 -1 15 15
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.01 0.016 -10000 0 -0.2 3 3
TRAF2/ASK1 0.014 0.019 -10000 0 -0.23 3 3
ATM 0.011 0 -10000 0 -10000 0 0
MAP2K3 0.026 0.02 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.028 0.025 -10000 0 -0.22 3 3
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.001 0.07 -10000 0 -0.41 15 15
TXN 0.007 0 -10000 0 -10000 0 0
CALM1 0.011 0 -10000 0 -10000 0 0
GADD45A 0.011 0 -10000 0 -10000 0 0
GADD45B 0.011 0 -10000 0 -10000 0 0
MAP3K1 0.011 0 -10000 0 -10000 0 0
MAP3K6 0.011 0 -10000 0 -10000 0 0
MAP3K7 0.011 0 -10000 0 -10000 0 0
MAP3K4 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.015 0.022 -10000 0 -0.28 3 3
TAK1/TAB family 0.001 0.009 0.15 2 -10000 0 2
RAC1/OSM/MEKK3 0.021 0 -10000 0 -10000 0 0
TRAF2 0.011 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.001 0.009 -10000 0 -10000 0 0
TRAF6 0.007 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.046 0.13 -10000 0 -0.33 88 88
CCM2 0.011 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.018 0.073 -10000 0 -0.18 88 88
MAPK11 0.009 0.026 -10000 0 -0.41 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.01 0.067 -10000 0 -0.16 91 91
OSM/MEKK3 0.016 0 -10000 0 -10000 0 0
TAOK1 0.013 0.018 -10000 0 -0.28 2 2
TAOK2 0.014 0 -10000 0 -10000 0 0
TAOK3 0.014 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.011 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.009 0.032 -10000 0 -0.41 3 3
MAP3K10 0.011 0 -10000 0 -10000 0 0
MAP3K3 0.011 0 -10000 0 -10000 0 0
TRX/ASK1 0.012 0.018 -10000 0 -0.23 3 3
GADD45/MTK1/MTK1 0.02 0.035 -10000 0 -0.19 15 15
Caspase cascade in apoptosis

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
TOP1 0.013 0.049 -10000 0 -0.29 6 6
ACTA1 0.004 0.059 0.16 3 -0.3 10 13
NUMA1 0.013 0.049 -10000 0 -0.29 6 6
SPTAN1 0.007 0.058 0.17 1 -0.3 10 11
LIMK1 0.007 0.058 0.17 1 -0.3 10 11
BIRC3 0.003 0.055 -10000 0 -0.39 10 10
BIRC2 0.011 0 -10000 0 -10000 0 0
BAX 0.011 0 -10000 0 -10000 0 0
CASP10 -0.002 0.075 -10000 0 -0.2 57 57
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.011 0 -10000 0 -10000 0 0
PTK2 0.013 0.049 -10000 0 -0.29 6 6
DIABLO 0.011 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.007 0.058 0.17 1 -0.3 10 11
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.011 0 -10000 0 -10000 0 0
GSN 0.004 0.061 -10000 0 -0.3 10 10
MADD 0.011 0 -10000 0 -10000 0 0
TFAP2A 0.028 0.039 -10000 0 -0.59 2 2
BID 0.008 0.037 -10000 0 -0.18 11 11
MAP3K1 0.008 0.024 -10000 0 -0.2 1 1
TRADD 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.016 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.007 0.058 -10000 0 -0.3 10 10
CASP9 0.011 0 -10000 0 -10000 0 0
DNA repair -0.005 0.022 0.14 1 -0.16 5 6
neuron apoptosis 0.019 0.008 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.013 0.056 -10000 0 -0.34 6 6
APAF1 0.011 0 -10000 0 -10000 0 0
CASP6 0.022 0.032 -10000 0 -10000 0 0
TRAF2 0.011 0 -10000 0 -10000 0 0
ICAD/CAD 0.012 0.056 -10000 0 -0.29 10 10
CASP7 -0.004 0.033 0.25 8 -10000 0 8
KRT18 0.013 0.032 -10000 0 -0.7 1 1
apoptosis 0.014 0.054 -10000 0 -0.41 2 2
DFFA 0.007 0.058 0.17 1 -0.3 10 11
DFFB 0.007 0.058 0.17 1 -0.3 10 11
PARP1 0.005 0.022 0.16 5 -0.14 1 6
actin filament polymerization -0.009 0.058 0.28 11 -10000 0 11
TNF -0.032 0.11 -10000 0 -0.33 66 66
CYCS 0.009 0.032 -10000 0 -0.19 3 3
SATB1 -0.006 0.082 -10000 0 -0.37 5 5
SLK 0.007 0.058 -10000 0 -0.3 10 10
p15 BID/BAX 0.013 0.033 -10000 0 -0.26 2 2
CASP2 0.03 0.03 -10000 0 -0.3 1 1
JNK cascade -0.008 0.024 0.19 1 -10000 0 1
CASP3 0.001 0.062 0.17 5 -0.32 10 15
LMNB2 0.032 0.024 -10000 0 -10000 0 0
RIPK1 0.011 0 -10000 0 -10000 0 0
CASP4 0.01 0.018 -10000 0 -0.41 1 1
Mammalian IAPs/DIABLO 0.024 0.03 -10000 0 -0.2 8 8
negative regulation of DNA binding 0.028 0.039 -10000 0 -0.58 2 2
stress fiber formation 0.007 0.058 0.17 1 -0.3 10 11
GZMB -0.011 0.086 -10000 0 -0.25 57 57
CASP1 0.012 0.022 -10000 0 -0.28 3 3
LMNB1 0.032 0.024 -10000 0 -10000 0 0
APP 0.019 0.008 -10000 0 -10000 0 0
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0 -10000 0 -10000 0 0
VIM 0.009 0.053 -10000 0 -0.29 5 5
LMNA 0.032 0.024 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.026 0.032 -10000 0 -0.32 1 1
LRDD 0.011 0 -10000 0 -10000 0 0
SREBF1 0.007 0.058 0.17 1 -0.3 10 11
APAF-1/Caspase 9 -0.001 0.017 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.013 0.048 -10000 0 -0.29 6 6
CFL2 0.009 0.059 -10000 0 -0.28 11 11
GAS2 -0.008 0.081 0.17 1 -0.34 14 15
positive regulation of apoptosis 0.035 0.024 -10000 0 -10000 0 0
PRF1 0.004 0.05 -10000 0 -0.37 9 9
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.009 0.032 -9999 0 -0.41 3 3
Caspase 8 (4 units) 0.03 0.035 -9999 0 -0.36 1 1
NEF 0.001 0.019 -9999 0 -0.16 4 4
NFKBIA 0.012 0.012 -9999 0 -10000 0 0
BIRC3 0.027 0.061 -9999 0 -0.4 10 10
CYCS 0.035 0.037 -9999 0 -0.25 4 4
RIPK1 0.011 0 -9999 0 -10000 0 0
CD247 0.01 0.037 -9999 0 -0.41 3 3
MAP2K7 0.037 0.034 -9999 0 -0.29 2 2
protein ubiquitination 0.049 0.027 -9999 0 -0.18 2 2
CRADD 0.011 0 -9999 0 -10000 0 0
DAXX 0.011 0 -9999 0 -10000 0 0
FAS 0.007 0.041 -9999 0 -0.41 5 5
BID 0.031 0.038 -9999 0 -0.2 11 11
NF-kappa-B/RelA/I kappa B alpha 0.026 0.035 -9999 0 -0.22 9 9
TRADD 0.011 0 -9999 0 -10000 0 0
MAP3K5 0.009 0.032 -9999 0 -0.41 3 3
CFLAR 0.011 0 -9999 0 -10000 0 0
FADD 0.011 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.027 0.035 -9999 0 -0.22 9 9
MAPK8 0.039 0.038 -9999 0 -0.29 2 2
APAF1 0.011 0 -9999 0 -10000 0 0
TRAF1 0.011 0 -9999 0 -10000 0 0
TRAF2 0.011 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.026 0.04 -9999 0 -0.22 11 11
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.043 0.03 -9999 0 -0.24 2 2
CHUK 0.05 0.028 -9999 0 -0.2 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.03 0.026 -9999 0 -0.18 8 8
TCRz/NEF 0.01 0.04 -9999 0 -0.22 14 14
TNF -0.032 0.11 -9999 0 -0.33 66 66
FASLG 0.013 0.062 -9999 0 -0.34 14 14
NFKB1 0.011 0.022 -9999 0 -0.4 1 1
TNFR1A/BAG4/TNF-alpha -0.004 0.067 -9999 0 -0.18 69 69
CASP6 -0.003 0.022 -9999 0 -10000 0 0
CASP7 0.056 0.069 -9999 0 -0.44 8 8
RELA 0.012 0.012 -9999 0 -10000 0 0
CASP2 0.011 0 -9999 0 -10000 0 0
CASP3 0.056 0.069 -9999 0 -0.44 8 8
TNFRSF1A 0.011 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.015 0.022 -9999 0 -0.28 3 3
CASP8 0.011 0 -9999 0 -10000 0 0
CASP9 0.011 0 -9999 0 -10000 0 0
MAP3K14 0.047 0.029 -9999 0 -0.22 2 2
APAF-1/Caspase 9 -0.007 0.04 -9999 0 -0.28 9 9
BCL2 0.026 0.068 -9999 0 -0.28 7 7
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.024 0.013 -10000 0 -0.19 2 2
epithelial cell differentiation -0.001 0.011 -10000 0 -0.18 2 2
CYFIP2 0.009 0.032 -10000 0 -0.41 3 3
ENAH 0.049 0.016 -10000 0 -10000 0 0
EGFR 0 0.067 -10000 0 -0.4 14 14
EPHA2 0.011 0 -10000 0 -10000 0 0
MYO6 0.029 0.012 -10000 0 -10000 0 0
CTNNB1 0.011 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.021 0.019 -10000 0 -0.23 3 3
AQP5 0.013 0.045 -10000 0 -0.38 6 6
CTNND1 0.011 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.029 0.012 -10000 0 -0.17 2 2
regulation of calcium-dependent cell-cell adhesion 0.023 0.038 -10000 0 -0.18 17 17
EGF -0.005 0.071 -10000 0 -0.34 23 23
NCKAP1 0.011 0 -10000 0 -10000 0 0
AQP3 -0.004 0.044 -10000 0 -0.45 5 5
cortical microtubule organization -0.001 0.011 -10000 0 -0.18 2 2
GO:0000145 0.027 0.012 -10000 0 -0.16 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.025 0.013 -10000 0 -0.19 2 2
MLLT4 0.011 0 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.013 -10000 0 -10000 0 0
ARF6 0.011 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.027 0.018 -10000 0 -0.2 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.037 0.012 -10000 0 -10000 0 0
PVRL2 0.011 0 -10000 0 -10000 0 0
ZYX 0.029 0.012 -10000 0 -0.17 2 2
ARF6/GTP 0.03 0.016 -10000 0 -0.18 2 2
CDH1 0.009 0.026 -10000 0 -0.41 2 2
EGFR/EGFR/EGF/EGF -0.01 0.041 -10000 0 -0.32 3 3
RhoA/GDP -0.001 0.01 -10000 0 -0.17 2 2
actin cytoskeleton organization 0.033 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer -0.006 0.082 -10000 0 -0.41 21 21
GIT1 0.011 0 -10000 0 -10000 0 0
IGF1R -0.006 0.082 -10000 0 -0.41 21 21
IGF1 -0.069 0.16 -10000 0 -0.41 100 100
DIAPH1 -0.003 0.04 -10000 0 -0.52 3 3
Wnt receptor signaling pathway 0.001 0.011 0.18 2 -10000 0 2
RHOA 0.011 0 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.013 -10000 0 -10000 0 0
CTNNA1 0.011 0 -10000 0 -10000 0 0
VCL 0.033 0.012 -10000 0 -10000 0 0
EFNA1 0.01 0.021 -10000 0 -0.33 2 2
LPP 0.034 0.012 -10000 0 -10000 0 0
Ephrin A1/EPHA2 -0.001 0.012 -10000 0 -10000 0 0
SEC6/SEC8 -0.001 0.009 -10000 0 -10000 0 0
MGAT3 0.023 0.039 -10000 0 -0.18 17 17
HGF/MET -0.035 0.073 -10000 0 -0.47 3 3
HGF -0.074 0.17 -10000 0 -0.41 106 106
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.024 0.014 -10000 0 -0.2 2 2
actin cable formation 0.062 0.016 -10000 0 -10000 0 0
KIAA1543 0.033 0.025 -10000 0 -0.35 2 2
KIFC3 0.029 0.012 -10000 0 -0.17 2 2
NCK1 0.009 0.026 -10000 0 -0.41 2 2
EXOC3 0.011 0 -10000 0 -10000 0 0
ACTN1 0.029 0.012 -10000 0 -10000 0 0
NCK1/GIT1 0.015 0.018 -10000 0 -0.28 2 2
mol:GDP -0.001 0.011 -10000 0 -0.18 2 2
EXOC4 0.011 0 -10000 0 -10000 0 0
STX4 0.029 0.012 -10000 0 -10000 0 0
PIP5K1C 0.029 0.012 -10000 0 -0.17 2 2
LIMA1 0.011 0 -10000 0 -10000 0 0
ABI1 0.011 0 -10000 0 -10000 0 0
ROCK1 0.047 0.016 -10000 0 -10000 0 0
adherens junction assembly 0.045 0.027 -10000 0 -0.36 2 2
IGF-1R heterotetramer/IGF1 -0.038 0.079 -10000 0 -0.35 12 12
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.016 0 -10000 0 -10000 0 0
MET 0.005 0.047 -10000 0 -0.37 8 8
PLEKHA7 0.029 0.015 -10000 0 -10000 0 0
mol:GTP 0.026 0.017 -10000 0 -0.2 2 2
establishment of epithelial cell apical/basal polarity 0.047 0.011 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.024 0.013 -10000 0 -0.19 2 2
regulation of cell-cell adhesion 0.033 0.012 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.024 0.014 -10000 0 -0.2 2 2
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.059 0.034 -9999 0 -10000 0 0
ERC1 0.011 0 -9999 0 -10000 0 0
RIP2/NOD2 0.016 0.01 -9999 0 -0.22 1 1
NFKBIA 0.036 0.01 -9999 0 -10000 0 0
BIRC2 0.011 0 -9999 0 -10000 0 0
IKBKB 0.011 0 -9999 0 -10000 0 0
RIPK2 0.011 0 -9999 0 -10000 0 0
IKBKG 0.037 0.003 -9999 0 -10000 0 0
IKK complex/A20 -0.012 0.032 -9999 0 -10000 0 0
NEMO/A20/RIP2 0.011 0 -9999 0 -10000 0 0
XPO1 0.011 0 -9999 0 -10000 0 0
NEMO/ATM 0.041 0.002 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.015 0 -9999 0 -10000 0 0
IKK complex/ELKS 0 0 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0.022 0 -9999 0 -10000 0 0
NOD2 0.01 0.015 -9999 0 -0.33 1 1
NFKB1 0.013 0.018 -9999 0 -0.4 1 1
RELA 0.014 0 -9999 0 -10000 0 0
MALT1 0.011 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0.016 0 -9999 0 -10000 0 0
ATM 0.011 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.013 0.078 -9999 0 -0.22 66 66
TRAF6 0.011 0 -9999 0 -10000 0 0
PRKCA -0.016 0.1 -9999 0 -0.41 34 34
CHUK 0.011 0 -9999 0 -10000 0 0
UBE2D3 0.011 0 -9999 0 -10000 0 0
TNF -0.032 0.11 -9999 0 -0.33 66 66
NF kappa B1 p50/RelA 0.031 0.011 -9999 0 -0.22 1 1
BCL10 0.011 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.01 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
TNFRSF1A 0.011 0 -9999 0 -10000 0 0
IKK complex 0.046 0.002 -9999 0 -10000 0 0
CYLD 0.011 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.009 0.034 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.01 0.018 -9999 0 -0.41 1 1
PLK4 0.008 0.033 -9999 0 -0.33 5 5
regulation of centriole replication 0.015 0.026 -9999 0 -0.23 6 6
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.007 0.041 -10000 0 -0.37 6 6
positive regulation of NF-kappaB transcription factor activity 0.007 0.052 -10000 0 -0.27 18 18
MAP2K4 0.035 0.02 -10000 0 -10000 0 0
IKBKB 0.011 0 -10000 0 -10000 0 0
TNFRSF10B 0.011 0 -10000 0 -10000 0 0
TNFRSF10A 0.009 0.026 -10000 0 -0.41 2 2
SMPD1 0.014 0.015 -10000 0 -0.16 3 3
IKBKG 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.001 0.063 -10000 0 -0.41 12 12
TRAIL/TRAILR2 0.013 0.028 -10000 0 -0.25 6 6
TRAIL/TRAILR3 0.013 0.031 -10000 0 -0.25 7 7
TRAIL/TRAILR1 0.012 0.034 -10000 0 -0.26 8 8
TRAIL/TRAILR4 0.007 0.052 -10000 0 -0.27 18 18
TRAIL/TRAILR1/DAP3/GTP 0.018 0.026 -10000 0 -0.19 8 8
IKK complex -0.001 0.007 -10000 0 -10000 0 0
RIPK1 0.011 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.008 0 -10000 0 -10000 0 0
MAPK3 0.015 0.028 -10000 0 -0.25 6 6
MAP3K1 0.031 0.02 -10000 0 -0.2 3 3
TRAILR4 (trimer) 0.001 0.063 -10000 0 -0.41 12 12
TRADD 0.011 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.009 0.026 -10000 0 -0.41 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.028 0.022 -10000 0 -0.19 5 5
CFLAR 0.011 0 -10000 0 -10000 0 0
MAPK1 0.015 0.028 -10000 0 -0.25 6 6
TRAIL/TRAILR1/FADD/TRADD/RIP 0.03 0.024 -10000 0 -0.18 5 5
mol:ceramide 0.014 0.015 -10000 0 -0.16 3 3
FADD 0.011 0 -10000 0 -10000 0 0
MAPK8 0.038 0.027 -10000 0 -10000 0 0
TRAF2 0.011 0 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.01 0.018 -10000 0 -0.41 1 1
CHUK 0.011 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.019 0.028 -10000 0 -0.21 8 8
DAP3 0.011 0 -10000 0 -10000 0 0
CASP10 0.002 0.046 0.22 12 -0.31 4 16
JNK cascade 0.007 0.052 -10000 0 -0.27 18 18
TRAIL (trimer) 0.007 0.041 -10000 0 -0.37 6 6
TNFRSF10C 0.01 0.018 -10000 0 -0.41 1 1
TRAIL/TRAILR1/DAP3/GTP/FADD 0.023 0.024 -10000 0 -0.19 5 5
TRAIL/TRAILR2/FADD 0.02 0.024 -10000 0 -0.2 6 6
cell death 0.014 0.015 -10000 0 -0.16 3 3
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.028 0.018 -10000 0 -0.19 3 3
TRAILR2 (trimer) 0.011 0 -10000 0 -10000 0 0
CASP8 0.001 0.009 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.031 0.02 -10000 0 -10000 0 0
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 0.002 0.024 0.21 6 -10000 0 6
DAPP1 0.028 0.043 -10000 0 -0.3 3 3
Src family/SYK family/BLNK-LAT/BTK-ITK 0.044 0.047 -10000 0 -0.49 1 1
mol:DAG 0.046 0.031 0.16 5 -0.18 1 6
HRAS 0.012 0.001 -10000 0 -10000 0 0
RAP1A 0.012 0.001 -10000 0 -10000 0 0
ARF5/GDP 0.027 0.046 -10000 0 -0.2 13 13
PLCG2 0.01 0.024 -10000 0 -0.37 2 2
PLCG1 0.011 0 -10000 0 -10000 0 0
ARF5 0.011 0 -10000 0 -10000 0 0
mol:GTP 0.002 0.023 0.2 6 -10000 0 6
ARF1/GTP 0.002 0.024 0.21 6 -10000 0 6
RHOA 0.011 0 -10000 0 -10000 0 0
YES1 0.011 0 -10000 0 -10000 0 0
RAP1A/GTP 0.023 0.021 0.2 6 -10000 0 6
ADAP1 0.002 0.023 0.2 6 -10000 0 6
ARAP3 0.002 0.023 0.2 6 -10000 0 6
INPPL1 0.011 0 -10000 0 -10000 0 0
PREX1 0.011 0 -10000 0 -10000 0 0
ARHGEF6 0.001 0.065 -10000 0 -0.41 13 13
ARHGEF7 0.011 0 -10000 0 -10000 0 0
ARF1 0.011 0 -10000 0 -10000 0 0
NRAS 0.012 0.001 -10000 0 -10000 0 0
FYN 0.011 0 -10000 0 -10000 0 0
ARF6 0.011 0 -10000 0 -10000 0 0
FGR 0.002 0.06 -10000 0 -0.41 11 11
mol:Ca2+ 0.032 0.018 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0 0.068 -10000 0 -0.41 14 14
ZAP70 -0.001 0.064 -10000 0 -0.34 18 18
mol:IP3 0.039 0.024 -10000 0 -10000 0 0
LYN 0.011 0 -10000 0 -10000 0 0
ARF1/GDP 0.027 0.046 -10000 0 -0.2 13 13
RhoA/GDP 0 0.025 0.19 6 -0.2 1 7
PDK1/Src/Hsp90 0.022 0 -10000 0 -10000 0 0
BLNK 0.009 0.03 -10000 0 -0.38 3 3
actin cytoskeleton reorganization 0.046 0.036 0.2 5 -0.23 3 8
SRC 0.011 0 -10000 0 -10000 0 0
PLEKHA2 0.023 0.011 -10000 0 -0.23 1 1
RAC1 0.011 0 -10000 0 -10000 0 0
PTEN 0.003 0.042 -10000 0 -0.39 6 6
HSP90AA1 0.011 0 -10000 0 -10000 0 0
ARF6/GTP 0.002 0.024 0.21 6 -10000 0 6
RhoA/GTP 0.028 0.02 0.2 6 -10000 0 6
Src family/SYK family/BLNK-LAT 0.034 0.04 -10000 0 -0.3 1 1
BLK -0.015 0.087 -10000 0 -0.33 37 37
PDPK1 0.011 0 -10000 0 -10000 0 0
CYTH1 0.002 0.023 0.2 6 -10000 0 6
HCK 0.006 0.039 -10000 0 -0.33 7 7
CYTH3 0.002 0.023 0.2 6 -10000 0 6
CYTH2 0.002 0.023 0.2 6 -10000 0 6
KRAS 0.011 0.015 -10000 0 -0.33 1 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.035 0.03 -10000 0 -0.38 2 2
SGK1 0 0.031 0.16 6 -0.42 2 8
INPP5D 0.01 0.018 -10000 0 -0.41 1 1
mol:GDP 0.022 0.048 -10000 0 -0.22 13 13
SOS1 0.011 0 -10000 0 -10000 0 0
SYK 0.01 0.015 -10000 0 -0.33 1 1
ARF6/GDP 0 0.026 0.2 6 -0.21 1 7
mol:PI-3-4-5-P3 0.002 0.026 0.23 6 -10000 0 6
ARAP3/RAP1A/GTP 0.023 0.021 0.2 6 -10000 0 6
VAV1 0.007 0.038 -10000 0 -0.34 6 6
mol:PI-3-4-P2 0.018 0.013 -10000 0 -0.28 1 1
RAS family/GTP/PI3K Class I 0.025 0.01 -10000 0 -10000 0 0
PLEKHA1 0.023 0.011 -10000 0 -0.23 1 1
Rac1/GDP 0.027 0.046 -10000 0 -0.2 13 13
LAT 0.011 0 -10000 0 -10000 0 0
Rac1/GTP 0.019 0.067 -10000 0 -0.26 25 25
ITK -0.003 0.035 0.2 6 -10000 0 6
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.053 0.039 0.18 5 -0.24 1 6
LCK 0.008 0.035 -10000 0 -0.35 5 5
BTK 0.001 0.025 0.2 6 -10000 0 6
Arf6 trafficking events

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
SLC2A4 -0.19 0.21 -10000 0 -0.41 255 255
CLTC 0.026 0.001 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.021 0.006 -10000 0 -10000 0 0
Dynamin 2/GTP 0.02 0 -10000 0 -10000 0 0
EXOC4 0.011 0 -10000 0 -10000 0 0
CD59 0.023 0.001 -10000 0 -10000 0 0
CPE -0.01 0.074 -10000 0 -0.24 52 52
CTNNB1 0.011 0 -10000 0 -10000 0 0
membrane fusion 0.021 0.006 -10000 0 -10000 0 0
CTNND1 0.025 0 -10000 0 -10000 0 0
DNM2 0.011 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.026 0.003 -10000 0 -10000 0 0
TSHR 0.005 0.041 -10000 0 -0.19 22 22
INS 0.01 0.002 -10000 0 -10000 0 0
BIN1 0.008 0.037 -10000 0 -0.41 4 4
mol:Choline 0.021 0.006 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ 0.02 0 -10000 0 -10000 0 0
JUP 0.023 0.008 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.02 0.02 -10000 0 -0.2 4 4
ARF6/GTP 0.008 0 -10000 0 -10000 0 0
CDH1 0.022 0.011 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.008 0 -10000 0 -10000 0 0
MAPK8IP3 0.011 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0.008 0 -10000 0 -10000 0 0
EXOC2 0.011 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.035 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.011 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0.006 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.015 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.015 0 -10000 0 -10000 0 0
ACAP1 0.02 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.019 0.012 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.03 0.004 -10000 0 -10000 0 0
JIP4/KLC1 0.021 0 -10000 0 -10000 0 0
EXOC1 0.011 0 -10000 0 -10000 0 0
exocyst 0.035 0 -10000 0 -10000 0 0
RALA/GTP 0.008 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.015 0 -10000 0 -10000 0 0
receptor recycling 0.008 0 -10000 0 -10000 0 0
CTNNA1 0.025 0 -10000 0 -10000 0 0
NME1 0.015 0 -10000 0 -10000 0 0
clathrin coat assembly 0.026 0.002 -10000 0 -10000 0 0
IL2RA 0.02 0.016 -10000 0 -10000 0 0
VAMP3 0.015 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.074 0.076 -10000 0 -10000 0 0
EXOC6 0.011 0 -10000 0 -10000 0 0
PLD1 0.018 0 -10000 0 -10000 0 0
PLD2 0.017 0.011 -10000 0 -0.24 1 1
EXOC5 0.011 0 -10000 0 -10000 0 0
PIP5K1C 0.026 0.001 -10000 0 -10000 0 0
SDC1 0.003 0.032 -10000 0 -10000 0 0
ARF6/GDP 0.015 0 -10000 0 -10000 0 0
EXOC7 0.011 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0 0.006 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.021 0.006 -10000 0 -10000 0 0
endocytosis -0.019 0.019 0.2 4 -10000 0 4
SCAMP2 0.011 0 -10000 0 -10000 0 0
ADRB2 -0.004 0.075 -10000 0 -10000 0 0
EXOC3 0.011 0 -10000 0 -10000 0 0
ASAP2 0.011 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.021 0 -10000 0 -10000 0 0
KLC1 0.011 0 -10000 0 -10000 0 0
AVPR2 -0.032 0.092 -10000 0 -0.21 1 1
RALA 0.011 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0.005 -10000 0 -10000 0 0
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 -0.012 0.032 -9999 0 -0.24 2 2
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.027 0.032 -9999 0 -0.24 2 2
SUMO1 0.011 0 -9999 0 -10000 0 0
ZFPM1 0.009 0.026 -9999 0 -0.41 2 2
NPC/RanGAP1/SUMO1/Ubc9 0.017 0 -9999 0 -10000 0 0
FKBP3 0.011 0 -9999 0 -10000 0 0
Histones 0.028 0.025 -9999 0 -10000 0 0
YY1/LSF 0.018 0.04 -9999 0 -0.2 17 17
SMG5 0.011 0 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.015 0.035 -9999 0 -0.19 2 2
I kappa B alpha/HDAC1 0.016 0.028 -9999 0 -10000 0 0
SAP18 0.011 0 -9999 0 -10000 0 0
RELA 0.02 0.032 -9999 0 -0.19 4 4
HDAC1/Smad7 0.022 0.015 -9999 0 -0.23 2 2
RANGAP1 0.011 0 -9999 0 -10000 0 0
HDAC3/TR2 0.016 0.028 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.037 0.013 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.023 0.03 -9999 0 -0.18 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.029 0.12 -9999 0 -0.41 50 50
GATA1 0.006 0.005 -9999 0 -10000 0 0
Mad/Max 0.016 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.043 0.017 -9999 0 -10000 0 0
RBBP7 0.011 0 -9999 0 -10000 0 0
NPC 0.007 0 -9999 0 -10000 0 0
RBBP4 0.009 0.032 -9999 0 -0.41 3 3
MAX 0.011 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.011 0 -9999 0 -10000 0 0
NFKBIA 0.011 0.031 -9999 0 -10000 0 0
KAT2B 0.004 0.055 -9999 0 -0.41 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.034 0.015 -9999 0 -10000 0 0
SIN3 complex 0.028 0 -9999 0 -10000 0 0
SMURF1 0.011 0 -9999 0 -10000 0 0
CHD3 0.011 0 -9999 0 -10000 0 0
SAP30 0.011 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.011 0 -9999 0 -10000 0 0
YY1/HDAC3 0.022 0.036 -9999 0 -10000 0 0
YY1/HDAC2 0.021 0.031 -9999 0 -0.19 11 11
YY1/HDAC1 0.021 0.031 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.037 0.013 -9999 0 -10000 0 0
PPARG 0.005 0.071 -9999 0 -0.26 30 30
HDAC8/hEST1B 0.022 0 -9999 0 -10000 0 0
UBE2I 0.011 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.011 0 -9999 0 -10000 0 0
TNFRSF1A 0.011 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.016 0.028 -9999 0 -10000 0 0
MBD3L2 0.002 0.004 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.021 0.015 -9999 0 -0.23 2 2
CREBBP 0.009 0.026 -9999 0 -0.41 2 2
NuRD/MBD3/MBD3L2 Complex 0.041 0.013 -9999 0 -10000 0 0
HDAC1 0.011 0 -9999 0 -10000 0 0
HDAC3 0.011 0.031 -9999 0 -10000 0 0
HDAC2 0.011 0 -9999 0 -10000 0 0
YY1 0.019 0.037 -9999 0 -0.23 11 11
HDAC8 0.011 0 -9999 0 -10000 0 0
SMAD7 0.009 0.026 -9999 0 -0.41 2 2
NCOR2 0.011 0 -9999 0 -10000 0 0
MXD1 0.011 0 -9999 0 -10000 0 0
STAT3 0.02 0.018 -9999 0 -0.27 2 2
NFKB1 0.01 0.018 -9999 0 -0.41 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.011 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.024 0.036 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 0.026 0.028 -9999 0 -10000 0 0
EP300 0.011 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.02 0.018 -9999 0 -0.27 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.031 -9999 0 -10000 0 0
histone deacetylation 0.037 0.013 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.023 0.028 -9999 0 -0.18 2 2
nuclear export -0.022 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GATAD2B 0.011 0 -9999 0 -10000 0 0
GATAD2A 0.011 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.005 0.073 -9999 0 -0.21 50 50
GATA1/HDAC1 0.013 0.004 -9999 0 -10000 0 0
GATA1/HDAC3 0.005 0.027 -9999 0 -10000 0 0
CHD4 0.011 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.013 0.078 -9999 0 -0.22 66 66
SIN3/HDAC complex/Mad/Max 0.037 0.013 -9999 0 -10000 0 0
NuRD Complex 0.044 0.013 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.027 0.025 -9999 0 -10000 0 0
SIN3B 0.011 0 -9999 0 -10000 0 0
MTA2 0.011 0 -9999 0 -10000 0 0
SIN3A 0.011 0 -9999 0 -10000 0 0
XPO1 0.011 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.025 0 -9999 0 -10000 0 0
HDAC complex 0.027 0.017 -9999 0 -0.2 3 3
GATA1/Fog1 0.011 0.019 -9999 0 -0.28 2 2
FKBP25/HDAC1/HDAC2 0.022 0 -9999 0 -10000 0 0
TNF -0.032 0.11 -9999 0 -0.33 66 66
negative regulation of cell growth 0.037 0.013 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.037 0.013 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.027 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.023 0.033 -9999 0 -0.25 2 2
SIN3/HDAC complex/NCoR1 0.035 0.015 -9999 0 -10000 0 0
TFCP2 0.006 0.045 -9999 0 -0.41 6 6
NR2C1 0.011 0 -9999 0 -10000 0 0
MBD3 0.011 0 -9999 0 -10000 0 0
MBD2 0.011 0 -9999 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.011 0 -10000 0 -10000 0 0
Rac1/GDP 0 0.003 -10000 0 -10000 0 0
DOCK1 0.006 0.045 -10000 0 -0.41 6 6
ITGA4 0.009 0.03 -10000 0 -0.38 3 3
RAC1 0.011 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.014 0.023 -10000 0 -0.25 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.011 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.021 0.018 -10000 0 -0.21 3 3
alpha4/beta7 Integrin/Paxillin 0.026 0.018 -10000 0 -0.2 2 2
lamellipodium assembly -0.006 0.047 -10000 0 -0.4 6 6
PIK3CA 0.01 0.018 -10000 0 -0.41 1 1
PI3K 0.013 0.031 -10000 0 -0.28 6 6
ARF6 0.011 0 -10000 0 -10000 0 0
TLN1 0.011 0 -10000 0 -10000 0 0
PXN 0.018 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.041 -10000 0 -0.41 5 5
ARF6/GTP -0.001 0.011 -10000 0 -10000 0 0
cell adhesion 0.031 0.015 -10000 0 -0.18 2 2
CRKL/CBL 0.016 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.026 0.016 -10000 0 -0.2 2 2
ITGB1 0.011 0 -10000 0 -10000 0 0
ITGB7 0.01 0.015 -10000 0 -0.33 1 1
ARF6/GDP 0 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.016 0.061 -10000 0 -0.19 40 40
p130Cas/Crk/Dock1 0.02 0.027 -10000 0 -0.23 6 6
VCAM1 -0.021 0.11 -10000 0 -0.41 40 40
alpha4/beta1 Integrin/Paxillin/Talin 0.032 0.015 -10000 0 -0.18 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.032 0.015 -10000 0 -0.18 2 2
BCAR1 0.011 0 -10000 0 -10000 0 0
mol:GDP -0.031 0.015 0.18 2 -10000 0 2
CBL 0.011 0 -10000 0 -10000 0 0
PRKACA 0.011 0 -10000 0 -10000 0 0
GIT1 0.011 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.032 0.015 -10000 0 -0.18 2 2
Rac1/GTP -0.006 0.053 -10000 0 -0.44 6 6
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.011 0 -9999 0 -10000 0 0
ITGB7 0.01 0.015 -9999 0 -0.33 1 1
ITGA4 0.009 0.03 -9999 0 -0.38 3 3
alpha4/beta7 Integrin 0.014 0.023 -9999 0 -0.25 4 4
alpha4/beta1 Integrin 0.015 0.021 -9999 0 -0.26 3 3
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.027 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.018 0 -9999 0 -10000 0 0
mol:DAG 0.031 0.008 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0 -9999 0 -10000 0 0
CaM/Ca2+ 0.036 0.007 -9999 0 -10000 0 0
HIF1A 0.018 0 -9999 0 -10000 0 0
GAB1 0.008 0.037 -9999 0 -0.41 4 4
AKT1 0.043 0.026 -9999 0 -10000 0 0
PLCG1 0.031 0.008 -9999 0 -10000 0 0
NOS3 0.048 0.017 -9999 0 -0.25 1 1
CBL 0.011 0 -9999 0 -10000 0 0
mol:NO 0.048 0.017 -9999 0 -0.24 1 1
FLT1 0.025 0 -9999 0 -10000 0 0
PGF 0.01 0.015 -9999 0 -0.33 1 1
VEGFR1 homodimer/NRP2/VEGFR121 0.021 0.048 -9999 0 -10000 0 0
CALM1 0.011 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
eNOS/Hsp90 0.052 0.017 -9999 0 -10000 0 0
endothelial cell proliferation 0.019 0.065 -9999 0 -0.31 4 4
mol:Ca2+ 0.031 0.008 -9999 0 -10000 0 0
MAPK3 0.026 0.05 -9999 0 -10000 0 0
MAPK1 0.026 0.05 -9999 0 -10000 0 0
PIK3R1 0.007 0.041 -9999 0 -0.41 5 5
PLGF homodimer 0.01 0.015 -9999 0 -0.33 1 1
PRKACA 0.011 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.063 0.16 -9999 0 -0.41 93 93
VEGFA homodimer 0.011 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.027 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.031 0.048 -9999 0 -10000 0 0
PI3K 0.034 0.024 -9999 0 -10000 0 0
PRKCA 0.022 0.053 -9999 0 -10000 0 0
PRKCB 0.022 0.051 -9999 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer 0.026 0.008 -9999 0 -10000 0 0
VEGFA 0.011 0 -9999 0 -10000 0 0
VEGFB 0.011 0 -9999 0 -10000 0 0
mol:IP3 0.031 0.008 -9999 0 -10000 0 0
RASA1 0.029 0.022 -9999 0 -10000 0 0
NRP2 -0.009 0.09 -9999 0 -0.41 25 25
VEGFR1 homodimer 0.025 0 -9999 0 -10000 0 0
VEGFB homodimer 0.011 0 -9999 0 -10000 0 0
NCK1 0.009 0.026 -9999 0 -0.41 2 2
eNOS/Caveolin-1 0.019 0.075 -9999 0 -0.41 1 1
PTPN11 0.011 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.033 0.023 -9999 0 -10000 0 0
mol:L-citrulline 0.048 0.017 -9999 0 -0.24 1 1
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.037 0 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.031 0.014 -9999 0 -10000 0 0
CD2AP 0.011 0 -9999 0 -10000 0 0
PI3K/GAB1 0.037 0.029 -9999 0 -10000 0 0
PDPK1 0.037 0.022 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.032 0 -9999 0 -10000 0 0
mol:NADP 0.048 0.017 -9999 0 -0.24 1 1
HSP90AA1 0.011 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.036 0 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.015 0.053 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.036 0.03 -10000 0 -0.22 7 7
adherens junction organization 0.033 0.028 -10000 0 -0.35 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.036 0.042 -10000 0 -0.38 2 2
FMN1 0.027 0.038 -10000 0 -0.34 2 2
mol:IP3 0.03 0.026 -10000 0 -0.18 7 7
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.028 0.027 -10000 0 -0.36 2 2
CTNNB1 0.011 0.001 -10000 0 -10000 0 0
AKT1 0.036 0.027 -10000 0 -0.33 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.032 0.029 -10000 0 -0.42 2 2
CTNND1 0.012 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.033 0.025 -10000 0 -0.33 2 2
VASP 0.033 0.026 -10000 0 -0.34 2 2
ZYX 0.033 0.026 -10000 0 -0.34 2 2
JUB 0.033 0.026 -10000 0 -0.34 2 2
EGFR(dimer) 0.028 0.045 -10000 0 -0.36 3 3
E-cadherin/beta catenin-gamma catenin -0.001 0.021 -10000 0 -0.31 2 2
mol:PI-3-4-5-P3 0.03 0.028 -10000 0 -0.2 7 7
PIK3CA 0.011 0.018 -10000 0 -0.41 1 1
PI3K 0.031 0.029 -10000 0 -0.2 7 7
FYN 0.031 0.037 -10000 0 -0.24 1 1
mol:Ca2+ 0.03 0.026 -10000 0 -0.18 7 7
JUP 0.01 0.018 -10000 0 -0.4 1 1
PIK3R1 0.008 0.041 -10000 0 -0.41 5 5
mol:DAG 0.03 0.026 -10000 0 -0.18 7 7
CDH1 0.009 0.026 -10000 0 -0.41 2 2
RhoA/GDP 0.036 0.042 -10000 0 -0.38 2 2
establishment of polarity of embryonic epithelium 0.033 0.025 -10000 0 -0.33 2 2
SRC 0.011 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
RHOA 0.011 0 -10000 0 -10000 0 0
EGFR 0 0.067 -10000 0 -0.4 14 14
CASR 0.023 0.044 -10000 0 -0.27 1 1
RhoA/GTP -0.002 0.02 -10000 0 -0.26 1 1
AKT2 0.036 0.027 -10000 0 -0.33 1 1
actin cable formation 0.032 0.037 -10000 0 -0.46 1 1
apoptosis -0.034 0.029 0.2 7 -10000 0 7
CTNNA1 0.012 0.001 -10000 0 -10000 0 0
mol:GDP 0.031 0.044 -10000 0 -0.41 2 2
PIP5K1A 0.033 0.026 -10000 0 -0.34 2 2
PLCG1 0.031 0.026 -10000 0 -0.19 7 7
Rac1/GTP -0.005 0.036 -10000 0 -0.41 2 2
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.01 0.018 -9999 0 -0.41 1 1
SMAD2 0.011 0 -9999 0 -10000 0 0
SMAD3 0.031 0.017 -9999 0 -10000 0 0
SMAD3/SMAD4 0.036 0.019 -9999 0 -0.33 1 1
SMAD4/Ubc9/PIASy 0.022 0.011 -9999 0 -0.23 1 1
SMAD2/SMAD2/SMAD4 0.025 0.033 -9999 0 -10000 0 0
PPM1A 0.011 0 -9999 0 -10000 0 0
CALM1 0.011 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.017 0.009 -9999 0 -0.2 1 1
MAP3K1 0.011 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.011 0.038 -9999 0 -0.28 9 9
MAPK3 0.011 0 -9999 0 -10000 0 0
MAPK1 0.011 0 -9999 0 -10000 0 0
NUP214 0.011 0 -9999 0 -10000 0 0
CTDSP1 0.011 0 -9999 0 -10000 0 0
CTDSP2 0.011 0 -9999 0 -10000 0 0
CTDSPL 0.011 0 -9999 0 -10000 0 0
KPNB1 0.011 0 -9999 0 -10000 0 0
TGFBRAP1 0.005 0.052 -9999 0 -0.41 8 8
UBE2I 0.011 0 -9999 0 -10000 0 0
NUP153 0.01 0.018 -9999 0 -0.41 1 1
KPNA2 -0.004 0.07 -9999 0 -0.33 23 23
PIAS4 0.011 0 -9999 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.033 0.013 -10000 0 -10000 0 0
regulation of axonogenesis -0.023 0.008 -10000 0 -10000 0 0
myoblast fusion -0.017 0.013 -10000 0 -10000 0 0
mol:GTP -0.001 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.022 0.04 0.22 14 -10000 0 14
ARF1/GTP 0 0.003 -10000 0 -10000 0 0
mol:GM1 0.008 0.005 -10000 0 -10000 0 0
mol:Choline 0.022 0.011 -10000 0 -0.22 1 1
lamellipodium assembly 0.001 0.012 -10000 0 -10000 0 0
MAPK3 0.023 0.008 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.023 0.04 -10000 0 -0.22 14 14
ARF1 0.011 0 -10000 0 -10000 0 0
ARF6/GDP 0.017 0.013 -10000 0 -10000 0 0
ARF1/GDP 0.023 0.012 -10000 0 -10000 0 0
ARF6 0.01 0.003 -10000 0 -10000 0 0
RAB11A 0.011 0 -10000 0 -10000 0 0
TIAM1 0.001 0.068 -10000 0 -0.41 14 14
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.023 0.008 -10000 0 -10000 0 0
actin filament bundle formation -0.021 0.01 -10000 0 -10000 0 0
KALRN -0.001 0.023 -10000 0 -0.21 5 5
RAB11FIP3/RAB11A 0.016 0 -10000 0 -10000 0 0
RhoA/GDP 0.021 0.01 -10000 0 -10000 0 0
NME1 0.012 0.001 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.01 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.001 0.005 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.001 0.012 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
liver development -0.001 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.001 0.005 -10000 0 -10000 0 0
RhoA/GTP 0 0.003 -10000 0 -10000 0 0
mol:GDP 0.002 0.013 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.021 0.005 -10000 0 -10000 0 0
RHOA 0.011 0 -10000 0 -10000 0 0
PLD1 0.017 0.004 -10000 0 -10000 0 0
RAB11FIP3 0.011 0 -10000 0 -10000 0 0
tube morphogenesis 0.001 0.012 -10000 0 -10000 0 0
ruffle organization 0.023 0.008 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.001 0.005 -10000 0 -10000 0 0
PLD2 0.017 0.013 -10000 0 -0.26 1 1
PIP5K1A 0.023 0.008 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.022 0.011 -10000 0 -0.22 1 1
Rac1/GTP 0.001 0.012 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.016 0.01 -9999 0 -0.22 1 1
FBXW11 0.011 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.021 0.011 -9999 0 -0.23 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.037 0.012 -9999 0 -10000 0 0
NFKBIA 0.022 0.01 -9999 0 -0.17 1 1
MAPK14 0.011 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.011 -9999 0 -0.23 1 1
ARRB2 0.014 0 -9999 0 -10000 0 0
REL 0.011 0.001 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.014 -9999 0 -0.2 2 2
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.011 -9999 0 -0.23 1 1
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
NF kappa B1 p50 dimer 0.016 0.013 -9999 0 -0.28 1 1
PIK3R1 0.007 0.041 -9999 0 -0.41 5 5
NFKB1 0.018 0.013 -9999 0 -0.28 1 1
RELA 0.011 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.028 0.012 -9999 0 -0.18 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.04 0.012 -9999 0 -10000 0 0
SRC 0.011 0 -9999 0 -10000 0 0
PI3K 0.013 0.031 -9999 0 -0.28 6 6
NF kappa B1 p50/RelA 0.028 0.012 -9999 0 -0.18 1 1
IKBKB 0.011 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.011 0 -9999 0 -10000 0 0
SYK 0.01 0.015 -9999 0 -0.33 1 1
I kappa B alpha/PIK3R1 0.025 0.022 -9999 0 -0.17 6 6
cell death 0.039 0.012 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.021 0.011 -9999 0 -0.23 1 1
LCK 0.008 0.035 -9999 0 -0.35 5 5
BCL3 0.01 0.015 -9999 0 -0.33 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.032 0.025 -9999 0 -0.38 2 2
KLHL20 -0.002 0.012 -9999 0 -10000 0 0
CYFIP2 0.009 0.032 -9999 0 -0.41 3 3
Rac1/GDP 0.048 0.016 -9999 0 -0.21 2 2
ENAH 0.032 0.027 -9999 0 -0.38 2 2
AP1M1 0.011 0 -9999 0 -10000 0 0
RAP1B 0.011 0 -9999 0 -10000 0 0
RAP1A 0.011 0 -9999 0 -10000 0 0
CTNNB1 0.011 0 -9999 0 -10000 0 0
CDC42/GTP 0 0.008 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.002 0.011 -9999 0 -0.13 1 1
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.027 0.016 -9999 0 -0.2 2 2
RAPGEF1 0.041 0.023 -9999 0 -0.32 2 2
CTNND1 0.011 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.027 0.026 -9999 0 -0.4 2 2
CRK 0.037 0.024 -9999 0 -0.35 2 2
E-cadherin/gamma catenin/alpha catenin 0.021 0.023 -9999 0 -0.34 2 2
alphaE/beta7 Integrin 0.016 0.01 -9999 0 -0.22 1 1
IQGAP1 0.011 0 -9999 0 -10000 0 0
NCKAP1 0.011 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.021 0 -9999 0 -10000 0 0
DLG1 0.032 0.025 -9999 0 -0.38 2 2
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.01 -9999 0 -10000 0 0
MLLT4 0.011 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.015 0.036 -9999 0 -0.2 14 14
PI3K -0.001 0.012 -9999 0 -10000 0 0
ARF6 0.011 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0.015 0.027 -9999 0 -0.4 2 2
TIAM1 0 0.068 -9999 0 -0.41 14 14
E-cadherin(dimer)/Ca2+ 0.026 0.013 -9999 0 -0.19 2 2
AKT1 -0.001 0.007 -9999 0 -10000 0 0
PIK3R1 0.007 0.041 -9999 0 -0.41 5 5
CDH1 0.009 0.026 -9999 0 -0.41 2 2
RhoA/GDP 0.048 0.016 -9999 0 -0.21 2 2
actin cytoskeleton organization 0.034 0.015 -9999 0 -10000 0 0
CDC42/GDP 0.048 0.016 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.019 0.021 -9999 0 -0.31 2 2
ITGB7 0.01 0.015 -9999 0 -0.33 1 1
RAC1 0.011 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.028 0.014 -9999 0 -0.2 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin 0.019 0.013 -9999 0 -0.19 2 2
mol:GDP 0.046 0.018 -9999 0 -0.24 2 2
CDC42/GTP/IQGAP1 0.015 0 -9999 0 -10000 0 0
JUP 0.01 0.018 -9999 0 -0.41 1 1
p120 catenin/RhoA/GDP 0.045 0.017 -9999 0 -0.21 2 2
RAC1/GTP/IQGAP1 0.015 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.016 0 -9999 0 -10000 0 0
RHOA 0.011 0 -9999 0 -10000 0 0
CDC42 0.011 0 -9999 0 -10000 0 0
CTNNA1 0.011 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.027 0.014 -9999 0 -0.13 2 2
NME1 0.011 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.032 0.027 -9999 0 -0.38 2 2
regulation of cell-cell adhesion 0 0.007 -9999 0 -10000 0 0
WASF2 -0.001 0.005 -9999 0 -10000 0 0
Rap1/GTP -0.001 0.009 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.031 0.021 -9999 0 -0.38 1 1
CCND1 0.031 0.016 -9999 0 -0.15 2 2
VAV2 0.041 0.024 -9999 0 -0.35 2 2
RAP1/GDP 0.043 0.015 -9999 0 -10000 0 0
adherens junction assembly 0.032 0.026 -9999 0 -0.37 2 2
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.011 0 -9999 0 -10000 0 0
PIP5K1C 0.011 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.036 0.021 -9999 0 -0.36 1 1
E-cadherin/beta catenin -0.001 0.018 -9999 0 -0.3 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.032 0.025 -9999 0 -0.38 2 2
PIK3CA 0.01 0.018 -9999 0 -0.41 1 1
Rac1/GTP -0.003 0.018 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0.022 0.015 -9999 0 -0.23 2 2
ITGAE 0.011 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.027 0.027 -9999 0 -0.4 2 2
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.021 0.023 -9999 0 -0.34 2 2
E-cadherin/beta catenin 0.015 0.018 -9999 0 -0.28 2 2
CTNNB1 0.011 0 -9999 0 -10000 0 0
JUP 0.01 0.018 -9999 0 -0.41 1 1
CDH1 0.009 0.026 -9999 0 -0.41 2 2
Circadian rhythm 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
chromatin modification 0.039 0.011 -9999 0 -10000 0 0
CLOCK 0.014 0.001 -9999 0 -10000 0 0
TIMELESS/CRY2 0.034 0.012 -9999 0 -10000 0 0
DEC1/BMAL1 0.011 0.013 -9999 0 -0.28 1 1
ATR 0.011 0 -9999 0 -10000 0 0
NR1D1 0.033 0.009 -9999 0 -10000 0 0
ARNTL 0.013 0.018 -9999 0 -0.41 1 1
TIMELESS 0.033 0.013 -9999 0 -10000 0 0
NPAS2 0.01 0.041 -9999 0 -0.41 5 5
CRY2 0.011 0 -9999 0 -10000 0 0
mol:CO -0.011 0.003 -9999 0 -10000 0 0
CHEK1 0.011 0 -9999 0 -10000 0 0
mol:HEME 0.011 0.003 -9999 0 -10000 0 0
PER1 0.009 0.026 -9999 0 -0.41 2 2
BMAL/CLOCK/NPAS2 0.033 0.027 -9999 0 -0.22 6 6
BMAL1/CLOCK 0.04 0.019 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.039 0.011 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.039 0.011 -9999 0 -10000 0 0
mol:NADPH 0.011 0.003 -9999 0 -10000 0 0
PER1/TIMELESS 0.034 0.018 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.001 0.004 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.011 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0.025 0 -9999 0 -9999 0 0
HDAC4 0.011 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.011 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.014 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.023 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.011 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.011 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.025 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.025 0 -9999 0 -9999 0 0
RANGAP1 0.011 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.028 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.017 0 -9999 0 -9999 0 0
Ran/GTP 0.022 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.011 0 -9999 0 -9999 0 0
UBE2I 0.011 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0.027 0 -9999 0 -9999 0 0
NPC 0.007 0 -9999 0 -9999 0 0
PIAS2 0.011 0 -9999 0 -9999 0 0
PIAS1 0.011 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.016 0.004 -9999 0 -10000 0 0
AP2 0.016 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.016 0 -9999 0 -10000 0 0
CLTB 0.011 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.021 0 -9999 0 -10000 0 0
CD4 0.01 0.015 -9999 0 -0.33 1 1
CLTA 0.011 0 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
ARFGAP1 0.009 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0.006 -9999 0 -0.15 1 1
ARF1/GTP 0 0.003 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.022 0 -9999 0 -10000 0 0
mol:Choline 0 0.007 -9999 0 -0.15 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.011 0 -9999 0 -10000 0 0
DDEF1 0 0.007 -9999 0 -0.16 1 1
ARF1/GDP 0 0.002 -9999 0 -10000 0 0
AP2M1 0.011 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.014 0 -9999 0 -10000 0 0
Rac/GTP 0.009 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.021 0 -9999 0 -10000 0 0
ARFIP2 0.01 0 -9999 0 -10000 0 0
COPA 0.011 0 -9999 0 -10000 0 0
RAC1 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.021 0.002 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.008 0 -9999 0 -10000 0 0
GGA3 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.015 0.003 -9999 0 -10000 0 0
AP2A1 0.011 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.022 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.015 0.003 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.014 0 -9999 0 -10000 0 0
CYTH2 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0.016 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.008 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.028 0.003 -9999 0 -10000 0 0
PLD2 0 0.007 -9999 0 -0.15 1 1
ARF-GAP1/v-SNARE 0.009 0 -9999 0 -10000 0 0
PIP5K1A 0 0.006 -9999 0 -0.15 1 1
ARF1/GTP/Membrin/GBF1/p115 0 0.003 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0.007 -9999 0 -0.15 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.009 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.016 0.001 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.022 0.009 -9999 0 -0.17 1 1
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 0.016 0 -9999 0 -10000 0 0
FBXW11 0.011 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.011 0 -9999 0 -10000 0 0
CHUK 0.011 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.033 0 -9999 0 -10000 0 0
NFKB1 0.01 0.018 -9999 0 -0.41 1 1
MAP3K14 0.011 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.016 0.013 -9999 0 -0.28 1 1
RELB 0.011 0 -9999 0 -10000 0 0
NFKB2 0.011 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.015 0 -9999 0 -10000 0 0
regulation of B cell activation 0.015 0 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 527 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.SL.A6JA TCGA.SL.A6J9 TCGA.SJ.A6ZJ TCGA.SJ.A6ZI
109_MAP3K5 -0.13 0.043 0.043 0.043
47_PPARGC1A -0.41 0.011 0.011 -0.41
105_BMP4 0.011 -0.41 0.011 0.011
105_BMP6 0.011 0.011 0.011 0.011
105_BMP7 0.011 0.011 0.011 0.011
105_BMP2 0.011 -0.41 0.011 0.011
131_RELN/VLDLR -0.2 -0.2 0.028 -0.2
30_TGFB1/TGF beta receptor Type II 0.011 0.011 0.013 0.01
84_STAT5B -0.023 -0.091 -0.024 0.038
84_STAT5A -0.023 -0.091 -0.024 0.038
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/9831132/UCEC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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