PARADIGM pathway analysis of mRNASeq expression and copy number data
Breast Invasive Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1SF2TPB
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1SF2TPB
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 57 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 340
Signaling events mediated by Stem cell factor receptor (c-Kit) 260
Signaling mediated by p38-alpha and p38-beta 257
Class IB PI3K non-lipid kinase events 253
Reelin signaling pathway 228
EGFR-dependent Endothelin signaling events 189
Aurora B signaling 186
FOXA2 and FOXA3 transcription factor networks 180
PLK1 signaling events 163
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 159
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 1019 . 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 ( 1019 ).

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 0.3337 340 17345 51 -0.064 0.74 1000 -1000 -0.035 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2552 260 20318 78 -0.57 0.18 1000 -1000 -0.05 -1000
Signaling mediated by p38-alpha and p38-beta 0.2522 257 11311 44 -0.32 0.024 1000 -1000 -0.015 -1000
Class IB PI3K non-lipid kinase events 0.2483 253 759 3 -0.13 -1000 1000 -1000 -0.019 -1000
Reelin signaling pathway 0.2237 228 12801 56 -0.32 0.055 1000 -1000 -0.024 -1000
EGFR-dependent Endothelin signaling events 0.1855 189 3986 21 -0.22 0.034 1000 -1000 -0.034 -1000
Aurora B signaling 0.1825 186 12492 67 -0.22 0.27 1000 -1000 -0.038 -1000
FOXA2 and FOXA3 transcription factor networks 0.1766 180 8322 46 -1.1 0.034 1000 -1000 -0.052 -1000
PLK1 signaling events 0.1600 163 13869 85 -0.067 0.24 1000 -1000 -0.024 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1560 159 10864 68 -0.39 0.18 1000 -1000 -0.047 -1000
HIF-1-alpha transcription factor network 0.1541 157 11997 76 -0.48 0.035 1000 -1000 -0.044 -1000
Glucocorticoid receptor regulatory network 0.1492 152 17332 114 -0.74 0.28 1000 -1000 -0.048 -1000
EPHB forward signaling 0.1452 148 12608 85 -0.22 0.15 1000 -1000 -0.058 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1413 144 12692 88 -0.31 0.12 1000 -1000 -0.051 -1000
Endothelins 0.1384 141 13553 96 -0.34 0.18 1000 -1000 -0.029 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1354 138 7478 54 -0.32 0.055 1000 -1000 -0.032 -1000
p75(NTR)-mediated signaling 0.1344 137 17150 125 -0.23 0.099 1000 -1000 -0.06 -1000
IL4-mediated signaling events 0.1286 131 11993 91 -0.68 0.26 1000 -1000 -0.039 -1000
Ephrin B reverse signaling 0.1207 123 5949 48 -0.22 0.1 1000 -1000 -0.019 -1000
Wnt signaling 0.1079 110 773 7 -0.098 0.019 1000 -1000 -0.009 -1000
IGF1 pathway 0.1040 106 6079 57 -0.11 0.043 1000 -1000 -0.028 -1000
Noncanonical Wnt signaling pathway 0.1030 105 2732 26 -0.098 0.024 1000 -1000 -0.032 -1000
ErbB2/ErbB3 signaling events 0.0991 101 6568 65 -0.27 0.034 1000 -1000 -0.06 -1000
Nongenotropic Androgen signaling 0.0952 97 5069 52 -0.25 0.13 1000 -1000 -0.021 -1000
Arf6 signaling events 0.0932 95 5929 62 -0.22 0.05 1000 -1000 -0.024 -1000
IL23-mediated signaling events 0.0913 93 5603 60 -0.3 0.086 1000 -1000 -0.045 -1000
BMP receptor signaling 0.0903 92 7475 81 -0.38 0.1 1000 -1000 -0.041 -1000
Plasma membrane estrogen receptor signaling 0.0873 89 7681 86 -0.11 0.1 1000 -1000 -0.045 -1000
Visual signal transduction: Rods 0.0864 88 4581 52 -0.33 0.057 1000 -1000 -0.021 -1000
Signaling events regulated by Ret tyrosine kinase 0.0854 87 7170 82 -0.068 0.1 1000 -1000 -0.047 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0854 87 10529 120 -0.37 0.17 1000 -1000 -0.041 -1000
Calcium signaling in the CD4+ TCR pathway 0.0844 86 2676 31 -0.19 0.028 1000 -1000 -0.038 -1000
Signaling events mediated by PTP1B 0.0834 85 6501 76 -0.45 0.083 1000 -1000 -0.048 -1000
Syndecan-1-mediated signaling events 0.0824 84 2885 34 -0.071 0.18 1000 -1000 -0.024 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0824 84 7143 85 -0.24 0.024 1000 -1000 -0.033 -1000
S1P1 pathway 0.0785 80 2906 36 -0.34 0.024 1000 -1000 -0.026 -1000
Aurora C signaling 0.0756 77 542 7 0 0.14 1000 -1000 -0.01 -1000
amb2 Integrin signaling 0.0736 75 6206 82 -0.34 0.12 1000 -1000 -0.024 -1000
Glypican 1 network 0.0726 74 3556 48 -0.2 0.045 1000 -1000 -0.022 -1000
Integrins in angiogenesis 0.0726 74 6274 84 -0.2 0.12 1000 -1000 -0.031 -1000
Effects of Botulinum toxin 0.0726 74 1939 26 -0.004 0.1 1000 -1000 -0.001 -1000
IL6-mediated signaling events 0.0707 72 5457 75 -0.18 0.056 1000 -1000 -0.037 -1000
Ephrin A reverse signaling 0.0697 71 500 7 -0.033 0.023 1000 -1000 -0.002 -1000
TCR signaling in naïve CD8+ T cells 0.0697 71 6688 93 -0.088 0.088 1000 -1000 -0.043 -1000
LPA receptor mediated events 0.0658 67 6935 102 -0.19 0.12 1000 -1000 -0.061 -1000
Signaling events mediated by the Hedgehog family 0.0648 66 3446 52 -0.12 0.03 1000 -1000 -0.032 -1000
E-cadherin signaling in keratinocytes 0.0638 65 2800 43 -0.19 0.031 1000 -1000 -0.028 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0589 60 2067 34 -0.024 0.06 1000 -1000 -0.021 -1000
ErbB4 signaling events 0.0559 57 3955 69 -0.28 0.06 1000 -1000 -0.04 -1000
Fc-epsilon receptor I signaling in mast cells 0.0550 56 5454 97 -0.15 0.034 1000 -1000 -0.046 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0550 56 2936 52 -0.11 0.07 1000 -1000 -0.03 -1000
Visual signal transduction: Cones 0.0540 55 2115 38 -0.027 0.16 1000 -1000 -0.007 -1000
PDGFR-alpha signaling pathway 0.0540 55 2455 44 -0.3 0.036 1000 -1000 -0.032 -1000
Syndecan-3-mediated signaling events 0.0540 55 1953 35 -0.23 0.054 1000 -1000 -0.014 -1000
IL12-mediated signaling events 0.0510 52 4544 87 -0.32 0.073 1000 -1000 -0.072 -1000
FAS signaling pathway (CD95) 0.0510 52 2458 47 -0.43 0.04 1000 -1000 -0.024 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0510 52 1739 33 -0.38 0.059 1000 -1000 -0.039 -1000
Nectin adhesion pathway 0.0500 51 3215 63 -0.056 0.045 1000 -1000 -0.038 -1000
Syndecan-2-mediated signaling events 0.0491 50 3496 69 -0.12 0.12 1000 -1000 -0.024 -1000
Presenilin action in Notch and Wnt signaling 0.0491 50 3061 61 -0.28 0.13 1000 -1000 -0.042 -1000
TCGA08_rtk_signaling 0.0471 48 1259 26 -0.19 0.036 1000 -1000 -0.014 -1000
Rapid glucocorticoid signaling 0.0461 47 957 20 -0.11 0.027 1000 -1000 -0.005 -1000
Ras signaling in the CD4+ TCR pathway 0.0461 47 813 17 -0.056 0.025 1000 -1000 -0.015 -1000
Aurora A signaling 0.0442 45 2759 60 -0.081 0.18 1000 -1000 -0.012 -1000
Canonical Wnt signaling pathway 0.0442 45 2340 51 -0.28 0.13 1000 -1000 -0.036 -1000
Glypican 2 network 0.0442 45 182 4 0.033 0.057 1000 -1000 0.017 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0442 45 3355 74 -0.19 0.05 1000 -1000 -0.062 -1000
LPA4-mediated signaling events 0.0412 42 504 12 -0.12 0.005 1000 -1000 -0.02 -1000
Signaling events mediated by HDAC Class III 0.0412 42 1705 40 -0.33 0.045 1000 -1000 -0.027 -1000
Insulin Pathway 0.0393 40 3017 74 -0.12 0.061 1000 -1000 -0.042 -1000
Regulation of Androgen receptor activity 0.0383 39 2775 70 -0.17 0.12 1000 -1000 -0.044 -1000
Coregulation of Androgen receptor activity 0.0373 38 2888 76 -0.17 0.065 1000 -1000 -0.016 -1000
Syndecan-4-mediated signaling events 0.0373 38 2559 67 -0.2 0.12 1000 -1000 -0.045 -1000
Thromboxane A2 receptor signaling 0.0363 37 3986 105 -0.19 0.036 1000 -1000 -0.034 -1000
BCR signaling pathway 0.0363 37 3753 99 -0.08 0.058 1000 -1000 -0.039 -1000
IL27-mediated signaling events 0.0353 36 1877 51 -0.19 0.075 1000 -1000 -0.039 -1000
TCGA08_retinoblastoma 0.0353 36 292 8 -0.017 0.06 1000 -1000 -0.003 -1000
Regulation of Telomerase 0.0353 36 3678 102 -0.21 0.15 1000 -1000 -0.023 -1000
Osteopontin-mediated events 0.0343 35 1339 38 -0.15 0.088 1000 -1000 -0.024 -1000
Regulation of p38-alpha and p38-beta 0.0343 35 1930 54 -0.25 0.053 1000 -1000 -0.044 -1000
Regulation of nuclear SMAD2/3 signaling 0.0324 33 4500 136 -0.2 0.08 1000 -1000 -0.029 -1000
IL2 signaling events mediated by STAT5 0.0304 31 683 22 0.005 0.11 1000 -1000 -0.022 -1000
TCGA08_p53 0.0265 27 191 7 -0.01 0.02 1000 -1000 -0.004 -1000
Signaling events mediated by PRL 0.0236 24 826 34 -0.12 0.035 1000 -1000 -0.039 -1000
Caspase cascade in apoptosis 0.0226 23 1705 74 -0.029 0.057 1000 -1000 -0.03 -1000
Class I PI3K signaling events mediated by Akt 0.0226 23 1576 68 -0.16 0.044 1000 -1000 -0.024 -1000
Ceramide signaling pathway 0.0226 23 1780 76 -0.1 0.064 1000 -1000 -0.026 -1000
Signaling mediated by p38-gamma and p38-delta 0.0226 23 358 15 -0.025 0.024 1000 -1000 -0.025 -1000
HIF-2-alpha transcription factor network 0.0216 22 954 43 -0.16 0.16 1000 -1000 -0.037 -1000
Arf6 trafficking events 0.0216 22 1581 71 -0.26 0.042 1000 -1000 -0.024 -1000
S1P4 pathway 0.0206 21 545 25 -0.011 0.044 1000 -1000 -0.019 -1000
mTOR signaling pathway 0.0196 20 1099 53 -0.025 0.027 1000 -1000 -0.025 -1000
IL2 signaling events mediated by PI3K 0.0196 20 1178 58 -0.001 0.065 1000 -1000 -0.032 -1000
Cellular roles of Anthrax toxin 0.0186 19 750 39 -0.079 0.028 1000 -1000 -0.019 -1000
Hedgehog signaling events mediated by Gli proteins 0.0186 19 1298 65 -0.088 0.056 1000 -1000 -0.03 -1000
S1P5 pathway 0.0186 19 337 17 -0.003 0.033 1000 -1000 -0.013 -1000
BARD1 signaling events 0.0177 18 1050 57 -0.047 0.11 1000 -1000 -0.032 -1000
JNK signaling in the CD4+ TCR pathway 0.0177 18 306 17 0.004 0.062 1000 -1000 -0.029 -1000
S1P3 pathway 0.0177 18 764 42 -0.011 0.042 1000 -1000 -0.026 -1000
E-cadherin signaling in the nascent adherens junction 0.0167 17 1320 76 -0.025 0.051 1000 -1000 -0.047 -1000
ceramide signaling pathway 0.0157 16 799 49 -0.003 0.036 1000 -1000 -0.03 -1000
FoxO family signaling 0.0157 16 1035 64 -0.016 0.24 1000 -1000 -0.028 -1000
Retinoic acid receptors-mediated signaling 0.0147 15 871 58 -0.05 0.052 1000 -1000 -0.032 -1000
TRAIL signaling pathway 0.0137 14 680 48 -0.017 0.043 1000 -1000 -0.025 -1000
PLK2 and PLK4 events 0.0128 13 39 3 0.015 0.032 1000 -1000 -0.009 -1000
PDGFR-beta signaling pathway 0.0128 13 1287 97 -0.027 0.057 1000 -1000 -0.043 -1000
E-cadherin signaling events 0.0128 13 66 5 0.008 0.031 1000 -1000 0.008 -1000
IL1-mediated signaling events 0.0118 12 795 62 -0.01 0.063 1000 -1000 -0.036 -1000
p38 MAPK signaling pathway 0.0118 12 546 44 -0.02 0.066 1000 -1000 -0.023 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0108 11 330 28 -0.003 0.051 1000 -1000 -0.012 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0108 11 515 45 0.004 0.055 1000 -1000 -0.033 -1000
Class I PI3K signaling events 0.0108 11 822 73 -0.019 0.051 1000 -1000 -0.028 -1000
EPO signaling pathway 0.0098 10 553 55 0.014 0.081 1000 -1000 -0.026 -1000
IFN-gamma pathway 0.0098 10 717 68 -0.009 0.077 1000 -1000 -0.045 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0098 10 384 37 -0.008 0.067 1000 -1000 -0.026 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0098 10 843 83 -0.019 0.047 1000 -1000 -0.019 -1000
Insulin-mediated glucose transport 0.0088 9 319 32 -0.12 0.039 1000 -1000 -0.016 -1000
Canonical NF-kappaB pathway 0.0079 8 348 39 0 0.052 1000 -1000 -0.024 -1000
Signaling events mediated by HDAC Class II 0.0079 8 642 75 -0.031 0.063 1000 -1000 -0.029 -1000
a4b1 and a4b7 Integrin signaling 0.0079 8 43 5 0.024 0.041 1000 -1000 0.011 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0069 7 997 125 -0.097 0.055 1000 -1000 -0.031 -1000
VEGFR1 specific signals 0.0069 7 427 56 -0.097 0.056 1000 -1000 -0.034 -1000
Signaling events mediated by HDAC Class I 0.0059 6 631 104 -0.059 0.058 1000 -1000 -0.029 -1000
Atypical NF-kappaB pathway 0.0049 5 160 31 0 0.03 1000 -1000 -0.012 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0039 4 107 23 -0.003 0.043 1000 -1000 -0.019 -1000
Circadian rhythm pathway 0.0039 4 97 22 -0.007 0.049 1000 -1000 -0.021 -1000
Paxillin-dependent events mediated by a4b1 0.0039 4 160 36 -0.048 0.052 1000 -1000 -0.023 -1000
Arf6 downstream pathway 0.0020 2 124 43 -0.054 0.055 1000 -1000 -0.027 -1000
Alternative NF-kappaB pathway 0.0020 2 30 13 0 0.068 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0010 1 28 27 -0.009 0.057 1000 -1000 -0.034 -1000
Arf1 pathway 0.0010 1 89 54 -0.001 0.045 1000 -1000 -0.014 -1000
Total NA 8068 478163 7203 -20 -990 131000 -131000 -3.8 -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 0.61 0.39 0.98 426 -1 3 429
PLK1 0.38 0.25 0.63 384 -0.88 1 385
BIRC5 0.39 0.26 0.68 279 -0.88 3 282
HSPA1B 0.61 0.39 0.99 412 -1 3 415
MAP2K1 0.17 0.12 0.3 397 -10000 0 397
BRCA2 0.62 0.41 1 406 -0.97 4 410
FOXM1 0.72 0.5 1.2 467 -1.2 3 470
XRCC1 0.61 0.4 1 392 -1 3 395
FOXM1B/p19 0.12 0.27 0.8 61 -1.2 3 64
Cyclin D1/CDK4 0.53 0.38 0.9 388 -0.98 3 391
CDC2 0.67 0.45 1.1 469 -1.1 3 472
TGFA 0.54 0.39 0.9 413 -0.98 7 420
SKP2 0.62 0.4 1 397 -1 3 400
CCNE1 0.091 0.096 0.3 159 -10000 0 159
CKS1B 0.66 0.43 1 443 -0.98 3 446
RB1 0.31 0.31 0.68 336 -0.61 7 343
FOXM1C/SP1 0.55 0.37 0.9 386 -1.1 5 391
AURKB 0.31 0.31 0.65 277 -0.85 16 293
CENPF 0.71 0.47 1.1 487 -0.98 3 490
CDK4 0.085 0.055 0.24 31 -10000 0 31
MYC 0.36 0.38 0.84 269 -0.96 6 275
CHEK2 0.17 0.12 0.31 323 -10000 0 323
ONECUT1 0.56 0.4 0.94 404 -1 3 407
CDKN2A -0.064 0.12 0.23 14 -0.24 195 209
LAMA4 0.61 0.41 1 401 -1.1 6 407
FOXM1B/HNF6 0.57 0.4 0.98 367 -1.3 3 370
FOS 0.3 0.65 1 313 -1 62 375
SP1 0.024 0.022 -10000 0 -0.2 7 7
CDC25B 0.62 0.4 1 411 -1 3 414
response to radiation 0.12 0.087 0.23 320 -10000 0 320
CENPB 0.62 0.4 1 401 -1 3 404
CENPA 0.67 0.44 1.1 455 -1 3 458
NEK2 0.74 0.46 1.1 517 -0.96 3 520
HIST1H2BA 0.61 0.39 0.99 399 -1 3 402
CCNA2 0.14 0.13 0.31 380 -10000 0 380
EP300 0.023 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.65 0.43 1.1 413 -1.2 3 416
CCNB2 0.68 0.44 1.1 465 -1 3 468
CCNB1 0.68 0.46 1.1 440 -1.1 3 443
ETV5 0.62 0.41 1 403 -1 3 406
ESR1 0.48 0.55 1 362 -1 16 378
CCND1 0.56 0.42 0.96 413 -1 3 416
GSK3A 0.14 0.092 0.26 282 -10000 0 282
Cyclin A-E1/CDK1-2 0.24 0.16 0.41 420 -10000 0 420
CDK2 0.059 0.029 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.15 0.11 0.26 430 -10000 0 430
FOXM1B/Cbp/p300 0.24 0.3 0.73 65 -1.1 3 68
GAS1 0.56 0.49 0.97 422 -1.1 34 456
MMP2 0.61 0.42 0.99 405 -1.2 10 415
RB1/FOXM1C 0.5 0.39 0.89 390 -1 3 393
CREBBP 0.023 0.006 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.16 0.2 0.33 2 -0.38 426 428
CRKL -0.17 0.21 -10000 0 -0.4 445 445
HRAS -0.12 0.18 -10000 0 -0.36 288 288
mol:PIP3 -0.14 0.2 -10000 0 -0.38 332 332
SPRED1 0.024 0.005 -10000 0 -10000 0 0
SPRED2 0.024 0.003 -10000 0 -10000 0 0
GAB1 -0.18 0.22 -10000 0 -0.42 453 453
FOXO3 -0.14 0.2 0.51 1 -0.36 405 406
AKT1 -0.16 0.21 0.35 1 -0.38 428 429
BAD -0.15 0.2 0.33 1 -0.36 394 395
megakaryocyte differentiation -0.18 0.22 -10000 0 -0.41 454 454
GSK3B -0.14 0.2 0.51 1 -0.36 416 417
RAF1 -0.097 0.16 0.25 3 -0.34 76 79
SHC1 0.02 0.009 -10000 0 -10000 0 0
STAT3 -0.18 0.22 -10000 0 -0.42 450 450
STAT1 -0.44 0.52 -10000 0 -1 460 460
HRAS/SPRED1 -0.094 0.16 -10000 0 -0.34 75 75
cell proliferation -0.18 0.22 -10000 0 -0.41 456 456
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
TEC 0.023 0.033 -10000 0 -0.58 3 3
RPS6KB1 -0.17 0.22 -10000 0 -0.4 460 460
HRAS/SPRED2 -0.093 0.16 -10000 0 -0.34 71 71
LYN/TEC/p62DOK -0.14 0.22 -10000 0 -0.4 376 376
MAPK3 -0.066 0.12 0.31 6 -0.28 32 38
STAP1 -0.18 0.22 -10000 0 -0.42 455 455
GRAP2 0.016 0.072 0.26 3 -0.58 14 17
JAK2 -0.37 0.45 -10000 0 -0.84 460 460
STAT1 (dimer) -0.43 0.51 -10000 0 -0.98 460 460
mol:Gleevec 0.007 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.14 0.22 -10000 0 -0.4 374 374
actin filament polymerization -0.18 0.22 0.33 1 -0.41 452 453
LYN 0.021 0.009 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 462 462
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
CBL/CRKL/GRB2 -0.14 0.2 -10000 0 -0.38 385 385
PI3K -0.15 0.22 -10000 0 -0.39 435 435
PTEN 0.023 0.027 -10000 0 -0.57 2 2
SCF/KIT/EPO/EPOR -0.51 0.63 -10000 0 -1.2 457 457
MAPK8 -0.18 0.22 -10000 0 -0.42 456 456
STAT3 (dimer) -0.18 0.22 -10000 0 -0.41 450 450
positive regulation of transcription -0.052 0.11 0.24 14 -0.23 24 38
mol:GDP -0.13 0.19 -10000 0 -0.37 291 291
PIK3C2B -0.16 0.2 -10000 0 -0.42 351 351
CBL/CRKL -0.16 0.2 -10000 0 -0.38 428 428
FER -0.18 0.22 -10000 0 -0.42 455 455
SH2B3 -0.18 0.22 -10000 0 -0.42 456 456
PDPK1 -0.12 0.19 0.34 8 -0.35 304 312
SNAI2 -0.17 0.21 0.28 4 -0.42 406 410
positive regulation of cell proliferation -0.32 0.39 -10000 0 -0.73 460 460
KITLG -0.004 0.06 0.26 10 -0.6 5 15
cell motility -0.32 0.39 -10000 0 -0.73 460 460
PTPN6 0.033 0.018 0.27 2 -10000 0 2
EPOR -0.11 0.19 -10000 0 -1 13 13
STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 462 462
SOCS1 0.025 0.033 0.26 12 -0.58 1 13
cell migration 0.18 0.22 0.42 458 -10000 0 458
SOS1 0.024 0.003 -10000 0 -10000 0 0
EPO 0.043 0.094 0.25 161 -10000 0 161
VAV1 0.023 0.035 0.26 2 -0.58 3 5
GRB10 -0.18 0.22 -10000 0 -0.42 451 451
PTPN11 0.031 0.009 -10000 0 -10000 0 0
SCF/KIT -0.19 0.23 -10000 0 -0.44 459 459
GO:0007205 0.009 0.012 -10000 0 -10000 0 0
MAP2K1 -0.075 0.13 0.29 8 -0.28 48 56
CBL 0.022 0.008 -10000 0 -10000 0 0
KIT -0.57 0.66 -10000 0 -1.3 458 458
MAP2K2 -0.075 0.13 0.32 7 -0.28 46 53
SHC/Grb2/SOS1 -0.14 0.21 -10000 0 -0.4 327 327
STAT5A -0.27 0.33 -10000 0 -0.62 462 462
GRB2 0.023 0.01 0.26 1 -10000 0 1
response to radiation -0.17 0.21 0.28 4 -0.41 407 411
SHC/GRAP2 0.023 0.052 -10000 0 -0.33 17 17
PTPRO -0.18 0.22 -10000 0 -0.42 454 454
SH2B2 -0.18 0.22 -10000 0 -0.42 452 452
DOK1 0.025 0.015 0.26 4 -10000 0 4
MATK -0.19 0.22 -10000 0 -0.42 458 458
CREBBP -0.028 0.072 -10000 0 -0.18 19 19
BCL2 -0.16 0.32 -10000 0 -1.3 56 56
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.32 0.51 0.43 4 -1 334 338
MKNK1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.089 0.18 -10000 0 -0.34 325 325
ATF2/c-Jun -0.084 0.16 -10000 0 -0.4 118 118
MAPK11 -0.083 0.18 -10000 0 -0.35 302 302
MITF -0.12 0.22 -10000 0 -0.41 329 329
MAPKAPK5 -0.12 0.21 -10000 0 -0.4 333 333
KRT8 -0.11 0.21 -10000 0 -0.4 313 313
MAPKAPK3 0.024 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.02 0.01 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.14 0.29 -10000 0 -0.53 332 332
CEBPB -0.11 0.2 0.29 1 -0.4 307 308
SLC9A1 -0.12 0.22 -10000 0 -0.41 326 326
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.11 0.21 -10000 0 -0.4 323 323
p38alpha-beta/MNK1 -0.11 0.25 -10000 0 -0.46 302 302
JUN -0.084 0.16 -10000 0 -0.4 118 118
PPARGC1A -0.21 0.33 0.27 1 -0.56 395 396
USF1 -0.1 0.19 0.32 3 -0.38 311 314
RAB5/GDP/GDI1 -0.082 0.16 -10000 0 -0.3 320 320
NOS2 -0.11 0.22 -10000 0 -0.56 89 89
DDIT3 -0.11 0.21 -10000 0 -0.4 329 329
RAB5A 0.024 0.003 -10000 0 -10000 0 0
HSPB1 -0.095 0.17 0.28 4 -0.34 308 312
p38alpha-beta/HBP1 -0.11 0.25 -10000 0 -0.45 304 304
CREB1 -0.12 0.22 -10000 0 -0.43 329 329
RAB5/GDP 0.018 0.002 -10000 0 -10000 0 0
EIF4E -0.12 0.21 -10000 0 -0.41 294 294
RPS6KA4 -0.11 0.21 -10000 0 -0.41 328 328
PLA2G4A -0.13 0.22 -10000 0 -0.43 329 329
GDI1 -0.11 0.21 0.29 1 -0.4 331 332
TP53 -0.15 0.27 0.28 1 -0.53 313 314
RPS6KA5 -0.12 0.22 -10000 0 -0.41 336 336
ESR1 -0.15 0.24 0.29 1 -0.43 368 369
HBP1 0.024 0.004 -10000 0 -10000 0 0
MEF2C -0.11 0.21 -10000 0 -0.4 332 332
MEF2A -0.12 0.21 0.29 1 -0.41 327 328
EIF4EBP1 -0.12 0.22 0.28 1 -0.44 317 318
KRT19 -0.11 0.21 0.32 1 -0.41 308 309
ELK4 -0.1 0.19 0.31 3 -0.38 314 317
ATF6 -0.1 0.19 0.32 3 -0.38 314 317
ATF1 -0.12 0.22 -10000 0 -0.43 334 334
p38alpha-beta/MAPKAPK2 -0.097 0.22 -10000 0 -0.41 290 290
p38alpha-beta/MAPKAPK3 -0.11 0.25 -10000 0 -0.45 304 304
Class IB PI3K non-lipid kinase events

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.13 0.26 0.57 253 -10000 0 253
PI3K Class IB/PDE3B -0.13 0.26 -10000 0 -0.57 253 253
PDE3B -0.13 0.26 -10000 0 -0.58 253 253
Reelin signaling pathway

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
CDK5R1/CDK5 0.038 0.028 -10000 0 -10000 0 0
VLDLR 0.008 0.094 -10000 0 -0.58 25 25
CRKL 0.023 0.006 -10000 0 -10000 0 0
LRPAP1 0.024 0.005 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.58 2 2
ITGA3 0.022 0.022 0.26 1 -0.58 1 2
RELN/VLDLR/Fyn -0.2 0.21 -10000 0 -0.38 569 569
MAPK8IP1/MKK7/MAP3K11/JNK1 0.055 0.044 -10000 0 -0.32 6 6
AKT1 -0.15 0.14 -10000 0 -0.27 547 547
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
DAB1 0.036 0.056 0.26 58 -10000 0 58
RELN/LRP8/DAB1 -0.16 0.19 0.35 5 -0.32 571 576
LRPAP1/LRP8 0.049 0.048 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.15 0.19 0.32 4 -0.31 558 562
DAB1/alpha3/beta1 Integrin -0.14 0.18 -10000 0 -0.3 495 495
long-term memory -0.18 0.22 0.34 5 -0.36 555 560
DAB1/LIS1 -0.15 0.19 0.3 4 -0.31 570 574
DAB1/CRLK/C3G -0.15 0.18 -10000 0 -0.3 552 552
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
DAB1/NCK2 -0.15 0.19 0.3 4 -0.31 567 571
ARHGEF2 0.021 0.009 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.035 0.18 0.26 12 -0.58 101 113
CDK5R1 0.028 0.035 0.26 22 -10000 0 22
RELN -0.32 0.3 0.26 3 -0.58 581 584
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
RELN/LRP8/Fyn -0.18 0.2 -10000 0 -0.36 561 561
GRIN2A/RELN/LRP8/DAB1/Fyn -0.17 0.22 0.34 4 -0.35 529 533
MAPK8 0.021 0.046 -10000 0 -0.58 6 6
RELN/VLDLR/DAB1 -0.18 0.2 0.32 2 -0.34 572 574
ITGB1 0.024 0.004 -10000 0 -10000 0 0
MAP1B -0.18 0.18 0.22 2 -0.33 572 574
RELN/LRP8 -0.19 0.2 -10000 0 -0.36 574 574
GRIN2B/RELN/LRP8/DAB1/Fyn -0.17 0.2 0.36 3 -0.33 581 584
PI3K 0.03 0.043 -10000 0 -0.38 10 10
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.032 0.022 -10000 0 -0.43 1 1
RAP1A -0.16 0.15 0.33 3 -0.3 395 398
PAFAH1B1 0.023 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.031 0.26 4 -0.58 2 6
CRLK/C3G 0.034 0.009 -10000 0 -10000 0 0
GRIN2B -0.02 0.15 0.26 1 -0.58 67 68
NCK2 0.024 0.003 -10000 0 -10000 0 0
neuron differentiation -0.086 0.12 -10000 0 -0.34 66 66
neuron adhesion -0.15 0.15 0.32 4 -0.49 21 25
LRP8 0.047 0.07 0.26 97 -10000 0 97
GSK3B -0.14 0.14 -10000 0 -0.26 512 512
RELN/VLDLR/DAB1/Fyn -0.16 0.19 0.32 2 -0.32 561 563
MAP3K11 0.024 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.16 0.16 0.18 1 -0.28 558 559
CDK5 0.025 0.016 0.26 4 -10000 0 4
MAPT -0.024 0.19 0.88 14 -0.52 95 109
neuron migration -0.19 0.18 0.3 2 -0.34 508 510
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.087 0.12 -10000 0 -0.35 66 66
RELN/VLDLR -0.17 0.2 -10000 0 -0.34 574 574
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.025 0.02 0.26 7 -10000 0 7
EGFR -0.19 0.29 -10000 0 -0.58 362 362
EGF/EGFR -0.17 0.23 -10000 0 -0.38 492 492
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.12 0.2 -10000 0 -0.36 374 374
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.023 0.019 -10000 0 -0.58 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.093 0.24 0.26 2 -0.58 195 197
EGF/EGFR dimer/SHC -0.16 0.22 -10000 0 -0.41 400 400
mol:GDP -0.12 0.2 -10000 0 -0.36 374 374
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.019 0.15 0.26 1 -0.58 71 72
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.18 -10000 0 -0.34 373 373
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP -0.12 0.19 -10000 0 -0.34 373 373
FRAP1 -0.15 0.16 0.16 3 -0.34 374 377
EGF/EGFR dimer -0.22 0.26 -10000 0 -0.46 507 507
SOS1 0.024 0.003 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
ETA receptor/Endothelin-1 0.001 0.12 0.2 1 -0.42 75 76
Aurora B signaling

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
Condensin I complex 0.11 0.1 0.24 297 -0.26 2 299
STMN1 0.081 0.082 0.27 67 -10000 0 67
Aurora B/RasGAP/Survivin 0.2 0.14 0.33 476 -10000 0 476
Chromosomal passenger complex/Cul3 protein complex 0.006 0.14 0.2 179 -0.25 125 304
BIRC5 0.18 0.12 0.27 665 -10000 0 665
DES -0.15 0.32 -10000 0 -0.59 241 241
Aurora C/Aurora B/INCENP 0.11 0.08 0.33 6 -0.3 1 7
Aurora B/TACC1 0.072 0.1 0.19 1 -0.34 26 27
Aurora B/PP2A 0.11 0.084 0.21 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.033 0.028 0.14 12 -10000 0 12
mitotic metaphase/anaphase transition -0.006 0.006 -10000 0 -10000 0 0
NDC80 0.15 0.12 0.27 457 -10000 0 457
Cul3 protein complex -0.12 0.2 -10000 0 -0.37 391 391
KIF2C 0.15 0.11 0.24 577 -10000 0 577
PEBP1 0.028 0.004 -10000 0 -10000 0 0
KIF20A 0.2 0.1 0.26 738 -10000 0 738
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.11 0.084 -10000 0 -10000 0 0
SEPT1 0.03 0.041 0.26 30 -10000 0 30
SMC2 0.024 0.003 -10000 0 -10000 0 0
SMC4 0.026 0.023 0.26 9 -10000 0 9
NSUN2/NPM1/Nucleolin 0.074 0.19 0.33 24 -0.46 87 111
PSMA3 0.024 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.006 -10000 0 -10000 0 0
H3F3B 0.072 0.063 0.24 36 -10000 0 36
AURKB 0.14 0.12 0.26 521 -10000 0 521
AURKC 0.026 0.031 0.26 10 -0.58 1 11
CDCA8 0.11 0.11 0.27 327 -10000 0 327
cytokinesis 0.15 0.15 0.31 380 -0.34 6 386
Aurora B/Septin1 0.18 0.17 0.36 401 -0.32 5 406
AURKA 0.12 0.12 0.26 401 -10000 0 401
INCENP 0.031 0.008 -10000 0 -10000 0 0
KLHL13 -0.22 0.29 -10000 0 -0.58 400 400
BUB1 0.18 0.11 0.26 680 -10000 0 680
hSgo1/Aurora B/Survivin 0.27 0.19 0.42 593 -10000 0 593
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.19 0.14 0.36 322 -10000 0 322
SGOL1 0.17 0.12 0.26 627 -10000 0 627
CENPA 0.17 0.14 0.31 478 -0.27 1 479
NCAPG 0.14 0.12 0.26 481 -10000 0 481
Aurora B/HC8 Proteasome 0.11 0.084 -10000 0 -10000 0 0
NCAPD2 0.024 0.009 0.26 1 -10000 0 1
Aurora B/PP1-gamma 0.12 0.083 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
NCAPH 0.12 0.12 0.26 388 -10000 0 388
NPM1 0.068 0.13 0.26 4 -0.37 35 39
RASA1 0.024 0.004 -10000 0 -10000 0 0
KLHL9 0.023 0.006 -10000 0 -10000 0 0
mitotic prometaphase 0.003 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.11 0.083 -10000 0 -10000 0 0
PPP1CC 0.024 0.002 -10000 0 -10000 0 0
Centraspindlin 0.21 0.16 0.36 420 -10000 0 420
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
NSUN2 0.074 0.12 0.27 20 -0.43 7 27
MYLK 0.023 0.14 0.24 7 -0.32 115 122
KIF23 0.1 0.11 0.27 298 -10000 0 298
VIM 0.081 0.087 0.38 31 -0.41 2 33
RACGAP1 0.041 0.049 0.28 41 -10000 0 41
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.063 0.14 -10000 0 -0.6 20 20
Chromosomal passenger complex 0.18 0.13 0.29 521 -10000 0 521
Chromosomal passenger complex/EVI5 0.24 0.17 0.4 474 -10000 0 474
TACC1 0.004 0.095 -10000 0 -0.58 26 26
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
CUL3 0.024 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.24 0.27 -10000 0 -0.69 155 155
PCK1 -0.93 0.63 -10000 0 -1.4 634 634
HNF4A -0.23 0.27 -10000 0 -0.84 50 50
KCNJ11 -0.28 0.29 -10000 0 -0.76 159 159
AKT1 -0.17 0.16 -10000 0 -0.4 103 103
response to starvation 0.005 0.011 -10000 0 -10000 0 0
DLK1 -0.45 0.48 -10000 0 -1.1 334 334
NKX2-1 -0.035 0.16 0.53 2 -0.54 1 3
ACADM -0.25 0.27 -10000 0 -0.72 131 131
TAT -1.1 0.63 -10000 0 -1.4 719 719
CEBPB 0.024 0.008 -10000 0 -10000 0 0
CEBPA 0.02 0.057 -10000 0 -0.57 9 9
TTR -0.41 0.29 -10000 0 -0.71 348 348
PKLR -0.22 0.27 0.55 4 -0.7 121 125
APOA1 -0.28 0.31 -10000 0 -0.89 76 76
CPT1C -0.24 0.27 0.59 1 -0.72 128 129
ALAS1 -0.15 0.16 -10000 0 -0.65 11 11
TFRC -0.42 0.26 -10000 0 -0.67 391 391
FOXF1 0.017 0.047 0.26 6 -0.58 4 10
NF1 0.027 0.006 -10000 0 -10000 0 0
HNF1A (dimer) 0.034 0.03 0.26 7 -10000 0 7
CPT1A -0.23 0.27 -10000 0 -0.73 114 114
HMGCS1 -0.25 0.26 -10000 0 -0.7 140 140
NR3C1 -0.12 0.12 -10000 0 -0.25 292 292
CPT1B -0.24 0.27 -10000 0 -0.72 131 131
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.023 -10000 0 -10000 0 0
GCK -0.27 0.32 -10000 0 -0.83 163 163
CREB1 -0.076 0.093 -10000 0 -0.24 85 85
IGFBP1 -0.42 0.54 -10000 0 -1.4 228 228
PDX1 -0.12 0.15 0.5 1 -0.54 6 7
UCP2 -0.24 0.27 0.54 1 -0.7 137 138
ALDOB -0.28 0.28 -10000 0 -0.72 180 180
AFP -0.57 0.51 0.34 2 -0.85 646 648
BDH1 -0.24 0.26 -10000 0 -0.73 115 115
HADH -0.28 0.28 -10000 0 -0.74 156 156
F2 -0.28 0.3 -10000 0 -0.94 49 49
HNF1A 0.034 0.03 0.26 7 -10000 0 7
G6PC -0.18 0.12 -10000 0 -0.53 12 12
SLC2A2 -0.16 0.17 -10000 0 -0.95 1 1
INS 0.019 0.078 0.24 5 -10000 0 5
FOXA1 -0.22 0.23 0.28 18 -0.36 617 635
FOXA3 -0.36 0.21 0.29 13 -0.46 752 765
FOXA2 -0.32 0.33 -10000 0 -0.8 196 196
ABCC8 -0.32 0.39 -10000 0 -0.98 178 178
ALB -0.78 0.54 0.34 2 -1.1 681 683
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.067 0.049 0.1 6 -0.1 542 548
BUB1B 0.084 0.068 0.15 396 -10000 0 396
PLK1 0.051 0.039 0.11 143 -10000 0 143
PLK1S1 0.026 0.036 0.14 11 -0.16 19 30
KIF2A 0.042 0.039 0.29 5 -10000 0 5
regulation of mitotic centrosome separation 0.051 0.039 0.11 143 -10000 0 143
GOLGA2 0.024 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.24 0.15 0.32 701 -10000 0 701
WEE1 0.044 0.062 0.23 2 -0.27 24 26
cytokinesis 0.12 0.089 0.21 285 -0.32 3 288
PP2A-alpha B56 0.12 0.12 -10000 0 -0.43 31 31
AURKA 0.066 0.053 0.12 422 -0.14 4 426
PICH/PLK1 0.1 0.09 0.22 302 -10000 0 302
CENPE 0.063 0.056 0.14 279 -10000 0 279
RhoA/GTP 0.018 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.043 0.039 0.29 5 -10000 0 5
PPP2CA 0.024 0.004 -10000 0 -10000 0 0
FZR1 0.024 0.004 -10000 0 -10000 0 0
TPX2 0.082 0.055 0.13 539 -0.13 2 541
PAK1 0.022 0.02 0.26 6 -10000 0 6
SPC24 0.17 0.12 0.26 610 -10000 0 610
FBXW11 0.024 0.004 -10000 0 -10000 0 0
CLSPN 0.073 0.071 0.14 412 -0.19 22 434
GORASP1 0.024 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.015 51 -10000 0 51
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.023 0.019 0.055 136 -10000 0 136
G2 phase of mitotic cell cycle 0.001 0.003 0.014 15 -10000 0 15
STAG2 0.024 0.019 -10000 0 -0.58 1 1
GRASP65/GM130/RAB1/GTP 0.01 0.082 -10000 0 -0.5 25 25
spindle elongation 0.051 0.039 0.11 143 -10000 0 143
ODF2 0.026 0.004 -10000 0 -10000 0 0
BUB1 0.11 0.13 -10000 0 -0.47 32 32
TPT1 0.013 0.057 0.13 2 -0.17 77 79
CDC25C 0.12 0.07 0.16 583 -0.19 18 601
CDC25B 0.03 0.032 0.27 17 -10000 0 17
SGOL1 0.067 0.049 0.1 542 -0.1 6 548
RHOA 0.024 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.068 0.065 0.22 50 -10000 0 50
CDC14B -0.01 0.075 -10000 0 -0.43 31 31
CDC20 0.15 0.12 0.26 525 -10000 0 525
PLK1/PBIP1 0.039 0.048 0.14 137 -10000 0 137
mitosis -0.005 0.006 0.027 4 -10000 0 4
FBXO5 0.031 0.037 0.16 20 -10000 0 20
CDC2 0.003 0.004 0.011 186 -10000 0 186
NDC80 0.16 0.12 0.26 589 -10000 0 589
metaphase plate congression 0.029 0.055 0.17 2 -0.19 48 50
ERCC6L 0.091 0.086 0.24 163 -10000 0 163
NLP/gamma Tubulin 0.024 0.025 0.077 33 -0.083 11 44
microtubule cytoskeleton organization 0.013 0.057 0.13 2 -0.16 77 79
G2/M transition DNA damage checkpoint -0.001 0.003 0.012 15 -10000 0 15
PPP1R12A 0.025 0.004 -10000 0 -10000 0 0
interphase -0.001 0.003 0.012 15 -10000 0 15
PLK1/PRC1-2 0.21 0.13 0.27 709 -10000 0 709
GRASP65/GM130/RAB1/GTP/PLK1 0.07 0.031 -10000 0 -10000 0 0
RAB1A 0.024 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.043 0.036 0.1 151 -10000 0 151
mitotic prometaphase 0.002 0.005 0.022 50 -10000 0 50
proteasomal ubiquitin-dependent protein catabolic process 0.053 0.052 -10000 0 -0.31 3 3
microtubule-based process 0.17 0.091 0.22 737 -10000 0 737
Golgi organization 0.051 0.039 0.11 143 -10000 0 143
Cohesin/SA2 0.055 0.032 0.14 6 -0.31 1 7
PPP1CB/MYPT1 0.037 0.007 -10000 0 -10000 0 0
KIF20A 0.2 0.1 0.26 738 -10000 0 738
APC/C/CDC20 0.14 0.1 0.23 524 -10000 0 524
PPP2R1A 0.024 0.004 -10000 0 -10000 0 0
chromosome segregation 0.032 0.048 0.14 137 -10000 0 137
PRC1 0.081 0.1 0.26 243 -10000 0 243
ECT2 0.05 0.056 0.26 39 -10000 0 39
C13orf34 0.041 0.033 0.094 149 -10000 0 149
NUDC 0.029 0.056 0.17 2 -0.19 48 50
regulation of attachment of spindle microtubules to kinetochore 0.084 0.068 0.15 396 -10000 0 396
spindle assembly 0.037 0.03 0.091 97 -10000 0 97
spindle stabilization 0.026 0.036 0.14 11 -0.16 19 30
APC/C/HCDH1 0.009 0.068 -10000 0 -0.37 31 31
MKLP2/PLK1 0.17 0.091 0.22 737 -10000 0 737
CCNB1 0.07 0.094 0.26 191 -10000 0 191
PPP1CB 0.025 0.003 -10000 0 -10000 0 0
BTRC 0.024 0.003 -10000 0 -10000 0 0
ROCK2 0.028 0.086 0.24 1 -0.37 36 37
TUBG1 0.024 0.04 0.13 4 -0.16 35 39
G2/M transition of mitotic cell cycle 0.042 0.044 0.19 14 -10000 0 14
MLF1IP 0.025 0.048 0.14 147 -10000 0 147
INCENP 0.024 0.005 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.1 0.13 0.31 261 -0.24 1 262
NFATC2 -0.032 0.23 0.5 8 -0.61 88 96
NFATC3 -0.051 0.13 -10000 0 -0.28 221 221
CD40LG -0.32 0.52 0.75 5 -0.98 324 329
ITCH -0.004 0.085 -10000 0 -0.26 97 97
CBLB -0.004 0.086 -10000 0 -0.26 98 98
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.1 0.39 0.62 46 -1 82 128
JUNB 0.025 0.011 0.26 2 -10000 0 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.1 -10000 0 -0.31 104 104
T cell anergy -0.03 0.14 -10000 0 -0.42 101 101
TLE4 -0.03 0.19 0.36 1 -0.6 62 63
Jun/NFAT1-c-4/p21SNFT -0.21 0.46 0.69 6 -0.87 269 275
AP-1/NFAT1-c-4 -0.35 0.64 0.78 13 -1.2 318 331
IKZF1 -0.02 0.16 0.49 7 -0.54 41 48
T-helper 2 cell differentiation -0.092 0.27 0.47 2 -0.8 85 87
AP-1/NFAT1 -0.1 0.27 0.46 12 -0.47 269 281
CALM1 0.009 0.065 -10000 0 -0.19 1 1
EGR2 -0.3 0.6 0.64 4 -1.2 250 254
EGR3 -0.39 0.66 0.63 4 -1.3 326 330
NFAT1/FOXP3 0.046 0.23 0.48 92 -0.5 58 150
EGR1 -0.16 0.28 -10000 0 -0.57 313 313
JUN 0.014 0.062 0.2 2 -0.58 8 10
EGR4 0.04 0.061 0.26 68 -10000 0 68
mol:Ca2+ -0.012 0.056 -10000 0 -0.18 104 104
GBP3 -0.026 0.17 0.38 2 -0.54 62 64
FOSL1 0.028 0.044 0.26 22 -0.58 2 24
NFAT1-c-4/MAF/IRF4 -0.23 0.48 0.62 7 -0.88 301 308
DGKA -0.022 0.16 0.57 1 -0.51 50 51
CREM 0.023 0.008 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.3 0.51 0.64 3 -0.95 322 325
CTLA4 0.035 0.21 0.44 108 -0.56 35 143
NFAT1-c-4 (dimer)/EGR1 -0.32 0.54 0.65 3 -1 331 334
NFAT1-c-4 (dimer)/EGR4 -0.22 0.47 0.62 5 -0.86 309 314
FOS -0.15 0.27 -10000 0 -0.58 289 289
IFNG -0.061 0.28 0.56 7 -0.77 75 82
T cell activation -0.17 0.3 0.64 4 -0.68 179 183
MAF 0.021 0.008 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.18 0.36 0.66 317 -0.6 3 320
TNF -0.29 0.47 0.54 4 -0.91 321 325
FASLG -0.38 0.67 0.74 4 -1.3 327 331
TBX21 0.02 0.12 0.36 14 -0.57 36 50
BATF3 0.021 0.014 0.26 2 -10000 0 2
PRKCQ 0.004 0.12 0.29 8 -0.57 40 48
PTPN1 -0.021 0.16 0.4 5 -0.46 69 74
NFAT1-c-4/ICER1 -0.23 0.46 0.58 3 -0.86 307 310
GATA3 0.011 0.11 0.26 25 -0.58 31 56
T-helper 1 cell differentiation -0.06 0.27 0.56 7 -0.75 75 82
IL2RA -0.1 0.37 0.62 41 -0.89 96 137
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.021 0.16 0.36 1 -0.49 56 57
E2F1 0.097 0.11 0.26 294 -10000 0 294
PPARG -0.11 0.25 -10000 0 -0.58 224 224
SLC3A2 -0.022 0.16 0.36 1 -0.51 49 50
IRF4 -0.021 0.16 0.26 11 -0.58 79 90
PTGS2 -0.37 0.55 0.64 5 -1 346 351
CSF2 -0.31 0.5 0.71 7 -0.96 319 326
JunB/Fra1/NFAT1-c-4 -0.21 0.45 0.59 4 -0.83 304 308
IL4 -0.097 0.28 0.48 2 -0.85 84 86
IL5 -0.32 0.5 0.64 5 -0.96 318 323
IL2 -0.17 0.31 0.64 4 -0.69 174 178
IL3 -0.054 0.13 -10000 0 -0.82 18 18
RNF128 -0.046 0.21 0.28 4 -0.66 104 108
NFATC1 -0.19 0.36 0.6 3 -0.66 317 320
CDK4 0.14 0.25 0.58 133 -0.6 2 135
PTPRK -0.024 0.17 0.43 3 -0.54 60 63
IL8 -0.31 0.51 0.6 9 -0.97 318 327
POU2F1 0.021 0.012 0.26 1 -10000 0 1
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.24 0.37 0.67 1 -0.78 209 210
HDAC7 0.025 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.19 0.33 0.65 2 -0.74 149 151
SMAD4 0.024 0.005 -10000 0 -10000 0 0
ID2 -0.24 0.37 -10000 0 -0.78 207 207
AP1 -0.1 0.21 -10000 0 -0.43 298 298
ABCG2 -0.26 0.39 -10000 0 -0.79 242 242
HIF1A -0.047 0.084 -10000 0 -0.26 9 9
TFF3 -0.25 0.41 0.68 5 -0.79 254 259
GATA2 0.008 0.098 0.26 12 -0.57 25 37
AKT1 -0.055 0.094 -10000 0 -0.23 65 65
response to hypoxia -0.062 0.084 -10000 0 -0.21 112 112
MCL1 -0.24 0.35 -10000 0 -0.78 201 201
NDRG1 -0.22 0.36 -10000 0 -0.78 184 184
SERPINE1 -0.24 0.38 0.67 5 -0.78 211 216
FECH -0.24 0.37 -10000 0 -0.78 211 211
FURIN -0.24 0.37 -10000 0 -0.77 214 214
NCOA2 0.001 0.12 -10000 0 -0.57 40 40
EP300 -0.06 0.13 0.32 1 -0.33 112 113
HMOX1 -0.24 0.37 -10000 0 -0.78 216 216
BHLHE40 -0.24 0.37 -10000 0 -0.78 209 209
BHLHE41 -0.24 0.38 -10000 0 -0.79 213 213
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.02 0.11 -10000 0 -0.31 1 1
ENG -0.015 0.11 0.38 3 -10000 0 3
JUN 0.017 0.055 -10000 0 -0.58 8 8
RORA -0.24 0.37 -10000 0 -0.78 216 216
ABCB1 -0.26 0.45 -10000 0 -1.1 203 203
TFRC -0.24 0.37 -10000 0 -0.78 214 214
CXCR4 -0.24 0.37 -10000 0 -0.78 212 212
TF -0.4 0.45 -10000 0 -0.86 397 397
CITED2 -0.24 0.37 -10000 0 -0.78 212 212
HIF1A/ARNT -0.27 0.42 0.77 2 -0.88 203 205
LDHA -0.039 0.12 -10000 0 -0.74 23 23
ETS1 -0.24 0.37 -10000 0 -0.78 216 216
PGK1 -0.24 0.37 -10000 0 -0.78 211 211
NOS2 -0.24 0.37 -10000 0 -0.78 207 207
ITGB2 -0.24 0.37 0.67 1 -0.78 211 212
ALDOA -0.24 0.37 -10000 0 -0.78 204 204
Cbp/p300/CITED2 -0.25 0.39 -10000 0 -0.86 184 184
FOS -0.15 0.27 -10000 0 -0.58 285 285
HK2 -0.24 0.37 -10000 0 -0.78 216 216
SP1 0.002 0.058 -10000 0 -0.17 19 19
GCK -0.12 0.34 0.53 1 -1.3 59 60
HK1 -0.24 0.37 -10000 0 -0.78 212 212
NPM1 -0.24 0.37 -10000 0 -0.78 214 214
EGLN1 -0.23 0.36 -10000 0 -0.77 203 203
CREB1 0.028 0.004 -10000 0 -10000 0 0
PGM1 -0.24 0.37 -10000 0 -0.78 212 212
SMAD3 0.025 0.004 -10000 0 -10000 0 0
EDN1 -0.18 0.37 -10000 0 -0.96 144 144
IGFBP1 -0.3 0.42 -10000 0 -0.86 275 275
VEGFA -0.16 0.29 -10000 0 -0.64 142 142
HIF1A/JAB1 -0.008 0.068 -10000 0 -0.27 1 1
CP -0.3 0.45 0.66 2 -0.88 284 286
CXCL12 -0.26 0.4 -10000 0 -0.81 235 235
COPS5 0.024 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.012 -10000 0 -10000 0 0
BNIP3 -0.24 0.37 0.75 1 -0.78 212 213
EGLN3 -0.23 0.38 0.75 1 -0.78 212 213
CA9 -0.2 0.4 0.68 6 -0.77 210 216
TERT -0.23 0.37 0.68 4 -0.78 204 208
ENO1 -0.24 0.37 -10000 0 -0.78 214 214
PFKL -0.24 0.37 -10000 0 -0.78 212 212
NCOA1 0.025 0.019 -10000 0 -0.58 1 1
ADM -0.26 0.4 0.67 1 -0.82 233 234
ARNT -0.034 0.071 -10000 0 -10000 0 0
HNF4A 0.018 0.039 0.26 13 -10000 0 13
ADFP -0.26 0.36 -10000 0 -0.77 221 221
SLC2A1 -0.16 0.29 0.64 2 -0.67 121 123
LEP -0.48 0.41 -10000 0 -0.84 442 442
HIF1A/ARNT/Cbp/p300 -0.2 0.34 0.64 1 -0.76 152 153
EPO -0.1 0.27 0.66 3 -0.73 48 51
CREBBP -0.05 0.12 0.29 2 -0.32 85 87
HIF1A/ARNT/Cbp/p300/HDAC7 -0.19 0.33 0.7 1 -0.75 141 142
PFKFB3 -0.24 0.37 -10000 0 -0.79 203 203
NT5E -0.24 0.38 -10000 0 -0.79 212 212
Glucocorticoid receptor regulatory network

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
PCK2 0.091 0.1 0.41 6 -10000 0 6
SMARCC2 0.024 0.013 -10000 0 -0.17 3 3
SMARCC1 0.024 0.012 -10000 0 -10000 0 0
TBX21 -0.12 0.21 0.37 8 -0.57 103 111
SUMO2 0.001 0.023 -10000 0 -10000 0 0
STAT1 (dimer) 0.033 0.033 0.27 18 -10000 0 18
FKBP4 0.025 0.018 0.26 5 -10000 0 5
FKBP5 0.018 0.068 0.26 5 -0.58 12 17
GR alpha/HSP90/FKBP51/HSP90 0.12 0.13 0.31 131 -0.3 8 139
PRL -0.061 0.12 0.49 4 -0.44 6 10
cortisol/GR alpha (dimer)/TIF2 0.18 0.28 0.51 343 -0.48 16 359
RELA -0.038 0.1 0.25 3 -0.23 71 74
FGG 0.21 0.24 0.47 359 -0.48 2 361
GR beta/TIF2 0.08 0.16 0.29 199 -0.4 38 237
IFNG -0.3 0.36 0.47 4 -0.7 366 370
apoptosis -0.27 0.31 0.85 1 -0.64 303 304
CREB1 0.062 0.054 -10000 0 -10000 0 0
histone acetylation 0.028 0.13 0.37 53 -0.37 23 76
BGLAP -0.08 0.14 0.37 3 -0.44 35 38
GR/PKAc 0.13 0.13 0.33 118 -0.34 3 121
NF kappa B1 p50/RelA -0.063 0.18 0.46 3 -0.35 160 163
SMARCD1 0.025 0.012 -10000 0 -10000 0 0
MDM2 0.098 0.11 0.22 328 -10000 0 328
GATA3 0.014 0.11 0.26 25 -0.57 31 56
AKT1 0.02 0.009 -10000 0 -10000 0 0
CSF2 -0.024 0.1 0.48 1 -0.54 5 6
GSK3B 0 0.024 -10000 0 -10000 0 0
NR1I3 -0.2 0.26 0.8 1 -0.59 174 175
CSN2 0.16 0.19 0.36 378 -0.41 3 381
BRG1/BAF155/BAF170/BAF60A 0.061 0.042 -10000 0 -0.48 5 5
NFATC1 0.023 0.027 -10000 0 -0.58 2 2
POU2F1 0.023 0.016 0.26 1 -10000 0 1
CDKN1A 0.016 0.088 -10000 0 -1.4 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.007 0.007 -10000 0 -10000 0 0
SFN 0.021 0.068 0.26 17 -0.58 10 27
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.32 87 -0.31 4 91
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.36 0.4 0.62 2 -0.81 383 385
JUN -0.26 0.29 0.41 9 -0.54 423 432
IL4 -0.11 0.15 -10000 0 -0.46 46 46
CDK5R1 0.022 0.037 0.26 22 -10000 0 22
PRKACA 0.024 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.25 0.24 -10000 0 -0.48 468 468
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.12 0.32 90 -0.3 5 95
cortisol/GR alpha (monomer) 0.28 0.32 0.59 440 -0.52 3 443
NCOA2 -0.003 0.12 -10000 0 -0.58 40 40
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.28 -10000 0 -0.6 292 292
AP-1/NFAT1-c-4 -0.43 0.45 0.48 8 -0.81 527 535
AFP -0.54 0.65 0.48 2 -1.4 343 345
SUV420H1 0.023 0.006 -10000 0 -10000 0 0
IRF1 0.16 0.16 0.42 124 -10000 0 124
TP53 0.031 0.029 -10000 0 -0.52 2 2
PPP5C 0.024 0.003 -10000 0 -10000 0 0
KRT17 -0.65 0.69 0.44 3 -1.3 471 474
KRT14 -0.71 0.67 -10000 0 -1.3 527 527
TBP 0.028 0.011 -10000 0 -10000 0 0
CREBBP 0.15 0.14 0.29 457 -10000 0 457
HDAC1 0.022 0.011 -10000 0 -10000 0 0
HDAC2 0.021 0.011 -10000 0 -10000 0 0
AP-1 -0.43 0.46 0.48 8 -0.81 527 535
MAPK14 0.003 0.022 -10000 0 -10000 0 0
MAPK10 -0.084 0.21 -10000 0 -0.58 146 146
MAPK11 -0.002 0.04 -10000 0 -0.59 3 3
KRT5 -0.74 0.71 0.43 3 -1.4 532 535
interleukin-1 receptor activity -0.001 0.005 -10000 0 -10000 0 0
NCOA1 0.025 0.02 -10000 0 -0.57 1 1
STAT1 0.033 0.033 0.27 18 -10000 0 18
CGA -0.053 0.17 0.4 1 -0.46 30 31
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.18 0.36 368 -10000 0 368
MAPK3 0.001 0.022 -10000 0 -10000 0 0
MAPK1 0.003 0.022 -10000 0 -10000 0 0
ICAM1 -0.18 0.25 0.57 2 -0.55 219 221
NFKB1 -0.038 0.1 0.29 1 -0.27 24 25
MAPK8 -0.19 0.22 0.38 5 -0.41 398 403
MAPK9 0.003 0.022 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.28 0.33 0.86 1 -0.67 305 306
BAX 0.017 0.065 -10000 0 -10000 0 0
POMC -0.16 0.29 -10000 0 -0.93 65 65
EP300 0.15 0.14 0.29 417 -10000 0 417
cortisol/GR alpha (dimer)/p53 0.22 0.27 0.52 359 -0.47 2 361
proteasomal ubiquitin-dependent protein catabolic process 0.077 0.11 0.26 162 -10000 0 162
SGK1 0.19 0.2 0.52 12 -1.1 5 17
IL13 -0.25 0.28 0.5 5 -0.63 199 204
IL6 -0.43 0.53 0.62 1 -1.1 378 379
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.21 0.23 0.56 1 -0.64 72 73
IL2 -0.33 0.36 0.46 3 -0.7 411 414
CDK5 0.018 0.02 0.26 4 -10000 0 4
PRKACB 0.033 0.06 0.26 45 -0.58 3 48
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
IL8 -0.19 0.29 0.57 2 -0.6 222 224
CDK5R1/CDK5 0.019 0.037 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.018 0.16 0.39 3 -0.36 48 51
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.26 0.49 426 -0.42 3 429
SMARCA4 0.024 0.011 -10000 0 -0.16 1 1
chromatin remodeling 0.15 0.16 0.34 298 -10000 0 298
NF kappa B1 p50/RelA/Cbp 0.064 0.19 0.41 63 -0.41 19 82
JUN (dimer) -0.26 0.29 0.41 9 -0.53 424 433
YWHAH 0.023 0.006 -10000 0 -10000 0 0
VIPR1 -0.13 0.21 -10000 0 -0.48 162 162
NR3C1 0.17 0.2 0.38 378 -0.43 4 382
NR4A1 -0.024 0.17 -10000 0 -0.55 93 93
TIF2/SUV420H1 0.01 0.09 -10000 0 -0.43 40 40
MAPKKK cascade -0.27 0.31 0.85 1 -0.64 303 304
cortisol/GR alpha (dimer)/Src-1 0.25 0.27 0.51 427 -0.45 3 430
PBX1 0.023 0.016 0.26 1 -10000 0 1
POU1F1 0.022 0.016 0.26 2 -10000 0 2
SELE -0.19 0.31 0.5 3 -0.65 222 225
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.15 0.16 0.34 294 -10000 0 294
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.26 0.49 426 -0.42 3 429
mol:cortisol 0.16 0.19 0.34 447 -0.25 3 450
MMP1 0.035 0.31 0.39 10 -0.9 83 93
EPHB forward 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
Ephrin A5/EPHB2 -0.005 0.12 0.18 19 -0.36 99 118
cell-cell adhesion 0.14 0.15 0.31 400 -10000 0 400
Ephrin B/EPHB2/RasGAP 0.032 0.1 -10000 0 -0.32 72 72
ITSN1 0.024 0.019 -10000 0 -0.58 1 1
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.033 0.013 0.18 6 -10000 0 6
Ephrin B1/EPHB1 -0.13 0.2 -10000 0 -0.36 410 410
HRAS/GDP -0.12 0.19 -10000 0 -0.41 175 175
Ephrin B/EPHB1/GRB7 -0.11 0.21 -10000 0 -0.36 393 393
Endophilin/SYNJ1 -0.025 0.083 0.23 2 -0.3 71 73
KRAS 0.024 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.11 0.22 -10000 0 -0.36 404 404
endothelial cell migration 0.041 0.037 -10000 0 -0.32 7 7
GRB2 0.023 0.01 0.26 1 -10000 0 1
GRB7 0.02 0.021 -10000 0 -0.58 1 1
PAK1 -0.031 0.099 0.35 3 -0.33 77 80
HRAS 0.025 0.02 0.26 7 -10000 0 7
RRAS -0.026 0.084 0.23 2 -0.3 71 73
DNM1 0.02 0.051 0.26 1 -0.58 7 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.15 0.18 0.35 2 -0.34 426 428
lamellipodium assembly -0.14 0.15 -10000 0 -0.31 400 400
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.097 0.16 -10000 0 -0.32 308 308
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
EPHB2 0.028 0.033 0.26 19 -10000 0 19
EPHB3 0.026 0.02 0.26 7 -10000 0 7
EPHB1 -0.22 0.3 0.26 1 -0.58 412 413
EPHB4 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.12 0.17 -10000 0 -0.42 161 161
Ephrin B/EPHB2 0.022 0.1 -10000 0 -0.32 72 72
Ephrin B/EPHB3 0.021 0.097 -10000 0 -0.32 68 68
JNK cascade -0.13 0.16 0.38 7 -0.32 409 416
Ephrin B/EPHB1 -0.12 0.21 -10000 0 -0.36 426 426
RAP1/GDP -0.1 0.16 -10000 0 -0.39 146 146
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EFNB3 -0.022 0.16 -10000 0 -0.58 74 74
EFNB1 0.025 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.11 0.19 -10000 0 -0.33 410 410
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.11 0.2 -10000 0 -0.41 158 158
Rap1/GTP -0.12 0.17 -10000 0 -0.32 346 346
axon guidance -0.005 0.12 -10000 0 -0.35 99 99
MAPK3 -0.092 0.14 -10000 0 -0.39 109 109
MAPK1 -0.096 0.14 -10000 0 -0.39 110 110
Rac1/GDP -0.11 0.16 -10000 0 -0.4 158 158
actin cytoskeleton reorganization -0.12 0.13 -10000 0 -0.34 139 139
CDC42/GDP -0.11 0.16 -10000 0 -0.39 159 159
PI3K 0.046 0.039 -10000 0 -0.32 7 7
EFNA5 -0.033 0.18 0.26 1 -0.58 95 96
Ephrin B2/EPHB4 0.03 0.01 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.005 0.086 -10000 0 -0.27 74 74
CDC42 0.023 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.12 0.17 -10000 0 -0.31 373 373
PTK2 0.15 0.27 0.68 197 -10000 0 197
MAP4K4 -0.13 0.16 0.39 7 -0.32 409 416
SRC 0.024 0.005 -10000 0 -10000 0 0
KALRN 0.013 0.082 -10000 0 -0.58 19 19
Intersectin/N-WASP 0.035 0.016 -10000 0 -0.43 1 1
neuron projection morphogenesis -0.11 0.14 0.29 7 -0.43 74 81
MAP2K1 -0.093 0.15 -10000 0 -0.31 295 295
WASL 0.024 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.1 0.2 -10000 0 -0.34 409 409
cell migration -0.11 0.18 0.31 4 -0.43 135 139
NRAS 0.024 0.004 -10000 0 -10000 0 0
SYNJ1 -0.026 0.084 0.23 2 -0.3 71 73
PXN 0.024 0.002 -10000 0 -10000 0 0
TF -0.18 0.17 0.22 2 -0.32 545 547
HRAS/GTP -0.11 0.19 -10000 0 -0.32 414 414
Ephrin B1/EPHB1-2 -0.11 0.19 -10000 0 -0.33 410 410
cell adhesion mediated by integrin 0.008 0.087 0.29 69 -0.24 8 77
RAC1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.12 0.2 -10000 0 -0.33 423 423
RAC1-CDC42/GTP -0.14 0.15 -10000 0 -0.31 377 377
RASA1 0.024 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.1 0.16 -10000 0 -0.39 149 149
ruffle organization -0.13 0.16 0.39 5 -0.5 65 70
NCK1 0.024 0.003 -10000 0 -10000 0 0
receptor internalization -0.029 0.088 0.22 2 -0.31 72 74
Ephrin B/EPHB2/KALRN 0.026 0.12 -10000 0 -0.34 85 85
ROCK1 0.017 0.032 0.21 5 -0.34 1 6
RAS family/GDP -0.11 0.12 -10000 0 -0.34 124 124
Rac1/GTP -0.12 0.18 -10000 0 -0.32 400 400
Ephrin B/EPHB1/Src/Paxillin -0.12 0.18 -10000 0 -0.33 408 408
Angiopoietin receptor Tie2-mediated signaling

Figure S14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.14 0.38 -10000 0 -0.86 207 207
NCK1/PAK1/Dok-R -0.089 0.16 -10000 0 -0.41 207 207
NCK1/Dok-R -0.17 0.45 -10000 0 -1 207 207
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.04 0.095 0.24 184 -10000 0 184
RELA 0.024 0.004 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
F2 0.042 0.11 0.27 175 -10000 0 175
TNIP2 0.024 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.15 0.43 -10000 0 -0.97 207 207
FN1 0.12 0.12 0.26 394 -10000 0 394
PLD2 -0.2 0.46 -10000 0 -1.1 206 206
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB14 0.014 0.18 0.26 138 -0.58 71 209
ELK1 -0.17 0.41 -10000 0 -0.96 207 207
GRB7 0.02 0.021 -10000 0 -0.58 1 1
PAK1 0.023 0.02 0.26 6 -10000 0 6
Tie2/Ang1/alpha5/beta1 Integrin -0.11 0.47 -10000 0 -1 207 207
CDKN1A -0.1 0.26 -10000 0 -0.6 177 177
ITGA5 0.024 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.17 0.45 -10000 0 -1 207 207
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:NO -0.1 0.28 0.39 1 -0.64 207 208
PLG -0.2 0.46 -10000 0 -1.1 207 207
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.15 0.36 -10000 0 -0.83 207 207
GRB2 0.023 0.01 0.26 1 -10000 0 1
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
ANGPT2 -0.14 0.28 -10000 0 -0.67 156 156
BMX -0.31 0.5 -10000 0 -1.2 208 208
ANGPT1 -0.22 0.49 -10000 0 -1.2 184 184
tube development -0.12 0.28 -10000 0 -0.65 204 204
ANGPT4 -0.15 0.27 -10000 0 -0.58 282 282
response to hypoxia -0.013 0.028 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.2 0.5 -10000 0 -1.1 206 206
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
FGF2 -0.2 0.29 -10000 0 -0.57 376 376
STAT5A (dimer) -0.13 0.33 -10000 0 -0.75 200 200
mol:L-citrulline -0.1 0.28 0.39 1 -0.64 207 208
AGTR1 -0.092 0.26 0.26 58 -0.57 217 275
MAPK14 -0.19 0.46 -10000 0 -1.1 209 209
Tie2/SHP2 -0.089 0.31 -10000 0 -1.1 76 76
TEK -0.097 0.33 -10000 0 -1.2 76 76
RPS6KB1 -0.13 0.37 -10000 0 -0.82 207 207
Angiotensin II/AT1 -0.067 0.19 0.18 58 -0.42 220 278
Tie2/Ang1/GRB2 -0.19 0.48 -10000 0 -1.1 207 207
MAPK3 -0.17 0.42 -10000 0 -0.98 206 206
MAPK1 -0.18 0.42 -10000 0 -0.99 206 206
Tie2/Ang1/GRB7 -0.2 0.47 -10000 0 -1.1 207 207
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.2 0.46 -10000 0 -1.1 207 207
PI3K -0.17 0.43 -10000 0 -0.99 207 207
FES -0.19 0.46 -10000 0 -1.1 208 208
Crk/Dok-R -0.17 0.45 -10000 0 -1 207 207
Tie2/Ang1/ABIN2 -0.19 0.48 -10000 0 -1.1 207 207
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.13 0.34 -10000 0 -0.77 207 207
STAT5A 0.02 0.047 -10000 0 -0.58 6 6
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.11 0.37 0.47 1 -0.81 206 207
Tie2/Ang2 -0.17 0.39 -10000 0 -0.89 200 200
Tie2/Ang1 -0.21 0.5 -10000 0 -1.2 207 207
FOXO1 -0.12 0.34 0.47 1 -0.78 207 208
ELF1 0.013 0.035 -10000 0 -10000 0 0
ELF2 -0.19 0.45 -10000 0 -1.1 207 207
mol:Choline -0.18 0.44 -10000 0 -1 206 206
cell migration -0.035 0.1 -10000 0 -0.23 207 207
FYN -0.14 0.32 -10000 0 -0.74 200 200
DOK2 0.021 0.026 0.26 4 -0.58 1 5
negative regulation of cell cycle -0.092 0.24 -10000 0 -0.54 179 179
ETS1 -0.019 0.11 -10000 0 -0.27 148 148
PXN -0.088 0.31 0.45 1 -0.67 207 208
ITGB1 0.024 0.004 -10000 0 -10000 0 0
NOS3 -0.12 0.32 -10000 0 -0.73 207 207
RAC1 0.024 0.004 -10000 0 -10000 0 0
TNF -0.022 0.13 0.26 19 -0.27 181 200
MAPKKK cascade -0.18 0.44 -10000 0 -1 206 206
RASA1 0.024 0.004 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.19 0.47 -10000 0 -1.1 207 207
NCK1 0.024 0.003 -10000 0 -10000 0 0
vasculogenesis -0.088 0.25 0.37 2 -0.57 207 209
mol:Phosphatidic acid -0.18 0.44 -10000 0 -1 206 206
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.1 0.28 0.39 1 -0.64 207 208
Rac1/GTP -0.12 0.34 -10000 0 -0.78 207 207
MMP2 -0.2 0.46 -10000 0 -1.1 207 207
Endothelins

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
AKT1 -0.075 0.13 -10000 0 -0.42 97 97
PTK2B 0.02 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.055 0.2 -10000 0 -0.83 42 42
EDN1 -0.075 0.17 -10000 0 -0.53 95 95
EDN3 -0.23 0.29 0.26 2 -0.58 414 416
EDN2 0.075 0.11 0.26 227 -0.58 4 231
HRAS/GDP -0.095 0.2 -10000 0 -0.47 148 148
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.063 0.14 -10000 0 -0.38 115 115
ADCY4 -0.13 0.2 0.28 3 -0.43 262 265
ADCY5 -0.21 0.24 0.24 1 -0.45 448 449
ADCY6 -0.12 0.19 0.28 3 -0.41 256 259
ADCY7 -0.12 0.19 0.27 4 -0.4 260 264
ADCY1 -0.12 0.2 0.27 3 -0.41 266 269
ADCY2 -0.14 0.22 0.28 9 -0.45 274 283
ADCY3 -0.12 0.19 0.26 3 -0.4 261 264
ADCY8 -0.1 0.18 0.27 4 -0.4 207 211
ADCY9 -0.12 0.18 0.27 1 -0.4 244 245
arachidonic acid secretion -0.16 0.27 0.31 2 -0.5 332 334
ETB receptor/Endothelin-1/Gq/GTP -0.05 0.15 -10000 0 -0.35 156 156
GNAO1 0.018 0.093 0.26 32 -0.58 19 51
HRAS 0.025 0.02 0.26 7 -10000 0 7
ETA receptor/Endothelin-1/G12/GTP -0.06 0.14 0.3 7 -0.39 95 102
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.2 0.28 7 -0.42 266 273
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.065 0.16 0.38 10 -0.44 91 101
EDNRB -0.024 0.17 -10000 0 -0.57 85 85
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.079 0.16 0.28 1 -0.49 101 102
CYSLTR1 -0.082 0.16 -10000 0 -0.49 95 95
SLC9A1 -0.047 0.096 -10000 0 -0.28 105 105
mol:GDP -0.11 0.21 0.34 2 -0.5 156 158
SLC9A3 -0.11 0.28 -10000 0 -0.65 171 171
RAF1 -0.14 0.24 0.33 1 -0.47 269 270
JUN -0.053 0.19 -10000 0 -0.76 46 46
JAK2 -0.073 0.14 -10000 0 -0.42 97 97
mol:IP3 -0.075 0.17 -10000 0 -0.45 116 116
ETA receptor/Endothelin-1 -0.086 0.16 0.33 8 -0.49 99 107
PLCB1 -0.017 0.15 -10000 0 -0.58 64 64
PLCB2 0.014 0.027 0.26 1 -0.58 1 2
ETA receptor/Endothelin-3 -0.19 0.22 -10000 0 -0.44 423 423
FOS -0.29 0.44 -10000 0 -0.93 314 314
Gai/GDP -0.098 0.29 -10000 0 -0.74 155 155
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.2 0.28 1 -0.52 143 144
BCAR1 0.022 0.008 -10000 0 -10000 0 0
PRKCB1 -0.078 0.16 -10000 0 -0.42 131 131
GNAQ 0.014 0.032 -10000 0 -0.58 2 2
GNAZ 0.018 0.057 -10000 0 -0.58 9 9
GNAL -0.11 0.25 -10000 0 -0.58 219 219
Gs family/GDP -0.15 0.24 -10000 0 -0.5 247 247
ETA receptor/Endothelin-1/Gq/GTP -0.048 0.12 -10000 0 -0.36 86 86
MAPK14 -0.065 0.16 -10000 0 -0.41 128 128
TRPC6 -0.059 0.21 -10000 0 -0.9 42 42
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.003 0.12 -10000 0 -0.58 45 45
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.065 0.17 -10000 0 -0.4 153 153
ETB receptor/Endothelin-2 0.027 0.15 0.25 16 -0.39 94 110
ETB receptor/Endothelin-3 -0.19 0.24 -10000 0 -0.44 467 467
ETB receptor/Endothelin-1 -0.077 0.18 0.25 7 -0.47 155 162
MAPK3 -0.25 0.38 -10000 0 -0.79 318 318
MAPK1 -0.26 0.4 -10000 0 -0.81 322 322
Rac1/GDP -0.095 0.19 -10000 0 -0.48 140 140
cAMP biosynthetic process -0.16 0.22 0.39 2 -0.46 274 276
MAPK8 -0.061 0.21 -10000 0 -0.71 64 64
SRC 0.024 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.066 0.17 -10000 0 -0.36 184 184
p130Cas/CRK/Src/PYK2 -0.1 0.22 0.49 1 -0.56 128 129
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.095 0.19 -10000 0 -0.48 139 139
COL1A2 -0.088 0.2 0.38 9 -0.48 141 150
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.022 0.096 0.26 15 -0.33 10 25
mol:DAG -0.075 0.17 -10000 0 -0.45 118 118
MAP2K2 -0.19 0.3 0.34 2 -0.59 325 327
MAP2K1 -0.19 0.3 0.32 2 -0.59 325 327
EDNRA -0.035 0.065 -10000 0 -0.28 20 20
positive regulation of muscle contraction -0.065 0.12 -10000 0 -0.38 91 91
Gq family/GDP -0.06 0.19 -10000 0 -0.48 103 103
HRAS/GTP -0.1 0.2 0.34 1 -0.48 157 158
PRKCH -0.077 0.16 -10000 0 -0.44 121 121
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA -0.073 0.18 0.29 3 -0.46 126 129
PRKCB -0.074 0.18 -10000 0 -0.45 121 121
PRKCE -0.08 0.16 -10000 0 -0.44 123 123
PRKCD -0.077 0.16 -10000 0 -0.44 116 116
PRKCG -0.078 0.17 0.27 1 -0.45 117 118
regulation of vascular smooth muscle contraction -0.34 0.52 -10000 0 -1.1 311 311
PRKCQ -0.086 0.19 -10000 0 -0.48 131 131
PLA2G4A -0.18 0.31 0.33 1 -0.55 332 333
GNA14 0.014 0.071 0.26 19 -0.58 10 29
GNA15 0.022 0.028 0.26 6 -0.58 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.028 -10000 0 -0.58 2 2
Rac1/GTP -0.061 0.14 0.3 7 -0.39 97 104
MMP1 0.18 0.13 0.39 85 -10000 0 85
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.024 0.004 -10000 0 -10000 0 0
VLDLR 0.008 0.094 -10000 0 -0.58 25 25
LRPAP1 0.024 0.005 -10000 0 -10000 0 0
NUDC 0.023 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.19 0.2 -10000 0 -0.36 574 574
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
KATNA1 0.023 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.18 0.17 0.2 1 -0.33 571 572
IQGAP1/CaM 0.034 0.009 -10000 0 -10000 0 0
DAB1 0.036 0.056 0.26 58 -10000 0 58
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
PLA2G7 0.024 0.07 0.26 24 -0.58 10 34
CALM1 0.024 0.004 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.049 0.048 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.024 0.002 -10000 0 -10000 0 0
CDK5R1 0.028 0.035 0.26 22 -10000 0 22
LIS1/Poliovirus Protein 3A 0.007 0.003 -10000 0 -10000 0 0
CDK5R2 0.055 0.084 0.26 143 -10000 0 143
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.2 0.21 0.34 2 -0.37 572 574
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.14 0.15 0.34 5 -0.28 406 411
MAP1B 0 0.042 -10000 0 -0.32 16 16
RAC1 0.01 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.16 0.16 0.22 1 -0.3 543 544
RELN -0.32 0.3 0.26 3 -0.58 581 584
PAFAH/LIS1 0.023 0.047 0.2 24 -0.36 9 33
LIS1/CLIP170 0.023 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.12 0.13 -10000 0 -0.28 42 42
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.15 0.17 -10000 0 -0.3 480 480
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.15 0.15 0.4 3 -0.3 419 422
LIS1/IQGAP1 0.023 0.009 -10000 0 -10000 0 0
RHOA 0.01 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.01 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.051 0.075 0.26 111 -10000 0 111
PAFAH1B2 0.02 0.034 -10000 0 -0.58 3 3
MAP1B/LIS1/Dynein heavy chain 0.014 0.042 -10000 0 -0.31 3 3
NDEL1/Katanin 60/Dynein heavy chain -0.13 0.15 0.4 3 -0.32 64 67
LRP8 0.047 0.07 0.26 97 -10000 0 97
NDEL1/Katanin 60 -0.14 0.15 0.41 3 -0.28 392 395
P39/CDK5 -0.16 0.16 0.31 9 -0.29 547 556
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.023 0.009 -10000 0 -10000 0 0
CDK5 -0.18 0.15 0.19 5 -0.31 567 572
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.02 0.008 -10000 0 -10000 0 0
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.17 0.19 0.33 1 -0.32 565 566
RELN/VLDLR -0.17 0.2 -10000 0 -0.34 574 574
CDC42 0.01 0.005 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.034 0.017 -10000 0 -0.43 1 1
Necdin/E2F1 0.061 0.11 -10000 0 -0.39 31 31
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.05 0.18 -10000 0 -0.33 276 276
NGF (dimer)/p75(NTR)/BEX1 -0.11 0.24 0.34 1 -0.41 355 356
NT-4/5 (dimer)/p75(NTR) -0.23 0.29 -10000 0 -0.51 488 488
IKBKB 0.021 0.009 -10000 0 -10000 0 0
AKT1 -0.086 0.16 0.36 1 -0.33 264 265
IKBKG 0.024 0.002 -10000 0 -10000 0 0
BDNF -0.017 0.16 0.26 21 -0.58 77 98
MGDIs/NGR/p75(NTR)/LINGO1 -0.041 0.2 0.34 7 -0.35 269 276
FURIN 0.024 0.009 0.26 1 -10000 0 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.096 0.21 -10000 0 -0.4 313 313
LINGO1 0.078 0.1 0.26 227 -10000 0 227
Sortilin/TRAF6/NRIF 0.023 0.024 -10000 0 -0.56 1 1
proBDNF (dimer) -0.017 0.16 0.26 21 -0.57 77 98
NTRK1 0.024 0.049 0.26 21 -0.58 3 24
RTN4R 0.032 0.046 0.26 38 -10000 0 38
neuron apoptosis -0.085 0.2 0.34 8 -0.47 102 110
IRAK1 0.025 0.013 0.26 3 -10000 0 3
SHC1 -0.084 0.16 -10000 0 -0.37 212 212
ARHGDIA 0.023 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.054 0.034 -10000 0 -0.32 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.057 0.18 -10000 0 -0.34 271 271
MAGEH1 0.024 0.002 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.069 0.19 -10000 0 -0.36 281 281
Mammalian IAPs/DIABLO 0.057 0.033 -10000 0 -0.34 2 2
proNGF (dimer) 0.017 0.076 0.26 7 -0.57 15 22
MAGED1 0.025 0.011 0.26 2 -10000 0 2
APP 0.024 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.18 0.28 -10000 0 -0.57 348 348
ZNF274 0.024 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.068 0.16 -10000 0 -0.32 263 263
NGF 0.017 0.076 0.26 7 -0.58 15 22
cell cycle arrest -0.076 0.15 0.23 42 -0.3 272 314
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.055 0.12 -10000 0 -0.28 194 194
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.19 0.27 -10000 0 -0.46 444 444
NCSTN 0.02 0.009 -10000 0 -10000 0 0
mol:GTP -0.071 0.19 -10000 0 -0.37 276 276
PSENEN 0.024 0.008 0.26 1 -10000 0 1
mol:ceramide -0.081 0.16 -10000 0 -0.34 273 273
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.045 0.11 -10000 0 -0.36 29 29
p75(NTR)/beta APP -0.095 0.2 -10000 0 -0.42 275 275
BEX1 -0.02 0.24 0.26 157 -0.58 135 292
mol:GDP -0.11 0.16 -10000 0 -0.37 278 278
NGF (dimer) 0.002 0.14 0.34 1 -0.34 122 123
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.026 0.19 0.34 6 -0.32 255 261
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
RAC1/GTP -0.063 0.16 -10000 0 -0.32 273 273
MYD88 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.071 0.19 -10000 0 -0.37 276 276
RHOB 0.024 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.077 0.074 -10000 0 -10000 0 0
NT3 (dimer) -0.063 0.22 0.26 12 -0.57 148 160
TP53 -0.095 0.17 0.33 5 -0.33 300 305
PRDM4 -0.08 0.17 -10000 0 -0.34 272 272
BDNF (dimer) 0.021 0.2 0.34 18 -0.36 181 199
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
SORT1 0.023 0.019 -10000 0 -0.58 1 1
activation of caspase activity -0.053 0.17 -10000 0 -0.32 276 276
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.057 0.18 -10000 0 -0.34 269 269
RHOC 0.024 0.004 -10000 0 -10000 0 0
XIAP 0.025 0.002 -10000 0 -10000 0 0
MAPK10 -0.14 0.2 0.29 5 -0.42 282 287
DIABLO 0.024 0.002 -10000 0 -10000 0 0
SMPD2 -0.081 0.17 -10000 0 -0.34 273 273
APH1B 0.023 0.019 -10000 0 -0.58 1 1
APH1A 0.02 0.01 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.074 0.19 -10000 0 -0.37 276 276
PSEN1 0.024 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.009 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.15 0.25 -10000 0 -0.46 381 381
MAPK8 -0.1 0.18 0.29 11 -0.37 260 271
MAPK9 -0.1 0.18 0.28 8 -0.37 254 262
APAF1 0.024 0.003 -10000 0 -10000 0 0
NTF3 -0.063 0.22 0.26 12 -0.58 148 160
NTF4 -0.18 0.28 -10000 0 -0.58 348 348
NDN 0.005 0.1 -10000 0 -0.58 31 31
RAC1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.045 0.17 -10000 0 -0.31 273 273
p75 CTF/Sortilin/TRAF6/NRIF 0.057 0.023 -10000 0 -0.34 1 1
RhoA-B-C/GTP -0.071 0.19 -10000 0 -0.37 276 276
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.067 0.2 -10000 0 -0.35 301 301
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.078 0.2 -10000 0 -0.37 303 303
PRKACB 0.033 0.06 0.26 45 -0.58 3 48
proBDNF (dimer)/p75 ECD 0.003 0.13 -10000 0 -0.42 77 77
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.023 0.042 0.26 11 -0.58 3 14
BIRC2 0.022 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.089 0.17 0.28 14 -0.34 267 281
BAD -0.12 0.19 0.36 9 -0.39 275 284
RIPK2 0.021 0.016 0.26 3 -10000 0 3
NGFR -0.14 0.27 -10000 0 -0.58 275 275
CYCS -0.089 0.15 0.36 2 -0.33 265 267
ADAM17 0.024 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.048 0.16 -10000 0 -0.34 199 199
BCL2L11 -0.12 0.19 0.36 9 -0.39 269 278
BDNF (dimer)/p75(NTR) -0.12 0.24 -10000 0 -0.45 323 323
PI3K -0.061 0.18 -10000 0 -0.35 267 267
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.058 0.18 -10000 0 -0.34 272 272
NDNL2 0.024 0.005 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.1 0.21 -10000 0 -0.42 294 294
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.057 0.18 -10000 0 -0.34 273 273
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.023 0.02 -10000 0 -0.58 1 1
PLG 0.018 0.016 0.26 4 -10000 0 4
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.11 0.19 -10000 0 -0.38 313 313
SQSTM1 0.024 0.008 0.26 1 -10000 0 1
NGFRAP1 0.023 0.027 -10000 0 -0.58 2 2
CASP3 -0.11 0.18 0.36 8 -0.36 280 288
E2F1 0.093 0.11 0.26 294 -10000 0 294
CASP9 0.023 0.006 -10000 0 -10000 0 0
IKK complex -0.004 0.11 0.27 1 -0.4 17 18
NGF (dimer)/TRKA 0.026 0.066 -10000 0 -0.43 16 16
MMP7 -0.038 0.2 0.26 30 -0.58 112 142
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.047 0.18 -10000 0 -0.33 266 266
MMP3 0.099 0.14 0.26 355 -0.58 11 366
APAF-1/Caspase 9 -0.088 0.12 -10000 0 -0.46 10 10
IL4-mediated signaling events

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
BCL2L1 -0.24 0.61 0.79 17 -1.1 228 245
STAT6 (cleaved dimer) -0.31 0.58 -10000 0 -1.2 244 244
IGHG1 -0.028 0.26 0.5 65 -0.39 56 121
IGHG3 -0.24 0.58 0.69 15 -1.1 245 260
AKT1 -0.087 0.35 0.57 29 -0.72 96 125
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.049 0.3 0.54 28 -0.72 58 86
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.089 0.36 0.59 30 -0.73 97 127
THY1 -0.24 0.61 0.82 12 -1.2 203 215
MYB 0.012 0.083 0.26 2 -0.58 19 21
HMGA1 0.034 0.048 0.26 42 -10000 0 42
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.11 0.42 0.65 55 -0.71 187 242
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.081 0.35 0.59 30 -0.74 79 109
SP1 0.034 0.026 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SOCS5 0.015 0.047 -10000 0 -0.55 1 1
STAT6 (dimer)/ETS1 -0.27 0.61 0.72 7 -1.2 238 245
SOCS1 -0.14 0.4 0.63 21 -0.73 191 212
SOCS3 -0.095 0.36 0.64 9 -0.83 66 75
FCER2 -0.4 0.75 0.8 27 -1.3 344 371
PARP14 0.017 0.032 0.25 3 -10000 0 3
CCL17 -0.23 0.63 0.88 35 -1.2 200 235
GRB2 0.023 0.01 0.26 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.043 0.29 0.53 34 -0.67 46 80
T cell proliferation -0.26 0.62 0.75 9 -1.2 230 239
IL4R/JAK1 -0.25 0.6 0.73 5 -1.1 230 235
EGR2 -0.38 0.76 0.87 14 -1.4 279 293
JAK2 0.011 0.077 0.26 1 -10000 0 1
JAK3 0.022 0.037 0.28 14 -10000 0 14
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
JAK1 0.017 0.041 -10000 0 -10000 0 0
COL1A2 -0.024 0.27 0.57 12 -1 17 29
CCL26 -0.24 0.62 0.83 17 -1.2 222 239
IL4R -0.25 0.67 0.89 28 -1.2 221 249
PTPN6 0.014 0.036 0.22 2 -10000 0 2
IL13RA2 -0.24 0.61 0.81 17 -1.2 218 235
IL13RA1 0.011 0.078 0.26 1 -10000 0 1
IRF4 -0.13 0.5 0.63 9 -1.4 110 119
ARG1 -0.006 0.22 0.58 7 -0.62 7 14
CBL -0.11 0.38 0.59 39 -0.69 169 208
GTF3A 0.055 0.05 0.26 1 -10000 0 1
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL13RA1/JAK2 0.024 0.11 0.31 20 -10000 0 20
IRF4/BCL6 -0.12 0.45 0.56 1 -1.3 109 110
CD40LG -0.01 0.14 0.31 14 -0.58 47 61
MAPK14 -0.11 0.39 0.6 33 -0.71 153 186
mitosis -0.08 0.34 0.56 32 -0.68 96 128
STAT6 -0.28 0.77 0.97 43 -1.4 233 276
SPI1 0.027 0.018 0.26 5 -10000 0 5
RPS6KB1 -0.063 0.32 0.54 40 -0.65 90 130
STAT6 (dimer) -0.28 0.77 0.98 43 -1.4 233 276
STAT6 (dimer)/PARP14 -0.3 0.67 0.75 11 -1.2 251 262
mast cell activation 0 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.095 0.36 0.58 33 -0.73 109 142
FRAP1 -0.087 0.35 0.57 29 -0.72 95 124
LTA -0.23 0.63 0.88 33 -1.2 217 250
FES 0.022 0.033 -10000 0 -0.58 3 3
T-helper 1 cell differentiation 0.26 0.72 1.3 235 -0.97 43 278
CCL11 -0.18 0.6 0.79 20 -1.1 188 208
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.075 0.34 0.58 33 -0.73 81 114
IL2RG 0.026 0.075 0.27 45 -0.57 7 52
IL10 -0.21 0.61 0.85 17 -1.2 180 197
IRS1 0.001 0.12 -10000 0 -0.58 39 39
IRS2 0.003 0.1 -10000 0 -0.58 32 32
IL4 -0.011 0.27 0.62 26 -1.1 22 48
IL5 -0.24 0.61 0.82 11 -1.2 201 212
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.16 0.52 0.82 45 -0.88 219 264
COL1A1 -0.003 0.36 0.64 59 -0.97 52 111
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.26 0.61 0.74 1 -1.2 196 197
IL2R gamma/JAK3 0.037 0.071 0.32 26 -0.39 7 33
TFF3 -0.3 0.71 0.86 26 -1.3 252 278
ALOX15 -0.31 0.7 0.83 20 -1.3 277 297
MYBL1 0.039 0.065 0.26 77 -10000 0 77
T-helper 2 cell differentiation -0.2 0.53 0.71 31 -0.94 236 267
SHC1 0.02 0.009 -10000 0 -10000 0 0
CEBPB 0.025 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.084 0.35 0.56 32 -0.67 110 142
mol:PI-3-4-5-P3 -0.087 0.35 0.57 29 -0.72 95 124
PI3K -0.096 0.37 0.58 25 -0.78 94 119
DOK2 0.021 0.026 0.26 4 -0.58 1 5
ETS1 0.004 0.053 -10000 0 -0.54 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.033 0.27 0.51 38 -0.63 38 76
ITGB3 -0.26 0.63 0.85 6 -1.2 204 210
PIGR -0.68 0.8 0.83 20 -1.3 576 596
IGHE -0.015 0.087 0.18 27 -0.22 27 54
MAPKKK cascade -0.031 0.27 0.5 44 -0.61 38 82
BCL6 0.023 0.041 -10000 0 -0.57 4 4
OPRM1 -0.24 0.61 0.81 14 -1.2 213 227
RETNLB -0.25 0.61 0.84 6 -1.2 196 202
SELP -0.36 0.77 0.83 18 -1.4 281 299
AICDA -0.24 0.58 0.8 10 -1.1 215 225
Ephrin B reverse signaling

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
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EPHB2 0.027 0.033 0.26 19 -10000 0 19
EFNB1 0.001 0.038 -10000 0 -0.43 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.089 0.18 -10000 0 -0.3 400 400
Ephrin B2/EPHB1-2 -0.11 0.18 -10000 0 -0.33 410 410
neuron projection morphogenesis -0.094 0.16 -10000 0 -0.29 400 400
Ephrin B1/EPHB1-2/Tiam1 -0.1 0.18 -10000 0 -0.32 406 406
DNM1 0.02 0.051 0.27 1 -0.58 7 8
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.024 0.12 -10000 0 -0.56 46 46
YES1 -0.026 0.18 -10000 0 -0.77 51 51
Ephrin B1/EPHB1-2/NCK2 -0.1 0.18 -10000 0 -0.32 409 409
PI3K 0.004 0.13 -10000 0 -0.52 56 56
mol:GDP -0.1 0.18 -10000 0 -0.32 406 406
ITGA2B 0.033 0.061 0.26 48 -0.58 3 51
endothelial cell proliferation 0.029 0.01 -10000 0 -10000 0 0
FYN -0.027 0.17 -10000 0 -0.76 50 50
MAP3K7 -0.025 0.13 0.23 3 -0.57 49 52
FGR -0.024 0.17 -10000 0 -0.76 50 50
TIAM1 0.025 0.015 0.26 4 -10000 0 4
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
RGS3 0.024 0.003 -10000 0 -10000 0 0
cell adhesion -0.011 0.14 0.25 1 -0.45 78 79
LYN -0.024 0.17 -10000 0 -0.75 50 50
Ephrin B1/EPHB1-2/Src Family Kinases -0.029 0.16 -10000 0 -0.71 51 51
Ephrin B1/EPHB1-2 -0.025 0.14 -10000 0 -0.63 46 46
SRC -0.023 0.17 -10000 0 -0.75 51 51
ITGB3 0.005 0.11 0.26 4 -0.58 32 36
EPHB1 -0.22 0.3 0.27 1 -0.57 412 413
EPHB4 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.029 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.026 0.092 -10000 0 -0.42 35 35
BLK -0.023 0.18 -10000 0 -0.78 48 48
HCK -0.023 0.17 -10000 0 -0.75 51 51
regulation of stress fiber formation 0.1 0.18 0.32 409 -10000 0 409
MAPK8 -0.026 0.12 -10000 0 -0.51 54 54
Ephrin B1/EPHB1-2/RGS3 -0.1 0.18 -10000 0 -0.32 408 408
endothelial cell migration -0.019 0.11 -10000 0 -0.51 43 43
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTPN13 0.008 0.11 -10000 0 -0.69 26 26
regulation of focal adhesion formation 0.1 0.18 0.32 409 -10000 0 409
chemotaxis 0.1 0.18 0.32 408 -10000 0 408
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.091 0.17 -10000 0 -0.3 400 400
angiogenesis -0.026 0.14 -10000 0 -0.62 48 48
LCK -0.023 0.18 -10000 0 -0.77 50 50
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.098 0.2 0.22 1 -0.38 277 278
FZD6 0.015 0.051 -10000 0 -0.58 7 7
WNT6 -0.082 0.25 0.26 40 -0.58 193 233
WNT4 0.017 0.087 0.26 19 -0.58 18 37
FZD3 0.017 0.047 -10000 0 -0.58 6 6
WNT5A 0.019 0.069 0.26 9 -0.58 12 21
WNT11 -0.084 0.23 0.26 10 -0.58 181 191
IGF1 pathway

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
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTK2 0.019 0.01 -10000 0 -10000 0 0
CRKL -0.067 0.16 -10000 0 -0.34 219 219
GRB2/SOS1/SHC 0.038 0.022 -10000 0 -10000 0 0
HRAS 0.025 0.02 0.26 7 -10000 0 7
IRS1/Crk -0.062 0.16 -10000 0 -0.34 224 224
IGF-1R heterotetramer/IGF1/PTP1B -0.043 0.17 -10000 0 -0.37 194 194
AKT1 -0.068 0.14 0.25 2 -0.32 185 187
BAD -0.065 0.13 0.24 2 -0.31 178 180
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.068 0.16 -10000 0 -0.34 224 224
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.058 0.17 -10000 0 -0.35 224 224
RAF1 -0.049 0.13 0.28 1 -0.48 45 46
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.032 0.16 -10000 0 -0.33 205 205
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.062 0.18 -10000 0 -0.36 231 231
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.063 0.13 0.25 2 -0.33 162 164
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.029 0.12 0.31 9 -0.4 41 50
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.039 0.13 -10000 0 -0.32 146 146
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.01 0.14 -10000 0 -0.31 144 144
IGF-1R heterotetramer -0.012 0.1 0.26 1 -0.63 20 21
IGF-1R heterotetramer/IGF1/IRS/Nck -0.045 0.17 -10000 0 -0.35 221 221
Crk/p130 Cas/Paxillin -0.036 0.16 -10000 0 -0.32 210 210
IGF1R -0.012 0.1 0.26 1 -0.63 20 21
IGF1 -0.11 0.26 -10000 0 -0.6 211 211
IRS2/Crk -0.067 0.17 -10000 0 -0.35 232 232
PI3K -0.035 0.17 -10000 0 -0.34 214 214
apoptosis 0.043 0.11 0.37 39 -0.27 5 44
HRAS/GDP 0.019 0.014 0.18 7 -10000 0 7
PRKCD -0.079 0.18 -10000 0 -0.4 208 208
RAF1/14-3-3 E -0.024 0.13 0.29 3 -0.42 45 48
BAD/14-3-3 -0.046 0.11 0.28 5 -0.4 39 44
PRKCZ -0.067 0.14 0.25 2 -0.32 185 187
Crk/p130 Cas/Paxillin/FAK1 -0.027 0.12 -10000 0 -0.41 38 38
PTPN1 0.024 0.02 0.26 6 -10000 0 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.081 0.19 -10000 0 -0.42 218 218
BCAR1 0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.023 0.15 -10000 0 -0.33 161 161
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.054 0.17 -10000 0 -0.34 221 221
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 -0.068 0.16 -10000 0 -0.34 224 224
IRS1 -0.071 0.17 -10000 0 -0.37 224 224
IRS2 -0.076 0.17 -10000 0 -0.37 232 232
IGF-1R heterotetramer/IGF1 -0.078 0.21 -10000 0 -0.46 225 225
GRB2 0.023 0.01 0.26 1 -10000 0 1
PDPK1 -0.07 0.14 0.28 1 -0.33 188 189
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKD1 -0.089 0.2 -10000 0 -0.43 218 218
SHC1 0.02 0.009 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.023 0.16 -10000 0 -0.58 76 76
GNB1/GNG2 -0.075 0.21 -10000 0 -0.47 148 148
mol:DAG -0.077 0.18 0.35 1 -0.44 138 139
PLCG1 -0.079 0.19 0.36 1 -0.45 138 139
YES1 -0.096 0.19 0.2 1 -0.38 255 256
FZD3 0.017 0.047 -10000 0 -0.58 6 6
FZD6 0.015 0.051 -10000 0 -0.58 7 7
G protein -0.063 0.2 0.3 2 -0.46 135 137
MAP3K7 -0.071 0.15 0.24 1 -0.41 104 105
mol:Ca2+ -0.074 0.18 0.35 1 -0.42 138 139
mol:IP3 -0.077 0.18 0.35 1 -0.44 138 139
NLK -0.01 0.13 -10000 0 -0.84 23 23
GNB1 0.024 0.005 -10000 0 -10000 0 0
CAMK2A -0.073 0.17 0.3 2 -0.42 118 120
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.098 0.2 0.22 1 -0.38 277 278
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
GNAS -0.091 0.19 0.2 1 -0.48 132 133
GO:0007205 -0.08 0.18 0.35 1 -0.43 138 139
WNT6 -0.082 0.25 0.26 40 -0.58 193 233
WNT4 0.017 0.087 0.26 19 -0.58 18 37
NFAT1/CK1 alpha -0.09 0.2 0.33 1 -0.5 126 127
GNG2 0.018 0.06 -10000 0 -0.58 10 10
WNT5A 0.019 0.069 0.26 9 -0.58 12 21
WNT11 -0.084 0.23 0.26 10 -0.58 181 191
CDC42 -0.083 0.19 -10000 0 -0.47 129 129
ErbB2/ErbB3 signaling events

Figure S23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.009 0.008 -10000 0 -10000 0 0
RAS family/GTP -0.023 0.14 0.28 3 -0.29 54 57
NFATC4 -0.067 0.12 0.27 4 -0.25 230 234
ERBB2IP 0.025 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.024 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.071 0.15 -10000 0 -0.31 241 241
JUN -0.01 0.098 0.25 23 -0.45 3 26
HRAS 0.026 0.02 0.26 7 -10000 0 7
DOCK7 -0.083 0.14 0.28 2 -0.3 238 240
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.054 0.16 -10000 0 -0.33 197 197
AKT1 -0.001 0.009 -10000 0 -10000 0 0
BAD -0.007 0.006 -10000 0 -10000 0 0
MAPK10 -0.074 0.11 0.21 6 -0.28 129 135
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.076 0.16 -10000 0 -0.33 241 241
RAF1 -0.02 0.14 0.33 14 -0.3 51 65
ErbB2/ErbB3/neuregulin 2 -0.15 0.18 -10000 0 -0.35 418 418
STAT3 -0.003 0.16 -10000 0 -0.86 35 35
cell migration -0.058 0.1 0.27 10 -0.26 78 88
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.045 0.25 0.45 10 -0.51 99 109
FOS -0.1 0.28 0.33 43 -0.49 305 348
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.071 0.15 -10000 0 -0.31 241 241
MAPK3 -0.016 0.2 0.42 10 -0.55 22 32
MAPK1 -0.029 0.22 0.42 11 -0.49 78 89
JAK2 -0.081 0.14 0.26 1 -0.3 236 237
NF2 -0.002 0.06 -10000 0 -0.68 7 7
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.055 0.13 0.2 7 -0.28 230 237
NRG1 -0.14 0.27 0.26 4 -0.58 279 283
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
MAPK8 -0.082 0.15 0.24 3 -0.3 242 245
MAPK9 -0.045 0.082 0.2 8 -0.24 1 9
ERBB2 0 0.069 0.24 77 -10000 0 77
ERBB3 0.022 0.033 -10000 0 -0.58 3 3
SHC1 0.021 0.01 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
apoptosis 0.02 0.025 -10000 0 -0.16 6 6
STAT3 (dimer) -0.003 0.16 -10000 0 -0.84 35 35
RNF41 -0.013 0.011 -10000 0 -10000 0 0
FRAP1 -0.005 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.073 0.094 -10000 0 -0.23 224 224
ErbB2/ErbB2/HSP90 (dimer) -0.011 0.016 -10000 0 -10000 0 0
CHRNA1 0.017 0.18 0.36 53 -0.44 15 68
myelination -0.063 0.12 0.32 11 -0.25 185 196
PPP3CB -0.077 0.13 0.27 2 -0.28 236 238
KRAS 0.024 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.037 0.14 0.24 1 -0.26 189 190
NRG2 -0.27 0.3 -10000 0 -0.58 491 491
mol:GDP -0.054 0.13 0.2 7 -0.28 230 237
SOS1 0.025 0.003 -10000 0 -10000 0 0
MAP2K2 -0.018 0.14 0.28 34 -0.3 49 83
SRC 0.024 0.005 -10000 0 -10000 0 0
mol:cAMP -0.002 0.002 -10000 0 -10000 0 0
PTPN11 -0.083 0.14 0.28 2 -0.3 240 242
MAP2K1 -0.054 0.23 0.4 10 -0.51 93 103
heart morphogenesis -0.071 0.15 -10000 0 -0.31 241 241
RAS family/GDP -0.023 0.14 0.3 1 -0.29 53 54
GRB2 0.024 0.01 0.26 1 -10000 0 1
PRKACA -0.002 0.069 -10000 0 -0.68 10 10
CHRNE 0.004 0.028 0.15 4 -0.21 3 7
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.001 0.009 -10000 0 -10000 0 0
nervous system development -0.071 0.15 -10000 0 -0.31 241 241
CDC42 0.023 0.006 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 0.003 0.004 -10000 0 -10000 0 0
GNB1/GNG2 -0.007 0.13 -10000 0 -0.34 133 133
regulation of S phase of mitotic cell cycle -0.022 0.1 -10000 0 -0.3 119 119
GNAO1 0.018 0.093 0.26 32 -0.58 19 51
HRAS 0.024 0.02 0.26 7 -10000 0 7
SHBG/T-DHT 0.015 0.005 -10000 0 -10000 0 0
PELP1 0.021 0.007 -10000 0 -10000 0 0
AKT1 0.005 0.003 -10000 0 -10000 0 0
MAP2K1 -0.068 0.11 -10000 0 -0.33 117 117
T-DHT/AR -0.039 0.15 0.17 1 -0.42 125 126
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 299 299
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.003 0.12 -10000 0 -0.58 45 45
mol:GDP -0.06 0.16 -10000 0 -0.47 127 127
cell proliferation -0.14 0.21 0.27 2 -0.44 287 289
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
FOS -0.25 0.38 -10000 0 -0.81 303 303
mol:Ca2+ -0.012 0.027 -10000 0 -0.072 126 126
MAPK3 -0.1 0.16 0.26 3 -0.32 292 295
MAPK1 -0.08 0.14 -10000 0 -0.38 110 110
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
mol:IP3 -0.001 0.002 -10000 0 -0.004 298 298
cAMP biosynthetic process 0.004 0.02 -10000 0 -10000 0 0
GNG2 0.018 0.06 -10000 0 -0.58 10 10
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 298 298
HRAS/GTP -0.026 0.12 -10000 0 -0.32 122 122
actin cytoskeleton reorganization 0.03 0.033 -10000 0 -0.3 8 8
SRC 0.023 0.005 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 298 298
PI3K 0.027 0.037 -10000 0 -0.32 10 10
apoptosis 0.13 0.21 0.43 307 -10000 0 307
T-DHT/AR/PELP1 -0.023 0.13 -10000 0 -0.37 124 124
HRAS/GDP -0.049 0.16 -10000 0 -0.46 125 125
CREB1 -0.14 0.23 -10000 0 -0.47 307 307
RAC1-CDC42/GTP 0.038 0.036 -10000 0 -0.31 8 8
AR -0.051 0.2 0.26 1 -0.58 124 125
GNB1 0.024 0.005 -10000 0 -10000 0 0
RAF1 -0.06 0.11 -10000 0 -0.32 117 117
RAC1-CDC42/GDP -0.025 0.16 -10000 0 -0.44 124 124
T-DHT/AR/PELP1/Src -0.02 0.12 -10000 0 -0.34 123 123
MAP2K2 -0.069 0.11 -10000 0 -0.33 117 117
T-DHT/AR/PELP1/Src/PI3K -0.022 0.11 -10000 0 -0.3 119 119
GNAZ 0.018 0.057 -10000 0 -0.58 9 9
SHBG 0.022 0.008 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.049 0.16 -10000 0 -0.47 89 89
mol:T-DHT -0.001 0.001 0.002 1 -0.004 86 87
RAC1 0.024 0.004 -10000 0 -10000 0 0
GNRH1 0.001 0.027 -10000 0 -0.42 4 4
Gi family/GTP -0.032 0.096 -10000 0 -0.28 84 84
CDC42 0.023 0.006 -10000 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B 0.027 0.034 -10000 0 -0.46 3 3
ARNO/beta Arrestin1-2 -0.066 0.16 -10000 0 -0.56 43 43
EGFR -0.19 0.29 -10000 0 -0.58 362 362
EPHA2 0.02 0.043 -10000 0 -0.58 5 5
USP6 0.022 0.007 -10000 0 -10000 0 0
IQSEC1 0.024 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.22 0.26 -10000 0 -0.46 507 507
ARRB2 -0.043 0.13 -10000 0 -0.36 139 139
mol:GTP 0.011 0.05 0.14 27 -0.2 22 49
ARRB1 0.021 0.028 -10000 0 -0.58 2 2
FBXO8 0.024 0.005 -10000 0 -10000 0 0
TSHR 0.001 0.12 0.26 4 -0.58 39 43
EGF -0.093 0.24 0.26 2 -0.58 195 197
somatostatin receptor activity 0 0 0.001 1 -0.001 205 206
ARAP2 0.021 0.038 -10000 0 -0.58 4 4
mol:GDP -0.12 0.16 -10000 0 -0.34 249 249
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 137 137
ITGA2B 0.033 0.061 0.26 48 -0.58 3 51
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.039 -10000 0 -0.34 5 5
ADAP1 0.025 0.034 0.26 8 -0.58 2 10
KIF13B 0.019 0.028 -10000 0 -0.58 2 2
HGF/MET -0.064 0.2 -10000 0 -0.45 202 202
PXN 0.025 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.12 0.13 -10000 0 -0.3 233 233
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.18 0.24 -10000 0 -0.41 490 490
ADRB2 -0.11 0.25 -10000 0 -0.58 217 217
receptor agonist activity 0 0 0 1 0 203 204
actin filament binding 0 0 0 2 -0.001 216 218
SRC 0.024 0.005 -10000 0 -10000 0 0
ITGB3 0.005 0.11 0.26 4 -0.58 32 36
GNAQ 0.023 0.027 -10000 0 -0.58 2 2
EFA6/PI-4-5-P2 0 0 0.001 1 -0.001 123 124
ARF6/GDP -0.039 0.15 0.25 2 -0.45 84 86
ARF6/GDP/GULP/ACAP1 -0.11 0.19 -10000 0 -0.41 201 201
alphaIIb/beta3 Integrin/paxillin/GIT1 0.05 0.081 -10000 0 -0.33 35 35
ACAP1 0.027 0.066 0.26 38 -0.58 6 44
ACAP2 0.024 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.058 0.18 -10000 0 -0.49 139 139
EFNA1 0.02 0.009 -10000 0 -10000 0 0
HGF -0.011 0.14 -10000 0 -0.58 59 59
CYTH3 0.004 0.014 -10000 0 -0.42 1 1
CYTH2 0.007 0.097 -10000 0 -1 9 9
NCK1 0.024 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0 1 0 177 178
endosomal lumen acidification 0 0 0.001 5 0 228 233
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.013 0.14 -10000 0 -0.58 62 62
GNAQ/ARNO 0.019 0.094 -10000 0 -0.95 9 9
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 117 117
MET -0.071 0.22 -10000 0 -0.58 159 159
GNA14 0.022 0.068 0.26 19 -0.58 10 29
GNA15 0.025 0.027 0.26 6 -0.58 1 7
GIT1 0.023 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 1 -0.001 161 162
GNA11 0.023 0.027 -10000 0 -0.58 2 2
LHCGR -0.069 0.2 -10000 0 -0.58 139 139
AGTR1 -0.093 0.26 0.26 58 -0.58 217 275
desensitization of G-protein coupled receptor protein signaling pathway -0.058 0.17 -10000 0 -0.49 139 139
IPCEF1/ARNO -0.14 0.2 -10000 0 -0.59 69 69
alphaIIb/beta3 Integrin 0.026 0.092 -10000 0 -0.42 35 35
IL23-mediated signaling events

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
CCL2 -0.027 0.5 0.82 44 -1.1 72 116
IL23A -0.038 0.5 0.86 33 -1.1 66 99
NF kappa B1 p50/RelA/I kappa B alpha -0.067 0.46 0.76 9 -1.1 79 88
positive regulation of T cell mediated cytotoxicity -0.029 0.56 0.91 59 -1.2 85 144
ITGA3 -0.023 0.49 0.81 43 -1.1 72 115
IL17F -0.01 0.37 0.61 67 -0.69 77 144
IL12B 0.086 0.16 0.36 197 -10000 0 197
STAT1 (dimer) -0.045 0.51 0.76 48 -1.1 94 142
CD4 -0.021 0.49 0.83 48 -1 74 122
IL23 -0.023 0.5 0.83 48 -1.1 66 114
IL23R 0.048 0.21 0.62 16 -0.94 16 32
IL1B -0.04 0.51 0.85 39 -1.2 73 112
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.014 0.5 0.85 65 -1 70 135
TYK2 0.026 0.06 0.22 6 -10000 0 6
STAT4 0.001 0.12 0.26 1 -0.58 40 41
STAT3 0.024 0.005 -10000 0 -10000 0 0
IL18RAP 0.007 0.11 0.27 4 -0.57 34 38
IL12RB1 0.035 0.095 0.38 40 -0.59 2 42
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.039 0.091 0.32 41 -0.44 2 43
IL23R/JAK2 0.061 0.22 0.56 29 -0.86 15 44
positive regulation of chronic inflammatory response -0.029 0.56 0.91 59 -1.2 85 144
natural killer cell activation -0.004 0.016 -10000 0 -0.053 35 35
JAK2 0.039 0.085 0.27 29 -10000 0 29
PIK3R1 0.019 0.056 -10000 0 -0.57 9 9
NFKB1 0.027 0.009 -10000 0 -10000 0 0
RELA 0.027 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.016 0.48 0.82 50 -1 66 116
ALOX12B -0.022 0.49 0.83 48 -1.1 71 119
CXCL1 -0.2 0.71 0.86 45 -1.2 270 315
T cell proliferation -0.029 0.56 0.91 59 -1.2 85 144
NFKBIA 0.026 0.009 -10000 0 -10000 0 0
IL17A 0.019 0.32 0.57 84 -0.55 61 145
PI3K -0.064 0.48 0.7 22 -1 93 115
IFNG 0.026 0.071 0.18 128 -0.12 13 141
STAT3 (dimer) -0.068 0.45 0.77 9 -1 80 89
IL18R1 0.017 0.076 -10000 0 -0.57 16 16
IL23/IL23R/JAK2/TYK2/SOCS3 0.034 0.35 0.66 84 -0.69 38 122
IL18/IL18R 0.041 0.1 0.29 10 -0.37 48 58
macrophage activation 0 0.03 0.058 99 -0.045 33 132
TNF -0.038 0.51 0.85 41 -1.1 77 118
STAT3/STAT4 -0.062 0.49 0.69 26 -1.1 90 116
STAT4 (dimer) -0.057 0.52 0.75 44 -1.2 92 136
IL18 0.03 0.039 0.27 25 -10000 0 25
IL19 0.019 0.5 0.84 66 -1 69 135
STAT5A (dimer) -0.048 0.51 0.76 38 -1.1 87 125
STAT1 0.029 0.032 0.26 18 -10000 0 18
SOCS3 0.02 0.043 -10000 0 -0.58 5 5
CXCL9 0.003 0.52 0.86 75 -1.1 72 147
MPO -0.052 0.55 0.84 41 -1.2 104 145
positive regulation of humoral immune response -0.029 0.56 0.91 59 -1.2 85 144
IL23/IL23R/JAK2/TYK2 -0.037 0.57 0.91 58 -1.3 81 139
IL6 -0.3 0.75 0.8 38 -1.2 369 407
STAT5A 0.02 0.047 -10000 0 -0.58 6 6
IL2 0.022 0.04 0.31 9 -10000 0 9
positive regulation of tyrosine phosphorylation of STAT protein -0.004 0.016 -10000 0 -0.053 35 35
CD3E -0.033 0.52 0.86 51 -1.2 78 129
keratinocyte proliferation -0.029 0.56 0.91 59 -1.2 85 144
NOS2 -0.022 0.49 0.82 46 -1.1 71 117
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.063 0.16 0.32 9 -0.34 101 110
SMAD6-7/SMURF1 0.046 0.016 -10000 0 -10000 0 0
NOG 0.013 0.092 0.26 17 -0.58 21 38
SMAD9 -0.092 0.26 -10000 0 -0.61 169 169
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD5 -0.027 0.14 0.23 1 -0.43 69 70
BMP7/USAG1 -0.2 0.25 -10000 0 -0.43 502 502
SMAD5/SKI -0.021 0.15 0.26 1 -0.42 76 77
SMAD1 0.012 0.064 -10000 0 -0.44 7 7
BMP2 -0.076 0.22 0.26 1 -0.58 166 167
SMAD1/SMAD1/SMAD4 0.018 0.071 -10000 0 -0.41 9 9
BMPR1A 0.023 0.019 -10000 0 -0.58 1 1
BMPR1B 0.1 0.15 0.26 398 -0.58 22 420
BMPR1A-1B/BAMBI 0.084 0.12 0.34 10 -0.33 51 61
AHSG 0.021 0.025 0.26 10 -10000 0 10
CER1 0.019 0.014 0.26 3 -10000 0 3
BMP2-4/CER1 -0.047 0.18 -10000 0 -0.4 199 199
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.041 0.17 0.22 1 -0.42 106 107
BMP2-4 (homodimer) -0.068 0.2 -10000 0 -0.46 206 206
RGMB 0.023 0.019 -10000 0 -0.58 1 1
BMP6/BMPR2/BMPR1A-1B 0.071 0.14 -10000 0 -0.32 90 90
RGMA -0.054 0.2 -10000 0 -0.58 130 130
SMURF1 0.024 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.042 0.17 0.24 1 -0.42 119 120
BMP2-4/USAG1 -0.23 0.27 -10000 0 -0.45 544 544
SMAD6/SMURF1/SMAD5 -0.022 0.15 -10000 0 -0.42 78 78
SOSTDC1 -0.26 0.3 0.26 3 -0.58 482 485
BMP7/BMPR2/BMPR1A-1B 0.07 0.14 0.3 5 -0.32 82 87
SKI 0.024 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) -0.017 0.15 0.26 2 -0.57 68 70
HFE2 0.02 0.02 0.26 6 -10000 0 6
ZFYVE16 0.024 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD -0.045 0.2 -10000 0 -0.41 204 204
SMAD5/SMAD5/SMAD4 -0.022 0.15 -10000 0 -0.43 71 71
MAPK1 0.023 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.028 0.15 -10000 0 -0.38 109 109
BMP7 (homodimer) -0.01 0.16 0.26 28 -0.57 66 94
NUP214 0.024 0.004 -10000 0 -10000 0 0
BMP6/FETUA 0 0.12 -10000 0 -0.41 73 73
SMAD1/SKI 0.019 0.078 -10000 0 -0.44 11 11
SMAD6 0.024 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/FETUA -0.047 0.18 0.34 1 -0.4 200 201
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.037 0.1 0.26 92 -0.58 14 106
BMPR2 (homodimer) 0.024 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.044 0.016 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.087 0.11 -10000 0 -0.42 23 23
CHRDL1 -0.38 0.28 -10000 0 -0.58 677 677
ENDOFIN/SMAD1 0.019 0.08 -10000 0 -0.46 11 11
SMAD6-7/SMURF1/SMAD1 0.035 0.083 -10000 0 -0.44 10 10
SMAD6/SMURF1 0.024 0.004 -10000 0 -10000 0 0
BAMBI 0.015 0.11 0.26 38 -0.58 30 68
SMURF2 0.022 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.3 0.27 -10000 0 -0.46 675 675
BMP2-4/GREM1 -0.038 0.2 -10000 0 -0.41 209 209
SMAD7 0.024 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.085 0.25 -10000 0 -0.6 167 167
SMAD1/SMAD6 0.018 0.08 -10000 0 -0.46 11 11
TAK1/SMAD6 0.034 0.01 -10000 0 -10000 0 0
BMP7 -0.011 0.16 0.26 28 -0.58 66 94
BMP6 -0.017 0.15 0.26 2 -0.58 68 70
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.041 0.17 -10000 0 -0.43 118 118
PPM1A 0.024 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.017 0.077 -10000 0 -0.46 10 10
SMAD7/SMURF1 0.034 0.009 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
PPP1CA 0.023 0.007 -10000 0 -10000 0 0
XIAP 0.025 0.002 -10000 0 -10000 0 0
CTDSP1 0.024 0.004 -10000 0 -10000 0 0
PPP1R15A 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.052 0.2 0.24 2 -0.48 123 125
CHRD 0.025 0.099 0.26 53 -0.58 19 72
BMPR2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.055 0.19 -10000 0 -0.49 117 117
BMP4 -0.011 0.14 0.26 1 -0.58 59 60
FST 0.004 0.11 0.26 4 -0.58 35 39
BMP2-4/NOG -0.049 0.19 -10000 0 -0.41 196 196
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.074 0.14 0.3 5 -0.3 82 87
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.003 0.15 -10000 0 -0.32 161 161
ER alpha/Gai/GDP/Gbeta gamma -0.081 0.22 -10000 0 -0.47 192 192
AKT1 -0.11 0.33 -10000 0 -0.78 182 182
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.11 0.33 -10000 0 -0.8 181 181
mol:Ca2+ -0.023 0.1 0.27 2 -0.44 28 30
IGF1R 0.012 0.083 0.26 2 -0.58 19 21
E2/ER alpha (dimer)/Striatin -0.013 0.16 -10000 0 -0.37 152 152
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis 0.1 0.31 0.74 182 -10000 0 182
RhoA/GTP -0.015 0.1 -10000 0 -0.29 113 113
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.062 0.21 0.32 4 -0.47 176 180
regulation of stress fiber formation 0.024 0.1 0.43 3 -0.32 6 9
E2/ERA-ERB (dimer) -0.017 0.16 -10000 0 -0.36 158 158
KRAS 0.024 0.005 -10000 0 -10000 0 0
G13/GTP -0.007 0.13 -10000 0 -0.32 138 138
pseudopodium formation -0.024 0.1 0.32 6 -0.43 3 9
E2/ER alpha (dimer)/PELP1 -0.011 0.15 -10000 0 -0.36 138 138
GRB2 0.023 0.01 0.26 1 -10000 0 1
GNG2 0.018 0.06 -10000 0 -0.58 10 10
GNAO1 0.018 0.093 0.26 32 -0.58 19 51
HRAS 0.025 0.02 0.26 7 -10000 0 7
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.083 0.23 -10000 0 -0.52 188 188
E2/ER beta (dimer) 0.008 0.064 -10000 0 -0.41 22 22
mol:GDP -0.036 0.17 0.25 14 -0.4 154 168
mol:NADP -0.083 0.23 -10000 0 -0.52 188 188
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
mol:IP3 -0.026 0.1 0.27 2 -0.46 27 29
IGF-1R heterotetramer 0.012 0.083 0.26 2 -0.57 19 21
PLCB1 -0.024 0.11 0.28 2 -0.35 70 72
PLCB2 -0.005 0.082 -10000 0 -0.5 16 16
IGF1 -0.1 0.24 -10000 0 -0.58 211 211
mol:L-citrulline -0.083 0.23 -10000 0 -0.52 188 188
RHOA 0.024 0.005 -10000 0 -10000 0 0
Gai/GDP -0.076 0.25 -10000 0 -0.63 150 150
JNK cascade 0.008 0.063 -10000 0 -0.41 22 22
BCAR1 0.021 0.008 -10000 0 -10000 0 0
ESR2 0.011 0.086 -10000 0 -0.58 21 21
GNAQ 0.023 0.027 -10000 0 -0.58 2 2
ESR1 -0.031 0.23 0.26 120 -0.58 138 258
Gq family/GDP/Gbeta gamma -0.009 0.16 -10000 0 -0.73 36 36
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.015 0.13 -10000 0 -0.56 20 20
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.055 0.2 0.31 5 -0.47 147 152
GNAZ 0.018 0.057 -10000 0 -0.58 9 9
E2/ER alpha (dimer) -0.025 0.17 0.18 120 -0.41 144 264
STRN 0.014 0.078 -10000 0 -0.58 17 17
GNAL -0.11 0.25 -10000 0 -0.58 219 219
PELP1 0.022 0.007 -10000 0 -10000 0 0
MAPK11 0.002 0.058 -10000 0 -0.36 24 24
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.003 0.12 -10000 0 -0.58 45 45
HBEGF -0.051 0.21 0.34 22 -0.51 106 128
cAMP biosynthetic process -0.088 0.18 -10000 0 -0.33 330 330
SRC -0.075 0.21 0.3 7 -0.45 187 194
PI3K 0.03 0.043 -10000 0 -0.38 10 10
GNB1 0.024 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.018 0.16 -10000 0 -0.38 141 141
SOS1 0.024 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.11 0.19 -10000 0 -0.44 201 201
Gs family/GTP -0.084 0.19 -10000 0 -0.33 330 330
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.044 0.019 -10000 0 -10000 0 0
vasodilation -0.078 0.22 -10000 0 -0.49 194 194
mol:DAG -0.026 0.1 0.27 2 -0.46 27 29
Gs family/GDP/Gbeta gamma -0.089 0.18 -10000 0 -0.36 260 260
MSN -0.026 0.11 0.33 6 -0.47 3 9
Gq family/GTP 0 0.088 -10000 0 -0.52 15 15
mol:PI-3-4-5-P3 -0.1 0.32 -10000 0 -0.76 181 181
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.078 0.22 0.49 194 -10000 0 194
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
RhoA/GDP -0.02 0.17 0.26 11 -0.39 147 158
NOS3 -0.088 0.25 -10000 0 -0.55 187 187
GNA11 0.023 0.027 -10000 0 -0.58 2 2
MAPKKK cascade -0.076 0.25 0.32 1 -0.58 178 179
E2/ER alpha (dimer)/PELP1/Src -0.066 0.22 0.33 6 -0.49 179 185
ruffle organization -0.024 0.1 0.32 6 -0.43 3 9
ROCK2 -0.025 0.12 0.36 5 -0.28 117 122
GNA14 0.023 0.068 0.26 19 -0.58 10 29
GNA15 0.025 0.027 0.26 6 -0.58 1 7
GNA13 0.023 0.007 -10000 0 -10000 0 0
MMP9 -0.043 0.21 0.36 25 -0.5 101 126
MMP2 -0.066 0.2 0.28 9 -0.43 186 195
Visual signal transduction: Rods

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
mol:K + 0.024 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.017 0.02 0.18 14 -10000 0 14
Metarhodopsin II/Arrestin 0.037 0.038 0.33 2 -10000 0 2
PDE6G/GNAT1/GTP 0.036 0.034 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.024 0.029 0.26 14 -10000 0 14
GRK1 0.019 0.017 0.26 4 -10000 0 4
CNG Channel -0.052 0.16 -10000 0 -0.31 274 274
mol:Na + -0.052 0.16 0.24 4 -0.3 277 281
mol:ADP 0.019 0.017 0.26 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.014 0.12 0.34 1 -0.36 85 86
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.047 0.17 0.29 4 -0.31 275 279
CNGB1 0.031 0.053 0.26 50 -10000 0 50
RDH5 -0.33 0.3 -10000 0 -0.58 585 585
SAG 0.033 0.054 0.26 52 -10000 0 52
mol:Ca2+ -0.085 0.14 0.35 17 -0.3 214 231
Na + (4 Units) -0.055 0.15 -10000 0 -0.29 272 272
RGS9 -0.027 0.17 0.26 11 -0.58 86 97
GNB1/GNGT1 0.055 0.061 0.2 149 -10000 0 149
GNAT1/GDP 0.023 0.11 0.32 4 -0.32 84 88
GUCY2D 0.024 0.045 0.26 16 -0.58 3 19
GNGT1 0.057 0.089 0.26 159 -10000 0 159
GUCY2F 0.019 0.011 0.26 2 -10000 0 2
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) 0.02 0.05 0.21 3 -0.32 14 17
mol:11-cis-retinal -0.33 0.3 -10000 0 -0.57 585 585
mol:cGMP 0.042 0.045 -10000 0 -0.33 7 7
GNB1 0.024 0.005 -10000 0 -10000 0 0
Rhodopsin -0.23 0.23 0.2 7 -0.42 592 599
SLC24A1 0.024 0.004 -10000 0 -10000 0 0
CNGA1 -0.14 0.27 0.26 4 -0.58 284 288
Metarhodopsin II 0.026 0.02 0.17 16 -10000 0 16
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.054 0.05 -10000 0 -0.34 7 7
RGS9BP 0.036 0.052 0.26 51 -10000 0 51
Metarhodopsin II/Transducin 0.025 0.033 0.17 8 -0.17 1 9
GCAP Family/Ca ++ 0.043 0.037 -10000 0 -0.34 4 4
PDE6A/B 0.029 0.064 -10000 0 -0.43 16 16
mol:Pi 0.014 0.12 0.34 1 -0.36 85 86
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.059 0.054 0.32 2 -10000 0 2
PDE6B 0.014 0.076 0.26 2 -0.58 16 18
PDE6A 0.028 0.033 0.26 19 -10000 0 19
PDE6G 0.032 0.047 0.26 39 -10000 0 39
RHO 0.024 0.028 0.26 13 -10000 0 13
PDE6 0.034 0.12 0.3 7 -0.31 92 99
GUCA1A 0.031 0.044 0.26 35 -10000 0 35
GC2/GCAP Family 0.054 0.039 -10000 0 -0.34 4 4
GUCA1C 0.017 0.008 0.26 1 -10000 0 1
GUCA1B 0.021 0.038 -10000 0 -0.58 4 4
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.002 0.086 -10000 0 -0.55 14 14
Crk/p130 Cas/Paxillin -0.055 0.12 -10000 0 -0.34 132 132
JUN -0.013 0.12 0.25 1 -0.41 28 29
HRAS 0.025 0.02 0.26 7 -10000 0 7
RET51/GFRalpha1/GDNF/GRB10 0.045 0.2 0.35 53 -0.34 161 214
RAP1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.012 0.26 2 -10000 0 2
RAP1A/GDP 0.018 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.046 0.19 0.35 52 -0.34 159 211
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.009 0.15 0.32 4 -0.34 163 167
RHOA 0.024 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.023 0.17 0.29 38 -0.31 160 198
GRB7 0.02 0.021 -10000 0 -0.58 1 1
RET51/GFRalpha1/GDNF 0.045 0.2 0.35 52 -0.34 161 213
MAPKKK cascade 0.002 0.15 0.28 10 -0.33 118 128
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.022 0.18 0.32 3 -0.38 173 176
lamellipodium assembly -0.032 0.13 -10000 0 -0.32 130 130
RET51/GFRalpha1/GDNF/SHC 0.038 0.18 0.35 43 -0.34 126 169
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.007 0.14 0.32 4 -0.33 122 126
RET9/GFRalpha1/GDNF/Shank3 -0.011 0.15 0.32 4 -0.33 163 167
MAPK3 -0.031 0.13 -10000 0 -0.31 125 125
DOK1 0.025 0.015 0.26 4 -10000 0 4
DOK6 0.017 0.071 0.26 6 -0.58 13 19
PXN 0.024 0.002 -10000 0 -10000 0 0
neurite development -0.03 0.12 -10000 0 -0.44 20 20
DOK5 0.011 0.09 0.26 5 -0.58 22 27
GFRA1 -0.068 0.24 0.26 54 -0.58 175 229
MAPK8 -0.007 0.13 0.22 4 -0.45 24 28
HRAS/GTP 0.031 0.18 0.3 52 -0.34 154 206
tube development -0.004 0.15 0.34 10 -0.32 156 166
MAPK1 -0.03 0.13 0.34 2 -0.31 123 125
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.021 0.11 0.2 4 -0.27 156 160
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
PDLIM7 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.041 0.19 0.34 49 -0.34 163 212
SHC1 0.02 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.031 0.19 0.34 39 -0.34 162 201
RET51/GFRalpha1/GDNF/Dok5 0.028 0.2 0.35 47 -0.36 169 216
PRKCA 0.01 0.086 0.26 1 -0.58 21 22
HRAS/GDP 0.019 0.014 0.18 7 -10000 0 7
CREB1 -0.011 0.13 0.22 15 -0.32 93 108
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.018 0.1 0.25 1 -0.26 116 117
RET51/GFRalpha1/GDNF/Grb7 0.045 0.18 0.34 66 -0.34 130 196
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.1 0.14 0.26 354 -0.58 13 367
DOK4 0.022 0.008 -10000 0 -10000 0 0
JNK cascade -0.012 0.12 0.25 1 -0.4 28 29
RET9/GFRalpha1/GDNF/FRS2 -0.01 0.15 0.32 4 -0.34 163 167
SHANK3 0.023 0.006 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.018 0.1 0.25 1 -0.27 115 116
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.008 0.14 0.24 16 -0.29 124 140
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.005 0.14 0.26 4 -0.3 126 130
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.013 0.14 0.25 17 -0.31 95 112
PI3K -0.025 0.21 0.28 18 -0.48 131 149
SOS1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.002 0.14 0.32 3 -0.32 156 159
GRB10 0.024 0.003 -10000 0 -10000 0 0
activation of MAPKK activity -0.001 0.12 0.24 10 -0.27 119 129
RET51/GFRalpha1/GDNF/FRS2 0.042 0.19 0.34 56 -0.34 161 217
GAB1 0.024 0.004 -10000 0 -10000 0 0
IRS1 0.001 0.12 -10000 0 -0.58 39 39
IRS2 0.003 0.1 -10000 0 -0.58 32 32
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.012 0.14 0.25 17 -0.3 95 112
RET51/GFRalpha1/GDNF/PKC alpha 0.027 0.2 0.35 43 -0.35 171 214
GRB2 0.023 0.01 0.26 1 -10000 0 1
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GDNF 0.033 0.054 0.26 53 -10000 0 53
RAC1 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.031 0.22 0.35 50 -0.39 172 222
Rac1/GTP -0.02 0.16 0.23 11 -0.38 130 141
RET9/GFRalpha1/GDNF -0.024 0.16 0.33 4 -0.35 175 179
GFRalpha1/GDNF -0.03 0.18 0.37 4 -0.41 177 181
Neurotrophic factor-mediated Trk 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
CRKL 0.023 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.071 0.11 -10000 0 -0.28 94 94
NT3 (dimer)/TRKC -0.18 0.27 -10000 0 -0.48 413 413
NT3 (dimer)/TRKB -0.3 0.31 -10000 0 -0.53 582 582
SHC/Grb2/SOS1/GAB1/PI3K 0.016 0.032 -10000 0 -0.26 6 6
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
BDNF -0.017 0.16 0.26 21 -0.58 77 98
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
NTRK1 0.024 0.049 0.26 21 -0.58 3 24
NTRK2 -0.29 0.3 -10000 0 -0.58 519 519
NTRK3 -0.18 0.28 0.26 5 -0.58 333 338
NT-4/5 (dimer)/TRKB -0.37 0.34 -10000 0 -0.58 653 653
neuron apoptosis 0.17 0.22 0.47 282 -10000 0 282
SHC 2-3/Grb2 -0.19 0.24 -10000 0 -0.52 282 282
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 -0.19 0.25 -10000 0 -0.54 274 274
SHC3 -0.18 0.24 -10000 0 -0.52 268 268
STAT3 (dimer) 0.034 0.042 -10000 0 -0.36 3 3
NT3 (dimer)/TRKA -0.11 0.22 -10000 0 -0.43 277 277
RIN/GDP -0.047 0.12 0.27 5 -0.26 75 80
GIPC1 0.025 0.011 0.26 2 -10000 0 2
KRAS 0.024 0.005 -10000 0 -10000 0 0
DNAJA3 -0.081 0.15 -10000 0 -0.34 240 240
RIN/GTP 0.014 0.008 0.18 2 -10000 0 2
CCND1 0.025 0.091 0.43 36 -0.83 3 39
MAGED1 0.025 0.011 0.26 2 -10000 0 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.18 0.28 -10000 0 -0.57 348 348
SHC/GRB2/SOS1 0.038 0.022 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
NGF (dimer)/TRKA/MATK 0.034 0.083 0.34 1 -0.39 27 28
TRKA/NEDD4-2 0.031 0.038 -10000 0 -0.36 4 4
ELMO1 0.024 0.003 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.032 0.007 -10000 0 -10000 0 0
NGF 0.017 0.076 0.26 7 -0.58 15 22
HRAS 0.025 0.02 0.26 7 -10000 0 7
DOCK1 0.024 0.004 -10000 0 -10000 0 0
GAB2 0.021 0.02 -10000 0 -0.58 1 1
RIT2 0.019 0.012 0.26 2 -10000 0 2
RIT1 0.021 0.009 -10000 0 -10000 0 0
FRS2 0.024 0.012 0.26 2 -10000 0 2
DNM1 0.02 0.051 0.26 1 -0.58 7 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.075 0.16 -10000 0 -0.32 273 273
mol:GDP -0.076 0.16 0.33 6 -0.37 99 105
NGF (dimer) 0.017 0.076 0.26 7 -0.57 15 22
RhoG/GDP 0.018 0.002 -10000 0 -10000 0 0
RIT1/GDP -0.046 0.11 0.37 2 -0.26 65 67
TIAM1 0.025 0.015 0.26 4 -10000 0 4
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
BDNF (dimer)/TRKB -0.19 0.23 -10000 0 -0.4 542 542
KIDINS220/CRKL/C3G 0.034 0.009 -10000 0 -10000 0 0
SHC/RasGAP 0.029 0.015 -10000 0 -10000 0 0
FRS2 family/SHP2 0.046 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.047 0.028 -10000 0 -10000 0 0
RIT1/GTP 0.015 0.007 -10000 0 -10000 0 0
NT3 (dimer) -0.063 0.22 0.26 12 -0.57 148 160
RAP1/GDP -0.043 0.094 -10000 0 -0.22 73 73
KIDINS220/CRKL 0.023 0.006 -10000 0 -10000 0 0
BDNF (dimer) -0.017 0.16 0.26 21 -0.57 77 98
ubiquitin-dependent protein catabolic process 0.035 0.061 -10000 0 -0.36 16 16
Schwann cell development -0.05 0.039 -10000 0 -10000 0 0
EHD4 0.024 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.055 0.024 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.019 0.051 -10000 0 -0.27 9 9
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.28 0.29 -10000 0 -0.48 592 592
ABL1 0.024 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.079 0.13 -10000 0 -0.45 50 50
STAT3 0.034 0.042 -10000 0 -0.36 3 3
axon guidance -0.27 0.27 -10000 0 -0.46 592 592
MAPK3 0.026 0.088 0.25 5 -0.36 25 30
MAPK1 0.028 0.09 0.25 5 -0.36 26 31
CDC42/GDP -0.045 0.12 0.29 5 -0.26 70 75
NTF3 -0.063 0.22 0.26 12 -0.58 148 160
NTF4 -0.18 0.28 -10000 0 -0.58 348 348
NGF (dimer)/TRKA/FAIM 0.037 0.061 -10000 0 -0.37 16 16
PI3K 0.03 0.043 -10000 0 -0.38 10 10
FRS3 0.024 0.005 -10000 0 -10000 0 0
FAIM 0.024 0.004 -10000 0 -10000 0 0
GAB1 0.024 0.004 -10000 0 -10000 0 0
RASGRF1 -0.08 0.16 0.25 2 -0.34 262 264
SOS1 0.024 0.003 -10000 0 -10000 0 0
MCF2L -0.16 0.22 0.21 1 -0.42 402 403
RGS19 0.023 0.01 0.26 1 -10000 0 1
CDC42 0.023 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.016 0.096 0.4 1 -0.43 10 11
Rac1/GDP -0.046 0.12 0.3 4 -0.26 70 74
NGF (dimer)/TRKA/GRIT 0.024 0.057 -10000 0 -0.36 16 16
neuron projection morphogenesis -0.074 0.22 -10000 0 -0.76 48 48
NGF (dimer)/TRKA/NEDD4-2 0.036 0.061 -10000 0 -0.37 16 16
MAP2K1 0.031 0.087 0.36 17 -10000 0 17
NGFR -0.14 0.27 -10000 0 -0.58 275 275
NGF (dimer)/TRKA/GIPC/GAIP 0.015 0.051 -10000 0 -0.29 19 19
RAS family/GTP/PI3K 0.018 0.027 -10000 0 -0.26 6 6
FRS2 family/SHP2/GRB2/SOS1 0.064 0.027 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.023 0.02 -10000 0 -0.58 1 1
MAPKKK cascade -0.04 0.14 -10000 0 -0.66 37 37
RASA1 0.024 0.004 -10000 0 -10000 0 0
TRKA/c-Abl 0.032 0.037 -10000 0 -0.43 3 3
SQSTM1 0.024 0.008 0.26 1 -10000 0 1
BDNF (dimer)/TRKB/GIPC -0.17 0.22 -10000 0 -0.36 536 536
NGF (dimer)/TRKA/p62/Atypical PKCs 0.052 0.062 -10000 0 -0.32 16 16
MATK 0.02 0.087 0.26 27 -0.58 17 44
NEDD4L 0.023 0.02 -10000 0 -0.58 1 1
RAS family/GDP -0.057 0.07 -10000 0 -0.21 57 57
NGF (dimer)/TRKA -0.089 0.17 -10000 0 -0.34 286 286
Rac1/GTP -0.087 0.12 -10000 0 -0.28 211 211
FRS2 family/SHP2/CRK family 0.06 0.029 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.004 0.041 0.22 4 -0.37 2 6
NFATC2 -0.024 0.11 0.24 3 -0.38 76 79
NFATC3 0.006 0.035 0.21 5 -10000 0 5
CD40LG -0.14 0.29 0.51 17 -0.57 226 243
PTGS2 -0.19 0.34 0.51 12 -0.64 305 317
JUNB 0.025 0.011 0.26 2 -10000 0 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.028 0.16 3 -10000 0 3
CaM/Ca2+ 0.009 0.028 0.16 3 -10000 0 3
CALM1 0.016 0.022 -10000 0 -10000 0 0
JUN 0.012 0.058 -10000 0 -0.58 8 8
mol:Ca2+ -0.003 0.011 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.012 -10000 0 -10000 0 0
FOSL1 0.028 0.044 0.26 22 -0.58 2 24
CREM 0.023 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.003 0.15 0.46 13 -0.4 52 65
FOS -0.15 0.27 -10000 0 -0.58 285 285
IFNG -0.11 0.28 0.48 38 -0.54 201 239
AP-1/NFAT1-c-4 -0.13 0.34 0.54 38 -0.62 239 277
FASLG -0.12 0.27 0.55 19 -0.55 182 201
NFAT1-c-4/ICER1 -0.015 0.12 0.32 8 -0.35 68 76
IL2RA -0.12 0.28 0.5 28 -0.55 212 240
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSF2 -0.13 0.28 0.51 18 -0.54 220 238
JunB/Fra1/NFAT1-c-4 -0.003 0.13 0.34 13 -0.34 67 80
IL4 -0.13 0.27 0.5 13 -0.54 219 232
IL2 -0.015 0.16 -10000 0 -0.94 27 27
IL3 -0.018 0.12 -10000 0 -0.72 23 23
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
BATF3 0.021 0.014 0.26 2 -10000 0 2
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.021 0.012 0.26 1 -10000 0 1
Signaling events mediated by PTP1B

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
PDGFRB 0.022 0.038 -10000 0 -0.58 4 4
Jak2/Leptin Receptor -0.11 0.19 0.27 1 -0.42 223 224
PTP1B/AKT1 -0.068 0.13 0.22 1 -0.34 127 128
FYN 0.022 0.027 -10000 0 -0.58 2 2
p210 bcr-abl/PTP1B -0.083 0.14 0.22 2 -0.36 144 146
EGFR -0.2 0.29 -10000 0 -0.59 362 362
EGF/EGFR -0.2 0.24 -10000 0 -0.42 502 502
CSF1 0.022 0.038 -10000 0 -0.58 4 4
AKT1 0.024 0.005 -10000 0 -10000 0 0
INSR 0.024 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.049 0.16 0.23 16 -0.36 124 140
Insulin Receptor/Insulin -0.045 0.12 -10000 0 -0.38 47 47
HCK 0.027 0.026 0.26 12 -10000 0 12
CRK 0.022 0.007 -10000 0 -10000 0 0
TYK2 -0.08 0.13 0.31 2 -0.35 135 137
EGF -0.11 0.24 0.26 2 -0.58 195 197
YES1 0.023 0.02 -10000 0 -0.58 1 1
CAV1 -0.16 0.21 0.27 3 -0.43 299 302
TXN 0.017 0.018 0.26 3 -10000 0 3
PTP1B/IRS1/GRB2 -0.074 0.15 -10000 0 -0.37 141 141
cell migration 0.083 0.14 0.36 144 -0.22 2 146
STAT3 0.022 0.005 -10000 0 -10000 0 0
PRLR 0.023 0.047 0.26 6 -0.58 5 11
ITGA2B 0.031 0.061 0.26 48 -0.58 3 51
CSF1R 0.024 0.008 0.26 1 -10000 0 1
Prolactin Receptor/Prolactin 0.032 0.04 0.32 1 -0.38 5 6
FGR 0.024 0.009 0.26 1 -10000 0 1
PTP1B/p130 Cas -0.07 0.14 0.22 1 -0.35 132 133
Crk/p130 Cas -0.063 0.14 -10000 0 -0.35 116 116
DOK1 -0.069 0.13 0.25 3 -0.39 80 83
JAK2 -0.049 0.12 0.27 1 -0.48 49 50
Jak2/Leptin Receptor/Leptin -0.27 0.16 -10000 0 -0.4 406 406
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
PTPN1 -0.084 0.14 0.22 2 -0.36 144 146
LYN 0.021 0.009 -10000 0 -10000 0 0
CDH2 0.064 0.095 0.26 175 -0.58 2 177
SRC -0.018 0.099 -10000 0 -0.62 20 20
ITGB3 0.004 0.11 0.26 4 -0.58 32 36
CAT1/PTP1B -0.093 0.19 0.55 2 -0.48 132 134
CAPN1 0.021 0.006 -10000 0 -10000 0 0
CSK 0.024 0.004 -10000 0 -10000 0 0
PI3K -0.039 0.12 -10000 0 -0.4 44 44
mol:H2O2 -0.005 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.24 0.14 -10000 0 -0.36 375 375
negative regulation of transcription -0.049 0.12 0.27 1 -0.47 49 50
FCGR2A 0.02 0.009 -10000 0 -10000 0 0
FER 0.01 0.064 -10000 0 -0.59 11 11
alphaIIb/beta3 Integrin 0.022 0.092 -10000 0 -0.42 35 35
BLK 0.051 0.088 0.26 135 -0.58 2 137
Insulin Receptor/Insulin/Shc 0.035 0.019 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
LEPR -0.12 0.26 -10000 0 -0.58 247 247
BCAR1 0.021 0.008 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.023 0.01 0.26 1 -10000 0 1
mol:NADPH -0.005 0.004 -10000 0 -10000 0 0
TRPV6 -0.041 0.17 0.48 3 -0.46 87 90
PRL 0.008 0.034 0.27 10 -10000 0 10
SOCS3 0.009 0.16 -10000 0 -1.2 16 16
SPRY2 -0.041 0.18 -10000 0 -0.58 97 97
Insulin Receptor/Insulin/IRS1 0.026 0.081 -10000 0 -0.38 38 38
CSF1/CSF1R -0.066 0.14 -10000 0 -0.36 122 122
Ras protein signal transduction 0.052 0.15 0.64 57 -10000 0 57
IRS1 0.001 0.12 -10000 0 -0.58 39 39
INS 0.009 0.015 -10000 0 -10000 0 0
LEP -0.45 0.24 -10000 0 -0.58 783 783
STAT5B -0.071 0.14 0.22 4 -0.36 125 129
STAT5A -0.072 0.14 0.22 4 -0.36 129 133
GRB2 0.023 0.01 0.26 1 -10000 0 1
PDGFB-D/PDGFRB -0.074 0.14 0.22 1 -0.36 136 137
CSN2 0.025 0.058 0.4 1 -10000 0 1
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
LAT -0.01 0.073 -10000 0 -0.59 8 8
YBX1 0.027 0.016 0.22 4 -10000 0 4
LCK 0.026 0.077 0.26 36 -0.58 11 47
SHC1 0.02 0.009 -10000 0 -10000 0 0
NOX4 0.02 0.033 0.26 10 -0.58 1 11
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 0.025 0.008 0.26 1 -10000 0 1
CCL5 0.03 0.056 0.26 36 -0.58 3 39
SDCBP 0.021 0.009 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.064 0.12 0.23 99 -0.32 23 122
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.05 0.12 0.27 7 -0.37 17 24
Syndecan-1/Syntenin 0.052 0.12 0.28 12 -0.37 15 27
MAPK3 0.049 0.12 0.26 13 -0.35 15 28
HGF/MET -0.064 0.2 -10000 0 -0.45 202 202
TGFB1/TGF beta receptor Type II 0.024 0.008 0.26 1 -10000 0 1
BSG 0.024 0.009 0.26 1 -10000 0 1
keratinocyte migration 0.05 0.12 0.27 7 -0.36 17 24
Syndecan-1/RANTES 0.06 0.14 0.3 44 -0.4 18 62
Syndecan-1/CD147 0.065 0.13 0.3 12 -0.36 16 28
Syndecan-1/Syntenin/PIP2 0.048 0.11 0.27 12 -0.35 15 27
LAMA5 0.023 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.046 0.11 0.26 11 -0.35 15 26
MMP7 -0.038 0.2 0.26 30 -0.58 112 142
HGF -0.011 0.14 -10000 0 -0.58 59 59
Syndecan-1/CASK 0.043 0.12 0.19 94 -0.31 29 123
Syndecan-1/HGF/MET -0.003 0.2 0.29 7 -0.46 105 112
regulation of cell adhesion 0.042 0.11 0.26 10 -0.36 12 22
HPSE 0.027 0.036 0.26 17 -0.58 1 18
positive regulation of cell migration 0.064 0.12 0.23 99 -0.32 23 122
SDC1 0.067 0.12 0.23 98 -0.26 50 148
Syndecan-1/Collagen 0.064 0.12 0.23 99 -0.32 23 122
PPIB 0.025 0.014 0.26 3 -10000 0 3
MET -0.071 0.22 -10000 0 -0.58 159 159
PRKACA 0.024 0.003 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 409 -0.58 1 410
MAPK1 0.049 0.12 0.27 11 -0.35 14 25
homophilic cell adhesion 0.063 0.12 0.23 99 -0.32 23 122
MMP1 0.18 0.11 0.26 686 -10000 0 686
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.039 0.17 -10000 0 -0.42 159 159
CRKL -0.047 0.15 0.36 1 -0.41 83 84
mol:PIP3 0.002 0.064 0.57 2 -0.91 4 6
AKT1 0.011 0.077 0.37 4 -0.8 4 8
PTK2B 0.02 0.01 -10000 0 -10000 0 0
RAPGEF1 -0.046 0.14 0.34 1 -0.41 69 70
RANBP10 0.022 0.008 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.041 0.18 -10000 0 -0.39 193 193
MAP3K5 -0.04 0.15 0.33 2 -0.45 60 62
HGF/MET/CIN85/CBL/ENDOPHILINS -0.029 0.17 -10000 0 -0.36 199 199
AP1 -0.11 0.19 -10000 0 -0.4 288 288
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis -0.24 0.38 -10000 0 -0.77 332 332
STAT3 (dimer) -0.046 0.15 -10000 0 -0.45 76 76
GAB1/CRKL/SHP2/PI3K -0.019 0.15 -10000 0 -0.4 74 74
INPP5D 0.024 0.004 -10000 0 -10000 0 0
CBL/CRK -0.036 0.15 0.34 1 -0.41 67 68
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.023 0.005 -10000 0 -10000 0 0
PTEN 0.023 0.027 -10000 0 -0.58 2 2
ELK1 -0.029 0.098 0.26 40 -0.21 115 155
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.026 0.093 -10000 0 -0.28 56 56
PAK1 0.024 0.089 0.33 11 -0.76 4 15
HGF/MET/RANBP10 -0.043 0.18 -10000 0 -0.39 200 200
HRAS -0.1 0.26 -10000 0 -0.64 174 174
DOCK1 -0.046 0.14 0.52 1 -0.41 71 72
GAB1 -0.05 0.16 -10000 0 -0.36 155 155
CRK -0.048 0.15 0.3 2 -0.4 89 91
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.1 0.25 -10000 0 -0.58 209 209
JUN 0.019 0.054 -10000 0 -0.58 8 8
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.051 0.12 -10000 0 -0.29 203 203
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
cell morphogenesis -0.049 0.16 0.39 4 -0.45 82 86
GRB2/SHC -0.015 0.11 -10000 0 -0.29 109 109
FOS -0.15 0.27 -10000 0 -0.58 285 285
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.029 0.097 0.26 40 -0.21 115 155
HGF/MET/MUC20 -0.054 0.17 -10000 0 -0.39 202 202
cell migration -0.015 0.11 -10000 0 -0.28 109 109
GRB2 0.023 0.01 0.26 1 -10000 0 1
CBL 0.022 0.008 -10000 0 -10000 0 0
MET/RANBP10 -0.041 0.17 -10000 0 -0.42 159 159
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.047 0.14 -10000 0 -0.34 165 165
MET/MUC20 -0.054 0.16 -10000 0 -0.41 167 167
RAP1B -0.039 0.14 0.3 2 -0.44 46 48
RAP1A -0.045 0.14 0.41 2 -0.44 45 47
HGF/MET/RANBP9 -0.041 0.18 -10000 0 -0.39 196 196
RAF1 -0.097 0.24 -10000 0 -0.61 174 174
STAT3 -0.047 0.15 -10000 0 -0.46 76 76
cell proliferation -0.04 0.19 0.28 30 -0.43 142 172
RPS6KB1 -0.015 0.064 -10000 0 -0.24 32 32
MAPK3 -0.041 0.095 0.72 6 -10000 0 6
MAPK1 -0.009 0.18 0.68 53 -10000 0 53
RANBP9 0.024 0.005 -10000 0 -10000 0 0
MAPK8 -0.028 0.14 0.36 2 -0.44 45 47
SRC -0.051 0.13 0.2 1 -0.41 69 70
PI3K -0.026 0.13 -10000 0 -0.28 192 192
MET/Glomulin -0.046 0.15 -10000 0 -0.38 161 161
SOS1 0.024 0.003 -10000 0 -10000 0 0
MAP2K1 -0.089 0.23 0.47 1 -0.56 173 174
MET -0.071 0.22 -10000 0 -0.58 159 159
MAP4K1 -0.042 0.16 0.38 1 -0.43 80 81
PTK2 0.019 0.01 -10000 0 -10000 0 0
MAP2K2 -0.089 0.23 0.47 1 -0.56 174 175
BAD 0.009 0.073 0.33 4 -0.76 4 8
MAP2K4 -0.037 0.14 0.32 2 -0.41 55 57
SHP2/GRB2/SOS1/GAB1 -0.039 0.18 -10000 0 -0.4 161 161
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
SH3KBP1 0.024 0.003 -10000 0 -10000 0 0
HGS -0.047 0.11 -10000 0 -0.27 184 184
PLCgamma1/PKC 0.017 0.004 -10000 0 -10000 0 0
HGF -0.011 0.14 -10000 0 -0.58 59 59
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.021 0.13 -10000 0 -0.27 190 190
PDPK1 0.013 0.081 0.28 10 -0.84 4 14
HGF/MET/SHIP -0.042 0.18 -10000 0 -0.39 201 201
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.018 0.041 -10000 0 -0.37 4 4
PDGFRB 0.018 0.039 -10000 0 -0.58 4 4
SPHK1 -0.019 0.1 -10000 0 -0.75 14 14
mol:S1P -0.021 0.097 0.39 1 -0.66 14 15
S1P1/S1P/Gi -0.13 0.23 0.32 2 -0.43 327 329
GNAO1 0.006 0.095 0.25 32 -0.58 19 51
PDGFB-D/PDGFRB/PLCgamma1 -0.11 0.21 0.38 3 -0.4 297 300
PLCG1 -0.13 0.22 0.36 2 -0.42 306 308
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.018 0.039 -10000 0 -0.58 4 4
GNAI2 0.009 0.023 -10000 0 -10000 0 0
GNAI3 0.009 0.023 -10000 0 -10000 0 0
GNAI1 -0.017 0.13 -10000 0 -0.59 45 45
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.014 0.028 0.2 1 -0.38 3 4
S1P1/S1P -0.035 0.098 0.28 2 -0.48 17 19
negative regulation of cAMP metabolic process -0.13 0.23 0.32 2 -0.42 327 329
MAPK3 -0.18 0.3 0.3 12 -0.58 330 342
calcium-dependent phospholipase C activity -0.003 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
KDR 0.012 0.038 -10000 0 -0.58 3 3
PLCB2 -0.026 0.098 0.3 6 -0.42 18 24
RAC1 0.024 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.082 -10000 0 -0.4 17 17
receptor internalization -0.035 0.09 -10000 0 -0.44 17 17
PTGS2 -0.34 0.5 0.39 2 -1 343 345
Rac1/GTP -0.033 0.082 -10000 0 -0.4 17 17
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFA 0.015 0.027 0.26 6 -10000 0 6
negative regulation of T cell proliferation -0.13 0.23 0.32 2 -0.42 327 329
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.004 0.06 -10000 0 -0.58 9 9
MAPK1 -0.2 0.33 0.32 3 -0.62 348 351
S1P1/S1P/PDGFB-D/PDGFRB -0.034 0.12 0.31 4 -0.48 16 20
ABCC1 0.012 0.019 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.024 0.005 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.11 0.08 0.32 7 -0.3 1 8
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.019 0.02 -10000 0 -0.3 2 2
AURKB 0.14 0.12 0.26 521 -10000 0 521
AURKC 0.026 0.031 0.26 10 -0.58 1 11
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.006 0.07 0.35 1 -0.35 9 10
alphaM/beta2 Integrin/GPIbA 0.01 0.076 0.34 4 -0.41 6 10
alphaM/beta2 Integrin/proMMP-9 0.072 0.11 0.35 13 -0.42 1 14
PLAUR 0.041 0.061 0.26 71 -10000 0 71
HMGB1 -0.004 0.041 -10000 0 -0.18 1 1
alphaM/beta2 Integrin/Talin 0.009 0.063 0.35 1 -10000 0 1
AGER -0.007 0.051 -10000 0 -0.48 3 3
RAP1A 0.024 0.004 -10000 0 -10000 0 0
SELPLG 0.024 0.003 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.026 0.14 0.33 4 -0.22 272 276
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 409 -0.58 1 410
CYR61 -0.005 0.13 -10000 0 -0.58 48 48
TLN1 0.024 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.001 0.11 -10000 0 -0.36 38 38
RHOA 0.024 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.093 0.23 -10000 0 -0.57 190 190
MYH2 -0.012 0.14 0.26 9 -0.46 37 46
MST1R 0.022 0.055 0.26 9 -0.58 7 16
leukocyte activation during inflammatory response -0.19 0.17 0.3 1 -0.33 556 557
APOB -0.34 0.29 -10000 0 -0.58 611 611
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.018 0.047 -10000 0 -0.58 6 6
JAM3 0.019 0.043 -10000 0 -0.58 5 5
GP1BA 0.024 0.06 0.26 24 -0.58 6 30
alphaM/beta2 Integrin/CTGF 0.005 0.076 0.35 1 -0.39 12 13
alphaM/beta2 Integrin -0.011 0.12 0.21 5 -0.38 44 49
JAM3 homodimer 0.019 0.043 -10000 0 -0.57 5 5
ICAM2 0.019 0.043 -10000 0 -0.58 5 5
ICAM1 0.028 0.029 0.26 15 -10000 0 15
phagocytosis triggered by activation of immune response cell surface activating receptor -0.009 0.12 0.23 7 -0.38 45 52
cell adhesion 0.009 0.075 0.34 4 -0.41 6 10
NFKB1 -0.1 0.2 0.42 4 -0.38 312 316
THY1 0.024 0.021 0.26 7 -10000 0 7
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.22 0.19 0.18 1 -0.36 617 618
alphaM/beta2 Integrin/LRP/tPA 0.008 0.091 0.34 1 -0.39 25 26
IL6 -0.26 0.39 0.35 3 -0.76 370 373
ITGB2 -0.003 0.051 0.26 12 -10000 0 12
elevation of cytosolic calcium ion concentration 0.03 0.084 0.34 18 -10000 0 18
alphaM/beta2 Integrin/JAM2/JAM3 0 0.1 0.34 1 -0.39 42 43
JAM2 -0.006 0.13 -10000 0 -0.58 50 50
alphaM/beta2 Integrin/ICAM1 0.023 0.087 0.33 4 -0.33 17 21
alphaM/beta2 Integrin/uPA/Plg 0.019 0.07 0.34 1 -10000 0 1
RhoA/GTP -0.017 0.15 0.24 13 -0.4 66 79
positive regulation of phagocytosis -0.001 0.1 0.32 4 -0.34 24 28
Ron/MSP 0.029 0.064 0.21 12 -0.41 18 30
alphaM/beta2 Integrin/uPAR/uPA 0.032 0.086 0.35 18 -10000 0 18
alphaM/beta2 Integrin/uPAR 0.019 0.078 0.41 3 -10000 0 3
PLAU 0.03 0.039 0.26 27 -10000 0 27
PLAT 0.006 0.092 -10000 0 -0.58 24 24
actin filament polymerization -0.011 0.14 0.29 6 -0.44 37 43
MST1 0.02 0.056 0.26 4 -0.58 8 12
alphaM/beta2 Integrin/lipoprotein(a) -0.19 0.17 0.32 1 -0.33 556 557
TNF -0.1 0.2 0.35 6 -0.73 20 26
RAP1B 0.024 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.014 0.068 0.35 1 -10000 0 1
fibrinolysis 0.018 0.068 0.33 1 -10000 0 1
HCK 0.027 0.026 0.26 12 -10000 0 12
dendritic cell antigen processing and presentation -0.009 0.12 0.23 7 -0.38 45 52
VTN 0.034 0.072 0.26 60 -0.58 5 65
alphaM/beta2 Integrin/CYR61 -0.008 0.11 0.35 1 -0.38 51 52
LPA 0.018 0.018 0.26 5 -10000 0 5
LRP1 0.018 0.06 -10000 0 -0.58 10 10
cell migration 0.043 0.084 0.29 12 -0.36 8 20
FN1 0.12 0.12 0.26 394 -10000 0 394
alphaM/beta2 Integrin/Thy1 0.01 0.063 0.35 1 -10000 0 1
MPO -0.011 0.14 0.26 2 -0.58 55 57
KNG1 0.022 0.028 0.26 13 -10000 0 13
RAP1/GDP 0.031 0.008 -10000 0 -10000 0 0
ROCK1 -0.012 0.15 0.27 14 -0.46 41 55
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.018 0.016 0.26 4 -10000 0 4
CTGF 0.017 0.066 0.26 2 -0.58 12 14
alphaM/beta2 Integrin/Hck 0.011 0.067 0.36 4 -10000 0 4
ITGAM -0.003 0.044 0.25 5 -10000 0 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.044 0.16 0.34 1 -0.36 170 171
HP -0.067 0.23 0.26 35 -0.58 161 196
leukocyte adhesion -0.039 0.14 0.29 4 -0.38 56 60
SELP -0.093 0.23 -10000 0 -0.58 190 190
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.1 0.19 -10000 0 -0.37 305 305
fibroblast growth factor receptor signaling pathway -0.1 0.19 -10000 0 -0.37 305 305
LAMA1 -0.039 0.18 0.26 2 -0.58 105 107
PRNP 0.015 0.071 -10000 0 -0.58 14 14
GPC1/SLIT2 -0.012 0.14 -10000 0 -0.43 99 99
SMAD2 0 0.067 0.25 1 -0.34 36 37
GPC1/PrPc/Cu2+ 0.026 0.05 -10000 0 -0.36 15 15
GPC1/Laminin alpha1 -0.016 0.14 -10000 0 -0.43 106 106
TDGF1 0.017 0.06 0.26 1 -0.58 10 11
CRIPTO/GPC1 0.03 0.05 -10000 0 -0.43 11 11
APP/GPC1 0.035 0.021 -10000 0 -0.43 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.005 0.041 -10000 0 -0.37 11 11
FLT1 0.023 0.006 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.032 0.08 -10000 0 -0.37 37 37
SERPINC1 0.029 0.048 0.26 39 -10000 0 39
FYN 0.004 0.044 -10000 0 -0.36 13 13
FGR 0.005 0.041 -10000 0 -0.37 11 11
positive regulation of MAPKKK cascade 0.008 0.084 0.28 2 -0.36 26 28
SLIT2 -0.035 0.18 -10000 0 -0.58 98 98
GPC1/NRG -0.11 0.2 -10000 0 -0.43 280 280
NRG1 -0.15 0.27 0.26 4 -0.58 279 283
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.045 0.026 -10000 0 -0.37 1 1
LYN 0.005 0.036 -10000 0 -0.37 8 8
mol:Spermine 0.006 0.016 -10000 0 -0.42 1 1
cell growth -0.1 0.19 -10000 0 -0.37 305 305
BMP signaling pathway -0.025 0.026 0.57 1 -0.26 5 6
SRC 0.005 0.041 -10000 0 -0.37 11 11
TGFBR1 0.024 0.008 0.26 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.14 0.28 0.26 26 -0.58 288 314
GPC1 0.025 0.026 0.26 5 -0.58 1 6
TGFBR1 (dimer) 0.024 0.008 0.26 1 -10000 0 1
VEGFA 0.025 0.019 0.26 6 -10000 0 6
BLK 0.019 0.067 -10000 0 -0.38 13 13
HCK 0.006 0.044 -10000 0 -0.37 11 11
FGF2 -0.2 0.29 -10000 0 -0.58 376 376
FGFR1 0.016 0.051 -10000 0 -0.58 7 7
VEGFR1 homodimer 0.023 0.006 -10000 0 -10000 0 0
TGFBR2 0.003 0.11 -10000 0 -0.58 36 36
cell death 0.035 0.021 -10000 0 -0.43 1 1
ATIII/GPC1 0.036 0.039 -10000 0 -0.43 1 1
PLA2G2A/GPC1 -0.1 0.21 -10000 0 -0.43 288 288
LCK 0.005 0.062 -10000 0 -0.36 22 22
neuron differentiation -0.11 0.2 -10000 0 -0.42 280 280
PrPc/Cu2+ 0.011 0.052 -10000 0 -0.42 14 14
APP 0.024 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.003 0.11 -10000 0 -0.57 36 36
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.034 0.03 -10000 0 -0.42 3 3
alphaV beta3 Integrin -0.12 0.21 -10000 0 -0.38 370 370
PTK2 -0.057 0.15 0.32 2 -0.48 53 55
IGF1R 0.012 0.083 0.26 2 -0.58 19 21
PI4KB 0.02 0.009 -10000 0 -10000 0 0
MFGE8 0.018 0.068 0.26 6 -0.58 12 18
SRC 0.024 0.005 -10000 0 -10000 0 0
CDKN1B -0.043 0.12 -10000 0 -0.51 31 31
VEGFA 0.025 0.019 0.26 6 -10000 0 6
ILK -0.041 0.11 -10000 0 -0.48 28 28
ROCK1 0.023 0.019 -10000 0 -0.58 1 1
AKT1 -0.042 0.1 -10000 0 -0.46 25 25
PTK2B -0.014 0.072 0.36 2 -0.34 32 34
alphaV/beta3 Integrin/JAM-A -0.076 0.17 0.3 1 -0.33 269 270
CBL 0.022 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.031 0.075 -10000 0 -0.37 32 32
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.044 0.2 -10000 0 -0.39 224 224
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.014 0.064 -10000 0 -0.42 8 8
alphaV/beta3 Integrin/Syndecan-1 0.043 0.084 -10000 0 -0.36 32 32
PI4KA 0.023 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.27 -10000 0 -0.46 328 328
PI4 Kinase 0.028 0.015 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.069 0.1 0.34 3 -0.36 32 35
RPS6KB1 -0.16 0.23 0.42 3 -0.44 293 296
TLN1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 -0.2 0.29 -10000 0 -0.56 351 351
GPR124 0.016 0.051 -10000 0 -0.58 7 7
MAPK1 -0.2 0.3 -10000 0 -0.56 365 365
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
alphaV/beta3 Integrin/Tumstatin -0.038 0.17 -10000 0 -0.38 196 196
cell adhesion 0.022 0.085 0.26 1 -0.37 41 42
ANGPTL3 0.021 0.016 0.26 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.045 0.028 -10000 0 -0.37 2 2
IGF-1R heterotetramer 0.012 0.083 0.26 2 -0.57 19 21
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
TGFBR2 0.003 0.11 -10000 0 -0.58 36 36
ITGB3 0.005 0.11 0.26 4 -0.58 32 36
IGF1 -0.1 0.24 -10000 0 -0.58 211 211
RAC1 0.024 0.004 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.024 0.081 -10000 0 -0.4 30 30
apoptosis 0.024 0.003 -10000 0 -10000 0 0
CD47 0.024 0.019 -10000 0 -0.58 1 1
alphaV/beta3 Integrin/CD47 0.034 0.075 -10000 0 -0.37 32 32
VCL 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.014 0.14 -10000 0 -0.46 66 66
CSF1 0.022 0.038 -10000 0 -0.58 4 4
PIK3C2A -0.039 0.11 -10000 0 -0.47 25 25
PI4 Kinase/Pyk2 -0.076 0.15 -10000 0 -0.31 226 226
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.044 0.079 -10000 0 -0.36 32 32
FAK1/Vinculin -0.038 0.14 0.34 4 -0.39 48 52
alphaV beta3/Integrin/ppsTEM5 0.024 0.082 -10000 0 -0.4 30 30
RHOA 0.024 0.005 -10000 0 -10000 0 0
VTN 0.034 0.072 0.26 60 -0.58 5 65
BCAR1 0.021 0.008 -10000 0 -10000 0 0
FGF2 -0.2 0.29 -10000 0 -0.58 376 376
F11R -0.12 0.2 -10000 0 -0.43 283 283
alphaV/beta3 Integrin/Lactadherin 0.029 0.09 0.34 1 -0.39 41 42
alphaV/beta3 Integrin/TGFBR2 0.021 0.12 -10000 0 -0.47 50 50
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.05 0.035 -10000 0 -0.33 4 4
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.032 0.068 -10000 0 -0.34 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.12 0.12 0.26 394 -10000 0 394
alphaV/beta3 Integrin/Pyk2 0.026 0.075 -10000 0 -0.34 32 32
SDC1 0.04 0.063 0.26 69 -0.58 1 70
VAV3 -0.01 0.04 -10000 0 -0.32 10 10
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0.001 0.12 -10000 0 -0.58 39 39
FAK1/Paxillin -0.038 0.14 0.34 4 -0.39 49 53
cell migration -0.037 0.12 0.3 7 -0.36 43 50
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PI3K -0.065 0.17 -10000 0 -0.32 260 260
SPP1 0.086 0.1 0.26 261 -10000 0 261
KDR 0.022 0.033 -10000 0 -0.58 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.003 -10000 0 -10000 0 0
COL4A3 -0.082 0.23 0.26 4 -0.58 178 182
angiogenesis -0.18 0.3 0.3 1 -0.56 344 345
Rac1/GTP 0.021 0.037 -10000 0 -0.3 9 9
EDIL3 -0.006 0.14 0.26 15 -0.58 55 70
cell proliferation 0.02 0.12 -10000 0 -0.46 50 50
Effects of Botulinum toxin

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
STX1A 0.011 0.025 0.14 37 -10000 0 37
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.033 0.11 -10000 0 -0.43 40 40
STXBP1 0.021 0.042 -10000 0 -0.58 5 5
ACh/CHRNA1 0.073 0.092 0.2 322 -0.16 7 329
RAB3GAP2/RIMS1/UNC13B 0.036 0.088 -10000 0 -0.37 30 30
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.026 0.14 0.26 111 -0.58 40 151
mol:ACh -0.004 0.037 0.091 11 -0.14 41 52
RAB3GAP2 0.02 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.021 0.083 0.24 1 -0.28 39 40
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.073 0.091 0.2 322 -0.16 7 329
UNC13B 0.024 0.004 -10000 0 -10000 0 0
CHRNA1 0.1 0.11 0.26 333 -10000 0 333
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.035 0.11 0.2 190 -0.37 38 228
SNAP25 0 0.059 0.097 55 -0.3 32 87
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 0.05 0.15 0.26 198 -0.58 35 233
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.023 0.033 -10000 0 -0.36 5 5
STX1A/SNAP25 fragment 1/VAMP2 0.021 0.083 0.24 1 -0.28 39 40
IL6-mediated signaling 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
BCL2L1 -0.027 0.23 0.55 9 -0.64 32 41
CRP -0.005 0.24 0.57 25 -0.7 22 47
cell cycle arrest -0.038 0.25 0.56 11 -0.69 46 57
TIMP1 -0.02 0.22 0.53 10 -0.63 25 35
IL6ST -0.033 0.18 -10000 0 -0.57 103 103
Rac1/GDP -0.069 0.2 0.32 7 -0.48 98 105
AP1 -0.074 0.21 -10000 0 -0.61 46 46
GAB2 0.022 0.021 -10000 0 -0.57 1 1
TNFSF11 -0.016 0.24 0.62 10 -0.67 26 36
HSP90B1 0.023 0.11 -10000 0 -0.81 10 10
GAB1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.094 0.18 -10000 0 -0.52 84 84
AKT1 0.023 0.06 -10000 0 -0.52 4 4
FOXO1 0.024 0.062 0.43 1 -0.48 3 4
MAP2K6 -0.095 0.19 0.28 2 -0.42 163 165
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.052 0.2 0.39 11 -0.5 75 86
MITF -0.089 0.2 0.28 10 -0.42 167 177
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.024 0.004 -10000 0 -10000 0 0
A2M -0.003 0.18 -10000 0 -1.2 24 24
CEBPB 0.021 0.018 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.017 0.13 -10000 0 -0.52 34 34
STAT3 -0.044 0.27 0.56 11 -0.75 46 57
STAT1 0.014 0.087 -10000 0 -0.82 8 8
CEBPD -0.013 0.24 0.56 16 -0.68 31 47
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.031 0.043 -10000 0 -0.38 10 10
JUN 0.019 0.054 -10000 0 -0.58 8 8
PIAS3/MITF -0.074 0.19 0.33 2 -0.4 158 160
MAPK11 -0.094 0.18 -10000 0 -0.53 85 85
STAT3 (dimer)/FOXO1 -0.024 0.22 0.53 11 -0.58 39 50
GRB2/SOS1/GAB family -0.059 0.18 -10000 0 -0.48 73 73
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.1 0.19 0.25 1 -0.34 304 305
GRB2 0.024 0.01 0.26 1 -10000 0 1
JAK2 0.023 0.006 -10000 0 -10000 0 0
LBP -0.16 0.45 0.57 21 -0.93 233 254
PIK3R1 0.019 0.057 -10000 0 -0.57 9 9
JAK1 0.026 0.009 -10000 0 -10000 0 0
MYC -0.002 0.28 0.58 15 -0.98 30 45
FGG -0.025 0.24 0.62 10 -0.68 25 35
macrophage differentiation -0.038 0.25 0.56 11 -0.69 46 57
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.093 0.21 -10000 0 -0.36 331 331
JUNB -0.029 0.22 0.53 8 -0.65 26 34
FOS -0.15 0.27 -10000 0 -0.58 285 285
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.092 0.2 0.3 10 -0.43 168 178
STAT1/PIAS1 -0.059 0.2 0.36 9 -0.45 105 114
GRB2/SOS1/GAB family/SHP2/PI3K 0.024 0.064 -10000 0 -0.49 6 6
STAT3 (dimer) -0.042 0.27 0.56 11 -0.74 46 57
PRKCD -0.035 0.21 0.47 14 -0.54 54 68
IL6R 0.001 0.11 -10000 0 -0.57 35 35
SOCS3 -0.091 0.19 -10000 0 -0.72 36 36
gp130 (dimer)/JAK1/JAK1/LMO4 0.015 0.13 0.25 2 -0.36 103 105
Rac1/GTP -0.063 0.2 0.35 8 -0.48 94 102
HCK 0.027 0.026 0.26 12 -10000 0 12
MAPKKK cascade -0.001 0.14 -10000 0 -0.61 29 29
bone resorption -0.014 0.23 0.56 18 -0.63 27 45
IRF1 -0.03 0.23 0.55 8 -0.67 27 35
mol:GDP -0.084 0.2 0.3 10 -0.41 164 174
SOS1 0.024 0.004 -10000 0 -10000 0 0
VAV1 -0.086 0.2 0.3 10 -0.42 165 175
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.2 -10000 0 -0.59 91 91
PTPN11 0.012 0.08 -10000 0 -0.85 7 7
IL6/IL6RA -0.12 0.22 -10000 0 -0.42 318 318
gp130 (dimer)/TYK2/TYK2/LMO4 0.01 0.13 0.24 1 -0.36 104 105
gp130 (dimer)/JAK2/JAK2/LMO4 0.01 0.13 -10000 0 -0.36 100 100
IL6 -0.18 0.29 0.28 1 -0.57 352 353
PIAS3 0.023 0.006 -10000 0 -10000 0 0
PTPRE 0.008 0.031 -10000 0 -0.58 1 1
PIAS1 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.1 0.19 0.23 2 -0.33 330 332
LMO4 0.028 0.038 0.28 2 -0.57 3 5
STAT3 (dimer)/PIAS3 -0.046 0.26 0.55 8 -0.7 49 57
MCL1 0.056 0.095 0.49 1 -0.51 3 4
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.007 0.12 -10000 0 -0.35 100 100
EFNA5 -0.033 0.18 0.26 1 -0.58 95 96
FYN -0.026 0.1 0.18 5 -0.34 95 100
neuron projection morphogenesis -0.007 0.12 -10000 0 -0.35 100 100
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.007 0.12 -10000 0 -0.35 100 100
EPHA5 0.023 0.016 0.26 4 -10000 0 4
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.046 0.18 0.3 133 -0.48 51 184
FYN 0.022 0.2 0.34 59 -0.59 55 114
LAT/GRAP2/SLP76 0.027 0.18 0.35 47 -0.51 55 102
IKBKB 0.021 0.009 -10000 0 -10000 0 0
AKT1 0.024 0.16 0.33 74 -0.38 74 148
B2M 0.025 0.009 -10000 0 -10000 0 0
IKBKG 0.017 0.06 0.16 69 -0.14 26 95
MAP3K8 0.021 0.042 -10000 0 -0.58 5 5
mol:Ca2+ -0.022 0.032 -10000 0 -0.09 161 161
integrin-mediated signaling pathway 0.025 0.026 -10000 0 -0.36 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.012 0.21 0.4 39 -0.53 79 118
TRPV6 -0.088 0.27 1.2 15 -0.57 179 194
CD28 0.024 0.049 0.27 9 -0.58 5 14
SHC1 0.031 0.22 0.32 143 -0.54 70 213
receptor internalization -0.011 0.22 0.37 37 -0.48 135 172
PRF1 -0.011 0.24 0.55 9 -0.99 41 50
KRAS 0.024 0.005 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
COT/AKT1 0.032 0.14 0.3 70 -0.33 59 129
LAT 0.015 0.21 0.36 53 -0.59 61 114
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D 0.022 0.099 0.27 44 -0.58 19 63
CD3E 0.022 0.091 0.27 35 -0.59 16 51
CD3G 0.013 0.11 0.27 36 -0.58 29 65
RASGRP2 0 0.051 0.13 18 -0.17 65 83
RASGRP1 0.026 0.16 0.36 48 -0.42 55 103
HLA-A 0.027 0.022 0.27 7 -10000 0 7
RASSF5 0.019 0.035 0.26 1 -0.58 3 4
RAP1A/GTP/RAPL 0.026 0.026 -10000 0 -0.36 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.042 0.083 0.18 147 -0.13 24 171
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.056 -10000 0 -0.22 40 40
PRKCA 0.013 0.1 0.23 46 -0.27 51 97
GRAP2 0.016 0.072 0.26 3 -0.57 14 17
mol:IP3 0.013 0.14 0.26 116 -0.38 51 167
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.005 0.18 0.32 35 -0.66 50 85
ORAI1 0.036 0.17 0.64 3 -0.98 14 17
CSK 0.009 0.2 0.38 36 -0.57 66 102
B7 family/CD28 0.062 0.21 0.45 42 -0.61 49 91
CHUK 0.024 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.001 0.23 0.4 37 -0.53 104 141
PTPN6 0.009 0.2 0.36 42 -0.58 63 105
VAV1 0.005 0.2 0.38 36 -0.6 62 98
Monovalent TCR/CD3 -0.002 0.14 0.27 40 -0.52 53 93
CBL 0.022 0.008 -10000 0 -10000 0 0
LCK 0.02 0.21 0.37 46 -0.6 60 106
PAG1 0.022 0.21 0.35 58 -0.61 56 114
RAP1A 0.024 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.002 0.23 0.38 38 -0.55 91 129
CD80 0.088 0.1 0.26 266 -10000 0 266
CD86 0.026 0.018 0.27 5 -10000 0 5
PDK1/CARD11/BCL10/MALT1 -0.007 0.072 0.2 1 -0.26 40 41
HRAS 0.025 0.02 0.26 7 -10000 0 7
GO:0035030 0.022 0.16 0.34 43 -0.49 51 94
CD8A 0.028 0.063 0.28 27 -0.59 6 33
CD8B 0.014 0.12 0.27 29 -0.58 31 60
PTPRC 0.022 0.044 0.27 13 -0.58 3 16
PDK1/PKC theta 0.025 0.19 0.39 74 -0.48 65 139
CSK/PAG1 0.025 0.2 0.34 62 -0.62 50 112
SOS1 0.024 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.038 0.02 0.25 1 -10000 0 1
GRAP2/SLP76 0.021 0.2 0.39 36 -0.58 61 97
STIM1 0.025 0.098 1.3 4 -10000 0 4
RAS family/GTP 0.046 0.096 0.23 88 -0.18 37 125
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.016 0.24 0.37 37 -0.51 136 173
mol:DAG -0.017 0.099 0.14 21 -0.34 54 75
RAP1A/GDP 0.022 0.038 0.11 75 -0.066 7 82
PLCG1 0.023 0.005 -10000 0 -10000 0 0
CD247 0.016 0.081 0.27 17 -0.58 15 32
cytotoxic T cell degranulation -0.008 0.23 0.55 9 -0.92 41 50
RAP1A/GTP -0.001 0.017 -10000 0 -0.064 63 63
mol:PI-3-4-5-P3 0.018 0.18 0.36 51 -0.43 79 130
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.019 0.17 0.29 107 -0.5 50 157
NRAS 0.024 0.004 -10000 0 -10000 0 0
ZAP70 0.025 0.1 0.26 51 -0.58 20 71
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.006 0.16 0.4 13 -0.51 53 66
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.031 0.11 0.35 26 -0.49 32 58
CARD11 0.027 0.042 0.26 19 -0.58 2 21
PRKCB 0.014 0.1 0.27 43 -0.28 43 86
PRKCE 0.018 0.097 0.24 45 -0.26 41 86
PRKCQ 0.013 0.2 0.41 39 -0.53 73 112
LCP2 0.024 0.009 0.26 1 -10000 0 1
BCL10 0.024 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression 0.027 0.14 0.31 78 -0.32 73 151
IKK complex 0.036 0.085 0.22 109 -0.12 13 122
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.027 0.11 0.26 74 -0.27 45 119
PDPK1 0.029 0.16 0.35 75 -0.36 66 141
TCR/CD3/MHC I/CD8/Fyn -0.025 0.25 0.4 31 -0.64 92 123
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.035 0.072 -10000 0 -0.32 35 35
NF kappa B1 p50/RelA/I kappa B alpha 0.002 0.12 -10000 0 -0.41 17 17
AP1 -0.096 0.2 -10000 0 -0.34 364 364
mol:PIP3 -0.13 0.18 -10000 0 -0.34 394 394
AKT1 0.007 0.076 0.32 3 -0.41 10 13
PTK2B -0.028 0.1 -10000 0 -0.34 52 52
RHOA 0.002 0.062 0.26 2 -0.31 26 28
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.11 0.28 2 -0.29 93 95
MAGI3 0.024 0.004 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
apoptosis -0.026 0.12 -10000 0 -0.32 135 135
HRAS/GDP 0.019 0.014 0.18 7 -10000 0 7
positive regulation of microtubule depolymerization -0.052 0.12 0.28 3 -0.32 129 132
NF kappa B1 p50/RelA -0.012 0.12 -10000 0 -0.33 93 93
endothelial cell migration 0.002 0.079 -10000 0 -0.44 28 28
ADCY4 -0.021 0.12 -10000 0 -0.5 38 38
ADCY5 -0.075 0.15 -10000 0 -0.5 72 72
ADCY6 -0.013 0.097 -10000 0 -0.46 31 31
ADCY7 -0.012 0.097 -10000 0 -0.47 31 31
ADCY1 -0.014 0.11 -10000 0 -0.49 33 33
ADCY2 -0.025 0.12 -10000 0 -0.5 42 42
ADCY3 -0.013 0.096 -10000 0 -0.45 31 31
ADCY8 -0.011 0.09 -10000 0 -0.45 27 27
ADCY9 -0.013 0.096 -10000 0 -0.46 31 31
GSK3B -0.028 0.099 0.26 5 -0.34 47 52
arachidonic acid secretion -0.017 0.1 -10000 0 -0.36 61 61
GNG2 0.018 0.06 -10000 0 -0.57 10 10
TRIP6 0.018 0.016 -10000 0 -0.41 1 1
GNAO1 0.003 0.083 -10000 0 -0.37 42 42
HRAS 0.025 0.02 0.26 7 -10000 0 7
NFKBIA -0.021 0.13 0.27 2 -0.34 95 97
GAB1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.027 0.12 -10000 0 -0.81 21 21
JUN 0.019 0.054 -10000 0 -0.58 8 8
LPA/LPA2/NHERF2 0.031 0.018 -10000 0 -10000 0 0
TIAM1 0.012 0.14 -10000 0 -0.95 21 21
PIK3R1 0.018 0.057 -10000 0 -0.57 9 9
mol:IP3 -0.014 0.11 0.28 2 -0.29 93 95
PLCB3 0.026 0.045 -10000 0 -10000 0 0
FOS -0.15 0.27 -10000 0 -0.58 285 285
positive regulation of mitosis -0.017 0.1 -10000 0 -0.36 61 61
LPA/LPA1-2-3 0.001 0.14 -10000 0 -0.34 132 132
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
stress fiber formation -0.016 0.1 0.24 1 -0.36 41 42
GNAZ 0.003 0.069 -10000 0 -0.35 35 35
EGFR/PI3K-beta/Gab1 -0.13 0.2 -10000 0 -0.35 394 394
positive regulation of dendritic cell cytokine production 0 0.14 -10000 0 -0.33 132 132
LPA/LPA2/MAGI-3 0.033 0.016 -10000 0 -10000 0 0
ARHGEF1 0.019 0.069 -10000 0 -0.32 17 17
GNAI2 0.007 0.058 -10000 0 -0.33 27 27
GNAI3 0.007 0.058 -10000 0 -0.33 27 27
GNAI1 -0.01 0.1 -10000 0 -0.38 66 66
LPA/LPA3 -0.026 0.14 0.18 35 -0.41 116 151
LPA/LPA2 0.019 0.015 0.18 2 -10000 0 2
LPA/LPA1 0.011 0.069 -10000 0 -0.38 29 29
HB-EGF/EGFR -0.08 0.2 0.25 3 -0.35 334 337
HBEGF 0.066 0.075 0.27 22 -0.43 3 25
mol:DAG -0.014 0.11 0.28 2 -0.29 93 95
cAMP biosynthetic process -0.031 0.11 0.31 2 -0.42 54 56
NFKB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
LYN -0.008 0.13 0.27 22 -0.34 77 99
GNAQ -0.021 0.11 0.21 1 -0.31 114 115
LPAR2 0.025 0.011 0.26 2 -10000 0 2
LPAR3 -0.036 0.2 0.26 35 -0.58 112 147
LPAR1 0.013 0.085 -10000 0 -0.5 24 24
IL8 -0.14 0.23 0.35 30 -0.41 335 365
PTK2 -0.022 0.1 0.24 1 -0.32 92 93
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
CASP3 -0.026 0.12 -10000 0 -0.32 135 135
EGFR -0.19 0.29 -10000 0 -0.58 362 362
PLCG1 -0.024 0.12 0.2 4 -0.33 114 118
PLD2 -0.027 0.12 0.24 1 -0.32 128 129
G12/G13 0.037 0.059 -10000 0 -0.32 22 22
PI3K-beta 0.002 0.074 -10000 0 -0.45 11 11
cell migration 0.002 0.063 -10000 0 -0.25 19 19
SLC9A3R2 0.023 0.01 0.26 1 -10000 0 1
PXN -0.017 0.1 0.24 1 -0.37 41 42
HRAS/GTP -0.017 0.1 -10000 0 -0.37 61 61
RAC1 0.024 0.004 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 409 -0.58 1 410
PRKCE 0.024 0.019 -10000 0 -0.58 1 1
PRKCD -0.015 0.11 0.3 1 -0.41 11 12
Gi(beta/gamma) -0.011 0.1 -10000 0 -0.44 40 40
mol:LPA 0.001 0.016 -10000 0 -0.18 5 5
TRIP6/p130 Cas/FAK1/Paxillin -0.014 0.12 -10000 0 -0.41 29 29
MAPKKK cascade -0.017 0.1 -10000 0 -0.36 61 61
contractile ring contraction involved in cytokinesis 0.002 0.063 0.26 2 -0.3 26 28
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.021 0.11 0.18 4 -0.32 120 124
GNA15 -0.019 0.11 0.18 5 -0.31 113 118
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.007 -10000 0 -10000 0 0
MAPT -0.054 0.13 0.28 3 -0.32 129 132
GNA11 -0.02 0.11 0.21 1 -0.31 114 115
Rac1/GTP 0.028 0.13 -10000 0 -0.86 21 21
MMP2 0.002 0.079 -10000 0 -0.44 28 28
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.043 0.22 0.42 5 -0.63 108 113
IHH 0.016 0.083 0.27 30 -0.22 35 65
SHH Np/Cholesterol/GAS1 0.001 0.075 -10000 0 -0.33 44 44
LRPAP1 0.024 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.001 0.075 0.33 44 -10000 0 44
SMO/beta Arrestin2 -0.02 0.21 -10000 0 -0.62 88 88
SMO -0.043 0.21 0.33 1 -0.66 89 90
AKT1 -0.004 0.13 -10000 0 -0.51 29 29
ARRB2 0.022 0.007 -10000 0 -10000 0 0
BOC -0.02 0.16 -10000 0 -0.58 73 73
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
heart looping -0.042 0.21 0.32 1 -0.64 89 90
STIL 0.007 0.18 0.3 28 -0.5 76 104
DHH N/PTCH2 -0.012 0.15 -10000 0 -0.43 103 103
DHH N/PTCH1 -0.028 0.2 -10000 0 -0.51 135 135
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
DHH 0.008 0.1 0.26 2 -0.58 28 30
PTHLH -0.064 0.3 0.43 12 -0.84 113 125
determination of left/right symmetry -0.042 0.21 0.32 1 -0.64 89 90
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
skeletal system development -0.063 0.3 0.43 12 -0.83 113 125
IHH N/Hhip 0.028 0.056 0.26 1 -0.47 1 2
DHH N/Hhip 0.023 0.079 -10000 0 -0.42 29 29
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.042 0.21 0.32 1 -0.64 89 90
pancreas development 0.024 0.029 0.26 8 -0.57 1 9
HHAT 0.02 0.021 -10000 0 -0.58 1 1
PI3K 0.03 0.043 -10000 0 -0.38 10 10
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.007 0.13 -10000 0 -0.58 52 52
somite specification -0.042 0.21 0.32 1 -0.64 89 90
SHH Np/Cholesterol/PTCH1 -0.025 0.16 0.3 1 -0.51 81 82
SHH Np/Cholesterol/PTCH2 -0.006 0.087 -10000 0 -0.34 60 60
SHH Np/Cholesterol/Megalin -0.059 0.15 0.28 3 -0.34 205 208
SHH 0 0.038 0.35 7 -0.43 1 8
catabolic process -0.033 0.21 0.32 2 -0.57 115 117
SMO/Vitamin D3 -0.009 0.2 0.37 14 -0.58 82 96
SHH Np/Cholesterol/Hhip 0.016 0.031 0.28 5 -0.34 2 7
LRP2 -0.12 0.27 0.26 25 -0.58 251 276
receptor-mediated endocytosis -0.079 0.22 0.31 10 -0.63 95 105
SHH Np/Cholesterol/BOC -0.005 0.086 -10000 0 -0.34 59 59
SHH Np/Cholesterol/CDO 0.012 0.042 -10000 0 -0.34 12 12
mesenchymal cell differentiation -0.016 0.03 0.34 2 -0.28 5 7
mol:Vitamin D3 0.003 0.18 0.34 21 -0.51 80 101
IHH N/PTCH2 -0.01 0.14 0.22 1 -0.47 80 81
CDON 0.015 0.065 -10000 0 -0.58 12 12
IHH N/PTCH1 -0.024 0.21 0.36 4 -0.57 116 120
Megalin/LRPAP1 -0.078 0.2 -10000 0 -0.42 251 251
PTCH2 -0.022 0.16 -10000 0 -0.58 77 77
SHH Np/Cholesterol 0.01 0.014 -10000 0 -0.34 1 1
PTCH1 -0.033 0.21 0.32 2 -0.57 115 117
HHIP 0.024 0.029 0.26 8 -0.58 1 9
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0 0.062 0.22 2 -0.31 9 11
adherens junction organization -0.016 0.095 0.22 1 -0.34 54 55
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.088 0.15 0.32 4 -0.29 323 327
FMN1 -0.015 0.091 -10000 0 -0.31 58 58
mol:IP3 -0.002 0.053 -10000 0 -0.27 10 10
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.01 0.091 -10000 0 -0.32 52 52
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.063 -10000 0 -0.28 10 10
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.016 0.13 -10000 0 -0.53 41 41
CTNND1 0.024 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.011 0.078 -10000 0 -0.3 46 46
VASP -0.012 0.084 -10000 0 -0.3 50 50
ZYX -0.012 0.084 -10000 0 -0.31 50 50
JUB -0.012 0.086 -10000 0 -0.3 52 52
EGFR(dimer) -0.11 0.18 -10000 0 -0.33 357 357
E-cadherin/beta catenin-gamma catenin 0.031 0.063 -10000 0 -0.35 22 22
mol:PI-3-4-5-P3 0.015 0.074 -10000 0 -0.27 16 16
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.015 0.075 -10000 0 -0.28 16 16
FYN -0.005 0.066 0.22 2 -0.31 9 11
mol:Ca2+ -0.001 0.052 -10000 0 -0.27 10 10
JUP 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.019 0.057 -10000 0 -0.57 9 9
mol:DAG -0.002 0.053 -10000 0 -0.27 10 10
CDH1 0.009 0.088 -10000 0 -0.58 22 22
RhoA/GDP -0.088 0.15 0.36 2 -0.29 324 326
establishment of polarity of embryonic epithelium -0.012 0.083 -10000 0 -0.3 50 50
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
EGFR -0.19 0.29 -10000 0 -0.58 362 362
CASR -0.004 0.054 0.23 2 -0.26 8 10
RhoA/GTP 0.012 0.057 -10000 0 -0.26 7 7
AKT2 0 0.064 -10000 0 -0.28 8 8
actin cable formation -0.019 0.091 0.25 2 -0.34 43 45
apoptosis -0.003 0.073 0.28 21 -0.24 8 29
CTNNA1 0.024 0.006 -10000 0 -10000 0 0
mol:GDP -0.1 0.15 -10000 0 -0.3 326 326
PIP5K1A -0.011 0.08 -10000 0 -0.31 46 46
PLCG1 -0.002 0.054 -10000 0 -0.28 10 10
Rac1/GTP -0.096 0.17 -10000 0 -0.31 346 346
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.014 0.14 0.42 79 -0.23 11 90
KIRREL -0.024 0.16 -10000 0 -0.58 80 80
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.014 0.14 0.23 11 -0.42 79 90
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARRB2 0.022 0.007 -10000 0 -10000 0 0
WASL 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.034 0.12 0.29 4 -0.33 77 81
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.008 0.088 0.24 1 -0.28 65 66
FYN 0.016 0.13 0.27 110 -0.31 76 186
mol:Ca2+ 0.031 0.11 0.28 3 -0.32 72 75
mol:DAG 0.032 0.12 0.29 3 -0.32 72 75
NPHS2 0.014 0.031 0.27 4 -10000 0 4
mol:IP3 0.032 0.12 0.29 3 -0.32 72 75
regulation of endocytosis 0.023 0.1 0.24 5 -0.3 76 81
Nephrin/NEPH1/podocin/Cholesterol 0.024 0.11 0.25 9 -0.32 77 86
establishment of cell polarity 0.014 0.14 0.23 11 -0.42 79 90
Nephrin/NEPH1/podocin/NCK1-2 0.044 0.11 0.32 1 -0.3 75 76
Nephrin/NEPH1/beta Arrestin2 0.027 0.11 0.25 5 -0.3 76 81
NPHS1 0.06 0.092 0.26 156 -10000 0 156
Nephrin/NEPH1/podocin 0.025 0.11 0.31 4 -0.31 76 80
TJP1 0.023 0.02 -10000 0 -0.58 1 1
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.033 0.12 0.29 3 -0.33 72 75
CD2AP 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.031 0.12 0.3 5 -0.32 74 79
GRB2 0.023 0.01 0.26 1 -10000 0 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.013 0.14 0.28 107 -0.31 83 190
cytoskeleton organization 0.003 0.11 0.27 15 -0.33 71 86
Nephrin/NEPH1 0.016 0.1 0.19 7 -0.3 78 85
Nephrin/NEPH1/ZO-1 0.025 0.12 -10000 0 -0.35 78 78
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.016 0.08 -10000 0 -0.33 2 2
epithelial cell differentiation 0.033 0.079 0.4 1 -0.4 1 2
ITCH 0.032 0.019 -10000 0 -10000 0 0
WWP1 0.024 0.098 0.48 8 -10000 0 8
FYN 0.022 0.027 -10000 0 -0.58 2 2
EGFR -0.19 0.29 -10000 0 -0.58 362 362
PRL 0.022 0.025 0.26 10 -10000 0 10
neuron projection morphogenesis -0.046 0.14 0.36 9 -0.37 30 39
PTPRZ1 -0.28 0.3 0.26 6 -0.58 515 521
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.056 0.14 -10000 0 -0.39 35 35
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.091 0.16 -10000 0 -0.34 225 225
ADAM17 0.032 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.005 0.074 0.39 8 -10000 0 8
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.001 0.11 -10000 0 -0.37 45 45
NCOR1 0.022 0.008 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.083 0.15 -10000 0 -0.4 51 51
GRIN2B -0.1 0.16 -10000 0 -0.44 64 64
ErbB4/ErbB2/betacellulin 0.013 0.097 -10000 0 -0.41 5 5
STAT1 0.029 0.032 0.26 18 -10000 0 18
HBEGF 0.023 0.027 -10000 0 -0.58 2 2
PRLR 0.022 0.046 0.26 6 -0.58 5 11
E4ICDs/ETO2 0.007 0.088 0.35 1 -0.41 11 12
axon guidance 0.055 0.11 0.4 7 -0.38 1 8
NEDD4 0.03 0.018 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.032 0.037 0.2 15 -0.38 5 20
CBFA2T3 0.013 0.075 0.26 4 -0.58 15 19
ErbB4/ErbB2/HBEGF 0.031 0.071 -10000 0 -10000 0 0
MAPK3 -0.053 0.14 -10000 0 -0.38 31 31
STAT1 (dimer) 0.02 0.081 -10000 0 -10000 0 0
MAPK1 -0.052 0.14 0.36 2 -0.38 31 33
JAK2 0.023 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.075 0.15 -10000 0 -0.4 47 47
NRG1 -0.11 0.2 -10000 0 -0.43 275 275
NRG3 -0.006 0.14 0.26 19 -0.58 56 75
NRG2 -0.27 0.3 -10000 0 -0.58 491 491
NRG4 0.027 0.028 0.26 14 -10000 0 14
heart development 0.055 0.11 0.4 7 -0.38 1 8
neural crest cell migration -0.075 0.15 -10000 0 -0.39 47 47
ERBB2 0.035 0.069 0.27 79 -10000 0 79
WWOX/E4ICDs 0.012 0.076 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.098 0.17 -10000 0 -0.4 28 28
apoptosis 0.016 0.13 0.47 42 -10000 0 42
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.16 0.18 -10000 0 -0.35 370 370
ErbB4/ErbB2/epiregulin 0.005 0.13 0.36 12 -0.39 9 21
ErbB4/ErbB4/betacellulin/betacellulin -0.004 0.11 -10000 0 -0.36 38 38
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.041 0.086 0.4 1 -0.43 3 4
MDM2 0.01 0.08 0.32 2 -10000 0 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.086 0.15 -10000 0 -0.33 224 224
STAT5A 0.05 0.11 0.37 10 -0.41 1 11
ErbB4/EGFR/neuregulin 1 beta -0.19 0.23 -10000 0 -0.51 266 266
DLG4 0.022 0.008 -10000 0 -10000 0 0
GRB2/SHC 0.028 0.016 0.2 1 -10000 0 1
E4ICDs/TAB2/NCoR1 0.011 0.07 -10000 0 -10000 0 0
STAT5A (dimer) 0.06 0.1 0.46 1 -0.42 1 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.06 0.11 0.36 5 -0.36 1 6
LRIG1 0.022 0.027 -10000 0 -0.58 2 2
EREG -0.028 0.21 0.26 74 -0.58 114 188
BTC -0.008 0.14 0.26 2 -0.58 53 55
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.047 0.11 0.41 6 -0.38 1 7
ERBB4 -0.005 0.074 0.39 8 -10000 0 8
STAT5B 0.022 0.027 -10000 0 -0.58 2 2
YAP1 -0.014 0.11 -10000 0 -0.38 71 71
GRB2 0.023 0.01 0.26 1 -10000 0 1
ErbB4/ErbB2/neuregulin 4 0.033 0.07 0.32 1 -10000 0 1
glial cell differentiation -0.011 0.069 -10000 0 -10000 0 0
WWOX 0.022 0.014 0.26 2 -10000 0 2
cell proliferation -0.041 0.17 0.35 9 -0.52 25 34
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.022 0.027 -10000 0 -0.58 2 2
LAT2 -0.019 0.1 -10000 0 -0.36 49 49
AP1 -0.058 0.18 -10000 0 -0.43 117 117
mol:PIP3 0.011 0.17 0.35 42 -0.42 50 92
IKBKB 0.034 0.13 0.3 87 -0.26 27 114
AKT1 0.013 0.17 0.32 144 -0.34 56 200
IKBKG 0.017 0.11 0.28 48 -0.27 27 75
MS4A2 -0.021 0.15 0.26 4 -0.56 73 77
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
MAP3K1 0.012 0.12 0.33 15 -0.39 26 41
mol:Ca2+ 0.016 0.14 0.31 46 -0.32 48 94
LYN 0.022 0.013 -10000 0 -10000 0 0
CBLB -0.018 0.099 -10000 0 -0.35 49 49
SHC1 0.02 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK 0 0.12 -10000 0 -0.34 116 116
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
PLD2 -0.003 0.17 0.33 125 -0.33 126 251
PTPN13 -0.014 0.15 -10000 0 -0.57 38 38
PTPN11 0.023 0.018 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.013 0.13 0.34 29 -0.34 27 56
SYK 0.025 0.011 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.026 0.13 -10000 0 -0.36 95 95
LAT -0.018 0.1 -10000 0 -0.36 50 50
PAK2 0.013 0.13 0.32 17 -0.43 26 43
NFATC2 -0.046 0.16 -10000 0 -0.6 65 65
HRAS 0.01 0.13 0.27 19 -0.38 47 66
GAB2 0.021 0.02 -10000 0 -0.58 1 1
PLA2G1B 0 0.1 -10000 0 -0.85 13 13
Fc epsilon R1 -0.022 0.16 -10000 0 -0.4 135 135
Antigen/IgE/Fc epsilon R1 -0.018 0.14 -10000 0 -0.36 135 135
mol:GDP -0.014 0.11 -10000 0 -0.39 46 46
JUN 0.019 0.054 -10000 0 -0.58 8 8
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
FOS -0.15 0.27 -10000 0 -0.58 285 285
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.015 0.1 -10000 0 -0.29 99 99
CHUK 0.017 0.11 0.28 47 -0.27 27 74
KLRG1 -0.017 0.093 -10000 0 -0.32 49 49
VAV1 -0.019 0.1 -10000 0 -0.36 50 50
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.016 0.096 -10000 0 -0.36 45 45
negative regulation of mast cell degranulation -0.006 0.096 -10000 0 -0.37 26 26
BTK -0.012 0.11 -10000 0 -0.39 46 46
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.03 0.13 -10000 0 -0.34 131 131
GAB2/PI3K/SHP2 -0.048 0.1 -10000 0 -0.32 99 99
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.023 0.1 -10000 0 -0.28 107 107
RAF1 0 0.11 -10000 0 -0.92 13 13
Fc epsilon R1/FcgammaRIIB/SHIP 0 0.15 -10000 0 -0.35 135 135
FCER1G 0.019 0.018 0.26 1 -10000 0 1
FCER1A -0.045 0.19 -10000 0 -0.58 107 107
Antigen/IgE/Fc epsilon R1/Fyn -0.01 0.14 -10000 0 -0.35 129 129
MAPK3 0.001 0.1 -10000 0 -0.85 13 13
MAPK1 -0.005 0.11 -10000 0 -0.86 13 13
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.023 0.18 -10000 0 -0.58 68 68
DUSP1 -0.047 0.19 -10000 0 -0.58 118 118
NF-kappa-B/RelA 0.009 0.059 0.14 5 -0.17 17 22
actin cytoskeleton reorganization -0.006 0.15 -10000 0 -0.59 31 31
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.002 0.11 -10000 0 -0.44 28 28
FER -0.02 0.11 -10000 0 -0.36 55 55
RELA 0.024 0.004 -10000 0 -10000 0 0
ITK -0.013 0.094 0.15 2 -0.4 47 49
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG1 0.006 0.13 0.28 8 -0.39 50 58
cytokine secretion -0.003 0.035 -10000 0 -10000 0 0
SPHK1 -0.017 0.099 0.22 1 -0.36 49 50
PTK2 -0.007 0.15 -10000 0 -0.63 31 31
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.023 0.13 -10000 0 -0.37 96 96
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.007 0.16 0.33 39 -0.42 53 92
MAP2K2 -0.003 0.1 -10000 0 -0.85 13 13
MAP2K1 -0.003 0.1 -10000 0 -0.86 13 13
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.008 0.092 -10000 0 -0.36 27 27
MAP2K4 -0.074 0.29 -10000 0 -0.84 126 126
Fc epsilon R1/FcgammaRIIB -0.009 0.15 -10000 0 -0.37 135 135
mol:Choline -0.002 0.17 0.33 125 -0.33 126 251
SHC/Grb2/SOS1 0.013 0.11 -10000 0 -0.35 44 44
FYN 0.022 0.027 -10000 0 -0.58 2 2
DOK1 0.025 0.015 0.26 4 -10000 0 4
PXN -0.007 0.14 -10000 0 -0.57 31 31
HCLS1 -0.018 0.099 -10000 0 -0.35 50 50
PRKCB 0.015 0.14 0.31 47 -0.32 54 101
FCGR2B 0.018 0.04 0.26 1 -0.58 4 5
IGHE 0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.006 0.097 -10000 0 -0.38 26 26
LCP2 0.024 0.009 0.26 1 -10000 0 1
PLA2G4A -0.043 0.14 -10000 0 -0.36 127 127
RASA1 0.024 0.004 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.17 0.33 125 -0.33 126 251
IKK complex 0.033 0.11 0.28 76 -0.21 13 89
WIPF1 0.024 0.003 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.033 0.1 1.1 1 -10000 0 1
VDR 0.024 0.003 -10000 0 -10000 0 0
FAM120B 0.023 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.027 0.12 -10000 0 -0.39 11 11
RXRs/LXRs/DNA/Oxysterols -0.006 0.12 -10000 0 -0.43 16 16
MED1 0.022 0.008 -10000 0 -10000 0 0
mol:9cRA 0.003 0.01 -10000 0 -0.15 1 1
RARs/THRs/DNA/Src-1 0.001 0.083 -10000 0 -0.3 55 55
RXRs/NUR77 -0.049 0.18 -10000 0 -0.35 241 241
RXRs/PPAR -0.1 0.17 -10000 0 -0.32 324 324
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.049 0.041 -10000 0 -0.32 9 9
RARA 0.023 0.007 -10000 0 -10000 0 0
NCOA1 0.024 0.019 -10000 0 -0.58 1 1
VDR/VDR/DNA 0.024 0.003 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.037 0.038 -10000 0 -0.32 9 9
RARG 0.024 0.003 -10000 0 -10000 0 0
RPS6KB1 0.07 0.18 0.62 90 -10000 0 90
RARs/THRs/DNA/SMRT 0.003 0.08 -10000 0 -0.3 54 54
THRA 0.022 0.008 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.03 0.15 -10000 0 -0.32 202 202
NR1H4 0.02 0.023 0.26 9 -10000 0 9
RXRs/LXRs/DNA -0.009 0.16 -10000 0 -0.31 184 184
NR1H2 0.027 0.013 -10000 0 -10000 0 0
NR1H3 0.027 0.012 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.023 0.15 -10000 0 -0.31 201 201
NR4A1 -0.022 0.16 -10000 0 -0.58 78 78
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.032 0.1 -10000 0 -0.23 177 177
RXRG -0.1 0.24 0.26 2 -0.57 204 206
RXR alpha/CCPG 0.036 0.014 -10000 0 -10000 0 0
RXRA 0.027 0.013 -10000 0 -10000 0 0
RXRB 0.027 0.012 -10000 0 -10000 0 0
THRB -0.005 0.13 -10000 0 -0.58 49 49
PPARG -0.11 0.25 -10000 0 -0.58 224 224
PPARD 0.024 0.004 -10000 0 -10000 0 0
TNF -0.012 0.15 -10000 0 -1 11 11
mol:Oxysterols 0.004 0.009 -10000 0 -10000 0 0
cholesterol transport -0.006 0.12 -10000 0 -0.43 16 16
PPARA 0.021 0.038 -10000 0 -0.58 4 4
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.018 0.063 -10000 0 -0.58 11 11
RXRs/NUR77/BCL2 -0.068 0.15 -10000 0 -0.3 257 257
SREBF1 -0.007 0.11 -10000 0 -0.52 4 4
RXRs/RXRs/DNA/9cRA -0.03 0.15 -10000 0 -0.32 202 202
ABCA1 -0.011 0.13 -10000 0 -0.8 8 8
RARs/THRs 0.042 0.095 -10000 0 -0.34 52 52
RXRs/FXR -0.026 0.16 -10000 0 -0.33 202 202
BCL2 0.007 0.097 -10000 0 -0.58 27 27
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.032 0.044 -10000 0 -0.32 13 13
RGS9BP 0.036 0.052 0.26 51 -10000 0 51
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.019 0.017 0.26 4 -10000 0 4
mol:Na + 0.037 0.045 -10000 0 -10000 0 0
mol:ADP -0.006 0.026 0.25 5 -10000 0 5
GNAT2 0.024 0.014 0.26 3 -10000 0 3
RGS9-1/Gbeta5/R9AP 0.014 0.12 0.34 1 -0.36 85 86
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.014 -10000 0 -10000 0 0
GRK7 0.023 0.018 0.26 5 -10000 0 5
CNGB3 0.022 0.038 0.26 23 -10000 0 23
Cone Metarhodopsin II/X-Arrestin 0.016 0.015 0.18 8 -10000 0 8
mol:Ca2+ 0.13 0.11 0.29 169 -10000 0 169
Cone PDE6 0.029 0.11 0.33 2 -0.32 80 82
Cone Metarhodopsin II 0.025 0.016 -10000 0 -10000 0 0
Na + (4 Units) 0.12 0.094 0.32 63 -10000 0 63
GNAT2/GDP 0.023 0.11 0.32 1 -0.31 83 84
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.006 0.034 0.21 3 -10000 0 3
Cone Transducin 0.035 0.047 -10000 0 -0.34 13 13
SLC24A2 0.16 0.12 0.26 590 -10000 0 590
GNB3/GNGT2 0.026 0.055 -10000 0 -0.41 14 14
GNB3 0.017 0.066 0.26 2 -0.58 12 14
GNAT2/GTP 0.018 0.009 0.18 3 -10000 0 3
CNGA3 0.046 0.069 0.26 92 -10000 0 92
ARR3 0.021 0.022 0.26 8 -10000 0 8
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.038 0.045 -10000 0 -10000 0 0
mol:Pi 0.014 0.12 0.34 1 -0.36 85 86
Cone CNG Channel 0.05 0.044 0.29 2 -10000 0 2
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.16 0.12 0.26 590 -10000 0 590
RGS9 -0.027 0.17 0.26 11 -0.58 86 97
PDE6C 0.02 0.009 0.26 1 -10000 0 1
GNGT2 0.021 0.028 -10000 0 -0.58 2 2
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.019 0.016 0.26 4 -10000 0 4
PDGFR-alpha signaling pathway

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 -0.031 0.14 -10000 0 -0.6 58 58
PDGF/PDGFRA/CRKL -0.01 0.11 -10000 0 -0.43 57 57
positive regulation of JUN kinase activity 0.025 0.083 -10000 0 -0.33 42 42
CRKL 0.023 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.013 0.11 -10000 0 -0.43 59 59
AP1 -0.3 0.44 -10000 0 -0.96 301 301
mol:IP3 -0.035 0.11 -10000 0 -0.46 55 55
PLCG1 -0.035 0.11 -10000 0 -0.46 55 55
PDGF/PDGFRA/alphaV Integrin -0.01 0.11 -10000 0 -0.43 58 58
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.035 0.11 -10000 0 -0.46 55 55
CAV3 0.02 0.012 0.26 2 -10000 0 2
CAV1 -0.097 0.24 -10000 0 -0.58 202 202
SHC/Grb2/SOS1 0.026 0.084 -10000 0 -0.34 42 42
PDGF/PDGFRA/Shf -0.01 0.11 -10000 0 -0.43 59 59
FOS -0.3 0.44 -10000 0 -0.95 301 301
JUN -0.038 0.045 -10000 0 -0.45 6 6
oligodendrocyte development -0.01 0.11 -10000 0 -0.43 58 58
GRB2 0.023 0.01 0.26 1 -10000 0 1
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
mol:DAG -0.035 0.11 -10000 0 -0.46 55 55
PDGF/PDGFRA -0.031 0.14 -10000 0 -0.6 58 58
actin cytoskeleton reorganization -0.01 0.11 -10000 0 -0.43 58 58
SRF 0.016 0.013 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
PI3K 0.014 0.1 -10000 0 -0.37 64 64
PDGF/PDGFRA/Crk/C3G 0.016 0.097 -10000 0 -0.37 58 58
JAK1 -0.026 0.1 0.23 1 -0.43 58 59
ELK1/SRF -0.035 0.089 0.32 2 -0.36 56 58
SHB 0.024 0.009 0.26 1 -10000 0 1
SHF 0.023 0.021 0.26 1 -0.58 1 2
CSNK2A1 0.036 0.023 -10000 0 -10000 0 0
GO:0007205 -0.046 0.11 0.22 1 -0.47 58 59
SOS1 0.024 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.025 0.083 -10000 0 -0.33 42 42
PDGF/PDGFRA/SHB -0.01 0.11 -10000 0 -0.43 58 58
PDGF/PDGFRA/Caveolin-1 -0.097 0.22 -10000 0 -0.49 230 230
ITGAV 0.024 0.003 -10000 0 -10000 0 0
ELK1 -0.053 0.1 -10000 0 -0.43 57 57
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.011 0.11 -10000 0 -0.43 58 58
JAK-STAT cascade -0.026 0.1 0.23 1 -0.43 58 59
cell proliferation -0.01 0.11 -10000 0 -0.43 59 59
Syndecan-3-mediated signaling events

Figure S54.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S54.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.021 0.009 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.074 0.16 -10000 0 -0.3 263 263
Syndecan-3/Neurocan 0.027 0.076 0.28 19 -0.37 20 39
POMC 0.021 0.09 0.26 30 -0.58 18 48
EGFR -0.19 0.29 -10000 0 -0.58 362 362
Syndecan-3/EGFR -0.091 0.16 -10000 0 -0.32 284 284
AGRP 0.021 0.025 0.26 10 -10000 0 10
NCSTN 0.02 0.009 -10000 0 -10000 0 0
PSENEN 0.024 0.008 0.26 1 -10000 0 1
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.023 0.019 -10000 0 -0.58 1 1
APH1A 0.02 0.01 -10000 0 -10000 0 0
NCAN 0.037 0.058 0.26 62 -10000 0 62
long-term memory 0.035 0.064 -10000 0 -0.35 16 16
Syndecan-3/IL8 0.02 0.083 0.28 9 -0.34 35 44
PSEN1 0.024 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.03 0.014 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.58 2 2
limb bud formation 0.001 0.057 -10000 0 -0.39 21 21
MC4R 0.023 0.027 0.26 12 -10000 0 12
SRC 0.024 0.005 -10000 0 -10000 0 0
PTN -0.23 0.3 0.26 2 -0.58 425 427
FGFR/FGF/Syndecan-3 0.001 0.058 -10000 0 -0.39 21 21
neuron projection morphogenesis -0.074 0.16 0.34 5 -0.33 91 96
Syndecan-3/AgRP 0.015 0.062 0.27 1 -0.37 21 22
Syndecan-3/AgRP/MC4R 0.038 0.07 0.33 1 -0.36 20 21
Fyn/Cortactin 0.029 0.022 -10000 0 -0.31 2 2
SDC3 0.001 0.058 -10000 0 -0.39 21 21
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.02 0.082 0.28 9 -0.34 35 44
IL8 0.026 0.1 0.26 56 -0.58 19 75
Syndecan-3/Fyn/Cortactin 0.036 0.065 -10000 0 -0.36 16 16
Syndecan-3/CASK 0 0.056 -10000 0 -0.37 22 22
alpha-MSH/MC4R 0.03 0.071 0.37 2 -0.43 18 20
Gamma Secretase 0.054 0.034 -10000 0 -0.32 1 1
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.04 0.15 0.36 63 -0.37 39 102
TBX21 0.011 0.35 0.75 23 -1.2 50 73
B2M 0.025 0.012 -10000 0 -10000 0 0
TYK2 0.024 0.037 0.2 1 -10000 0 1
IL12RB1 0.032 0.074 0.33 38 -0.6 2 40
GADD45B 0.035 0.26 0.65 23 -0.88 33 56
IL12RB2 0.026 0.15 0.27 112 -0.58 41 153
GADD45G 0.052 0.27 0.68 27 -0.94 25 52
natural killer cell activation 0.007 0.026 -10000 0 -10000 0 0
RELB 0.026 0.023 0.26 9 -10000 0 9
RELA 0.024 0.004 -10000 0 -10000 0 0
IL18 0.034 0.042 0.28 25 -10000 0 25
IL2RA 0.029 0.088 0.26 55 -0.58 13 68
IFNG 0.055 0.082 0.26 137 -10000 0 137
STAT3 (dimer) 0.033 0.25 0.56 41 -0.7 46 87
HLA-DRB5 0.024 0.08 0.25 73 -0.58 5 78
FASLG 0.051 0.31 0.74 33 -1 37 70
NF kappa B2 p52/RelB 0.018 0.26 0.68 5 -0.78 52 57
CD4 0.009 0.025 -10000 0 -10000 0 0
SOCS1 0.025 0.033 0.26 12 -0.58 1 13
EntrezGene:6955 -0.006 0.016 -10000 0 -10000 0 0
CD3D 0.008 0.1 0.26 44 -0.59 19 63
CD3E 0.009 0.093 0.27 35 -0.58 16 51
CD3G 0.001 0.12 0.27 36 -0.59 29 65
IL12Rbeta2/JAK2 0.036 0.12 0.3 31 -0.44 41 72
CCL3 0.03 0.28 0.73 20 -1 30 50
CCL4 0.032 0.28 0.71 23 -0.95 31 54
HLA-A 0.028 0.022 0.26 7 -10000 0 7
IL18/IL18R 0.065 0.12 0.38 18 -0.38 48 66
NOS2 0.031 0.28 0.7 24 -0.98 34 58
IL12/IL12R/TYK2/JAK2/SPHK2 0.037 0.15 0.34 65 -0.35 51 116
IL1R1 0.017 0.31 0.71 21 -1.2 37 58
IL4 -0.011 0.038 -10000 0 -0.18 1 1
JAK2 0.023 0.036 -10000 0 -10000 0 0
EntrezGene:6957 -0.004 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.024 0.23 0.39 32 -0.77 56 88
RAB7A 0.049 0.24 0.64 21 -0.82 21 42
lysosomal transport 0.05 0.23 0.62 24 -0.77 21 45
FOS -0.32 0.62 0.6 15 -1.2 327 342
STAT4 (dimer) 0.061 0.29 0.58 45 -0.86 46 91
STAT5A (dimer) 0.045 0.28 0.61 50 -0.78 50 100
GZMA 0.023 0.3 0.68 35 -1.1 32 67
GZMB 0.023 0.32 0.7 33 -1.1 41 74
HLX 0.021 0.014 0.26 2 -10000 0 2
LCK 0.025 0.3 0.67 37 -0.86 55 92
TCR/CD3/MHC II/CD4 -0.047 0.18 0.28 26 -0.44 108 134
IL2/IL2R 0.066 0.1 0.42 38 -0.37 19 57
MAPK14 0.045 0.28 0.65 29 -0.88 35 64
CCR5 0.034 0.27 0.69 30 -0.87 35 65
IL1B 0.017 0.082 0.3 3 -0.59 14 17
STAT6 0.04 0.12 0.39 40 -0.53 6 46
STAT4 0.001 0.12 0.26 1 -0.58 40 41
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.032 0.26 18 -10000 0 18
NFKB1 0.024 0.004 -10000 0 -10000 0 0
NFKB2 0.024 0.008 0.26 1 -10000 0 1
IL12B 0.073 0.11 0.28 208 -10000 0 208
CD8A 0.029 0.064 0.28 27 -0.58 6 33
CD8B 0.014 0.11 0.28 29 -0.58 31 60
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.04 0.15 0.37 39 -0.36 63 102
IL2RB 0.031 0.052 0.26 36 -0.58 2 38
proteasomal ubiquitin-dependent protein catabolic process 0.065 0.27 0.57 48 -0.77 45 93
IL2RG 0.031 0.071 0.26 45 -0.58 7 52
IL12 0.049 0.15 0.3 85 -0.44 55 140
STAT5A 0.02 0.047 -10000 0 -0.58 6 6
CD247 0.006 0.083 0.26 17 -0.58 15 32
IL2 0.023 0.023 0.26 9 -10000 0 9
SPHK2 0.024 0.003 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.006 0.15 0.3 15 -0.59 56 71
IL12/IL12R/TYK2/JAK2 0.032 0.31 0.7 41 -0.88 53 94
MAP2K3 0.038 0.28 0.64 31 -0.87 41 72
RIPK2 0.021 0.016 0.26 3 -10000 0 3
MAP2K6 0.044 0.27 0.65 29 -0.88 35 64
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.007 0.034 0.26 1 -0.58 1 2
IL18RAP 0.011 0.11 0.28 4 -0.58 34 38
IL12Rbeta1/TYK2 0.041 0.07 0.29 34 -0.46 2 36
EOMES -0.02 0.18 -10000 0 -1 27 27
STAT1 (dimer) 0.066 0.27 0.61 68 -0.73 37 105
T cell proliferation 0.049 0.22 0.51 32 -0.66 38 70
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.021 0.078 -10000 0 -0.58 16 16
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.013 0.19 0.4 5 -0.73 38 43
ATF2 0.043 0.26 0.62 28 -0.82 34 62
FAS signaling pathway (CD95)

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
SPTAN1 -0.003 0.042 0.21 28 -0.19 1 29
RFC1 -0.003 0.04 0.21 25 -10000 0 25
PRKDC 0.015 0.077 0.23 100 -10000 0 100
RIPK1 0.027 0.007 -10000 0 -10000 0 0
CASP7 -0.018 0.098 -10000 0 -0.62 20 20
FASLG/FAS/FADD/FAF1 -0.004 0.058 0.21 14 -0.28 12 26
MAP2K4 -0.084 0.18 0.44 2 -0.33 251 253
mol:ceramide -0.023 0.099 -10000 0 -0.36 26 26
GSN -0.007 0.057 0.21 28 -0.28 20 48
FASLG/FAS/FADD/FAF1/Caspase 8 -0.007 0.075 0.28 1 -0.35 15 16
FAS 0.004 0.037 -10000 0 -0.59 2 2
BID -0.018 0.022 -10000 0 -10000 0 0
MAP3K1 -0.048 0.12 0.29 3 -0.41 36 39
MAP3K7 0.011 0.019 -10000 0 -10000 0 0
RB1 -0.003 0.04 0.21 25 -0.19 3 28
CFLAR 0.027 0.007 -10000 0 -10000 0 0
HGF/MET -0.051 0.2 -10000 0 -0.41 211 211
ARHGDIB 0 0.047 0.22 36 -10000 0 36
FADD 0.006 0.024 -10000 0 -10000 0 0
actin filament polymerization 0.012 0.063 0.35 11 -0.21 28 39
NFKB1 -0.045 0.12 -10000 0 -0.6 17 17
MAPK8 -0.15 0.26 0.61 2 -0.46 369 371
DFFA -0.003 0.04 0.21 25 -10000 0 25
DNA fragmentation during apoptosis -0.008 0.05 0.21 25 -10000 0 25
FAS/FADD/MET -0.037 0.14 -10000 0 -0.37 142 142
CFLAR/RIP1 0.04 0.013 -10000 0 -10000 0 0
FAIM3 0.027 0.037 0.26 22 -10000 0 22
FAF1 0.003 0.029 -10000 0 -10000 0 0
PARP1 -0.001 0.049 0.23 33 -10000 0 33
DFFB -0.003 0.041 0.21 25 -10000 0 25
CHUK -0.04 0.11 -10000 0 -0.56 16 16
FASLG 0.007 0.086 0.26 39 -0.59 12 51
FAS/FADD 0.009 0.037 -10000 0 -0.33 2 2
HGF -0.011 0.14 -10000 0 -0.58 59 59
LMNA -0.004 0.054 0.19 34 -10000 0 34
CASP6 -0.003 0.04 0.21 25 -10000 0 25
CASP10 0.004 0.042 -10000 0 -0.59 3 3
CASP3 0.001 0.045 0.26 27 -10000 0 27
PTPN13 0.008 0.095 -10000 0 -0.58 26 26
CASP8 -0.021 0.026 -10000 0 -0.18 22 22
IL6 -0.43 0.62 -10000 0 -1.2 371 371
MET -0.071 0.22 -10000 0 -0.58 159 159
ICAD/CAD -0.006 0.033 0.2 11 -10000 0 11
FASLG/FAS/FADD/FAF1/Caspase 10 -0.023 0.1 -10000 0 -0.37 26 26
activation of caspase activity by cytochrome c -0.018 0.022 -10000 0 -10000 0 0
PAK2 -0.002 0.05 0.22 37 -0.19 4 41
BCL2 0.008 0.097 -10000 0 -0.57 27 27
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.38 0.28 -10000 0 -0.58 679 679
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.027 0.033 0.26 19 -10000 0 19
TCEB1 0.021 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.03 0.048 -10000 0 -0.26 14 14
HIF1A 0.018 0.04 -10000 0 -0.26 11 11
COPS5 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.055 0.038 -10000 0 -10000 0 0
FIH (dimer) 0.024 0.003 -10000 0 -10000 0 0
CDKN2A 0.059 0.087 0.26 155 -10000 0 155
ARNT/IPAS -0.25 0.2 -10000 0 -0.38 679 679
HIF1AN 0.024 0.003 -10000 0 -10000 0 0
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.02 0.045 -10000 0 -0.28 13 13
CUL2 0.024 0.004 -10000 0 -10000 0 0
OS9 0.024 0.003 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.041 0.028 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.032 0.049 -10000 0 -0.27 14 14
PHD1-3/OS9 0.056 0.049 -10000 0 -0.34 2 2
HIF1A/RACK1/Elongin B/Elongin C 0.043 0.053 -10000 0 -0.3 4 4
VHL 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.027 0.049 -10000 0 -0.28 13 13
EGLN3 0.04 0.063 0.26 69 -0.58 1 70
EGLN2 0.025 0.017 0.26 5 -10000 0 5
EGLN1 0.02 0.021 -10000 0 -0.58 1 1
TP53 0.022 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.029 0.069 -10000 0 -0.52 13 13
ARNT 0.02 0.01 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.023 0.006 -10000 0 -10000 0 0
HIF1A/p19ARF 0.053 0.072 0.24 35 -0.27 12 47
Nectin adhesion pathway

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
PDGFRB 0.022 0.038 -10000 0 -0.58 4 4
alphaV beta3 Integrin 0.02 0.082 -10000 0 -0.43 32 32
PTK2 -0.041 0.15 -10000 0 -0.44 103 103
positive regulation of JNK cascade -0.021 0.12 -10000 0 -0.32 111 111
CDC42/GDP -0.017 0.17 -10000 0 -0.43 116 116
Rac1/GDP -0.017 0.17 -10000 0 -0.43 116 116
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.021 0.15 -10000 0 -0.4 109 109
nectin-3/I-afadin -0.015 0.14 -10000 0 -0.43 104 104
RAPGEF1 -0.034 0.17 0.46 1 -0.47 103 104
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.049 0.18 -10000 0 -0.53 109 109
PDGFB-D/PDGFRB 0.022 0.038 -10000 0 -0.57 4 4
TLN1 -0.023 0.07 -10000 0 -0.38 13 13
Rap1/GTP -0.024 0.12 -10000 0 -0.34 99 99
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.028 -10000 0 -0.34 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.015 0.14 -10000 0 -0.43 104 104
PVR 0.024 0.003 -10000 0 -10000 0 0
Necl-5(dimer) 0.024 0.003 -10000 0 -10000 0 0
mol:GDP -0.037 0.2 0.47 1 -0.53 118 119
MLLT4 0.021 0.034 0.26 1 -0.58 3 4
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.02 0.13 -10000 0 -0.35 105 105
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.029 0.031 0.2 1 -0.3 6 7
positive regulation of lamellipodium assembly -0.02 0.13 -10000 0 -0.34 119 119
PVRL1 0.022 0.008 -10000 0 -10000 0 0
PVRL3 -0.038 0.18 -10000 0 -0.58 103 103
PVRL2 0.024 0.004 -10000 0 -10000 0 0
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
CDH1 0.008 0.088 -10000 0 -0.58 22 22
CLDN1 0.008 0.12 0.26 23 -0.58 36 59
JAM-A/CLDN1 0.004 0.14 -10000 0 -0.37 99 99
SRC -0.056 0.2 -10000 0 -0.57 116 116
ITGB3 0.005 0.11 0.26 4 -0.58 32 36
nectin-1(dimer)/I-afadin/I-afadin 0.029 0.031 0.2 1 -0.3 6 7
FARP2 -0.037 0.2 0.46 1 -0.53 110 111
RAC1 0.024 0.004 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.002 0.13 -10000 0 -0.37 103 103
nectin-1/I-afadin 0.029 0.031 0.2 1 -0.3 6 7
nectin-2/I-afadin 0.032 0.03 0.2 1 -0.3 6 7
RAC1/GTP/IQGAP1/filamentous actin 0.032 0.008 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0 0.13 -10000 0 -0.37 104 104
CDC42/GTP/IQGAP1/filamentous actin 0.031 0.009 -10000 0 -10000 0 0
F11R 0.02 0.01 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.021 0.12 -10000 0 -0.32 111 111
alphaV/beta3 Integrin/Talin -0.006 0.1 0.26 1 -0.41 38 39
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.03 0.2 1 -0.3 6 7
nectin-2(dimer)/I-afadin/I-afadin 0.032 0.03 0.2 1 -0.3 6 7
PIP5K1C -0.019 0.077 -10000 0 -0.23 102 102
VAV2 -0.037 0.21 0.47 1 -0.54 117 118
RAP1/GDP -0.014 0.16 -10000 0 -0.4 110 110
ITGAV 0.024 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.002 0.13 -10000 0 -0.37 103 103
nectin-3(dimer)/I-afadin/I-afadin -0.015 0.14 -10000 0 -0.43 104 104
Rac1/GTP -0.021 0.16 -10000 0 -0.41 118 118
PTPRM -0.016 0.087 -10000 0 -0.25 105 105
E-cadherin/beta catenin/alpha catenin 0.045 0.068 -10000 0 -0.32 23 23
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.023 0.006 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.096 0.1 0.22 394 -0.35 2 396
EPHB2 0.028 0.033 0.26 19 -10000 0 19
Syndecan-2/TACI 0.022 0.061 0.29 6 -0.36 12 18
LAMA1 -0.039 0.18 0.26 2 -0.58 105 107
Syndecan-2/alpha2 ITGB1 -0.037 0.15 -10000 0 -0.33 182 182
HRAS 0.025 0.02 0.26 7 -10000 0 7
Syndecan-2/CASK 0.005 0.017 -10000 0 -0.36 2 2
ITGA5 0.024 0.003 -10000 0 -10000 0 0
BAX 0.002 0.031 0.46 1 -10000 0 1
EPB41 0.024 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.017 0.018 -10000 0 -0.33 2 2
LAMA3 -0.12 0.25 -10000 0 -0.58 231 231
EZR 0.024 0.012 0.26 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.046 0.19 -10000 0 -0.58 117 117
Syndecan-2/MMP2 0.015 0.038 -10000 0 -0.37 8 8
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.023 0.071 -10000 0 -0.43 23 23
dendrite morphogenesis 0.022 0.035 0.22 19 -0.36 2 21
Syndecan-2/GM-CSF 0.021 0.036 0.31 4 -0.36 2 6
determination of left/right symmetry 0.007 0.02 -10000 0 -0.42 2 2
Syndecan-2/PKC delta 0.019 0.023 0.31 1 -0.36 2 3
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.033 0.074 0.19 167 -0.33 2 169
MAPK1 0.037 0.077 0.19 187 -0.32 2 189
Syndecan-2/RACK1 0.029 0.026 0.23 2 -0.31 2 4
NF1 0.023 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.007 0.02 -10000 0 -0.42 2 2
ITGA2 0.009 0.094 -10000 0 -0.58 25 25
MAPK8 0.005 0.034 0.27 5 -0.36 5 10
Syndecan-2/alpha2/beta1 Integrin 0.001 0.12 -10000 0 -0.36 80 80
Syndecan-2/Kininogen 0.019 0.031 0.22 13 -0.36 2 15
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.042 0.069 0.32 6 -0.3 2 8
Syndecan-2/CASK/Protein 4.1 0.017 0.019 -10000 0 -0.33 2 2
extracellular matrix organization 0.02 0.023 0.35 1 -0.36 2 3
actin cytoskeleton reorganization 0.096 0.1 0.21 394 -0.35 2 396
Syndecan-2/Caveolin-2/Ras -0.007 0.11 0.24 2 -0.34 90 92
Syndecan-2/Laminin alpha3 -0.058 0.15 -10000 0 -0.36 173 173
Syndecan-2/RasGAP 0.038 0.031 0.25 1 -0.3 2 3
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
PRKCD 0.024 0.009 0.26 1 -10000 0 1
Syndecan-2 dimer 0.022 0.035 0.22 19 -0.36 2 21
GO:0007205 0.002 0.003 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.025 0.025 -10000 0 -0.3 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
SDCBP 0.021 0.009 -10000 0 -10000 0 0
TNFRSF13B 0.027 0.085 0.26 52 -0.58 12 64
RASA1 0.024 0.004 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.023 0.071 -10000 0 -0.43 23 23
Syndecan-2/Synbindin 0.018 0.021 -10000 0 -0.35 2 2
TGFB1 0.025 0.008 0.26 1 -10000 0 1
CASP3 0.043 0.071 0.19 180 -0.33 2 182
FN1 0.12 0.12 0.26 394 -10000 0 394
Syndecan-2/IL8 0.024 0.071 0.22 56 -0.36 17 73
SDC2 0.007 0.02 -10000 0 -0.42 2 2
KNG1 0.022 0.028 0.26 13 -10000 0 13
Syndecan-2/Neurofibromin 0.018 0.021 -10000 0 -0.36 2 2
TRAPPC4 0.022 0.008 -10000 0 -10000 0 0
CSF2 0.026 0.037 0.26 23 -10000 0 23
Syndecan-2/TGFB1 0.02 0.023 0.35 1 -0.36 2 3
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.019 -10000 0 -0.33 2 2
Syndecan-2/Ezrin 0.029 0.026 0.3 1 -0.33 2 3
PRKACA 0.045 0.073 0.19 193 -0.32 2 195
angiogenesis 0.024 0.071 0.22 56 -0.36 17 73
MMP2 0.018 0.047 -10000 0 -0.58 6 6
IL8 0.026 0.1 0.26 56 -0.58 19 75
calcineurin-NFAT signaling pathway 0.022 0.06 0.29 6 -0.36 12 18
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.021 0.081 -10000 0 -0.44 12 12
HDAC1 0.021 0.012 -10000 0 -10000 0 0
AES 0.023 0.005 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
DTX1 -0.028 0.17 -10000 0 -0.58 87 87
LRP6/FZD1 0.034 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.047 -10000 0 -0.58 6 6
AP1 -0.076 0.16 -10000 0 -0.32 270 270
NCSTN 0.02 0.009 -10000 0 -10000 0 0
ADAM10 0.023 0.027 -10000 0 -0.58 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.016 0.095 -10000 0 -0.66 12 12
NICD/RBPSUH 0.02 0.078 -10000 0 -0.4 22 22
WIF1 -0.28 0.3 0.26 11 -0.58 509 520
NOTCH1 0.009 0.07 -10000 0 -0.41 24 24
PSENEN 0.024 0.008 0.26 1 -10000 0 1
KREMEN2 0.13 0.12 0.26 435 -10000 0 435
DKK1 0.026 0.16 0.26 134 -0.58 50 184
beta catenin/beta TrCP1 0.009 0.069 0.26 1 -0.36 6 7
APH1B 0.023 0.019 -10000 0 -0.58 1 1
APH1A 0.02 0.01 -10000 0 -10000 0 0
AXIN1 0.011 0.06 -10000 0 -0.47 8 8
CtBP/CBP/TCF1/TLE1/AES 0.012 0.039 -10000 0 -0.29 7 7
PSEN1 0.024 0.005 -10000 0 -10000 0 0
FOS -0.15 0.27 -10000 0 -0.58 285 285
JUN 0.019 0.054 -10000 0 -0.58 8 8
MAP3K7 0.021 0.009 -10000 0 -10000 0 0
CTNNB1 -0.001 0.068 0.26 2 -0.38 6 8
MAPK3 0.023 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.094 0.099 0.34 1 -0.34 17 18
HNF1A 0.026 0.02 0.26 7 -10000 0 7
CTBP1 0.023 0.006 -10000 0 -10000 0 0
MYC -0.014 0.21 -10000 0 -1.3 26 26
NKD1 0.021 0.055 0.26 14 -0.58 6 20
FZD1 0.024 0.004 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.006 0.12 -10000 0 -0.47 18 18
apoptosis -0.076 0.15 -10000 0 -0.32 270 270
Delta 1/NOTCHprecursor 0.019 0.08 -10000 0 -0.43 12 12
DLL1 0.021 0.038 -10000 0 -0.58 4 4
PPARD 0.014 0.096 -10000 0 -0.83 12 12
Gamma Secretase 0.055 0.034 -10000 0 -0.32 1 1
APC 0.004 0.084 0.25 1 -0.47 22 23
DVL1 -0.03 0.078 -10000 0 -0.37 33 33
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.1 0.14 0.34 73 -0.34 42 115
LRP6 0.024 0.005 -10000 0 -10000 0 0
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
NLK 0.009 0.009 -10000 0 -10000 0 0
CCND1 0.021 0.097 -10000 0 -1 6 6
WNT1 0.023 0.012 0.26 2 -10000 0 2
Axin1/APC/beta catenin 0.013 0.1 0.32 5 -0.47 13 18
DKK2 0.011 0.091 0.26 2 -0.58 23 25
NOTCH1 precursor/DVL1 -0.02 0.11 -10000 0 -0.59 22 22
GSK3B 0.024 0.003 -10000 0 -10000 0 0
FRAT1 0.024 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.003 0.12 -10000 0 -0.48 18 18
PPP2R5D -0.004 0.058 0.29 5 -0.36 15 20
MAPK1 0.023 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.14 0.2 -10000 0 -0.34 492 492
RBPJ 0.024 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.011 0.14 -10000 0 -0.58 58 58
HRAS 0.025 0.02 0.26 7 -10000 0 7
EGFR -0.19 0.29 -10000 0 -0.58 362 362
AKT -0.014 0.12 0.3 7 -0.27 94 101
FOXO3 0.022 0.02 -10000 0 -0.58 1 1
AKT1 0.024 0.004 -10000 0 -10000 0 0
FOXO1 0.02 0.038 -10000 0 -0.58 4 4
AKT3 0.015 0.057 -10000 0 -0.58 9 9
FOXO4 0.025 0.001 -10000 0 -10000 0 0
MET -0.071 0.22 -10000 0 -0.58 159 159
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
NRAS 0.024 0.004 -10000 0 -10000 0 0
PIK3CG 0.017 0.072 0.26 4 -0.58 14 18
PIK3R3 0.024 0.008 0.26 1 -10000 0 1
PIK3R2 0.024 0.003 -10000 0 -10000 0 0
NF1 0.023 0.006 -10000 0 -10000 0 0
RAS -0.061 0.14 0.21 4 -0.34 148 152
ERBB2 0.021 0.009 -10000 0 -10000 0 0
proliferation/survival/translation -0.005 0.091 0.33 44 -0.24 2 46
PI3K -0.05 0.14 0.26 13 -0.24 306 319
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
KRAS 0.024 0.005 -10000 0 -10000 0 0
FOXO 0.036 0.058 0.26 9 -0.16 2 11
AKT2 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.023 0.027 -10000 0 -0.58 2 2
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.043 0.15 -10000 0 -0.32 221 221
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.005 0.014 0.14 8 -10000 0 8
GNB1/GNG2 0.027 0.04 -10000 0 -0.36 10 10
GNB1 0.024 0.005 -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 0.006 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.063 0.14 -10000 0 -0.32 236 236
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 0.02 0.035 0.081 236 -10000 0 236
GNAL -0.11 0.25 -10000 0 -0.58 219 219
GNG2 0.018 0.06 -10000 0 -0.58 10 10
CRH 0.017 0.023 0.26 8 -10000 0 8
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.028 -10000 0 -0.36 6 6
MAPK11 0.005 0.02 -10000 0 -0.36 3 3
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 -0.056 0.2 0.3 2 -0.39 180 182
MAP3K8 0.01 0.046 -10000 0 -0.58 5 5
FOS -0.02 0.14 0.32 2 -0.44 49 51
PRKCA -0.002 0.088 0.24 1 -0.58 21 22
PTPN7 0.021 0.06 0.25 54 -10000 0 54
HRAS 0.024 0.021 0.26 7 -10000 0 7
PRKCB 0.006 0.08 0.25 18 -0.58 14 32
NRAS 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.025 0.036 -10000 0 -10000 0 0
MAPK3 0.008 0.091 -10000 0 -0.8 5 5
MAP2K1 -0.011 0.12 -10000 0 -0.51 40 40
ELK1 0.006 0.029 -10000 0 -10000 0 0
BRAF -0.012 0.1 -10000 0 -0.49 36 36
mol:GTP -0.002 0.003 -10000 0 -0.006 301 301
MAPK1 -0.009 0.12 -10000 0 -0.46 42 42
RAF1 -0.011 0.099 -10000 0 -0.48 36 36
KRAS 0.023 0.006 -10000 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.044 0.043 -10000 0 -10000 0 0
BIRC5 0.18 0.11 0.26 665 -10000 0 665
NFKBIA 0.025 0.042 0.29 6 -10000 0 6
CPEB1 -0.081 0.23 0.26 1 -0.58 176 177
AKT1 0.025 0.042 0.29 6 -10000 0 6
NDEL1 0.022 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.033 0.037 0.21 1 -0.21 1 2
NDEL1/TACC3 0.065 0.068 0.22 107 -10000 0 107
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GSK3B -0.003 0.027 -10000 0 -10000 0 0
PAK1/Aurora A 0.041 0.045 0.28 2 -10000 0 2
MDM2 0.024 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.094 0.069 0.27 27 -10000 0 27
TP53 0.022 0.051 -10000 0 -0.22 12 12
DLG7 0.022 0.031 0.18 1 -10000 0 1
AURKAIP1 0.026 0.023 0.26 9 -10000 0 9
ARHGEF7 0.023 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.069 0.072 0.24 107 -10000 0 107
G2/M transition of mitotic cell cycle 0.033 0.037 0.21 1 -0.21 1 2
AURKA 0.038 0.048 0.24 1 -10000 0 1
AURKB 0.088 0.076 0.17 411 -10000 0 411
CDC25B 0.032 0.038 0.22 3 -10000 0 3
G2/M transition checkpoint 0.019 0.029 0.13 1 -0.15 1 2
mRNA polyadenylation -0.026 0.13 -10000 0 -0.3 176 176
Aurora A/CPEB -0.026 0.13 -10000 0 -0.3 176 176
Aurora A/TACC1/TRAP/chTOG 0.043 0.074 -10000 0 -0.3 25 25
BRCA1 0.023 0.021 0.26 1 -0.58 1 2
centrosome duplication 0.041 0.044 0.28 2 -10000 0 2
regulation of centrosome cycle 0.063 0.066 0.25 18 -10000 0 18
spindle assembly 0.041 0.073 -10000 0 -0.3 25 25
TDRD7 0.024 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.14 0.088 0.26 63 -10000 0 63
CENPA 0.099 0.083 0.19 412 -0.21 3 415
Aurora A/PP2A 0.044 0.044 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.031 0.04 0.24 1 -10000 0 1
negative regulation of DNA binding 0.018 0.062 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.013 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
Ajuba/Aurora A 0.019 0.029 0.14 1 -0.15 1 2
mitotic prometaphase -0.009 0.029 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.05 0.24 1 -10000 0 1
TACC1 0.004 0.095 -10000 0 -0.58 26 26
TACC3 0.058 0.084 0.26 146 -10000 0 146
Aurora A/Antizyme1 0.054 0.044 -10000 0 -10000 0 0
Aurora A/RasGAP 0.044 0.043 -10000 0 -10000 0 0
OAZ1 0.024 0.005 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.002 0.027 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.04 0.024 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.094 0.069 0.27 27 -10000 0 27
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.096 0.073 0.21 108 -10000 0 108
PAK1 0.023 0.02 0.26 6 -10000 0 6
CKAP5 0.024 0.003 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.021 0.25 2 -10000 0 2
AES 0.022 0.02 0.23 2 -10000 0 2
FBXW11 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.01 -10000 0 -10000 0 0
SMAD4 0.023 0.005 -10000 0 -10000 0 0
DKK2 0.011 0.091 0.26 2 -0.57 23 25
TLE1 0.019 0.051 0.21 3 -0.58 6 9
MACF1 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.1 0.1 0.32 31 -0.42 2 33
WIF1 -0.28 0.3 0.26 11 -0.57 509 520
beta catenin/RanBP3 0.02 0.09 0.42 35 -0.39 1 36
KREMEN2 0.13 0.12 0.26 435 -10000 0 435
DKK1 0.026 0.16 0.26 134 -0.57 50 184
beta catenin/beta TrCP1 0.11 0.095 0.32 20 -0.37 2 22
FZD1 0.025 0.004 -10000 0 -10000 0 0
AXIN2 0.016 0.26 0.6 80 -1.3 21 101
AXIN1 0.023 0.007 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.048 0.076 -10000 0 -0.56 11 11
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.066 0.13 0.36 4 -0.59 22 26
Axin1/APC/GSK3 0.047 0.054 0.24 1 -0.31 1 2
Axin1/APC/GSK3/beta catenin/Macf1 0.043 0.063 0.3 2 -0.4 4 6
HNF1A 0.025 0.028 0.25 10 -10000 0 10
CTBP1 0.022 0.02 0.23 3 -10000 0 3
MYC 0.11 0.34 0.58 243 -1.3 23 266
RANBP3 0.024 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.093 0.099 0.34 1 -0.34 17 18
NKD1 0.021 0.055 0.26 14 -0.57 6 20
TCF4 0.017 0.059 0.24 3 -0.57 9 12
TCF3 0.022 0.023 0.3 3 -10000 0 3
WNT1/LRP6/FZD1/Axin1 0.057 0.024 -10000 0 -10000 0 0
Ran/GTP 0.018 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.005 0.13 0.48 33 -0.5 16 49
LEF1 0.053 0.085 0.26 134 -0.54 1 135
DVL1 0.055 0.053 -10000 0 -0.46 1 1
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.069 0.15 0.31 4 -0.64 24 28
DKK1/LRP6/Kremen 2 0.1 0.14 0.34 73 -0.34 42 115
LRP6 0.024 0.005 -10000 0 -10000 0 0
CSNK1A1 0.023 0.022 0.27 3 -10000 0 3
NLK 0.023 0.014 0.26 2 -10000 0 2
CCND1 0.091 0.26 0.61 169 -1 6 175
WNT1 0.024 0.012 0.26 2 -10000 0 2
GSK3A 0.025 0.003 -10000 0 -10000 0 0
GSK3B 0.024 0.003 -10000 0 -10000 0 0
FRAT1 0.024 0.003 -10000 0 -10000 0 0
PPP2R5D 0.038 0.056 0.3 5 -0.3 8 13
APC 0.016 0.057 0.36 6 -10000 0 6
WNT1/LRP6/FZD1 0.12 0.11 0.26 62 -0.24 1 63
CREBBP 0.021 0.019 0.22 2 -10000 0 2
Glypican 2 network

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
MDK 0.033 0.045 0.26 37 -10000 0 37
GPC2 0.048 0.081 0.26 108 -0.58 3 111
GPC2/Midkine 0.057 0.069 0.37 14 -0.43 3 17
neuron projection morphogenesis 0.056 0.069 0.37 14 -0.43 3 17
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.011 0.047 -10000 0 -0.26 23 23
epithelial cell differentiation 0.035 0.059 -10000 0 -0.32 22 22
CYFIP2 0.029 0.051 0.26 27 -0.58 3 30
ENAH -0.004 0.06 0.29 10 -10000 0 10
EGFR -0.19 0.29 -10000 0 -0.58 362 362
EPHA2 0.02 0.043 -10000 0 -0.58 5 5
MYO6 -0.013 0.054 0.36 1 -0.31 23 24
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.05 0.036 -10000 0 -0.37 3 3
AQP5 -0.19 0.26 0.33 1 -0.5 396 397
CTNND1 0.024 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.053 0.36 1 -0.3 22 23
regulation of calcium-dependent cell-cell adhesion -0.025 0.078 0.36 1 -0.3 61 62
EGF -0.093 0.24 0.26 2 -0.58 195 197
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
AQP3 -0.016 0.12 0.29 1 -0.46 50 51
cortical microtubule organization 0.035 0.059 -10000 0 -0.32 22 22
GO:0000145 -0.013 0.05 0.35 1 -0.29 22 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.039 0.06 -10000 0 -0.32 22 22
MLLT4 0.021 0.034 0.26 1 -0.58 3 4
ARF6/GDP -0.021 0.041 -10000 0 -0.28 3 3
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.039 -10000 0 -0.34 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.003 0.052 -10000 0 -0.29 22 22
PVRL2 0.024 0.004 -10000 0 -10000 0 0
ZYX -0.013 0.053 0.36 1 -0.3 22 23
ARF6/GTP 0.049 0.041 -10000 0 -0.31 5 5
CDH1 0.008 0.088 -10000 0 -0.58 22 22
EGFR/EGFR/EGF/EGF -0.15 0.2 -10000 0 -0.34 497 497
RhoA/GDP 0.036 0.057 -10000 0 -0.3 22 22
actin cytoskeleton organization -0.015 0.051 0.34 1 -0.3 23 24
IGF-1R heterotetramer 0.012 0.083 0.26 2 -0.57 19 21
GIT1 0.023 0.006 -10000 0 -10000 0 0
IGF1R 0.012 0.083 0.26 2 -0.58 19 21
IGF1 -0.1 0.24 -10000 0 -0.58 211 211
DIAPH1 0.026 0.1 -10000 0 -0.56 15 15
Wnt receptor signaling pathway -0.035 0.059 0.32 22 -10000 0 22
RHOA 0.024 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.021 0.041 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
VCL -0.015 0.052 0.35 1 -0.3 23 24
EFNA1 0.02 0.009 -10000 0 -10000 0 0
LPP -0.017 0.055 -10000 0 -0.3 28 28
Ephrin A1/EPHA2 0.024 0.056 -10000 0 -0.3 22 22
SEC6/SEC8 -0.023 0.045 -10000 0 -0.3 23 23
MGAT3 -0.025 0.079 0.36 1 -0.31 61 62
HGF/MET -0.04 0.16 -10000 0 -0.33 214 214
HGF -0.011 0.14 -10000 0 -0.58 59 59
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.011 0.047 -10000 0 -0.26 23 23
actin cable formation 0.04 0.096 0.31 37 -0.29 1 38
KIAA1543 -0.014 0.055 0.35 1 -0.32 22 23
KIFC3 -0.014 0.052 0.36 1 -0.31 22 23
NCK1 0.024 0.003 -10000 0 -10000 0 0
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ACTN1 -0.014 0.052 -10000 0 -0.31 22 22
NCK1/GIT1 0.033 0.01 -10000 0 -10000 0 0
mol:GDP 0.035 0.059 -10000 0 -0.32 22 22
EXOC4 0.024 0.004 -10000 0 -10000 0 0
STX4 -0.013 0.051 0.36 1 -0.31 20 21
PIP5K1C -0.013 0.054 0.36 1 -0.31 22 23
LIMA1 0.024 0.019 -10000 0 -0.58 1 1
ABI1 0.024 0.004 -10000 0 -10000 0 0
ROCK1 0.016 0.089 0.3 24 -10000 0 24
adherens junction assembly -0.023 0.1 0.3 3 -0.63 14 17
IGF-1R heterotetramer/IGF1 -0.043 0.15 -10000 0 -0.31 222 222
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.03 0.2 1 -0.3 6 7
MET -0.071 0.22 -10000 0 -0.58 159 159
PLEKHA7 -0.014 0.058 0.36 1 -0.33 22 23
mol:GTP 0.043 0.038 -10000 0 -0.33 5 5
establishment of epithelial cell apical/basal polarity -0.01 0.068 0.37 6 -0.52 1 7
cortical actin cytoskeleton stabilization 0.011 0.047 -10000 0 -0.26 23 23
regulation of cell-cell adhesion -0.015 0.051 0.34 1 -0.3 23 24
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.011 0.047 -10000 0 -0.26 23 23
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.019 0.065 -10000 0 -0.36 34 34
ADCY5 -0.12 0.17 -10000 0 -0.37 305 305
ADCY6 -0.007 0.011 -10000 0 -0.36 1 1
ADCY7 -0.006 0.012 -10000 0 -0.36 1 1
ADCY1 -0.008 0.063 -10000 0 -0.37 25 25
ADCY2 -0.029 0.099 0.24 7 -0.37 75 82
ADCY3 -0.007 0.012 -10000 0 -0.36 1 1
ADCY8 -0.004 0.022 0.23 5 -10000 0 5
PRKCE 0.005 0.014 -10000 0 -0.42 1 1
ADCY9 -0.007 0.011 -10000 0 -0.36 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.011 0.086 0.23 15 -0.26 33 48
Signaling events mediated by HDAC Class III

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
EP300 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.019 -10000 0 -0.58 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.016 0.061 0.43 1 -0.27 15 16
CDKN1A -0.009 0.035 -10000 0 -0.77 2 2
KAT2B 0.024 0.019 -10000 0 -0.58 1 1
BAX 0.025 0.017 0.26 5 -10000 0 5
FOXO3 -0.005 0.008 -10000 0 -0.25 1 1
FOXO1 0.02 0.038 -10000 0 -0.58 4 4
FOXO4 0.012 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
TAT -0.33 0.3 0.26 25 -0.58 593 618
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.024 -10000 0 -0.43 1 1
PPARGC1A -0.093 0.24 0.26 9 -0.58 198 207
FHL2 0.021 0.046 -10000 0 -0.58 6 6
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.032 0.011 -10000 0 -10000 0 0
HIST2H4A 0.016 0.061 0.27 15 -0.43 1 16
SIRT1/FOXO3a 0.016 0.027 -10000 0 -0.2 4 4
SIRT1 0.022 0.009 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.039 0.024 -10000 0 -0.37 1 1
SIRT1/Histone H1b 0.028 0.043 -10000 0 -0.21 6 6
apoptosis -0.045 0.017 -10000 0 -10000 0 0
SIRT1/PGC1A -0.049 0.16 -10000 0 -0.36 198 198
p53/SIRT1 0.027 0.02 0.41 2 -10000 0 2
SIRT1/FOXO4 0.023 0.037 -10000 0 -0.21 4 4
FOXO1/FHL2/SIRT1 0.037 0.041 -10000 0 -0.34 9 9
HIST1H1E 0.021 0.03 0.21 6 -10000 0 6
SIRT1/p300 0.033 0.011 -10000 0 -10000 0 0
muscle cell differentiation -0.029 0.023 0.37 1 -10000 0 1
TP53 0.02 0.011 0.21 2 -10000 0 2
KU70/SIRT1/BAX 0.045 0.018 -10000 0 -10000 0 0
CREBBP 0.023 0.006 -10000 0 -10000 0 0
MEF2D 0.021 0.009 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.26 0.22 -10000 0 -0.42 593 593
ACSS2 -0.007 0.009 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.029 0.023 -10000 0 -0.37 1 1
Insulin Pathway

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
CBL/APS/CAP -0.047 0.17 -10000 0 -0.33 243 243
TC10/GTP -0.039 0.14 -10000 0 -0.3 218 218
Insulin Receptor/Insulin/IRS1/Shp2 0.043 0.08 -10000 0 -0.34 38 38
HRAS 0.025 0.02 0.26 7 -10000 0 7
APS homodimer 0.034 0.048 0.26 42 -10000 0 42
GRB14 0.014 0.18 0.26 138 -0.58 71 209
FOXO3 -0.018 0.16 -10000 0 -0.59 64 64
AKT1 -0.018 0.11 0.31 10 -0.29 94 104
INSR 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.056 0.047 0.36 10 -10000 0 10
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.024 0.003 -10000 0 -10000 0 0
SORBS1 -0.12 0.26 -10000 0 -0.58 243 243
CRK 0.022 0.007 -10000 0 -10000 0 0
PTPN1 -0.002 0.023 -10000 0 -10000 0 0
CAV1 -0.083 0.15 -10000 0 -0.35 215 215
CBL/APS/CAP/Crk-II/C3G -0.027 0.16 -10000 0 -0.31 239 239
Insulin Receptor/Insulin/IRS1/NCK2 0.043 0.079 -10000 0 -0.34 37 37
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.029 0.074 -10000 0 -0.3 43 43
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.013 0.066 -10000 0 -0.37 12 12
RPS6KB1 -0.017 0.098 0.29 11 -0.27 78 89
PARD6A 0.023 0.02 0.26 6 -10000 0 6
CBL 0.022 0.008 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.015 0.039 -10000 0 -0.55 4 4
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.009 0.094 -10000 0 -0.27 78 78
HRAS/GTP -0.02 0.046 -10000 0 -0.28 24 24
Insulin Receptor 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.041 0.072 -10000 0 -0.33 26 26
PRKCI 0.014 0.058 -10000 0 -0.46 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.003 0.1 -10000 0 -0.3 105 105
SHC1 0.02 0.009 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.041 0.036 -10000 0 -0.46 4 4
PI3K 0.038 0.078 -10000 0 -0.31 43 43
NCK2 0.024 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.014 0.18 7 -10000 0 7
AKT2 -0.018 0.11 0.3 8 -0.29 87 95
PRKCZ 0.004 0.086 -10000 0 -0.49 13 13
SH2B2 0.034 0.048 0.26 42 -10000 0 42
SHC/SHIP 0.012 0.06 -10000 0 -0.31 28 28
F2RL2 0.047 0.12 0.26 141 -0.58 17 158
TRIP10 0.024 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.037 0.022 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.053 0.034 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.037 0.17 -10000 0 -0.33 242 242
TC10/GDP 0.018 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.049 0.028 -10000 0 -10000 0 0
INPP5D -0.019 0.063 -10000 0 -0.32 38 38
SOS1 0.024 0.003 -10000 0 -10000 0 0
SGK1 -0.018 0.14 -10000 0 -0.68 42 42
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0.001 0.12 -10000 0 -0.58 39 39
p62DOK/RasGAP 0.042 0.037 -10000 0 -0.46 4 4
INS 0.019 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.063 0.19 1 -0.32 38 39
GRB2 0.023 0.01 0.26 1 -10000 0 1
EIF4EBP1 -0.021 0.091 0.29 5 -0.27 65 70
PTPRA 0.026 0.008 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.032 0.006 -10000 0 -10000 0 0
PDPK1 0.023 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.008 0.055 -10000 0 -0.28 27 27
Insulin Receptor/Insulin/IRS1 0.029 0.076 -10000 0 -0.34 39 39
Insulin Receptor/Insulin/IRS3 0.034 0.014 -10000 0 -10000 0 0
Par3/Par6 0.061 0.073 -10000 0 -0.31 17 17
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.007 0.011 -10000 0 -10000 0 0
SMARCC1 0.005 0.028 -10000 0 -0.59 1 1
REL 0.018 0.067 -10000 0 -0.58 12 12
HDAC7 -0.037 0.11 0.32 3 -0.42 30 33
JUN 0.018 0.054 -10000 0 -0.58 8 8
EP300 0.023 0.006 -10000 0 -10000 0 0
KAT2B 0.023 0.019 -10000 0 -0.58 1 1
KAT5 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.008 0.061 -10000 0 -0.43 18 18
FOXO1 0.02 0.038 -10000 0 -0.58 4 4
T-DHT/AR -0.023 0.12 0.33 1 -0.39 49 50
MAP2K6 0.003 0.082 0.25 1 -0.58 18 19
BRM/BAF57 0.024 0.028 -10000 0 -10000 0 0
MAP2K4 0.014 0.021 -10000 0 -10000 0 0
SMARCA2 0.017 0.019 -10000 0 -10000 0 0
PDE9A -0.063 0.26 -10000 0 -1.1 57 57
NCOA2 -0.005 0.12 -10000 0 -0.57 40 40
CEBPA 0.019 0.057 -10000 0 -0.57 9 9
EHMT2 0.02 0.012 -10000 0 -10000 0 0
cell proliferation -0.001 0.15 0.36 27 -0.45 23 50
NR0B1 0.028 0.044 0.26 34 -10000 0 34
EGR1 -0.17 0.28 -10000 0 -0.58 313 313
RXRs/9cRA -0.045 0.15 -10000 0 -0.34 202 202
AR/RACK1/Src -0.017 0.11 0.32 7 -0.37 29 36
AR/GR -0.026 0.12 0.28 1 -0.3 123 124
GNB2L1 0.023 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
RCHY1 0.024 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.001 0.003 -10000 0 -0.013 14 14
MAPK8 -0.002 0.04 -10000 0 -0.43 6 6
T-DHT/AR/TIF2/CARM1 -0.015 0.12 0.34 2 -0.37 47 49
SRC -0.019 0.065 0.2 22 -0.34 21 43
NR3C1 0.018 0.06 -10000 0 -0.58 10 10
KLK3 -0.16 0.41 0.38 5 -1.1 140 145
APPBP2 0.015 0.019 -10000 0 -10000 0 0
TRIM24 0.018 0.02 0.26 1 -10000 0 1
T-DHT/AR/TIP60 -0.014 0.095 0.33 4 -0.39 23 27
TMPRSS2 -0.13 0.37 -10000 0 -1.1 130 130
RXRG -0.1 0.24 0.26 2 -0.58 204 206
mol:9cRA -0.001 0.003 -10000 0 -0.011 12 12
RXRA 0.024 0.005 -10000 0 -10000 0 0
RXRB 0.024 0.005 -10000 0 -10000 0 0
CARM1 0.022 0.011 -10000 0 -10000 0 0
NR2C2 0.019 0.053 -10000 0 -0.57 8 8
KLK2 -0.054 0.21 0.33 4 -0.66 84 88
AR -0.038 0.1 -10000 0 -0.31 120 120
SENP1 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
MDM2 0.026 0.016 -10000 0 -10000 0 0
SRY 0.003 0.012 0.032 132 -0.024 33 165
GATA2 0.012 0.098 0.26 12 -0.58 25 37
MYST2 0 0.002 -10000 0 -10000 0 0
HOXB13 0.12 0.12 0.26 417 -10000 0 417
T-DHT/AR/RACK1/Src -0.012 0.1 0.33 11 -0.38 24 35
positive regulation of transcription 0.012 0.097 0.26 12 -0.57 25 37
DNAJA1 0.017 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.01 -10000 0 -10000 0 0
NCOA1 0.021 0.031 -10000 0 -0.61 1 1
SPDEF -0.011 0.15 0.26 30 -0.58 62 92
T-DHT/AR/TIF2 -0.003 0.098 0.26 9 -0.38 23 32
T-DHT/AR/Hsp90 -0.016 0.094 0.34 2 -0.39 23 25
GSK3B 0.022 0.011 -10000 0 -10000 0 0
NR2C1 0.025 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.024 0.059 0.23 1 -0.36 22 23
SIRT1 0.024 0.003 -10000 0 -10000 0 0
ZMIZ2 0.026 0.016 -10000 0 -10000 0 0
POU2F1 0.008 0.051 -10000 0 -0.18 13 13
T-DHT/AR/DAX-1 -0.014 0.098 0.31 4 -0.39 24 28
CREBBP 0.023 0.006 -10000 0 -10000 0 0
SMARCE1 0.017 0.019 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.01 0.042 -10000 0 -0.57 1 1
SVIL 0.009 0.051 -10000 0 -0.57 4 4
ZNF318 0.042 0.057 0.21 12 -10000 0 12
JMJD2C -0.002 0.043 0.11 23 -0.13 78 101
T-DHT/AR/Ubc9 -0.032 0.14 -10000 0 -0.38 125 125
CARM1 0.018 0.016 -10000 0 -10000 0 0
PRDX1 0.025 0.006 -10000 0 -10000 0 0
PELP1 0.025 0.012 -10000 0 -10000 0 0
CTNNB1 0.013 0.031 -10000 0 -10000 0 0
AKT1 0.028 0.019 -10000 0 -10000 0 0
PTK2B 0.011 0.027 -10000 0 -10000 0 0
MED1 0.026 0.021 -10000 0 -10000 0 0
MAK 0.037 0.087 0.29 10 -0.55 11 21
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 0.008 0.055 -10000 0 -0.57 5 5
GSN 0.004 0.074 -10000 0 -0.57 12 12
NCOA2 -0.008 0.12 -10000 0 -0.58 40 40
NCOA6 0.012 0.034 -10000 0 -10000 0 0
DNA-PK 0.052 0.055 0.24 1 -10000 0 1
NCOA4 0.02 0.013 -10000 0 -10000 0 0
PIAS3 0.013 0.03 -10000 0 -10000 0 0
cell proliferation 0.005 0.12 0.37 2 -0.58 24 26
XRCC5 0.027 0.015 -10000 0 -10000 0 0
UBE3A 0.007 0.046 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.04 0.16 -10000 0 -0.4 138 138
FHL2 0.003 0.12 -10000 0 -0.9 8 8
RANBP9 0.011 0.035 -10000 0 -10000 0 0
JMJD1A -0.01 0.055 0.12 36 -0.14 134 170
CDK6 0.021 0.051 0.26 2 -0.58 7 9
TGFB1I1 0.009 0.048 -10000 0 -0.58 3 3
T-DHT/AR/CyclinD1 -0.04 0.14 -10000 0 -0.38 131 131
XRCC6 0.026 0.016 -10000 0 -10000 0 0
T-DHT/AR -0.036 0.17 -10000 0 -0.39 137 137
CTDSP1 0.017 0.02 -10000 0 -10000 0 0
CTDSP2 0.036 0.038 -10000 0 -10000 0 0
BRCA1 0.011 0.04 -10000 0 -0.57 1 1
TCF4 0.026 0.064 -10000 0 -0.57 9 9
CDKN2A 0.065 0.09 0.27 155 -10000 0 155
SRF 0.033 0.023 -10000 0 -10000 0 0
NKX3-1 -0.058 0.2 0.36 3 -0.67 58 61
KLK3 -0.17 0.48 -10000 0 -1.4 132 132
TMF1 0.018 0.017 -10000 0 -10000 0 0
HNRNPA1 0.03 0.021 -10000 0 -10000 0 0
AOF2 -0.008 0.024 -10000 0 -0.07 132 132
APPL1 0.021 0.034 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.025 0.15 -10000 0 -0.38 126 126
AR -0.064 0.2 0.21 1 -0.59 124 125
UBA3 0.016 0.02 -10000 0 -10000 0 0
PATZ1 0.028 0.021 -10000 0 -10000 0 0
PAWR 0.018 0.025 -10000 0 -0.58 1 1
PRKDC 0.024 0.017 -10000 0 -10000 0 0
PA2G4 0.032 0.027 -10000 0 -10000 0 0
UBE2I 0.023 0.007 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.021 0.13 -10000 0 -0.35 115 115
RPS6KA3 0.006 0.062 -10000 0 -0.57 7 7
T-DHT/AR/ARA70 -0.035 0.14 -10000 0 -0.38 124 124
LATS2 0.028 0.023 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.018 0.14 0.19 6 -0.34 130 136
Cyclin D3/CDK11 p58 0.019 0.006 -10000 0 -10000 0 0
VAV3 0.014 0.064 0.26 16 -0.58 6 22
KLK2 -0.081 0.28 0.38 1 -1 80 81
CASP8 0.027 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.038 0.14 -10000 0 -0.36 133 133
TMPRSS2 -0.13 0.34 -10000 0 -0.99 130 130
CCND1 0.012 0.04 0.26 1 -0.58 3 4
PIAS1 0.008 0.047 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.031 0.072 1 -0.071 169 170
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 0.001 0.066 -10000 0 -0.17 114 114
T-DHT/AR/CDK6 -0.032 0.15 -10000 0 -0.36 142 142
CMTM2 0.023 0.013 0.26 1 -10000 0 1
SNURF 0.012 0.082 -10000 0 -0.58 19 19
ZMIZ1 0.01 0.042 -10000 0 -10000 0 0
CCND3 0.024 0.005 -10000 0 -10000 0 0
TGIF1 0.028 0.021 -10000 0 -10000 0 0
FKBP4 0.013 0.038 0.26 4 -10000 0 4
Syndecan-4-mediated signaling events

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
PTK2 0.084 0.1 0.28 20 -0.57 6 26
Syndecan-4/Syndesmos 0.095 0.11 0.39 4 -0.7 6 10
positive regulation of JNK cascade 0.084 0.14 0.37 6 -0.64 8 14
Syndecan-4/ADAM12 0.11 0.12 0.41 7 -0.72 6 13
CCL5 0.03 0.056 0.26 36 -0.58 3 39
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DNM2 0.024 0.004 -10000 0 -10000 0 0
ITGA5 0.024 0.003 -10000 0 -10000 0 0
SDCBP 0.021 0.009 -10000 0 -10000 0 0
PLG -0.009 0.031 0.26 4 -10000 0 4
ADAM12 0.037 0.064 0.26 62 -0.58 2 64
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.024 0.015 0.26 3 -10000 0 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.028 0.018 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.064 0.15 0.41 2 -0.69 8 10
Syndecan-4/CXCL12/CXCR4 0.088 0.14 0.38 6 -0.69 8 14
Syndecan-4/Laminin alpha3 0.034 0.15 0.41 2 -0.8 6 8
MDK 0.033 0.045 0.26 37 -10000 0 37
Syndecan-4/FZD7 0.095 0.12 0.4 3 -0.69 7 10
Syndecan-4/Midkine 0.1 0.11 0.39 8 -0.69 6 14
FZD7 0.013 0.082 -10000 0 -0.58 19 19
Syndecan-4/FGFR1/FGF -0.011 0.16 -10000 0 -0.59 13 13
THBS1 0.021 0.038 -10000 0 -0.58 4 4
integrin-mediated signaling pathway 0.093 0.12 0.4 5 -0.69 7 12
positive regulation of MAPKKK cascade 0.084 0.14 0.37 6 -0.64 8 14
Syndecan-4/TACI 0.098 0.12 0.39 6 -0.72 6 12
CXCR4 0.03 0.037 0.26 24 -10000 0 24
cell adhesion 0.061 0.084 0.24 81 -0.25 20 101
Syndecan-4/Dynamin 0.099 0.11 0.4 3 -0.73 6 9
Syndecan-4/TSP1 0.098 0.11 0.39 4 -0.72 6 10
Syndecan-4/GIPC 0.1 0.11 0.4 3 -0.73 6 9
Syndecan-4/RANTES 0.1 0.11 0.38 5 -0.72 6 11
ITGB1 0.024 0.004 -10000 0 -10000 0 0
LAMA1 -0.039 0.18 0.26 2 -0.58 105 107
LAMA3 -0.12 0.25 -10000 0 -0.58 231 231
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.022 0.22 0.7 89 -0.54 21 110
Syndecan-4/alpha-Actinin 0.099 0.11 0.4 3 -0.72 6 9
TFPI -0.002 0.12 -10000 0 -0.58 44 44
F2 0.024 0.032 0.27 8 -10000 0 8
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.002 0.18 0.44 1 -0.6 21 22
ACTN1 0.024 0.005 -10000 0 -10000 0 0
TNC 0.012 0.093 0.26 8 -0.58 23 31
Syndecan-4/CXCL12 0.077 0.14 0.4 3 -0.72 8 11
FGF6 0.015 0.027 -10000 0 -0.58 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
CXCL12 -0.02 0.16 -10000 0 -0.58 73 73
TNFRSF13B 0.027 0.085 0.26 52 -0.58 12 64
FGF2 -0.2 0.29 -10000 0 -0.58 376 376
FGFR1 0.016 0.051 -10000 0 -0.58 7 7
Syndecan-4/PI-4-5-P2 0.075 0.1 -10000 0 -0.72 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.11 0.12 0.26 389 -10000 0 389
cell migration -0.02 0.012 -10000 0 -10000 0 0
PRKCD 0.012 0.026 -10000 0 -10000 0 0
vasculogenesis 0.097 0.1 0.39 4 -0.68 6 10
SDC4 0.087 0.1 0.48 1 -0.78 5 6
Syndecan-4/Tenascin C 0.094 0.12 0.41 4 -0.72 7 11
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.014 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.086 0.11 0.37 3 -0.7 6 9
MMP9 0.12 0.12 0.26 409 -0.57 1 410
Rac1/GTP 0.061 0.085 0.25 77 -0.26 20 97
cytoskeleton organization 0.093 0.1 0.39 4 -0.67 6 10
GIPC1 0.025 0.011 0.26 2 -10000 0 2
Syndecan-4/TFPI 0.088 0.13 0.4 3 -0.72 7 10
Thromboxane A2 receptor signaling

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
TGM2 0.027 0.029 0.26 14 -10000 0 14
GNB1/GNG2 -0.016 0.049 -10000 0 -0.19 63 63
AKT1 0.022 0.093 0.33 13 -0.26 34 47
EGF -0.093 0.24 0.26 2 -0.58 195 197
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.014 0.058 0.25 2 -0.28 5 7
mol:Ca2+ 0.021 0.12 0.39 12 -0.3 70 82
LYN 0.012 0.055 0.25 2 -0.3 3 5
RhoA/GTP 0.009 0.045 0.14 4 -0.14 18 22
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.018 0.12 0.4 13 -0.34 63 76
GNG2 0.018 0.06 -10000 0 -0.58 10 10
ARRB2 0.022 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.006 0.12 -10000 0 -0.57 36 36
G beta5/gamma2 -0.013 0.068 -10000 0 -0.26 62 62
PRKCH 0.016 0.12 0.38 14 -0.36 65 79
DNM1 0.02 0.051 0.26 1 -0.58 7 8
TXA2/TP beta/beta Arrestin3 0.008 0.032 -10000 0 -0.53 1 1
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.008 0.1 0.26 7 -0.58 29 36
G12 family/GTP -0.001 0.091 -10000 0 -0.31 60 60
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
ADRBK2 0.021 0.038 -10000 0 -0.58 4 4
RhoA/GTP/ROCK1 0.031 0.015 -10000 0 -0.36 1 1
mol:GDP -0.01 0.1 0.36 35 -0.33 8 43
mol:NADP 0.024 0.004 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
PRKG1 -0.013 0.14 -10000 0 -0.58 62 62
mol:IP3 0.018 0.14 0.46 9 -0.38 71 80
cell morphogenesis 0.031 0.015 -10000 0 -0.36 1 1
PLCB2 0.009 0.17 0.55 6 -0.52 71 77
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.025 0.071 0.26 7 -0.29 5 12
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.015 0.06 0.24 4 -0.29 5 9
RHOA 0.024 0.005 -10000 0 -10000 0 0
PTGIR 0.027 0.026 0.26 12 -10000 0 12
PRKCB1 0.017 0.13 0.4 12 -0.37 68 80
GNAQ 0.023 0.027 -10000 0 -0.58 2 2
mol:L-citrulline 0.024 0.004 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.012 0.17 0.54 7 -0.53 65 72
LCK 0.016 0.074 0.25 2 -0.35 15 17
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.023 0.054 -10000 0 -0.25 27 27
TXA2-R family/G12 family/GDP/G beta/gamma 0.006 0.1 -10000 0 -0.42 48 48
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.023 0.051 -10000 0 -0.24 26 26
MAPK14 0.018 0.089 0.34 14 -0.23 58 72
TGM2/GTP 0.013 0.15 0.49 9 -0.43 69 78
MAPK11 0.016 0.09 0.34 15 -0.24 60 75
ARHGEF1 0.011 0.067 0.27 10 -0.18 50 60
GNAI2 0.024 0.005 -10000 0 -10000 0 0
JNK cascade 0.019 0.13 0.42 12 -0.39 64 76
RAB11/GDP 0.023 0.006 -10000 0 -10000 0 0
ICAM1 0.021 0.1 0.38 13 -0.28 60 73
cAMP biosynthetic process 0.015 0.13 0.42 10 -0.36 69 79
Gq family/GTP/EBP50 0.015 0.043 0.22 4 -0.26 7 11
actin cytoskeleton reorganization 0.031 0.015 -10000 0 -0.36 1 1
SRC 0.013 0.057 0.25 2 -0.29 5 7
GNB5 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.024 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.05 0.11 0.24 3 -0.29 70 73
VCAM1 0.019 0.11 0.38 12 -0.31 60 72
TP beta/Gq family/GDP/G beta5/gamma2 -0.006 0.12 -10000 0 -0.57 36 36
platelet activation 0.022 0.12 0.4 15 -0.31 63 78
PGI2/IP 0.02 0.018 0.18 12 -10000 0 12
PRKACA 0.009 0.053 -10000 0 -0.27 32 32
Gq family/GDP/G beta5/gamma2 0 0.1 -10000 0 -0.47 31 31
TXA2/TP beta/beta Arrestin2 -0.007 0.069 -10000 0 -0.45 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.002 0.047 -10000 0 -0.27 28 28
mol:DAG 0.016 0.14 0.46 9 -0.42 70 79
EGFR -0.19 0.29 -10000 0 -0.58 362 362
TXA2/TP alpha 0.013 0.17 0.52 7 -0.49 70 77
Gq family/GTP 0.002 0.049 0.25 1 -0.22 41 42
YES1 0.014 0.06 0.25 2 -0.28 6 8
GNAI2/GTP 0.014 0.051 -10000 0 -0.25 29 29
PGD2/DP 0.006 0.076 0.18 7 -0.4 32 39
SLC9A3R1 0.035 0.054 0.26 53 -10000 0 53
FYN 0.012 0.058 0.26 1 -0.32 7 8
mol:NO 0.024 0.004 -10000 0 -10000 0 0
GNA15 0.025 0.027 0.26 6 -0.58 1 7
PGK/cGMP 0.008 0.096 -10000 0 -0.36 62 62
RhoA/GDP 0.023 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.036 0.069 -10000 0 -0.3 30 30
NOS3 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.02 0.13 0.39 14 -0.38 59 73
PRKCB 0.02 0.13 0.41 11 -0.37 61 72
PRKCE 0.017 0.12 0.43 10 -0.36 63 73
PRKCD 0.016 0.13 0.44 9 -0.38 61 70
PRKCG 0.018 0.13 0.45 9 -0.39 62 71
muscle contraction 0.013 0.16 0.49 9 -0.49 67 76
PRKCZ 0.017 0.12 0.4 12 -0.35 61 73
ARR3 0.021 0.022 0.26 8 -10000 0 8
TXA2/TP beta 0.024 0.058 -10000 0 -0.27 29 29
PRKCQ 0.013 0.14 0.41 13 -0.4 64 77
MAPKKK cascade 0.013 0.16 0.48 8 -0.46 69 77
SELE 0.015 0.12 0.36 14 -0.39 60 74
TP beta/GNAI2/GDP/G beta/gamma 0.035 0.069 -10000 0 -0.3 31 31
ROCK1 0.023 0.019 -10000 0 -0.58 1 1
GNA14 0.023 0.068 0.26 19 -0.58 10 29
chemotaxis 0.011 0.18 0.59 6 -0.61 60 66
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.007 -10000 0 -10000 0 0
GNA11 0.023 0.027 -10000 0 -0.58 2 2
Rac1/GTP 0.018 0.003 -10000 0 -10000 0 0
BCR signaling pathway

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.022 0.13 0.33 11 -0.38 41 52
IKBKB 0.024 0.089 0.36 5 -0.31 12 17
AKT1 0.038 0.11 0.27 72 -0.24 21 93
IKBKG 0.028 0.074 0.36 4 -0.29 6 10
CALM1 0.001 0.098 -10000 0 -0.34 43 43
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
MAP3K1 0.023 0.16 0.37 12 -0.52 43 55
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.1 -10000 0 -0.35 45 45
DOK1 0.025 0.015 0.26 4 -10000 0 4
AP-1 -0.023 0.1 0.26 6 -0.24 62 68
LYN 0.021 0.009 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
BCR complex 0.003 0.16 0.25 66 -0.45 90 156
CD22 -0.012 0.13 0.28 21 -0.41 73 94
CAMK2G 0.003 0.096 0.3 1 -0.4 19 20
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.002 0.088 -10000 0 -0.33 52 52
GO:0007205 0.001 0.1 -10000 0 -0.36 45 45
SYK 0.024 0.004 -10000 0 -10000 0 0
ELK1 0.002 0.1 0.26 2 -0.35 43 45
NFATC1 0.031 0.13 0.3 24 -0.43 37 61
B-cell antigen/BCR complex 0.003 0.16 0.25 66 -0.45 90 156
PAG1/CSK 0.03 0.016 -10000 0 -10000 0 0
NFKBIB 0.025 0.047 0.18 9 -0.13 22 31
HRAS 0.011 0.11 0.26 12 -0.33 48 60
NFKBIA 0.025 0.046 0.18 9 -0.12 15 24
NF-kappa-B/RelA/I kappa B beta 0.028 0.042 0.18 9 -10000 0 9
RasGAP/Csk 0.031 0.12 0.33 19 -0.37 64 83
mol:GDP 0.003 0.1 -10000 0 -0.34 44 44
PTEN 0.023 0.027 -10000 0 -0.58 2 2
CD79B 0.011 0.1 0.26 18 -0.57 26 44
NF-kappa-B/RelA/I kappa B alpha 0.028 0.041 0.18 9 -10000 0 9
GRB2 0.023 0.01 0.26 1 -10000 0 1
PI3K/BCAP/CD19 0.023 0.17 0.35 12 -0.45 68 80
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
mol:IP3 0.002 0.1 -10000 0 -0.36 44 44
CSK 0.024 0.004 -10000 0 -10000 0 0
FOS -0.08 0.16 -10000 0 -0.42 89 89
CHUK 0.024 0.082 0.36 4 -0.3 18 22
IBTK 0.023 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.018 0.096 -10000 0 -0.41 17 17
PTPN6 -0.014 0.13 0.26 22 -0.42 61 83
RELA 0.024 0.004 -10000 0 -10000 0 0
BCL2A1 0.025 0.035 0.16 10 -10000 0 10
VAV2 0.015 0.14 0.29 14 -0.57 30 44
ubiquitin-dependent protein catabolic process 0.027 0.046 0.18 9 -0.12 28 37
BTK 0.015 0.064 -10000 0 -0.97 4 4
CD19 0.004 0.14 0.28 33 -0.43 59 92
MAP4K1 0.032 0.054 0.26 39 -0.58 2 41
CD72 0.03 0.043 0.26 26 -0.58 1 27
PAG1 0.021 0.014 0.26 2 -10000 0 2
MAPK14 0.025 0.14 0.36 14 -0.45 40 54
SH3BP5 0.024 0.004 -10000 0 -10000 0 0
PIK3AP1 0.002 0.11 -10000 0 -0.38 47 47
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.002 0.14 0.27 3 -0.41 76 79
RAF1 0.01 0.1 0.25 12 -0.34 37 49
RasGAP/p62DOK/SHIP 0.03 0.12 0.3 18 -0.36 64 82
CD79A -0.005 0.18 0.26 71 -0.57 76 147
re-entry into mitotic cell cycle -0.023 0.099 0.27 5 -0.24 60 65
RASA1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.017 0.097 0.28 21 -0.35 16 37
MAPK1 0.01 0.091 0.26 7 -0.36 16 23
CD72/SHP1 0.029 0.15 0.34 35 -0.41 56 91
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.023 0.15 0.35 16 -0.45 43 59
actin cytoskeleton organization 0.031 0.14 0.31 27 -0.5 29 56
NF-kappa-B/RelA 0.058 0.079 0.31 9 -0.21 1 10
Calcineurin 0.018 0.092 -10000 0 -0.39 16 16
PI3K -0.013 0.096 -10000 0 -0.36 52 52
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.005 0.11 -10000 0 -0.39 49 49
SOS1 0.024 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.011 0.2 0.44 7 -0.7 51 58
DAPP1 -0.018 0.21 -10000 0 -0.78 52 52
cytokine secretion 0.031 0.13 0.28 29 -0.4 37 66
mol:DAG 0.002 0.1 -10000 0 -0.36 44 44
PLCG2 0.02 0.029 0.26 1 -0.57 2 3
MAP2K1 0.01 0.098 0.28 7 -0.37 20 27
B-cell antigen/BCR complex/FcgammaRIIB 0.014 0.13 0.34 18 -0.42 65 83
mol:PI-3-4-5-P3 0.006 0.092 0.22 21 -0.32 25 46
ETS1 0 0.09 0.28 1 -0.39 19 20
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.033 0.13 0.33 19 -0.36 69 88
B-cell antigen/BCR complex/LYN -0.012 0.14 0.26 19 -0.42 75 94
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.14 0.31 24 -0.54 29 53
B-cell antigen/BCR complex/LYN/SYK 0.013 0.14 0.36 21 -0.43 58 79
CARD11 0.003 0.1 0.3 3 -0.36 42 45
FCGR2B 0.018 0.04 0.26 1 -0.58 4 5
PPP3CA 0.024 0.011 0.26 2 -10000 0 2
BCL10 0.024 0.005 -10000 0 -10000 0 0
IKK complex 0.027 0.051 0.16 45 -0.14 4 49
PTPRC 0.022 0.044 0.26 13 -0.58 3 16
PDPK1 0.02 0.083 0.21 56 -0.23 19 75
PPP3CB 0.024 0.004 -10000 0 -10000 0 0
PPP3CC 0.02 0.01 -10000 0 -10000 0 0
POU2F2 0.022 0.033 0.18 8 -10000 0 8
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.011 0.26 1 -10000 0 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.012 0.12 0.44 8 -0.42 6 14
IL27/IL27R/JAK1 0.038 0.16 0.54 11 -0.56 11 22
TBX21 -0.003 0.17 0.43 18 -0.51 45 63
IL12B 0.075 0.1 0.27 208 -10000 0 208
IL12A -0.015 0.1 0.14 15 -0.42 56 71
IL6ST -0.037 0.18 0.2 1 -0.58 103 104
IL27RA/JAK1 0.022 0.07 0.65 1 -1.2 2 3
IL27 0.046 0.075 0.27 94 -10000 0 94
TYK2 0.03 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.098 0.16 0.73 2 -0.52 11 13
T-helper 2 cell differentiation -0.012 0.12 0.44 8 -0.42 6 14
T cell proliferation during immune response -0.012 0.12 0.44 8 -0.42 6 14
MAPKKK cascade 0.012 0.12 0.42 6 -0.44 8 14
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT2 0.024 0.002 -10000 0 -10000 0 0
STAT1 0.028 0.034 0.27 18 -10000 0 18
IL12RB1 0.034 0.054 0.27 38 -0.58 2 40
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.007 0.18 0.45 31 -0.53 50 81
IL27/IL27R/JAK2/TYK2 0.011 0.12 0.42 6 -0.45 8 14
positive regulation of T cell mediated cytotoxicity 0.012 0.12 0.42 6 -0.44 8 14
STAT1 (dimer) 0.035 0.2 0.58 31 -0.62 20 51
JAK2 0.027 0.012 -10000 0 -10000 0 0
JAK1 0.024 0.01 -10000 0 -10000 0 0
STAT2 (dimer) 0.023 0.12 0.42 4 -0.43 8 12
T cell proliferation -0.092 0.19 0.33 6 -0.44 102 108
IL12/IL12R/TYK2/JAK2 0.058 0.18 0.45 5 -0.74 26 31
IL17A -0.098 0.16 0.74 2 -0.52 11 13
mast cell activation -0.012 0.12 0.44 8 -0.42 6 14
IFNG 0.021 0.046 0.13 116 -0.1 7 123
T cell differentiation 0 0.006 0.022 5 -0.021 4 9
STAT3 (dimer) 0.022 0.12 0.42 4 -0.44 7 11
STAT5A (dimer) 0.02 0.12 0.42 4 -0.44 13 17
STAT4 (dimer) 0.011 0.14 0.42 4 -0.41 31 35
STAT4 0.001 0.12 0.26 1 -0.58 40 41
T cell activation -0.005 0.011 0.12 2 -0.11 6 8
IL27R/JAK2/TYK2 0.018 0.13 0.4 1 -0.57 8 9
GATA3 -0.021 0.26 0.62 35 -1.3 31 66
IL18 0.009 0.021 0.14 25 -10000 0 25
positive regulation of mast cell cytokine production 0.022 0.11 0.41 4 -0.44 7 11
IL27/EBI3 0.051 0.073 0.26 51 -0.39 6 57
IL27RA 0.009 0.072 0.55 2 -1.3 2 4
IL6 -0.19 0.29 0.26 1 -0.57 352 353
STAT5A 0.02 0.047 -10000 0 -0.58 6 6
monocyte differentiation 0.001 0.002 -10000 0 -10000 0 0
IL2 -0.014 0.042 0.45 2 -0.53 1 3
IL1B 0.001 0.051 0.14 3 -0.42 14 17
EBI3 0.025 0.056 0.27 13 -0.58 6 19
TNF 0.005 0.047 0.14 22 -0.42 10 32
TCGA08_retinoblastoma

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
CDKN2B 0.023 0.025 0.27 2 -0.55 1 3
CDKN2C 0.015 0.029 -10000 0 -0.56 1 1
CDKN2A 0.06 0.087 0.26 155 -10000 0 155
CCND2 -0.016 0.037 0.2 2 -0.2 16 18
RB1 0.016 0.05 0.27 16 -0.24 8 24
CDK4 -0.017 0.038 0.21 2 -0.23 11 13
CDK6 -0.017 0.041 0.22 2 -0.2 21 23
G1/S progression -0.01 0.06 0.19 40 -0.27 15 55
Regulation of Telomerase

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
Telomerase catalytic core complex 0.057 0.13 0.51 6 -0.52 2 8
RAD9A 0.023 0.007 -10000 0 -10000 0 0
AP1 -0.097 0.21 -10000 0 -0.42 294 294
IFNAR2 0.029 0.009 -10000 0 -10000 0 0
AKT1 -0.002 0.089 -10000 0 -0.23 90 90
ER alpha/Oestrogen -0.023 0.17 0.18 120 -0.41 144 264
NFX1/SIN3/HDAC complex 0.023 0.058 0.24 1 -0.32 15 16
EGF -0.091 0.24 0.26 2 -0.57 195 197
SMG5 0.021 0.009 -10000 0 -10000 0 0
SMG6 0.022 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.041 0.018 -10000 0 -10000 0 0
TERT/c-Abl 0.054 0.12 0.43 3 -0.49 2 5
SAP18 0.024 0.007 -10000 0 -10000 0 0
MRN complex 0.036 0.022 -10000 0 -10000 0 0
WT1 0.15 0.12 0.26 498 -10000 0 498
WRN 0.02 0.009 -10000 0 -10000 0 0
SP1 0.031 0.013 -10000 0 -10000 0 0
SP3 0.026 0.005 -10000 0 -10000 0 0
TERF2IP 0.021 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.049 0.1 -10000 0 -0.51 1 1
Mad/Max 0.041 0.014 -10000 0 -10000 0 0
TERT 0.057 0.13 0.51 6 -0.59 1 7
CCND1 0.081 0.16 0.54 20 -1.1 3 23
MAX 0.026 0.006 -10000 0 -10000 0 0
RBBP7 0.027 0.02 0.26 7 -10000 0 7
RBBP4 0.024 0.019 -10000 0 -0.57 1 1
TERF2 0.021 0.014 -10000 0 -10000 0 0
PTGES3 0.024 0.002 -10000 0 -10000 0 0
SIN3A 0.025 0.004 -10000 0 -10000 0 0
Telomerase/911 0.04 0.051 -10000 0 -0.4 4 4
CDKN1B 0.029 0.052 -10000 0 -0.68 3 3
RAD1 0.024 0.004 -10000 0 -10000 0 0
XRCC5 0.024 0.004 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
SAP30 0.025 0.016 0.26 4 -10000 0 4
TRF2/PARP2 0.032 0.016 -10000 0 -10000 0 0
UBE3A 0.025 0.007 -10000 0 -10000 0 0
JUN 0.021 0.054 -10000 0 -0.57 8 8
E6 0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.01 -10000 0 -10000 0 0
FOS -0.14 0.27 -10000 0 -0.57 285 285
IFN-gamma/IRF1 0.065 0.065 0.39 2 -0.32 3 5
PARP2 0.024 0.004 -10000 0 -10000 0 0
BLM 0.046 0.069 0.26 93 -10000 0 93
Telomerase 0.029 0.08 0.27 1 -0.64 5 6
IRF1 0.029 0.019 0.27 3 -0.19 3 6
ESR1 -0.03 0.23 0.26 120 -0.57 138 258
KU/TER 0.034 0.01 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.014 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.027 0.056 0.24 1 -0.34 8 9
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.027 0.057 0.24 1 -0.34 8 9
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.012 -10000 0 -10000 0 0
ATM 0.013 0.016 -10000 0 -10000 0 0
SMAD3 0.005 0.013 -10000 0 -10000 0 0
ABL1 0.024 0.004 -10000 0 -10000 0 0
MXD1 0.027 0.009 0.26 1 -10000 0 1
MRE11A 0.022 0.007 -10000 0 -10000 0 0
HUS1 0.024 0.003 -10000 0 -10000 0 0
RPS6KB1 0.022 0.008 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.059 0.13 0.5 1 -0.59 5 6
NR2F2 0.012 0.038 -10000 0 -0.58 3 3
MAPK3 0.006 0.02 -10000 0 -10000 0 0
MAPK1 0.006 0.02 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.022 0.012 0.26 1 -10000 0 1
NFKB1 0.024 0.004 -10000 0 -10000 0 0
HNRNPC 0.024 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.013 0.016 -10000 0 -10000 0 0
NBN 0.02 0.01 -10000 0 -10000 0 0
EGFR -0.19 0.29 -10000 0 -0.57 362 362
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.21 0.26 -10000 0 -0.46 497 497
MYC 0.008 0.084 -10000 0 -0.57 20 20
IL2 0.03 0.027 0.26 9 -10000 0 9
KU 0.034 0.01 -10000 0 -10000 0 0
RAD50 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
TGFB1 0.022 0.012 0.26 1 -10000 0 1
TRF2/BLM 0.044 0.047 0.23 8 -10000 0 8
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.067 0.13 0.46 4 -0.55 1 5
SP1/HDAC2 0.046 0.026 -10000 0 -10000 0 0
PINX1 0.02 0.009 -10000 0 -10000 0 0
Telomerase/EST1A 0.046 0.1 -10000 0 -0.49 1 1
Smad3/Myc 0.007 0.055 -10000 0 -0.37 19 19
911 complex 0.044 0.016 -10000 0 -10000 0 0
IFNG 0.059 0.084 0.27 137 -0.2 1 138
Telomerase/PinX1 0.039 0.096 -10000 0 -0.49 1 1
Telomerase/AKT1/mTOR/p70S6K 0.027 0.1 0.31 3 -0.54 16 19
SIN3B 0.025 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.044 0.094 -10000 0 -0.42 1 1
response to DNA damage stimulus -0.002 0.028 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.047 0.034 -10000 0 -10000 0 0
TRF2/WRN 0.028 0.017 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.049 0.1 -10000 0 -0.51 1 1
E2F1 0.098 0.11 0.27 294 -10000 0 294
ZNFX1 0.024 0.007 -10000 0 -10000 0 0
PIF1 0.068 0.093 0.26 188 -10000 0 188
NCL 0.024 0.004 -10000 0 -10000 0 0
DKC1 0.025 0.011 0.26 2 -10000 0 2
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Osteopontin-mediated events

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.043 0.076 0.3 2 -0.3 32 34
NF kappa B1 p50/RelA/I kappa B alpha 0.048 0.086 0.34 13 -0.33 3 16
alphaV/beta3 Integrin/Osteopontin/Src 0.082 0.073 0.23 16 -10000 0 16
AP1 -0.038 0.18 0.35 1 -0.55 32 33
ILK 0.03 0.078 0.3 1 -0.33 28 29
bone resorption 0.018 0.089 0.27 1 -0.36 34 35
PTK2B 0.02 0.01 -10000 0 -10000 0 0
PYK2/p130Cas 0.066 0.096 0.31 8 -0.29 31 39
ITGAV 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.023 0.073 -10000 0 -0.42 26 26
alphaV/beta3 Integrin/Osteopontin 0.077 0.1 0.33 5 -0.35 32 37
MAP3K1 0.03 0.081 0.26 15 -0.33 32 47
JUN 0.019 0.054 -10000 0 -0.57 8 8
MAPK3 0.02 0.074 0.28 13 -0.31 26 39
MAPK1 0.022 0.074 0.27 14 -0.3 26 40
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.016 0.084 0.26 17 -0.36 29 46
ITGB3 0.008 0.11 0.27 4 -0.57 32 36
NFKBIA 0.018 0.072 0.28 13 -0.31 23 36
FOS -0.15 0.27 -10000 0 -0.57 285 285
CD44 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
PLAU 0.023 0.1 0.46 7 -0.55 2 9
NF kappa B1 p50/RelA 0.066 0.081 0.37 6 -10000 0 6
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.025 0.083 0.24 1 -0.42 32 33
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.03 0.079 0.26 15 -0.32 32 47
VAV3 0.016 0.078 0.26 17 -0.31 30 47
MAP3K14 0.032 0.079 0.27 12 -0.32 32 44
ROCK2 0.008 0.095 -10000 0 -0.58 26 26
SPP1 0.088 0.1 0.26 261 -10000 0 261
RAC1 0.024 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.029 0.072 0.3 3 -0.29 28 31
MMP2 -0.055 0.15 0.33 3 -0.51 30 33
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.029 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.012 0.08 0.26 1 -0.58 18 19
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.096 0.13 -10000 0 -0.24 403 403
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.023 0.02 -10000 0 -0.58 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.58 2 2
MAP3K12 0.024 0.003 -10000 0 -10000 0 0
FGR 0.024 0.009 0.26 1 -10000 0 1
p38 alpha/TAB1 -0.04 0.097 -10000 0 -0.34 69 69
PRKG1 -0.013 0.14 -10000 0 -0.58 62 62
DUSP8 0.022 0.033 -10000 0 -0.58 3 3
PGK/cGMP/p38 alpha -0.018 0.13 -10000 0 -0.34 95 95
apoptosis -0.039 0.093 -10000 0 -0.33 67 67
RAL/GTP 0.032 0.007 -10000 0 -10000 0 0
LYN 0.021 0.009 -10000 0 -10000 0 0
DUSP1 -0.047 0.19 -10000 0 -0.58 118 118
PAK1 0.023 0.02 0.26 6 -10000 0 6
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.053 0.025 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.024 0.008 0.26 1 -10000 0 1
RAC1-CDC42/GTP 0.031 0.009 -10000 0 -10000 0 0
MAPK11 -0.01 0.13 0.42 2 -0.38 54 56
BLK 0.051 0.088 0.26 135 -0.58 2 137
HCK 0.027 0.026 0.26 12 -10000 0 12
MAP2K3 0.023 0.007 -10000 0 -10000 0 0
DUSP16 0.023 0.005 -10000 0 -10000 0 0
DUSP10 0.021 0.014 0.26 2 -10000 0 2
TRAF6/MEKK3 0.028 0.01 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.005 0.13 0.37 2 -0.38 64 66
positive regulation of innate immune response -0.012 0.15 0.46 2 -0.45 57 59
LCK 0.026 0.077 0.26 36 -0.58 11 47
p38alpha-beta/MKP7 -0.003 0.14 0.65 1 -0.44 52 53
p38alpha-beta/MKP5 -0.004 0.14 0.65 1 -0.45 46 47
PGK/cGMP -0.009 0.11 -10000 0 -0.42 62 62
PAK2 0.024 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.035 0.17 0.65 1 -0.46 81 82
CDC42 0.023 0.006 -10000 0 -10000 0 0
RALB 0.024 0.003 -10000 0 -10000 0 0
RALA 0.024 0.004 -10000 0 -10000 0 0
PAK3 -0.25 0.3 -10000 0 -0.58 460 460
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.025 0.011 -10000 0 -10000 0 0
HSPA8 0.021 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.014 0.17 0.29 5 -0.39 138 143
AKT1 0.025 0.011 -10000 0 -10000 0 0
GSC -0.03 0.28 -10000 0 -1.3 40 40
NKX2-5 0.056 0.085 0.26 145 -10000 0 145
muscle cell differentiation -0.028 0.063 0.35 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.066 0.067 -10000 0 -0.44 1 1
SMAD4 0.012 0.046 -10000 0 -10000 0 0
CBFB 0.022 0.008 -10000 0 -10000 0 0
SAP18 0.023 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.1 0.2 0.27 1 -0.36 360 361
SMAD3/SMAD4/VDR 0.054 0.06 -10000 0 -0.34 1 1
MYC 0.005 0.084 -10000 0 -0.58 20 20
CDKN2B -0.044 0.18 -10000 0 -0.82 26 26
AP1 -0.053 0.16 -10000 0 -0.31 261 261
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.009 0.087 -10000 0 -0.36 31 31
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.012 0.059 -10000 0 -0.34 13 13
SP3 0.025 0.004 -10000 0 -10000 0 0
CREB1 0.024 0.003 -10000 0 -10000 0 0
FOXH1 0.044 0.08 0.26 108 -10000 0 108
SMAD3/SMAD4/GR 0.023 0.073 -10000 0 -0.38 11 11
GATA3 0.013 0.11 0.26 25 -0.57 31 56
SKI/SIN3/HDAC complex/NCoR1 0.004 0.078 -10000 0 -0.34 35 35
MEF2C/TIF2 0.027 0.09 0.31 3 -0.32 14 17
endothelial cell migration -0.029 0.086 0.56 6 -10000 0 6
MAX 0.02 0.015 -10000 0 -10000 0 0
RBBP7 0.026 0.02 0.26 7 -10000 0 7
RBBP4 0.023 0.019 -10000 0 -0.58 1 1
RUNX2 0.027 0.026 0.26 12 -10000 0 12
RUNX3 0.022 0.04 0.26 3 -0.58 4 7
RUNX1 0.024 0.019 -10000 0 -0.58 1 1
CTBP1 0.024 0.005 -10000 0 -10000 0 0
NR3C1 0.014 0.061 -10000 0 -0.58 10 10
VDR 0.024 0.003 -10000 0 -10000 0 0
CDKN1A 0.015 0.08 -10000 0 -1.1 3 3
KAT2B 0.024 0.019 -10000 0 -0.58 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.054 0.079 -10000 0 -0.27 22 22
DCP1A 0.024 0.005 -10000 0 -10000 0 0
SKI 0.023 0.005 -10000 0 -10000 0 0
SERPINE1 0.029 0.086 -10000 0 -0.56 6 6
SMAD3/SMAD4/ATF2 0.032 0.06 -10000 0 -0.4 2 2
SMAD3/SMAD4/ATF3 -0.015 0.14 -10000 0 -0.4 108 108
SAP30 0.024 0.016 0.26 4 -10000 0 4
Cbp/p300/PIAS3 0.046 0.029 -10000 0 -10000 0 0
JUN -0.063 0.16 -10000 0 -0.3 260 260
SMAD3/SMAD4/IRF7 0.05 0.081 0.33 19 -10000 0 19
TFE3 0.029 0.009 -10000 0 -0.2 1 1
COL1A2 0.046 0.091 0.4 2 -0.6 6 8
mesenchymal cell differentiation -0.034 0.059 -10000 0 -10000 0 0
DLX1 0.055 0.1 0.26 155 -0.58 9 164
TCF3 0.024 0.009 0.26 1 -10000 0 1
FOS -0.14 0.27 -10000 0 -0.57 287 287
SMAD3/SMAD4/Max 0.027 0.059 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.045 0.019 -10000 0 -10000 0 0
ZBTB17 0.022 0.007 -10000 0 -10000 0 0
LAMC1 0.012 0.038 -10000 0 -0.25 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 0.033 0.056 -10000 0 -10000 0 0
IRF7 0.047 0.07 0.27 86 -10000 0 86
ESR1 -0.036 0.23 0.26 120 -0.58 138 258
HNF4A 0.022 0.029 0.26 14 -10000 0 14
MEF2C 0.054 0.091 0.4 10 -0.44 2 12
SMAD2-3/SMAD4 0.033 0.066 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.045 0.025 -10000 0 -0.37 1 1
IGHV3OR16-13 0.005 0.042 -10000 0 -0.35 13 13
TGIF2/HDAC complex 0.023 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
SKIL 0.026 0.024 0.26 10 -10000 0 10
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
SNIP1 0.023 0.006 -10000 0 -10000 0 0
GCN5L2 0.002 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.042 0.062 -10000 0 -0.46 1 1
MSG1/HSC70 -0.14 0.22 0.2 12 -0.42 380 392
SMAD2 0.021 0.031 -10000 0 -10000 0 0
SMAD3 0.014 0.041 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.016 0.04 -10000 0 -0.26 1 1
SMAD2/SMAD2/SMAD4 0.02 0.053 0.23 10 -0.4 4 14
NCOR1 0.022 0.008 -10000 0 -10000 0 0
NCOA2 -0.003 0.12 -10000 0 -0.58 40 40
NCOA1 0.024 0.019 -10000 0 -0.58 1 1
MYOD/E2A 0.032 0.021 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.077 0.065 -10000 0 -0.41 1 1
IFNB1 0.02 0.071 0.32 31 -10000 0 31
SMAD3/SMAD4/MEF2C 0.071 0.087 0.33 1 -0.42 2 3
CITED1 -0.2 0.3 0.26 14 -0.57 379 393
SMAD2-3/SMAD4/ARC105 0.041 0.067 -10000 0 -10000 0 0
RBL1 0.024 0.009 0.26 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.016 0.067 -10000 0 -0.43 13 13
RUNX1-3/PEBPB2 0.041 0.038 -10000 0 -0.45 4 4
SMAD7 -0.034 0.15 -10000 0 -0.44 30 30
MYC/MIZ-1 0.015 0.065 -10000 0 -0.43 20 20
SMAD3/SMAD4 0.028 0.073 0.3 25 -0.35 4 29
IL10 0.007 0.082 0.33 4 -0.37 26 30
PIASy/HDAC complex 0.02 0.015 -10000 0 -10000 0 0
PIAS3 0.024 0.006 -10000 0 -10000 0 0
CDK2 0.026 0.008 -10000 0 -10000 0 0
IL5 0.004 0.084 0.33 2 -0.36 30 32
CDK4 0.025 0.009 -10000 0 -10000 0 0
PIAS4 0.02 0.015 -10000 0 -10000 0 0
ATF3 -0.045 0.19 0.26 1 -0.58 109 110
SMAD3/SMAD4/SP1 0.046 0.066 -10000 0 -0.37 2 2
FOXG1 0.017 0.068 0.26 66 -10000 0 66
FOXO3 0.011 0.018 -10000 0 -0.43 1 1
FOXO1 0.009 0.029 -10000 0 -0.43 4 4
FOXO4 0.012 0.01 -10000 0 -10000 0 0
heart looping 0.054 0.091 0.4 10 -0.44 2 12
CEBPB 0.023 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.053 0.09 0.29 3 -0.39 9 12
MYOD1 0.021 0.029 0.26 14 -10000 0 14
SMAD3/SMAD4/HNF4 0.032 0.059 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.029 0.1 0.36 1 -0.4 32 33
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.024 0.26 10 -10000 0 10
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.043 0.07 -10000 0 -0.44 3 3
SMAD3/SMAD4/SP1-3 0.061 0.065 -10000 0 -0.44 1 1
MED15 0.023 0.006 -10000 0 -10000 0 0
SP1 0.031 0.014 -10000 0 -0.2 1 1
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.08 0.095 0.34 21 -0.32 2 23
ITGB5 0.015 0.043 0.28 1 -0.4 1 2
TGIF/SIN3/HDAC complex/CtBP 0.012 0.063 -10000 0 -0.3 25 25
SMAD3/SMAD4/AR -0.018 0.15 -10000 0 -0.39 123 123
AR -0.05 0.2 0.26 1 -0.58 124 125
negative regulation of cell growth 0.001 0.082 -10000 0 -0.32 20 20
SMAD3/SMAD4/MYOD 0.032 0.059 -10000 0 -10000 0 0
E2F5 0.022 0.022 0.26 7 -10000 0 7
E2F4 0.022 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.067 0.075 -10000 0 -0.33 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.016 0.055 -10000 0 -0.37 11 11
TFDP1 0.022 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.038 0.18 -10000 0 -0.31 260 260
SMAD3/SMAD4/RUNX2 0.035 0.06 -10000 0 -10000 0 0
TGIF2 0.024 0.005 -10000 0 -10000 0 0
TGIF1 0.023 0.006 -10000 0 -10000 0 0
ATF2 0.023 0.027 -10000 0 -0.58 2 2
IL2 signaling events mediated by STAT5

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
GAB2 0.022 0.02 -10000 0 -0.57 1 1
ELF1 0.031 0.053 -10000 0 -0.36 10 10
CCNA2 0.11 0.12 0.26 380 -10000 0 380
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
JAK3 0.028 0.028 0.26 14 -10000 0 14
PIK3R1 0.019 0.057 -10000 0 -0.57 9 9
JAK1 0.024 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.047 0.1 0.31 18 -0.48 15 33
SHC1 0.021 0.01 -10000 0 -10000 0 0
SP1 0.024 0.047 0.22 1 -0.39 12 13
IL2RA 0.021 0.11 0.44 9 -0.76 13 22
IL2RB 0.031 0.052 0.26 36 -0.57 2 38
SOS1 0.025 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.071 0.26 45 -0.57 7 52
G1/S transition of mitotic cell cycle 0.044 0.14 0.31 5 -0.82 16 21
PTPN11 0.025 0.002 -10000 0 -10000 0 0
CCND2 0.005 0.091 0.35 2 -0.8 12 14
LCK 0.026 0.077 0.26 36 -0.57 11 47
GRB2 0.024 0.01 0.26 1 -10000 0 1
IL2 0.023 0.023 0.26 9 -10000 0 9
CDK6 0.02 0.051 0.26 2 -0.58 7 9
CCND3 0.047 0.1 0.42 4 -0.56 6 10
TCGA08_p53

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
CDKN2A 0.026 0.048 0.14 155 -10000 0 155
TP53 0.009 0.018 -10000 0 -0.19 2 2
Senescence 0.009 0.022 -10000 0 -0.19 2 2
Apoptosis 0.009 0.022 -10000 0 -0.19 2 2
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.01 0.061 0.29 30 -10000 0 30
MDM4 0.02 0.01 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.061 0.087 0.26 159 -10000 0 159
mol:Halofuginone 0.002 0.004 -10000 0 -10000 0 0
ITGA1 0.018 0.057 -10000 0 -0.58 9 9
CDKN1A -0.032 0.095 -10000 0 -0.44 27 27
PRL-3/alpha Tubulin 0.029 0.017 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.077 0.24 43 -0.43 12 55
AGT 0.03 0.092 0.26 72 -0.58 12 84
CCNA2 -0.066 0.14 -10000 0 -10000 0 0
TUBA1B 0.024 0.003 -10000 0 -10000 0 0
EGR1 -0.12 0.2 0.18 2 -0.42 313 315
CDK2/Cyclin E1 0.014 0.11 -10000 0 -0.49 16 16
MAPK3 0.01 0.021 0.26 6 -10000 0 6
PRL-2 /Rab GGTase beta 0.035 0.007 -10000 0 -10000 0 0
MAPK1 0.01 0.021 0.26 6 -10000 0 6
PTP4A1 -0.095 0.15 -10000 0 -10000 0 0
PTP4A3 0.02 0.015 0.26 2 -10000 0 2
PTP4A2 0.024 0.004 -10000 0 -10000 0 0
ITGB1 0.01 0.019 0.26 5 -10000 0 5
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1 -0.019 0.076 -10000 0 -0.42 15 15
Rab GGTase beta/Rab GGTase alpha 0.035 0.008 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.075 0.15 -10000 0 -10000 0 0
RABGGTA 0.024 0.004 -10000 0 -10000 0 0
BCAR1 -0.014 0.012 -10000 0 -0.18 2 2
RHOC -0.021 0.084 -10000 0 -0.43 21 21
RHOA -0.024 0.094 -10000 0 -0.46 27 27
cell motility -0.027 0.1 0.25 1 -0.38 33 34
PRL-1/alpha Tubulin -0.075 0.15 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.025 0.041 -10000 0 -0.35 9 9
ROCK1 -0.026 0.1 0.25 1 -0.39 30 31
RABGGTB 0.024 0.004 -10000 0 -10000 0 0
CDK2 0.024 0.002 -10000 0 -10000 0 0
mitosis -0.095 0.15 -10000 0 -10000 0 0
ATF5 0.025 0.013 0.26 3 -10000 0 3
Caspase cascade in apoptosis

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
TOP1 0.008 0.11 0.26 2 -0.4 44 46
ACTA1 0.013 0.11 0.26 7 -0.5 29 36
NUMA1 0.003 0.11 0.26 2 -0.4 44 46
SPTAN1 -0.002 0.11 0.27 6 -0.5 29 35
LIMK1 -0.001 0.11 0.27 5 -0.5 29 34
BIRC3 0.023 0.042 0.26 11 -0.58 3 14
BIRC2 0.022 0.007 -10000 0 -10000 0 0
BAX 0.025 0.017 0.26 5 -10000 0 5
CASP10 -0.011 0.093 0.21 11 -0.46 30 41
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
PTK2 0.003 0.12 0.28 1 -0.45 42 43
DIABLO 0.024 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.002 0.11 0.27 6 -0.49 29 35
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
GSN -0.006 0.12 0.28 4 -0.48 38 42
MADD 0.024 0.003 -10000 0 -10000 0 0
TFAP2A 0.013 0.13 -10000 0 -0.67 30 30
BID 0.004 0.053 0.18 3 -0.27 29 32
MAP3K1 -0.004 0.097 -10000 0 -0.4 45 45
TRADD 0.022 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.034 0.009 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.002 0.11 0.26 7 -0.5 28 35
CASP9 0.023 0.006 -10000 0 -10000 0 0
DNA repair -0.017 0.044 0.25 4 -0.21 5 9
neuron apoptosis 0.004 0.12 -10000 0 -0.69 24 24
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0 0.12 0.27 1 -0.45 38 39
APAF1 0.024 0.003 -10000 0 -10000 0 0
CASP6 -0.001 0.16 -10000 0 -0.9 25 25
TRAF2 0.025 0.015 0.26 4 -10000 0 4
ICAD/CAD -0.004 0.1 0.25 1 -0.51 26 27
CASP7 0.002 0.061 0.26 5 -0.34 6 11
KRT18 0.014 0.08 -10000 0 -0.71 9 9
apoptosis 0.002 0.12 0.31 5 -0.45 44 49
DFFA -0.004 0.11 0.25 3 -0.5 29 32
DFFB -0.003 0.11 0.25 3 -0.5 29 32
PARP1 0.017 0.044 0.21 5 -0.25 4 9
actin filament polymerization 0.001 0.11 0.46 30 -0.29 7 37
TNF 0.023 0.07 0.26 22 -0.58 10 32
CYCS 0.006 0.05 0.22 6 -0.24 16 22
SATB1 -0.009 0.16 -10000 0 -0.78 31 31
SLK -0.002 0.11 0.28 5 -0.5 29 34
p15 BID/BAX 0.013 0.063 0.24 2 -0.24 33 35
CASP2 0.002 0.066 0.23 7 -0.39 7 14
JNK cascade 0.004 0.096 0.4 45 -10000 0 45
CASP3 0 0.11 0.28 3 -0.5 32 35
LMNB2 0 0.13 0.27 5 -0.5 43 48
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CASP4 0.022 0.008 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.057 0.033 -10000 0 -0.34 2 2
negative regulation of DNA binding 0.013 0.13 -10000 0 -0.66 30 30
stress fiber formation -0.002 0.11 0.28 5 -0.49 29 34
GZMB 0.011 0.1 0.28 11 -0.51 29 40
CASP1 0.011 0.012 -10000 0 -0.35 1 1
LMNB1 0.019 0.12 0.29 8 -0.5 28 36
APP 0.003 0.12 -10000 0 -0.7 24 24
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.001 -10000 0 -10000 0 0
VIM 0.004 0.12 0.29 5 -0.45 46 51
LMNA 0.008 0.083 0.32 2 -0.37 24 26
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.004 0.069 -10000 0 -0.31 21 21
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.002 0.11 0.28 3 -0.49 29 32
APAF-1/Caspase 9 -0.004 0.12 -10000 0 -0.61 35 35
nuclear fragmentation during apoptosis 0.004 0.11 0.26 2 -0.4 44 46
CFL2 -0.001 0.11 0.29 7 -0.48 30 37
GAS2 -0.029 0.14 0.27 6 -0.38 96 102
positive regulation of apoptosis 0.013 0.12 0.27 8 -0.48 33 41
PRF1 0.016 0.081 0.26 8 -0.58 17 25
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.011 0.002 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.03 0.02 0.3 1 -10000 0 1
CDKN1B 0.01 0.057 -10000 0 -0.34 15 15
CDKN1A 0.009 0.062 -10000 0 -0.34 19 19
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.008 -10000 0 -10000 0 0
FOXO3 0.013 0.056 -10000 0 -0.34 13 13
AKT1 0.005 0.058 -10000 0 -0.33 25 25
BAD 0.024 0.009 0.26 1 -10000 0 1
AKT3 0.006 0.034 -10000 0 -0.35 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.008 0.06 -10000 0 -0.34 19 19
AKT1/ASK1 0.031 0.069 -10000 0 -0.32 20 20
BAD/YWHAZ 0.037 0.023 -10000 0 -10000 0 0
RICTOR 0.024 0.004 -10000 0 -10000 0 0
RAF1 0.024 0.004 -10000 0 -10000 0 0
JNK cascade -0.03 0.067 0.31 20 -10000 0 20
TSC1 0.01 0.053 -10000 0 -0.34 13 13
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.036 0.072 0.27 1 -0.34 18 19
EP300 0.023 0.006 -10000 0 -10000 0 0
mol:GDP 0.009 0.061 -10000 0 -0.32 27 27
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.007 0.056 0.32 1 -0.33 17 18
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
TBC1D4 0.003 0.019 -10000 0 -0.35 3 3
MAP3K5 0.022 0.033 -10000 0 -0.58 3 3
MAPKAP1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.026 0.077 0.31 18 -0.26 4 22
YWHAH 0.023 0.006 -10000 0 -10000 0 0
AKT1S1 0.011 0.062 -10000 0 -0.32 25 25
CASP9 0.011 0.046 -10000 0 -0.32 11 11
YWHAB 0.023 0.006 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.073 0.31 6 -0.33 16 22
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.044 0.017 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.011 0.06 0.25 3 -0.32 18 21
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.006 0.054 -10000 0 -0.33 20 20
CHUK 0.009 0.056 -10000 0 -0.33 17 17
BAD/BCL-XL 0.038 0.069 0.28 3 -0.32 19 22
mTORC2 0.03 0.007 -10000 0 -10000 0 0
AKT2 0.011 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.031 0.099 0.31 7 -0.39 24 31
PDPK1 0.023 0.006 -10000 0 -10000 0 0
MDM2 0.011 0.066 0.27 2 -0.34 19 21
MAPKKK cascade -0.036 0.071 0.34 18 -0.25 3 21
MDM2/Cbp/p300 0.042 0.074 0.34 4 -0.56 3 7
TSC1/TSC2 0.014 0.07 0.26 36 -0.36 13 49
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.071 0.32 4 -0.53 3 7
glucose import -0.16 0.16 0.21 3 -0.32 471 474
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.01 0.051 0.18 3 -0.3 9 12
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.16 0.16 0.21 3 -0.32 471 474
GSK3A 0.01 0.06 -10000 0 -0.35 17 17
FOXO1 0.011 0.041 -10000 0 -0.29 9 9
GSK3B 0.009 0.06 -10000 0 -0.35 18 18
SFN 0.021 0.068 0.26 17 -0.58 10 27
G1/S transition of mitotic cell cycle 0.013 0.065 0.29 4 -0.34 17 21
p27Kip1/14-3-3 family 0.02 0.049 -10000 0 -0.45 3 3
PRKACA 0.024 0.003 -10000 0 -10000 0 0
KPNA1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.006 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.011 0.002 -10000 0 -10000 0 0
MAP4K4 0.002 0.062 -10000 0 -0.4 6 6
BAG4 0.019 0.028 -10000 0 -0.58 2 2
PKC zeta/ceramide -0.003 0.054 -10000 0 -0.25 17 17
NFKBIA 0.024 0.005 -10000 0 -10000 0 0
BIRC3 0.023 0.042 0.26 11 -0.58 3 14
BAX 0.001 0.042 -10000 0 -0.35 10 10
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.065 0.68 9 -10000 0 9
BAD -0.017 0.048 0.19 3 -0.24 15 18
SMPD1 0.014 0.058 0.2 12 -0.25 18 30
RB1 -0.017 0.046 -10000 0 -0.25 14 14
FADD/Caspase 8 0.026 0.089 0.26 9 -0.41 7 16
MAP2K4 -0.017 0.046 0.18 4 -0.3 8 12
NSMAF 0.021 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.011 0.056 0.19 27 -0.31 6 33
EGF -0.093 0.24 0.26 2 -0.58 195 197
mol:ceramide -0.016 0.05 -10000 0 -0.25 16 16
MADD 0.024 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.009 0.008 -10000 0 -10000 0 0
ASAH1 0.021 0.016 0.26 3 -10000 0 3
negative regulation of cell cycle -0.017 0.046 -10000 0 -0.24 14 14
cell proliferation -0.046 0.12 0.28 1 -0.27 190 191
BID -0.023 0.17 -10000 0 -0.66 61 61
MAP3K1 -0.017 0.048 0.19 2 -0.24 17 19
EIF2A -0.016 0.049 0.29 3 -0.25 6 9
TRADD 0.022 0.008 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.009 0.054 0.27 3 -0.31 5 8
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.013 0.06 0.25 4 -0.32 5 9
Cathepsin D/ceramide 0.003 0.06 0.18 30 -0.23 15 45
FADD 0.004 0.062 0.26 3 -0.41 5 8
KSR1 -0.011 0.055 0.2 20 -0.24 14 34
MAPK8 -0.015 0.06 -10000 0 -0.29 16 16
PRKRA -0.017 0.048 0.2 2 -0.26 12 14
PDGFA 0.024 0.004 -10000 0 -10000 0 0
TRAF2 0.025 0.015 0.26 4 -10000 0 4
IGF1 -0.1 0.24 -10000 0 -0.58 211 211
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.016 0.049 -10000 0 -0.25 16 16
CTSD 0.032 0.043 0.26 34 -10000 0 34
regulation of nitric oxide biosynthetic process 0.035 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.048 0.13 0.29 1 -0.29 189 190
PRKCD 0.024 0.009 0.26 1 -10000 0 1
PRKCZ 0.023 0.02 -10000 0 -0.58 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.009 0.008 -10000 0 -10000 0 0
RelA/NF kappa B1 0.035 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.024 0.019 -10000 0 -0.58 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.014 0.051 -10000 0 -0.39 7 7
TNFR1A/BAG4/TNF-alpha 0.036 0.052 -10000 0 -0.36 11 11
mol:Sphingosine-1-phosphate 0.011 0.002 -10000 0 -10000 0 0
MAP2K1 -0.012 0.055 0.25 4 -0.31 5 9
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
CYCS 0 0.05 0.18 19 -0.23 12 31
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.026 -10000 0 -0.43 2 2
EIF2AK2 -0.018 0.044 -10000 0 -0.28 7 7
TNF-alpha/TNFR1A/FAN 0.04 0.044 -10000 0 -0.36 6 6
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.016 0.075 -10000 0 -0.38 23 23
MAP2K2 -0.012 0.055 0.25 4 -0.3 6 10
SMPD3 -0.003 0.1 0.27 4 -0.29 92 96
TNF 0.023 0.07 0.26 22 -0.58 10 32
PKC zeta/PAR4 0.034 0.022 -10000 0 -0.43 2 2
mol:PHOSPHOCHOLINE 0.045 0.1 0.24 195 -0.24 2 197
NF kappa B1/RelA/I kappa B alpha 0.064 0.029 -10000 0 -0.32 2 2
AIFM1 -0.002 0.051 0.18 20 -0.21 15 35
BCL2 0.007 0.097 -10000 0 -0.58 27 27
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K -0.008 0.011 0.23 2 -10000 0 2
SNTA1 0.024 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.001 0.034 0.3 7 -10000 0 7
MAPK12 0.004 0.072 0.21 60 -0.33 22 82
CCND1 0.011 0.046 -10000 0 -0.37 6 6
p38 gamma/SNTA1 0.022 0.071 0.32 2 -0.31 21 23
MAP2K3 0.023 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.004 -10000 0 -10000 0 0
G2/M transition checkpoint 0.005 0.072 0.21 64 -0.33 22 86
MAP2K6 -0.003 0.052 -10000 0 -0.35 22 22
MAPT -0.025 0.12 0.26 13 -0.32 111 124
MAPK13 0.011 0.011 0.26 2 -10000 0 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.011 0.023 -10000 0 -0.35 4 4
HIF-2-alpha transcription factor network

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
MMP14 0.023 0.089 -10000 0 -0.58 12 12
oxygen homeostasis 0.011 0.013 -10000 0 -10000 0 0
TCEB2 0.027 0.033 0.26 19 -10000 0 19
TCEB1 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.088 0.089 0.35 12 -0.36 3 15
EPO 0.15 0.17 0.51 75 -0.55 2 77
FIH (dimer) 0.033 0.02 -10000 0 -10000 0 0
APEX1 0.034 0.024 -10000 0 -10000 0 0
SERPINE1 0.14 0.16 0.53 24 -0.57 3 27
FLT1 -0.017 0.17 -10000 0 -0.74 26 26
ADORA2A 0.16 0.17 0.48 81 -0.54 3 84
germ cell development 0.14 0.16 0.5 40 -0.55 3 43
SLC11A2 0.14 0.16 0.48 36 -0.57 3 39
BHLHE40 0.14 0.16 0.53 13 -0.58 4 17
HIF1AN 0.033 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.12 0.13 0.4 56 -0.36 2 58
ETS1 0.027 0.035 -10000 0 -0.58 3 3
CITED2 0.015 0.092 -10000 0 -0.64 9 9
KDR -0.014 0.17 -10000 0 -0.77 24 24
PGK1 0.14 0.16 0.53 15 -0.56 3 18
SIRT1 0.026 0.005 -10000 0 -10000 0 0
response to hypoxia 0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.18 0.61 13 -0.65 3 16
EPAS1 0.072 0.09 0.29 51 -0.36 5 56
SP1 0.029 0.012 -10000 0 -10000 0 0
ABCG2 0.12 0.2 0.49 35 -0.58 31 66
EFNA1 0.11 0.14 0.51 6 -0.55 2 8
FXN 0.15 0.16 0.46 49 -0.55 3 52
POU5F1 0.14 0.16 0.55 23 -0.57 3 26
neuron apoptosis -0.16 0.18 0.63 3 -0.6 13 16
EP300 0.023 0.006 -10000 0 -10000 0 0
EGLN3 0.048 0.068 0.28 69 -0.59 1 70
EGLN2 0.034 0.026 0.27 5 -10000 0 5
EGLN1 0.027 0.028 -10000 0 -0.59 1 1
VHL/Elongin B/Elongin C 0.041 0.028 -10000 0 -10000 0 0
VHL 0.024 0.004 -10000 0 -10000 0 0
ARNT 0.029 0.024 -10000 0 -10000 0 0
SLC2A1 0.15 0.16 0.47 49 -0.55 3 52
TWIST1 0.14 0.18 0.47 44 -0.56 28 72
ELK1 0.028 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.1 0.11 0.41 9 -0.36 2 11
VEGFA 0.14 0.16 0.5 29 -0.57 3 32
CREBBP 0.023 0.006 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.26 0.3 -10000 0 -0.58 473 473
CLTC 0.025 0.067 0.28 1 -0.43 12 13
calcium ion-dependent exocytosis 0.009 0.026 0.2 1 -0.26 2 3
Dynamin 2/GTP 0.022 0.013 -10000 0 -10000 0 0
EXOC4 0.024 0.004 -10000 0 -10000 0 0
CD59 0.016 0.046 -10000 0 -0.34 10 10
CPE 0.005 0.049 -10000 0 -0.36 17 17
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
membrane fusion 0.011 0.019 -10000 0 -0.17 5 5
CTNND1 0.008 0.056 0.19 84 -10000 0 84
DNM2 0.024 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.044 0.21 3 -0.33 7 10
TSHR -0.003 0.074 0.15 4 -0.37 39 43
INS -0.002 0.091 -10000 0 -0.48 33 33
BIN1 0.019 0.054 -10000 0 -0.58 8 8
mol:Choline 0.011 0.019 -10000 0 -0.17 5 5
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.017 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.022 0.013 -10000 0 -10000 0 0
JUP 0.016 0.039 0.23 1 -0.32 7 8
ASAP2/amphiphysin II 0.042 0.035 -10000 0 -0.34 7 7
ARF6/GTP 0.018 0.003 -10000 0 -10000 0 0
CDH1 0.008 0.056 -10000 0 -0.37 9 9
clathrin-independent pinocytosis 0.018 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.023 0.007 -10000 0 -10000 0 0
positive regulation of endocytosis 0.018 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.028 0.26 14 -10000 0 14
substrate adhesion-dependent cell spreading 0.016 0.039 -10000 0 -0.33 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.022 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.036 0.066 0.34 8 -10000 0 8
positive regulation of phagocytosis 0.011 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.03 0.01 -10000 0 -10000 0 0
ACAP1 0.015 0.028 -10000 0 -0.25 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.013 0.044 -10000 0 -0.33 10 10
clathrin heavy chain/ACAP1 0.024 0.064 0.28 6 -0.35 12 18
JIP4/KLC1 0.041 0.016 -10000 0 -10000 0 0
EXOC1 0.024 0.004 -10000 0 -10000 0 0
exocyst 0.019 0.034 -10000 0 -0.34 4 4
RALA/GTP 0.018 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.03 0.011 -10000 0 -10000 0 0
receptor recycling 0.018 0.003 -10000 0 -10000 0 0
CTNNA1 0.008 0.057 0.19 87 -10000 0 87
NME1 0.013 0.017 -10000 0 -10000 0 0
clathrin coat assembly 0.028 0.07 0.28 3 -0.42 12 15
IL2RA 0.019 0.055 -10000 0 -0.32 13 13
VAMP3 0.011 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.12 0.14 -10000 0 -0.27 394 394
EXOC6 0.024 0.003 -10000 0 -10000 0 0
PLD1 0.009 0.029 -10000 0 -0.3 8 8
PLD2 0.011 0.006 -10000 0 -10000 0 0
EXOC5 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.013 0.04 0.19 2 -0.35 6 8
SDC1 0.02 0.044 0.21 1 -0.33 8 9
ARF6/GDP 0.021 0.013 -10000 0 -10000 0 0
EXOC7 0.023 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.039 0.068 -10000 0 -0.34 8 8
mol:Phosphatidic acid 0.011 0.019 -10000 0 -0.17 5 5
endocytosis -0.04 0.035 0.33 7 -10000 0 7
SCAMP2 0.024 0.004 -10000 0 -10000 0 0
ADRB2 -0.041 0.14 0.26 1 -0.3 174 175
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ASAP2 0.024 0.019 -10000 0 -0.58 1 1
Dynamin 2/GDP 0.026 0.017 -10000 0 -10000 0 0
KLC1 0.024 0.004 -10000 0 -10000 0 0
AVPR2 -0.085 0.16 0.29 3 -0.38 53 56
RALA 0.024 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.035 0.067 0.32 2 -0.35 5 7
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.018 0.093 0.26 32 -0.58 19 51
CDC42/GTP -0.003 0.095 -10000 0 -0.31 43 43
PLCG1 -0.011 0.087 -10000 0 -0.31 45 45
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.033 0.011 -10000 0 -10000 0 0
cell migration -0.003 0.093 -10000 0 -0.3 43 43
S1PR5 0.027 0.042 0.26 19 -0.58 2 21
S1PR4 0.029 0.065 0.26 37 -0.58 6 43
MAPK3 -0.008 0.082 0.27 1 -0.31 38 39
MAPK1 -0.006 0.083 -10000 0 -0.32 41 41
S1P/S1P5/Gi -0.001 0.086 -10000 0 -0.28 72 72
GNAI1 -0.003 0.12 -10000 0 -0.58 45 45
CDC42/GDP 0.017 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.028 -10000 0 -0.36 2 2
RHOA 0.006 0.058 0.24 1 -0.31 6 7
S1P/S1P4/Gi -0.002 0.092 -10000 0 -0.29 78 78
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.018 0.057 -10000 0 -0.58 9 9
S1P/S1P4/G12/G13 0.044 0.043 -10000 0 -0.33 6 6
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.007 -10000 0 -10000 0 0
CDC42 0.023 0.006 -10000 0 -10000 0 0
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.024 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.019 0.067 0.21 2 -0.29 49 51
FRAP1 -0.003 0.082 0.26 1 -0.46 23 24
AKT1 -0.011 0.066 0.18 6 -0.27 43 49
INSR 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.007 -10000 0 -10000 0 0
mol:GTP 0.021 0.068 0.23 3 -0.24 33 36
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.002 0.036 -10000 0 -0.18 12 12
TSC2 0.023 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.006 0.048 -10000 0 -0.25 13 13
TSC1 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.004 0.079 -10000 0 -0.31 57 57
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.013 0.046 -10000 0 -0.22 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.009 0.074 0.26 5 -0.3 25 30
MAP3K5 0 0.047 0.2 11 -0.2 39 50
PIK3R1 0.019 0.057 -10000 0 -0.57 9 9
apoptosis 0 0.047 0.2 11 -0.2 40 51
mol:LY294002 0 0 -10000 0 -0.001 49 49
EIF4B 0.008 0.068 0.27 4 -0.27 22 26
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.026 0.066 0.22 2 -0.27 15 17
eIF4E/eIF4G1/eIF4A1 0.003 0.05 -10000 0 -0.28 20 20
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.015 0.081 -10000 0 -0.28 64 64
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.052 0.22 11 -0.19 3 14
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.025 0.06 -10000 0 -0.25 12 12
mol:Amino Acids 0 0 -10000 0 -0.001 49 49
FKBP12/Rapamycin 0.018 0.004 -10000 0 -10000 0 0
PDPK1 -0.02 0.061 0.18 6 -0.27 46 52
EIF4E 0.024 0.004 -10000 0 -10000 0 0
ASK1/PP5C -0.006 0.14 -10000 0 -0.52 59 59
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.002 0.049 -10000 0 -10000 0 0
TSC1/TSC2 0.024 0.074 0.25 4 -0.25 33 37
tumor necrosis factor receptor activity 0 0 0.001 49 -10000 0 49
RPS6 0.024 0.005 -10000 0 -10000 0 0
PPP5C 0.024 0.003 -10000 0 -10000 0 0
EIF4G1 0.024 0.004 -10000 0 -10000 0 0
IRS1 -0.012 0.081 -10000 0 -0.33 58 58
INS 0.017 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.027 -10000 0 -0.57 2 2
PDK2 -0.018 0.061 0.19 10 -0.27 42 52
EIF4EBP1 -0.025 0.23 -10000 0 -1 47 47
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PPP2R5D -0.001 0.078 0.32 3 -0.42 22 25
peptide biosynthetic process -0.011 0.016 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
EIF4A1 0.022 0.008 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 16 -0.002 14 30
EEF2 -0.011 0.016 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.015 0.22 -10000 0 -0.97 47 47
IL2 signaling events mediated by PI3K

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
BCL2L1 0.021 0.078 -10000 0 -0.52 7 7
UGCG 0.01 0.12 -10000 0 -0.68 27 27
AKT1/mTOR/p70S6K/Hsp90/TERT 0.047 0.12 0.3 7 -0.43 27 34
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.011 0.12 -10000 0 -0.67 27 27
mol:DAG 0.007 0.073 -10000 0 -0.75 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.037 0.14 0.3 7 -0.43 50 57
FRAP1 0.03 0.16 0.33 7 -0.5 50 57
FOXO3 0.036 0.14 0.35 11 -0.52 32 43
AKT1 0.035 0.15 0.34 6 -0.56 34 40
GAB2 0.021 0.021 -10000 0 -0.57 1 1
SMPD1 0.009 0.11 -10000 0 -0.64 26 26
SGMS1 0.02 0.059 -10000 0 -0.56 8 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.001 0.034 -10000 0 -0.33 10 10
CALM1 0.024 0.004 -10000 0 -10000 0 0
cell proliferation 0.048 0.11 0.36 3 -0.52 17 20
EIF3A 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.031 0.045 -10000 0 -0.38 10 10
RPS6KB1 0.011 0.098 -10000 0 -0.84 11 11
mol:sphingomyelin 0.007 0.073 -10000 0 -0.75 8 8
natural killer cell activation 0 0.002 -10000 0 -0.016 1 1
JAK3 0.028 0.029 0.26 14 -10000 0 14
PIK3R1 0.019 0.057 -10000 0 -0.58 9 9
JAK1 0.024 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MYC 0.065 0.2 0.45 6 -0.92 27 33
MYB 0.031 0.18 -10000 0 -1.1 20 20
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.036 0.11 0.3 18 -0.48 19 37
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.036 0.094 -10000 0 -0.76 11 11
mol:PI-3-4-5-P3 0.04 0.11 0.3 18 -0.47 19 37
Rac1/GDP 0.016 0.035 0.19 1 -0.34 8 9
T cell proliferation 0.041 0.1 0.3 12 -0.48 14 26
SHC1 0.02 0.011 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.011 0.078 2 -0.077 19 21
PRKCZ 0.04 0.1 0.3 10 -0.5 14 24
NF kappa B1 p50/RelA 0.048 0.14 0.32 7 -0.44 45 52
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.025 0.077 0.3 11 -0.55 7 18
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
IL2RA 0.028 0.088 0.26 55 -0.57 13 68
IL2RB 0.031 0.053 0.26 36 -0.58 2 38
TERT 0.053 0.08 0.26 127 -10000 0 127
E2F1 0.052 0.093 -10000 0 -0.36 27 27
SOS1 0.024 0.007 -10000 0 -10000 0 0
RPS6 0.024 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.034 19 -0.04 2 21
PTPN11 0.024 0.008 -10000 0 -10000 0 0
IL2RG 0.031 0.071 0.26 45 -0.58 7 52
actin cytoskeleton organization 0.041 0.1 0.3 12 -0.48 14 26
GRB2 0.023 0.011 0.26 1 -10000 0 1
IL2 0.022 0.026 0.26 9 -10000 0 9
PIK3CA 0.024 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.039 0.039 -10000 0 -0.3 9 9
LCK 0.026 0.078 0.26 36 -0.57 11 47
BCL2 0.017 0.2 0.44 3 -0.79 44 47
Cellular roles of Anthrax toxin

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
ANTXR1 0.023 0.028 0.26 1 -0.58 2 3
ANTXR2 0.018 0.06 -10000 0 -0.58 10 10
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.008 -10000 0 -0.077 12 12
monocyte activation 0.003 0.086 0.26 2 -0.35 52 54
MAP2K2 0.002 0.085 -10000 0 -0.58 21 21
MAP2K1 -0.004 0.008 -10000 0 -0.11 1 1
MAP2K7 -0.004 0.008 0.12 1 -10000 0 1
MAP2K6 -0.01 0.042 -10000 0 -0.31 18 18
CYAA -0.009 0.036 -10000 0 -0.34 11 11
MAP2K4 -0.004 0.008 -10000 0 -0.11 1 1
IL1B -0.009 0.048 0.18 3 -0.29 24 27
Channel 0.026 0.043 -10000 0 -0.36 11 11
NLRP1 -0.007 0.032 -10000 0 -0.32 10 10
CALM1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.067 -10000 0 -0.39 28 28
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.008 0.077 12 -10000 0 12
MAPK3 -0.004 0.008 0.084 1 -10000 0 1
MAPK1 -0.004 0.009 0.12 2 -0.11 1 3
PGR -0.079 0.14 0.2 2 -0.31 256 258
PA/Cellular Receptors 0.028 0.046 -10000 0 -0.39 11 11
apoptosis -0.002 0.008 -10000 0 -0.077 12 12
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.04 -10000 0 -0.32 12 12
macrophage activation -0.005 0.01 0.12 3 -10000 0 3
TNF 0.023 0.07 0.26 22 -0.58 10 32
VCAM1 0.003 0.086 0.26 2 -0.35 52 54
platelet activation -0.001 0.067 -10000 0 -0.39 28 28
MAPKKK cascade -0.002 0.026 0.093 14 -0.13 7 21
IL18 -0.003 0.026 -10000 0 -0.23 9 9
negative regulation of macrophage activation -0.002 0.008 -10000 0 -0.077 12 12
LEF -0.002 0.008 -10000 0 -0.077 12 12
CASP1 -0.003 0.028 -10000 0 -0.23 11 11
mol:cAMP -0.001 0.068 -10000 0 -0.39 28 28
necrosis -0.002 0.008 -10000 0 -0.077 12 12
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.026 0.04 -10000 0 -0.34 11 11
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.038 0.058 -10000 0 -0.39 17 17
forebrain development -0.044 0.21 0.35 1 -0.53 119 120
GNAO1 0.017 0.093 0.26 32 -0.58 19 51
SMO/beta Arrestin2 0.027 0.045 -10000 0 -0.43 8 8
SMO 0.017 0.055 -10000 0 -0.58 8 8
ARRB2 0.021 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.023 0.08 0.31 1 -0.46 12 13
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.024 0.003 -10000 0 -10000 0 0
GNAI2 0.022 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.056 0.023 -10000 0 -10000 0 0
GNAI1 -0.004 0.12 -10000 0 -0.58 45 45
XPO1 0.022 0.015 -10000 0 -10000 0 0
GLI1/Su(fu) -0.035 0.19 -10000 0 -0.61 68 68
SAP30 0.025 0.016 0.26 4 -10000 0 4
mol:GDP 0.017 0.055 -10000 0 -0.58 8 8
MIM/GLI2A 0.022 0.025 0.28 4 -10000 0 4
IFT88 0.023 0.006 -10000 0 -10000 0 0
GNAI3 0.023 0.009 -10000 0 -10000 0 0
GLI2 0.008 0.067 -10000 0 -0.34 12 12
GLI3 0.012 0.083 0.32 1 -0.44 16 17
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
SAP18 0.023 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.023 0.006 -10000 0 -10000 0 0
GNG2 0.018 0.06 -10000 0 -0.58 10 10
Gi family/GTP -0.006 0.095 -10000 0 -0.3 69 69
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.016 0.088 -10000 0 -0.43 23 23
GLI2/Su(fu) 0.012 0.083 -10000 0 -0.39 20 20
FOXA2 0.01 0.11 0.42 1 -0.64 17 18
neural tube patterning -0.044 0.21 0.35 1 -0.53 119 120
SPOP 0.022 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.02 0.043 -10000 0 -0.37 1 1
GNB1 0.024 0.005 -10000 0 -10000 0 0
CSNK1G2 0.024 0.005 -10000 0 -10000 0 0
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
MTSS1 0.022 0.025 0.28 4 -10000 0 4
embryonic limb morphogenesis -0.044 0.21 0.35 1 -0.53 119 120
SUFU 0.015 0.027 -10000 0 -0.24 9 9
LGALS3 0.017 0.063 -10000 0 -0.58 11 11
catabolic process 0.025 0.1 0.32 1 -0.51 18 19
GLI3A/CBP 0.002 0.092 -10000 0 -0.36 58 58
KIF3A 0.024 0.004 -10000 0 -10000 0 0
GLI1 -0.046 0.22 0.35 1 -0.55 117 118
RAB23 0.024 0.004 -10000 0 -10000 0 0
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
IFT172 0.024 0.019 -10000 0 -0.58 1 1
RBBP7 0.026 0.02 0.26 7 -10000 0 7
Su(fu)/Galectin3 0.017 0.06 -10000 0 -0.39 12 12
GNAZ 0.017 0.057 -10000 0 -0.57 9 9
RBBP4 0.023 0.019 -10000 0 -0.58 1 1
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.017 0.071 -10000 0 -0.37 14 14
STK36 0.021 0.024 -10000 0 -0.57 1 1
Gi family/GNB1/GNG2/GDP -0.012 0.11 -10000 0 -0.4 40 40
PTCH1 -0.088 0.32 -10000 0 -1.1 82 82
MIM/GLI1 -0.032 0.2 -10000 0 -0.62 65 65
CREBBP 0.002 0.092 -10000 0 -0.36 58 58
Su(fu)/SIN3/HDAC complex 0.006 0.091 -10000 0 -0.41 33 33
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.002 0.088 0.29 41 -10000 0 41
GNAI2 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.028 -10000 0 -0.36 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.018 0.093 0.26 32 -0.58 19 51
RhoA/GTP -0.001 0.09 -10000 0 -0.34 24 24
negative regulation of cAMP metabolic process -0.001 0.085 -10000 0 -0.28 72 72
GNAZ 0.018 0.057 -10000 0 -0.58 9 9
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNA12 0.024 0.004 -10000 0 -10000 0 0
S1PR5 0.027 0.042 0.26 19 -0.58 2 21
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.001 0.086 -10000 0 -0.28 72 72
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
GNAI1 -0.003 0.12 -10000 0 -0.58 45 45
BARD1 signaling events

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
BARD1/CSTF1 0.027 0.054 -10000 0 -0.4 15 15
ATM 0.022 0.008 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
PRKDC 0.021 0.008 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
UBE2L3 0.023 0.006 -10000 0 -10000 0 0
FANCD2 0.018 0.016 -10000 0 -10000 0 0
protein ubiquitination 0.065 0.069 0.31 2 -0.3 15 17
XRCC5 0.024 0.004 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.036 0.022 -10000 0 -10000 0 0
MRE11A 0.022 0.007 -10000 0 -10000 0 0
DNA-PK 0.04 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.014 0.089 -10000 0 -0.53 11 11
FANCF 0.024 0.004 -10000 0 -10000 0 0
BRCA1 0.023 0.021 0.26 1 -0.58 1 2
CCNE1 0.061 0.087 0.26 159 -10000 0 159
CDK2/Cyclin E1 0.06 0.06 -10000 0 -10000 0 0
FANCG 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.028 0.058 -10000 0 -0.41 16 16
FANCE 0.024 0.004 -10000 0 -10000 0 0
FANCC 0.024 0.003 -10000 0 -10000 0 0
NBN 0.02 0.01 -10000 0 -10000 0 0
FANCA 0.06 0.09 0.26 166 -10000 0 166
DNA repair 0.029 0.087 0.3 3 -0.36 7 10
BRCA1/BARD1/ubiquitin 0.028 0.058 -10000 0 -0.41 16 16
BARD1/DNA-PK 0.046 0.052 -10000 0 -0.34 13 13
FANCL 0.024 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.027 0.054 0.39 15 -10000 0 15
BRCA1/BARD1/CTIP/M/R/N Complex 0.011 0.071 -10000 0 -0.27 21 21
BRCA1/BACH1/BARD1/TopBP1 0.041 0.053 -10000 0 -0.37 15 15
BRCA1/BARD1/P53 0.049 0.053 -10000 0 -0.34 15 15
BARD1/CSTF1/BRCA1 0.038 0.051 -10000 0 -0.37 13 13
BRCA1/BACH1 0.023 0.021 0.26 1 -0.57 1 2
BARD1 0.015 0.073 0.26 1 -0.58 15 16
PCNA 0.024 0.012 0.26 2 -10000 0 2
BRCA1/BARD1/UbcH5C 0.041 0.052 -10000 0 -0.37 14 14
BRCA1/BARD1/UbcH7 0.039 0.053 -10000 0 -0.37 15 15
BRCA1/BARD1/RAD51/PCNA 0.094 0.088 0.32 2 -0.32 14 16
BARD1/DNA-PK/P53 0.05 0.054 -10000 0 -0.32 13 13
BRCA1/BARD1/Ubiquitin 0.028 0.058 -10000 0 -0.41 16 16
BRCA1/BARD1/CTIP 0.029 0.049 -10000 0 -0.34 15 15
FA complex 0.035 0.039 0.24 3 -0.26 1 4
BARD1/EWS 0.027 0.057 -10000 0 -0.42 15 15
RBBP8 0.01 0.006 -10000 0 -10000 0 0
TP53 0.022 0.008 -10000 0 -10000 0 0
TOPBP1 0.024 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.047 0.052 0.33 15 -10000 0 15
BRCA1/BARD1 0.071 0.073 0.34 2 -0.3 15 17
CSTF1 0.023 0.007 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.011 0.054 0.18 1 -0.42 15 16
CDK2 0.024 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.11 0.11 0.26 354 -10000 0 354
RAD50 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.028 0.058 -10000 0 -0.41 16 16
EWSR1 0.023 0.006 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.055 0.074 0.39 13 -0.38 13 26
MAP4K1 0.032 0.054 0.26 39 -0.58 2 41
MAP3K8 0.021 0.042 -10000 0 -0.58 5 5
PRKCB 0.019 0.078 0.26 18 -0.58 14 32
DBNL 0.024 0.004 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
MAP3K1 0.014 0.057 0.22 3 -0.32 15 18
JUN 0.004 0.13 0.5 1 -0.6 36 37
MAP3K7 0.014 0.056 0.22 4 -0.3 14 18
GRAP2 0.016 0.072 0.26 3 -0.58 14 17
CRK 0.022 0.007 -10000 0 -10000 0 0
MAP2K4 0.012 0.067 0.25 1 -0.4 10 11
LAT 0.025 0.039 0.26 14 -0.58 2 16
LCP2 0.024 0.009 0.26 1 -10000 0 1
MAPK8 0.008 0.13 -10000 0 -0.64 36 36
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.021 0.062 0.25 3 -0.31 19 22
LAT/GRAP2/SLP76/HPK1/HIP-55 0.062 0.073 0.38 13 -0.37 13 26
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.022 0.038 -10000 0 -0.58 4 4
mol:S1P 0 0.003 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.011 0.093 -10000 0 -0.3 78 78
GNAO1 0.018 0.093 0.26 32 -0.58 19 51
S1P/S1P3/G12/G13 0.042 0.02 -10000 0 -10000 0 0
AKT1 0.006 0.094 -10000 0 -0.47 30 30
AKT3 -0.01 0.16 -10000 0 -1 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.022 0.038 -10000 0 -0.57 4 4
GNAI2 0.024 0.009 -10000 0 -10000 0 0
GNAI3 0.024 0.008 -10000 0 -10000 0 0
GNAI1 -0.003 0.12 -10000 0 -0.58 45 45
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.026 0.021 0.26 7 -10000 0 7
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.096 -10000 0 -0.35 47 47
MAPK3 -0.008 0.089 0.27 2 -0.33 42 44
MAPK1 -0.005 0.088 0.27 1 -0.34 41 42
JAK2 -0.008 0.1 -10000 0 -0.39 36 36
CXCR4 -0.008 0.093 0.21 1 -0.34 45 46
FLT1 0.023 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC -0.01 0.092 0.21 1 -0.33 45 46
S1P/S1P3/Gi -0.001 0.096 -10000 0 -0.35 47 47
RAC1 0.024 0.004 -10000 0 -10000 0 0
RhoA/GTP 0 0.099 -10000 0 -0.39 27 27
VEGFA 0.026 0.02 0.25 6 -10000 0 6
S1P/S1P2/Gi -0.001 0.089 -10000 0 -0.29 74 74
VEGFR1 homodimer/VEGFA homodimer 0.036 0.022 -10000 0 -0.19 1 1
RHOA 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.02 0.041 -10000 0 -0.29 15 15
GNAQ 0.023 0.027 -10000 0 -0.58 2 2
GNAZ 0.018 0.057 -10000 0 -0.58 9 9
G12/G13 0.033 0.011 -10000 0 -10000 0 0
GNA14 0.023 0.068 0.26 19 -0.58 10 29
GNA15 0.025 0.027 0.26 6 -0.58 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.007 -10000 0 -10000 0 0
GNA11 0.023 0.027 -10000 0 -0.58 2 2
Rac1/GTP -0.001 0.1 -10000 0 -0.33 46 46
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.021 0.12 -10000 0 -0.41 48 48
KLHL20 0.015 0.066 0.23 12 -0.22 17 29
CYFIP2 0.029 0.051 0.26 27 -0.58 3 30
Rac1/GDP -0.001 0.087 0.26 8 -0.31 20 28
ENAH -0.018 0.11 -10000 0 -0.4 44 44
AP1M1 0.024 0.004 -10000 0 -10000 0 0
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.008 0.05 -10000 0 -0.33 2 2
ABI1/Sra1/Nap1 -0.013 0.033 -10000 0 -0.15 19 19
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.045 0.071 -10000 0 -0.34 24 24
RAPGEF1 -0.021 0.11 0.26 1 -0.4 33 34
CTNND1 0.024 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.023 0.13 -10000 0 -0.41 56 56
CRK -0.017 0.1 -10000 0 -0.41 39 39
E-cadherin/gamma catenin/alpha catenin 0.031 0.066 -10000 0 -0.37 22 22
alphaE/beta7 Integrin 0.036 0.035 -10000 0 -0.43 2 2
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.041 0.028 -10000 0 -0.34 3 3
DLG1 -0.025 0.12 -10000 0 -0.41 54 54
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.017 0.032 -10000 0 -0.19 20 20
MLLT4 0.021 0.034 0.26 1 -0.58 3 4
ARF6/GTP/NME1/Tiam1 0.044 0.025 -10000 0 -10000 0 0
PI3K -0.004 0.047 -10000 0 -0.24 20 20
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.019 0.071 -10000 0 -0.43 22 22
TIAM1 0.025 0.015 0.26 4 -10000 0 4
E-cadherin(dimer)/Ca2+ 0.039 0.06 -10000 0 -0.32 22 22
AKT1 -0.008 0.036 -10000 0 -0.21 1 1
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
CDH1 0.008 0.088 -10000 0 -0.58 22 22
RhoA/GDP -0.001 0.087 0.26 8 -0.31 20 28
actin cytoskeleton organization 0.014 0.054 0.19 20 -0.16 14 34
CDC42/GDP 0 0.086 0.26 8 -0.31 20 28
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.007 0.047 -10000 0 -0.27 23 23
ITGB7 0.029 0.046 0.26 25 -0.58 2 27
RAC1 0.024 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.043 0.065 -10000 0 -0.34 22 22
E-cadherin/Ca2+/beta catenin/alpha catenin 0.028 0.056 -10000 0 -0.32 22 22
mol:GDP -0.014 0.094 0.27 8 -0.36 21 29
CDC42/GTP/IQGAP1 0.031 0.009 -10000 0 -10000 0 0
JUP 0.023 0.005 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.004 0.089 0.26 5 -0.32 20 25
RAC1/GTP/IQGAP1 0.032 0.008 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.035 0.007 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
CDC42 0.023 0.006 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.014 0.049 0.18 38 -0.25 3 41
NME1 0.026 0.03 0.26 15 -10000 0 15
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.024 0.12 -10000 0 -0.42 49 49
regulation of cell-cell adhesion 0.003 0.042 -10000 0 -0.22 19 19
WASF2 0.007 0.027 -10000 0 -10000 0 0
Rap1/GTP 0.012 0.06 0.24 1 -0.28 19 20
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.072 -10000 0 -0.32 24 24
CCND1 0.014 0.055 0.21 32 -0.31 3 35
VAV2 -0.021 0.15 -10000 0 -0.61 24 24
RAP1/GDP 0.006 0.072 0.26 3 -0.35 3 6
adherens junction assembly -0.023 0.12 -10000 0 -0.4 49 49
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.024 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.039 0.067 -10000 0 -0.31 24 24
E-cadherin/beta catenin -0.001 0.065 -10000 0 -0.35 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.025 0.12 -10000 0 -0.4 54 54
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.006 0.091 0.26 30 -0.34 24 54
E-cadherin/beta catenin/alpha catenin 0.032 0.065 -10000 0 -0.37 22 22
ITGAE 0.022 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.024 0.13 -10000 0 -0.42 56 56
ceramide signaling pathway

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
MAP4K4 -0.003 0.1 0.26 2 -0.42 30 32
BAG4 0.019 0.028 -10000 0 -0.58 2 2
BAD 0.005 0.039 0.19 6 -0.19 6 12
NFKBIA 0.024 0.005 -10000 0 -10000 0 0
BIRC3 0.023 0.042 0.26 11 -0.57 3 14
BAX 0.005 0.042 0.22 5 -0.17 12 17
EnzymeConsortium:3.1.4.12 0.001 0.026 0.085 4 -0.095 25 29
IKBKB 0.015 0.1 0.32 4 -0.42 20 24
MAP2K2 0.008 0.051 0.2 17 -0.23 2 19
MAP2K1 0.008 0.052 0.21 16 -0.23 2 18
SMPD1 0.001 0.032 0.14 3 -0.16 15 18
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.026 0.12 0.3 11 -0.44 22 33
MAP2K4 0.005 0.035 0.19 4 -0.2 4 8
protein ubiquitination 0.002 0.1 0.34 4 -0.41 27 31
EnzymeConsortium:2.7.1.37 0.007 0.054 0.22 14 -0.25 2 16
response to UV 0 0.001 0.002 20 -0.002 3 23
RAF1 0.008 0.052 0.19 36 -0.21 5 41
CRADD 0.024 0.003 -10000 0 -10000 0 0
mol:ceramide 0.005 0.041 0.14 4 -0.15 22 26
I-kappa-B-alpha/RELA/p50/ubiquitin 0.031 0.008 -10000 0 -10000 0 0
MADD 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.003 0.04 0.19 3 -0.2 7 10
TRADD 0.022 0.008 -10000 0 -10000 0 0
RELA/p50 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.009 0.052 0.21 14 -0.24 2 16
MAPK1 0.006 0.06 0.21 14 -0.22 10 24
p50/RELA/I-kappa-B-alpha 0.035 0.009 -10000 0 -10000 0 0
FADD 0.022 0.11 0.28 11 -0.43 23 34
KSR1 0.009 0.05 0.18 32 -0.19 8 40
MAPK8 0.001 0.048 0.23 9 -0.31 6 15
TRAF2 0.025 0.015 0.26 4 -10000 0 4
response to radiation 0 0 0.002 7 -10000 0 7
CHUK -0.003 0.095 -10000 0 -0.42 24 24
TNF R/SODD 0.027 0.026 -10000 0 -0.43 2 2
TNF 0.024 0.07 0.26 22 -0.58 10 32
CYCS 0.008 0.046 0.18 14 -0.18 5 19
IKBKG -0.003 0.098 0.35 2 -0.42 24 26
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0 0.1 -10000 0 -0.45 28 28
RELA 0.024 0.004 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AIFM1 0.007 0.045 0.17 15 -0.18 6 21
TNF/TNF R/SODD 0.036 0.052 -10000 0 -0.36 11 11
TNFRSF1A 0.024 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 7 -10000 0 7
CASP8 0.009 0.11 -10000 0 -0.62 29 29
NSMAF 0.015 0.11 0.26 10 -0.41 27 37
response to hydrogen peroxide 0 0.001 0.002 20 -0.002 3 23
BCL2 0.007 0.097 -10000 0 -0.58 27 27
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.012 0.059 -10000 0 -10000 0 0
PLK1 0.25 0.19 0.59 54 -0.57 1 55
CDKN1B 0.16 0.13 0.39 53 -0.45 5 58
FOXO3 0.21 0.16 0.47 152 -0.62 1 153
KAT2B 0.057 0.035 -10000 0 -0.58 1 1
FOXO1/SIRT1 0.011 0.054 -10000 0 -0.28 6 6
CAT 0.19 0.17 0.64 14 -0.95 4 18
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.058 0.029 -10000 0 -10000 0 0
FOXO1 0.017 0.061 -10000 0 -0.28 9 9
MAPK10 -0.016 0.12 0.21 10 -0.3 144 154
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.036 0.084 0.38 3 -0.32 2 5
response to oxidative stress 0.036 0.027 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.18 0.14 0.45 36 -0.52 2 38
XPO1 0.025 0.003 -10000 0 -10000 0 0
EP300 0.025 0.007 -10000 0 -10000 0 0
BCL2L11 0.065 0.082 -10000 0 -0.72 7 7
FOXO1/SKP2 0.027 0.057 -10000 0 -0.28 6 6
mol:GDP 0.036 0.027 -10000 0 -10000 0 0
RAN 0.025 0.003 -10000 0 -10000 0 0
GADD45A 0.13 0.13 0.47 3 -0.52 12 15
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.021 0.13 -10000 0 -0.53 31 31
MST1 0.052 0.061 0.28 4 -0.52 8 12
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.009 0.13 -10000 0 -0.46 43 43
YWHAB 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.03 0.036 0.21 11 -0.3 6 17
MAPK9 0.032 0.026 0.21 12 -10000 0 12
YWHAG 0.024 0.003 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
SIRT1 0.011 0.021 -10000 0 -10000 0 0
SOD2 0.15 0.13 0.46 17 -0.42 2 19
RBL2 0.11 0.25 0.55 2 -0.62 61 63
RAL/GDP 0.057 0.022 -10000 0 -10000 0 0
CHUK 0.057 0.029 -10000 0 -10000 0 0
Ran/GTP 0.02 0.003 -10000 0 -10000 0 0
CSNK1G2 0.024 0.005 -10000 0 -10000 0 0
RAL/GTP 0.058 0.021 -10000 0 -10000 0 0
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
FASLG 0.06 0.17 -10000 0 -1.3 13 13
SKP2 0.024 0.004 -10000 0 -10000 0 0
USP7 0.024 0.007 -10000 0 -10000 0 0
IKBKB 0.048 0.033 -10000 0 -10000 0 0
CCNB1 0.21 0.17 0.57 50 -0.57 1 51
FOXO1-3a-4/beta catenin 0.15 0.12 0.39 61 -0.38 4 65
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.057 -10000 0 -0.27 7 7
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
SGK1 0.053 0.049 -10000 0 -0.57 4 4
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.007 -10000 0 -10000 0 0
ZFAND5 0.033 0.075 0.44 1 -10000 0 1
SFN 0.021 0.068 0.26 17 -0.58 10 27
CDK2 0.023 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.063 0.11 0.36 1 -0.41 17 18
CREBBP 0.022 0.007 -10000 0 -10000 0 0
FBXO32 0.24 0.21 0.61 112 -1.1 4 116
BCL6 0.17 0.15 0.53 3 -0.82 8 11
RALB 0.025 0.004 -10000 0 -10000 0 0
RALA 0.025 0.004 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.024 0.004 -10000 0 -10000 0 0
VDR 0.024 0.003 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.043 0.022 -10000 0 -0.37 1 1
EP300 0.023 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.015 0.062 -10000 0 -0.38 12 12
KAT2B 0.024 0.019 -10000 0 -0.58 1 1
MAPK14 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.006 0.066 0.2 4 -0.35 15 19
RAR alpha/9cRA/Cyclin H 0.047 0.074 -10000 0 -0.34 18 18
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.021 0.065 -10000 0 -0.43 11 11
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.023 0.063 -10000 0 -0.42 10 10
NCOR2 0.024 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.018 0.002 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.009 0.11 -10000 0 -0.54 20 20
NCOA2 -0.003 0.12 -10000 0 -0.58 40 40
NCOA3 0.023 0.006 -10000 0 -10000 0 0
NCOA1 0.024 0.019 -10000 0 -0.58 1 1
VDR/VDR/DNA 0.024 0.003 -10000 0 -10000 0 0
RARG 0.025 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.033 0.006 -10000 0 -10000 0 0
MAPK3 0.023 0.007 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.021 0.046 -10000 0 -0.57 6 6
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.009 0.1 -10000 0 -0.48 21 21
RARA 0.013 0.056 0.2 12 -0.27 25 37
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.008 0.078 -10000 0 -0.37 21 21
PRKCA 0.011 0.087 0.26 1 -0.57 21 22
RXRs/RARs/NRIP1/9cRA/HDAC1 0.011 0.12 0.49 1 -0.55 20 21
RXRG -0.05 0.15 0.25 13 -0.35 187 200
RXRA 0.022 0.064 0.35 1 -0.27 25 26
RXRB 0.016 0.062 0.24 11 -0.34 21 32
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RBP1 0.034 0.076 0.26 60 -0.58 7 67
CRBP1/9-cic-RA 0.024 0.054 0.18 60 -0.42 7 67
RARB 0.019 0.063 -10000 0 -0.57 11 11
PRKCG 0.032 0.045 0.26 36 -10000 0 36
MNAT1 0.024 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.008 0.1 -10000 0 -0.52 23 23
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.01 0.098 -10000 0 -0.44 24 24
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.079 0.24 12 -0.37 14 26
RXRs/RARs/NRIP1/9cRA/HDAC3 0.011 0.12 0.45 1 -0.54 21 22
positive regulation of DNA binding 0.033 0.065 -10000 0 -0.32 18 18
NRIP1 0.012 0.12 0.54 1 -0.78 8 9
RXRs/RARs 0.011 0.12 -10000 0 -0.52 25 25
RXRs/RXRs/DNA/9cRA -0.013 0.09 -10000 0 -0.48 22 22
PRKACA 0.024 0.003 -10000 0 -10000 0 0
CDK7 0.024 0.005 -10000 0 -10000 0 0
TFIIH 0.047 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.052 0.056 -10000 0 -0.35 2 2
CCNH 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.045 0.015 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.02 0.05 -10000 0 -0.58 7 7
positive regulation of NF-kappaB transcription factor activity -0.007 0.12 -10000 0 -0.34 102 102
MAP2K4 0.015 0.047 -10000 0 -0.38 4 4
IKBKB 0.021 0.009 -10000 0 -10000 0 0
TNFRSF10B 0.02 0.01 -10000 0 -10000 0 0
TNFRSF10A 0.018 0.034 -10000 0 -0.58 3 3
SMPD1 0.008 0.03 -10000 0 -0.35 6 6
IKBKG 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.017 0.14 0.26 1 -0.58 62 63
TRAIL/TRAILR2 0.026 0.04 -10000 0 -0.38 8 8
TRAIL/TRAILR3 0.027 0.045 -10000 0 -0.38 9 9
TRAIL/TRAILR1 0.024 0.048 -10000 0 -0.35 14 14
TRAIL/TRAILR4 -0.007 0.12 -10000 0 -0.34 102 102
TRAIL/TRAILR1/DAP3/GTP 0.028 0.04 -10000 0 -0.33 7 7
IKK complex 0.011 0.039 -10000 0 -0.42 1 1
RIPK1 0.024 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.015 0.007 -10000 0 -10000 0 0
MAPK3 0.007 0.037 0.26 1 -0.42 7 8
MAP3K1 0.017 0.063 -10000 0 -0.46 8 8
TRAILR4 (trimer) -0.017 0.14 0.26 1 -0.57 62 63
TRADD 0.022 0.008 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.034 -10000 0 -0.57 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.012 0.045 -10000 0 -0.38 8 8
CFLAR 0.024 0.003 -10000 0 -10000 0 0
MAPK1 0.007 0.037 0.26 1 -0.42 7 8
TRAIL/TRAILR1/FADD/TRADD/RIP 0.042 0.048 -10000 0 -0.3 7 7
mol:ceramide 0.008 0.03 -10000 0 -0.35 6 6
FADD 0.021 0.009 -10000 0 -10000 0 0
MAPK8 0.011 0.063 0.26 1 -0.37 12 13
TRAF2 0.025 0.015 0.26 4 -10000 0 4
TRAILR3 (trimer) 0.022 0.022 0.26 7 -10000 0 7
CHUK 0.024 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.03 0.042 -10000 0 -0.36 7 7
DAP3 0.021 0.009 -10000 0 -10000 0 0
CASP10 0.035 0.085 0.28 59 -0.34 3 62
JNK cascade -0.007 0.12 -10000 0 -0.34 102 102
TRAIL (trimer) 0.02 0.05 -10000 0 -0.57 7 7
TNFRSF10C 0.022 0.022 0.26 7 -10000 0 7
TRAIL/TRAILR1/DAP3/GTP/FADD 0.031 0.04 -10000 0 -0.31 5 5
TRAIL/TRAILR2/FADD 0.032 0.037 -10000 0 -0.28 8 8
cell death 0.008 0.03 -10000 0 -0.34 6 6
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.014 0.042 -10000 0 -0.41 6 6
TRAILR2 (trimer) 0.02 0.01 -10000 0 -10000 0 0
CASP8 0.013 0.045 -10000 0 -0.57 4 4
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.043 0.044 -10000 0 -0.3 5 5
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.024 0.009 0.26 1 -9999 0 1
PLK4 0.032 0.044 0.26 36 -9999 0 36
regulation of centriole replication 0.015 0.026 0.26 2 -9999 0 2
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate 0.025 0.076 0.3 5 -0.36 15 20
PDGFB-D/PDGFRB/SLAP 0.028 0.034 -10000 0 -0.37 4 4
PDGFB-D/PDGFRB/APS/CBL 0.048 0.043 -10000 0 -0.36 4 4
AKT1 0.025 0.095 0.35 34 -0.27 7 41
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.031 0.087 0.32 6 -0.38 19 25
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
FGR -0.001 0.1 -10000 0 -0.44 39 39
mol:Ca2+ 0.022 0.089 0.29 6 -0.41 20 26
MYC 0.053 0.17 0.39 19 -0.78 25 44
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.034 0.044 -10000 0 -0.31 3 3
LRP1/PDGFRB/PDGFB 0.041 0.054 -10000 0 -0.42 12 12
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0.022 0.09 0.3 5 -0.42 20 25
PTEN 0.023 0.027 -10000 0 -0.58 2 2
GRB2 0.023 0.01 0.26 1 -10000 0 1
GRB7 0.02 0.021 -10000 0 -0.58 1 1
PDGFB-D/PDGFRB/SHP2 0.034 0.03 -10000 0 -0.42 4 4
PDGFB-D/PDGFRB/GRB10 0.034 0.03 -10000 0 -0.42 4 4
cell cycle arrest 0.028 0.033 -10000 0 -0.37 4 4
HRAS 0.025 0.02 0.26 7 -10000 0 7
HIF1A 0.019 0.088 0.33 32 -0.26 1 33
GAB1 0.024 0.096 0.29 7 -0.4 21 28
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.024 0.088 0.32 8 -0.36 16 24
PDGFB-D/PDGFRB 0.042 0.033 -10000 0 -0.37 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.034 0.027 -10000 0 -0.37 4 4
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.022 0.068 0.28 3 -0.37 11 14
positive regulation of MAPKKK cascade 0.034 0.03 -10000 0 -0.42 4 4
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
mol:IP3 0.022 0.091 0.3 5 -0.42 20 25
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.023 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.029 0.035 -10000 0 -0.43 5 5
SHB 0.024 0.009 0.26 1 -10000 0 1
BLK -0.027 0.17 0.29 3 -0.41 127 130
PTPN2 0.024 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.034 0.03 -10000 0 -0.42 4 4
BCAR1 0.021 0.008 -10000 0 -10000 0 0
VAV2 0.026 0.1 0.31 6 -0.45 21 27
CBL 0.022 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.034 0.03 -10000 0 -0.42 4 4
LCK 0.004 0.11 -10000 0 -0.5 35 35
PDGFRB 0.022 0.039 -10000 0 -0.58 4 4
ACP1 0.024 0.004 -10000 0 -10000 0 0
HCK 0.014 0.064 -10000 0 -0.49 9 9
ABL1 0.019 0.095 0.3 6 -0.38 27 33
PDGFB-D/PDGFRB/CBL 0.019 0.11 0.3 2 -0.44 30 32
PTPN1 0.024 0.02 0.26 6 -10000 0 6
SNX15 0.024 0.004 -10000 0 -10000 0 0
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.032 0.26 18 -10000 0 18
cell proliferation 0.054 0.16 0.36 28 -0.68 25 53
SLA 0.021 0.023 0.26 7 -10000 0 7
actin cytoskeleton reorganization 0.034 0.051 0.33 3 -0.3 3 6
SRC 0.012 0.061 0.28 1 -0.49 8 9
PI3K -0.013 0.032 -10000 0 -0.28 11 11
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.035 -10000 0 -0.37 4 4
SH2B2 0.034 0.048 0.26 42 -10000 0 42
PLCgamma1/SPHK1 0.031 0.089 0.32 6 -0.39 19 25
LYN 0.009 0.065 -10000 0 -0.48 11 11
LRP1 0.018 0.06 -10000 0 -0.58 10 10
SOS1 0.024 0.003 -10000 0 -10000 0 0
STAT5B 0.022 0.027 -10000 0 -0.58 2 2
STAT5A 0.02 0.047 -10000 0 -0.58 6 6
NCK1-2/p130 Cas 0.055 0.04 -10000 0 -0.3 3 3
SPHK1 0.027 0.043 0.26 20 -0.58 2 22
EDG1 0.001 0.002 -10000 0 -10000 0 0
mol:DAG 0.022 0.091 0.3 5 -0.42 20 25
PLCG1 0.022 0.092 0.3 5 -0.43 20 25
NHERF/PDGFRB 0.048 0.046 -10000 0 -0.36 4 4
YES1 -0.001 0.11 -10000 0 -0.52 38 38
cell migration 0.048 0.046 -10000 0 -0.36 4 4
SHC/Grb2/SOS1 0.049 0.042 -10000 0 -0.31 3 3
SLC9A3R2 0.023 0.01 0.26 1 -10000 0 1
SLC9A3R1 0.035 0.054 0.26 53 -10000 0 53
NHERF1-2/PDGFRB/PTEN 0.057 0.05 0.3 1 -0.34 5 6
FYN -0.002 0.1 -10000 0 -0.42 39 39
DOK1 0.021 0.049 0.33 1 -0.34 3 4
HRAS/GTP 0.019 0.014 0.18 7 -10000 0 7
PDGFB 0.023 0.006 -10000 0 -10000 0 0
RAC1 0.021 0.13 0.34 4 -0.54 29 33
PRKCD 0.021 0.05 0.34 1 -0.34 3 4
FER 0.016 0.061 0.2 2 -0.35 13 15
MAPKKK cascade 0.038 0.097 0.35 35 -0.3 3 38
RASA1 0.02 0.049 0.2 2 -0.34 3 5
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.035 0.043 0.3 1 -0.31 3 4
PDGFB-D/PDGFRB/SHB 0.034 0.031 -10000 0 -0.42 4 4
chemotaxis 0.019 0.093 0.29 7 -0.37 27 34
STAT1-3-5/STAT1-3-5 0.049 0.049 -10000 0 -0.37 8 8
Bovine Papilomavirus E5/PDGFRB 0.016 0.029 -10000 0 -0.42 4 4
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.031 0.066 -9999 0 -0.37 22 22
E-cadherin/beta catenin 0.02 0.071 -9999 0 -0.43 22 22
CTNNB1 0.024 0.004 -9999 0 -10000 0 0
JUP 0.023 0.005 -9999 0 -10000 0 0
CDH1 0.008 0.088 -9999 0 -0.58 22 22
IL1-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
UBC13/UEV1A 0.03 0.01 -10000 0 -10000 0 0
PRKCZ 0.023 0.02 -10000 0 -0.58 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.023 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.051 -10000 0 -0.38 7 7
IRAK/TOLLIP 0.024 0.014 -10000 0 -10000 0 0
IKBKB 0.021 0.009 -10000 0 -10000 0 0
IKBKG 0.024 0.002 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.026 0.096 0.37 3 -0.43 37 40
IL1A 0.028 0.032 0.26 18 -10000 0 18
IL1B 0.004 0.056 0.26 1 -0.44 15 16
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.04 -10000 0 -0.3 1 1
IL1R2 0.009 0.12 0.26 28 -0.58 37 65
IL1R1 0.014 0.08 -10000 0 -0.58 18 18
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.011 0.066 0.26 4 -0.31 19 23
TOLLIP 0.024 0.005 -10000 0 -10000 0 0
TICAM2 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.016 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.033 0.07 0.33 6 -0.37 1 7
JUN -0.01 0.067 0.3 5 -0.28 29 34
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.039 0.08 -10000 0 -0.33 38 38
IL1 alpha/IL1R1/IL1RAP/MYD88 0.055 0.058 -10000 0 -0.34 18 18
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.063 0.058 -10000 0 -0.32 18 18
IL1 beta fragment/IL1R1/IL1RAP 0.023 0.072 -10000 0 -0.36 31 31
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.005 0.067 0.33 4 -0.29 23 27
IRAK1 -0.001 0.018 0.21 2 -10000 0 2
IL1RN/IL1R1 0.033 0.072 -10000 0 -0.43 20 20
IRAK4 0.024 0.003 -10000 0 -10000 0 0
PRKCI 0.024 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.03 0.043 -10000 0 -0.38 10 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.058 -10000 0 -0.39 8 8
CHUK 0.024 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.023 0.072 -10000 0 -0.36 31 31
IL1 beta/IL1R2 0.012 0.096 -10000 0 -0.38 50 50
IRAK/TRAF6/TAK1/TAB1/TAB2 0.029 0.015 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.028 0.072 -10000 0 -0.31 37 37
IRAK3 0.003 0.11 0.26 1 -0.58 35 36
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.043 0.073 -10000 0 -0.33 31 31
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.02 0.045 -10000 0 -0.28 18 18
IL1 alpha/IL1R1/IL1RAP 0.043 0.06 -10000 0 -0.37 18 18
RELA 0.024 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.024 0.008 0.26 1 -10000 0 1
MYD88 0.024 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.044 0.036 -10000 0 -10000 0 0
IL1RAP 0.024 0.004 -10000 0 -10000 0 0
UBE2N 0.024 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.016 0.059 -10000 0 -0.6 2 2
CASP1 0.021 0.02 -10000 0 -0.58 1 1
IL1RN/IL1R2 0.028 0.1 0.37 5 -0.43 39 44
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.035 0.073 -10000 0 -0.34 31 31
TMEM189-UBE2V1 0.019 0.007 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.017 0.074 -10000 0 -0.36 24 24
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL1RN 0.032 0.052 0.26 36 -0.58 2 38
TRAF6/TAK1/TAB1/TAB2 0.039 0.018 -10000 0 -10000 0 0
MAP2K6 0 0.069 0.38 5 -0.3 17 22
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 0.017 0.02 -10000 0 -0.31 3 3
TRAF2/ASK1 0.03 0.026 -10000 0 -0.36 3 3
ATM 0.022 0.008 -10000 0 -10000 0 0
MAP2K3 -0.02 0.11 0.27 1 -0.39 40 41
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.014 0.1 0.26 2 -0.38 29 31
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.052 0.077 0.26 118 -10000 0 118
TXN 0.007 0.006 0.12 3 -10000 0 3
CALM1 0.024 0.004 -10000 0 -10000 0 0
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GADD45B 0.024 0.005 -10000 0 -10000 0 0
MAP3K1 0.023 0.02 -10000 0 -0.58 1 1
MAP3K6 0.023 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
MAP3K4 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.028 -10000 0 -0.42 3 3
TAK1/TAB family 0 0.02 0.18 2 -0.14 6 8
RAC1/OSM/MEKK3 0.042 0.016 -10000 0 -10000 0 0
TRAF2 0.025 0.015 0.26 4 -10000 0 4
RAC1/OSM/MEKK3/MKK3 -0.001 0.094 -10000 0 -0.32 29 29
TRAF6 0.006 0.001 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.008 0.16 0.26 40 -0.58 69 109
CCM2 0.024 0.008 0.26 1 -10000 0 1
CaM/Ca2+/CAMKIIB 0.01 0.11 -10000 0 -0.36 70 70
MAPK11 0.021 0.033 -10000 0 -0.58 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.021 0.1 -10000 0 -0.34 71 71
OSM/MEKK3 0.033 0.013 -10000 0 -10000 0 0
TAOK1 -0.005 0.077 -10000 0 -0.37 42 42
TAOK2 0.011 0.005 -10000 0 -10000 0 0
TAOK3 0.011 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.024 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.022 0.033 -10000 0 -0.58 3 3
MAP3K10 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.019 0.026 -10000 0 -0.35 3 3
GADD45/MTK1/MTK1 0.066 0.047 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.024 0.003 -10000 0 -10000 0 0
SPHK1 0.027 0.043 0.26 20 -0.58 2 22
GNAI2 0.024 0.005 -10000 0 -10000 0 0
mol:S1P 0.013 0.02 0.22 1 -0.3 2 3
GNAO1 0.018 0.093 0.26 32 -0.58 19 51
mol:Sphinganine-1-P 0.012 0.027 -10000 0 -0.43 2 2
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.051 0.035 -10000 0 -0.23 3 3
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.033 0.011 -10000 0 -10000 0 0
S1PR3 0.026 0.02 0.26 7 -10000 0 7
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.006 0.024 -10000 0 -0.24 5 5
S1PR5 0.027 0.042 0.26 19 -0.58 2 21
S1PR4 0.029 0.065 0.26 37 -0.58 6 43
GNAI1 -0.003 0.12 -10000 0 -0.58 45 45
S1P/S1P5/G12 0.046 0.042 0.25 5 -0.28 2 7
S1P/S1P3/Gq 0.026 0.064 -10000 0 -0.29 29 29
S1P/S1P4/Gi 0.002 0.096 0.26 1 -0.34 42 43
GNAQ 0.023 0.027 -10000 0 -0.58 2 2
GNAZ 0.018 0.057 -10000 0 -0.58 9 9
GNA14 0.023 0.068 0.26 19 -0.58 10 29
GNA15 0.025 0.027 0.26 6 -0.58 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.007 -10000 0 -10000 0 0
GNA11 0.023 0.027 -10000 0 -0.58 2 2
ABCC1 0.023 0.006 -10000 0 -10000 0 0
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 0.019 0.028 -10000 0 -0.58 2 2
Caspase 8 (4 units) 0.039 0.061 -10000 0 -0.37 4 4
NEF 0.004 0.022 -10000 0 -0.18 8 8
NFKBIA 0.025 0.012 -10000 0 -10000 0 0
BIRC3 0.019 0.055 -10000 0 -0.51 5 5
CYCS 0.038 0.078 0.25 27 -0.3 11 38
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CD247 0.018 0.09 0.3 17 -0.47 23 40
MAP2K7 0.042 0.13 0.37 2 -0.7 17 19
protein ubiquitination 0.014 0.083 0.29 7 -0.37 11 18
CRADD 0.024 0.003 -10000 0 -10000 0 0
DAXX 0.024 0.003 -10000 0 -10000 0 0
FAS 0.023 0.027 -10000 0 -0.58 2 2
BID 0.037 0.074 0.22 4 -0.3 13 17
NF-kappa-B/RelA/I kappa B alpha 0.051 0.033 -10000 0 -0.31 3 3
TRADD 0.022 0.008 -10000 0 -10000 0 0
MAP3K5 0.022 0.033 -10000 0 -0.58 3 3
CFLAR 0.024 0.003 -10000 0 -10000 0 0
FADD 0.021 0.009 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.051 0.033 -10000 0 -0.31 3 3
MAPK8 0.039 0.12 0.42 4 -0.64 17 21
APAF1 0.024 0.003 -10000 0 -10000 0 0
TRAF1 0.025 0.015 0.26 4 -10000 0 4
TRAF2 0.025 0.015 0.26 4 -10000 0 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.024 0.06 0.22 7 -0.31 14 21
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.013 0.093 -10000 0 -0.41 20 20
CHUK 0.013 0.087 0.31 4 -0.4 11 15
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.055 0.041 -10000 0 -0.35 4 4
TCRz/NEF 0.017 0.083 0.26 17 -0.44 23 40
TNF 0.023 0.07 0.26 22 -0.58 10 32
FASLG 0.012 0.11 0.3 39 -0.57 23 62
NFKB1 0.025 0.012 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.036 0.052 -10000 0 -0.36 11 11
CASP6 0.053 0.1 0.38 1 -0.49 22 23
CASP7 0.04 0.1 0.36 9 -0.47 10 19
RELA 0.025 0.011 -10000 0 -10000 0 0
CASP2 0.024 0.004 -10000 0 -10000 0 0
CASP3 0.036 0.1 0.36 7 -0.46 11 18
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.026 -10000 0 -0.43 2 2
CASP8 0.024 0.003 -10000 0 -10000 0 0
CASP9 0.023 0.006 -10000 0 -10000 0 0
MAP3K14 0.015 0.089 0.3 1 -0.39 18 19
APAF-1/Caspase 9 0.034 0.062 0.26 6 -0.37 5 11
BCL2 0.031 0.13 0.44 5 -0.55 22 27
Class I PI3K signaling events

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
ARF5/GTP -0.013 0.041 0.35 2 -0.28 3 5
DAPP1 0.016 0.1 0.32 6 -0.35 35 41
Src family/SYK family/BLNK-LAT/BTK-ITK 0.015 0.14 0.29 12 -0.48 38 50
mol:DAG 0.019 0.076 0.24 24 -0.25 11 35
HRAS 0.026 0.021 0.26 7 -10000 0 7
RAP1A 0.025 0.006 -10000 0 -10000 0 0
ARF5/GDP 0.028 0.061 0.27 1 -0.35 9 10
PLCG2 0.02 0.029 0.26 1 -0.58 2 3
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARF5 0.024 0.008 0.26 1 -10000 0 1
mol:GTP -0.01 0.042 0.32 6 -0.28 2 8
ARF1/GTP -0.004 0.034 0.27 6 -0.28 2 8
RHOA 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.02 -10000 0 -0.58 1 1
RAP1A/GTP -0.011 0.036 0.2 2 -0.28 2 4
ADAP1 -0.012 0.04 0.36 2 -0.28 3 5
ARAP3 -0.01 0.042 0.32 6 -0.28 2 8
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PREX1 0.028 0.034 0.26 20 -10000 0 20
ARHGEF6 0.017 0.068 -10000 0 -0.58 13 13
ARHGEF7 0.023 0.007 -10000 0 -10000 0 0
ARF1 0.02 0.01 -10000 0 -10000 0 0
NRAS 0.025 0.006 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.58 2 2
ARF6 0.024 0.004 -10000 0 -10000 0 0
FGR 0.024 0.009 0.26 1 -10000 0 1
mol:Ca2+ 0.013 0.052 0.26 11 -10000 0 11
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.025 0.015 0.26 4 -10000 0 4
ZAP70 0.024 0.1 0.26 51 -0.58 20 71
mol:IP3 0.013 0.061 0.19 40 -0.18 9 49
LYN 0.021 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.023 0.059 0.33 2 -0.35 8 10
RhoA/GDP 0.031 0.043 -10000 0 -0.29 1 1
PDK1/Src/Hsp90 0.044 0.017 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.017 0.068 0.35 7 -0.33 5 12
SRC 0.024 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.007 0.012 0.23 2 -10000 0 2
RAC1 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.022 0.028 -10000 0 -0.55 2 2
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.014 0.04 0.33 3 -0.27 2 5
RhoA/GTP -0.012 0.041 0.36 4 -0.27 2 6
Src family/SYK family/BLNK-LAT 0.025 0.097 0.26 17 -0.41 17 34
BLK 0.051 0.088 0.26 135 -0.58 2 137
PDPK1 0.023 0.006 -10000 0 -10000 0 0
CYTH1 -0.011 0.041 0.36 4 -0.27 2 6
HCK 0.027 0.026 0.26 12 -10000 0 12
CYTH3 -0.012 0.04 0.36 2 -0.28 3 5
CYTH2 -0.012 0.04 0.33 3 -0.27 2 5
KRAS 0.024 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.01 0.053 0.31 1 -0.5 6 7
SGK1 0.007 0.075 -10000 0 -0.36 30 30
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.016 0.062 0.34 2 -0.33 12 14
SOS1 0.024 0.003 -10000 0 -10000 0 0
SYK 0.024 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.019 0.049 0.39 5 -0.29 1 6
mol:PI-3-4-5-P3 -0.011 0.037 0.27 4 -0.28 2 6
ARAP3/RAP1A/GTP -0.011 0.036 0.2 2 -0.28 2 4
VAV1 0.023 0.035 0.26 2 -0.58 3 5
mol:PI-3-4-P2 0.01 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.037 0.034 -10000 0 -0.28 2 2
PLEKHA1 -0.009 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.029 0.06 0.27 1 -0.34 9 10
LAT 0.025 0.039 0.26 14 -0.58 2 16
Rac1/GTP 0.016 0.052 -10000 0 -0.34 11 11
ITK -0.019 0.067 0.36 4 -0.32 30 34
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.018 0.095 0.29 15 -0.33 15 30
LCK 0.026 0.077 0.26 36 -0.58 11 47
BTK -0.011 0.042 0.36 4 -0.27 2 6
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.05 0.082 0.34 1 -0.48 1 2
CRKL 0.026 0.048 0.29 7 -10000 0 7
mol:DAG 0.038 0.053 0.33 1 -10000 0 1
HRAS 0.035 0.079 0.3 19 -10000 0 19
MAPK8 0.041 0.071 0.24 31 -0.35 5 36
RAP1A 0.026 0.047 0.29 7 -10000 0 7
GAB1 0.026 0.046 0.29 5 -10000 0 5
MAPK14 0.043 0.066 0.24 30 -10000 0 30
EPO 0.062 0.088 0.26 161 -10000 0 161
PLCG1 0.038 0.052 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.026 0.013 0.26 1 -10000 0 1
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.064 0.063 -10000 0 -0.35 5 5
GAB1/SHC/GRB2/SOS1 0.042 0.042 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.061 0.061 0.23 3 -10000 0 3
IRS2 0.014 0.071 0.29 5 -0.3 31 36
STAT1 0.044 0.065 0.31 4 -10000 0 4
STAT5B 0.04 0.06 0.33 1 -0.35 1 2
cell proliferation 0.023 0.076 0.24 33 -0.33 5 38
GAB1/SHIP/PIK3R1/SHP2/SHC 0.032 0.043 -10000 0 -0.29 6 6
TEC 0.025 0.049 0.29 6 -0.3 1 7
SOCS3 0.02 0.043 -10000 0 -0.58 5 5
STAT1 (dimer) 0.044 0.065 0.31 4 -10000 0 4
JAK2 0.025 0.01 -10000 0 -10000 0 0
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
EPO/EPOR (dimer)/JAK2 0.081 0.064 0.34 3 -10000 0 3
EPO/EPOR 0.061 0.061 0.23 3 -10000 0 3
LYN 0.021 0.012 -10000 0 -10000 0 0
TEC/VAV2 0.039 0.048 0.28 4 -0.3 1 5
elevation of cytosolic calcium ion concentration 0.026 0.013 0.26 1 -10000 0 1
SHC1 0.02 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.062 0.056 -10000 0 -10000 0 0
mol:IP3 0.038 0.053 0.33 1 -10000 0 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.031 0.077 0.29 2 -0.3 30 32
SH2B3 0.027 0.009 -10000 0 -10000 0 0
NFKB1 0.043 0.066 0.25 30 -10000 0 30
EPO/EPOR (dimer)/JAK2/SOCS3 0.025 0.044 -10000 0 -0.28 2 2
PTPN6 0.023 0.04 0.28 3 -10000 0 3
TEC/VAV2/GRB2 0.047 0.05 -10000 0 -0.29 1 1
EPOR 0.026 0.013 0.26 1 -10000 0 1
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.041 0.042 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG2 0.02 0.029 0.26 1 -0.58 2 3
CRKL/CBL/C3G 0.046 0.049 -10000 0 -10000 0 0
VAV2 0.027 0.048 0.29 8 -10000 0 8
CBL 0.025 0.047 0.29 6 -10000 0 6
SHC/Grb2/SOS1 0.035 0.038 -10000 0 -10000 0 0
STAT5A 0.038 0.065 0.33 1 -0.34 6 7
GRB2 0.023 0.01 0.26 1 -10000 0 1
STAT5 (dimer) 0.05 0.082 0.34 1 -0.34 13 14
LYN/PLCgamma2 0.027 0.027 -10000 0 -0.43 2 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
BTK 0.028 0.049 0.29 8 -10000 0 8
BCL2 0.03 0.17 -10000 0 -0.83 34 34
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.07 0.051 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.056 0.046 0.34 4 -10000 0 4
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.048 0.02 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I 0.014 0.043 -10000 0 -0.22 2 2
CaM/Ca2+ 0.067 0.047 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.042 0.042 0.29 2 -10000 0 2
AKT1 0.01 0.063 0.31 9 -0.28 7 16
MAP2K1 0.007 0.045 0.29 4 -0.3 1 5
MAP3K11 0.023 0.042 0.29 4 -10000 0 4
IFNGR1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.016 0.099 -10000 0 -0.38 12 12
Rap1/GTP 0.017 0.013 -10000 0 -10000 0 0
CRKL/C3G 0.034 0.009 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.077 0.055 -10000 0 -10000 0 0
CEBPB 0.027 0.096 0.35 3 -0.48 7 10
STAT3 0.024 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.075 0.097 -10000 0 -0.69 9 9
STAT1 0.026 0.047 0.29 6 -10000 0 6
CALM1 0.024 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.055 0.082 0.26 137 -10000 0 137
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.041 0.045 0.29 5 -10000 0 5
CEBPB/PTGES2/Cbp/p300 0.028 0.063 0.31 3 -0.33 5 8
mol:Ca2+ 0.066 0.049 -10000 0 -10000 0 0
MAPK3 0.021 0.08 -10000 0 -0.56 12 12
STAT1 (dimer) 0.026 0.06 -10000 0 -0.3 1 1
MAPK1 -0.009 0.17 -10000 0 -0.67 57 57
JAK2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
JAK1 0.026 0.006 -10000 0 -10000 0 0
CAMK2D 0.022 0.033 -10000 0 -0.58 3 3
DAPK1 0.026 0.07 0.31 4 -0.34 2 6
SMAD7 0.016 0.035 0.18 5 -10000 0 5
CBL/CRKL/C3G 0.046 0.039 0.28 4 -10000 0 4
PI3K 0.057 0.053 -10000 0 -0.29 8 8
IFNG 0.055 0.082 0.26 137 -10000 0 137
apoptosis 0.023 0.075 0.3 3 -0.41 11 14
CAMK2G 0.024 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.005 -10000 0 -10000 0 0
CAMK2A 0.031 0.039 0.26 28 -10000 0 28
CAMK2B -0.008 0.16 0.26 40 -0.58 69 109
FRAP1 0.008 0.058 0.3 9 -0.26 7 16
PRKCD 0.011 0.065 0.32 11 -0.28 6 17
RAP1B 0.024 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.014 0.043 -10000 0 -0.22 2 2
PTPN2 0.024 0.005 -10000 0 -10000 0 0
EP300 0.024 0.006 -10000 0 -10000 0 0
IRF1 0.022 0.058 0.31 10 -0.32 1 11
STAT1 (dimer)/PIASy 0.039 0.046 0.28 5 -10000 0 5
SOCS1 0.016 0.11 -10000 0 -1 10 10
mol:GDP 0.042 0.036 0.29 1 -10000 0 1
CASP1 0.015 0.038 0.2 5 -0.24 3 8
PTGES2 0.025 0.008 0.26 1 -10000 0 1
IRF9 0.028 0.042 0.23 10 -10000 0 10
mol:PI-3-4-5-P3 0.042 0.044 -10000 0 -0.28 8 8
RAP1/GDP 0.036 0.023 -10000 0 -10000 0 0
CBL 0.021 0.04 0.29 4 -10000 0 4
MAP3K1 0.021 0.042 0.29 4 -0.31 1 5
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PIAS4 0.024 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.014 0.043 -10000 0 -0.22 2 2
PTPN11 0.026 0.045 0.31 4 -10000 0 4
CREBBP 0.023 0.007 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.019 0.024 0.22 5 -0.31 1 6
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DOCK1 0.024 0.004 -10000 0 -10000 0 0
ITGA4 0.027 0.024 0.26 10 -10000 0 10
alpha4/beta7 Integrin/MAdCAM1 0.067 0.049 0.36 10 -0.34 2 12
EPO 0.061 0.088 0.26 161 -10000 0 161
alpha4/beta7 Integrin 0.041 0.04 0.37 4 -0.43 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.037 0.017 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.06 0.061 -10000 0 -10000 0 0
lamellipodium assembly 0.011 0.075 -10000 0 -0.44 19 19
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.03 0.043 -10000 0 -0.38 10 10
ARF6 0.024 0.004 -10000 0 -10000 0 0
JAK2 0.034 0.031 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
MADCAM1 0.032 0.045 0.26 37 -10000 0 37
cell adhesion 0.065 0.048 0.35 10 -0.34 2 12
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.013 0.043 -10000 0 -0.34 9 9
ITGB7 0.029 0.046 0.26 25 -0.58 2 27
RAC1 0.024 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.045 0.047 -10000 0 -0.37 10 10
p130Cas/Crk/Dock1 0.026 0.042 0.35 1 -0.29 8 9
VCAM1 0.019 0.063 0.26 6 -0.58 10 16
RHOA 0.024 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.058 0.024 -10000 0 -10000 0 0
BCAR1 -0.008 0.044 0.38 2 -0.31 9 11
EPOR 0.024 0.008 0.26 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.022 0.008 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.011 0.077 -10000 0 -0.45 19 19
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.024 0.004 -10000 0 -10000 0 0
NFATC1 0.02 0.085 0.31 5 -0.4 12 17
NFATC2 -0.004 0.069 0.21 1 -0.26 30 31
NFATC3 0.014 0.016 -10000 0 -0.41 1 1
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.011 0.094 0.26 3 -0.38 26 29
Exportin 1/Ran/NUP214 0.047 0.011 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.032 0.086 0.26 5 -0.42 10 15
BCL2/BAX 0.021 0.077 -10000 0 -0.37 34 34
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.013 -10000 0 -10000 0 0
CaM/Ca2+ 0.015 0.013 -10000 0 -10000 0 0
BAX 0.025 0.017 0.26 5 -10000 0 5
MAPK14 0.023 0.007 -10000 0 -10000 0 0
BAD 0.024 0.009 0.26 1 -10000 0 1
CABIN1/MEF2D 0.019 0.082 -10000 0 -0.39 14 14
Calcineurin A alpha-beta B1/BCL2 0.007 0.097 -10000 0 -0.57 27 27
FKBP8 0.024 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.019 0.081 0.38 14 -10000 0 14
KPNB1 0.023 0.006 -10000 0 -10000 0 0
KPNA2 0.036 0.057 0.26 60 -10000 0 60
XPO1 0.024 0.003 -10000 0 -10000 0 0
SFN 0.021 0.068 0.26 17 -0.58 10 27
MAP3K8 0.02 0.043 -10000 0 -0.57 5 5
NFAT4/CK1 alpha 0.018 0.028 -10000 0 -0.28 2 2
MEF2D/NFAT1/Cbp/p300 0.012 0.1 -10000 0 -0.3 49 49
CABIN1 0.012 0.093 0.26 3 -0.38 25 28
CALM1 0.021 0.013 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.023 0.02 -10000 0 -0.58 1 1
CAMK4 0.031 0.047 0.26 34 -0.58 1 35
mol:Ca2+ -0.001 0.005 -10000 0 -10000 0 0
MAPK3 0.023 0.006 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.042 0.039 -10000 0 -0.43 1 1
YWHAB 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.019 0.047 -10000 0 -0.57 6 6
MAPK9 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.021 0.097 0.32 1 -0.43 12 13
PRKCH 0.023 0.019 -10000 0 -0.58 1 1
CABIN1/Cbp/p300 0.028 0.022 -10000 0 -10000 0 0
CASP3 0.022 0.008 -10000 0 -10000 0 0
PIM1 0.024 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.008 -10000 0 -10000 0 0
apoptosis 0.011 0.032 -10000 0 -0.33 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.039 -10000 0 -0.32 3 3
PRKCB 0.019 0.078 0.26 18 -0.58 14 32
PRKCE 0.024 0.019 -10000 0 -0.58 1 1
JNK2/NFAT4 0.008 0.06 -10000 0 -0.38 1 1
BAD/BCL-XL 0.034 0.009 -10000 0 -10000 0 0
PRKCD 0.024 0.009 0.26 1 -10000 0 1
NUP214 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.022 0.021 -10000 0 -0.57 1 1
PRKCA 0.01 0.086 0.26 1 -0.58 21 22
PRKCG 0.03 0.045 0.26 36 -10000 0 36
PRKCQ 0.001 0.12 0.26 8 -0.58 40 48
FKBP38/BCL2 0.02 0.077 -10000 0 -0.38 34 34
EP300 0.02 0.015 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.029 0.087 0.34 1 -0.41 9 10
CaM/Ca2+/FKBP38 0.028 0.017 -10000 0 -10000 0 0
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSNK1A1 0.009 0.012 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.032 0.034 0.18 32 -0.36 1 33
NFATc/ERK1 0.03 0.083 0.34 1 -0.41 9 10
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.038 0.094 0.26 5 -0.39 19 24
NR4A1 -0.005 0.16 -10000 0 -0.52 74 74
GSK3B 0.023 0.008 -10000 0 -10000 0 0
positive T cell selection 0.014 0.016 -10000 0 -0.4 1 1
NFAT1/CK1 alpha 0 0.055 -10000 0 -0.27 8 8
RCH1/ KPNB1 0.041 0.041 -10000 0 -10000 0 0
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
PRKACA 0.023 0.007 -10000 0 -10000 0 0
AKAP5 0.035 0.055 0.26 50 -0.58 1 51
MEF2D 0.018 0.015 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha 0.03 0.082 0.34 1 -0.42 8 9
CREBBP 0.019 0.015 -10000 0 -10000 0 0
BCL2 0.007 0.097 -10000 0 -0.58 27 27
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.1 0.15 -10000 0 -0.41 69 69
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
AKT1 0.024 0.004 -10000 0 -10000 0 0
AKT2 0.024 0.004 -10000 0 -10000 0 0
STXBP4 0.022 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.11 0.15 0.44 1 -0.4 85 86
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
TBC1D4 0.008 0.031 -10000 0 -0.43 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
YWHAB 0.023 0.006 -10000 0 -10000 0 0
SNARE/Synip 0.039 0.021 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
ASIP 0.024 0.023 0.26 9 -10000 0 9
PRKCI 0.024 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
GYS1 0.009 0.015 0.24 4 -10000 0 4
PRKCZ 0.023 0.02 -10000 0 -0.58 1 1
TRIP10 0.024 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.018 0.065 -10000 0 -0.33 12 12
VAMP2 0.022 0.008 -10000 0 -10000 0 0
SLC2A4 -0.12 0.17 0.45 1 -0.43 98 99
STX4 0.023 0.006 -10000 0 -10000 0 0
GSK3B 0.018 0.005 -10000 0 -10000 0 0
SFN 0.021 0.068 0.26 17 -0.58 10 27
LNPEP 0.02 0.05 -10000 0 -0.58 7 7
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.035 0.11 0.29 12 -0.32 22 34
ERC1 0.023 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.03 0.034 0.37 1 -0.43 1 2
NFKBIA 0.01 0.02 -10000 0 -10000 0 0
BIRC2 0.022 0.007 -10000 0 -10000 0 0
IKBKB 0.021 0.009 -10000 0 -10000 0 0
RIPK2 0.021 0.016 0.26 3 -10000 0 3
IKBKG 0.019 0.029 -10000 0 -10000 0 0
IKK complex/A20 0.022 0.12 -10000 0 -0.39 43 43
NEMO/A20/RIP2 0.02 0.016 0.26 3 -10000 0 3
XPO1 0.024 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.014 0.12 0.32 2 -0.4 46 48
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.032 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.012 0.11 -10000 0 -0.38 38 38
BCL10/MALT1/TRAF6 0.045 0.015 -10000 0 -10000 0 0
NOD2 0.027 0.043 0.26 25 -0.58 1 26
NFKB1 0.026 0.004 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
MALT1 0.023 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.032 0.012 -10000 0 -10000 0 0
ATM 0.022 0.008 -10000 0 -10000 0 0
TNF/TNFR1A 0.033 0.053 -10000 0 -0.42 10 10
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.01 0.086 0.26 1 -0.58 21 22
CHUK 0.024 0.003 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
TNF 0.023 0.07 0.26 22 -0.58 10 32
NF kappa B1 p50/RelA 0.052 0.014 -10000 0 -10000 0 0
BCL10 0.024 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.02 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
IKK complex 0.016 0.12 -10000 0 -0.4 41 41
CYLD 0.022 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.014 0.13 -10000 0 -0.42 46 46
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.05 0.044 -10000 0 -0.34 9 9
HDAC3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.009 -10000 0 -0.28 1 1
GATA1/HDAC4 0.036 0.025 -10000 0 -0.43 1 1
GATA1/HDAC5 0.036 0.021 -10000 0 -10000 0 0
GATA2/HDAC5 0.025 0.075 -10000 0 -0.43 25 25
HDAC5/BCL6/BCoR 0.044 0.035 -10000 0 -0.37 6 6
HDAC9 0.022 0.059 0.26 11 -0.58 8 19
Glucocorticoid receptor/Hsp90/HDAC6 0.043 0.043 -10000 0 -0.37 10 10
HDAC4/ANKRA2 0.034 0.017 -10000 0 -0.43 1 1
HDAC5/YWHAB 0.033 0.011 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
GATA2 0.012 0.098 0.26 12 -0.58 25 37
HDAC4/RFXANK 0.035 0.018 -10000 0 -0.43 1 1
BCOR 0.023 0.027 -10000 0 -0.58 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.023 0.01 0.26 1 -10000 0 1
HDAC5 0.024 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.03 0.047 -10000 0 -0.42 10 10
Histones 0.017 0.048 -10000 0 -0.31 8 8
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.019 -10000 0 -0.58 1 1
XPO1 0.024 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.034 0.009 -10000 0 -10000 0 0
HDAC4/Ubc9 0.032 0.018 -10000 0 -0.43 1 1
HDAC7 0.024 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.033 0.011 -10000 0 -10000 0 0
TUBA1B 0.024 0.003 -10000 0 -10000 0 0
HDAC6 0.024 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.035 0.011 -10000 0 -10000 0 0
CAMK4 0.031 0.047 0.26 34 -0.58 1 35
Tubulin/HDAC6 0.048 0.013 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.023 0.006 -10000 0 -10000 0 0
GATA1 0.026 0.029 0.26 15 -10000 0 15
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NR3C1 0.018 0.06 -10000 0 -0.58 10 10
SUMO1/HDAC4 0.034 0.041 -10000 0 -0.23 5 5
SRF 0.024 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.033 0.018 -10000 0 -0.43 1 1
Tubulin 0.035 0.011 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.032 0.019 -10000 0 -0.43 1 1
GNB1 0.024 0.005 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
BCL6/BCoR 0.032 0.036 -10000 0 -0.43 6 6
HDAC4/HDAC3/SMRT (N-CoR2) 0.047 0.017 -10000 0 -0.37 1 1
HDAC4/SRF 0.05 0.035 -10000 0 -0.37 2 2
HDAC4/ER alpha -0.012 0.18 -10000 0 -0.43 139 139
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.017 0.047 -10000 0 -0.31 8 8
cell motility 0.047 0.013 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.023 0.007 -10000 0 -10000 0 0
HDAC7/HDAC3 0.036 0.006 -10000 0 -10000 0 0
BCL6 0.021 0.038 -10000 0 -0.58 4 4
HDAC4/CaMK II delta B 0.023 0.019 -10000 0 -0.57 1 1
Hsp90/HDAC6 0.035 0.007 -10000 0 -10000 0 0
ESR1 -0.031 0.23 0.26 120 -0.58 138 258
HDAC6/HDAC11 0.036 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.039 -10000 0 -0.24 4 4
NPC 0.014 0.002 -10000 0 -10000 0 0
MEF2C 0.023 0.019 -10000 0 -0.58 1 1
RAN 0.024 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.063 0.03 -10000 0 -0.31 2 2
GNG2 0.018 0.06 -10000 0 -0.58 10 10
NCOR2 0.024 0.003 -10000 0 -10000 0 0
TUBB2A 0.024 0.012 0.26 2 -10000 0 2
HDAC11 0.024 0.008 0.26 1 -10000 0 1
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
ANKRA2 0.024 0.005 -10000 0 -10000 0 0
RFXANK 0.025 0.011 0.26 2 -10000 0 2
nuclear import -0.027 0.017 0.33 1 -10000 0 1
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 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.029 0.046 0.26 25 -0.58 2 27
ITGA4 0.027 0.024 0.26 10 -10000 0 10
alpha4/beta7 Integrin 0.041 0.04 0.37 4 -0.43 2 6
alpha4/beta1 Integrin 0.037 0.017 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.02 0.082 -10000 0 -0.43 32 32
AKT1 0.032 0.084 0.34 3 -0.55 6 9
PTK2B 0.003 0.085 0.35 1 -0.77 5 6
VEGFR2 homodimer/Frs2 0.026 0.054 -10000 0 -0.68 5 5
CAV1 -0.097 0.24 -10000 0 -0.58 202 202
CALM1 0.024 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.04 0.054 -10000 0 -0.63 5 5
endothelial cell proliferation 0.044 0.11 0.36 19 -0.59 7 26
mol:Ca2+ 0.014 0.049 -10000 0 -0.48 7 7
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.051 0.056 -10000 0 -0.52 7 7
RP11-342D11.1 0.005 0.049 -10000 0 -0.5 7 7
CDH5 0.017 0.05 -10000 0 -0.58 7 7
VEGFA homodimer 0.049 0.029 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 0.011 0.088 0.26 1 -0.58 22 23
HRAS/GDP 0.031 0.046 -10000 0 -0.6 3 3
SH2D2A 0.04 0.074 0.26 87 -0.58 2 89
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.043 0.086 -10000 0 -0.55 8 8
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.046 0.07 -10000 0 -0.51 7 7
VEGFR1 homodimer 0.023 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.049 0.056 -10000 0 -0.66 3 3
GRB10 0.015 0.051 -10000 0 -0.65 4 4
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
PAK1 0.023 0.02 0.26 6 -10000 0 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.051 0.071 -10000 0 -0.74 5 5
HRAS 0.025 0.02 0.26 7 -10000 0 7
VEGF/Rho/ROCK1/Integrin Complex 0.009 0.072 -10000 0 -0.49 9 9
HIF1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.012 0.26 2 -10000 0 2
oxygen and reactive oxygen species metabolic process 0.049 0.055 -10000 0 -0.52 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.022 0.033 -10000 0 -0.58 3 3
Nck/Pak 0.033 0.018 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.037 0.06 -10000 0 -0.58 7 7
mol:GDP 0.039 0.05 -10000 0 -0.64 3 3
mol:NADP 0.025 0.083 0.56 1 -0.47 10 11
eNOS/Hsp90 0.037 0.08 0.55 1 -0.46 8 9
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
mol:IP3 0.015 0.05 -10000 0 -0.48 7 7
HIF1A/ARNT 0.029 0.015 -10000 0 -10000 0 0
SHB 0.024 0.009 0.26 1 -10000 0 1
VEGFA 0.026 0.019 0.26 6 -10000 0 6
VEGFC 0.023 0.005 -10000 0 -10000 0 0
FAK1/Vinculin 0.022 0.099 0.35 1 -0.68 7 8
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.04 0.093 -10000 0 -0.39 34 34
PTPN6 0.024 0.012 0.26 2 -10000 0 2
EPAS1 0.025 0.054 -10000 0 -0.59 7 7
mol:L-citrulline 0.025 0.083 0.56 1 -0.47 10 11
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.049 0.056 -10000 0 -0.61 5 5
VEGFR2 homodimer/VEGFA homodimer 0.042 0.056 -10000 0 -0.54 7 7
VEGFR2/3 heterodimer 0.025 0.064 -10000 0 -0.64 8 8
VEGFB 0.024 0.005 -10000 0 -10000 0 0
MAPK11 0.005 0.064 -10000 0 -0.73 4 4
VEGFR2 homodimer 0.012 0.06 -10000 0 -0.66 7 7
FLT1 0.023 0.006 -10000 0 -10000 0 0
NEDD4 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.007 0.072 0.32 1 -0.66 4 5
MAPK1 0.01 0.073 -10000 0 -0.6 5 5
VEGFA145/NRP2 0.035 0.025 -10000 0 -0.32 3 3
VEGFR1/2 heterodimer 0.024 0.057 -10000 0 -0.6 7 7
KDR 0.012 0.061 -10000 0 -0.66 7 7
VEGFA165/NRP1/VEGFR2 homodimer 0.041 0.059 -10000 0 -0.55 7 7
SRC 0.024 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.015 0.081 0.38 2 -0.56 6 8
PI3K 0.026 0.065 -10000 0 -0.66 5 5
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.04 0.055 -10000 0 -0.55 7 7
FES 0.014 0.055 -10000 0 -0.52 7 7
GAB1 0.015 0.058 -10000 0 -0.78 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.039 0.053 -10000 0 -0.52 7 7
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
ARNT 0.02 0.01 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.017 0.13 -10000 0 -0.47 20 20
VEGFR2 homodimer/VEGFA homodimer/Yes 0.039 0.057 -10000 0 -0.52 8 8
PI3K/GAB1 0.04 0.077 -10000 0 -0.58 5 5
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.055 0.056 -10000 0 -0.62 4 4
PRKACA 0.024 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.037 0.062 -10000 0 -0.6 8 8
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
CDC42 0.014 0.053 -10000 0 -0.67 4 4
actin cytoskeleton reorganization 0.045 0.07 -10000 0 -0.5 7 7
PTK2 0.006 0.084 -10000 0 -0.75 7 7
EDG1 0.005 0.049 -10000 0 -0.5 7 7
mol:DAG 0.015 0.05 -10000 0 -0.48 7 7
CaM/Ca2+ 0.026 0.048 -10000 0 -0.58 4 4
MAP2K3 -0.005 0.057 -10000 0 -0.64 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.04 0.055 -10000 0 -0.68 4 4
PLCG1 0.015 0.051 -10000 0 -0.49 7 7
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.051 0.054 -10000 0 -0.5 7 7
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.02 -10000 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.041 0.055 -10000 0 -0.55 7 7
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.04 0.056 -10000 0 -0.55 7 7
cell migration 0.024 0.092 0.32 2 -0.65 6 8
mol:PI-3-4-5-P3 0.026 0.06 -10000 0 -0.6 5 5
FYN 0.022 0.027 -10000 0 -0.58 2 2
VEGFB/NRP1 0.019 0.049 -10000 0 -0.62 4 4
mol:NO 0.025 0.083 0.56 1 -0.47 10 11
PXN 0.024 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.017 0.041 -10000 0 -0.6 3 3
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.033 0.052 -10000 0 -0.68 4 4
VHL 0.024 0.004 -10000 0 -10000 0 0
ITGB3 0.005 0.11 0.26 4 -0.58 32 36
NOS3 0.025 0.09 0.57 1 -0.54 10 11
VEGFR2 homodimer/VEGFA homodimer/Sck 0.031 0.077 -10000 0 -0.39 27 27
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA -0.008 0.071 0.35 1 -0.72 4 5
PRKCB -0.005 0.064 -10000 0 -0.7 4 4
VCL 0.024 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.023 0.051 -10000 0 -0.5 7 7
VEGFR1/2 heterodimer/VEGFA homodimer 0.038 0.057 -10000 0 -0.56 7 7
VEGFA165/NRP2 0.035 0.025 -10000 0 -0.32 3 3
MAPKKK cascade 0.051 0.078 0.33 11 -0.61 3 14
NRP2 0.023 0.028 0.26 1 -0.58 2 3
VEGFC homodimer 0.023 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
ROCK1 0.023 0.019 -10000 0 -0.58 1 1
FAK1/Paxillin 0.023 0.1 0.42 2 -0.68 7 9
MAP3K13 0.013 0.055 -10000 0 -0.67 4 4
PDPK1 0.015 0.055 0.27 1 -0.63 3 4
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.026 0.018 -10000 0 -0.47 1 1
VEGFR1 homodimer/NRP1 0.01 0.016 -10000 0 -0.49 1 1
mol:DAG 0.012 0.031 -10000 0 -0.39 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0.02 -10000 0 -0.45 1 1
CaM/Ca2+ 0.026 0.029 -10000 0 -0.37 2 2
HIF1A 0.028 0.012 -10000 0 -0.31 1 1
GAB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.01 0.048 -10000 0 -0.42 1 1
PLCG1 0.012 0.031 -10000 0 -0.39 2 2
NOS3 0.015 0.054 -10000 0 -0.5 3 3
CBL 0.022 0.008 -10000 0 -10000 0 0
mol:NO 0.019 0.063 0.3 1 -0.45 6 7
FLT1 0.013 0.019 -10000 0 -0.56 1 1
PGF 0.024 0.022 0.26 2 -0.58 1 3
VEGFR1 homodimer/NRP2/VEGFR121 0.038 0.031 -10000 0 -0.45 2 2
CALM1 0.024 0.004 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
eNOS/Hsp90 0.032 0.065 -10000 0 -0.43 7 7
endothelial cell proliferation 0.011 0.083 0.32 8 -0.6 4 12
mol:Ca2+ 0.012 0.03 -10000 0 -0.39 2 2
MAPK3 -0.013 0.051 -10000 0 -0.33 18 18
MAPK1 -0.012 0.049 -10000 0 -0.33 16 16
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
PLGF homodimer 0.024 0.022 0.26 2 -0.57 1 3
PRKACA 0.024 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.097 0.24 -10000 0 -0.58 202 202
VEGFA homodimer 0.025 0.019 0.26 6 -10000 0 6
VEGFR1 homodimer/VEGFA homodimer 0.027 0.022 -10000 0 -0.49 1 1
platelet activating factor biosynthetic process -0.014 0.048 -10000 0 -0.64 1 1
PI3K 0.044 0.044 -10000 0 -0.33 10 10
PRKCA -0.012 0.053 0.24 1 -0.34 19 20
PRKCB -0.009 0.05 -10000 0 -0.35 13 13
VEGFR1 homodimer/PLGF homodimer 0.026 0.024 -10000 0 -0.43 2 2
VEGFA 0.025 0.019 0.26 6 -10000 0 6
VEGFB 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.012 0.031 -10000 0 -0.39 2 2
RASA1 0.013 0.029 -10000 0 -0.44 1 1
NRP2 0.023 0.028 0.26 1 -0.58 2 3
VEGFR1 homodimer 0.013 0.019 -10000 0 -0.56 1 1
VEGFB homodimer 0.024 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.028 0.14 -10000 0 -0.45 23 23
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.043 0.044 -10000 0 -0.33 10 10
mol:L-citrulline 0.019 0.063 0.3 1 -0.45 6 7
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.047 0.029 -10000 0 -0.42 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.038 0.023 -10000 0 -0.45 1 1
CD2AP 0.024 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.056 0.048 -10000 0 -0.32 10 10
PDPK1 -0.004 0.05 -10000 0 -0.41 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.039 0.024 -10000 0 -0.45 1 1
mol:NADP 0.019 0.063 0.3 1 -0.45 6 7
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.046 0.028 -10000 0 -0.41 1 1
VEGFR1 homodimer/NRP2 0.025 0.029 -10000 0 -0.44 3 3
Signaling events mediated by HDAC Class I

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.05 0.063 -10000 0 -0.38 9 9
Ran/GTP/Exportin 1/HDAC1 -0.009 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.062 -10000 0 -0.37 8 8
SUMO1 0.024 0.003 -10000 0 -10000 0 0
ZFPM1 0.023 0.02 0.26 6 -10000 0 6
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
FKBP3 0.024 0.004 -10000 0 -10000 0 0
Histones 0.053 0.042 -10000 0 -0.42 1 1
YY1/LSF 0.024 0.05 -10000 0 -0.3 7 7
SMG5 0.021 0.009 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.021 0.035 -10000 0 -0.32 8 8
I kappa B alpha/HDAC1 0.029 0.04 -10000 0 -0.44 2 2
SAP18 0.023 0.006 -10000 0 -10000 0 0
RELA 0.02 0.038 -10000 0 -0.29 8 8
HDAC1/Smad7 0.046 0.014 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
HDAC3/TR2 0.031 0.037 -10000 0 -0.44 1 1
NuRD/MBD3 Complex 0.026 0.052 -10000 0 -0.29 11 11
NF kappa B1 p50/RelA 0.027 0.064 0.38 1 -0.38 4 5
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.012 0.098 0.26 12 -0.58 25 37
GATA1 0.026 0.029 0.26 15 -10000 0 15
Mad/Max 0.035 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.017 0.08 -10000 0 -0.36 19 19
RBBP7 0.026 0.02 0.26 7 -10000 0 7
NPC 0.014 0.002 -10000 0 -10000 0 0
RBBP4 0.023 0.019 -10000 0 -0.58 1 1
MAX 0.024 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NFKBIA 0.018 0.031 -10000 0 -0.48 2 2
KAT2B 0.024 0.019 -10000 0 -0.58 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.018 0.03 -10000 0 -0.36 1 1
SIN3 complex 0.056 0.023 -10000 0 -10000 0 0
SMURF1 0.024 0.004 -10000 0 -10000 0 0
CHD3 0.022 0.008 -10000 0 -10000 0 0
SAP30 0.025 0.016 0.26 4 -10000 0 4
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.022 0.008 -10000 0 -10000 0 0
YY1/HDAC3 0.022 0.047 -10000 0 -0.35 5 5
YY1/HDAC2 0.025 0.045 -10000 0 -0.24 13 13
YY1/HDAC1 0.025 0.047 -10000 0 -0.28 6 6
NuRD/MBD2 Complex (MeCP1) 0.025 0.055 -10000 0 -0.27 13 13
PPARG -0.059 0.16 -10000 0 -0.35 208 208
HDAC8/hEST1B 0.041 0.019 -10000 0 -10000 0 0
UBE2I 0.023 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.031 0.037 -10000 0 -0.44 1 1
MBD3L2 0.018 0.011 0.26 2 -10000 0 2
ubiquitin-dependent protein catabolic process 0.045 0.014 -10000 0 -10000 0 0
CREBBP 0.023 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.023 0.067 -10000 0 -0.35 15 15
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.018 0.029 -10000 0 -0.24 9 9
HDAC2 0.023 0.006 -10000 0 -10000 0 0
YY1 0.015 0.012 -10000 0 -0.29 1 1
HDAC8 0.025 0.001 -10000 0 -10000 0 0
SMAD7 0.024 0.005 -10000 0 -10000 0 0
NCOR2 0.024 0.003 -10000 0 -10000 0 0
MXD1 0.025 0.008 0.26 1 -10000 0 1
STAT3 0.016 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.036 0.049 -10000 0 -0.27 6 6
YY1/SAP30/HDAC1 0.037 0.047 -10000 0 -0.25 6 6
EP300 0.023 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.016 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.031 -10000 0 -0.48 2 2
histone deacetylation 0.025 0.054 -10000 0 -0.27 13 13
STAT3 (dimer non-phopshorylated)/HDAC3 0.019 0.037 -10000 0 -0.31 3 3
nuclear export -0.041 0.019 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GATAD2B 0.021 0.009 -10000 0 -10000 0 0
GATAD2A 0.024 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.024 0.067 -10000 0 -0.34 22 22
GATA1/HDAC1 0.036 0.02 -10000 0 -10000 0 0
GATA1/HDAC3 0.032 0.042 -10000 0 -0.46 1 1
CHD4 0.024 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.033 0.053 -10000 0 -0.42 10 10
SIN3/HDAC complex/Mad/Max 0.015 0.055 -10000 0 -0.28 19 19
NuRD Complex 0.025 0.066 -10000 0 -0.36 10 10
positive regulation of chromatin silencing 0.05 0.041 -10000 0 -0.41 1 1
SIN3B 0.024 0.004 -10000 0 -10000 0 0
MTA2 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
XPO1 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.035 0.039 -10000 0 -0.23 4 4
HDAC complex 0.058 0.023 -10000 0 -10000 0 0
GATA1/Fog1 0.033 0.025 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.045 0.016 -10000 0 -10000 0 0
TNF 0.023 0.07 0.26 22 -0.58 10 32
negative regulation of cell growth 0.015 0.054 -10000 0 -0.28 19 19
NuRD/MBD2/PRMT5 Complex 0.025 0.055 -10000 0 -0.27 13 13
Ran/GTP/Exportin 1 0.035 0.039 -10000 0 -0.24 4 4
NF kappa B/RelA/I kappa B alpha 0.019 0.054 -10000 0 -0.37 9 9
SIN3/HDAC complex/NCoR1 0.007 0.067 -10000 0 -0.31 28 28
TFCP2 0.024 0.019 -10000 0 -0.58 1 1
NR2C1 0.024 0.003 -10000 0 -10000 0 0
MBD3 0.024 0.009 0.26 1 -10000 0 1
MBD2 0.024 0.005 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.035 0.009 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.018 0.038 -10000 0 -0.37 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.026 0.044 -10000 0 -0.34 2 2
NFKBIA 0.014 0.038 -10000 0 -0.25 11 11
MAPK14 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.011 -10000 0 -10000 0 0
ARRB2 0.011 0.004 -10000 0 -10000 0 0
REL 0.017 0.065 -10000 0 -0.58 12 12
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.022 0.012 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.011 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.016 0.013 0.25 2 -10000 0 2
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
NFKB1 0.01 0.012 0.26 2 -10000 0 2
RELA 0.024 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.024 0.047 -10000 0 -0.26 10 10
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.024 0.048 -10000 0 -0.34 3 3
SRC 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.03 0.043 -10000 0 -0.38 10 10
NF kappa B1 p50/RelA 0.024 0.047 -10000 0 -0.26 10 10
IKBKB 0.021 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -10000 0 0
SYK 0.024 0.004 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.023 0.056 -10000 0 -0.26 22 22
cell death 0.023 0.046 -10000 0 -0.32 3 3
NF kappa B1 p105/c-Rel 0.018 0.038 -10000 0 -0.37 8 8
LCK 0.026 0.077 0.26 36 -0.58 11 47
BCL3 0.024 0.008 0.26 1 -10000 0 1
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD2 -0.003 0.04 0.21 1 -0.3 2 3
SMAD3 0.022 0.025 -10000 0 -10000 0 0
SMAD3/SMAD4 0.036 0.064 -10000 0 -0.43 12 12
SMAD4/Ubc9/PIASy 0.043 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.041 0.06 -10000 0 -0.28 1 1
PPM1A 0.024 0.004 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.008 0.045 -10000 0 -0.27 6 6
MAP3K1 0.023 0.02 -10000 0 -0.58 1 1
TRAP-1/SMAD4 0.029 0.051 -10000 0 -0.43 12 12
MAPK3 0.023 0.006 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
NUP214 0.024 0.004 -10000 0 -10000 0 0
CTDSP1 0.024 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
KPNB1 0.023 0.006 -10000 0 -10000 0 0
TGFBRAP1 0.017 0.065 -10000 0 -0.58 12 12
UBE2I 0.023 0.007 -10000 0 -10000 0 0
NUP153 0.024 0.005 -10000 0 -10000 0 0
KPNA2 0.036 0.057 0.26 60 -10000 0 60
PIAS4 0.024 0.004 -10000 0 -10000 0 0
Circadian rhythm pathway

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
chromatin modification 0.042 0.037 -10000 0 -10000 0 0
CLOCK 0.02 0.06 -10000 0 -0.57 10 10
TIMELESS/CRY2 0.031 0.027 -10000 0 -10000 0 0
DEC1/BMAL1 0.033 0.013 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
NR1D1 0.015 0.019 -10000 0 -10000 0 0
ARNTL 0.026 0.005 -10000 0 -10000 0 0
TIMELESS 0.018 0.027 -10000 0 -10000 0 0
NPAS2 0.023 0.047 0.26 1 -0.57 6 7
CRY2 0.024 0.004 -10000 0 -10000 0 0
mol:CO -0.007 0.007 -10000 0 -0.093 7 7
CHEK1 0.028 0.037 0.26 24 -10000 0 24
mol:HEME 0.007 0.007 0.093 7 -10000 0 7
PER1 0.014 0.068 -10000 0 -0.58 13 13
BMAL/CLOCK/NPAS2 0.049 0.055 -10000 0 -0.36 16 16
BMAL1/CLOCK 0.018 0.065 -10000 0 -0.46 2 2
S phase of mitotic cell cycle 0.042 0.037 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.043 0.037 -10000 0 -10000 0 0
mol:NADPH 0.007 0.007 0.093 7 -10000 0 7
PER1/TIMELESS 0.025 0.046 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.019 0.016 0.26 4 -10000 0 4
Paxillin-dependent events mediated by a4b1

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
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
DOCK1 0.024 0.004 -10000 0 -10000 0 0
ITGA4 0.027 0.024 0.26 10 -10000 0 10
RAC1 0.024 0.004 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.041 0.04 0.37 4 -0.43 2 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.049 0.018 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.044 0.036 0.34 4 -0.34 2 6
lamellipodium assembly -0.002 0.085 -10000 0 -0.39 33 33
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.03 0.043 -10000 0 -0.38 10 10
ARF6 0.024 0.004 -10000 0 -10000 0 0
TLN1 0.024 0.004 -10000 0 -10000 0 0
PXN 0.011 0.002 -10000 0 -10000 0 0
PIK3R1 0.018 0.057 -10000 0 -0.58 9 9
ARF6/GTP 0.047 0.021 -10000 0 -10000 0 0
cell adhesion 0.05 0.019 -10000 0 -10000 0 0
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.04 0.017 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.029 0.046 0.26 25 -0.58 2 27
ARF6/GDP 0.022 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.049 0.044 -10000 0 -0.32 10 10
p130Cas/Crk/Dock1 0.041 0.02 -10000 0 -10000 0 0
VCAM1 0.019 0.063 0.26 6 -0.58 10 16
alpha4/beta1 Integrin/Paxillin/Talin 0.052 0.02 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.05 0.022 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
mol:GDP -0.048 0.021 -10000 0 -10000 0 0
CBL 0.022 0.008 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.052 0.02 -10000 0 -10000 0 0
Rac1/GTP -0.003 0.093 -10000 0 -0.44 33 33
Arf6 downstream 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
PLAUR 0.039 0.069 -10000 0 -10000 0 0
regulation of axonogenesis -0.01 0.027 0.23 6 -10000 0 6
myoblast fusion -0.025 0.047 -10000 0 -0.22 1 1
mol:GTP 0.022 0.031 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.054 0.043 -10000 0 -10000 0 0
ARF1/GTP 0.03 0.029 -10000 0 -10000 0 0
mol:GM1 0.012 0.024 -10000 0 -10000 0 0
mol:Choline 0.008 0.038 -10000 0 -0.35 8 8
lamellipodium assembly 0.017 0.06 -10000 0 -0.36 8 8
MAPK3 0.031 0.045 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.055 0.044 -10000 0 -10000 0 0
ARF1 0.02 0.01 -10000 0 -10000 0 0
ARF6/GDP 0.025 0.047 0.22 1 -10000 0 1
ARF1/GDP 0.024 0.048 -10000 0 -0.28 1 1
ARF6 0.031 0.017 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
TIAM1 0.027 0.016 0.26 4 -10000 0 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.031 0.044 -10000 0 -10000 0 0
actin filament bundle formation -0.032 0.05 0.26 2 -10000 0 2
KALRN 0.009 0.056 -10000 0 -0.31 20 20
RAB11FIP3/RAB11A 0.033 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.032 0.051 -10000 0 -0.26 2 2
NME1 0.028 0.03 0.26 15 -10000 0 15
Rac1/GDP 0.033 0.051 -10000 0 -0.26 3 3
substrate adhesion-dependent cell spreading 0.022 0.031 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.017 0.06 -10000 0 -0.36 8 8
RAC1 0.024 0.004 -10000 0 -10000 0 0
liver development 0.022 0.031 -10000 0 -10000 0 0
ARF6/GTP 0.022 0.031 -10000 0 -10000 0 0
RhoA/GTP 0.034 0.028 -10000 0 -10000 0 0
mol:GDP 0.02 0.047 0.24 1 -10000 0 1
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.03 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
PLD1 0.017 0.045 -10000 0 -0.4 8 8
RAB11FIP3 0.023 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.017 0.06 -10000 0 -0.36 8 8
ruffle organization 0.01 0.027 -10000 0 -0.23 6 6
regulation of epithelial cell migration 0.022 0.031 -10000 0 -10000 0 0
PLD2 0.02 0.025 -10000 0 -10000 0 0
PIP5K1A 0.01 0.027 -10000 0 -0.23 6 6
mol:Phosphatidic acid 0.008 0.038 -10000 0 -0.35 8 8
Rac1/GTP 0.017 0.06 -10000 0 -0.36 8 8
Alternative NF-kappaB pathway

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
IKK alpha homodimer 0.034 0.009 -10000 0 -9999 0 0
FBXW11 0.024 0.004 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.024 0.004 -10000 0 -9999 0 0
CHUK 0.024 0.003 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.068 0.025 -10000 0 -9999 0 0
NFKB1 0.024 0.004 -10000 0 -9999 0 0
MAP3K14 0.024 0.005 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.036 0.016 -10000 0 -9999 0 0
RELB 0.026 0.023 0.26 9 -9999 0 9
NFKB2 0.024 0.008 0.26 1 -9999 0 1
NF kappa B2 p52/RelB 0.034 0.016 0.18 10 -9999 0 10
regulation of B cell activation 0.033 0.016 0.18 10 -9999 0 10
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.011 -10000 0 -0.27 1 1
MDM2/SUMO1 0.033 0.041 -10000 0 -0.23 4 4
HDAC4 0.023 0.019 -10000 0 -0.58 1 1
Ran/GTP/Exportin 1/HDAC1 -0.008 0.007 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.009 0.017 -10000 0 -0.22 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.006 0.012 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.034 0.041 -10000 0 -0.23 5 5
SUMO1/HDAC1 0.035 0.039 -10000 0 -0.23 4 4
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.057 0.02 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.011 0.004 -10000 0 -10000 0 0
Ran/GTP 0.023 0.037 -10000 0 -0.24 4 4
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.024 0.005 -10000 0 -10000 0 0
UBE2I 0.023 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.021 0.039 0.25 1 -0.24 4 5
NPC 0.014 0.002 -10000 0 -10000 0 0
PIAS2 0.024 0.005 -10000 0 -10000 0 0
PIAS1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Arf1 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
coatomer protein complex 0.011 0.032 0.18 2 -10000 0 2
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.027 0.048 -10000 0 -0.19 3 3
AP2 0.035 0.008 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.031 0.01 -10000 0 -10000 0 0
CLTB 0.025 0.017 0.26 5 -10000 0 5
coatomer protein complex/ARF1/GTP/ER cargo protein 0.014 0.01 -10000 0 -10000 0 0
CD4 0.023 0.005 -10000 0 -10000 0 0
CLTA 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.006 0.006 0.14 2 -10000 0 2
mol:PI-4-5-P2 0.007 0.016 -10000 0 -10000 0 0
ARF1/GTP 0.024 0.016 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.008 0.011 0.2 2 -10000 0 2
mol:Choline 0.007 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.011 -10000 0 -10000 0 0
DDEF1 0.006 0.016 -10000 0 -10000 0 0
ARF1/GDP 0.001 0.022 0.19 2 -10000 0 2
AP2M1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.01 0.006 -10000 0 -10000 0 0
Rac/GTP 0.021 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.026 0.017 -10000 0 -10000 0 0
ARFIP2 0.014 0.018 -10000 0 -10000 0 0
COPA 0.02 0.009 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.023 -10000 0 -0.2 2 2
ARF1/GTP/ARHGAP10 0.014 0.008 -10000 0 -10000 0 0
GGA3 0.023 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.012 0.042 -10000 0 -0.24 20 20
AP2A1 0.024 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.009 0.024 -10000 0 -0.22 5 5
ARF1/GDP/Membrin 0.012 0.051 -10000 0 -0.25 29 29
Arfaptin 2/Rac/GDP 0.028 0.011 -10000 0 -10000 0 0
CYTH2 0.029 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.015 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.02 0.024 -10000 0 -10000 0 0
PLD2 0.007 0.016 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.006 0.006 0.14 2 -10000 0 2
PIP5K1A 0.007 0.016 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.013 0.021 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.016 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.006 0.006 0.14 2 -10000 0 2
GOSR2 0.009 0.027 -10000 0 -0.31 6 6
USO1 0.009 0.023 -10000 0 -0.32 4 4
GBF1 0.01 0.02 -10000 0 -0.31 3 3
ARF1/GTP/Arfaptin 2 0.028 0.015 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.045 0.015 -10000 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 1001 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.S3.A6ZH TCGA.S3.A6ZG TCGA.S3.A6ZF TCGA.PE.A5DE
109_MAP3K5 -0.34 0.025 0.059 0.096
47_PPARGC1A -0.58 0.025 -0.58 0.025
105_BMP4 0.025 0.025 0.025 0.025
105_BMP6 0.025 0.025 0.025 0.025
105_BMP7 0.025 0.025 0.025 0.025
105_BMP2 -0.58 -0.58 0.025 0.025
131_RELN/VLDLR -0.34 -0.34 -0.34 -0.34
30_TGFB1/TGF beta receptor Type II 0.02 0.024 0.024 0.024
84_STAT5B -0.52 -0.061 -0.06 -0.091
84_STAT5A -0.52 -0.061 -0.06 -0.091
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/BRCA-TP/6044496/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/BRCA-TP/6154449/Gistic2_Analysis_6154752/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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