PARADIGM pathway analysis of mRNASeq expression and copy number data
Breast Invasive Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1WM1C3M
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/C1WM1C3M
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) 281
Class IB PI3K non-lipid kinase events 272
Signaling mediated by p38-alpha and p38-beta 265
Reelin signaling pathway 222
Aurora B signaling 194
EGFR-dependent Endothelin signaling events 192
FOXA2 and FOXA3 transcription factor networks 169
HIF-1-alpha transcription factor network 155
EPHB forward signaling 155
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 1058 . 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 ( 1058 ).

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 0.3214 340 17352 51 -0.057 0.71 1000 -1000 -0.034 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2656 281 21929 78 -0.57 0.18 1000 -1000 -0.035 -1000
Class IB PI3K non-lipid kinase events 0.2571 272 816 3 -0.13 -1000 1000 -1000 -0.014 -1000
Signaling mediated by p38-alpha and p38-beta 0.2505 265 11687 44 -0.32 0.024 1000 -1000 -0.018 -1000
Reelin signaling pathway 0.2098 222 12474 56 -0.32 0.054 1000 -1000 -0.03 -1000
Aurora B signaling 0.1834 194 13018 67 -0.21 0.27 1000 -1000 -0.031 -1000
EGFR-dependent Endothelin signaling events 0.1815 192 4037 21 -0.21 0.034 1000 -1000 -0.035 -1000
FOXA2 and FOXA3 transcription factor networks 0.1597 169 7816 46 -1.1 0.034 1000 -1000 -0.067 -1000
HIF-1-alpha transcription factor network 0.1465 155 11828 76 -0.47 0.035 1000 -1000 -0.039 -1000
EPHB forward signaling 0.1465 155 13224 85 -0.21 0.14 1000 -1000 -0.053 -1000
PLK1 signaling events 0.1446 153 13030 85 -0.064 0.23 1000 -1000 -0.027 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1446 153 10417 68 -0.34 0.16 1000 -1000 -0.049 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1446 153 13498 88 -0.31 0.12 1000 -1000 -0.058 -1000
Endothelins 0.1361 144 13881 96 -0.34 0.17 1000 -1000 -0.026 -1000
Glucocorticoid receptor regulatory network 0.1352 143 16333 114 -0.73 0.28 1000 -1000 -0.043 -1000
p75(NTR)-mediated signaling 0.1333 141 17645 125 -0.23 0.098 1000 -1000 -0.06 -1000
Ephrin B reverse signaling 0.1134 120 5804 48 -0.21 0.09 1000 -1000 -0.026 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1115 118 6396 54 -0.32 0.055 1000 -1000 -0.033 -1000
Wnt signaling 0.1078 114 802 7 -0.095 0.019 1000 -1000 -0.008 -1000
Noncanonical Wnt signaling pathway 0.1068 113 2945 26 -0.095 0.024 1000 -1000 -0.034 -1000
IL23-mediated signaling events 0.1059 112 6764 60 -0.3 0.085 1000 -1000 -0.039 -1000
IL4-mediated signaling events 0.1049 111 10145 91 -0.67 0.25 1000 -1000 -0.066 -1000
Arf6 signaling events 0.1021 108 6736 62 -0.21 0.05 1000 -1000 -0.023 -1000
IGF1 pathway 0.1021 108 6199 57 -0.11 0.043 1000 -1000 -0.039 -1000
Plasma membrane estrogen receptor signaling 0.0983 104 8950 86 -0.12 0.11 1000 -1000 -0.049 -1000
Nongenotropic Androgen signaling 0.0964 102 5344 52 -0.24 0.13 1000 -1000 -0.023 -1000
ErbB2/ErbB3 signaling events 0.0945 100 6557 65 -0.26 0.034 1000 -1000 -0.043 -1000
BMP receptor signaling 0.0898 95 7766 81 -0.38 0.1 1000 -1000 -0.036 -1000
Signaling events regulated by Ret tyrosine kinase 0.0879 93 7630 82 -0.072 0.098 1000 -1000 -0.051 -1000
ErbB4 signaling events 0.0870 92 6403 69 -0.28 0.061 1000 -1000 -0.023 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0851 90 10833 120 -0.36 0.17 1000 -1000 -0.04 -1000
Signaling events mediated by PTP1B 0.0841 89 6829 76 -0.44 0.082 1000 -1000 -0.032 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0832 88 7485 85 -0.24 0.024 1000 -1000 -0.037 -1000
Visual signal transduction: Rods 0.0832 88 4587 52 -0.33 0.056 1000 -1000 -0.028 -1000
Calcium signaling in the CD4+ TCR pathway 0.0794 84 2631 31 -0.19 0.027 1000 -1000 -0.042 -1000
Aurora C signaling 0.0766 81 572 7 0 0.14 1000 -1000 -0.008 -1000
S1P1 pathway 0.0766 81 2943 36 -0.33 0.024 1000 -1000 -0.03 -1000
Glypican 1 network 0.0756 80 3876 48 -0.2 0.046 1000 -1000 -0.018 -1000
Effects of Botulinum toxin 0.0756 80 2098 26 -0.004 0.1 1000 -1000 -0.005 -1000
IL6-mediated signaling events 0.0709 75 5672 75 -0.18 0.054 1000 -1000 -0.029 -1000
amb2 Integrin signaling 0.0699 74 6140 82 -0.34 0.12 1000 -1000 -0.024 -1000
Integrins in angiogenesis 0.0681 72 6055 84 -0.2 0.12 1000 -1000 -0.04 -1000
TCR signaling in naïve CD8+ T cells 0.0681 72 6696 93 -0.09 0.087 1000 -1000 -0.046 -1000
Syndecan-1-mediated signaling events 0.0662 70 2410 34 -0.073 0.18 1000 -1000 -0.036 -1000
LPA receptor mediated events 0.0652 69 7065 102 -0.19 0.12 1000 -1000 -0.061 -1000
Ephrin A reverse signaling 0.0643 68 479 7 -0.029 0.023 1000 -1000 -0.007 -1000
Signaling events mediated by the Hedgehog family 0.0633 67 3513 52 -0.12 0.03 1000 -1000 -0.033 -1000
Fc-epsilon receptor I signaling in mast cells 0.0577 61 5985 97 -0.14 0.035 1000 -1000 -0.056 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0567 60 2070 34 -0.023 0.06 1000 -1000 -0.024 -1000
Visual signal transduction: Cones 0.0548 58 2205 38 -0.025 0.16 1000 -1000 -0.01 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0548 58 3051 52 -0.11 0.069 1000 -1000 -0.028 -1000
PDGFR-alpha signaling pathway 0.0539 57 2533 44 -0.3 0.036 1000 -1000 -0.034 -1000
Canonical Wnt signaling pathway 0.0529 56 2887 51 -0.28 0.12 1000 -1000 -0.03 -1000
TCGA08_rtk_signaling 0.0529 56 1479 26 -0.19 0.037 1000 -1000 -0.006 -1000
E-cadherin signaling in keratinocytes 0.0520 55 2401 43 -0.19 0.033 1000 -1000 -0.027 -1000
Presenilin action in Notch and Wnt signaling 0.0501 53 3250 61 -0.28 0.12 1000 -1000 -0.032 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0501 53 1751 33 -0.38 0.06 1000 -1000 -0.026 -1000
Nectin adhesion pathway 0.0491 52 3338 63 -0.056 0.046 1000 -1000 -0.038 -1000
IL12-mediated signaling events 0.0482 51 4443 87 -0.31 0.073 1000 -1000 -0.056 -1000
Syndecan-2-mediated signaling events 0.0482 51 3584 69 -0.11 0.12 1000 -1000 -0.025 -1000
FAS signaling pathway (CD95) 0.0463 49 2318 47 -0.43 0.04 1000 -1000 -0.028 -1000
Rapid glucocorticoid signaling 0.0463 49 998 20 -0.11 0.027 1000 -1000 0 -1000
Syndecan-3-mediated signaling events 0.0454 48 1688 35 -0.23 0.055 1000 -1000 -0.019 -1000
Glypican 2 network 0.0444 47 191 4 0.033 0.057 1000 -1000 0.018 -1000
Signaling events mediated by HDAC Class III 0.0425 45 1832 40 -0.33 0.045 1000 -1000 -0.024 -1000
LPA4-mediated signaling events 0.0416 44 529 12 -0.12 0.006 1000 -1000 -0.019 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0416 44 3329 74 -0.19 0.049 1000 -1000 -0.062 -1000
Regulation of Androgen receptor activity 0.0406 43 3013 70 -0.16 0.11 1000 -1000 -0.038 -1000
Coregulation of Androgen receptor activity 0.0388 41 3121 76 -0.15 0.065 1000 -1000 -0.012 -1000
Aurora A signaling 0.0388 41 2512 60 -0.079 0.18 1000 -1000 -0.021 -1000
Syndecan-4-mediated signaling events 0.0388 41 2810 67 -0.2 0.12 1000 -1000 -0.031 -1000
Ras signaling in the CD4+ TCR pathway 0.0388 41 698 17 -0.054 0.026 1000 -1000 -0.02 -1000
Insulin Pathway 0.0369 39 2956 74 -0.12 0.061 1000 -1000 -0.038 -1000
Thromboxane A2 receptor signaling 0.0350 37 3913 105 -0.19 0.036 1000 -1000 -0.037 -1000
Regulation of p38-alpha and p38-beta 0.0350 37 2034 54 -0.24 0.053 1000 -1000 -0.043 -1000
TCGA08_retinoblastoma 0.0350 37 296 8 -0.017 0.061 1000 -1000 -0.002 -1000
IL27-mediated signaling events 0.0340 36 1859 51 -0.18 0.075 1000 -1000 -0.037 -1000
Regulation of Telomerase 0.0331 35 3667 102 -0.2 0.14 1000 -1000 -0.046 -1000
Osteopontin-mediated events 0.0321 34 1299 38 -0.14 0.088 1000 -1000 -0.027 -1000
BCR signaling pathway 0.0321 34 3379 99 -0.077 0.055 1000 -1000 -0.048 -1000
IL2 signaling events mediated by STAT5 0.0312 33 740 22 0.006 0.11 1000 -1000 -0.031 -1000
Regulation of nuclear SMAD2/3 signaling 0.0302 32 4412 136 -0.2 0.081 1000 -1000 -0.035 -1000
TCGA08_p53 0.0274 29 204 7 -0.011 0.02 1000 -1000 -0.007 -1000
Arf6 trafficking events 0.0246 26 1900 71 -0.27 0.042 1000 -1000 -0.02 -1000
Signaling mediated by p38-gamma and p38-delta 0.0236 25 388 15 -0.027 0.024 1000 -1000 -0.026 -1000
Ceramide signaling pathway 0.0227 24 1879 76 -0.1 0.063 1000 -1000 -0.027 -1000
Signaling events mediated by PRL 0.0227 24 840 34 -0.12 0.035 1000 -1000 -0.041 -1000
Caspase cascade in apoptosis 0.0217 23 1748 74 -0.027 0.057 1000 -1000 -0.035 -1000
S1P5 pathway 0.0208 22 380 17 -0.005 0.033 1000 -1000 -0.008 -1000
Cellular roles of Anthrax toxin 0.0189 20 782 39 -0.08 0.028 1000 -1000 -0.018 -1000
mTOR signaling pathway 0.0189 20 1081 53 -0.024 0.028 1000 -1000 -0.032 -1000
Class I PI3K signaling events mediated by Akt 0.0189 20 1412 68 -0.16 0.044 1000 -1000 -0.031 -1000
HIF-2-alpha transcription factor network 0.0189 20 871 43 -0.15 0.16 1000 -1000 -0.032 -1000
IL2 signaling events mediated by PI3K 0.0189 20 1210 58 -0.001 0.065 1000 -1000 -0.026 -1000
BARD1 signaling events 0.0180 19 1098 57 -0.047 0.1 1000 -1000 -0.026 -1000
FoxO family signaling 0.0170 18 1194 64 -0.016 0.23 1000 -1000 -0.025 -1000
S1P4 pathway 0.0170 18 466 25 -0.011 0.044 1000 -1000 -0.023 -1000
JNK signaling in the CD4+ TCR pathway 0.0161 17 303 17 0.003 0.063 1000 -1000 -0.027 -1000
Hedgehog signaling events mediated by Gli proteins 0.0151 16 1087 65 -0.087 0.056 1000 -1000 -0.045 -1000
ceramide signaling pathway 0.0151 16 827 49 -0.002 0.037 1000 -1000 -0.031 -1000
Retinoic acid receptors-mediated signaling 0.0151 16 929 58 -0.051 0.052 1000 -1000 -0.037 -1000
E-cadherin signaling in the nascent adherens junction 0.0151 16 1223 76 -0.023 0.053 1000 -1000 -0.048 -1000
S1P3 pathway 0.0142 15 638 42 -0.013 0.042 1000 -1000 -0.032 -1000
PLK2 and PLK4 events 0.0132 14 43 3 0.016 0.033 1000 -1000 -0.005 -1000
IL1-mediated signaling events 0.0123 13 853 62 -0.009 0.063 1000 -1000 -0.031 -1000
PDGFR-beta signaling pathway 0.0123 13 1325 97 -0.027 0.056 1000 -1000 -0.05 -1000
p38 MAPK signaling pathway 0.0123 13 583 44 -0.02 0.067 1000 -1000 -0.022 -1000
Class I PI3K signaling events 0.0113 12 900 73 -0.018 0.05 1000 -1000 -0.031 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0104 11 333 28 -0.005 0.051 1000 -1000 -0.014 -1000
EPO signaling pathway 0.0104 11 607 55 0.014 0.08 1000 -1000 -0.027 -1000
Insulin-mediated glucose transport 0.0104 11 367 32 -0.12 0.039 1000 -1000 -0.017 -1000
TRAIL signaling pathway 0.0104 11 574 48 -0.016 0.043 1000 -1000 -0.028 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0104 11 950 83 -0.018 0.047 1000 -1000 -0.027 -1000
E-cadherin signaling events 0.0104 11 57 5 0.011 0.033 1000 -1000 0.012 -1000
Canonical NF-kappaB pathway 0.0095 10 425 39 0 0.051 1000 -1000 -0.022 -1000
IFN-gamma pathway 0.0095 10 731 68 -0.007 0.076 1000 -1000 -0.049 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0095 10 391 37 -0.009 0.067 1000 -1000 -0.02 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0095 10 494 45 0.003 0.055 1000 -1000 -0.045 -1000
Signaling events mediated by HDAC Class II 0.0085 9 698 75 -0.036 0.063 1000 -1000 -0.03 -1000
a4b1 and a4b7 Integrin signaling 0.0085 9 46 5 0.024 0.041 1000 -1000 0.013 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0076 8 1099 125 -0.098 0.054 1000 -1000 -0.036 -1000
VEGFR1 specific signals 0.0066 7 440 56 -0.098 0.056 1000 -1000 -0.039 -1000
Signaling events mediated by HDAC Class I 0.0057 6 640 104 -0.059 0.058 1000 -1000 -0.031 -1000
Arf6 downstream pathway 0.0047 5 222 43 -0.054 0.055 1000 -1000 -0.018 -1000
Atypical NF-kappaB pathway 0.0047 5 164 31 0 0.03 1000 -1000 -0.007 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0038 4 108 23 -0.003 0.043 1000 -1000 -0.027 -1000
Circadian rhythm pathway 0.0038 4 105 22 -0.007 0.049 1000 -1000 -0.02 -1000
Paxillin-dependent events mediated by a4b1 0.0038 4 158 36 -0.048 0.052 1000 -1000 -0.025 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0009 1 32 27 -0.008 0.057 1000 -1000 -0.033 -1000
Arf1 pathway 0.0009 1 89 54 -0.001 0.045 1000 -1000 -0.014 -1000
Alternative NF-kappaB pathway 0.0000 0 11 13 0 0.068 1000 -1000 0 -1000
Total NA 8216 486786 7203 -20 -990 131000 -131000 -3.9 -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 0.59 0.39 0.99 381 -1 3 384
PLK1 0.36 0.24 0.61 398 -0.68 2 400
BIRC5 0.38 0.25 0.62 378 -0.79 4 382
HSPA1B 0.59 0.39 0.98 397 -1 3 400
MAP2K1 0.16 0.12 0.3 354 -10000 0 354
BRCA2 0.6 0.4 1 398 -0.98 4 402
FOXM1 0.69 0.49 1.1 448 -1.2 3 451
XRCC1 0.59 0.39 0.98 392 -1 3 395
FOXM1B/p19 0.12 0.27 0.8 64 -0.98 5 69
Cyclin D1/CDK4 0.52 0.37 0.89 386 -0.98 3 389
CDC2 0.64 0.44 1 445 -1.1 3 448
TGFA 0.52 0.39 0.89 401 -0.95 8 409
SKP2 0.6 0.39 0.99 393 -1 3 396
CCNE1 0.091 0.095 0.3 172 -10000 0 172
CKS1B 0.63 0.42 1 441 -0.98 3 444
RB1 0.29 0.3 0.66 337 -0.66 7 344
FOXM1C/SP1 0.54 0.36 0.89 380 -1.1 5 385
AURKB 0.3 0.3 0.62 316 -0.78 21 337
CENPF 0.68 0.46 1.1 477 -0.98 3 480
CDK4 0.082 0.054 0.21 52 -10000 0 52
MYC 0.35 0.37 0.83 274 -0.96 6 280
CHEK2 0.16 0.12 0.28 408 -10000 0 408
ONECUT1 0.54 0.39 0.93 399 -1.1 3 402
CDKN2A -0.057 0.12 0.21 29 -0.22 232 261
LAMA4 0.59 0.4 0.98 402 -1.1 6 408
FOXM1B/HNF6 0.55 0.4 0.96 365 -1.3 3 368
FOS 0.29 0.64 1 305 -0.98 71 376
SP1 0.024 0.021 -10000 0 -0.2 4 4
CDC25B 0.6 0.39 0.98 406 -1 3 409
response to radiation 0.11 0.085 0.22 349 -10000 0 349
CENPB 0.59 0.39 1 373 -1 3 376
CENPA 0.65 0.43 1.1 448 -1 3 451
NEK2 0.71 0.45 1.1 505 -0.96 3 508
HIST1H2BA 0.59 0.39 0.98 393 -1 3 396
CCNA2 0.14 0.13 0.3 391 -10000 0 391
EP300 0.023 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.62 0.42 1.1 380 -1.2 3 383
CCNB2 0.65 0.43 1.1 463 -1 3 466
CCNB1 0.65 0.45 1.1 420 -1.1 3 423
ETV5 0.6 0.4 1 368 -1 3 371
ESR1 0.45 0.55 1 360 -0.98 19 379
CCND1 0.54 0.41 0.96 395 -1 3 398
GSK3A 0.14 0.089 0.26 282 -10000 0 282
Cyclin A-E1/CDK1-2 0.23 0.16 0.4 424 -10000 0 424
CDK2 0.057 0.028 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.14 0.11 0.25 462 -10000 0 462
FOXM1B/Cbp/p300 0.25 0.3 0.73 73 -1.1 3 76
GAS1 0.54 0.48 0.98 381 -1.1 34 415
MMP2 0.58 0.41 0.98 399 -1.2 10 409
RB1/FOXM1C 0.47 0.39 0.88 381 -1 3 384
CREBBP 0.023 0.007 -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 0.34 3 -0.38 449 452
CRKL -0.18 0.21 0.26 1 -0.4 468 469
HRAS -0.13 0.18 -10000 0 -0.35 324 324
mol:PIP3 -0.14 0.2 0.27 3 -0.37 368 371
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 -0.42 476 476
FOXO3 -0.14 0.2 0.53 1 -0.37 327 328
AKT1 -0.16 0.21 0.37 1 -0.39 416 417
BAD -0.15 0.2 0.35 1 -0.37 330 331
megakaryocyte differentiation -0.18 0.22 -10000 0 -0.41 480 480
GSK3B -0.15 0.2 0.53 1 -0.38 327 328
RAF1 -0.098 0.16 0.25 6 -0.3 304 310
SHC1 0.02 0.009 -10000 0 -10000 0 0
STAT3 -0.18 0.22 -10000 0 -0.42 473 473
STAT1 -0.44 0.52 -10000 0 -0.99 486 486
HRAS/SPRED1 -0.095 0.16 -10000 0 -0.3 299 299
cell proliferation -0.18 0.22 -10000 0 -0.41 481 481
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
TEC 0.022 0.032 -10000 0 -0.57 3 3
RPS6KB1 -0.17 0.22 -10000 0 -0.4 482 482
HRAS/SPRED2 -0.095 0.16 -10000 0 -0.3 304 304
LYN/TEC/p62DOK -0.15 0.22 -10000 0 -0.4 404 404
MAPK3 -0.067 0.12 0.26 13 -0.26 56 69
STAP1 -0.18 0.22 -10000 0 -0.42 479 479
GRAP2 0.017 0.067 0.26 3 -0.57 13 16
JAK2 -0.37 0.45 -10000 0 -0.84 484 484
STAT1 (dimer) -0.43 0.51 -10000 0 -0.97 486 486
mol:Gleevec 0.007 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.15 0.22 -10000 0 -0.4 407 407
actin filament polymerization -0.18 0.22 0.33 1 -0.41 476 477
LYN 0.021 0.009 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 484 484
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
CBL/CRKL/GRB2 -0.14 0.2 -10000 0 -0.37 420 420
PI3K -0.15 0.22 -10000 0 -0.39 451 451
PTEN 0.023 0.019 -10000 0 -0.57 1 1
SCF/KIT/EPO/EPOR -0.51 0.63 -10000 0 -1.2 478 478
MAPK8 -0.19 0.22 -10000 0 -0.42 481 481
STAT3 (dimer) -0.18 0.22 0.27 1 -0.41 473 474
positive regulation of transcription -0.053 0.11 0.23 15 -0.22 45 60
mol:GDP -0.13 0.19 -10000 0 -0.37 326 326
PIK3C2B -0.17 0.2 -10000 0 -0.42 375 375
CBL/CRKL -0.16 0.2 -10000 0 -0.38 458 458
FER -0.19 0.22 -10000 0 -0.42 478 478
SH2B3 -0.18 0.22 -10000 0 -0.42 478 478
PDPK1 -0.12 0.19 0.34 9 -0.35 330 339
SNAI2 -0.18 0.21 0.28 4 -0.42 430 434
positive regulation of cell proliferation -0.32 0.39 -10000 0 -0.73 487 487
KITLG -0.004 0.059 0.25 10 -0.59 5 15
cell motility -0.32 0.39 -10000 0 -0.73 487 487
PTPN6 0.033 0.017 0.27 2 -10000 0 2
EPOR -0.12 0.2 -10000 0 -1 16 16
STAT5A (dimer) -0.27 0.32 -10000 0 -0.6 483 483
SOCS1 0.025 0.033 0.26 13 -0.57 1 14
cell migration 0.18 0.22 0.41 481 -10000 0 481
SOS1 0.024 0.003 -10000 0 -10000 0 0
EPO 0.041 0.092 0.25 165 -10000 0 165
VAV1 0.023 0.034 0.26 2 -0.57 3 5
GRB10 -0.18 0.22 -10000 0 -0.42 474 474
PTPN11 0.031 0.01 -10000 0 -10000 0 0
SCF/KIT -0.19 0.23 -10000 0 -0.44 482 482
GO:0007205 0.009 0.012 -10000 0 -10000 0 0
MAP2K1 -0.077 0.13 0.26 14 -0.27 74 88
CBL 0.022 0.008 -10000 0 -10000 0 0
KIT -0.57 0.66 -10000 0 -1.3 480 480
MAP2K2 -0.076 0.13 0.28 12 -0.27 66 78
SHC/Grb2/SOS1 -0.14 0.21 -10000 0 -0.4 349 349
STAT5A -0.27 0.33 -10000 0 -0.62 483 483
GRB2 0.023 0.01 0.26 1 -10000 0 1
response to radiation -0.17 0.21 0.28 4 -0.41 431 435
SHC/GRAP2 0.024 0.049 -10000 0 -0.3 18 18
PTPRO -0.18 0.22 -10000 0 -0.42 477 477
SH2B2 -0.18 0.22 -10000 0 -0.42 476 476
DOK1 0.025 0.015 0.26 4 -10000 0 4
MATK -0.19 0.22 -10000 0 -0.42 481 481
CREBBP -0.028 0.072 -10000 0 -10000 0 0
BCL2 -0.16 0.32 -10000 0 -1.2 66 66
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.13 0.26 0.57 272 -10000 0 272
PI3K Class IB/PDE3B -0.13 0.26 -10000 0 -0.57 272 272
PDE3B -0.13 0.26 -10000 0 -0.57 272 272
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.32 0.5 0.43 4 -1 344 348
MKNK1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.087 0.18 -10000 0 -0.34 342 342
ATF2/c-Jun -0.082 0.16 -10000 0 -0.42 96 96
MAPK11 -0.082 0.18 -10000 0 -0.35 312 312
MITF -0.12 0.22 0.28 1 -0.41 339 340
MAPKAPK5 -0.11 0.21 -10000 0 -0.4 345 345
KRT8 -0.11 0.21 -10000 0 -0.4 325 325
MAPKAPK3 0.024 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.02 0.009 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.14 0.29 -10000 0 -0.52 343 343
CEBPB -0.1 0.2 0.28 1 -0.4 320 321
SLC9A1 -0.11 0.21 -10000 0 -0.41 339 339
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.11 0.2 -10000 0 -0.39 334 334
p38alpha-beta/MNK1 -0.1 0.25 -10000 0 -0.45 313 313
JUN -0.081 0.16 -10000 0 -0.41 96 96
PPARGC1A -0.2 0.33 0.26 1 -0.56 406 407
USF1 -0.1 0.19 0.32 3 -0.38 322 325
RAB5/GDP/GDI1 -0.081 0.16 -10000 0 -0.3 328 328
NOS2 -0.11 0.22 -10000 0 -0.56 90 90
DDIT3 -0.11 0.2 -10000 0 -0.4 340 340
RAB5A 0.024 0.003 -10000 0 -10000 0 0
HSPB1 -0.094 0.17 0.28 3 -0.33 311 314
p38alpha-beta/HBP1 -0.11 0.25 -10000 0 -0.45 313 313
CREB1 -0.12 0.22 -10000 0 -0.43 345 345
RAB5/GDP 0.018 0.002 -10000 0 -10000 0 0
EIF4E -0.11 0.21 -10000 0 -0.4 311 311
RPS6KA4 -0.11 0.21 -10000 0 -0.4 339 339
PLA2G4A -0.13 0.22 -10000 0 -0.43 340 340
GDI1 -0.11 0.21 -10000 0 -0.4 343 343
TP53 -0.15 0.27 0.28 1 -0.52 323 324
RPS6KA5 -0.12 0.22 -10000 0 -0.41 348 348
ESR1 -0.15 0.24 0.28 1 -0.42 394 395
HBP1 0.024 0.004 -10000 0 -10000 0 0
MEF2C -0.11 0.21 -10000 0 -0.4 344 344
MEF2A -0.11 0.21 0.28 1 -0.4 340 341
EIF4EBP1 -0.12 0.22 0.28 1 -0.44 327 328
KRT19 -0.11 0.21 0.32 1 -0.4 321 322
ELK4 -0.1 0.19 0.3 3 -0.38 325 328
ATF6 -0.1 0.19 0.32 3 -0.38 326 329
ATF1 -0.12 0.22 -10000 0 -0.43 347 347
p38alpha-beta/MAPKAPK2 -0.095 0.22 -10000 0 -0.41 298 298
p38alpha-beta/MAPKAPK3 -0.1 0.25 -10000 0 -0.44 334 334
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 0.093 -10000 0 -0.57 26 26
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 -0.57 2 2
ITGA3 0.022 0.021 0.26 1 -0.57 1 2
RELN/VLDLR/Fyn -0.2 0.21 -10000 0 -0.37 584 584
MAPK8IP1/MKK7/MAP3K11/JNK1 0.054 0.045 -10000 0 -0.32 7 7
AKT1 -0.14 0.14 -10000 0 -0.27 529 529
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
DAB1 0.035 0.055 0.26 59 -10000 0 59
RELN/LRP8/DAB1 -0.16 0.19 0.32 4 -0.32 589 593
LRPAP1/LRP8 0.049 0.048 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.14 0.18 0.32 4 -0.31 573 577
DAB1/alpha3/beta1 Integrin -0.14 0.18 -10000 0 -0.3 517 517
long-term memory -0.18 0.22 0.33 5 -0.36 561 566
DAB1/LIS1 -0.14 0.19 0.3 4 -0.3 586 590
DAB1/CRLK/C3G -0.15 0.18 -10000 0 -0.3 564 564
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DAB1/NCK2 -0.14 0.19 0.3 4 -0.31 584 588
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 -0.032 0.18 0.26 12 -0.57 101 113
CDK5R1 0.028 0.035 0.26 23 -10000 0 23
RELN -0.32 0.29 0.26 2 -0.57 600 602
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
RELN/LRP8/Fyn -0.18 0.2 -10000 0 -0.36 577 577
GRIN2A/RELN/LRP8/DAB1/Fyn -0.16 0.22 0.33 4 -0.35 539 543
MAPK8 0.02 0.049 -10000 0 -0.57 7 7
RELN/VLDLR/DAB1 -0.18 0.19 0.32 2 -0.34 588 590
ITGB1 0.024 0.004 -10000 0 -10000 0 0
MAP1B -0.18 0.18 0.22 2 -0.33 589 591
RELN/LRP8 -0.18 0.2 -10000 0 -0.36 593 593
GRIN2B/RELN/LRP8/DAB1/Fyn -0.16 0.2 0.36 3 -0.33 595 598
PI3K 0.03 0.042 -10000 0 -0.4 9 9
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.032 0.021 -10000 0 -0.26 3 3
RAP1A -0.16 0.15 0.34 3 -0.33 115 118
PAFAH1B1 0.023 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.03 0.26 4 -0.57 2 6
CRLK/C3G 0.034 0.01 -10000 0 -10000 0 0
GRIN2B -0.02 0.15 0.26 1 -0.57 70 71
NCK2 0.024 0.003 -10000 0 -10000 0 0
neuron differentiation -0.087 0.12 -10000 0 -0.34 80 80
neuron adhesion -0.14 0.15 0.32 4 -0.48 22 26
LRP8 0.047 0.07 0.26 103 -10000 0 103
GSK3B -0.14 0.14 -10000 0 -0.3 175 175
RELN/VLDLR/DAB1/Fyn -0.16 0.19 0.32 2 -0.32 574 576
MAP3K11 0.024 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.15 0.16 -10000 0 -0.28 571 571
CDK5 0.025 0.015 0.26 4 -10000 0 4
MAPT -0.024 0.2 0.87 19 -0.52 104 123
neuron migration -0.18 0.18 0.27 2 -0.34 486 488
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.087 0.12 -10000 0 -0.35 79 79
RELN/VLDLR -0.17 0.2 -10000 0 -0.34 592 592
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.1 0.1 0.23 305 -0.26 2 307
STMN1 0.079 0.079 0.26 68 -10000 0 68
Aurora B/RasGAP/Survivin 0.19 0.14 0.33 490 -10000 0 490
Chromosomal passenger complex/Cul3 protein complex 0.005 0.14 0.21 88 -0.28 61 149
BIRC5 0.18 0.11 0.26 690 -10000 0 690
DES -0.16 0.32 -10000 0 -0.58 266 266
Aurora C/Aurora B/INCENP 0.11 0.079 0.32 9 -0.3 1 10
Aurora B/TACC1 0.072 0.1 0.19 1 -0.34 25 26
Aurora B/PP2A 0.11 0.083 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.032 0.027 0.14 8 -10000 0 8
mitotic metaphase/anaphase transition -0.006 0.005 -10000 0 -10000 0 0
NDC80 0.14 0.12 0.26 472 -10000 0 472
Cul3 protein complex -0.12 0.2 -10000 0 -0.36 407 407
KIF2C 0.15 0.1 0.24 568 -10000 0 568
PEBP1 0.027 0.004 -10000 0 -10000 0 0
KIF20A 0.19 0.1 0.25 766 -10000 0 766
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.11 0.082 -10000 0 -10000 0 0
SEPT1 0.031 0.042 0.26 34 -10000 0 34
SMC2 0.024 0.003 -10000 0 -10000 0 0
SMC4 0.026 0.023 0.26 10 -10000 0 10
NSUN2/NPM1/Nucleolin 0.074 0.19 0.31 33 -0.45 98 131
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 0.071 0.061 0.23 34 -10000 0 34
AURKB 0.14 0.12 0.26 544 -10000 0 544
AURKC 0.026 0.033 0.26 14 -0.57 1 15
CDCA8 0.11 0.11 0.27 340 -10000 0 340
cytokinesis 0.14 0.14 0.31 366 -0.33 7 373
Aurora B/Septin1 0.18 0.17 0.36 370 -0.32 5 375
AURKA 0.11 0.11 0.25 416 -10000 0 416
INCENP 0.03 0.008 -10000 0 -10000 0 0
KLHL13 -0.21 0.29 -10000 0 -0.57 415 415
BUB1 0.18 0.11 0.25 696 -10000 0 696
hSgo1/Aurora B/Survivin 0.27 0.18 0.41 614 -10000 0 614
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.18 0.14 0.35 336 -10000 0 336
SGOL1 0.17 0.11 0.26 643 -10000 0 643
CENPA 0.17 0.14 0.3 489 -0.28 1 490
NCAPG 0.13 0.12 0.26 486 -10000 0 486
Aurora B/HC8 Proteasome 0.11 0.082 0.2 150 -10000 0 150
NCAPD2 0.024 0.009 0.26 1 -10000 0 1
Aurora B/PP1-gamma 0.12 0.082 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
NCAPH 0.11 0.11 0.26 399 -10000 0 399
NPM1 0.067 0.13 0.25 6 -0.36 40 46
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 0.082 0.2 150 -10000 0 150
PPP1CC 0.024 0.002 -10000 0 -10000 0 0
Centraspindlin 0.2 0.15 0.37 406 -10000 0 406
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
NSUN2 0.073 0.12 0.26 25 -0.31 33 58
MYLK 0.021 0.14 0.23 8 -0.32 122 130
KIF23 0.1 0.11 0.27 320 -10000 0 320
VIM 0.079 0.084 0.37 30 -0.41 2 32
RACGAP1 0.041 0.048 0.27 42 -10000 0 42
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.062 0.14 -10000 0 -0.43 42 42
Chromosomal passenger complex 0.17 0.12 0.28 549 -10000 0 549
Chromosomal passenger complex/EVI5 0.24 0.17 0.4 489 -10000 0 489
TACC1 0.006 0.091 -10000 0 -0.57 25 25
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
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.026 0.021 0.26 8 -10000 0 8
EGFR -0.19 0.28 -10000 0 -0.57 375 375
EGF/EGFR -0.16 0.22 -10000 0 -0.37 498 498
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.12 0.2 -10000 0 -0.35 380 380
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.024 0.02 0.26 1 -0.57 1 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.082 0.23 0.26 2 -0.57 186 188
EGF/EGFR dimer/SHC -0.15 0.22 -10000 0 -0.4 406 406
mol:GDP -0.12 0.19 -10000 0 -0.35 380 380
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.018 0.15 0.26 1 -0.57 74 75
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.18 -10000 0 -0.33 379 379
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP -0.11 0.19 -10000 0 -0.33 379 379
FRAP1 -0.14 0.16 0.16 3 -0.34 380 383
EGF/EGFR dimer -0.21 0.26 -10000 0 -0.46 506 506
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 -10000 0 -0.42 77 77
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 0.52 1 -0.75 109 110
PCK1 -0.92 0.63 -10000 0 -1.4 637 637
HNF4A -0.23 0.28 0.66 2 -0.83 58 60
KCNJ11 -0.28 0.3 -10000 0 -0.8 133 133
AKT1 -0.17 0.16 0.37 1 -0.46 38 39
response to starvation 0.005 0.012 -10000 0 -10000 0 0
DLK1 -0.45 0.48 -10000 0 -1.1 346 346
NKX2-1 -0.035 0.16 0.54 1 -10000 0 1
ACADM -0.25 0.27 0.52 1 -0.77 97 98
TAT -1.1 0.63 0.44 1 -1.4 751 752
CEBPB 0.024 0.01 -10000 0 -10000 0 0
CEBPA 0.021 0.056 -10000 0 -0.57 9 9
TTR -0.41 0.29 0.53 2 -0.75 302 304
PKLR -0.22 0.27 0.57 6 -0.76 86 92
APOA1 -0.28 0.32 0.79 1 -0.88 84 85
CPT1C -0.25 0.27 0.55 2 -0.75 110 112
ALAS1 -0.15 0.16 -10000 0 -0.74 7 7
TFRC -0.42 0.26 -10000 0 -0.73 288 288
FOXF1 0.017 0.046 0.26 6 -0.57 4 10
NF1 0.026 0.007 -10000 0 -10000 0 0
HNF1A (dimer) 0.034 0.031 0.26 7 -10000 0 7
CPT1A -0.23 0.27 0.59 2 -0.75 103 105
HMGCS1 -0.25 0.27 0.62 2 -0.76 103 105
NR3C1 -0.12 0.12 0.21 1 -0.24 347 348
CPT1B -0.25 0.27 0.52 1 -0.77 102 103
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.023 -10000 0 -10000 0 0
GCK -0.27 0.32 0.52 1 -0.9 134 135
CREB1 -0.076 0.093 -10000 0 -0.22 135 135
IGFBP1 -0.41 0.54 0.41 1 -1.4 237 238
PDX1 -0.12 0.15 0.49 1 -0.53 7 8
UCP2 -0.24 0.27 0.53 2 -0.77 87 89
ALDOB -0.28 0.29 0.68 1 -0.8 118 119
AFP -0.58 0.51 0.35 1 -0.86 658 659
BDH1 -0.25 0.27 0.52 1 -0.77 90 91
HADH -0.28 0.28 -10000 0 -0.8 109 109
F2 -0.28 0.31 0.79 1 -0.89 75 76
HNF1A 0.034 0.031 0.26 7 -10000 0 7
G6PC -0.18 0.12 -10000 0 -0.55 10 10
SLC2A2 -0.16 0.17 0.62 1 -0.94 1 2
INS 0.018 0.077 0.22 28 -10000 0 28
FOXA1 -0.22 0.23 0.34 4 -0.41 487 491
FOXA3 -0.36 0.21 0.28 15 -0.46 800 815
FOXA2 -0.32 0.33 0.77 1 -0.83 175 176
ABCC8 -0.32 0.39 0.56 1 -1 165 166
ALB -0.77 0.54 0.34 2 -1.1 709 711
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.24 0.37 0.65 1 -0.78 213 214
HDAC7 0.025 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.18 0.34 0.64 3 -0.77 135 138
SMAD4 0.024 0.006 -10000 0 -10000 0 0
ID2 -0.24 0.37 -10000 0 -0.79 210 210
AP1 -0.1 0.21 -10000 0 -0.43 294 294
ABCG2 -0.26 0.39 -10000 0 -0.8 239 239
HIF1A -0.046 0.085 -10000 0 -0.24 17 17
TFF3 -0.25 0.41 0.67 5 -0.8 247 252
GATA2 0.009 0.098 0.25 14 -0.57 26 40
AKT1 -0.054 0.095 -10000 0 -0.27 23 23
response to hypoxia -0.061 0.085 -10000 0 -0.21 109 109
MCL1 -0.23 0.36 -10000 0 -0.78 199 199
NDRG1 -0.22 0.36 -10000 0 -0.78 187 187
SERPINE1 -0.23 0.38 0.66 5 -0.78 213 218
FECH -0.24 0.37 -10000 0 -0.78 211 211
FURIN -0.24 0.37 -10000 0 -0.78 210 210
NCOA2 0 0.12 -10000 0 -0.57 43 43
EP300 -0.059 0.13 0.31 1 -0.33 110 111
HMOX1 -0.24 0.37 0.65 1 -0.78 212 213
BHLHE40 -0.24 0.37 -10000 0 -0.79 211 211
BHLHE41 -0.24 0.38 -10000 0 -0.8 213 213
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.018 0.11 -10000 0 -0.31 1 1
ENG -0.016 0.11 0.38 3 -10000 0 3
JUN 0.018 0.047 -10000 0 -0.57 6 6
RORA -0.24 0.37 -10000 0 -0.79 212 212
ABCB1 -0.26 0.45 -10000 0 -1.1 212 212
TFRC -0.24 0.37 -10000 0 -0.78 211 211
CXCR4 -0.24 0.38 -10000 0 -0.78 213 213
TF -0.4 0.46 -10000 0 -0.86 407 407
CITED2 -0.24 0.37 -10000 0 -0.78 212 212
HIF1A/ARNT -0.26 0.42 0.76 3 -0.94 167 170
LDHA -0.038 0.12 -10000 0 -0.73 23 23
ETS1 -0.24 0.37 -10000 0 -0.78 214 214
PGK1 -0.24 0.37 -10000 0 -0.79 210 210
NOS2 -0.24 0.37 -10000 0 -0.79 205 205
ITGB2 -0.24 0.37 0.65 2 -0.79 209 211
ALDOA -0.23 0.37 -10000 0 -0.79 204 204
Cbp/p300/CITED2 -0.24 0.39 -10000 0 -0.87 179 179
FOS -0.14 0.27 -10000 0 -0.57 290 290
HK2 -0.24 0.37 -10000 0 -0.79 212 212
SP1 0.001 0.058 -10000 0 -0.2 4 4
GCK -0.12 0.34 0.52 1 -1.3 60 61
HK1 -0.24 0.37 -10000 0 -0.78 211 211
NPM1 -0.24 0.37 -10000 0 -0.78 214 214
EGLN1 -0.23 0.36 -10000 0 -0.78 201 201
CREB1 0.028 0.004 -10000 0 -10000 0 0
PGM1 -0.24 0.37 -10000 0 -0.78 213 213
SMAD3 0.024 0.004 -10000 0 -10000 0 0
EDN1 -0.18 0.37 -10000 0 -1 138 138
IGFBP1 -0.3 0.42 -10000 0 -0.86 275 275
VEGFA -0.16 0.3 -10000 0 -0.69 115 115
HIF1A/JAB1 -0.008 0.068 -10000 0 -0.27 1 1
CP -0.3 0.45 0.65 4 -0.88 293 297
CXCL12 -0.26 0.4 -10000 0 -0.82 231 231
COPS5 0.024 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.012 -10000 0 -10000 0 0
BNIP3 -0.24 0.37 0.73 1 -0.79 211 212
EGLN3 -0.23 0.38 0.73 1 -0.78 213 214
CA9 -0.2 0.4 0.66 8 -0.78 205 213
TERT -0.22 0.38 0.66 4 -0.78 205 209
ENO1 -0.24 0.37 -10000 0 -0.78 212 212
PFKL -0.24 0.37 -10000 0 -0.78 212 212
NCOA1 0.025 0.019 -10000 0 -0.57 1 1
ADM -0.26 0.4 0.65 1 -0.83 233 234
ARNT -0.033 0.072 -10000 0 -10000 0 0
HNF4A 0.019 0.04 0.26 15 -10000 0 15
ADFP -0.25 0.36 -10000 0 -0.78 218 218
SLC2A1 -0.16 0.3 0.62 2 -0.68 117 119
LEP -0.47 0.42 -10000 0 -0.85 432 432
HIF1A/ARNT/Cbp/p300 -0.2 0.34 -10000 0 -0.77 155 155
EPO -0.1 0.27 0.64 4 -0.72 55 59
CREBBP -0.049 0.12 0.31 1 -0.35 70 71
HIF1A/ARNT/Cbp/p300/HDAC7 -0.18 0.34 0.68 1 -0.78 127 128
PFKFB3 -0.24 0.37 -10000 0 -0.8 205 205
NT5E -0.24 0.38 -10000 0 -0.8 211 211
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.003 0.11 -10000 0 -0.35 97 97
cell-cell adhesion 0.13 0.15 0.31 392 -10000 0 392
Ephrin B/EPHB2/RasGAP 0.032 0.11 -10000 0 -0.32 78 78
ITSN1 0.024 0.019 -10000 0 -0.57 1 1
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.033 0.013 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.12 0.19 -10000 0 -0.36 402 402
HRAS/GDP -0.12 0.18 -10000 0 -0.32 401 401
Ephrin B/EPHB1/GRB7 -0.1 0.21 -10000 0 -0.35 389 389
Endophilin/SYNJ1 -0.027 0.083 0.23 2 -0.3 76 78
KRAS 0.024 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.1 0.21 -10000 0 -0.36 400 400
endothelial cell migration 0.042 0.036 -10000 0 -0.31 7 7
GRB2 0.023 0.01 0.26 1 -10000 0 1
GRB7 0.019 0.033 -10000 0 -0.57 3 3
PAK1 -0.032 0.1 0.35 2 -0.33 83 85
HRAS 0.026 0.021 0.26 8 -10000 0 8
RRAS -0.027 0.084 0.23 2 -0.3 77 79
DNM1 0.02 0.049 0.26 1 -0.57 7 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.14 0.18 0.35 2 -0.34 419 421
lamellipodium assembly -0.13 0.15 -10000 0 -0.31 392 392
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.091 0.16 -10000 0 -0.32 309 309
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
EPHB2 0.028 0.033 0.26 20 -10000 0 20
EPHB3 0.026 0.021 0.26 8 -10000 0 8
EPHB1 -0.21 0.29 0.26 1 -0.57 402 403
EPHB4 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.12 0.17 -10000 0 -0.42 168 168
Ephrin B/EPHB2 0.022 0.1 -10000 0 -0.31 78 78
Ephrin B/EPHB3 0.021 0.098 -10000 0 -0.32 73 73
JNK cascade -0.12 0.15 0.36 8 -0.31 398 406
Ephrin B/EPHB1 -0.11 0.21 -10000 0 -0.35 419 419
RAP1/GDP -0.094 0.16 -10000 0 -0.39 148 148
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EFNB3 -0.023 0.16 -10000 0 -0.57 79 79
EFNB1 0.025 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.099 0.18 -10000 0 -0.33 401 401
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.1 0.19 -10000 0 -0.33 404 404
Rap1/GTP -0.11 0.17 -10000 0 -0.32 340 340
axon guidance -0.003 0.11 -10000 0 -0.35 97 97
MAPK3 -0.086 0.14 -10000 0 -0.38 110 110
MAPK1 -0.091 0.14 -10000 0 -0.39 110 110
Rac1/GDP -0.11 0.16 -10000 0 -0.4 161 161
actin cytoskeleton reorganization -0.11 0.13 -10000 0 -0.33 155 155
CDC42/GDP -0.11 0.16 -10000 0 -0.39 162 162
PI3K 0.046 0.038 -10000 0 -0.32 7 7
EFNA5 -0.029 0.17 0.26 1 -0.57 93 94
Ephrin B2/EPHB4 0.03 0.01 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.005 0.088 -10000 0 -0.27 81 81
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.11 0.16 -10000 0 -0.31 382 382
PTK2 0.14 0.27 0.67 199 -10000 0 199
MAP4K4 -0.12 0.15 0.36 8 -0.31 398 406
SRC 0.024 0.005 -10000 0 -10000 0 0
KALRN 0.013 0.082 -10000 0 -0.57 20 20
Intersectin/N-WASP 0.035 0.016 -10000 0 -0.42 1 1
neuron projection morphogenesis -0.11 0.14 0.28 8 -0.41 85 93
MAP2K1 -0.087 0.15 0.2 1 -0.3 295 296
WASL 0.024 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.09 0.19 -10000 0 -0.33 399 399
cell migration -0.1 0.18 0.29 5 -0.35 282 287
NRAS 0.024 0.004 -10000 0 -10000 0 0
SYNJ1 -0.027 0.084 -10000 0 -0.3 76 76
PXN 0.024 0.002 -10000 0 -10000 0 0
TF -0.18 0.17 0.22 2 -0.32 551 553
HRAS/GTP -0.1 0.19 -10000 0 -0.32 412 412
Ephrin B1/EPHB1-2 -0.099 0.18 -10000 0 -0.33 400 400
cell adhesion mediated by integrin 0.01 0.086 0.29 75 -0.21 18 93
RAC1 0.024 0.003 -10000 0 -10000 0 0
mol:GTP -0.11 0.2 -10000 0 -0.33 415 415
RAC1-CDC42/GTP -0.13 0.15 -10000 0 -0.31 372 372
RASA1 0.024 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.097 0.16 -10000 0 -0.39 153 153
ruffle organization -0.13 0.16 0.36 5 -0.49 68 73
NCK1 0.024 0.003 -10000 0 -10000 0 0
receptor internalization -0.03 0.087 -10000 0 -0.31 78 78
Ephrin B/EPHB2/KALRN 0.025 0.12 -10000 0 -0.34 90 90
ROCK1 0.017 0.031 0.21 5 -0.33 1 6
RAS family/GDP -0.11 0.12 -10000 0 -0.33 139 139
Rac1/GTP -0.12 0.17 -10000 0 -0.32 392 392
Ephrin B/EPHB1/Src/Paxillin -0.12 0.18 -10000 0 -0.33 405 405
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.064 0.048 0.12 1 -0.12 143 144
BUB1B 0.084 0.066 0.15 421 -10000 0 421
PLK1 0.049 0.038 0.11 149 -10000 0 149
PLK1S1 0.026 0.035 0.14 10 -0.17 18 28
KIF2A 0.041 0.039 0.24 8 -10000 0 8
regulation of mitotic centrosome separation 0.049 0.038 0.11 149 -10000 0 149
GOLGA2 0.024 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.23 0.14 0.33 668 -10000 0 668
WEE1 0.043 0.062 0.23 2 -0.27 26 28
cytokinesis 0.12 0.087 0.21 246 -0.37 2 248
PP2A-alpha B56 0.11 0.12 -10000 0 -0.44 26 26
AURKA 0.064 0.052 0.12 425 -0.14 4 429
PICH/PLK1 0.097 0.088 0.21 342 -10000 0 342
CENPE 0.061 0.054 0.16 83 -10000 0 83
RhoA/GTP 0.018 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.041 0.038 0.24 8 -10000 0 8
PPP2CA 0.024 0.004 -10000 0 -10000 0 0
FZR1 0.024 0.004 -10000 0 -10000 0 0
TPX2 0.079 0.054 0.12 599 -0.13 2 601
PAK1 0.022 0.019 0.26 6 -10000 0 6
SPC24 0.16 0.11 0.26 629 -10000 0 629
FBXW11 0.024 0.004 -10000 0 -10000 0 0
CLSPN 0.071 0.069 0.14 420 -0.19 21 441
GORASP1 0.024 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.015 53 -10000 0 53
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.023 0.019 0.054 141 -10000 0 141
G2 phase of mitotic cell cycle 0.001 0.003 0.014 14 -10000 0 14
STAG2 0.024 0.019 -10000 0 -0.57 1 1
GRASP65/GM130/RAB1/GTP 0.011 0.08 -10000 0 -0.5 24 24
spindle elongation 0.049 0.038 0.11 149 -10000 0 149
ODF2 0.026 0.004 -10000 0 -10000 0 0
BUB1 0.11 0.13 -10000 0 -0.47 33 33
TPT1 0.013 0.057 0.12 2 -0.17 74 76
CDC25C 0.11 0.069 0.16 472 -0.2 17 489
CDC25B 0.03 0.032 0.26 18 -10000 0 18
SGOL1 0.064 0.048 0.12 143 -0.12 1 144
RHOA 0.024 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.068 0.065 0.24 33 -10000 0 33
CDC14B -0.01 0.074 -10000 0 -0.43 32 32
CDC20 0.15 0.12 0.26 547 -10000 0 547
PLK1/PBIP1 0.038 0.046 0.14 137 -10000 0 137
mitosis -0.004 0.005 0.027 4 -10000 0 4
FBXO5 0.03 0.035 0.16 15 -10000 0 15
CDC2 0.003 0.004 0.011 194 -10000 0 194
NDC80 0.16 0.12 0.26 606 -10000 0 606
metaphase plate congression 0.028 0.054 0.14 2 -0.19 48 50
ERCC6L 0.088 0.084 0.24 165 -10000 0 165
NLP/gamma Tubulin 0.023 0.024 0.076 31 -0.087 10 41
microtubule cytoskeleton organization 0.013 0.057 0.12 2 -0.17 74 76
G2/M transition DNA damage checkpoint -0.001 0.002 0.011 24 -10000 0 24
PPP1R12A 0.025 0.004 -10000 0 -10000 0 0
interphase -0.001 0.002 0.011 24 -10000 0 24
PLK1/PRC1-2 0.2 0.12 0.28 672 -10000 0 672
GRASP65/GM130/RAB1/GTP/PLK1 0.07 0.03 -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 0.041 0.035 0.099 152 -10000 0 152
mitotic prometaphase 0.002 0.005 0.022 50 -10000 0 50
proteasomal ubiquitin-dependent protein catabolic process 0.052 0.051 0.19 2 -0.31 3 5
microtubule-based process 0.17 0.089 0.22 760 -10000 0 760
Golgi organization 0.049 0.038 0.11 149 -10000 0 149
Cohesin/SA2 0.054 0.031 0.16 3 -0.3 1 4
PPP1CB/MYPT1 0.037 0.007 -10000 0 -10000 0 0
KIF20A 0.2 0.1 0.26 766 -10000 0 766
APC/C/CDC20 0.14 0.099 0.23 543 -10000 0 543
PPP2R1A 0.024 0.004 -10000 0 -10000 0 0
chromosome segregation 0.031 0.047 0.14 137 -10000 0 137
PRC1 0.08 0.1 0.26 251 -10000 0 251
ECT2 0.049 0.057 0.26 45 -10000 0 45
C13orf34 0.04 0.033 0.092 153 -10000 0 153
NUDC 0.028 0.054 0.14 2 -0.19 48 50
regulation of attachment of spindle microtubules to kinetochore 0.083 0.066 0.15 421 -10000 0 421
spindle assembly 0.036 0.03 0.086 122 -10000 0 122
spindle stabilization 0.026 0.035 0.14 10 -0.17 18 28
APC/C/HCDH1 0.01 0.067 -10000 0 -0.35 34 34
MKLP2/PLK1 0.17 0.089 0.22 760 -10000 0 760
CCNB1 0.069 0.092 0.26 199 -10000 0 199
PPP1CB 0.025 0.003 -10000 0 -10000 0 0
BTRC 0.024 0.003 -10000 0 -10000 0 0
ROCK2 0.027 0.085 0.23 1 -0.37 37 38
TUBG1 0.023 0.039 0.13 3 -0.16 31 34
G2/M transition of mitotic cell cycle 0.041 0.044 0.19 12 -10000 0 12
MLF1IP 0.024 0.046 0.14 147 -10000 0 147
INCENP 0.024 0.005 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.1 0.13 0.31 273 -0.24 1 274
NFATC2 -0.027 0.23 0.5 7 -0.6 92 99
NFATC3 -0.043 0.13 -10000 0 -0.28 175 175
CD40LG -0.3 0.5 0.65 6 -0.98 311 317
ITCH -0.003 0.084 -10000 0 -0.26 98 98
CBLB -0.003 0.084 -10000 0 -0.27 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.094 0.38 0.59 50 -0.98 87 137
JUNB 0.025 0.011 0.26 2 -10000 0 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.002 0.1 -10000 0 -0.31 105 105
T cell anergy -0.028 0.14 0.33 1 -0.42 102 103
TLE4 -0.026 0.19 -10000 0 -0.62 58 58
Jun/NFAT1-c-4/p21SNFT -0.18 0.44 0.69 5 -0.86 250 255
AP-1/NFAT1-c-4 -0.32 0.61 0.74 14 -1.1 308 322
IKZF1 -0.017 0.16 0.48 7 -0.49 59 66
T-helper 2 cell differentiation -0.086 0.27 -10000 0 -0.85 75 75
AP-1/NFAT1 -0.097 0.26 0.45 12 -0.47 271 283
CALM1 0.01 0.064 -10000 0 -10000 0 0
EGR2 -0.26 0.56 0.6 4 -1.2 226 230
EGR3 -0.34 0.62 0.68 2 -1.3 289 291
NFAT1/FOXP3 0.049 0.22 0.46 102 -0.49 61 163
EGR1 -0.16 0.28 -10000 0 -0.57 321 321
JUN 0.015 0.054 -10000 0 -0.57 6 6
EGR4 0.039 0.059 0.26 70 -10000 0 70
mol:Ca2+ -0.011 0.055 -10000 0 -0.18 105 105
GBP3 -0.021 0.17 0.38 3 -0.53 63 66
FOSL1 0.027 0.047 0.26 23 -0.57 3 26
NFAT1-c-4/MAF/IRF4 -0.2 0.46 0.6 7 -0.87 277 284
DGKA -0.018 0.16 0.56 1 -0.48 60 61
CREM 0.023 0.007 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.27 0.49 0.61 3 -0.94 298 301
CTLA4 0.037 0.21 0.43 117 -0.54 38 155
NFAT1-c-4 (dimer)/EGR1 -0.28 0.52 0.62 3 -1 312 315
NFAT1-c-4 (dimer)/EGR4 -0.19 0.45 0.6 5 -0.86 279 284
FOS -0.15 0.27 0.19 2 -0.57 294 296
IFNG -0.055 0.27 0.51 10 -0.75 81 91
T cell activation -0.15 0.3 0.62 4 -0.69 152 156
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 0.16 0.34 0.65 284 -0.62 2 286
TNF -0.26 0.45 0.54 3 -0.9 305 308
FASLG -0.33 0.63 0.8 2 -1.2 311 313
TBX21 0.021 0.12 0.35 15 -0.57 36 51
BATF3 0.021 0.016 0.26 3 -10000 0 3
PRKCQ 0.004 0.12 0.29 8 -0.57 41 49
PTPN1 -0.017 0.16 0.39 3 -0.48 59 62
NFAT1-c-4/ICER1 -0.2 0.44 0.55 3 -0.85 282 285
GATA3 0.009 0.11 0.26 26 -0.57 35 61
T-helper 1 cell differentiation -0.053 0.27 0.5 11 -0.72 84 95
IL2RA -0.095 0.37 0.58 47 -0.82 119 166
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.017 0.16 0.36 1 -0.49 57 58
E2F1 0.097 0.11 0.26 312 -10000 0 312
PPARG -0.11 0.25 -10000 0 -0.57 239 239
SLC3A2 -0.019 0.16 0.36 1 -0.48 61 62
IRF4 -0.021 0.16 0.26 12 -0.57 82 94
PTGS2 -0.34 0.54 0.63 4 -1 332 336
CSF2 -0.29 0.49 0.64 9 -0.95 309 318
JunB/Fra1/NFAT1-c-4 -0.18 0.43 0.59 3 -0.82 277 280
IL4 -0.091 0.28 -10000 0 -0.9 74 74
IL5 -0.29 0.49 0.58 7 -0.95 311 318
IL2 -0.16 0.3 0.67 3 -0.71 144 147
IL3 -0.05 0.13 -10000 0 -0.82 18 18
RNF128 -0.044 0.21 0.27 5 -0.66 105 110
NFATC1 -0.16 0.34 0.62 2 -0.66 284 286
CDK4 0.12 0.24 0.57 128 -0.58 2 130
PTPRK -0.02 0.17 0.45 2 -0.57 49 51
IL8 -0.28 0.5 0.58 9 -0.96 304 313
POU2F1 0.021 0.012 0.26 1 -10000 0 1
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.15 0.38 -10000 0 -0.86 223 223
NCK1/PAK1/Dok-R -0.092 0.17 -10000 0 -0.41 223 223
NCK1/Dok-R -0.18 0.45 -10000 0 -1 222 222
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.042 0.097 0.24 197 -10000 0 197
RELA 0.024 0.005 -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 0.045 0.11 0.27 197 -10000 0 197
TNIP2 0.024 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.16 0.43 -10000 0 -0.97 222 222
FN1 0.12 0.11 0.26 411 -10000 0 411
PLD2 -0.2 0.46 -10000 0 -1.1 222 222
PTPN11 0.024 0.003 -10000 0 -10000 0 0
GRB14 0.013 0.18 0.26 143 -0.57 75 218
ELK1 -0.18 0.41 -10000 0 -0.95 223 223
GRB7 0.019 0.033 -10000 0 -0.57 3 3
PAK1 0.023 0.019 0.26 6 -10000 0 6
Tie2/Ang1/alpha5/beta1 Integrin -0.12 0.48 -10000 0 -1 222 222
CDKN1A -0.11 0.26 -10000 0 -0.6 190 190
ITGA5 0.025 0.008 0.26 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.18 0.45 -10000 0 -1 222 222
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:NO -0.11 0.28 -10000 0 -0.64 223 223
PLG -0.21 0.46 -10000 0 -1.1 222 222
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.15 0.36 -10000 0 -0.82 223 223
GRB2 0.023 0.01 0.26 1 -10000 0 1
PIK3R1 0.018 0.056 -10000 0 -0.57 9 9
ANGPT2 -0.14 0.28 -10000 0 -0.7 151 151
BMX -0.31 0.5 -10000 0 -1.2 224 224
ANGPT1 -0.22 0.49 -10000 0 -1.2 197 197
tube development -0.12 0.29 -10000 0 -0.66 201 201
ANGPT4 -0.15 0.26 -10000 0 -0.57 295 295
response to hypoxia -0.013 0.028 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.21 0.5 -10000 0 -1.1 222 222
alpha5/beta1 Integrin 0.035 0.008 -10000 0 -10000 0 0
FGF2 -0.2 0.29 -10000 0 -0.57 393 393
STAT5A (dimer) -0.14 0.33 -10000 0 -0.77 191 191
mol:L-citrulline -0.11 0.28 -10000 0 -0.64 223 223
AGTR1 -0.094 0.26 0.26 62 -0.57 231 293
MAPK14 -0.2 0.46 -10000 0 -1.1 225 225
Tie2/SHP2 -0.095 0.31 -10000 0 -1.1 83 83
TEK -0.1 0.34 -10000 0 -1.2 83 83
RPS6KB1 -0.14 0.37 -10000 0 -0.82 222 222
Angiotensin II/AT1 -0.069 0.19 0.18 62 -0.42 234 296
Tie2/Ang1/GRB2 -0.2 0.48 -10000 0 -1.1 222 222
MAPK3 -0.18 0.42 -10000 0 -0.97 222 222
MAPK1 -0.19 0.42 -10000 0 -0.98 222 222
Tie2/Ang1/GRB7 -0.2 0.48 -10000 0 -1.1 222 222
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.21 0.47 -10000 0 -1.1 223 223
PI3K -0.18 0.43 -10000 0 -0.99 223 223
FES -0.2 0.46 -10000 0 -1.1 225 225
Crk/Dok-R -0.18 0.46 -10000 0 -1 222 222
Tie2/Ang1/ABIN2 -0.2 0.49 -10000 0 -1.1 222 222
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.13 0.34 -10000 0 -0.77 223 223
STAT5A 0.02 0.045 -10000 0 -0.57 6 6
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.12 0.37 0.47 1 -0.8 222 223
Tie2/Ang2 -0.18 0.39 -10000 0 -0.92 194 194
Tie2/Ang1 -0.22 0.51 -10000 0 -1.2 223 223
FOXO1 -0.13 0.34 0.47 1 -0.77 223 224
ELF1 0.012 0.036 -10000 0 -10000 0 0
ELF2 -0.2 0.46 -10000 0 -1.1 222 222
mol:Choline -0.19 0.44 -10000 0 -1 222 222
cell migration -0.037 0.1 -10000 0 -0.23 223 223
FYN -0.14 0.33 -10000 0 -0.77 192 192
DOK2 0.02 0.031 0.26 4 -0.57 2 6
negative regulation of cell cycle -0.096 0.24 -10000 0 -0.54 191 191
ETS1 -0.021 0.11 -10000 0 -0.27 159 159
PXN -0.095 0.31 0.45 1 -0.67 222 223
ITGB1 0.024 0.004 -10000 0 -10000 0 0
NOS3 -0.13 0.32 -10000 0 -0.72 223 223
RAC1 0.024 0.003 -10000 0 -10000 0 0
TNF -0.023 0.13 0.26 19 -0.27 185 204
MAPKKK cascade -0.19 0.44 -10000 0 -1 222 222
RASA1 0.024 0.004 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.2 0.47 -10000 0 -1.1 220 220
NCK1 0.024 0.003 -10000 0 -10000 0 0
vasculogenesis -0.093 0.26 0.37 2 -0.57 223 225
mol:Phosphatidic acid -0.19 0.44 -10000 0 -1 222 222
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.11 0.28 -10000 0 -0.64 223 223
Rac1/GTP -0.13 0.34 -10000 0 -0.77 223 223
MMP2 -0.21 0.47 -10000 0 -1.1 223 223
Endothelins

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 -0.073 0.13 -10000 0 -0.43 94 94
PTK2B 0.02 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.052 0.19 -10000 0 -0.78 47 47
EDN1 -0.074 0.17 -10000 0 -0.55 94 94
EDN3 -0.22 0.29 0.26 2 -0.57 430 432
EDN2 0.074 0.11 0.26 236 -0.57 5 241
HRAS/GDP -0.093 0.19 0.28 1 -0.46 157 158
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.061 0.14 -10000 0 -0.39 108 108
ADCY4 -0.13 0.2 0.28 2 -0.42 271 273
ADCY5 -0.21 0.24 -10000 0 -0.45 456 456
ADCY6 -0.12 0.18 0.28 2 -0.4 262 264
ADCY7 -0.12 0.18 0.28 2 -0.4 262 264
ADCY1 -0.12 0.2 0.26 1 -0.41 262 263
ADCY2 -0.14 0.22 0.29 7 -0.45 278 285
ADCY3 -0.12 0.18 0.26 1 -0.4 261 262
ADCY8 -0.1 0.17 0.27 2 -0.41 199 201
ADCY9 -0.12 0.18 0.26 1 -0.4 250 251
arachidonic acid secretion -0.16 0.27 0.31 2 -0.5 341 343
ETB receptor/Endothelin-1/Gq/GTP -0.05 0.15 -10000 0 -0.35 165 165
GNAO1 0.018 0.09 0.26 32 -0.57 19 51
HRAS 0.025 0.021 0.26 8 -10000 0 8
ETA receptor/Endothelin-1/G12/GTP -0.059 0.13 -10000 0 -0.4 91 91
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.2 -10000 0 -0.42 263 263
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.064 0.15 0.37 10 -0.44 92 102
EDNRB -0.027 0.17 -10000 0 -0.57 93 93
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.077 0.16 -10000 0 -0.49 100 100
CYSLTR1 -0.08 0.16 -10000 0 -0.49 97 97
SLC9A1 -0.045 0.093 -10000 0 -0.29 90 90
mol:GDP -0.1 0.2 0.33 2 -0.49 165 167
SLC9A3 -0.11 0.28 -10000 0 -0.64 183 183
RAF1 -0.14 0.23 0.33 1 -0.45 292 293
JUN -0.05 0.18 -10000 0 -0.78 40 40
JAK2 -0.071 0.13 -10000 0 -0.42 97 97
mol:IP3 -0.074 0.17 -10000 0 -0.44 127 127
ETA receptor/Endothelin-1 -0.083 0.16 -10000 0 -0.48 101 101
PLCB1 -0.017 0.15 -10000 0 -0.57 68 68
PLCB2 0.014 0.026 0.26 1 -0.57 1 2
ETA receptor/Endothelin-3 -0.19 0.21 -10000 0 -0.43 440 440
FOS -0.29 0.44 -10000 0 -0.93 321 321
Gai/GDP -0.098 0.29 -10000 0 -0.75 159 159
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.2 0.28 1 -0.54 137 138
BCAR1 0.022 0.008 -10000 0 -10000 0 0
PRKCB1 -0.077 0.16 -10000 0 -0.41 141 141
GNAQ 0.014 0.032 -10000 0 -0.58 2 2
GNAZ 0.018 0.055 -10000 0 -0.57 9 9
GNAL -0.11 0.25 -10000 0 -0.57 229 229
Gs family/GDP -0.15 0.24 -10000 0 -0.49 267 267
ETA receptor/Endothelin-1/Gq/GTP -0.047 0.12 -10000 0 -0.36 88 88
MAPK14 -0.066 0.16 -10000 0 -0.4 138 138
TRPC6 -0.056 0.21 -10000 0 -0.87 44 44
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.005 0.13 -10000 0 -0.57 52 52
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.066 0.17 -10000 0 -0.39 165 165
ETB receptor/Endothelin-2 0.024 0.15 0.24 16 -0.39 103 119
ETB receptor/Endothelin-3 -0.19 0.24 -10000 0 -0.44 493 493
ETB receptor/Endothelin-1 -0.078 0.18 -10000 0 -0.46 166 166
MAPK3 -0.25 0.38 -10000 0 -0.79 325 325
MAPK1 -0.25 0.39 -10000 0 -0.8 329 329
Rac1/GDP -0.094 0.19 0.28 1 -0.46 158 159
cAMP biosynthetic process -0.16 0.22 0.53 1 -0.49 242 243
MAPK8 -0.059 0.21 -10000 0 -0.72 63 63
SRC 0.024 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.067 0.17 -10000 0 -0.37 185 185
p130Cas/CRK/Src/PYK2 -0.097 0.21 0.49 1 -0.56 126 127
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.093 0.19 0.28 1 -0.48 147 148
COL1A2 -0.088 0.19 0.38 9 -0.48 148 157
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.022 0.095 0.26 13 -0.35 10 23
mol:DAG -0.074 0.17 -10000 0 -0.44 127 127
MAP2K2 -0.19 0.3 0.34 2 -0.59 330 332
MAP2K1 -0.19 0.29 0.32 2 -0.58 332 334
EDNRA -0.034 0.064 0.28 1 -0.28 20 21
positive regulation of muscle contraction -0.063 0.12 -10000 0 -0.38 89 89
Gq family/GDP -0.058 0.19 -10000 0 -0.47 115 115
HRAS/GTP -0.1 0.2 0.34 1 -0.47 169 170
PRKCH -0.076 0.16 -10000 0 -0.43 126 126
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA -0.072 0.18 0.28 3 -0.45 131 134
PRKCB -0.074 0.18 0.24 1 -0.44 129 130
PRKCE -0.079 0.16 -10000 0 -0.43 130 130
PRKCD -0.076 0.16 -10000 0 -0.42 127 127
PRKCG -0.077 0.17 0.27 1 -0.43 128 129
regulation of vascular smooth muscle contraction -0.34 0.51 -10000 0 -1.1 322 322
PRKCQ -0.085 0.18 -10000 0 -0.46 146 146
PLA2G4A -0.18 0.3 0.33 1 -0.55 341 342
GNA14 0.014 0.069 0.25 19 -0.58 10 29
GNA15 0.022 0.027 0.26 6 -0.57 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.028 -10000 0 -0.57 2 2
Rac1/GTP -0.059 0.13 -10000 0 -0.4 95 95
MMP1 0.17 0.13 0.41 70 -10000 0 70
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.091 0.11 0.47 3 -10000 0 3
SMARCC2 0.024 0.013 -10000 0 -0.19 1 1
SMARCC1 0.024 0.012 -10000 0 -10000 0 0
TBX21 -0.12 0.21 0.39 6 -0.7 67 73
SUMO2 0.001 0.023 -10000 0 -10000 0 0
STAT1 (dimer) 0.033 0.033 0.27 19 -10000 0 19
FKBP4 0.025 0.017 0.26 5 -10000 0 5
FKBP5 0.017 0.071 0.26 5 -0.57 14 19
GR alpha/HSP90/FKBP51/HSP90 0.12 0.13 0.31 115 -0.31 8 123
PRL -0.062 0.12 0.52 3 -0.49 1 4
cortisol/GR alpha (dimer)/TIF2 0.18 0.28 0.53 303 -0.48 17 320
RELA -0.036 0.1 0.25 2 -0.25 44 46
FGG 0.21 0.24 0.48 342 -0.46 4 346
GR beta/TIF2 0.08 0.16 0.32 118 -0.4 40 158
IFNG -0.3 0.36 0.46 4 -0.7 376 380
apoptosis -0.26 0.31 0.85 1 -0.63 318 319
CREB1 0.061 0.053 -10000 0 -10000 0 0
histone acetylation 0.026 0.13 0.36 56 -0.41 16 72
BGLAP -0.082 0.14 -10000 0 -0.48 22 22
GR/PKAc 0.13 0.13 0.36 83 -0.33 3 86
NF kappa B1 p50/RelA -0.061 0.18 0.42 4 -0.35 138 142
SMARCD1 0.025 0.011 -10000 0 -10000 0 0
MDM2 0.099 0.11 0.23 278 -10000 0 278
GATA3 0.013 0.12 0.26 26 -0.57 35 61
AKT1 0.02 0.009 -10000 0 -10000 0 0
CSF2 -0.025 0.1 0.47 1 -0.54 4 5
GSK3B 0.001 0.024 -10000 0 -10000 0 0
NR1I3 -0.2 0.26 0.8 1 -0.61 155 156
CSN2 0.16 0.19 0.39 280 -0.43 4 284
BRG1/BAF155/BAF170/BAF60A 0.06 0.041 -10000 0 -0.47 5 5
NFATC1 0.023 0.027 -10000 0 -0.57 2 2
POU2F1 0.023 0.016 0.26 1 -10000 0 1
CDKN1A 0.016 0.087 -10000 0 -1.3 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 0.071 0.26 19 -0.57 12 31
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.33 85 -0.28 9 94
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.36 0.39 0.62 2 -0.81 390 392
JUN -0.26 0.29 0.41 9 -0.56 403 412
IL4 -0.12 0.15 -10000 0 -0.58 10 10
CDK5R1 0.022 0.037 0.25 23 -10000 0 23
PRKACA 0.024 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.25 0.24 -10000 0 -0.47 487 487
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.12 0.32 88 -0.3 6 94
cortisol/GR alpha (monomer) 0.28 0.32 0.61 402 -0.51 5 407
NCOA2 -0.004 0.12 -10000 0 -0.57 43 43
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.28 -10000 0 -0.6 299 299
AP-1/NFAT1-c-4 -0.43 0.45 0.47 8 -0.82 528 536
AFP -0.55 0.65 0.48 2 -1.4 357 359
SUV420H1 0.023 0.006 -10000 0 -10000 0 0
IRF1 0.16 0.16 0.44 96 -10000 0 96
TP53 0.031 0.028 -10000 0 -0.52 2 2
PPP5C 0.024 0.003 -10000 0 -10000 0 0
KRT17 -0.65 0.69 0.45 2 -1.4 462 464
KRT14 -0.7 0.67 -10000 0 -1.3 544 544
TBP 0.028 0.011 -10000 0 -10000 0 0
CREBBP 0.14 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 0.45 0.47 8 -0.82 528 536
MAPK14 0.003 0.022 -10000 0 -10000 0 0
MAPK10 -0.084 0.2 -10000 0 -0.58 152 152
MAPK11 -0.001 0.039 -10000 0 -0.58 3 3
KRT5 -0.73 0.7 0.45 1 -1.4 546 547
interleukin-1 receptor activity -0.001 0.004 -10000 0 -10000 0 0
NCOA1 0.025 0.019 -10000 0 -0.57 1 1
STAT1 0.033 0.033 0.27 19 -10000 0 19
CGA -0.056 0.17 0.42 2 -0.48 21 23
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.18 0.37 341 -10000 0 341
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 0.59 4 -0.57 193 197
NFKB1 -0.037 0.1 0.28 1 -0.28 16 17
MAPK8 -0.2 0.22 0.36 7 -0.42 414 421
MAPK9 0.003 0.022 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.28 0.32 0.86 1 -0.67 325 326
BAX 0.017 0.065 -10000 0 -10000 0 0
POMC -0.16 0.29 -10000 0 -1.2 45 45
EP300 0.14 0.14 0.29 484 -10000 0 484
cortisol/GR alpha (dimer)/p53 0.22 0.27 0.53 327 -0.49 3 330
proteasomal ubiquitin-dependent protein catabolic process 0.078 0.11 0.27 156 -10000 0 156
SGK1 0.19 0.2 0.54 7 -1.1 5 12
IL13 -0.25 0.28 0.51 6 -0.62 228 234
IL6 -0.43 0.52 0.5 2 -1.1 392 394
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.21 0.23 0.52 3 -0.62 90 93
IL2 -0.33 0.36 0.47 2 -0.72 385 387
CDK5 0.018 0.02 0.25 4 -10000 0 4
PRKACB 0.032 0.058 0.26 45 -0.57 3 48
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
IL8 -0.19 0.29 0.48 6 -0.61 214 220
CDK5R1/CDK5 0.019 0.036 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.017 0.15 0.38 3 -0.39 29 32
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.26 0.51 387 -0.46 3 390
SMARCA4 0.024 0.011 -10000 0 -10000 0 0
chromatin remodeling 0.15 0.16 0.37 211 -10000 0 211
NF kappa B1 p50/RelA/Cbp 0.063 0.19 0.41 65 -0.42 14 79
JUN (dimer) -0.26 0.29 0.41 9 -0.55 403 412
YWHAH 0.023 0.006 -10000 0 -10000 0 0
VIPR1 -0.13 0.21 -10000 0 -0.62 95 95
NR3C1 0.17 0.2 0.4 326 -0.44 4 330
NR4A1 -0.026 0.17 -10000 0 -0.55 101 101
TIF2/SUV420H1 0.01 0.091 -10000 0 -0.42 43 43
MAPKKK cascade -0.26 0.31 0.85 1 -0.63 318 319
cortisol/GR alpha (dimer)/Src-1 0.25 0.27 0.54 382 -0.5 3 385
PBX1 0.023 0.015 0.26 1 -10000 0 1
POU1F1 0.022 0.015 0.26 2 -10000 0 2
SELE -0.19 0.31 0.56 3 -0.74 159 162
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.15 0.16 0.37 209 -10000 0 209
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.26 0.51 387 -0.46 3 390
mol:cortisol 0.16 0.19 0.35 416 -0.26 4 420
MMP1 0.031 0.31 -10000 0 -0.93 80 80
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.034 0.016 -10000 0 -0.42 1 1
Necdin/E2F1 0.062 0.11 -10000 0 -0.39 32 32
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.046 0.17 -10000 0 -0.32 282 282
NGF (dimer)/p75(NTR)/BEX1 -0.1 0.24 0.34 1 -0.41 356 357
NT-4/5 (dimer)/p75(NTR) -0.23 0.29 -10000 0 -0.49 513 513
IKBKB 0.021 0.009 -10000 0 -10000 0 0
AKT1 -0.083 0.16 0.36 1 -0.32 268 269
IKBKG 0.024 0.002 -10000 0 -10000 0 0
BDNF -0.014 0.16 0.26 23 -0.57 75 98
MGDIs/NGR/p75(NTR)/LINGO1 -0.038 0.2 0.34 6 -0.35 274 280
FURIN 0.024 0.009 0.26 1 -10000 0 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.09 0.21 -10000 0 -0.39 310 310
LINGO1 0.077 0.098 0.26 239 -10000 0 239
Sortilin/TRAF6/NRIF 0.024 0.024 -10000 0 -0.56 1 1
proBDNF (dimer) -0.014 0.16 0.26 23 -0.57 75 98
NTRK1 0.023 0.051 0.26 23 -0.57 4 27
RTN4R 0.032 0.046 0.26 42 -10000 0 42
neuron apoptosis -0.08 0.2 0.34 8 -0.52 74 82
IRAK1 0.025 0.015 0.26 4 -10000 0 4
SHC1 -0.081 0.16 -10000 0 -0.37 219 219
ARHGDIA 0.023 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.055 0.034 -10000 0 -0.32 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.054 0.18 -10000 0 -0.34 278 278
MAGEH1 0.024 0.002 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.065 0.19 -10000 0 -0.36 288 288
Mammalian IAPs/DIABLO 0.057 0.033 -10000 0 -0.33 2 2
proNGF (dimer) 0.017 0.076 0.26 8 -0.57 16 24
MAGED1 0.025 0.01 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 -0.57 363 363
ZNF274 0.024 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.065 0.15 -10000 0 -0.32 269 269
NGF 0.017 0.076 0.26 8 -0.57 16 24
cell cycle arrest -0.073 0.15 0.34 11 -0.3 278 289
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.053 0.12 -10000 0 -0.27 204 204
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.19 0.26 -10000 0 -0.45 480 480
NCSTN 0.02 0.009 -10000 0 -10000 0 0
mol:GTP -0.069 0.19 -10000 0 -0.37 280 280
PSENEN 0.024 0.008 0.26 1 -10000 0 1
mol:ceramide -0.078 0.16 -10000 0 -0.34 279 279
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.044 0.11 -10000 0 -0.24 197 197
p75(NTR)/beta APP -0.091 0.2 -10000 0 -0.41 289 289
BEX1 -0.019 0.23 0.26 162 -0.57 139 301
mol:GDP -0.11 0.16 -10000 0 -0.36 284 284
NGF (dimer) 0.002 0.14 0.34 1 -0.34 129 130
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.023 0.18 0.34 5 -0.32 260 265
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
RAC1/GTP -0.06 0.16 -10000 0 -0.32 282 282
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 -0.069 0.19 -10000 0 -0.37 280 280
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 0.073 -10000 0 -10000 0 0
NT3 (dimer) -0.06 0.21 0.26 12 -0.57 150 162
TP53 -0.091 0.17 0.33 5 -0.33 298 303
PRDM4 -0.078 0.16 -10000 0 -0.34 278 278
BDNF (dimer) 0.023 0.2 0.33 20 -0.36 184 204
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
SORT1 0.023 0.019 -10000 0 -0.57 1 1
activation of caspase activity -0.049 0.17 -10000 0 -0.32 282 282
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.054 0.18 -10000 0 -0.34 275 275
RHOC 0.024 0.004 -10000 0 -10000 0 0
XIAP 0.025 0.002 -10000 0 -10000 0 0
MAPK10 -0.13 0.2 0.29 5 -0.41 283 288
DIABLO 0.024 0.002 -10000 0 -10000 0 0
SMPD2 -0.079 0.16 -10000 0 -0.34 279 279
APH1B 0.023 0.019 -10000 0 -0.57 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.071 0.19 -10000 0 -0.37 282 282
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 -0.46 376 376
MAPK8 -0.097 0.18 0.29 10 -0.37 258 268
MAPK9 -0.095 0.17 0.28 8 -0.36 256 264
APAF1 0.024 0.003 -10000 0 -10000 0 0
NTF3 -0.06 0.21 0.26 12 -0.57 150 162
NTF4 -0.18 0.28 -10000 0 -0.57 363 363
NDN 0.005 0.1 -10000 0 -0.57 32 32
RAC1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.042 0.16 -10000 0 -0.3 279 279
p75 CTF/Sortilin/TRAF6/NRIF 0.057 0.022 -10000 0 -0.33 1 1
RhoA-B-C/GTP -0.069 0.19 -10000 0 -0.37 280 280
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.061 0.19 -10000 0 -0.34 302 302
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.072 0.2 -10000 0 -0.36 304 304
PRKACB 0.032 0.058 0.26 45 -0.57 3 48
proBDNF (dimer)/p75 ECD 0.005 0.12 -10000 0 -0.41 79 79
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.023 0.041 0.26 12 -0.57 3 15
BIRC2 0.022 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.086 0.17 0.27 17 -0.34 273 290
BAD -0.11 0.19 0.38 8 -0.38 276 284
RIPK2 0.021 0.016 0.26 3 -10000 0 3
NGFR -0.14 0.26 -10000 0 -0.57 280 280
CYCS -0.086 0.15 0.36 2 -0.32 270 272
ADAM17 0.024 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.045 0.16 -10000 0 -0.34 203 203
BCL2L11 -0.11 0.19 0.38 8 -0.38 275 283
BDNF (dimer)/p75(NTR) -0.12 0.23 -10000 0 -0.44 326 326
PI3K -0.057 0.18 -10000 0 -0.34 271 271
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.055 0.18 -10000 0 -0.34 278 278
NDNL2 0.023 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) -0.096 0.21 -10000 0 -0.41 300 300
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.054 0.18 -10000 0 -0.34 278 278
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
PLG 0.019 0.022 0.26 8 -10000 0 8
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.11 0.19 -10000 0 -0.38 316 316
SQSTM1 0.024 0.008 0.26 1 -10000 0 1
NGFRAP1 0.023 0.026 -10000 0 -0.57 2 2
CASP3 -0.11 0.18 0.38 7 -0.36 277 284
E2F1 0.094 0.11 0.26 312 -10000 0 312
CASP9 0.023 0.006 -10000 0 -10000 0 0
IKK complex -0.003 0.11 -10000 0 -0.38 22 22
NGF (dimer)/TRKA 0.026 0.067 -10000 0 -0.4 20 20
MMP7 -0.038 0.19 0.26 31 -0.57 117 148
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.044 0.17 -10000 0 -0.32 271 271
MMP3 0.098 0.13 0.26 367 -0.57 11 378
APAF-1/Caspase 9 -0.086 0.11 -10000 0 -0.44 10 10
Ephrin B reverse 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
EFNB2 0.023 0.007 -10000 0 -10000 0 0
EPHB2 0.027 0.033 0.26 20 -10000 0 20
EFNB1 -0.004 0.037 -10000 0 -0.42 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.079 0.18 -10000 0 -0.3 390 390
Ephrin B2/EPHB1-2 -0.098 0.18 0.21 1 -0.32 401 402
neuron projection morphogenesis -0.085 0.16 -10000 0 -0.29 390 390
Ephrin B1/EPHB1-2/Tiam1 -0.09 0.18 -10000 0 -0.32 396 396
DNM1 0.02 0.049 0.27 1 -0.57 7 8
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.023 0.12 -10000 0 -0.55 46 46
YES1 -0.025 0.17 -10000 0 -0.76 51 51
Ephrin B1/EPHB1-2/NCK2 -0.091 0.18 -10000 0 -0.32 399 399
PI3K 0.006 0.13 -10000 0 -0.52 55 55
mol:GDP -0.09 0.18 -10000 0 -0.31 396 396
ITGA2B 0.033 0.061 0.26 52 -0.57 3 55
endothelial cell proliferation 0.029 0.01 -10000 0 -10000 0 0
FYN -0.025 0.17 -10000 0 -0.76 50 50
MAP3K7 -0.024 0.13 -10000 0 -0.57 49 49
FGR -0.022 0.17 -10000 0 -0.76 50 50
TIAM1 0.025 0.015 0.26 4 -10000 0 4
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
RGS3 0.024 0.003 -10000 0 -10000 0 0
cell adhesion -0.009 0.14 -10000 0 -0.52 52 52
LYN -0.022 0.17 -10000 0 -0.75 50 50
Ephrin B1/EPHB1-2/Src Family Kinases -0.028 0.16 -10000 0 -0.71 51 51
Ephrin B1/EPHB1-2 -0.024 0.13 -10000 0 -0.63 46 46
SRC -0.021 0.17 -10000 0 -0.75 51 51
ITGB3 0.005 0.11 0.26 4 -0.57 34 38
EPHB1 -0.21 0.29 0.27 1 -0.57 402 403
EPHB4 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.03 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.026 0.092 -10000 0 -0.42 37 37
BLK -0.021 0.17 -10000 0 -0.78 48 48
HCK -0.021 0.17 -10000 0 -0.75 51 51
regulation of stress fiber formation 0.09 0.18 0.31 399 -10000 0 399
MAPK8 -0.025 0.12 -10000 0 -0.54 48 48
Ephrin B1/EPHB1-2/RGS3 -0.09 0.18 -10000 0 -0.32 399 399
endothelial cell migration -0.018 0.11 -10000 0 -0.51 42 42
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTPN13 0.009 0.11 -10000 0 -0.68 26 26
regulation of focal adhesion formation 0.09 0.18 0.31 399 -10000 0 399
chemotaxis 0.09 0.18 0.31 399 -10000 0 399
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.081 0.17 -10000 0 -0.29 390 390
angiogenesis -0.025 0.13 -10000 0 -0.62 48 48
LCK -0.021 0.17 -10000 0 -0.76 50 50
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.024 0.004 -10000 0 -10000 0 0
VLDLR 0.008 0.093 -10000 0 -0.57 26 26
LRPAP1 0.024 0.005 -10000 0 -10000 0 0
NUDC 0.023 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.18 0.2 -10000 0 -0.36 593 593
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 -10000 0 -0.32 590 590
IQGAP1/CaM 0.034 0.009 -10000 0 -10000 0 0
DAB1 0.035 0.055 0.26 59 -10000 0 59
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
PLA2G7 0.023 0.068 0.26 23 -0.57 10 33
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 23 -10000 0 23
LIS1/Poliovirus Protein 3A 0.007 0.003 -10000 0 -10000 0 0
CDK5R2 0.055 0.083 0.26 149 -10000 0 149
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.19 0.21 0.34 2 -0.37 588 590
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.13 0.15 0.35 3 -0.32 64 67
MAP1B 0 0.042 -10000 0 -0.32 17 17
RAC1 0.011 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.15 0.16 -10000 0 -0.3 479 479
RELN -0.32 0.29 0.26 2 -0.57 600 602
PAFAH/LIS1 0.023 0.046 0.32 2 -0.36 9 11
LIS1/CLIP170 0.023 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.11 0.13 -10000 0 -0.29 17 17
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.15 0.17 -10000 0 -0.3 496 496
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.15 0.15 0.33 3 -0.34 76 79
LIS1/IQGAP1 0.023 0.009 -10000 0 -10000 0 0
RHOA 0.01 0.004 -10000 0 -10000 0 0
PAFAH1B1 0.01 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.05 0.073 0.26 115 -10000 0 115
PAFAH1B2 0.02 0.037 -10000 0 -0.57 4 4
MAP1B/LIS1/Dynein heavy chain 0.014 0.042 -10000 0 -0.23 15 15
NDEL1/Katanin 60/Dynein heavy chain -0.13 0.15 0.34 3 -0.32 59 62
LRP8 0.047 0.07 0.26 103 -10000 0 103
NDEL1/Katanin 60 -0.13 0.15 0.35 3 -0.33 64 67
P39/CDK5 -0.15 0.16 0.34 6 -0.3 436 442
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.023 0.009 -10000 0 -10000 0 0
CDK5 -0.18 0.15 -10000 0 -0.31 582 582
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 -0.16 0.19 0.33 1 -0.32 582 583
RELN/VLDLR -0.17 0.2 -10000 0 -0.34 592 592
CDC42 0.01 0.005 -10000 0 -10000 0 0
Wnt 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
Noncanonical Wnts/FZD -0.095 0.2 0.22 1 -0.38 285 286
FZD6 0.014 0.056 -10000 0 -0.57 9 9
WNT6 -0.079 0.24 0.26 46 -0.57 197 243
WNT4 0.017 0.086 0.26 20 -0.57 19 39
FZD3 0.017 0.046 -10000 0 -0.57 6 6
WNT5A 0.019 0.067 0.26 9 -0.57 12 21
WNT11 -0.083 0.23 0.26 10 -0.57 188 198
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.024 0.16 -10000 0 -0.57 81 81
GNB1/GNG2 -0.073 0.21 -10000 0 -0.47 151 151
mol:DAG -0.075 0.18 0.24 1 -0.44 141 142
PLCG1 -0.078 0.19 0.24 1 -0.45 139 140
YES1 -0.094 0.19 0.2 1 -0.37 264 265
FZD3 0.017 0.046 -10000 0 -0.57 6 6
FZD6 0.014 0.056 -10000 0 -0.57 9 9
G protein -0.061 0.2 0.3 2 -0.46 135 137
MAP3K7 -0.07 0.15 0.24 1 -0.4 108 109
mol:Ca2+ -0.073 0.18 0.23 1 -0.42 141 142
mol:IP3 -0.075 0.18 0.24 1 -0.44 141 142
NLK -0.01 0.13 -10000 0 -0.84 24 24
GNB1 0.024 0.005 -10000 0 -10000 0 0
CAMK2A -0.071 0.17 0.25 2 -0.42 120 122
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.095 0.2 0.22 1 -0.38 285 286
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
GNAS -0.088 0.19 0.2 1 -0.38 251 252
GO:0007205 -0.079 0.18 0.23 1 -0.43 138 139
WNT6 -0.079 0.24 0.26 46 -0.57 197 243
WNT4 0.017 0.086 0.26 20 -0.57 19 39
NFAT1/CK1 alpha -0.087 0.2 0.32 2 -0.46 154 156
GNG2 0.018 0.058 -10000 0 -0.57 10 10
WNT5A 0.019 0.067 0.26 9 -0.57 12 21
WNT11 -0.083 0.23 0.26 10 -0.57 188 198
CDC42 -0.081 0.18 -10000 0 -0.47 131 131
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.024 0.49 0.8 47 -1.1 75 122
IL23A -0.035 0.49 0.85 33 -1.1 72 105
NF kappa B1 p50/RelA/I kappa B alpha -0.063 0.45 0.75 9 -0.88 151 160
positive regulation of T cell mediated cytotoxicity -0.026 0.54 0.85 72 -0.96 157 229
ITGA3 -0.02 0.48 0.8 44 -1.1 76 120
IL17F -0.008 0.36 0.59 76 -0.67 82 158
IL12B 0.085 0.15 0.35 211 -10000 0 211
STAT1 (dimer) -0.041 0.5 0.75 49 -0.93 157 206
CD4 -0.019 0.48 0.82 45 -1 75 120
IL23 -0.02 0.49 0.82 49 -1.1 71 120
IL23R 0.048 0.2 0.6 17 -0.94 16 33
IL1B -0.037 0.5 0.82 42 -1.1 78 120
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.015 0.49 0.83 64 -1 72 136
TYK2 0.026 0.059 0.2 10 -10000 0 10
STAT4 -0.001 0.12 0.26 1 -0.57 44 45
STAT3 0.024 0.005 -10000 0 -10000 0 0
IL18RAP 0.007 0.11 0.27 5 -0.57 36 41
IL12RB1 0.035 0.093 0.37 44 -0.59 2 46
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.039 0.089 0.31 46 -0.43 2 48
IL23R/JAK2 0.061 0.22 0.55 30 -0.87 15 45
positive regulation of chronic inflammatory response -0.026 0.54 0.85 72 -0.96 157 229
natural killer cell activation -0.004 0.015 -10000 0 -0.051 35 35
JAK2 0.038 0.083 0.26 38 -10000 0 38
PIK3R1 0.019 0.055 -10000 0 -0.56 9 9
NFKB1 0.026 0.009 -10000 0 -10000 0 0
RELA 0.026 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.014 0.47 0.8 54 -1 72 126
ALOX12B -0.02 0.48 0.81 49 -1 75 124
CXCL1 -0.19 0.7 0.84 46 -1.2 271 317
T cell proliferation -0.026 0.54 0.85 72 -0.96 157 229
NFKBIA 0.026 0.009 -10000 0 -10000 0 0
IL17A 0.02 0.31 0.55 90 -0.53 71 161
PI3K -0.059 0.47 0.69 24 -0.91 144 168
IFNG 0.026 0.068 0.17 134 -0.12 14 148
STAT3 (dimer) -0.059 0.45 0.71 14 -0.93 111 125
IL18R1 0.017 0.076 -10000 0 -0.57 17 17
IL23/IL23R/JAK2/TYK2/SOCS3 0.035 0.35 0.64 85 -0.62 58 143
IL18/IL18R 0.04 0.1 0.29 10 -0.36 51 61
macrophage activation 0 0.029 0.056 102 -0.044 54 156
TNF -0.034 0.5 0.83 43 -1.1 77 120
STAT3/STAT4 -0.06 0.49 0.68 24 -0.93 156 180
STAT4 (dimer) -0.054 0.51 0.74 43 -0.96 159 202
IL18 0.029 0.036 0.26 22 -10000 0 22
IL19 0.019 0.49 0.82 67 -1 71 138
STAT5A (dimer) -0.044 0.5 0.73 44 -0.93 158 202
STAT1 0.028 0.031 0.26 19 -10000 0 19
SOCS3 0.02 0.041 -10000 0 -0.57 5 5
CXCL9 0.005 0.51 0.83 80 -1 77 157
MPO -0.051 0.55 0.82 43 -1.2 111 154
positive regulation of humoral immune response -0.026 0.54 0.85 72 -0.96 157 229
IL23/IL23R/JAK2/TYK2 -0.034 0.56 0.88 63 -1 151 214
IL6 -0.3 0.74 0.79 38 -1.2 384 422
STAT5A 0.02 0.045 -10000 0 -0.57 6 6
IL2 0.022 0.038 0.3 8 -10000 0 8
positive regulation of tyrosine phosphorylation of STAT protein -0.004 0.015 -10000 0 -0.051 35 35
CD3E -0.03 0.51 0.82 58 -1.1 82 140
keratinocyte proliferation -0.026 0.54 0.85 72 -0.96 157 229
NOS2 -0.02 0.48 0.8 47 -1.1 74 121
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.23 0.6 0.85 5 -1.2 183 188
STAT6 (cleaved dimer) -0.3 0.57 -10000 0 -1.2 234 234
IGHG1 -0.027 0.26 0.52 55 -0.52 11 66
IGHG3 -0.23 0.57 0.72 5 -1.1 218 223
AKT1 -0.085 0.35 0.58 19 -0.8 70 89
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.048 0.29 0.55 21 -0.92 31 52
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.087 0.36 0.6 22 -0.87 60 82
THY1 -0.24 0.6 0.86 6 -1.2 176 182
MYB 0.011 0.086 0.26 1 -0.57 22 23
HMGA1 0.034 0.047 0.26 44 -10000 0 44
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.11 0.41 0.65 50 -0.78 133 183
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.079 0.35 0.6 21 -0.89 48 69
SP1 0.034 0.025 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SOCS5 0.014 0.046 -10000 0 -0.55 1 1
STAT6 (dimer)/ETS1 -0.26 0.6 0.71 7 -1.2 212 219
SOCS1 -0.14 0.4 0.65 17 -0.76 158 175
SOCS3 -0.093 0.35 0.64 9 -0.83 68 77
FCER2 -0.38 0.74 0.8 25 -1.3 330 355
PARP14 0.017 0.032 0.24 3 -10000 0 3
CCL17 -0.22 0.62 0.86 38 -1.2 180 218
GRB2 0.023 0.01 0.26 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.042 0.29 0.54 29 -0.77 32 61
T cell proliferation -0.25 0.61 0.76 6 -1.2 199 205
IL4R/JAK1 -0.24 0.59 0.76 2 -1.2 194 196
EGR2 -0.36 0.74 0.87 12 -1.4 261 273
JAK2 0.011 0.076 0.26 1 -10000 0 1
JAK3 0.022 0.036 0.28 14 -10000 0 14
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
JAK1 0.017 0.041 -10000 0 -10000 0 0
COL1A2 -0.024 0.27 0.6 5 -1.1 16 21
CCL26 -0.23 0.61 0.93 6 -1.2 178 184
IL4R -0.24 0.66 0.9 22 -1.3 191 213
PTPN6 0.014 0.035 0.21 2 -10000 0 2
IL13RA2 -0.24 0.61 0.86 7 -1.2 182 189
IL13RA1 0.011 0.077 0.26 1 -10000 0 1
IRF4 -0.13 0.5 0.58 12 -1.4 119 131
ARG1 -0.005 0.22 0.57 7 -0.75 3 10
CBL -0.11 0.38 0.6 30 -0.76 119 149
GTF3A 0.055 0.049 0.26 1 -10000 0 1
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL13RA1/JAK2 0.024 0.11 0.3 28 -10000 0 28
IRF4/BCL6 -0.12 0.45 0.51 2 -1.3 118 120
CD40LG -0.011 0.14 0.31 12 -0.58 49 61
MAPK14 -0.11 0.38 0.61 27 -0.78 113 140
mitosis -0.078 0.33 0.57 22 -0.74 70 92
STAT6 -0.27 0.75 0.96 42 -1.5 197 239
SPI1 0.027 0.018 0.26 5 -10000 0 5
RPS6KB1 -0.061 0.32 0.56 27 -0.73 62 89
STAT6 (dimer) -0.27 0.75 0.96 42 -1.5 197 239
STAT6 (dimer)/PARP14 -0.29 0.66 0.78 5 -1.3 213 218
mast cell activation 0 0.023 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.093 0.36 0.61 21 -0.83 72 93
FRAP1 -0.086 0.35 0.58 19 -0.8 70 89
LTA -0.22 0.62 0.87 32 -1.2 186 218
FES 0.022 0.032 -10000 0 -0.57 3 3
T-helper 1 cell differentiation 0.25 0.71 1.4 200 -0.96 43 243
CCL11 -0.18 0.59 0.78 19 -1.2 170 189
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.073 0.34 0.6 21 -0.86 50 71
IL2RG 0.025 0.073 0.26 45 -0.57 7 52
IL10 -0.21 0.6 0.86 13 -1.2 168 181
IRS1 0.001 0.11 -10000 0 -0.57 40 40
IRS2 0.003 0.11 -10000 0 -0.57 34 34
IL4 -0.011 0.26 0.71 7 -1.1 19 26
IL5 -0.24 0.61 0.86 7 -1.2 179 186
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.15 0.52 0.8 46 -0.93 180 226
COL1A1 -0.001 0.36 0.69 31 -1 46 77
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.25 0.61 -10000 0 -1.3 168 168
IL2R gamma/JAK3 0.037 0.069 0.36 17 -0.42 6 23
TFF3 -0.29 0.71 0.89 19 -1.4 228 247
ALOX15 -0.3 0.7 0.88 11 -1.4 241 252
MYBL1 0.039 0.064 0.26 81 -10000 0 81
T-helper 2 cell differentiation -0.19 0.52 0.72 24 -1 198 222
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 -0.083 0.35 0.57 26 -0.81 65 91
mol:PI-3-4-5-P3 -0.085 0.35 0.59 19 -0.8 70 89
PI3K -0.094 0.36 0.6 15 -0.87 69 84
DOK2 0.02 0.031 0.26 4 -0.57 2 6
ETS1 0.004 0.052 -10000 0 -0.53 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.032 0.27 0.51 33 -0.72 26 59
ITGB3 -0.26 0.63 0.85 5 -1.3 192 197
PIGR -0.67 0.8 0.86 12 -1.3 546 558
IGHE -0.015 0.086 0.18 32 -0.22 30 62
MAPKKK cascade -0.03 0.27 0.51 34 -0.7 26 60
BCL6 0.022 0.047 -10000 0 -0.57 6 6
OPRM1 -0.24 0.6 0.9 7 -1.3 176 183
RETNLB -0.24 0.6 0.84 5 -1.2 182 187
SELP -0.36 0.77 0.86 12 -1.5 272 284
AICDA -0.23 0.57 0.8 8 -1.2 172 180
Arf6 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
CENTA1/KIF3B 0.027 0.029 -10000 0 -0.39 3 3
ARNO/beta Arrestin1-2 -0.064 0.16 -10000 0 -0.55 44 44
EGFR -0.19 0.28 -10000 0 -0.57 375 375
EPHA2 0.021 0.041 -10000 0 -0.57 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 -0.21 0.26 -10000 0 -0.46 506 506
ARRB2 -0.043 0.13 -10000 0 -0.36 146 146
mol:GTP 0.011 0.049 0.14 31 -0.2 21 52
ARRB1 0.021 0.027 -10000 0 -0.57 2 2
FBXO8 0.024 0.005 -10000 0 -10000 0 0
TSHR 0.001 0.12 0.26 4 -0.57 40 44
EGF -0.082 0.23 0.26 2 -0.57 186 188
somatostatin receptor activity 0 0 0.001 1 -0.001 281 282
ARAP2 0.021 0.041 -10000 0 -0.57 5 5
mol:GDP -0.12 0.16 -10000 0 -0.32 300 300
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 174 174
ITGA2B 0.033 0.061 0.26 52 -0.57 3 55
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.039 -10000 0 -0.33 5 5
ADAP1 0.025 0.028 0.26 8 -0.57 1 9
KIF13B 0.019 0.028 -10000 0 -0.57 2 2
HGF/MET -0.064 0.2 -10000 0 -0.45 214 214
PXN 0.024 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.12 0.13 0.19 1 -0.28 312 313
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.17 0.23 -10000 0 -0.4 495 495
ADRB2 -0.1 0.24 -10000 0 -0.57 220 220
receptor agonist activity 0 0 0 1 0 280 281
actin filament binding 0 0 0 2 -0.001 285 287
SRC 0.023 0.005 -10000 0 -10000 0 0
ITGB3 0.005 0.11 0.26 4 -0.57 34 38
GNAQ 0.023 0.026 -10000 0 -0.57 2 2
EFA6/PI-4-5-P2 0 0 0.001 1 -0.001 166 167
ARF6/GDP -0.038 0.15 0.25 2 -0.44 89 91
ARF6/GDP/GULP/ACAP1 -0.11 0.18 -10000 0 -0.4 214 214
alphaIIb/beta3 Integrin/paxillin/GIT1 0.05 0.081 -10000 0 -0.33 37 37
ACAP1 0.028 0.065 0.26 42 -0.57 6 48
ACAP2 0.024 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.058 0.17 -10000 0 -0.49 146 146
EFNA1 0.02 0.009 -10000 0 -10000 0 0
HGF -0.01 0.14 0.26 2 -0.57 60 62
CYTH3 0.004 0.013 -10000 0 -0.42 1 1
CYTH2 0.007 0.096 -10000 0 -1 9 9
NCK1 0.024 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0 1 0 228 229
endosomal lumen acidification 0 0 0.001 5 0 261 266
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.013 0.14 -10000 0 -0.57 65 65
GNAQ/ARNO 0.019 0.092 -10000 0 -0.95 9 9
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 223 223
MET -0.073 0.22 -10000 0 -0.57 169 169
GNA14 0.022 0.066 0.26 19 -0.57 10 29
GNA15 0.025 0.026 0.26 6 -0.57 1 7
GIT1 0.023 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 1 -0.001 228 229
GNA11 0.023 0.026 -10000 0 -0.57 2 2
LHCGR -0.069 0.2 -10000 0 -0.57 146 146
AGTR1 -0.095 0.26 0.26 62 -0.57 231 293
desensitization of G-protein coupled receptor protein signaling pathway -0.058 0.17 -10000 0 -0.48 146 146
IPCEF1/ARNO -0.13 0.19 -10000 0 -0.59 64 64
alphaIIb/beta3 Integrin 0.026 0.092 -10000 0 -0.42 37 37
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.024 0.003 -10000 0 -10000 0 0
PTK2 0.019 0.01 -10000 0 -10000 0 0
CRKL -0.066 0.16 -10000 0 -0.34 230 230
GRB2/SOS1/SHC 0.038 0.022 -10000 0 -10000 0 0
HRAS 0.026 0.021 0.26 8 -10000 0 8
IRS1/Crk -0.061 0.16 -10000 0 -0.34 234 234
IGF-1R heterotetramer/IGF1/PTP1B -0.043 0.17 -10000 0 -0.37 203 203
AKT1 -0.066 0.14 0.25 2 -0.32 188 190
BAD -0.064 0.13 0.24 2 -0.45 43 45
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.068 0.16 -10000 0 -0.34 234 234
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.058 0.16 -10000 0 -0.34 234 234
RAF1 -0.047 0.13 0.28 1 -0.49 43 44
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.032 0.16 -10000 0 -0.33 216 216
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.061 0.17 -10000 0 -0.35 247 247
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.063 0.13 0.25 2 -0.32 169 171
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.028 0.12 0.31 9 -0.4 40 49
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.018 0.055 -10000 0 -0.57 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 -0.31 157 157
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.01 0.14 -10000 0 -0.31 152 152
IGF-1R heterotetramer -0.011 0.1 0.26 1 -0.63 20 21
IGF-1R heterotetramer/IGF1/IRS/Nck -0.045 0.17 -10000 0 -0.34 231 231
Crk/p130 Cas/Paxillin -0.036 0.16 -10000 0 -0.32 219 219
IGF1R -0.011 0.1 0.26 1 -0.63 20 21
IGF1 -0.11 0.25 -10000 0 -0.59 222 222
IRS2/Crk -0.067 0.17 -10000 0 -0.35 243 243
PI3K -0.034 0.17 -10000 0 -0.33 224 224
apoptosis 0.043 0.11 0.38 35 -0.27 5 40
HRAS/GDP 0.019 0.014 -10000 0 -10000 0 0
PRKCD -0.078 0.18 -10000 0 -0.4 222 222
RAF1/14-3-3 E -0.023 0.13 0.29 3 -0.42 43 46
BAD/14-3-3 -0.046 0.11 0.28 5 -0.41 35 40
PRKCZ -0.066 0.14 0.25 2 -0.32 195 197
Crk/p130 Cas/Paxillin/FAK1 -0.027 0.11 -10000 0 -0.4 38 38
PTPN1 0.024 0.019 0.26 6 -10000 0 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.082 0.19 -10000 0 -0.41 230 230
BCAR1 0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.022 0.14 -10000 0 -0.33 168 168
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.054 0.16 -10000 0 -0.34 231 231
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 -0.067 0.16 -10000 0 -0.34 234 234
IRS1 -0.071 0.17 -10000 0 -0.36 234 234
IRS2 -0.076 0.17 -10000 0 -0.36 245 245
IGF-1R heterotetramer/IGF1 -0.077 0.21 -10000 0 -0.45 236 236
GRB2 0.023 0.01 0.26 1 -10000 0 1
PDPK1 -0.068 0.14 0.28 1 -0.33 197 198
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKD1 -0.089 0.19 -10000 0 -0.42 229 229
SHC1 0.02 0.009 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.001 0.15 -10000 0 -0.32 168 168
ER alpha/Gai/GDP/Gbeta gamma -0.083 0.22 -10000 0 -0.46 205 205
AKT1 -0.12 0.33 -10000 0 -0.77 201 201
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.11 0.34 -10000 0 -0.78 199 199
mol:Ca2+ -0.023 0.1 0.27 2 -0.44 28 30
IGF1R 0.013 0.08 0.26 2 -0.57 19 21
E2/ER alpha (dimer)/Striatin -0.016 0.16 0.18 114 -0.36 169 283
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis 0.11 0.31 0.73 201 -10000 0 201
RhoA/GTP -0.016 0.1 -10000 0 -0.29 119 119
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.066 0.21 0.31 4 -0.46 190 194
regulation of stress fiber formation 0.024 0.1 0.24 122 -0.31 8 130
E2/ERA-ERB (dimer) -0.019 0.16 0.18 106 -0.36 169 275
KRAS 0.024 0.005 -10000 0 -10000 0 0
G13/GTP -0.009 0.13 -10000 0 -0.31 148 148
pseudopodium formation -0.024 0.1 0.31 8 -0.24 122 130
E2/ER alpha (dimer)/PELP1 -0.014 0.15 -10000 0 -0.36 148 148
GRB2 0.023 0.01 0.26 1 -10000 0 1
GNG2 0.018 0.058 -10000 0 -0.57 10 10
GNAO1 0.018 0.09 0.26 32 -0.57 19 51
HRAS 0.026 0.021 0.26 8 -10000 0 8
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.087 0.23 0.25 1 -0.5 214 215
E2/ER beta (dimer) 0.009 0.062 -10000 0 -0.41 22 22
mol:GDP -0.038 0.17 0.25 14 -0.39 165 179
mol:NADP -0.087 0.23 0.25 1 -0.5 214 215
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
mol:IP3 -0.026 0.1 0.27 2 -0.46 27 29
IGF-1R heterotetramer 0.013 0.08 0.26 2 -0.57 19 21
PLCB1 -0.024 0.11 0.28 2 -0.35 74 76
PLCB2 -0.005 0.083 -10000 0 -0.51 16 16
IGF1 -0.1 0.24 -10000 0 -0.57 222 222
mol:L-citrulline -0.087 0.23 0.25 1 -0.5 214 215
RHOA 0.024 0.005 -10000 0 -10000 0 0
Gai/GDP -0.076 0.25 -10000 0 -0.63 153 153
JNK cascade 0.009 0.062 -10000 0 -0.41 22 22
BCAR1 0.021 0.008 -10000 0 -10000 0 0
ESR2 0.012 0.084 -10000 0 -0.57 21 21
GNAQ 0.023 0.026 -10000 0 -0.57 2 2
ESR1 -0.036 0.23 0.26 116 -0.57 148 264
Gq family/GDP/Gbeta gamma -0.009 0.16 -10000 0 -0.75 36 36
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.018 0.13 -10000 0 -0.58 20 20
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.058 0.2 0.31 5 -0.46 157 162
GNAZ 0.018 0.055 -10000 0 -0.57 9 9
E2/ER alpha (dimer) -0.029 0.17 0.18 116 -0.41 154 270
STRN 0.014 0.078 -10000 0 -0.57 18 18
GNAL -0.11 0.25 -10000 0 -0.57 229 229
PELP1 0.022 0.007 -10000 0 -10000 0 0
MAPK11 0.002 0.056 -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 -0.005 0.13 -10000 0 -0.57 52 52
HBEGF -0.054 0.21 0.34 20 -0.5 109 129
cAMP biosynthetic process -0.088 0.18 -10000 0 -0.33 338 338
SRC -0.078 0.21 0.29 7 -0.44 203 210
PI3K 0.03 0.042 -10000 0 -0.4 9 9
GNB1 0.024 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.02 0.16 -10000 0 -0.36 160 160
SOS1 0.024 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.11 0.19 -10000 0 -0.43 212 212
Gs family/GTP -0.084 0.19 -10000 0 -0.33 338 338
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.044 0.019 -10000 0 -10000 0 0
vasodilation -0.082 0.22 0.24 1 -0.48 214 215
mol:DAG -0.026 0.1 0.27 2 -0.46 27 29
Gs family/GDP/Gbeta gamma -0.09 0.18 -10000 0 -0.36 274 274
MSN -0.026 0.11 0.32 8 -0.26 124 132
Gq family/GTP -0.001 0.088 -10000 0 -0.54 15 15
mol:PI-3-4-5-P3 -0.11 0.32 -10000 0 -0.75 200 200
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.082 0.22 0.48 214 -0.24 1 215
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
RhoA/GDP -0.022 0.17 0.26 11 -0.38 163 174
NOS3 -0.093 0.24 0.25 1 -0.53 214 215
GNA11 0.023 0.026 -10000 0 -0.57 2 2
MAPKKK cascade -0.083 0.25 0.3 3 -0.56 210 213
E2/ER alpha (dimer)/PELP1/Src -0.07 0.22 0.31 8 -0.48 194 202
ruffle organization -0.024 0.1 0.31 8 -0.24 122 130
ROCK2 -0.025 0.12 0.34 8 -0.28 131 139
GNA14 0.023 0.066 0.26 19 -0.57 10 29
GNA15 0.025 0.026 0.26 6 -0.57 1 7
GNA13 0.023 0.007 -10000 0 -10000 0 0
MMP9 -0.047 0.2 0.36 23 -0.49 108 131
MMP2 -0.069 0.2 0.28 9 -0.42 200 209
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.003 0.004 -10000 0 -10000 0 0
GNB1/GNG2 -0.008 0.13 -10000 0 -0.33 140 140
regulation of S phase of mitotic cell cycle -0.022 0.1 -10000 0 -0.29 123 123
GNAO1 0.018 0.09 0.26 32 -0.57 19 51
HRAS 0.025 0.021 0.26 8 -10000 0 8
SHBG/T-DHT 0.015 0.005 -10000 0 -10000 0 0
PELP1 0.022 0.007 -10000 0 -10000 0 0
AKT1 0.005 0.003 -10000 0 -10000 0 0
MAP2K1 -0.067 0.11 -10000 0 -0.33 120 120
T-DHT/AR -0.04 0.15 0.17 1 -0.42 132 133
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 306 306
GNAI2 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.006 0.13 -10000 0 -0.57 52 52
mol:GDP -0.061 0.16 -10000 0 -0.47 135 135
cell proliferation -0.13 0.21 0.27 3 -0.44 293 296
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
FOS -0.24 0.37 -10000 0 -0.81 309 309
mol:Ca2+ -0.013 0.028 -10000 0 -0.072 136 136
MAPK3 -0.099 0.16 0.26 4 -0.32 304 308
MAPK1 -0.078 0.14 -10000 0 -0.39 104 104
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
mol:IP3 -0.001 0.002 -10000 0 -0.004 304 304
cAMP biosynthetic process 0.004 0.02 -10000 0 -10000 0 0
GNG2 0.018 0.058 -10000 0 -0.57 10 10
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 304 304
HRAS/GTP -0.026 0.12 -10000 0 -0.32 129 129
actin cytoskeleton reorganization 0.03 0.032 -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 -0.004 304 304
PI3K 0.027 0.036 -10000 0 -0.34 9 9
apoptosis 0.13 0.21 0.43 313 -10000 0 313
T-DHT/AR/PELP1 -0.023 0.13 -10000 0 -0.36 131 131
HRAS/GDP -0.049 0.16 -10000 0 -0.45 132 132
CREB1 -0.14 0.23 -10000 0 -0.46 313 313
RAC1-CDC42/GTP 0.038 0.035 -10000 0 -0.3 8 8
AR -0.052 0.2 0.25 1 -0.57 131 132
GNB1 0.024 0.005 -10000 0 -10000 0 0
RAF1 -0.059 0.11 -10000 0 -0.32 124 124
RAC1-CDC42/GDP -0.025 0.16 -10000 0 -0.44 131 131
T-DHT/AR/PELP1/Src -0.02 0.12 -10000 0 -0.34 130 130
MAP2K2 -0.068 0.11 -10000 0 -0.33 117 117
T-DHT/AR/PELP1/Src/PI3K -0.022 0.11 -10000 0 -0.3 123 123
GNAZ 0.018 0.055 -10000 0 -0.57 9 9
SHBG 0.022 0.008 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.049 0.16 -10000 0 -0.49 82 82
mol:T-DHT -0.001 0.001 0.002 2 -0.003 203 205
RAC1 0.024 0.003 -10000 0 -10000 0 0
GNRH1 0.001 0.027 -10000 0 -0.42 4 4
Gi family/GTP -0.034 0.098 -10000 0 -0.28 92 92
CDC42 0.023 0.005 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.008 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.022 0.14 0.26 5 -0.26 152 157
NFATC4 -0.064 0.12 0.26 8 -0.26 80 88
ERBB2IP 0.024 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.024 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.069 0.15 -10000 0 -0.31 241 241
JUN -0.009 0.097 0.23 27 -0.45 3 30
HRAS 0.026 0.021 0.26 8 -10000 0 8
DOCK7 -0.08 0.14 0.28 2 -0.3 238 240
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.052 0.15 -10000 0 -0.33 195 195
AKT1 -0.001 0.009 -10000 0 -10000 0 0
BAD -0.007 0.006 -10000 0 -10000 0 0
MAPK10 -0.07 0.11 0.2 9 -0.27 134 143
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.073 0.16 -10000 0 -0.33 241 241
RAF1 -0.017 0.15 0.33 15 -0.3 56 71
ErbB2/ErbB3/neuregulin 2 -0.14 0.18 -10000 0 -0.35 429 429
STAT3 -0.003 0.16 -10000 0 -0.86 35 35
cell migration -0.056 0.1 0.23 15 -0.25 86 101
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.042 0.24 0.43 13 -0.49 113 126
FOS -0.098 0.28 0.34 28 -0.49 311 339
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.069 0.15 -10000 0 -0.31 241 241
MAPK3 -0.013 0.2 0.41 13 -0.43 60 73
MAPK1 -0.026 0.22 0.41 13 -0.56 45 58
JAK2 -0.078 0.14 0.26 1 -0.3 236 237
NF2 -0.003 0.062 -10000 0 -0.68 8 8
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.054 0.13 0.21 6 -0.28 225 231
NRG1 -0.14 0.26 0.26 4 -0.57 280 284
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
MAPK8 -0.081 0.15 0.23 4 -0.3 244 248
MAPK9 -0.042 0.083 0.2 11 -0.26 3 14
ERBB2 0 0.07 0.24 80 -0.44 1 81
ERBB3 0.021 0.042 -10000 0 -0.57 5 5
SHC1 0.021 0.01 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
apoptosis 0.019 0.025 -10000 0 -0.17 4 4
STAT3 (dimer) -0.002 0.16 -10000 0 -0.84 35 35
RNF41 -0.012 0.011 -10000 0 -10000 0 0
FRAP1 -0.004 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.07 0.093 -10000 0 -0.23 217 217
ErbB2/ErbB2/HSP90 (dimer) -0.011 0.02 -10000 0 -0.38 1 1
CHRNA1 0.019 0.18 0.36 60 -0.38 24 84
myelination -0.059 0.12 0.3 16 -0.26 63 79
PPP3CB -0.075 0.13 0.27 2 -0.28 237 239
KRAS 0.024 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.036 0.14 -10000 0 -0.26 191 191
NRG2 -0.26 0.3 -10000 0 -0.57 500 500
mol:GDP -0.053 0.13 0.21 6 -0.28 225 231
SOS1 0.025 0.003 -10000 0 -10000 0 0
MAP2K2 -0.015 0.14 0.33 16 -0.3 52 68
SRC 0.024 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.08 0.14 0.28 2 -0.3 240 242
MAP2K1 -0.051 0.22 0.42 6 -0.52 84 90
heart morphogenesis -0.069 0.15 -10000 0 -0.31 241 241
RAS family/GDP -0.021 0.14 0.29 1 -0.26 151 152
GRB2 0.023 0.01 0.26 1 -10000 0 1
PRKACA -0.003 0.072 -10000 0 -0.68 11 11
CHRNE 0.004 0.027 0.13 3 -0.21 3 6
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 -0.069 0.15 -10000 0 -0.31 241 241
CDC42 0.023 0.005 -10000 0 -10000 0 0
BMP 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
BMP7/BMPR2/BMPR1A-1B/FS 0.059 0.16 0.32 8 -0.35 111 119
SMAD6-7/SMURF1 0.046 0.015 -10000 0 -10000 0 0
NOG 0.012 0.097 0.26 19 -0.57 25 44
SMAD9 -0.087 0.25 -10000 0 -0.6 177 177
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD5 -0.02 0.14 -10000 0 -0.43 65 65
BMP7/USAG1 -0.2 0.25 -10000 0 -0.43 520 520
SMAD5/SKI -0.015 0.15 -10000 0 -0.44 64 64
SMAD1 0.013 0.063 -10000 0 -0.41 8 8
BMP2 -0.075 0.22 0.26 2 -0.57 173 175
SMAD1/SMAD1/SMAD4 0.018 0.069 -10000 0 -0.39 11 11
BMPR1A 0.023 0.026 -10000 0 -0.57 2 2
BMPR1B 0.1 0.15 0.26 413 -0.57 22 435
BMPR1A-1B/BAMBI 0.083 0.12 0.34 10 -0.33 53 63
AHSG 0.022 0.03 0.26 16 -10000 0 16
CER1 0.019 0.014 0.26 3 -10000 0 3
BMP2-4/CER1 -0.047 0.18 -10000 0 -0.39 208 208
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.038 0.16 -10000 0 -0.38 124 124
BMP2-4 (homodimer) -0.067 0.2 -10000 0 -0.45 215 215
RGMB 0.023 0.019 -10000 0 -0.57 1 1
BMP6/BMPR2/BMPR1A-1B 0.071 0.14 -10000 0 -0.31 92 92
RGMA -0.051 0.2 -10000 0 -0.57 131 131
SMURF1 0.024 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.035 0.16 0.23 1 -0.41 118 119
BMP2-4/USAG1 -0.22 0.26 -10000 0 -0.44 561 561
SMAD6/SMURF1/SMAD5 -0.016 0.15 -10000 0 -0.44 66 66
SOSTDC1 -0.26 0.3 0.26 3 -0.57 493 496
BMP7/BMPR2/BMPR1A-1B 0.067 0.14 0.3 4 -0.32 91 95
SKI 0.024 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) -0.015 0.15 0.26 2 -0.57 69 71
HFE2 0.018 0.024 0.26 9 -10000 0 9
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 -0.41 214 214
SMAD5/SMAD5/SMAD4 -0.016 0.15 -10000 0 -0.44 66 66
MAPK1 0.023 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.021 0.15 -10000 0 -0.37 106 106
BMP7 (homodimer) -0.014 0.16 0.26 29 -0.57 75 104
NUP214 0.024 0.004 -10000 0 -10000 0 0
BMP6/FETUA 0.002 0.12 0.2 16 -0.4 74 90
SMAD1/SKI 0.02 0.077 -10000 0 -0.42 12 12
SMAD6 0.024 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/FETUA -0.046 0.18 0.34 1 -0.39 210 211
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.037 0.098 0.26 94 -0.57 14 108
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) 0.086 0.11 -10000 0 -0.42 24 24
CHRDL1 -0.38 0.28 -10000 0 -0.57 703 703
ENDOFIN/SMAD1 0.019 0.079 -10000 0 -0.44 12 12
SMAD6-7/SMURF1/SMAD1 0.036 0.082 -10000 0 -0.42 12 12
SMAD6/SMURF1 0.024 0.004 -10000 0 -10000 0 0
BAMBI 0.015 0.11 0.26 38 -0.57 31 69
SMURF2 0.022 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.3 0.27 -10000 0 -0.46 703 703
BMP2-4/GREM1 -0.037 0.2 -10000 0 -0.4 218 218
SMAD7 0.024 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.08 0.25 -10000 0 -0.58 181 181
SMAD1/SMAD6 0.019 0.079 -10000 0 -0.43 13 13
TAK1/SMAD6 0.034 0.01 -10000 0 -10000 0 0
BMP7 -0.014 0.16 0.26 29 -0.57 75 104
BMP6 -0.015 0.15 0.26 2 -0.57 69 71
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.033 0.16 -10000 0 -0.42 118 118
PPM1A 0.024 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.018 0.076 -10000 0 -0.42 13 13
SMAD7/SMURF1 0.034 0.009 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
PPP1CA 0.023 0.006 -10000 0 -10000 0 0
XIAP 0.025 0.002 -10000 0 -10000 0 0
CTDSP1 0.024 0.003 -10000 0 -10000 0 0
PPP1R15A 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.045 0.2 0.23 1 -0.47 127 128
CHRD 0.025 0.096 0.26 54 -0.57 19 73
BMPR2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.049 0.18 -10000 0 -0.48 117 117
BMP4 -0.011 0.14 0.26 1 -0.57 61 62
FST 0.002 0.11 0.26 4 -0.57 39 43
BMP2-4/NOG -0.049 0.19 0.34 1 -0.41 205 206
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.071 0.14 0.3 4 -0.31 91 95
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.002 0.083 -10000 0 -0.55 14 14
Crk/p130 Cas/Paxillin -0.056 0.12 -10000 0 -0.34 136 136
JUN -0.016 0.12 0.23 2 -0.42 26 28
HRAS 0.026 0.021 0.26 8 -10000 0 8
RET51/GFRalpha1/GDNF/GRB10 0.041 0.19 0.34 51 -0.34 174 225
RAP1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.011 0.26 2 -10000 0 2
RAP1A/GDP 0.018 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.041 0.19 0.34 50 -0.34 172 222
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.003 -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 -0.011 0.15 0.32 4 -0.33 176 180
RHOA 0.024 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.02 0.16 0.28 36 -0.31 173 209
GRB7 0.019 0.033 -10000 0 -0.57 3 3
RET51/GFRalpha1/GDNF 0.04 0.19 0.34 50 -0.34 173 223
MAPKKK cascade -0.001 0.15 0.28 9 -0.32 152 161
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.024 0.18 0.32 3 -0.38 187 190
lamellipodium assembly -0.034 0.13 -10000 0 -0.31 140 140
RET51/GFRalpha1/GDNF/SHC 0.035 0.18 0.35 42 -0.34 136 178
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.009 0.14 0.32 4 -0.33 132 136
RET9/GFRalpha1/GDNF/Shank3 -0.014 0.15 0.32 4 -0.33 175 179
MAPK3 -0.032 0.13 0.24 8 -0.31 138 146
DOK1 0.025 0.015 0.26 4 -10000 0 4
DOK6 0.017 0.071 0.26 6 -0.57 14 20
PXN 0.024 0.002 -10000 0 -10000 0 0
neurite development -0.032 0.12 -10000 0 -0.44 21 21
DOK5 0.011 0.087 0.26 5 -0.57 22 27
GFRA1 -0.072 0.24 0.26 51 -0.57 187 238
MAPK8 -0.01 0.13 0.21 4 -0.28 140 144
HRAS/GTP 0.028 0.18 0.29 51 -0.34 166 217
tube development -0.007 0.15 0.34 9 -0.31 166 175
MAPK1 -0.031 0.13 0.25 9 -0.31 137 146
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.023 0.11 0.25 1 -0.27 161 162
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 0.036 0.19 0.34 47 -0.33 176 223
SHC1 0.02 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.026 0.19 0.34 37 -0.34 175 212
RET51/GFRalpha1/GDNF/Dok5 0.024 0.2 0.34 46 -0.35 182 228
PRKCA 0.01 0.084 0.26 1 -0.57 21 22
HRAS/GDP 0.019 0.014 0.18 8 -10000 0 8
CREB1 -0.014 0.13 0.23 9 -0.32 100 109
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.02 0.1 0.25 1 -0.26 119 120
RET51/GFRalpha1/GDNF/Grb7 0.04 0.18 0.33 63 -0.35 142 205
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.098 0.13 0.26 362 -0.57 13 375
DOK4 0.022 0.008 -10000 0 -10000 0 0
JNK cascade -0.015 0.12 0.25 1 -0.41 26 27
RET9/GFRalpha1/GDNF/FRS2 -0.013 0.15 0.32 4 -0.33 175 179
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 -0.02 0.1 0.25 1 -0.27 120 121
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.005 0.14 0.24 14 -0.28 135 149
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.002 0.14 0.25 4 -0.29 138 142
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.01 0.14 0.25 15 -0.3 102 117
PI3K -0.029 0.21 0.29 7 -0.47 141 148
SOS1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.004 0.14 0.32 3 -0.31 166 169
GRB10 0.024 0.003 -10000 0 -10000 0 0
activation of MAPKK activity -0.003 0.12 0.24 7 -0.27 83 90
RET51/GFRalpha1/GDNF/FRS2 0.037 0.19 0.34 53 -0.34 174 227
GAB1 0.024 0.004 -10000 0 -10000 0 0
IRS1 0.001 0.11 -10000 0 -0.57 40 40
IRS2 0.003 0.11 -10000 0 -0.57 34 34
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.009 0.14 0.25 15 -0.3 102 117
RET51/GFRalpha1/GDNF/PKC alpha 0.023 0.19 0.35 41 -0.34 181 222
GRB2 0.023 0.01 0.26 1 -10000 0 1
PRKACA 0.024 0.004 -10000 0 -10000 0 0
GDNF 0.032 0.053 0.26 54 -10000 0 54
RAC1 0.024 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.026 0.22 0.34 48 -0.38 186 234
Rac1/GTP -0.022 0.16 0.23 4 -0.37 140 144
RET9/GFRalpha1/GDNF -0.026 0.16 0.32 4 -0.36 176 180
GFRalpha1/GDNF -0.033 0.18 0.37 4 -0.41 186 190
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.015 0.081 0.26 8 -0.28 8 16
epithelial cell differentiation 0.033 0.081 0.39 1 -0.37 7 8
ITCH 0.032 0.019 -10000 0 -10000 0 0
WWP1 0.022 0.098 0.47 8 -10000 0 8
FYN 0.022 0.027 -10000 0 -0.57 2 2
EGFR -0.19 0.28 -10000 0 -0.57 375 375
PRL 0.022 0.025 0.26 11 -10000 0 11
neuron projection morphogenesis -0.041 0.14 0.35 13 -0.35 39 52
PTPRZ1 -0.28 0.3 0.26 6 -0.57 533 539
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.053 0.14 -10000 0 -0.31 173 173
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.087 0.16 0.24 1 -0.32 285 286
ADAM17 0.032 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.006 0.074 0.38 8 -0.3 6 14
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0 0.11 0.26 7 -0.33 54 61
NCOR1 0.022 0.008 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.08 0.15 -10000 0 -0.31 265 265
GRIN2B -0.098 0.16 0.24 6 -0.32 278 284
ErbB4/ErbB2/betacellulin 0.012 0.097 -10000 0 -0.3 46 46
STAT1 0.028 0.031 0.26 19 -10000 0 19
HBEGF 0.023 0.026 -10000 0 -0.57 2 2
PRLR 0.021 0.052 0.26 6 -0.57 7 13
E4ICDs/ETO2 0.007 0.088 0.27 6 -0.34 19 25
axon guidance 0.056 0.11 0.3 53 -0.32 6 59
NEDD4 0.03 0.018 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.031 0.041 -10000 0 -0.39 7 7
CBFA2T3 0.014 0.073 0.26 4 -0.57 15 19
ErbB4/ErbB2/HBEGF 0.03 0.072 -10000 0 -0.34 3 3
MAPK3 -0.048 0.14 0.34 4 -0.3 152 156
STAT1 (dimer) 0.019 0.081 0.26 10 -0.26 5 15
MAPK1 -0.047 0.14 0.36 5 -0.35 47 52
JAK2 0.023 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.072 0.15 0.25 2 -0.31 249 251
NRG1 -0.1 0.19 0.16 2 -0.42 276 278
NRG3 -0.001 0.13 0.26 21 -0.57 51 72
NRG2 -0.26 0.3 -10000 0 -0.57 500 500
NRG4 0.027 0.028 0.26 15 -10000 0 15
heart development 0.056 0.11 0.3 53 -0.32 6 59
neural crest cell migration -0.071 0.15 0.25 2 -0.31 249 251
ERBB2 0.034 0.07 0.27 82 -0.42 1 83
WWOX/E4ICDs 0.011 0.076 0.26 5 -0.25 8 13
SHC1 0.02 0.009 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.097 0.16 -10000 0 -0.31 288 288
apoptosis 0.013 0.12 0.42 54 -0.26 4 58
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.16 0.18 0.25 2 -0.33 488 490
ErbB4/ErbB2/epiregulin 0.005 0.13 0.3 21 -0.3 106 127
ErbB4/ErbB4/betacellulin/betacellulin -0.005 0.11 0.26 6 -0.32 62 68
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.04 0.088 0.39 1 -0.38 8 9
MDM2 0.009 0.08 0.26 31 -0.26 5 36
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.083 0.15 -10000 0 -0.32 268 268
STAT5A 0.05 0.11 0.29 44 -0.32 8 52
ErbB4/EGFR/neuregulin 1 beta -0.18 0.23 -10000 0 -0.42 459 459
DLG4 0.022 0.008 -10000 0 -10000 0 0
GRB2/SHC 0.028 0.016 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.01 0.07 0.22 6 -0.24 6 12
STAT5A (dimer) 0.06 0.1 0.46 1 -0.39 7 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.061 0.11 0.33 11 -0.32 7 18
LRIG1 0.022 0.032 -10000 0 -0.57 3 3
EREG -0.026 0.2 0.26 76 -0.57 115 191
BTC -0.008 0.14 0.26 2 -0.57 56 58
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.046 0.11 0.31 42 -0.33 6 48
ERBB4 -0.006 0.074 0.38 8 -0.3 6 14
STAT5B 0.022 0.027 -10000 0 -0.57 2 2
YAP1 -0.014 0.11 -10000 0 -0.39 74 74
GRB2 0.023 0.01 0.26 1 -10000 0 1
ErbB4/ErbB2/neuregulin 4 0.033 0.071 0.32 1 -0.41 1 2
glial cell differentiation -0.01 0.07 0.24 6 -0.22 6 12
WWOX 0.022 0.013 0.26 2 -10000 0 2
cell proliferation -0.039 0.17 0.35 15 -0.43 56 71
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 -0.069 0.11 -10000 0 -0.28 95 95
NT3 (dimer)/TRKC -0.17 0.26 -10000 0 -0.46 431 431
NT3 (dimer)/TRKB -0.29 0.31 -10000 0 -0.52 597 597
SHC/Grb2/SOS1/GAB1/PI3K 0.016 0.031 -10000 0 -0.26 6 6
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
BDNF -0.014 0.16 0.26 23 -0.57 75 98
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
NTRK1 0.023 0.051 0.26 23 -0.57 4 27
NTRK2 -0.28 0.3 -10000 0 -0.57 535 535
NTRK3 -0.17 0.28 0.26 5 -0.57 337 342
NT-4/5 (dimer)/TRKB -0.36 0.34 -10000 0 -0.57 681 681
neuron apoptosis 0.17 0.22 0.47 281 -10000 0 281
SHC 2-3/Grb2 -0.18 0.24 -10000 0 -0.52 281 281
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 -0.18 0.25 -10000 0 -0.55 277 277
SHC3 -0.18 0.24 -10000 0 -0.52 274 274
STAT3 (dimer) 0.033 0.045 -10000 0 -0.36 5 5
NT3 (dimer)/TRKA -0.1 0.21 -10000 0 -0.42 285 285
RIN/GDP -0.046 0.12 0.3 4 -0.26 78 82
GIPC1 0.024 0.011 0.26 2 -10000 0 2
KRAS 0.024 0.005 -10000 0 -10000 0 0
DNAJA3 -0.079 0.15 -10000 0 -0.34 242 242
RIN/GTP 0.014 0.006 0.18 1 -10000 0 1
CCND1 0.023 0.097 0.43 36 -0.82 5 41
MAGED1 0.025 0.01 0.26 2 -10000 0 2
PTPN11 0.024 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.18 0.28 -10000 0 -0.57 363 363
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 0.084 0.34 3 -0.39 29 32
TRKA/NEDD4-2 0.031 0.04 -10000 0 -0.37 5 5
ELMO1 0.024 0.004 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.032 0.008 -10000 0 -10000 0 0
NGF 0.017 0.076 0.26 8 -0.57 16 24
HRAS 0.026 0.021 0.26 8 -10000 0 8
DOCK1 0.024 0.005 -10000 0 -10000 0 0
GAB2 0.021 0.02 -10000 0 -0.57 1 1
RIT2 0.018 0.009 0.26 1 -10000 0 1
RIT1 0.021 0.009 -10000 0 -10000 0 0
FRS2 0.024 0.011 0.26 2 -10000 0 2
DNM1 0.02 0.049 0.26 1 -0.57 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 -0.072 0.16 -10000 0 -0.32 270 270
mol:GDP -0.075 0.16 0.34 6 -0.37 105 111
NGF (dimer) 0.017 0.076 0.26 8 -0.57 16 24
RhoG/GDP 0.018 0.003 -10000 0 -10000 0 0
RIT1/GDP -0.045 0.11 0.38 2 -0.26 73 75
TIAM1 0.025 0.015 0.26 4 -10000 0 4
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
BDNF (dimer)/TRKB -0.19 0.23 -10000 0 -0.39 556 556
KIDINS220/CRKL/C3G 0.034 0.01 -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 0.048 0.028 -10000 0 -10000 0 0
RIT1/GTP 0.015 0.007 -10000 0 -10000 0 0
NT3 (dimer) -0.06 0.21 0.26 12 -0.57 150 162
RAP1/GDP -0.041 0.094 -10000 0 -0.22 70 70
KIDINS220/CRKL 0.023 0.006 -10000 0 -10000 0 0
BDNF (dimer) -0.014 0.16 0.26 23 -0.57 75 98
ubiquitin-dependent protein catabolic process 0.035 0.062 -10000 0 -0.36 18 18
Schwann cell development -0.049 0.038 -10000 0 -10000 0 0
EHD4 0.024 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.055 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.019 0.051 -10000 0 -0.27 11 11
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.27 0.28 -10000 0 -0.47 611 611
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 -0.078 0.13 -10000 0 -0.45 55 55
STAT3 0.033 0.045 -10000 0 -0.36 5 5
axon guidance -0.26 0.26 -10000 0 -0.45 611 611
MAPK3 0.024 0.087 0.25 3 -0.36 27 30
MAPK1 0.026 0.09 0.25 4 -0.36 28 32
CDC42/GDP -0.044 0.12 0.28 6 -0.26 73 79
NTF3 -0.06 0.21 0.26 12 -0.57 150 162
NTF4 -0.18 0.28 -10000 0 -0.57 363 363
NGF (dimer)/TRKA/FAIM 0.037 0.062 -10000 0 -0.36 18 18
PI3K 0.03 0.042 -10000 0 -0.4 9 9
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 -0.078 0.16 0.25 3 -0.33 264 267
SOS1 0.024 0.003 -10000 0 -10000 0 0
MCF2L -0.16 0.22 0.21 1 -0.41 409 410
RGS19 0.023 0.01 0.26 1 -10000 0 1
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.096 0.33 3 -0.42 11 14
Rac1/GDP -0.045 0.12 0.31 4 -0.26 79 83
NGF (dimer)/TRKA/GRIT 0.024 0.058 -10000 0 -0.34 20 20
neuron projection morphogenesis -0.071 0.22 -10000 0 -0.74 50 50
NGF (dimer)/TRKA/NEDD4-2 0.036 0.062 -10000 0 -0.36 18 18
MAP2K1 0.03 0.086 0.36 17 -10000 0 17
NGFR -0.14 0.26 -10000 0 -0.57 280 280
NGF (dimer)/TRKA/GIPC/GAIP 0.015 0.051 -10000 0 -0.29 21 21
RAS family/GTP/PI3K 0.018 0.027 -10000 0 -0.26 6 6
FRS2 family/SHP2/GRB2/SOS1 0.063 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 0.003 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
MAPKKK cascade -0.04 0.14 -10000 0 -0.66 40 40
RASA1 0.024 0.004 -10000 0 -10000 0 0
TRKA/c-Abl 0.032 0.039 -10000 0 -0.42 4 4
SQSTM1 0.024 0.008 0.26 1 -10000 0 1
BDNF (dimer)/TRKB/GIPC -0.16 0.22 -10000 0 -0.36 551 551
NGF (dimer)/TRKA/p62/Atypical PKCs 0.052 0.063 -10000 0 -0.32 18 18
MATK 0.02 0.087 0.26 29 -0.57 18 47
NEDD4L 0.023 0.019 -10000 0 -0.57 1 1
RAS family/GDP -0.056 0.07 -10000 0 -0.21 65 65
NGF (dimer)/TRKA -0.087 0.16 -10000 0 -0.34 292 292
Rac1/GTP -0.084 0.12 -10000 0 -0.28 213 213
FRS2 family/SHP2/CRK family 0.06 0.029 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.022 0.037 -10000 0 -0.57 4 4
Jak2/Leptin Receptor -0.11 0.19 0.27 1 -0.39 265 266
PTP1B/AKT1 -0.066 0.13 0.22 1 -0.35 126 127
FYN 0.022 0.027 -10000 0 -0.57 2 2
p210 bcr-abl/PTP1B -0.082 0.14 0.22 2 -0.36 149 151
EGFR -0.2 0.29 -10000 0 -0.58 375 375
EGF/EGFR -0.2 0.24 -10000 0 -0.42 510 510
CSF1 0.021 0.041 -10000 0 -0.57 5 5
AKT1 0.024 0.005 -10000 0 -10000 0 0
INSR 0.024 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.047 0.16 0.23 13 -0.37 128 141
Insulin Receptor/Insulin -0.043 0.12 -10000 0 -0.38 53 53
HCK 0.027 0.026 0.26 13 -10000 0 13
CRK 0.022 0.007 -10000 0 -10000 0 0
TYK2 -0.078 0.14 0.28 3 -0.35 140 143
EGF -0.099 0.23 0.25 2 -0.58 186 188
YES1 0.023 0.019 -10000 0 -0.57 1 1
CAV1 -0.16 0.21 0.27 2 -0.42 319 321
TXN 0.017 0.017 0.25 3 -10000 0 3
PTP1B/IRS1/GRB2 -0.072 0.15 -10000 0 -0.38 144 144
cell migration 0.082 0.14 0.36 149 -0.22 2 151
STAT3 0.022 0.005 -10000 0 -10000 0 0
PRLR 0.021 0.052 0.26 6 -0.57 7 13
ITGA2B 0.031 0.061 0.26 52 -0.57 3 55
CSF1R 0.024 0.008 0.26 1 -10000 0 1
Prolactin Receptor/Prolactin 0.031 0.044 0.31 1 -0.43 6 7
FGR 0.024 0.009 0.26 1 -10000 0 1
PTP1B/p130 Cas -0.068 0.14 0.22 1 -0.35 136 137
Crk/p130 Cas -0.061 0.14 -10000 0 -0.36 114 114
DOK1 -0.067 0.13 0.23 2 -0.35 117 119
JAK2 -0.048 0.12 -10000 0 -0.43 64 64
Jak2/Leptin Receptor/Leptin -0.26 0.16 -10000 0 -0.4 420 420
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
PTPN1 -0.082 0.14 0.22 2 -0.36 149 151
LYN 0.021 0.009 -10000 0 -10000 0 0
CDH2 0.063 0.093 0.26 183 -0.57 2 185
SRC -0.017 0.098 -10000 0 -0.62 20 20
ITGB3 0.004 0.11 0.25 4 -0.57 34 38
CAT1/PTP1B -0.092 0.19 0.32 4 -0.47 147 151
CAPN1 0.021 0.006 -10000 0 -10000 0 0
CSK 0.024 0.004 -10000 0 -10000 0 0
PI3K -0.037 0.12 -10000 0 -0.4 46 46
mol:H2O2 -0.004 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.23 0.15 -10000 0 -0.36 385 385
negative regulation of transcription -0.047 0.12 -10000 0 -0.42 64 64
FCGR2A 0.021 0.012 0.26 1 -10000 0 1
FER 0.011 0.059 -10000 0 -0.58 10 10
alphaIIb/beta3 Integrin 0.023 0.093 -10000 0 -0.42 37 37
BLK 0.05 0.087 0.26 142 -0.57 2 144
Insulin Receptor/Insulin/Shc 0.035 0.019 -10000 0 -10000 0 0
RHOA 0.021 0.006 -10000 0 -10000 0 0
LEPR -0.12 0.26 -10000 0 -0.57 254 254
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 -0.042 0.18 0.32 5 -0.45 98 103
PRL 0.008 0.034 0.26 11 -10000 0 11
SOCS3 0.01 0.16 -10000 0 -1.2 16 16
SPRY2 -0.038 0.17 -10000 0 -0.58 97 97
Insulin Receptor/Insulin/IRS1 0.026 0.08 -10000 0 -0.37 40 40
CSF1/CSF1R -0.064 0.14 -10000 0 -0.36 135 135
Ras protein signal transduction 0.051 0.15 0.63 59 -10000 0 59
IRS1 0.001 0.11 -10000 0 -0.57 40 40
INS 0.009 0.015 -10000 0 -10000 0 0
LEP -0.44 0.24 -10000 0 -0.57 800 800
STAT5B -0.069 0.14 0.2 3 -0.35 140 143
STAT5A -0.07 0.14 0.2 3 -0.35 146 149
GRB2 0.023 0.01 0.26 1 -10000 0 1
PDGFB-D/PDGFRB -0.072 0.14 0.22 1 -0.36 138 139
CSN2 0.024 0.057 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
LAT -0.009 0.073 -10000 0 -0.55 9 9
YBX1 0.027 0.015 0.23 1 -10000 0 1
LCK 0.026 0.076 0.26 39 -0.57 11 50
SHC1 0.02 0.009 -10000 0 -10000 0 0
NOX4 0.02 0.031 0.26 10 -0.57 1 11
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.04 0.17 -10000 0 -0.42 169 169
CRKL -0.047 0.15 0.36 1 -0.42 74 75
mol:PIP3 0.002 0.06 0.57 1 -0.89 4 5
AKT1 0.01 0.075 0.37 3 -0.78 4 7
PTK2B 0.02 0.009 -10000 0 -10000 0 0
RAPGEF1 -0.046 0.14 0.34 1 -0.45 50 51
RANBP10 0.022 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.041 0.18 -10000 0 -0.39 204 204
MAP3K5 -0.04 0.15 0.36 1 -0.46 56 57
HGF/MET/CIN85/CBL/ENDOPHILINS -0.029 0.17 -10000 0 -0.36 210 210
AP1 -0.11 0.19 -10000 0 -0.4 292 292
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 -0.77 338 338
STAT3 (dimer) -0.046 0.15 -10000 0 -0.35 166 166
GAB1/CRKL/SHP2/PI3K -0.018 0.15 -10000 0 -0.46 46 46
INPP5D 0.024 0.004 -10000 0 -10000 0 0
CBL/CRK -0.036 0.14 0.34 1 -0.46 46 47
PTPN11 0.024 0.003 -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 0.019 -10000 0 -0.57 1 1
ELK1 -0.029 0.096 0.27 33 -0.21 132 165
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.026 0.092 -10000 0 -0.27 63 63
PAK1 0.023 0.087 0.36 7 -0.75 4 11
HGF/MET/RANBP10 -0.043 0.18 -10000 0 -0.38 211 211
HRAS -0.1 0.26 -10000 0 -0.64 184 184
DOCK1 -0.045 0.14 0.52 1 -0.41 70 71
GAB1 -0.049 0.16 -10000 0 -0.43 87 87
CRK -0.048 0.15 0.36 1 -0.42 74 75
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.1 0.25 -10000 0 -0.57 219 219
JUN 0.02 0.045 -10000 0 -0.57 6 6
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.051 0.12 -10000 0 -0.29 213 213
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
cell morphogenesis -0.047 0.16 0.37 6 -0.45 82 88
GRB2/SHC -0.016 0.11 -10000 0 -0.28 118 118
FOS -0.14 0.27 -10000 0 -0.57 290 290
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.029 0.096 0.27 33 -0.21 132 165
HGF/MET/MUC20 -0.053 0.17 -10000 0 -0.38 214 214
cell migration -0.016 0.11 -10000 0 -0.28 118 118
GRB2 0.023 0.01 0.26 1 -10000 0 1
CBL 0.022 0.008 -10000 0 -10000 0 0
MET/RANBP10 -0.042 0.17 -10000 0 -0.41 172 172
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.046 0.14 -10000 0 -0.33 174 174
MET/MUC20 -0.055 0.16 -10000 0 -0.41 177 177
RAP1B -0.039 0.14 0.34 3 -0.44 44 47
RAP1A -0.044 0.14 0.41 2 -0.43 44 46
HGF/MET/RANBP9 -0.041 0.18 -10000 0 -0.39 206 206
RAF1 -0.097 0.24 -10000 0 -0.6 184 184
STAT3 -0.047 0.15 -10000 0 -0.35 166 166
cell proliferation -0.04 0.19 0.28 35 -0.43 152 187
RPS6KB1 -0.015 0.064 -10000 0 -0.22 40 40
MAPK3 -0.042 0.094 0.66 7 -10000 0 7
MAPK1 -0.011 0.18 0.68 52 -10000 0 52
RANBP9 0.024 0.005 -10000 0 -10000 0 0
MAPK8 -0.028 0.14 0.44 1 -0.44 46 47
SRC -0.051 0.13 0.2 1 -0.32 167 168
PI3K -0.026 0.13 -10000 0 -0.29 171 171
MET/Glomulin -0.047 0.14 -10000 0 -0.37 171 171
SOS1 0.024 0.003 -10000 0 -10000 0 0
MAP2K1 -0.089 0.23 0.47 1 -0.56 183 184
MET -0.073 0.22 -10000 0 -0.57 169 169
MAP4K1 -0.042 0.15 0.38 1 -0.48 58 59
PTK2 0.019 0.01 -10000 0 -10000 0 0
MAP2K2 -0.089 0.23 0.47 1 -0.56 184 185
BAD 0.008 0.071 0.33 3 -0.75 4 7
MAP2K4 -0.036 0.13 0.34 1 -0.43 48 49
SHP2/GRB2/SOS1/GAB1 -0.039 0.17 -10000 0 -0.4 166 166
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 -0.27 197 197
PLCgamma1/PKC 0.017 0.004 -10000 0 -10000 0 0
HGF -0.01 0.14 0.26 2 -0.57 60 62
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 0.12 -10000 0 -0.27 199 199
PDPK1 0.013 0.078 0.42 1 -0.83 4 5
HGF/MET/SHIP -0.042 0.18 -10000 0 -0.39 212 212
Visual signal transduction: Rods

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
mol:K + 0.024 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.017 0.019 0.18 14 -10000 0 14
Metarhodopsin II/Arrestin 0.036 0.037 0.32 2 -10000 0 2
PDE6G/GNAT1/GTP 0.036 0.034 0.18 31 -10000 0 31
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.024 0.028 0.26 14 -10000 0 14
GRK1 0.019 0.016 0.26 4 -10000 0 4
CNG Channel -0.049 0.16 -10000 0 -0.31 276 276
mol:Na + -0.049 0.16 -10000 0 -0.3 268 268
mol:ADP 0.019 0.016 0.26 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.016 0.12 0.34 1 -0.36 85 86
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.043 0.17 0.28 5 -0.31 265 270
CNGB1 0.031 0.052 0.26 52 -10000 0 52
RDH5 -0.33 0.29 -10000 0 -0.57 625 625
SAG 0.032 0.051 0.26 50 -10000 0 50
mol:Ca2+ -0.082 0.14 0.35 17 -0.31 95 112
Na + (4 Units) -0.052 0.15 -10000 0 -0.29 246 246
RGS9 -0.025 0.17 0.26 11 -0.57 87 98
GNB1/GNGT1 0.055 0.059 0.2 154 -10000 0 154
GNAT1/GDP 0.025 0.11 0.3 5 -0.31 85 90
GUCY2D 0.023 0.047 0.26 15 -0.57 4 19
GNGT1 0.056 0.087 0.26 164 -10000 0 164
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 0.051 0.21 3 -0.31 16 19
mol:11-cis-retinal -0.33 0.29 -10000 0 -0.57 625 625
mol:cGMP 0.042 0.046 -10000 0 -0.32 8 8
GNB1 0.024 0.005 -10000 0 -10000 0 0
Rhodopsin -0.24 0.22 -10000 0 -0.42 629 629
SLC24A1 0.024 0.004 -10000 0 -10000 0 0
CNGA1 -0.14 0.27 0.26 4 -0.57 287 291
Metarhodopsin II 0.026 0.019 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.054 0.051 -10000 0 -0.34 8 8
RGS9BP 0.037 0.054 0.26 59 -10000 0 59
Metarhodopsin II/Transducin 0.024 0.032 0.17 8 -0.17 1 9
GCAP Family/Ca ++ 0.044 0.037 -10000 0 -0.34 4 4
PDE6A/B 0.028 0.066 -10000 0 -0.42 18 18
mol:Pi 0.016 0.12 0.34 1 -0.36 85 86
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.059 0.053 0.32 2 -10000 0 2
PDE6B 0.014 0.079 0.26 3 -0.57 18 21
PDE6A 0.028 0.032 0.26 19 -10000 0 19
PDE6G 0.032 0.046 0.26 41 -10000 0 41
RHO 0.024 0.028 0.26 14 -10000 0 14
PDE6 0.035 0.12 0.3 9 -0.31 96 105
GUCA1A 0.031 0.045 0.26 39 -10000 0 39
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 0.022 0.037 -10000 0 -0.57 4 4
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.003 0.039 0.23 2 -0.37 2 4
NFATC2 -0.025 0.11 0.21 3 -0.37 81 84
NFATC3 0.006 0.034 0.23 2 -10000 0 2
CD40LG -0.14 0.29 0.48 16 -0.58 220 236
PTGS2 -0.19 0.33 0.48 12 -0.64 307 319
JUNB 0.025 0.011 0.26 2 -10000 0 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.027 0.16 2 -10000 0 2
CaM/Ca2+ 0.008 0.027 0.16 2 -10000 0 2
CALM1 0.016 0.022 -10000 0 -10000 0 0
JUN 0.013 0.05 -10000 0 -0.58 6 6
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 0.027 0.047 0.26 23 -0.57 3 26
CREM 0.023 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.005 0.15 0.46 11 -0.42 46 57
FOS -0.15 0.27 -10000 0 -0.58 290 290
IFNG -0.11 0.28 0.46 40 -0.55 200 240
AP-1/NFAT1-c-4 -0.13 0.33 0.53 37 -0.63 226 263
FASLG -0.12 0.26 0.52 20 -0.55 183 203
NFAT1-c-4/ICER1 -0.017 0.12 0.32 5 -0.35 70 75
IL2RA -0.12 0.28 0.48 29 -0.54 221 250
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSF2 -0.13 0.27 0.48 18 -0.54 215 233
JunB/Fra1/NFAT1-c-4 -0.006 0.13 0.33 12 -0.34 69 81
IL4 -0.13 0.26 0.48 12 -0.56 190 202
IL2 -0.015 0.16 -10000 0 -0.94 27 27
IL3 -0.017 0.11 -10000 0 -0.72 23 23
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
BATF3 0.021 0.016 0.26 3 -10000 0 3
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.021 0.012 0.26 1 -10000 0 1
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.024 0.005 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.11 0.079 0.32 10 -0.3 1 11
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 0.26 544 -10000 0 544
AURKC 0.026 0.033 0.26 14 -0.57 1 15
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.018 0.043 -10000 0 -0.38 5 5
PDGFRB 0.018 0.038 -10000 0 -0.58 4 4
SPHK1 -0.018 0.098 -10000 0 -0.75 14 14
mol:S1P -0.021 0.096 0.39 1 -0.66 14 15
S1P1/S1P/Gi -0.13 0.23 0.31 2 -0.44 322 324
GNAO1 0.006 0.092 0.24 32 -0.58 19 51
PDGFB-D/PDGFRB/PLCgamma1 -0.11 0.21 0.37 3 -0.41 300 303
PLCG1 -0.12 0.22 0.36 2 -0.42 305 307
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.018 0.038 -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 -0.019 0.13 -10000 0 -0.58 52 52
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.014 0.03 0.2 1 -0.38 4 5
S1P1/S1P -0.034 0.098 0.28 2 -0.47 18 20
negative regulation of cAMP metabolic process -0.13 0.23 0.31 2 -0.43 322 324
MAPK3 -0.18 0.3 0.3 12 -0.58 343 355
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 0.041 -10000 0 -0.58 4 4
PLCB2 -0.025 0.097 0.3 6 -0.41 19 25
RAC1 0.024 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.082 -10000 0 -0.39 18 18
receptor internalization -0.035 0.088 -10000 0 -0.43 18 18
PTGS2 -0.33 0.5 0.38 2 -1 354 356
Rac1/GTP -0.032 0.082 -10000 0 -0.39 18 18
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFA 0.015 0.027 0.26 7 -10000 0 7
negative regulation of T cell proliferation -0.13 0.23 0.31 2 -0.43 322 324
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.004 0.059 -10000 0 -0.58 9 9
MAPK1 -0.2 0.33 0.34 2 -0.62 358 360
S1P1/S1P/PDGFB-D/PDGFRB -0.033 0.12 0.31 4 -0.48 17 21
ABCC1 0.012 0.019 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.1 0.19 -10000 0 -0.37 317 317
fibroblast growth factor receptor signaling pathway -0.1 0.19 -10000 0 -0.36 317 317
LAMA1 -0.036 0.18 0.26 3 -0.57 105 108
PRNP 0.015 0.071 -10000 0 -0.57 15 15
GPC1/SLIT2 -0.013 0.14 -10000 0 -0.41 111 111
SMAD2 0 0.067 0.25 1 -0.33 38 39
GPC1/PrPc/Cu2+ 0.026 0.05 -10000 0 -0.36 16 16
GPC1/Laminin alpha1 -0.013 0.14 0.37 1 -0.4 116 117
TDGF1 0.017 0.059 0.26 1 -0.57 10 11
CRIPTO/GPC1 0.03 0.049 -10000 0 -0.42 11 11
APP/GPC1 0.035 0.021 0.2 7 -0.42 1 8
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.005 0.04 -10000 0 -0.36 11 11
FLT1 0.023 0.006 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.033 0.08 -10000 0 -0.36 39 39
SERPINC1 0.03 0.049 0.26 45 -10000 0 45
FYN 0.004 0.043 -10000 0 -0.36 13 13
FGR 0.005 0.04 -10000 0 -0.36 11 11
positive regulation of MAPKKK cascade 0.01 0.083 0.26 4 -0.35 28 32
SLIT2 -0.037 0.18 -10000 0 -0.57 105 105
GPC1/NRG -0.11 0.2 -10000 0 -0.37 360 360
NRG1 -0.14 0.26 0.26 4 -0.57 280 284
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.046 0.026 -10000 0 -0.36 1 1
LYN 0.005 0.036 -10000 0 -0.36 8 8
mol:Spermine 0.006 0.017 -10000 0 -0.42 1 1
cell growth -0.1 0.19 -10000 0 -0.36 317 317
BMP signaling pathway -0.025 0.027 0.57 1 -0.26 7 8
SRC 0.005 0.04 -10000 0 -0.36 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 0.27 0.26 27 -0.57 294 321
GPC1 0.025 0.027 0.26 7 -0.57 1 8
TGFBR1 (dimer) 0.024 0.008 0.26 1 -10000 0 1
VEGFA 0.025 0.02 0.26 7 -10000 0 7
BLK 0.02 0.066 -10000 0 -0.37 13 13
HCK 0.007 0.043 -10000 0 -0.36 11 11
FGF2 -0.2 0.29 -10000 0 -0.57 393 393
FGFR1 0.016 0.049 -10000 0 -0.57 7 7
VEGFR1 homodimer 0.023 0.006 -10000 0 -10000 0 0
TGFBR2 0.002 0.11 -10000 0 -0.57 38 38
cell death 0.035 0.021 0.2 7 -0.42 1 8
ATIII/GPC1 0.037 0.04 -10000 0 -0.43 1 1
PLA2G2A/GPC1 -0.096 0.21 -10000 0 -0.4 316 316
LCK 0.006 0.061 -10000 0 -0.36 22 22
neuron differentiation -0.11 0.2 -10000 0 -0.37 360 360
PrPc/Cu2+ 0.011 0.052 -10000 0 -0.42 15 15
APP 0.024 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.002 0.11 -10000 0 -0.57 38 38
Effects of Botulinum toxin

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
STX1A 0.01 0.024 0.13 37 -10000 0 37
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.031 0.11 0.2 107 -0.42 45 152
STXBP1 0.021 0.041 -10000 0 -0.57 5 5
ACh/CHRNA1 0.073 0.09 0.2 340 -0.16 8 348
RAB3GAP2/RIMS1/UNC13B 0.035 0.088 -10000 0 -0.31 44 44
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.023 0.14 0.26 112 -0.57 44 156
mol:ACh -0.004 0.037 0.09 11 -0.14 43 54
RAB3GAP2 0.02 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.02 0.083 0.23 1 -0.27 43 44
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.073 0.09 0.2 340 -0.16 8 348
UNC13B 0.024 0.004 -10000 0 -10000 0 0
CHRNA1 0.1 0.11 0.26 351 -10000 0 351
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.033 0.11 0.2 195 -0.37 41 236
SNAP25 -0.001 0.059 -10000 0 -0.3 34 34
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 0.048 0.15 0.26 203 -0.57 37 240
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.023 0.032 -10000 0 -0.36 5 5
STX1A/SNAP25 fragment 1/VAMP2 0.02 0.083 0.23 1 -0.27 43 44
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.028 0.23 0.64 2 -0.65 29 31
CRP -0.007 0.24 0.56 23 -0.64 31 54
cell cycle arrest -0.039 0.25 0.56 10 -0.68 47 57
TIMP1 -0.02 0.22 0.52 10 -0.6 30 40
IL6ST -0.035 0.18 -10000 0 -0.56 111 111
Rac1/GDP -0.069 0.2 0.38 2 -0.42 143 145
AP1 -0.072 0.21 0.37 1 -0.56 63 64
GAB2 0.022 0.02 -10000 0 -0.57 1 1
TNFSF11 -0.017 0.24 0.6 11 -0.66 27 38
HSP90B1 0.022 0.11 -10000 0 -0.79 11 11
GAB1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.094 0.18 -10000 0 -0.52 90 90
AKT1 0.022 0.066 -10000 0 -0.66 4 4
FOXO1 0.023 0.067 0.43 1 -0.59 4 5
MAP2K6 -0.095 0.18 0.27 2 -0.49 111 113
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.053 0.2 0.38 12 -0.48 86 98
MITF -0.09 0.19 0.27 10 -0.41 170 180
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 -0.002 0.18 -10000 0 -1.2 24 24
CEBPB 0.021 0.018 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.018 0.13 -10000 0 -0.5 39 39
STAT3 -0.046 0.26 0.57 9 -0.74 47 56
STAT1 0.012 0.094 -10000 0 -0.83 10 10
CEBPD -0.013 0.23 0.57 9 -0.67 31 40
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.031 0.042 -10000 0 -0.4 9 9
JUN 0.02 0.045 -10000 0 -0.57 6 6
PIAS3/MITF -0.072 0.18 0.32 2 -0.4 148 150
MAPK11 -0.094 0.18 -10000 0 -0.53 87 87
STAT3 (dimer)/FOXO1 -0.025 0.22 0.51 13 -0.55 51 64
GRB2/SOS1/GAB family -0.06 0.18 -10000 0 -0.48 76 76
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.1 0.19 0.24 1 -0.34 307 308
GRB2 0.023 0.01 0.26 1 -10000 0 1
JAK2 0.023 0.006 -10000 0 -10000 0 0
LBP -0.17 0.45 0.54 24 -0.92 247 271
PIK3R1 0.019 0.055 -10000 0 -0.57 9 9
JAK1 0.026 0.008 -10000 0 -10000 0 0
MYC -0.003 0.27 0.57 14 -0.94 33 47
FGG -0.026 0.23 0.6 11 -0.66 29 40
macrophage differentiation -0.039 0.25 0.56 10 -0.68 47 57
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.093 0.21 -10000 0 -0.35 350 350
JUNB -0.03 0.22 0.61 2 -0.62 31 33
FOS -0.14 0.27 -10000 0 -0.57 290 290
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.092 0.2 0.3 10 -0.42 173 183
STAT1/PIAS1 -0.06 0.2 0.36 9 -0.39 164 173
GRB2/SOS1/GAB family/SHP2/PI3K 0.024 0.07 -10000 0 -0.52 8 8
STAT3 (dimer) -0.044 0.26 0.57 9 -0.73 46 55
PRKCD -0.037 0.2 0.45 14 -0.51 62 76
IL6R 0.002 0.11 -10000 0 -0.57 36 36
SOCS3 -0.091 0.19 -10000 0 -0.66 48 48
gp130 (dimer)/JAK1/JAK1/LMO4 0.013 0.13 -10000 0 -0.35 111 111
Rac1/GTP -0.063 0.2 0.34 9 -0.46 106 115
HCK 0.027 0.026 0.26 13 -10000 0 13
MAPKKK cascade -0.002 0.14 -10000 0 -0.61 32 32
bone resorption -0.015 0.23 0.6 11 -0.63 27 38
IRF1 -0.031 0.22 0.64 2 -0.67 27 29
mol:GDP -0.083 0.19 0.29 11 -0.41 168 179
SOS1 0.024 0.004 -10000 0 -10000 0 0
VAV1 -0.085 0.2 0.29 11 -0.41 168 179
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.2 -10000 0 -0.59 90 90
PTPN11 0.011 0.082 -10000 0 -0.84 8 8
IL6/IL6RA -0.12 0.22 -10000 0 -0.43 309 309
gp130 (dimer)/TYK2/TYK2/LMO4 0.009 0.13 0.24 1 -0.36 111 112
gp130 (dimer)/JAK2/JAK2/LMO4 0.009 0.13 -10000 0 -0.36 105 105
IL6 -0.18 0.29 0.28 1 -0.57 368 369
PIAS3 0.02 0.009 -10000 0 -10000 0 0
PTPRE 0.008 0.031 -10000 0 -0.57 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 -0.11 0.19 0.22 2 -0.33 324 326
LMO4 0.028 0.037 0.28 2 -0.57 3 5
STAT3 (dimer)/PIAS3 -0.049 0.24 0.54 9 -0.69 49 58
MCL1 0.054 0.097 0.49 1 -0.58 4 5
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.006 0.071 0.34 1 -0.34 10 11
alphaM/beta2 Integrin/GPIbA 0.01 0.076 0.34 4 -0.41 6 10
alphaM/beta2 Integrin/proMMP-9 0.074 0.11 0.35 16 -0.42 1 17
PLAUR 0.041 0.061 0.26 76 -10000 0 76
HMGB1 -0.003 0.04 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.01 0.063 0.34 1 -10000 0 1
AGER -0.006 0.051 0.26 1 -0.47 3 4
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 0.32 4 -0.36 13 17
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 439 -0.57 1 440
CYR61 -0.004 0.13 -10000 0 -0.57 49 49
TLN1 0.024 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.001 0.11 -10000 0 -0.36 37 37
RHOA 0.024 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.094 0.23 -10000 0 -0.57 200 200
MYH2 -0.013 0.14 0.29 7 -0.47 37 44
MST1R 0.022 0.054 0.26 9 -0.57 7 16
leukocyte activation during inflammatory response -0.18 0.17 0.29 1 -0.33 573 574
APOB -0.34 0.29 -10000 0 -0.57 629 629
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.018 0.05 0.26 1 -0.57 7 8
JAM3 0.019 0.042 -10000 0 -0.57 5 5
GP1BA 0.025 0.059 0.26 26 -0.57 6 32
alphaM/beta2 Integrin/CTGF 0.005 0.076 0.34 1 -0.39 12 13
alphaM/beta2 Integrin -0.012 0.12 0.22 6 -0.39 43 49
JAM3 homodimer 0.019 0.042 -10000 0 -0.57 5 5
ICAM2 0.019 0.042 -10000 0 -0.57 5 5
ICAM1 0.027 0.028 0.26 15 -10000 0 15
phagocytosis triggered by activation of immune response cell surface activating receptor -0.01 0.12 0.24 5 -0.38 44 49
cell adhesion 0.01 0.075 0.33 4 -0.4 6 10
NFKB1 -0.099 0.2 0.42 4 -0.37 324 328
THY1 0.024 0.022 0.26 8 -10000 0 8
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.21 0.19 -10000 0 -0.36 635 635
alphaM/beta2 Integrin/LRP/tPA 0.008 0.091 0.34 1 -0.38 26 27
IL6 -0.26 0.39 0.36 2 -0.76 379 381
ITGB2 -0.002 0.052 0.26 15 -10000 0 15
elevation of cytosolic calcium ion concentration 0.031 0.085 0.34 19 -10000 0 19
alphaM/beta2 Integrin/JAM2/JAM3 0.001 0.1 0.34 1 -0.38 41 42
JAM2 -0.004 0.13 -10000 0 -0.57 49 49
alphaM/beta2 Integrin/ICAM1 0.023 0.086 0.33 4 -0.33 17 21
alphaM/beta2 Integrin/uPA/Plg 0.019 0.071 0.33 1 -10000 0 1
RhoA/GTP -0.018 0.15 0.24 16 -0.4 68 84
positive regulation of phagocytosis -0.002 0.1 0.3 5 -0.36 19 24
Ron/MSP 0.03 0.062 0.37 1 -0.4 18 19
alphaM/beta2 Integrin/uPAR/uPA 0.032 0.087 0.34 19 -10000 0 19
alphaM/beta2 Integrin/uPAR 0.02 0.078 0.4 3 -10000 0 3
PLAU 0.03 0.038 0.26 28 -10000 0 28
PLAT 0.006 0.091 0.26 1 -0.57 25 26
actin filament polymerization -0.012 0.14 0.28 8 -0.44 37 45
MST1 0.02 0.055 0.26 6 -0.57 8 14
alphaM/beta2 Integrin/lipoprotein(a) -0.18 0.17 0.32 1 -0.33 573 574
TNF -0.099 0.2 0.39 3 -0.73 16 19
RAP1B 0.024 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.014 0.068 0.34 1 -10000 0 1
fibrinolysis 0.018 0.069 0.32 1 -10000 0 1
HCK 0.027 0.026 0.26 13 -10000 0 13
dendritic cell antigen processing and presentation -0.01 0.12 0.24 5 -0.38 44 49
VTN 0.033 0.078 0.26 66 -0.57 8 74
alphaM/beta2 Integrin/CYR61 -0.008 0.1 0.34 1 -0.39 48 49
LPA 0.018 0.017 0.26 5 -10000 0 5
LRP1 0.019 0.058 -10000 0 -0.57 10 10
cell migration 0.043 0.084 0.28 14 -0.36 8 22
FN1 0.12 0.11 0.26 411 -10000 0 411
alphaM/beta2 Integrin/Thy1 0.01 0.063 0.34 1 -10000 0 1
MPO -0.012 0.14 0.26 2 -0.57 60 62
KNG1 0.023 0.033 0.26 20 -10000 0 20
RAP1/GDP 0.031 0.008 -10000 0 -10000 0 0
ROCK1 -0.012 0.15 0.29 12 -0.46 40 52
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.019 0.022 0.26 8 -10000 0 8
CTGF 0.017 0.065 0.26 3 -0.57 12 15
alphaM/beta2 Integrin/Hck 0.011 0.067 0.35 5 -10000 0 5
ITGAM -0.003 0.044 0.25 5 -10000 0 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.044 0.16 0.34 1 -0.36 180 181
HP -0.068 0.23 0.26 35 -0.57 169 204
leukocyte adhesion -0.038 0.14 0.29 4 -0.38 51 55
SELP -0.094 0.23 -10000 0 -0.57 200 200
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.034 0.033 -10000 0 -0.42 4 4
alphaV beta3 Integrin -0.12 0.21 -10000 0 -0.38 389 389
PTK2 -0.056 0.15 0.32 2 -0.52 43 45
IGF1R 0.013 0.08 0.26 2 -0.57 19 21
PI4KB 0.02 0.009 -10000 0 -10000 0 0
MFGE8 0.018 0.066 0.26 6 -0.57 12 18
SRC 0.024 0.005 -10000 0 -10000 0 0
CDKN1B -0.044 0.12 -10000 0 -0.53 34 34
VEGFA 0.025 0.02 0.26 7 -10000 0 7
ILK -0.042 0.12 -10000 0 -0.5 31 31
ROCK1 0.023 0.019 -10000 0 -0.57 1 1
AKT1 -0.043 0.1 -10000 0 -0.5 27 27
PTK2B -0.014 0.071 0.36 2 -0.34 33 35
alphaV/beta3 Integrin/JAM-A -0.076 0.18 0.3 1 -0.33 286 287
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 -0.36 34 34
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.043 0.19 -10000 0 -0.38 234 234
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.013 0.069 -10000 0 -0.44 10 10
alphaV/beta3 Integrin/Syndecan-1 0.042 0.083 -10000 0 -0.36 34 34
PI4KA 0.023 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.27 -10000 0 -0.46 342 342
PI4 Kinase 0.028 0.015 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.069 0.1 0.34 3 -0.35 34 37
RPS6KB1 -0.16 0.22 0.42 3 -0.55 177 180
TLN1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 -0.2 0.29 -10000 0 -0.58 337 337
GPR124 0.016 0.049 -10000 0 -0.57 7 7
MAPK1 -0.2 0.29 -10000 0 -0.58 351 351
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
alphaV/beta3 Integrin/Tumstatin -0.033 0.17 -10000 0 -0.37 195 195
cell adhesion 0.023 0.084 0.26 1 -0.36 43 44
ANGPTL3 0.021 0.016 0.26 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.045 0.03 -10000 0 -0.36 3 3
IGF-1R heterotetramer 0.013 0.08 0.26 2 -0.57 19 21
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
TGFBR2 0.002 0.11 -10000 0 -0.57 38 38
ITGB3 0.005 0.11 0.26 4 -0.57 34 38
IGF1 -0.1 0.24 -10000 0 -0.57 222 222
RAC1 0.024 0.003 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.024 0.08 -10000 0 -0.4 31 31
apoptosis 0.024 0.003 -10000 0 -10000 0 0
CD47 0.024 0.019 -10000 0 -0.57 1 1
alphaV/beta3 Integrin/CD47 0.033 0.075 -10000 0 -0.36 34 34
VCL 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.014 0.14 -10000 0 -0.46 68 68
CSF1 0.021 0.041 -10000 0 -0.57 5 5
PIK3C2A -0.041 0.11 -10000 0 -0.5 28 28
PI4 Kinase/Pyk2 -0.077 0.15 -10000 0 -0.52 24 24
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.044 0.081 -10000 0 -0.37 34 34
FAK1/Vinculin -0.037 0.13 0.34 4 -0.41 39 43
alphaV beta3/Integrin/ppsTEM5 0.025 0.081 -10000 0 -0.4 31 31
RHOA 0.024 0.005 -10000 0 -10000 0 0
VTN 0.033 0.078 0.26 66 -0.57 8 74
BCAR1 0.021 0.008 -10000 0 -10000 0 0
FGF2 -0.2 0.29 -10000 0 -0.57 393 393
F11R -0.12 0.19 -10000 0 -0.42 297 297
alphaV/beta3 Integrin/Lactadherin 0.029 0.09 0.34 1 -0.38 43 44
alphaV/beta3 Integrin/TGFBR2 0.021 0.12 -10000 0 -0.46 53 53
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.05 0.037 -10000 0 -0.33 5 5
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.032 0.068 -10000 0 -0.33 33 33
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.12 0.11 0.26 411 -10000 0 411
alphaV/beta3 Integrin/Pyk2 0.026 0.074 -10000 0 -0.34 34 34
SDC1 0.039 0.061 0.26 68 -0.57 1 69
VAV3 -0.011 0.042 -10000 0 -0.32 12 12
PTPN11 0.024 0.003 -10000 0 -10000 0 0
IRS1 0.001 0.11 -10000 0 -0.57 40 40
FAK1/Paxillin -0.037 0.14 0.34 4 -0.41 40 44
cell migration -0.036 0.12 0.3 6 -0.38 36 42
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PI3K -0.066 0.17 -10000 0 -0.32 249 249
SPP1 0.086 0.1 0.26 276 -10000 0 276
KDR 0.022 0.037 -10000 0 -0.57 4 4
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 -0.076 0.22 0.26 4 -0.57 175 179
angiogenesis -0.19 0.3 -10000 0 -0.58 322 322
Rac1/GTP 0.021 0.039 -10000 0 -0.29 11 11
EDIL3 -0.006 0.14 0.26 15 -0.57 57 72
cell proliferation 0.02 0.12 -10000 0 -0.46 53 53
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.045 0.18 0.3 128 -0.48 50 178
FYN 0.023 0.2 0.33 61 -0.58 57 118
LAT/GRAP2/SLP76 0.027 0.18 0.36 44 -0.51 55 99
IKBKB 0.021 0.009 -10000 0 -10000 0 0
AKT1 0.024 0.16 0.32 76 -0.38 72 148
B2M 0.025 0.009 -10000 0 -10000 0 0
IKBKG 0.017 0.059 0.16 71 -0.14 27 98
MAP3K8 0.02 0.049 -10000 0 -0.57 7 7
mol:Ca2+ -0.022 0.032 -10000 0 -0.09 166 166
integrin-mediated signaling pathway 0.026 0.023 -10000 0 -0.29 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.012 0.2 0.4 37 -0.53 79 116
TRPV6 -0.09 0.27 1.2 15 -0.57 189 204
CD28 0.024 0.051 0.26 10 -0.57 6 16
SHC1 0.03 0.21 0.32 142 -0.57 63 205
receptor internalization -0.011 0.22 0.36 37 -0.5 129 166
PRF1 -0.01 0.24 0.56 7 -0.99 41 48
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 74 -0.35 53 127
LAT 0.015 0.2 0.36 53 -0.61 59 112
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D 0.023 0.096 0.27 46 -0.58 19 65
CD3E 0.022 0.088 0.27 36 -0.58 16 52
CD3G 0.013 0.11 0.26 38 -0.57 32 70
RASGRP2 0 0.051 0.13 16 -0.17 70 86
RASGRP1 0.026 0.16 0.35 48 -0.42 56 104
HLA-A 0.026 0.022 0.26 7 -10000 0 7
RASSF5 0.019 0.034 0.26 1 -0.57 3 4
RAP1A/GTP/RAPL 0.026 0.023 -10000 0 -0.29 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.041 0.081 0.18 148 -0.14 19 167
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.056 -10000 0 -0.22 41 41
PRKCA 0.014 0.099 0.24 45 -0.28 47 92
GRAP2 0.016 0.067 0.26 3 -0.57 13 16
mol:IP3 0.014 0.14 0.26 125 -0.38 52 177
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.005 0.18 0.31 36 -0.65 51 87
ORAI1 0.037 0.17 0.64 4 -0.98 14 18
CSK 0.01 0.2 0.37 36 -0.61 59 95
B7 family/CD28 0.062 0.21 0.44 44 -0.63 47 91
CHUK 0.024 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.002 0.23 0.39 38 -0.57 92 130
PTPN6 0.009 0.2 0.36 39 -0.62 56 95
VAV1 0.006 0.2 0.37 37 -0.6 64 101
Monovalent TCR/CD3 -0.002 0.14 0.27 37 -0.51 55 92
CBL 0.022 0.008 -10000 0 -10000 0 0
LCK 0.02 0.2 0.36 47 -0.6 60 107
PAG1 0.023 0.2 0.33 66 -0.6 59 125
RAP1A 0.024 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.002 0.22 0.37 38 -0.64 69 107
CD80 0.087 0.1 0.26 278 -10000 0 278
CD86 0.026 0.018 0.26 6 -10000 0 6
PDK1/CARD11/BCL10/MALT1 -0.006 0.072 0.19 4 -0.26 41 45
HRAS 0.026 0.021 0.26 8 -10000 0 8
GO:0035030 0.022 0.16 0.33 45 -0.52 47 92
CD8A 0.028 0.062 0.27 29 -0.58 6 35
CD8B 0.014 0.11 0.27 30 -0.58 32 62
PTPRC 0.021 0.042 0.26 11 -0.58 3 14
PDK1/PKC theta 0.025 0.19 0.38 75 -0.49 64 139
CSK/PAG1 0.026 0.2 0.33 65 -0.61 52 117
SOS1 0.024 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.038 0.02 0.22 4 -10000 0 4
GRAP2/SLP76 0.021 0.2 0.39 34 -0.6 59 93
STIM1 0.025 0.096 1.3 4 -10000 0 4
RAS family/GTP 0.045 0.094 0.22 94 -0.18 42 136
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.015 0.24 0.36 37 -0.51 138 175
mol:DAG -0.017 0.098 0.13 20 -0.34 55 75
RAP1A/GDP 0.022 0.037 0.1 73 -10000 0 73
PLCG1 0.023 0.005 -10000 0 -10000 0 0
CD247 0.016 0.078 0.27 16 -0.58 15 31
cytotoxic T cell degranulation -0.007 0.23 0.54 8 -0.92 41 49
RAP1A/GTP -0.001 0.017 -10000 0 -0.064 67 67
mol:PI-3-4-5-P3 0.019 0.18 0.37 44 -0.44 78 122
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.021 0.17 0.29 114 -0.5 51 165
NRAS 0.024 0.004 -10000 0 -10000 0 0
ZAP70 0.026 0.099 0.26 56 -0.57 20 76
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.007 0.16 0.39 14 -0.51 53 67
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 0.38 21 -0.48 33 54
CARD11 0.027 0.042 0.26 20 -0.57 2 22
PRKCB 0.015 0.1 0.27 48 -0.28 42 90
PRKCE 0.019 0.097 0.23 55 -0.26 42 97
PRKCQ 0.014 0.2 0.4 39 -0.54 73 112
LCP2 0.024 0.008 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 0.3 82 -0.33 68 150
IKK complex 0.036 0.082 0.21 114 -0.12 14 128
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.026 0.11 0.25 82 -0.27 48 130
PDPK1 0.029 0.16 0.35 76 -0.38 59 135
TCR/CD3/MHC I/CD8/Fyn -0.024 0.24 0.41 29 -0.74 71 100
Syndecan-1-mediated signaling events

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
TGFB1 0.025 0.013 0.26 3 -10000 0 3
CCL5 0.029 0.057 0.26 37 -0.57 4 41
SDCBP 0.021 0.009 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.063 0.12 0.28 24 -0.38 14 38
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.05 0.12 0.26 5 -0.37 17 22
Syndecan-1/Syntenin 0.051 0.12 0.28 10 -0.39 13 23
MAPK3 0.048 0.11 0.26 11 -0.36 14 25
HGF/MET -0.064 0.2 -10000 0 -0.45 214 214
TGFB1/TGF beta receptor Type II 0.025 0.013 0.26 3 -10000 0 3
BSG 0.024 0.009 0.26 1 -10000 0 1
keratinocyte migration 0.049 0.12 0.26 5 -0.37 17 22
Syndecan-1/RANTES 0.059 0.13 0.3 43 -0.4 18 61
Syndecan-1/CD147 0.064 0.13 0.3 10 -0.36 16 26
Syndecan-1/Syntenin/PIP2 0.047 0.11 0.27 9 -0.38 13 22
LAMA5 0.023 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.046 0.11 0.26 8 -0.37 13 21
MMP7 -0.038 0.19 0.26 31 -0.57 117 148
HGF -0.01 0.14 0.26 2 -0.57 60 62
Syndecan-1/CASK 0.042 0.12 0.22 19 -0.36 18 37
Syndecan-1/HGF/MET -0.003 0.2 0.3 8 -0.45 107 115
regulation of cell adhesion 0.041 0.11 0.26 8 -0.39 8 16
HPSE 0.027 0.035 0.26 17 -0.57 1 18
positive regulation of cell migration 0.063 0.12 0.28 24 -0.38 14 38
SDC1 0.066 0.12 0.27 23 -0.39 10 33
Syndecan-1/Collagen 0.063 0.12 0.28 24 -0.38 14 38
PPIB 0.025 0.013 0.26 3 -10000 0 3
MET -0.073 0.22 -10000 0 -0.57 169 169
PRKACA 0.024 0.004 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 439 -0.57 1 440
MAPK1 0.048 0.11 0.27 10 -0.4 8 18
homophilic cell adhesion 0.062 0.12 0.28 24 -0.38 15 39
MMP1 0.18 0.11 0.26 714 -10000 0 714
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 0.034 0.073 -10000 0 -0.33 36 36
NF kappa B1 p50/RelA/I kappa B alpha 0.001 0.12 -10000 0 -0.41 17 17
AP1 -0.092 0.19 -10000 0 -0.33 370 370
mol:PIP3 -0.13 0.18 -10000 0 -0.34 404 404
AKT1 0.007 0.076 0.31 2 -0.4 11 13
PTK2B -0.028 0.1 -10000 0 -0.35 52 52
RHOA 0.003 0.062 0.24 3 -0.31 26 29
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.013 0.11 0.23 2 -0.28 94 96
MAGI3 0.024 0.004 -10000 0 -10000 0 0
RELA 0.024 0.005 -10000 0 -10000 0 0
apoptosis -0.026 0.12 -10000 0 -0.32 136 136
HRAS/GDP 0.019 0.014 0.18 8 -10000 0 8
positive regulation of microtubule depolymerization -0.052 0.12 0.26 3 -0.32 115 118
NF kappa B1 p50/RelA -0.012 0.12 -10000 0 -0.33 94 94
endothelial cell migration 0.002 0.081 0.26 1 -0.43 31 32
ADCY4 -0.022 0.12 -10000 0 -0.5 42 42
ADCY5 -0.077 0.15 -10000 0 -0.49 79 79
ADCY6 -0.014 0.098 -10000 0 -0.46 32 32
ADCY7 -0.012 0.096 -10000 0 -0.47 31 31
ADCY1 -0.015 0.11 -10000 0 -0.48 36 36
ADCY2 -0.027 0.12 -10000 0 -0.5 46 46
ADCY3 -0.014 0.097 -10000 0 -0.46 32 32
ADCY8 -0.011 0.089 -10000 0 -0.44 28 28
ADCY9 -0.014 0.097 -10000 0 -0.46 32 32
GSK3B -0.027 0.099 0.28 3 -0.34 48 51
arachidonic acid secretion -0.018 0.1 -10000 0 -0.41 47 47
GNG2 0.018 0.058 -10000 0 -0.57 10 10
TRIP6 0.018 0.016 -10000 0 -0.4 1 1
GNAO1 0.002 0.082 -10000 0 -0.36 45 45
HRAS 0.026 0.021 0.26 8 -10000 0 8
NFKBIA -0.021 0.13 0.27 2 -0.34 100 102
GAB1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.026 0.13 -10000 0 -0.81 23 23
JUN 0.02 0.045 -10000 0 -0.57 6 6
LPA/LPA2/NHERF2 0.031 0.018 -10000 0 -10000 0 0
TIAM1 0.011 0.14 -10000 0 -0.95 23 23
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
mol:IP3 -0.014 0.11 0.23 2 -0.29 95 97
PLCB3 0.025 0.045 0.2 3 -10000 0 3
FOS -0.14 0.27 -10000 0 -0.57 290 290
positive regulation of mitosis -0.018 0.1 -10000 0 -0.41 47 47
LPA/LPA1-2-3 0.002 0.14 -10000 0 -0.33 137 137
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 -0.017 0.1 -10000 0 -0.37 44 44
GNAZ 0.003 0.069 -10000 0 -0.34 37 37
EGFR/PI3K-beta/Gab1 -0.12 0.2 -10000 0 -0.35 404 404
positive regulation of dendritic cell cytokine production 0 0.13 -10000 0 -0.33 137 137
LPA/LPA2/MAGI-3 0.033 0.016 -10000 0 -10000 0 0
ARHGEF1 0.018 0.07 -10000 0 -0.32 19 19
GNAI2 0.006 0.059 -10000 0 -0.33 30 30
GNAI3 0.006 0.06 -10000 0 -0.33 30 30
GNAI1 -0.012 0.1 -10000 0 -0.37 76 76
LPA/LPA3 -0.025 0.14 0.18 36 -0.41 119 155
LPA/LPA2 0.019 0.015 0.18 2 -10000 0 2
LPA/LPA1 0.011 0.071 -10000 0 -0.37 32 32
HB-EGF/EGFR -0.078 0.2 0.27 2 -0.35 346 348
HBEGF 0.067 0.074 0.27 23 -0.42 3 26
mol:DAG -0.014 0.11 0.23 2 -0.29 95 97
cAMP biosynthetic process -0.032 0.11 0.4 1 -0.42 54 55
NFKB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.024 0.005 -10000 0 -10000 0 0
LYN -0.009 0.13 0.26 23 -0.33 81 104
GNAQ -0.02 0.11 0.21 1 -0.31 117 118
LPAR2 0.025 0.011 0.26 2 -10000 0 2
LPAR3 -0.034 0.19 0.26 36 -0.57 115 151
LPAR1 0.013 0.087 -10000 0 -0.57 21 21
IL8 -0.13 0.23 0.35 30 -0.41 344 374
PTK2 -0.022 0.1 0.24 1 -0.32 93 94
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
CASP3 -0.026 0.12 -10000 0 -0.32 136 136
EGFR -0.19 0.28 -10000 0 -0.57 375 375
PLCG1 -0.023 0.11 0.2 4 -0.33 116 120
PLD2 -0.027 0.12 0.24 1 -0.32 131 132
G12/G13 0.036 0.061 -10000 0 -0.31 25 25
PI3K-beta 0.002 0.074 -10000 0 -0.44 12 12
cell migration 0.002 0.064 -10000 0 -0.26 22 22
SLC9A3R2 0.023 0.01 0.26 1 -10000 0 1
PXN -0.018 0.1 -10000 0 -0.38 44 44
HRAS/GTP -0.019 0.11 -10000 0 -0.42 47 47
RAC1 0.024 0.003 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 439 -0.57 1 440
PRKCE 0.024 0.003 -10000 0 -10000 0 0
PRKCD -0.015 0.1 0.23 1 -0.41 11 12
Gi(beta/gamma) -0.013 0.1 -10000 0 -0.45 40 40
mol:LPA 0.001 0.017 -10000 0 -0.18 6 6
TRIP6/p130 Cas/FAK1/Paxillin -0.014 0.12 -10000 0 -0.43 26 26
MAPKKK cascade -0.018 0.1 -10000 0 -0.41 47 47
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 0.21 1 -0.32 123 124
GNA15 -0.019 0.11 0.2 2 -0.31 116 118
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 0.26 3 -0.33 116 119
GNA11 -0.02 0.11 0.21 1 -0.31 117 118
Rac1/GTP 0.027 0.13 -10000 0 -0.86 23 23
MMP2 0.002 0.082 0.26 1 -0.44 31 32
Ephrin A reverse signaling

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
MAPKKK cascade -0.005 0.11 -10000 0 -0.36 93 93
EFNA5 -0.029 0.17 0.26 1 -0.57 93 94
FYN -0.023 0.1 0.18 9 -0.33 93 102
neuron projection morphogenesis -0.005 0.11 -10000 0 -0.36 93 93
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.005 0.11 -10000 0 -0.36 93 93
EPHA5 0.023 0.015 0.26 4 -10000 0 4
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.039 0.22 0.43 4 -0.66 95 99
IHH 0.016 0.082 0.26 31 -0.2 69 100
SHH Np/Cholesterol/GAS1 0.001 0.075 -10000 0 -0.33 46 46
LRPAP1 0.024 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.001 0.074 0.33 46 -10000 0 46
SMO/beta Arrestin2 -0.017 0.21 -10000 0 -0.62 92 92
SMO -0.041 0.21 0.32 1 -0.65 92 93
AKT1 -0.003 0.13 -10000 0 -0.61 20 20
ARRB2 0.022 0.007 -10000 0 -10000 0 0
BOC -0.018 0.15 -10000 0 -0.57 74 74
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
heart looping -0.04 0.2 0.32 1 -0.64 92 93
STIL 0.008 0.17 0.3 28 -0.48 81 109
DHH N/PTCH2 -0.011 0.14 -10000 0 -0.44 100 100
DHH N/PTCH1 -0.026 0.2 -10000 0 -0.55 114 114
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DHH 0.008 0.099 0.26 2 -0.57 29 31
PTHLH -0.059 0.3 0.52 2 -0.88 99 101
determination of left/right symmetry -0.04 0.2 0.32 1 -0.64 92 93
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
skeletal system development -0.058 0.29 0.52 2 -0.86 100 102
IHH N/Hhip 0.027 0.057 0.24 2 -0.46 2 4
DHH N/Hhip 0.022 0.079 -10000 0 -0.42 31 31
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.04 0.2 0.32 1 -0.64 92 93
pancreas development 0.023 0.032 0.26 6 -0.57 2 8
HHAT 0.02 0.021 -10000 0 -0.57 1 1
PI3K 0.03 0.042 -10000 0 -0.4 9 9
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.007 0.13 -10000 0 -0.57 54 54
somite specification -0.04 0.2 0.32 1 -0.64 92 93
SHH Np/Cholesterol/PTCH1 -0.023 0.16 0.3 1 -0.5 85 86
SHH Np/Cholesterol/PTCH2 -0.005 0.086 -10000 0 -0.33 61 61
SHH Np/Cholesterol/Megalin -0.059 0.15 0.2 9 -0.3 259 268
SHH 0 0.038 0.34 7 -0.43 1 8
catabolic process -0.031 0.2 0.33 1 -0.61 100 101
SMO/Vitamin D3 -0.008 0.2 0.36 14 -0.57 86 100
SHH Np/Cholesterol/Hhip 0.015 0.031 0.28 4 -0.34 3 7
LRP2 -0.12 0.26 0.26 25 -0.57 264 289
receptor-mediated endocytosis -0.078 0.22 0.31 7 -0.62 97 104
SHH Np/Cholesterol/BOC -0.004 0.085 -10000 0 -0.33 60 60
SHH Np/Cholesterol/CDO 0.012 0.042 -10000 0 -0.33 13 13
mesenchymal cell differentiation -0.015 0.03 0.33 3 -0.28 4 7
mol:Vitamin D3 0.004 0.18 0.35 19 -0.5 83 102
IHH N/PTCH2 -0.008 0.14 -10000 0 -0.47 80 80
CDON 0.014 0.066 -10000 0 -0.57 13 13
IHH N/PTCH1 -0.022 0.21 0.35 4 -0.57 116 120
Megalin/LRPAP1 -0.078 0.2 0.2 22 -0.42 269 291
PTCH2 -0.021 0.16 -10000 0 -0.57 78 78
SHH Np/Cholesterol 0.01 0.013 -10000 0 -0.33 1 1
PTCH1 -0.031 0.2 0.33 1 -0.61 100 101
HHIP 0.023 0.032 0.26 6 -0.57 2 8
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.022 0.026 -10000 0 -0.57 2 2
LAT2 -0.018 0.1 -10000 0 -0.35 55 55
AP1 -0.055 0.18 -10000 0 -0.43 115 115
mol:PIP3 0.011 0.16 0.34 50 -0.42 53 103
IKBKB 0.035 0.13 0.27 123 -0.25 30 153
AKT1 0.014 0.17 0.32 146 -0.44 19 165
IKBKG 0.017 0.11 0.24 77 -0.26 32 109
MS4A2 -0.02 0.15 0.26 5 -0.55 76 81
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
MAP3K1 0.013 0.12 0.28 36 -0.39 28 64
mol:Ca2+ 0.015 0.14 0.3 57 -0.32 51 108
LYN 0.022 0.012 -10000 0 -10000 0 0
CBLB -0.017 0.099 -10000 0 -0.35 53 53
SHC1 0.02 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK 0 0.12 -10000 0 -0.33 120 120
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
PLD2 -0.002 0.17 0.33 126 -0.33 130 256
PTPN13 -0.013 0.15 -10000 0 -0.56 40 40
PTPN11 0.023 0.018 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.014 0.13 0.31 44 -0.34 29 73
SYK 0.026 0.01 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.025 0.12 -10000 0 -0.36 97 97
LAT -0.018 0.1 -10000 0 -0.35 55 55
PAK2 0.014 0.13 0.27 42 -0.36 49 91
NFATC2 -0.046 0.16 -10000 0 -0.56 77 77
HRAS 0.009 0.13 0.26 27 -0.38 52 79
GAB2 0.021 0.02 -10000 0 -0.57 1 1
PLA2G1B 0.002 0.099 -10000 0 -0.84 12 12
Fc epsilon R1 -0.02 0.16 -10000 0 -0.39 141 141
Antigen/IgE/Fc epsilon R1 -0.016 0.14 -10000 0 -0.36 140 140
mol:GDP -0.013 0.11 0.25 1 -0.38 52 53
JUN 0.02 0.045 -10000 0 -0.57 6 6
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.019 0.055 -10000 0 -0.57 9 9
FOS -0.14 0.27 -10000 0 -0.57 290 290
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.015 0.1 -10000 0 -0.28 111 111
CHUK 0.017 0.11 0.24 74 -0.26 32 106
KLRG1 -0.016 0.094 -10000 0 -0.27 97 97
VAV1 -0.019 0.1 -10000 0 -0.35 55 55
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.016 0.096 -10000 0 -0.35 50 50
negative regulation of mast cell degranulation -0.005 0.096 -10000 0 -0.3 51 51
BTK -0.011 0.11 -10000 0 -0.44 33 33
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.029 0.13 -10000 0 -0.33 135 135
GAB2/PI3K/SHP2 -0.047 0.099 -10000 0 -0.32 97 97
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.023 0.1 -10000 0 -0.28 111 111
RAF1 0.001 0.11 -10000 0 -0.92 12 12
Fc epsilon R1/FcgammaRIIB/SHIP 0.002 0.14 -10000 0 -0.35 137 137
FCER1G 0.019 0.017 0.26 1 -10000 0 1
FCER1A -0.043 0.18 -10000 0 -0.58 108 108
Antigen/IgE/Fc epsilon R1/Fyn -0.008 0.14 -10000 0 -0.35 131 131
MAPK3 0.002 0.1 -10000 0 -0.86 12 12
MAPK1 -0.003 0.1 -10000 0 -0.86 12 12
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.023 0.18 -10000 0 -0.59 67 67
DUSP1 -0.046 0.19 -10000 0 -0.57 122 122
NF-kappa-B/RelA 0.008 0.058 0.14 6 -0.17 18 24
actin cytoskeleton reorganization -0.005 0.15 -10000 0 -0.58 33 33
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.001 0.11 0.25 1 -0.44 30 31
FER -0.019 0.11 -10000 0 -0.36 59 59
RELA 0.024 0.005 -10000 0 -10000 0 0
ITK -0.012 0.092 -10000 0 -0.4 47 47
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG1 0.006 0.13 0.27 10 -0.39 53 63
cytokine secretion -0.003 0.035 -10000 0 -0.15 1 1
SPHK1 -0.016 0.099 0.21 2 -0.34 56 58
PTK2 -0.007 0.15 -10000 0 -0.62 33 33
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.022 0.13 -10000 0 -0.37 99 99
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.008 0.16 0.32 47 -0.41 58 105
MAP2K2 -0.002 0.099 -10000 0 -0.85 12 12
MAP2K1 -0.001 0.1 -10000 0 -0.86 12 12
MAP2K7 0.024 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.007 0.092 -10000 0 -0.35 31 31
MAP2K4 -0.075 0.3 -10000 0 -0.84 132 132
Fc epsilon R1/FcgammaRIIB -0.007 0.15 -10000 0 -0.37 137 137
mol:Choline -0.002 0.17 0.33 126 -0.32 130 256
SHC/Grb2/SOS1 0.013 0.11 -10000 0 -0.35 47 47
FYN 0.022 0.027 -10000 0 -0.57 2 2
DOK1 0.025 0.015 0.26 4 -10000 0 4
PXN -0.007 0.14 -10000 0 -0.56 33 33
HCLS1 -0.017 0.1 -10000 0 -0.35 54 54
PRKCB 0.015 0.14 0.28 75 -0.32 59 134
FCGR2B 0.018 0.038 0.26 1 -0.57 4 5
IGHE 0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.005 0.097 -10000 0 -0.31 51 51
LCP2 0.024 0.009 0.26 1 -10000 0 1
PLA2G4A -0.043 0.14 -10000 0 -0.36 133 133
RASA1 0.024 0.004 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.17 0.33 126 -0.32 130 256
IKK complex 0.032 0.11 0.25 116 -0.21 19 135
WIPF1 0.024 0.003 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.015 0.14 0.42 81 -0.24 2 83
KIRREL -0.023 0.16 -10000 0 -0.57 83 83
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.015 0.14 0.24 2 -0.42 81 83
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 -0.32 80 84
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 68 69
FYN 0.014 0.13 0.28 98 -0.31 79 177
mol:Ca2+ 0.031 0.11 0.28 3 -0.32 75 78
mol:DAG 0.033 0.11 0.28 3 -0.32 75 78
NPHS2 0.014 0.031 0.26 4 -10000 0 4
mol:IP3 0.033 0.11 0.28 3 -0.32 75 78
regulation of endocytosis 0.024 0.1 0.24 4 -0.29 79 83
Nephrin/NEPH1/podocin/Cholesterol 0.024 0.11 0.25 9 -0.32 80 89
establishment of cell polarity 0.015 0.14 0.24 2 -0.42 81 83
Nephrin/NEPH1/podocin/NCK1-2 0.044 0.11 0.32 1 -0.3 78 79
Nephrin/NEPH1/beta Arrestin2 0.027 0.11 0.25 4 -0.3 79 83
NPHS1 0.06 0.091 0.26 164 -10000 0 164
Nephrin/NEPH1/podocin 0.025 0.11 0.3 4 -0.31 79 83
TJP1 0.023 0.019 -10000 0 -0.57 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 0.034 0.12 0.29 3 -0.32 75 78
CD2AP 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.032 0.12 0.3 5 -0.32 77 82
GRB2 0.023 0.01 0.26 1 -10000 0 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.013 0.13 0.29 97 -0.31 85 182
cytoskeleton organization 0.004 0.11 0.27 17 -0.33 64 81
Nephrin/NEPH1 0.016 0.1 0.2 2 -0.3 81 83
Nephrin/NEPH1/ZO-1 0.026 0.12 -10000 0 -0.35 81 81
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.033 0.044 -10000 0 -0.31 13 13
RGS9BP 0.037 0.054 0.26 59 -10000 0 59
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.019 0.016 0.26 4 -10000 0 4
mol:Na + 0.037 0.045 -10000 0 -10000 0 0
mol:ADP -0.006 0.025 0.25 5 -10000 0 5
GNAT2 0.024 0.013 0.26 3 -10000 0 3
RGS9-1/Gbeta5/R9AP 0.016 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 0.18 5 -10000 0 5
GRK7 0.023 0.017 0.26 5 -10000 0 5
CNGB3 0.022 0.038 0.26 25 -10000 0 25
Cone Metarhodopsin II/X-Arrestin 0.015 0.014 0.18 8 -10000 0 8
mol:Ca2+ 0.12 0.1 0.29 175 -10000 0 175
Cone PDE6 0.031 0.11 0.32 3 -0.32 81 84
Cone Metarhodopsin II 0.025 0.016 0.17 5 -10000 0 5
Na + (4 Units) 0.11 0.093 0.31 68 -10000 0 68
GNAT2/GDP 0.025 0.11 0.29 2 -0.31 84 86
GNB5 0.024 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.006 0.033 0.19 11 -10000 0 11
Cone Transducin 0.036 0.047 -10000 0 -0.33 13 13
SLC24A2 0.16 0.12 0.26 609 -10000 0 609
GNB3/GNGT2 0.026 0.054 -10000 0 -0.41 14 14
GNB3 0.017 0.065 0.26 4 -0.57 12 16
GNAT2/GTP 0.018 0.009 0.18 3 -10000 0 3
CNGA3 0.045 0.068 0.26 97 -10000 0 97
ARR3 0.021 0.021 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 0.016 0.12 0.34 1 -0.36 85 86
Cone CNG Channel 0.05 0.044 0.28 2 -10000 0 2
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.16 0.12 0.26 609 -10000 0 609
RGS9 -0.025 0.17 0.26 11 -0.57 87 98
PDE6C 0.02 0.009 0.26 1 -10000 0 1
GNGT2 0.021 0.027 -10000 0 -0.57 2 2
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.019 0.017 0.26 5 -10000 0 5
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 0.034 0.1 0.99 2 -10000 0 2
VDR 0.024 0.003 -10000 0 -10000 0 0
FAM120B 0.023 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.025 0.12 -10000 0 -0.38 10 10
RXRs/LXRs/DNA/Oxysterols -0.005 0.12 -10000 0 -0.42 14 14
MED1 0.022 0.008 -10000 0 -10000 0 0
mol:9cRA 0.004 0.009 -10000 0 -0.15 1 1
RARs/THRs/DNA/Src-1 0.001 0.082 -10000 0 -0.3 58 58
RXRs/NUR77 -0.049 0.18 -10000 0 -0.35 253 253
RXRs/PPAR -0.1 0.18 -10000 0 -0.33 323 323
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 0.048 0.041 -10000 0 -0.32 10 10
RARA 0.022 0.007 -10000 0 -10000 0 0
NCOA1 0.024 0.019 -10000 0 -0.57 1 1
VDR/VDR/DNA 0.024 0.003 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.037 0.039 -10000 0 -0.31 10 10
RARG 0.024 0.003 -10000 0 -10000 0 0
RPS6KB1 0.069 0.17 0.61 93 -10000 0 93
RARs/THRs/DNA/SMRT 0.003 0.079 -10000 0 -0.29 56 56
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 -0.029 0.15 -10000 0 -0.32 210 210
NR1H4 0.021 0.026 0.26 12 -10000 0 12
RXRs/LXRs/DNA -0.007 0.16 -10000 0 -0.31 192 192
NR1H2 0.027 0.012 -10000 0 -10000 0 0
NR1H3 0.028 0.011 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.022 0.15 -10000 0 -0.31 209 209
NR4A1 -0.024 0.16 -10000 0 -0.57 84 84
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.032 0.1 -10000 0 -0.23 185 185
RXRG -0.099 0.24 0.26 2 -0.57 212 214
RXR alpha/CCPG 0.036 0.014 -10000 0 -10000 0 0
RXRA 0.027 0.012 -10000 0 -10000 0 0
RXRB 0.027 0.011 -10000 0 -10000 0 0
THRB -0.005 0.13 -10000 0 -0.57 51 51
PPARG -0.11 0.25 -10000 0 -0.57 239 239
PPARD 0.024 0.004 -10000 0 -10000 0 0
TNF -0.009 0.14 -10000 0 -1 9 9
mol:Oxysterols 0.004 0.008 -10000 0 -0.12 1 1
cholesterol transport -0.005 0.12 -10000 0 -0.42 14 14
PPARA 0.021 0.037 -10000 0 -0.57 4 4
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.017 0.064 -10000 0 -0.57 12 12
RXRs/NUR77/BCL2 -0.068 0.15 -10000 0 -0.3 270 270
SREBF1 -0.006 0.11 0.44 1 -0.5 3 4
RXRs/RXRs/DNA/9cRA -0.029 0.15 -10000 0 -0.32 210 210
ABCA1 -0.01 0.13 -10000 0 -0.78 8 8
RARs/THRs 0.042 0.094 -10000 0 -0.34 54 54
RXRs/FXR -0.025 0.16 -10000 0 -0.33 210 210
BCL2 0.007 0.096 -10000 0 -0.57 28 28
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.031 0.14 -10000 0 -0.59 60 60
PDGF/PDGFRA/CRKL -0.01 0.11 -10000 0 -0.42 59 59
positive regulation of JUN kinase activity 0.025 0.082 -10000 0 -0.33 43 43
CRKL 0.023 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.012 0.11 -10000 0 -0.43 61 61
AP1 -0.3 0.44 -10000 0 -0.96 307 307
mol:IP3 -0.034 0.11 -10000 0 -0.45 57 57
PLCG1 -0.034 0.11 -10000 0 -0.45 57 57
PDGF/PDGFRA/alphaV Integrin -0.01 0.11 -10000 0 -0.43 60 60
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.034 0.11 -10000 0 -0.45 57 57
CAV3 0.02 0.011 0.26 2 -10000 0 2
CAV1 -0.098 0.24 -10000 0 -0.57 213 213
SHC/Grb2/SOS1 0.027 0.083 -10000 0 -0.33 43 43
PDGF/PDGFRA/Shf -0.009 0.11 -10000 0 -0.42 61 61
FOS -0.29 0.43 0.32 1 -0.94 307 308
JUN -0.037 0.044 -10000 0 -0.44 6 6
oligodendrocyte development -0.01 0.11 -10000 0 -0.43 60 60
GRB2 0.023 0.01 0.26 1 -10000 0 1
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
mol:DAG -0.034 0.11 -10000 0 -0.45 57 57
PDGF/PDGFRA -0.031 0.14 -10000 0 -0.59 60 60
actin cytoskeleton reorganization -0.009 0.11 -10000 0 -0.42 60 60
SRF 0.016 0.013 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
PI3K 0.015 0.1 -10000 0 -0.37 64 64
PDGF/PDGFRA/Crk/C3G 0.017 0.096 -10000 0 -0.36 60 60
JAK1 -0.025 0.1 0.23 1 -0.43 59 60
ELK1/SRF -0.034 0.088 0.32 1 -0.35 58 59
SHB 0.024 0.008 0.26 1 -10000 0 1
SHF 0.023 0.02 0.26 1 -0.57 1 2
CSNK2A1 0.036 0.023 -10000 0 -10000 0 0
GO:0007205 -0.045 0.11 0.22 1 -0.46 60 61
SOS1 0.024 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.025 0.082 -10000 0 -0.33 43 43
PDGF/PDGFRA/SHB -0.009 0.11 -10000 0 -0.42 60 60
PDGF/PDGFRA/Caveolin-1 -0.097 0.22 -10000 0 -0.48 242 242
ITGAV 0.024 0.003 -10000 0 -10000 0 0
ELK1 -0.052 0.1 -10000 0 -0.43 59 59
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.01 0.11 -10000 0 -0.42 60 60
JAK-STAT cascade -0.025 0.1 0.23 1 -0.42 59 60
cell proliferation -0.009 0.11 -10000 0 -0.42 61 61
Canonical Wnt 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
HDAC1 0.023 0.021 0.24 2 -10000 0 2
AES 0.023 0.02 0.22 3 -10000 0 3
FBXW11 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.035 0.009 -10000 0 -10000 0 0
SMAD4 0.023 0.005 -10000 0 -10000 0 0
DKK2 0.011 0.09 0.26 2 -0.57 24 26
TLE1 0.019 0.049 0.22 1 -0.58 6 7
MACF1 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.11 0.1 0.3 42 -0.36 5 47
WIF1 -0.28 0.3 0.26 12 -0.57 533 545
beta catenin/RanBP3 0.021 0.093 0.43 37 -0.39 1 38
KREMEN2 0.12 0.12 0.26 454 -10000 0 454
DKK1 0.027 0.16 0.26 141 -0.57 51 192
beta catenin/beta TrCP1 0.11 0.094 0.3 32 -0.35 3 35
FZD1 0.025 0.004 -10000 0 -10000 0 0
AXIN2 0.014 0.26 0.59 81 -1.3 22 103
AXIN1 0.024 0.007 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.047 0.077 -10000 0 -0.54 13 13
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.065 0.13 0.36 4 -0.58 23 27
Axin1/APC/GSK3 0.047 0.054 0.24 2 -0.31 1 3
Axin1/APC/GSK3/beta catenin/Macf1 0.043 0.063 0.31 2 -0.4 4 6
HNF1A 0.025 0.028 0.25 9 -10000 0 9
CTBP1 0.022 0.021 0.25 2 -10000 0 2
MYC 0.11 0.33 0.57 250 -1.3 23 273
RANBP3 0.024 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.092 0.097 0.34 1 -0.33 18 19
NKD1 0.022 0.054 0.26 15 -0.57 6 21
TCF4 0.017 0.058 0.24 3 -0.56 9 12
TCF3 0.023 0.024 0.31 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 0.006 0.13 0.48 36 -0.51 14 50
LEF1 0.051 0.082 0.26 132 -0.53 1 133
DVL1 0.056 0.053 0.22 1 -0.36 2 3
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.068 0.15 0.32 2 -0.6 28 30
DKK1/LRP6/Kremen 2 0.1 0.14 0.34 77 -0.34 44 121
LRP6 0.024 0.006 -10000 0 -10000 0 0
CSNK1A1 0.023 0.023 0.24 4 -10000 0 4
NLK 0.023 0.014 0.25 2 -10000 0 2
CCND1 0.087 0.26 0.61 171 -1.2 7 178
WNT1 0.024 0.012 0.26 2 -10000 0 2
GSK3A 0.025 0.003 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -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 9 14
APC 0.016 0.056 0.36 6 -10000 0 6
WNT1/LRP6/FZD1 0.12 0.11 0.22 502 -0.24 1 503
CREBBP 0.021 0.019 0.27 1 -10000 0 1
TCGA08_rtk_signaling

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
PDGFRA -0.01 0.14 -10000 0 -0.57 60 60
HRAS 0.026 0.021 0.26 8 -10000 0 8
EGFR -0.19 0.28 -10000 0 -0.57 375 375
AKT -0.014 0.12 0.3 7 -0.28 87 94
FOXO3 0.022 0.02 -10000 0 -0.57 1 1
AKT1 0.024 0.004 -10000 0 -10000 0 0
FOXO1 0.02 0.037 -10000 0 -0.57 4 4
AKT3 0.015 0.058 -10000 0 -0.57 10 10
FOXO4 0.025 0.001 -10000 0 -10000 0 0
MET -0.073 0.22 -10000 0 -0.57 169 169
PIK3CA 0.023 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 0.016 0.073 0.26 4 -0.57 15 19
PIK3R3 0.024 0.008 0.26 1 -10000 0 1
PIK3R2 0.024 0.004 -10000 0 -10000 0 0
NF1 0.023 0.006 -10000 0 -10000 0 0
RAS -0.061 0.14 0.21 4 -0.24 341 345
ERBB2 0.021 0.02 -10000 0 -0.57 1 1
proliferation/survival/translation -0.007 0.088 0.32 46 -0.26 1 47
PI3K -0.049 0.14 0.25 16 -0.24 306 322
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
KRAS 0.024 0.005 -10000 0 -10000 0 0
FOXO 0.037 0.058 0.25 11 -0.16 2 13
AKT2 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.023 0.019 -10000 0 -0.57 1 1
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.001 0.062 0.22 2 -0.32 8 10
adherens junction organization -0.014 0.093 0.22 1 -0.34 50 51
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.085 0.15 0.34 3 -0.33 113 116
FMN1 -0.013 0.089 -10000 0 -0.32 56 56
mol:IP3 -0.001 0.052 -10000 0 -0.27 10 10
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.007 0.088 -10000 0 -0.32 48 48
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.002 0.062 -10000 0 -0.28 10 10
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.013 0.13 -10000 0 -0.5 43 43
CTNND1 0.024 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.009 0.077 -10000 0 -0.31 44 44
VASP -0.01 0.082 -10000 0 -0.31 46 46
ZYX -0.009 0.082 -10000 0 -0.31 47 47
JUB -0.009 0.083 -10000 0 -0.31 48 48
EGFR(dimer) -0.11 0.18 -10000 0 -0.33 364 364
E-cadherin/beta catenin-gamma catenin 0.033 0.058 -10000 0 -0.35 19 19
mol:PI-3-4-5-P3 0.016 0.072 -10000 0 -0.27 16 16
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.016 0.073 -10000 0 -0.28 16 16
FYN -0.003 0.065 0.22 2 -0.32 7 9
mol:Ca2+ 0 0.051 -10000 0 -0.26 10 10
JUP 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.019 0.055 -10000 0 -0.57 9 9
mol:DAG -0.001 0.052 -10000 0 -0.27 10 10
CDH1 0.011 0.08 -10000 0 -0.57 19 19
RhoA/GDP -0.084 0.15 0.36 2 -0.33 105 107
establishment of polarity of embryonic epithelium -0.01 0.08 -10000 0 -0.3 46 46
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
EGFR -0.19 0.28 -10000 0 -0.57 375 375
CASR -0.003 0.054 0.23 2 -0.26 8 10
RhoA/GTP 0.014 0.056 -10000 0 -0.26 7 7
AKT2 0.001 0.062 -10000 0 -0.26 14 14
actin cable formation -0.018 0.09 0.25 2 -0.31 60 62
apoptosis -0.005 0.072 0.28 22 -0.23 9 31
CTNNA1 0.024 0.006 -10000 0 -10000 0 0
mol:GDP -0.098 0.15 -10000 0 -0.3 332 332
PIP5K1A -0.009 0.078 -10000 0 -0.31 44 44
PLCG1 -0.001 0.052 -10000 0 -0.27 10 10
Rac1/GTP -0.093 0.17 -10000 0 -0.3 362 362
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.022 0.082 -10000 0 -0.41 28 28
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 -0.57 91 91
LRP6/FZD1 0.034 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.045 -10000 0 -0.57 6 6
AP1 -0.073 0.15 -10000 0 -0.31 274 274
NCSTN 0.02 0.009 -10000 0 -10000 0 0
ADAM10 0.022 0.032 -10000 0 -0.57 3 3
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.013 0.1 -10000 0 -0.64 17 17
NICD/RBPSUH 0.021 0.079 -10000 0 -0.4 29 29
WIF1 -0.28 0.3 0.26 12 -0.57 533 545
NOTCH1 0.009 0.072 -10000 0 -0.42 27 27
PSENEN 0.024 0.008 0.26 1 -10000 0 1
KREMEN2 0.12 0.12 0.26 454 -10000 0 454
DKK1 0.026 0.16 0.26 141 -0.57 51 192
beta catenin/beta TrCP1 0.008 0.067 -10000 0 -0.36 5 5
APH1B 0.023 0.019 -10000 0 -0.57 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
AXIN1 0.011 0.061 0.25 1 -0.45 9 10
CtBP/CBP/TCF1/TLE1/AES 0.012 0.039 -10000 0 -0.3 5 5
PSEN1 0.024 0.005 -10000 0 -10000 0 0
FOS -0.14 0.27 -10000 0 -0.57 290 290
JUN 0.02 0.045 -10000 0 -0.57 6 6
MAP3K7 0.021 0.009 -10000 0 -10000 0 0
CTNNB1 -0.001 0.066 0.25 1 -0.37 6 7
MAPK3 0.023 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.093 0.097 0.34 1 -0.33 18 19
HNF1A 0.025 0.019 0.26 7 -10000 0 7
CTBP1 0.023 0.006 -10000 0 -10000 0 0
MYC -0.013 0.21 -10000 0 -1.3 26 26
NKD1 0.022 0.054 0.26 15 -0.57 6 21
FZD1 0.024 0.003 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.005 0.12 -10000 0 -0.44 29 29
apoptosis -0.073 0.15 -10000 0 -0.31 274 274
Delta 1/NOTCHprecursor 0.019 0.081 -10000 0 -0.4 30 30
DLL1 0.021 0.037 -10000 0 -0.57 4 4
PPARD 0.014 0.094 -10000 0 -0.83 12 12
Gamma Secretase 0.055 0.034 -10000 0 -0.32 1 1
APC 0.004 0.083 -10000 0 -0.45 24 24
DVL1 -0.029 0.077 -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 0.099 0.14 0.34 77 -0.34 44 121
LRP6 0.023 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 0.018 0.11 -10000 0 -1.1 8 8
WNT1 0.023 0.011 0.26 2 -10000 0 2
Axin1/APC/beta catenin 0.012 0.099 0.32 5 -0.42 19 24
DKK2 0.011 0.09 0.26 2 -0.57 24 26
NOTCH1 precursor/DVL1 -0.02 0.11 -10000 0 -0.53 32 32
GSK3B 0.024 0.004 -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 -0.44 29 29
PPP2R5D -0.004 0.058 0.29 5 -0.36 16 21
MAPK1 0.023 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.14 0.19 -10000 0 -0.33 516 516
RBPJ 0.024 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
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 -0.57 702 702
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.028 0.034 0.26 21 -10000 0 21
TCEB1 0.021 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.03 0.048 -10000 0 -0.31 4 4
HIF1A 0.004 0.029 -10000 0 -0.27 10 10
COPS5 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.056 0.037 -10000 0 -10000 0 0
FIH (dimer) 0.024 0.003 -10000 0 -10000 0 0
CDKN2A 0.06 0.087 0.26 168 -10000 0 168
ARNT/IPAS -0.25 0.2 -10000 0 -0.38 702 702
HIF1AN 0.024 0.003 -10000 0 -10000 0 0
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.021 0.045 -10000 0 -0.28 13 13
CUL2 0.024 0.004 -10000 0 -10000 0 0
OS9 0.024 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.042 0.028 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.032 0.048 -10000 0 -0.32 4 4
PHD1-3/OS9 0.056 0.048 -10000 0 -0.33 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 0.026 0.048 -10000 0 -0.28 12 12
EGLN3 0.04 0.063 0.26 73 -0.57 1 74
EGLN2 0.025 0.015 0.26 4 -10000 0 4
EGLN1 0.02 0.021 -10000 0 -0.57 1 1
TP53 0.022 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.03 0.066 -10000 0 -0.51 13 13
ARNT 0.02 0.009 -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 0.28 6 -0.27 11 17
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 0.037 -10000 0 -0.57 4 4
alphaV beta3 Integrin 0.02 0.082 -10000 0 -0.42 34 34
PTK2 -0.041 0.16 -10000 0 -0.48 88 88
positive regulation of JNK cascade -0.021 0.12 -10000 0 -0.32 119 119
CDC42/GDP -0.018 0.17 0.43 1 -0.43 123 124
Rac1/GDP -0.018 0.17 -10000 0 -0.43 123 123
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 -0.022 0.16 -10000 0 -0.39 117 117
nectin-3/I-afadin -0.015 0.14 -10000 0 -0.43 110 110
RAPGEF1 -0.036 0.17 0.46 1 -0.47 109 110
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.05 0.18 -10000 0 -0.54 109 109
PDGFB-D/PDGFRB 0.022 0.037 -10000 0 -0.57 4 4
TLN1 -0.023 0.069 -10000 0 -0.38 13 13
Rap1/GTP -0.024 0.12 -10000 0 -0.34 106 106
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.027 -10000 0 -0.33 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.015 0.14 -10000 0 -0.43 110 110
PVR 0.024 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.039 0.2 0.45 1 -0.53 124 125
MLLT4 0.021 0.033 0.26 1 -0.57 3 4
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.019 0.13 -10000 0 -0.34 110 110
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.029 0.03 -10000 0 -0.42 3 3
positive regulation of lamellipodium assembly -0.02 0.13 -10000 0 -0.34 125 125
PVRL1 0.022 0.008 -10000 0 -10000 0 0
PVRL3 -0.038 0.18 -10000 0 -0.57 109 109
PVRL2 0.024 0.004 -10000 0 -10000 0 0
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
CDH1 0.011 0.08 -10000 0 -0.57 19 19
CLDN1 0.007 0.12 0.26 23 -0.57 38 61
JAM-A/CLDN1 0.004 0.13 -10000 0 -0.36 104 104
SRC -0.056 0.21 -10000 0 -0.59 112 112
ITGB3 0.005 0.11 0.26 4 -0.57 34 38
nectin-1(dimer)/I-afadin/I-afadin 0.029 0.03 -10000 0 -0.42 3 3
FARP2 -0.038 0.2 0.46 1 -0.52 123 124
RAC1 0.024 0.003 -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 -0.37 109 109
nectin-1/I-afadin 0.029 0.03 -10000 0 -0.42 3 3
nectin-2/I-afadin 0.032 0.029 -10000 0 -0.42 3 3
RAC1/GTP/IQGAP1/filamentous actin 0.032 0.007 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.001 0.13 -10000 0 -0.37 110 110
CDC42/GTP/IQGAP1/filamentous actin 0.031 0.009 -10000 0 -10000 0 0
F11R 0.02 0.009 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.021 0.12 -10000 0 -0.32 119 119
alphaV/beta3 Integrin/Talin -0.007 0.1 0.26 1 -0.4 40 41
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.42 3 3
nectin-2(dimer)/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.42 3 3
PIP5K1C -0.019 0.077 -10000 0 -0.22 110 110
VAV2 -0.038 0.21 0.44 1 -0.54 123 124
RAP1/GDP -0.015 0.16 -10000 0 -0.4 116 116
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 -0.37 109 109
nectin-3(dimer)/I-afadin/I-afadin -0.015 0.14 -10000 0 -0.43 110 110
Rac1/GTP -0.022 0.16 -10000 0 -0.41 125 125
PTPRM -0.017 0.087 -10000 0 -0.25 112 112
E-cadherin/beta catenin/alpha catenin 0.046 0.064 -10000 0 -0.32 21 21
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 0.041 0.15 0.35 66 -0.34 54 120
TBX21 0.013 0.35 0.76 21 -1.2 48 69
B2M 0.025 0.011 -10000 0 -10000 0 0
TYK2 0.024 0.036 0.2 1 -10000 0 1
IL12RB1 0.032 0.073 0.32 41 -0.6 2 43
GADD45B 0.036 0.26 0.64 22 -0.89 32 54
IL12RB2 0.028 0.15 0.27 120 -0.58 42 162
GADD45G 0.053 0.26 0.72 18 -0.96 24 42
natural killer cell activation 0.007 0.025 0.16 1 -10000 0 1
RELB 0.026 0.023 0.26 10 -10000 0 10
RELA 0.024 0.005 -10000 0 -10000 0 0
IL18 0.033 0.039 0.28 22 -10000 0 22
IL2RA 0.027 0.087 0.26 54 -0.57 14 68
IFNG 0.055 0.081 0.26 143 -10000 0 143
STAT3 (dimer) 0.033 0.25 0.57 35 -0.71 44 79
HLA-DRB5 0.025 0.079 0.25 76 -0.58 5 81
FASLG 0.049 0.31 0.76 28 -1 38 66
NF kappa B2 p52/RelB 0.02 0.25 0.67 5 -0.83 44 49
CD4 0.01 0.024 -10000 0 -10000 0 0
SOCS1 0.025 0.033 0.26 13 -0.57 1 14
EntrezGene:6955 -0.005 0.015 -10000 0 -10000 0 0
CD3D 0.009 0.099 0.26 45 -0.58 19 64
CD3E 0.009 0.091 0.27 36 -0.58 16 52
CD3G 0 0.12 0.27 37 -0.58 32 69
IL12Rbeta2/JAK2 0.036 0.12 0.29 32 -0.43 43 75
CCL3 0.033 0.28 0.72 20 -0.99 31 51
CCL4 0.034 0.27 0.72 20 -0.97 29 49
HLA-A 0.027 0.021 0.26 7 -10000 0 7
IL18/IL18R 0.064 0.12 0.37 17 -0.38 51 68
NOS2 0.032 0.28 0.69 22 -1 31 53
IL12/IL12R/TYK2/JAK2/SPHK2 0.038 0.15 0.35 57 -0.34 59 116
IL1R1 0.019 0.31 0.7 21 -1.1 40 61
IL4 -0.011 0.037 -10000 0 -10000 0 0
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 -0.76 58 90
RAB7A 0.05 0.24 0.65 17 -0.81 23 40
lysosomal transport 0.051 0.23 0.65 17 -0.76 23 40
FOS -0.31 0.62 0.58 16 -1.2 333 349
STAT4 (dimer) 0.061 0.28 0.63 30 -0.87 44 74
STAT5A (dimer) 0.046 0.28 0.63 42 -0.83 43 85
GZMA 0.024 0.29 0.71 27 -1.1 33 60
GZMB 0.023 0.32 0.72 26 -1.1 43 69
HLX 0.021 0.016 0.26 3 -10000 0 3
LCK 0.027 0.3 0.68 33 -0.9 49 82
TCR/CD3/MHC II/CD4 -0.046 0.18 0.27 25 -0.48 93 118
IL2/IL2R 0.065 0.098 0.41 38 -0.36 20 58
MAPK14 0.046 0.27 0.68 21 -0.93 32 53
CCR5 0.036 0.27 0.71 25 -0.94 29 54
IL1B 0.017 0.08 0.27 4 -0.58 14 18
STAT6 0.039 0.12 0.4 34 -0.6 7 41
STAT4 -0.001 0.12 0.26 1 -0.57 44 45
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.031 0.26 19 -10000 0 19
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 0.28 220 -10000 0 220
CD8A 0.029 0.063 0.28 29 -0.57 6 35
CD8B 0.014 0.11 0.27 30 -0.57 32 62
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.041 0.15 0.34 54 -0.35 67 121
IL2RB 0.03 0.051 0.26 37 -0.57 2 39
proteasomal ubiquitin-dependent protein catabolic process 0.065 0.27 0.62 32 -0.78 44 76
IL2RG 0.031 0.068 0.26 45 -0.57 7 52
IL12 0.049 0.15 0.29 101 -0.42 59 160
STAT5A 0.02 0.045 -10000 0 -0.57 6 6
CD247 0.006 0.08 0.26 16 -0.58 15 31
IL2 0.022 0.021 0.26 8 -10000 0 8
SPHK2 0.024 0.003 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.006 0.15 0.29 19 -0.58 58 77
IL12/IL12R/TYK2/JAK2 0.034 0.3 0.72 35 -0.93 46 81
MAP2K3 0.039 0.28 0.65 25 -0.9 39 64
RIPK2 0.021 0.016 0.26 3 -10000 0 3
MAP2K6 0.045 0.27 0.65 25 -0.91 33 58
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.008 0.033 0.26 1 -0.57 1 2
IL18RAP 0.011 0.11 0.28 5 -0.57 36 41
IL12Rbeta1/TYK2 0.041 0.069 0.28 37 -0.46 2 39
EOMES -0.019 0.18 -10000 0 -1.1 25 25
STAT1 (dimer) 0.066 0.26 0.66 50 -0.76 34 84
T cell proliferation 0.048 0.22 0.53 23 -0.66 39 62
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.021 0.078 -10000 0 -0.57 17 17
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.014 0.19 0.5 1 -0.73 38 39
ATF2 0.043 0.26 0.63 21 -0.84 32 53
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.095 0.1 0.21 411 -0.35 2 413
EPHB2 0.028 0.033 0.26 20 -10000 0 20
Syndecan-2/TACI 0.023 0.061 0.2 58 -0.36 12 70
LAMA1 -0.036 0.18 0.26 3 -0.57 105 108
Syndecan-2/alpha2 ITGB1 -0.037 0.15 -10000 0 -0.32 192 192
HRAS 0.026 0.021 0.26 8 -10000 0 8
Syndecan-2/CASK 0.005 0.016 -10000 0 -0.35 2 2
ITGA5 0.025 0.008 0.26 1 -10000 0 1
BAX 0.002 0.03 0.45 1 -10000 0 1
EPB41 0.024 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.018 0.018 -10000 0 -0.32 2 2
LAMA3 -0.11 0.25 -10000 0 -0.57 241 241
EZR 0.024 0.012 0.26 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.051 0.2 -10000 0 -0.57 131 131
Syndecan-2/MMP2 0.015 0.039 0.18 1 -0.36 9 10
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.023 0.07 -10000 0 -0.4 27 27
dendrite morphogenesis 0.022 0.034 0.21 20 -0.36 2 22
Syndecan-2/GM-CSF 0.021 0.035 0.31 4 -0.36 2 6
determination of left/right symmetry 0.007 0.019 -10000 0 -0.41 2 2
Syndecan-2/PKC delta 0.019 0.022 0.31 1 -0.36 2 3
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.032 0.073 0.19 168 -0.33 2 170
MAPK1 0.037 0.076 0.23 10 -0.32 2 12
Syndecan-2/RACK1 0.03 0.027 0.24 3 -0.31 2 5
NF1 0.023 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.007 0.019 -10000 0 -0.41 2 2
ITGA2 0.009 0.093 -10000 0 -0.57 26 26
MAPK8 0.005 0.033 0.25 6 -0.35 5 11
Syndecan-2/alpha2/beta1 Integrin 0.003 0.12 -10000 0 -0.36 81 81
Syndecan-2/Kininogen 0.02 0.034 0.3 5 -0.36 2 7
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.042 0.069 0.31 7 -0.3 2 9
Syndecan-2/CASK/Protein 4.1 0.017 0.018 -10000 0 -0.32 2 2
extracellular matrix organization 0.02 0.023 0.24 3 -0.36 2 5
actin cytoskeleton reorganization 0.094 0.1 0.21 411 -0.35 2 413
Syndecan-2/Caveolin-2/Ras -0.009 0.11 0.26 3 -0.33 100 103
Syndecan-2/Laminin alpha3 -0.057 0.14 -10000 0 -0.36 181 181
Syndecan-2/RasGAP 0.038 0.031 0.26 2 -0.3 2 4
alpha5/beta1 Integrin 0.035 0.008 -10000 0 -10000 0 0
PRKCD 0.024 0.009 0.26 1 -10000 0 1
Syndecan-2 dimer 0.023 0.034 0.21 20 -0.36 2 22
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 0.024 -10000 0 -0.29 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
SDCBP 0.021 0.009 -10000 0 -10000 0 0
TNFRSF13B 0.028 0.085 0.26 58 -0.57 12 70
RASA1 0.024 0.004 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.023 0.07 -10000 0 -0.4 27 27
Syndecan-2/Synbindin 0.018 0.02 -10000 0 -0.35 2 2
TGFB1 0.025 0.013 0.26 3 -10000 0 3
CASP3 0.043 0.071 0.19 185 -0.33 2 187
FN1 0.12 0.11 0.26 411 -10000 0 411
Syndecan-2/IL8 0.024 0.07 0.21 60 -0.36 17 77
SDC2 0.007 0.02 -10000 0 -0.42 2 2
KNG1 0.023 0.033 0.26 20 -10000 0 20
Syndecan-2/Neurofibromin 0.019 0.021 -10000 0 -0.36 2 2
TRAPPC4 0.022 0.008 -10000 0 -10000 0 0
CSF2 0.025 0.036 0.26 24 -10000 0 24
Syndecan-2/TGFB1 0.02 0.023 0.24 3 -0.36 2 5
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.018 -10000 0 -0.32 2 2
Syndecan-2/Ezrin 0.029 0.026 0.29 1 -0.33 2 3
PRKACA 0.044 0.072 0.19 196 -0.32 2 198
angiogenesis 0.024 0.069 0.21 60 -0.36 17 77
MMP2 0.018 0.05 0.26 1 -0.57 7 8
IL8 0.026 0.098 0.26 60 -0.57 19 79
calcineurin-NFAT signaling pathway 0.023 0.06 0.2 58 -0.36 12 70
FAS signaling pathway (CD95)

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
SPTAN1 -0.003 0.042 0.21 29 -10000 0 29
RFC1 -0.003 0.039 0.21 25 -10000 0 25
PRKDC 0.016 0.08 0.23 107 -10000 0 107
RIPK1 0.027 0.007 -10000 0 -10000 0 0
CASP7 -0.018 0.099 -10000 0 -0.63 21 21
FASLG/FAS/FADD/FAF1 -0.005 0.059 0.22 11 -0.3 12 23
MAP2K4 -0.084 0.18 0.39 2 -0.42 110 112
mol:ceramide -0.023 0.1 -10000 0 -0.39 23 23
GSN -0.007 0.055 0.21 28 -0.35 11 39
FASLG/FAS/FADD/FAF1/Caspase 8 -0.008 0.076 0.28 1 -0.37 15 16
FAS 0.004 0.037 -10000 0 -0.59 2 2
BID -0.018 0.021 -10000 0 -10000 0 0
MAP3K1 -0.047 0.12 0.31 2 -0.41 37 39
MAP3K7 0.011 0.019 -10000 0 -10000 0 0
RB1 -0.002 0.039 0.22 25 -10000 0 25
CFLAR 0.027 0.007 -10000 0 -10000 0 0
HGF/MET -0.05 0.19 -10000 0 -0.4 221 221
ARHGDIB -0.001 0.045 0.22 35 -10000 0 35
FADD 0.006 0.024 -10000 0 -10000 0 0
actin filament polymerization 0.012 0.062 0.35 11 -0.21 29 40
NFKB1 -0.045 0.12 -10000 0 -0.57 19 19
MAPK8 -0.15 0.26 0.56 2 -0.46 382 384
DFFA -0.003 0.04 0.21 25 -10000 0 25
DNA fragmentation during apoptosis -0.008 0.049 0.21 26 -10000 0 26
FAS/FADD/MET -0.037 0.14 -10000 0 -0.38 139 139
CFLAR/RIP1 0.04 0.013 -10000 0 -10000 0 0
FAIM3 0.027 0.035 0.26 22 -10000 0 22
FAF1 0.003 0.029 -10000 0 -10000 0 0
PARP1 -0.001 0.048 0.22 35 -0.19 6 41
DFFB -0.004 0.04 0.21 25 -10000 0 25
CHUK -0.04 0.11 -10000 0 -0.56 16 16
FASLG 0.006 0.088 0.26 40 -0.58 14 54
FAS/FADD 0.009 0.036 -10000 0 -0.33 2 2
HGF -0.01 0.14 0.26 2 -0.57 60 62
LMNA -0.003 0.054 -10000 0 -10000 0 0
CASP6 -0.003 0.039 0.21 25 -10000 0 25
CASP10 0.004 0.041 -10000 0 -0.58 3 3
CASP3 0 0.043 0.26 24 -10000 0 24
PTPN13 0.009 0.093 -10000 0 -0.57 26 26
CASP8 -0.021 0.025 -10000 0 -0.18 2 2
IL6 -0.43 0.62 -10000 0 -1.2 386 386
MET -0.073 0.22 -10000 0 -0.57 169 169
ICAD/CAD -0.006 0.032 0.2 19 -10000 0 19
FASLG/FAS/FADD/FAF1/Caspase 10 -0.023 0.1 -10000 0 -0.4 23 23
activation of caspase activity by cytochrome c -0.018 0.021 -10000 0 -10000 0 0
PAK2 -0.003 0.048 0.22 35 -0.19 6 41
BCL2 0.008 0.096 -10000 0 -0.57 28 28
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 -0.32 231 231
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.005 0.013 0.13 8 -10000 0 8
GNB1/GNG2 0.027 0.039 -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 -0.062 0.14 -10000 0 -0.31 246 246
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 0.034 0.081 246 -10000 0 246
GNAL -0.11 0.25 -10000 0 -0.57 229 229
GNG2 0.018 0.058 -10000 0 -0.57 10 10
CRH 0.017 0.022 0.26 8 -10000 0 8
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.029 -10000 0 -0.35 7 7
MAPK11 0.005 0.019 -10000 0 -0.35 3 3
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.021 0.009 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.072 0.16 -10000 0 -0.48 25 25
Syndecan-3/Neurocan 0.027 0.074 0.27 18 -0.37 20 38
POMC 0.019 0.093 0.26 29 -0.57 21 50
EGFR -0.19 0.28 -10000 0 -0.57 375 375
Syndecan-3/EGFR -0.089 0.16 -10000 0 -0.31 294 294
AGRP 0.021 0.024 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 -0.57 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
NCAN 0.036 0.056 0.26 62 -10000 0 62
long-term memory 0.035 0.063 -10000 0 -0.35 15 15
Syndecan-3/IL8 0.021 0.082 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 -0.57 2 2
limb bud formation 0.002 0.056 -10000 0 -0.39 21 21
MC4R 0.023 0.026 0.26 12 -10000 0 12
SRC 0.024 0.005 -10000 0 -10000 0 0
PTN -0.23 0.29 0.26 2 -0.57 439 441
FGFR/FGF/Syndecan-3 0.001 0.057 -10000 0 -0.39 21 21
neuron projection morphogenesis -0.072 0.16 0.33 5 -0.47 23 28
Syndecan-3/AgRP 0.015 0.061 0.27 1 -0.37 21 22
Syndecan-3/AgRP/MC4R 0.038 0.069 0.33 1 -0.36 20 21
Fyn/Cortactin 0.028 0.022 -10000 0 -0.42 1 1
SDC3 0.001 0.057 -10000 0 -0.39 21 21
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.021 0.081 0.28 9 -0.34 35 44
IL8 0.026 0.098 0.26 60 -0.57 19 79
Syndecan-3/Fyn/Cortactin 0.036 0.064 -10000 0 -0.36 15 15
Syndecan-3/CASK 0 0.055 -10000 0 -0.37 21 21
alpha-MSH/MC4R 0.029 0.072 0.37 2 -0.42 21 23
Gamma Secretase 0.055 0.034 -10000 0 -0.32 1 1
Glypican 2 network

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
MDK 0.033 0.044 0.26 38 -10000 0 38
GPC2 0.048 0.081 0.26 116 -0.57 3 119
GPC2/Midkine 0.057 0.068 0.37 14 -0.42 3 17
neuron projection morphogenesis 0.057 0.068 0.36 14 -0.42 3 17
Signaling events mediated by HDAC Class III

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
EP300 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.019 -10000 0 -0.57 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.021 0.07 0.42 1 -0.26 49 50
CDKN1A -0.009 0.034 -10000 0 -0.77 2 2
KAT2B 0.024 0.019 -10000 0 -0.57 1 1
BAX 0.025 0.016 0.26 5 -10000 0 5
FOXO3 -0.005 0.008 -10000 0 -0.25 1 1
FOXO1 0.02 0.037 -10000 0 -0.57 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 24 -0.57 619 643
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.023 -10000 0 -0.42 1 1
PPARGC1A -0.09 0.24 0.26 10 -0.57 202 212
FHL2 0.021 0.045 -10000 0 -0.57 6 6
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.033 0.011 -10000 0 -10000 0 0
HIST2H4A 0.021 0.07 0.26 49 -0.42 1 50
SIRT1/FOXO3a 0.016 0.026 -10000 0 -0.19 3 3
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 0.023 -10000 0 -0.36 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 -0.047 0.16 -10000 0 -0.36 201 201
p53/SIRT1 0.027 0.02 0.41 2 -10000 0 2
SIRT1/FOXO4 0.022 0.037 -10000 0 -0.21 4 4
FOXO1/FHL2/SIRT1 0.037 0.04 -10000 0 -0.33 9 9
HIST1H1E 0.021 0.031 0.21 7 -10000 0 7
SIRT1/p300 0.033 0.011 -10000 0 -10000 0 0
muscle cell differentiation -0.029 0.023 0.36 1 -10000 0 1
TP53 0.02 0.011 0.21 2 -10000 0 2
KU70/SIRT1/BAX 0.045 0.017 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
MEF2D 0.021 0.009 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.25 0.21 -10000 0 -0.42 619 619
ACSS2 -0.007 0.009 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.029 0.023 -10000 0 -0.36 1 1
LPA4-mediated signaling events

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.019 0.064 -10000 0 -0.36 35 35
ADCY5 -0.12 0.16 -10000 0 -0.36 322 322
ADCY6 -0.007 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.002 -10000 0 -10000 0 0
ADCY1 -0.008 0.062 -10000 0 -0.36 26 26
ADCY2 -0.028 0.098 0.24 8 -0.36 77 85
ADCY3 -0.007 0.003 -10000 0 -10000 0 0
ADCY8 -0.004 0.023 0.23 6 -10000 0 6
PRKCE 0.006 0.001 -10000 0 -10000 0 0
ADCY9 -0.006 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.011 0.085 0.22 19 -0.25 36 55
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 0.012 0.043 -10000 0 -0.26 20 20
epithelial cell differentiation 0.036 0.054 -10000 0 -0.31 19 19
CYFIP2 0.028 0.049 0.26 27 -0.57 3 30
ENAH -0.004 0.06 0.29 11 -10000 0 11
EGFR -0.19 0.28 -10000 0 -0.57 375 375
EPHA2 0.021 0.041 -10000 0 -0.57 5 5
MYO6 -0.012 0.052 0.36 1 -0.3 20 21
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.049 0.035 -10000 0 -0.36 3 3
AQP5 -0.18 0.26 0.33 1 -0.5 407 408
CTNND1 0.024 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.012 0.05 0.36 1 -0.3 19 20
regulation of calcium-dependent cell-cell adhesion -0.023 0.075 0.36 1 -0.3 61 62
EGF -0.082 0.23 0.26 2 -0.57 186 188
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
AQP3 -0.016 0.12 0.29 1 -0.47 53 54
cortical microtubule organization 0.036 0.054 -10000 0 -0.31 19 19
GO:0000145 -0.012 0.048 0.35 1 -0.28 19 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.041 0.056 -10000 0 -0.32 19 19
MLLT4 0.021 0.033 0.26 1 -0.57 3 4
ARF6/GDP -0.02 0.039 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.045 0.039 -10000 0 -0.33 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.001 0.049 -10000 0 -0.28 19 19
PVRL2 0.024 0.004 -10000 0 -10000 0 0
ZYX -0.012 0.05 0.36 1 -0.3 19 20
ARF6/GTP 0.049 0.04 -10000 0 -0.31 5 5
CDH1 0.011 0.08 -10000 0 -0.57 19 19
EGFR/EGFR/EGF/EGF -0.14 0.2 -10000 0 -0.33 501 501
RhoA/GDP 0.037 0.053 -10000 0 -0.3 19 19
actin cytoskeleton organization -0.013 0.049 0.34 1 -0.29 20 21
IGF-1R heterotetramer 0.013 0.08 0.26 2 -0.57 19 21
GIT1 0.023 0.006 -10000 0 -10000 0 0
IGF1R 0.013 0.08 0.26 2 -0.57 19 21
IGF1 -0.1 0.24 -10000 0 -0.57 222 222
DIAPH1 0.026 0.1 -10000 0 -0.59 9 9
Wnt receptor signaling pathway -0.036 0.054 0.31 19 -10000 0 19
RHOA 0.024 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.02 0.039 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
VCL -0.014 0.05 0.35 1 -0.3 20 21
EFNA1 0.02 0.009 -10000 0 -10000 0 0
LPP -0.015 0.053 -10000 0 -0.29 26 26
Ephrin A1/EPHA2 0.025 0.053 -10000 0 -0.29 21 21
SEC6/SEC8 -0.022 0.042 -10000 0 -0.3 20 20
MGAT3 -0.023 0.076 0.36 1 -0.3 61 62
HGF/MET -0.038 0.15 -10000 0 -0.32 222 222
HGF -0.01 0.14 0.26 2 -0.57 60 62
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.012 0.043 -10000 0 -0.26 20 20
actin cable formation 0.041 0.095 0.3 40 -0.29 1 41
KIAA1543 -0.013 0.054 0.27 2 -0.33 19 21
KIFC3 -0.013 0.049 0.36 1 -0.3 19 20
NCK1 0.024 0.003 -10000 0 -10000 0 0
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ACTN1 -0.012 0.049 -10000 0 -0.3 19 19
NCK1/GIT1 0.033 0.01 -10000 0 -10000 0 0
mol:GDP 0.036 0.054 -10000 0 -0.31 19 19
EXOC4 0.024 0.004 -10000 0 -10000 0 0
STX4 -0.012 0.049 0.36 1 -0.3 18 19
PIP5K1C -0.012 0.051 0.36 1 -0.3 19 20
LIMA1 0.024 0.019 -10000 0 -0.57 1 1
ABI1 0.024 0.004 -10000 0 -10000 0 0
ROCK1 0.016 0.088 0.3 25 -10000 0 25
adherens junction assembly -0.022 0.1 0.3 3 -0.63 16 19
IGF-1R heterotetramer/IGF1 -0.042 0.15 -10000 0 -0.31 226 226
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.029 -10000 0 -0.42 3 3
MET -0.073 0.22 -10000 0 -0.57 169 169
PLEKHA7 -0.013 0.057 0.36 1 -0.35 19 20
mol:GTP 0.043 0.038 -10000 0 -0.33 5 5
establishment of epithelial cell apical/basal polarity -0.008 0.067 0.37 7 -0.52 1 8
cortical actin cytoskeleton stabilization 0.012 0.043 -10000 0 -0.26 20 20
regulation of cell-cell adhesion -0.013 0.049 0.34 1 -0.29 20 21
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.012 0.043 -10000 0 -0.26 20 20
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.007 0.011 -10000 0 -10000 0 0
SMARCC1 0.006 0.027 -10000 0 -0.5 2 2
REL 0.017 0.067 -10000 0 -0.57 13 13
HDAC7 -0.036 0.11 0.37 3 -0.36 67 70
JUN 0.019 0.045 -10000 0 -0.57 6 6
EP300 0.023 0.006 -10000 0 -10000 0 0
KAT2B 0.023 0.019 -10000 0 -0.57 1 1
KAT5 0.024 0.005 -10000 0 -10000 0 0
MAPK14 -0.008 0.063 -10000 0 -0.43 20 20
FOXO1 0.02 0.037 -10000 0 -0.57 4 4
T-DHT/AR -0.022 0.12 0.33 1 -0.37 68 69
MAP2K6 0.003 0.084 0.24 1 -0.58 20 21
BRM/BAF57 0.025 0.027 -10000 0 -10000 0 0
MAP2K4 0.014 0.021 -10000 0 -10000 0 0
SMARCA2 0.018 0.018 -10000 0 -10000 0 0
PDE9A -0.061 0.26 -10000 0 -1.1 58 58
NCOA2 -0.006 0.12 -10000 0 -0.57 43 43
CEBPA 0.019 0.055 -10000 0 -0.57 9 9
EHMT2 0.021 0.012 -10000 0 -10000 0 0
cell proliferation 0.001 0.15 0.35 35 -0.4 36 71
NR0B1 0.027 0.046 0.26 33 -0.57 1 34
EGR1 -0.16 0.27 -10000 0 -0.57 321 321
RXRs/9cRA -0.043 0.15 -10000 0 -0.33 210 210
AR/RACK1/Src -0.015 0.11 0.31 9 -0.34 41 50
AR/GR -0.026 0.12 0.24 3 -0.29 140 143
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 15 15
MAPK8 -0.001 0.041 -10000 0 -0.43 7 7
T-DHT/AR/TIF2/CARM1 -0.015 0.12 0.32 1 -0.36 54 55
SRC -0.018 0.066 0.19 29 -0.34 24 53
NR3C1 0.018 0.058 -10000 0 -0.57 10 10
KLK3 -0.14 0.4 0.37 5 -1.1 137 142
APPBP2 0.016 0.019 -10000 0 -10000 0 0
TRIM24 0.019 0.019 0.26 1 -10000 0 1
T-DHT/AR/TIP60 -0.014 0.095 0.3 3 -0.38 28 31
TMPRSS2 -0.13 0.36 -10000 0 -1 136 136
RXRG -0.1 0.24 0.26 2 -0.57 212 214
mol:9cRA -0.001 0.002 -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 0.018 0.055 -10000 0 -0.57 9 9
KLK2 -0.05 0.2 0.32 6 -0.66 82 88
AR -0.039 0.11 -10000 0 -0.3 138 138
SENP1 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
MDM2 0.025 0.016 -10000 0 -10000 0 0
SRY 0.003 0.012 0.032 126 -0.023 41 167
GATA2 0.012 0.097 0.26 14 -0.57 26 40
MYST2 0 0.002 -10000 0 -10000 0 0
HOXB13 0.11 0.12 0.25 434 -10000 0 434
T-DHT/AR/RACK1/Src -0.012 0.1 0.32 12 -0.38 28 40
positive regulation of transcription 0.012 0.097 0.26 14 -0.57 26 40
DNAJA1 0.017 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.011 -10000 0 -10000 0 0
NCOA1 0.021 0.03 -10000 0 -0.6 1 1
SPDEF -0.013 0.16 0.26 31 -0.57 69 100
T-DHT/AR/TIF2 -0.004 0.1 0.28 10 -0.36 30 40
T-DHT/AR/Hsp90 -0.015 0.095 0.31 4 -0.38 27 31
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 0.06 0.23 1 -0.36 25 26
SIRT1 0.024 0.003 -10000 0 -10000 0 0
ZMIZ2 0.026 0.017 -10000 0 -10000 0 0
POU2F1 0.009 0.05 -10000 0 -0.2 3 3
T-DHT/AR/DAX-1 -0.015 0.1 0.3 6 -0.38 29 35
CREBBP 0.023 0.007 -10000 0 -10000 0 0
SMARCE1 0.017 0.018 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.011 0.041 -10000 0 -0.57 1 1
SVIL 0.01 0.05 -10000 0 -0.57 4 4
ZNF318 0.039 0.055 0.2 40 -10000 0 40
JMJD2C -0.001 0.042 0.11 31 -0.13 76 107
T-DHT/AR/Ubc9 -0.031 0.14 -10000 0 -0.35 148 148
CARM1 0.019 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 0.014 0.03 -10000 0 -10000 0 0
AKT1 0.027 0.019 -10000 0 -10000 0 0
PTK2B 0.012 0.026 -10000 0 -10000 0 0
MED1 0.025 0.02 -10000 0 -10000 0 0
MAK 0.035 0.084 0.2 90 -0.55 11 101
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 0.01 0.053 -10000 0 -0.57 5 5
GSN 0.005 0.072 -10000 0 -0.57 12 12
NCOA2 -0.008 0.12 -10000 0 -0.57 43 43
NCOA6 0.013 0.033 -10000 0 -10000 0 0
DNA-PK 0.051 0.053 0.24 1 -10000 0 1
NCOA4 0.02 0.013 -10000 0 -10000 0 0
PIAS3 0.012 0.027 -10000 0 -10000 0 0
cell proliferation 0.005 0.11 0.35 1 -0.57 24 25
XRCC5 0.026 0.015 -10000 0 -10000 0 0
UBE3A 0.009 0.045 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.038 0.16 -10000 0 -0.38 154 154
FHL2 0.003 0.11 -10000 0 -0.7 12 12
RANBP9 0.013 0.033 -10000 0 -10000 0 0
JMJD1A -0.009 0.054 0.11 36 -0.13 139 175
CDK6 0.021 0.05 0.26 2 -0.57 7 9
TGFB1I1 0.009 0.05 -10000 0 -0.57 4 4
T-DHT/AR/CyclinD1 -0.04 0.14 -10000 0 -0.37 140 140
XRCC6 0.025 0.016 -10000 0 -10000 0 0
T-DHT/AR -0.035 0.17 -10000 0 -0.35 173 173
CTDSP1 0.018 0.019 -10000 0 -10000 0 0
CTDSP2 0.034 0.037 -10000 0 -10000 0 0
BRCA1 0.012 0.039 -10000 0 -0.57 1 1
TCF4 0.025 0.062 -10000 0 -0.56 9 9
CDKN2A 0.065 0.09 0.26 168 -10000 0 168
SRF 0.032 0.023 -10000 0 -10000 0 0
NKX3-1 -0.056 0.19 0.35 3 -0.58 81 84
KLK3 -0.15 0.46 0.4 1 -1.4 126 127
TMF1 0.018 0.016 -10000 0 -10000 0 0
HNRNPA1 0.029 0.021 -10000 0 -10000 0 0
AOF2 -0.007 0.023 -10000 0 -0.069 126 126
APPL1 0.019 0.033 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.024 0.15 -10000 0 -0.35 146 146
AR -0.064 0.2 0.21 1 -0.58 133 134
UBA3 0.017 0.019 -10000 0 -10000 0 0
PATZ1 0.027 0.021 -10000 0 -10000 0 0
PAWR 0.018 0.024 -10000 0 -0.57 1 1
PRKDC 0.023 0.017 -10000 0 -10000 0 0
PA2G4 0.031 0.027 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.021 0.13 -10000 0 -0.33 135 135
RPS6KA3 0.008 0.06 -10000 0 -0.57 7 7
T-DHT/AR/ARA70 -0.034 0.14 -10000 0 -0.35 147 147
LATS2 0.028 0.023 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.018 0.14 0.19 8 -0.33 143 151
Cyclin D3/CDK11 p58 0.019 0.006 -10000 0 -10000 0 0
VAV3 0.014 0.065 0.26 17 -0.57 7 24
KLK2 -0.075 0.28 0.37 1 -1 78 79
CASP8 0.026 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.037 0.15 -10000 0 -0.37 140 140
TMPRSS2 -0.12 0.34 -10000 0 -0.96 137 137
CCND1 0.011 0.046 0.26 1 -0.57 5 6
PIAS1 0.009 0.045 -10000 0 -10000 0 0
mol:T-DHT -0.008 0.03 0.057 2 -0.071 168 170
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 0.003 0.064 -10000 0 -0.2 11 11
T-DHT/AR/CDK6 -0.031 0.15 -10000 0 -0.38 138 138
CMTM2 0.023 0.013 0.25 1 -10000 0 1
SNURF 0.012 0.08 -10000 0 -0.57 19 19
ZMIZ1 0.01 0.041 -10000 0 -0.15 2 2
CCND3 0.024 0.005 -10000 0 -10000 0 0
TGIF1 0.027 0.021 -10000 0 -10000 0 0
FKBP4 0.014 0.037 0.26 4 -10000 0 4
Aurora A signaling

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
Aurora A/GADD45A 0.044 0.042 -10000 0 -10000 0 0
BIRC5 0.18 0.11 0.26 690 -10000 0 690
NFKBIA 0.024 0.04 0.28 7 -10000 0 7
CPEB1 -0.079 0.22 0.26 1 -0.57 180 181
AKT1 0.024 0.041 0.29 7 -10000 0 7
NDEL1 0.022 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.033 0.036 0.21 1 -10000 0 1
NDEL1/TACC3 0.065 0.067 0.26 16 -10000 0 16
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GSK3B -0.002 0.027 -10000 0 -10000 0 0
PAK1/Aurora A 0.04 0.044 0.27 2 -10000 0 2
MDM2 0.024 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.091 0.067 0.27 26 -10000 0 26
TP53 0.023 0.05 -10000 0 -0.22 12 12
DLG7 0.022 0.03 0.18 1 -10000 0 1
AURKAIP1 0.026 0.025 0.26 12 -10000 0 12
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 0.071 0.27 16 -10000 0 16
G2/M transition of mitotic cell cycle 0.032 0.036 0.2 1 -10000 0 1
AURKA 0.037 0.046 0.24 1 -10000 0 1
AURKB 0.087 0.075 0.17 410 -10000 0 410
CDC25B 0.031 0.04 0.22 3 -10000 0 3
G2/M transition checkpoint 0.018 0.029 -10000 0 -10000 0 0
mRNA polyadenylation -0.025 0.13 -10000 0 -0.3 179 179
Aurora A/CPEB -0.025 0.13 -10000 0 -0.3 179 179
Aurora A/TACC1/TRAP/chTOG 0.043 0.072 -10000 0 -0.31 22 22
BRCA1 0.023 0.02 0.26 1 -0.57 1 2
centrosome duplication 0.04 0.044 0.27 2 -10000 0 2
regulation of centrosome cycle 0.064 0.066 0.25 16 -10000 0 16
spindle assembly 0.042 0.07 -10000 0 -0.3 22 22
TDRD7 0.024 0.003 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.14 0.087 0.28 27 -10000 0 27
CENPA 0.096 0.081 0.19 422 -0.21 3 425
Aurora A/PP2A 0.043 0.043 -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 0.063 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.032 0.013 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
Ajuba/Aurora A 0.019 0.029 -10000 0 -10000 0 0
mitotic prometaphase -0.009 0.029 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.049 0.24 1 -10000 0 1
TACC1 0.006 0.091 -10000 0 -0.57 25 25
TACC3 0.058 0.084 0.26 156 -10000 0 156
Aurora A/Antizyme1 0.055 0.044 -10000 0 -10000 0 0
Aurora A/RasGAP 0.043 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 -0.001 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 0.091 0.067 0.27 26 -10000 0 26
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.094 0.072 0.24 37 -10000 0 37
PAK1 0.023 0.019 0.26 6 -10000 0 6
CKAP5 0.024 0.003 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 0.084 0.1 0.27 40 -0.57 6 46
Syndecan-4/Syndesmos 0.095 0.11 0.38 6 -0.7 6 12
positive regulation of JNK cascade 0.084 0.13 0.36 8 -0.64 8 16
Syndecan-4/ADAM12 0.11 0.12 0.37 22 -0.72 6 28
CCL5 0.029 0.057 0.26 37 -0.57 4 41
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DNM2 0.024 0.004 -10000 0 -10000 0 0
ITGA5 0.025 0.008 0.26 1 -10000 0 1
SDCBP 0.021 0.009 -10000 0 -10000 0 0
PLG -0.008 0.034 0.25 8 -10000 0 8
ADAM12 0.037 0.062 0.26 63 -0.57 2 65
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.024 0.014 0.26 3 -10000 0 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.029 0.018 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.066 0.15 0.38 4 -0.74 8 12
Syndecan-4/CXCL12/CXCR4 0.088 0.14 0.38 6 -0.69 8 14
Syndecan-4/Laminin alpha3 0.035 0.15 0.38 5 -0.74 7 12
MDK 0.033 0.044 0.26 38 -10000 0 38
Syndecan-4/FZD7 0.095 0.12 0.38 6 -0.69 7 13
Syndecan-4/Midkine 0.1 0.11 0.38 11 -0.7 6 17
FZD7 0.014 0.078 -10000 0 -0.57 18 18
Syndecan-4/FGFR1/FGF -0.009 0.16 0.35 1 -0.54 18 19
THBS1 0.022 0.037 -10000 0 -0.57 4 4
integrin-mediated signaling pathway 0.093 0.12 0.36 9 -0.69 7 16
positive regulation of MAPKKK cascade 0.084 0.13 0.36 8 -0.64 8 16
Syndecan-4/TACI 0.098 0.12 0.37 12 -0.72 6 18
CXCR4 0.029 0.035 0.26 24 -10000 0 24
cell adhesion 0.061 0.083 0.24 92 -0.25 20 112
Syndecan-4/Dynamin 0.099 0.1 0.38 4 -0.73 6 10
Syndecan-4/TSP1 0.098 0.11 0.38 6 -0.72 6 12
Syndecan-4/GIPC 0.099 0.1 0.38 4 -0.73 6 10
Syndecan-4/RANTES 0.1 0.11 0.37 7 -0.72 6 13
ITGB1 0.024 0.004 -10000 0 -10000 0 0
LAMA1 -0.036 0.18 0.26 3 -0.57 105 108
LAMA3 -0.11 0.25 -10000 0 -0.57 241 241
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA 0.024 0.23 0.7 93 -0.54 21 114
Syndecan-4/alpha-Actinin 0.099 0.1 0.38 5 -0.72 6 11
TFPI -0.003 0.12 -10000 0 -0.57 47 47
F2 0.025 0.034 0.27 12 -10000 0 12
alpha5/beta1 Integrin 0.035 0.008 -10000 0 -10000 0 0
positive regulation of cell adhesion 0 0.18 0.36 4 -0.55 31 35
ACTN1 0.024 0.005 -10000 0 -10000 0 0
TNC 0.013 0.091 0.26 11 -0.57 23 34
Syndecan-4/CXCL12 0.077 0.14 0.38 5 -0.72 8 13
FGF6 0.015 0.026 -10000 0 -0.57 2 2
RHOA 0.024 0.005 -10000 0 -10000 0 0
CXCL12 -0.019 0.16 -10000 0 -0.57 76 76
TNFRSF13B 0.028 0.085 0.26 58 -0.57 12 70
FGF2 -0.2 0.29 -10000 0 -0.57 393 393
FGFR1 0.016 0.049 -10000 0 -0.57 7 7
Syndecan-4/PI-4-5-P2 0.075 0.1 0.32 5 -0.72 6 11
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.11 0.12 0.25 410 -10000 0 410
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 0.37 7 -0.68 6 13
SDC4 0.088 0.1 0.36 8 -0.78 5 13
Syndecan-4/Tenascin C 0.095 0.12 0.38 6 -0.72 7 13
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.014 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.086 0.1 0.36 5 -0.7 6 11
MMP9 0.12 0.12 0.26 439 -0.56 1 440
Rac1/GTP 0.061 0.084 0.24 92 -0.26 20 112
cytoskeleton organization 0.093 0.1 0.37 6 -0.67 6 12
GIPC1 0.024 0.011 0.26 2 -10000 0 2
Syndecan-4/TFPI 0.087 0.12 0.38 5 -0.72 7 12
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.054 0.2 0.32 1 -0.52 66 67
MAP3K8 0.009 0.052 -10000 0 -0.57 7 7
FOS -0.019 0.14 0.32 2 -0.46 45 47
PRKCA -0.002 0.086 0.24 1 -0.58 21 22
PTPN7 0.021 0.059 0.25 58 -10000 0 58
HRAS 0.024 0.021 0.26 8 -10000 0 8
PRKCB 0.007 0.079 0.25 19 -0.58 14 33
NRAS 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.026 0.036 -10000 0 -10000 0 0
MAPK3 0.009 0.09 -10000 0 -0.81 5 5
MAP2K1 -0.011 0.12 -10000 0 -0.5 43 43
ELK1 0.007 0.029 -10000 0 -10000 0 0
BRAF -0.011 0.098 -10000 0 -0.48 37 37
mol:GTP -0.002 0.003 -10000 0 -0.006 307 307
MAPK1 -0.008 0.12 -10000 0 -0.54 27 27
RAF1 -0.011 0.097 -10000 0 -0.48 37 37
KRAS 0.023 0.005 -10000 0 -10000 0 0
Insulin Pathway

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
CBL/APS/CAP -0.047 0.17 -10000 0 -0.32 260 260
TC10/GTP -0.038 0.14 -10000 0 -0.29 246 246
Insulin Receptor/Insulin/IRS1/Shp2 0.043 0.079 -10000 0 -0.34 39 39
HRAS 0.026 0.021 0.26 8 -10000 0 8
APS homodimer 0.034 0.047 0.26 45 -10000 0 45
GRB14 0.013 0.18 0.26 143 -0.57 75 218
FOXO3 -0.019 0.16 -10000 0 -0.6 64 64
AKT1 -0.018 0.11 0.32 8 -0.29 84 92
INSR 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.056 0.046 0.42 5 -10000 0 5
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 -0.57 253 253
CRK 0.022 0.007 -10000 0 -10000 0 0
PTPN1 -0.001 0.024 -10000 0 -10000 0 0
CAV1 -0.083 0.15 -10000 0 -0.35 226 226
CBL/APS/CAP/Crk-II/C3G -0.027 0.16 -10000 0 -0.31 249 249
Insulin Receptor/Insulin/IRS1/NCK2 0.043 0.078 -10000 0 -0.34 38 38
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.029 0.073 -10000 0 -0.3 44 44
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.013 0.065 -10000 0 -0.36 13 13
RPS6KB1 -0.018 0.096 0.29 9 -0.48 1 10
PARD6A 0.023 0.019 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 0.038 -10000 0 -0.55 4 4
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.008 0.093 -10000 0 -0.28 19 19
HRAS/GTP -0.02 0.044 -10000 0 -0.28 25 25
Insulin Receptor 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.042 0.071 -10000 0 -0.32 26 26
PRKCI 0.014 0.058 -10000 0 -0.45 5 5
Insulin Receptor/Insulin/GRB14/PDK1 -0.003 0.1 -10000 0 -0.29 107 107
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 0.077 -10000 0 -0.3 44 44
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 8 -10000 0 8
AKT2 -0.018 0.11 0.28 11 -0.28 90 101
PRKCZ 0.005 0.085 -10000 0 -0.39 30 30
SH2B2 0.034 0.048 0.26 45 -10000 0 45
SHC/SHIP 0.012 0.058 -10000 0 -0.3 28 28
F2RL2 0.047 0.12 0.26 153 -0.57 18 171
TRIP10 0.024 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.037 0.021 -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 -0.33 252 252
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 0.062 0.19 1 -0.32 39 40
SOS1 0.024 0.003 -10000 0 -10000 0 0
SGK1 -0.019 0.14 -10000 0 -0.68 44 44
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.003 -10000 0 -10000 0 0
IRS1 0.001 0.11 -10000 0 -0.57 40 40
p62DOK/RasGAP 0.042 0.036 -10000 0 -0.47 4 4
INS 0.019 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.062 0.19 1 -0.31 39 40
GRB2 0.023 0.01 0.26 1 -10000 0 1
EIF4EBP1 -0.02 0.09 0.26 6 -0.48 1 7
PTPRA 0.026 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 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 0.009 0.054 -10000 0 -0.28 28 28
Insulin Receptor/Insulin/IRS1 0.029 0.075 -10000 0 -0.33 40 40
Insulin Receptor/Insulin/IRS3 0.034 0.014 -10000 0 -10000 0 0
Par3/Par6 0.061 0.073 -10000 0 -0.31 18 18
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 0.028 0.26 15 -10000 0 15
GNB1/GNG2 -0.016 0.048 -10000 0 -0.19 62 62
AKT1 0.024 0.093 0.32 15 -0.32 13 28
EGF -0.082 0.23 0.26 2 -0.57 186 188
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.014 0.058 0.25 2 -0.3 5 7
mol:Ca2+ 0.022 0.11 0.38 14 -0.3 70 84
LYN 0.012 0.054 0.25 2 -0.32 2 4
RhoA/GTP 0.009 0.045 0.13 4 -0.14 22 26
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.02 0.12 0.39 15 -0.35 61 76
GNG2 0.018 0.058 -10000 0 -0.57 10 10
ARRB2 0.022 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.007 0.12 -10000 0 -0.59 36 36
G beta5/gamma2 -0.012 0.067 -10000 0 -0.26 62 62
PRKCH 0.018 0.12 0.38 15 -0.36 63 78
DNM1 0.02 0.049 0.26 1 -0.57 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 -0.57 30 37
G12 family/GTP 0 0.089 -10000 0 -0.31 58 58
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
ADRBK2 0.021 0.037 -10000 0 -0.57 4 4
RhoA/GTP/ROCK1 0.031 0.015 -10000 0 -0.36 1 1
mol:GDP -0.012 0.099 0.36 33 -0.33 9 42
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 -0.57 65 65
mol:IP3 0.02 0.14 0.45 10 -0.38 70 80
cell morphogenesis 0.031 0.015 -10000 0 -0.36 1 1
PLCB2 0.012 0.17 0.54 7 -0.52 70 77
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.025 0.07 0.25 7 -0.29 5 12
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.015 0.059 0.24 4 -0.3 4 8
RHOA 0.024 0.005 -10000 0 -10000 0 0
PTGIR 0.026 0.022 0.26 9 -10000 0 9
PRKCB1 0.019 0.13 0.44 10 -0.38 64 74
GNAQ 0.023 0.026 -10000 0 -0.57 2 2
mol:L-citrulline 0.024 0.004 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.015 0.17 0.53 8 -0.53 63 71
LCK 0.016 0.073 0.25 2 -0.36 13 15
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.023 0.054 -10000 0 -0.25 25 25
TXA2-R family/G12 family/GDP/G beta/gamma 0.007 0.1 -10000 0 -0.42 48 48
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.023 0.051 -10000 0 -0.25 21 21
MAPK14 0.019 0.089 0.32 18 -0.23 59 77
TGM2/GTP 0.015 0.15 0.49 10 -0.43 67 77
MAPK11 0.017 0.09 0.33 17 -0.24 58 75
ARHGEF1 0.012 0.066 0.27 11 -0.18 48 59
GNAI2 0.024 0.005 -10000 0 -10000 0 0
JNK cascade 0.021 0.13 0.42 14 -0.39 63 77
RAB11/GDP 0.023 0.006 -10000 0 -10000 0 0
ICAM1 0.023 0.1 0.38 14 -0.28 59 73
cAMP biosynthetic process 0.017 0.13 0.43 10 -0.36 69 79
Gq family/GTP/EBP50 0.015 0.042 0.22 4 -0.28 5 9
actin cytoskeleton reorganization 0.031 0.015 -10000 0 -0.36 1 1
SRC 0.013 0.057 0.25 2 -0.28 5 7
GNB5 0.024 0.005 -10000 0 -10000 0 0
GNB1 0.024 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.047 0.1 0.22 5 -0.29 74 79
VCAM1 0.021 0.11 0.37 14 -0.31 60 74
TP beta/Gq family/GDP/G beta5/gamma2 -0.007 0.12 -10000 0 -0.59 36 36
platelet activation 0.024 0.12 0.39 17 -0.31 60 77
PGI2/IP 0.02 0.015 0.18 9 -10000 0 9
PRKACA 0.008 0.052 -10000 0 -0.28 30 30
Gq family/GDP/G beta5/gamma2 0 0.1 -10000 0 -0.5 29 29
TXA2/TP beta/beta Arrestin2 -0.006 0.067 -10000 0 -0.44 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 0.019 0.14 0.46 10 -0.42 66 76
EGFR -0.19 0.28 -10000 0 -0.57 375 375
TXA2/TP alpha 0.015 0.16 0.52 8 -0.49 69 77
Gq family/GTP 0.002 0.048 0.25 1 -0.22 42 43
YES1 0.014 0.059 0.25 2 -0.3 4 6
GNAI2/GTP 0.014 0.05 -10000 0 -0.26 18 18
PGD2/DP 0.006 0.075 0.18 7 -0.4 33 40
SLC9A3R1 0.036 0.054 0.26 57 -10000 0 57
FYN 0.012 0.058 0.26 1 -0.33 6 7
mol:NO 0.024 0.004 -10000 0 -10000 0 0
GNA15 0.025 0.026 0.26 6 -0.57 1 7
PGK/cGMP 0.008 0.095 -10000 0 -0.36 65 65
RhoA/GDP 0.023 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.036 0.069 -10000 0 -0.4 11 11
NOS3 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA 0.022 0.13 0.42 12 -0.38 58 70
PRKCB 0.021 0.13 0.41 13 -0.37 61 74
PRKCE 0.019 0.12 0.44 10 -0.36 59 69
PRKCD 0.018 0.13 0.42 11 -0.39 60 71
PRKCG 0.02 0.13 0.45 10 -0.39 62 72
muscle contraction 0.016 0.16 0.51 9 -0.49 65 74
PRKCZ 0.018 0.12 0.39 14 -0.35 62 76
ARR3 0.021 0.021 0.26 8 -10000 0 8
TXA2/TP beta 0.025 0.058 -10000 0 -0.26 30 30
PRKCQ 0.015 0.14 0.39 17 -0.4 64 81
MAPKKK cascade 0.015 0.15 0.48 9 -0.46 68 77
SELE 0.017 0.12 0.38 14 -0.39 58 72
TP beta/GNAI2/GDP/G beta/gamma 0.035 0.068 -10000 0 -0.41 11 11
ROCK1 0.023 0.019 -10000 0 -0.57 1 1
GNA14 0.023 0.066 0.26 19 -0.57 10 29
chemotaxis 0.014 0.18 0.58 7 -0.61 60 67
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.007 -10000 0 -10000 0 0
GNA11 0.023 0.026 -10000 0 -0.57 2 2
Rac1/GTP 0.018 0.003 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
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 0.011 0.082 0.26 1 -0.57 20 21
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.091 0.12 -10000 0 -0.24 405 405
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.023 0.019 -10000 0 -0.57 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 -0.57 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 0.099 -10000 0 -0.33 79 79
PRKG1 -0.013 0.14 -10000 0 -0.57 65 65
DUSP8 0.022 0.032 -10000 0 -0.57 3 3
PGK/cGMP/p38 alpha -0.019 0.13 -10000 0 -0.34 104 104
apoptosis -0.039 0.095 -10000 0 -0.33 74 74
RAL/GTP 0.032 0.006 -10000 0 -10000 0 0
LYN 0.021 0.009 -10000 0 -10000 0 0
DUSP1 -0.046 0.19 -10000 0 -0.57 122 122
PAK1 0.023 0.019 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 0.003 -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 0.008 -10000 0 -10000 0 0
MAPK11 -0.009 0.13 0.27 7 -0.39 58 65
BLK 0.05 0.087 0.26 142 -0.57 2 144
HCK 0.027 0.026 0.26 13 -10000 0 13
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 0.23 10 -0.38 69 79
positive regulation of innate immune response -0.011 0.15 0.31 6 -0.45 62 68
LCK 0.026 0.076 0.26 39 -0.57 11 50
p38alpha-beta/MKP7 -0.003 0.15 0.33 5 -0.44 55 60
p38alpha-beta/MKP5 -0.004 0.14 0.37 3 -0.46 49 52
PGK/cGMP -0.009 0.11 -10000 0 -0.42 65 65
PAK2 0.024 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.033 0.17 0.34 4 -0.46 86 90
CDC42 0.023 0.005 -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 -0.24 0.3 -10000 0 -0.57 462 462
TCGA08_retinoblastoma

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
CDKN2B 0.023 0.025 0.26 2 -0.54 1 3
CDKN2C 0.014 0.028 -10000 0 -0.55 1 1
CDKN2A 0.061 0.086 0.26 168 -10000 0 168
CCND2 -0.016 0.036 0.2 2 -0.21 14 16
RB1 0.016 0.047 0.26 14 -0.24 8 22
CDK4 -0.017 0.038 0.21 2 -0.22 12 14
CDK6 -0.017 0.04 0.22 2 -0.22 15 17
G1/S progression -0.01 0.058 0.19 41 -0.26 14 55
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.015 0.26 3 -10000 0 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.013 0.11 0.44 8 -0.52 3 11
IL27/IL27R/JAK1 0.038 0.16 0.68 5 -0.57 10 15
TBX21 -0.001 0.16 0.47 15 -0.5 43 58
IL12B 0.075 0.099 0.26 220 -10000 0 220
IL12A -0.014 0.1 0.14 18 -0.42 58 76
IL6ST -0.039 0.18 0.2 1 -0.57 111 112
IL27RA/JAK1 0.023 0.07 0.64 1 -1.2 2 3
IL27 0.048 0.076 0.27 107 -10000 0 107
TYK2 0.03 0.015 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.098 0.16 0.75 2 -0.68 3 5
T-helper 2 cell differentiation -0.013 0.11 0.44 8 -0.52 3 11
T cell proliferation during immune response -0.013 0.11 0.44 8 -0.52 3 11
MAPKKK cascade 0.013 0.11 0.52 3 -0.44 8 11
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT2 0.024 0.002 -10000 0 -10000 0 0
STAT1 0.028 0.033 0.26 19 -10000 0 19
IL12RB1 0.034 0.054 0.27 41 -0.57 2 43
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.009 0.18 0.46 31 -0.52 50 81
IL27/IL27R/JAK2/TYK2 0.012 0.11 0.52 3 -0.45 8 11
positive regulation of T cell mediated cytotoxicity 0.013 0.11 0.52 3 -0.44 8 11
STAT1 (dimer) 0.037 0.2 0.65 22 -0.65 16 38
JAK2 0.027 0.012 -10000 0 -10000 0 0
JAK1 0.024 0.01 -10000 0 -10000 0 0
STAT2 (dimer) 0.024 0.11 0.44 3 -0.44 7 10
T cell proliferation -0.092 0.18 0.36 3 -0.45 86 89
IL12/IL12R/TYK2/JAK2 0.058 0.18 0.43 8 -0.72 28 36
IL17A -0.098 0.16 0.75 2 -0.69 3 5
mast cell activation -0.013 0.11 0.44 8 -0.52 3 11
IFNG 0.021 0.045 0.12 116 -0.11 5 121
T cell differentiation 0 0.006 0.018 8 -0.019 8 16
STAT3 (dimer) 0.023 0.11 0.44 3 -0.44 7 10
STAT5A (dimer) 0.021 0.12 0.44 3 -0.44 13 16
STAT4 (dimer) 0.011 0.14 0.44 3 -0.4 34 37
STAT4 -0.001 0.12 0.26 1 -0.57 44 45
T cell activation -0.005 0.01 0.12 2 -0.1 6 8
IL27R/JAK2/TYK2 0.018 0.13 -10000 0 -0.75 4 4
GATA3 -0.025 0.27 0.62 37 -1.3 35 72
IL18 0.009 0.019 0.14 22 -10000 0 22
positive regulation of mast cell cytokine production 0.023 0.11 0.44 3 -0.44 7 10
IL27/EBI3 0.052 0.072 0.25 47 -0.39 6 53
IL27RA 0.011 0.072 0.74 1 -1.3 2 3
IL6 -0.18 0.28 0.26 1 -0.57 368 369
STAT5A 0.02 0.045 -10000 0 -0.57 6 6
monocyte differentiation 0.001 0.002 -10000 0 -10000 0 0
IL2 -0.014 0.039 0.45 2 -0.52 1 3
IL1B 0.001 0.05 0.13 3 -0.42 14 17
EBI3 0.025 0.054 0.26 12 -0.57 6 18
TNF 0.006 0.042 0.14 24 -0.42 8 32
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 0.056 0.13 0.5 5 -0.58 1 6
RAD9A 0.023 0.006 -10000 0 -10000 0 0
AP1 -0.093 0.21 -10000 0 -0.42 289 289
IFNAR2 0.029 0.009 -10000 0 -10000 0 0
AKT1 -0.004 0.089 -10000 0 -0.45 8 8
ER alpha/Oestrogen -0.026 0.17 0.18 116 -0.41 154 270
NFX1/SIN3/HDAC complex 0.023 0.058 0.24 1 -0.33 15 16
EGF -0.081 0.23 0.26 2 -0.57 186 188
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 2 -0.52 1 3
SAP18 0.024 0.007 -10000 0 -10000 0 0
MRN complex 0.037 0.022 -10000 0 -10000 0 0
WT1 0.14 0.12 0.26 510 -10000 0 510
WRN 0.02 0.009 -10000 0 -10000 0 0
SP1 0.031 0.013 -10000 0 -10000 0 0
SP3 0.026 0.006 -10000 0 -10000 0 0
TERF2IP 0.022 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.051 0.1 -10000 0 -0.51 1 1
Mad/Max 0.041 0.014 -10000 0 -10000 0 0
TERT 0.056 0.13 0.51 5 -0.59 1 6
CCND1 0.079 0.16 0.54 19 -1 5 24
MAX 0.026 0.007 -10000 0 -10000 0 0
RBBP7 0.027 0.019 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 0.039 0.05 -10000 0 -0.4 4 4
CDKN1B 0.029 0.05 -10000 0 -0.68 3 3
RAD1 0.024 0.004 -10000 0 -10000 0 0
XRCC5 0.024 0.003 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
SAP30 0.025 0.015 0.26 4 -10000 0 4
TRF2/PARP2 0.032 0.015 -10000 0 -10000 0 0
UBE3A 0.025 0.007 -10000 0 -10000 0 0
JUN 0.022 0.045 -10000 0 -0.57 6 6
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 -0.57 290 290
IFN-gamma/IRF1 0.064 0.064 0.38 2 -0.32 3 5
PARP2 0.024 0.004 -10000 0 -10000 0 0
BLM 0.045 0.068 0.26 96 -10000 0 96
Telomerase 0.029 0.08 0.26 1 -0.59 6 7
IRF1 0.029 0.018 0.26 3 -0.18 3 6
ESR1 -0.035 0.23 0.26 116 -0.57 148 264
KU/TER 0.034 0.009 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.014 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.027 0.055 0.23 1 -0.34 9 10
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.027 0.056 0.23 1 -0.34 9 10
HDAC1 0.025 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.012 -10000 0 -10000 0 0
ATM 0.012 0.016 -10000 0 -10000 0 0
SMAD3 0.005 0.014 -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 0.058 0.13 0.49 1 -0.62 4 5
NR2F2 0.012 0.037 -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 0.023 0.015 0.25 3 -10000 0 3
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 0.012 0.016 -10000 0 -10000 0 0
NBN 0.02 0.01 -10000 0 -10000 0 0
EGFR -0.19 0.28 -10000 0 -0.57 375 375
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.2 0.26 -10000 0 -0.45 505 505
MYC 0.009 0.082 -10000 0 -0.57 20 20
IL2 0.029 0.025 0.26 8 -10000 0 8
KU 0.034 0.009 -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 0.023 0.015 0.25 3 -10000 0 3
TRF2/BLM 0.044 0.046 0.23 8 -10000 0 8
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.067 0.12 0.45 4 -0.55 1 5
SP1/HDAC2 0.046 0.025 -10000 0 -10000 0 0
PINX1 0.02 0.009 -10000 0 -10000 0 0
Telomerase/EST1A 0.048 0.1 -10000 0 -0.49 1 1
Smad3/Myc 0.007 0.054 -10000 0 -0.36 19 19
911 complex 0.044 0.016 -10000 0 -10000 0 0
IFNG 0.058 0.082 0.26 143 -0.19 3 146
Telomerase/PinX1 0.04 0.097 -10000 0 -0.49 1 1
Telomerase/AKT1/mTOR/p70S6K 0.025 0.1 0.3 3 -0.58 14 17
SIN3B 0.025 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.045 0.096 -10000 0 -10000 0 0
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 0.051 0.1 -10000 0 -0.51 1 1
E2F1 0.098 0.11 0.26 312 -10000 0 312
ZNFX1 0.024 0.006 -10000 0 -10000 0 0
PIF1 0.068 0.092 0.26 198 -10000 0 198
NCL 0.024 0.004 -10000 0 -10000 0 0
DKC1 0.025 0.01 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 0.075 0.3 2 -0.31 29 31
NF kappa B1 p50/RelA/I kappa B alpha 0.046 0.084 0.35 12 -0.34 2 14
alphaV/beta3 Integrin/Osteopontin/Src 0.082 0.072 -10000 0 -10000 0 0
AP1 -0.035 0.18 0.34 1 -0.54 33 34
ILK 0.03 0.077 0.29 1 -0.32 28 29
bone resorption 0.018 0.089 -10000 0 -0.49 12 12
PTK2B 0.02 0.009 -10000 0 -10000 0 0
PYK2/p130Cas 0.067 0.095 0.33 2 -0.3 24 26
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 -0.41 28 28
alphaV/beta3 Integrin/Osteopontin 0.078 0.1 0.36 3 -0.35 34 37
MAP3K1 0.029 0.08 0.25 15 -0.33 34 49
JUN 0.021 0.045 -10000 0 -0.57 6 6
MAPK3 0.02 0.072 0.27 12 -0.31 25 37
MAPK1 0.021 0.073 0.27 13 -0.3 26 39
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.015 0.085 0.26 16 -0.35 36 52
ITGB3 0.007 0.11 0.26 4 -0.57 34 38
NFKBIA 0.018 0.071 0.31 6 -0.34 4 10
FOS -0.14 0.27 -10000 0 -0.57 290 290
CD44 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
PLAU 0.022 0.1 0.45 7 -0.55 2 9
NF kappa B1 p50/RelA 0.063 0.079 0.36 6 -10000 0 6
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RELA 0.024 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.025 0.083 -10000 0 -0.42 34 34
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.03 0.078 0.26 14 -0.32 34 48
VAV3 0.015 0.078 0.26 17 -0.31 32 49
MAP3K14 0.031 0.078 0.26 11 -0.32 34 45
ROCK2 0.008 0.096 -10000 0 -0.57 28 28
SPP1 0.088 0.1 0.26 276 -10000 0 276
RAC1 0.024 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.028 0.072 0.3 3 -0.29 31 34
MMP2 -0.054 0.15 0.32 6 -0.51 32 38
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.023 0.13 0.32 11 -0.39 38 49
IKBKB 0.024 0.089 0.29 10 -0.32 12 22
AKT1 0.039 0.11 0.26 90 -0.24 19 109
IKBKG 0.027 0.073 0.3 6 -0.31 5 11
CALM1 0.001 0.096 0.26 1 -0.44 17 18
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.023 0.16 0.37 11 -0.52 44 55
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.1 -10000 0 -0.36 41 41
DOK1 0.025 0.015 0.26 4 -10000 0 4
AP-1 -0.021 0.098 0.27 5 -0.25 50 55
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 0.005 0.16 0.36 19 -0.44 92 111
CD22 -0.012 0.13 0.28 20 -0.44 63 83
CAMK2G 0.003 0.095 0.3 1 -0.42 17 18
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 0.086 -10000 0 -0.33 52 52
GO:0007205 0.002 0.1 -10000 0 -0.36 41 41
SYK 0.024 0.003 -10000 0 -10000 0 0
ELK1 0.002 0.1 0.26 1 -0.44 19 20
NFATC1 0.03 0.13 0.3 24 -0.44 34 58
B-cell antigen/BCR complex 0.005 0.16 0.36 19 -0.44 92 111
PAG1/CSK 0.03 0.016 -10000 0 -10000 0 0
NFKBIB 0.023 0.049 0.16 14 -0.13 29 43
HRAS 0.011 0.11 0.26 13 -0.35 37 50
NFKBIA 0.023 0.048 0.15 15 -0.12 29 44
NF-kappa-B/RelA/I kappa B beta 0.027 0.043 0.17 11 -10000 0 11
RasGAP/Csk 0.032 0.12 0.33 20 -0.36 66 86
mol:GDP 0.004 0.099 -10000 0 -0.42 20 20
PTEN 0.023 0.019 -10000 0 -0.57 1 1
CD79B 0.012 0.099 0.26 19 -0.57 26 45
NF-kappa-B/RelA/I kappa B alpha 0.027 0.042 0.17 11 -10000 0 11
GRB2 0.023 0.01 0.26 1 -10000 0 1
PI3K/BCAP/CD19 0.023 0.16 0.35 11 -0.49 49 60
PIK3R1 0.018 0.055 -10000 0 -0.57 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 -0.077 0.16 -10000 0 -0.43 79 79
CHUK 0.024 0.081 0.31 6 -0.31 16 22
IBTK 0.023 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.019 0.096 -10000 0 -0.41 17 17
PTPN6 -0.014 0.12 0.29 8 -0.56 31 39
RELA 0.024 0.005 -10000 0 -10000 0 0
BCL2A1 0.024 0.036 0.17 9 -10000 0 9
VAV2 0.014 0.14 0.29 8 -0.57 30 38
ubiquitin-dependent protein catabolic process 0.025 0.048 0.16 14 -0.12 38 52
BTK 0.015 0.062 -10000 0 -0.97 4 4
CD19 0.005 0.14 0.27 31 -0.43 61 92
MAP4K1 0.032 0.054 0.26 43 -0.57 2 45
CD72 0.03 0.042 0.26 28 -0.57 1 29
PAG1 0.021 0.014 0.26 2 -10000 0 2
MAPK14 0.025 0.14 0.35 14 -0.44 42 56
SH3BP5 0.024 0.004 -10000 0 -10000 0 0
PIK3AP1 0.003 0.11 -10000 0 -0.44 27 27
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.003 0.13 0.26 3 -0.42 71 74
RAF1 0.01 0.1 0.28 7 -0.42 18 25
RasGAP/p62DOK/SHIP 0.032 0.12 0.3 19 -0.35 66 85
CD79A -0.003 0.17 0.26 78 -0.57 78 156
re-entry into mitotic cell cycle -0.021 0.097 0.26 5 -0.25 48 53
RASA1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.018 0.097 0.27 25 -0.37 13 38
MAPK1 0.01 0.09 0.27 7 -0.36 16 23
CD72/SHP1 0.029 0.14 0.36 26 -0.54 30 56
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.023 0.14 0.35 16 -0.44 44 60
actin cytoskeleton organization 0.031 0.14 0.31 26 -0.5 29 55
NF-kappa-B/RelA 0.055 0.082 0.28 13 -0.21 1 14
Calcineurin 0.019 0.092 -10000 0 -0.39 15 15
PI3K -0.013 0.095 -10000 0 -0.44 27 27
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.006 0.11 -10000 0 -0.39 47 47
SOS1 0.024 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.012 0.2 0.44 5 -0.7 49 54
DAPP1 -0.017 0.2 -10000 0 -0.78 51 51
cytokine secretion 0.031 0.13 0.28 30 -0.41 34 64
mol:DAG 0.002 0.1 -10000 0 -0.36 44 44
PLCG2 0.02 0.028 0.26 1 -0.57 2 3
MAP2K1 0.01 0.097 0.28 8 -0.4 16 24
B-cell antigen/BCR complex/FcgammaRIIB 0.016 0.13 0.34 19 -0.41 67 86
mol:PI-3-4-5-P3 0.005 0.09 0.22 18 -0.33 23 41
ETS1 0.001 0.089 0.28 1 -0.4 18 19
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.034 0.13 0.33 20 -0.36 71 91
B-cell antigen/BCR complex/LYN -0.011 0.13 0.3 5 -0.44 66 71
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 0.3 23 -0.53 29 52
B-cell antigen/BCR complex/LYN/SYK 0.014 0.14 0.35 21 -0.44 57 78
CARD11 0.004 0.1 0.28 3 -0.46 19 22
FCGR2B 0.018 0.038 0.26 1 -0.57 4 5
PPP3CA 0.024 0.011 0.26 2 -10000 0 2
BCL10 0.024 0.004 -10000 0 -10000 0 0
IKK complex 0.027 0.051 0.16 51 -0.14 4 55
PTPRC 0.021 0.041 0.26 11 -0.57 3 14
PDPK1 0.019 0.082 0.21 52 -0.23 19 71
PPP3CB 0.024 0.003 -10000 0 -10000 0 0
PPP3CC 0.02 0.01 -10000 0 -10000 0 0
POU2F2 0.021 0.034 0.18 10 -10000 0 10
IL2 signaling events mediated by STAT5

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
GAB2 0.022 0.02 -10000 0 -0.57 1 1
ELF1 0.03 0.053 -10000 0 -0.36 11 11
CCNA2 0.11 0.11 0.26 391 -10000 0 391
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
JAK3 0.028 0.027 0.26 14 -10000 0 14
PIK3R1 0.019 0.055 -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 0.046 0.1 0.33 12 -0.52 12 24
SHC1 0.021 0.009 -10000 0 -10000 0 0
SP1 0.024 0.046 -10000 0 -0.38 12 12
IL2RA 0.019 0.11 0.29 62 -0.76 14 76
IL2RB 0.031 0.051 0.26 37 -0.57 2 39
SOS1 0.025 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.068 0.26 45 -0.57 7 52
G1/S transition of mitotic cell cycle 0.043 0.14 0.35 3 -0.83 16 19
PTPN11 0.025 0.003 -10000 0 -10000 0 0
CCND2 0.006 0.089 0.43 1 -0.8 12 13
LCK 0.027 0.076 0.26 39 -0.57 11 50
GRB2 0.024 0.01 0.26 1 -10000 0 1
IL2 0.023 0.021 0.26 8 -10000 0 8
CDK6 0.021 0.05 0.26 2 -0.57 7 9
CCND3 0.046 0.1 0.42 5 -0.56 6 11
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.025 0.011 -10000 0 -10000 0 0
HSPA8 0.021 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.016 0.17 0.3 3 -0.39 145 148
AKT1 0.025 0.01 -10000 0 -10000 0 0
GSC -0.03 0.27 -10000 0 -1.3 40 40
NKX2-5 0.055 0.083 0.26 150 -10000 0 150
muscle cell differentiation -0.028 0.063 0.35 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.067 0.066 -10000 0 -0.44 1 1
SMAD4 0.013 0.045 -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 0.26 1 -0.36 376 377
SMAD3/SMAD4/VDR 0.055 0.059 -10000 0 -0.34 1 1
MYC 0.006 0.082 -10000 0 -0.57 20 20
CDKN2B -0.044 0.18 -10000 0 -1.2 13 13
AP1 -0.049 0.16 -10000 0 -0.3 244 244
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.009 0.087 -10000 0 -0.36 32 32
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.013 0.058 -10000 0 -0.35 10 10
SP3 0.025 0.004 -10000 0 -10000 0 0
CREB1 0.024 0.003 -10000 0 -10000 0 0
FOXH1 0.045 0.081 0.26 120 -10000 0 120
SMAD3/SMAD4/GR 0.024 0.071 -10000 0 -0.39 10 10
GATA3 0.012 0.11 0.26 26 -0.56 35 61
SKI/SIN3/HDAC complex/NCoR1 0.004 0.078 -10000 0 -0.34 36 36
MEF2C/TIF2 0.026 0.088 0.31 3 -0.32 15 18
endothelial cell migration -0.031 0.086 0.5 14 -10000 0 14
MAX 0.02 0.015 -10000 0 -10000 0 0
RBBP7 0.026 0.019 0.26 7 -10000 0 7
RBBP4 0.023 0.019 -10000 0 -0.57 1 1
RUNX2 0.027 0.027 0.26 14 -10000 0 14
RUNX3 0.021 0.043 0.26 3 -0.57 5 8
RUNX1 0.023 0.019 -10000 0 -0.57 1 1
CTBP1 0.023 0.005 -10000 0 -10000 0 0
NR3C1 0.014 0.06 -10000 0 -0.57 10 10
VDR 0.024 0.003 -10000 0 -10000 0 0
CDKN1A 0.016 0.079 -10000 0 -1.1 3 3
KAT2B 0.024 0.019 -10000 0 -0.57 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.055 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 0.03 0.086 -10000 0 -0.51 14 14
SMAD3/SMAD4/ATF2 0.033 0.059 -10000 0 -0.4 2 2
SMAD3/SMAD4/ATF3 -0.013 0.14 -10000 0 -0.4 111 111
SAP30 0.024 0.015 0.26 4 -10000 0 4
Cbp/p300/PIAS3 0.041 0.031 -10000 0 -10000 0 0
JUN -0.058 0.15 0.29 1 -0.33 92 93
SMAD3/SMAD4/IRF7 0.052 0.081 0.32 22 -10000 0 22
TFE3 0.029 0.009 -10000 0 -0.2 1 1
COL1A2 0.046 0.09 0.39 4 -0.59 6 10
mesenchymal cell differentiation -0.035 0.058 -10000 0 -10000 0 0
DLX1 0.054 0.1 0.26 163 -0.57 10 173
TCF3 0.024 0.009 0.26 1 -10000 0 1
FOS -0.14 0.27 -10000 0 -0.57 291 291
SMAD3/SMAD4/Max 0.028 0.058 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.044 0.019 -10000 0 -10000 0 0
ZBTB17 0.022 0.007 -10000 0 -10000 0 0
LAMC1 0.013 0.037 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.034 0.055 -10000 0 -10000 0 0
IRF7 0.048 0.071 0.27 95 -10000 0 95
ESR1 -0.041 0.23 0.26 116 -0.57 148 264
HNF4A 0.023 0.03 0.26 16 -10000 0 16
MEF2C 0.053 0.09 0.4 11 -0.44 2 13
SMAD2-3/SMAD4 0.034 0.065 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.045 0.025 -10000 0 -0.36 1 1
IGHV3OR16-13 0.006 0.039 -10000 0 -0.34 12 12
TGIF2/HDAC complex 0.024 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
SKIL 0.026 0.023 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 0.005 -10000 0 -10000 0 0
GCN5L2 0.001 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.043 0.061 -10000 0 -0.46 1 1
MSG1/HSC70 -0.14 0.22 0.2 13 -0.42 398 411
SMAD2 0.022 0.03 -10000 0 -10000 0 0
SMAD3 0.015 0.04 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.016 0.04 -10000 0 -0.26 1 1
SMAD2/SMAD2/SMAD4 0.027 0.058 0.26 8 -0.51 3 11
NCOR1 0.022 0.008 -10000 0 -10000 0 0
NCOA2 -0.004 0.12 -10000 0 -0.57 43 43
NCOA1 0.024 0.019 -10000 0 -0.57 1 1
MYOD/E2A 0.032 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.078 0.064 -10000 0 -0.41 1 1
IFNB1 0.022 0.071 0.32 27 -10000 0 27
SMAD3/SMAD4/MEF2C 0.071 0.086 0.33 2 -0.42 2 4
CITED1 -0.2 0.29 0.26 15 -0.57 397 412
SMAD2-3/SMAD4/ARC105 0.042 0.066 -10000 0 -10000 0 0
RBL1 0.023 0.02 0.26 1 -0.57 1 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.017 0.065 -10000 0 -0.48 9 9
RUNX1-3/PEBPB2 0.04 0.039 -10000 0 -0.42 5 5
SMAD7 -0.031 0.14 -10000 0 -0.42 30 30
MYC/MIZ-1 0.016 0.064 -10000 0 -0.42 20 20
SMAD3/SMAD4 0.033 0.072 0.3 23 -0.34 2 25
IL10 0.006 0.082 0.34 2 -0.36 30 32
PIASy/HDAC complex 0.02 0.015 -10000 0 -10000 0 0
PIAS3 0.021 0.01 -10000 0 -10000 0 0
CDK2 0.026 0.008 -10000 0 -10000 0 0
IL5 0.003 0.084 0.36 1 -0.35 34 35
CDK4 0.025 0.008 -10000 0 -10000 0 0
PIAS4 0.02 0.015 -10000 0 -10000 0 0
ATF3 -0.043 0.18 0.26 1 -0.57 112 113
SMAD3/SMAD4/SP1 0.047 0.064 -10000 0 -0.49 1 1
FOXG1 0.017 0.067 0.26 70 -10000 0 70
FOXO3 0.011 0.017 -10000 0 -0.42 1 1
FOXO1 0.01 0.029 -10000 0 -0.42 4 4
FOXO4 0.012 0.01 -10000 0 -10000 0 0
heart looping 0.053 0.089 0.4 11 -0.44 2 13
CEBPB 0.023 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.054 0.09 0.31 2 -0.39 10 12
MYOD1 0.021 0.028 0.26 14 -10000 0 14
SMAD3/SMAD4/HNF4 0.034 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.029 0.1 0.35 1 -0.39 36 37
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.023 0.26 10 -10000 0 10
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.044 0.07 -10000 0 -0.4 4 4
SMAD3/SMAD4/SP1-3 0.062 0.063 -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 0.081 0.094 0.34 21 -0.39 1 22
ITGB5 0.016 0.042 -10000 0 -0.4 1 1
TGIF/SIN3/HDAC complex/CtBP 0.012 0.063 -10000 0 -0.3 25 25
SMAD3/SMAD4/AR -0.017 0.15 -10000 0 -0.39 128 128
AR -0.05 0.2 0.26 1 -0.57 131 132
negative regulation of cell growth 0 0.083 -10000 0 -0.32 20 20
SMAD3/SMAD4/MYOD 0.032 0.058 -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 0.069 0.074 -10000 0 -0.33 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.016 0.055 -10000 0 -0.38 10 10
TFDP1 0.022 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.034 0.17 -10000 0 -0.31 216 216
SMAD3/SMAD4/RUNX2 0.036 0.059 -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 0.026 -10000 0 -0.57 2 2
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 0.047 0.13 168 -10000 0 168
TP53 0.01 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 -0.011 0.06 0.29 30 -10000 0 30
MDM4 0.02 0.009 -10000 0 -10000 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.27 0.3 -10000 0 -0.57 503 503
CLTC 0.025 0.067 0.24 8 -0.43 12 20
calcium ion-dependent exocytosis 0.009 0.025 -10000 0 -0.26 2 2
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 0.045 -10000 0 -0.34 10 10
CPE 0.005 0.049 -10000 0 -0.36 18 18
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
membrane fusion 0.01 0.019 -10000 0 -10000 0 0
CTNND1 0.008 0.056 0.19 86 -10000 0 86
DNM2 0.024 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.044 0.2 4 -0.33 7 11
TSHR -0.003 0.072 -10000 0 -0.36 40 40
INS -0.002 0.09 -10000 0 -0.48 34 34
BIN1 0.02 0.052 -10000 0 -0.57 8 8
mol:Choline 0.01 0.019 -10000 0 -10000 0 0
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 -0.33 7 8
ASAP2/amphiphysin II 0.042 0.034 -10000 0 -0.33 7 7
ARF6/GTP 0.018 0.003 -10000 0 -10000 0 0
CDH1 0.009 0.054 -10000 0 -0.37 9 9
clathrin-independent pinocytosis 0.018 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.023 0.006 -10000 0 -10000 0 0
positive regulation of endocytosis 0.018 0.003 -10000 0 -10000 0 0
EXOC2 0.027 0.029 0.26 16 -10000 0 16
substrate adhesion-dependent cell spreading 0.016 0.04 -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 -0.037 0.064 0.33 9 -10000 0 9
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 0.014 0.043 -10000 0 -0.34 10 10
clathrin heavy chain/ACAP1 0.024 0.063 0.24 12 -0.35 12 24
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 89 -10000 0 89
NME1 0.013 0.017 -10000 0 -10000 0 0
clathrin coat assembly 0.028 0.069 0.24 10 -0.42 12 22
IL2RA 0.019 0.055 -10000 0 -0.31 14 14
VAMP3 0.011 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.12 0.14 -10000 0 -0.27 414 414
EXOC6 0.024 0.003 -10000 0 -10000 0 0
PLD1 0.009 0.03 -10000 0 -0.29 9 9
PLD2 0.011 0.006 -10000 0 -10000 0 0
EXOC5 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.013 0.039 0.19 2 -0.33 7 9
SDC1 0.019 0.043 -10000 0 -0.33 8 8
ARF6/GDP 0.021 0.014 -10000 0 -10000 0 0
EXOC7 0.023 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.04 0.067 -10000 0 -0.34 9 9
mol:Phosphatidic acid 0.01 0.019 -10000 0 -10000 0 0
endocytosis -0.04 0.034 0.33 7 -10000 0 7
SCAMP2 0.024 0.004 -10000 0 -10000 0 0
ADRB2 -0.038 0.14 0.25 2 -0.3 179 181
EXOC3 0.024 0.005 -10000 0 -10000 0 0
ASAP2 0.024 0.019 -10000 0 -0.57 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 -0.083 0.16 0.27 4 -0.29 301 305
RALA 0.024 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.036 0.065 0.32 2 -0.36 5 7
Signaling mediated by p38-gamma and p38-delta

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
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 0.033 0.29 7 -10000 0 7
MAPK12 0.004 0.072 0.21 63 -0.32 24 87
CCND1 0.011 0.049 -10000 0 -0.37 8 8
p38 gamma/SNTA1 0.022 0.072 0.32 2 -0.31 24 26
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 0.073 0.21 67 -0.32 24 91
MAP2K6 -0.004 0.054 -10000 0 -0.34 25 25
MAPT -0.027 0.12 0.26 14 -0.32 121 135
MAPK13 0.011 0.011 0.26 2 -10000 0 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.01 0.025 -10000 0 -0.35 5 5
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.011 0.004 -10000 0 -10000 0 0
MAP4K4 0.003 0.06 -10000 0 -0.38 5 5
BAG4 0.018 0.033 -10000 0 -0.57 3 3
PKC zeta/ceramide -0.001 0.052 -10000 0 -0.24 17 17
NFKBIA 0.024 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.041 0.26 12 -0.57 3 15
BAX 0.002 0.041 -10000 0 -0.35 10 10
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.069 0.7 10 -10000 0 10
BAD -0.015 0.046 0.19 3 -0.24 15 18
SMPD1 0.015 0.057 0.2 12 -0.22 22 34
RB1 -0.015 0.044 -10000 0 -0.24 15 15
FADD/Caspase 8 0.027 0.087 0.26 12 -0.37 8 20
MAP2K4 -0.016 0.045 0.18 5 -0.27 11 16
NSMAF 0.021 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.009 0.056 0.19 31 -0.3 7 38
EGF -0.082 0.23 0.26 2 -0.57 186 188
mol:ceramide -0.014 0.048 0.14 1 -0.25 16 17
MADD 0.024 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.01 0.009 -10000 0 -10000 0 0
ASAH1 0.021 0.016 0.26 3 -10000 0 3
negative regulation of cell cycle -0.016 0.044 -10000 0 -0.24 15 15
cell proliferation -0.044 0.12 0.27 1 -0.27 200 201
BID -0.021 0.17 -10000 0 -0.66 61 61
MAP3K1 -0.015 0.047 0.19 4 -0.25 16 20
EIF2A -0.014 0.049 0.21 9 -0.24 7 16
TRADD 0.022 0.008 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.007 0.054 0.28 3 -0.29 7 10
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.011 0.059 0.26 4 -0.31 6 10
Cathepsin D/ceramide 0.005 0.057 0.17 32 -0.23 15 47
FADD 0.005 0.06 0.22 11 -0.39 4 15
KSR1 -0.009 0.054 0.2 22 -0.25 13 35
MAPK8 -0.014 0.058 -10000 0 -0.27 20 20
PRKRA -0.015 0.047 0.2 4 -0.24 15 19
PDGFA 0.024 0.008 0.26 1 -10000 0 1
TRAF2 0.025 0.015 0.26 4 -10000 0 4
IGF1 -0.1 0.24 -10000 0 -0.57 222 222
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.014 0.048 0.14 1 -0.25 16 17
CTSD 0.031 0.042 0.26 34 -10000 0 34
regulation of nitric oxide biosynthetic process 0.034 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.047 0.13 0.29 1 -0.29 200 201
PRKCD 0.024 0.009 0.26 1 -10000 0 1
PRKCZ 0.023 0.019 -10000 0 -0.57 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.01 0.009 -10000 0 -10000 0 0
RelA/NF kappa B1 0.034 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.019 -10000 0 -0.57 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.016 0.044 -10000 0 -0.35 5 5
TNFR1A/BAG4/TNF-alpha 0.037 0.05 -10000 0 -0.36 10 10
mol:Sphingosine-1-phosphate 0.011 0.004 -10000 0 -10000 0 0
MAP2K1 -0.01 0.055 0.26 4 -0.3 6 10
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.024 0.005 -10000 0 -10000 0 0
CYCS 0 0.049 0.17 21 -0.22 12 33
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.029 -10000 0 -0.36 4 4
EIF2AK2 -0.016 0.043 0.19 5 -0.24 11 16
TNF-alpha/TNFR1A/FAN 0.041 0.043 -10000 0 -0.36 6 6
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.014 0.08 -10000 0 -0.37 32 32
MAP2K2 -0.01 0.055 0.24 5 -0.29 7 12
SMPD3 -0.002 0.1 0.26 4 -0.29 93 97
TNF 0.025 0.063 0.26 24 -0.57 8 32
PKC zeta/PAR4 0.033 0.022 -10000 0 -0.42 2 2
mol:PHOSPHOCHOLINE 0.042 0.097 0.24 188 -0.21 3 191
NF kappa B1/RelA/I kappa B alpha 0.063 0.03 -10000 0 -0.32 2 2
AIFM1 -0.001 0.049 0.17 23 -0.2 16 39
BCL2 0.007 0.096 -10000 0 -0.57 28 28
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.062 0.087 0.26 172 -10000 0 172
mol:Halofuginone 0.002 0.004 -10000 0 -10000 0 0
ITGA1 0.019 0.055 -10000 0 -0.57 9 9
CDKN1A -0.031 0.094 -10000 0 -0.44 29 29
PRL-3/alpha Tubulin 0.03 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0.075 0.24 43 -0.42 12 55
AGT 0.03 0.089 0.26 74 -0.57 12 86
CCNA2 -0.065 0.14 -10000 0 -10000 0 0
TUBA1B 0.024 0.003 -10000 0 -10000 0 0
EGR1 -0.12 0.2 -10000 0 -0.41 321 321
CDK2/Cyclin E1 0.016 0.11 -10000 0 -0.4 28 28
MAPK3 0.01 0.02 0.26 5 -10000 0 5
PRL-2 /Rab GGTase beta 0.035 0.007 -10000 0 -10000 0 0
MAPK1 0.01 0.02 0.26 5 -10000 0 5
PTP4A1 -0.093 0.14 -10000 0 -10000 0 0
PTP4A3 0.021 0.019 0.26 5 -10000 0 5
PTP4A2 0.024 0.004 -10000 0 -10000 0 0
ITGB1 0.01 0.018 0.26 4 -10000 0 4
SRC 0.024 0.005 -10000 0 -10000 0 0
RAC1 -0.017 0.074 -10000 0 -0.43 14 14
Rab GGTase beta/Rab GGTase alpha 0.035 0.008 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.072 0.15 -10000 0 -10000 0 0
RABGGTA 0.024 0.004 -10000 0 -10000 0 0
BCAR1 -0.014 0.014 -10000 0 -10000 0 0
RHOC -0.02 0.082 -10000 0 -0.44 20 20
RHOA -0.022 0.092 -10000 0 -0.55 17 17
cell motility -0.026 0.1 -10000 0 -0.4 30 30
PRL-1/alpha Tubulin -0.073 0.15 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.026 0.041 -10000 0 -0.34 9 9
ROCK1 -0.024 0.099 -10000 0 -0.39 28 28
RABGGTB 0.024 0.004 -10000 0 -10000 0 0
CDK2 0.024 0.002 -10000 0 -10000 0 0
mitosis -0.092 0.14 -10000 0 -10000 0 0
ATF5 0.025 0.013 0.26 3 -10000 0 3
Caspase cascade in apoptosis

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
TOP1 0.008 0.11 0.26 2 -0.42 42 44
ACTA1 0.012 0.11 0.26 6 -0.49 30 36
NUMA1 0.004 0.11 0.26 2 -0.39 47 49
SPTAN1 -0.002 0.11 0.27 7 -0.49 31 38
LIMK1 -0.002 0.11 0.27 5 -0.49 31 36
BIRC3 0.023 0.041 0.26 12 -0.57 3 15
BIRC2 0.022 0.007 -10000 0 -10000 0 0
BAX 0.025 0.016 0.26 5 -10000 0 5
CASP10 -0.011 0.091 0.2 11 -0.45 32 43
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
PTK2 0.003 0.12 0.25 3 -0.44 44 47
DIABLO 0.024 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.002 0.11 0.27 7 -0.48 31 38
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 39 43
MADD 0.024 0.004 -10000 0 -10000 0 0
TFAP2A 0.013 0.13 -10000 0 -0.68 28 28
BID 0.003 0.054 0.18 3 -0.27 31 34
MAP3K1 -0.004 0.095 -10000 0 -0.38 52 52
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 0.001 0.11 0.26 7 -0.49 29 36
CASP9 0.023 0.006 -10000 0 -10000 0 0
DNA repair -0.016 0.044 0.25 4 -0.2 5 9
neuron apoptosis 0.003 0.12 -10000 0 -0.69 26 26
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0 0.11 0.26 2 -0.46 36 38
APAF1 0.024 0.003 -10000 0 -10000 0 0
CASP6 -0.001 0.15 -10000 0 -0.91 25 25
TRAF2 0.025 0.015 0.26 4 -10000 0 4
ICAD/CAD -0.005 0.1 0.25 1 -0.51 26 27
CASP7 0.002 0.061 0.27 4 -0.42 3 7
KRT18 0.014 0.081 -10000 0 -0.69 10 10
apoptosis 0.002 0.12 0.3 6 -0.45 46 52
DFFA -0.004 0.1 0.25 3 -0.49 30 33
DFFB -0.004 0.1 0.25 3 -0.48 31 34
PARP1 0.016 0.044 0.21 5 -0.25 4 9
actin filament polymerization 0.001 0.1 0.45 32 -0.29 9 41
TNF 0.025 0.063 0.26 24 -0.57 8 32
CYCS 0.005 0.049 0.21 6 -0.23 19 25
SATB1 -0.009 0.15 -10000 0 -0.78 31 31
SLK -0.002 0.11 0.28 4 -0.49 31 35
p15 BID/BAX 0.013 0.063 0.24 2 -0.24 35 37
CASP2 0.003 0.063 0.23 7 -0.38 6 13
JNK cascade 0.003 0.095 0.38 52 -10000 0 52
CASP3 0 0.11 0.28 3 -0.5 32 35
LMNB2 0.001 0.13 0.33 2 -0.51 42 44
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 0.014 0.13 -10000 0 -0.67 28 28
stress fiber formation -0.002 0.1 0.28 4 -0.48 31 35
GZMB 0.01 0.1 0.28 11 -0.5 31 42
CASP1 0.011 0.012 -10000 0 -0.35 1 1
LMNB1 0.02 0.12 0.3 7 -0.54 24 31
APP 0.003 0.12 -10000 0 -0.7 26 26
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 0.28 6 -0.44 48 54
LMNA 0.009 0.081 0.32 2 -0.38 22 24
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.005 0.067 -10000 0 -0.3 21 21
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.002 0.11 0.27 4 -0.49 30 34
APAF-1/Caspase 9 -0.003 0.12 -10000 0 -0.61 35 35
nuclear fragmentation during apoptosis 0.004 0.11 0.26 2 -0.38 47 49
CFL2 -0.001 0.11 0.29 9 -0.47 32 41
GAS2 -0.027 0.14 0.27 6 -0.38 94 100
positive regulation of apoptosis 0.014 0.11 0.27 7 -0.5 30 37
PRF1 0.016 0.078 0.26 8 -0.57 17 25
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.002 0.089 0.29 43 -10000 0 43
GNAI2 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.027 -10000 0 -0.36 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.018 0.09 0.26 32 -0.57 19 51
RhoA/GTP -0.002 0.091 -10000 0 -0.3 43 43
negative regulation of cAMP metabolic process -0.003 0.087 -10000 0 -0.28 79 79
GNAZ 0.018 0.055 -10000 0 -0.57 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 20 -0.57 2 22
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.003 0.087 -10000 0 -0.28 79 79
RhoA/GDP 0.018 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
GNAI1 -0.005 0.13 -10000 0 -0.57 52 52
Cellular roles of Anthrax toxin

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
ANTXR1 0.023 0.027 0.26 1 -0.57 2 3
ANTXR2 0.018 0.058 -10000 0 -0.57 10 10
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.008 -10000 0 -0.076 12 12
monocyte activation 0.004 0.084 0.25 2 -0.34 53 55
MAP2K2 0.002 0.083 -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 -0.3 21 21
CYAA -0.009 0.035 -10000 0 -0.32 12 12
MAP2K4 -0.004 0.008 -10000 0 -0.11 1 1
IL1B -0.008 0.046 0.18 3 -0.28 25 28
Channel 0.026 0.041 0.17 1 -0.34 12 13
NLRP1 -0.007 0.031 -10000 0 -0.31 10 10
CALM1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.066 -10000 0 -0.39 28 28
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.008 0.076 12 -10000 0 12
MAPK3 -0.004 0.007 0.085 1 -10000 0 1
MAPK1 -0.004 0.009 0.12 2 -10000 0 2
PGR -0.08 0.14 0.2 2 -0.31 270 272
PA/Cellular Receptors 0.028 0.045 0.18 1 -0.37 12 13
apoptosis -0.002 0.008 -10000 0 -0.076 12 12
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.039 0.16 1 -0.32 12 13
macrophage activation -0.005 0.01 0.14 1 -10000 0 1
TNF 0.025 0.063 0.26 24 -0.57 8 32
VCAM1 0.004 0.084 0.25 2 -0.34 53 55
platelet activation -0.001 0.066 -10000 0 -0.39 28 28
MAPKKK cascade -0.002 0.026 0.091 15 -0.13 6 21
IL18 -0.003 0.026 -10000 0 -0.22 9 9
negative regulation of macrophage activation -0.002 0.008 -10000 0 -0.076 12 12
LEF -0.002 0.008 -10000 0 -0.076 12 12
CASP1 -0.003 0.027 -10000 0 -0.17 18 18
mol:cAMP -0.001 0.067 -10000 0 -0.39 28 28
necrosis -0.002 0.008 -10000 0 -0.076 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 0.039 0.16 1 -0.32 12 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.024 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.018 0.064 0.16 1 -0.29 46 47
FRAP1 -0.001 0.083 0.4 1 -0.46 25 26
AKT1 -0.005 0.069 0.18 4 -0.28 35 39
INSR 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.007 -10000 0 -10000 0 0
mol:GTP 0.024 0.068 0.23 5 -0.26 16 21
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.002 0.035 -10000 0 -0.22 3 3
TSC2 0.023 0.006 -10000 0 -10000 0 0
RHEB/GDP 0.006 0.046 -10000 0 -0.25 12 12
TSC1 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.005 0.077 -10000 0 -0.31 57 57
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.014 0.046 -10000 0 -0.23 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.012 0.076 0.25 9 -0.31 22 31
MAP3K5 -0.001 0.046 0.2 10 -0.2 44 54
PIK3R1 0.019 0.055 -10000 0 -0.57 9 9
apoptosis -0.001 0.046 0.2 10 -0.19 45 55
mol:LY294002 0 0 0.001 1 -0.001 50 51
EIF4B 0.011 0.069 0.27 6 -0.29 15 21
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.028 0.066 -10000 0 -0.29 9 9
eIF4E/eIF4G1/eIF4A1 0.003 0.05 -10000 0 -0.28 21 21
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.016 0.079 -10000 0 -0.29 60 60
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.054 0.22 15 -0.19 3 18
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.027 0.06 -10000 0 -0.25 11 11
mol:Amino Acids 0 0 0.001 1 -0.001 50 51
FKBP12/Rapamycin 0.018 0.004 -10000 0 -10000 0 0
PDPK1 -0.019 0.058 0.17 5 -0.27 43 48
EIF4E 0.024 0.004 -10000 0 -10000 0 0
ASK1/PP5C -0.005 0.14 -10000 0 -0.52 62 62
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.003 0.048 -10000 0 -10000 0 0
TSC1/TSC2 0.027 0.074 0.25 6 -0.29 13 19
tumor necrosis factor receptor activity 0 0 0.001 50 -0.001 1 51
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 -0.011 0.079 -10000 0 -0.33 58 58
INS 0.017 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.019 -10000 0 -0.57 1 1
PDK2 -0.017 0.057 0.18 8 -0.27 38 46
EIF4EBP1 -0.024 0.23 -10000 0 -1 47 47
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PPP2R5D 0.001 0.079 0.33 4 -0.41 24 28
peptide biosynthetic process -0.011 0.017 0.18 8 -10000 0 8
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 0.003 52 -0.003 3 55
EEF2 -0.011 0.017 0.18 8 -10000 0 8
eIF4E/4E-BP1 -0.014 0.21 -10000 0 -0.97 47 47
Class I PI3K signaling events mediated by Akt

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
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 0.056 -10000 0 -0.34 13 13
CDKN1A 0.009 0.062 -10000 0 -0.35 17 17
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.009 -10000 0 -10000 0 0
FOXO3 0.013 0.055 -10000 0 -0.41 6 6
AKT1 0.006 0.057 -10000 0 -0.36 17 17
BAD 0.024 0.009 0.26 1 -10000 0 1
AKT3 0.007 0.034 -10000 0 -0.35 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.008 0.06 -10000 0 -0.44 7 7
AKT1/ASK1 0.031 0.068 -10000 0 -0.4 7 7
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 0.066 0.38 8 -10000 0 8
TSC1 0.011 0.052 -10000 0 -0.34 12 12
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.037 0.071 0.27 1 -0.43 7 8
EP300 0.023 0.006 -10000 0 -10000 0 0
mol:GDP 0.01 0.06 -10000 0 -0.35 19 19
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.007 0.055 0.32 1 -0.33 17 18
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
TBC1D4 0.004 0.015 -10000 0 -0.35 2 2
MAP3K5 0.022 0.032 -10000 0 -0.57 3 3
MAPKAP1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.026 0.076 0.31 18 -0.24 5 23
YWHAH 0.023 0.006 -10000 0 -10000 0 0
AKT1S1 0.011 0.061 -10000 0 -0.35 17 17
CASP9 0.011 0.046 -10000 0 -0.4 3 3
YWHAB 0.023 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.073 0.32 5 -0.54 3 8
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 0.059 0.25 3 -0.48 5 8
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.006 0.052 -10000 0 -0.33 19 19
CHUK 0.009 0.056 -10000 0 -0.4 6 6
BAD/BCL-XL 0.038 0.067 0.29 2 -0.53 3 5
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 0.3 8 -0.4 22 30
PDPK1 0.023 0.006 -10000 0 -10000 0 0
MDM2 0.012 0.065 0.27 2 -0.44 7 9
MAPKKK cascade -0.036 0.07 0.35 16 -0.26 1 17
MDM2/Cbp/p300 0.042 0.073 0.34 4 -0.56 3 7
TSC1/TSC2 0.014 0.069 0.26 34 -0.59 3 37
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.07 0.32 4 -0.53 3 7
glucose import -0.16 0.15 0.21 2 -0.31 500 502
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.011 0.05 0.18 3 -0.4 5 8
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.15 0.16 0.21 2 -0.31 500 502
GSK3A 0.01 0.06 -10000 0 -0.42 8 8
FOXO1 0.011 0.041 -10000 0 -0.3 1 1
GSK3B 0.009 0.06 -10000 0 -0.44 7 7
SFN 0.021 0.071 0.26 19 -0.57 12 31
G1/S transition of mitotic cell cycle 0.014 0.065 0.33 2 -0.6 3 5
p27Kip1/14-3-3 family 0.02 0.05 0.37 1 -0.45 3 4
PRKACA 0.024 0.004 -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 0.007 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.024 0.089 -10000 0 -0.6 11 11
oxygen homeostasis 0.011 0.013 -10000 0 -10000 0 0
TCEB2 0.028 0.034 0.26 21 -10000 0 21
TCEB1 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.088 0.088 0.36 10 -0.36 3 13
EPO 0.15 0.17 0.52 63 -0.51 3 66
FIH (dimer) 0.032 0.02 -10000 0 -10000 0 0
APEX1 0.033 0.024 -10000 0 -10000 0 0
SERPINE1 0.14 0.16 0.53 22 -0.52 5 27
FLT1 -0.017 0.17 -10000 0 -0.7 33 33
ADORA2A 0.16 0.17 0.49 64 -0.52 4 68
germ cell development 0.14 0.16 0.54 23 -0.53 4 27
SLC11A2 0.14 0.16 0.52 15 -0.55 4 19
BHLHE40 0.13 0.16 0.52 13 -0.56 5 18
HIF1AN 0.032 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.12 0.13 0.41 47 -0.39 3 50
ETS1 0.027 0.035 -10000 0 -0.57 3 3
CITED2 0.015 0.089 -10000 0 -0.56 15 15
KDR -0.016 0.17 -10000 0 -0.78 27 27
PGK1 0.14 0.16 0.52 14 -0.54 4 18
SIRT1 0.026 0.004 -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 -0.58 6 19
EPAS1 0.069 0.089 0.28 49 -0.37 6 55
SP1 0.03 0.013 -10000 0 -10000 0 0
ABCG2 0.12 0.2 0.53 15 -0.56 40 55
EFNA1 0.11 0.14 0.5 7 -0.53 3 10
FXN 0.15 0.16 0.47 39 -0.52 4 43
POU5F1 0.14 0.16 0.54 23 -0.55 4 27
neuron apoptosis -0.15 0.18 0.56 6 -0.6 13 19
EP300 0.023 0.006 -10000 0 -10000 0 0
EGLN3 0.047 0.067 0.27 73 -0.58 1 74
EGLN2 0.033 0.025 0.26 4 -10000 0 4
EGLN1 0.027 0.028 -10000 0 -0.58 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 0.48 41 -0.53 4 45
TWIST1 0.13 0.19 0.46 40 -0.55 37 77
ELK1 0.028 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.1 0.11 0.42 7 -0.38 3 10
VEGFA 0.13 0.16 0.57 12 -0.55 4 16
CREBBP 0.023 0.007 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.022 0.078 -10000 0 -0.6 4 4
UGCG 0.009 0.12 -10000 0 -0.67 29 29
AKT1/mTOR/p70S6K/Hsp90/TERT 0.047 0.12 0.3 11 -0.44 27 38
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.011 0.12 -10000 0 -0.66 29 29
mol:DAG 0.005 0.083 -10000 0 -0.76 11 11
CaM/Ca2+/Calcineurin A alpha-beta B1 0.037 0.14 0.3 6 -0.43 51 57
FRAP1 0.03 0.16 0.33 6 -0.48 57 63
FOXO3 0.035 0.14 0.34 12 -0.54 30 42
AKT1 0.036 0.15 0.34 6 -0.56 33 39
GAB2 0.021 0.021 -10000 0 -0.57 1 1
SMPD1 0.009 0.11 -10000 0 -0.64 26 26
SGMS1 0.019 0.064 -10000 0 -0.54 11 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.001 0.033 -10000 0 -0.34 9 9
CALM1 0.024 0.004 -10000 0 -10000 0 0
cell proliferation 0.046 0.11 0.29 7 -0.46 23 30
EIF3A 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.031 0.043 -10000 0 -0.38 10 10
RPS6KB1 0.011 0.097 -10000 0 -0.84 11 11
mol:sphingomyelin 0.005 0.083 -10000 0 -0.76 11 11
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 0.028 0.028 0.26 14 -10000 0 14
PIK3R1 0.019 0.056 -10000 0 -0.57 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 0.42 9 -0.91 27 36
MYB 0.029 0.19 0.48 2 -1.1 23 25
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.036 0.11 0.32 10 -0.51 17 27
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.036 0.093 -10000 0 -0.76 11 11
mol:PI-3-4-5-P3 0.04 0.11 0.32 10 -0.49 17 27
Rac1/GDP 0.016 0.033 -10000 0 -0.33 8 8
T cell proliferation 0.04 0.1 0.29 12 -0.48 14 26
SHC1 0.02 0.011 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.013 0.1 3 -0.076 22 25
PRKCZ 0.039 0.1 0.3 10 -0.5 14 24
NF kappa B1 p50/RelA 0.047 0.14 0.33 2 -0.45 44 46
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.025 0.075 0.3 11 -0.52 8 19
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RELA 0.024 0.005 -10000 0 -10000 0 0
IL2RA 0.027 0.087 0.26 54 -0.57 14 68
IL2RB 0.031 0.052 0.26 37 -0.57 2 39
TERT 0.053 0.079 0.26 136 -10000 0 136
E2F1 0.052 0.094 0.41 1 -0.38 22 23
SOS1 0.024 0.007 -10000 0 -10000 0 0
RPS6 0.024 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.006 0.033 22 -0.05 3 25
PTPN11 0.024 0.008 -10000 0 -10000 0 0
IL2RG 0.031 0.069 0.26 45 -0.57 7 52
actin cytoskeleton organization 0.04 0.1 0.29 12 -0.48 14 26
GRB2 0.023 0.011 0.26 1 -10000 0 1
IL2 0.022 0.024 0.26 8 -10000 0 8
PIK3CA 0.024 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.039 0.038 -10000 0 -0.31 8 8
LCK 0.027 0.076 0.26 39 -0.57 11 50
BCL2 0.017 0.2 0.37 5 -0.74 51 56
BARD1 signaling events

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
BARD1/CSTF1 0.027 0.054 0.2 1 -0.39 16 17
ATM 0.022 0.008 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
PRKDC 0.021 0.009 -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 16 18
XRCC5 0.024 0.003 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.037 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 0.088 -10000 0 -0.42 21 21
FANCF 0.024 0.004 -10000 0 -10000 0 0
BRCA1 0.023 0.02 0.26 1 -0.57 1 2
CCNE1 0.062 0.087 0.26 172 -10000 0 172
CDK2/Cyclin E1 0.061 0.06 -10000 0 -10000 0 0
FANCG 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.027 0.058 -10000 0 -0.42 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 0.089 0.26 174 -10000 0 174
DNA repair 0.028 0.085 0.3 4 -0.37 7 11
BRCA1/BARD1/ubiquitin 0.027 0.058 -10000 0 -0.42 16 16
BARD1/DNA-PK 0.046 0.051 -10000 0 -0.33 13 13
FANCL 0.024 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.027 0.054 0.39 16 -0.2 1 17
BRCA1/BARD1/CTIP/M/R/N Complex 0.011 0.071 -10000 0 -0.28 9 9
BRCA1/BACH1/BARD1/TopBP1 0.04 0.053 -10000 0 -0.36 16 16
BRCA1/BARD1/P53 0.048 0.053 -10000 0 -0.33 16 16
BARD1/CSTF1/BRCA1 0.038 0.051 -10000 0 -0.36 14 14
BRCA1/BACH1 0.023 0.02 0.26 1 -0.57 1 2
BARD1 0.015 0.074 0.26 1 -0.57 16 17
PCNA 0.024 0.011 0.26 2 -10000 0 2
BRCA1/BARD1/UbcH5C 0.04 0.052 -10000 0 -0.36 15 15
BRCA1/BARD1/UbcH7 0.039 0.052 -10000 0 -0.36 15 15
BRCA1/BARD1/RAD51/PCNA 0.093 0.087 0.31 2 -0.31 15 17
BARD1/DNA-PK/P53 0.05 0.053 -10000 0 -0.31 13 13
BRCA1/BARD1/Ubiquitin 0.027 0.058 -10000 0 -0.42 16 16
BRCA1/BARD1/CTIP 0.029 0.049 -10000 0 -0.33 16 16
FA complex 0.035 0.038 0.24 3 -0.26 1 4
BARD1/EWS 0.027 0.057 -10000 0 -0.42 16 16
RBBP8 0.01 0.005 -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 16 -10000 0 16
BRCA1/BARD1 0.071 0.073 0.33 2 -0.3 16 18
CSTF1 0.023 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.011 0.054 0.18 1 -0.42 16 17
CDK2 0.024 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.1 0.11 0.26 366 -10000 0 366
RAD50 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.027 0.058 -10000 0 -0.42 16 16
EWSR1 0.023 0.006 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.012 0.061 -10000 0 -10000 0 0
PLK1 0.25 0.18 0.55 83 -0.57 1 84
CDKN1B 0.15 0.13 0.39 49 -0.45 5 54
FOXO3 0.2 0.16 0.45 175 -0.52 2 177
KAT2B 0.055 0.034 -10000 0 -0.58 1 1
FOXO1/SIRT1 0.012 0.055 -10000 0 -0.28 8 8
CAT 0.19 0.16 0.52 36 -0.95 4 40
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.056 0.029 -10000 0 -10000 0 0
FOXO1 0.017 0.062 -10000 0 -0.31 8 8
MAPK10 -0.016 0.12 0.2 11 -0.29 150 161
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.034 0.085 0.38 3 -0.42 2 5
response to oxidative stress 0.035 0.026 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.17 0.14 0.41 73 -0.52 2 75
XPO1 0.025 0.003 -10000 0 -10000 0 0
EP300 0.025 0.007 -10000 0 -10000 0 0
BCL2L11 0.063 0.082 -10000 0 -0.7 8 8
FOXO1/SKP2 0.026 0.058 -10000 0 -0.28 8 8
mol:GDP 0.034 0.026 -10000 0 -10000 0 0
RAN 0.025 0.003 -10000 0 -10000 0 0
GADD45A 0.13 0.13 0.45 3 -0.51 14 17
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.021 0.13 -10000 0 -0.51 36 36
MST1 0.052 0.06 0.27 6 -0.52 8 14
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 0.12 -10000 0 -0.45 46 46
YWHAB 0.023 0.005 -10000 0 -10000 0 0
MAPK8 0.029 0.036 0.2 13 -0.3 7 20
MAPK9 0.031 0.025 0.2 15 -10000 0 15
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 0.012 0.02 -10000 0 -10000 0 0
SOD2 0.15 0.13 0.47 14 -0.44 1 15
RBL2 0.1 0.25 0.54 2 -0.63 69 71
RAL/GDP 0.056 0.021 -10000 0 -10000 0 0
CHUK 0.056 0.028 -10000 0 -10000 0 0
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CSNK1G2 0.024 0.005 -10000 0 -10000 0 0
RAL/GTP 0.057 0.021 -10000 0 -10000 0 0
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
FASLG 0.056 0.18 -10000 0 -1.3 15 15
SKP2 0.024 0.004 -10000 0 -10000 0 0
USP7 0.024 0.006 -10000 0 -10000 0 0
IKBKB 0.047 0.032 -10000 0 -10000 0 0
CCNB1 0.2 0.17 0.56 51 -0.57 1 52
FOXO1-3a-4/beta catenin 0.15 0.12 0.42 35 -0.39 6 41
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.058 -10000 0 -0.28 8 8
CSNK1A1 0.024 0.004 -10000 0 -10000 0 0
SGK1 0.052 0.048 -10000 0 -0.56 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 0.031 0.075 0.44 1 -0.41 1 2
SFN 0.021 0.071 0.26 19 -0.57 12 31
CDK2 0.023 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.062 0.11 0.32 2 -0.41 19 21
CREBBP 0.022 0.008 -10000 0 -10000 0 0
FBXO32 0.23 0.21 0.57 137 -1.2 4 141
BCL6 0.16 0.16 0.48 6 -0.87 10 16
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
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.018 0.09 0.26 32 -0.57 19 51
CDC42/GTP -0.004 0.096 -10000 0 -0.36 27 27
PLCG1 -0.011 0.086 -10000 0 -0.36 28 28
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 -0.004 0.094 -10000 0 -0.35 27 27
S1PR5 0.027 0.042 0.26 20 -0.57 2 22
S1PR4 0.029 0.063 0.26 38 -0.57 6 44
MAPK3 -0.008 0.082 0.26 1 -0.31 38 39
MAPK1 -0.007 0.084 -10000 0 -0.38 25 25
S1P/S1P5/Gi -0.003 0.087 -10000 0 -0.28 79 79
GNAI1 -0.005 0.13 -10000 0 -0.57 52 52
CDC42/GDP 0.017 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.027 -10000 0 -0.36 2 2
RHOA 0.006 0.058 0.24 1 -0.31 6 7
S1P/S1P4/Gi -0.003 0.093 -10000 0 -0.33 48 48
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.018 0.055 -10000 0 -0.57 9 9
S1P/S1P4/G12/G13 0.044 0.042 -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 0.005 -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 0.056 0.072 0.38 13 -0.38 12 25
MAP4K1 0.032 0.054 0.26 43 -0.57 2 45
MAP3K8 0.02 0.049 -10000 0 -0.57 7 7
PRKCB 0.019 0.076 0.26 19 -0.57 14 33
DBNL 0.024 0.003 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
MAP3K1 0.014 0.055 0.26 1 -0.31 16 17
JUN 0.003 0.13 -10000 0 -0.61 38 38
MAP3K7 0.014 0.054 0.26 1 -0.36 6 7
GRAP2 0.017 0.067 0.26 3 -0.57 13 16
CRK 0.022 0.007 -10000 0 -10000 0 0
MAP2K4 0.012 0.067 0.24 1 -0.38 13 14
LAT 0.025 0.038 0.26 14 -0.57 2 16
LCP2 0.024 0.008 0.26 1 -10000 0 1
MAPK8 0.007 0.13 -10000 0 -0.64 38 38
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.021 0.06 0.25 3 -0.31 18 21
LAT/GRAP2/SLP76/HPK1/HIP-55 0.063 0.071 0.37 13 -0.37 12 25
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.038 0.057 -10000 0 -0.38 17 17
forebrain development -0.042 0.21 0.35 1 -0.62 76 77
GNAO1 0.017 0.091 0.26 32 -0.57 19 51
SMO/beta Arrestin2 0.027 0.044 -10000 0 -0.42 8 8
SMO 0.017 0.053 -10000 0 -0.57 8 8
ARRB2 0.021 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.023 0.081 0.28 1 -0.49 11 12
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.024 0.004 -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 -0.007 0.13 -10000 0 -0.57 52 52
XPO1 0.022 0.015 -10000 0 -10000 0 0
GLI1/Su(fu) -0.034 0.19 -10000 0 -0.65 56 56
SAP30 0.025 0.015 0.26 4 -10000 0 4
mol:GDP 0.017 0.053 -10000 0 -0.57 8 8
MIM/GLI2A 0.022 0.022 0.27 3 -10000 0 3
IFT88 0.023 0.006 -10000 0 -10000 0 0
GNAI3 0.023 0.009 -10000 0 -10000 0 0
GLI2 0.009 0.066 -10000 0 -0.3 23 23
GLI3 0.012 0.084 0.29 1 -0.48 13 14
CSNK1D 0.023 0.006 -10000 0 -10000 0 0
CSNK1E 0.023 0.006 -10000 0 -10000 0 0
SAP18 0.023 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.023 0.006 -10000 0 -10000 0 0
GNG2 0.018 0.058 -10000 0 -0.57 10 10
Gi family/GTP -0.008 0.096 -10000 0 -0.33 55 55
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.017 0.087 -10000 0 -0.46 20 20
GLI2/Su(fu) 0.013 0.081 -10000 0 -0.4 19 19
FOXA2 0.01 0.1 -10000 0 -0.68 14 14
neural tube patterning -0.042 0.21 0.35 1 -0.62 76 77
SPOP 0.022 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.021 0.042 -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 0.022 0.27 3 -10000 0 3
embryonic limb morphogenesis -0.042 0.21 0.35 1 -0.62 76 77
SUFU 0.015 0.027 -10000 0 -0.26 4 4
LGALS3 0.017 0.064 -10000 0 -0.57 12 12
catabolic process 0.026 0.1 0.29 1 -0.52 18 19
GLI3A/CBP 0.003 0.089 -10000 0 -0.36 57 57
KIF3A 0.024 0.004 -10000 0 -10000 0 0
GLI1 -0.044 0.21 0.35 1 -0.64 76 77
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 -0.57 1 1
RBBP7 0.026 0.019 0.26 7 -10000 0 7
Su(fu)/Galectin3 0.017 0.06 -10000 0 -0.38 13 13
GNAZ 0.017 0.056 -10000 0 -0.57 9 9
RBBP4 0.023 0.019 -10000 0 -0.57 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 0.004 -10000 0 -10000 0 0
GLI2/SPOP 0.018 0.071 -10000 0 -0.36 15 15
STK36 0.021 0.024 -10000 0 -0.57 1 1
Gi family/GNB1/GNG2/GDP -0.013 0.11 -10000 0 -0.45 35 35
PTCH1 -0.087 0.32 -10000 0 -1.1 83 83
MIM/GLI1 -0.03 0.19 -10000 0 -0.66 55 55
CREBBP 0.003 0.089 -10000 0 -0.36 57 57
Su(fu)/SIN3/HDAC complex 0.007 0.091 -10000 0 -0.42 32 32
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.002 0.1 0.26 2 -0.42 29 31
BAG4 0.018 0.033 -10000 0 -0.57 3 3
BAD 0.005 0.038 0.2 4 -0.19 5 9
NFKBIA 0.024 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.041 0.26 12 -0.57 3 15
BAX 0.005 0.042 0.22 6 -0.18 6 12
EnzymeConsortium:3.1.4.12 0.002 0.026 0.085 4 -0.094 25 29
IKBKB 0.016 0.1 0.32 4 -0.42 19 23
MAP2K2 0.008 0.052 0.22 13 -0.24 2 15
MAP2K1 0.009 0.053 0.22 15 -0.24 2 17
SMPD1 0.002 0.032 0.14 3 -0.15 16 19
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.025 0.12 0.28 20 -0.42 27 47
MAP2K4 0.006 0.034 0.18 5 -0.22 3 8
protein ubiquitination 0.004 0.1 0.34 4 -0.41 24 28
EnzymeConsortium:2.7.1.37 0.008 0.055 0.23 15 -0.25 2 17
response to UV 0 0.001 0.002 22 -0.002 2 24
RAF1 0.009 0.052 0.19 39 -0.22 4 43
CRADD 0.024 0.003 -10000 0 -10000 0 0
mol:ceramide 0.006 0.041 0.14 5 -0.15 22 27
I-kappa-B-alpha/RELA/p50/ubiquitin 0.031 0.009 -10000 0 -10000 0 0
MADD 0.024 0.004 -10000 0 -10000 0 0
MAP3K1 0.004 0.04 0.17 5 -0.18 9 14
TRADD 0.022 0.008 -10000 0 -10000 0 0
RELA/p50 0.024 0.005 -10000 0 -10000 0 0
MAPK3 0.01 0.053 0.22 13 -0.23 3 16
MAPK1 0.007 0.06 0.22 13 -0.25 5 18
p50/RELA/I-kappa-B-alpha 0.034 0.01 -10000 0 -10000 0 0
FADD 0.023 0.11 0.27 13 -0.43 23 36
KSR1 0.009 0.05 0.19 30 -0.21 5 35
MAPK8 0.002 0.047 0.22 11 -0.28 8 19
TRAF2 0.025 0.015 0.26 4 -10000 0 4
response to radiation 0 0 0.002 9 -10000 0 9
CHUK -0.001 0.094 -10000 0 -0.42 24 24
TNF R/SODD 0.027 0.029 -10000 0 -0.36 4 4
TNF 0.025 0.063 0.26 24 -0.57 8 32
CYCS 0.008 0.045 0.18 15 -0.17 6 21
IKBKG -0.002 0.097 0.34 2 -0.42 24 26
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.001 0.1 -10000 0 -0.44 28 28
RELA 0.024 0.005 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AIFM1 0.007 0.044 0.16 16 -0.18 7 23
TNF/TNF R/SODD 0.037 0.05 -10000 0 -0.36 10 10
TNFRSF1A 0.024 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 9 -10000 0 9
CASP8 0.001 0.13 -10000 0 -0.62 43 43
NSMAF 0.016 0.11 0.26 11 -0.41 26 37
response to hydrogen peroxide 0 0.001 0.002 22 -0.002 2 24
BCL2 0.007 0.096 -10000 0 -0.57 28 28
Retinoic acid receptors-mediated signaling

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
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 0.021 -10000 0 -0.36 1 1
EP300 0.023 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.015 0.062 -10000 0 -0.34 17 17
KAT2B 0.024 0.019 -10000 0 -0.57 1 1
MAPK14 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.006 0.066 0.21 2 -0.36 16 18
RAR alpha/9cRA/Cyclin H 0.047 0.073 -10000 0 -0.34 18 18
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.021 0.066 -10000 0 -0.42 12 12
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 0.064 -10000 0 -0.29 28 28
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 -0.57 18 18
NCOA2 -0.004 0.12 -10000 0 -0.57 43 43
NCOA3 0.023 0.006 -10000 0 -10000 0 0
NCOA1 0.024 0.019 -10000 0 -0.57 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 0.006 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
MAPK8 0.021 0.049 -10000 0 -0.57 7 7
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.008 0.1 -10000 0 -0.49 22 22
RARA 0.013 0.056 0.2 12 -0.27 26 38
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.007 0.079 -10000 0 -0.38 22 22
PRKCA 0.012 0.084 0.26 1 -0.57 21 22
RXRs/RARs/NRIP1/9cRA/HDAC1 0.011 0.12 0.45 1 -0.58 18 19
RXRG -0.051 0.15 0.24 12 -0.35 197 209
RXRA 0.022 0.063 0.24 3 -0.27 26 29
RXRB 0.016 0.061 0.24 11 -0.34 21 32
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RBP1 0.035 0.076 0.26 66 -0.57 7 73
CRBP1/9-cic-RA 0.025 0.053 0.18 66 -0.42 7 73
RARB 0.018 0.064 -10000 0 -0.57 12 12
PRKCG 0.031 0.044 0.26 37 -10000 0 37
MNAT1 0.024 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.009 0.1 -10000 0 -0.52 25 25
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.01 0.099 -10000 0 -0.48 20 20
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.079 0.24 14 -0.36 16 30
RXRs/RARs/NRIP1/9cRA/HDAC3 0.011 0.12 0.45 1 -0.57 19 20
positive regulation of DNA binding 0.032 0.064 -10000 0 -0.32 19 19
NRIP1 0.011 0.12 0.54 1 -0.76 9 10
RXRs/RARs 0.009 0.12 -10000 0 -0.52 26 26
RXRs/RXRs/DNA/9cRA -0.014 0.091 -10000 0 -0.49 23 23
PRKACA 0.024 0.004 -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 -0.3 4 4
CCNH 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.007 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.045 0.015 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.019 0.11 -10000 0 -0.41 42 42
KLHL20 0.015 0.065 0.23 11 -0.22 13 24
CYFIP2 0.028 0.049 0.26 27 -0.57 3 30
Rac1/GDP 0.001 0.085 0.26 8 -0.31 19 27
ENAH -0.015 0.1 -10000 0 -0.4 41 41
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 0.009 0.048 -10000 0 -0.41 1 1
ABI1/Sra1/Nap1 -0.012 0.032 -10000 0 -0.16 8 8
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.047 0.067 -10000 0 -0.33 21 21
RAPGEF1 -0.018 0.11 0.26 2 -0.4 30 32
CTNND1 0.024 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.021 0.12 -10000 0 -0.41 53 53
CRK -0.016 0.1 -10000 0 -0.41 35 35
E-cadherin/gamma catenin/alpha catenin 0.032 0.06 -10000 0 -0.36 19 19
alphaE/beta7 Integrin 0.036 0.034 -10000 0 -0.42 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 0.04 0.027 -10000 0 -0.33 3 3
DLG1 -0.023 0.12 -10000 0 -0.4 49 49
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.017 0.031 -10000 0 -0.22 3 3
MLLT4 0.021 0.033 0.26 1 -0.57 3 4
ARF6/GTP/NME1/Tiam1 0.044 0.025 -10000 0 -10000 0 0
PI3K -0.003 0.045 -10000 0 -0.29 3 3
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.021 0.065 -10000 0 -0.34 29 29
TIAM1 0.025 0.015 0.26 4 -10000 0 4
E-cadherin(dimer)/Ca2+ 0.041 0.056 -10000 0 -0.32 19 19
AKT1 -0.007 0.035 -10000 0 -0.21 1 1
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
CDH1 0.011 0.08 -10000 0 -0.57 19 19
RhoA/GDP 0.001 0.085 0.26 8 -0.31 18 26
actin cytoskeleton organization 0.014 0.053 0.19 20 -0.16 12 32
CDC42/GDP 0.001 0.083 0.26 8 -0.31 18 26
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.008 0.043 -10000 0 -0.27 20 20
ITGB7 0.029 0.046 0.26 28 -0.57 2 30
RAC1 0.024 0.003 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.044 0.06 -10000 0 -0.33 19 19
E-cadherin/Ca2+/beta catenin/alpha catenin 0.03 0.052 -10000 0 -0.31 19 19
mol:GDP -0.013 0.091 0.27 8 -0.35 20 28
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 0.006 0.087 0.26 7 -0.32 18 25
RAC1/GTP/IQGAP1 0.032 0.007 -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 0.005 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.013 0.047 0.18 37 -0.23 5 42
NME1 0.026 0.031 0.26 17 -10000 0 17
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.021 0.12 -10000 0 -0.41 46 46
regulation of cell-cell adhesion 0.003 0.04 -10000 0 -0.28 2 2
WASF2 0.007 0.026 -10000 0 -10000 0 0
Rap1/GTP 0.013 0.058 0.24 2 -0.28 17 19
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.053 0.067 -10000 0 -0.32 21 21
CCND1 0.014 0.055 0.2 34 -0.29 5 39
VAV2 -0.019 0.15 -10000 0 -0.54 39 39
RAP1/GDP 0.007 0.07 0.26 3 -0.29 17 20
adherens junction assembly -0.021 0.11 -10000 0 -0.4 46 46
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 0.041 0.063 -10000 0 -0.31 21 21
E-cadherin/beta catenin 0.001 0.06 -10000 0 -0.34 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.022 0.12 -10000 0 -0.4 51 51
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.005 0.089 0.26 31 -0.34 25 56
E-cadherin/beta catenin/alpha catenin 0.034 0.06 -10000 0 -0.36 19 19
ITGAE 0.022 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.021 0.12 -10000 0 -0.42 53 53
S1P3 pathway

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
PDGFRB 0.022 0.037 -10000 0 -0.57 4 4
mol:S1P 0 0.004 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.013 0.095 -10000 0 -0.3 84 84
GNAO1 0.018 0.091 0.26 32 -0.57 19 51
S1P/S1P3/G12/G13 0.042 0.02 -10000 0 -10000 0 0
AKT1 0.006 0.093 -10000 0 -0.48 29 29
AKT3 -0.011 0.17 -10000 0 -1.1 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.022 0.037 -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 -0.005 0.13 -10000 0 -0.57 52 52
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.026 0.022 0.25 8 -10000 0 8
S1PR2 0.024 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.097 -10000 0 -0.4 33 33
MAPK3 -0.008 0.089 0.27 2 -0.39 27 29
MAPK1 -0.006 0.09 0.27 1 -0.41 28 29
JAK2 -0.009 0.1 -10000 0 -0.39 37 37
CXCR4 -0.009 0.094 -10000 0 -0.41 29 29
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 0.091 -10000 0 -0.4 27 27
S1P/S1P3/Gi -0.002 0.098 -10000 0 -0.41 33 33
RAC1 0.024 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.1 -10000 0 -0.4 27 27
VEGFA 0.026 0.021 0.26 6 -10000 0 6
S1P/S1P2/Gi -0.003 0.091 -10000 0 -0.34 43 43
VEGFR1 homodimer/VEGFA homodimer 0.036 0.022 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.02 0.04 -10000 0 -0.29 15 15
GNAQ 0.023 0.026 -10000 0 -0.57 2 2
GNAZ 0.018 0.056 -10000 0 -0.57 9 9
G12/G13 0.033 0.011 -10000 0 -10000 0 0
GNA14 0.023 0.066 0.26 19 -0.57 10 29
GNA15 0.025 0.026 0.26 6 -0.57 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 0.026 -10000 0 -0.57 2 2
Rac1/GTP -0.002 0.1 -10000 0 -0.39 30 30
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.024 0.009 0.26 1 -9999 0 1
PLK4 0.033 0.045 0.26 40 -9999 0 40
regulation of centriole replication 0.016 0.026 0.26 2 -9999 0 2
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.03 0.01 -10000 0 -10000 0 0
PRKCZ 0.023 0.019 -10000 0 -0.57 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 0.05 -10000 0 -0.37 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 0.095 0.37 3 -0.42 38 41
IL1A 0.028 0.031 0.26 19 -10000 0 19
IL1B 0.004 0.055 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 29 -0.57 38 67
IL1R1 0.014 0.078 -10000 0 -0.57 18 18
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.011 0.064 0.26 3 -0.31 20 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 0.069 0.33 8 -0.37 1 9
JUN -0.009 0.067 0.3 6 -0.28 30 36
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.039 0.078 -10000 0 -0.32 39 39
IL1 alpha/IL1R1/IL1RAP/MYD88 0.055 0.057 -10000 0 -0.33 18 18
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.063 0.057 -10000 0 -0.32 18 18
IL1 beta fragment/IL1R1/IL1RAP 0.024 0.07 -10000 0 -0.36 31 31
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.005 0.068 0.33 5 -0.29 25 30
IRAK1 -0.001 0.019 0.21 2 -10000 0 2
IL1RN/IL1R1 0.033 0.07 -10000 0 -0.42 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 0.042 -10000 0 -0.4 9 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.012 0.057 -10000 0 -0.3 21 21
CHUK 0.024 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.024 0.07 -10000 0 -0.36 31 31
IL1 beta/IL1R2 0.013 0.094 -10000 0 -0.38 51 51
IRAK/TRAF6/TAK1/TAB1/TAB2 0.029 0.015 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.028 0.071 -10000 0 -0.31 38 38
IRAK3 0.004 0.11 0.26 1 -0.57 35 36
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.043 0.071 -10000 0 -0.33 31 31
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.02 0.044 -10000 0 -0.27 18 18
IL1 alpha/IL1R1/IL1RAP 0.043 0.058 -10000 0 -0.36 18 18
RELA 0.024 0.005 -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 0.058 -10000 0 -0.31 23 23
CASP1 0.021 0.02 -10000 0 -0.57 1 1
IL1RN/IL1R2 0.029 0.1 0.37 5 -0.42 40 45
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.035 0.071 -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 0.018 0.073 -10000 0 -0.34 30 30
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL1RN 0.032 0.051 0.26 38 -0.57 2 40
TRAF6/TAK1/TAB1/TAB2 0.039 0.017 -10000 0 -10000 0 0
MAP2K6 0 0.069 0.37 6 -0.3 18 24
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 0.075 0.3 4 -0.38 12 16
PDGFB-D/PDGFRB/SLAP 0.028 0.033 -10000 0 -0.36 4 4
PDGFB-D/PDGFRB/APS/CBL 0.048 0.043 -10000 0 -0.36 4 4
AKT1 0.025 0.095 0.34 38 -10000 0 38
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.031 0.086 0.32 6 -0.4 16 22
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
FGR 0 0.1 -10000 0 -0.45 38 38
mol:Ca2+ 0.023 0.089 0.29 7 -0.42 19 26
MYC 0.053 0.17 0.37 30 -0.77 25 55
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.035 0.044 -10000 0 -0.3 3 3
LRP1/PDGFRB/PDGFB 0.041 0.053 -10000 0 -0.41 12 12
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 0.024 0.003 -10000 0 -10000 0 0
GO:0007205 0.023 0.09 0.3 6 -0.43 19 25
PTEN 0.023 0.019 -10000 0 -0.57 1 1
GRB2 0.023 0.01 0.26 1 -10000 0 1
GRB7 0.019 0.033 -10000 0 -0.57 3 3
PDGFB-D/PDGFRB/SHP2 0.034 0.029 -10000 0 -0.42 4 4
PDGFB-D/PDGFRB/GRB10 0.034 0.029 -10000 0 -0.42 4 4
cell cycle arrest 0.028 0.033 -10000 0 -0.36 4 4
HRAS 0.026 0.021 0.26 8 -10000 0 8
HIF1A 0.02 0.089 0.33 37 -10000 0 37
GAB1 0.025 0.095 0.3 7 -0.42 18 25
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.025 0.087 0.32 10 -0.37 15 25
PDGFB-D/PDGFRB 0.042 0.032 -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 -0.42 3 3
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.023 0.067 0.28 3 -0.37 11 14
positive regulation of MAPKKK cascade 0.034 0.029 -10000 0 -0.42 4 4
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
mol:IP3 0.023 0.09 0.3 6 -0.43 19 25
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.023 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.028 0.04 -10000 0 -0.42 7 7
SHB 0.024 0.008 0.26 1 -10000 0 1
BLK -0.027 0.17 0.29 5 -0.4 143 148
PTPN2 0.024 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.033 0.029 -10000 0 -0.42 4 4
BCAR1 0.021 0.008 -10000 0 -10000 0 0
VAV2 0.026 0.1 0.31 8 -0.45 21 29
CBL 0.022 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.034 0.029 -10000 0 -0.42 4 4
LCK 0.005 0.11 -10000 0 -0.51 34 34
PDGFRB 0.022 0.038 -10000 0 -0.57 4 4
ACP1 0.024 0.003 -10000 0 -10000 0 0
HCK 0.015 0.063 -10000 0 -0.51 8 8
ABL1 0.02 0.095 0.3 7 -0.38 26 33
PDGFB-D/PDGFRB/CBL 0.02 0.11 0.3 3 -0.44 29 32
PTPN1 0.024 0.02 0.26 6 -10000 0 6
SNX15 0.024 0.005 -10000 0 -10000 0 0
STAT3 0.024 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.031 0.26 19 -10000 0 19
cell proliferation 0.054 0.15 0.35 34 -0.65 27 61
SLA 0.021 0.022 0.26 7 -10000 0 7
actin cytoskeleton reorganization 0.034 0.051 0.33 2 -0.3 3 5
SRC 0.012 0.06 0.28 1 -0.49 8 9
PI3K -0.012 0.03 -10000 0 -0.29 8 8
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.039 -10000 0 -0.36 6 6
SH2B2 0.034 0.048 0.26 45 -10000 0 45
PLCgamma1/SPHK1 0.032 0.088 0.32 6 -0.41 16 22
LYN 0.009 0.064 -10000 0 -0.47 12 12
LRP1 0.019 0.058 -10000 0 -0.57 10 10
SOS1 0.024 0.003 -10000 0 -10000 0 0
STAT5B 0.022 0.027 -10000 0 -0.57 2 2
STAT5A 0.02 0.045 -10000 0 -0.57 6 6
NCK1-2/p130 Cas 0.055 0.04 -10000 0 -0.3 3 3
SPHK1 0.027 0.042 0.26 20 -0.57 2 22
EDG1 0.001 0.002 -10000 0 -10000 0 0
mol:DAG 0.023 0.09 0.3 6 -0.43 19 25
PLCG1 0.023 0.092 0.3 6 -0.44 19 25
NHERF/PDGFRB 0.049 0.045 -10000 0 -0.36 4 4
YES1 -0.001 0.11 -10000 0 -0.51 40 40
cell migration 0.048 0.045 -10000 0 -0.36 4 4
SHC/Grb2/SOS1 0.05 0.042 -10000 0 -0.31 3 3
SLC9A3R2 0.023 0.01 0.26 1 -10000 0 1
SLC9A3R1 0.036 0.054 0.26 57 -10000 0 57
NHERF1-2/PDGFRB/PTEN 0.056 0.049 0.29 2 -0.33 4 6
FYN -0.003 0.1 -10000 0 -0.42 42 42
DOK1 0.021 0.049 0.26 2 -0.33 3 5
HRAS/GTP 0.019 0.014 0.18 8 -10000 0 8
PDGFB 0.023 0.006 -10000 0 -10000 0 0
RAC1 0.021 0.13 0.33 4 -0.53 29 33
PRKCD 0.021 0.051 0.27 2 -0.34 3 5
FER 0.017 0.059 -10000 0 -0.34 12 12
MAPKKK cascade 0.037 0.097 0.36 36 -0.3 3 39
RASA1 0.02 0.049 -10000 0 -0.34 3 3
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 0.03 -10000 0 -0.42 4 4
chemotaxis 0.02 0.093 0.29 7 -0.37 26 33
STAT1-3-5/STAT1-3-5 0.049 0.048 -10000 0 -0.37 8 8
Bovine Papilomavirus E5/PDGFRB 0.016 0.028 -10000 0 -0.42 4 4
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.017 0.02 -10000 0 -0.3 3 3
TRAF2/ASK1 0.03 0.025 -10000 0 -0.36 3 3
ATM 0.022 0.008 -10000 0 -10000 0 0
MAP2K3 -0.02 0.11 0.27 1 -0.36 52 53
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.014 0.099 0.26 1 -0.37 33 34
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.052 0.076 0.26 126 -10000 0 126
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 0.004 -10000 0 -10000 0 0
MAP3K1 0.023 0.019 -10000 0 -0.57 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 0.093 -10000 0 -0.32 29 29
TRAF6 0.006 0.001 -10000 0 -10000 0 0
RAC1 0.024 0.003 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.007 0.16 0.26 44 -0.57 71 115
CCM2 0.024 0.008 0.26 1 -10000 0 1
CaM/Ca2+/CAMKIIB 0.011 0.1 -10000 0 -0.36 71 71
MAPK11 0.021 0.032 -10000 0 -0.57 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.022 0.1 -10000 0 -0.34 73 73
OSM/MEKK3 0.032 0.013 -10000 0 -10000 0 0
TAOK1 -0.006 0.078 -10000 0 -0.36 47 47
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 0.032 -10000 0 -0.57 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 0.025 -10000 0 -0.35 3 3
GADD45/MTK1/MTK1 0.067 0.047 -10000 0 -10000 0 0
Class I PI3K 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
ARF5/GTP -0.013 0.039 0.3 4 -0.28 2 6
DAPP1 0.016 0.1 0.27 7 -0.35 37 44
Src family/SYK family/BLNK-LAT/BTK-ITK 0.017 0.14 0.28 13 -0.48 40 53
mol:DAG 0.021 0.081 0.24 35 -0.23 15 50
HRAS 0.026 0.021 0.26 8 -10000 0 8
RAP1A 0.025 0.006 -10000 0 -10000 0 0
ARF5/GDP 0.028 0.062 0.27 1 -0.33 11 12
PLCG2 0.02 0.028 0.26 1 -0.57 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 0.038 0.31 5 -0.28 1 6
ARF1/GTP -0.004 0.033 0.26 8 -0.28 1 9
RHOA 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.019 -10000 0 -0.57 1 1
RAP1A/GTP -0.011 0.033 0.2 1 -0.28 1 2
ADAP1 -0.011 0.039 0.33 3 -0.29 2 5
ARAP3 -0.01 0.038 0.31 5 -0.28 1 6
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PREX1 0.028 0.033 0.26 21 -10000 0 21
ARHGEF6 0.016 0.069 -10000 0 -0.57 14 14
ARHGEF7 0.023 0.007 -10000 0 -10000 0 0
ARF1 0.02 0.009 -10000 0 -10000 0 0
NRAS 0.025 0.006 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.57 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+ 0.016 0.056 0.24 19 -10000 0 19
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.025 0.015 0.26 4 -10000 0 4
ZAP70 0.025 0.099 0.26 56 -0.57 20 76
mol:IP3 0.017 0.069 0.2 58 -0.18 9 67
LYN 0.021 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.024 0.06 0.36 2 -0.33 11 13
RhoA/GDP 0.03 0.041 0.23 4 -0.25 1 5
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 0.019 0.071 0.3 16 -0.32 4 20
SRC 0.024 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.007 0.011 0.23 2 -10000 0 2
RAC1 0.024 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.021 -10000 0 -0.55 1 1
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.013 0.039 0.3 5 -0.27 1 6
RhoA/GTP -0.012 0.038 0.33 4 -0.27 1 5
Src family/SYK family/BLNK-LAT 0.025 0.097 0.25 17 -0.38 22 39
BLK 0.05 0.087 0.26 142 -0.57 2 144
PDPK1 0.023 0.006 -10000 0 -10000 0 0
CYTH1 -0.011 0.038 0.32 4 -0.27 1 5
HCK 0.027 0.026 0.26 13 -10000 0 13
CYTH3 -0.012 0.039 0.33 3 -0.28 2 5
CYTH2 -0.011 0.039 0.32 4 -0.27 1 5
KRAS 0.024 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.01 0.051 0.31 1 -0.49 6 7
SGK1 0.006 0.074 -10000 0 -0.48 7 7
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.016 0.064 0.38 2 -0.34 12 14
SOS1 0.024 0.003 -10000 0 -10000 0 0
SYK 0.024 0.003 -10000 0 -10000 0 0
ARF6/GDP 0.018 0.045 0.28 9 -0.25 1 10
mol:PI-3-4-5-P3 -0.011 0.035 0.28 4 -0.28 1 5
ARAP3/RAP1A/GTP -0.011 0.033 0.2 1 -0.28 1 2
VAV1 0.023 0.034 0.26 2 -0.57 3 5
mol:PI-3-4-P2 0.01 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.04 0.038 -10000 0 -0.28 1 1
PLEKHA1 -0.009 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.029 0.061 0.27 1 -0.33 11 12
LAT 0.025 0.038 0.26 14 -0.57 2 16
Rac1/GTP 0.016 0.053 -10000 0 -0.35 11 11
ITK -0.018 0.063 0.32 4 -0.31 30 34
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.021 0.099 0.28 32 -0.33 16 48
LCK 0.026 0.076 0.26 39 -0.57 11 50
BTK -0.011 0.039 0.32 4 -0.27 1 5
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.024 0.003 -10000 0 -10000 0 0
SPHK1 0.026 0.042 0.26 20 -0.57 2 22
GNAI2 0.024 0.005 -10000 0 -10000 0 0
mol:S1P 0.013 0.02 0.22 1 -0.29 2 3
GNAO1 0.018 0.09 0.26 32 -0.57 19 51
mol:Sphinganine-1-P 0.012 0.027 0.26 1 -0.42 2 3
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.051 0.036 -10000 0 -0.23 1 1
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.033 0.011 -10000 0 -10000 0 0
S1PR3 0.026 0.021 0.26 8 -10000 0 8
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 20 -0.57 2 22
S1PR4 0.029 0.063 0.26 38 -0.57 6 44
GNAI1 -0.005 0.13 -10000 0 -0.57 52 52
S1P/S1P5/G12 0.046 0.041 0.24 4 -0.25 5 9
S1P/S1P3/Gq 0.026 0.064 -10000 0 -0.32 20 20
S1P/S1P4/Gi 0.002 0.097 0.26 1 -0.34 43 44
GNAQ 0.023 0.026 -10000 0 -0.57 2 2
GNAZ 0.018 0.055 -10000 0 -0.57 9 9
GNA14 0.023 0.066 0.26 19 -0.57 10 29
GNA15 0.025 0.026 0.26 6 -0.57 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 0.026 -10000 0 -0.57 2 2
ABCC1 0.023 0.006 -10000 0 -10000 0 0
EPO signaling 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
BCL2L1 0.05 0.082 -10000 0 -0.48 1 1
CRKL 0.025 0.047 0.28 10 -10000 0 10
mol:DAG 0.038 0.051 -10000 0 -10000 0 0
HRAS 0.034 0.078 0.31 18 -10000 0 18
MAPK8 0.041 0.071 0.24 34 -0.35 5 39
RAP1A 0.026 0.048 0.28 11 -10000 0 11
GAB1 0.026 0.046 0.28 8 -10000 0 8
MAPK14 0.043 0.065 0.24 34 -10000 0 34
EPO 0.061 0.085 0.26 165 -10000 0 165
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 0.062 -10000 0 -0.35 5 5
GAB1/SHC/GRB2/SOS1 0.042 0.041 0.26 2 -10000 0 2
EPO/EPOR (dimer) 0.061 0.059 0.23 3 -10000 0 3
IRS2 0.014 0.072 0.3 6 -0.29 34 40
STAT1 0.044 0.065 0.31 4 -10000 0 4
STAT5B 0.04 0.059 0.33 1 -0.34 1 2
cell proliferation 0.023 0.076 0.24 36 -0.32 5 41
GAB1/SHIP/PIK3R1/SHP2/SHC 0.033 0.042 -10000 0 -0.28 6 6
TEC 0.025 0.047 0.26 8 -0.27 2 10
SOCS3 0.02 0.041 -10000 0 -0.57 5 5
STAT1 (dimer) 0.044 0.064 0.31 4 -10000 0 4
JAK2 0.025 0.01 -10000 0 -10000 0 0
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
EPO/EPOR (dimer)/JAK2 0.08 0.063 0.34 3 -10000 0 3
EPO/EPOR 0.061 0.059 0.23 3 -10000 0 3
LYN 0.021 0.012 -10000 0 -10000 0 0
TEC/VAV2 0.039 0.047 0.27 4 -0.29 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 0.055 -10000 0 -10000 0 0
mol:IP3 0.038 0.051 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.031 0.077 0.29 2 -0.29 32 34
SH2B3 0.027 0.009 -10000 0 -10000 0 0
NFKB1 0.043 0.066 0.25 31 -10000 0 31
EPO/EPOR (dimer)/JAK2/SOCS3 0.025 0.043 -10000 0 -0.25 3 3
PTPN6 0.023 0.04 0.28 3 -10000 0 3
TEC/VAV2/GRB2 0.047 0.048 0.27 4 -0.29 1 5
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 0.041 0.27 2 -10000 0 2
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG2 0.02 0.028 0.26 1 -0.57 2 3
CRKL/CBL/C3G 0.046 0.048 0.27 5 -10000 0 5
VAV2 0.027 0.049 0.28 12 -10000 0 12
CBL 0.025 0.047 0.31 6 -10000 0 6
SHC/Grb2/SOS1 0.035 0.038 -10000 0 -10000 0 0
STAT5A 0.038 0.064 0.33 1 -0.33 6 7
GRB2 0.023 0.01 0.26 1 -10000 0 1
STAT5 (dimer) 0.05 0.081 0.34 1 -0.34 12 13
LYN/PLCgamma2 0.027 0.026 -10000 0 -0.42 2 2
PTPN11 0.024 0.003 -10000 0 -10000 0 0
BTK 0.027 0.049 0.28 12 -10000 0 12
BCL2 0.03 0.17 0.33 2 -0.83 35 37
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.1 0.15 -10000 0 -0.4 70 70
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 0.4 1 -0.37 112 113
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
TBC1D4 0.008 0.027 -10000 0 -0.42 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
YWHAB 0.023 0.005 -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 0.024 0.26 10 -10000 0 10
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 0.01 0.016 0.24 5 -10000 0 5
PRKCZ 0.023 0.019 -10000 0 -0.57 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 0.26 1 -0.33 12 13
VAMP2 0.022 0.007 -10000 0 -10000 0 0
SLC2A4 -0.12 0.16 0.41 1 -0.41 112 113
STX4 0.023 0.006 -10000 0 -10000 0 0
GSK3B 0.018 0.005 -10000 0 -10000 0 0
SFN 0.021 0.071 0.26 19 -0.57 12 31
LNPEP 0.02 0.049 -10000 0 -0.57 7 7
YWHAE 0.022 0.007 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.02 0.049 -10000 0 -0.57 7 7
positive regulation of NF-kappaB transcription factor activity -0.006 0.12 -10000 0 -0.41 70 70
MAP2K4 0.016 0.046 -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 0.033 -10000 0 -0.57 3 3
SMPD1 0.008 0.029 -10000 0 -0.34 6 6
IKBKG 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.016 0.14 0.26 1 -0.57 63 64
TRAIL/TRAILR2 0.026 0.039 -10000 0 -0.41 7 7
TRAIL/TRAILR3 0.027 0.043 -10000 0 -0.43 7 7
TRAIL/TRAILR1 0.024 0.047 -10000 0 -0.41 10 10
TRAIL/TRAILR4 -0.006 0.12 -10000 0 -0.41 70 70
TRAIL/TRAILR1/DAP3/GTP 0.029 0.039 -10000 0 -0.32 7 7
IKK complex 0.011 0.04 -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 0.036 0.26 1 -0.42 7 8
MAP3K1 0.018 0.062 -10000 0 -0.45 8 8
TRAILR4 (trimer) -0.016 0.14 0.26 1 -0.57 63 64
TRADD 0.022 0.008 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.033 -10000 0 -0.57 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.012 0.045 -10000 0 -0.36 9 9
CFLAR 0.024 0.003 -10000 0 -10000 0 0
MAPK1 0.007 0.036 0.26 1 -0.42 7 8
TRAIL/TRAILR1/FADD/TRADD/RIP 0.042 0.047 -10000 0 -0.3 7 7
mol:ceramide 0.008 0.029 -10000 0 -0.34 6 6
FADD 0.021 0.009 -10000 0 -10000 0 0
MAPK8 0.012 0.062 0.26 1 -0.44 7 8
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 0.031 0.042 -10000 0 -0.35 7 7
DAP3 0.021 0.009 -10000 0 -10000 0 0
CASP10 0.035 0.084 0.28 60 -0.34 3 63
JNK cascade -0.006 0.12 -10000 0 -0.41 70 70
TRAIL (trimer) 0.02 0.049 -10000 0 -0.57 7 7
TNFRSF10C 0.022 0.022 0.26 7 -10000 0 7
TRAIL/TRAILR1/DAP3/GTP/FADD 0.032 0.04 -10000 0 -0.31 5 5
TRAIL/TRAILR2/FADD 0.032 0.037 -10000 0 -0.35 5 5
cell death 0.008 0.029 -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 0.012 0.047 -10000 0 -0.56 5 5
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.043 0.043 -10000 0 -0.3 5 5
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.024 0.004 -10000 0 -10000 0 0
NFATC1 0.02 0.085 0.31 5 -0.43 11 16
NFATC2 -0.005 0.071 0.18 3 -0.25 39 42
NFATC3 0.014 0.016 -10000 0 -0.4 1 1
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.011 0.096 0.26 3 -0.34 40 43
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 0.089 0.26 6 -0.39 15 21
BCL2/BAX 0.021 0.076 -10000 0 -0.37 35 35
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 0.016 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 0.018 0.085 -10000 0 -0.33 27 27
Calcineurin A alpha-beta B1/BCL2 0.007 0.096 -10000 0 -0.57 28 28
FKBP8 0.024 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.018 0.084 0.33 27 -10000 0 27
KPNB1 0.023 0.006 -10000 0 -10000 0 0
KPNA2 0.036 0.056 0.26 63 -10000 0 63
XPO1 0.024 0.003 -10000 0 -10000 0 0
SFN 0.021 0.071 0.26 19 -0.57 12 31
MAP3K8 0.019 0.049 -10000 0 -0.57 7 7
NFAT4/CK1 alpha 0.018 0.028 -10000 0 -0.28 2 2
MEF2D/NFAT1/Cbp/p300 0.011 0.1 -10000 0 -0.29 72 72
CABIN1 0.012 0.095 0.26 3 -0.34 39 42
CALM1 0.021 0.013 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.023 0.019 -10000 0 -0.57 1 1
CAMK4 0.032 0.047 0.26 37 -0.57 1 38
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 0.038 -10000 0 -0.42 1 1
YWHAB 0.023 0.005 -10000 0 -10000 0 0
MAPK8 0.019 0.049 -10000 0 -0.57 7 7
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 -0.45 12 13
PRKCH 0.023 0.019 -10000 0 -0.57 1 1
CABIN1/Cbp/p300 0.027 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 0.034 -10000 0 -0.36 2 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.04 -10000 0 -0.31 4 4
PRKCB 0.019 0.076 0.26 19 -0.57 14 33
PRKCE 0.024 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.008 0.059 -10000 0 -0.37 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 0.02 -10000 0 -0.57 1 1
PRKCA 0.01 0.084 0.26 1 -0.57 21 22
PRKCG 0.03 0.044 0.26 37 -10000 0 37
PRKCQ 0.002 0.12 0.26 8 -0.57 41 49
FKBP38/BCL2 0.02 0.076 -10000 0 -0.37 35 35
EP300 0.019 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 11 12
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 -10000 0 -0.36 1 1
NFATc/ERK1 0.03 0.084 0.34 1 -0.41 10 11
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.038 0.095 0.25 5 -0.41 20 25
NR4A1 -0.009 0.17 0.26 1 -0.51 83 84
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 -0.001 0.057 -10000 0 -0.25 15 15
RCH1/ KPNB1 0.041 0.04 -10000 0 -10000 0 0
YWHAQ 0.024 0.003 -10000 0 -10000 0 0
PRKACA 0.023 0.007 -10000 0 -10000 0 0
AKAP5 0.035 0.054 0.26 52 -0.57 1 53
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 0.031 0.083 0.34 1 -0.41 10 11
CREBBP 0.019 0.015 -10000 0 -10000 0 0
BCL2 0.007 0.096 -10000 0 -0.57 28 28
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.033 0.06 -9999 0 -0.36 19 19
E-cadherin/beta catenin 0.022 0.065 -9999 0 -0.42 19 19
CTNNB1 0.024 0.004 -9999 0 -10000 0 0
JUP 0.023 0.005 -9999 0 -10000 0 0
CDH1 0.011 0.08 -9999 0 -0.57 19 19
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.034 0.11 0.28 17 -0.32 26 43
ERC1 0.023 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.03 0.035 0.37 1 -0.42 1 2
NFKBIA 0.012 0.025 -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 0.03 -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 0.28 1 -0.37 76 77
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 42 42
BCL10/MALT1/TRAF6 0.045 0.015 -10000 0 -10000 0 0
NOD2 0.028 0.044 0.26 30 -0.57 1 31
NFKB1 0.025 0.004 -10000 0 -10000 0 0
RELA 0.025 0.005 -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 0.034 0.048 -10000 0 -0.42 8 8
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.01 0.084 0.26 1 -0.57 21 22
CHUK 0.024 0.003 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
TNF 0.025 0.063 0.26 24 -0.57 8 32
NF kappa B1 p50/RelA 0.051 0.016 -10000 0 -10000 0 0
BCL10 0.024 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.025 -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 0.015 0.12 -10000 0 -0.36 69 69
CYLD 0.022 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.013 0.13 -10000 0 -0.41 50 50
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.069 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 0.055 0.046 0.33 5 -10000 0 5
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 0.042 -10000 0 -0.22 1 1
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 0.28 2 -10000 0 2
AKT1 0.011 0.062 0.29 10 -10000 0 10
MAP2K1 0.007 0.045 0.29 4 -0.29 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 0.017 0.098 -10000 0 -0.39 11 11
Rap1/GTP 0.017 0.013 -10000 0 -10000 0 0
CRKL/C3G 0.034 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.076 0.054 -10000 0 -10000 0 0
CEBPB 0.028 0.095 0.32 2 -0.49 7 9
STAT3 0.024 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.075 0.096 -10000 0 -0.7 9 9
STAT1 0.026 0.048 0.29 6 -10000 0 6
CALM1 0.024 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.055 0.081 0.26 143 -10000 0 143
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.041 0.045 0.29 6 -10000 0 6
CEBPB/PTGES2/Cbp/p300 0.027 0.062 0.34 2 -0.33 5 7
mol:Ca2+ 0.065 0.049 -10000 0 -10000 0 0
MAPK3 0.022 0.079 -10000 0 -0.56 12 12
STAT1 (dimer) 0.026 0.059 -10000 0 -0.3 1 1
MAPK1 -0.007 0.17 -10000 0 -0.67 56 56
JAK2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
JAK1 0.026 0.007 -10000 0 -10000 0 0
CAMK2D 0.022 0.032 -10000 0 -0.57 3 3
DAPK1 0.026 0.069 0.29 4 -0.34 2 6
SMAD7 0.017 0.036 0.17 9 -10000 0 9
CBL/CRKL/C3G 0.045 0.039 0.29 4 -10000 0 4
PI3K 0.057 0.052 -10000 0 -0.29 7 7
IFNG 0.055 0.081 0.26 143 -10000 0 143
apoptosis 0.023 0.073 0.26 4 -0.4 11 15
CAMK2G 0.024 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.005 -10000 0 -10000 0 0
CAMK2A 0.031 0.04 0.26 32 -10000 0 32
CAMK2B -0.007 0.16 0.26 44 -0.57 71 115
FRAP1 0.009 0.058 0.28 10 -10000 0 10
PRKCD 0.012 0.065 0.3 12 -0.28 2 14
RAP1B 0.024 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.014 0.042 -10000 0 -0.22 1 1
PTPN2 0.024 0.005 -10000 0 -10000 0 0
EP300 0.024 0.006 -10000 0 -10000 0 0
IRF1 0.021 0.057 0.29 12 -0.32 1 13
STAT1 (dimer)/PIASy 0.039 0.046 0.28 6 -10000 0 6
SOCS1 0.016 0.11 -10000 0 -1 10 10
mol:GDP 0.041 0.036 0.27 4 -10000 0 4
CASP1 0.016 0.039 0.19 10 -0.24 3 13
PTGES2 0.024 0.008 0.26 1 -10000 0 1
IRF9 0.028 0.041 0.24 8 -10000 0 8
mol:PI-3-4-5-P3 0.042 0.043 -10000 0 -0.28 7 7
RAP1/GDP 0.036 0.023 -10000 0 -10000 0 0
CBL 0.021 0.041 0.29 4 -10000 0 4
MAP3K1 0.022 0.042 0.29 4 -0.3 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 0.042 -10000 0 -0.22 1 1
PTPN11 0.026 0.044 0.29 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 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
PTK2 0.019 0.023 0.21 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 0.005 -10000 0 -10000 0 0
ITGA4 0.026 0.023 0.26 10 -10000 0 10
alpha4/beta7 Integrin/MAdCAM1 0.067 0.048 0.35 10 -0.34 2 12
EPO 0.06 0.086 0.26 165 -10000 0 165
alpha4/beta7 Integrin 0.041 0.04 0.37 4 -0.42 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 0.016 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.059 0.059 -10000 0 -10000 0 0
lamellipodium assembly 0.012 0.075 -10000 0 -0.44 19 19
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.03 0.042 -10000 0 -0.4 9 9
ARF6 0.024 0.004 -10000 0 -10000 0 0
JAK2 0.033 0.03 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
MADCAM1 0.031 0.044 0.26 37 -10000 0 37
cell adhesion 0.065 0.047 0.34 10 -0.33 2 12
CRKL/CBL 0.032 0.013 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.013 0.042 -10000 0 -0.33 9 9
ITGB7 0.029 0.046 0.26 28 -0.57 2 30
RAC1 0.024 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.045 0.046 -10000 0 -0.36 10 10
p130Cas/Crk/Dock1 0.026 0.041 0.35 1 -0.28 9 10
VCAM1 0.02 0.061 0.26 6 -0.57 10 16
RHOA 0.024 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.058 0.023 -10000 0 -10000 0 0
BCAR1 -0.009 0.043 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 -0.46 19 19
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.018 0.033 -10000 0 -0.57 3 3
Caspase 8 (4 units) 0.039 0.061 -10000 0 -0.5 2 2
NEF 0.003 0.023 -10000 0 -0.18 10 10
NFKBIA 0.025 0.012 -10000 0 -10000 0 0
BIRC3 0.019 0.055 -10000 0 -0.51 5 5
CYCS 0.036 0.077 0.26 25 -0.3 11 36
RIPK1 0.024 0.005 -10000 0 -10000 0 0
CD247 0.017 0.088 0.3 16 -0.44 25 41
MAP2K7 0.041 0.13 0.42 1 -0.73 17 18
protein ubiquitination 0.015 0.083 0.31 5 -0.37 11 16
CRADD 0.024 0.003 -10000 0 -10000 0 0
DAXX 0.024 0.003 -10000 0 -10000 0 0
FAS 0.023 0.026 -10000 0 -0.57 2 2
BID 0.036 0.073 0.24 2 -0.29 15 17
NF-kappa-B/RelA/I kappa B alpha 0.05 0.033 -10000 0 -0.31 3 3
TRADD 0.022 0.008 -10000 0 -10000 0 0
MAP3K5 0.022 0.032 -10000 0 -0.57 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 0.037 0.12 0.42 4 -0.65 18 22
APAF1 0.024 0.003 -10000 0 -10000 0 0
TRAF1 0.025 0.013 0.26 3 -10000 0 3
TRAF2 0.025 0.015 0.26 4 -10000 0 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.024 0.06 0.23 4 -0.31 15 19
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.014 0.092 -10000 0 -0.45 14 14
CHUK 0.014 0.086 0.31 4 -0.4 11 15
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.055 0.04 -10000 0 -0.34 4 4
TCRz/NEF 0.016 0.081 0.31 9 -0.42 25 34
TNF 0.025 0.063 0.26 24 -0.57 8 32
FASLG 0.011 0.11 0.29 40 -0.57 25 65
NFKB1 0.025 0.012 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.037 0.05 -10000 0 -0.36 10 10
CASP6 0.053 0.1 0.38 1 -0.51 16 17
CASP7 0.041 0.1 0.36 9 -0.44 13 22
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 6 -0.46 11 17
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.029 -10000 0 -0.36 4 4
CASP8 0.024 0.003 -10000 0 -10000 0 0
CASP9 0.023 0.006 -10000 0 -10000 0 0
MAP3K14 0.016 0.088 0.29 1 -0.42 13 14
APAF-1/Caspase 9 0.033 0.061 0.24 6 -0.37 5 11
BCL2 0.03 0.13 0.44 5 -0.55 23 28
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 0.051 0.043 -10000 0 -0.33 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 -0.42 1 1
GATA1/HDAC5 0.036 0.021 -10000 0 -10000 0 0
GATA2/HDAC5 0.025 0.074 -10000 0 -0.42 26 26
HDAC5/BCL6/BCoR 0.043 0.038 -10000 0 -0.36 8 8
HDAC9 0.021 0.06 0.26 10 -0.57 9 19
Glucocorticoid receptor/Hsp90/HDAC6 0.043 0.042 -10000 0 -0.36 10 10
HDAC4/ANKRA2 0.034 0.017 -10000 0 -0.42 1 1
HDAC5/YWHAB 0.033 0.01 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
GATA2 0.012 0.097 0.26 14 -0.57 26 40
HDAC4/RFXANK 0.035 0.018 -10000 0 -0.42 1 1
BCOR 0.023 0.026 -10000 0 -0.57 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.023 0.012 0.26 2 -10000 0 2
HDAC5 0.024 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.03 0.046 -10000 0 -0.42 10 10
Histones 0.016 0.049 -10000 0 -0.28 15 15
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.019 -10000 0 -0.57 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 0.033 0.018 -10000 0 -0.42 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 0.032 0.047 0.26 37 -0.57 1 38
Tubulin/HDAC6 0.047 0.018 -10000 0 -0.36 1 1
SUMO1 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.023 0.005 -10000 0 -10000 0 0
GATA1 0.026 0.03 0.26 17 -10000 0 17
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NR3C1 0.018 0.058 -10000 0 -0.57 10 10
SUMO1/HDAC4 0.035 0.04 -10000 0 -0.23 5 5
SRF 0.024 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.033 0.017 -10000 0 -0.42 1 1
Tubulin 0.035 0.018 -10000 0 -0.42 1 1
HDAC4/14-3-3 E 0.032 0.018 -10000 0 -0.42 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 0.041 -10000 0 -0.42 8 8
HDAC4/HDAC3/SMRT (N-CoR2) 0.047 0.018 -10000 0 -0.36 1 1
HDAC4/SRF 0.05 0.035 -10000 0 -0.36 2 2
HDAC4/ER alpha -0.016 0.17 -10000 0 -0.42 152 152
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.016 0.049 -10000 0 -0.28 15 15
cell motility 0.047 0.018 -10000 0 -0.36 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.036 0.006 -10000 0 -10000 0 0
BCL6 0.02 0.045 -10000 0 -0.57 6 6
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 -0.036 0.23 0.26 116 -0.57 148 264
HDAC6/HDAC11 0.036 0.009 0.2 2 -10000 0 2
Ran/GTP/Exportin 1 0.035 0.038 -10000 0 -0.24 4 4
NPC 0.014 0.002 -10000 0 -10000 0 0
MEF2C 0.023 0.019 -10000 0 -0.57 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 0.058 -10000 0 -0.57 10 10
NCOR2 0.024 0.003 -10000 0 -10000 0 0
TUBB2A 0.024 0.022 0.26 2 -0.57 1 3
HDAC11 0.025 0.011 0.26 2 -10000 0 2
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 0.016 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 28 -0.57 2 30
ITGA4 0.026 0.023 0.26 10 -10000 0 10
alpha4/beta7 Integrin 0.041 0.04 0.37 4 -0.42 2 6
alpha4/beta1 Integrin 0.037 0.016 -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 -0.42 34 34
AKT1 0.031 0.085 0.34 2 -0.55 7 9
PTK2B 0.003 0.085 0.35 1 -0.73 6 7
VEGFR2 homodimer/Frs2 0.025 0.06 -10000 0 -0.6 8 8
CAV1 -0.098 0.24 -10000 0 -0.57 213 213
CALM1 0.024 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.039 0.059 -10000 0 -0.56 8 8
endothelial cell proliferation 0.044 0.11 0.37 20 -0.57 8 28
mol:Ca2+ 0.014 0.053 -10000 0 -0.61 5 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.051 0.06 -10000 0 -0.51 9 9
RP11-342D11.1 0.004 0.053 -10000 0 -0.51 8 8
CDH5 0.018 0.049 -10000 0 -0.57 7 7
VEGFA homodimer 0.05 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 -0.57 23 24
HRAS/GDP 0.03 0.049 -10000 0 -0.58 4 4
SH2D2A 0.04 0.073 0.26 91 -0.57 2 93
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.043 0.087 -10000 0 -0.54 9 9
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.045 0.073 -10000 0 -0.5 9 9
VEGFR1 homodimer 0.023 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.049 0.06 -10000 0 -0.64 4 4
GRB10 0.014 0.055 -10000 0 -0.64 5 5
PTPN11 0.024 0.003 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
PAK1 0.023 0.019 0.26 6 -10000 0 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.051 0.073 -10000 0 -0.58 9 9
HRAS 0.026 0.021 0.26 8 -10000 0 8
VEGF/Rho/ROCK1/Integrin Complex 0.008 0.075 -10000 0 -0.53 9 9
HIF1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.011 0.26 2 -10000 0 2
oxygen and reactive oxygen species metabolic process 0.049 0.059 -10000 0 -0.5 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.022 0.032 -10000 0 -0.57 3 3
Nck/Pak 0.033 0.018 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.036 0.064 -10000 0 -0.56 9 9
mol:GDP 0.039 0.054 -10000 0 -0.62 4 4
mol:NADP 0.025 0.084 0.56 1 -0.46 11 12
eNOS/Hsp90 0.036 0.081 0.55 1 -0.46 9 10
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
mol:IP3 0.014 0.054 -10000 0 -0.62 5 5
HIF1A/ARNT 0.029 0.015 -10000 0 -10000 0 0
SHB 0.024 0.008 0.26 1 -10000 0 1
VEGFA 0.026 0.02 0.26 7 -10000 0 7
VEGFC 0.023 0.005 -10000 0 -10000 0 0
FAK1/Vinculin 0.021 0.1 0.35 1 -0.74 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 0.039 0.096 -10000 0 -0.41 33 33
PTPN6 0.024 0.011 0.26 2 -10000 0 2
EPAS1 0.024 0.057 -10000 0 -0.56 9 9
mol:L-citrulline 0.025 0.084 0.56 1 -0.46 11 12
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.048 0.061 -10000 0 -0.54 8 8
VEGFR2 homodimer/VEGFA homodimer 0.041 0.06 -10000 0 -0.53 9 9
VEGFR2/3 heterodimer 0.024 0.068 -10000 0 -0.61 10 10
VEGFB 0.024 0.005 -10000 0 -10000 0 0
MAPK11 0.004 0.068 -10000 0 -0.66 6 6
VEGFR2 homodimer 0.011 0.066 -10000 0 -0.65 9 9
FLT1 0.023 0.006 -10000 0 -10000 0 0
NEDD4 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.007 0.073 -10000 0 -0.62 5 5
MAPK1 0.009 0.074 -10000 0 -0.58 6 6
VEGFA145/NRP2 0.036 0.025 -10000 0 -0.39 2 2
VEGFR1/2 heterodimer 0.023 0.062 -10000 0 -0.59 9 9
KDR 0.011 0.066 -10000 0 -0.65 9 9
VEGFA165/NRP1/VEGFR2 homodimer 0.041 0.062 -10000 0 -0.56 8 8
SRC 0.024 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.014 0.081 0.46 1 -0.59 6 7
PI3K 0.026 0.068 -10000 0 -0.71 5 5
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.04 0.059 -10000 0 -0.53 9 9
FES 0.013 0.059 -10000 0 -0.66 5 5
GAB1 0.014 0.062 -10000 0 -0.75 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.038 0.058 -10000 0 -0.51 9 9
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
ARNT 0.02 0.009 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.017 0.13 -10000 0 -0.49 21 21
VEGFR2 homodimer/VEGFA homodimer/Yes 0.038 0.061 -10000 0 -0.51 10 10
PI3K/GAB1 0.04 0.079 -10000 0 -0.61 5 5
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.054 0.06 -10000 0 -0.62 5 5
PRKACA 0.024 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.036 0.065 -10000 0 -0.6 9 9
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
CDC42 0.014 0.057 -10000 0 -0.66 5 5
actin cytoskeleton reorganization 0.045 0.073 -10000 0 -0.5 9 9
PTK2 0.005 0.087 -10000 0 -0.76 8 8
EDG1 0.004 0.053 -10000 0 -0.51 8 8
mol:DAG 0.014 0.054 -10000 0 -0.62 5 5
CaM/Ca2+ 0.026 0.052 -10000 0 -0.57 5 5
MAP2K3 -0.006 0.06 -10000 0 -0.63 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.039 0.058 -10000 0 -0.67 5 5
PLCG1 0.014 0.055 -10000 0 -0.63 5 5
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.05 0.059 -10000 0 -0.49 9 9
IQGAP1 0.024 0.005 -10000 0 -10000 0 0
YES1 0.023 0.019 -10000 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.04 0.06 -10000 0 -0.53 9 9
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.039 0.059 -10000 0 -0.56 8 8
cell migration 0.024 0.093 0.33 1 -0.65 7 8
mol:PI-3-4-5-P3 0.026 0.063 -10000 0 -0.64 5 5
FYN 0.022 0.027 -10000 0 -0.57 2 2
VEGFB/NRP1 0.019 0.053 -10000 0 -0.52 7 7
mol:NO 0.025 0.084 0.56 1 -0.46 11 12
PXN 0.024 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.017 0.044 -10000 0 -0.58 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.033 0.056 -10000 0 -0.67 5 5
VHL 0.024 0.004 -10000 0 -10000 0 0
ITGB3 0.005 0.11 0.26 4 -0.57 34 38
NOS3 0.025 0.091 0.57 1 -0.53 11 12
VEGFR2 homodimer/VEGFA homodimer/Sck 0.031 0.08 -10000 0 -0.39 30 30
RAC1 0.024 0.003 -10000 0 -10000 0 0
PRKCA -0.009 0.073 0.35 1 -0.69 5 6
PRKCB -0.005 0.065 -10000 0 -0.64 5 5
VCL 0.024 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.022 0.055 -10000 0 -0.51 8 8
VEGFR1/2 heterodimer/VEGFA homodimer 0.037 0.061 -10000 0 -0.54 9 9
VEGFA165/NRP2 0.036 0.025 -10000 0 -0.39 2 2
MAPKKK cascade 0.051 0.08 0.34 10 -0.58 4 14
NRP2 0.023 0.027 0.26 1 -0.57 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 -0.57 1 1
FAK1/Paxillin 0.022 0.1 0.42 2 -0.69 8 10
MAP3K13 0.012 0.059 -10000 0 -0.51 9 9
PDPK1 0.015 0.056 0.27 1 -0.57 4 5
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 -0.48 1 1
mol:DAG 0.013 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 0.011 0.048 -10000 0 -0.42 1 1
PLCG1 0.013 0.031 -10000 0 -0.39 2 2
NOS3 0.016 0.054 0.28 2 -0.5 3 5
CBL 0.022 0.008 -10000 0 -10000 0 0
mol:NO 0.02 0.063 0.29 4 -0.45 6 10
FLT1 0.013 0.018 -10000 0 -0.56 1 1
PGF 0.024 0.025 0.26 5 -0.57 1 6
VEGFR1 homodimer/NRP2/VEGFR121 0.038 0.03 -10000 0 -0.39 3 3
CALM1 0.024 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
eNOS/Hsp90 0.032 0.065 -10000 0 -0.43 7 7
endothelial cell proliferation 0.012 0.081 0.33 6 -0.6 4 10
mol:Ca2+ 0.013 0.031 -10000 0 -0.38 2 2
MAPK3 -0.012 0.05 -10000 0 -0.32 17 17
MAPK1 -0.012 0.048 -10000 0 -0.65 1 1
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
PLGF homodimer 0.024 0.025 0.26 5 -0.57 1 6
PRKACA 0.024 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.098 0.24 -10000 0 -0.57 213 213
VEGFA homodimer 0.025 0.02 0.26 7 -10000 0 7
VEGFR1 homodimer/VEGFA homodimer 0.027 0.022 -10000 0 -0.48 1 1
platelet activating factor biosynthetic process -0.013 0.047 -10000 0 -0.64 1 1
PI3K 0.045 0.044 -10000 0 -0.33 10 10
PRKCA -0.011 0.052 0.24 1 -0.34 19 20
PRKCB -0.008 0.049 -10000 0 -0.35 11 11
VEGFR1 homodimer/PLGF homodimer 0.027 0.025 -10000 0 -0.42 2 2
VEGFA 0.025 0.02 0.26 7 -10000 0 7
VEGFB 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.013 0.031 -10000 0 -0.39 2 2
RASA1 0.013 0.029 -10000 0 -0.43 1 1
NRP2 0.023 0.027 0.26 1 -0.57 2 3
VEGFR1 homodimer 0.013 0.018 -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 0.3 1 -0.44 24 25
PTPN11 0.024 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.043 0.043 -10000 0 -0.32 10 10
mol:L-citrulline 0.02 0.063 0.29 4 -0.45 6 10
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.047 0.028 -10000 0 -0.41 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 -0.003 0.051 -10000 0 -0.4 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.039 0.024 -10000 0 -0.45 1 1
mol:NADP 0.02 0.063 0.29 4 -0.45 6 10
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.046 0.027 -10000 0 -0.41 1 1
VEGFR1 homodimer/NRP2 0.025 0.028 -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 0.061 -10000 0 -0.38 7 7
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 0.06 -10000 0 -0.36 6 6
SUMO1 0.024 0.003 -10000 0 -10000 0 0
ZFPM1 0.023 0.021 0.26 7 -10000 0 7
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
FKBP3 0.024 0.004 -10000 0 -10000 0 0
Histones 0.054 0.04 -10000 0 -0.4 1 1
YY1/LSF 0.024 0.05 -10000 0 -0.25 16 16
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 0.022 0.029 -10000 0 -0.3 6 6
I kappa B alpha/HDAC1 0.03 0.036 -10000 0 -0.42 1 1
SAP18 0.023 0.006 -10000 0 -10000 0 0
RELA 0.02 0.036 -10000 0 -0.31 6 6
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 0.035 -10000 0 -0.43 1 1
NuRD/MBD3 Complex 0.025 0.052 -10000 0 -0.28 12 12
NF kappa B1 p50/RelA 0.026 0.064 0.38 1 -0.38 4 5
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.012 0.097 0.26 14 -0.57 26 40
GATA1 0.026 0.03 0.26 17 -10000 0 17
Mad/Max 0.035 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.017 0.079 -10000 0 -0.36 20 20
RBBP7 0.026 0.019 0.26 7 -10000 0 7
NPC 0.014 0.002 -10000 0 -10000 0 0
RBBP4 0.023 0.019 -10000 0 -0.57 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 0.025 -10000 0 -0.47 1 1
KAT2B 0.024 0.019 -10000 0 -0.57 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 0.022 -10000 0 -10000 0 0
SMURF1 0.024 0.004 -10000 0 -10000 0 0
CHD3 0.022 0.007 -10000 0 -10000 0 0
SAP30 0.024 0.015 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 0.023 0.046 -10000 0 -0.38 3 3
YY1/HDAC2 0.025 0.046 -10000 0 -0.24 14 14
YY1/HDAC1 0.024 0.048 -10000 0 -0.24 13 13
NuRD/MBD2 Complex (MeCP1) 0.024 0.054 -10000 0 -0.27 13 13
PPARG -0.059 0.16 -10000 0 -0.34 217 217
HDAC8/hEST1B 0.041 0.019 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -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 0.035 -10000 0 -0.43 1 1
MBD3L2 0.017 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 0.007 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.023 0.066 -10000 0 -0.34 15 15
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.019 0.026 -10000 0 -0.49 1 1
HDAC2 0.023 0.006 -10000 0 -10000 0 0
YY1 0.015 0.011 -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 7 7
YY1/SAP30/HDAC1 0.036 0.048 -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 0.025 -10000 0 -0.47 1 1
histone deacetylation 0.024 0.054 -10000 0 -0.27 13 13
STAT3 (dimer non-phopshorylated)/HDAC3 0.019 0.034 -10000 0 -0.42 1 1
nuclear export -0.041 0.019 -10000 0 -10000 0 0
PRKACA 0.024 0.004 -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 0.025 0.066 -10000 0 -0.33 23 23
GATA1/HDAC1 0.036 0.02 -10000 0 -10000 0 0
GATA1/HDAC3 0.033 0.041 -10000 0 -0.45 1 1
CHD4 0.023 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.034 0.048 -10000 0 -0.42 8 8
SIN3/HDAC complex/Mad/Max 0.016 0.054 -10000 0 -0.29 19 19
NuRD Complex 0.025 0.066 -10000 0 -0.38 9 9
positive regulation of chromatin silencing 0.051 0.039 -10000 0 -0.4 1 1
SIN3B 0.024 0.004 -10000 0 -10000 0 0
MTA2 0.024 0.005 -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 0.038 -10000 0 -0.23 4 4
HDAC complex 0.058 0.022 -10000 0 -10000 0 0
GATA1/Fog1 0.033 0.026 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.045 0.015 -10000 0 -10000 0 0
TNF 0.025 0.063 0.26 24 -0.57 8 32
negative regulation of cell growth 0.016 0.054 -10000 0 -0.28 19 19
NuRD/MBD2/PRMT5 Complex 0.024 0.054 -10000 0 -0.27 13 13
Ran/GTP/Exportin 1 0.035 0.038 -10000 0 -0.24 4 4
NF kappa B/RelA/I kappa B alpha 0.019 0.051 -10000 0 -0.36 7 7
SIN3/HDAC complex/NCoR1 0.007 0.067 -10000 0 -0.32 29 29
TFCP2 0.024 0.019 -10000 0 -0.57 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
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.04 0.068 0.32 8 -10000 0 8
regulation of axonogenesis -0.01 0.026 0.23 6 -10000 0 6
myoblast fusion -0.025 0.046 -10000 0 -0.22 1 1
mol:GTP 0.022 0.031 -10000 0 -0.15 11 11
regulation of calcium-dependent cell-cell adhesion -0.054 0.044 -10000 0 -0.3 1 1
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 0.039 -10000 0 -0.34 9 9
lamellipodium assembly 0.017 0.058 -10000 0 -0.37 7 7
MAPK3 0.031 0.045 0.2 10 -10000 0 10
ARF6/GTP/NME1/Tiam1 0.055 0.044 0.31 1 -10000 0 1
ARF1 0.02 0.009 -10000 0 -10000 0 0
ARF6/GDP 0.025 0.047 0.22 1 -10000 0 1
ARF1/GDP 0.025 0.048 -10000 0 -0.26 3 3
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 0.2 3 -10000 0 3
actin filament bundle formation -0.032 0.05 0.24 5 -10000 0 5
KALRN 0.009 0.056 -10000 0 -0.31 21 21
RAB11FIP3/RAB11A 0.033 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.032 0.051 -10000 0 -0.25 5 5
NME1 0.028 0.031 0.26 17 -10000 0 17
Rac1/GDP 0.033 0.051 -10000 0 -0.24 6 6
substrate adhesion-dependent cell spreading 0.022 0.031 -10000 0 -0.15 11 11
cortical actin cytoskeleton organization 0.017 0.058 -10000 0 -0.37 7 7
RAC1 0.024 0.003 -10000 0 -10000 0 0
liver development 0.022 0.031 -10000 0 -0.15 11 11
ARF6/GTP 0.022 0.031 -10000 0 -0.15 11 11
RhoA/GTP 0.034 0.028 -10000 0 -10000 0 0
mol:GDP 0.02 0.046 0.2 3 -0.21 5 8
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.03 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
PLD1 0.016 0.046 -10000 0 -0.39 9 9
RAB11FIP3 0.023 0.006 -10000 0 -10000 0 0
tube morphogenesis 0.017 0.058 -10000 0 -0.37 7 7
ruffle organization 0.01 0.026 -10000 0 -0.23 6 6
regulation of epithelial cell migration 0.022 0.031 -10000 0 -0.15 11 11
PLD2 0.02 0.024 -10000 0 -10000 0 0
PIP5K1A 0.01 0.026 -10000 0 -0.23 6 6
mol:Phosphatidic acid 0.008 0.039 -10000 0 -0.34 9 9
Rac1/GTP 0.017 0.058 -10000 0 -0.37 7 7
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.035 0.012 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.018 0.037 -10000 0 -0.36 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.026 0.044 -10000 0 -0.33 2 2
NFKBIA 0.015 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 0.066 -10000 0 -0.57 13 13
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.022 0.013 -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 0.023 0.005 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.016 0.012 0.25 2 -10000 0 2
PIK3R1 0.018 0.055 -10000 0 -0.57 9 9
NFKB1 0.01 0.012 0.26 2 -10000 0 2
RELA 0.024 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.023 0.046 -10000 0 -0.26 10 10
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.024 0.047 -10000 0 -0.34 3 3
SRC 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.03 0.042 -10000 0 -0.4 9 9
NF kappa B1 p50/RelA 0.023 0.046 -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 0.003 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.023 0.055 -10000 0 -0.26 22 22
cell death 0.024 0.045 -10000 0 -0.32 3 3
NF kappa B1 p105/c-Rel 0.018 0.037 -10000 0 -0.36 8 8
LCK 0.026 0.076 0.26 39 -0.57 11 50
BCL3 0.024 0.011 0.26 2 -10000 0 2
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD2 -0.003 0.038 0.21 1 -0.3 2 3
SMAD3 0.022 0.025 -10000 0 -10000 0 0
SMAD3/SMAD4 0.037 0.064 -10000 0 -0.46 10 10
SMAD4/Ubc9/PIASy 0.043 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.041 0.059 -10000 0 -10000 0 0
PPM1A 0.024 0.004 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.008 0.044 -10000 0 -0.28 5 5
MAP3K1 0.023 0.019 -10000 0 -0.57 1 1
TRAP-1/SMAD4 0.028 0.052 -10000 0 -0.42 13 13
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 0.003 -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 0.066 -10000 0 -0.57 13 13
UBE2I 0.023 0.006 -10000 0 -10000 0 0
NUP153 0.024 0.005 -10000 0 -10000 0 0
KPNA2 0.036 0.056 0.26 63 -10000 0 63
PIAS4 0.024 0.004 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.042 0.036 0.36 2 -10000 0 2
CLOCK 0.019 0.061 -10000 0 -0.57 11 11
TIMELESS/CRY2 0.031 0.026 -10000 0 -10000 0 0
DEC1/BMAL1 0.033 0.014 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
NR1D1 0.015 0.017 -10000 0 -10000 0 0
ARNTL 0.026 0.004 -10000 0 -10000 0 0
TIMELESS 0.018 0.025 -10000 0 -10000 0 0
NPAS2 0.023 0.042 0.26 1 -0.57 5 6
CRY2 0.024 0.003 -10000 0 -10000 0 0
mol:CO -0.007 0.006 -10000 0 -0.091 6 6
CHEK1 0.027 0.036 0.26 24 -10000 0 24
mol:HEME 0.007 0.006 0.091 6 -10000 0 6
PER1 0.013 0.073 -10000 0 -0.57 16 16
BMAL/CLOCK/NPAS2 0.049 0.053 -10000 0 -0.36 16 16
BMAL1/CLOCK 0.018 0.064 -10000 0 -0.45 2 2
S phase of mitotic cell cycle 0.042 0.036 0.36 2 -10000 0 2
TIMELESS/CHEK1/ATR 0.042 0.037 0.36 2 -10000 0 2
mol:NADPH 0.007 0.006 0.091 6 -10000 0 6
PER1/TIMELESS 0.024 0.047 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.019 0.018 0.26 6 -10000 0 6
Paxillin-dependent events mediated by a4b1

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
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.009 -10000 0 -10000 0 0
DOCK1 0.024 0.005 -10000 0 -10000 0 0
ITGA4 0.026 0.023 0.26 10 -10000 0 10
RAC1 0.024 0.003 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.041 0.04 0.37 4 -0.42 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 0.035 0.33 4 -0.33 2 6
lamellipodium assembly -0.002 0.084 -10000 0 -0.4 31 31
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.03 0.042 -10000 0 -0.4 9 9
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 0.055 -10000 0 -0.57 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 0.013 -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 28 -0.57 2 30
ARF6/GDP 0.022 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.049 0.043 -10000 0 -0.32 10 10
p130Cas/Crk/Dock1 0.041 0.019 -10000 0 -10000 0 0
VCAM1 0.02 0.061 0.26 6 -0.57 10 16
alpha4/beta1 Integrin/Paxillin/Talin 0.052 0.02 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 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 0.004 -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 0.092 -10000 0 -0.45 31 31
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.008 0.011 -10000 0 -0.26 1 1
MDM2/SUMO1 0.033 0.04 -10000 0 -0.23 4 4
HDAC4 0.023 0.019 -10000 0 -0.57 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 0.007 0.011 -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 0.035 0.04 -10000 0 -0.23 5 5
SUMO1/HDAC1 0.035 0.038 -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 0.036 -10000 0 -0.2 8 8
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.024 0.005 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.022 0.038 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 S130.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.011 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 0.047 -10000 0 -0.19 3 3
AP2 0.034 0.009 -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 0.13 2 -10000 0 2
mol:PI-4-5-P2 0.007 0.016 -10000 0 -10000 0 0
ARF1/GTP 0.024 0.015 -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 0.022 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 0.005 -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 0.027 0.017 -10000 0 -10000 0 0
ARFIP2 0.015 0.018 -10000 0 -10000 0 0
COPA 0.02 0.009 -10000 0 -10000 0 0
RAC1 0.024 0.003 -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 0.05 -10000 0 -0.25 29 29
Arfaptin 2/Rac/GDP 0.028 0.011 -10000 0 -10000 0 0
CYTH2 0.029 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.027 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 0.019 0.023 -10000 0 -10000 0 0
PLD2 0.007 0.016 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.006 0.006 0.13 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 0.13 2 -10000 0 2
GOSR2 0.009 0.026 -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
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.034 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 0.017 -10000 0 -9999 0 0
RELB 0.026 0.023 0.26 10 -9999 0 10
NFKB2 0.024 0.008 0.26 1 -9999 0 1
NF kappa B2 p52/RelB 0.034 0.016 -10000 0 -9999 0 0
regulation of B cell activation 0.033 0.016 -10000 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 1040 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.XX.A89A TCGA.XX.A899 TCGA.W8.A86G TCGA.V7.A7HQ
109_MAP3K5 0.025 0.025 0.025 -0.16
47_PPARGC1A 0.025 0.025 0.025 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 0.025 0.025 0.025 -0.57
131_RELN/VLDLR 0.063 0.063 -0.33 -0.33
30_TGFB1/TGF beta receptor Type II 0.018 0.019 0.024 0.024
84_STAT5B 0.12 0.03 0.012 -0.34
84_STAT5A 0.12 0.03 0.012 -0.34
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/9828739/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/BRCA-TP/10005885/Gistic2_Analysis_10006113/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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