PARADIGM pathway analysis of mRNASeq expression and copy number data
Breast Invasive Carcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1GM85MS
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1GM85MS
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 54 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 357
Signaling events mediated by Stem cell factor receptor (c-Kit) 263
Signaling mediated by p38-alpha and p38-beta 253
Class IB PI3K non-lipid kinase events 247
Reelin signaling pathway 211
Aurora B signaling 188
EGFR-dependent Endothelin signaling events 183
FOXA2 and FOXA3 transcription factor networks 180
PLK1 signaling events 177
HIF-1-alpha transcription factor network 148
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 988 . 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 ( 988 ).

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 0.3613 357 18252 51 -0.069 0.76 1000 -1000 -0.041 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2662 263 20536 78 -0.57 0.18 1000 -1000 -0.019 -1000
Signaling mediated by p38-alpha and p38-beta 0.2561 253 11143 44 -0.32 0.024 1000 -1000 -0.015 -1000
Class IB PI3K non-lipid kinase events 0.2500 247 741 3 -0.13 -1000 1000 -1000 -0.016 -1000
Reelin signaling pathway 0.2136 211 11832 56 -0.33 0.055 1000 -1000 -0.03 -1000
Aurora B signaling 0.1903 188 12616 67 -0.22 0.28 1000 -1000 -0.022 -1000
EGFR-dependent Endothelin signaling events 0.1852 183 3844 21 -0.22 0.034 1000 -1000 -0.039 -1000
FOXA2 and FOXA3 transcription factor networks 0.1822 180 8319 46 -1.1 0.033 1000 -1000 -0.036 -1000
PLK1 signaling events 0.1791 177 15061 85 -0.068 0.24 1000 -1000 -0.026 -1000
HIF-1-alpha transcription factor network 0.1498 148 11249 76 -0.48 0.035 1000 -1000 -0.038 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1498 148 10094 68 -0.36 0.17 1000 -1000 -0.048 -1000
Glucocorticoid receptor regulatory network 0.1457 144 16494 114 -0.74 0.28 1000 -1000 -0.048 -1000
Endothelins 0.1397 138 13324 96 -0.34 0.18 1000 -1000 -0.034 -1000
EPHB forward signaling 0.1397 138 11735 85 -0.23 0.15 1000 -1000 -0.065 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1387 137 12106 88 -0.3 0.12 1000 -1000 -0.059 -1000
p75(NTR)-mediated signaling 0.1346 133 16630 125 -0.23 0.1 1000 -1000 -0.058 -1000
IL4-mediated signaling events 0.1235 122 11105 91 -0.68 0.26 1000 -1000 -0.059 -1000
Ephrin B reverse signaling 0.1215 120 5801 48 -0.23 0.1 1000 -1000 -0.025 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1194 118 6412 54 -0.33 0.055 1000 -1000 -0.037 -1000
Noncanonical Wnt signaling pathway 0.1093 108 2816 26 -0.098 0.024 1000 -1000 -0.035 -1000
Wnt signaling 0.1083 107 749 7 -0.098 0.019 1000 -1000 -0.006 -1000
IGF1 pathway 0.1032 102 5860 57 -0.11 0.043 1000 -1000 -0.039 -1000
IL23-mediated signaling events 0.0992 98 5927 60 -0.3 0.083 1000 -1000 -0.049 -1000
Arf6 signaling events 0.0982 97 6043 62 -0.22 0.051 1000 -1000 -0.029 -1000
Nongenotropic Androgen signaling 0.0911 90 4688 52 -0.25 0.13 1000 -1000 -0.027 -1000
ErbB2/ErbB3 signaling events 0.0901 89 5789 65 -0.27 0.034 1000 -1000 -0.056 -1000
BMP receptor signaling 0.0901 89 7274 81 -0.38 0.11 1000 -1000 -0.044 -1000
Plasma membrane estrogen receptor signaling 0.0881 87 7509 86 -0.11 0.1 1000 -1000 -0.05 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0870 86 7377 85 -0.24 0.024 1000 -1000 -0.034 -1000
Signaling events regulated by Ret tyrosine kinase 0.0870 86 7060 82 -0.07 0.1 1000 -1000 -0.053 -1000
Calcium signaling in the CD4+ TCR pathway 0.0860 85 2648 31 -0.19 0.028 1000 -1000 -0.031 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0850 84 10193 120 -0.37 0.17 1000 -1000 -0.046 -1000
Signaling events mediated by PTP1B 0.0840 83 6355 76 -0.45 0.082 1000 -1000 -0.033 -1000
Visual signal transduction: Rods 0.0810 80 4186 52 -0.33 0.056 1000 -1000 -0.022 -1000
Glypican 1 network 0.0800 79 3797 48 -0.2 0.045 1000 -1000 -0.024 -1000
S1P1 pathway 0.0800 79 2855 36 -0.33 0.024 1000 -1000 -0.027 -1000
Aurora C signaling 0.0759 75 528 7 0 0.15 1000 -1000 -0.011 -1000
Integrins in angiogenesis 0.0739 73 6146 84 -0.2 0.12 1000 -1000 -0.027 -1000
amb2 Integrin signaling 0.0719 71 5869 82 -0.35 0.12 1000 -1000 -0.031 -1000
Effects of Botulinum toxin 0.0719 71 1849 26 -0.004 0.1 1000 -1000 -0.005 -1000
ErbB4 signaling events 0.0698 69 4806 69 -0.28 0.06 1000 -1000 -0.032 -1000
Ephrin A reverse signaling 0.0688 68 479 7 -0.031 0.023 1000 -1000 0 -1000
LPA receptor mediated events 0.0688 68 6947 102 -0.19 0.12 1000 -1000 -0.048 -1000
TCR signaling in naïve CD8+ T cells 0.0678 67 6301 93 -0.089 0.089 1000 -1000 -0.048 -1000
IL6-mediated signaling events 0.0678 67 5084 75 -0.18 0.057 1000 -1000 -0.031 -1000
Syndecan-1-mediated signaling events 0.0668 66 2263 34 -0.072 0.19 1000 -1000 -0.026 -1000
Signaling events mediated by the Hedgehog family 0.0658 65 3383 52 -0.12 0.031 1000 -1000 -0.027 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0557 55 2897 52 -0.11 0.07 1000 -1000 -0.027 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0547 54 1856 34 -0.021 0.06 1000 -1000 -0.03 -1000
Visual signal transduction: Cones 0.0547 54 2066 38 -0.027 0.16 1000 -1000 -0.004 -1000
PDGFR-alpha signaling pathway 0.0536 53 2374 44 -0.3 0.036 1000 -1000 -0.035 -1000
Canonical Wnt signaling pathway 0.0526 52 2670 51 -0.28 0.13 1000 -1000 -0.034 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0516 51 1691 33 -0.38 0.059 1000 -1000 -0.026 -1000
E-cadherin signaling in keratinocytes 0.0516 51 2202 43 -0.19 0.032 1000 -1000 -0.03 -1000
IL12-mediated signaling events 0.0496 49 4327 87 -0.32 0.07 1000 -1000 -0.063 -1000
Presenilin action in Notch and Wnt signaling 0.0496 49 3016 61 -0.28 0.13 1000 -1000 -0.035 -1000
Fc-epsilon receptor I signaling in mast cells 0.0496 49 4845 97 -0.15 0.034 1000 -1000 -0.055 -1000
FAS signaling pathway (CD95) 0.0486 48 2265 47 -0.43 0.04 1000 -1000 -0.021 -1000
Nectin adhesion pathway 0.0476 47 2985 63 -0.054 0.045 1000 -1000 -0.039 -1000
Ras signaling in the CD4+ TCR pathway 0.0466 46 783 17 -0.059 0.025 1000 -1000 -0.015 -1000
Rapid glucocorticoid signaling 0.0455 45 916 20 -0.11 0.027 1000 -1000 -0.003 -1000
Syndecan-3-mediated signaling events 0.0445 44 1574 35 -0.23 0.054 1000 -1000 -0.019 -1000
Glypican 2 network 0.0445 44 178 4 0.032 0.056 1000 -1000 0.013 -1000
Signaling events mediated by HDAC Class III 0.0435 43 1736 40 -0.33 0.045 1000 -1000 -0.02 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0435 43 3206 74 -0.19 0.049 1000 -1000 -0.062 -1000
LPA4-mediated signaling events 0.0415 41 499 12 -0.12 0.005 1000 -1000 -0.022 -1000
TCGA08_rtk_signaling 0.0405 40 1056 26 -0.19 0.036 1000 -1000 -0.008 -1000
Syndecan-2-mediated signaling events 0.0395 39 2691 69 -0.12 0.12 1000 -1000 -0.034 -1000
Aurora A signaling 0.0395 39 2372 60 -0.085 0.18 1000 -1000 -0.018 -1000
Syndecan-4-mediated signaling events 0.0395 39 2625 67 -0.2 0.12 1000 -1000 -0.027 -1000
Regulation of Androgen receptor activity 0.0385 38 2698 70 -0.17 0.12 1000 -1000 -0.033 -1000
Regulation of p38-alpha and p38-beta 0.0374 37 1999 54 -0.25 0.052 1000 -1000 -0.039 -1000
Coregulation of Androgen receptor activity 0.0354 35 2694 76 -0.16 0.065 1000 -1000 -0.015 -1000
Thromboxane A2 receptor signaling 0.0354 35 3730 105 -0.19 0.035 1000 -1000 -0.038 -1000
Regulation of Telomerase 0.0354 35 3596 102 -0.21 0.15 1000 -1000 -0.038 -1000
BCR signaling pathway 0.0354 35 3500 99 -0.081 0.057 1000 -1000 -0.051 -1000
Insulin Pathway 0.0354 35 2602 74 -0.12 0.06 1000 -1000 -0.047 -1000
TCGA08_retinoblastoma 0.0344 34 276 8 -0.017 0.061 1000 -1000 -0.003 -1000
Osteopontin-mediated events 0.0334 33 1279 38 -0.15 0.089 1000 -1000 -0.023 -1000
IL27-mediated signaling events 0.0334 33 1684 51 -0.19 0.072 1000 -1000 -0.042 -1000
IL2 signaling events mediated by STAT5 0.0324 32 714 22 0.006 0.12 1000 -1000 -0.033 -1000
Regulation of nuclear SMAD2/3 signaling 0.0314 31 4241 136 -0.2 0.078 1000 -1000 -0.03 -1000
TCGA08_p53 0.0263 26 186 7 -0.011 0.02 1000 -1000 -0.004 -1000
HIF-2-alpha transcription factor network 0.0243 24 1074 43 -0.16 0.16 1000 -1000 -0.04 -1000
Signaling mediated by p38-gamma and p38-delta 0.0233 23 357 15 -0.025 0.024 1000 -1000 -0.029 -1000
Signaling events mediated by PRL 0.0233 23 804 34 -0.12 0.035 1000 -1000 -0.036 -1000
Caspase cascade in apoptosis 0.0223 22 1650 74 -0.029 0.056 1000 -1000 -0.032 -1000
Class I PI3K signaling events mediated by Akt 0.0213 21 1481 68 -0.16 0.043 1000 -1000 -0.03 -1000
Ceramide signaling pathway 0.0213 21 1621 76 -0.1 0.063 1000 -1000 -0.027 -1000
FoxO family signaling 0.0213 21 1346 64 -0.016 0.24 1000 -1000 -0.038 -1000
S1P4 pathway 0.0213 21 544 25 -0.011 0.044 1000 -1000 -0.019 -1000
Hedgehog signaling events mediated by Gli proteins 0.0202 20 1354 65 -0.09 0.055 1000 -1000 -0.03 -1000
S1P5 pathway 0.0202 20 354 17 -0.005 0.033 1000 -1000 -0.007 -1000
IL2 signaling events mediated by PI3K 0.0192 19 1107 58 -0.001 0.066 1000 -1000 -0.031 -1000
Cellular roles of Anthrax toxin 0.0182 18 711 39 -0.079 0.028 1000 -1000 -0.018 -1000
mTOR signaling pathway 0.0182 18 982 53 -0.028 0.027 1000 -1000 -0.032 -1000
BARD1 signaling events 0.0172 17 969 57 -0.048 0.11 1000 -1000 -0.033 -1000
JNK signaling in the CD4+ TCR pathway 0.0162 16 274 17 0.002 0.062 1000 -1000 -0.02 -1000
ceramide signaling pathway 0.0152 15 755 49 -0.004 0.036 1000 -1000 -0.029 -1000
Retinoic acid receptors-mediated signaling 0.0152 15 880 58 -0.052 0.052 1000 -1000 -0.028 -1000
S1P3 pathway 0.0152 15 666 42 -0.013 0.042 1000 -1000 -0.035 -1000
E-cadherin signaling in the nascent adherens junction 0.0142 14 1120 76 -0.024 0.051 1000 -1000 -0.051 -1000
TRAIL signaling pathway 0.0132 13 630 48 -0.015 0.042 1000 -1000 -0.031 -1000
PLK2 and PLK4 events 0.0121 12 38 3 0.015 0.032 1000 -1000 -0.006 -1000
PDGFR-beta signaling pathway 0.0121 12 1253 97 -0.029 0.056 1000 -1000 -0.049 -1000
p38 MAPK signaling pathway 0.0121 12 531 44 -0.019 0.065 1000 -1000 -0.021 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0111 11 322 28 -0.005 0.051 1000 -1000 -0.011 -1000
IL1-mediated signaling events 0.0111 11 732 62 -0.011 0.062 1000 -1000 -0.035 -1000
Class I PI3K signaling events 0.0111 11 807 73 -0.017 0.05 1000 -1000 -0.032 -1000
Arf6 trafficking events 0.0111 11 846 71 -0.27 0.041 1000 -1000 -0.025 -1000
E-cadherin signaling events 0.0111 11 57 5 0.01 0.032 1000 -1000 0.012 -1000
IFN-gamma pathway 0.0101 10 698 68 -0.01 0.077 1000 -1000 -0.044 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0101 10 468 45 0.004 0.055 1000 -1000 -0.036 -1000
EPO signaling pathway 0.0091 9 520 55 0.012 0.08 1000 -1000 -0.03 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0091 9 360 37 -0.008 0.066 1000 -1000 -0.024 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0091 9 820 83 -0.018 0.047 1000 -1000 -0.023 -1000
Canonical NF-kappaB pathway 0.0081 8 327 39 0 0.051 1000 -1000 -0.023 -1000
Signaling events mediated by HDAC Class II 0.0081 8 621 75 -0.032 0.062 1000 -1000 -0.029 -1000
a4b1 and a4b7 Integrin signaling 0.0081 8 40 5 0.024 0.04 1000 -1000 0.014 -1000
Insulin-mediated glucose transport 0.0081 8 262 32 -0.13 0.039 1000 -1000 -0.023 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0071 7 897 125 -0.096 0.055 1000 -1000 -0.043 -1000
VEGFR1 specific signals 0.0061 6 347 56 -0.096 0.053 1000 -1000 -0.044 -1000
Signaling events mediated by HDAC Class I 0.0051 5 603 104 -0.059 0.057 1000 -1000 -0.03 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0040 4 100 23 -0.003 0.043 1000 -1000 -0.029 -1000
Circadian rhythm pathway 0.0040 4 95 22 -0.007 0.049 1000 -1000 -0.023 -1000
Atypical NF-kappaB pathway 0.0040 4 139 31 0 0.031 1000 -1000 -0.01 -1000
Arf6 downstream pathway 0.0030 3 133 43 -0.054 0.055 1000 -1000 -0.02 -1000
Paxillin-dependent events mediated by a4b1 0.0030 3 136 36 -0.047 0.051 1000 -1000 -0.026 -1000
Arf1 pathway 0.0010 1 86 54 -0.001 0.045 1000 -1000 -0.015 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 23 27 -0.009 0.056 1000 -1000 -0.035 -1000
Alternative NF-kappaB pathway 0.0000 0 10 13 0 0.067 1000 -1000 0 -1000
Total NA 7791 462054 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 0.63 0.4 0.99 430 -1 3 433
PLK1 0.39 0.26 0.63 421 -0.87 1 422
BIRC5 0.4 0.26 0.6 518 -0.79 4 522
HSPA1B 0.63 0.4 0.98 439 -0.95 4 443
MAP2K1 0.18 0.12 0.31 356 -10000 0 356
BRCA2 0.64 0.41 1 413 -0.97 4 417
FOXM1 0.74 0.51 1.2 476 -1.1 4 480
XRCC1 0.63 0.4 1 422 -1 3 425
FOXM1B/p19 0.13 0.27 0.8 67 -1 5 72
Cyclin D1/CDK4 0.55 0.38 0.9 406 -0.98 3 409
CDC2 0.68 0.45 1.1 477 -0.99 4 481
TGFA 0.55 0.39 0.89 448 -0.96 7 455
SKP2 0.63 0.4 1 435 -0.95 4 439
CCNE1 0.093 0.097 0.3 157 -10000 0 157
CKS1B 0.68 0.43 1 465 -0.98 3 468
RB1 0.32 0.32 0.68 353 -0.63 7 360
FOXM1C/SP1 0.57 0.37 0.9 408 -1 6 414
AURKB 0.33 0.31 0.62 382 -0.72 22 404
CENPF 0.73 0.47 1.1 496 -0.92 4 500
CDK4 0.087 0.056 0.25 23 -10000 0 23
MYC 0.36 0.38 0.84 278 -0.96 6 284
CHEK2 0.17 0.12 0.32 302 -10000 0 302
ONECUT1 0.58 0.4 0.93 433 -0.96 4 437
CDKN2A -0.069 0.12 0.23 15 -0.24 212 227
LAMA4 0.63 0.41 0.98 455 -1.1 6 461
FOXM1B/HNF6 0.58 0.41 0.97 399 -1.1 4 403
FOS 0.32 0.65 1 312 -0.99 60 372
SP1 0.023 0.023 -10000 0 -0.21 6 6
CDC25B 0.63 0.4 1 433 -0.98 3 436
response to radiation 0.12 0.088 0.23 296 -10000 0 296
CENPB 0.63 0.4 0.98 443 -0.92 4 447
CENPA 0.69 0.45 1.1 460 -0.95 4 464
NEK2 0.76 0.46 1.1 504 -0.96 3 507
HIST1H2BA 0.62 0.4 0.98 440 -0.95 4 444
CCNA2 0.15 0.13 0.31 383 -10000 0 383
EP300 0.023 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.66 0.44 1.1 423 -1.1 4 427
CCNB2 0.7 0.45 1.1 465 -1 3 468
CCNB1 0.7 0.46 1.1 462 -0.99 4 466
ETV5 0.64 0.41 1 432 -0.95 4 436
ESR1 0.49 0.55 1 372 -1 14 386
CCND1 0.58 0.42 0.96 437 -1 3 440
GSK3A 0.15 0.093 0.27 270 -10000 0 270
Cyclin A-E1/CDK1-2 0.24 0.16 0.41 414 -10000 0 414
CDK2 0.06 0.03 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.16 0.11 0.27 406 -10000 0 406
FOXM1B/Cbp/p300 0.24 0.29 0.71 92 -0.98 4 96
GAS1 0.58 0.49 0.98 428 -1.1 32 460
MMP2 0.62 0.42 0.99 421 -1.1 10 431
RB1/FOXM1C 0.51 0.39 0.89 400 -1 3 403
CREBBP 0.023 0.006 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

Figure S2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S2.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.16 0.2 0.33 2 -0.38 432 434
CRKL -0.18 0.21 -10000 0 -0.4 441 441
HRAS -0.13 0.18 -10000 0 -0.36 279 279
mol:PIP3 -0.14 0.2 -10000 0 -0.37 344 344
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 -0.42 450 450
FOXO3 -0.15 0.2 0.51 1 -0.36 402 403
AKT1 -0.16 0.21 0.35 1 -0.38 425 426
BAD -0.15 0.2 0.33 1 -0.36 418 419
megakaryocyte differentiation -0.18 0.22 -10000 0 -0.41 449 449
GSK3B -0.15 0.2 0.51 1 -0.36 407 408
RAF1 -0.098 0.16 0.25 3 -0.34 71 74
SHC1 0.02 0.009 -10000 0 -10000 0 0
STAT3 -0.18 0.22 -10000 0 -0.42 448 448
STAT1 -0.45 0.52 -10000 0 -1 454 454
HRAS/SPRED1 -0.095 0.16 -10000 0 -0.3 266 266
cell proliferation -0.18 0.22 -10000 0 -0.41 451 451
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
TEC 0.022 0.033 -10000 0 -0.58 3 3
RPS6KB1 -0.17 0.22 -10000 0 -0.4 452 452
HRAS/SPRED2 -0.094 0.16 -10000 0 -0.34 75 75
LYN/TEC/p62DOK -0.15 0.22 -10000 0 -0.4 378 378
MAPK3 -0.067 0.12 0.33 5 -0.28 29 34
STAP1 -0.18 0.22 -10000 0 -0.41 452 452
GRAP2 0.016 0.071 0.26 3 -0.58 13 16
JAK2 -0.37 0.45 -10000 0 -0.84 457 457
STAT1 (dimer) -0.44 0.51 -10000 0 -0.97 454 454
mol:Gleevec 0.007 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.14 0.22 -10000 0 -0.4 381 381
actin filament polymerization -0.18 0.22 0.33 1 -0.41 449 450
LYN 0.021 0.008 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.26 0.32 -10000 0 -0.6 453 453
PIK3R1 0.019 0.047 -10000 0 -0.58 6 6
CBL/CRKL/GRB2 -0.14 0.2 -10000 0 -0.37 391 391
PI3K -0.15 0.22 -10000 0 -0.39 425 425
PTEN 0.022 0.028 -10000 0 -0.58 2 2
SCF/KIT/EPO/EPOR -0.51 0.64 -10000 0 -1.2 446 446
MAPK8 -0.19 0.22 -10000 0 -0.42 451 451
STAT3 (dimer) -0.18 0.21 -10000 0 -0.41 448 448
positive regulation of transcription -0.053 0.11 0.24 12 -0.23 23 35
mol:GDP -0.13 0.19 -10000 0 -0.37 296 296
PIK3C2B -0.17 0.2 -10000 0 -0.38 433 433
CBL/CRKL -0.16 0.2 -10000 0 -0.38 434 434
FER -0.19 0.22 -10000 0 -0.42 455 455
SH2B3 -0.18 0.22 -10000 0 -0.42 451 451
PDPK1 -0.12 0.19 0.33 8 -0.35 309 317
SNAI2 -0.18 0.21 0.28 4 -0.4 443 447
positive regulation of cell proliferation -0.32 0.39 -10000 0 -0.73 457 457
KITLG -0.004 0.061 0.26 10 -0.6 5 15
cell motility -0.32 0.39 -10000 0 -0.73 457 457
PTPN6 0.032 0.018 0.27 2 -10000 0 2
EPOR -0.12 0.19 -10000 0 -0.88 19 19
STAT5A (dimer) -0.27 0.32 -10000 0 -0.6 456 456
SOCS1 0.025 0.033 0.26 12 -0.58 1 13
cell migration 0.18 0.22 0.41 454 -10000 0 454
SOS1 0.024 0.003 -10000 0 -10000 0 0
EPO 0.042 0.094 0.25 155 -10000 0 155
VAV1 0.024 0.022 0.26 2 -0.58 1 3
GRB10 -0.18 0.22 -10000 0 -0.42 446 446
PTPN11 0.031 0.009 -10000 0 -10000 0 0
SCF/KIT -0.19 0.23 -10000 0 -0.44 451 451
GO:0007205 0.009 0.012 -10000 0 -10000 0 0
MAP2K1 -0.076 0.13 0.31 6 -0.29 43 49
CBL 0.022 0.007 -10000 0 -10000 0 0
KIT -0.57 0.66 -10000 0 -1.3 450 450
MAP2K2 -0.076 0.14 0.33 6 -0.29 43 49
SHC/Grb2/SOS1 -0.14 0.21 -10000 0 -0.4 321 321
STAT5A -0.28 0.34 -10000 0 -0.62 455 455
GRB2 0.023 0.01 0.26 1 -10000 0 1
response to radiation -0.17 0.21 0.28 4 -0.39 444 448
SHC/GRAP2 0.023 0.051 -10000 0 -0.36 13 13
PTPRO -0.18 0.22 -10000 0 -0.42 449 449
SH2B2 -0.18 0.22 -10000 0 -0.41 449 449
DOK1 0.025 0.011 0.26 2 -10000 0 2
MATK -0.19 0.22 -10000 0 -0.42 455 455
CREBBP -0.029 0.073 -10000 0 -0.18 19 19
BCL2 -0.16 0.32 -10000 0 -1.2 60 60
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.32 0.51 0.44 4 -1 319 323
MKNK1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.087 0.18 -10000 0 -0.34 318 318
ATF2/c-Jun -0.084 0.16 -10000 0 -0.44 89 89
MAPK11 -0.082 0.18 -10000 0 -0.35 290 290
MITF -0.12 0.21 -10000 0 -0.41 316 316
MAPKAPK5 -0.11 0.21 -10000 0 -0.4 323 323
KRT8 -0.11 0.21 -10000 0 -0.4 304 304
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 -0.52 323 323
CEBPB -0.1 0.2 0.29 1 -0.4 298 299
SLC9A1 -0.11 0.21 -10000 0 -0.41 315 315
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.11 0.21 -10000 0 -0.4 309 309
p38alpha-beta/MNK1 -0.11 0.25 -10000 0 -0.43 318 318
JUN -0.084 0.16 -10000 0 -0.43 89 89
PPARGC1A -0.2 0.33 0.27 2 -0.55 383 385
USF1 -0.1 0.19 0.32 3 -0.38 297 300
RAB5/GDP/GDI1 -0.082 0.16 -10000 0 -0.3 320 320
NOS2 -0.11 0.22 0.36 1 -0.41 294 295
DDIT3 -0.11 0.21 -10000 0 -0.4 317 317
RAB5A 0.024 0.003 -10000 0 -10000 0 0
HSPB1 -0.095 0.17 0.28 3 -0.33 303 306
p38alpha-beta/HBP1 -0.11 0.25 -10000 0 -0.45 291 291
CREB1 -0.12 0.22 -10000 0 -0.43 321 321
RAB5/GDP 0.018 0.002 -10000 0 -10000 0 0
EIF4E -0.11 0.21 -10000 0 -0.41 289 289
RPS6KA4 -0.11 0.21 -10000 0 -0.4 315 315
PLA2G4A -0.13 0.22 -10000 0 -0.43 315 315
GDI1 -0.11 0.21 0.29 1 -0.4 321 322
TP53 -0.15 0.27 0.27 2 -0.53 301 303
RPS6KA5 -0.12 0.22 -10000 0 -0.41 326 326
ESR1 -0.15 0.24 0.29 1 -0.42 363 364
HBP1 0.024 0.004 -10000 0 -10000 0 0
MEF2C -0.11 0.21 -10000 0 -0.4 319 319
MEF2A -0.11 0.21 0.29 1 -0.4 317 318
EIF4EBP1 -0.12 0.22 0.28 1 -0.44 305 306
KRT19 -0.11 0.21 0.32 1 -0.4 311 312
ELK4 -0.1 0.19 0.31 3 -0.38 303 306
ATF6 -0.1 0.19 0.32 3 -0.38 302 305
ATF1 -0.12 0.22 -10000 0 -0.43 323 323
p38alpha-beta/MAPKAPK2 -0.096 0.22 -10000 0 -0.41 278 278
p38alpha-beta/MAPKAPK3 -0.11 0.25 -10000 0 -0.45 291 291
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.13 0.26 0.57 247 -10000 0 247
PI3K Class IB/PDE3B -0.13 0.26 -10000 0 -0.58 247 247
PDE3B -0.13 0.26 -10000 0 -0.58 247 247
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 0.037 0.029 -10000 0 -10000 0 0
VLDLR 0.008 0.093 -10000 0 -0.58 24 24
CRKL 0.023 0.006 -10000 0 -10000 0 0
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
FYN 0.021 0.028 -10000 0 -0.58 2 2
ITGA3 0.022 0.022 0.26 1 -0.58 1 2
RELN/VLDLR/Fyn -0.2 0.21 -10000 0 -0.38 556 556
MAPK8IP1/MKK7/MAP3K11/JNK1 0.055 0.044 -10000 0 -0.32 6 6
AKT1 -0.15 0.14 -10000 0 -0.27 500 500
MAP2K7 0.024 0.003 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
DAB1 0.036 0.057 0.26 57 -10000 0 57
RELN/LRP8/DAB1 -0.16 0.19 0.36 5 -0.33 557 562
LRPAP1/LRP8 0.049 0.049 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.15 0.19 0.32 4 -0.31 544 548
DAB1/alpha3/beta1 Integrin -0.14 0.18 -10000 0 -0.32 398 398
long-term memory -0.19 0.22 0.35 4 -0.36 544 548
DAB1/LIS1 -0.15 0.19 0.3 4 -0.31 548 552
DAB1/CRLK/C3G -0.15 0.18 -10000 0 -0.31 464 464
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DAB1/NCK2 -0.15 0.19 0.3 4 -0.31 548 552
ARHGEF2 0.02 0.009 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.034 0.18 0.26 12 -0.58 97 109
CDK5R1 0.028 0.037 0.26 23 -10000 0 23
RELN -0.33 0.3 0.26 3 -0.58 567 570
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
RELN/LRP8/Fyn -0.19 0.21 -10000 0 -0.36 547 547
GRIN2A/RELN/LRP8/DAB1/Fyn -0.17 0.22 0.34 4 -0.36 515 519
MAPK8 0.021 0.043 -10000 0 -0.58 5 5
RELN/VLDLR/DAB1 -0.18 0.2 0.33 2 -0.34 559 561
ITGB1 0.024 0.004 -10000 0 -10000 0 0
MAP1B -0.19 0.18 0.22 2 -0.33 560 562
RELN/LRP8 -0.19 0.2 -10000 0 -0.36 560 560
GRIN2B/RELN/LRP8/DAB1/Fyn -0.17 0.21 0.37 3 -0.33 568 571
PI3K 0.031 0.036 -10000 0 -0.36 7 7
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.031 0.022 -10000 0 -0.43 1 1
RAP1A -0.17 0.15 0.34 3 -0.3 385 388
PAFAH1B1 0.022 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.032 0.26 5 -0.58 2 7
CRLK/C3G 0.034 0.009 -10000 0 -10000 0 0
GRIN2B -0.024 0.16 0.26 1 -0.58 71 72
NCK2 0.024 0.002 -10000 0 -10000 0 0
neuron differentiation -0.086 0.12 -10000 0 -0.35 60 60
neuron adhesion -0.15 0.15 0.33 4 -0.49 20 24
LRP8 0.048 0.072 0.26 99 -10000 0 99
GSK3B -0.14 0.14 -10000 0 -0.3 156 156
RELN/VLDLR/DAB1/Fyn -0.16 0.19 0.32 2 -0.32 548 550
MAP3K11 0.024 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.16 0.15 -10000 0 -0.29 512 512
CDK5 0.024 0.014 0.26 3 -10000 0 3
MAPT -0.023 0.2 0.88 15 -0.52 92 107
neuron migration -0.19 0.18 0.28 1 -0.35 420 421
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.087 0.12 -10000 0 -0.35 60 60
RELN/VLDLR -0.17 0.2 -10000 0 -0.34 561 561
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 0.11 0.1 0.24 309 -0.26 2 311
STMN1 0.082 0.082 0.27 63 -10000 0 63
Aurora B/RasGAP/Survivin 0.2 0.14 0.34 460 -10000 0 460
Chromosomal passenger complex/Cul3 protein complex 0.009 0.14 0.2 177 -0.24 120 297
BIRC5 0.18 0.12 0.27 643 -10000 0 643
DES -0.15 0.32 0.36 2 -0.57 255 257
Aurora C/Aurora B/INCENP 0.11 0.08 0.33 6 -0.3 1 7
Aurora B/TACC1 0.074 0.1 0.18 95 -0.34 21 116
Aurora B/PP2A 0.11 0.084 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.033 0.028 0.14 10 -10000 0 10
mitotic metaphase/anaphase transition -0.007 0.006 -10000 0 -10000 0 0
NDC80 0.15 0.13 0.28 444 -10000 0 444
Cul3 protein complex -0.12 0.2 -10000 0 -0.37 378 378
KIF2C 0.16 0.11 0.24 575 -10000 0 575
PEBP1 0.027 0.004 -10000 0 -10000 0 0
KIF20A 0.2 0.1 0.26 726 -10000 0 726
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.11 0.084 -10000 0 -10000 0 0
SEPT1 0.029 0.039 0.26 26 -10000 0 26
SMC2 0.024 0.003 -10000 0 -10000 0 0
SMC4 0.026 0.023 0.26 9 -10000 0 9
NSUN2/NPM1/Nucleolin 0.077 0.19 0.29 63 -0.44 91 154
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 0.073 0.064 0.24 36 -10000 0 36
AURKB 0.15 0.12 0.26 507 -10000 0 507
AURKC 0.025 0.031 0.26 10 -0.58 1 11
CDCA8 0.11 0.12 0.27 331 -10000 0 331
cytokinesis 0.15 0.15 0.31 378 -0.34 6 384
Aurora B/Septin1 0.19 0.18 0.36 423 -0.32 5 428
AURKA 0.12 0.12 0.26 395 -10000 0 395
INCENP 0.031 0.008 -10000 0 -10000 0 0
KLHL13 -0.22 0.29 -10000 0 -0.58 387 387
BUB1 0.18 0.11 0.26 662 -10000 0 662
hSgo1/Aurora B/Survivin 0.28 0.19 0.42 574 -10000 0 574
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.19 0.14 0.36 342 -10000 0 342
SGOL1 0.18 0.12 0.26 615 -10000 0 615
CENPA 0.18 0.14 0.31 487 -0.23 2 489
NCAPG 0.14 0.12 0.26 485 -10000 0 485
Aurora B/HC8 Proteasome 0.11 0.084 0.21 2 -10000 0 2
NCAPD2 0.023 0.009 0.26 1 -10000 0 1
Aurora B/PP1-gamma 0.12 0.083 -10000 0 -10000 0 0
RHOA 0.023 0.005 -10000 0 -10000 0 0
NCAPH 0.12 0.12 0.26 404 -10000 0 404
NPM1 0.071 0.13 0.26 5 -0.34 41 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 0.084 0.21 2 -10000 0 2
PPP1CC 0.024 0.002 -10000 0 -10000 0 0
Centraspindlin 0.21 0.16 0.37 412 -10000 0 412
RhoA/GDP 0.017 0.003 -10000 0 -10000 0 0
NSUN2 0.076 0.12 0.27 20 -0.29 47 67
MYLK 0.027 0.14 0.24 7 -0.32 104 111
KIF23 0.1 0.11 0.27 295 -10000 0 295
VIM 0.082 0.088 0.38 31 -0.41 2 33
RACGAP1 0.042 0.05 0.28 42 -10000 0 42
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.066 0.14 0.23 1 -0.38 50 51
Chromosomal passenger complex 0.18 0.13 0.29 542 -10000 0 542
Chromosomal passenger complex/EVI5 0.24 0.17 0.4 465 -10000 0 465
TACC1 0.007 0.087 -10000 0 -0.58 21 21
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 0.025 0.018 0.26 5 -10000 0 5
EGFR -0.19 0.29 -10000 0 -0.58 349 349
EGF/EGFR -0.16 0.23 -10000 0 -0.38 474 474
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.12 0.2 -10000 0 -0.36 363 363
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.023 0.02 -10000 0 -0.58 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.093 0.24 0.26 2 -0.58 189 191
EGF/EGFR dimer/SHC -0.16 0.22 -10000 0 -0.41 387 387
mol:GDP -0.12 0.2 -10000 0 -0.36 363 363
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.018 0.15 0.26 1 -0.58 68 69
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.18 -10000 0 -0.34 362 362
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP -0.12 0.19 -10000 0 -0.34 362 362
FRAP1 -0.15 0.16 0.16 3 -0.34 363 366
EGF/EGFR dimer -0.22 0.26 -10000 0 -0.47 480 480
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 71 71
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.24 0.27 -10000 0 -0.67 174 174
PCK1 -0.92 0.64 -10000 0 -1.4 617 617
HNF4A -0.24 0.28 -10000 0 -0.78 87 87
KCNJ11 -0.28 0.3 -10000 0 -0.74 175 175
AKT1 -0.17 0.16 -10000 0 -0.41 103 103
response to starvation 0.005 0.011 -10000 0 -10000 0 0
DLK1 -0.45 0.48 0.57 1 -1 346 347
NKX2-1 -0.037 0.16 0.5 6 -0.52 2 8
ACADM -0.25 0.27 -10000 0 -0.67 186 186
TAT -1.1 0.64 -10000 0 -1.4 698 698
CEBPB 0.024 0.008 -10000 0 -10000 0 0
CEBPA 0.02 0.058 -10000 0 -0.58 9 9
TTR -0.41 0.29 -10000 0 -0.72 320 320
PKLR -0.22 0.27 0.54 5 -0.68 147 152
APOA1 -0.28 0.32 -10000 0 -0.85 102 102
CPT1C -0.25 0.27 0.55 2 -0.72 124 126
ALAS1 -0.15 0.16 -10000 0 -0.73 7 7
TFRC -0.42 0.27 -10000 0 -0.69 350 350
FOXF1 0.017 0.048 0.26 6 -0.58 4 10
NF1 0.026 0.006 -10000 0 -10000 0 0
HNF1A (dimer) 0.033 0.03 0.26 6 -10000 0 6
CPT1A -0.24 0.27 -10000 0 -0.72 122 122
HMGCS1 -0.25 0.27 -10000 0 -0.73 119 119
NR3C1 -0.12 0.12 -10000 0 -0.27 237 237
CPT1B -0.25 0.27 -10000 0 -0.69 162 162
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.024 -10000 0 -10000 0 0
GCK -0.28 0.32 -10000 0 -0.8 186 186
CREB1 -0.076 0.093 -10000 0 -0.21 158 158
IGFBP1 -0.42 0.55 -10000 0 -1.4 226 226
PDX1 -0.12 0.16 -10000 0 -0.57 2 2
UCP2 -0.24 0.27 0.55 1 -0.71 133 134
ALDOB -0.28 0.29 -10000 0 -0.74 164 164
AFP -0.57 0.51 0.35 2 -0.87 598 600
BDH1 -0.25 0.27 -10000 0 -0.69 156 156
HADH -0.28 0.28 -10000 0 -0.72 175 175
F2 -0.28 0.31 -10000 0 -0.83 110 110
HNF1A 0.033 0.03 0.26 6 -10000 0 6
G6PC -0.18 0.12 -10000 0 -0.61 5 5
SLC2A2 -0.16 0.17 -10000 0 -0.95 1 1
INS 0.02 0.079 0.24 8 -10000 0 8
FOXA1 -0.22 0.24 0.28 18 -0.39 486 504
FOXA3 -0.36 0.21 0.29 14 -0.46 727 741
FOXA2 -0.32 0.33 0.61 1 -0.8 198 199
ABCC8 -0.32 0.39 0.58 1 -0.95 197 198
ALB -0.77 0.54 0.37 1 -1.2 628 629
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.068 0.05 0.11 3 -0.11 442 445
BUB1B 0.089 0.068 0.15 489 -10000 0 489
PLK1 0.052 0.039 0.088 424 -0.079 2 426
PLK1S1 0.027 0.035 0.14 8 -0.16 19 27
KIF2A 0.043 0.037 0.16 16 -10000 0 16
regulation of mitotic centrosome separation 0.052 0.039 0.088 425 -0.079 2 427
GOLGA2 0.024 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.24 0.15 0.32 683 -10000 0 683
WEE1 0.045 0.062 0.22 2 -0.27 23 25
cytokinesis 0.13 0.086 0.22 270 -0.29 2 272
PP2A-alpha B56 0.12 0.12 -10000 0 -0.44 22 22
AURKA 0.067 0.053 0.12 422 -0.15 3 425
PICH/PLK1 0.1 0.091 0.22 292 -10000 0 292
CENPE 0.065 0.057 0.16 78 -10000 0 78
RhoA/GTP 0.017 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.043 0.037 0.16 16 -10000 0 16
PPP2CA 0.024 0.004 -10000 0 -10000 0 0
FZR1 0.024 0.004 -10000 0 -10000 0 0
TPX2 0.083 0.056 0.13 576 -0.13 3 579
PAK1 0.022 0.019 0.26 5 -10000 0 5
SPC24 0.17 0.12 0.26 590 -10000 0 590
FBXW11 0.024 0.004 -10000 0 -10000 0 0
CLSPN 0.075 0.071 0.14 440 -0.19 20 460
GORASP1 0.024 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.004 0.015 46 -10000 0 46
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.024 0.019 0.053 155 -0.041 2 157
G2 phase of mitotic cell cycle 0.001 0.003 0.013 18 -10000 0 18
STAG2 0.024 0.019 -10000 0 -0.58 1 1
GRASP65/GM130/RAB1/GTP 0.009 0.084 -10000 0 -0.5 25 25
spindle elongation 0.052 0.039 0.088 425 -0.079 2 427
ODF2 0.026 0.004 -10000 0 -10000 0 0
BUB1 0.11 0.13 -10000 0 -0.47 28 28
TPT1 0.014 0.056 0.13 1 -0.17 69 70
CDC25C 0.12 0.07 0.16 601 -0.19 17 618
CDC25B 0.029 0.032 0.27 16 -10000 0 16
SGOL1 0.068 0.05 0.11 442 -0.11 3 445
RHOA 0.023 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.069 0.067 0.28 15 -10000 0 15
CDC14B -0.011 0.073 -10000 0 -0.43 28 28
CDC20 0.15 0.12 0.26 519 -10000 0 519
PLK1/PBIP1 0.04 0.049 0.14 140 -10000 0 140
mitosis -0.005 0.005 0.024 3 -10000 0 3
FBXO5 0.031 0.036 0.15 18 -0.12 1 19
CDC2 0.003 0.004 0.011 186 -10000 0 186
NDC80 0.16 0.12 0.26 576 -10000 0 576
metaphase plate congression 0.03 0.055 0.15 1 -0.19 45 46
ERCC6L 0.092 0.087 0.25 159 -10000 0 159
NLP/gamma Tubulin 0.025 0.025 0.073 51 -0.083 11 62
microtubule cytoskeleton organization 0.014 0.056 0.13 1 -0.17 69 70
G2/M transition DNA damage checkpoint -0.001 0.002 0.011 20 -10000 0 20
PPP1R12A 0.025 0.004 -10000 0 -10000 0 0
interphase -0.001 0.002 0.011 20 -10000 0 20
PLK1/PRC1-2 0.21 0.13 0.28 641 -10000 0 641
GRASP65/GM130/RAB1/GTP/PLK1 0.07 0.031 -10000 0 -10000 0 0
RAB1A 0.024 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.044 0.036 0.078 430 -10000 0 430
mitotic prometaphase 0.002 0.005 0.022 47 -10000 0 47
proteasomal ubiquitin-dependent protein catabolic process 0.055 0.052 0.19 1 -0.3 4 5
microtubule-based process 0.18 0.09 0.23 721 -10000 0 721
Golgi organization 0.052 0.039 0.088 425 -0.079 2 427
Cohesin/SA2 0.056 0.032 0.15 3 -0.31 1 4
PPP1CB/MYPT1 0.036 0.007 -10000 0 -10000 0 0
KIF20A 0.2 0.1 0.26 726 -10000 0 726
APC/C/CDC20 0.14 0.1 0.23 519 -10000 0 519
PPP2R1A 0.024 0.004 -10000 0 -10000 0 0
chromosome segregation 0.033 0.049 0.14 140 -10000 0 140
PRC1 0.082 0.1 0.26 238 -10000 0 238
ECT2 0.051 0.057 0.26 40 -10000 0 40
C13orf34 0.042 0.033 0.081 275 -0.068 1 276
NUDC 0.03 0.055 0.15 1 -0.19 45 46
regulation of attachment of spindle microtubules to kinetochore 0.088 0.068 0.15 491 -10000 0 491
spindle assembly 0.037 0.03 0.087 128 -10000 0 128
spindle stabilization 0.027 0.035 0.14 8 -0.16 19 27
APC/C/HCDH1 0.01 0.066 -10000 0 -0.37 28 28
MKLP2/PLK1 0.18 0.091 0.23 721 -10000 0 721
CCNB1 0.071 0.095 0.26 191 -10000 0 191
PPP1CB 0.025 0.003 -10000 0 -10000 0 0
BTRC 0.024 0.003 -10000 0 -10000 0 0
ROCK2 0.032 0.077 0.23 1 -0.36 28 29
TUBG1 0.024 0.04 0.13 4 -0.16 34 38
G2/M transition of mitotic cell cycle 0.043 0.046 0.2 11 -10000 0 11
MLF1IP 0.025 0.049 0.14 146 -10000 0 146
INCENP 0.024 0.005 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.24 0.37 0.69 1 -0.79 199 200
HDAC7 0.025 0.004 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.19 0.34 0.65 2 -0.74 145 147
SMAD4 0.024 0.005 -10000 0 -10000 0 0
ID2 -0.24 0.37 -10000 0 -0.79 199 199
AP1 -0.1 0.21 -10000 0 -0.43 282 282
ABCG2 -0.26 0.39 -10000 0 -0.8 223 223
HIF1A -0.048 0.084 -10000 0 -0.24 15 15
TFF3 -0.25 0.41 0.69 6 -0.8 231 237
GATA2 0.008 0.1 0.26 11 -0.58 25 36
AKT1 -0.055 0.094 -10000 0 -0.25 35 35
response to hypoxia -0.062 0.084 0.18 1 -0.21 112 113
MCL1 -0.24 0.35 -10000 0 -0.78 192 192
NDRG1 -0.22 0.36 -10000 0 -0.79 174 174
SERPINE1 -0.24 0.38 0.69 4 -0.79 196 200
FECH -0.24 0.37 -10000 0 -0.78 202 202
FURIN -0.24 0.37 -10000 0 -0.79 194 194
NCOA2 0.006 0.1 -10000 0 -0.57 29 29
EP300 -0.06 0.13 0.3 2 -0.33 104 106
HMOX1 -0.24 0.37 -10000 0 -0.79 198 198
BHLHE40 -0.24 0.37 -10000 0 -0.79 197 197
BHLHE41 -0.24 0.38 -10000 0 -0.81 196 196
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.021 0.11 -10000 0 -0.31 1 1
ENG -0.016 0.11 0.4 2 -10000 0 2
JUN 0.017 0.056 -10000 0 -0.58 8 8
RORA -0.24 0.37 -10000 0 -0.79 199 199
ABCB1 -0.26 0.44 -10000 0 -1.1 194 194
TFRC -0.24 0.37 -10000 0 -0.79 197 197
CXCR4 -0.24 0.38 -10000 0 -0.79 199 199
TF -0.4 0.45 -10000 0 -0.86 386 386
CITED2 -0.24 0.37 -10000 0 -0.79 196 196
HIF1A/ARNT -0.27 0.42 0.78 2 -0.91 175 177
LDHA -0.041 0.12 -10000 0 -0.74 24 24
ETS1 -0.24 0.37 -10000 0 -0.79 200 200
PGK1 -0.24 0.37 -10000 0 -0.79 196 196
NOS2 -0.24 0.37 -10000 0 -0.79 195 195
ITGB2 -0.24 0.37 0.68 1 -0.79 199 200
ALDOA -0.24 0.37 -10000 0 -0.79 190 190
Cbp/p300/CITED2 -0.25 0.39 -10000 0 -0.87 172 172
FOS -0.15 0.27 -10000 0 -0.58 277 277
HK2 -0.24 0.37 -10000 0 -0.79 199 199
SP1 0.001 0.058 -10000 0 -0.2 5 5
GCK -0.12 0.34 0.53 1 -1.4 59 60
HK1 -0.24 0.37 -10000 0 -0.79 199 199
NPM1 -0.24 0.37 -10000 0 -0.79 199 199
EGLN1 -0.23 0.36 -10000 0 -0.78 193 193
CREB1 0.028 0.004 -10000 0 -10000 0 0
PGM1 -0.24 0.37 -10000 0 -0.79 199 199
SMAD3 0.024 0.004 -10000 0 -10000 0 0
EDN1 -0.18 0.37 -10000 0 -1 125 125
IGFBP1 -0.31 0.42 -10000 0 -0.86 266 266
VEGFA -0.16 0.29 0.55 1 -0.67 121 122
HIF1A/JAB1 -0.007 0.068 -10000 0 -0.28 1 1
CP -0.3 0.45 0.67 2 -0.89 272 274
CXCL12 -0.26 0.4 -10000 0 -0.83 216 216
COPS5 0.024 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4 0.035 0.012 -10000 0 -0.18 1 1
BNIP3 -0.24 0.37 0.76 1 -0.79 201 202
EGLN3 -0.23 0.38 0.76 1 -0.79 195 196
CA9 -0.2 0.4 0.67 8 -0.78 192 200
TERT -0.23 0.37 0.7 5 -0.78 193 198
ENO1 -0.24 0.37 -10000 0 -0.79 199 199
PFKL -0.24 0.37 -10000 0 -0.79 199 199
NCOA1 0.024 0.02 -10000 0 -0.58 1 1
ADM -0.26 0.4 0.69 1 -0.83 219 220
ARNT -0.035 0.07 -10000 0 -0.18 2 2
HNF4A 0.018 0.039 0.26 12 -0.18 1 13
ADFP -0.26 0.36 0.56 1 -0.78 206 207
SLC2A1 -0.16 0.3 0.66 2 -0.65 136 138
LEP -0.48 0.41 -10000 0 -0.84 427 427
HIF1A/ARNT/Cbp/p300 -0.21 0.34 0.65 1 -0.77 148 149
EPO -0.098 0.26 0.7 3 -0.77 35 38
CREBBP -0.05 0.12 0.29 3 -0.33 75 78
HIF1A/ARNT/Cbp/p300/HDAC7 -0.19 0.33 0.71 1 -0.75 138 139
PFKFB3 -0.24 0.37 -10000 0 -0.8 193 193
NT5E -0.24 0.38 -10000 0 -0.8 203 203
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.1 0.13 0.32 256 -10000 0 256
NFATC2 -0.023 0.23 0.52 7 -0.61 78 85
NFATC3 -0.046 0.13 -10000 0 -0.28 171 171
CD40LG -0.3 0.51 0.77 6 -0.99 291 297
ITCH -0.005 0.087 -10000 0 -0.26 97 97
CBLB -0.005 0.087 -10000 0 -0.26 95 95
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.089 0.38 0.64 48 -0.95 82 130
JUNB 0.024 0.008 0.26 1 -10000 0 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.1 -10000 0 -0.31 104 104
T cell anergy -0.03 0.14 -10000 0 -0.42 102 102
TLE4 -0.025 0.19 -10000 0 -0.66 48 48
Jun/NFAT1-c-4/p21SNFT -0.19 0.45 0.71 6 -0.88 241 247
AP-1/NFAT1-c-4 -0.33 0.63 0.78 15 -1.2 290 305
IKZF1 -0.015 0.16 0.5 7 -0.5 51 58
T-helper 2 cell differentiation -0.082 0.27 0.48 2 -0.83 70 72
AP-1/NFAT1 -0.099 0.27 0.47 13 -0.48 255 268
CALM1 0.008 0.066 -10000 0 -0.18 100 100
EGR2 -0.28 0.59 0.69 3 -1.5 157 160
EGR3 -0.36 0.65 0.64 4 -1.3 281 285
NFAT1/FOXP3 0.054 0.23 0.48 98 -0.47 66 164
EGR1 -0.17 0.28 -10000 0 -0.58 307 307
JUN 0.014 0.063 0.21 2 -0.58 8 10
EGR4 0.04 0.061 0.26 66 -10000 0 66
mol:Ca2+ -0.013 0.057 -10000 0 -0.18 100 100
GBP3 -0.02 0.17 0.38 2 -0.54 58 60
FOSL1 0.028 0.045 0.26 22 -0.58 2 24
NFAT1-c-4/MAF/IRF4 -0.21 0.47 0.62 7 -0.89 266 273
DGKA -0.016 0.16 0.58 1 -0.49 52 53
CREM 0.023 0.008 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.28 0.5 0.65 3 -0.97 285 288
CTLA4 0.041 0.21 0.44 113 -0.5 44 157
NFAT1-c-4 (dimer)/EGR1 -0.3 0.54 0.66 3 -1 300 303
NFAT1-c-4 (dimer)/EGR4 -0.2 0.47 0.62 6 -0.88 267 273
FOS -0.15 0.27 0.21 2 -0.58 282 284
IFNG -0.053 0.27 0.46 26 -0.69 94 120
T cell activation -0.16 0.3 0.72 3 -0.7 139 142
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 0.17 0.35 0.66 284 -0.62 3 287
TNF -0.27 0.46 0.56 4 -0.91 295 299
FASLG -0.34 0.65 0.75 4 -1.2 298 302
TBX21 0.02 0.13 0.36 14 -0.58 35 49
BATF3 0.021 0.014 0.26 2 -10000 0 2
PRKCQ 0.007 0.12 0.29 11 -0.58 35 46
PTPN1 -0.015 0.16 0.41 4 -0.49 50 54
NFAT1-c-4/ICER1 -0.21 0.45 0.58 3 -0.87 270 273
GATA3 0.011 0.11 0.26 27 -0.58 31 58
T-helper 1 cell differentiation -0.051 0.27 0.46 26 -0.67 94 120
IL2RA -0.091 0.37 0.62 45 -0.78 116 161
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.016 0.15 0.36 1 -0.48 58 59
E2F1 0.099 0.11 0.27 295 -10000 0 295
PPARG -0.11 0.25 -10000 0 -0.58 215 215
SLC3A2 -0.017 0.16 0.36 1 -0.49 52 53
IRF4 -0.021 0.16 0.26 10 -0.58 76 86
PTGS2 -0.35 0.55 0.64 6 -1 319 325
CSF2 -0.3 0.5 0.67 10 -0.98 285 295
JunB/Fra1/NFAT1-c-4 -0.19 0.45 0.6 4 -0.84 265 269
IL4 -0.086 0.28 0.5 1 -0.89 67 68
IL5 -0.3 0.5 0.63 7 -0.98 285 292
IL2 -0.16 0.31 0.73 3 -0.72 133 136
IL3 -0.052 0.13 -10000 0 -0.82 17 17
RNF128 -0.049 0.21 0.28 4 -0.66 104 108
NFATC1 -0.17 0.35 0.62 3 -0.66 284 287
CDK4 0.13 0.25 0.63 76 -0.62 2 78
PTPRK -0.018 0.17 0.43 3 -0.54 54 57
IL8 -0.29 0.5 0.61 11 -0.98 286 297
POU2F1 0.021 0.012 0.26 1 -10000 0 1
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.091 0.1 0.48 3 -10000 0 3
SMARCC2 0.024 0.013 -10000 0 -0.18 2 2
SMARCC1 0.024 0.013 -10000 0 -0.15 2 2
TBX21 -0.12 0.21 0.36 10 -0.57 100 110
SUMO2 0.001 0.023 -10000 0 -10000 0 0
STAT1 (dimer) 0.033 0.034 0.27 18 -10000 0 18
FKBP4 0.024 0.016 0.26 4 -10000 0 4
FKBP5 0.016 0.073 0.26 4 -0.58 14 18
GR alpha/HSP90/FKBP51/HSP90 0.11 0.13 0.32 102 -0.36 7 109
PRL -0.061 0.12 0.53 3 -0.49 1 4
cortisol/GR alpha (dimer)/TIF2 0.18 0.27 0.51 319 -0.48 13 332
RELA -0.038 0.1 0.29 1 -0.26 29 30
FGG 0.21 0.24 0.46 366 -0.45 3 369
GR beta/TIF2 0.085 0.16 0.3 174 -0.4 28 202
IFNG -0.3 0.36 0.42 13 -0.66 417 430
apoptosis -0.26 0.31 0.85 1 -0.62 307 308
CREB1 0.062 0.055 -10000 0 -10000 0 0
histone acetylation 0.028 0.13 0.37 54 -0.37 22 76
BGLAP -0.081 0.14 -10000 0 -0.49 20 20
GR/PKAc 0.13 0.13 0.34 106 -0.36 2 108
NF kappa B1 p50/RelA -0.063 0.18 0.46 3 -0.35 140 143
SMARCD1 0.024 0.012 -10000 0 -10000 0 0
MDM2 0.098 0.11 0.22 332 -10000 0 332
GATA3 0.014 0.12 0.26 27 -0.57 31 58
AKT1 0.02 0.009 -10000 0 -10000 0 0
CSF2 -0.023 0.1 0.48 1 -0.57 3 4
GSK3B 0 0.024 -10000 0 -10000 0 0
NR1I3 -0.2 0.26 0.8 1 -0.58 177 178
CSN2 0.16 0.19 0.39 263 -0.45 2 265
BRG1/BAF155/BAF170/BAF60A 0.06 0.042 -10000 0 -0.48 5 5
NFATC1 0.022 0.028 -10000 0 -0.58 2 2
POU2F1 0.023 0.016 0.26 1 -10000 0 1
CDKN1A 0.015 0.088 -10000 0 -1.4 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.007 0.007 -10000 0 -10000 0 0
SFN 0.021 0.069 0.26 17 -0.58 10 27
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.33 79 -0.39 4 83
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.36 0.4 0.62 2 -0.82 360 362
JUN -0.26 0.29 0.43 7 -0.54 400 407
IL4 -0.12 0.15 -10000 0 -0.5 29 29
CDK5R1 0.022 0.039 0.26 23 -10000 0 23
PRKACA 0.024 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.25 0.24 -10000 0 -0.48 456 456
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.13 0.33 74 -0.36 5 79
cortisol/GR alpha (monomer) 0.28 0.32 0.59 418 -0.52 3 421
NCOA2 0.002 0.1 -10000 0 -0.58 29 29
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.28 -10000 0 -0.6 286 286
AP-1/NFAT1-c-4 -0.43 0.45 0.49 7 -0.81 507 514
AFP -0.54 0.65 0.49 2 -1.4 326 328
SUV420H1 0.023 0.006 -10000 0 -10000 0 0
IRF1 0.16 0.16 0.42 122 -10000 0 122
TP53 0.031 0.029 -10000 0 -0.52 2 2
PPP5C 0.024 0.003 -10000 0 -10000 0 0
KRT17 -0.65 0.69 0.44 2 -1.4 446 448
KRT14 -0.71 0.67 -10000 0 -1.3 516 516
TBP 0.027 0.01 -10000 0 -10000 0 0
CREBBP 0.15 0.14 0.29 446 -10000 0 446
HDAC1 0.022 0.01 -10000 0 -10000 0 0
HDAC2 0.021 0.011 -10000 0 -10000 0 0
AP-1 -0.43 0.46 0.49 7 -0.82 507 514
MAPK14 0.003 0.022 -10000 0 -10000 0 0
MAPK10 -0.084 0.21 -10000 0 -0.58 141 141
MAPK11 -0.002 0.04 -10000 0 -0.59 3 3
KRT5 -0.74 0.71 0.45 2 -1.4 511 513
interleukin-1 receptor activity -0.001 0.005 -10000 0 -10000 0 0
NCOA1 0.025 0.02 -10000 0 -0.57 1 1
STAT1 0.033 0.034 0.27 18 -10000 0 18
CGA -0.052 0.17 0.4 1 -0.47 27 28
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.18 0.36 349 -10000 0 349
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 0.58 2 -0.58 175 177
NFKB1 -0.038 0.1 0.29 1 -0.26 29 30
MAPK8 -0.19 0.22 0.36 7 -0.41 404 411
MAPK9 0.003 0.022 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.28 0.32 0.86 1 -0.66 310 311
BAX 0.017 0.065 -10000 0 -10000 0 0
POMC -0.16 0.29 -10000 0 -0.9 67 67
EP300 0.15 0.14 0.29 440 -10000 0 440
cortisol/GR alpha (dimer)/p53 0.22 0.26 0.52 337 -0.48 2 339
proteasomal ubiquitin-dependent protein catabolic process 0.078 0.11 0.24 189 -10000 0 189
SGK1 0.19 0.2 0.51 15 -1.1 5 20
IL13 -0.25 0.28 0.51 5 -0.64 193 198
IL6 -0.44 0.53 0.63 1 -1.1 366 367
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.21 0.23 0.57 1 -0.72 35 36
IL2 -0.33 0.36 0.47 3 -0.7 387 390
CDK5 0.017 0.019 0.26 3 -10000 0 3
PRKACB 0.033 0.061 0.26 45 -0.58 3 48
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
IL8 -0.19 0.29 0.51 3 -0.6 217 220
CDK5R1/CDK5 0.018 0.038 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.018 0.15 0.4 3 -0.36 39 42
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.26 0.5 385 -0.45 2 387
SMARCA4 0.024 0.011 -10000 0 -10000 0 0
chromatin remodeling 0.15 0.16 0.34 292 -10000 0 292
NF kappa B1 p50/RelA/Cbp 0.065 0.19 0.4 74 -0.41 16 90
JUN (dimer) -0.25 0.29 0.43 7 -0.54 400 407
YWHAH 0.023 0.006 -10000 0 -10000 0 0
VIPR1 -0.13 0.21 -10000 0 -0.49 149 149
NR3C1 0.17 0.2 0.39 337 -0.45 3 340
NR4A1 -0.026 0.18 -10000 0 -0.56 93 93
TIF2/SUV420H1 0.014 0.079 -10000 0 -0.43 29 29
MAPKKK cascade -0.26 0.31 0.85 1 -0.62 307 308
cortisol/GR alpha (dimer)/Src-1 0.25 0.27 0.52 410 -0.45 3 413
PBX1 0.023 0.016 0.26 1 -10000 0 1
POU1F1 0.022 0.016 0.26 2 -10000 0 2
SELE -0.19 0.31 0.51 3 -0.66 210 213
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.15 0.16 0.34 289 -10000 0 289
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.26 0.5 385 -0.45 2 387
mol:cortisol 0.16 0.19 0.34 427 -0.24 4 431
MMP1 0.043 0.31 0.37 19 -0.9 76 95
Endothelins

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 -0.074 0.13 -10000 0 -0.42 93 93
PTK2B 0.02 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.054 0.19 -10000 0 -0.82 40 40
EDN1 -0.075 0.17 -10000 0 -0.54 88 88
EDN3 -0.23 0.29 0.26 2 -0.58 400 402
EDN2 0.079 0.11 0.26 236 -0.58 4 240
HRAS/GDP -0.095 0.19 0.28 1 -0.49 126 127
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.062 0.14 -10000 0 -0.41 94 94
ADCY4 -0.13 0.2 0.29 3 -0.43 252 255
ADCY5 -0.21 0.24 -10000 0 -0.45 432 432
ADCY6 -0.12 0.18 0.29 3 -0.4 249 252
ADCY7 -0.12 0.18 0.29 3 -0.4 244 247
ADCY1 -0.12 0.2 0.25 4 -0.4 263 267
ADCY2 -0.14 0.22 0.28 9 -0.44 267 276
ADCY3 -0.12 0.18 0.28 2 -0.4 243 245
ADCY8 -0.1 0.17 0.28 3 -0.4 202 205
ADCY9 -0.12 0.18 0.26 2 -0.4 237 239
arachidonic acid secretion -0.16 0.27 0.32 1 -0.51 312 313
ETB receptor/Endothelin-1/Gq/GTP -0.049 0.15 -10000 0 -0.36 133 133
GNAO1 0.018 0.095 0.26 32 -0.58 19 51
HRAS 0.024 0.018 0.26 5 -10000 0 5
ETA receptor/Endothelin-1/G12/GTP -0.06 0.13 0.3 7 -0.39 93 100
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.2 0.28 7 -0.42 253 260
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.064 0.16 0.31 38 -0.43 90 128
EDNRB -0.022 0.16 -10000 0 -0.57 79 79
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.077 0.16 -10000 0 -0.48 94 94
CYSLTR1 -0.082 0.16 -10000 0 -0.48 92 92
SLC9A1 -0.047 0.098 -10000 0 -0.28 101 101
mol:GDP -0.1 0.21 0.33 2 -0.5 144 146
SLC9A3 -0.11 0.28 -10000 0 -0.66 159 159
RAF1 -0.14 0.24 0.32 1 -0.48 242 243
JUN -0.053 0.19 -10000 0 -0.8 40 40
JAK2 -0.072 0.13 -10000 0 -0.42 93 93
mol:IP3 -0.074 0.17 -10000 0 -0.45 108 108
ETA receptor/Endothelin-1 -0.085 0.16 0.34 8 -0.48 95 103
PLCB1 -0.015 0.14 -10000 0 -0.58 58 58
PLCB2 0.013 0.027 0.26 1 -0.58 1 2
ETA receptor/Endothelin-3 -0.19 0.22 -10000 0 -0.44 408 408
FOS -0.29 0.44 -10000 0 -0.94 304 304
Gai/GDP -0.1 0.3 -10000 0 -0.75 150 150
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.2 0.28 1 -0.54 126 127
BCAR1 0.021 0.008 -10000 0 -10000 0 0
PRKCB1 -0.078 0.16 -10000 0 -0.44 117 117
GNAQ 0.013 0.033 -10000 0 -0.58 2 2
GNAZ 0.018 0.055 -10000 0 -0.58 8 8
GNAL -0.11 0.25 -10000 0 -0.58 209 209
Gs family/GDP -0.15 0.24 0.26 1 -0.5 238 239
ETA receptor/Endothelin-1/Gq/GTP -0.049 0.12 -10000 0 -0.38 70 70
MAPK14 -0.065 0.16 -10000 0 -0.42 113 113
TRPC6 -0.058 0.21 -10000 0 -0.9 39 39
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 -0.58 47 47
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.065 0.17 -10000 0 -0.43 124 124
ETB receptor/Endothelin-2 0.031 0.15 0.25 16 -0.41 81 97
ETB receptor/Endothelin-3 -0.19 0.25 -10000 0 -0.45 449 449
ETB receptor/Endothelin-1 -0.075 0.18 0.25 7 -0.47 144 151
MAPK3 -0.25 0.38 -10000 0 -0.79 310 310
MAPK1 -0.26 0.4 -10000 0 -0.81 312 312
Rac1/GDP -0.095 0.19 0.28 1 -0.48 130 131
cAMP biosynthetic process -0.16 0.22 0.39 2 -0.45 274 276
MAPK8 -0.06 0.21 -10000 0 -0.72 60 60
SRC 0.023 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.066 0.17 -10000 0 -0.37 173 173
p130Cas/CRK/Src/PYK2 -0.099 0.22 0.49 1 -0.58 111 112
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.094 0.19 0.28 1 -0.48 130 131
COL1A2 -0.086 0.19 0.39 9 -0.48 134 143
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.025 0.097 0.26 13 -0.35 9 22
mol:DAG -0.075 0.17 -10000 0 -0.45 108 108
MAP2K2 -0.19 0.3 0.34 2 -0.59 312 314
MAP2K1 -0.19 0.29 0.32 2 -0.58 314 316
EDNRA -0.035 0.065 -10000 0 -0.28 20 20
positive regulation of muscle contraction -0.064 0.12 -10000 0 -0.38 84 84
Gq family/GDP -0.059 0.19 -10000 0 -0.52 81 81
HRAS/GTP -0.1 0.2 0.34 1 -0.48 148 149
PRKCH -0.076 0.16 -10000 0 -0.47 94 94
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA -0.072 0.18 0.31 2 -0.49 103 105
PRKCB -0.074 0.18 -10000 0 -0.46 115 115
PRKCE -0.08 0.16 -10000 0 -0.46 106 106
PRKCD -0.076 0.16 -10000 0 -0.45 105 105
PRKCG -0.078 0.17 0.27 1 -0.45 111 112
regulation of vascular smooth muscle contraction -0.34 0.52 -10000 0 -1.1 301 301
PRKCQ -0.084 0.18 -10000 0 -0.48 124 124
PLA2G4A -0.18 0.31 0.33 1 -0.56 312 313
GNA14 0.014 0.073 0.26 21 -0.58 10 31
GNA15 0.022 0.028 0.26 6 -0.58 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.029 -10000 0 -0.58 2 2
Rac1/GTP -0.06 0.13 0.3 7 -0.38 93 100
MMP1 0.18 0.13 0.27 603 -10000 0 603
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.003 0.12 -10000 0 -0.36 88 88
cell-cell adhesion 0.14 0.15 0.32 324 -10000 0 324
Ephrin B/EPHB2/RasGAP 0.031 0.11 -10000 0 -0.32 72 72
ITSN1 0.023 0.027 -10000 0 -0.58 2 2
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 0.012 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.14 0.2 -10000 0 -0.37 404 404
HRAS/GDP -0.13 0.19 -10000 0 -0.43 157 157
Ephrin B/EPHB1/GRB7 -0.12 0.21 -10000 0 -0.36 383 383
Endophilin/SYNJ1 -0.027 0.084 0.23 2 -0.3 71 73
KRAS 0.023 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.12 0.22 -10000 0 -0.36 400 400
endothelial cell migration 0.042 0.032 -10000 0 -0.32 4 4
GRB2 0.023 0.01 0.26 1 -10000 0 1
GRB7 0.02 0.021 -10000 0 -0.58 1 1
PAK1 -0.032 0.1 0.29 4 -0.33 79 83
HRAS 0.025 0.018 0.26 5 -10000 0 5
RRAS -0.027 0.085 0.23 2 -0.31 71 73
DNM1 0.02 0.052 0.26 1 -0.58 7 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.15 0.18 0.35 2 -0.34 419 421
lamellipodium assembly -0.14 0.15 -10000 0 -0.32 324 324
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.1 0.17 -10000 0 -0.32 307 307
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
EPHB2 0.028 0.033 0.26 18 -10000 0 18
EPHB3 0.025 0.019 0.26 6 -10000 0 6
EPHB1 -0.23 0.3 0.26 1 -0.58 406 407
EPHB4 0.024 0.004 -10000 0 -10000 0 0
mol:GDP -0.13 0.17 -10000 0 -0.43 151 151
Ephrin B/EPHB2 0.021 0.1 -10000 0 -0.32 72 72
Ephrin B/EPHB3 0.019 0.098 -10000 0 -0.32 68 68
JNK cascade -0.14 0.16 0.36 7 -0.32 403 410
Ephrin B/EPHB1 -0.13 0.21 -10000 0 -0.36 419 419
RAP1/GDP -0.1 0.16 -10000 0 -0.39 141 141
EFNB2 0.022 0.007 -10000 0 -10000 0 0
EFNB3 -0.024 0.16 -10000 0 -0.58 74 74
EFNB1 0.024 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.11 0.19 -10000 0 -0.33 404 404
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.12 0.2 -10000 0 -0.42 150 150
Rap1/GTP -0.12 0.17 -10000 0 -0.33 318 318
axon guidance -0.004 0.12 -10000 0 -0.36 88 88
MAPK3 -0.095 0.14 -10000 0 -0.39 106 106
MAPK1 -0.099 0.15 -10000 0 -0.39 106 106
Rac1/GDP -0.12 0.16 -10000 0 -0.4 147 147
actin cytoskeleton reorganization -0.12 0.13 -10000 0 -0.36 107 107
CDC42/GDP -0.12 0.16 -10000 0 -0.4 146 146
PI3K 0.047 0.033 -10000 0 -0.32 4 4
EFNA5 -0.031 0.17 0.26 1 -0.58 88 89
Ephrin B2/EPHB4 0.03 0.01 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.005 0.089 -10000 0 -0.28 73 73
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.12 0.17 -10000 0 -0.32 323 323
PTK2 0.15 0.27 0.68 192 -10000 0 192
MAP4K4 -0.14 0.16 0.36 7 -0.32 403 410
SRC 0.023 0.005 -10000 0 -10000 0 0
KALRN 0.013 0.081 -10000 0 -0.58 18 18
Intersectin/N-WASP 0.034 0.022 -10000 0 -0.43 2 2
neuron projection morphogenesis -0.12 0.14 0.29 7 -0.43 73 80
MAP2K1 -0.096 0.16 -10000 0 -0.41 111 111
WASL 0.024 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.1 0.2 -10000 0 -0.34 403 403
cell migration -0.11 0.18 0.31 5 -0.44 129 134
NRAS 0.024 0.004 -10000 0 -10000 0 0
SYNJ1 -0.027 0.085 0.23 2 -0.31 71 73
PXN 0.024 0.002 -10000 0 -10000 0 0
TF -0.18 0.17 0.22 2 -0.33 537 539
HRAS/GTP -0.11 0.19 -10000 0 -0.32 398 398
Ephrin B1/EPHB1-2 -0.11 0.19 -10000 0 -0.34 404 404
cell adhesion mediated by integrin 0.009 0.088 0.29 69 -0.21 18 87
RAC1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.12 0.2 -10000 0 -0.34 415 415
RAC1-CDC42/GTP -0.14 0.15 -10000 0 -0.32 328 328
RASA1 0.024 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.11 0.16 -10000 0 -0.4 130 130
ruffle organization -0.14 0.17 0.36 5 -0.5 65 70
NCK1 0.024 0.003 -10000 0 -10000 0 0
receptor internalization -0.03 0.089 0.22 2 -0.31 72 74
Ephrin B/EPHB2/KALRN 0.025 0.12 -10000 0 -0.35 83 83
ROCK1 0.017 0.032 0.21 5 -0.34 1 6
RAS family/GDP -0.11 0.12 -10000 0 -0.38 85 85
Rac1/GTP -0.13 0.18 -10000 0 -0.34 324 324
Ephrin B/EPHB1/Src/Paxillin -0.13 0.18 -10000 0 -0.33 406 406
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.14 0.37 -10000 0 -0.87 198 198
NCK1/PAK1/Dok-R -0.088 0.16 -10000 0 -0.41 198 198
NCK1/Dok-R -0.17 0.45 -10000 0 -1 197 197
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.04 0.095 0.24 175 -10000 0 175
RELA 0.024 0.004 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
F2 0.041 0.11 0.27 170 -10000 0 170
TNIP2 0.023 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.15 0.43 -10000 0 -0.98 197 197
FN1 0.12 0.12 0.26 388 -10000 0 388
PLD2 -0.19 0.46 -10000 0 -1.1 197 197
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB14 0.015 0.18 0.26 135 -0.58 68 203
ELK1 -0.17 0.41 -10000 0 -0.96 198 198
GRB7 0.02 0.021 -10000 0 -0.58 1 1
PAK1 0.023 0.019 0.26 5 -10000 0 5
Tie2/Ang1/alpha5/beta1 Integrin -0.11 0.47 -10000 0 -1 198 198
CDKN1A -0.1 0.26 -10000 0 -0.6 165 165
ITGA5 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.17 0.45 -10000 0 -1 197 197
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:NO -0.1 0.28 -10000 0 -0.64 198 198
PLG -0.2 0.46 -10000 0 -1.1 198 198
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.14 0.35 -10000 0 -0.83 198 198
GRB2 0.023 0.01 0.26 1 -10000 0 1
PIK3R1 0.019 0.048 -10000 0 -0.58 6 6
ANGPT2 -0.14 0.27 -10000 0 -0.69 138 138
BMX -0.3 0.5 -10000 0 -1.2 199 199
ANGPT1 -0.21 0.48 -10000 0 -1.2 175 175
tube development -0.12 0.28 -10000 0 -0.66 188 188
ANGPT4 -0.16 0.27 -10000 0 -0.58 282 282
response to hypoxia -0.013 0.027 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.19 0.5 -10000 0 -1.1 197 197
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
FGF2 -0.2 0.29 -10000 0 -0.58 364 364
STAT5A (dimer) -0.13 0.33 -10000 0 -0.77 172 172
mol:L-citrulline -0.1 0.28 -10000 0 -0.64 198 198
AGTR1 -0.089 0.26 0.26 57 -0.58 206 263
MAPK14 -0.19 0.46 -10000 0 -1.1 200 200
Tie2/SHP2 -0.089 0.31 -10000 0 -1.1 75 75
TEK -0.098 0.34 -10000 0 -1.2 75 75
RPS6KB1 -0.13 0.36 -10000 0 -0.82 198 198
Angiotensin II/AT1 -0.065 0.19 0.18 57 -0.42 209 266
Tie2/Ang1/GRB2 -0.19 0.48 -10000 0 -1.1 197 197
MAPK3 -0.17 0.42 -10000 0 -0.98 197 197
MAPK1 -0.18 0.42 -10000 0 -0.99 197 197
Tie2/Ang1/GRB7 -0.19 0.47 -10000 0 -1.1 197 197
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.2 0.46 -10000 0 -1.1 198 198
PI3K -0.17 0.43 -10000 0 -0.99 198 198
FES -0.19 0.46 -10000 0 -1.1 200 200
Crk/Dok-R -0.17 0.45 -10000 0 -1 197 197
Tie2/Ang1/ABIN2 -0.19 0.48 -10000 0 -1.1 197 197
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.12 0.33 -10000 0 -0.77 198 198
STAT5A 0.02 0.047 -10000 0 -0.58 6 6
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.11 0.36 0.47 1 -0.8 197 198
Tie2/Ang2 -0.17 0.38 -10000 0 -0.9 184 184
Tie2/Ang1 -0.21 0.5 -10000 0 -1.2 198 198
FOXO1 -0.12 0.34 0.47 1 -0.78 198 199
ELF1 0.013 0.035 -10000 0 -10000 0 0
ELF2 -0.19 0.45 -10000 0 -1.1 197 197
mol:Choline -0.18 0.43 -10000 0 -1 197 197
cell migration -0.036 0.1 -10000 0 -0.23 198 198
FYN -0.14 0.32 -10000 0 -0.75 187 187
DOK2 0.02 0.026 0.26 4 -0.58 1 5
negative regulation of cell cycle -0.092 0.23 -10000 0 -0.55 167 167
ETS1 -0.019 0.11 -10000 0 -0.27 144 144
PXN -0.087 0.31 0.43 2 -0.67 197 199
ITGB1 0.024 0.004 -10000 0 -10000 0 0
NOS3 -0.12 0.32 -10000 0 -0.73 198 198
RAC1 0.024 0.004 -10000 0 -10000 0 0
TNF -0.022 0.13 0.27 18 -0.28 172 190
MAPKKK cascade -0.18 0.43 -10000 0 -1 197 197
RASA1 0.024 0.004 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.19 0.47 -10000 0 -1.1 197 197
NCK1 0.024 0.003 -10000 0 -10000 0 0
vasculogenesis -0.087 0.25 0.37 2 -0.57 198 200
mol:Phosphatidic acid -0.18 0.43 -10000 0 -1 197 197
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP -0.1 0.28 -10000 0 -0.64 198 198
Rac1/GTP -0.12 0.34 -10000 0 -0.78 198 198
MMP2 -0.2 0.46 -10000 0 -1.1 198 198
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 0.017 -10000 0 -0.43 1 1
Necdin/E2F1 0.063 0.11 -10000 0 -0.39 31 31
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.049 0.18 -10000 0 -0.33 263 263
NGF (dimer)/p75(NTR)/BEX1 -0.11 0.24 0.34 1 -0.41 342 343
NT-4/5 (dimer)/p75(NTR) -0.23 0.29 -10000 0 -0.51 475 475
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 -0.084 0.16 0.36 1 -0.33 252 253
IKBKG 0.024 0.002 -10000 0 -10000 0 0
BDNF -0.019 0.17 0.26 19 -0.58 76 95
MGDIs/NGR/p75(NTR)/LINGO1 -0.04 0.2 0.34 6 -0.35 262 268
FURIN 0.024 0.009 0.26 1 -10000 0 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.095 0.21 -10000 0 -0.4 294 294
LINGO1 0.078 0.1 0.26 219 -10000 0 219
Sortilin/TRAF6/NRIF 0.023 0.025 -10000 0 -0.56 1 1
proBDNF (dimer) -0.019 0.17 0.26 19 -0.58 76 95
NTRK1 0.025 0.047 0.26 23 -0.58 2 25
RTN4R 0.032 0.046 0.26 36 -10000 0 36
neuron apoptosis -0.082 0.2 0.35 8 -0.4 183 191
IRAK1 0.025 0.013 0.26 3 -10000 0 3
SHC1 -0.083 0.16 -10000 0 -0.38 203 203
ARHGDIA 0.023 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.017 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.054 0.034 -10000 0 -0.32 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.056 0.18 -10000 0 -0.35 259 259
MAGEH1 0.024 0.002 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.068 0.19 -10000 0 -0.36 269 269
Mammalian IAPs/DIABLO 0.056 0.033 -10000 0 -0.34 2 2
proNGF (dimer) 0.016 0.077 0.26 7 -0.58 15 22
MAGED1 0.025 0.011 0.26 2 -10000 0 2
APP 0.024 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.19 0.29 -10000 0 -0.58 343 343
ZNF274 0.024 0.004 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.067 0.16 -10000 0 -0.32 251 251
NGF 0.016 0.077 0.26 7 -0.58 15 22
cell cycle arrest -0.074 0.15 0.24 43 -0.3 259 302
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.054 0.12 -10000 0 -0.28 188 188
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.19 0.27 -10000 0 -0.45 448 448
NCSTN 0.02 0.009 -10000 0 -10000 0 0
mol:GTP -0.07 0.19 -10000 0 -0.37 263 263
PSENEN 0.024 0.008 0.26 1 -10000 0 1
mol:ceramide -0.093 0.16 -10000 0 -0.34 260 260
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.045 0.11 -10000 0 -0.36 31 31
p75(NTR)/beta APP -0.094 0.2 -10000 0 -0.42 272 272
BEX1 -0.02 0.24 0.26 152 -0.58 131 283
mol:GDP -0.11 0.16 -10000 0 -0.37 265 265
NGF (dimer) 0 0.14 0.34 1 -0.34 120 121
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.025 0.19 0.34 5 -0.32 245 250
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
RAC1/GTP -0.062 0.16 -10000 0 -0.32 263 263
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 -0.07 0.19 -10000 0 -0.37 263 263
RHOB 0.024 0.003 -10000 0 -10000 0 0
RHOA 0.023 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.079 0.075 -10000 0 -10000 0 0
NT3 (dimer) -0.063 0.22 0.26 12 -0.58 143 155
TP53 -0.093 0.17 0.37 6 -0.34 286 292
PRDM4 -0.093 0.16 -10000 0 -0.34 259 259
BDNF (dimer) 0.02 0.2 0.34 18 -0.36 177 195
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
SORT1 0.023 0.02 -10000 0 -0.58 1 1
activation of caspase activity -0.052 0.17 -10000 0 -0.32 263 263
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.056 0.18 -10000 0 -0.35 257 257
RHOC 0.024 0.004 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
MAPK10 -0.13 0.2 0.29 5 -0.42 276 281
DIABLO 0.024 0.002 -10000 0 -10000 0 0
SMPD2 -0.094 0.16 -10000 0 -0.34 260 260
APH1B 0.023 0.02 -10000 0 -0.58 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.073 0.19 -10000 0 -0.38 263 263
PSEN1 0.024 0.004 -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 -0.46 365 365
MAPK8 -0.099 0.18 0.29 10 -0.37 249 259
MAPK9 -0.098 0.18 0.28 8 -0.37 249 257
APAF1 0.024 0.003 -10000 0 -10000 0 0
NTF3 -0.063 0.22 0.26 12 -0.58 143 155
NTF4 -0.19 0.29 -10000 0 -0.58 343 343
NDN 0.004 0.11 -10000 0 -0.58 31 31
RAC1/GDP 0.018 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.044 0.16 -10000 0 -0.31 260 260
p75 CTF/Sortilin/TRAF6/NRIF 0.056 0.023 -10000 0 -0.34 1 1
RhoA-B-C/GTP -0.07 0.19 -10000 0 -0.37 263 263
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.066 0.2 -10000 0 -0.35 287 287
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.077 0.2 -10000 0 -0.37 289 289
PRKACB 0.033 0.061 0.26 45 -0.58 3 48
proBDNF (dimer)/p75 ECD 0.001 0.13 -10000 0 -0.42 76 76
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.023 0.042 0.26 10 -0.58 3 13
BIRC2 0.022 0.007 -10000 0 -10000 0 0
neuron projection morphogenesis -0.088 0.17 0.28 15 -0.35 253 268
BAD -0.12 0.19 0.38 8 -0.39 268 276
RIPK2 0.02 0.017 0.26 3 -10000 0 3
NGFR -0.14 0.27 -10000 0 -0.58 262 262
CYCS -0.088 0.15 0.36 2 -0.33 254 256
ADAM17 0.024 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.047 0.16 -10000 0 -0.35 187 187
BCL2L11 -0.12 0.19 0.38 8 -0.39 267 275
BDNF (dimer)/p75(NTR) -0.12 0.24 -10000 0 -0.45 309 309
PI3K -0.059 0.18 -10000 0 -0.35 255 255
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.057 0.18 -10000 0 -0.35 259 259
NDNL2 0.023 0.005 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKCI 0.023 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.098 0.21 -10000 0 -0.42 281 281
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.057 0.18 -10000 0 -0.35 261 261
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.023 0.02 -10000 0 -0.58 1 1
PLG 0.018 0.016 0.26 4 -10000 0 4
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.11 0.19 -10000 0 -0.38 298 298
SQSTM1 0.024 0.009 0.26 1 -10000 0 1
NGFRAP1 0.023 0.027 -10000 0 -0.58 2 2
CASP3 -0.11 0.18 0.38 7 -0.36 275 282
E2F1 0.096 0.11 0.26 295 -10000 0 295
CASP9 0.023 0.006 -10000 0 -10000 0 0
IKK complex -0.004 0.11 -10000 0 -0.4 16 16
NGF (dimer)/TRKA 0.027 0.066 -10000 0 -0.4 17 17
MMP7 -0.039 0.2 0.26 30 -0.58 110 140
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.046 0.18 -10000 0 -0.33 254 254
MMP3 0.1 0.14 0.26 349 -0.58 11 360
APAF-1/Caspase 9 -0.088 0.12 -10000 0 -0.46 10 10
IL4-mediated signaling events

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
BCL2L1 -0.24 0.61 0.79 18 -1.2 182 200
STAT6 (cleaved dimer) -0.3 0.58 -10000 0 -1.2 231 231
IGHG1 -0.029 0.27 0.51 61 -0.6 10 71
IGHG3 -0.24 0.58 0.68 20 -1.1 228 248
AKT1 -0.086 0.35 0.57 28 -0.77 76 104
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.049 0.3 0.55 26 -0.81 41 67
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.088 0.36 0.59 30 -0.79 71 101
THY1 -0.24 0.61 0.8 19 -1.2 200 219
MYB 0.012 0.082 0.26 2 -0.58 18 20
HMGA1 0.033 0.046 0.26 38 -10000 0 38
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.11 0.42 0.66 52 -0.74 153 205
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.08 0.35 0.59 30 -0.81 56 86
SP1 0.034 0.027 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SOCS5 0.014 0.047 -10000 0 -0.55 1 1
STAT6 (dimer)/ETS1 -0.27 0.6 0.68 16 -1.2 223 239
SOCS1 -0.14 0.4 0.62 28 -0.74 177 205
SOCS3 -0.094 0.36 0.63 12 -0.84 63 75
FCER2 -0.39 0.75 0.81 28 -1.3 317 345
PARP14 0.017 0.032 0.25 3 -10000 0 3
CCL17 -0.22 0.63 0.88 37 -1.2 185 222
GRB2 0.023 0.01 0.26 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.042 0.29 0.53 39 -0.76 31 70
T cell proliferation -0.26 0.62 0.72 15 -1.2 209 224
IL4R/JAK1 -0.25 0.6 0.74 5 -1.2 206 211
EGR2 -0.37 0.76 0.85 18 -1.5 252 270
JAK2 0.011 0.077 0.24 4 -10000 0 4
JAK3 0.023 0.039 0.28 16 -10000 0 16
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
JAK1 0.017 0.042 -10000 0 -10000 0 0
COL1A2 -0.023 0.27 0.57 12 -1.1 15 27
CCL26 -0.24 0.61 0.81 20 -1.2 185 205
IL4R -0.25 0.67 0.87 36 -1.3 202 238
PTPN6 0.014 0.036 0.22 2 -10000 0 2
IL13RA2 -0.24 0.61 0.8 21 -1.2 185 206
IL13RA1 0.011 0.078 0.24 4 -10000 0 4
IRF4 -0.13 0.5 0.6 15 -1.4 107 122
ARG1 -0.006 0.22 0.59 7 -1.2 1 8
CBL -0.11 0.38 0.58 42 -0.72 145 187
GTF3A 0.055 0.051 0.27 1 -10000 0 1
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL13RA1/JAK2 0.024 0.11 0.29 40 -10000 0 40
IRF4/BCL6 -0.12 0.45 0.57 1 -1.3 106 107
CD40LG -0.01 0.14 0.31 15 -0.59 44 59
MAPK14 -0.11 0.39 0.6 36 -0.74 128 164
mitosis -0.079 0.33 0.56 30 -0.71 77 107
STAT6 -0.28 0.76 0.96 47 -1.4 221 268
SPI1 0.027 0.02 0.26 6 -10000 0 6
RPS6KB1 -0.062 0.32 0.55 35 -0.7 66 101
STAT6 (dimer) -0.28 0.76 0.96 46 -1.4 221 267
STAT6 (dimer)/PARP14 -0.3 0.66 0.72 16 -1.2 239 255
mast cell activation 0 0.024 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.096 0.36 0.59 32 -0.79 82 114
FRAP1 -0.087 0.35 0.57 28 -0.76 77 105
LTA -0.22 0.63 0.88 33 -1.2 184 217
FES 0.022 0.034 -10000 0 -0.58 3 3
T-helper 1 cell differentiation 0.26 0.72 1.3 221 -0.96 46 267
CCL11 -0.18 0.6 0.75 36 -1.1 184 220
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.075 0.35 0.58 35 -0.77 68 103
IL2RG 0.025 0.075 0.27 42 -0.57 7 49
IL10 -0.21 0.61 0.81 31 -1.2 178 209
IRS1 0 0.12 -10000 0 -0.58 38 38
IRS2 0.004 0.1 -10000 0 -0.58 30 30
IL4 -0.011 0.27 0.63 24 -1.1 19 43
IL5 -0.24 0.61 0.84 9 -1.3 170 179
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.16 0.52 0.81 46 -0.9 191 237
COL1A1 -0.002 0.37 0.62 72 -0.97 51 123
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.26 0.61 0.74 2 -1.3 176 178
IL2R gamma/JAK3 0.037 0.073 0.37 19 -0.42 6 25
TFF3 -0.3 0.71 0.86 28 -1.3 232 260
ALOX15 -0.32 0.71 0.81 23 -1.3 255 278
MYBL1 0.039 0.066 0.26 77 -10000 0 77
T-helper 2 cell differentiation -0.2 0.53 0.69 40 -0.97 207 247
SHC1 0.02 0.009 -10000 0 -10000 0 0
CEBPB 0.024 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.083 0.35 0.56 35 -0.74 75 110
mol:PI-3-4-5-P3 -0.086 0.35 0.57 28 -0.76 76 104
PI3K -0.095 0.36 0.59 23 -0.83 75 98
DOK2 0.02 0.026 0.26 4 -0.58 1 5
ETS1 0.004 0.053 -10000 0 -0.54 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.032 0.27 0.51 43 -0.74 23 66
ITGB3 -0.26 0.63 0.79 19 -1.2 213 232
PIGR -0.68 0.79 0.82 26 -1.3 551 577
IGHE -0.015 0.088 0.18 29 -0.21 38 67
MAPKKK cascade -0.031 0.27 0.5 44 -0.72 23 67
BCL6 0.023 0.041 -10000 0 -0.57 4 4
OPRM1 -0.24 0.61 0.8 20 -1.2 188 208
RETNLB -0.24 0.61 0.78 19 -1.2 187 206
SELP -0.36 0.77 0.83 23 -1.5 266 289
AICDA -0.23 0.58 0.77 16 -1.1 195 211
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.022 0.007 -10000 0 -10000 0 0
EPHB2 0.027 0.033 0.26 18 -10000 0 18
EFNB1 -0.005 0.039 -10000 0 -0.43 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.092 0.18 -10000 0 -0.3 396 396
Ephrin B2/EPHB1-2 -0.11 0.19 -10000 0 -0.33 404 404
neuron projection morphogenesis -0.097 0.16 -10000 0 -0.29 397 397
Ephrin B1/EPHB1-2/Tiam1 -0.1 0.19 -10000 0 -0.32 401 401
DNM1 0.02 0.052 0.27 1 -0.58 7 8
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.024 0.12 -10000 0 -0.55 45 45
YES1 -0.026 0.17 -10000 0 -0.76 49 49
Ephrin B1/EPHB1-2/NCK2 -0.1 0.19 -10000 0 -0.32 403 403
PI3K 0.005 0.13 -10000 0 -0.53 50 50
mol:GDP -0.1 0.18 -10000 0 -0.32 401 401
ITGA2B 0.032 0.061 0.26 44 -0.58 3 47
endothelial cell proliferation 0.029 0.01 -10000 0 -10000 0 0
FYN -0.027 0.17 -10000 0 -0.76 49 49
MAP3K7 -0.025 0.13 -10000 0 -0.57 47 47
FGR -0.024 0.17 -10000 0 -0.76 48 48
TIAM1 0.025 0.016 0.26 4 -10000 0 4
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
RGS3 0.024 0.003 -10000 0 -10000 0 0
cell adhesion -0.009 0.13 -10000 0 -0.48 58 58
LYN -0.024 0.17 -10000 0 -0.75 48 48
Ephrin B1/EPHB1-2/Src Family Kinases -0.029 0.16 -10000 0 -0.71 49 49
Ephrin B1/EPHB1-2 -0.025 0.14 -10000 0 -0.63 45 45
SRC -0.023 0.17 -10000 0 -0.75 49 49
ITGB3 0.008 0.098 0.26 4 -0.58 26 30
EPHB1 -0.23 0.3 0.27 1 -0.58 406 407
EPHB4 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.029 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.028 0.087 -10000 0 -0.42 29 29
BLK -0.024 0.18 -10000 0 -0.78 47 47
HCK -0.023 0.17 -10000 0 -0.75 49 49
regulation of stress fiber formation 0.1 0.18 0.32 403 -10000 0 403
MAPK8 -0.026 0.12 -10000 0 -0.53 47 47
Ephrin B1/EPHB1-2/RGS3 -0.1 0.19 -10000 0 -0.32 400 400
endothelial cell migration -0.019 0.11 -10000 0 -0.51 41 41
NCK2 0.024 0.002 -10000 0 -10000 0 0
PTPN13 0.009 0.11 -10000 0 -0.69 24 24
regulation of focal adhesion formation 0.1 0.18 0.32 403 -10000 0 403
chemotaxis 0.1 0.18 0.32 401 -10000 0 401
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.094 0.17 -10000 0 -0.3 396 396
angiogenesis -0.026 0.14 -10000 0 -0.62 47 47
LCK -0.023 0.17 -10000 0 -0.76 48 48
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.024 0.004 -10000 0 -10000 0 0
VLDLR 0.008 0.093 -10000 0 -0.58 24 24
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
NUDC 0.023 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.19 0.2 -10000 0 -0.36 560 560
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
KATNA1 0.023 0.005 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.19 0.16 -10000 0 -0.33 557 557
IQGAP1/CaM 0.034 0.009 -10000 0 -10000 0 0
DAB1 0.036 0.057 0.26 57 -10000 0 57
IQGAP1 0.023 0.005 -10000 0 -10000 0 0
PLA2G7 0.024 0.069 0.26 24 -0.58 9 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 0.049 -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 0.037 0.26 23 -10000 0 23
LIS1/Poliovirus Protein 3A 0.007 0.003 -10000 0 -10000 0 0
CDK5R2 0.055 0.084 0.26 137 -10000 0 137
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.2 0.21 0.34 2 -0.37 559 561
YWHAE 0.022 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.14 0.15 0.35 3 -0.32 58 61
MAP1B 0 0.042 -10000 0 -0.32 16 16
RAC1 0.01 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.16 0.16 -10000 0 -0.3 509 509
RELN -0.33 0.3 0.26 3 -0.58 567 570
PAFAH/LIS1 0.023 0.048 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 -0.12 0.13 -10000 0 -0.3 7 7
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.15 0.17 -10000 0 -0.3 468 468
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.15 0.15 0.34 3 -0.3 394 397
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 0.048 0.072 0.26 99 -10000 0 99
PAFAH1B2 0.02 0.034 -10000 0 -0.58 3 3
MAP1B/LIS1/Dynein heavy chain 0.014 0.043 -10000 0 -0.35 2 2
NDEL1/Katanin 60/Dynein heavy chain -0.13 0.15 0.35 3 -0.32 58 61
LRP8 0.048 0.072 0.26 99 -10000 0 99
NDEL1/Katanin 60 -0.14 0.15 0.35 3 -0.33 64 67
P39/CDK5 -0.16 0.16 0.35 5 -0.3 415 420
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.023 0.009 -10000 0 -10000 0 0
CDK5 -0.18 0.15 0.2 1 -0.31 552 553
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.02 0.007 -10000 0 -10000 0 0
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.17 0.19 0.33 1 -0.32 555 556
RELN/VLDLR -0.17 0.2 -10000 0 -0.34 561 561
CDC42 0.01 0.004 -10000 0 -10000 0 0
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 -0.018 0.15 -10000 0 -0.58 65 65
GNB1/GNG2 -0.076 0.21 -10000 0 -0.47 147 147
mol:DAG -0.078 0.18 0.24 1 -0.44 137 138
PLCG1 -0.081 0.19 0.24 1 -0.46 137 138
YES1 -0.096 0.19 0.2 1 -0.38 254 255
FZD3 0.016 0.048 -10000 0 -0.58 6 6
FZD6 0.014 0.051 -10000 0 -0.58 7 7
G protein -0.064 0.2 0.3 2 -0.46 133 135
MAP3K7 -0.072 0.15 0.25 1 -0.41 103 104
mol:Ca2+ -0.076 0.18 0.24 1 -0.42 137 138
mol:IP3 -0.078 0.18 0.24 1 -0.44 137 138
NLK -0.011 0.13 -10000 0 -0.84 23 23
GNB1 0.023 0.005 -10000 0 -10000 0 0
CAMK2A -0.074 0.17 0.24 2 -0.42 118 120
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.098 0.21 0.22 1 -0.39 264 265
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
GNAS -0.091 0.19 0.2 1 -0.38 234 235
GO:0007205 -0.082 0.18 0.23 1 -0.43 137 138
WNT6 -0.08 0.24 0.26 39 -0.58 183 222
WNT4 0.017 0.088 0.26 19 -0.58 18 37
NFAT1/CK1 alpha -0.088 0.2 0.33 1 -0.46 150 151
GNG2 0.018 0.061 -10000 0 -0.58 10 10
WNT5A 0.019 0.068 0.26 9 -0.58 11 20
WNT11 -0.088 0.24 0.26 10 -0.58 182 192
CDC42 -0.083 0.19 -10000 0 -0.46 132 132
Wnt signaling

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
Noncanonical Wnts/FZD -0.098 0.21 0.22 1 -0.39 264 265
FZD6 0.014 0.051 -10000 0 -0.58 7 7
WNT6 -0.08 0.24 0.26 39 -0.58 183 222
WNT4 0.017 0.088 0.26 19 -0.58 18 37
FZD3 0.016 0.048 -10000 0 -0.58 6 6
WNT5A 0.019 0.068 0.26 9 -0.58 11 20
WNT11 -0.088 0.24 0.26 10 -0.58 182 192
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.024 0.002 -10000 0 -10000 0 0
PTK2 0.019 0.01 -10000 0 -10000 0 0
CRKL -0.067 0.16 -10000 0 -0.34 212 212
GRB2/SOS1/SHC 0.038 0.022 -10000 0 -10000 0 0
HRAS 0.025 0.018 0.26 5 -10000 0 5
IRS1/Crk -0.062 0.16 -10000 0 -0.34 216 216
IGF-1R heterotetramer/IGF1/PTP1B -0.043 0.17 -10000 0 -0.37 189 189
AKT1 -0.068 0.14 0.25 2 -0.32 179 181
BAD -0.065 0.13 0.24 2 -0.3 173 175
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.068 0.16 -10000 0 -0.34 216 216
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.058 0.17 -10000 0 -0.35 216 216
RAF1 -0.049 0.14 -10000 0 -0.49 43 43
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.032 0.16 -10000 0 -0.34 198 198
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.062 0.18 -10000 0 -0.36 229 229
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.063 0.13 0.25 2 -0.33 156 158
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.03 0.12 0.32 8 -0.41 38 46
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.039 0.13 -10000 0 -0.32 138 138
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.01 0.14 -10000 0 -0.31 137 137
IGF-1R heterotetramer -0.013 0.1 0.26 1 -0.63 21 22
IGF-1R heterotetramer/IGF1/IRS/Nck -0.045 0.17 -10000 0 -0.35 213 213
Crk/p130 Cas/Paxillin -0.037 0.16 -10000 0 -0.32 202 202
IGF1R -0.013 0.1 0.26 1 -0.63 21 22
IGF1 -0.11 0.25 -10000 0 -0.6 202 202
IRS2/Crk -0.067 0.17 -10000 0 -0.35 225 225
PI3K -0.034 0.17 -10000 0 -0.34 207 207
apoptosis 0.043 0.11 0.39 31 -0.26 6 37
HRAS/GDP 0.018 0.012 0.18 5 -10000 0 5
PRKCD -0.078 0.18 -10000 0 -0.4 203 203
RAF1/14-3-3 E -0.024 0.13 0.3 2 -0.42 42 44
BAD/14-3-3 -0.045 0.11 0.27 6 -0.41 31 37
PRKCZ -0.067 0.14 0.25 2 -0.32 177 179
Crk/p130 Cas/Paxillin/FAK1 -0.028 0.12 -10000 0 -0.42 34 34
PTPN1 0.024 0.02 0.26 6 -10000 0 6
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.081 0.19 -10000 0 -0.42 213 213
BCAR1 0.021 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.022 0.15 -10000 0 -0.33 152 152
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
IRS1/NCK2 -0.054 0.17 -10000 0 -0.34 213 213
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 -0.068 0.16 -10000 0 -0.35 216 216
IRS1 -0.071 0.17 -10000 0 -0.36 223 223
IRS2 -0.076 0.17 -10000 0 -0.37 225 225
IGF-1R heterotetramer/IGF1 -0.077 0.21 -10000 0 -0.46 218 218
GRB2 0.023 0.01 0.26 1 -10000 0 1
PDPK1 -0.07 0.14 0.28 1 -0.33 184 185
YWHAE 0.022 0.007 -10000 0 -10000 0 0
PRKD1 -0.089 0.2 -10000 0 -0.43 211 211
SHC1 0.02 0.009 -10000 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.027 0.5 0.83 41 -1.1 66 107
IL23A -0.037 0.5 0.85 35 -1.1 64 99
NF kappa B1 p50/RelA/I kappa B alpha -0.07 0.46 0.74 9 -1.1 78 87
positive regulation of T cell mediated cytotoxicity -0.029 0.56 0.87 71 -1 125 196
ITGA3 -0.023 0.49 0.83 37 -1.1 67 104
IL17F -0.011 0.37 0.61 66 -0.69 70 136
IL12B 0.083 0.15 0.37 177 -10000 0 177
STAT1 (dimer) -0.045 0.51 0.76 47 -0.98 129 176
CD4 -0.021 0.49 0.84 45 -1 70 115
IL23 -0.023 0.5 0.83 47 -1.1 63 110
IL23R 0.051 0.2 0.6 20 -0.96 12 32
IL1B -0.04 0.51 0.84 43 -1.2 71 114
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.013 0.5 0.86 62 -1 67 129
TYK2 0.026 0.06 0.22 5 -10000 0 5
STAT4 -0.001 0.12 0.26 1 -0.58 41 42
STAT3 0.024 0.005 -10000 0 -10000 0 0
IL18RAP 0.006 0.11 0.28 4 -0.57 35 39
IL12RB1 0.036 0.093 0.39 38 -0.61 1 39
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.04 0.09 0.32 40 -0.47 1 41
IL23R/JAK2 0.064 0.22 0.56 32 -0.91 11 43
positive regulation of chronic inflammatory response -0.029 0.56 0.87 71 -1 125 196
natural killer cell activation -0.004 0.016 -10000 0 -0.052 36 36
JAK2 0.039 0.085 0.26 40 -10000 0 40
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
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 -0.017 0.48 0.81 52 -1 63 115
ALOX12B -0.022 0.49 0.84 45 -1 69 114
CXCL1 -0.2 0.71 0.86 45 -1.2 260 305
T cell proliferation -0.029 0.56 0.87 71 -1 125 196
NFKBIA 0.026 0.01 -10000 0 -10000 0 0
IL17A 0.019 0.32 0.57 84 -0.55 54 138
PI3K -0.065 0.48 0.7 24 -1 100 124
IFNG 0.027 0.071 0.18 129 -0.11 13 142
STAT3 (dimer) -0.068 0.45 0.78 9 -1 76 85
IL18R1 0.017 0.075 -10000 0 -0.57 15 15
IL23/IL23R/JAK2/TYK2/SOCS3 0.034 0.35 0.67 77 -0.7 35 112
IL18/IL18R 0.04 0.11 0.3 10 -0.37 48 58
macrophage activation 0 0.03 0.059 94 -0.044 49 143
TNF -0.038 0.51 0.84 45 -1.1 75 120
STAT3/STAT4 -0.064 0.5 0.69 27 -1.1 93 120
STAT4 (dimer) -0.058 0.52 0.75 43 -1.1 116 159
IL18 0.03 0.04 0.27 25 -10000 0 25
IL19 0.017 0.5 0.84 65 -1 67 132
STAT5A (dimer) -0.048 0.51 0.75 43 -0.98 128 171
STAT1 0.028 0.032 0.26 18 -10000 0 18
SOCS3 0.02 0.043 -10000 0 -0.58 5 5
CXCL9 0.003 0.52 0.86 75 -1.1 71 146
MPO -0.051 0.55 0.83 46 -1.2 102 148
positive regulation of humoral immune response -0.029 0.56 0.87 71 -1 125 196
IL23/IL23R/JAK2/TYK2 -0.037 0.58 0.88 69 -1.1 110 179
IL6 -0.3 0.75 0.81 36 -1.2 358 394
STAT5A 0.02 0.047 -10000 0 -0.58 6 6
IL2 0.022 0.041 0.31 9 -10000 0 9
positive regulation of tyrosine phosphorylation of STAT protein -0.004 0.016 -10000 0 -0.052 36 36
CD3E -0.033 0.52 0.86 52 -1.2 78 130
keratinocyte proliferation -0.029 0.56 0.87 71 -1 125 196
NOS2 -0.022 0.5 0.81 51 -1.1 70 121
Arf6 signaling events

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
CENTA1/KIF3B 0.026 0.034 0.18 7 -0.46 3 10
ARNO/beta Arrestin1-2 -0.068 0.17 -10000 0 -0.56 42 42
EGFR -0.19 0.29 -10000 0 -0.58 349 349
EPHA2 0.02 0.043 -10000 0 -0.58 5 5
USP6 0.022 0.007 -10000 0 -10000 0 0
IQSEC1 0.024 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.22 0.26 -10000 0 -0.46 487 487
ARRB2 -0.044 0.13 -10000 0 -0.36 136 136
mol:GTP 0.011 0.051 0.13 45 -0.19 25 70
ARRB1 0.021 0.028 -10000 0 -0.58 2 2
FBXO8 0.023 0.005 -10000 0 -10000 0 0
TSHR 0 0.12 0.26 3 -0.58 38 41
EGF -0.093 0.24 0.26 2 -0.58 189 191
somatostatin receptor activity 0 0 0.001 1 -0.001 241 242
ARAP2 0.02 0.043 -10000 0 -0.58 5 5
mol:GDP -0.12 0.16 -10000 0 -0.33 258 258
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 132 132
ITGA2B 0.032 0.06 0.26 44 -0.58 3 47
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.044 0.039 -10000 0 -0.34 5 5
ADAP1 0.024 0.034 0.26 7 -0.58 2 9
KIF13B 0.019 0.029 -10000 0 -0.58 2 2
HGF/MET -0.066 0.2 -10000 0 -0.46 199 199
PXN 0.024 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.12 0.13 -10000 0 -0.29 259 259
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.18 0.24 -10000 0 -0.41 472 472
ADRB2 -0.11 0.25 -10000 0 -0.58 212 212
receptor agonist activity 0 0 0 1 0 220 221
actin filament binding 0 0 0 2 -0.001 254 256
SRC 0.023 0.005 -10000 0 -10000 0 0
ITGB3 0.008 0.098 0.26 4 -0.58 26 30
GNAQ 0.022 0.027 -10000 0 -0.58 2 2
EFA6/PI-4-5-P2 0 0 0.001 1 -0.001 139 140
ARF6/GDP -0.039 0.15 0.25 2 -0.44 85 87
ARF6/GDP/GULP/ACAP1 -0.11 0.19 -10000 0 -0.42 185 185
alphaIIb/beta3 Integrin/paxillin/GIT1 0.051 0.077 -10000 0 -0.34 29 29
ACAP1 0.027 0.067 0.26 37 -0.58 6 43
ACAP2 0.024 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.059 0.18 -10000 0 -0.49 136 136
EFNA1 0.02 0.009 -10000 0 -10000 0 0
HGF -0.013 0.14 -10000 0 -0.58 60 60
CYTH3 0.004 0.014 -10000 0 -0.43 1 1
CYTH2 0.006 0.099 -10000 0 -1 9 9
NCK1 0.024 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0 1 0 188 189
endosomal lumen acidification 0 0 0.001 5 0 240 245
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.014 0.15 -10000 0 -0.58 62 62
GNAQ/ARNO 0.018 0.095 -10000 0 -0.95 9 9
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 147 147
MET -0.072 0.22 -10000 0 -0.58 155 155
GNA14 0.023 0.07 0.26 21 -0.58 10 31
GNA15 0.024 0.027 0.26 6 -0.58 1 7
GIT1 0.023 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 1 -0.001 190 191
GNA11 0.022 0.028 -10000 0 -0.58 2 2
LHCGR -0.07 0.2 -10000 0 -0.58 136 136
AGTR1 -0.09 0.26 0.26 57 -0.58 206 263
desensitization of G-protein coupled receptor protein signaling pathway -0.059 0.18 -10000 0 -0.49 136 136
IPCEF1/ARNO -0.14 0.2 -10000 0 -0.59 67 67
alphaIIb/beta3 Integrin 0.028 0.087 -10000 0 -0.42 29 29
Nongenotropic Androgen 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
PTK2 0.003 0.004 -10000 0 -10000 0 0
GNB1/GNG2 -0.007 0.13 -10000 0 -0.34 127 127
regulation of S phase of mitotic cell cycle -0.021 0.1 -10000 0 -0.3 111 111
GNAO1 0.017 0.095 0.26 32 -0.58 19 51
HRAS 0.024 0.018 0.26 5 -10000 0 5
SHBG/T-DHT 0.015 0.005 -10000 0 -10000 0 0
PELP1 0.021 0.007 -10000 0 -10000 0 0
AKT1 0.005 0.003 -10000 0 -10000 0 0
MAP2K1 -0.068 0.11 -10000 0 -0.34 104 104
T-DHT/AR -0.039 0.15 0.17 1 -0.43 120 121
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.007 291 291
GNAI2 0.023 0.005 -10000 0 -10000 0 0
GNAI3 0.024 0.004 -10000 0 -10000 0 0
GNAI1 -0.005 0.13 -10000 0 -0.58 47 47
mol:GDP -0.059 0.16 -10000 0 -0.47 121 121
cell proliferation -0.14 0.21 0.27 2 -0.44 275 277
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
FOS -0.25 0.38 -10000 0 -0.81 295 295
mol:Ca2+ -0.012 0.027 -10000 0 -0.072 126 126
MAPK3 -0.1 0.17 0.26 3 -0.42 104 107
MAPK1 -0.081 0.15 -10000 0 -0.39 102 102
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
mol:IP3 -0.001 0.002 -10000 0 -0.004 289 289
cAMP biosynthetic process 0.004 0.021 -10000 0 -10000 0 0
GNG2 0.018 0.061 -10000 0 -0.58 10 10
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 289 289
HRAS/GTP -0.026 0.12 -10000 0 -0.33 117 117
actin cytoskeleton reorganization 0.031 0.028 -10000 0 -0.3 5 5
SRC 0.023 0.005 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 289 289
PI3K 0.028 0.031 -10000 0 -0.33 6 6
apoptosis 0.13 0.22 0.44 298 -10000 0 298
T-DHT/AR/PELP1 -0.023 0.13 -10000 0 -0.37 119 119
HRAS/GDP -0.048 0.16 -10000 0 -0.46 120 120
CREB1 -0.14 0.23 -10000 0 -0.47 298 298
RAC1-CDC42/GTP 0.039 0.03 -10000 0 -0.3 5 5
AR -0.051 0.2 0.26 1 -0.58 119 120
GNB1 0.023 0.005 -10000 0 -10000 0 0
RAF1 -0.06 0.11 -10000 0 -0.33 109 109
RAC1-CDC42/GDP -0.024 0.16 -10000 0 -0.44 119 119
T-DHT/AR/PELP1/Src -0.02 0.12 -10000 0 -0.34 118 118
MAP2K2 -0.069 0.11 -10000 0 -0.34 105 105
T-DHT/AR/PELP1/Src/PI3K -0.021 0.1 -10000 0 -0.3 111 111
GNAZ 0.018 0.055 -10000 0 -0.58 8 8
SHBG 0.021 0.008 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.05 0.16 -10000 0 -0.47 87 87
mol:T-DHT -0.001 0.001 0.002 1 -0.004 85 86
RAC1 0.024 0.004 -10000 0 -10000 0 0
GNRH1 0.001 0.028 -10000 0 -0.43 4 4
Gi family/GTP -0.034 0.098 -10000 0 -0.28 85 85
CDC42 0.023 0.005 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.009 0.008 -10000 0 -10000 0 0
RAS family/GTP -0.021 0.14 0.32 1 -0.3 46 47
NFATC4 -0.066 0.12 0.27 4 -0.25 177 181
ERBB2IP 0.024 0.006 -10000 0 -10000 0 0
HSP90 (dimer) 0.024 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.07 0.15 -10000 0 -0.31 228 228
JUN -0.01 0.098 0.24 27 -0.47 3 30
HRAS 0.025 0.018 0.26 5 -10000 0 5
DOCK7 -0.082 0.14 0.28 2 -0.3 224 226
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.054 0.15 -10000 0 -0.33 186 186
AKT1 -0.001 0.009 -10000 0 -10000 0 0
BAD -0.007 0.006 -10000 0 -10000 0 0
MAPK10 -0.073 0.11 0.21 7 -0.27 124 131
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.075 0.16 -10000 0 -0.33 228 228
RAF1 -0.018 0.15 0.36 10 -0.35 8 18
ErbB2/ErbB3/neuregulin 2 -0.15 0.18 -10000 0 -0.35 403 403
STAT3 -0.003 0.16 -10000 0 -0.86 33 33
cell migration -0.058 0.1 0.24 11 -0.25 76 87
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.043 0.25 0.46 9 -0.54 75 84
FOS -0.1 0.28 0.33 42 -0.49 295 337
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.07 0.15 -10000 0 -0.31 228 228
MAPK3 -0.014 0.2 0.43 9 -0.6 17 26
MAPK1 -0.028 0.22 0.43 9 -0.6 40 49
JAK2 -0.08 0.14 0.26 1 -0.3 223 224
NF2 -0.002 0.061 -10000 0 -0.68 7 7
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.054 0.13 0.23 3 -0.29 184 187
NRG1 -0.14 0.27 0.26 4 -0.58 268 272
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
MAPK8 -0.081 0.15 0.25 2 -0.3 228 230
MAPK9 -0.045 0.083 0.2 9 -0.25 1 10
ERBB2 0.001 0.07 0.24 77 -10000 0 77
ERBB3 0.022 0.028 -10000 0 -0.58 2 2
SHC1 0.021 0.01 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
apoptosis 0.02 0.026 -10000 0 -0.16 6 6
STAT3 (dimer) -0.002 0.16 -10000 0 -0.84 33 33
RNF41 -0.012 0.011 -10000 0 -10000 0 0
FRAP1 -0.005 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.072 0.094 -10000 0 -0.23 218 218
ErbB2/ErbB2/HSP90 (dimer) -0.011 0.016 -10000 0 -10000 0 0
CHRNA1 0.019 0.18 0.37 53 -0.45 14 67
myelination -0.062 0.12 0.33 10 -0.25 75 85
PPP3CB -0.076 0.13 0.27 2 -0.28 223 225
KRAS 0.024 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.037 0.14 -10000 0 -0.26 145 145
NRG2 -0.27 0.3 -10000 0 -0.58 478 478
mol:GDP -0.054 0.13 0.23 3 -0.29 184 187
SOS1 0.024 0.003 -10000 0 -10000 0 0
MAP2K2 -0.016 0.14 0.33 14 -0.36 7 21
SRC 0.023 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.082 0.14 0.28 2 -0.3 225 227
MAP2K1 -0.05 0.22 0.44 5 -0.53 69 74
heart morphogenesis -0.07 0.15 -10000 0 -0.31 228 228
RAS family/GDP -0.021 0.14 0.3 1 -0.35 12 13
GRB2 0.023 0.01 0.26 1 -10000 0 1
PRKACA -0.003 0.07 -10000 0 -0.68 10 10
CHRNE 0.004 0.028 0.11 4 -0.21 3 7
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.001 0.009 -10000 0 -10000 0 0
nervous system development -0.07 0.15 -10000 0 -0.31 228 228
CDC42 0.023 0.005 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.063 0.16 0.31 10 -0.35 97 107
SMAD6-7/SMURF1 0.045 0.015 -10000 0 -10000 0 0
NOG 0.014 0.092 0.26 17 -0.58 20 37
SMAD9 -0.09 0.25 -10000 0 -0.61 162 162
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD5 -0.026 0.14 0.23 1 -0.42 69 70
BMP7/USAG1 -0.2 0.25 -10000 0 -0.43 491 491
SMAD5/SKI -0.021 0.15 0.26 1 -0.42 73 74
SMAD1 0.013 0.062 -10000 0 -0.42 6 6
BMP2 -0.076 0.22 0.26 1 -0.58 160 161
SMAD1/SMAD1/SMAD4 0.018 0.07 -10000 0 -0.42 8 8
BMPR1A 0.023 0.02 -10000 0 -0.58 1 1
BMPR1B 0.11 0.15 0.26 388 -0.58 19 407
BMPR1A-1B/BAMBI 0.085 0.12 0.34 11 -0.33 47 58
AHSG 0.02 0.023 0.26 8 -10000 0 8
CER1 0.018 0.015 0.26 3 -10000 0 3
BMP2-4/CER1 -0.048 0.18 -10000 0 -0.4 194 194
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.042 0.17 -10000 0 -0.42 103 103
BMP2-4 (homodimer) -0.069 0.2 -10000 0 -0.44 208 208
RGMB 0.023 0.02 -10000 0 -0.58 1 1
BMP6/BMPR2/BMPR1A-1B 0.071 0.14 -10000 0 -0.32 86 86
RGMA -0.055 0.2 -10000 0 -0.58 126 126
SMURF1 0.024 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.041 0.17 -10000 0 -0.42 114 114
BMP2-4/USAG1 -0.23 0.27 -10000 0 -0.44 537 537
SMAD6/SMURF1/SMAD5 -0.022 0.15 -10000 0 -0.42 75 75
SOSTDC1 -0.26 0.3 0.26 3 -0.58 466 469
BMP7/BMPR2/BMPR1A-1B 0.07 0.14 0.3 6 -0.32 79 85
SKI 0.023 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) -0.017 0.15 0.26 2 -0.58 67 69
HFE2 0.02 0.02 0.26 6 -10000 0 6
ZFYVE16 0.024 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD -0.045 0.2 -10000 0 -0.42 196 196
SMAD5/SMAD5/SMAD4 -0.022 0.15 -10000 0 -0.42 76 76
MAPK1 0.023 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.028 0.15 -10000 0 -0.38 104 104
BMP7 (homodimer) -0.011 0.16 0.26 28 -0.58 65 93
NUP214 0.024 0.004 -10000 0 -10000 0 0
BMP6/FETUA -0.001 0.12 -10000 0 -0.41 72 72
SMAD1/SKI 0.019 0.077 -10000 0 -0.44 10 10
SMAD6 0.024 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/FETUA -0.048 0.18 0.34 1 -0.4 194 195
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.039 0.098 0.26 92 -0.58 12 104
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) 0.088 0.11 -10000 0 -0.41 21 21
CHRDL1 -0.38 0.28 -10000 0 -0.58 655 655
ENDOFIN/SMAD1 0.019 0.079 -10000 0 -0.46 10 10
SMAD6-7/SMURF1/SMAD1 0.035 0.083 -10000 0 -0.44 10 10
SMAD6/SMURF1 0.024 0.004 -10000 0 -10000 0 0
BAMBI 0.015 0.11 0.26 37 -0.58 29 66
SMURF2 0.022 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.3 0.27 -10000 0 -0.46 658 658
BMP2-4/GREM1 -0.038 0.2 -10000 0 -0.4 202 202
SMAD7 0.023 0.005 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.083 0.25 -10000 0 -0.6 158 158
SMAD1/SMAD6 0.018 0.08 -10000 0 -0.48 9 9
TAK1/SMAD6 0.033 0.01 -10000 0 -10000 0 0
BMP7 -0.011 0.16 0.26 28 -0.58 65 93
BMP6 -0.017 0.15 0.26 2 -0.58 67 69
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.042 0.17 -10000 0 -0.44 113 113
PPM1A 0.024 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.017 0.076 -10000 0 -0.46 9 9
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 0.024 0.002 -10000 0 -10000 0 0
CTDSP1 0.024 0.004 -10000 0 -10000 0 0
PPP1R15A 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.052 0.2 0.24 2 -0.48 122 124
CHRD 0.027 0.098 0.26 55 -0.58 17 72
BMPR2 0.024 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.055 0.19 -10000 0 -0.49 115 115
BMP4 -0.012 0.14 0.26 1 -0.58 58 59
FST 0.003 0.11 0.26 4 -0.58 35 39
BMP2-4/NOG -0.05 0.19 -10000 0 -0.41 191 191
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.074 0.14 0.3 6 -0.3 79 85
Plasma membrane estrogen receptor signaling

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.001 0.15 -10000 0 -0.32 160 160
ER alpha/Gai/GDP/Gbeta gamma -0.082 0.22 -10000 0 -0.47 186 186
AKT1 -0.11 0.33 -10000 0 -0.79 175 175
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.11 0.33 -10000 0 -0.8 174 174
mol:Ca2+ -0.025 0.1 0.27 2 -0.46 25 27
IGF1R 0.011 0.086 0.26 2 -0.58 20 22
E2/ER alpha (dimer)/Striatin -0.012 0.16 -10000 0 -0.37 144 144
SHC1 0.02 0.009 -10000 0 -10000 0 0
apoptosis 0.1 0.31 0.75 175 -10000 0 175
RhoA/GTP -0.014 0.1 -10000 0 -0.29 107 107
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.064 0.21 0.32 5 -0.47 167 172
regulation of stress fiber formation 0.022 0.1 0.43 2 -0.32 7 9
E2/ERA-ERB (dimer) -0.019 0.16 0.18 102 -0.36 158 260
KRAS 0.023 0.005 -10000 0 -10000 0 0
G13/GTP -0.008 0.13 -10000 0 -0.32 134 134
pseudopodium formation -0.022 0.1 0.32 7 -0.43 2 9
E2/ER alpha (dimer)/PELP1 -0.012 0.15 -10000 0 -0.36 134 134
GRB2 0.023 0.01 0.26 1 -10000 0 1
GNG2 0.018 0.061 -10000 0 -0.58 10 10
GNAO1 0.018 0.095 0.26 32 -0.58 19 51
HRAS 0.025 0.018 0.26 5 -10000 0 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.085 0.23 -10000 0 -0.52 190 190
E2/ER beta (dimer) 0.007 0.068 -10000 0 -0.41 24 24
mol:GDP -0.037 0.17 0.25 12 -0.4 152 164
mol:NADP -0.085 0.23 -10000 0 -0.52 190 190
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
mol:IP3 -0.026 0.11 0.27 2 -0.49 24 26
IGF-1R heterotetramer 0.011 0.086 0.26 2 -0.58 20 22
PLCB1 -0.024 0.11 0.28 2 -0.49 26 28
PLCB2 -0.006 0.085 -10000 0 -0.52 16 16
IGF1 -0.1 0.24 -10000 0 -0.58 202 202
mol:L-citrulline -0.085 0.23 -10000 0 -0.52 190 190
RHOA 0.023 0.005 -10000 0 -10000 0 0
Gai/GDP -0.078 0.25 -10000 0 -0.63 147 147
JNK cascade 0.007 0.067 -10000 0 -0.41 24 24
BCAR1 0.021 0.008 -10000 0 -10000 0 0
ESR2 0.009 0.091 -10000 0 -0.58 23 23
GNAQ 0.023 0.027 -10000 0 -0.58 2 2
ESR1 -0.032 0.23 0.26 113 -0.58 134 247
Gq family/GDP/Gbeta gamma -0.01 0.16 -10000 0 -0.74 35 35
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.016 0.13 -10000 0 -0.6 16 16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.057 0.2 0.31 5 -0.48 138 143
GNAZ 0.018 0.055 -10000 0 -0.58 8 8
E2/ER alpha (dimer) -0.026 0.17 0.18 113 -0.41 140 253
STRN 0.017 0.066 -10000 0 -0.58 12 12
GNAL -0.11 0.25 -10000 0 -0.58 209 209
PELP1 0.022 0.007 -10000 0 -10000 0 0
MAPK11 0.001 0.063 -10000 0 -0.38 25 25
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 -0.58 47 47
HBEGF -0.051 0.21 0.34 22 -0.51 101 123
cAMP biosynthetic process -0.088 0.18 -10000 0 -0.33 318 318
SRC -0.077 0.22 0.3 8 -0.45 180 188
PI3K 0.031 0.036 -10000 0 -0.36 7 7
GNB1 0.023 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.019 0.16 -10000 0 -0.37 140 140
SOS1 0.024 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.11 0.19 -10000 0 -0.44 186 186
Gs family/GTP -0.084 0.19 -10000 0 -0.34 318 318
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.043 0.017 -10000 0 -10000 0 0
vasodilation -0.079 0.22 -10000 0 -0.49 190 190
mol:DAG -0.026 0.11 0.27 2 -0.49 24 26
Gs family/GDP/Gbeta gamma -0.09 0.18 -10000 0 -0.36 253 253
MSN -0.024 0.11 0.32 7 -0.3 15 22
Gq family/GTP -0.001 0.091 -10000 0 -0.54 15 15
mol:PI-3-4-5-P3 -0.1 0.32 -10000 0 -0.76 174 174
NRAS 0.024 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.079 0.22 0.49 190 -10000 0 190
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
RhoA/GDP -0.021 0.17 0.26 9 -0.38 150 159
NOS3 -0.091 0.25 -10000 0 -0.55 190 190
GNA11 0.022 0.028 -10000 0 -0.58 2 2
MAPKKK cascade -0.076 0.25 0.31 3 -0.58 170 173
E2/ER alpha (dimer)/PELP1/Src -0.068 0.22 0.34 6 -0.49 171 177
ruffle organization -0.022 0.1 0.32 7 -0.43 2 9
ROCK2 -0.023 0.12 0.34 7 -0.28 108 115
GNA14 0.023 0.07 0.26 21 -0.58 10 31
GNA15 0.025 0.027 0.26 6 -0.58 1 7
GNA13 0.022 0.007 -10000 0 -10000 0 0
MMP9 -0.042 0.21 0.37 24 -0.5 96 120
MMP2 -0.067 0.2 0.28 10 -0.44 162 172
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.04 0.17 -10000 0 -0.41 163 163
CRKL -0.049 0.15 0.36 1 -0.41 88 89
mol:PIP3 0.003 0.059 0.57 2 -0.94 3 5
AKT1 0.011 0.073 0.37 4 -0.82 3 7
PTK2B 0.02 0.01 -10000 0 -10000 0 0
RAPGEF1 -0.048 0.14 0.34 1 -0.39 83 84
RANBP10 0.021 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.043 0.18 -10000 0 -0.4 190 190
MAP3K5 -0.041 0.15 0.36 1 -0.41 77 78
HGF/MET/CIN85/CBL/ENDOPHILINS -0.031 0.17 -10000 0 -0.36 196 196
AP1 -0.11 0.19 -10000 0 -0.4 280 280
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 -0.77 322 322
STAT3 (dimer) -0.049 0.15 -10000 0 -0.36 156 156
GAB1/CRKL/SHP2/PI3K -0.02 0.15 -10000 0 -0.4 72 72
INPP5D 0.024 0.004 -10000 0 -10000 0 0
CBL/CRK -0.037 0.15 0.34 1 -0.39 81 82
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.023 0.005 -10000 0 -10000 0 0
PTEN 0.022 0.028 -10000 0 -0.58 2 2
ELK1 -0.029 0.097 0.25 47 -0.21 128 175
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.027 0.094 -10000 0 -0.29 57 57
PAK1 0.023 0.086 0.37 8 -0.79 3 11
HGF/MET/RANBP10 -0.045 0.18 -10000 0 -0.39 196 196
HRAS -0.11 0.26 -10000 0 -0.65 171 171
DOCK1 -0.047 0.14 0.52 1 -0.41 73 74
GAB1 -0.051 0.16 -10000 0 -0.36 151 151
CRK -0.05 0.15 0.36 1 -0.4 89 90
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.1 0.26 -10000 0 -0.58 208 208
JUN 0.019 0.054 -10000 0 -0.58 8 8
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.053 0.13 -10000 0 -0.29 199 199
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
cell morphogenesis -0.051 0.16 0.38 5 -0.45 81 86
GRB2/SHC -0.017 0.11 -10000 0 -0.29 109 109
FOS -0.15 0.27 -10000 0 -0.58 277 277
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.029 0.097 0.25 47 -0.21 129 176
HGF/MET/MUC20 -0.055 0.18 -10000 0 -0.39 199 199
cell migration -0.017 0.11 -10000 0 -0.29 109 109
GRB2 0.023 0.01 0.26 1 -10000 0 1
CBL 0.022 0.007 -10000 0 -10000 0 0
MET/RANBP10 -0.042 0.17 -10000 0 -0.42 158 158
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.048 0.14 -10000 0 -0.34 161 161
MET/MUC20 -0.054 0.16 -10000 0 -0.41 163 163
RAP1B -0.041 0.14 0.28 3 -0.39 71 74
RAP1A -0.046 0.14 0.41 2 -0.39 72 74
HGF/MET/RANBP9 -0.043 0.18 -10000 0 -0.4 192 192
RAF1 -0.098 0.25 -10000 0 -0.61 170 170
STAT3 -0.05 0.15 -10000 0 -0.36 156 156
cell proliferation -0.043 0.19 0.28 27 -0.44 141 168
RPS6KB1 -0.015 0.064 -10000 0 -0.27 21 21
MAPK3 -0.042 0.095 0.66 7 -10000 0 7
MAPK1 -0.008 0.18 0.68 52 -10000 0 52
RANBP9 0.023 0.005 -10000 0 -10000 0 0
MAPK8 -0.028 0.14 0.43 1 -0.42 50 51
SRC -0.053 0.13 0.2 1 -0.33 151 152
PI3K -0.027 0.13 -10000 0 -0.29 160 160
MET/Glomulin -0.047 0.15 -10000 0 -0.38 157 157
SOS1 0.024 0.003 -10000 0 -10000 0 0
MAP2K1 -0.09 0.23 0.47 1 -0.56 169 170
MET -0.072 0.22 -10000 0 -0.58 155 155
MAP4K1 -0.044 0.16 0.38 1 -0.42 84 85
PTK2 0.019 0.01 -10000 0 -10000 0 0
MAP2K2 -0.09 0.23 0.47 1 -0.56 169 170
BAD 0.009 0.069 0.35 3 -0.79 3 6
MAP2K4 -0.038 0.13 0.34 1 -0.41 56 57
SHP2/GRB2/SOS1/GAB1 -0.041 0.18 -10000 0 -0.4 158 158
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 -0.048 0.11 -10000 0 -0.27 182 182
PLCgamma1/PKC 0.017 0.004 -10000 0 -10000 0 0
HGF -0.013 0.14 -10000 0 -0.58 60 60
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 -0.023 0.13 -10000 0 -0.27 187 187
PDPK1 0.013 0.076 0.43 2 -0.87 3 5
HGF/MET/SHIP -0.044 0.18 -10000 0 -0.4 197 197
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.003 0.086 -10000 0 -0.44 25 25
Crk/p130 Cas/Paxillin -0.055 0.12 -10000 0 -0.34 117 117
JUN -0.014 0.12 0.25 1 -0.41 26 27
HRAS 0.025 0.018 0.26 5 -10000 0 5
RET51/GFRalpha1/GDNF/GRB10 0.045 0.2 0.35 51 -0.34 158 209
RAP1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.012 0.26 2 -10000 0 2
RAP1A/GDP 0.018 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.044 0.2 0.35 50 -0.34 157 207
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.01 0.15 0.33 4 -0.34 160 164
RHOA 0.023 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.021 0.17 0.29 35 -0.31 158 193
GRB7 0.02 0.021 -10000 0 -0.58 1 1
RET51/GFRalpha1/GDNF 0.043 0.2 0.35 50 -0.34 159 209
MAPKKK cascade 0.001 0.15 0.29 9 -0.33 116 125
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.023 0.18 0.33 3 -0.39 169 172
lamellipodium assembly -0.032 0.13 -10000 0 -0.32 123 123
RET51/GFRalpha1/GDNF/SHC 0.037 0.18 0.35 41 -0.34 123 164
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.008 0.14 0.33 4 -0.34 119 123
RET9/GFRalpha1/GDNF/Shank3 -0.013 0.15 0.33 4 -0.34 160 164
MAPK3 -0.031 0.13 0.23 2 -0.32 124 126
DOK1 0.025 0.011 0.26 2 -10000 0 2
DOK6 0.018 0.067 0.26 6 -0.58 11 17
PXN 0.024 0.002 -10000 0 -10000 0 0
neurite development -0.03 0.13 0.25 1 -0.31 112 113
DOK5 0.011 0.087 0.26 5 -0.58 20 25
GFRA1 -0.07 0.24 0.26 51 -0.58 172 223
MAPK8 -0.008 0.13 0.22 3 -0.45 23 26
HRAS/GTP 0.03 0.18 0.29 49 -0.34 152 201
tube development -0.005 0.15 0.35 10 -0.32 152 162
MAPK1 -0.03 0.13 0.27 3 -0.31 124 127
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.022 0.11 0.26 1 -0.27 147 148
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
PDLIM7 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.04 0.19 0.34 47 -0.33 162 209
SHC1 0.02 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.029 0.19 0.35 36 -0.34 160 196
RET51/GFRalpha1/GDNF/Dok5 0.028 0.2 0.35 46 -0.36 165 211
PRKCA 0.01 0.086 0.26 1 -0.58 20 21
HRAS/GDP 0.018 0.012 0.18 5 -10000 0 5
CREB1 -0.011 0.13 0.23 13 -0.32 90 103
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.018 0.1 0.26 1 -0.27 106 107
RET51/GFRalpha1/GDNF/Grb7 0.044 0.19 0.34 65 -0.35 128 193
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.1 0.14 0.26 346 -0.58 13 359
DOK4 0.021 0.008 -10000 0 -10000 0 0
JNK cascade -0.013 0.12 0.25 1 -0.4 26 27
RET9/GFRalpha1/GDNF/FRS2 -0.011 0.15 0.33 4 -0.34 161 165
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 -0.019 0.1 0.26 1 -0.27 106 107
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.008 0.14 0.25 16 -0.29 124 140
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.004 0.14 0.26 3 -0.3 125 128
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.013 0.14 0.25 17 -0.31 92 109
PI3K -0.025 0.21 0.29 12 -0.48 124 136
SOS1 0.024 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.004 0.14 0.32 3 -0.32 152 155
GRB10 0.024 0.003 -10000 0 -10000 0 0
activation of MAPKK activity -0.002 0.12 0.24 10 -0.27 118 128
RET51/GFRalpha1/GDNF/FRS2 0.041 0.2 0.35 54 -0.34 160 214
GAB1 0.024 0.004 -10000 0 -10000 0 0
IRS1 0 0.12 -10000 0 -0.58 38 38
IRS2 0.004 0.1 -10000 0 -0.58 30 30
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.012 0.14 0.25 17 -0.31 92 109
RET51/GFRalpha1/GDNF/PKC alpha 0.027 0.2 0.35 42 -0.35 167 209
GRB2 0.023 0.01 0.26 1 -10000 0 1
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GDNF 0.033 0.055 0.26 52 -10000 0 52
RAC1 0.024 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.029 0.22 0.35 48 -0.4 169 217
Rac1/GTP -0.019 0.17 0.23 8 -0.38 123 131
RET9/GFRalpha1/GDNF -0.025 0.16 0.33 4 -0.35 172 176
GFRalpha1/GDNF -0.032 0.19 0.37 4 -0.41 174 178
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.004 0.042 0.23 5 -0.37 2 7
NFATC2 -0.02 0.1 0.23 4 -0.38 65 69
NFATC3 0.007 0.036 0.23 5 -10000 0 5
CD40LG -0.13 0.29 0.53 18 -0.57 215 233
PTGS2 -0.19 0.34 0.53 13 -0.64 294 307
JUNB 0.024 0.008 0.26 1 -10000 0 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.028 0.16 4 -10000 0 4
CaM/Ca2+ 0.009 0.028 0.16 4 -10000 0 4
CALM1 0.016 0.022 -10000 0 -10000 0 0
JUN 0.012 0.059 -10000 0 -0.59 8 8
mol:Ca2+ -0.002 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.012 -10000 0 -10000 0 0
FOSL1 0.028 0.045 0.26 22 -0.58 2 24
CREM 0.023 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0 0.15 0.48 14 -0.38 55 69
FOS -0.15 0.27 -10000 0 -0.58 278 278
IFNG -0.11 0.28 0.49 40 -0.52 219 259
AP-1/NFAT1-c-4 -0.13 0.34 0.56 37 -0.61 233 270
FASLG -0.11 0.27 0.55 21 -0.54 185 206
NFAT1-c-4/ICER1 -0.012 0.12 0.32 8 -0.35 59 67
IL2RA -0.12 0.28 0.5 32 -0.53 225 257
FKBP12/FK506 0.017 0.003 -10000 0 -10000 0 0
CSF2 -0.12 0.28 0.53 18 -0.54 210 228
JunB/Fra1/NFAT1-c-4 0 0.12 0.33 17 -0.34 58 75
IL4 -0.13 0.27 0.51 14 -0.54 211 225
IL2 -0.015 0.16 -10000 0 -0.94 26 26
IL3 -0.017 0.11 -10000 0 -0.7 23 23
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
BATF3 0.021 0.014 0.26 2 -10000 0 2
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.021 0.012 0.26 1 -10000 0 1
Neurotrophic factor-mediated Trk receptor signaling

Figure S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.023 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.071 0.11 -10000 0 -0.29 85 85
NT3 (dimer)/TRKC -0.18 0.27 -10000 0 -0.47 409 409
NT3 (dimer)/TRKB -0.3 0.31 -10000 0 -0.52 579 579
SHC/Grb2/SOS1/GAB1/PI3K 0.016 0.029 -10000 0 -0.26 4 4
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
BDNF -0.019 0.17 0.26 19 -0.58 76 95
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DYNLT1 0.023 0.006 -10000 0 -10000 0 0
NTRK1 0.025 0.047 0.26 23 -0.58 2 25
NTRK2 -0.28 0.3 -10000 0 -0.58 497 497
NTRK3 -0.18 0.28 0.26 5 -0.58 322 327
NT-4/5 (dimer)/TRKB -0.37 0.34 -10000 0 -0.58 635 635
neuron apoptosis 0.17 0.22 0.47 268 -10000 0 268
SHC 2-3/Grb2 -0.18 0.24 -10000 0 -0.51 268 268
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 -0.18 0.25 -10000 0 -0.54 263 263
SHC3 -0.18 0.23 -10000 0 -0.52 255 255
STAT3 (dimer) 0.033 0.042 -10000 0 -0.36 3 3
NT3 (dimer)/TRKA -0.11 0.22 -10000 0 -0.42 266 266
RIN/GDP -0.047 0.12 0.29 4 -0.26 75 79
GIPC1 0.024 0.008 0.26 1 -10000 0 1
KRAS 0.023 0.005 -10000 0 -10000 0 0
DNAJA3 -0.08 0.15 -10000 0 -0.33 232 232
RIN/GTP 0.014 0.008 0.18 2 -10000 0 2
CCND1 0.024 0.091 0.44 33 -0.83 3 36
MAGED1 0.025 0.011 0.26 2 -10000 0 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.19 0.29 -10000 0 -0.58 343 343
SHC/GRB2/SOS1 0.038 0.022 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
NGF (dimer)/TRKA/MATK 0.034 0.083 0.34 2 -0.38 27 29
TRKA/NEDD4-2 0.032 0.037 -10000 0 -0.34 3 3
ELMO1 0.024 0.003 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.031 0.007 -10000 0 -10000 0 0
NGF 0.016 0.077 0.26 7 -0.58 15 22
HRAS 0.025 0.018 0.26 5 -10000 0 5
DOCK1 0.024 0.004 -10000 0 -10000 0 0
GAB2 0.022 0.008 -10000 0 -10000 0 0
RIT2 0.019 0.012 0.26 2 -10000 0 2
RIT1 0.02 0.009 -10000 0 -10000 0 0
FRS2 0.024 0.012 0.26 2 -10000 0 2
DNM1 0.02 0.052 0.26 1 -0.58 7 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.073 0.16 -10000 0 -0.32 256 256
mol:GDP -0.075 0.16 0.34 5 -0.37 100 105
NGF (dimer) 0.016 0.077 0.26 7 -0.58 15 22
RhoG/GDP 0.018 0.002 -10000 0 -10000 0 0
RIT1/GDP -0.046 0.11 0.37 2 -0.26 63 65
TIAM1 0.025 0.016 0.26 4 -10000 0 4
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
BDNF (dimer)/TRKB -0.19 0.23 -10000 0 -0.4 520 520
KIDINS220/CRKL/C3G 0.034 0.009 -10000 0 -10000 0 0
SHC/RasGAP 0.029 0.015 -10000 0 -10000 0 0
FRS2 family/SHP2 0.046 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.047 0.028 -10000 0 -10000 0 0
RIT1/GTP 0.015 0.007 -10000 0 -10000 0 0
NT3 (dimer) -0.063 0.22 0.26 12 -0.58 143 155
RAP1/GDP -0.042 0.095 -10000 0 -0.22 73 73
KIDINS220/CRKL 0.023 0.006 -10000 0 -10000 0 0
BDNF (dimer) -0.019 0.17 0.26 19 -0.58 76 95
ubiquitin-dependent protein catabolic process 0.036 0.061 -10000 0 -0.36 15 15
Schwann cell development -0.049 0.039 -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 0.02 0.05 -10000 0 -0.27 9 9
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.28 0.29 -10000 0 -0.48 574 574
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 -0.43 55 55
STAT3 0.033 0.042 -10000 0 -0.36 3 3
axon guidance -0.27 0.27 -10000 0 -0.45 587 587
MAPK3 0.009 0.09 0.23 6 -0.35 25 31
MAPK1 0.011 0.092 0.23 6 -0.35 26 32
CDC42/GDP -0.044 0.12 0.29 5 -0.26 68 73
NTF3 -0.063 0.22 0.26 12 -0.58 143 155
NTF4 -0.19 0.29 -10000 0 -0.58 343 343
NGF (dimer)/TRKA/FAIM 0.037 0.061 -10000 0 -0.37 15 15
PI3K 0.031 0.036 -10000 0 -0.36 7 7
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 -0.077 0.16 0.25 2 -0.33 249 251
SOS1 0.024 0.003 -10000 0 -10000 0 0
MCF2L -0.16 0.22 0.21 1 -0.42 390 391
RGS19 0.023 0.013 0.26 2 -10000 0 2
CDC42 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.094 0.4 1 -0.44 8 9
Rac1/GDP -0.045 0.12 0.3 4 -0.26 74 78
NGF (dimer)/TRKA/GRIT 0.025 0.057 -10000 0 -0.34 17 17
neuron projection morphogenesis -0.071 0.22 -10000 0 -0.78 42 42
NGF (dimer)/TRKA/NEDD4-2 0.036 0.061 -10000 0 -0.37 15 15
MAP2K1 0.031 0.088 0.36 18 -10000 0 18
NGFR -0.14 0.27 -10000 0 -0.58 262 262
NGF (dimer)/TRKA/GIPC/GAIP 0.015 0.051 -10000 0 -0.3 18 18
RAS family/GTP/PI3K 0.018 0.023 -10000 0 -0.26 4 4
FRS2 family/SHP2/GRB2/SOS1 0.063 0.026 -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 0.023 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCZ 0.023 0.02 -10000 0 -0.58 1 1
MAPKKK cascade -0.039 0.14 -10000 0 -0.65 36 36
RASA1 0.024 0.004 -10000 0 -10000 0 0
TRKA/c-Abl 0.032 0.036 -10000 0 -0.43 2 2
SQSTM1 0.024 0.009 0.26 1 -10000 0 1
BDNF (dimer)/TRKB/GIPC -0.17 0.22 -10000 0 -0.37 515 515
NGF (dimer)/TRKA/p62/Atypical PKCs 0.052 0.061 -10000 0 -0.32 15 15
MATK 0.02 0.089 0.26 26 -0.58 17 43
NEDD4L 0.023 0.02 -10000 0 -0.58 1 1
RAS family/GDP -0.057 0.07 -10000 0 -0.21 55 55
NGF (dimer)/TRKA -0.086 0.16 -10000 0 -0.34 272 272
Rac1/GTP -0.085 0.12 -10000 0 -0.28 199 199
FRS2 family/SHP2/CRK family 0.06 0.028 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.021 0.039 -10000 0 -0.58 4 4
Jak2/Leptin Receptor -0.11 0.2 0.27 1 -0.4 249 250
PTP1B/AKT1 -0.067 0.13 0.22 1 -0.34 116 117
FYN 0.021 0.028 -10000 0 -0.58 2 2
p210 bcr-abl/PTP1B -0.082 0.14 0.22 2 -0.36 139 141
EGFR -0.2 0.29 -10000 0 -0.59 349 349
EGF/EGFR -0.2 0.24 -10000 0 -0.42 488 488
CSF1 0.021 0.039 -10000 0 -0.58 4 4
AKT1 0.023 0.005 -10000 0 -10000 0 0
INSR 0.024 0.005 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.047 0.16 0.24 17 -0.35 127 144
Insulin Receptor/Insulin -0.044 0.11 -10000 0 -0.38 46 46
HCK 0.026 0.026 0.26 11 -10000 0 11
CRK 0.022 0.007 -10000 0 -10000 0 0
TYK2 -0.079 0.13 0.41 1 -0.36 122 123
EGF -0.11 0.24 0.26 2 -0.59 189 191
YES1 0.023 0.02 -10000 0 -0.58 1 1
CAV1 -0.16 0.21 0.27 2 -0.43 292 294
TXN 0.016 0.019 0.26 3 -10000 0 3
PTP1B/IRS1/GRB2 -0.073 0.15 -10000 0 -0.37 132 132
cell migration 0.082 0.14 0.36 139 -0.22 2 141
STAT3 0.022 0.005 -10000 0 -10000 0 0
PRLR 0.022 0.046 0.26 4 -0.58 5 9
ITGA2B 0.03 0.061 0.26 44 -0.58 3 47
CSF1R 0.024 0.008 0.26 1 -10000 0 1
Prolactin Receptor/Prolactin 0.032 0.041 0.32 1 -0.38 5 6
FGR 0.023 0.009 0.26 1 -10000 0 1
PTP1B/p130 Cas -0.069 0.14 -10000 0 -0.35 124 124
Crk/p130 Cas -0.062 0.14 -10000 0 -0.36 106 106
DOK1 -0.068 0.13 0.23 2 -0.39 76 78
JAK2 -0.05 0.12 -10000 0 -0.45 56 56
Jak2/Leptin Receptor/Leptin -0.27 0.16 -10000 0 -0.4 399 399
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
PTPN1 -0.083 0.14 0.22 2 -0.36 139 141
LYN 0.021 0.008 -10000 0 -10000 0 0
CDH2 0.065 0.096 0.26 173 -0.58 2 175
SRC -0.018 0.098 -10000 0 -0.62 19 19
ITGB3 0.007 0.099 0.26 4 -0.58 26 30
CAT1/PTP1B -0.094 0.19 0.35 3 -0.47 136 139
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 37 37
mol:H2O2 -0.005 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.24 0.14 -10000 0 -0.36 367 367
negative regulation of transcription -0.049 0.12 -10000 0 -0.44 56 56
FCGR2A 0.02 0.009 -10000 0 -10000 0 0
FER 0.009 0.065 -10000 0 -0.59 11 11
alphaIIb/beta3 Integrin 0.024 0.087 -10000 0 -0.43 29 29
BLK 0.05 0.088 0.26 129 -0.58 2 131
Insulin Receptor/Insulin/Shc 0.035 0.019 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
LEPR -0.12 0.26 -10000 0 -0.58 240 240
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 -0.043 0.17 0.28 8 -0.42 107 115
PRL 0.009 0.034 0.27 10 -10000 0 10
SOCS3 0.009 0.16 -10000 0 -1.2 15 15
SPRY2 -0.041 0.18 -10000 0 -0.59 93 93
Insulin Receptor/Insulin/IRS1 0.025 0.081 -10000 0 -0.38 36 36
CSF1/CSF1R -0.064 0.14 -10000 0 -0.36 114 114
Ras protein signal transduction 0.052 0.15 0.63 57 -10000 0 57
IRS1 0 0.12 -10000 0 -0.58 38 38
INS 0.009 0.015 -10000 0 -10000 0 0
LEP -0.45 0.24 -10000 0 -0.58 759 759
STAT5B -0.071 0.14 0.2 3 -0.35 130 133
STAT5A -0.071 0.14 0.2 3 -0.36 132 135
GRB2 0.023 0.01 0.26 1 -10000 0 1
PDGFB-D/PDGFRB -0.073 0.14 0.22 1 -0.36 131 132
CSN2 0.025 0.06 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
LAT -0.01 0.075 -10000 0 -0.6 8 8
YBX1 0.027 0.016 0.22 4 -10000 0 4
LCK 0.025 0.078 0.26 34 -0.58 11 45
SHC1 0.02 0.009 -10000 0 -10000 0 0
NOX4 0.019 0.032 0.26 9 -0.58 1 10
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 13 -10000 0 13
Metarhodopsin II/Arrestin 0.037 0.038 0.33 2 -10000 0 2
PDE6G/GNAT1/GTP 0.036 0.034 0.18 51 -10000 0 51
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.023 0.028 0.26 13 -10000 0 13
GRK1 0.019 0.017 0.26 4 -10000 0 4
CNG Channel -0.053 0.16 -10000 0 -0.31 266 266
mol:Na + -0.053 0.16 -10000 0 -0.3 260 260
mol:ADP 0.019 0.017 0.26 4 -10000 0 4
RGS9-1/Gbeta5/R9AP 0.014 0.12 0.34 1 -0.36 82 83
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.047 0.17 0.29 3 -0.31 255 258
CNGB1 0.031 0.054 0.26 50 -10000 0 50
RDH5 -0.33 0.3 -10000 0 -0.58 576 576
SAG 0.032 0.053 0.26 49 -10000 0 49
mol:Ca2+ -0.086 0.14 0.35 15 -0.31 90 105
Na + (4 Units) -0.056 0.15 -10000 0 -0.29 250 250
RGS9 -0.027 0.17 0.26 10 -0.58 84 94
GNB1/GNGT1 0.054 0.06 -10000 0 -10000 0 0
GNAT1/GDP 0.022 0.11 0.32 3 -0.32 82 85
GUCY2D 0.024 0.04 0.26 13 -0.58 2 15
GNGT1 0.056 0.088 0.26 150 -10000 0 150
GUCY2F 0.018 0.011 0.26 2 -10000 0 2
GNB5 0.024 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.02 0.052 0.21 3 -0.32 15 18
mol:11-cis-retinal -0.33 0.3 -10000 0 -0.58 576 576
mol:cGMP 0.042 0.044 -10000 0 -0.33 6 6
GNB1 0.023 0.005 -10000 0 -10000 0 0
Rhodopsin -0.24 0.23 -10000 0 -0.42 576 576
SLC24A1 0.024 0.004 -10000 0 -10000 0 0
CNGA1 -0.15 0.27 0.26 4 -0.58 277 281
Metarhodopsin II 0.026 0.02 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.054 0.049 -10000 0 -0.34 6 6
RGS9BP 0.036 0.053 0.26 49 -10000 0 49
Metarhodopsin II/Transducin 0.024 0.033 0.18 6 -10000 0 6
GCAP Family/Ca ++ 0.044 0.038 -10000 0 -0.34 4 4
PDE6A/B 0.029 0.065 -10000 0 -0.43 16 16
mol:Pi 0.013 0.12 0.34 1 -0.36 82 83
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.058 0.054 0.33 2 -10000 0 2
PDE6B 0.014 0.077 0.26 2 -0.58 16 18
PDE6A 0.028 0.033 0.26 18 -10000 0 18
PDE6G 0.033 0.047 0.26 39 -10000 0 39
RHO 0.024 0.028 0.26 13 -10000 0 13
PDE6 0.033 0.12 0.3 7 -0.31 92 99
GUCA1A 0.031 0.046 0.26 37 -10000 0 37
GC2/GCAP Family 0.054 0.04 -10000 0 -0.35 4 4
GUCA1C 0.017 0.008 0.26 1 -10000 0 1
GUCA1B 0.021 0.039 -10000 0 -0.58 4 4
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.1 0.19 -10000 0 -0.34 362 362
fibroblast growth factor receptor signaling pathway -0.1 0.19 -10000 0 -0.33 362 362
LAMA1 -0.04 0.18 0.26 2 -0.58 102 104
PRNP 0.015 0.072 -10000 0 -0.58 14 14
GPC1/SLIT2 -0.011 0.14 -10000 0 -0.42 98 98
SMAD2 -0.02 0.061 0.25 1 -0.34 31 32
GPC1/PrPc/Cu2+ 0.025 0.05 -10000 0 -0.37 15 15
GPC1/Laminin alpha1 -0.016 0.14 -10000 0 -0.41 112 112
TDGF1 0.016 0.061 0.26 1 -0.58 10 11
CRIPTO/GPC1 0.029 0.051 -10000 0 -0.43 11 11
APP/GPC1 0.034 0.02 -10000 0 -0.43 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.004 0.042 -10000 0 -0.37 11 11
FLT1 0.023 0.006 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.033 0.076 -10000 0 -0.37 32 32
SERPINC1 0.029 0.047 0.26 37 -10000 0 37
FYN 0.003 0.045 -10000 0 -0.37 13 13
FGR 0.004 0.042 -10000 0 -0.37 11 11
positive regulation of MAPKKK cascade 0.008 0.083 0.26 4 -0.35 27 31
SLIT2 -0.034 0.18 -10000 0 -0.58 92 92
GPC1/NRG -0.11 0.2 -10000 0 -0.37 342 342
NRG1 -0.14 0.27 0.26 4 -0.58 268 272
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.045 0.025 -10000 0 -0.37 1 1
LYN 0.004 0.037 -10000 0 -0.37 8 8
mol:Spermine 0.006 0.016 -10000 0 -0.42 1 1
cell growth -0.1 0.19 -10000 0 -0.33 362 362
BMP signaling pathway -0.024 0.025 0.58 1 -0.26 4 5
SRC 0.004 0.04 -10000 0 -0.37 10 10
TGFBR1 0.024 0.008 0.26 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.15 0.28 0.26 26 -0.58 286 312
GPC1 0.024 0.025 0.26 4 -0.58 1 5
TGFBR1 (dimer) 0.024 0.008 0.26 1 -10000 0 1
VEGFA 0.025 0.019 0.26 6 -10000 0 6
BLK 0.019 0.068 -10000 0 -0.38 13 13
HCK 0.006 0.043 -10000 0 -0.37 10 10
FGF2 -0.2 0.29 -10000 0 -0.58 364 364
FGFR1 0.015 0.051 -10000 0 -0.58 7 7
VEGFR1 homodimer 0.023 0.006 -10000 0 -10000 0 0
TGFBR2 0.005 0.11 -10000 0 -0.58 31 31
cell death 0.034 0.02 -10000 0 -0.43 1 1
ATIII/GPC1 0.035 0.039 -10000 0 -0.43 1 1
PLA2G2A/GPC1 -0.1 0.22 -10000 0 -0.43 286 286
LCK 0.005 0.063 -10000 0 -0.37 22 22
neuron differentiation -0.11 0.2 -10000 0 -0.37 342 342
PrPc/Cu2+ 0.011 0.053 -10000 0 -0.42 14 14
APP 0.024 0.004 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.005 0.11 -10000 0 -0.58 31 31
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.018 0.041 -10000 0 -0.44 3 3
PDGFRB 0.018 0.04 -10000 0 -0.58 4 4
SPHK1 -0.018 0.098 0.24 1 -0.76 13 14
mol:S1P -0.022 0.096 0.39 1 -0.67 13 14
S1P1/S1P/Gi -0.13 0.23 0.27 5 -0.43 328 333
GNAO1 0.006 0.096 0.25 32 -0.59 19 51
PDGFB-D/PDGFRB/PLCgamma1 -0.11 0.21 0.35 4 -0.4 285 289
PLCG1 -0.13 0.22 0.3 4 -0.42 295 299
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.018 0.04 -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 -0.59 47 47
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.013 0.028 0.2 1 -0.38 3 4
S1P1/S1P -0.035 0.098 0.28 2 -0.48 16 18
negative regulation of cAMP metabolic process -0.13 0.23 0.27 5 -0.42 328 333
MAPK3 -0.18 0.3 0.31 12 -0.59 320 332
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 0.017 0.003 -10000 0 -10000 0 0
KDR 0.012 0.038 -10000 0 -0.59 3 3
PLCB2 -0.026 0.098 0.31 7 -0.43 17 24
RAC1 0.024 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.032 0.082 -10000 0 -0.4 16 16
receptor internalization -0.035 0.089 0.19 1 -0.45 16 17
PTGS2 -0.33 0.5 0.4 2 -1 329 331
Rac1/GTP -0.032 0.082 -10000 0 -0.41 16 16
RHOA 0.023 0.005 -10000 0 -10000 0 0
VEGFA 0.015 0.027 0.26 6 -10000 0 6
negative regulation of T cell proliferation -0.13 0.23 0.27 5 -0.42 328 333
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.004 0.058 -10000 0 -0.58 8 8
MAPK1 -0.2 0.32 0.33 3 -0.62 334 337
S1P1/S1P/PDGFB-D/PDGFRB -0.035 0.12 0.32 4 -0.5 15 19
ABCC1 0.012 0.019 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.024 0.004 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.11 0.08 0.32 7 -0.3 1 8
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.019 0.02 -10000 0 -0.3 2 2
AURKB 0.15 0.12 0.26 507 -10000 0 507
AURKC 0.025 0.031 0.26 10 -0.58 1 11
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.034 0.03 -10000 0 -0.42 3 3
alphaV beta3 Integrin -0.12 0.21 -10000 0 -0.38 354 354
PTK2 -0.055 0.15 0.32 2 -0.48 47 49
IGF1R 0.011 0.086 0.26 2 -0.58 20 22
PI4KB 0.02 0.009 -10000 0 -10000 0 0
MFGE8 0.017 0.069 0.26 5 -0.58 12 17
SRC 0.023 0.005 -10000 0 -10000 0 0
CDKN1B -0.044 0.12 -10000 0 -0.52 33 33
VEGFA 0.025 0.019 0.26 6 -10000 0 6
ILK -0.04 0.11 -10000 0 -0.48 28 28
ROCK1 0.023 0.02 -10000 0 -0.58 1 1
AKT1 -0.041 0.1 -10000 0 -0.47 24 24
PTK2B -0.012 0.069 0.36 2 -0.35 26 28
alphaV/beta3 Integrin/JAM-A -0.074 0.17 0.3 1 -0.33 259 260
CBL 0.022 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.033 0.07 -10000 0 -0.37 26 26
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.044 0.2 -10000 0 -0.39 216 216
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.014 0.063 -10000 0 -0.44 8 8
alphaV/beta3 Integrin/Syndecan-1 0.045 0.079 -10000 0 -0.36 26 26
PI4KA 0.023 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.27 -10000 0 -0.41 423 423
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 0.071 0.098 0.34 3 -0.36 26 29
RPS6KB1 -0.15 0.22 0.42 3 -0.44 277 280
TLN1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 -0.2 0.29 -10000 0 -0.54 369 369
GPR124 0.016 0.048 -10000 0 -0.58 6 6
MAPK1 -0.2 0.29 -10000 0 -0.55 359 359
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
alphaV/beta3 Integrin/Tumstatin -0.037 0.17 -10000 0 -0.38 189 189
cell adhesion 0.024 0.081 0.26 1 -0.37 35 36
ANGPTL3 0.021 0.016 0.26 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.045 0.028 -10000 0 -0.37 2 2
IGF-1R heterotetramer 0.011 0.086 0.26 2 -0.58 20 22
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
TGFBR2 0.005 0.11 -10000 0 -0.58 31 31
ITGB3 0.008 0.098 0.26 4 -0.58 26 30
IGF1 -0.1 0.24 -10000 0 -0.58 202 202
RAC1 0.024 0.004 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.026 0.074 -10000 0 -0.38 26 26
apoptosis 0.024 0.003 -10000 0 -10000 0 0
CD47 0.023 0.02 -10000 0 -0.58 1 1
alphaV/beta3 Integrin/CD47 0.035 0.069 -10000 0 -0.37 26 26
VCL 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.019 0.13 -10000 0 -0.46 56 56
CSF1 0.021 0.039 -10000 0 -0.58 4 4
PIK3C2A -0.04 0.11 -10000 0 -0.47 26 26
PI4 Kinase/Pyk2 -0.075 0.15 -10000 0 -0.31 220 220
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.046 0.075 -10000 0 -0.37 26 26
FAK1/Vinculin -0.037 0.13 0.31 6 -0.38 46 52
alphaV beta3/Integrin/ppsTEM5 0.026 0.075 -10000 0 -0.38 26 26
RHOA 0.023 0.005 -10000 0 -10000 0 0
VTN 0.034 0.072 0.26 58 -0.58 5 63
BCAR1 0.021 0.008 -10000 0 -10000 0 0
FGF2 -0.2 0.29 -10000 0 -0.58 364 364
F11R -0.12 0.2 -10000 0 -0.43 276 276
alphaV/beta3 Integrin/Lactadherin 0.03 0.086 0.34 1 -0.39 35 36
alphaV/beta3 Integrin/TGFBR2 0.024 0.11 -10000 0 -0.46 42 42
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.049 0.035 -10000 0 -0.34 4 4
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.034 0.062 -10000 0 -0.34 25 25
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.12 0.12 0.26 388 -10000 0 388
alphaV/beta3 Integrin/Pyk2 0.027 0.071 -10000 0 -0.35 26 26
SDC1 0.04 0.064 0.26 67 -0.58 1 68
VAV3 -0.011 0.042 -10000 0 -0.32 11 11
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0 0.12 -10000 0 -0.58 38 38
FAK1/Paxillin -0.036 0.14 0.31 7 -0.39 43 50
cell migration -0.036 0.12 0.3 7 -0.36 40 47
ITGAV 0.024 0.003 -10000 0 -10000 0 0
PI3K -0.063 0.17 0.26 1 -0.32 250 251
SPP1 0.086 0.1 0.26 255 -10000 0 255
KDR 0.022 0.034 -10000 0 -0.58 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.003 -10000 0 -10000 0 0
COL4A3 -0.085 0.23 0.26 4 -0.58 177 181
angiogenesis -0.18 0.3 0.28 1 -0.55 351 352
Rac1/GTP 0.021 0.039 -10000 0 -0.3 10 10
EDIL3 -0.002 0.13 0.26 15 -0.58 47 62
cell proliferation 0.023 0.11 -10000 0 -0.46 42 42
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.005 0.071 0.35 1 -0.35 9 10
alphaM/beta2 Integrin/GPIbA 0.009 0.077 0.34 5 -0.41 6 11
alphaM/beta2 Integrin/proMMP-9 0.075 0.11 0.3 27 -0.42 1 28
PLAUR 0.042 0.063 0.26 73 -10000 0 73
HMGB1 -0.004 0.04 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.009 0.063 0.35 1 -10000 0 1
AGER -0.007 0.051 -10000 0 -0.63 2 2
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 -0.027 0.14 0.33 4 -0.36 13 17
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 412 -0.58 1 413
CYR61 -0.006 0.13 -10000 0 -0.58 47 47
TLN1 0.024 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.001 0.11 -10000 0 -0.37 33 33
RHOA 0.023 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.095 0.24 -10000 0 -0.58 187 187
MYH2 -0.013 0.14 0.26 10 -0.48 34 44
MST1R 0.022 0.053 0.26 10 -0.58 6 16
leukocyte activation during inflammatory response -0.19 0.17 0.3 1 -0.33 570 571
APOB -0.35 0.29 -10000 0 -0.58 603 603
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.018 0.048 -10000 0 -0.58 6 6
JAM3 0.019 0.044 -10000 0 -0.58 5 5
GP1BA 0.024 0.06 0.26 23 -0.58 6 29
alphaM/beta2 Integrin/CTGF 0.004 0.077 0.35 1 -0.39 12 13
alphaM/beta2 Integrin -0.011 0.12 0.22 5 -0.39 40 45
JAM3 homodimer 0.019 0.043 -10000 0 -0.58 5 5
ICAM2 0.019 0.043 -10000 0 -0.58 5 5
ICAM1 0.028 0.03 0.26 15 -10000 0 15
phagocytosis triggered by activation of immune response cell surface activating receptor -0.01 0.12 0.23 6 -0.4 40 46
cell adhesion 0.009 0.076 0.34 5 -0.41 6 11
NFKB1 -0.1 0.2 0.42 4 -0.38 305 309
THY1 0.024 0.022 0.26 7 -10000 0 7
RhoA/GDP 0.017 0.003 -10000 0 -10000 0 0
Lipoprotein(a) -0.22 0.19 0.18 1 -0.36 609 610
alphaM/beta2 Integrin/LRP/tPA 0.007 0.09 0.34 1 -0.35 29 30
IL6 -0.26 0.39 0.35 3 -0.77 353 356
ITGB2 -0.002 0.052 0.26 13 -10000 0 13
elevation of cytosolic calcium ion concentration 0.031 0.086 0.34 19 -10000 0 19
alphaM/beta2 Integrin/JAM2/JAM3 -0.001 0.11 0.34 1 -0.37 45 46
JAM2 -0.006 0.13 -10000 0 -0.58 48 48
alphaM/beta2 Integrin/ICAM1 0.022 0.087 0.33 4 -0.33 16 20
alphaM/beta2 Integrin/uPA/Plg 0.018 0.07 0.34 1 -10000 0 1
RhoA/GTP -0.017 0.16 0.25 13 -0.48 41 54
positive regulation of phagocytosis -0.001 0.1 0.32 4 -0.34 23 27
Ron/MSP 0.029 0.063 0.37 1 -0.41 17 18
alphaM/beta2 Integrin/uPAR/uPA 0.032 0.088 0.35 19 -10000 0 19
alphaM/beta2 Integrin/uPAR 0.019 0.079 0.3 10 -10000 0 10
PLAU 0.03 0.039 0.26 27 -10000 0 27
PLAT 0.006 0.091 -10000 0 -0.58 23 23
actin filament polymerization -0.012 0.14 0.26 11 -0.45 34 45
MST1 0.019 0.056 0.26 2 -0.58 8 10
alphaM/beta2 Integrin/lipoprotein(a) -0.19 0.17 0.32 1 -0.33 569 570
TNF -0.1 0.2 0.36 6 -0.74 19 25
RAP1B 0.024 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.013 0.069 0.35 1 -10000 0 1
fibrinolysis 0.017 0.069 0.33 1 -10000 0 1
HCK 0.026 0.026 0.26 11 -10000 0 11
dendritic cell antigen processing and presentation -0.01 0.12 0.23 6 -0.4 40 46
VTN 0.034 0.072 0.26 58 -0.58 5 63
alphaM/beta2 Integrin/CYR61 -0.009 0.11 0.35 1 -0.38 50 51
LPA 0.018 0.018 0.26 5 -10000 0 5
LRP1 0.019 0.058 -10000 0 -0.58 9 9
cell migration 0.044 0.086 0.28 16 -0.36 8 24
FN1 0.12 0.12 0.26 388 -10000 0 388
alphaM/beta2 Integrin/Thy1 0.009 0.064 0.26 4 -10000 0 4
MPO -0.011 0.14 0.26 2 -0.58 53 55
KNG1 0.021 0.025 0.26 10 -10000 0 10
RAP1/GDP 0.031 0.008 -10000 0 -10000 0 0
ROCK1 -0.013 0.15 0.3 8 -0.48 35 43
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.018 0.016 0.26 4 -10000 0 4
CTGF 0.016 0.067 0.26 2 -0.58 12 14
alphaM/beta2 Integrin/Hck 0.01 0.067 0.32 6 -0.17 1 7
ITGAM -0.003 0.044 0.25 5 -10000 0 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.045 0.16 0.34 1 -0.37 170 171
HP -0.069 0.23 0.26 32 -0.58 158 190
leukocyte adhesion -0.04 0.14 0.29 4 -0.39 53 57
SELP -0.095 0.24 -10000 0 -0.58 187 187
Effects of Botulinum toxin

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
STX1A 0.011 0.026 0.14 37 -10000 0 37
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.032 0.11 -10000 0 -0.42 41 41
STXBP1 0.021 0.039 -10000 0 -0.58 4 4
ACh/CHRNA1 0.073 0.092 0.2 312 -0.16 7 319
RAB3GAP2/RIMS1/UNC13B 0.036 0.089 -10000 0 -0.37 30 30
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.025 0.15 0.26 108 -0.58 40 148
mol:ACh -0.004 0.037 0.091 11 -0.14 42 53
RAB3GAP2 0.02 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.021 0.084 0.24 1 -0.28 38 39
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.073 0.092 0.2 312 -0.16 7 319
UNC13B 0.024 0.004 -10000 0 -10000 0 0
CHRNA1 0.1 0.11 0.26 323 -10000 0 323
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.034 0.12 0.2 187 -0.37 41 228
SNAP25 -0.001 0.06 -10000 0 -0.31 32 32
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 0.048 0.16 0.26 195 -0.58 38 233
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.024 0.031 -10000 0 -0.37 4 4
STX1A/SNAP25 fragment 1/VAMP2 0.021 0.084 0.24 1 -0.28 38 39
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.016 0.08 -10000 0 -0.35 3 3
epithelial cell differentiation 0.032 0.078 -10000 0 -0.4 1 1
ITCH 0.032 0.018 -10000 0 -10000 0 0
WWP1 0.025 0.098 0.48 8 -10000 0 8
FYN 0.021 0.028 -10000 0 -0.58 2 2
EGFR -0.19 0.29 -10000 0 -0.58 349 349
PRL 0.022 0.025 0.26 10 -10000 0 10
neuron projection morphogenesis -0.05 0.14 0.35 12 -0.37 28 40
PTPRZ1 -0.28 0.3 0.26 6 -0.58 497 503
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.056 0.14 -10000 0 -0.38 37 37
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.09 0.16 -10000 0 -0.35 217 217
ADAM17 0.031 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.004 0.073 0.39 8 -0.33 4 12
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.002 0.12 -10000 0 -0.37 46 46
NCOR1 0.022 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.082 0.15 -10000 0 -0.33 203 203
GRIN2B -0.1 0.16 -10000 0 -0.43 75 75
ErbB4/ErbB2/betacellulin 0.014 0.096 -10000 0 -0.32 29 29
STAT1 0.028 0.032 0.26 18 -10000 0 18
HBEGF 0.023 0.027 -10000 0 -0.58 2 2
PRLR 0.022 0.046 0.26 4 -0.58 5 9
E4ICDs/ETO2 0.007 0.088 0.36 1 -0.42 11 12
axon guidance 0.055 0.11 0.4 8 -0.38 1 9
NEDD4 0.029 0.026 -10000 0 -0.56 1 1
Prolactin receptor/Prolactin receptor/Prolactin 0.032 0.037 0.2 10 -0.38 5 15
CBFA2T3 0.013 0.076 0.26 4 -0.58 15 19
ErbB4/ErbB2/HBEGF 0.031 0.071 -10000 0 -0.31 2 2
MAPK3 -0.053 0.14 0.28 1 -0.37 35 36
STAT1 (dimer) 0.02 0.081 0.29 1 -0.38 1 2
MAPK1 -0.051 0.14 0.39 2 -0.38 30 32
JAK2 0.023 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.074 0.15 -10000 0 -0.33 197 197
NRG1 -0.11 0.2 -10000 0 -0.43 264 264
NRG3 -0.008 0.15 0.26 18 -0.58 58 76
NRG2 -0.27 0.3 -10000 0 -0.58 478 478
NRG4 0.027 0.029 0.26 14 -10000 0 14
heart development 0.055 0.11 0.4 8 -0.38 1 9
neural crest cell migration -0.074 0.15 -10000 0 -0.33 198 198
ERBB2 0.035 0.07 0.27 79 -10000 0 79
WWOX/E4ICDs 0.012 0.076 -10000 0 -0.38 1 1
SHC1 0.02 0.009 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.097 0.17 -10000 0 -0.32 250 250
apoptosis 0.017 0.13 0.48 43 -10000 0 43
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.16 0.18 -10000 0 -0.35 367 367
ErbB4/ErbB2/epiregulin 0.007 0.13 0.36 12 -0.32 70 82
ErbB4/ErbB4/betacellulin/betacellulin -0.003 0.11 0.29 1 -0.36 39 40
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.04 0.086 -10000 0 -0.39 5 5
MDM2 0.01 0.08 0.3 8 -0.38 1 9
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.086 0.15 -10000 0 -0.33 218 218
STAT5A 0.05 0.11 0.36 10 -0.39 2 12
ErbB4/EGFR/neuregulin 1 beta -0.19 0.23 -10000 0 -0.44 403 403
DLG4 0.022 0.008 -10000 0 -10000 0 0
GRB2/SHC 0.028 0.016 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.011 0.07 -10000 0 -0.36 1 1
STAT5A (dimer) 0.058 0.1 -10000 0 -0.42 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.06 0.11 0.36 6 -0.36 2 8
LRIG1 0.022 0.028 -10000 0 -0.58 2 2
EREG -0.025 0.2 0.26 73 -0.58 107 180
BTC -0.007 0.13 0.26 2 -0.58 50 52
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.047 0.11 0.41 7 -0.38 1 8
ERBB4 -0.004 0.073 0.39 8 -0.33 4 12
STAT5B 0.022 0.028 -10000 0 -0.58 2 2
YAP1 -0.012 0.11 -10000 0 -0.38 65 65
GRB2 0.023 0.01 0.26 1 -10000 0 1
ErbB4/ErbB2/neuregulin 4 0.034 0.07 0.32 1 -10000 0 1
glial cell differentiation -0.011 0.069 0.35 1 -10000 0 1
WWOX 0.022 0.014 0.26 2 -10000 0 2
cell proliferation -0.04 0.17 0.35 9 -0.52 24 33
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.006 0.12 0.18 4 -0.35 93 97
EFNA5 -0.031 0.17 0.26 1 -0.58 88 89
FYN -0.024 0.1 0.18 7 -0.34 88 95
neuron projection morphogenesis -0.006 0.12 0.18 4 -0.35 93 97
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.006 0.12 0.18 4 -0.36 93 97
EPHA5 0.023 0.016 0.26 4 -10000 0 4
LPA receptor mediated events

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
GNB1/GNG2 0.034 0.073 -10000 0 -0.34 31 31
NF kappa B1 p50/RelA/I kappa B alpha 0 0.13 -10000 0 -0.41 17 17
AP1 -0.097 0.2 -10000 0 -0.34 352 352
mol:PIP3 -0.13 0.19 -10000 0 -0.34 377 377
AKT1 0.008 0.076 0.31 3 -0.42 10 13
PTK2B -0.029 0.1 -10000 0 -0.33 58 58
RHOA 0.002 0.063 0.22 6 -0.31 25 31
PIK3CB 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.11 0.26 3 -0.28 101 104
MAGI3 0.024 0.004 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
apoptosis -0.027 0.12 -10000 0 -0.32 132 132
HRAS/GDP 0.018 0.012 0.18 5 -10000 0 5
positive regulation of microtubule depolymerization -0.053 0.12 0.28 3 -0.31 134 137
NF kappa B1 p50/RelA -0.013 0.13 -10000 0 -0.33 94 94
endothelial cell migration 0.002 0.079 -10000 0 -0.44 27 27
ADCY4 -0.021 0.12 -10000 0 -0.5 39 39
ADCY5 -0.076 0.16 -10000 0 -0.44 90 90
ADCY6 -0.013 0.098 -10000 0 -0.46 30 30
ADCY7 -0.012 0.098 -10000 0 -0.47 30 30
ADCY1 -0.014 0.11 -10000 0 -0.48 34 34
ADCY2 -0.026 0.12 -10000 0 -0.49 43 43
ADCY3 -0.013 0.097 -10000 0 -0.47 28 28
ADCY8 -0.011 0.091 -10000 0 -0.46 26 26
ADCY9 -0.013 0.098 -10000 0 -0.46 30 30
GSK3B -0.029 0.099 0.31 2 -0.34 47 49
arachidonic acid secretion -0.018 0.1 -10000 0 -0.36 61 61
GNG2 0.017 0.061 -10000 0 -0.58 10 10
TRIP6 0.018 0.016 -10000 0 -0.41 1 1
GNAO1 0.002 0.083 -10000 0 -0.37 41 41
HRAS 0.025 0.018 0.26 5 -10000 0 5
NFKBIA -0.022 0.13 0.26 2 -0.34 107 109
GAB1 0.024 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.029 0.11 -10000 0 -0.82 17 17
JUN 0.019 0.054 -10000 0 -0.58 8 8
LPA/LPA2/NHERF2 0.031 0.018 -10000 0 -10000 0 0
TIAM1 0.015 0.13 -10000 0 -0.96 17 17
PIK3R1 0.02 0.047 -10000 0 -0.57 6 6
mol:IP3 -0.015 0.11 0.26 3 -0.29 101 104
PLCB3 0.025 0.044 0.2 1 -10000 0 1
FOS -0.15 0.27 -10000 0 -0.58 277 277
positive regulation of mitosis -0.018 0.1 -10000 0 -0.36 61 61
LPA/LPA1-2-3 0 0.14 -10000 0 -0.34 129 129
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 0.24 1 -0.36 43 44
GNAZ 0.003 0.068 -10000 0 -0.35 33 33
EGFR/PI3K-beta/Gab1 -0.13 0.2 -10000 0 -0.36 377 377
positive regulation of dendritic cell cytokine production -0.001 0.14 -10000 0 -0.34 129 129
LPA/LPA2/MAGI-3 0.033 0.016 0.18 1 -0.14 1 2
ARHGEF1 0.018 0.069 -10000 0 -0.31 21 21
GNAI2 0.006 0.058 -10000 0 -0.33 26 26
GNAI3 0.007 0.058 -10000 0 -0.33 26 26
GNAI1 -0.011 0.1 -10000 0 -0.38 67 67
LPA/LPA3 -0.027 0.14 0.18 33 -0.41 114 147
LPA/LPA2 0.019 0.015 0.18 2 -10000 0 2
LPA/LPA1 0.011 0.069 -10000 0 -0.38 28 28
HB-EGF/EGFR -0.078 0.2 0.27 2 -0.35 322 324
HBEGF 0.07 0.077 0.27 24 -0.43 3 27
mol:DAG -0.015 0.11 0.26 3 -0.29 101 104
cAMP biosynthetic process -0.032 0.11 0.31 2 -0.42 54 56
NFKB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
LYN -0.01 0.13 0.27 25 -0.33 88 113
GNAQ -0.021 0.11 0.21 1 -0.31 112 113
LPAR2 0.025 0.011 0.26 2 -10000 0 2
LPAR3 -0.037 0.2 0.26 33 -0.58 110 143
LPAR1 0.013 0.084 -10000 0 -0.5 23 23
IL8 -0.13 0.24 0.36 28 -0.41 315 343
PTK2 -0.023 0.1 0.24 1 -0.32 89 90
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
CASP3 -0.027 0.12 -10000 0 -0.32 132 132
EGFR -0.19 0.29 -10000 0 -0.58 349 349
PLCG1 -0.024 0.12 0.2 4 -0.33 112 116
PLD2 -0.028 0.12 0.24 1 -0.32 127 128
G12/G13 0.036 0.06 -10000 0 -0.32 22 22
PI3K-beta 0.002 0.074 -10000 0 -0.46 12 12
cell migration 0.002 0.062 -10000 0 -0.25 17 17
SLC9A3R2 0.023 0.01 0.26 1 -10000 0 1
PXN -0.018 0.1 0.24 1 -0.36 43 44
HRAS/GTP -0.018 0.11 -10000 0 -0.37 61 61
RAC1 0.024 0.004 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 412 -0.58 1 413
PRKCE 0.024 0.019 -10000 0 -0.58 1 1
PRKCD -0.016 0.11 0.27 2 -0.28 87 89
Gi(beta/gamma) -0.012 0.1 -10000 0 -0.44 39 39
mol:LPA 0.001 0.016 -10000 0 -0.18 5 5
TRIP6/p130 Cas/FAK1/Paxillin -0.015 0.12 -10000 0 -0.4 33 33
MAPKKK cascade -0.018 0.1 -10000 0 -0.36 61 61
contractile ring contraction involved in cytokinesis 0.001 0.064 0.22 6 -0.3 27 33
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.022 0.12 0.21 1 -0.32 118 119
GNA15 -0.02 0.11 0.21 2 -0.31 111 113
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
MAPT -0.055 0.13 0.28 3 -0.32 134 137
GNA11 -0.021 0.11 0.19 2 -0.31 112 114
Rac1/GTP 0.03 0.12 -10000 0 -0.87 17 17
MMP2 0.002 0.08 -10000 0 -0.44 27 27
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC 0.047 0.18 0.31 123 -0.5 45 168
FYN 0.023 0.2 0.37 45 -0.62 49 94
LAT/GRAP2/SLP76 0.027 0.18 0.36 44 -0.54 49 93
IKBKB 0.02 0.009 -10000 0 -10000 0 0
AKT1 0.024 0.16 0.32 76 -0.38 70 146
B2M 0.025 0.009 -10000 0 -10000 0 0
IKBKG 0.016 0.06 0.16 66 -0.14 26 92
MAP3K8 0.021 0.039 -10000 0 -0.58 4 4
mol:Ca2+ -0.023 0.032 -10000 0 -0.094 143 143
integrin-mediated signaling pathway 0.025 0.026 -10000 0 -0.36 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.012 0.21 0.4 39 -0.54 72 111
TRPV6 -0.089 0.27 1.2 15 -0.58 176 191
CD28 0.025 0.046 0.27 9 -0.58 4 13
SHC1 0.031 0.22 0.33 131 -0.62 51 182
receptor internalization -0.011 0.22 0.36 37 -0.51 117 154
PRF1 -0.011 0.25 0.57 7 -1 39 46
KRAS 0.023 0.005 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
COT/AKT1 0.033 0.14 0.3 73 -0.33 57 130
LAT 0.015 0.21 0.37 50 -0.63 54 104
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D 0.022 0.1 0.27 41 -0.58 19 60
CD3E 0.022 0.092 0.27 34 -0.59 16 50
CD3G 0.013 0.11 0.27 35 -0.58 29 64
RASGRP2 0 0.052 0.13 18 -0.17 65 83
RASGRP1 0.027 0.16 0.35 48 -0.44 47 95
HLA-A 0.026 0.023 0.27 7 -10000 0 7
RASSF5 0.018 0.035 0.26 1 -0.58 3 4
RAP1A/GTP/RAPL 0.026 0.026 -10000 0 -0.37 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.042 0.083 0.17 165 -0.13 25 190
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.056 -10000 0 -0.21 40 40
PRKCA 0.014 0.1 0.23 46 -0.28 44 90
GRAP2 0.016 0.071 0.26 3 -0.58 13 16
mol:IP3 0.013 0.14 0.26 117 -0.39 47 164
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.006 0.18 0.32 33 -0.65 50 83
ORAI1 0.036 0.17 0.64 3 -0.98 14 17
CSK 0.01 0.2 0.38 36 -0.64 53 89
B7 family/CD28 0.063 0.21 0.44 43 -0.64 44 87
CHUK 0.024 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.002 0.23 0.4 35 -0.67 64 99
PTPN6 0.009 0.2 0.37 37 -0.64 52 89
VAV1 0.005 0.2 0.39 35 -0.63 55 90
Monovalent TCR/CD3 -0.003 0.15 0.27 38 -0.53 51 89
CBL 0.022 0.007 -10000 0 -10000 0 0
LCK 0.02 0.21 0.38 41 -0.67 48 89
PAG1 0.022 0.21 0.35 57 -0.64 51 108
RAP1A 0.024 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.002 0.23 0.38 36 -0.67 61 97
CD80 0.089 0.11 0.26 264 -10000 0 264
CD86 0.026 0.018 0.27 5 -10000 0 5
PDK1/CARD11/BCL10/MALT1 -0.007 0.072 0.2 1 -0.26 39 40
HRAS 0.025 0.018 0.26 5 -10000 0 5
GO:0035030 0.023 0.16 0.34 42 -0.52 45 87
CD8A 0.028 0.06 0.28 25 -0.59 5 30
CD8B 0.013 0.12 0.28 27 -0.58 31 58
PTPRC 0.021 0.044 0.27 11 -0.58 3 14
PDK1/PKC theta 0.026 0.19 0.38 77 -0.5 58 135
CSK/PAG1 0.026 0.2 0.34 62 -0.62 49 111
SOS1 0.024 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.037 0.021 0.25 1 -10000 0 1
GRAP2/SLP76 0.021 0.2 0.41 32 -0.62 53 85
STIM1 0.025 0.099 1.3 4 -10000 0 4
RAS family/GTP 0.047 0.096 0.22 101 -0.19 31 132
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.015 0.24 0.38 35 -0.54 117 152
mol:DAG -0.017 0.099 0.14 20 -0.35 49 69
RAP1A/GDP 0.022 0.038 0.098 93 -10000 0 93
PLCG1 0.023 0.005 -10000 0 -10000 0 0
CD247 0.016 0.083 0.27 18 -0.58 15 33
cytotoxic T cell degranulation -0.008 0.23 0.55 8 -0.92 40 48
RAP1A/GTP -0.001 0.017 -10000 0 -0.065 60 60
mol:PI-3-4-5-P3 0.019 0.18 0.36 51 -0.45 72 123
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.02 0.17 0.3 108 -0.51 47 155
NRAS 0.024 0.004 -10000 0 -10000 0 0
ZAP70 0.024 0.1 0.26 48 -0.58 20 68
GRB2/SOS1 0.034 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.005 0.16 0.42 11 -0.52 49 60
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.03 0.11 0.33 27 -0.49 31 58
CARD11 0.028 0.045 0.26 22 -0.58 2 24
PRKCB 0.014 0.1 0.26 48 -0.29 41 89
PRKCE 0.018 0.097 0.22 59 -0.26 40 99
PRKCQ 0.015 0.2 0.4 42 -0.56 62 104
LCP2 0.024 0.009 0.26 1 -10000 0 1
BCL10 0.024 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0.027 0.14 0.3 79 -0.33 65 144
IKK complex 0.036 0.085 0.22 111 -0.12 14 125
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.027 0.11 0.25 78 -0.27 42 120
PDPK1 0.029 0.16 0.34 78 -0.38 56 134
TCR/CD3/MHC I/CD8/Fyn -0.024 0.25 0.42 27 -0.75 66 93
IL6-mediated signaling 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
BCL2L1 -0.021 0.23 0.57 7 -0.7 18 25
CRP 0 0.24 0.57 26 -0.69 20 46
cell cycle arrest -0.031 0.25 0.57 11 -0.7 36 47
TIMP1 -0.015 0.22 0.54 10 -0.61 25 35
IL6ST -0.026 0.17 -10000 0 -0.57 89 89
Rac1/GDP -0.063 0.2 0.33 8 -0.43 105 113
AP1 -0.07 0.21 0.38 2 -0.48 92 94
GAB2 0.022 0.008 -10000 0 -10000 0 0
TNFSF11 -0.009 0.24 0.63 10 -0.74 14 24
HSP90B1 0.024 0.11 -10000 0 -0.74 12 12
GAB1 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.091 0.17 -10000 0 -0.52 76 76
AKT1 0.024 0.058 -10000 0 -0.52 4 4
FOXO1 0.025 0.06 0.43 1 -0.49 3 4
MAP2K6 -0.091 0.18 0.28 2 -0.42 136 138
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.046 0.2 0.4 11 -0.48 68 79
MITF -0.084 0.19 0.28 10 -0.4 153 163
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 -0.006 0.19 -10000 0 -1.2 25 25
CEBPB 0.021 0.018 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.014 0.12 -10000 0 -0.48 32 32
STAT3 -0.038 0.27 0.58 10 -0.78 36 46
STAT1 0.014 0.089 -10000 0 -0.82 8 8
CEBPD -0.007 0.24 0.57 14 -0.76 17 31
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.032 0.036 -10000 0 -0.36 7 7
JUN 0.019 0.055 -10000 0 -0.58 8 8
PIAS3/MITF -0.069 0.19 0.34 2 -0.45 90 92
MAPK11 -0.091 0.18 -10000 0 -0.52 77 77
STAT3 (dimer)/FOXO1 -0.018 0.22 0.54 11 -0.59 30 41
GRB2/SOS1/GAB family -0.055 0.18 -10000 0 -0.47 65 65
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.097 0.19 0.25 1 -0.34 285 286
GRB2 0.023 0.01 0.26 1 -10000 0 1
JAK2 0.023 0.006 -10000 0 -10000 0 0
LBP -0.16 0.45 0.56 23 -0.93 220 243
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
JAK1 0.026 0.009 -10000 0 -10000 0 0
MYC 0.004 0.28 0.57 21 -1 25 46
FGG -0.018 0.24 0.57 18 -0.67 23 41
macrophage differentiation -0.031 0.25 0.57 11 -0.7 36 47
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.09 0.21 -10000 0 -0.35 325 325
JUNB -0.024 0.22 0.54 8 -0.65 22 30
FOS -0.15 0.27 -10000 0 -0.58 277 277
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.087 0.2 0.31 10 -0.42 159 169
STAT1/PIAS1 -0.054 0.2 0.37 9 -0.39 147 156
GRB2/SOS1/GAB family/SHP2/PI3K 0.026 0.062 -10000 0 -0.49 6 6
STAT3 (dimer) -0.036 0.26 0.58 10 -0.76 35 45
PRKCD -0.029 0.2 0.46 15 -0.52 45 60
IL6R 0.003 0.11 -10000 0 -0.58 31 31
SOCS3 -0.088 0.19 -10000 0 -0.67 40 40
gp130 (dimer)/JAK1/JAK1/LMO4 0.019 0.13 -10000 0 -0.36 89 89
Rac1/GTP -0.057 0.2 0.35 9 -0.46 89 98
HCK 0.026 0.026 0.26 11 -10000 0 11
MAPKKK cascade 0.003 0.13 -10000 0 -0.57 28 28
bone resorption -0.007 0.23 0.61 11 -0.68 15 26
IRF1 -0.024 0.23 0.56 8 -0.69 19 27
mol:GDP -0.078 0.19 0.3 10 -0.4 156 166
SOS1 0.024 0.004 -10000 0 -10000 0 0
VAV1 -0.08 0.19 0.3 10 -0.4 156 166
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.099 0.19 -10000 0 -0.56 85 85
PTPN11 0.012 0.081 -10000 0 -0.85 7 7
IL6/IL6RA -0.12 0.22 -10000 0 -0.43 296 296
gp130 (dimer)/TYK2/TYK2/LMO4 0.014 0.12 -10000 0 -0.36 90 90
gp130 (dimer)/JAK2/JAK2/LMO4 0.014 0.12 -10000 0 -0.36 87 87
IL6 -0.18 0.29 0.28 1 -0.57 342 343
PIAS3 0.023 0.006 -10000 0 -10000 0 0
PTPRE 0.007 0.032 -10000 0 -0.58 1 1
PIAS1 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.1 0.18 0.23 2 -0.32 318 320
LMO4 0.028 0.038 0.28 2 -0.57 3 5
STAT3 (dimer)/PIAS3 -0.04 0.25 0.56 8 -0.72 37 45
MCL1 0.057 0.094 0.49 1 -0.51 3 4
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.008 0.26 1 -10000 0 1
CCL5 0.03 0.056 0.26 35 -0.58 3 38
SDCBP 0.021 0.008 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.066 0.13 0.3 21 -0.39 13 34
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 0.052 0.12 0.28 6 -0.37 17 23
Syndecan-1/Syntenin 0.054 0.12 0.29 11 -0.39 13 24
MAPK3 0.05 0.12 0.27 12 -0.36 13 25
HGF/MET -0.066 0.2 -10000 0 -0.46 199 199
TGFB1/TGF beta receptor Type II 0.024 0.008 0.26 1 -10000 0 1
BSG 0.023 0.005 -10000 0 -10000 0 0
keratinocyte migration 0.052 0.12 0.27 6 -0.37 17 23
Syndecan-1/RANTES 0.063 0.14 0.32 38 -0.4 18 56
Syndecan-1/CD147 0.067 0.13 0.3 13 -0.36 16 29
Syndecan-1/Syntenin/PIP2 0.05 0.12 0.27 11 -0.38 13 24
LAMA5 0.023 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.048 0.11 0.26 10 -0.37 13 23
MMP7 -0.039 0.2 0.26 30 -0.58 110 140
HGF -0.013 0.14 -10000 0 -0.58 60 60
Syndecan-1/CASK 0.045 0.12 0.25 16 -0.37 17 33
Syndecan-1/HGF/MET -0.001 0.2 0.3 5 -0.46 99 104
regulation of cell adhesion 0.044 0.11 0.26 10 -0.39 8 18
HPSE 0.027 0.037 0.26 17 -0.58 1 18
positive regulation of cell migration 0.066 0.13 0.3 21 -0.39 13 34
SDC1 0.069 0.12 0.3 20 -0.42 9 29
Syndecan-1/Collagen 0.066 0.13 0.3 21 -0.39 13 34
PPIB 0.024 0.014 0.26 3 -10000 0 3
MET -0.072 0.22 -10000 0 -0.58 155 155
PRKACA 0.024 0.003 -10000 0 -10000 0 0
MMP9 0.12 0.12 0.26 412 -0.58 1 413
MAPK1 0.051 0.12 0.28 12 -0.4 8 20
homophilic cell adhesion 0.066 0.13 0.3 21 -0.38 14 35
MMP1 0.19 0.11 0.26 667 -10000 0 667
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 -0.044 0.23 0.42 4 -0.64 105 109
IHH 0.014 0.082 0.27 27 -0.23 15 42
SHH Np/Cholesterol/GAS1 0 0.076 -10000 0 -0.34 44 44
LRPAP1 0.023 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0 0.076 0.33 44 -10000 0 44
SMO/beta Arrestin2 -0.021 0.21 -10000 0 -0.61 90 90
SMO -0.044 0.21 -10000 0 -0.64 90 90
AKT1 -0.004 0.13 -10000 0 -0.52 26 26
ARRB2 0.022 0.007 -10000 0 -10000 0 0
BOC -0.019 0.15 -10000 0 -0.58 69 69
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
heart looping -0.043 0.21 -10000 0 -0.63 90 90
STIL 0.006 0.18 0.3 28 -0.49 76 104
DHH N/PTCH2 -0.012 0.15 -10000 0 -0.43 99 99
DHH N/PTCH1 -0.029 0.2 -10000 0 -0.5 133 133
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
DHH 0.008 0.098 0.26 2 -0.58 26 28
PTHLH -0.066 0.31 0.43 11 -0.83 114 125
determination of left/right symmetry -0.043 0.21 -10000 0 -0.63 90 90
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
skeletal system development -0.065 0.3 0.43 11 -0.82 114 125
IHH N/Hhip 0.026 0.057 -10000 0 -0.47 2 2
DHH N/Hhip 0.022 0.079 -10000 0 -0.42 28 28
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.043 0.21 -10000 0 -0.63 90 90
pancreas development 0.023 0.034 0.26 7 -0.58 2 9
HHAT 0.02 0.021 -10000 0 -0.58 1 1
PI3K 0.031 0.036 -10000 0 -0.36 7 7
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.008 0.14 -10000 0 -0.58 52 52
somite specification -0.043 0.21 -10000 0 -0.63 90 90
SHH Np/Cholesterol/PTCH1 -0.026 0.16 0.28 2 -0.49 85 87
SHH Np/Cholesterol/PTCH2 -0.007 0.088 -10000 0 -0.34 59 59
SHH Np/Cholesterol/Megalin -0.059 0.15 0.28 3 -0.34 201 204
SHH 0 0.038 0.36 6 -0.43 1 7
catabolic process -0.034 0.21 0.35 1 -0.56 117 118
SMO/Vitamin D3 -0.01 0.2 0.36 15 -0.57 82 97
SHH Np/Cholesterol/Hhip 0.016 0.034 0.31 5 -0.34 3 8
LRP2 -0.12 0.27 0.26 25 -0.58 243 268
receptor-mediated endocytosis -0.08 0.22 0.3 9 -0.62 97 106
SHH Np/Cholesterol/BOC -0.005 0.087 -10000 0 -0.34 58 58
SHH Np/Cholesterol/CDO 0.012 0.042 -10000 0 -0.34 12 12
mesenchymal cell differentiation -0.015 0.034 0.34 3 -0.31 5 8
mol:Vitamin D3 0.001 0.18 0.34 19 -0.5 84 103
IHH N/PTCH2 -0.011 0.14 -10000 0 -0.46 78 78
CDON 0.014 0.067 -10000 0 -0.58 12 12
IHH N/PTCH1 -0.025 0.21 0.35 3 -0.56 117 120
Megalin/LRPAP1 -0.078 0.2 -10000 0 -0.43 243 243
PTCH2 -0.022 0.16 -10000 0 -0.58 74 74
SHH Np/Cholesterol 0.01 0.014 -10000 0 -0.34 1 1
PTCH1 -0.034 0.21 0.35 1 -0.56 117 118
HHIP 0.023 0.034 0.26 7 -0.58 2 9
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.034 0.1 1.1 1 -10000 0 1
VDR 0.024 0.003 -10000 0 -10000 0 0
FAM120B 0.023 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.029 0.12 0.25 3 -0.39 11 14
RXRs/LXRs/DNA/Oxysterols -0.011 0.12 -10000 0 -0.44 16 16
MED1 0.021 0.008 -10000 0 -10000 0 0
mol:9cRA 0.003 0.01 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.001 0.083 -10000 0 -0.31 51 51
RXRs/NUR77 -0.052 0.18 -10000 0 -0.36 240 240
RXRs/PPAR -0.1 0.17 -10000 0 -0.32 317 317
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 9 9
RARA 0.022 0.007 -10000 0 -10000 0 0
NCOA1 0.023 0.02 -10000 0 -0.58 1 1
VDR/VDR/DNA 0.024 0.003 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.037 0.039 -10000 0 -0.32 9 9
RARG 0.024 0.002 -10000 0 -10000 0 0
RPS6KB1 0.07 0.18 0.61 88 -10000 0 88
RARs/THRs/DNA/SMRT 0.003 0.08 -10000 0 -0.3 53 53
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 -0.032 0.15 -10000 0 -0.33 200 200
NR1H4 0.02 0.022 0.26 8 -10000 0 8
RXRs/LXRs/DNA -0.011 0.16 -10000 0 -0.31 182 182
NR1H2 0.027 0.013 -10000 0 -10000 0 0
NR1H3 0.027 0.012 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.025 0.15 -10000 0 -0.31 199 199
NR4A1 -0.025 0.16 -10000 0 -0.58 79 79
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.033 0.1 -10000 0 -0.24 175 175
RXRG -0.1 0.24 0.26 2 -0.57 202 204
RXR alpha/CCPG 0.035 0.014 -10000 0 -10000 0 0
RXRA 0.026 0.013 -10000 0 -10000 0 0
RXRB 0.027 0.012 -10000 0 -10000 0 0
THRB -0.006 0.13 -10000 0 -0.58 48 48
PPARG -0.11 0.25 -10000 0 -0.58 215 215
PPARD 0.024 0.004 -10000 0 -10000 0 0
TNF -0.015 0.15 0.37 3 -1 11 14
mol:Oxysterols 0.003 0.009 -10000 0 -10000 0 0
cholesterol transport -0.009 0.12 -10000 0 -0.43 16 16
PPARA 0.021 0.028 -10000 0 -0.58 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.017 0.064 -10000 0 -0.58 11 11
RXRs/NUR77/BCL2 -0.071 0.15 -10000 0 -0.3 255 255
SREBF1 -0.01 0.11 -10000 0 -0.52 4 4
RXRs/RXRs/DNA/9cRA -0.032 0.15 -10000 0 -0.33 200 200
ABCA1 -0.014 0.13 -10000 0 -0.8 8 8
RARs/THRs 0.041 0.096 -10000 0 -0.34 51 51
RXRs/FXR -0.029 0.16 -10000 0 -0.34 199 199
BCL2 0.006 0.1 -10000 0 -0.58 28 28
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 -0.016 0.14 0.43 71 -0.25 2 73
KIRREL -0.021 0.16 -10000 0 -0.58 73 73
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.016 0.14 0.25 2 -0.43 71 73
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 0.036 0.12 0.29 4 -0.33 70 74
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.009 0.087 0.24 1 -0.29 58 59
FYN 0.017 0.13 0.28 104 -0.31 69 173
mol:Ca2+ 0.033 0.11 0.31 1 -0.32 67 68
mol:DAG 0.034 0.11 0.32 1 -0.32 67 68
NPHS2 0.014 0.031 0.27 4 -10000 0 4
mol:IP3 0.034 0.11 0.32 1 -0.32 67 68
regulation of endocytosis 0.024 0.1 0.24 5 -0.3 69 74
Nephrin/NEPH1/podocin/Cholesterol 0.025 0.11 0.25 9 -0.32 70 79
establishment of cell polarity 0.016 0.14 0.25 2 -0.43 71 73
Nephrin/NEPH1/podocin/NCK1-2 0.045 0.11 0.32 1 -0.3 68 69
Nephrin/NEPH1/beta Arrestin2 0.028 0.11 0.25 5 -0.3 69 74
NPHS1 0.06 0.092 0.26 152 -10000 0 152
Nephrin/NEPH1/podocin 0.026 0.11 0.31 4 -0.32 69 73
TJP1 0.023 0.02 -10000 0 -0.58 1 1
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.035 0.12 0.32 1 -0.33 67 68
CD2AP 0.024 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.033 0.11 0.3 5 -0.33 67 72
GRB2 0.023 0.01 0.26 1 -10000 0 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.015 0.14 0.29 97 -0.32 76 173
cytoskeleton organization 0.005 0.11 0.29 11 -0.34 54 65
Nephrin/NEPH1 0.017 0.1 0.19 7 -0.3 71 78
Nephrin/NEPH1/ZO-1 0.027 0.12 -10000 0 -0.35 71 71
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 0.032 0.045 -10000 0 -0.32 13 13
RGS9BP 0.036 0.053 0.26 49 -10000 0 49
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.019 0.017 0.26 4 -10000 0 4
mol:Na + 0.037 0.045 -10000 0 -10000 0 0
mol:ADP -0.006 0.027 0.25 5 -10000 0 5
GNAT2 0.024 0.014 0.26 3 -10000 0 3
RGS9-1/Gbeta5/R9AP 0.014 0.12 0.34 1 -0.36 82 83
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.014 -10000 0 -10000 0 0
GRK7 0.023 0.022 0.26 8 -10000 0 8
CNGB3 0.021 0.036 0.26 20 -10000 0 20
Cone Metarhodopsin II/X-Arrestin 0.015 0.015 0.18 8 -10000 0 8
mol:Ca2+ 0.13 0.11 0.3 166 -10000 0 166
Cone PDE6 0.028 0.11 0.33 2 -0.32 78 80
Cone Metarhodopsin II 0.026 0.018 -10000 0 -10000 0 0
Na + (4 Units) 0.12 0.094 0.32 60 -10000 0 60
GNAT2/GDP 0.022 0.11 0.32 1 -0.31 81 82
GNB5 0.024 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.005 0.036 0.21 3 -10000 0 3
Cone Transducin 0.034 0.048 -10000 0 -0.34 13 13
SLC24A2 0.16 0.12 0.26 576 -10000 0 576
GNB3/GNGT2 0.025 0.056 -10000 0 -0.41 14 14
GNB3 0.016 0.068 0.26 3 -0.58 12 15
GNAT2/GTP 0.018 0.01 0.18 3 -10000 0 3
CNGA3 0.046 0.07 0.26 91 -10000 0 91
ARR3 0.021 0.022 0.26 8 -10000 0 8
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.037 0.045 -10000 0 -10000 0 0
mol:Pi 0.013 0.12 0.34 1 -0.36 82 83
Cone CNG Channel 0.049 0.044 0.29 2 -10000 0 2
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.16 0.12 0.26 576 -10000 0 576
RGS9 -0.027 0.17 0.26 10 -0.58 84 94
PDE6C 0.02 0.009 0.26 1 -10000 0 1
GNGT2 0.021 0.028 -10000 0 -0.58 2 2
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.019 0.017 0.26 4 -10000 0 4
PDGFR-alpha signaling pathway

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
PDGFRA -0.032 0.14 -10000 0 -0.6 56 56
PDGF/PDGFRA/CRKL -0.011 0.11 -10000 0 -0.43 55 55
positive regulation of JUN kinase activity 0.024 0.083 -10000 0 -0.34 42 42
CRKL 0.023 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.013 0.11 -10000 0 -0.43 58 58
AP1 -0.3 0.44 -10000 0 -0.97 293 293
mol:IP3 -0.035 0.11 -10000 0 -0.46 52 52
PLCG1 -0.035 0.11 -10000 0 -0.46 52 52
PDGF/PDGFRA/alphaV Integrin -0.011 0.11 -10000 0 -0.43 56 56
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.035 0.11 -10000 0 -0.46 52 52
CAV3 0.02 0.012 0.26 2 -10000 0 2
CAV1 -0.096 0.24 -10000 0 -0.58 194 194
SHC/Grb2/SOS1 0.025 0.084 -10000 0 -0.34 42 42
PDGF/PDGFRA/Shf -0.01 0.11 -10000 0 -0.43 58 58
FOS -0.3 0.44 -10000 0 -0.95 293 293
JUN -0.038 0.046 -10000 0 -0.45 6 6
oligodendrocyte development -0.011 0.11 -10000 0 -0.43 56 56
GRB2 0.023 0.01 0.26 1 -10000 0 1
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
mol:DAG -0.035 0.11 -10000 0 -0.46 52 52
PDGF/PDGFRA -0.032 0.14 -10000 0 -0.6 56 56
actin cytoskeleton reorganization -0.01 0.11 -10000 0 -0.42 59 59
SRF 0.016 0.013 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
PI3K 0.014 0.1 -10000 0 -0.37 59 59
PDGF/PDGFRA/Crk/C3G 0.016 0.097 -10000 0 -0.37 56 56
JAK1 -0.026 0.1 0.23 1 -0.43 55 56
ELK1/SRF -0.035 0.089 0.32 1 -0.36 54 55
SHB 0.024 0.009 0.26 1 -10000 0 1
SHF 0.023 0.021 0.26 1 -0.58 1 2
CSNK2A1 0.036 0.023 -10000 0 -10000 0 0
GO:0007205 -0.046 0.11 0.22 1 -0.48 54 55
SOS1 0.024 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.024 0.083 -10000 0 -0.34 42 42
PDGF/PDGFRA/SHB -0.01 0.11 -10000 0 -0.42 59 59
PDGF/PDGFRA/Caveolin-1 -0.097 0.22 -10000 0 -0.48 224 224
ITGAV 0.024 0.003 -10000 0 -10000 0 0
ELK1 -0.053 0.1 -10000 0 -0.44 54 54
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.011 0.11 -10000 0 -0.43 56 56
JAK-STAT cascade -0.026 0.1 0.23 1 -0.43 55 56
cell proliferation -0.01 0.11 -10000 0 -0.42 58 58
Canonical Wnt 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
HDAC1 0.022 0.021 0.25 2 -10000 0 2
AES 0.022 0.02 0.25 1 -10000 0 1
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 0.088 0.26 2 -0.58 21 23
TLE1 0.018 0.055 0.22 2 -0.58 7 9
MACF1 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.1 0.1 0.32 28 -0.35 4 32
WIF1 -0.28 0.3 0.26 11 -0.58 491 502
beta catenin/RanBP3 0.02 0.089 0.42 32 -0.39 1 33
KREMEN2 0.13 0.12 0.26 425 -10000 0 425
DKK1 0.025 0.16 0.26 129 -0.58 49 178
beta catenin/beta TrCP1 0.11 0.094 0.31 26 -0.35 2 28
FZD1 0.024 0.004 -10000 0 -10000 0 0
AXIN2 0.018 0.25 0.6 77 -1.3 19 96
AXIN1 0.023 0.007 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.048 0.072 -10000 0 -0.53 11 11
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.064 0.13 0.38 3 -0.63 18 21
Axin1/APC/GSK3 0.046 0.055 0.24 1 -0.31 1 2
Axin1/APC/GSK3/beta catenin/Macf1 0.043 0.061 0.31 2 -0.36 3 5
HNF1A 0.024 0.027 0.25 8 -10000 0 8
CTBP1 0.021 0.02 0.24 2 -10000 0 2
MYC 0.11 0.34 0.58 239 -1.3 23 262
RANBP3 0.024 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.094 0.098 0.34 1 -0.34 16 17
NKD1 0.021 0.056 0.26 14 -0.58 6 20
TCF4 0.016 0.06 0.24 3 -0.57 9 12
TCF3 0.022 0.024 0.3 3 -10000 0 3
WNT1/LRP6/FZD1/Axin1 0.057 0.023 -10000 0 -10000 0 0
Ran/GTP 0.018 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.004 0.13 0.48 31 -0.5 16 47
LEF1 0.053 0.085 0.26 129 -0.54 1 130
DVL1 0.054 0.053 -10000 0 -0.36 2 2
CSNK2A1 0.024 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.068 0.15 0.3 6 -0.63 24 30
DKK1/LRP6/Kremen 2 0.099 0.14 0.35 69 -0.34 43 112
LRP6 0.024 0.005 -10000 0 -10000 0 0
CSNK1A1 0.023 0.022 0.27 3 -10000 0 3
NLK 0.023 0.015 0.26 2 -10000 0 2
CCND1 0.089 0.26 0.61 158 -1.2 5 163
WNT1 0.024 0.012 0.26 2 -10000 0 2
GSK3A 0.025 0.003 -10000 0 -10000 0 0
GSK3B 0.024 0.003 -10000 0 -10000 0 0
FRAT1 0.024 0.003 -10000 0 -10000 0 0
PPP2R5D 0.037 0.058 0.3 5 -0.29 10 15
APC 0.015 0.057 0.36 7 -10000 0 7
WNT1/LRP6/FZD1 0.12 0.11 0.22 462 -0.24 1 463
CREBBP 0.021 0.019 0.22 2 -10000 0 2
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.38 0.28 -10000 0 -0.58 657 657
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.027 0.26 12 -10000 0 12
TCEB1 0.02 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.03 0.048 -10000 0 -0.26 14 14
HIF1A 0.004 0.03 -10000 0 -0.26 11 11
COPS5 0.021 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.054 0.036 -10000 0 -10000 0 0
FIH (dimer) 0.024 0.003 -10000 0 -10000 0 0
CDKN2A 0.059 0.087 0.26 151 -10000 0 151
ARNT/IPAS -0.25 0.21 -10000 0 -0.38 663 663
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 -0.27 14 14
CUL2 0.024 0.004 -10000 0 -10000 0 0
OS9 0.024 0.003 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.04 0.026 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.032 0.049 -10000 0 -0.27 14 14
PHD1-3/OS9 0.055 0.049 -10000 0 -0.34 2 2
HIF1A/RACK1/Elongin B/Elongin C 0.041 0.052 -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 0.049 -10000 0 -0.28 13 13
EGLN3 0.04 0.065 0.26 70 -0.58 1 71
EGLN2 0.025 0.018 0.26 5 -10000 0 5
EGLN1 0.019 0.021 -10000 0 -0.58 1 1
TP53 0.022 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.028 0.068 -10000 0 -0.52 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 0.073 0.24 34 -0.27 12 46
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.001 0.06 0.22 2 -0.32 6 8
adherens junction organization -0.015 0.093 -10000 0 -0.34 50 50
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.087 0.15 0.34 3 -0.33 103 106
FMN1 -0.014 0.091 -10000 0 -0.32 55 55
mol:IP3 0 0.051 -10000 0 -0.27 7 7
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.008 0.089 -10000 0 -0.32 48 48
CTNNB1 0.025 0.005 -10000 0 -10000 0 0
AKT1 0.003 0.061 -10000 0 -0.28 7 7
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.013 0.13 -10000 0 -0.53 37 37
CTNND1 0.024 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.01 0.077 -10000 0 -0.3 44 44
VASP -0.011 0.082 -10000 0 -0.3 46 46
ZYX -0.01 0.083 -10000 0 -0.3 47 47
JUB -0.01 0.084 -10000 0 -0.3 48 48
EGFR(dimer) -0.11 0.18 -10000 0 -0.33 342 342
E-cadherin/beta catenin-gamma catenin 0.032 0.06 -10000 0 -0.36 19 19
mol:PI-3-4-5-P3 0.016 0.072 -10000 0 -0.29 7 7
PIK3CA 0.024 0.006 -10000 0 -10000 0 0
PI3K 0.017 0.073 -10000 0 -0.3 7 7
FYN -0.004 0.064 0.22 1 -0.36 4 5
mol:Ca2+ 0 0.05 -10000 0 -0.27 7 7
JUP 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.021 0.047 -10000 0 -0.58 6 6
mol:DAG 0 0.051 -10000 0 -0.27 7 7
CDH1 0.01 0.083 -10000 0 -0.58 19 19
RhoA/GDP -0.086 0.15 0.36 2 -0.34 97 99
establishment of polarity of embryonic epithelium -0.01 0.081 -10000 0 -0.3 46 46
SRC 0.023 0.005 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
RHOA 0.023 0.005 -10000 0 -10000 0 0
EGFR -0.19 0.29 -10000 0 -0.58 349 349
CASR -0.003 0.053 0.23 2 -0.27 5 7
RhoA/GTP 0.014 0.055 -10000 0 -0.26 5 5
AKT2 0.001 0.062 -10000 0 -0.28 6 6
actin cable formation -0.018 0.09 0.25 2 -0.33 42 44
apoptosis -0.004 0.071 0.28 18 -0.23 7 25
CTNNA1 0.024 0.005 -10000 0 -10000 0 0
mol:GDP -0.099 0.15 -10000 0 -0.3 309 309
PIP5K1A -0.01 0.079 -10000 0 -0.31 44 44
PLCG1 -0.001 0.051 -10000 0 -0.28 6 6
Rac1/GTP -0.095 0.17 -10000 0 -0.31 340 340
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.037 0.15 0.36 59 -0.35 51 110
TBX21 0.009 0.35 0.77 22 -1.2 49 71
B2M 0.025 0.011 -10000 0 -10000 0 0
TYK2 0.023 0.037 -10000 0 -10000 0 0
IL12RB1 0.032 0.072 0.33 37 -0.62 1 38
GADD45B 0.033 0.26 0.68 20 -0.92 28 48
IL12RB2 0.024 0.16 0.27 107 -0.58 42 149
GADD45G 0.049 0.27 0.67 27 -0.88 28 55
natural killer cell activation 0.007 0.026 0.16 5 -10000 0 5
RELB 0.026 0.023 0.26 9 -10000 0 9
RELA 0.024 0.004 -10000 0 -10000 0 0
IL18 0.034 0.043 0.28 25 -10000 0 25
IL2RA 0.03 0.085 0.26 54 -0.58 11 65
IFNG 0.055 0.083 0.26 133 -10000 0 133
STAT3 (dimer) 0.031 0.25 0.58 36 -0.7 44 80
HLA-DRB5 0.024 0.081 0.25 70 -0.58 5 75
FASLG 0.048 0.3 0.76 29 -1 35 64
NF kappa B2 p52/RelB 0.015 0.25 0.69 5 -0.78 49 54
CD4 0.009 0.025 -10000 0 -10000 0 0
SOCS1 0.025 0.033 0.26 12 -0.58 1 13
EntrezGene:6955 -0.006 0.016 -10000 0 -10000 0 0
CD3D 0.007 0.1 0.27 39 -0.59 19 58
CD3E 0.008 0.094 0.27 34 -0.58 16 50
CD3G 0 0.12 0.27 35 -0.59 29 64
IL12Rbeta2/JAK2 0.033 0.13 0.3 29 -0.43 44 73
CCL3 0.028 0.28 0.75 19 -1 29 48
CCL4 0.03 0.28 0.75 19 -0.98 27 46
HLA-A 0.027 0.022 0.27 6 -10000 0 6
IL18/IL18R 0.063 0.12 0.36 22 -0.38 48 70
NOS2 0.028 0.28 0.72 21 -0.94 36 57
IL12/IL12R/TYK2/JAK2/SPHK2 0.035 0.15 0.36 56 -0.34 55 111
IL1R1 0.015 0.31 0.73 19 -1.1 36 55
IL4 -0.011 0.038 -10000 0 -10000 0 0
JAK2 0.022 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 31 -0.76 55 86
RAB7A 0.046 0.24 0.66 18 -0.8 22 40
lysosomal transport 0.048 0.23 0.63 22 -0.75 22 44
FOS -0.32 0.63 0.62 14 -1.2 318 332
STAT4 (dimer) 0.058 0.29 0.61 36 -0.86 44 80
STAT5A (dimer) 0.043 0.28 0.63 42 -0.77 50 92
GZMA 0.02 0.3 0.7 31 -1.1 31 62
GZMB 0.022 0.32 0.74 26 -1.1 38 64
HLX 0.021 0.014 0.26 2 -10000 0 2
LCK 0.023 0.3 0.7 33 -0.85 54 87
TCR/CD3/MHC II/CD4 -0.049 0.18 0.28 26 -0.47 95 121
IL2/IL2R 0.067 0.099 0.43 37 -0.36 16 53
MAPK14 0.042 0.28 0.67 24 -0.88 34 58
CCR5 0.033 0.27 0.72 26 -0.89 32 58
IL1B 0.017 0.081 0.31 3 -0.59 13 16
STAT6 0.039 0.12 0.42 31 -0.52 5 36
STAT4 -0.001 0.12 0.26 1 -0.58 41 42
STAT3 0.023 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.032 0.26 18 -10000 0 18
NFKB1 0.024 0.004 -10000 0 -10000 0 0
NFKB2 0.024 0.008 0.26 1 -10000 0 1
IL12B 0.07 0.11 0.29 189 -10000 0 189
CD8A 0.029 0.061 0.28 25 -0.58 5 30
CD8B 0.013 0.12 0.28 27 -0.58 31 58
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.037 0.15 0.34 51 -0.36 60 111
IL2RB 0.032 0.047 0.26 38 -10000 0 38
proteasomal ubiquitin-dependent protein catabolic process 0.062 0.27 0.59 41 -0.77 44 85
IL2RG 0.03 0.071 0.26 42 -0.58 7 49
IL12 0.047 0.15 0.3 84 -0.43 53 137
STAT5A 0.02 0.047 -10000 0 -0.58 6 6
CD247 0.006 0.085 0.27 18 -0.58 15 33
IL2 0.023 0.024 0.26 9 -10000 0 9
SPHK2 0.024 0.003 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.005 0.15 0.27 21 -0.59 52 73
IL12/IL12R/TYK2/JAK2 0.029 0.31 0.72 36 -0.87 52 88
MAP2K3 0.035 0.28 0.67 24 -0.86 40 64
RIPK2 0.02 0.017 0.26 3 -10000 0 3
MAP2K6 0.041 0.27 0.67 24 -0.86 35 59
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.007 0.034 0.26 1 -0.58 1 2
IL18RAP 0.009 0.12 0.28 4 -0.58 35 39
IL12Rbeta1/TYK2 0.04 0.069 0.3 30 -0.48 1 31
EOMES -0.018 0.18 -10000 0 -1 25 25
STAT1 (dimer) 0.064 0.27 0.63 59 -0.72 38 97
T cell proliferation 0.047 0.22 0.52 28 -0.66 36 64
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.021 0.076 -10000 0 -0.58 15 15
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.013 0.19 0.42 4 -0.73 37 41
ATF2 0.04 0.26 0.63 24 -0.81 33 57
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 0.078 -10000 0 -0.41 20 20
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 -0.031 0.17 -10000 0 -0.58 89 89
LRP6/FZD1 0.034 0.009 -10000 0 -10000 0 0
TLE1 0.019 0.051 -10000 0 -0.58 7 7
AP1 -0.077 0.16 -10000 0 -0.32 264 264
NCSTN 0.02 0.009 -10000 0 -10000 0 0
ADAM10 0.022 0.028 -10000 0 -0.58 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.015 0.097 -10000 0 -0.66 12 12
NICD/RBPSUH 0.021 0.075 -10000 0 -0.4 24 24
WIF1 -0.28 0.3 0.26 11 -0.58 491 502
NOTCH1 0.01 0.067 -10000 0 -0.42 22 22
PSENEN 0.024 0.008 0.26 1 -10000 0 1
KREMEN2 0.13 0.12 0.26 425 -10000 0 425
DKK1 0.025 0.16 0.26 129 -0.58 49 178
beta catenin/beta TrCP1 0.007 0.069 -10000 0 -0.35 7 7
APH1B 0.023 0.02 -10000 0 -0.58 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
AXIN1 0.012 0.058 0.25 1 -0.46 7 8
CtBP/CBP/TCF1/TLE1/AES 0.012 0.041 -10000 0 -0.3 6 6
PSEN1 0.024 0.004 -10000 0 -10000 0 0
FOS -0.15 0.27 -10000 0 -0.58 277 277
JUN 0.019 0.054 -10000 0 -0.58 8 8
MAP3K7 0.021 0.009 -10000 0 -10000 0 0
CTNNB1 -0.002 0.069 0.25 1 -0.37 7 8
MAPK3 0.023 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.094 0.098 0.34 1 -0.34 16 17
HNF1A 0.025 0.019 0.26 6 -10000 0 6
CTBP1 0.023 0.006 -10000 0 -10000 0 0
MYC -0.016 0.22 -10000 0 -1.3 26 26
NKD1 0.021 0.056 0.26 14 -0.58 6 20
FZD1 0.024 0.003 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.007 0.12 -10000 0 -0.44 24 24
apoptosis -0.076 0.16 -10000 0 -0.32 264 264
Delta 1/NOTCHprecursor 0.02 0.077 -10000 0 -0.4 22 22
DLL1 0.02 0.039 -10000 0 -0.58 4 4
PPARD 0.014 0.098 -10000 0 -0.83 12 12
Gamma Secretase 0.055 0.034 -10000 0 -0.32 1 1
APC 0.004 0.084 -10000 0 -0.45 23 23
DVL1 -0.029 0.079 -10000 0 -0.38 31 31
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 69 -0.34 43 112
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 0.021 0.098 -10000 0 -1 6 6
WNT1 0.023 0.012 0.26 2 -10000 0 2
Axin1/APC/beta catenin 0.012 0.099 0.33 4 -0.43 17 21
DKK2 0.011 0.088 0.26 2 -0.58 21 23
NOTCH1 precursor/DVL1 -0.02 0.11 -10000 0 -0.6 20 20
GSK3B 0.024 0.003 -10000 0 -10000 0 0
FRAT1 0.024 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.004 0.12 -10000 0 -0.45 23 23
PPP2R5D -0.005 0.061 0.29 5 -0.35 17 22
MAPK1 0.023 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.14 0.2 -10000 0 -0.34 476 476
RBPJ 0.023 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.022 0.028 -10000 0 -0.58 2 2
LAT2 -0.019 0.1 0.22 1 -0.37 45 46
AP1 -0.059 0.18 -10000 0 -0.44 109 109
mol:PIP3 0.01 0.16 0.35 40 -0.44 40 80
IKBKB 0.034 0.13 0.28 104 -0.27 19 123
AKT1 0.013 0.16 0.32 137 -0.46 16 153
IKBKG 0.016 0.11 0.24 66 -0.27 23 89
MS4A2 -0.021 0.15 0.26 4 -0.56 71 75
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.013 0.12 0.29 27 -0.4 23 50
mol:Ca2+ 0.015 0.14 0.31 46 -0.38 23 69
LYN 0.021 0.013 -10000 0 -10000 0 0
CBLB -0.018 0.1 -10000 0 -0.36 44 44
SHC1 0.02 0.009 -10000 0 -10000 0 0
RasGAP/p62DOK -0.003 0.12 -10000 0 -0.34 117 117
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
PLD2 -0.004 0.17 0.33 118 -0.33 122 240
PTPN13 -0.014 0.15 -10000 0 -0.57 37 37
PTPN11 0.023 0.018 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.013 0.13 0.33 30 -0.34 25 55
SYK 0.025 0.011 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.026 0.12 -10000 0 -0.44 43 43
LAT -0.018 0.1 0.22 1 -0.36 47 48
PAK2 0.014 0.13 0.3 26 -0.45 22 48
NFATC2 -0.041 0.15 -10000 0 -0.59 56 56
HRAS 0.01 0.13 0.27 19 -0.47 24 43
GAB2 0.022 0.008 -10000 0 -10000 0 0
PLA2G1B 0 0.11 -10000 0 -0.85 13 13
Fc epsilon R1 -0.022 0.16 -10000 0 -0.41 129 129
Antigen/IgE/Fc epsilon R1 -0.018 0.14 -10000 0 -0.37 129 129
mol:GDP -0.013 0.11 -10000 0 -0.48 23 23
JUN 0.019 0.054 -10000 0 -0.58 8 8
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
FOS -0.15 0.27 -10000 0 -0.58 277 277
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.016 0.11 -10000 0 -0.37 49 49
CHUK 0.016 0.11 0.24 65 -0.27 24 89
KLRG1 -0.017 0.094 -10000 0 -0.32 47 47
VAV1 -0.019 0.1 -10000 0 -0.36 46 46
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.017 0.097 -10000 0 -0.36 44 44
negative regulation of mast cell degranulation -0.006 0.096 -10000 0 -0.38 24 24
BTK -0.012 0.11 -10000 0 -0.49 24 24
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.03 0.13 -10000 0 -0.38 77 77
GAB2/PI3K/SHP2 -0.047 0.1 -10000 0 -0.35 64 64
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.023 0.1 -10000 0 -0.29 101 101
RAF1 0 0.11 -10000 0 -0.92 13 13
Fc epsilon R1/FcgammaRIIB/SHIP 0 0.15 -10000 0 -0.35 131 131
FCER1G 0.019 0.019 0.26 2 -10000 0 2
FCER1A -0.045 0.19 -10000 0 -0.59 103 103
Antigen/IgE/Fc epsilon R1/Fyn -0.01 0.14 -10000 0 -0.35 126 126
MAPK3 0.001 0.11 -10000 0 -0.86 13 13
MAPK1 -0.005 0.11 -10000 0 -0.86 13 13
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.022 0.18 -10000 0 -0.59 63 63
DUSP1 -0.049 0.2 -10000 0 -0.58 118 118
NF-kappa-B/RelA 0.008 0.058 -10000 0 -0.22 1 1
actin cytoskeleton reorganization -0.006 0.15 -10000 0 -0.6 31 31
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0 0.11 -10000 0 -0.45 23 23
FER -0.02 0.11 -10000 0 -0.38 49 49
RELA 0.024 0.004 -10000 0 -10000 0 0
ITK -0.011 0.091 -10000 0 -0.4 42 42
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG1 0.007 0.13 0.28 11 -0.48 23 34
cytokine secretion -0.003 0.035 -10000 0 -10000 0 0
SPHK1 -0.017 0.099 0.22 2 -0.36 46 48
PTK2 -0.008 0.16 -10000 0 -0.63 31 31
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.023 0.13 -10000 0 -0.45 44 44
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.007 0.16 0.33 36 -0.48 30 66
MAP2K2 -0.003 0.1 -10000 0 -0.86 13 13
MAP2K1 -0.003 0.11 -10000 0 -0.86 13 13
MAP2K7 0.024 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 -0.008 0.093 -10000 0 -0.37 25 25
MAP2K4 -0.072 0.29 -10000 0 -0.83 121 121
Fc epsilon R1/FcgammaRIIB -0.009 0.15 -10000 0 -0.37 131 131
mol:Choline -0.004 0.17 0.33 118 -0.33 122 240
SHC/Grb2/SOS1 0.012 0.11 -10000 0 -0.42 22 22
FYN 0.021 0.028 -10000 0 -0.58 2 2
DOK1 0.025 0.011 0.26 2 -10000 0 2
PXN -0.008 0.14 -10000 0 -0.57 31 31
HCLS1 -0.018 0.1 -10000 0 -0.36 45 45
PRKCB 0.014 0.14 0.28 64 -0.37 29 93
FCGR2B 0.018 0.04 0.26 1 -0.58 4 5
IGHE 0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.006 0.098 -10000 0 -0.39 24 24
LCP2 0.024 0.009 0.26 1 -10000 0 1
PLA2G4A -0.044 0.14 -10000 0 -0.38 110 110
RASA1 0.024 0.004 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.004 0.17 0.33 118 -0.33 122 240
IKK complex 0.032 0.11 0.27 87 -0.21 11 98
WIPF1 0.024 0.003 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 -0.002 0.043 0.21 29 -0.19 5 34
RFC1 -0.002 0.042 0.22 27 -10000 0 27
PRKDC 0.016 0.077 0.23 98 -10000 0 98
RIPK1 0.027 0.007 -10000 0 -10000 0 0
CASP7 -0.018 0.099 -10000 0 -0.62 20 20
FASLG/FAS/FADD/FAF1 -0.005 0.057 0.22 9 -0.3 9 18
MAP2K4 -0.084 0.18 0.39 2 -0.4 112 114
mol:ceramide -0.022 0.098 -10000 0 -0.39 20 20
GSN -0.006 0.057 0.21 29 -0.3 17 46
FASLG/FAS/FADD/FAF1/Caspase 8 -0.007 0.074 -10000 0 -0.38 11 11
FAS 0.004 0.038 -10000 0 -0.59 2 2
BID -0.019 0.022 -10000 0 -10000 0 0
MAP3K1 -0.048 0.12 0.29 3 -0.43 32 35
MAP3K7 0.01 0.019 -10000 0 -10000 0 0
RB1 -0.002 0.041 0.22 26 -0.19 5 31
CFLAR 0.027 0.007 -10000 0 -10000 0 0
HGF/MET -0.053 0.2 -10000 0 -0.42 205 205
ARHGDIB 0.001 0.051 0.23 38 -10000 0 38
FADD 0.006 0.024 -10000 0 -10000 0 0
actin filament polymerization 0.012 0.065 0.36 11 -0.21 29 40
NFKB1 -0.046 0.12 -10000 0 -0.6 18 18
MAPK8 -0.15 0.25 0.56 2 -0.46 359 361
DFFA -0.003 0.042 0.22 26 -10000 0 26
DNA fragmentation during apoptosis -0.008 0.051 0.21 26 -10000 0 26
FAS/FADD/MET -0.038 0.14 -10000 0 -0.38 129 129
CFLAR/RIP1 0.04 0.013 -10000 0 -10000 0 0
FAIM3 0.027 0.037 0.26 22 -10000 0 22
FAF1 0.003 0.029 -10000 0 -10000 0 0
PARP1 -0.001 0.052 0.24 32 -10000 0 32
DFFB -0.003 0.041 0.22 26 -0.19 6 32
CHUK -0.04 0.11 -10000 0 -0.56 16 16
FASLG 0.007 0.084 0.26 36 -0.59 11 47
FAS/FADD 0.009 0.037 -10000 0 -0.33 2 2
HGF -0.013 0.14 -10000 0 -0.58 60 60
LMNA -0.004 0.054 0.19 50 -10000 0 50
CASP6 -0.003 0.041 0.21 26 -0.19 4 30
CASP10 0.003 0.042 -10000 0 -0.59 3 3
CASP3 0.001 0.047 0.26 27 -10000 0 27
PTPN13 0.009 0.093 -10000 0 -0.58 24 24
CASP8 -0.021 0.026 -10000 0 -10000 0 0
IL6 -0.43 0.62 -10000 0 -1.2 361 361
MET -0.072 0.22 -10000 0 -0.58 155 155
ICAD/CAD -0.006 0.035 0.2 20 -10000 0 20
FASLG/FAS/FADD/FAF1/Caspase 10 -0.023 0.099 -10000 0 -0.39 20 20
activation of caspase activity by cytochrome c -0.019 0.022 -10000 0 -10000 0 0
PAK2 -0.002 0.054 0.23 37 -10000 0 37
BCL2 0.006 0.1 -10000 0 -0.58 28 28
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.021 0.039 -10000 0 -0.58 4 4
alphaV beta3 Integrin 0.022 0.076 -10000 0 -0.43 26 26
PTK2 -0.039 0.15 -10000 0 -0.47 79 79
positive regulation of JNK cascade -0.02 0.12 -10000 0 -0.32 105 105
CDC42/GDP -0.016 0.17 0.43 1 -0.43 110 111
Rac1/GDP -0.016 0.17 -10000 0 -0.42 110 110
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 -0.02 0.15 -10000 0 -0.39 102 102
nectin-3/I-afadin -0.014 0.14 -10000 0 -0.44 99 99
RAPGEF1 -0.033 0.17 0.46 1 -0.47 96 97
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.047 0.18 -10000 0 -0.54 96 96
PDGFB-D/PDGFRB 0.021 0.039 -10000 0 -0.58 4 4
TLN1 -0.023 0.07 -10000 0 -0.39 13 13
Rap1/GTP -0.022 0.12 -10000 0 -0.34 94 94
IQGAP1 0.023 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.028 -10000 0 -0.34 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.014 0.14 -10000 0 -0.44 99 99
PVR 0.024 0.003 -10000 0 -10000 0 0
Necl-5(dimer) 0.024 0.003 -10000 0 -10000 0 0
mol:GDP -0.036 0.2 0.45 1 -0.52 111 112
MLLT4 0.021 0.035 0.26 1 -0.58 3 4
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.021 0.13 -10000 0 -0.34 99 99
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.029 0.031 -10000 0 -0.43 3 3
positive regulation of lamellipodium assembly -0.019 0.13 -10000 0 -0.34 112 112
PVRL1 0.022 0.007 -10000 0 -10000 0 0
PVRL3 -0.037 0.18 -10000 0 -0.58 98 98
PVRL2 0.024 0.004 -10000 0 -10000 0 0
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
CDH1 0.01 0.083 -10000 0 -0.58 19 19
CLDN1 0.007 0.12 0.26 22 -0.58 35 57
JAM-A/CLDN1 0.005 0.13 -10000 0 -0.37 93 93
SRC -0.054 0.2 -10000 0 -0.58 104 104
ITGB3 0.008 0.098 0.26 4 -0.58 26 30
nectin-1(dimer)/I-afadin/I-afadin 0.029 0.031 -10000 0 -0.43 3 3
FARP2 -0.036 0.2 0.46 1 -0.53 105 106
RAC1 0.024 0.004 -10000 0 -10000 0 0
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.003 0.13 -10000 0 -0.38 98 98
nectin-1/I-afadin 0.029 0.031 -10000 0 -0.43 3 3
nectin-2/I-afadin 0.031 0.03 0.2 1 -0.3 6 7
RAC1/GTP/IQGAP1/filamentous actin 0.031 0.007 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0 0.13 -10000 0 -0.37 99 99
CDC42/GTP/IQGAP1/filamentous actin 0.03 0.009 -10000 0 -10000 0 0
F11R 0.02 0.009 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.02 0.12 -10000 0 -0.32 105 105
alphaV/beta3 Integrin/Talin -0.004 0.1 0.26 2 -0.41 32 34
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.031 0.03 0.2 1 -0.3 6 7
nectin-2(dimer)/I-afadin/I-afadin 0.031 0.03 0.2 1 -0.3 6 7
PIP5K1C -0.019 0.077 -10000 0 -0.23 96 96
VAV2 -0.035 0.2 0.44 1 -0.54 109 110
RAP1/GDP -0.013 0.16 -10000 0 -0.4 102 102
ITGAV 0.024 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.003 0.13 -10000 0 -0.38 98 98
nectin-3(dimer)/I-afadin/I-afadin -0.014 0.14 -10000 0 -0.44 99 99
Rac1/GTP -0.02 0.16 -10000 0 -0.41 111 111
PTPRM -0.016 0.087 -10000 0 -0.25 100 100
E-cadherin/beta catenin/alpha catenin 0.045 0.067 -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
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.059 0.2 0.32 1 -0.4 170 171
MAP3K8 0.01 0.043 -10000 0 -0.58 4 4
FOS -0.022 0.14 0.32 2 -0.45 47 49
PRKCA -0.002 0.087 0.24 1 -0.58 20 21
PTPN7 0.02 0.06 0.25 52 -10000 0 52
HRAS 0.024 0.018 0.26 5 -10000 0 5
PRKCB 0.004 0.083 0.26 15 -0.58 15 30
NRAS 0.023 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.025 0.036 -10000 0 -10000 0 0
MAPK3 0.007 0.091 -10000 0 -0.8 5 5
MAP2K1 -0.012 0.12 -10000 0 -0.5 40 40
ELK1 0.006 0.029 -10000 0 -10000 0 0
BRAF -0.013 0.1 -10000 0 -0.49 36 36
mol:GTP -0.002 0.003 -10000 0 -0.006 293 293
MAPK1 -0.011 0.12 -10000 0 -0.47 41 41
RAF1 -0.013 0.1 -10000 0 -0.49 36 36
KRAS 0.022 0.006 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.042 0.15 -10000 0 -0.32 211 211
MAPK9 0.006 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.005 0.014 0.14 8 -10000 0 8
GNB1/GNG2 0.027 0.041 -10000 0 -0.36 10 10
GNB1 0.023 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 -0.32 226 226
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.02 0.035 0.082 226 -10000 0 226
GNAL -0.11 0.25 -10000 0 -0.58 209 209
GNG2 0.018 0.061 -10000 0 -0.58 10 10
CRH 0.017 0.023 0.26 8 -10000 0 8
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.026 -10000 0 -0.36 5 5
MAPK11 0.005 0.02 -10000 0 -0.36 3 3
Syndecan-3-mediated signaling events

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
CTTN 0.021 0.009 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.072 0.16 -10000 0 -0.51 22 22
Syndecan-3/Neurocan 0.028 0.075 0.28 19 -0.38 18 37
POMC 0.021 0.09 0.26 29 -0.58 17 46
EGFR -0.19 0.29 -10000 0 -0.58 349 349
Syndecan-3/EGFR -0.09 0.16 -10000 0 -0.32 276 276
AGRP 0.021 0.026 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 0.02 -10000 0 -0.58 1 1
APH1A 0.02 0.009 -10000 0 -10000 0 0
NCAN 0.037 0.059 0.26 62 -10000 0 62
long-term memory 0.036 0.062 -10000 0 -0.35 14 14
Syndecan-3/IL8 0.021 0.083 0.28 10 -0.34 33 43
PSEN1 0.024 0.004 -10000 0 -10000 0 0
Src/Cortactin 0.03 0.014 -10000 0 -10000 0 0
FYN 0.021 0.028 -10000 0 -0.58 2 2
limb bud formation 0.002 0.055 -10000 0 -0.39 19 19
MC4R 0.022 0.025 0.26 10 -10000 0 10
SRC 0.023 0.005 -10000 0 -10000 0 0
PTN -0.23 0.3 0.26 2 -0.58 406 408
FGFR/FGF/Syndecan-3 0.002 0.056 -10000 0 -0.39 19 19
neuron projection morphogenesis -0.072 0.16 0.34 5 -0.48 22 27
Syndecan-3/AgRP 0.015 0.06 0.27 1 -0.37 19 20
Syndecan-3/AgRP/MC4R 0.038 0.068 -10000 0 -0.36 18 18
Fyn/Cortactin 0.028 0.022 -10000 0 -0.31 2 2
SDC3 0.002 0.056 -10000 0 -0.4 19 19
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.02 0.082 0.28 10 -0.34 33 43
IL8 0.026 0.1 0.26 56 -0.58 18 74
Syndecan-3/Fyn/Cortactin 0.037 0.064 -10000 0 -0.36 14 14
Syndecan-3/CASK 0 0.054 -10000 0 -0.38 19 19
alpha-MSH/MC4R 0.03 0.07 0.37 1 -0.43 17 18
Gamma Secretase 0.054 0.034 -10000 0 -0.32 1 1
Glypican 2 network

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
MDK 0.032 0.045 0.26 35 -10000 0 35
GPC2 0.048 0.082 0.26 106 -0.58 3 109
GPC2/Midkine 0.056 0.07 0.37 14 -0.43 3 17
neuron projection morphogenesis 0.056 0.07 0.37 14 -0.43 3 17
Signaling events mediated by HDAC Class III

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
EP300 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.02 -10000 0 -0.58 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.017 0.062 0.43 1 -0.27 16 17
CDKN1A -0.009 0.035 -10000 0 -0.78 2 2
KAT2B 0.023 0.02 -10000 0 -0.58 1 1
BAX 0.025 0.016 0.26 4 -10000 0 4
FOXO3 -0.005 0.008 -10000 0 -0.25 1 1
FOXO1 0.02 0.039 -10000 0 -0.58 4 4
FOXO4 0.012 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
TAT -0.33 0.3 0.26 25 -0.58 572 597
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.024 -10000 0 -0.43 1 1
PPARGC1A -0.09 0.24 0.26 9 -0.58 186 195
FHL2 0.02 0.047 -10000 0 -0.58 6 6
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.032 0.011 -10000 0 -10000 0 0
HIST2H4A 0.017 0.062 0.27 16 -0.43 1 17
SIRT1/FOXO3a 0.016 0.026 -10000 0 -0.2 4 4
SIRT1 0.022 0.009 0.21 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.039 0.024 -10000 0 -0.37 1 1
SIRT1/Histone H1b 0.027 0.043 -10000 0 -0.21 6 6
apoptosis -0.044 0.017 -10000 0 -10000 0 0
SIRT1/PGC1A -0.048 0.16 -10000 0 -0.36 186 186
p53/SIRT1 0.027 0.02 0.41 2 -10000 0 2
SIRT1/FOXO4 0.022 0.036 -10000 0 -0.21 4 4
FOXO1/FHL2/SIRT1 0.036 0.042 -10000 0 -0.34 9 9
HIST1H1E 0.02 0.03 0.21 6 -10000 0 6
SIRT1/p300 0.032 0.011 -10000 0 -10000 0 0
muscle cell differentiation -0.029 0.025 0.37 1 -10000 0 1
TP53 0.02 0.011 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.045 0.017 -10000 0 -10000 0 0
CREBBP 0.023 0.006 -10000 0 -10000 0 0
MEF2D 0.02 0.009 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.26 0.22 -10000 0 -0.39 668 668
ACSS2 -0.007 0.009 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.029 0.025 -10000 0 -0.37 1 1
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.011 0.045 -10000 0 -0.26 20 20
epithelial cell differentiation 0.035 0.056 -10000 0 -0.32 19 19
CYFIP2 0.029 0.047 0.26 25 -0.58 2 27
ENAH -0.004 0.061 0.3 10 -10000 0 10
EGFR -0.19 0.29 -10000 0 -0.58 349 349
EPHA2 0.02 0.043 -10000 0 -0.58 5 5
MYO6 -0.013 0.052 0.36 1 -0.31 20 21
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.049 0.031 -10000 0 -0.37 1 1
AQP5 -0.19 0.26 0.33 1 -0.51 387 388
CTNND1 0.024 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.051 0.36 1 -0.3 19 20
regulation of calcium-dependent cell-cell adhesion -0.024 0.076 0.36 1 -0.31 56 57
EGF -0.093 0.24 0.26 2 -0.58 189 191
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
AQP3 -0.016 0.12 0.29 1 -0.47 47 48
cortical microtubule organization 0.035 0.056 -10000 0 -0.32 19 19
GO:0000145 -0.013 0.048 0.35 1 -0.29 19 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.04 0.058 -10000 0 -0.32 19 19
MLLT4 0.021 0.035 0.26 1 -0.58 3 4
ARF6/GDP -0.021 0.041 -10000 0 -10000 0 0
ARF6 0.024 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.044 0.039 -10000 0 -0.34 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.002 0.05 -10000 0 -0.29 19 19
PVRL2 0.024 0.004 -10000 0 -10000 0 0
ZYX -0.013 0.051 0.36 1 -0.31 19 20
ARF6/GTP 0.048 0.041 -10000 0 -0.32 5 5
CDH1 0.01 0.083 -10000 0 -0.58 19 19
EGFR/EGFR/EGF/EGF -0.15 0.2 -10000 0 -0.34 482 482
RhoA/GDP 0.036 0.055 -10000 0 -0.3 19 19
actin cytoskeleton organization -0.015 0.05 0.34 1 -0.3 20 21
IGF-1R heterotetramer 0.011 0.086 0.26 2 -0.58 20 22
GIT1 0.023 0.006 -10000 0 -10000 0 0
IGF1R 0.011 0.086 0.26 2 -0.58 20 22
IGF1 -0.1 0.24 -10000 0 -0.58 202 202
DIAPH1 0.026 0.1 -10000 0 -0.54 14 14
Wnt receptor signaling pathway -0.035 0.056 0.32 19 -10000 0 19
RHOA 0.023 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.021 0.042 -10000 0 -0.28 20 20
CTNNA1 0.024 0.004 -10000 0 -10000 0 0
VCL -0.015 0.051 0.35 1 -0.3 20 21
EFNA1 0.02 0.009 -10000 0 -10000 0 0
LPP -0.016 0.052 -10000 0 -0.3 24 24
Ephrin A1/EPHA2 0.024 0.056 -10000 0 -0.3 22 22
SEC6/SEC8 -0.022 0.044 -10000 0 -0.3 21 21
MGAT3 -0.024 0.077 0.36 1 -0.31 56 57
HGF/MET -0.041 0.16 -10000 0 -0.33 208 208
HGF -0.013 0.14 -10000 0 -0.58 60 60
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.011 0.045 -10000 0 -0.26 20 20
actin cable formation 0.041 0.096 0.31 35 -0.29 1 36
KIAA1543 -0.013 0.053 0.35 1 -0.32 19 20
KIFC3 -0.013 0.049 0.36 1 -0.31 19 20
NCK1 0.024 0.003 -10000 0 -10000 0 0
EXOC3 0.023 0.005 -10000 0 -10000 0 0
ACTN1 -0.013 0.05 -10000 0 -0.31 19 19
NCK1/GIT1 0.033 0.01 -10000 0 -10000 0 0
mol:GDP 0.035 0.056 -10000 0 -0.32 19 19
EXOC4 0.024 0.004 -10000 0 -10000 0 0
STX4 -0.013 0.05 0.36 1 -0.31 19 20
PIP5K1C -0.013 0.052 0.36 1 -0.31 19 20
LIMA1 0.023 0.027 -10000 0 -0.58 2 2
ABI1 0.024 0.004 -10000 0 -10000 0 0
ROCK1 0.016 0.09 0.3 25 -10000 0 25
adherens junction assembly -0.023 0.1 0.3 3 -0.64 14 17
IGF-1R heterotetramer/IGF1 -0.043 0.15 -10000 0 -0.32 213 213
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.031 0.03 0.2 1 -0.3 6 7
MET -0.072 0.22 -10000 0 -0.58 155 155
PLEKHA7 -0.013 0.056 0.36 1 -0.34 19 20
mol:GTP 0.043 0.038 -10000 0 -0.33 5 5
establishment of epithelial cell apical/basal polarity -0.01 0.068 0.37 6 -0.52 1 7
cortical actin cytoskeleton stabilization 0.011 0.045 -10000 0 -0.26 20 20
regulation of cell-cell adhesion -0.015 0.05 0.34 1 -0.3 20 21
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.011 0.045 -10000 0 -0.26 20 20
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 -0.02 0.067 -10000 0 -0.37 35 35
ADCY5 -0.12 0.17 -10000 0 -0.37 295 295
ADCY6 -0.007 0.012 -10000 0 -0.37 1 1
ADCY7 -0.006 0.012 -10000 0 -0.37 1 1
ADCY1 -0.008 0.064 -10000 0 -0.37 25 25
ADCY2 -0.029 0.099 0.25 7 -0.37 72 79
ADCY3 -0.007 0.012 -10000 0 -0.37 1 1
ADCY8 -0.004 0.023 0.23 5 -10000 0 5
PRKCE 0.005 0.014 -10000 0 -0.43 1 1
ADCY9 -0.007 0.012 -10000 0 -0.37 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.011 0.087 0.22 18 -0.24 37 55
TCGA08_rtk_signaling

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
PDGFRA -0.011 0.14 -10000 0 -0.58 56 56
HRAS 0.025 0.018 0.26 5 -10000 0 5
EGFR -0.19 0.29 -10000 0 -0.58 349 349
AKT -0.014 0.12 0.3 6 -0.28 83 89
FOXO3 0.022 0.02 -10000 0 -0.58 1 1
AKT1 0.024 0.004 -10000 0 -10000 0 0
FOXO1 0.02 0.039 -10000 0 -0.58 4 4
AKT3 0.014 0.058 -10000 0 -0.58 9 9
FOXO4 0.024 0.001 -10000 0 -10000 0 0
MET -0.072 0.22 -10000 0 -0.58 155 155
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 0.017 0.068 0.26 3 -0.58 12 15
PIK3R3 0.024 0.009 0.26 1 -10000 0 1
PIK3R2 0.024 0.003 -10000 0 -10000 0 0
NF1 0.023 0.006 -10000 0 -10000 0 0
RAS -0.061 0.14 0.21 4 -0.34 144 148
ERBB2 0.021 0.009 -10000 0 -10000 0 0
proliferation/survival/translation -0.005 0.091 0.33 43 -0.26 1 44
PI3K -0.051 0.14 0.27 11 -0.32 152 163
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
KRAS 0.023 0.005 -10000 0 -10000 0 0
FOXO 0.036 0.057 0.27 7 -0.16 2 9
AKT2 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.022 0.028 -10000 0 -0.58 2 2
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.097 0.1 0.32 86 -0.35 2 88
EPHB2 0.028 0.033 0.26 18 -10000 0 18
Syndecan-2/TACI 0.021 0.061 0.3 5 -0.36 12 17
LAMA1 -0.04 0.18 0.26 2 -0.58 102 104
Syndecan-2/alpha2 ITGB1 -0.037 0.15 -10000 0 -0.33 174 174
HRAS 0.025 0.018 0.26 5 -10000 0 5
Syndecan-2/CASK 0.005 0.017 -10000 0 -0.36 2 2
ITGA5 0.024 0.002 -10000 0 -10000 0 0
BAX -0.002 0.029 0.46 1 -10000 0 1
EPB41 0.024 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.017 0.019 -10000 0 -0.33 2 2
LAMA3 -0.12 0.25 -10000 0 -0.58 223 223
EZR 0.024 0.012 0.26 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.05 0.2 -10000 0 -0.58 119 119
Syndecan-2/MMP2 0.014 0.039 -10000 0 -0.37 8 8
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.023 0.07 -10000 0 -0.41 24 24
dendrite morphogenesis 0.022 0.035 0.32 4 -0.36 2 6
Syndecan-2/GM-CSF 0.021 0.037 0.32 5 -0.36 2 7
determination of left/right symmetry 0.007 0.02 -10000 0 -0.42 2 2
Syndecan-2/PKC delta 0.019 0.023 0.31 1 -0.36 2 3
GNB2L1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.034 0.075 0.19 165 -0.33 2 167
MAPK1 0.038 0.078 0.2 97 -0.32 2 99
Syndecan-2/RACK1 0.029 0.025 0.22 1 -0.31 2 3
NF1 0.023 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.007 0.02 -10000 0 -0.42 2 2
ITGA2 0.009 0.093 -10000 0 -0.58 24 24
MAPK8 0.005 0.032 0.27 5 -0.36 4 9
Syndecan-2/alpha2/beta1 Integrin 0.001 0.12 -10000 0 -0.36 80 80
Syndecan-2/Kininogen 0.018 0.03 0.31 3 -0.36 2 5
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC 0.042 0.07 0.35 5 -0.3 2 7
Syndecan-2/CASK/Protein 4.1 0.017 0.019 -10000 0 -0.33 2 2
extracellular matrix organization 0.019 0.023 0.35 1 -0.36 2 3
actin cytoskeleton reorganization 0.097 0.1 0.32 86 -0.35 2 88
Syndecan-2/Caveolin-2/Ras -0.009 0.11 0.23 1 -0.34 89 90
Syndecan-2/Laminin alpha3 -0.058 0.15 -10000 0 -0.36 165 165
Syndecan-2/RasGAP 0.037 0.03 -10000 0 -0.3 2 2
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
PRKCD 0.024 0.009 0.26 1 -10000 0 1
Syndecan-2 dimer 0.022 0.035 0.32 4 -0.36 2 6
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 -0.3 2 2
RHOA 0.023 0.005 -10000 0 -10000 0 0
SDCBP 0.021 0.008 -10000 0 -10000 0 0
TNFRSF13B 0.026 0.086 0.26 48 -0.58 12 60
RASA1 0.024 0.004 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.023 0.07 -10000 0 -0.41 24 24
Syndecan-2/Synbindin 0.017 0.021 -10000 0 -0.35 2 2
TGFB1 0.024 0.008 0.26 1 -10000 0 1
CASP3 0.043 0.072 0.19 177 -0.33 2 179
FN1 0.12 0.12 0.26 388 -10000 0 388
Syndecan-2/IL8 0.024 0.072 0.22 56 -0.36 16 72
SDC2 0.007 0.02 -10000 0 -0.42 2 2
KNG1 0.021 0.025 0.26 10 -10000 0 10
Syndecan-2/Neurofibromin 0.018 0.021 -10000 0 -0.36 2 2
TRAPPC4 0.022 0.007 -10000 0 -10000 0 0
CSF2 0.026 0.037 0.26 23 -10000 0 23
Syndecan-2/TGFB1 0.019 0.023 0.35 1 -0.36 2 3
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.019 -10000 0 -0.33 2 2
Syndecan-2/Ezrin 0.029 0.026 0.3 1 -0.33 2 3
PRKACA 0.045 0.074 0.19 189 -0.32 2 191
angiogenesis 0.024 0.072 0.22 56 -0.36 16 72
MMP2 0.018 0.048 -10000 0 -0.58 6 6
IL8 0.026 0.1 0.26 56 -0.58 18 74
calcineurin-NFAT signaling pathway 0.021 0.06 0.3 5 -0.36 12 17
Aurora A signaling

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
Aurora A/GADD45A 0.044 0.043 -10000 0 -10000 0 0
BIRC5 0.18 0.12 0.26 643 -10000 0 643
NFKBIA 0.024 0.041 0.29 6 -10000 0 6
CPEB1 -0.085 0.23 -10000 0 -0.58 175 175
AKT1 0.024 0.041 0.29 6 -10000 0 6
NDEL1 0.022 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.034 0.037 0.21 1 -0.21 1 2
NDEL1/TACC3 0.065 0.068 0.26 14 -10000 0 14
GADD45A 0.024 0.004 -10000 0 -10000 0 0
GSK3B -0.003 0.027 -10000 0 -10000 0 0
PAK1/Aurora A 0.041 0.044 0.24 1 -10000 0 1
MDM2 0.023 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.095 0.07 0.27 25 -10000 0 25
TP53 0.022 0.052 0.19 1 -0.22 13 14
DLG7 0.023 0.032 0.18 1 -10000 0 1
AURKAIP1 0.025 0.018 0.26 5 -10000 0 5
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.069 0.072 0.28 14 -10000 0 14
G2/M transition of mitotic cell cycle 0.031 0.035 0.21 1 -0.21 1 2
AURKA 0.039 0.048 0.24 1 -10000 0 1
AURKB 0.089 0.077 0.17 390 -10000 0 390
CDC25B 0.033 0.039 0.22 4 -10000 0 4
G2/M transition checkpoint 0.019 0.029 -10000 0 -10000 0 0
mRNA polyadenylation -0.029 0.13 -10000 0 -0.3 170 170
Aurora A/CPEB -0.028 0.13 -10000 0 -0.3 170 170
Aurora A/TACC1/TRAP/chTOG 0.043 0.07 -10000 0 -0.3 19 19
BRCA1 0.023 0.021 0.26 1 -0.58 1 2
centrosome duplication 0.041 0.044 0.24 1 -10000 0 1
regulation of centrosome cycle 0.064 0.066 0.26 14 -10000 0 14
spindle assembly 0.042 0.069 -10000 0 -0.3 19 19
TDRD7 0.024 0.003 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.14 0.089 0.28 28 -10000 0 28
CENPA 0.099 0.084 0.19 403 -0.21 3 406
Aurora A/PP2A 0.044 0.044 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.031 0.04 0.24 1 -10000 0 1
negative regulation of DNA binding 0.017 0.062 -10000 0 -0.22 13 13
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.031 0.013 -10000 0 -10000 0 0
RASA1 0.024 0.004 -10000 0 -10000 0 0
Ajuba/Aurora A 0.019 0.029 -10000 0 -10000 0 0
mitotic prometaphase -0.009 0.029 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.048 0.24 1 -10000 0 1
TACC1 0.007 0.087 -10000 0 -0.58 21 21
TACC3 0.058 0.085 0.26 143 -10000 0 143
Aurora A/Antizyme1 0.054 0.043 -10000 0 -10000 0 0
Aurora A/RasGAP 0.044 0.044 -10000 0 -10000 0 0
OAZ1 0.023 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 -0.003 0.027 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.039 0.024 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.095 0.07 0.27 25 -10000 0 25
PPP2R5D 0.024 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.097 0.074 0.25 31 -10000 0 31
PAK1 0.023 0.019 0.26 5 -10000 0 5
CKAP5 0.024 0.003 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 0.086 0.11 0.27 41 -0.63 6 47
Syndecan-4/Syndesmos 0.097 0.11 0.38 5 -0.67 6 11
positive regulation of JNK cascade 0.086 0.14 0.36 10 -0.62 8 18
Syndecan-4/ADAM12 0.11 0.12 0.36 35 -0.69 6 41
CCL5 0.03 0.056 0.26 35 -0.58 3 38
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DNM2 0.024 0.004 -10000 0 -10000 0 0
ITGA5 0.024 0.002 -10000 0 -10000 0 0
SDCBP 0.021 0.008 -10000 0 -10000 0 0
PLG -0.009 0.031 0.26 4 -10000 0 4
ADAM12 0.037 0.065 0.26 61 -0.58 2 63
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.023 0.013 0.26 2 -10000 0 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.028 0.018 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.067 0.15 0.38 4 -0.6 10 14
Syndecan-4/CXCL12/CXCR4 0.091 0.14 0.38 6 -0.66 8 14
Syndecan-4/Laminin alpha3 0.037 0.15 0.4 3 -0.65 8 11
MDK 0.032 0.045 0.26 35 -10000 0 35
Syndecan-4/FZD7 0.097 0.12 0.38 5 -0.66 7 12
Syndecan-4/Midkine 0.11 0.11 0.38 11 -0.67 6 17
FZD7 0.012 0.083 -10000 0 -0.58 19 19
Syndecan-4/FGFR1/FGF -0.009 0.16 0.35 1 -0.53 19 20
THBS1 0.022 0.034 -10000 0 -0.58 3 3
integrin-mediated signaling pathway 0.096 0.12 0.37 7 -0.67 7 14
positive regulation of MAPKKK cascade 0.086 0.14 0.36 10 -0.62 8 18
Syndecan-4/TACI 0.099 0.12 0.37 16 -0.69 6 22
CXCR4 0.03 0.038 0.26 25 -10000 0 25
cell adhesion 0.062 0.085 0.25 74 -0.26 19 93
Syndecan-4/Dynamin 0.1 0.11 0.39 4 -0.7 6 10
Syndecan-4/TSP1 0.1 0.11 0.38 5 -0.69 6 11
Syndecan-4/GIPC 0.1 0.11 0.39 5 -0.7 6 11
Syndecan-4/RANTES 0.1 0.11 0.37 6 -0.69 6 12
ITGB1 0.024 0.004 -10000 0 -10000 0 0
LAMA1 -0.04 0.18 0.26 2 -0.58 102 104
LAMA3 -0.12 0.25 -10000 0 -0.58 223 223
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.02 0.22 0.69 84 -0.54 19 103
Syndecan-4/alpha-Actinin 0.1 0.11 0.39 4 -0.69 6 10
TFPI -0.003 0.12 -10000 0 -0.58 43 43
F2 0.025 0.032 0.27 8 -10000 0 8
alpha5/beta1 Integrin 0.035 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion 0 0.18 0.39 2 -0.53 32 34
ACTN1 0.024 0.005 -10000 0 -10000 0 0
TNC 0.013 0.088 0.26 7 -0.58 20 27
Syndecan-4/CXCL12 0.079 0.14 0.39 4 -0.66 9 13
FGF6 0.015 0.027 -10000 0 -0.58 2 2
RHOA 0.023 0.005 -10000 0 -10000 0 0
CXCL12 -0.02 0.16 -10000 0 -0.58 70 70
TNFRSF13B 0.026 0.086 0.26 48 -0.58 12 60
FGF2 -0.2 0.29 -10000 0 -0.58 364 364
FGFR1 0.015 0.051 -10000 0 -0.58 7 7
Syndecan-4/PI-4-5-P2 0.078 0.1 0.31 7 -0.69 6 13
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.11 0.12 0.26 383 -10000 0 383
cell migration -0.02 0.012 -10000 0 -10000 0 0
PRKCD 0.012 0.026 -10000 0 -10000 0 0
vasculogenesis 0.099 0.1 0.38 5 -0.66 6 11
SDC4 0.09 0.1 0.36 8 -0.78 5 13
Syndecan-4/Tenascin C 0.097 0.12 0.38 6 -0.7 7 13
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.013 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.088 0.11 0.37 4 -0.67 6 10
MMP9 0.12 0.12 0.26 412 -0.57 1 413
Rac1/GTP 0.062 0.086 0.25 74 -0.26 19 93
cytoskeleton organization 0.096 0.1 0.38 5 -0.64 6 11
GIPC1 0.024 0.008 0.26 1 -10000 0 1
Syndecan-4/TFPI 0.09 0.13 0.39 4 -0.69 7 11
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.007 0.011 -10000 0 -10000 0 0
SMARCC1 0.005 0.028 -10000 0 -0.5 2 2
REL 0.019 0.059 -10000 0 -0.58 9 9
HDAC7 -0.037 0.11 0.32 2 -0.36 60 62
JUN 0.017 0.055 -10000 0 -0.58 8 8
EP300 0.023 0.006 -10000 0 -10000 0 0
KAT2B 0.023 0.02 -10000 0 -0.58 1 1
KAT5 0.024 0.004 -10000 0 -10000 0 0
MAPK14 -0.009 0.064 -10000 0 -0.44 19 19
FOXO1 0.019 0.039 -10000 0 -0.58 4 4
T-DHT/AR -0.024 0.12 -10000 0 -0.38 60 60
MAP2K6 0.002 0.086 0.25 1 -0.58 19 20
BRM/BAF57 0.024 0.027 -10000 0 -10000 0 0
MAP2K4 0.013 0.021 -10000 0 -10000 0 0
SMARCA2 0.017 0.019 -10000 0 -10000 0 0
PDE9A -0.064 0.26 -10000 0 -1 62 62
NCOA2 0 0.1 -10000 0 -0.58 29 29
CEBPA 0.019 0.058 -10000 0 -0.58 9 9
EHMT2 0.02 0.013 -10000 0 -10000 0 0
cell proliferation -0.001 0.15 0.39 21 -0.45 24 45
NR0B1 0.028 0.045 0.26 34 -10000 0 34
EGR1 -0.17 0.28 -10000 0 -0.58 307 307
RXRs/9cRA -0.047 0.15 -10000 0 -0.34 200 200
AR/RACK1/Src -0.017 0.11 0.32 7 -0.37 29 36
AR/GR -0.025 0.12 0.28 1 -0.3 121 122
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 -0.015 7 7
MAPK8 -0.002 0.037 -10000 0 -0.43 5 5
T-DHT/AR/TIF2/CARM1 -0.013 0.11 0.34 2 -0.37 41 43
SRC -0.019 0.065 0.21 2 -0.35 20 22
NR3C1 0.018 0.058 -10000 0 -0.58 9 9
KLK3 -0.16 0.41 0.39 3 -1.1 134 137
APPBP2 0.015 0.019 -10000 0 -10000 0 0
TRIM24 0.018 0.02 0.26 1 -10000 0 1
T-DHT/AR/TIP60 -0.014 0.096 0.33 4 -0.4 23 27
TMPRSS2 -0.13 0.37 -10000 0 -1 128 128
RXRG -0.11 0.24 0.26 2 -0.58 202 204
mol:9cRA -0.001 0.002 -10000 0 -0.016 1 1
RXRA 0.023 0.005 -10000 0 -10000 0 0
RXRB 0.023 0.005 -10000 0 -10000 0 0
CARM1 0.022 0.011 -10000 0 -10000 0 0
NR2C2 0.02 0.047 -10000 0 -0.58 6 6
KLK2 -0.053 0.21 0.33 5 -0.66 82 87
AR -0.038 0.1 0.17 1 -0.3 123 124
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 -0.024 31 157
GATA2 0.011 0.099 0.26 11 -0.58 25 36
MYST2 0 0.002 -10000 0 -10000 0 0
HOXB13 0.12 0.12 0.26 402 -10000 0 402
T-DHT/AR/RACK1/Src -0.012 0.1 0.34 10 -0.39 23 33
positive regulation of transcription 0.011 0.099 0.26 11 -0.58 25 36
DNAJA1 0.016 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.01 -10000 0 -10000 0 0
NCOA1 0.021 0.031 -10000 0 -0.61 1 1
SPDEF -0.013 0.15 0.26 25 -0.58 61 86
T-DHT/AR/TIF2 -0.001 0.097 0.3 5 -0.38 22 27
T-DHT/AR/Hsp90 -0.015 0.095 0.31 3 -0.4 23 26
GSK3B 0.021 0.011 -10000 0 -10000 0 0
NR2C1 0.025 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.024 0.06 0.23 1 -0.36 22 23
SIRT1 0.024 0.003 -10000 0 -10000 0 0
ZMIZ2 0.026 0.016 -10000 0 -10000 0 0
POU2F1 0.009 0.051 -10000 0 -0.18 13 13
T-DHT/AR/DAX-1 -0.014 0.099 0.31 4 -0.4 24 28
CREBBP 0.022 0.006 -10000 0 -10000 0 0
SMARCE1 0.017 0.018 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.029 0.011 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.023 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.011 0.084 0.26 1 -0.58 19 20
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.021 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.097 0.13 -10000 0 -0.24 395 395
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.023 0.02 -10000 0 -0.58 1 1
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
FYN 0.021 0.028 -10000 0 -0.58 2 2
MAP3K12 0.024 0.003 -10000 0 -10000 0 0
FGR 0.023 0.009 0.26 1 -10000 0 1
p38 alpha/TAB1 -0.04 0.096 -10000 0 -0.31 79 79
PRKG1 -0.009 0.14 -10000 0 -0.58 54 54
DUSP8 0.022 0.034 -10000 0 -0.58 3 3
PGK/cGMP/p38 alpha -0.018 0.13 -10000 0 -0.33 100 100
apoptosis -0.039 0.092 -10000 0 -0.31 73 73
RAL/GTP 0.032 0.007 -10000 0 -10000 0 0
LYN 0.021 0.008 -10000 0 -10000 0 0
DUSP1 -0.049 0.2 -10000 0 -0.58 118 118
PAK1 0.023 0.019 0.26 5 -10000 0 5
SRC 0.023 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.052 0.025 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.024 0.008 0.26 1 -10000 0 1
RAC1-CDC42/GTP 0.031 0.008 -10000 0 -10000 0 0
MAPK11 -0.011 0.13 0.26 11 -0.36 60 71
BLK 0.05 0.088 0.26 129 -0.58 2 131
HCK 0.026 0.026 0.26 11 -10000 0 11
MAP2K3 0.022 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 -0.006 0.13 0.24 11 -0.36 69 80
positive regulation of innate immune response -0.013 0.15 0.3 9 -0.42 66 75
LCK 0.025 0.078 0.26 34 -0.58 11 45
p38alpha-beta/MKP7 -0.005 0.14 0.36 4 -0.41 59 63
p38alpha-beta/MKP5 -0.005 0.14 0.43 2 -0.42 52 54
PGK/cGMP -0.007 0.1 -10000 0 -0.42 55 55
PAK2 0.024 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.037 0.17 0.36 4 -0.41 107 111
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 -0.25 0.3 -10000 0 -0.58 449 449
Coregulation of Androgen receptor activity

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.01 0.042 -10000 0 -0.58 1 1
SVIL 0.01 0.048 -10000 0 -0.58 3 3
ZNF318 0.041 0.056 0.2 21 -10000 0 21
JMJD2C -0.002 0.043 0.11 22 -0.13 76 98
T-DHT/AR/Ubc9 -0.032 0.14 -10000 0 -0.39 117 117
CARM1 0.018 0.016 -10000 0 -10000 0 0
PRDX1 0.025 0.006 -10000 0 -10000 0 0
PELP1 0.025 0.012 -10000 0 -10000 0 0
CTNNB1 0.013 0.03 -10000 0 -10000 0 0
AKT1 0.028 0.018 -10000 0 -10000 0 0
PTK2B 0.011 0.027 -10000 0 -10000 0 0
MED1 0.026 0.02 -10000 0 -10000 0 0
MAK 0.036 0.088 0.3 9 -0.55 11 20
response to oxidative stress 0.001 0.004 -10000 0 -10000 0 0
HIP1 0.009 0.052 -10000 0 -0.58 4 4
GSN 0.003 0.075 -10000 0 -0.58 12 12
NCOA2 -0.002 0.1 -10000 0 -0.58 29 29
NCOA6 0.012 0.034 -10000 0 -10000 0 0
DNA-PK 0.051 0.054 -10000 0 -10000 0 0
NCOA4 0.02 0.013 -10000 0 -10000 0 0
PIAS3 0.013 0.03 -10000 0 -10000 0 0
cell proliferation 0.004 0.12 0.37 2 -0.58 24 26
XRCC5 0.027 0.015 -10000 0 -10000 0 0
UBE3A 0.007 0.046 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.039 0.16 -10000 0 -0.39 139 139
FHL2 0.002 0.12 -10000 0 -0.9 8 8
RANBP9 0.012 0.034 -10000 0 -10000 0 0
JMJD1A -0.01 0.055 0.12 35 -0.14 127 162
CDK6 0.022 0.045 0.26 2 -0.58 5 7
TGFB1I1 0.009 0.048 -10000 0 -0.58 3 3
T-DHT/AR/CyclinD1 -0.04 0.14 -10000 0 -0.39 118 118
XRCC6 0.026 0.016 -10000 0 -10000 0 0
T-DHT/AR -0.036 0.17 -10000 0 -0.4 132 132
CTDSP1 0.017 0.02 -10000 0 -10000 0 0
CTDSP2 0.035 0.038 -10000 0 -10000 0 0
BRCA1 0.011 0.04 -10000 0 -0.58 1 1
TCF4 0.026 0.065 -10000 0 -0.57 9 9
CDKN2A 0.065 0.091 0.27 151 -10000 0 151
SRF 0.032 0.023 -10000 0 -10000 0 0
NKX3-1 -0.059 0.2 0.38 2 -0.68 58 60
KLK3 -0.16 0.48 -10000 0 -1.4 126 126
TMF1 0.018 0.017 -10000 0 -10000 0 0
HNRNPA1 0.029 0.021 -10000 0 -10000 0 0
AOF2 -0.008 0.024 -10000 0 -0.069 126 126
APPL1 0.02 0.034 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.025 0.15 -10000 0 -0.36 130 130
AR -0.064 0.2 0.22 1 -0.59 119 120
UBA3 0.016 0.02 -10000 0 -10000 0 0
PATZ1 0.028 0.021 -10000 0 -10000 0 0
PAWR 0.017 0.025 -10000 0 -0.58 1 1
PRKDC 0.024 0.017 -10000 0 -10000 0 0
PA2G4 0.032 0.027 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.021 0.13 -10000 0 -0.35 111 111
RPS6KA3 0.008 0.054 -10000 0 -0.58 4 4
T-DHT/AR/ARA70 -0.035 0.14 -10000 0 -0.36 130 130
LATS2 0.028 0.022 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.018 0.14 0.22 1 -0.33 128 129
Cyclin D3/CDK11 p58 0.019 0.006 -10000 0 -10000 0 0
VAV3 0.013 0.067 0.26 17 -0.58 7 24
KLK2 -0.082 0.28 0.36 2 -0.99 80 82
CASP8 0.026 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.034 0.14 -10000 0 -0.36 120 120
TMPRSS2 -0.13 0.34 -10000 0 -0.99 126 126
CCND1 0.011 0.04 0.26 1 -0.58 3 4
PIAS1 0.008 0.046 -10000 0 -10000 0 0
mol:T-DHT -0.009 0.031 0.06 2 -0.071 163 165
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 0.001 0.066 -10000 0 -0.19 28 28
T-DHT/AR/CDK6 -0.031 0.15 -10000 0 -0.38 124 124
CMTM2 0.023 0.013 0.26 1 -10000 0 1
SNURF 0.011 0.083 -10000 0 -0.58 19 19
ZMIZ1 0.01 0.042 -10000 0 -10000 0 0
CCND3 0.024 0.005 -10000 0 -10000 0 0
TGIF1 0.028 0.021 -10000 0 -10000 0 0
FKBP4 0.013 0.037 0.26 3 -10000 0 3
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.027 0.029 0.26 14 -10000 0 14
GNB1/GNG2 -0.016 0.049 -10000 0 -0.19 60 60
AKT1 0.022 0.094 0.33 13 -0.27 27 40
EGF -0.093 0.24 0.26 2 -0.58 189 191
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.013 0.058 0.25 2 -0.3 5 7
mol:Ca2+ 0.021 0.11 0.4 12 -0.3 67 79
LYN 0.012 0.054 0.25 2 -0.33 2 4
RhoA/GTP 0.009 0.045 0.14 5 -0.14 27 32
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.018 0.12 0.41 13 -0.35 59 72
GNG2 0.018 0.061 -10000 0 -0.58 10 10
ARRB2 0.022 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.008 0.12 -10000 0 -0.59 35 35
G beta5/gamma2 -0.013 0.068 -10000 0 -0.26 59 59
PRKCH 0.017 0.12 0.43 10 -0.36 59 69
DNM1 0.02 0.052 0.26 1 -0.58 7 8
TXA2/TP beta/beta Arrestin3 0.008 0.033 -10000 0 -0.53 1 1
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
PTGDR 0.009 0.1 0.26 7 -0.58 27 34
G12 family/GTP 0 0.09 -10000 0 -0.31 56 56
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
ADRBK2 0.02 0.039 -10000 0 -0.58 4 4
RhoA/GTP/ROCK1 0.031 0.015 -10000 0 -0.37 1 1
mol:GDP -0.01 0.1 0.36 33 -0.34 8 41
mol:NADP 0.024 0.004 -10000 0 -10000 0 0
RAB11A 0.024 0.004 -10000 0 -10000 0 0
PRKG1 -0.009 0.14 -10000 0 -0.58 54 54
mol:IP3 0.018 0.14 0.46 9 -0.38 68 77
cell morphogenesis 0.031 0.015 -10000 0 -0.36 1 1
PLCB2 0.01 0.17 0.56 6 -0.52 69 75
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.025 0.071 0.26 7 -0.29 5 12
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.014 0.059 0.25 4 -0.3 4 8
RHOA 0.023 0.005 -10000 0 -10000 0 0
PTGIR 0.026 0.023 0.26 9 -10000 0 9
PRKCB1 0.017 0.13 0.45 9 -0.38 62 71
GNAQ 0.023 0.027 -10000 0 -0.58 2 2
mol:L-citrulline 0.024 0.004 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.013 0.17 0.57 6 -0.53 60 66
LCK 0.015 0.074 0.25 2 -0.36 14 16
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.023 0.054 -10000 0 -0.25 22 22
TXA2-R family/G12 family/GDP/G beta/gamma 0.004 0.11 -10000 0 -0.42 49 49
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.023 0.051 -10000 0 -0.25 19 19
MAPK14 0.018 0.09 0.35 14 -0.23 56 70
TGM2/GTP 0.015 0.15 0.5 9 -0.43 63 72
MAPK11 0.016 0.091 0.34 15 -0.24 52 67
ARHGEF1 0.011 0.067 0.27 11 -0.18 47 58
GNAI2 0.024 0.005 -10000 0 -10000 0 0
JNK cascade 0.02 0.13 0.43 12 -0.39 60 72
RAB11/GDP 0.023 0.006 -10000 0 -10000 0 0
ICAM1 0.022 0.1 0.39 12 -0.28 57 69
cAMP biosynthetic process 0.016 0.13 0.44 9 -0.36 65 74
Gq family/GTP/EBP50 0.015 0.043 0.22 4 -0.22 15 19
actin cytoskeleton reorganization 0.031 0.015 -10000 0 -0.36 1 1
SRC 0.012 0.056 0.25 2 -0.3 4 6
GNB5 0.024 0.004 -10000 0 -10000 0 0
GNB1 0.023 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.05 0.11 0.24 3 -0.29 71 74
VCAM1 0.02 0.11 0.39 12 -0.31 58 70
TP beta/Gq family/GDP/G beta5/gamma2 -0.008 0.12 -10000 0 -0.59 35 35
platelet activation 0.023 0.12 0.41 15 -0.31 57 72
PGI2/IP 0.019 0.016 0.18 9 -10000 0 9
PRKACA 0.009 0.052 -10000 0 -0.29 27 27
Gq family/GDP/G beta5/gamma2 -0.001 0.1 -10000 0 -0.47 32 32
TXA2/TP beta/beta Arrestin2 -0.008 0.069 -10000 0 -0.45 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.002 0.047 -10000 0 -0.27 25 25
mol:DAG 0.017 0.14 0.47 9 -0.42 65 74
EGFR -0.19 0.29 -10000 0 -0.58 349 349
TXA2/TP alpha 0.014 0.16 0.53 7 -0.49 66 73
Gq family/GTP 0.002 0.05 0.25 1 -0.22 39 40
YES1 0.013 0.059 0.25 2 -0.28 6 8
GNAI2/GTP 0.013 0.051 -10000 0 -0.25 24 24
PGD2/DP 0.006 0.075 0.18 7 -0.4 30 37
SLC9A3R1 0.034 0.052 0.26 47 -10000 0 47
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 0.027 0.26 6 -0.58 1 7
PGK/cGMP 0.01 0.092 -10000 0 -0.37 54 54
RhoA/GDP 0.023 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.035 0.068 -10000 0 -0.39 10 10
NOS3 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.021 0.13 0.44 10 -0.38 55 65
PRKCB 0.02 0.13 0.42 11 -0.38 59 70
PRKCE 0.017 0.12 0.45 9 -0.36 56 65
PRKCD 0.016 0.13 0.45 9 -0.39 57 66
PRKCG 0.018 0.13 0.46 9 -0.39 58 67
muscle contraction 0.014 0.16 0.54 7 -0.49 62 69
PRKCZ 0.017 0.12 0.4 12 -0.35 58 70
ARR3 0.021 0.022 0.26 8 -10000 0 8
TXA2/TP beta 0.024 0.058 -10000 0 -0.27 27 27
PRKCQ 0.015 0.14 0.42 13 -0.39 61 74
MAPKKK cascade 0.014 0.16 0.49 8 -0.46 66 74
SELE 0.015 0.12 0.38 13 -0.39 58 71
TP beta/GNAI2/GDP/G beta/gamma 0.034 0.068 -10000 0 -0.41 10 10
ROCK1 0.023 0.02 -10000 0 -0.58 1 1
GNA14 0.023 0.07 0.26 21 -0.58 10 31
chemotaxis 0.012 0.18 0.6 6 -0.61 58 64
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.028 -10000 0 -0.58 2 2
Rac1/GTP 0.018 0.003 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex 0.057 0.13 0.5 7 -0.52 2 9
RAD9A 0.023 0.006 -10000 0 -10000 0 0
AP1 -0.098 0.21 -10000 0 -0.43 277 277
IFNAR2 0.029 0.009 -10000 0 -10000 0 0
AKT1 -0.002 0.089 -10000 0 -0.23 87 87
ER alpha/Oestrogen -0.024 0.17 0.18 113 -0.41 140 253
NFX1/SIN3/HDAC complex 0.023 0.058 0.24 1 -0.32 15 16
EGF -0.091 0.24 0.26 2 -0.57 189 191
SMG5 0.02 0.009 -10000 0 -10000 0 0
SMG6 0.022 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.041 0.018 -10000 0 -10000 0 0
TERT/c-Abl 0.054 0.12 0.43 3 -0.49 2 5
SAP18 0.023 0.007 -10000 0 -10000 0 0
MRN complex 0.036 0.022 -10000 0 -10000 0 0
WT1 0.15 0.12 0.27 486 -10000 0 486
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 0.021 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.048 0.1 -10000 0 -0.51 1 1
Mad/Max 0.04 0.014 -10000 0 -10000 0 0
TERT 0.057 0.14 0.51 6 -0.6 1 7
CCND1 0.08 0.16 0.55 16 -1.1 3 19
MAX 0.026 0.006 -10000 0 -10000 0 0
RBBP7 0.027 0.021 0.27 7 -10000 0 7
RBBP4 0.024 0.02 -10000 0 -0.57 1 1
TERF2 0.021 0.013 -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 0.052 -10000 0 -0.38 5 5
CDKN1B 0.029 0.053 -10000 0 -0.68 3 3
RAD1 0.024 0.004 -10000 0 -10000 0 0
XRCC5 0.024 0.004 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
SAP30 0.025 0.016 0.26 4 -10000 0 4
TRF2/PARP2 0.032 0.015 -10000 0 -10000 0 0
UBE3A 0.025 0.007 -10000 0 -10000 0 0
JUN 0.02 0.054 -10000 0 -0.57 8 8
E6 0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.01 -10000 0 -10000 0 0
FOS -0.15 0.27 -10000 0 -0.57 277 277
IFN-gamma/IRF1 0.065 0.065 0.24 30 -0.32 3 33
PARP2 0.024 0.004 -10000 0 -10000 0 0
BLM 0.046 0.07 0.26 91 -10000 0 91
Telomerase 0.03 0.076 0.26 2 -0.61 4 6
IRF1 0.029 0.019 0.27 3 -0.19 3 6
ESR1 -0.031 0.23 0.26 113 -0.57 134 247
KU/TER 0.034 0.01 -10000 0 -10000 0 0
ATM/TRF2 0.03 0.014 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.027 0.053 0.24 1 -0.32 7 8
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.028 0.054 0.24 1 -0.33 7 8
HDAC1 0.025 0.004 -10000 0 -10000 0 0
HDAC2 0.028 0.013 -10000 0 -10000 0 0
ATM 0.013 0.016 -10000 0 -10000 0 0
SMAD3 0.005 0.013 -10000 0 -10000 0 0
ABL1 0.024 0.004 -10000 0 -10000 0 0
MXD1 0.027 0.009 0.26 1 -10000 0 1
MRE11A 0.022 0.007 -10000 0 -10000 0 0
HUS1 0.024 0.003 -10000 0 -10000 0 0
RPS6KB1 0.022 0.008 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.059 0.13 0.51 1 -0.62 4 5
NR2F2 0.012 0.039 -10000 0 -0.58 3 3
MAPK3 0.006 0.021 -10000 0 -10000 0 0
MAPK1 0.006 0.021 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.021 0.012 0.26 1 -10000 0 1
NFKB1 0.024 0.004 -10000 0 -10000 0 0
HNRNPC 0.024 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.013 0.016 -10000 0 -10000 0 0
NBN 0.019 0.01 -10000 0 -10000 0 0
EGFR -0.19 0.29 -10000 0 -0.57 349 349
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.21 0.26 -10000 0 -0.46 480 480
MYC 0.007 0.086 -10000 0 -0.58 20 20
IL2 0.029 0.027 0.26 9 -10000 0 9
KU 0.034 0.01 -10000 0 -10000 0 0
RAD50 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
TGFB1 0.021 0.012 0.26 1 -10000 0 1
TRF2/BLM 0.044 0.048 0.23 8 -10000 0 8
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.067 0.13 0.47 4 -0.56 1 5
SP1/HDAC2 0.046 0.026 -10000 0 -10000 0 0
PINX1 0.02 0.009 -10000 0 -10000 0 0
Telomerase/EST1A 0.045 0.1 -10000 0 -0.5 1 1
Smad3/Myc 0.006 0.056 -10000 0 -0.37 19 19
911 complex 0.044 0.016 -10000 0 -10000 0 0
IFNG 0.059 0.085 0.27 133 -0.19 3 136
Telomerase/PinX1 0.037 0.096 -10000 0 -0.5 1 1
Telomerase/AKT1/mTOR/p70S6K 0.027 0.097 0.32 3 -0.49 16 19
SIN3B 0.025 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.043 0.095 -10000 0 -10000 0 0
response to DNA damage stimulus -0.002 0.027 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.046 0.033 -10000 0 -10000 0 0
TRF2/WRN 0.027 0.016 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.048 0.1 -10000 0 -0.46 2 2
E2F1 0.1 0.11 0.27 295 -10000 0 295
ZNFX1 0.023 0.007 -10000 0 -10000 0 0
PIF1 0.069 0.094 0.26 184 -10000 0 184
NCL 0.024 0.004 -10000 0 -10000 0 0
DKC1 0.025 0.011 0.26 2 -10000 0 2
telomeric DNA binding 0 0 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.022 0.13 0.3 17 -0.38 41 58
IKBKB 0.023 0.091 0.29 11 -0.31 12 23
AKT1 0.037 0.11 0.27 66 -0.24 19 85
IKBKG 0.027 0.075 0.32 6 -0.29 7 13
CALM1 0 0.1 0.26 1 -0.35 43 44
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
MAP3K1 0.021 0.16 0.37 11 -0.54 42 53
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.1 -10000 0 -0.36 45 45
DOK1 0.025 0.011 0.26 2 -10000 0 2
AP-1 -0.024 0.099 0.26 6 -0.24 55 61
LYN 0.021 0.008 -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 0.001 0.16 0.37 18 -0.46 89 107
CD22 -0.014 0.14 0.29 20 -0.46 59 79
CAMK2G 0.001 0.098 0.26 5 -0.42 19 24
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
INPP5D 0.024 0.004 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.001 0.09 -10000 0 -0.33 52 52
GO:0007205 0 0.11 -10000 0 -0.37 45 45
SYK 0.024 0.003 -10000 0 -10000 0 0
ELK1 0 0.1 0.26 1 -0.36 41 42
NFATC1 0.029 0.14 0.29 28 -0.46 34 62
B-cell antigen/BCR complex 0.001 0.16 0.37 18 -0.46 89 107
PAG1/CSK 0.029 0.017 -10000 0 -10000 0 0
NFKBIB 0.024 0.047 0.17 11 -0.13 22 33
HRAS 0.01 0.11 0.26 15 -0.36 38 53
NFKBIA 0.025 0.047 0.16 13 -0.12 22 35
NF-kappa-B/RelA/I kappa B beta 0.028 0.042 0.17 10 -10000 0 10
RasGAP/Csk 0.029 0.13 0.33 19 -0.37 63 82
mol:GDP 0.002 0.1 -10000 0 -0.35 45 45
PTEN 0.022 0.028 -10000 0 -0.58 2 2
CD79B 0.011 0.1 0.26 19 -0.58 26 45
NF-kappa-B/RelA/I kappa B alpha 0.028 0.041 0.17 10 -10000 0 10
GRB2 0.023 0.01 0.26 1 -10000 0 1
PI3K/BCAP/CD19 0.022 0.17 0.32 22 -0.5 48 70
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
mol:IP3 0.001 0.11 -10000 0 -0.37 45 45
CSK 0.024 0.004 -10000 0 -10000 0 0
FOS -0.081 0.16 -10000 0 -0.43 81 81
CHUK 0.024 0.083 0.3 8 -0.3 17 25
IBTK 0.023 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.018 0.098 -10000 0 -0.42 18 18
PTPN6 -0.016 0.13 0.26 19 -0.58 32 51
RELA 0.024 0.004 -10000 0 -10000 0 0
BCL2A1 0.025 0.036 0.16 12 -10000 0 12
VAV2 0.012 0.15 0.29 11 -0.59 30 41
ubiquitin-dependent protein catabolic process 0.026 0.047 0.17 11 -0.12 24 35
BTK 0.015 0.065 -10000 0 -0.97 4 4
CD19 0.003 0.14 0.28 31 -0.45 58 89
MAP4K1 0.031 0.053 0.26 36 -0.58 2 38
CD72 0.029 0.042 0.26 24 -0.58 1 25
PAG1 0.02 0.015 0.26 2 -10000 0 2
MAPK14 0.023 0.14 0.31 24 -0.45 42 66
SH3BP5 0.024 0.004 -10000 0 -10000 0 0
PIK3AP1 0.002 0.11 0.24 1 -0.38 47 48
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.001 0.14 0.27 3 -0.43 67 70
RAF1 0.009 0.1 0.26 12 -0.42 20 32
RasGAP/p62DOK/SHIP 0.028 0.12 0.3 18 -0.36 63 81
CD79A -0.007 0.18 0.26 66 -0.58 76 142
re-entry into mitotic cell cycle -0.023 0.098 0.25 6 -0.25 53 59
RASA1 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.016 0.099 0.28 22 -0.36 15 37
MAPK1 0.009 0.093 0.27 9 -0.36 18 27
CD72/SHP1 0.026 0.15 0.38 23 -0.56 31 54
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.022 0.15 0.35 15 -0.45 43 58
actin cytoskeleton organization 0.029 0.14 0.31 24 -0.51 29 53
NF-kappa-B/RelA 0.057 0.08 0.3 10 -0.21 1 11
Calcineurin 0.017 0.094 -10000 0 -0.4 17 17
PI3K -0.014 0.098 -10000 0 -0.41 36 36
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.004 0.12 -10000 0 -0.4 50 50
SOS1 0.024 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.009 0.2 0.44 6 -0.7 51 57
DAPP1 -0.02 0.21 -10000 0 -0.79 52 52
cytokine secretion 0.03 0.13 0.27 36 -0.42 34 70
mol:DAG 0.001 0.11 -10000 0 -0.37 45 45
PLCG2 0.02 0.029 0.26 1 -0.58 2 3
MAP2K1 0.009 0.1 0.28 9 -0.4 18 27
B-cell antigen/BCR complex/FcgammaRIIB 0.013 0.14 0.34 18 -0.42 64 82
mol:PI-3-4-5-P3 0.005 0.092 0.23 16 -0.33 23 39
ETS1 -0.001 0.092 0.24 5 -0.4 20 25
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.032 0.13 0.33 19 -0.36 69 88
B-cell antigen/BCR complex/LYN -0.013 0.14 0.26 18 -0.47 62 80
MALT1 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.14 0.3 21 -0.55 29 50
B-cell antigen/BCR complex/LYN/SYK 0.012 0.15 0.36 21 -0.45 56 77
CARD11 0.002 0.11 0.26 9 -0.37 42 51
FCGR2B 0.018 0.04 0.26 1 -0.58 4 5
PPP3CA 0.024 0.012 0.26 2 -10000 0 2
BCL10 0.024 0.004 -10000 0 -10000 0 0
IKK complex 0.027 0.051 0.16 49 -0.14 4 53
PTPRC 0.021 0.043 0.26 11 -0.58 3 14
PDPK1 0.02 0.084 0.22 51 -0.23 19 70
PPP3CB 0.024 0.004 -10000 0 -10000 0 0
PPP3CC 0.02 0.01 -10000 0 -10000 0 0
POU2F2 0.022 0.033 0.18 9 -10000 0 9
Insulin Pathway

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
CBL/APS/CAP -0.046 0.17 -10000 0 -0.33 237 237
TC10/GTP -0.037 0.14 -10000 0 -0.29 224 224
Insulin Receptor/Insulin/IRS1/Shp2 0.043 0.08 -10000 0 -0.35 36 36
HRAS 0.025 0.018 0.26 5 -10000 0 5
APS homodimer 0.033 0.047 0.26 39 -10000 0 39
GRB14 0.015 0.18 0.26 135 -0.58 68 203
FOXO3 -0.018 0.15 -10000 0 -0.59 61 61
AKT1 -0.018 0.11 0.33 7 -0.29 54 61
INSR 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.056 0.048 0.44 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 -0.58 230 230
CRK 0.022 0.007 -10000 0 -10000 0 0
PTPN1 -0.002 0.024 -10000 0 -10000 0 0
CAV1 -0.082 0.15 -10000 0 -0.36 207 207
CBL/APS/CAP/Crk-II/C3G -0.025 0.16 -10000 0 -0.31 227 227
Insulin Receptor/Insulin/IRS1/NCK2 0.043 0.079 -10000 0 -0.35 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.029 0.072 -10000 0 -0.31 38 38
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.012 0.067 -10000 0 -0.4 7 7
RPS6KB1 -0.017 0.097 0.32 7 -0.49 1 8
PARD6A 0.023 0.019 0.26 5 -10000 0 5
CBL 0.022 0.007 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.014 0.039 -10000 0 -0.56 4 4
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.009 0.093 -10000 0 -0.37 1 1
HRAS/GTP -0.02 0.046 -10000 0 -0.28 23 23
Insulin Receptor 0.027 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.041 0.073 -10000 0 -0.33 26 26
PRKCI 0.014 0.058 -10000 0 -0.46 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.003 0.1 -10000 0 -0.3 98 98
SHC1 0.02 0.009 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.041 0.037 -10000 0 -0.47 4 4
PI3K 0.039 0.076 -10000 0 -0.31 38 38
NCK2 0.024 0.002 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
mol:H2O2 0 0.002 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.012 0.18 5 -10000 0 5
AKT2 -0.018 0.11 0.3 6 -0.29 56 62
PRKCZ 0.004 0.086 -10000 0 -0.48 13 13
SH2B2 0.033 0.047 0.26 39 -10000 0 39
SHC/SHIP 0.011 0.06 -10000 0 -0.31 28 28
F2RL2 0.047 0.12 0.26 138 -0.58 17 155
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 -0.036 0.17 -10000 0 -0.33 229 229
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 -0.02 0.063 -10000 0 -0.32 36 36
SOS1 0.024 0.003 -10000 0 -10000 0 0
SGK1 -0.018 0.14 -10000 0 -0.68 40 40
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
IRS1 0 0.12 -10000 0 -0.58 38 38
p62DOK/RasGAP 0.041 0.037 -10000 0 -0.48 4 4
INS 0.019 0.009 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.062 -10000 0 -0.32 36 36
GRB2 0.023 0.01 0.26 1 -10000 0 1
EIF4EBP1 -0.02 0.089 0.31 3 -0.49 1 4
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 0.008 0.054 -10000 0 -0.28 26 26
Insulin Receptor/Insulin/IRS1 0.029 0.076 -10000 0 -0.34 37 37
Insulin Receptor/Insulin/IRS3 0.034 0.014 -10000 0 -10000 0 0
Par3/Par6 0.06 0.073 -10000 0 -0.32 17 17
TCGA08_retinoblastoma

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
CDKN2B 0.024 0.018 0.27 2 -10000 0 2
CDKN2C 0.014 0.029 -10000 0 -0.56 1 1
CDKN2A 0.061 0.087 0.26 151 -10000 0 151
CCND2 -0.016 0.037 0.17 1 -0.22 14 15
RB1 0.016 0.049 0.26 15 -0.24 7 22
CDK4 -0.017 0.038 0.21 1 -0.23 11 12
CDK6 -0.017 0.04 0.2 1 -0.21 19 20
G1/S progression -0.01 0.06 0.19 39 -0.27 14 53
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 0.045 0.072 0.28 3 -0.3 26 29
NF kappa B1 p50/RelA/I kappa B alpha 0.049 0.084 0.35 13 -0.32 4 17
alphaV/beta3 Integrin/Osteopontin/Src 0.082 0.074 0.23 16 -10000 0 16
AP1 -0.037 0.18 0.35 1 -0.53 29 30
ILK 0.032 0.075 0.26 13 -0.32 26 39
bone resorption 0.022 0.081 0.27 2 -0.34 24 26
PTK2B 0.02 0.01 -10000 0 -10000 0 0
PYK2/p130Cas 0.068 0.093 0.3 10 -0.29 26 36
ITGAV 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.026 0.063 -10000 0 -0.43 18 18
alphaV/beta3 Integrin/Osteopontin 0.08 0.1 0.28 18 -0.35 26 44
MAP3K1 0.032 0.078 0.26 15 -0.34 26 41
JUN 0.019 0.054 -10000 0 -0.58 8 8
MAPK3 0.022 0.071 0.28 12 -0.3 25 37
MAPK1 0.024 0.071 0.28 13 -0.31 21 34
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 0.019 0.081 0.26 16 -0.34 28 44
ITGB3 0.011 0.099 0.27 4 -0.57 26 30
NFKBIA 0.02 0.07 0.28 12 -0.31 20 32
FOS -0.15 0.27 -10000 0 -0.58 277 277
CD44 0.024 0.004 -10000 0 -10000 0 0
CHUK 0.024 0.003 -10000 0 -10000 0 0
PLAU 0.024 0.1 0.46 7 -0.55 2 9
NF kappa B1 p50/RelA 0.066 0.077 0.36 6 -10000 0 6
BCAR1 0.021 0.008 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.027 0.076 0.24 1 -0.42 26 27
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.033 0.075 0.26 15 -0.32 26 41
VAV3 0.017 0.077 0.26 18 -0.3 32 50
MAP3K14 0.034 0.075 0.27 11 -0.32 26 37
ROCK2 0.013 0.081 -10000 0 -0.58 18 18
SPP1 0.089 0.11 0.27 255 -10000 0 255
RAC1 0.024 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.03 0.07 0.24 16 -0.28 31 47
MMP2 -0.054 0.15 0.34 4 -0.51 27 31
IL27-mediated signaling events

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
TGFB1 0.025 0.011 0.26 1 -10000 0 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.014 0.12 0.46 7 -0.48 4 11
IL27/IL27R/JAK1 0.041 0.16 0.73 4 -0.74 5 9
TBX21 -0.001 0.17 0.43 19 -0.51 42 61
IL12B 0.072 0.098 0.27 189 -10000 0 189
IL12A -0.014 0.1 0.15 15 -0.42 52 67
IL6ST -0.031 0.17 0.2 1 -0.58 89 90
IL27RA/JAK1 0.022 0.071 0.65 1 -1.2 2 3
IL27 0.045 0.075 0.27 89 -10000 0 89
TYK2 0.03 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.098 0.16 1.1 1 -0.8 2 3
T-helper 2 cell differentiation -0.014 0.12 0.46 7 -0.48 4 11
T cell proliferation during immune response -0.014 0.12 0.46 7 -0.48 4 11
MAPKKK cascade 0.014 0.12 0.48 4 -0.46 7 11
STAT3 0.023 0.005 -10000 0 -10000 0 0
STAT2 0.024 0.002 -10000 0 -10000 0 0
STAT1 0.028 0.034 0.27 18 -10000 0 18
IL12RB1 0.034 0.051 0.27 37 -0.58 1 38
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.008 0.19 0.45 29 -0.52 51 80
IL27/IL27R/JAK2/TYK2 0.014 0.12 0.48 4 -0.47 7 11
positive regulation of T cell mediated cytotoxicity 0.014 0.12 0.48 4 -0.46 7 11
STAT1 (dimer) 0.037 0.2 0.62 22 -0.65 16 38
JAK2 0.027 0.013 -10000 0 -10000 0 0
JAK1 0.024 0.01 -10000 0 -10000 0 0
STAT2 (dimer) 0.026 0.12 0.45 3 -0.45 7 10
T cell proliferation -0.093 0.19 0.35 4 -0.46 79 83
IL12/IL12R/TYK2/JAK2 0.057 0.18 0.47 2 -0.74 25 27
IL17A -0.099 0.16 1.1 1 -0.8 2 3
mast cell activation -0.014 0.12 0.46 7 -0.48 4 11
IFNG 0.021 0.047 0.13 115 -0.1 4 119
T cell differentiation 0 0.006 0.015 18 -0.018 11 29
STAT3 (dimer) 0.024 0.11 0.45 3 -0.45 7 10
STAT5A (dimer) 0.022 0.12 0.45 3 -0.46 12 15
STAT4 (dimer) 0.012 0.14 0.45 3 -0.44 25 28
STAT4 -0.001 0.12 0.26 1 -0.58 41 42
T cell activation -0.005 0.011 0.12 2 -0.11 6 8
IL27R/JAK2/TYK2 0.021 0.13 -10000 0 -0.9 3 3
GATA3 -0.023 0.27 0.62 33 -1.3 31 64
IL18 0.009 0.022 0.14 25 -10000 0 25
positive regulation of mast cell cytokine production 0.024 0.11 0.45 3 -0.44 7 10
IL27/EBI3 0.051 0.075 0.33 16 -0.43 5 21
IL27RA 0.01 0.073 0.75 1 -1.3 2 3
IL6 -0.19 0.29 0.26 1 -0.58 342 343
STAT5A 0.02 0.047 -10000 0 -0.58 6 6
monocyte differentiation 0.001 0.002 -10000 0 -10000 0 0
IL2 -0.014 0.043 0.45 2 -0.54 1 3
IL1B 0.001 0.05 0.14 3 -0.43 13 16
EBI3 0.025 0.059 0.27 16 -0.58 6 22
TNF 0.005 0.048 0.14 21 -0.43 10 31
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 0.008 -10000 0 -10000 0 0
ELF1 0.032 0.05 -10000 0 -0.36 8 8
CCNA2 0.12 0.12 0.26 383 -10000 0 383
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
JAK3 0.028 0.031 0.26 16 -10000 0 16
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
JAK1 0.024 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.049 0.1 0.32 20 -0.55 9 29
SHC1 0.02 0.009 -10000 0 -10000 0 0
SP1 0.024 0.046 -10000 0 -0.39 11 11
IL2RA 0.022 0.11 0.3 61 -0.76 11 72
IL2RB 0.033 0.047 0.26 38 -10000 0 38
SOS1 0.024 0.003 -10000 0 -10000 0 0
IL2RG 0.031 0.071 0.26 42 -0.58 7 49
G1/S transition of mitotic cell cycle 0.048 0.13 0.32 3 -0.78 15 18
PTPN11 0.025 0.002 -10000 0 -10000 0 0
CCND2 0.006 0.089 0.35 2 -0.8 11 13
LCK 0.026 0.078 0.26 34 -0.58 11 45
GRB2 0.023 0.01 0.26 1 -10000 0 1
IL2 0.023 0.024 0.26 9 -10000 0 9
CDK6 0.021 0.045 0.26 2 -0.58 5 7
CCND3 0.048 0.1 0.42 5 -0.6 4 9
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 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.015 0.17 0.29 5 -0.4 132 137
AKT1 0.024 0.01 -10000 0 -10000 0 0
GSC -0.032 0.28 -10000 0 -1.4 40 40
NKX2-5 0.055 0.085 0.26 138 -10000 0 138
muscle cell differentiation -0.027 0.063 0.32 5 -10000 0 5
SMAD2-3/SMAD4/SP1 0.062 0.07 -10000 0 -0.44 1 1
SMAD4 0.011 0.046 -10000 0 -10000 0 0
CBFB 0.021 0.008 -10000 0 -10000 0 0
SAP18 0.022 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.11 0.2 0.27 1 -0.36 354 355
SMAD3/SMAD4/VDR 0.052 0.061 -10000 0 -0.35 1 1
MYC 0.004 0.085 -10000 0 -0.58 20 20
CDKN2B -0.045 0.18 -10000 0 -0.79 26 26
AP1 -0.054 0.16 -10000 0 -0.31 245 245
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.008 0.087 -10000 0 -0.36 27 27
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.012 0.06 -10000 0 -0.35 12 12
SP3 0.025 0.004 -10000 0 -10000 0 0
CREB1 0.024 0.003 -10000 0 -10000 0 0
FOXH1 0.043 0.079 0.26 100 -0.16 1 101
SMAD3/SMAD4/GR 0.023 0.072 -10000 0 -0.4 9 9
GATA3 0.013 0.11 0.26 27 -0.57 31 58
SKI/SIN3/HDAC complex/NCoR1 0.004 0.078 -10000 0 -0.39 22 22
MEF2C/TIF2 0.029 0.086 0.33 4 -0.32 11 15
endothelial cell migration -0.029 0.084 0.55 7 -10000 0 7
MAX 0.02 0.015 -10000 0 -10000 0 0
RBBP7 0.026 0.02 0.26 7 -10000 0 7
RBBP4 0.023 0.02 -10000 0 -0.58 1 1
RUNX2 0.026 0.026 0.26 11 -10000 0 11
RUNX3 0.022 0.036 0.26 3 -0.58 3 6
RUNX1 0.023 0.02 -10000 0 -0.58 1 1
CTBP1 0.023 0.005 -10000 0 -10000 0 0
NR3C1 0.015 0.059 -10000 0 -0.58 9 9
VDR 0.024 0.003 -10000 0 -10000 0 0
CDKN1A 0.015 0.082 -10000 0 -1.1 3 3
KAT2B 0.024 0.02 -10000 0 -0.58 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.053 0.079 -10000 0 -0.27 22 22
DCP1A 0.023 0.005 -10000 0 -10000 0 0
SKI 0.023 0.005 -10000 0 -10000 0 0
SERPINE1 0.029 0.085 -10000 0 -0.56 6 6
SMAD3/SMAD4/ATF2 0.032 0.059 -10000 0 -0.38 1 1
SMAD3/SMAD4/ATF3 -0.017 0.15 -10000 0 -0.4 109 109
SAP30 0.024 0.016 0.26 4 -10000 0 4
Cbp/p300/PIAS3 0.045 0.029 -10000 0 -10000 0 0
JUN -0.063 0.16 0.29 1 -0.31 232 233
SMAD3/SMAD4/IRF7 0.05 0.082 0.34 19 -10000 0 19
TFE3 0.028 0.009 -10000 0 -0.2 1 1
COL1A2 0.047 0.092 0.4 2 -0.64 5 7
mesenchymal cell differentiation -0.034 0.059 -10000 0 -10000 0 0
DLX1 0.054 0.11 0.26 149 -0.58 10 159
TCF3 0.024 0.009 0.26 1 -10000 0 1
FOS -0.15 0.27 -10000 0 -0.58 279 279
SMAD3/SMAD4/Max 0.027 0.059 -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 0.012 0.038 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.032 0.056 -10000 0 -10000 0 0
IRF7 0.046 0.07 0.28 81 -10000 0 81
ESR1 -0.037 0.23 0.26 113 -0.58 134 247
HNF4A 0.022 0.029 0.26 13 -10000 0 13
MEF2C 0.052 0.093 0.4 11 -0.43 3 14
SMAD2-3/SMAD4 0.032 0.066 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.045 0.025 -10000 0 -0.37 1 1
IGHV3OR16-13 0.005 0.042 -10000 0 -0.35 13 13
TGIF2/HDAC complex 0.023 0.005 -10000 0 -10000 0 0
CREBBP 0.024 0.009 -10000 0 -10000 0 0
SKIL 0.026 0.023 0.26 9 -10000 0 9
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
SNIP1 0.023 0.006 -10000 0 -10000 0 0
GCN5L2 0.002 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.041 0.062 -10000 0 -0.46 1 1
MSG1/HSC70 -0.14 0.22 -10000 0 -0.42 373 373
SMAD2 0.021 0.031 -10000 0 -10000 0 0
SMAD3 0.014 0.041 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.016 0.04 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.02 0.054 0.25 8 -0.47 3 11
NCOR1 0.022 0.007 -10000 0 -10000 0 0
NCOA2 0.002 0.1 -10000 0 -0.58 29 29
NCOA1 0.023 0.02 -10000 0 -0.58 1 1
MYOD/E2A 0.032 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.076 0.065 -10000 0 -0.42 1 1
IFNB1 0.021 0.073 0.32 31 -10000 0 31
SMAD3/SMAD4/MEF2C 0.069 0.088 -10000 0 -0.47 2 2
CITED1 -0.2 0.3 0.26 13 -0.58 373 386
SMAD2-3/SMAD4/ARC105 0.04 0.067 -10000 0 -10000 0 0
RBL1 0.024 0.009 0.26 1 -10000 0 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.016 0.066 -10000 0 -0.45 10 10
RUNX1-3/PEBPB2 0.041 0.036 -10000 0 -0.47 3 3
SMAD7 -0.035 0.15 -10000 0 -0.53 10 10
MYC/MIZ-1 0.014 0.066 -10000 0 -0.43 20 20
SMAD3/SMAD4 0.028 0.074 0.3 23 -0.35 4 27
IL10 0.006 0.083 0.34 2 -0.38 25 27
PIASy/HDAC complex 0.02 0.015 -10000 0 -10000 0 0
PIAS3 0.024 0.006 -10000 0 -10000 0 0
CDK2 0.025 0.008 -10000 0 -10000 0 0
IL5 0.004 0.085 -10000 0 -0.38 18 18
CDK4 0.025 0.009 -10000 0 -10000 0 0
PIAS4 0.02 0.015 -10000 0 -10000 0 0
ATF3 -0.048 0.19 -10000 0 -0.58 110 110
SMAD3/SMAD4/SP1 0.046 0.066 -10000 0 -0.49 1 1
FOXG1 0.018 0.069 0.26 66 -10000 0 66
FOXO3 0.011 0.018 -10000 0 -0.43 1 1
FOXO1 0.009 0.03 -10000 0 -0.43 4 4
FOXO4 0.012 0.01 -10000 0 -10000 0 0
heart looping 0.052 0.093 0.4 11 -0.42 3 14
CEBPB 0.023 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.052 0.092 0.29 3 -0.39 10 13
MYOD1 0.021 0.028 0.26 13 -10000 0 13
SMAD3/SMAD4/HNF4 0.032 0.059 -10000 0 -10000 0 0
SMAD3/SMAD4/GATA3 0.028 0.1 -10000 0 -0.41 30 30
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.023 0.26 9 -10000 0 9
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.043 0.069 -10000 0 -0.5 2 2
SMAD3/SMAD4/SP1-3 0.058 0.066 -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 0.078 0.094 0.35 15 -0.39 1 16
ITGB5 0.015 0.044 -10000 0 -0.4 1 1
TGIF/SIN3/HDAC complex/CtBP 0.013 0.061 -10000 0 -0.3 23 23
SMAD3/SMAD4/AR -0.018 0.15 -10000 0 -0.39 117 117
AR -0.049 0.2 0.26 1 -0.58 119 120
negative regulation of cell growth -0.001 0.083 -10000 0 -0.35 10 10
SMAD3/SMAD4/MYOD 0.031 0.058 -10000 0 -10000 0 0
E2F5 0.022 0.023 0.26 7 -10000 0 7
E2F4 0.021 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.066 0.074 -10000 0 -0.33 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.015 0.055 -10000 0 -0.37 11 11
TFDP1 0.022 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.039 0.18 -10000 0 -0.31 241 241
SMAD3/SMAD4/RUNX2 0.034 0.059 -10000 0 -10000 0 0
TGIF2 0.023 0.005 -10000 0 -10000 0 0
TGIF1 0.023 0.006 -10000 0 -10000 0 0
ATF2 0.023 0.02 -10000 0 -0.58 1 1
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 0.049 0.14 151 -10000 0 151
TP53 0.01 0.019 -10000 0 -0.19 2 2
Senescence 0.01 0.019 -10000 0 -0.19 2 2
Apoptosis 0.01 0.019 -10000 0 -0.19 2 2
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.011 0.061 0.29 29 -10000 0 29
MDM4 0.02 0.009 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.024 0.089 -10000 0 -0.64 6 6
oxygen homeostasis 0.012 0.013 -10000 0 -10000 0 0
TCEB2 0.026 0.027 0.26 12 -10000 0 12
TCEB1 0.02 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.088 0.087 0.34 9 -0.36 3 12
EPO 0.15 0.18 0.54 59 -0.55 2 61
FIH (dimer) 0.032 0.02 -10000 0 -10000 0 0
APEX1 0.034 0.024 -10000 0 -10000 0 0
SERPINE1 0.14 0.16 0.53 26 -0.57 3 29
FLT1 -0.017 0.17 -10000 0 -0.74 26 26
ADORA2A 0.16 0.17 0.49 84 -0.5 5 89
germ cell development 0.14 0.16 0.5 42 -0.55 3 45
SLC11A2 0.14 0.16 0.48 42 -0.54 4 46
BHLHE40 0.14 0.16 0.48 39 -0.58 4 43
HIF1AN 0.032 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.12 0.13 0.41 55 -0.37 2 57
ETS1 0.026 0.036 -10000 0 -0.58 3 3
CITED2 0.015 0.091 -10000 0 -0.64 9 9
KDR -0.014 0.17 -10000 0 -0.71 31 31
PGK1 0.14 0.16 0.49 37 -0.56 3 40
SIRT1 0.025 0.004 -10000 0 -10000 0 0
response to hypoxia 0.002 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.18 0.6 16 -0.55 7 23
EPAS1 0.073 0.091 0.29 57 -0.36 5 62
SP1 0.029 0.012 -10000 0 -10000 0 0
ABCG2 0.12 0.2 0.48 42 -0.57 36 78
EFNA1 0.11 0.14 0.51 7 -0.56 2 9
FXN 0.15 0.16 0.47 52 -0.55 3 55
POU5F1 0.14 0.16 0.5 42 -0.57 3 45
neuron apoptosis -0.16 0.18 0.54 7 -0.59 16 23
EP300 0.023 0.006 -10000 0 -10000 0 0
EGLN3 0.049 0.069 0.28 70 -0.59 1 71
EGLN2 0.034 0.026 0.27 5 -10000 0 5
EGLN1 0.027 0.029 -10000 0 -0.59 1 1
VHL/Elongin B/Elongin C 0.04 0.026 -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 59 -0.55 3 62
TWIST1 0.14 0.19 0.47 49 -0.55 31 80
ELK1 0.028 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.1 0.11 0.41 9 -0.36 2 11
VEGFA 0.14 0.16 0.49 37 -0.57 3 40
CREBBP 0.023 0.006 -10000 0 -10000 0 0
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 0.012 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 0.035 0.3 7 -10000 0 7
MAPK12 0.004 0.073 0.21 60 -0.33 23 83
CCND1 0.011 0.047 -10000 0 -0.37 6 6
p38 gamma/SNTA1 0.021 0.071 0.32 2 -0.32 20 22
MAP2K3 0.022 0.007 -10000 0 -10000 0 0
PKN1 0.024 0.003 -10000 0 -10000 0 0
G2/M transition checkpoint 0.005 0.074 0.21 64 -0.33 23 87
MAP2K6 -0.004 0.054 -10000 0 -0.35 23 23
MAPT -0.025 0.12 0.26 14 -0.32 107 121
MAPK13 0.01 0.012 0.26 2 -10000 0 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.011 0.023 -10000 0 -0.35 4 4
Signaling events mediated by PRL

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
CCNE1 0.062 0.088 0.26 157 -10000 0 157
mol:Halofuginone 0.002 0.004 -10000 0 -10000 0 0
ITGA1 0.019 0.051 -10000 0 -0.58 7 7
CDKN1A -0.032 0.094 -10000 0 -0.44 26 26
PRL-3/alpha Tubulin 0.029 0.017 -10000 0 -10000 0 0
mol:Ca2+ 0 0.077 0.24 40 -0.43 12 52
AGT 0.03 0.093 0.26 70 -0.58 12 82
CCNA2 -0.066 0.14 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -10000 0 -10000 0 0
EGR1 -0.12 0.2 -10000 0 -0.42 307 307
CDK2/Cyclin E1 0.014 0.11 -10000 0 -0.5 14 14
MAPK3 0.01 0.021 0.26 6 -10000 0 6
PRL-2 /Rab GGTase beta 0.035 0.007 -10000 0 -10000 0 0
MAPK1 0.01 0.021 0.26 6 -10000 0 6
PTP4A1 -0.096 0.15 -10000 0 -10000 0 0
PTP4A3 0.02 0.015 0.26 2 -10000 0 2
PTP4A2 0.024 0.004 -10000 0 -10000 0 0
ITGB1 0.01 0.019 0.26 5 -10000 0 5
SRC 0.023 0.005 -10000 0 -10000 0 0
RAC1 -0.02 0.077 -10000 0 -0.42 16 16
Rab GGTase beta/Rab GGTase alpha 0.035 0.008 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.076 0.15 -10000 0 -10000 0 0
RABGGTA 0.024 0.004 -10000 0 -10000 0 0
BCAR1 -0.014 0.012 -10000 0 -10000 0 0
RHOC -0.021 0.083 -10000 0 -0.44 19 19
RHOA -0.025 0.095 -10000 0 -0.46 27 27
cell motility -0.028 0.1 -10000 0 -0.37 35 35
PRL-1/alpha Tubulin -0.077 0.15 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.026 0.036 -10000 0 -0.33 7 7
ROCK1 -0.026 0.1 -10000 0 -0.38 33 33
RABGGTB 0.024 0.004 -10000 0 -10000 0 0
CDK2 0.024 0.002 -10000 0 -10000 0 0
mitosis -0.096 0.15 -10000 0 -10000 0 0
ATF5 0.025 0.014 0.26 3 -10000 0 3
Caspase cascade in apoptosis

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
TOP1 0.008 0.11 0.26 2 -0.4 43 45
ACTA1 0.013 0.12 0.26 7 -0.51 28 35
NUMA1 0.003 0.11 0.26 2 -0.4 44 46
SPTAN1 -0.003 0.11 0.27 6 -0.51 28 34
LIMK1 -0.002 0.11 0.27 5 -0.51 28 33
BIRC3 0.023 0.042 0.26 10 -0.58 3 13
BIRC2 0.022 0.007 -10000 0 -10000 0 0
BAX 0.025 0.016 0.26 4 -10000 0 4
CASP10 -0.011 0.094 0.22 10 -0.46 29 39
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.024 0.002 -10000 0 -10000 0 0
PTK2 0.002 0.12 0.25 3 -0.45 43 46
DIABLO 0.024 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.002 0.11 0.27 6 -0.5 28 34
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
GSN -0.007 0.12 0.28 4 -0.5 36 40
MADD 0.024 0.003 -10000 0 -10000 0 0
TFAP2A 0.012 0.14 -10000 0 -0.67 30 30
BID 0.003 0.054 0.19 3 -0.27 28 31
MAP3K1 -0.005 0.099 -10000 0 -0.4 48 48
TRADD 0.021 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 -0.52 26 33
CASP9 0.023 0.006 -10000 0 -10000 0 0
DNA repair -0.016 0.044 0.25 4 -0.21 5 9
neuron apoptosis 0.006 0.11 -10000 0 -0.7 19 19
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.001 0.12 0.26 2 -0.46 36 38
APAF1 0.024 0.003 -10000 0 -10000 0 0
CASP6 -0.002 0.16 -10000 0 -0.91 24 24
TRAF2 0.025 0.016 0.26 4 -10000 0 4
ICAD/CAD -0.005 0.1 0.25 1 -0.51 26 27
CASP7 0.002 0.06 0.26 5 -0.36 5 10
KRT18 0.014 0.075 -10000 0 -0.68 8 8
apoptosis 0.002 0.12 0.31 5 -0.46 43 48
DFFA -0.004 0.11 0.25 3 -0.51 28 31
DFFB -0.004 0.11 0.25 3 -0.51 28 31
PARP1 0.016 0.044 0.21 5 -0.25 4 9
actin filament polymerization 0.002 0.11 0.49 27 -0.29 7 34
TNF 0.023 0.07 0.26 21 -0.58 10 31
CYCS 0.005 0.05 0.22 6 -0.24 18 24
SATB1 -0.009 0.16 -10000 0 -0.79 29 29
SLK -0.002 0.11 0.28 5 -0.51 28 33
p15 BID/BAX 0.012 0.063 0.22 1 -0.32 14 15
CASP2 0.002 0.066 0.23 7 -0.3 19 26
JNK cascade 0.005 0.098 0.4 48 -10000 0 48
CASP3 -0.001 0.12 0.26 4 -0.53 28 32
LMNB2 0 0.13 0.27 5 -0.5 43 48
RIPK1 0.023 0.005 -10000 0 -10000 0 0
CASP4 0.022 0.007 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.056 0.033 -10000 0 -0.34 2 2
negative regulation of DNA binding 0.012 0.13 -10000 0 -0.66 30 30
stress fiber formation -0.002 0.11 0.28 5 -0.5 28 33
GZMB 0.011 0.11 0.29 10 -0.51 28 38
CASP1 0.011 0.012 -10000 0 -0.35 1 1
LMNB1 0.02 0.12 0.29 8 -0.49 27 35
APP 0.006 0.11 -10000 0 -0.71 19 19
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.001 -10000 0 -10000 0 0
VIM 0.004 0.12 0.29 5 -0.46 45 50
LMNA 0.007 0.084 0.32 2 -0.37 24 26
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.004 0.07 -10000 0 -0.31 21 21
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.002 0.11 0.27 4 -0.5 28 32
APAF-1/Caspase 9 -0.004 0.12 -10000 0 -0.61 34 34
nuclear fragmentation during apoptosis 0.003 0.11 0.26 2 -0.4 44 46
CFL2 -0.002 0.11 0.29 7 -0.5 27 34
GAS2 -0.029 0.14 0.27 6 -0.39 90 96
positive regulation of apoptosis 0.014 0.12 0.27 8 -0.48 32 40
PRF1 0.015 0.082 0.26 7 -0.58 17 24
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.01 0.002 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.03 0.019 -10000 0 -10000 0 0
CDKN1B 0.01 0.058 -10000 0 -0.34 15 15
CDKN1A 0.008 0.063 -10000 0 -0.34 19 19
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.008 -10000 0 -10000 0 0
FOXO3 0.012 0.06 -10000 0 -0.36 14 14
AKT1 0.005 0.058 -10000 0 -0.37 17 17
BAD 0.024 0.009 0.26 1 -10000 0 1
AKT3 0.006 0.035 -10000 0 -0.35 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.007 0.061 -10000 0 -0.34 19 19
AKT1/ASK1 0.031 0.068 -10000 0 -0.32 19 19
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 0.31 19 -10000 0 19
TSC1 0.01 0.053 -10000 0 -0.34 13 13
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.035 0.073 0.27 1 -0.35 17 18
EP300 0.023 0.006 -10000 0 -10000 0 0
mol:GDP 0.009 0.062 -10000 0 -0.35 19 19
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.006 0.056 0.32 1 -0.33 17 18
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
TBC1D4 0.004 0.016 -10000 0 -0.35 2 2
MAP3K5 0.022 0.028 -10000 0 -0.58 2 2
MAPKAP1 0.024 0.003 -10000 0 -10000 0 0
negative regulation of cell cycle -0.025 0.078 0.32 17 -0.25 4 21
YWHAH 0.023 0.006 -10000 0 -10000 0 0
AKT1S1 0.01 0.063 -10000 0 -0.35 17 17
CASP9 0.01 0.047 -10000 0 -0.32 11 11
YWHAB 0.023 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.035 0.074 0.3 6 -0.41 6 12
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.043 0.017 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
SRC 0.023 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.011 0.061 0.25 3 -0.44 6 9
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.005 0.054 -10000 0 -0.33 20 20
CHUK 0.009 0.057 -10000 0 -0.33 17 17
BAD/BCL-XL 0.036 0.07 0.29 1 -0.41 7 8
mTORC2 0.03 0.006 -10000 0 -10000 0 0
AKT2 0.011 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.03 0.1 0.32 6 -0.44 19 25
PDPK1 0.023 0.006 -10000 0 -10000 0 0
MDM2 0.011 0.066 0.27 2 -0.34 19 21
MAPKKK cascade -0.035 0.072 0.34 17 -0.26 1 18
MDM2/Cbp/p300 0.042 0.075 0.34 4 -0.42 6 10
TSC1/TSC2 0.012 0.068 0.26 31 -0.36 13 44
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.072 0.32 4 -0.4 6 10
glucose import -0.16 0.16 0.21 3 -0.32 463 466
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.01 0.051 0.18 2 -0.4 5 7
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.16 0.16 0.21 3 -0.32 463 466
GSK3A 0.009 0.061 -10000 0 -0.35 17 17
FOXO1 0.01 0.047 -10000 0 -0.33 10 10
GSK3B 0.008 0.061 -10000 0 -0.35 18 18
SFN 0.021 0.069 0.26 17 -0.58 10 27
G1/S transition of mitotic cell cycle 0.013 0.066 0.31 3 -0.35 16 19
p27Kip1/14-3-3 family 0.019 0.05 0.38 1 -0.45 3 4
PRKACA 0.024 0.003 -10000 0 -10000 0 0
KPNA1 0.024 0.003 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
YWHAG 0.024 0.003 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.006 -10000 0 -10000 0 0
Ceramide signaling pathway

Figure 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
SPHK2 0.01 0.002 -10000 0 -10000 0 0
MAP4K4 0.002 0.063 -10000 0 -0.4 6 6
BAG4 0.019 0.021 -10000 0 -0.58 1 1
PKC zeta/ceramide -0.003 0.054 -10000 0 -0.25 16 16
NFKBIA 0.024 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.042 0.26 10 -0.58 3 13
BAX 0.001 0.042 -10000 0 -0.35 10 10
RIPK1 0.023 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.066 0.68 9 -10000 0 9
BAD -0.016 0.048 0.19 3 -0.25 14 17
SMPD1 0.013 0.06 0.2 13 -0.25 19 32
RB1 -0.017 0.046 -10000 0 -0.27 11 11
FADD/Caspase 8 0.026 0.089 0.27 8 -0.41 7 15
MAP2K4 -0.017 0.046 0.18 1 -0.3 8 9
NSMAF 0.021 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.011 0.057 0.27 4 -0.33 5 9
EGF -0.093 0.24 0.26 2 -0.58 189 191
mol:ceramide -0.016 0.05 0.15 1 -0.26 15 16
MADD 0.024 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.009 0.009 -10000 0 -10000 0 0
ASAH1 0.021 0.016 0.26 3 -10000 0 3
negative regulation of cell cycle -0.017 0.046 -10000 0 -0.26 11 11
cell proliferation -0.045 0.12 0.28 1 -0.28 154 155
BID -0.025 0.18 -10000 0 -0.66 61 61
MAP3K1 -0.017 0.048 0.19 1 -0.25 16 17
EIF2A -0.016 0.049 0.29 3 -0.24 7 10
TRADD 0.021 0.008 -10000 0 -10000 0 0
CRADD 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.008 0.055 0.32 2 -0.32 5 7
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.013 0.06 0.32 2 -0.39 3 5
Cathepsin D/ceramide 0.003 0.06 0.18 15 -0.24 14 29
FADD 0.004 0.062 0.22 9 -0.41 5 14
KSR1 -0.011 0.056 0.2 21 -0.3 7 28
MAPK8 -0.016 0.062 -10000 0 -0.3 16 16
PRKRA -0.017 0.048 0.2 2 -0.24 15 17
PDGFA 0.024 0.004 -10000 0 -10000 0 0
TRAF2 0.025 0.016 0.26 4 -10000 0 4
IGF1 -0.1 0.24 -10000 0 -0.58 202 202
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.016 0.05 0.15 1 -0.25 15 16
CTSD 0.032 0.045 0.26 35 -10000 0 35
regulation of nitric oxide biosynthetic process 0.034 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.048 0.13 0.29 1 -0.3 152 153
PRKCD 0.024 0.009 0.26 1 -10000 0 1
PRKCZ 0.023 0.02 -10000 0 -0.58 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.009 0.009 -10000 0 -10000 0 0
RelA/NF kappa B1 0.035 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.02 -10000 0 -0.58 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.014 0.052 -10000 0 -0.4 7 7
TNFR1A/BAG4/TNF-alpha 0.036 0.051 -10000 0 -0.36 10 10
mol:Sphingosine-1-phosphate 0.01 0.002 -10000 0 -10000 0 0
MAP2K1 -0.011 0.055 0.32 2 -0.33 4 6
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
CYCS -0.001 0.051 0.18 19 -0.24 10 29
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.022 -10000 0 -0.3 2 2
EIF2AK2 -0.018 0.044 0.18 3 -0.24 11 14
TNF-alpha/TNFR1A/FAN 0.04 0.045 -10000 0 -0.37 6 6
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.016 0.076 -10000 0 -0.38 26 26
MAP2K2 -0.012 0.055 0.32 2 -0.33 4 6
SMPD3 -0.004 0.1 0.28 4 -0.29 95 99
TNF 0.023 0.07 0.26 21 -0.58 10 31
PKC zeta/PAR4 0.033 0.023 -10000 0 -0.43 2 2
mol:PHOSPHOCHOLINE 0.045 0.1 0.24 188 -0.24 2 190
NF kappa B1/RelA/I kappa B alpha 0.063 0.029 -10000 0 -0.32 2 2
AIFM1 -0.002 0.051 0.19 13 -0.24 9 22
BCL2 0.006 0.1 -10000 0 -0.58 28 28
FoxO family signaling

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.012 0.059 -10000 0 -10000 0 0
PLK1 0.26 0.19 0.52 189 -0.58 1 190
CDKN1B 0.16 0.13 0.4 53 -0.45 5 58
FOXO3 0.21 0.17 0.47 174 -0.63 1 175
KAT2B 0.058 0.035 -10000 0 -0.58 1 1
FOXO1/SIRT1 0.01 0.054 -10000 0 -0.33 3 3
CAT 0.2 0.17 0.66 15 -1 2 17
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.059 0.03 -10000 0 -10000 0 0
FOXO1 0.017 0.061 -10000 0 -0.32 6 6
MAPK10 -0.016 0.12 0.21 10 -0.3 139 149
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.036 0.084 0.41 3 -0.34 1 4
response to oxidative stress 0.037 0.028 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.18 0.14 0.4 134 -0.53 2 136
XPO1 0.024 0.003 -10000 0 -10000 0 0
EP300 0.025 0.007 -10000 0 -10000 0 0
BCL2L11 0.067 0.08 -10000 0 -0.65 8 8
FOXO1/SKP2 0.026 0.057 -10000 0 -0.33 3 3
mol:GDP 0.037 0.028 -10000 0 -10000 0 0
RAN 0.025 0.003 -10000 0 -10000 0 0
GADD45A 0.14 0.13 0.48 3 -0.55 9 12
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.022 0.12 -10000 0 -0.51 31 31
MST1 0.053 0.061 0.28 2 -0.52 8 10
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 0.008 0.13 -10000 0 -0.55 25 25
YWHAB 0.023 0.005 -10000 0 -10000 0 0
MAPK8 0.031 0.036 0.21 11 -0.3 5 16
MAPK9 0.032 0.027 0.21 12 -10000 0 12
YWHAG 0.024 0.003 -10000 0 -10000 0 0
YWHAE 0.022 0.007 -10000 0 -10000 0 0
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
SIRT1 0.011 0.021 -10000 0 -10000 0 0
SOD2 0.16 0.13 0.48 13 -0.51 1 14
RBL2 0.11 0.26 0.53 4 -0.62 63 67
RAL/GDP 0.057 0.022 -10000 0 -10000 0 0
CHUK 0.058 0.029 -10000 0 -10000 0 0
Ran/GTP 0.02 0.003 -10000 0 -10000 0 0
CSNK1G2 0.023 0.005 -10000 0 -10000 0 0
RAL/GTP 0.058 0.022 -10000 0 -10000 0 0
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
FASLG 0.063 0.17 0.45 1 -1.3 12 13
SKP2 0.024 0.004 -10000 0 -10000 0 0
USP7 0.023 0.006 -10000 0 -10000 0 0
IKBKB 0.049 0.034 -10000 0 -10000 0 0
CCNB1 0.22 0.18 0.52 157 -0.58 1 158
FOXO1-3a-4/beta catenin 0.15 0.13 0.42 37 -0.39 3 40
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.057 -10000 0 -0.32 3 3
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
SGK1 0.054 0.05 -10000 0 -0.57 4 4
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.007 -10000 0 -10000 0 0
ZFAND5 0.033 0.075 0.41 2 -10000 0 2
SFN 0.021 0.069 0.26 17 -0.58 10 27
CDK2 0.023 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.064 0.11 0.36 1 -0.43 14 15
CREBBP 0.022 0.007 -10000 0 -10000 0 0
FBXO32 0.24 0.21 0.59 133 -1.2 3 136
BCL6 0.17 0.16 0.54 4 -0.86 7 11
RALB 0.025 0.004 -10000 0 -10000 0 0
RALA 0.024 0.004 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.018 0.095 0.26 32 -0.58 19 51
CDC42/GTP -0.004 0.097 -10000 0 -0.31 44 44
PLCG1 -0.011 0.087 -10000 0 -0.32 43 43
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 0.032 0.011 -10000 0 -10000 0 0
cell migration -0.005 0.095 -10000 0 -0.3 46 46
S1PR5 0.027 0.042 0.26 18 -0.58 2 20
S1PR4 0.028 0.065 0.26 34 -0.58 6 40
MAPK3 -0.008 0.084 0.27 1 -0.32 38 39
MAPK1 -0.007 0.085 -10000 0 -0.32 41 41
S1P/S1P5/Gi -0.003 0.088 -10000 0 -0.28 72 72
GNAI1 -0.005 0.13 -10000 0 -0.58 47 47
CDC42/GDP 0.017 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.028 -10000 0 -0.37 2 2
RHOA 0.005 0.057 0.24 1 -0.32 6 7
S1P/S1P4/Gi -0.003 0.094 -10000 0 -0.29 78 78
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.018 0.055 -10000 0 -0.58 8 8
S1P/S1P4/G12/G13 0.044 0.043 -10000 0 -0.33 6 6
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
CDC42 0.023 0.005 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.059 -10000 0 -0.39 17 17
forebrain development -0.046 0.22 0.35 1 -0.53 126 127
GNAO1 0.017 0.095 0.26 32 -0.58 19 51
SMO/beta Arrestin2 0.027 0.045 -10000 0 -0.43 8 8
SMO 0.017 0.056 -10000 0 -0.58 8 8
ARRB2 0.021 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.022 0.081 0.28 1 -0.5 10 11
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.024 0.003 -10000 0 -10000 0 0
GNAI2 0.022 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.055 0.023 -10000 0 -10000 0 0
GNAI1 -0.006 0.13 -10000 0 -0.58 47 47
XPO1 0.022 0.015 -10000 0 -10000 0 0
GLI1/Su(fu) -0.037 0.2 -10000 0 -0.62 71 71
SAP30 0.024 0.016 0.26 4 -10000 0 4
mol:GDP 0.017 0.056 -10000 0 -0.58 8 8
MIM/GLI2A 0.022 0.025 0.28 4 -10000 0 4
IFT88 0.023 0.006 -10000 0 -10000 0 0
GNAI3 0.023 0.008 -10000 0 -10000 0 0
GLI2 0.008 0.066 -10000 0 -0.3 21 21
GLI3 0.011 0.084 0.29 1 -0.51 11 12
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 0.061 -10000 0 -0.58 10 10
Gi family/GTP -0.008 0.098 -10000 0 -0.29 84 84
SIN3B 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.015 0.088 -10000 0 -0.46 19 19
GLI2/Su(fu) 0.012 0.082 -10000 0 -0.39 19 19
FOXA2 0.009 0.11 0.43 1 -0.64 19 20
neural tube patterning -0.046 0.22 0.35 1 -0.53 126 127
SPOP 0.022 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.02 0.043 -10000 0 -0.37 1 1
GNB1 0.023 0.005 -10000 0 -10000 0 0
CSNK1G2 0.023 0.005 -10000 0 -10000 0 0
CSNK1G3 0.024 0.004 -10000 0 -10000 0 0
MTSS1 0.022 0.025 0.28 4 -10000 0 4
embryonic limb morphogenesis -0.046 0.22 0.35 1 -0.53 126 127
SUFU 0.015 0.028 -10000 0 -0.32 2 2
LGALS3 0.017 0.064 -10000 0 -0.58 11 11
catabolic process 0.025 0.1 0.29 1 -0.54 15 16
GLI3A/CBP 0 0.094 -10000 0 -0.36 60 60
KIF3A 0.024 0.004 -10000 0 -10000 0 0
GLI1 -0.048 0.22 0.35 1 -0.55 126 127
RAB23 0.024 0.004 -10000 0 -10000 0 0
CSNK1A1 0.024 0.003 -10000 0 -10000 0 0
IFT172 0.023 0.019 -10000 0 -0.58 1 1
RBBP7 0.026 0.02 0.26 7 -10000 0 7
Su(fu)/Galectin3 0.017 0.06 -10000 0 -0.39 12 12
GNAZ 0.017 0.055 -10000 0 -0.58 8 8
RBBP4 0.023 0.02 -10000 0 -0.58 1 1
CSNK1G1 0.024 0.004 -10000 0 -10000 0 0
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.017 0.069 -10000 0 -0.37 12 12
STK36 0.021 0.024 -10000 0 -0.58 1 1
Gi family/GNB1/GNG2/GDP -0.014 0.11 -10000 0 -0.4 43 43
PTCH1 -0.09 0.33 -10000 0 -1.1 81 81
MIM/GLI1 -0.035 0.2 0.36 1 -0.58 84 85
CREBBP 0 0.094 -10000 0 -0.36 60 60
Su(fu)/SIN3/HDAC complex 0.007 0.09 -10000 0 -0.43 27 27
S1P5 pathway

Figure S93.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.003 0.09 0.3 41 -10000 0 41
GNAI2 0.024 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.028 -10000 0 -0.37 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.018 0.095 0.26 32 -0.58 19 51
RhoA/GTP -0.003 0.091 -10000 0 -0.3 41 41
negative regulation of cAMP metabolic process -0.003 0.087 -10000 0 -0.28 72 72
GNAZ 0.018 0.055 -10000 0 -0.58 8 8
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 18 -0.58 2 20
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.003 0.088 -10000 0 -0.28 72 72
RhoA/GDP 0.017 0.003 -10000 0 -10000 0 0
RHOA 0.023 0.005 -10000 0 -10000 0 0
GNAI1 -0.005 0.13 -10000 0 -0.58 47 47
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 0.077 -10000 0 -0.74 2 2
UGCG 0.012 0.12 -10000 0 -0.68 24 24
AKT1/mTOR/p70S6K/Hsp90/TERT 0.047 0.12 0.29 11 -0.45 23 34
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.013 0.12 -10000 0 -0.67 24 24
mol:DAG 0.007 0.075 -10000 0 -0.77 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.037 0.14 0.31 6 -0.43 48 54
FRAP1 0.031 0.16 0.34 6 -0.5 48 54
FOXO3 0.036 0.14 0.34 11 -0.55 27 38
AKT1 0.036 0.15 0.34 6 -0.6 27 33
GAB2 0.021 0.01 -10000 0 -10000 0 0
SMPD1 0.009 0.11 -10000 0 -0.63 25 25
SGMS1 0.02 0.062 -10000 0 -0.59 8 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.002 0.028 -10000 0 -0.33 6 6
CALM1 0.024 0.004 -10000 0 -10000 0 0
cell proliferation 0.049 0.11 0.26 12 -0.42 23 35
EIF3A 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.032 0.037 -10000 0 -0.36 7 7
RPS6KB1 0.013 0.091 -10000 0 -0.84 9 9
mol:sphingomyelin 0.007 0.075 -10000 0 -0.77 8 8
natural killer cell activation 0 0.002 -10000 0 -0.016 1 1
JAK3 0.028 0.031 0.26 16 -10000 0 16
PIK3R1 0.02 0.048 -10000 0 -0.58 6 6
JAK1 0.024 0.007 -10000 0 -10000 0 0
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MYC 0.066 0.2 0.42 7 -0.95 25 32
MYB 0.033 0.18 -10000 0 -1.1 19 19
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.038 0.11 0.3 22 -0.5 15 37
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.087 -10000 0 -0.75 9 9
mol:PI-3-4-5-P3 0.041 0.11 0.3 22 -0.49 15 37
Rac1/GDP 0.016 0.029 -10000 0 -0.34 5 5
T cell proliferation 0.042 0.1 0.3 14 -0.48 12 26
SHC1 0.02 0.011 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.011 0.08 2 -0.077 18 20
PRKCZ 0.041 0.1 0.31 12 -0.5 12 24
NF kappa B1 p50/RelA 0.048 0.14 0.32 5 -0.48 31 36
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.027 0.074 0.3 13 -0.57 5 18
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
IL2RA 0.029 0.086 0.26 54 -0.58 11 65
IL2RB 0.033 0.047 0.26 38 -10000 0 38
TERT 0.052 0.079 0.26 119 -10000 0 119
E2F1 0.053 0.094 -10000 0 -0.36 27 27
SOS1 0.023 0.007 -10000 0 -10000 0 0
RPS6 0.023 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.034 18 -0.041 2 20
PTPN11 0.023 0.008 -10000 0 -10000 0 0
IL2RG 0.031 0.072 0.26 42 -0.58 7 49
actin cytoskeleton organization 0.042 0.1 0.3 14 -0.48 12 26
GRB2 0.022 0.012 0.26 1 -10000 0 1
IL2 0.022 0.026 0.26 9 -10000 0 9
PIK3CA 0.024 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.04 0.034 -10000 0 -0.32 5 5
LCK 0.026 0.079 0.26 34 -0.58 11 45
BCL2 0.018 0.2 0.38 4 -0.78 44 48
Cellular roles of Anthrax toxin

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
ANTXR1 0.024 0.021 0.26 1 -0.58 1 2
ANTXR2 0.018 0.058 -10000 0 -0.58 9 9
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.008 -10000 0 -0.073 11 11
monocyte activation 0.004 0.084 0.26 2 -0.35 48 50
MAP2K2 0.001 0.086 -10000 0 -0.58 21 21
MAP2K1 -0.004 0.007 -10000 0 -10000 0 0
MAP2K7 -0.004 0.008 0.12 1 -10000 0 1
MAP2K6 -0.01 0.043 -10000 0 -0.31 19 19
CYAA -0.009 0.031 -10000 0 -0.31 10 10
MAP2K4 -0.004 0.007 -10000 0 -10000 0 0
IL1B -0.008 0.045 0.22 2 -0.27 23 25
Channel 0.026 0.038 -10000 0 -0.33 10 10
NLRP1 -0.007 0.032 -10000 0 -0.31 10 10
CALM1 0.024 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.067 -10000 0 -0.39 27 27
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.008 0.073 11 -10000 0 11
MAPK3 -0.004 0.007 -10000 0 -10000 0 0
MAPK1 -0.004 0.009 0.12 2 -10000 0 2
PGR -0.079 0.14 0.2 2 -0.32 246 248
PA/Cellular Receptors 0.028 0.041 -10000 0 -0.37 10 10
apoptosis -0.002 0.008 -10000 0 -0.073 11 11
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.036 -10000 0 -0.31 10 10
macrophage activation -0.006 0.009 0.12 3 -10000 0 3
TNF 0.023 0.07 0.26 21 -0.58 10 31
VCAM1 0.004 0.085 0.26 2 -0.35 48 50
platelet activation -0.001 0.067 -10000 0 -0.39 27 27
MAPKKK cascade -0.002 0.026 0.095 14 -0.13 8 22
IL18 -0.003 0.024 -10000 0 -0.2 9 9
negative regulation of macrophage activation -0.002 0.008 -10000 0 -0.073 11 11
LEF -0.002 0.008 -10000 0 -0.074 11 11
CASP1 -0.003 0.024 -10000 0 -0.2 12 12
mol:cAMP -0.001 0.068 -10000 0 -0.4 27 27
necrosis -0.002 0.008 -10000 0 -0.073 11 11
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.026 0.036 -10000 0 -0.32 10 10
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.024 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.018 0.065 0.21 2 -0.29 44 46
FRAP1 -0.003 0.081 0.26 1 -0.46 22 23
AKT1 -0.011 0.065 0.19 2 -0.28 34 36
INSR 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0.021 0.067 0.23 3 -0.24 31 34
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 0.047 -10000 0 -0.25 10 10
TSC1 0.024 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.004 0.079 -10000 0 -0.31 55 55
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.013 0.045 -10000 0 -0.23 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.004 -10000 0 -10000 0 0
RPS6KB1 0.01 0.072 0.29 3 -0.32 16 19
MAP3K5 0 0.045 0.2 11 -0.19 39 50
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
apoptosis 0 0.045 0.2 11 -0.19 40 51
mol:LY294002 0 0 0.001 1 -0.001 48 49
EIF4B 0.008 0.066 0.27 4 -0.3 13 17
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.026 0.063 -10000 0 -0.28 12 12
eIF4E/eIF4G1/eIF4A1 0.004 0.05 -10000 0 -0.28 21 21
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.016 0.079 -10000 0 -0.3 54 54
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.051 0.21 12 -0.19 3 15
FKBP1A 0.024 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.025 0.059 -10000 0 -0.26 9 9
mol:Amino Acids 0 0 0.001 1 -0.001 48 49
FKBP12/Rapamycin 0.018 0.004 -10000 0 -10000 0 0
PDPK1 -0.02 0.06 0.18 6 -0.28 43 49
EIF4E 0.024 0.004 -10000 0 -10000 0 0
ASK1/PP5C -0.005 0.14 -10000 0 -0.52 56 56
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.003 0.049 -10000 0 -10000 0 0
TSC1/TSC2 0.024 0.073 0.25 4 -0.28 15 19
tumor necrosis factor receptor activity 0 0 0.001 48 -0.001 1 49
RPS6 0.023 0.005 -10000 0 -10000 0 0
PPP5C 0.024 0.003 -10000 0 -10000 0 0
EIF4G1 0.024 0.004 -10000 0 -10000 0 0
IRS1 -0.012 0.081 -10000 0 -0.33 56 56
INS 0.017 0.003 -10000 0 -10000 0 0
PTEN 0.022 0.028 -10000 0 -0.57 2 2
PDK2 -0.018 0.059 0.18 9 -0.28 36 45
EIF4EBP1 -0.028 0.24 -10000 0 -1 49 49
PIK3CA 0.024 0.005 -10000 0 -10000 0 0
PPP2R5D -0.001 0.077 0.29 4 -0.42 21 25
peptide biosynthetic process -0.011 0.015 -10000 0 -10000 0 0
RHEB 0.024 0.004 -10000 0 -10000 0 0
EIF4A1 0.022 0.008 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 15 -0.003 3 18
EEF2 -0.011 0.015 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.018 0.22 -10000 0 -0.97 49 49
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.028 0.05 -10000 0 -0.43 11 11
ATM 0.022 0.008 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
PRKDC 0.021 0.008 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
UBE2L3 0.023 0.006 -10000 0 -10000 0 0
FANCD2 0.018 0.016 0.19 5 -10000 0 5
protein ubiquitination 0.066 0.065 0.31 2 -0.3 11 13
XRCC5 0.024 0.004 -10000 0 -10000 0 0
XRCC6 0.023 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.036 0.022 -10000 0 -10000 0 0
MRE11A 0.022 0.007 -10000 0 -10000 0 0
DNA-PK 0.04 0.02 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.014 0.09 -10000 0 -0.46 16 16
FANCF 0.024 0.004 -10000 0 -10000 0 0
BRCA1 0.023 0.021 0.26 1 -0.58 1 2
CCNE1 0.062 0.088 0.26 157 -10000 0 157
CDK2/Cyclin E1 0.06 0.061 -10000 0 -10000 0 0
FANCG 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.029 0.051 -10000 0 -0.41 12 12
FANCE 0.024 0.004 -10000 0 -10000 0 0
FANCC 0.024 0.003 -10000 0 -10000 0 0
NBN 0.019 0.01 -10000 0 -10000 0 0
FANCA 0.062 0.092 0.26 168 -10000 0 168
DNA repair 0.031 0.086 0.28 8 -0.37 6 14
BRCA1/BARD1/ubiquitin 0.029 0.051 -10000 0 -0.41 12 12
BARD1/DNA-PK 0.047 0.046 -10000 0 -0.34 9 9
FANCL 0.024 0.003 -10000 0 -10000 0 0
mRNA polyadenylation -0.028 0.05 0.42 11 -10000 0 11
BRCA1/BARD1/CTIP/M/R/N Complex 0.013 0.069 -10000 0 -0.27 9 9
BRCA1/BACH1/BARD1/TopBP1 0.041 0.047 -10000 0 -0.37 11 11
BRCA1/BARD1/P53 0.05 0.047 -10000 0 -0.34 11 11
BARD1/CSTF1/BRCA1 0.039 0.048 -10000 0 -0.37 11 11
BRCA1/BACH1 0.023 0.021 0.26 1 -0.58 1 2
BARD1 0.017 0.064 0.26 1 -0.58 11 12
PCNA 0.024 0.012 0.26 2 -10000 0 2
BRCA1/BARD1/UbcH5C 0.042 0.047 -10000 0 -0.37 11 11
BRCA1/BARD1/UbcH7 0.04 0.047 -10000 0 -0.37 11 11
BRCA1/BARD1/RAD51/PCNA 0.096 0.085 0.32 2 -0.31 11 13
BARD1/DNA-PK/P53 0.051 0.049 -10000 0 -0.32 9 9
BRCA1/BARD1/Ubiquitin 0.029 0.051 -10000 0 -0.41 12 12
BRCA1/BARD1/CTIP 0.03 0.043 -10000 0 -0.34 11 11
FA complex 0.036 0.039 0.24 3 -0.26 1 4
BARD1/EWS 0.028 0.05 -10000 0 -0.43 11 11
RBBP8 0.01 0.006 -10000 0 -10000 0 0
TP53 0.022 0.008 -10000 0 -10000 0 0
TOPBP1 0.024 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.048 0.047 0.33 11 -10000 0 11
BRCA1/BARD1 0.072 0.069 0.34 2 -0.3 11 13
CSTF1 0.023 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.013 0.047 0.18 1 -0.42 11 12
CDK2 0.024 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.11 0.12 0.26 351 -10000 0 351
RAD50 0.024 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.029 0.051 -10000 0 -0.41 12 12
EWSR1 0.023 0.006 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.054 0.074 0.39 12 -0.39 12 24
MAP4K1 0.031 0.053 0.26 36 -0.58 2 38
MAP3K8 0.021 0.039 -10000 0 -0.58 4 4
PRKCB 0.017 0.08 0.26 15 -0.58 15 30
DBNL 0.024 0.004 -10000 0 -10000 0 0
CRKL 0.023 0.006 -10000 0 -10000 0 0
MAP3K1 0.013 0.057 0.27 1 -0.39 8 9
JUN 0.002 0.13 -10000 0 -0.59 38 38
MAP3K7 0.014 0.056 0.27 1 -0.4 5 6
GRAP2 0.016 0.071 0.26 3 -0.58 13 16
CRK 0.022 0.007 -10000 0 -10000 0 0
MAP2K4 0.012 0.067 0.25 1 -0.39 11 12
LAT 0.025 0.04 0.26 14 -0.58 2 16
LCP2 0.024 0.009 0.26 1 -10000 0 1
MAPK8 0.006 0.13 -10000 0 -0.63 37 37
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.021 0.062 0.26 3 -0.33 16 19
LAT/GRAP2/SLP76/HPK1/HIP-55 0.062 0.073 0.38 12 -0.37 12 24
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.004 0.1 0.26 2 -0.42 30 32
BAG4 0.019 0.021 -10000 0 -0.58 1 1
BAD 0.005 0.041 0.2 6 -0.18 9 15
NFKBIA 0.024 0.004 -10000 0 -10000 0 0
BIRC3 0.023 0.042 0.26 10 -0.58 3 13
BAX 0.005 0.043 0.24 4 -0.19 6 10
EnzymeConsortium:3.1.4.12 0.001 0.026 0.085 4 -0.096 25 29
IKBKB 0.015 0.1 0.28 12 -0.42 21 33
MAP2K2 0.008 0.052 0.22 14 -0.26 1 15
MAP2K1 0.008 0.053 0.22 16 -0.26 1 17
SMPD1 0.002 0.033 0.14 4 -0.15 16 20
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.025 0.12 0.28 15 -0.43 25 40
MAP2K4 0.005 0.035 0.18 3 -0.24 2 5
protein ubiquitination 0.002 0.1 0.34 4 -0.41 27 31
EnzymeConsortium:2.7.1.37 0.007 0.055 0.22 15 -0.28 1 16
response to UV 0 0.001 0.002 17 -0.002 2 19
RAF1 0.008 0.053 0.21 20 -0.27 1 21
CRADD 0.024 0.003 -10000 0 -10000 0 0
mol:ceramide 0.005 0.041 0.14 6 -0.15 22 28
I-kappa-B-alpha/RELA/p50/ubiquitin 0.031 0.008 -10000 0 -10000 0 0
MADD 0.024 0.004 -10000 0 -10000 0 0
MAP3K1 0.003 0.041 0.17 3 -0.2 9 12
TRADD 0.022 0.008 -10000 0 -10000 0 0
RELA/p50 0.024 0.004 -10000 0 -10000 0 0
MAPK3 0.009 0.053 0.21 15 -0.24 2 17
MAPK1 0.006 0.061 0.22 15 -0.25 5 20
p50/RELA/I-kappa-B-alpha 0.034 0.008 -10000 0 -10000 0 0
FADD 0.021 0.11 0.28 10 -0.44 23 33
KSR1 0.009 0.051 0.19 29 -0.21 6 35
MAPK8 0.001 0.047 0.24 7 -0.32 5 12
TRAF2 0.025 0.016 0.26 4 -10000 0 4
response to radiation 0 0 0.002 3 -10000 0 3
CHUK -0.003 0.096 -10000 0 -0.43 24 24
TNF R/SODD 0.027 0.022 -10000 0 -0.3 2 2
TNF 0.023 0.07 0.26 21 -0.58 10 31
CYCS 0.008 0.047 0.19 14 -0.18 5 19
IKBKG -0.003 0.099 0.35 2 -0.43 24 26
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0 0.1 -10000 0 -0.45 28 28
RELA 0.024 0.004 -10000 0 -10000 0 0
RIPK1 0.024 0.005 -10000 0 -10000 0 0
AIFM1 0.007 0.046 0.18 14 -0.19 5 19
TNF/TNF R/SODD 0.036 0.051 -10000 0 -0.36 10 10
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 3 -10000 0 3
CASP8 0.008 0.11 -10000 0 -0.63 28 28
NSMAF 0.015 0.11 0.26 10 -0.42 27 37
response to hydrogen peroxide 0 0.001 0.002 17 -0.002 2 19
BCL2 0.006 0.1 -10000 0 -0.58 28 28
Retinoic acid receptors-mediated signaling

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
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 -0.37 1 1
EP300 0.023 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.015 0.061 -10000 0 -0.34 15 15
KAT2B 0.023 0.02 -10000 0 -0.58 1 1
MAPK14 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.006 0.066 0.2 4 -0.36 15 19
RAR alpha/9cRA/Cyclin H 0.047 0.074 -10000 0 -0.34 18 18
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.021 0.065 -10000 0 -0.35 17 17
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 0.061 -10000 0 -0.3 20 20
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 0.008 0.11 -10000 0 -0.54 20 20
NCOA2 0.002 0.1 -10000 0 -0.58 29 29
NCOA3 0.023 0.006 -10000 0 -10000 0 0
NCOA1 0.023 0.02 -10000 0 -0.58 1 1
VDR/VDR/DNA 0.024 0.003 -10000 0 -10000 0 0
RARG 0.025 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.032 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 0.043 -10000 0 -0.58 5 5
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.008 0.1 -10000 0 -0.5 19 19
RARA 0.013 0.055 0.2 11 -0.28 23 34
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.01 0.074 -10000 0 -0.29 39 39
PRKCA 0.011 0.086 0.26 1 -0.58 20 21
RXRs/RARs/NRIP1/9cRA/HDAC1 0.01 0.12 0.45 1 -0.55 20 21
RXRG -0.052 0.16 0.25 12 -0.35 187 199
RXRA 0.022 0.064 0.35 1 -0.28 24 25
RXRB 0.016 0.062 0.24 11 -0.34 20 31
VDR/Vit D3/DNA 0.018 0.002 -10000 0 -10000 0 0
RBP1 0.033 0.077 0.26 57 -0.58 7 64
CRBP1/9-cic-RA 0.024 0.054 0.18 57 -0.42 7 64
RARB 0.018 0.064 -10000 0 -0.58 11 11
PRKCG 0.031 0.045 0.26 34 -10000 0 34
MNAT1 0.024 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.009 0.1 -10000 0 -0.52 23 23
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.008 0.098 -10000 0 -0.44 26 26
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.079 0.24 11 -0.38 14 25
RXRs/RARs/NRIP1/9cRA/HDAC3 0.01 0.12 0.45 1 -0.55 21 22
positive regulation of DNA binding 0.032 0.064 -10000 0 -0.32 18 18
NRIP1 0.011 0.12 0.54 1 -0.78 8 9
RXRs/RARs 0.009 0.12 -10000 0 -0.52 25 25
RXRs/RXRs/DNA/9cRA -0.014 0.09 -10000 0 -0.48 22 22
PRKACA 0.024 0.003 -10000 0 -10000 0 0
CDK7 0.023 0.005 -10000 0 -10000 0 0
TFIIH 0.047 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.052 0.055 -10000 0 -0.35 2 2
CCNH 0.024 0.004 -10000 0 -10000 0 0
CREBBP 0.023 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.044 0.014 -10000 0 -10000 0 0
S1P3 pathway

Figure S101.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S101.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.021 0.039 -10000 0 -0.58 4 4
mol:S1P 0 0.003 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.013 0.095 -10000 0 -0.3 79 79
GNAO1 0.018 0.095 0.26 32 -0.58 19 51
S1P/S1P3/G12/G13 0.042 0.019 -10000 0 -10000 0 0
AKT1 0.005 0.097 -10000 0 -0.48 30 30
AKT3 -0.01 0.16 -10000 0 -1.1 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.021 0.039 -10000 0 -0.58 4 4
GNAI2 0.023 0.009 -10000 0 -10000 0 0
GNAI3 0.024 0.008 -10000 0 -10000 0 0
GNAI1 -0.005 0.13 -10000 0 -0.58 47 47
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.026 0.021 0.26 7 -10000 0 7
S1PR2 0.024 0.003 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.096 -10000 0 -0.35 45 45
MAPK3 -0.008 0.09 0.27 2 -0.39 26 28
MAPK1 -0.006 0.089 0.27 1 -0.41 25 26
JAK2 -0.008 0.1 -10000 0 -0.39 34 34
CXCR4 -0.008 0.093 -10000 0 -0.4 26 26
FLT1 0.023 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
SRC -0.01 0.092 -10000 0 -0.4 25 25
S1P/S1P3/Gi -0.002 0.097 -10000 0 -0.36 45 45
RAC1 0.024 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.1 -10000 0 -0.39 27 27
VEGFA 0.025 0.02 0.26 5 -10000 0 5
S1P/S1P2/Gi -0.002 0.091 -10000 0 -0.29 74 74
VEGFR1 homodimer/VEGFA homodimer 0.035 0.021 -10000 0 -10000 0 0
RHOA 0.023 0.005 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.019 0.042 -10000 0 -0.29 15 15
GNAQ 0.023 0.027 -10000 0 -0.58 2 2
GNAZ 0.018 0.055 -10000 0 -0.58 8 8
G12/G13 0.032 0.011 -10000 0 -10000 0 0
GNA14 0.023 0.07 0.26 21 -0.58 10 31
GNA15 0.025 0.027 0.26 6 -0.58 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.028 -10000 0 -0.58 2 2
Rac1/GTP -0.002 0.1 -10000 0 -0.39 27 27
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 -0.02 0.11 -10000 0 -0.42 42 42
KLHL20 0.015 0.066 0.24 9 -0.22 14 23
CYFIP2 0.029 0.047 0.26 25 -0.58 2 27
Rac1/GDP 0 0.086 0.26 9 -0.31 19 28
ENAH -0.017 0.11 -10000 0 -0.45 26 26
AP1M1 0.024 0.004 -10000 0 -10000 0 0
RAP1B 0.024 0.005 -10000 0 -10000 0 0
RAP1A 0.024 0.004 -10000 0 -10000 0 0
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.008 0.049 -10000 0 -0.33 2 2
ABI1/Sra1/Nap1 -0.012 0.032 -10000 0 -0.15 13 13
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.045 0.069 -10000 0 -0.34 21 21
RAPGEF1 -0.02 0.11 -10000 0 -0.41 29 29
CTNND1 0.024 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.022 0.12 -10000 0 -0.42 50 50
CRK -0.017 0.1 -10000 0 -0.42 33 33
E-cadherin/gamma catenin/alpha catenin 0.031 0.063 -10000 0 -0.37 19 19
alphaE/beta7 Integrin 0.036 0.035 -10000 0 -0.43 2 2
IQGAP1 0.023 0.005 -10000 0 -10000 0 0
NCKAP1 0.024 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.028 -10000 0 -0.34 3 3
DLG1 -0.024 0.12 -10000 0 -0.45 34 34
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.017 0.031 -10000 0 -0.24 2 2
MLLT4 0.021 0.035 0.26 1 -0.58 3 4
ARF6/GTP/NME1/Tiam1 0.044 0.025 -10000 0 -10000 0 0
PI3K -0.003 0.046 -10000 0 -0.32 2 2
ARF6 0.024 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.019 0.068 -10000 0 -0.34 29 29
TIAM1 0.025 0.016 0.26 4 -10000 0 4
E-cadherin(dimer)/Ca2+ 0.04 0.058 -10000 0 -0.32 19 19
AKT1 -0.007 0.035 -10000 0 -0.21 1 1
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
CDH1 0.01 0.083 -10000 0 -0.58 19 19
RhoA/GDP 0 0.086 0.26 6 -0.31 19 25
actin cytoskeleton organization 0.014 0.053 0.18 16 -0.16 12 28
CDC42/GDP 0.001 0.085 0.26 7 -0.31 19 26
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.007 0.045 -10000 0 -0.27 20 20
ITGB7 0.029 0.046 0.26 24 -0.58 2 26
RAC1 0.024 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.043 0.062 -10000 0 -0.34 19 19
E-cadherin/Ca2+/beta catenin/alpha catenin 0.029 0.054 -10000 0 -0.32 19 19
mol:GDP -0.013 0.093 0.27 7 -0.36 20 27
CDC42/GTP/IQGAP1 0.03 0.009 -10000 0 -10000 0 0
JUP 0.023 0.005 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.005 0.088 0.27 1 -0.32 19 20
RAC1/GTP/IQGAP1 0.031 0.007 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.035 0.007 -10000 0 -10000 0 0
RHOA 0.023 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 0.048 0.18 37 -0.25 3 40
NME1 0.026 0.03 0.26 14 -10000 0 14
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.023 0.12 -10000 0 -0.42 44 44
regulation of cell-cell adhesion 0.003 0.042 -10000 0 -0.29 2 2
WASF2 0.007 0.027 -10000 0 -10000 0 0
Rap1/GTP 0.012 0.06 0.25 1 -0.28 18 19
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.069 -10000 0 -0.32 21 21
CCND1 0.015 0.055 0.21 30 -0.31 3 33
VAV2 -0.019 0.15 -10000 0 -0.54 38 38
RAP1/GDP 0.006 0.071 0.26 3 -0.35 3 6
adherens junction assembly -0.022 0.12 -10000 0 -0.4 44 44
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 0.04 0.065 -10000 0 -0.31 21 21
E-cadherin/beta catenin 0 0.062 -10000 0 -0.35 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.024 0.12 -10000 0 -0.43 41 41
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.005 0.091 0.27 29 -0.34 22 51
E-cadherin/beta catenin/alpha catenin 0.033 0.062 -10000 0 -0.37 19 19
ITGAE 0.022 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.023 0.13 -10000 0 -0.43 50 50
TRAIL signaling 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
TNFSF10 0.019 0.051 -10000 0 -0.58 7 7
positive regulation of NF-kappaB transcription factor activity -0.006 0.12 0.2 1 -0.33 96 97
MAP2K4 0.015 0.047 -10000 0 -0.42 3 3
IKBKB 0.02 0.009 -10000 0 -10000 0 0
TNFRSF10B 0.02 0.01 -10000 0 -10000 0 0
TNFRSF10A 0.018 0.029 -10000 0 -0.58 2 2
SMPD1 0.007 0.031 -10000 0 -0.35 6 6
IKBKG 0.024 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.015 0.14 0.26 1 -0.58 56 57
TRAIL/TRAILR2 0.025 0.041 -10000 0 -0.38 8 8
TRAIL/TRAILR3 0.026 0.045 -10000 0 -0.38 9 9
TRAIL/TRAILR1 0.023 0.047 -10000 0 -0.33 14 14
TRAIL/TRAILR4 -0.006 0.12 0.2 1 -0.33 96 97
TRAIL/TRAILR1/DAP3/GTP 0.028 0.039 -10000 0 -0.33 6 6
IKK complex 0.011 0.04 -10000 0 -0.42 1 1
RIPK1 0.023 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 0.038 0.26 1 -0.42 7 8
MAP3K1 0.017 0.063 -10000 0 -0.48 7 7
TRAILR4 (trimer) -0.015 0.14 0.26 1 -0.58 56 57
TRADD 0.021 0.008 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.029 -10000 0 -0.58 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.012 0.045 -10000 0 -0.39 7 7
CFLAR 0.024 0.003 -10000 0 -10000 0 0
MAPK1 0.007 0.038 0.26 1 -0.42 7 8
TRAIL/TRAILR1/FADD/TRADD/RIP 0.041 0.047 -10000 0 -0.3 6 6
mol:ceramide 0.007 0.03 -10000 0 -0.35 6 6
FADD 0.02 0.009 -10000 0 -10000 0 0
MAPK8 0.011 0.062 0.26 1 -0.43 7 8
TRAF2 0.025 0.016 0.26 4 -10000 0 4
TRAILR3 (trimer) 0.021 0.023 0.26 7 -10000 0 7
CHUK 0.024 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.03 0.041 -10000 0 -0.36 6 6
DAP3 0.02 0.009 -10000 0 -10000 0 0
CASP10 0.034 0.083 0.28 53 -0.35 3 56
JNK cascade -0.006 0.12 0.2 1 -0.33 96 97
TRAIL (trimer) 0.019 0.051 -10000 0 -0.58 7 7
TNFRSF10C 0.021 0.023 0.26 7 -10000 0 7
TRAIL/TRAILR1/DAP3/GTP/FADD 0.031 0.039 -10000 0 -0.31 4 4
TRAIL/TRAILR2/FADD 0.031 0.038 -10000 0 -0.36 5 5
cell death 0.007 0.03 -10000 0 -0.34 6 6
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.013 0.043 -10000 0 -0.42 6 6
TRAILR2 (trimer) 0.02 0.01 -10000 0 -10000 0 0
CASP8 0.013 0.045 -10000 0 -0.57 4 4
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.042 0.044 -10000 0 -0.3 5 5
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 0.032 0.045 0.26 35 -9999 0 35
regulation of centriole replication 0.015 0.027 0.26 2 -9999 0 2
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.024 0.076 0.3 4 -0.36 15 19
PDGFB-D/PDGFRB/SLAP 0.028 0.034 -10000 0 -0.37 4 4
PDGFB-D/PDGFRB/APS/CBL 0.047 0.043 -10000 0 -0.36 4 4
AKT1 0.024 0.093 0.35 32 -10000 0 32
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.03 0.086 0.32 5 -0.37 20 25
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
FGR -0.001 0.1 -10000 0 -0.43 38 38
mol:Ca2+ 0.022 0.089 0.28 7 -0.42 19 26
MYC 0.052 0.17 0.39 21 -0.78 25 46
SHC1 0.02 0.009 -10000 0 -10000 0 0
HRAS/GDP 0.034 0.044 -10000 0 -0.31 3 3
LRP1/PDGFRB/PDGFB 0.041 0.053 -10000 0 -0.42 11 11
GRB10 0.024 0.003 -10000 0 -10000 0 0
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GO:0007205 0.021 0.09 0.28 6 -0.42 19 25
PTEN 0.022 0.028 -10000 0 -0.58 2 2
GRB2 0.023 0.01 0.26 1 -10000 0 1
GRB7 0.02 0.021 -10000 0 -0.58 1 1
PDGFB-D/PDGFRB/SHP2 0.034 0.03 -10000 0 -0.43 4 4
PDGFB-D/PDGFRB/GRB10 0.034 0.03 -10000 0 -0.43 4 4
cell cycle arrest 0.027 0.034 -10000 0 -0.37 4 4
HRAS 0.025 0.018 0.26 5 -10000 0 5
HIF1A 0.02 0.087 0.33 32 -10000 0 32
GAB1 0.023 0.096 0.29 8 -0.41 19 27
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.024 0.088 0.32 9 -0.35 18 27
PDGFB-D/PDGFRB 0.042 0.033 -10000 0 -0.37 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.034 0.028 -10000 0 -0.37 4 4
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.02 0.068 0.28 3 -0.37 11 14
positive regulation of MAPKKK cascade 0.034 0.03 -10000 0 -0.42 4 4
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
mol:IP3 0.022 0.091 0.29 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 0.029 0.036 -10000 0 -0.43 5 5
SHB 0.024 0.009 0.26 1 -10000 0 1
BLK -0.029 0.17 0.29 3 -0.41 134 137
PTPN2 0.024 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.033 0.03 -10000 0 -0.42 4 4
BCAR1 0.021 0.008 -10000 0 -10000 0 0
VAV2 0.025 0.1 0.31 8 -0.44 22 30
CBL 0.022 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.033 0.031 -10000 0 -0.43 4 4
LCK 0.004 0.11 -10000 0 -0.51 33 33
PDGFRB 0.022 0.04 -10000 0 -0.58 4 4
ACP1 0.024 0.003 -10000 0 -10000 0 0
HCK 0.014 0.066 -10000 0 -0.51 9 9
ABL1 0.018 0.095 0.29 6 -0.37 27 33
PDGFB-D/PDGFRB/CBL 0.018 0.11 0.3 3 -0.44 29 32
PTPN1 0.024 0.021 0.26 6 -10000 0 6
SNX15 0.024 0.004 -10000 0 -10000 0 0
STAT3 0.023 0.005 -10000 0 -10000 0 0
STAT1 0.028 0.032 0.26 18 -10000 0 18
cell proliferation 0.053 0.16 0.36 31 -0.68 25 56
SLA 0.021 0.023 0.26 7 -10000 0 7
actin cytoskeleton reorganization 0.033 0.051 0.33 3 -0.3 3 6
SRC 0.012 0.057 -10000 0 -0.47 7 7
PI3K -0.013 0.03 -10000 0 -0.29 7 7
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.035 -10000 0 -0.37 4 4
SH2B2 0.033 0.047 0.26 39 -10000 0 39
PLCgamma1/SPHK1 0.03 0.088 0.32 5 -0.38 20 25
LYN 0.009 0.067 -10000 0 -0.49 11 11
LRP1 0.019 0.058 -10000 0 -0.58 9 9
SOS1 0.024 0.003 -10000 0 -10000 0 0
STAT5B 0.022 0.028 -10000 0 -0.58 2 2
STAT5A 0.02 0.047 -10000 0 -0.58 6 6
NCK1-2/p130 Cas 0.055 0.04 -10000 0 -0.31 3 3
SPHK1 0.026 0.042 0.26 17 -0.58 2 19
EDG1 0.001 0.002 -10000 0 -10000 0 0
mol:DAG 0.022 0.091 0.29 6 -0.43 19 25
PLCG1 0.022 0.092 0.29 6 -0.44 19 25
NHERF/PDGFRB 0.048 0.046 -10000 0 -0.37 4 4
YES1 -0.002 0.11 -10000 0 -0.51 37 37
cell migration 0.047 0.046 -10000 0 -0.36 4 4
SHC/Grb2/SOS1 0.048 0.042 -10000 0 -0.31 3 3
SLC9A3R2 0.023 0.01 0.26 1 -10000 0 1
SLC9A3R1 0.034 0.052 0.26 47 -10000 0 47
NHERF1-2/PDGFRB/PTEN 0.056 0.049 -10000 0 -0.34 5 5
FYN -0.002 0.1 -10000 0 -0.43 38 38
DOK1 0.02 0.048 -10000 0 -0.34 3 3
HRAS/GTP 0.018 0.012 0.18 5 -10000 0 5
PDGFB 0.023 0.006 -10000 0 -10000 0 0
RAC1 0.02 0.13 0.33 4 -0.55 27 31
PRKCD 0.02 0.051 0.34 1 -0.34 3 4
FER 0.016 0.062 -10000 0 -0.35 13 13
MAPKKK cascade 0.038 0.098 0.36 34 -0.3 3 37
RASA1 0.02 0.049 -10000 0 -0.34 3 3
NCK1 0.024 0.003 -10000 0 -10000 0 0
NCK2 0.024 0.002 -10000 0 -10000 0 0
p62DOK/Csk 0.034 0.042 -10000 0 -0.32 3 3
PDGFB-D/PDGFRB/SHB 0.033 0.032 0.2 1 -0.37 5 6
chemotaxis 0.018 0.093 0.28 7 -0.36 27 34
STAT1-3-5/STAT1-3-5 0.048 0.05 -10000 0 -0.37 8 8
Bovine Papilomavirus E5/PDGFRB 0.016 0.029 -10000 0 -0.43 4 4
PTPRJ 0.024 0.004 -10000 0 -10000 0 0
p38 MAPK 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
TRAF6/ASK1 0.017 0.018 -10000 0 -0.31 2 2
TRAF2/ASK1 0.03 0.023 -10000 0 -0.37 2 2
ATM 0.022 0.008 -10000 0 -10000 0 0
MAP2K3 -0.019 0.11 0.27 1 -0.38 45 46
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.012 0.098 0.3 1 -0.36 29 30
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.05 0.075 0.26 106 -10000 0 106
TXN 0.006 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 0.02 -10000 0 -0.58 1 1
MAP3K6 0.023 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
MAP3K4 0.023 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.025 -10000 0 -0.3 4 4
TAK1/TAB family 0 0.02 0.18 2 -0.15 6 8
RAC1/OSM/MEKK3 0.041 0.016 -10000 0 -10000 0 0
TRAF2 0.025 0.016 0.26 4 -10000 0 4
RAC1/OSM/MEKK3/MKK3 0 0.093 -10000 0 -0.31 33 33
TRAF6 0.006 0.001 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.009 0.16 0.26 41 -0.58 69 110
CCM2 0.024 0.008 0.26 1 -10000 0 1
CaM/Ca2+/CAMKIIB 0.009 0.11 -10000 0 -0.36 70 70
MAPK11 0.021 0.034 -10000 0 -0.58 3 3
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.021 0.11 -10000 0 -0.34 70 70
OSM/MEKK3 0.032 0.013 -10000 0 -10000 0 0
TAOK1 -0.003 0.069 -10000 0 -0.36 34 34
TAOK2 0.01 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 0.028 -10000 0 -0.58 2 2
MAP3K10 0.024 0.004 -10000 0 -10000 0 0
MAP3K3 0.022 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.019 0.023 -10000 0 -0.35 2 2
GADD45/MTK1/MTK1 0.065 0.046 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.024 0.003 -10000 0 -10000 0 0
SPHK1 0.026 0.042 0.26 17 -0.58 2 19
GNAI2 0.024 0.005 -10000 0 -10000 0 0
mol:S1P 0.013 0.02 0.22 1 -0.3 2 3
GNAO1 0.018 0.095 0.26 32 -0.58 19 51
mol:Sphinganine-1-P 0.012 0.027 -10000 0 -0.43 2 2
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.051 0.035 -10000 0 -0.23 3 3
GNAI3 0.024 0.004 -10000 0 -10000 0 0
G12/G13 0.032 0.011 -10000 0 -10000 0 0
S1PR3 0.026 0.02 0.26 7 -10000 0 7
S1PR2 0.024 0.003 -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 18 -0.58 2 20
S1PR4 0.028 0.065 0.26 34 -0.58 6 40
GNAI1 -0.005 0.13 -10000 0 -0.58 47 47
S1P/S1P5/G12 0.045 0.042 0.25 4 -0.26 4 8
S1P/S1P3/Gq 0.026 0.064 -10000 0 -0.3 24 24
S1P/S1P4/Gi 0.001 0.098 0.26 1 -0.34 42 43
GNAQ 0.023 0.027 -10000 0 -0.58 2 2
GNAZ 0.018 0.055 -10000 0 -0.58 8 8
GNA14 0.023 0.07 0.26 21 -0.58 10 31
GNA15 0.025 0.027 0.26 6 -0.58 1 7
GNA12 0.024 0.004 -10000 0 -10000 0 0
GNA13 0.022 0.007 -10000 0 -10000 0 0
GNA11 0.022 0.028 -10000 0 -0.58 2 2
ABCC1 0.023 0.006 -10000 0 -10000 0 0
IL1-mediated signaling events

Figure S108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S108.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.03 0.01 -10000 0 -10000 0 0
PRKCZ 0.023 0.02 -10000 0 -0.58 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.023 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.05 -10000 0 -0.37 6 6
IRAK/TOLLIP 0.024 0.014 -10000 0 -10000 0 0
IKBKB 0.02 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 -0.43 35 38
IL1A 0.028 0.031 0.26 17 -10000 0 17
IL1B 0.004 0.054 0.26 1 -0.43 14 15
IRAK/TRAF6/p62/Atypical PKCs 0.061 0.04 -10000 0 -0.3 1 1
IL1R2 0.009 0.12 0.26 27 -0.58 35 62
IL1R1 0.014 0.079 -10000 0 -0.58 17 17
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.01 0.064 0.26 4 -0.32 9 13
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 0.032 0.071 0.34 7 -0.37 1 8
JUN -0.011 0.066 0.29 4 -0.28 28 32
MAP3K7 0.023 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.04 0.075 -10000 0 -0.32 34 34
IL1 alpha/IL1R1/IL1RAP/MYD88 0.054 0.058 -10000 0 -0.34 17 17
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.062 0.057 -10000 0 -0.32 17 17
IL1 beta fragment/IL1R1/IL1RAP 0.023 0.069 -10000 0 -0.35 30 30
NFKB1 0.024 0.004 -10000 0 -10000 0 0
MAPK8 -0.006 0.066 0.33 3 -0.29 22 25
IRAK1 -0.001 0.018 0.21 2 -10000 0 2
IL1RN/IL1R1 0.033 0.072 -10000 0 -0.43 19 19
IRAK4 0.024 0.003 -10000 0 -10000 0 0
PRKCI 0.023 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PI3K 0.031 0.036 -10000 0 -0.36 7 7
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.011 0.057 -10000 0 -0.37 7 7
CHUK 0.024 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.023 0.069 -10000 0 -0.35 30 30
IL1 beta/IL1R2 0.013 0.093 -10000 0 -0.38 48 48
IRAK/TRAF6/TAK1/TAB1/TAB2 0.029 0.015 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.029 0.068 -10000 0 -0.31 27 27
IRAK3 0.003 0.11 0.26 1 -0.58 33 34
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.043 0.07 -10000 0 -0.32 30 30
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.019 0.045 -10000 0 -0.28 17 17
IL1 alpha/IL1R1/IL1RAP 0.043 0.059 -10000 0 -0.37 17 17
RELA 0.024 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.024 0.009 0.26 1 -10000 0 1
MYD88 0.024 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.043 0.035 -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 0.056 -10000 0 -0.6 1 1
CASP1 0.021 0.021 -10000 0 -0.58 1 1
IL1RN/IL1R2 0.029 0.1 0.37 5 -0.43 37 42
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.035 0.07 -10000 0 -0.33 30 30
TMEM189-UBE2V1 0.019 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.017 0.073 -10000 0 -0.36 21 21
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
IL1RN 0.032 0.053 0.26 36 -0.58 2 38
TRAF6/TAK1/TAB1/TAB2 0.038 0.017 -10000 0 -10000 0 0
MAP2K6 -0.001 0.068 0.39 4 -0.3 17 21
Class I PI3K signaling events

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
ARF5/GTP -0.013 0.043 0.33 3 -0.3 1 4
DAPP1 0.015 0.1 0.26 9 -0.35 36 45
Src family/SYK family/BLNK-LAT/BTK-ITK 0.014 0.14 0.29 15 -0.48 38 53
mol:DAG 0.019 0.079 0.23 32 -0.25 11 43
HRAS 0.025 0.018 0.26 5 -10000 0 5
RAP1A 0.024 0.006 -10000 0 -10000 0 0
ARF5/GDP 0.03 0.057 0.27 1 -0.34 6 7
PLCG2 0.02 0.029 0.26 1 -0.58 2 3
PLCG1 0.023 0.005 -10000 0 -10000 0 0
ARF5 0.024 0.009 0.26 1 -10000 0 1
mol:GTP -0.01 0.044 0.36 5 -0.28 2 7
ARF1/GTP -0.004 0.034 0.28 5 -0.28 2 7
RHOA 0.023 0.005 -10000 0 -10000 0 0
YES1 0.023 0.02 -10000 0 -0.58 1 1
RAP1A/GTP -0.011 0.036 0.2 2 -0.28 2 4
ADAP1 -0.011 0.042 0.33 3 -0.28 3 6
ARAP3 -0.01 0.044 0.36 5 -0.28 2 7
INPPL1 0.023 0.006 -10000 0 -10000 0 0
PREX1 0.027 0.034 0.26 19 -10000 0 19
ARHGEF6 0.017 0.064 -10000 0 -0.58 11 11
ARHGEF7 0.022 0.007 -10000 0 -10000 0 0
ARF1 0.02 0.009 -10000 0 -10000 0 0
NRAS 0.024 0.006 -10000 0 -10000 0 0
FYN 0.021 0.028 -10000 0 -0.58 2 2
ARF6 0.024 0.004 -10000 0 -10000 0 0
FGR 0.023 0.009 0.26 1 -10000 0 1
mol:Ca2+ 0.013 0.051 0.25 9 -10000 0 9
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.025 0.016 0.26 4 -10000 0 4
ZAP70 0.024 0.1 0.26 48 -0.58 20 68
mol:IP3 0.013 0.063 0.19 36 -0.19 6 42
LYN 0.021 0.008 -10000 0 -10000 0 0
ARF1/GDP 0.024 0.055 0.32 2 -0.33 6 8
RhoA/GDP 0.032 0.042 -10000 0 -0.29 1 1
PDK1/Src/Hsp90 0.043 0.017 -10000 0 -10000 0 0
BLNK 0.024 0.003 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.018 0.067 0.43 4 -0.33 4 8
SRC 0.023 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.007 0.012 0.23 2 -10000 0 2
RAC1 0.024 0.004 -10000 0 -10000 0 0
PTEN 0.021 0.028 -10000 0 -0.55 2 2
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.013 0.042 0.32 4 -10000 0 4
RhoA/GTP -0.011 0.043 0.35 5 -0.27 2 7
Src family/SYK family/BLNK-LAT 0.024 0.097 0.26 16 -0.38 21 37
BLK 0.05 0.088 0.26 129 -0.58 2 131
PDPK1 0.023 0.006 -10000 0 -10000 0 0
CYTH1 -0.01 0.043 0.34 5 -0.27 2 7
HCK 0.026 0.026 0.26 11 -10000 0 11
CYTH3 -0.012 0.041 0.33 3 -0.28 3 6
CYTH2 -0.011 0.041 0.32 4 -0.27 2 6
KRAS 0.024 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.01 0.053 0.31 1 -0.53 5 6
SGK1 0.007 0.076 -10000 0 -0.35 33 33
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.017 0.058 0.34 2 -0.34 7 9
SOS1 0.024 0.003 -10000 0 -10000 0 0
SYK 0.024 0.003 -10000 0 -10000 0 0
ARF6/GDP 0.02 0.05 0.38 6 -0.29 1 7
mol:PI-3-4-5-P3 -0.011 0.038 0.27 5 -0.28 2 7
ARAP3/RAP1A/GTP -0.011 0.037 0.2 2 -0.28 2 4
VAV1 0.024 0.022 0.26 2 -0.58 1 3
mol:PI-3-4-P2 0.01 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.036 0.033 -10000 0 -0.28 2 2
PLEKHA1 -0.009 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.03 0.056 0.27 1 -0.34 6 7
LAT 0.025 0.04 0.26 14 -0.58 2 16
Rac1/GTP 0.017 0.048 -10000 0 -0.32 9 9
ITK -0.017 0.068 0.34 5 -0.32 27 32
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.017 0.097 0.27 27 -0.34 14 41
LCK 0.025 0.078 0.26 34 -0.58 11 45
BTK -0.011 0.044 0.34 5 -0.27 2 7
Arf6 trafficking events

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
SLC2A4 -0.27 0.3 -10000 0 -0.58 465 465
CLTC 0.025 0.068 0.28 1 -0.43 12 13
calcium ion-dependent exocytosis 0.009 0.024 -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 0.046 -10000 0 -0.34 10 10
CPE 0.005 0.05 -10000 0 -0.37 17 17
CTNNB1 0.024 0.004 -10000 0 -10000 0 0
membrane fusion 0.011 0.018 -10000 0 -10000 0 0
CTNND1 0.007 0.056 0.36 2 -10000 0 2
DNM2 0.024 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.045 0.24 1 -0.36 6 7
TSHR -0.004 0.074 -10000 0 -0.37 38 38
INS -0.002 0.089 -10000 0 -0.48 31 31
BIN1 0.019 0.054 -10000 0 -0.58 8 8
mol:Choline 0.011 0.018 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.016 -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 0.041 0.036 -10000 0 -0.34 7 7
ARF6/GTP 0.018 0.003 -10000 0 -10000 0 0
CDH1 0.009 0.055 -10000 0 -0.38 8 8
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 0.028 0.26 13 -10000 0 13
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 0.066 0.34 8 -10000 0 8
positive regulation of phagocytosis 0.011 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.03 0.01 -10000 0 -10000 0 0
ACAP1 0.015 0.027 -10000 0 -0.25 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.013 0.044 -10000 0 -0.34 10 10
clathrin heavy chain/ACAP1 0.024 0.064 0.28 6 -0.35 12 18
JIP4/KLC1 0.041 0.016 -10000 0 -10000 0 0
EXOC1 0.024 0.004 -10000 0 -10000 0 0
exocyst 0.019 0.035 -10000 0 -0.34 4 4
RALA/GTP 0.018 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.029 0.01 -10000 0 -10000 0 0
receptor recycling 0.018 0.003 -10000 0 -10000 0 0
CTNNA1 0.008 0.057 0.36 2 -10000 0 2
NME1 0.013 0.016 -10000 0 -10000 0 0
clathrin coat assembly 0.028 0.07 0.28 3 -0.43 12 15
IL2RA 0.019 0.054 -10000 0 -0.32 12 12
VAMP3 0.011 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.12 0.14 -10000 0 -0.38 31 31
EXOC6 0.024 0.003 -10000 0 -10000 0 0
PLD1 0.009 0.026 -10000 0 -0.3 6 6
PLD2 0.011 0.006 -10000 0 -10000 0 0
EXOC5 0.024 0.004 -10000 0 -10000 0 0
PIP5K1C 0.013 0.041 -10000 0 -0.36 6 6
SDC1 0.019 0.044 -10000 0 -0.33 8 8
ARF6/GDP 0.021 0.013 -10000 0 -10000 0 0
EXOC7 0.023 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.039 0.069 -10000 0 -0.35 8 8
mol:Phosphatidic acid 0.011 0.018 -10000 0 -10000 0 0
endocytosis -0.04 0.035 0.33 7 -10000 0 7
SCAMP2 0.024 0.004 -10000 0 -10000 0 0
ADRB2 -0.042 0.14 0.26 1 -0.44 31 32
EXOC3 0.023 0.005 -10000 0 -10000 0 0
ASAP2 0.023 0.02 -10000 0 -0.58 1 1
Dynamin 2/GDP 0.025 0.017 -10000 0 -10000 0 0
KLC1 0.024 0.004 -10000 0 -10000 0 0
AVPR2 -0.088 0.16 0.29 3 -0.44 33 36
RALA 0.024 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.035 0.067 0.32 2 -0.35 5 7
E-cadherin signaling events

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.032 0.063 -9999 0 -0.37 19 19
E-cadherin/beta catenin 0.02 0.068 -9999 0 -0.43 19 19
CTNNB1 0.024 0.004 -9999 0 -10000 0 0
JUP 0.023 0.005 -9999 0 -10000 0 0
CDH1 0.01 0.083 -9999 0 -0.58 19 19
IFN-gamma 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
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 0.047 0.34 4 -10000 0 4
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.048 0.02 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I 0.014 0.042 -10000 0 -10000 0 0
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 0.043 0.29 2 -10000 0 2
AKT1 0.011 0.06 0.3 9 -0.28 4 13
MAP2K1 0.007 0.045 0.28 4 -0.3 1 5
MAP3K11 0.023 0.042 0.28 4 -10000 0 4
IFNGR1 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.016 0.1 -10000 0 -0.47 5 5
Rap1/GTP 0.017 0.013 -10000 0 -10000 0 0
CRKL/C3G 0.034 0.009 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.077 0.054 -10000 0 -10000 0 0
CEBPB 0.026 0.097 0.35 3 -0.46 9 12
STAT3 0.023 0.005 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.074 0.1 -10000 0 -0.66 11 11
STAT1 0.025 0.048 0.28 6 -10000 0 6
CALM1 0.024 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.055 0.083 0.26 133 -10000 0 133
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.041 0.046 0.29 5 -10000 0 5
CEBPB/PTGES2/Cbp/p300 0.027 0.065 0.29 5 -0.31 7 12
mol:Ca2+ 0.065 0.049 -10000 0 -10000 0 0
MAPK3 0.021 0.081 -10000 0 -0.56 12 12
STAT1 (dimer) 0.026 0.059 -10000 0 -10000 0 0
MAPK1 -0.01 0.17 -10000 0 -0.67 57 57
JAK2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
JAK1 0.026 0.006 -10000 0 -10000 0 0
CAMK2D 0.022 0.034 -10000 0 -0.58 3 3
DAPK1 0.025 0.07 0.34 3 -0.34 2 5
SMAD7 0.016 0.035 0.18 5 -10000 0 5
CBL/CRKL/C3G 0.046 0.039 0.29 3 -10000 0 3
PI3K 0.058 0.049 -10000 0 -0.29 5 5
IFNG 0.055 0.083 0.26 133 -10000 0 133
apoptosis 0.022 0.076 0.33 2 -0.41 12 14
CAMK2G 0.024 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.023 0.005 -10000 0 -10000 0 0
CAMK2A 0.031 0.042 0.26 30 -10000 0 30
CAMK2B -0.009 0.16 0.26 41 -0.58 69 110
FRAP1 0.008 0.055 0.29 9 -0.27 4 13
PRKCD 0.011 0.062 0.3 11 -0.29 4 15
RAP1B 0.024 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.014 0.042 -10000 0 -10000 0 0
PTPN2 0.023 0.005 -10000 0 -10000 0 0
EP300 0.023 0.006 -10000 0 -10000 0 0
IRF1 0.021 0.057 0.3 9 -0.32 1 10
STAT1 (dimer)/PIASy 0.038 0.046 0.28 5 -10000 0 5
SOCS1 0.014 0.12 -10000 0 -1 11 11
mol:GDP 0.042 0.036 0.27 3 -10000 0 3
CASP1 0.016 0.039 0.21 8 -0.26 2 10
PTGES2 0.024 0.008 0.26 1 -10000 0 1
IRF9 0.028 0.043 0.23 11 -10000 0 11
mol:PI-3-4-5-P3 0.043 0.04 -10000 0 -0.28 5 5
RAP1/GDP 0.035 0.022 -10000 0 -10000 0 0
CBL 0.021 0.041 0.27 4 -10000 0 4
MAP3K1 0.021 0.042 0.28 4 -0.31 1 5
PIAS1 0.024 0.004 -10000 0 -10000 0 0
PIAS4 0.023 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.014 0.042 -10000 0 -10000 0 0
PTPN11 0.025 0.045 0.24 10 -10000 0 10
CREBBP 0.023 0.006 -10000 0 -10000 0 0
RAPGEF1 0.024 0.004 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.019 0.021 -10000 0 -0.58 1 1
Caspase 8 (4 units) 0.039 0.06 -10000 0 -0.51 2 2
NEF 0.004 0.022 -10000 0 -0.18 7 7
NFKBIA 0.025 0.012 -10000 0 -10000 0 0
BIRC3 0.018 0.055 0.27 10 -0.56 4 14
CYCS 0.037 0.077 0.26 24 -0.31 9 33
RIPK1 0.023 0.005 -10000 0 -10000 0 0
CD247 0.018 0.092 0.3 18 -0.62 15 33
MAP2K7 0.042 0.13 0.37 2 -0.75 14 16
protein ubiquitination 0.013 0.085 0.31 5 -0.37 12 17
CRADD 0.024 0.003 -10000 0 -10000 0 0
DAXX 0.024 0.003 -10000 0 -10000 0 0
FAS 0.023 0.027 -10000 0 -0.58 2 2
BID 0.037 0.073 0.22 4 -0.31 11 15
NF-kappa-B/RelA/I kappa B alpha 0.051 0.033 -10000 0 -0.31 3 3
TRADD 0.021 0.008 -10000 0 -10000 0 0
MAP3K5 0.022 0.028 -10000 0 -0.58 2 2
CFLAR 0.024 0.003 -10000 0 -10000 0 0
FADD 0.02 0.009 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.051 0.033 -10000 0 -0.31 3 3
MAPK8 0.039 0.12 0.42 4 -0.68 14 18
APAF1 0.024 0.003 -10000 0 -10000 0 0
TRAF1 0.025 0.016 0.26 4 -10000 0 4
TRAF2 0.025 0.016 0.26 4 -10000 0 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.025 0.06 0.22 7 -0.32 12 19
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.012 0.095 -10000 0 -0.42 20 20
CHUK 0.013 0.087 0.31 4 -0.4 11 15
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.055 0.039 -10000 0 -0.36 3 3
TCRz/NEF 0.017 0.083 0.32 9 -0.44 22 31
TNF 0.023 0.07 0.26 21 -0.58 10 31
FASLG 0.012 0.11 0.3 36 -0.56 22 58
NFKB1 0.025 0.011 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.036 0.051 -10000 0 -0.36 10 10
CASP6 0.052 0.11 0.38 1 -0.52 17 18
CASP7 0.04 0.1 0.36 8 -0.49 9 17
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 0.37 5 -0.48 10 15
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.027 0.022 -10000 0 -0.3 2 2
CASP8 0.024 0.003 -10000 0 -10000 0 0
CASP9 0.023 0.006 -10000 0 -10000 0 0
MAP3K14 0.014 0.091 0.3 1 -0.4 19 20
APAF-1/Caspase 9 0.033 0.062 0.26 5 -0.37 6 11
BCL2 0.032 0.12 0.44 5 -0.56 19 24
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.049 0.082 -10000 0 -0.48 1 1
CRKL 0.023 0.048 0.29 6 -10000 0 6
mol:DAG 0.037 0.052 0.33 1 -10000 0 1
HRAS 0.033 0.078 0.3 16 -10000 0 16
MAPK8 0.041 0.07 0.24 29 -0.34 4 33
RAP1A 0.024 0.047 0.29 5 -10000 0 5
GAB1 0.024 0.047 0.28 6 -10000 0 6
MAPK14 0.042 0.065 0.24 29 -10000 0 29
EPO 0.062 0.088 0.26 155 -10000 0 155
PLCG1 0.037 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 0.063 0.063 -10000 0 -0.36 5 5
GAB1/SHC/GRB2/SOS1 0.041 0.042 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.061 0.06 0.23 3 -10000 0 3
IRS2 0.012 0.071 0.29 4 -0.3 30 34
STAT1 0.044 0.065 0.32 4 -10000 0 4
STAT5B 0.039 0.059 -10000 0 -0.35 1 1
cell proliferation 0.023 0.075 0.24 31 -0.32 4 35
GAB1/SHIP/PIK3R1/SHP2/SHC 0.033 0.04 -10000 0 -0.34 1 1
TEC 0.023 0.049 0.29 5 -0.3 1 6
SOCS3 0.02 0.043 -10000 0 -0.58 5 5
STAT1 (dimer) 0.043 0.065 0.31 4 -10000 0 4
JAK2 0.025 0.01 -10000 0 -10000 0 0
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
EPO/EPOR (dimer)/JAK2 0.08 0.064 0.34 3 -10000 0 3
EPO/EPOR 0.061 0.06 0.23 3 -10000 0 3
LYN 0.021 0.012 -10000 0 -10000 0 0
TEC/VAV2 0.038 0.048 0.28 3 -0.3 1 4
elevation of cytosolic calcium ion concentration 0.026 0.013 0.26 1 -10000 0 1
SHC1 0.02 0.009 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.062 0.056 -10000 0 -10000 0 0
mol:IP3 0.037 0.052 0.33 1 -10000 0 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.032 0.074 0.29 2 -0.3 26 28
SH2B3 0.026 0.009 -10000 0 -10000 0 0
NFKB1 0.042 0.066 0.25 28 -10000 0 28
EPO/EPOR (dimer)/JAK2/SOCS3 0.025 0.044 -10000 0 -0.2 8 8
PTPN6 0.022 0.039 0.28 3 -10000 0 3
TEC/VAV2/GRB2 0.046 0.049 0.28 3 -0.29 1 4
EPOR 0.026 0.013 0.26 1 -10000 0 1
INPP5D 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0.04 0.042 -10000 0 -10000 0 0
SOS1 0.024 0.003 -10000 0 -10000 0 0
PLCG2 0.02 0.029 0.26 1 -0.58 2 3
CRKL/CBL/C3G 0.046 0.048 0.28 4 -10000 0 4
VAV2 0.024 0.048 0.29 6 -10000 0 6
CBL 0.023 0.047 0.29 5 -10000 0 5
SHC/Grb2/SOS1 0.035 0.038 -10000 0 -10000 0 0
STAT5A 0.037 0.064 -10000 0 -0.34 6 6
GRB2 0.023 0.01 0.26 1 -10000 0 1
STAT5 (dimer) 0.049 0.082 0.34 1 -0.34 11 12
LYN/PLCgamma2 0.027 0.027 -10000 0 -0.43 2 2
PTPN11 0.024 0.002 -10000 0 -10000 0 0
BTK 0.025 0.049 0.29 6 -10000 0 6
BCL2 0.029 0.17 0.34 1 -0.83 33 34
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.018 0.024 0.22 4 -0.31 1 5
CRKL 0.023 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.003 -10000 0 -10000 0 0
DOCK1 0.024 0.004 -10000 0 -10000 0 0
ITGA4 0.026 0.023 0.26 9 -10000 0 9
alpha4/beta7 Integrin/MAdCAM1 0.066 0.049 0.36 9 -0.34 2 11
EPO 0.061 0.088 0.26 155 -10000 0 155
alpha4/beta7 Integrin 0.04 0.039 0.37 3 -0.43 2 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.036 0.017 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.06 0.061 -10000 0 -10000 0 0
lamellipodium assembly 0.011 0.074 -10000 0 -0.46 16 16
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.031 0.036 -10000 0 -0.36 7 7
ARF6 0.024 0.004 -10000 0 -10000 0 0
JAK2 0.034 0.032 -10000 0 -10000 0 0
PXN 0.024 0.002 -10000 0 -10000 0 0
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
MADCAM1 0.032 0.046 0.26 37 -10000 0 37
cell adhesion 0.064 0.048 0.35 9 -0.34 2 11
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
SRC -0.008 0.046 -10000 0 -0.34 9 9
ITGB7 0.029 0.046 0.26 24 -0.58 2 26
RAC1 0.024 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.044 0.047 -10000 0 -0.37 10 10
p130Cas/Crk/Dock1 0.027 0.043 0.35 1 -0.29 8 9
VCAM1 0.019 0.064 0.26 6 -0.58 10 16
RHOA 0.023 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.057 0.024 -10000 0 -10000 0 0
BCAR1 -0.008 0.046 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 0.007 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.011 0.076 -10000 0 -0.48 16 16
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.024 0.004 -10000 0 -10000 0 0
NFATC1 0.02 0.086 0.37 2 -0.45 8 10
NFATC2 -0.004 0.069 0.18 3 -0.25 34 37
NFATC3 0.014 0.017 -10000 0 -0.41 1 1
YWHAE 0.022 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.011 0.094 0.26 3 -0.37 28 31
Exportin 1/Ran/NUP214 0.047 0.011 -10000 0 -10000 0 0
mol:DAG 0 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.032 0.086 0.25 5 -0.42 11 16
BCL2/BAX 0.02 0.079 -10000 0 -0.39 33 33
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 4 -10000 0 4
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 0.083 -10000 0 -0.41 14 14
Calcineurin A alpha-beta B1/BCL2 0.006 0.1 -10000 0 -0.58 28 28
FKBP8 0.024 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.018 0.082 0.41 14 -10000 0 14
KPNB1 0.023 0.006 -10000 0 -10000 0 0
KPNA2 0.036 0.058 0.26 58 -10000 0 58
XPO1 0.024 0.003 -10000 0 -10000 0 0
SFN 0.021 0.069 0.26 17 -0.58 10 27
MAP3K8 0.02 0.039 -10000 0 -0.58 4 4
NFAT4/CK1 alpha 0.018 0.028 -10000 0 -0.29 2 2
MEF2D/NFAT1/Cbp/p300 0.012 0.1 -10000 0 -0.29 65 65
CABIN1 0.011 0.093 0.26 3 -0.37 27 30
CALM1 0.02 0.013 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
MAP3K1 0.023 0.02 -10000 0 -0.58 1 1
CAMK4 0.032 0.044 0.26 33 -10000 0 33
mol:Ca2+ -0.001 0.005 -10000 0 -10000 0 0
MAPK3 0.023 0.006 -10000 0 -10000 0 0
YWHAH 0.023 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.042 0.039 -10000 0 -0.43 1 1
YWHAB 0.023 0.005 -10000 0 -10000 0 0
MAPK8 0.019 0.044 -10000 0 -0.58 5 5
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 0.098 0.32 1 -0.44 12 13
PRKCH 0.023 0.02 -10000 0 -0.58 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 0.033 -10000 0 -0.33 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.039 -10000 0 -0.32 3 3
PRKCB 0.017 0.08 0.26 15 -0.58 15 30
PRKCE 0.024 0.019 -10000 0 -0.58 1 1
JNK2/NFAT4 0.007 0.06 -10000 0 -0.38 1 1
BAD/BCL-XL 0.034 0.01 -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 0.021 0.021 -10000 0 -0.58 1 1
PRKCA 0.01 0.086 0.26 1 -0.58 20 21
PRKCG 0.03 0.045 0.26 34 -10000 0 34
PRKCQ 0.004 0.12 0.26 11 -0.58 35 46
FKBP38/BCL2 0.019 0.079 -10000 0 -0.39 33 33
EP300 0.019 0.015 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.023 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.029 0.087 0.34 1 -0.43 8 9
CaM/Ca2+/FKBP38 0.028 0.017 -10000 0 -10000 0 0
FKBP12/FK506 0.017 0.003 -10000 0 -10000 0 0
CSNK1A1 0.009 0.013 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.032 0.032 -10000 0 -10000 0 0
NFATc/ERK1 0.029 0.084 0.33 1 -0.42 8 9
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.037 0.093 0.25 5 -0.4 17 22
NR4A1 -0.007 0.17 -10000 0 -0.51 77 77
GSK3B 0.022 0.008 -10000 0 -10000 0 0
positive T cell selection 0.014 0.016 -10000 0 -0.41 1 1
NFAT1/CK1 alpha 0 0.053 -10000 0 -0.23 14 14
RCH1/ KPNB1 0.041 0.041 -10000 0 -10000 0 0
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
PRKACA 0.023 0.007 -10000 0 -10000 0 0
AKAP5 0.035 0.056 0.26 49 -0.58 1 50
MEF2D 0.017 0.015 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha 0.03 0.083 0.34 1 -0.42 8 9
CREBBP 0.019 0.015 -10000 0 -10000 0 0
BCL2 0.006 0.1 -10000 0 -0.58 28 28
Canonical NF-kappaB pathway

Figure S117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.036 0.11 0.29 13 -0.34 18 31
ERC1 0.023 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.029 0.034 0.21 19 -0.43 1 20
NFKBIA 0.01 0.02 -10000 0 -10000 0 0
BIRC2 0.022 0.007 -10000 0 -10000 0 0
IKBKB 0.02 0.009 -10000 0 -10000 0 0
RIPK2 0.02 0.017 0.26 3 -10000 0 3
IKBKG 0.019 0.028 -10000 0 -10000 0 0
IKK complex/A20 0.021 0.12 -10000 0 -0.4 38 38
NEMO/A20/RIP2 0.02 0.017 0.26 3 -10000 0 3
XPO1 0.024 0.003 -10000 0 -10000 0 0
NEMO/ATM 0.015 0.12 0.35 1 -0.41 43 44
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 -0.41 27 27
BCL10/MALT1/TRAF6 0.045 0.015 -10000 0 -10000 0 0
NOD2 0.027 0.043 0.26 24 -0.58 1 25
NFKB1 0.025 0.004 -10000 0 -10000 0 0
RELA 0.025 0.004 -10000 0 -10000 0 0
MALT1 0.023 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.032 0.012 -10000 0 -10000 0 0
ATM 0.022 0.008 -10000 0 -10000 0 0
TNF/TNFR1A 0.033 0.053 -10000 0 -0.42 10 10
TRAF6 0.024 0.004 -10000 0 -10000 0 0
PRKCA 0.01 0.086 0.26 1 -0.58 20 21
CHUK 0.024 0.003 -10000 0 -10000 0 0
UBE2D3 0.024 0.004 -10000 0 -10000 0 0
TNF 0.023 0.07 0.26 21 -0.58 10 31
NF kappa B1 p50/RelA 0.051 0.014 -10000 0 -10000 0 0
BCL10 0.024 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.019 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.023 0.005 -10000 0 -10000 0 0
IKK complex 0.016 0.12 -10000 0 -0.41 39 39
CYLD 0.022 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.014 0.13 -10000 0 -0.44 35 35
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.05 0.044 -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 0.035 0.024 -10000 0 -0.43 1 1
GATA1/HDAC5 0.035 0.02 -10000 0 -10000 0 0
GATA2/HDAC5 0.024 0.076 -10000 0 -0.43 25 25
HDAC5/BCL6/BCoR 0.043 0.035 -10000 0 -0.37 6 6
HDAC9 0.022 0.06 0.26 11 -0.58 8 19
Glucocorticoid receptor/Hsp90/HDAC6 0.043 0.042 -10000 0 -0.37 9 9
HDAC4/ANKRA2 0.034 0.017 -10000 0 -0.43 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 0.011 0.099 0.26 11 -0.58 25 36
HDAC4/RFXANK 0.035 0.018 -10000 0 -0.43 1 1
BCOR 0.023 0.027 -10000 0 -0.58 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.023 0.006 -10000 0 -10000 0 0
HDAC5 0.023 0.005 -10000 0 -10000 0 0
GNB1/GNG2 0.029 0.047 -10000 0 -0.43 10 10
Histones 0.016 0.05 -10000 0 -0.32 9 9
ADRBK1 0.023 0.006 -10000 0 -10000 0 0
HDAC4 0.023 0.02 -10000 0 -0.58 1 1
XPO1 0.024 0.003 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.034 0.009 -10000 0 -10000 0 0
HDAC4/Ubc9 0.032 0.018 -10000 0 -0.43 1 1
HDAC7 0.024 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.032 0.011 -10000 0 -10000 0 0
TUBA1B 0.024 0.002 -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 0.044 0.26 33 -10000 0 33
Tubulin/HDAC6 0.047 0.013 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.023 0.005 -10000 0 -10000 0 0
GATA1 0.025 0.027 0.26 12 -10000 0 12
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 -0.58 9 9
SUMO1/HDAC4 0.034 0.04 -10000 0 -0.24 4 4
SRF 0.024 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.033 0.018 -10000 0 -0.43 1 1
Tubulin 0.035 0.011 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.032 0.019 -10000 0 -0.43 1 1
GNB1 0.023 0.005 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
BCL6/BCoR 0.032 0.037 -10000 0 -0.43 6 6
HDAC4/HDAC3/SMRT (N-CoR2) 0.047 0.018 -10000 0 -0.37 1 1
HDAC4/SRF 0.05 0.032 -10000 0 -0.37 1 1
HDAC4/ER alpha -0.013 0.18 -10000 0 -0.42 139 139
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.016 0.049 -10000 0 -0.32 9 9
cell motility 0.047 0.013 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.035 0.006 -10000 0 -10000 0 0
BCL6 0.021 0.039 -10000 0 -0.58 4 4
HDAC4/CaMK II delta B 0.023 0.02 -10000 0 -0.58 1 1
Hsp90/HDAC6 0.035 0.007 -10000 0 -10000 0 0
ESR1 -0.032 0.23 0.26 113 -0.58 134 247
HDAC6/HDAC11 0.035 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.034 0.038 -10000 0 -0.24 3 3
NPC 0.014 0.002 -10000 0 -10000 0 0
MEF2C 0.022 0.028 -10000 0 -0.58 2 2
RAN 0.024 0.003 -10000 0 -10000 0 0
HDAC4/MEF2C 0.062 0.031 -10000 0 -0.32 2 2
GNG2 0.018 0.061 -10000 0 -0.58 10 10
NCOR2 0.024 0.003 -10000 0 -10000 0 0
TUBB2A 0.024 0.012 0.26 2 -10000 0 2
HDAC11 0.024 0.004 -10000 0 -10000 0 0
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
ANKRA2 0.023 0.005 -10000 0 -10000 0 0
RFXANK 0.024 0.011 0.26 2 -10000 0 2
nuclear import -0.026 0.017 0.34 1 -10000 0 1
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.029 0.046 0.26 24 -0.58 2 26
ITGA4 0.026 0.023 0.26 9 -10000 0 9
alpha4/beta7 Integrin 0.04 0.039 0.37 3 -0.43 2 5
alpha4/beta1 Integrin 0.036 0.017 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.1 0.15 -10000 0 -0.42 65 65
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 -0.44 69 70
YWHAZ 0.019 0.01 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
YWHAQ 0.024 0.004 -10000 0 -10000 0 0
TBC1D4 0.009 0.025 -10000 0 -0.43 3 3
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 0.023 0.021 0.26 7 -10000 0 7
PRKCI 0.023 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
RHOQ 0.024 0.003 -10000 0 -10000 0 0
GYS1 0.009 0.015 0.24 4 -10000 0 4
PRKCZ 0.023 0.02 -10000 0 -0.58 1 1
TRIP10 0.024 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.032 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.018 0.067 0.26 1 -0.36 10 11
VAMP2 0.022 0.007 -10000 0 -10000 0 0
SLC2A4 -0.13 0.17 0.41 1 -0.49 69 70
STX4 0.023 0.006 -10000 0 -10000 0 0
GSK3B 0.017 0.005 -10000 0 -10000 0 0
SFN 0.021 0.069 0.26 17 -0.58 10 27
LNPEP 0.021 0.039 -10000 0 -0.58 4 4
YWHAE 0.022 0.007 -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 0.022 0.076 -10000 0 -0.43 26 26
AKT1 0.032 0.084 0.35 3 -0.58 6 9
PTK2B 0.005 0.082 0.35 1 -0.78 5 6
VEGFR2 homodimer/Frs2 0.026 0.053 -10000 0 -0.76 4 4
CAV1 -0.096 0.24 -10000 0 -0.58 194 194
CALM1 0.024 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.04 0.054 -10000 0 -0.71 4 4
endothelial cell proliferation 0.043 0.11 0.38 21 -0.57 8 29
mol:Ca2+ 0.015 0.049 -10000 0 -0.61 4 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.051 0.054 -10000 0 -0.61 5 5
RP11-342D11.1 0.005 0.049 -10000 0 -0.58 5 5
CDH5 0.018 0.048 -10000 0 -0.58 6 6
VEGFA homodimer 0.049 0.028 -10000 0 -10000 0 0
SHC1 0.02 0.009 -10000 0 -10000 0 0
SHC2 0.01 0.087 -10000 0 -0.58 21 21
HRAS/GDP 0.031 0.045 -10000 0 -0.6 3 3
SH2D2A 0.04 0.074 0.26 83 -0.58 2 85
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.043 0.087 -10000 0 -0.55 8 8
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.046 0.069 -10000 0 -0.58 5 5
VEGFR1 homodimer 0.023 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.049 0.055 -10000 0 -0.66 3 3
GRB10 0.015 0.051 -10000 0 -0.65 4 4
PTPN11 0.024 0.002 -10000 0 -10000 0 0
GRB2 0.023 0.01 0.26 1 -10000 0 1
PAK1 0.023 0.019 0.26 5 -10000 0 5
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.051 0.069 -10000 0 -0.74 5 5
HRAS 0.025 0.018 0.26 5 -10000 0 5
VEGF/Rho/ROCK1/Integrin Complex 0.011 0.069 -10000 0 -0.51 8 8
HIF1A 0.024 0.004 -10000 0 -10000 0 0
FRS2 0.024 0.012 0.26 2 -10000 0 2
oxygen and reactive oxygen species metabolic process 0.05 0.053 -10000 0 -0.6 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.022 0.034 -10000 0 -0.58 3 3
Nck/Pak 0.033 0.017 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.038 0.059 -10000 0 -0.69 5 5
mol:GDP 0.039 0.05 -10000 0 -0.64 3 3
mol:NADP 0.024 0.084 0.56 1 -0.47 10 11
eNOS/Hsp90 0.036 0.081 0.54 1 -0.47 8 9
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
mol:IP3 0.015 0.05 -10000 0 -0.62 4 4
HIF1A/ARNT 0.029 0.015 -10000 0 -10000 0 0
SHB 0.024 0.009 0.26 1 -10000 0 1
VEGFA 0.026 0.019 0.26 6 -10000 0 6
VEGFC 0.023 0.005 -10000 0 -10000 0 0
FAK1/Vinculin 0.023 0.098 0.35 1 -0.65 8 9
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.023 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.042 0.088 -10000 0 -0.42 25 25
PTPN6 0.024 0.012 0.26 2 -10000 0 2
EPAS1 0.026 0.048 -10000 0 -0.6 5 5
mol:L-citrulline 0.024 0.084 0.56 1 -0.47 10 11
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 0.049 0.055 -10000 0 -0.68 4 4
VEGFR2 homodimer/VEGFA homodimer 0.042 0.055 -10000 0 -0.58 6 6
VEGFR2/3 heterodimer 0.025 0.063 -10000 0 -0.73 6 6
VEGFB 0.024 0.005 -10000 0 -10000 0 0
MAPK11 0.005 0.064 -10000 0 -0.73 4 4
VEGFR2 homodimer 0.013 0.058 -10000 0 -0.76 5 5
FLT1 0.023 0.006 -10000 0 -10000 0 0
NEDD4 0.024 0.02 -10000 0 -0.57 1 1
MAPK3 0.006 0.071 0.32 1 -0.66 4 5
MAPK1 0.008 0.072 -10000 0 -0.6 5 5
VEGFA145/NRP2 0.035 0.026 -10000 0 -0.39 2 2
VEGFR1/2 heterodimer 0.024 0.056 -10000 0 -0.7 5 5
KDR 0.013 0.059 -10000 0 -0.76 5 5
VEGFA165/NRP1/VEGFR2 homodimer 0.041 0.059 -10000 0 -0.75 4 4
SRC 0.023 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.014 0.081 0.35 4 -0.62 5 9
PI3K 0.027 0.066 -10000 0 -0.7 5 5
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.04 0.053 -10000 0 -0.64 5 5
FES 0.013 0.055 -10000 0 -0.67 4 4
GAB1 0.015 0.058 -10000 0 -0.78 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.039 0.051 -10000 0 -0.6 5 5
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 -0.018 0.13 -10000 0 -0.48 19 19
VEGFR2 homodimer/VEGFA homodimer/Yes 0.039 0.055 -10000 0 -0.58 6 6
PI3K/GAB1 0.041 0.075 -10000 0 -0.57 6 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.055 0.055 -10000 0 -0.62 4 4
PRKACA 0.024 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.037 0.061 -10000 0 -0.69 6 6
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
CDC42 0.015 0.053 -10000 0 -0.67 4 4
actin cytoskeleton reorganization 0.046 0.068 -10000 0 -0.57 5 5
PTK2 0.006 0.083 -10000 0 -0.71 8 8
EDG1 0.005 0.049 -10000 0 -0.58 5 5
mol:DAG 0.015 0.05 -10000 0 -0.62 4 4
CaM/Ca2+ 0.026 0.048 -10000 0 -0.58 4 4
MAP2K3 -0.005 0.055 -10000 0 -0.64 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.04 0.054 -10000 0 -0.68 4 4
PLCG1 0.015 0.051 -10000 0 -0.63 4 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.05 0.053 -10000 0 -0.58 5 5
IQGAP1 0.023 0.005 -10000 0 -10000 0 0
YES1 0.023 0.02 -10000 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.041 0.054 -10000 0 -0.64 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.04 0.055 -10000 0 -0.64 5 5
cell migration 0.026 0.091 0.35 3 -0.66 6 9
mol:PI-3-4-5-P3 0.026 0.06 -10000 0 -0.63 5 5
FYN 0.021 0.028 -10000 0 -0.58 2 2
VEGFB/NRP1 0.02 0.049 -10000 0 -0.62 4 4
mol:NO 0.024 0.084 0.56 1 -0.47 10 11
PXN 0.024 0.002 -10000 0 -10000 0 0
HRAS/GTP 0.017 0.04 -10000 0 -0.6 3 3
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.033 0.052 -10000 0 -0.68 4 4
VHL 0.024 0.004 -10000 0 -10000 0 0
ITGB3 0.008 0.098 0.26 4 -0.58 26 30
NOS3 0.024 0.092 0.57 1 -0.54 10 11
VEGFR2 homodimer/VEGFA homodimer/Sck 0.032 0.076 -10000 0 -0.39 25 25
RAC1 0.024 0.004 -10000 0 -10000 0 0
PRKCA -0.009 0.071 0.35 1 -0.72 4 5
PRKCB -0.006 0.064 -10000 0 -0.7 4 4
VCL 0.024 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.023 0.051 -10000 0 -0.54 6 6
VEGFR1/2 heterodimer/VEGFA homodimer 0.038 0.056 -10000 0 -0.66 5 5
VEGFA165/NRP2 0.035 0.026 -10000 0 -0.39 2 2
MAPKKK cascade 0.051 0.078 0.34 11 -0.61 3 14
NRP2 0.023 0.029 0.26 1 -0.58 2 3
VEGFC homodimer 0.023 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
ROCK1 0.023 0.02 -10000 0 -0.58 1 1
FAK1/Paxillin 0.024 0.1 0.42 2 -0.65 8 10
MAP3K13 0.013 0.054 -10000 0 -0.67 4 4
PDPK1 0.015 0.055 0.27 1 -0.59 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 -0.49 1 1
mol:DAG 0.012 0.03 -10000 0 -0.39 2 2
VEGFR1 homodimer/NRP1/VEGFR 121 0.024 0.02 -10000 0 -0.45 1 1
CaM/Ca2+ 0.025 0.029 -10000 0 -0.37 2 2
HIF1A 0.027 0.012 -10000 0 -0.31 1 1
GAB1 0.024 0.004 -10000 0 -10000 0 0
AKT1 0.01 0.045 -10000 0 -0.42 1 1
PLCG1 0.012 0.03 -10000 0 -0.39 2 2
NOS3 0.015 0.055 -10000 0 -0.5 3 3
CBL 0.022 0.007 -10000 0 -10000 0 0
mol:NO 0.019 0.064 0.3 1 -0.45 6 7
FLT1 0.013 0.019 -10000 0 -0.56 1 1
PGF 0.024 0.024 0.26 3 -0.58 1 4
VEGFR1 homodimer/NRP2/VEGFR121 0.037 0.031 -10000 0 -0.45 2 2
CALM1 0.024 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
eNOS/Hsp90 0.031 0.066 -10000 0 -0.43 7 7
endothelial cell proliferation 0.011 0.084 0.36 6 -0.69 3 9
mol:Ca2+ 0.012 0.03 -10000 0 -0.39 2 2
MAPK3 -0.014 0.051 -10000 0 -0.68 1 1
MAPK1 -0.013 0.049 -10000 0 -0.66 1 1
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
PLGF homodimer 0.024 0.024 0.26 3 -0.58 1 4
PRKACA 0.024 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.096 0.24 -10000 0 -0.58 194 194
VEGFA homodimer 0.025 0.019 0.26 6 -10000 0 6
VEGFR1 homodimer/VEGFA homodimer 0.026 0.022 -10000 0 -0.49 1 1
platelet activating factor biosynthetic process -0.015 0.048 -10000 0 -0.65 1 1
PI3K 0.045 0.04 -10000 0 -0.34 7 7
PRKCA -0.012 0.054 0.25 1 -0.71 1 2
PRKCB -0.01 0.051 -10000 0 -0.35 12 12
VEGFR1 homodimer/PLGF homodimer 0.026 0.024 -10000 0 -0.43 2 2
VEGFA 0.025 0.019 0.26 6 -10000 0 6
VEGFB 0.024 0.005 -10000 0 -10000 0 0
mol:IP3 0.012 0.03 -10000 0 -0.39 2 2
RASA1 0.012 0.029 -10000 0 -0.44 1 1
NRP2 0.023 0.029 0.26 1 -0.58 2 3
VEGFR1 homodimer 0.013 0.019 -10000 0 -0.56 1 1
VEGFB homodimer 0.023 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.029 0.14 -10000 0 -0.46 21 21
PTPN11 0.024 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.044 0.039 -10000 0 -0.33 7 7
mol:L-citrulline 0.019 0.064 0.3 1 -0.45 6 7
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.047 0.028 -10000 0 -0.42 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.038 0.024 -10000 0 -0.46 1 1
CD2AP 0.024 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.053 0.042 -10000 0 -0.41 1 1
PDPK1 -0.004 0.049 -10000 0 -0.41 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.039 0.024 -10000 0 -0.46 1 1
mol:NADP 0.019 0.064 0.3 1 -0.45 6 7
HSP90AA1 0.024 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.028 -10000 0 -0.41 1 1
VEGFR1 homodimer/NRP2 0.025 0.029 -10000 0 -0.45 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 0.049 0.063 -10000 0 -0.38 9 9
Ran/GTP/Exportin 1/HDAC1 -0.009 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.03 0.063 -10000 0 -0.36 9 9
SUMO1 0.024 0.003 -10000 0 -10000 0 0
ZFPM1 0.023 0.021 0.26 6 -10000 0 6
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.004 -10000 0 -10000 0 0
FKBP3 0.024 0.004 -10000 0 -10000 0 0
Histones 0.052 0.043 -10000 0 -0.42 1 1
YY1/LSF 0.024 0.049 -10000 0 -0.24 15 15
SMG5 0.02 0.009 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.02 0.035 -10000 0 -0.32 8 8
I kappa B alpha/HDAC1 0.029 0.041 -10000 0 -0.44 2 2
SAP18 0.023 0.006 -10000 0 -10000 0 0
RELA 0.019 0.039 -10000 0 -0.29 8 8
HDAC1/Smad7 0.046 0.014 -10000 0 -10000 0 0
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
HDAC3/TR2 0.03 0.039 -10000 0 -0.44 1 1
NuRD/MBD3 Complex 0.026 0.051 -10000 0 -0.3 8 8
NF kappa B1 p50/RelA 0.026 0.064 0.38 1 -0.35 5 6
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.011 0.099 0.26 11 -0.58 25 36
GATA1 0.025 0.027 0.26 12 -10000 0 12
Mad/Max 0.035 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.017 0.081 -10000 0 -0.37 19 19
RBBP7 0.026 0.02 0.26 7 -10000 0 7
NPC 0.014 0.002 -10000 0 -10000 0 0
RBBP4 0.023 0.02 -10000 0 -0.58 1 1
MAX 0.024 0.004 -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 0.017 0.032 -10000 0 -0.28 8 8
KAT2B 0.023 0.02 -10000 0 -0.58 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.018 0.03 -10000 0 -0.36 1 1
SIN3 complex 0.055 0.023 -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 0.016 0.26 4 -10000 0 4
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.022 0.007 -10000 0 -10000 0 0
YY1/HDAC3 0.021 0.048 -10000 0 -0.35 5 5
YY1/HDAC2 0.024 0.045 -10000 0 -0.24 13 13
YY1/HDAC1 0.024 0.047 -10000 0 -0.24 13 13
NuRD/MBD2 Complex (MeCP1) 0.024 0.055 -10000 0 -0.28 11 11
PPARG -0.059 0.16 -10000 0 -0.35 199 199
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) 0.03 0.038 -10000 0 -0.44 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 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.022 0.069 -10000 0 -0.35 15 15
HDAC1 0.024 0.004 -10000 0 -10000 0 0
HDAC3 0.018 0.029 -10000 0 -0.24 9 9
HDAC2 0.023 0.006 -10000 0 -10000 0 0
YY1 0.015 0.012 -10000 0 -0.29 1 1
HDAC8 0.024 0.001 -10000 0 -10000 0 0
SMAD7 0.023 0.005 -10000 0 -10000 0 0
NCOR2 0.024 0.003 -10000 0 -10000 0 0
MXD1 0.024 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 0.048 -10000 0 -0.26 6 6
YY1/SAP30/HDAC1 0.036 0.047 -10000 0 -0.25 6 6
EP300 0.023 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.016 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.032 -10000 0 -0.28 8 8
histone deacetylation 0.024 0.054 -10000 0 -0.28 11 11
STAT3 (dimer non-phopshorylated)/HDAC3 0.019 0.037 -10000 0 -0.31 3 3
nuclear export -0.041 0.019 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GATAD2B 0.02 0.009 -10000 0 -10000 0 0
GATAD2A 0.024 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.023 0.069 -10000 0 -0.34 22 22
GATA1/HDAC1 0.036 0.019 -10000 0 -10000 0 0
GATA1/HDAC3 0.031 0.043 -10000 0 -0.46 1 1
CHD4 0.023 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.033 0.053 -10000 0 -0.42 10 10
SIN3/HDAC complex/Mad/Max 0.015 0.054 -10000 0 -0.41 4 4
NuRD Complex 0.024 0.068 -10000 0 -0.36 11 11
positive regulation of chromatin silencing 0.049 0.042 -10000 0 -0.41 1 1
SIN3B 0.024 0.004 -10000 0 -10000 0 0
MTA2 0.024 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.004 -10000 0 -10000 0 0
XPO1 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC1 0.035 0.038 -10000 0 -0.24 3 3
HDAC complex 0.057 0.025 -10000 0 -0.34 1 1
GATA1/Fog1 0.033 0.025 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.045 0.015 -10000 0 -10000 0 0
TNF 0.023 0.07 0.26 21 -0.58 10 31
negative regulation of cell growth 0.015 0.054 -10000 0 -0.4 4 4
NuRD/MBD2/PRMT5 Complex 0.024 0.055 -10000 0 -0.28 11 11
Ran/GTP/Exportin 1 0.034 0.038 -10000 0 -0.24 3 3
NF kappa B/RelA/I kappa B alpha 0.017 0.054 -10000 0 -0.37 9 9
SIN3/HDAC complex/NCoR1 0.006 0.067 -10000 0 -0.32 25 25
TFCP2 0.024 0.002 -10000 0 -10000 0 0
NR2C1 0.024 0.003 -10000 0 -10000 0 0
MBD3 0.024 0.009 0.26 1 -10000 0 1
MBD2 0.023 0.005 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.023 0.005 -10000 0 -10000 0 0
SMAD2 -0.003 0.04 0.21 1 -0.3 2 3
SMAD3 0.021 0.025 -10000 0 -10000 0 0
SMAD3/SMAD4 0.037 0.063 -10000 0 -0.47 8 8
SMAD4/Ubc9/PIASy 0.043 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.041 0.06 -10000 0 -0.28 2 2
PPM1A 0.024 0.004 -10000 0 -10000 0 0
CALM1 0.024 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.008 0.045 -10000 0 -0.27 7 7
MAP3K1 0.023 0.02 -10000 0 -0.58 1 1
TRAP-1/SMAD4 0.029 0.048 -10000 0 -0.4 11 11
MAPK3 0.023 0.006 -10000 0 -10000 0 0
MAPK1 0.023 0.006 -10000 0 -10000 0 0
NUP214 0.024 0.004 -10000 0 -10000 0 0
CTDSP1 0.024 0.004 -10000 0 -10000 0 0
CTDSP2 0.024 0.003 -10000 0 -10000 0 0
CTDSPL 0.024 0.004 -10000 0 -10000 0 0
KPNB1 0.023 0.006 -10000 0 -10000 0 0
TGFBRAP1 0.018 0.061 -10000 0 -0.58 10 10
UBE2I 0.023 0.006 -10000 0 -10000 0 0
NUP153 0.024 0.004 -10000 0 -10000 0 0
KPNA2 0.036 0.058 0.26 58 -10000 0 58
PIAS4 0.024 0.004 -10000 0 -10000 0 0
Circadian rhythm 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
chromatin modification 0.043 0.037 0.37 2 -10000 0 2
CLOCK 0.021 0.051 -10000 0 -0.57 7 7
TIMELESS/CRY2 0.031 0.026 -10000 0 -10000 0 0
DEC1/BMAL1 0.032 0.013 -10000 0 -10000 0 0
ATR 0.024 0.004 -10000 0 -10000 0 0
NR1D1 0.015 0.016 -10000 0 -10000 0 0
ARNTL 0.025 0.005 -10000 0 -10000 0 0
TIMELESS 0.018 0.025 -10000 0 -10000 0 0
NPAS2 0.022 0.048 0.26 1 -0.57 6 7
CRY2 0.024 0.004 -10000 0 -10000 0 0
mol:CO -0.007 0.007 -10000 0 -0.095 6 6
CHEK1 0.028 0.039 0.26 25 -10000 0 25
mol:HEME 0.007 0.007 0.095 6 -10000 0 6
PER1 0.013 0.074 -10000 0 -0.58 15 15
BMAL/CLOCK/NPAS2 0.049 0.051 -10000 0 -0.36 13 13
BMAL1/CLOCK 0.018 0.062 -10000 0 -0.46 2 2
S phase of mitotic cell cycle 0.043 0.037 0.37 2 -10000 0 2
TIMELESS/CHEK1/ATR 0.043 0.037 -10000 0 -10000 0 0
mol:NADPH 0.007 0.007 0.095 6 -10000 0 6
PER1/TIMELESS 0.024 0.048 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.019 0.016 0.26 4 -10000 0 4
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.035 0.009 -10000 0 -10000 0 0
FBXW11 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.018 0.034 -10000 0 -0.37 6 6
NF kappa B1 p50/RelA/I kappa B alpha 0.025 0.045 -10000 0 -0.34 2 2
NFKBIA 0.014 0.039 -10000 0 -0.25 11 11
MAPK14 0.024 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.01 -10000 0 -10000 0 0
ARRB2 0.011 0.004 -10000 0 -10000 0 0
REL 0.019 0.058 -10000 0 -0.58 9 9
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.021 0.012 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.011 -10000 0 -10000 0 0
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.015 0.01 0.25 1 -10000 0 1
PIK3R1 0.02 0.047 -10000 0 -0.58 6 6
NFKB1 0.009 0.012 0.26 2 -10000 0 2
RELA 0.024 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.024 0.047 -10000 0 -0.26 9 9
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.024 0.048 -10000 0 -0.34 3 3
SRC 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.031 0.036 -10000 0 -0.36 7 7
NF kappa B1 p50/RelA 0.024 0.047 -10000 0 -0.27 9 9
IKBKB 0.02 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 0.024 0.055 -10000 0 -0.26 19 19
cell death 0.023 0.046 -10000 0 -0.32 3 3
NF kappa B1 p105/c-Rel 0.018 0.034 -10000 0 -0.37 6 6
LCK 0.025 0.078 0.26 34 -0.58 11 45
BCL3 0.024 0.008 0.26 1 -10000 0 1
Arf6 downstream 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
PLAUR 0.041 0.072 0.37 2 -10000 0 2
regulation of axonogenesis -0.011 0.026 0.24 3 -10000 0 3
myoblast fusion -0.026 0.048 -10000 0 -0.22 1 1
mol:GTP 0.023 0.032 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.054 0.045 -10000 0 -0.33 1 1
ARF1/GTP 0.03 0.029 -10000 0 -10000 0 0
mol:GM1 0.012 0.025 -10000 0 -10000 0 0
mol:Choline 0.009 0.035 -10000 0 -0.34 6 6
lamellipodium assembly 0.017 0.061 -10000 0 -0.36 8 8
MAPK3 0.032 0.047 0.2 8 -10000 0 8
ARF6/GTP/NME1/Tiam1 0.055 0.046 0.33 1 -10000 0 1
ARF1 0.02 0.009 -10000 0 -10000 0 0
ARF6/GDP 0.026 0.048 0.22 1 -10000 0 1
ARF1/GDP 0.024 0.049 -10000 0 -0.26 2 2
ARF6 0.032 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 0.032 0.047 0.2 6 -10000 0 6
actin filament bundle formation -0.032 0.051 0.25 4 -10000 0 4
KALRN 0.01 0.057 -10000 0 -0.31 19 19
RAB11FIP3/RAB11A 0.033 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.032 0.052 -10000 0 -0.25 4 4
NME1 0.027 0.03 0.26 14 -10000 0 14
Rac1/GDP 0.033 0.052 -10000 0 -0.26 4 4
substrate adhesion-dependent cell spreading 0.023 0.032 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.017 0.061 -10000 0 -0.36 8 8
RAC1 0.024 0.004 -10000 0 -10000 0 0
liver development 0.023 0.032 -10000 0 -10000 0 0
ARF6/GTP 0.023 0.032 -10000 0 -10000 0 0
RhoA/GTP 0.034 0.029 -10000 0 -10000 0 0
mol:GDP 0.02 0.049 0.22 2 -0.22 1 3
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.03 -10000 0 -10000 0 0
RHOA 0.023 0.005 -10000 0 -10000 0 0
PLD1 0.018 0.042 -10000 0 -0.4 6 6
RAB11FIP3 0.023 0.006 -10000 0 -10000 0 0
tube morphogenesis 0.017 0.061 -10000 0 -0.36 8 8
ruffle organization 0.011 0.026 -10000 0 -0.24 3 3
regulation of epithelial cell migration 0.023 0.032 -10000 0 -10000 0 0
PLD2 0.02 0.025 -10000 0 -10000 0 0
PIP5K1A 0.011 0.027 -10000 0 -0.24 3 3
mol:Phosphatidic acid 0.009 0.035 -10000 0 -0.34 6 6
Rac1/GTP 0.017 0.062 -10000 0 -0.36 8 8
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 0.022 0.009 -10000 0 -10000 0 0
DOCK1 0.024 0.004 -10000 0 -10000 0 0
ITGA4 0.026 0.023 0.26 9 -10000 0 9
RAC1 0.024 0.004 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.04 0.039 0.37 3 -0.43 2 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.048 0.018 -10000 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.043 0.035 0.34 3 -0.34 2 5
lamellipodium assembly -0.001 0.083 -10000 0 -0.41 26 26
PIK3CA 0.023 0.005 -10000 0 -10000 0 0
PI3K 0.031 0.036 -10000 0 -0.36 7 7
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 0.02 0.047 -10000 0 -0.58 6 6
ARF6/GTP 0.046 0.021 -10000 0 -10000 0 0
cell adhesion 0.049 0.019 -10000 0 -10000 0 0
CRKL/CBL 0.032 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.039 0.017 -10000 0 -10000 0 0
ITGB1 0.024 0.004 -10000 0 -10000 0 0
ITGB7 0.029 0.046 0.26 24 -0.58 2 26
ARF6/GDP 0.022 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.048 0.044 -10000 0 -0.32 10 10
p130Cas/Crk/Dock1 0.04 0.019 -10000 0 -10000 0 0
VCAM1 0.019 0.064 0.26 6 -0.58 10 16
alpha4/beta1 Integrin/Paxillin/Talin 0.051 0.02 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.048 0.022 -10000 0 -10000 0 0
BCAR1 0.021 0.008 -10000 0 -10000 0 0
mol:GDP -0.047 0.021 -10000 0 -10000 0 0
CBL 0.022 0.007 -10000 0 -10000 0 0
PRKACA 0.024 0.003 -10000 0 -10000 0 0
GIT1 0.023 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.051 0.02 -10000 0 -10000 0 0
Rac1/GTP -0.003 0.091 -10000 0 -0.45 26 26
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.026 0.048 -10000 0 -0.18 4 4
AP2 0.034 0.008 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.03 0.01 -10000 0 -10000 0 0
CLTB 0.025 0.018 0.26 5 -10000 0 5
coatomer protein complex/ARF1/GTP/ER cargo protein 0.014 0.01 -10000 0 -10000 0 0
CD4 0.023 0.005 -10000 0 -10000 0 0
CLTA 0.024 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.006 0.006 0.14 2 -10000 0 2
mol:PI-4-5-P2 0.007 0.016 -10000 0 -10000 0 0
ARF1/GTP 0.024 0.015 -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 0.021 0.011 -10000 0 -10000 0 0
DDEF1 0.006 0.016 -10000 0 -10000 0 0
ARF1/GDP 0 0.02 -10000 0 -10000 0 0
AP2M1 0.024 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.01 0.006 -10000 0 -10000 0 0
Rac/GTP 0.021 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.026 0.017 -10000 0 -10000 0 0
ARFIP2 0.014 0.018 -10000 0 -10000 0 0
COPA 0.02 0.009 -10000 0 -10000 0 0
RAC1 0.024 0.004 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.024 -10000 0 -0.2 3 3
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 0.041 -10000 0 -0.24 19 19
AP2A1 0.024 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.009 0.025 -10000 0 -0.22 5 5
ARF1/GDP/Membrin 0.012 0.049 -10000 0 -0.26 27 27
Arfaptin 2/Rac/GDP 0.028 0.011 -10000 0 -10000 0 0
CYTH2 0.029 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.015 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.003 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.019 0.024 -10000 0 -10000 0 0
PLD2 0.007 0.016 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.006 0.006 0.14 2 -10000 0 2
PIP5K1A 0.007 0.016 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.013 0.021 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.016 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.006 0.006 0.14 2 -10000 0 2
GOSR2 0.008 0.027 -10000 0 -0.31 6 6
USO1 0.009 0.023 -10000 0 -0.32 4 4
GBF1 0.01 0.021 -10000 0 -0.31 3 3
ARF1/GTP/Arfaptin 2 0.027 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
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.011 -10000 0 -0.27 1 1
MDM2/SUMO1 0.032 0.04 -10000 0 -0.24 3 3
HDAC4 0.023 0.02 -10000 0 -0.58 1 1
Ran/GTP/Exportin 1/HDAC1 -0.008 0.007 -10000 0 -10000 0 0
SUMO1 0.024 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.008 0.018 -10000 0 -0.22 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.006 0.012 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.024 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.024 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.034 0.04 -10000 0 -0.24 4 4
SUMO1/HDAC1 0.035 0.038 -10000 0 -0.24 3 3
RANGAP1 0.023 0.006 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.056 0.02 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.011 0.004 -10000 0 -10000 0 0
Ran/GTP 0.022 0.036 -10000 0 -0.24 3 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.023 0.005 -10000 0 -10000 0 0
UBE2I 0.023 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.021 0.038 0.25 1 -0.24 3 4
NPC 0.014 0.002 -10000 0 -10000 0 0
PIAS2 0.023 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
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 0.067 0.025 -10000 0 -9999 0 0
NFKB1 0.024 0.004 -10000 0 -9999 0 0
MAP3K14 0.023 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 9 -9999 0 9
NFKB2 0.024 0.008 0.26 1 -9999 0 1
NF kappa B2 p52/RelB 0.033 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 971 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.PE.A5DE TCGA.PE.A5DD TCGA.PE.A5DC TCGA.OL.A66K
109_MAP3K5 0.096 0.025 0.059 0.025
47_PPARGC1A 0.024 0.024 -0.58 0.024
105_BMP4 0.024 0.024 0.024 0.024
105_BMP6 0.024 0.024 0.024 0.024
105_BMP7 0.024 0.024 0.024 0.024
105_BMP2 0.024 0.024 0.024 0.024
131_RELN/VLDLR -0.34 -0.34 -0.34 -0.34
30_TGFB1/TGF beta receptor Type II 0.024 0.024 0.024 0.024
84_STAT5B -0.091 -0.062 -0.065 -0.091
84_STAT5A -0.091 -0.062 -0.065 -0.091
Methods & Data
Input

  • Expression Data Normalization = Normal controls were used to median center the expression data used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA-TP/4397369/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/BRCA-TP/4464445/GDAC_Gistic2Report_4467984/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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