PARADIGM pathway analysis of mRNA expression data
Glioblastoma Multiforme (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1416W88
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNA expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1416W88
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 61 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 278
Glypican 2 network 224
RXR and RAR heterodimerization with other nuclear receptor 167
Endothelins 165
HIF-1-alpha transcription factor network 143
TCGA08_retinoblastoma 141
Osteopontin-mediated events 134
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 129
Thromboxane A2 receptor signaling 127
Syndecan-1-mediated signaling events 119
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 528 . 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 ( 528 ).

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 0.5265 278 14184 51 -0.047 0.88 1000 -1000 -0.17 -1000
Glypican 2 network 0.4242 224 897 4 -0.006 0 1000 -1000 -0.013 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.3163 167 8699 52 -0.027 0.15 1000 -1000 -0.03 -1000
Endothelins 0.3125 165 15887 96 -0.42 0.17 1000 -1000 -0.037 -1000
HIF-1-alpha transcription factor network 0.2708 143 10935 76 -0.019 0.36 1000 -1000 -0.067 -1000
TCGA08_retinoblastoma 0.2670 141 1129 8 -0.019 0.008 1000 -1000 -0.015 -1000
Osteopontin-mediated events 0.2538 134 5121 38 -0.014 0.11 1000 -1000 -0.026 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2443 129 8836 68 -0.44 0.32 1000 -1000 -0.065 -1000
Thromboxane A2 receptor signaling 0.2405 127 13380 105 -0.1 0.2 1000 -1000 -0.037 -1000
Syndecan-1-mediated signaling events 0.2254 119 4075 34 -0.017 0.085 1000 -1000 -0.02 -1000
LPA receptor mediated events 0.2197 116 11914 102 -0.03 0.15 1000 -1000 -0.042 -1000
Ras signaling in the CD4+ TCR pathway 0.2083 110 1885 17 -0.008 0.041 1000 -1000 -0.019 -1000
FoxO family signaling 0.2064 109 6991 64 -0.068 0.24 1000 -1000 -0.051 -1000
Effects of Botulinum toxin 0.1970 104 2711 26 -0.021 0 1000 -1000 -0.018 -1000
PLK2 and PLK4 events 0.1951 103 310 3 -0.014 -0.012 1000 -1000 -0.015 -1000
EGFR-dependent Endothelin signaling events 0.1818 96 2029 21 -0.014 0.025 1000 -1000 -0.02 -1000
HIF-2-alpha transcription factor network 0.1780 94 4084 43 -0.034 0.18 1000 -1000 -0.033 -1000
PDGFR-alpha signaling pathway 0.1572 83 3668 44 -0.02 0.051 1000 -1000 -0.023 -1000
Nongenotropic Androgen signaling 0.1534 81 4221 52 -0.13 0.046 1000 -1000 -0.021 -1000
BARD1 signaling events 0.1439 76 4355 57 -0.02 0.062 1000 -1000 -0.021 -1000
Noncanonical Wnt signaling pathway 0.1345 71 1856 26 -0.014 0.013 1000 -1000 -0.026 -1000
PLK1 signaling events 0.1345 71 6087 85 -0.014 0.059 1000 -1000 -0.017 -1000
IL2 signaling events mediated by PI3K 0.1307 69 4057 58 -0.014 0.066 1000 -1000 -0.036 -1000
Reelin signaling pathway 0.1231 65 3680 56 -0.051 0 1000 -1000 -0.025 -1000
Regulation of nuclear SMAD2/3 signaling 0.1212 64 8763 136 -0.13 0.13 1000 -1000 -0.023 -1000
IL6-mediated signaling events 0.1212 64 4860 75 -0.031 0.26 1000 -1000 -0.06 -1000
Syndecan-4-mediated signaling events 0.1136 60 4053 67 -0.017 0.023 1000 -1000 -0.019 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1117 59 5223 88 -0.047 0.18 1000 -1000 -0.048 -1000
S1P5 pathway 0.1080 57 978 17 -0.062 0.061 1000 -1000 -0.014 -1000
Plasma membrane estrogen receptor signaling 0.1080 57 4916 86 -0.47 0.076 1000 -1000 -0.025 -1000
PDGFR-beta signaling pathway 0.1004 53 5162 97 -0.03 0.077 1000 -1000 -0.028 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0985 52 1960 37 -0.023 0.055 1000 -1000 -0.02 -1000
IFN-gamma pathway 0.0947 50 3467 68 -0.1 0.02 1000 -1000 -0.033 -1000
Class I PI3K signaling events 0.0947 50 3682 73 -0.02 0.027 1000 -1000 -0.017 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0909 48 2618 54 -0.023 0 1000 -1000 -0.021 -1000
IL23-mediated signaling events 0.0909 48 2905 60 -0.02 0.11 1000 -1000 -0.11 -1000
Integrins in angiogenesis 0.0890 47 4019 84 -0.027 0.041 1000 -1000 -0.025 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0871 46 3593 78 -0.087 0.039 1000 -1000 -0.041 -1000
Aurora B signaling 0.0871 46 3088 67 -0.015 0.006 1000 -1000 -0.019 -1000
p75(NTR)-mediated signaling 0.0833 44 5512 125 -0.035 0.009 1000 -1000 -0.026 -1000
Canonical Wnt signaling pathway 0.0833 44 2274 51 -0.088 0.09 1000 -1000 -0.025 -1000
Circadian rhythm pathway 0.0814 43 957 22 -0.017 0.048 1000 -1000 -0.036 -1000
Signaling events mediated by HDAC Class I 0.0795 42 4462 104 -0.018 0.021 1000 -1000 -0.02 -1000
TCGA08_rtk_signaling 0.0795 42 1111 26 -0.014 0.024 1000 -1000 -0.018 -1000
Regulation of Telomerase 0.0795 42 4347 102 -0.026 0.07 1000 -1000 -0.051 -1000
Wnt signaling 0.0777 41 288 7 -0.014 -0.006 1000 -1000 -0.014 -1000
S1P4 pathway 0.0758 40 1008 25 -0.062 0 1000 -1000 -0.015 -1000
Presenilin action in Notch and Wnt signaling 0.0701 37 2315 61 -0.043 0.084 1000 -1000 -0.022 -1000
p38 MAPK signaling pathway 0.0701 37 1640 44 -0.019 0.003 1000 -1000 -0.018 -1000
Glypican 1 network 0.0682 36 1770 48 -0.02 0.014 1000 -1000 -0.017 -1000
BCR signaling pathway 0.0644 34 3389 99 -0.025 0.034 1000 -1000 -0.025 -1000
Arf6 downstream pathway 0.0625 33 1439 43 -0.017 0.022 1000 -1000 -0.019 -1000
amb2 Integrin signaling 0.0625 33 2772 82 -0.017 0.028 1000 -1000 -0.027 -1000
E-cadherin signaling in the nascent adherens junction 0.0625 33 2521 76 -0.028 0.022 1000 -1000 -0.027 -1000
Fc-epsilon receptor I signaling in mast cells 0.0606 32 3194 97 -0.02 0.028 1000 -1000 -0.039 -1000
IL12-mediated signaling events 0.0587 31 2720 87 -0.09 0.062 1000 -1000 -0.095 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0568 30 864 28 -0.017 0 1000 -1000 -0.015 -1000
IL1-mediated signaling events 0.0549 29 1817 62 -0.036 0.009 1000 -1000 -0.026 -1000
Insulin-mediated glucose transport 0.0530 28 916 32 -0.048 0 1000 -1000 -0.015 -1000
FAS signaling pathway (CD95) 0.0530 28 1327 47 -0.019 0.032 1000 -1000 -0.019 -1000
VEGFR1 specific signals 0.0511 27 1527 56 -0.029 0 1000 -1000 -0.023 -1000
Aurora A signaling 0.0492 26 1596 60 -0.021 0.027 1000 -1000 -0.017 -1000
Visual signal transduction: Cones 0.0473 25 955 38 -0.022 0.022 1000 -1000 -0.02 -1000
Ceramide signaling pathway 0.0473 25 1952 76 -0.022 0.017 1000 -1000 -0.018 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0473 25 1919 74 -0.18 0.021 1000 -1000 -0.032 -1000
E-cadherin signaling in keratinocytes 0.0473 25 1082 43 -0.021 0.018 1000 -1000 -0.018 -1000
ErbB2/ErbB3 signaling events 0.0455 24 1601 65 -0.027 0.052 1000 -1000 -0.043 -1000
IL4-mediated signaling events 0.0455 24 2209 91 -0.079 0.12 1000 -1000 -0.2 -1000
Ephrin B reverse signaling 0.0455 24 1190 48 -0.017 0.013 1000 -1000 -0.02 -1000
S1P1 pathway 0.0455 24 878 36 -0.066 0.045 1000 -1000 -0.026 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0436 23 532 23 -0.022 -0.002 1000 -1000 -0.017 -1000
Signaling mediated by p38-alpha and p38-beta 0.0436 23 1047 44 -0.02 0.001 1000 -1000 -0.018 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0436 23 1078 45 -0.034 0.008 1000 -1000 -0.027 -1000
Regulation of p38-alpha and p38-beta 0.0436 23 1246 54 -0.029 0 1000 -1000 -0.02 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0436 23 2789 120 -0.062 0.059 1000 -1000 -0.029 -1000
Syndecan-3-mediated signaling events 0.0398 21 762 35 -0.025 0 1000 -1000 -0.021 -1000
Arf6 signaling events 0.0379 20 1265 62 -0.024 0.005 1000 -1000 -0.019 -1000
TRAIL signaling pathway 0.0379 20 970 48 -0.024 0.002 1000 -1000 -0.021 -1000
Caspase cascade in apoptosis 0.0322 17 1298 74 -0.019 0.014 1000 -1000 -0.021 -1000
Syndecan-2-mediated signaling events 0.0322 17 1220 69 -0.024 0 1000 -1000 -0.02 -1000
TCGA08_p53 0.0322 17 120 7 -0.014 0.002 1000 -1000 -0.014 -1000
Paxillin-dependent events mediated by a4b1 0.0322 17 617 36 -0.029 0.027 1000 -1000 -0.022 -1000
IL2 signaling events mediated by STAT5 0.0322 17 390 22 -0.02 0.008 1000 -1000 -0.026 -1000
Signaling events mediated by PRL 0.0322 17 582 34 -0.018 0.011 1000 -1000 -0.02 -1000
BMP receptor signaling 0.0303 16 1351 81 -0.027 0.008 1000 -1000 -0.026 -1000
Glucocorticoid receptor regulatory network 0.0303 16 1901 114 -0.087 0.1 1000 -1000 -0.05 -1000
TCR signaling in naïve CD8+ T cells 0.0303 16 1550 93 -0.061 0.003 1000 -1000 -0.026 -1000
EPHB forward signaling 0.0303 16 1404 85 -0.038 0.033 1000 -1000 -0.027 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0303 16 2051 125 -0.024 0.037 1000 -1000 -0.033 -1000
Signaling events mediated by PTP1B 0.0284 15 1179 76 -0.02 0.038 1000 -1000 -0.029 -1000
ceramide signaling pathway 0.0284 15 773 49 -0.017 0.016 1000 -1000 -0.017 -1000
Retinoic acid receptors-mediated signaling 0.0284 15 889 58 -0.03 0.012 1000 -1000 -0.031 -1000
S1P3 pathway 0.0284 15 648 42 -0.065 0.001 1000 -1000 -0.023 -1000
Canonical NF-kappaB pathway 0.0246 13 536 39 -0.029 0 1000 -1000 -0.024 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0227 12 429 34 -0.022 0 1000 -1000 -0.016 -1000
Signaling events mediated by the Hedgehog family 0.0227 12 664 52 -0.025 0.016 1000 -1000 -0.021 -1000
Aurora C signaling 0.0227 12 87 7 -0.017 0 1000 -1000 -0.015 -1000
Signaling mediated by p38-gamma and p38-delta 0.0227 12 192 15 -0.034 0 1000 -1000 -0.017 -1000
Atypical NF-kappaB pathway 0.0227 12 379 31 -0.02 0 1000 -1000 -0.018 -1000
Cellular roles of Anthrax toxin 0.0208 11 433 39 -0.017 0.007 1000 -1000 -0.014 -1000
Nectin adhesion pathway 0.0208 11 722 63 -0.031 0.01 1000 -1000 -0.03 -1000
Calcium signaling in the CD4+ TCR pathway 0.0208 11 365 31 -0.059 0 1000 -1000 -0.028 -1000
Arf6 trafficking events 0.0208 11 801 71 -0.016 0.011 1000 -1000 -0.015 -1000
Hedgehog signaling events mediated by Gli proteins 0.0189 10 698 65 -0.042 0.008 1000 -1000 -0.031 -1000
EPO signaling pathway 0.0189 10 565 55 -0.033 0 1000 -1000 -0.02 -1000
Signaling events mediated by HDAC Class III 0.0189 10 439 40 -0.022 0.021 1000 -1000 -0.018 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0189 10 908 83 -0.068 0.066 1000 -1000 -0.022 -1000
IGF1 pathway 0.0189 10 626 57 -0.031 0.024 1000 -1000 -0.021 -1000
E-cadherin signaling events 0.0189 10 51 5 -0.02 -0.014 1000 -1000 -0.017 -1000
JNK signaling in the CD4+ TCR pathway 0.0170 9 161 17 -0.022 0.001 1000 -1000 -0.02 -1000
Class I PI3K signaling events mediated by Akt 0.0133 7 510 68 -0.043 0.03 1000 -1000 -0.02 -1000
Signaling events mediated by HDAC Class II 0.0114 6 500 75 -0.023 0.013 1000 -1000 -0.021 -1000
ErbB4 signaling events 0.0114 6 477 69 -0.024 0.016 1000 -1000 -0.029 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0114 6 557 85 -0.02 0.011 1000 -1000 -0.028 -1000
Signaling events regulated by Ret tyrosine kinase 0.0114 6 561 82 -0.029 0 1000 -1000 -0.023 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0114 6 225 33 -0.022 0 1000 -1000 -0.019 -1000
Regulation of Androgen receptor activity 0.0114 6 421 70 -0.033 0.002 1000 -1000 -0.031 -1000
FOXA2 and FOXA3 transcription factor networks 0.0095 5 230 46 -0.028 0 1000 -1000 -0.083 -1000
mTOR signaling pathway 0.0095 5 304 53 -0.022 0.029 1000 -1000 -0.024 -1000
IL27-mediated signaling events 0.0095 5 300 51 -0.043 0.009 1000 -1000 -0.04 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0076 4 110 27 -0.023 0 1000 -1000 -0.019 -1000
a4b1 and a4b7 Integrin signaling 0.0057 3 17 5 -0.017 -0.014 1000 -1000 -0.016 -1000
Insulin Pathway 0.0057 3 278 74 -0.032 0.014 1000 -1000 -0.023 -1000
LPA4-mediated signaling events 0.0019 1 12 12 -0.014 0 1000 -1000 -0.012 -1000
Coregulation of Androgen receptor activity 0.0019 1 112 76 -0.024 0.003 1000 -1000 -0.031 -1000
Rapid glucocorticoid signaling 0.0019 1 25 20 -0.014 0.002 1000 -1000 -0.014 -1000
Visual signal transduction: Rods 0.0019 1 57 52 -0.03 0 1000 -1000 -0.022 -1000
Arf1 pathway 0.0019 1 84 54 -0.017 0.006 1000 -1000 -0.014 -1000
Alternative NF-kappaB pathway 0.0019 1 18 13 -0.027 0 1000 -1000 -0.022 -1000
Ephrin A reverse signaling 0.0000 0 0 7 -0.017 0 1000 -1000 -0.014 -1000
Class IB PI3K non-lipid kinase events 0.0000 0 0 3 -0.014 -1000 1000 -1000 -0.013 -1000
Total NA 5362 300346 7203 -5.6 -990 131000 -131000 -3.8 -131000
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.68 0.48 1 333 -10000 0 333
PLK1 0.24 0.23 0.47 220 -10000 0 220
BIRC5 0.32 0.3 0.62 244 -10000 0 244
HSPA1B 0.68 0.48 1 334 -10000 0 334
MAP2K1 0.18 0.15 0.26 366 -10000 0 366
BRCA2 0.68 0.48 1 333 -10000 0 333
FOXM1 0.88 0.7 1.3 333 -10000 0 333
XRCC1 0.68 0.48 1 333 -10000 0 333
FOXM1B/p19 0.2 0.31 0.71 119 -10000 0 119
Cyclin D1/CDK4 0.12 0.28 0.75 72 -10000 0 72
CDC2 0.83 0.64 1.2 333 -10000 0 333
TGFA 0.62 0.43 0.9 336 -10000 0 336
SKP2 0.68 0.48 1 333 -10000 0 333
CCNE1 0.042 0.036 0.063 350 -10000 0 350
CKS1B 0.73 0.54 1.1 335 -10000 0 335
RB1 0.012 0.053 0.23 17 -10000 0 17
FOXM1C/SP1 0.38 0.42 0.85 215 -10000 0 215
AURKB 0.24 0.24 0.49 208 -10000 0 208
CENPF 0.74 0.55 1.1 336 -10000 0 336
CDK4 0.015 0.038 0.091 79 -10000 0 79
MYC 0.56 0.47 0.93 299 -10000 0 299
CHEK2 0.18 0.15 0.26 373 -10000 0 373
ONECUT1 0.65 0.45 0.94 336 -10000 0 336
CDKN2A -0.047 0.073 -10000 0 -0.13 166 166
LAMA4 0.68 0.48 1 332 -10000 0 332
FOXM1B/HNF6 0.65 0.46 0.95 334 -10000 0 334
FOS 0.71 0.5 1 332 -10000 0 332
SP1 -0.01 0.012 0.007 137 -10000 0 137
CDC25B 0.68 0.49 1 333 -10000 0 333
response to radiation 0.15 0.12 0.2 384 -10000 0 384
CENPB 0.68 0.49 1 333 -10000 0 333
CENPA 0.72 0.53 1.1 333 -10000 0 333
NEK2 0.69 0.5 1 333 -10000 0 333
HIST1H2BA 0.68 0.48 1 334 -10000 0 334
CCNA2 0.021 0.028 0.049 217 -10000 0 217
EP300 -0.014 0 -10000 0 -10000 0 0
CCNB1/CDK1 0.81 0.61 1.2 325 -10000 0 325
CCNB2 0.79 0.57 1.1 343 -10000 0 343
CCNB1 0.84 0.64 1.2 333 -10000 0 333
ETV5 0.68 0.48 1 333 -10000 0 333
ESR1 0.68 0.48 1 333 -10000 0 333
CCND1 0.66 0.48 0.97 335 -10000 0 335
GSK3A 0.16 0.12 0.21 384 -10000 0 384
Cyclin A-E1/CDK1-2 0.12 0.11 0.19 326 -10000 0 326
CDK2 0.039 0.035 0.059 347 -10000 0 347
G2/M transition of mitotic cell cycle 0.18 0.14 0.24 373 -10000 0 373
FOXM1B/Cbp/p300 0.059 0.14 0.47 14 -10000 0 14
GAS1 0.7 0.5 1 333 -10000 0 333
MMP2 0.76 0.54 1.1 334 -10000 0 334
RB1/FOXM1C 0.45 0.42 0.82 266 -10000 0 266
CREBBP -0.014 0 -10000 0 -10000 0 0
Glypican 2 network

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
MDK -0.006 0.007 0 299 -9999 0 299
GPC2 0 0 -9999 0 -9999 0 0
GPC2/Midkine -0.004 0.004 0 299 -9999 0 299
neuron projection morphogenesis -0.004 0.004 0 299 -9999 0 299
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.003 0.01 0.17 1 -9999 0 1
VDR -0.014 0 -10000 0 -9999 0 0
FAM120B 0 0 -10000 0 -9999 0 0
RXRs/LXRs/DNA/9cRA 0.12 0.083 0.17 378 -9999 0 378
RXRs/LXRs/DNA/Oxysterols 0.15 0.1 0.21 378 -9999 0 378
MED1 -0.014 0 -10000 0 -9999 0 0
mol:9cRA 0.027 0.018 0.039 381 -9999 0 381
RARs/THRs/DNA/Src-1 -0.011 0.002 -10000 0 -9999 0 0
RXRs/NUR77 0.076 0.066 0.12 378 -9999 0 378
RXRs/PPAR 0.035 0.031 0.054 381 -9999 0 381
NCOR2 -0.014 0 -10000 0 -9999 0 0
VDR/VDR/Vit D3 -0.009 0 -10000 0 -9999 0 0
RARs/VDR/DNA/Vit D3 -0.022 0 -10000 0 -9999 0 0
RARA -0.014 0 -10000 0 -9999 0 0
NCOA1 -0.014 0.002 0 14 -9999 0 14
VDR/VDR/DNA -0.014 0 -10000 0 -9999 0 0
RARs/RARs/DNA/9cRA 0.022 0.025 0.037 381 -9999 0 381
RARG -0.014 0 -10000 0 -9999 0 0
RPS6KB1 -0.004 0.014 0.26 1 -9999 0 1
RARs/THRs/DNA/SMRT -0.011 0 -10000 0 -9999 0 0
THRA -0.014 0 -10000 0 -9999 0 0
mol:Bile acids 0 0 -10000 0 -9999 0 0
VDR/Vit D3/DNA -0.009 0 -10000 0 -9999 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.11 0.092 0.17 352 -9999 0 352
NR1H4 -0.014 0 -10000 0 -9999 0 0
RXRs/LXRs/DNA 0.12 0.099 0.19 380 -9999 0 380
NR1H2 0.029 0.028 0.046 381 -9999 0 381
NR1H3 0.03 0.028 0.048 379 -9999 0 379
RXRs/VDR/DNA/Vit D3 0.07 0.061 0.11 378 -9999 0 378
NR4A1 -0.014 0 -10000 0 -9999 0 0
mol:ATRA 0 0 -10000 0 -9999 0 0
RXRs/FXR/9cRA/MED1 0.049 0.037 0.072 381 -9999 0 381
RXRG 0.028 0.028 0.045 378 -9999 0 378
RXR alpha/CCPG 0.021 0.019 0.033 381 -9999 0 381
RXRA 0.028 0.028 0.045 381 -9999 0 381
RXRB 0.029 0.029 0.047 381 -9999 0 381
THRB -0.014 0 -10000 0 -9999 0 0
PPARG -0.014 0.001 0 5 -9999 0 5
PPARD -0.014 0 -10000 0 -9999 0 0
TNF 0.14 0.098 0.2 379 -9999 0 379
mol:Oxysterols 0.026 0.017 0.037 381 -9999 0 381
cholesterol transport 0.15 0.1 0.21 378 -9999 0 378
PPARA -0.014 0 -10000 0 -9999 0 0
mol:Vit D3 0 0 -10000 0 -9999 0 0
RARB -0.014 0 -10000 0 -9999 0 0
RXRs/NUR77/BCL2 0.017 0.018 0.028 378 -9999 0 378
SREBF1 0.14 0.097 0.2 381 -9999 0 381
RXRs/RXRs/DNA/9cRA 0.11 0.092 0.17 352 -9999 0 352
ABCA1 -0.004 0.015 0.2 2 -9999 0 2
RARs/THRs -0.027 0 -10000 0 -9999 0 0
RXRs/FXR 0.076 0.066 0.12 378 -9999 0 378
BCL2 -0.014 0 -10000 0 -9999 0 0
Endothelins

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
AKT1 0.15 0.13 0.23 357 -10000 0 357
PTK2B -0.014 0.002 0.013 4 -10000 0 4
mol:Ca2+ 0.097 0.076 0.5 4 -10000 0 4
EDN1 0.08 0.077 0.13 354 -10000 0 354
EDN3 -0.014 0.001 0 4 -10000 0 4
EDN2 -0.014 0.001 0 1 -10000 0 1
HRAS/GDP 0.13 0.096 0.2 275 -0.18 2 277
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.068 0.08 0.16 192 -0.1 1 193
ADCY4 0.06 0.087 0.15 232 -10000 0 232
ADCY5 0.06 0.087 0.15 232 -10000 0 232
ADCY6 0.14 0.1 0.19 389 -10000 0 389
ADCY7 0.14 0.1 0.19 384 -10000 0 384
ADCY1 0.14 0.1 0.19 389 -10000 0 389
ADCY2 0.14 0.1 0.19 389 -10000 0 389
ADCY3 0.06 0.087 0.15 232 -10000 0 232
ADCY8 0.14 0.1 0.19 383 -10000 0 383
ADCY9 0.14 0.1 0.19 389 -10000 0 389
arachidonic acid secretion 0.13 0.13 0.33 127 -0.34 2 129
ETB receptor/Endothelin-1/Gq/GTP 0.066 0.065 0.12 264 -10000 0 264
GNAO1 -0.001 0.004 0 481 -10000 0 481
HRAS -0.008 0.012 0.013 127 -10000 0 127
ETA receptor/Endothelin-1/G12/GTP -0.003 0.026 0.15 10 -10000 0 10
ETA receptor/Endothelin-1/Gs/GTP -0.003 0.025 0.14 11 -10000 0 11
mol:GTP 0.004 0.007 0.016 125 -10000 0 125
COL3A1 -0.002 0.032 0.14 14 -10000 0 14
EDNRB 0.039 0.054 0.098 236 -10000 0 236
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0.15 0.13 0.23 361 -10000 0 361
CYSLTR1 0.13 0.13 0.22 322 -10000 0 322
SLC9A1 -0.002 0.014 0.079 11 -0.058 1 12
mol:GDP 0.13 0.099 0.21 265 -0.2 1 266
SLC9A3 0.099 0.11 0.33 6 -0.35 10 16
RAF1 0.13 0.12 0.3 130 -0.32 2 132
JUN 0.096 0.074 0.46 4 -10000 0 4
JAK2 0.15 0.13 0.23 361 -10000 0 361
mol:IP3 0.072 0.091 0.18 185 -10000 0 185
ETA receptor/Endothelin-1 -0.005 0.03 0.16 11 -10000 0 11
PLCB1 -0.007 0.013 0.018 124 -10000 0 124
PLCB2 -0.005 0.015 0.022 125 -10000 0 125
ETA receptor/Endothelin-3 0.033 0.053 0.09 225 -10000 0 225
FOS 0.14 0.16 0.4 125 -0.64 2 127
Gai/GDP -0.42 0.16 -10000 0 -0.46 480 480
CRK -0.014 0.002 0.013 4 -10000 0 4
mol:Ca ++ 0.17 0.14 0.27 301 -10000 0 301
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 0.004 0.024 0.15 12 -10000 0 12
GNAQ -0.006 0.016 0.023 125 -10000 0 125
GNAZ -0.012 0.005 0 72 -10000 0 72
GNAL -0.014 0 -10000 0 -10000 0 0
Gs family/GDP 0.11 0.084 0.18 250 -0.19 1 251
ETA receptor/Endothelin-1/Gq/GTP 0.054 0.075 0.16 142 -10000 0 142
MAPK14 0.058 0.058 0.11 279 -0.13 1 280
TRPC6 0.098 0.076 0.5 4 -10000 0 4
GNAI2 -0.014 0.001 0 1 -10000 0 1
GNAI3 -0.012 0.005 0 65 -10000 0 65
GNAI1 -0.012 0.005 0 81 -10000 0 81
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.065 0.064 0.12 258 -10000 0 258
ETB receptor/Endothelin-2 0.029 0.044 0.077 236 -10000 0 236
ETB receptor/Endothelin-3 0.029 0.044 0.077 234 -10000 0 234
ETB receptor/Endothelin-1 0.015 0.04 0.078 129 -10000 0 129
MAPK3 0.14 0.15 0.38 125 -0.62 2 127
MAPK1 0.13 0.16 0.38 125 -0.62 2 127
Rac1/GDP 0.13 0.093 0.2 265 -0.2 1 266
cAMP biosynthetic process 0.13 0.092 0.18 374 -10000 0 374
MAPK8 0.1 0.077 0.42 5 -10000 0 5
SRC -0.014 0.002 0.012 4 -10000 0 4
ETB receptor/Endothelin-1/Gi/GTP 0.004 0.019 0.11 14 -10000 0 14
p130Cas/CRK/Src/PYK2 0.12 0.093 0.26 93 -10000 0 93
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.13 0.093 0.2 264 -0.18 2 266
COL1A2 0.022 0.056 0.12 122 -10000 0 122
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.033 0.053 0.09 226 -10000 0 226
mol:DAG 0.073 0.091 0.18 185 -10000 0 185
MAP2K2 0.13 0.14 0.35 125 -0.47 2 127
MAP2K1 0.13 0.14 0.35 125 -0.47 2 127
EDNRA 0.046 0.069 0.12 232 -10000 0 232
positive regulation of muscle contraction 0.11 0.11 0.19 317 -10000 0 317
Gq family/GDP 0.015 0.03 0.13 13 -0.16 2 15
HRAS/GTP 0.12 0.1 0.2 273 -0.19 2 275
PRKCH 0.093 0.088 0.17 254 -10000 0 254
RAC1 -0.014 0 -10000 0 -10000 0 0
PRKCA 0.092 0.088 0.17 254 -10000 0 254
PRKCB 0.097 0.089 0.18 261 -0.12 1 262
PRKCE 0.092 0.087 0.17 254 -10000 0 254
PRKCD 0.093 0.089 0.17 254 -0.12 1 255
PRKCG 0.093 0.089 0.17 254 -10000 0 254
regulation of vascular smooth muscle contraction 0.14 0.17 0.41 114 -0.81 2 116
PRKCQ 0.093 0.088 0.17 254 -10000 0 254
PLA2G4A 0.13 0.13 0.33 127 -0.37 2 129
GNA14 -0.005 0.016 0.023 125 -10000 0 125
GNA15 -0.007 0.014 0.018 122 -10000 0 122
GNA12 -0.014 0.001 0 4 -10000 0 4
GNA11 -0.007 0.014 0.018 125 -10000 0 125
Rac1/GTP -0.003 0.027 0.15 11 -10000 0 11
MMP1 0.001 0.013 0.2 1 -0.058 9 10
HIF-1-alpha transcription factor network

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
PKM2 0.23 0.37 0.64 213 -10000 0 213
HDAC7 -0.002 0.003 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.002 0.13 0.36 31 -10000 0 31
SMAD4 -0.012 0.01 0.072 4 -10000 0 4
ID2 0.23 0.37 0.64 213 -10000 0 213
AP1 -0.013 0.009 0.096 1 -10000 0 1
ABCG2 0.23 0.37 0.66 200 -10000 0 200
HIF1A 0.059 0.11 0.2 165 -10000 0 165
TFF3 0.22 0.36 0.64 211 -10000 0 211
GATA2 -0.013 0.013 0.082 9 -10000 0 9
AKT1 0.13 0.14 0.25 274 -10000 0 274
response to hypoxia 0.098 0.13 0.23 227 -10000 0 227
MCL1 0.22 0.37 0.66 199 -10000 0 199
NDRG1 0.22 0.36 0.66 198 -10000 0 198
SERPINE1 0.065 0.25 0.53 96 -10000 0 96
FECH 0.23 0.37 0.64 213 -10000 0 213
FURIN 0.23 0.37 0.66 200 -10000 0 200
NCOA2 -0.015 0.001 -10000 0 -10000 0 0
EP300 0.27 0.22 0.43 320 -10000 0 320
HMOX1 -0.006 0.15 0.45 31 -10000 0 31
BHLHE40 0.21 0.36 0.63 206 -10000 0 206
BHLHE41 0.21 0.36 0.63 206 -10000 0 206
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.019 0.082 0.2 70 -10000 0 70
ENG 0.18 0.15 0.29 315 -10000 0 315
JUN -0.014 0.009 0.053 9 -10000 0 9
RORA 0.23 0.37 0.64 213 -10000 0 213
ABCB1 -0.012 0.031 -10000 0 -10000 0 0
TFRC 0.23 0.37 0.64 213 -10000 0 213
CXCR4 0.032 0.22 0.58 54 -10000 0 54
TF 0.23 0.36 0.64 211 -10000 0 211
CITED2 0.22 0.36 0.63 206 -10000 0 206
HIF1A/ARNT 0.031 0.2 0.51 53 -10000 0 53
LDHA -0.011 0.053 -10000 0 -0.56 4 4
ETS1 0.23 0.37 0.64 213 -10000 0 213
PGK1 0.23 0.37 0.64 213 -10000 0 213
NOS2 0.21 0.36 0.63 206 -10000 0 206
ITGB2 0.041 0.23 0.54 72 -10000 0 72
ALDOA 0.23 0.37 0.66 200 -10000 0 200
Cbp/p300/CITED2 0.17 0.33 0.61 170 -10000 0 170
FOS -0.011 0.007 0.046 1 -10000 0 1
HK2 0.23 0.37 0.64 213 -10000 0 213
SP1 -0.019 0.015 0.092 9 -10000 0 9
GCK 0.34 0.27 0.59 243 -10000 0 243
HK1 0.23 0.36 0.66 200 -10000 0 200
NPM1 0.22 0.37 0.66 199 -10000 0 199
EGLN1 0.23 0.37 0.64 213 -10000 0 213
CREB1 -0.017 0.007 -10000 0 -0.087 5 5
PGM1 0.23 0.37 0.66 200 -10000 0 200
SMAD3 -0.016 0.009 0.075 5 -10000 0 5
EDN1 0.23 0.19 0.41 219 -10000 0 219
IGFBP1 0.22 0.36 0.64 208 -10000 0 208
VEGFA 0.066 0.21 0.47 97 -10000 0 97
HIF1A/JAB1 0.004 0.036 0.096 38 -10000 0 38
CP 0.098 0.29 0.58 117 -10000 0 117
CXCL12 0.21 0.36 0.66 191 -10000 0 191
COPS5 -0.015 0 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.016 0.009 -10000 0 -10000 0 0
BNIP3 0.23 0.37 0.66 200 -10000 0 200
EGLN3 0.22 0.36 0.66 198 -10000 0 198
CA9 0.2 0.35 0.63 194 -10000 0 194
TERT 0.23 0.37 0.64 213 -10000 0 213
ENO1 0.23 0.37 0.64 213 -10000 0 213
PFKL 0.23 0.37 0.64 213 -10000 0 213
NCOA1 -0.015 0.002 -10000 0 -10000 0 0
ADM 0.021 0.2 0.52 54 -10000 0 54
ARNT 0.059 0.11 0.2 166 -10000 0 166
HNF4A -0.015 0 -10000 0 -10000 0 0
ADFP 0.056 0.24 0.55 84 -10000 0 84
SLC2A1 0.36 0.35 0.61 318 -10000 0 318
LEP 0.23 0.37 0.64 213 -10000 0 213
HIF1A/ARNT/Cbp/p300 -0.001 0.13 0.38 31 -10000 0 31
EPO 0.34 0.29 0.56 304 -10000 0 304
CREBBP 0.27 0.22 0.43 318 -10000 0 318
HIF1A/ARNT/Cbp/p300/HDAC7 -0.008 0.12 0.36 18 -10000 0 18
PFKFB3 0.23 0.37 0.64 213 -10000 0 213
NT5E 0.19 0.35 0.63 188 -10000 0 188
TCGA08_retinoblastoma

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
CDKN2B 0.001 0.014 0.012 332 -0.033 3 335
CDKN2C -0.001 0.01 0.014 95 -0.036 11 106
CDKN2A -0.019 0.021 0.014 95 -0.038 262 357
CCND2 -0.007 0.021 -10000 0 -0.063 65 65
RB1 0.008 0.026 0.074 68 -10000 0 68
CDK4 -0.008 0.025 -10000 0 -0.076 65 65
CDK6 -0.007 0.023 -10000 0 -0.069 65 65
G1/S progression -0.004 0.029 -10000 0 -0.073 68 68
Osteopontin-mediated 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
IKK alpha homodimer 0.056 0.089 0.14 227 -9999 0 227
NF kappa B1 p50/RelA/I kappa B alpha 0.059 0.1 0.21 129 -9999 0 129
alphaV/beta3 Integrin/Osteopontin/Src 0.005 0.028 0.04 164 -9999 0 164
AP1 0.016 0.092 0.26 54 -9999 0 54
ILK 0.062 0.085 0.15 222 -9999 0 222
bone resorption 0 0.022 0.1 13 -9999 0 13
PTK2B -0.014 0 -10000 0 -9999 0 0
PYK2/p130Cas 0.004 0.037 0.074 65 -9999 0 65
ITGAV 0.005 0.024 0.031 186 -9999 0 186
mol:GTP 0 0 -10000 0 -9999 0 0
CD44/Rho Family GTPase/ROCK2 -0.004 0.007 0 415 -9999 0 415
alphaV/beta3 Integrin/Osteopontin 0.011 0.044 0.069 164 -9999 0 164
MAP3K1 0.062 0.085 0.15 222 -9999 0 222
JUN 0.004 0.018 0.02 290 -9999 0 290
MAPK3 0.066 0.11 0.2 178 -9999 0 178
MAPK1 0.067 0.11 0.2 178 -9999 0 178
Rac1/GDP -0.009 0 -10000 0 -9999 0 0
NFKB1 -0.014 0.001 0 4 -9999 0 4
MAPK8 0.074 0.099 0.16 242 -9999 0 242
ITGB3 0.006 0.024 0.031 196 -9999 0 196
NFKBIA 0.066 0.11 0.24 131 -9999 0 131
FOS 0.002 0.015 0.019 202 -9999 0 202
CD44 -0.003 0.006 0 415 -9999 0 415
CHUK -0.014 0.001 0 1 -9999 0 1
PLAU 0.11 0.17 0.39 124 -9999 0 124
NF kappa B1 p50/RelA 0.053 0.11 0.24 119 -9999 0 119
BCAR1 0 0 -10000 0 -9999 0 0
RELA -0.014 0 -10000 0 -9999 0 0
alphaV beta3 Integrin 0.014 0.038 0.047 280 -9999 0 280
mol:GDP 0 0 -10000 0 -9999 0 0
SYK 0.04 0.072 0.12 195 -9999 0 195
VAV3 0.03 0.067 0.11 178 -9999 0 178
MAP3K14 0.062 0.096 0.16 232 -9999 0 232
ROCK2 -0.014 0 -10000 0 -9999 0 0
SPP1 0.001 0.017 0.03 72 -9999 0 72
RAC1 -0.014 0 -10000 0 -9999 0 0
Rac1/GTP 0.026 0.06 0.1 176 -9999 0 176
MMP2 0.007 0.062 0.17 47 -9999 0 47
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.019 0.008 0.059 6 -10000 0 6
NFATC2 -0.15 0.13 0.2 2 -0.28 212 214
NFATC3 -0.15 0.1 0.17 3 -0.23 277 280
CD40LG -0.26 0.3 0.36 34 -0.55 230 264
ITCH -0.023 0.031 0.15 16 -10000 0 16
CBLB -0.023 0.031 0.15 16 -10000 0 16
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.2 0.17 -10000 0 -0.38 228 228
JUNB -0.014 0.002 0 8 -10000 0 8
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.029 0.009 -10000 0 -10000 0 0
T cell anergy -0.032 0.049 0.22 14 -10000 0 14
TLE4 -0.093 0.088 0.13 5 -0.18 209 214
Jun/NFAT1-c-4/p21SNFT -0.31 0.26 0.28 1 -0.57 240 241
AP-1/NFAT1-c-4 -0.31 0.27 -10000 0 -0.59 230 230
IKZF1 -0.093 0.088 0.13 5 -0.18 215 220
T-helper 2 cell differentiation -0.14 0.14 -10000 0 -0.45 29 29
AP-1/NFAT1 -0.071 0.077 0.17 1 -0.18 117 118
CALM1 -0.024 0.02 0.082 16 -10000 0 16
EGR2 -0.31 0.26 0.46 3 -0.57 248 251
EGR3 -0.44 0.4 0.42 2 -0.86 244 246
NFAT1/FOXP3 -0.1 0.087 0.14 5 -0.19 206 211
EGR1 -0.015 0.004 0.037 1 -10000 0 1
JUN -0.008 0.027 0.076 24 -10000 0 24
EGR4 -0.015 0.003 0.028 2 -10000 0 2
mol:Ca2+ -0.014 0.003 -10000 0 -10000 0 0
GBP3 -0.088 0.085 0.13 4 -0.18 212 216
FOSL1 -0.014 0.002 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.31 0.26 0.25 2 -0.56 249 251
DGKA -0.093 0.088 0.13 5 -0.18 211 216
CREM -0.014 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.32 0.27 0.23 4 -0.58 249 253
CTLA4 -0.083 0.073 0.1 7 -0.16 206 213
NFAT1-c-4 (dimer)/EGR1 -0.32 0.27 0.23 5 -0.58 249 254
NFAT1-c-4 (dimer)/EGR4 -0.32 0.27 0.23 5 -0.58 249 254
FOS -0.008 0.019 0.071 11 -10000 0 11
IFNG -0.13 0.11 -10000 0 -0.33 30 30
T cell activation -0.15 0.17 0.37 5 -0.43 1 6
MAF -0.014 0 -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 0.3 0.25 0.55 244 -0.36 4 248
TNF -0.3 0.26 0.28 7 -0.55 248 255
FASLG -0.41 0.38 0.48 2 -0.79 249 251
TBX21 -0.015 0.005 0.11 1 -10000 0 1
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ -0.015 0 -10000 0 -10000 0 0
PTPN1 -0.093 0.088 0.13 5 -0.18 211 216
NFAT1-c-4/ICER1 -0.32 0.27 0.23 5 -0.58 249 254
GATA3 -0.014 0.001 -10000 0 -10000 0 0
T-helper 1 cell differentiation -0.13 0.11 -10000 0 -0.34 25 25
IL2RA -0.21 0.17 0.16 1 -0.38 230 231
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.096 0.082 0.14 2 -0.18 215 217
E2F1 0.055 0.052 0.093 342 -10000 0 342
PPARG -0.014 0.001 -10000 0 -10000 0 0
SLC3A2 -0.093 0.087 0.13 4 -0.18 209 213
IRF4 -0.014 0.001 -10000 0 -10000 0 0
PTGS2 -0.28 0.27 0.27 14 -0.55 230 244
CSF2 -0.26 0.3 0.36 34 -0.55 230 264
JunB/Fra1/NFAT1-c-4 -0.31 0.26 0.23 6 -0.56 248 254
IL4 -0.14 0.15 -10000 0 -0.46 29 29
IL5 -0.26 0.3 0.36 34 -0.55 230 264
IL2 -0.15 0.17 0.37 5 -0.43 1 6
IL3 -0.066 0.049 -10000 0 -10000 0 0
RNF128 -0.027 0.008 -10000 0 -10000 0 0
NFATC1 -0.3 0.25 0.36 4 -0.55 244 248
CDK4 0.32 0.25 0.49 314 -0.37 2 316
PTPRK -0.082 0.088 0.13 5 -0.18 185 190
IL8 -0.28 0.25 -10000 0 -0.56 215 215
POU2F1 -0.015 0 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.003 0.013 0.012 342 -10000 0 342
GNB1/GNG2 -0.004 0.007 -10000 0 -10000 0 0
AKT1 0.13 0.099 0.19 340 -10000 0 340
EGF -0.014 0.001 0 2 -10000 0 2
mol:TXA2 0 0 0.005 2 -10000 0 2
FGR -0.016 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.16 0.12 0.24 353 -10000 0 353
LYN -0.015 0.01 0.073 1 -10000 0 1
RhoA/GTP -0.002 0.004 -10000 0 -10000 0 0
mol:PGI2 0 0 0.004 2 -10000 0 2
SYK 0.17 0.13 0.25 341 -10000 0 341
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 -0.014 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.008 0.019 -10000 0 -0.16 7 7
G beta5/gamma2 -0.005 0.008 -10000 0 -10000 0 0
PRKCH 0.16 0.13 0.25 340 -10000 0 340
DNM1 -0.003 0.005 0 432 -10000 0 432
TXA2/TP beta/beta Arrestin3 0.001 0.002 -10000 0 -10000 0 0
mol:GTP 0.003 0.003 0.004 353 -10000 0 353
PTGDR -0.014 0.002 0.013 2 -10000 0 2
G12 family/GTP 0.002 0.007 -10000 0 -10000 0 0
ADRBK1 -0.014 0.001 0.011 1 -10000 0 1
ADRBK2 -0.014 0.001 0.011 1 -10000 0 1
RhoA/GTP/ROCK1 0.005 0.013 0.014 352 -10000 0 352
mol:GDP -0.1 0.083 -10000 0 -0.16 339 339
mol:NADP -0.013 0.004 0.011 14 -10000 0 14
RAB11A -0.014 0.001 0 1 -10000 0 1
PRKG1 -0.013 0.004 0.011 14 -10000 0 14
mol:IP3 0.18 0.13 0.26 339 -10000 0 339
cell morphogenesis 0.005 0.013 0.014 352 -10000 0 352
PLCB2 0.19 0.14 0.5 21 -10000 0 21
mol:cGMP 0.001 0.001 0.005 2 -10000 0 2
BLK -0.016 0.011 0.087 2 -10000 0 2
mol:PDG2 0 0 0.004 2 -10000 0 2
HCK -0.014 0.01 -10000 0 -10000 0 0
RHOA -0.014 0.001 0 2 -10000 0 2
PTGIR -0.014 0.002 0.013 2 -10000 0 2
PRKCB1 0.16 0.13 0.25 339 -10000 0 339
GNAQ -0.014 0 -10000 0 -10000 0 0
mol:L-citrulline -0.013 0.004 0.011 14 -10000 0 14
TXA2/TXA2-R family 0.19 0.14 0.51 21 -10000 0 21
LCK -0.016 0.011 0.087 2 -10000 0 2
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.023 0.002 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma -0.003 0.041 -10000 0 -0.38 6 6
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.023 0.002 -10000 0 -10000 0 0
MAPK14 0.13 0.11 0.2 353 -10000 0 353
TGM2/GTP 0.19 0.14 0.28 339 -10000 0 339
MAPK11 0.13 0.11 0.2 353 -10000 0 353
ARHGEF1 0.096 0.083 0.15 353 -10000 0 353
GNAI2 -0.014 0.001 0 1 -10000 0 1
JNK cascade 0.18 0.14 0.26 339 -10000 0 339
RAB11/GDP -0.018 0.004 -10000 0 -0.032 14 14
ICAM1 0.15 0.12 0.23 353 -10000 0 353
cAMP biosynthetic process 0.16 0.12 0.24 339 -10000 0 339
Gq family/GTP/EBP50 -0.007 0.004 0.047 2 -10000 0 2
actin cytoskeleton reorganization 0.005 0.013 0.014 352 -10000 0 352
SRC -0.016 0.011 0.087 2 -10000 0 2
GNB5 -0.014 0.002 0.001 8 -10000 0 8
GNB1 -0.014 0.002 0 6 -10000 0 6
EGF/EGFR 0.012 0.034 0.096 38 -10000 0 38
VCAM1 0.18 0.14 0.28 353 -10000 0 353
TP beta/Gq family/GDP/G beta5/gamma2 -0.008 0.019 -10000 0 -0.16 7 7
platelet activation 0.16 0.13 0.24 341 -10000 0 341
PGI2/IP -0.007 0.003 0.01 19 -10000 0 19
PRKACA -0.005 0.003 0.012 15 -10000 0 15
Gq family/GDP/G beta5/gamma2 -0.005 0.008 0.056 7 -10000 0 7
TXA2/TP beta/beta Arrestin2 -0.001 0.013 -10000 0 -0.3 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.009 0.004 0.01 15 -10000 0 15
mol:DAG 0.18 0.14 0.27 339 -10000 0 339
EGFR -0.009 0.007 0 194 -10000 0 194
TXA2/TP alpha 0.18 0.14 0.28 339 -10000 0 339
Gq family/GTP -0.006 0.008 0.062 7 -10000 0 7
YES1 -0.014 0.012 0.087 2 -10000 0 2
GNAI2/GTP 0.004 0.02 0.018 335 -10000 0 335
PGD2/DP -0.007 0.003 0.01 19 -10000 0 19
SLC9A3R1 -0.014 0.001 0 2 -10000 0 2
FYN -0.015 0.012 0.087 2 -10000 0 2
mol:NO -0.013 0.004 0.011 14 -10000 0 14
GNA15 -0.014 0.002 0 7 -10000 0 7
PGK/cGMP 0.005 0.013 0.014 353 -10000 0 353
RhoA/GDP -0.018 0.004 -10000 0 -0.032 14 14
TP alpha/TGM2/GDP/G beta/gamma -0.022 0.003 -10000 0 -10000 0 0
NOS3 -0.013 0.004 0.011 14 -10000 0 14
RAC1 -0.014 0 -10000 0 -10000 0 0
PRKCA 0.16 0.13 0.25 339 -10000 0 339
PRKCB 0.17 0.13 0.25 340 -10000 0 340
PRKCE 0.17 0.13 0.25 339 -10000 0 339
PRKCD 0.17 0.13 0.26 339 -10000 0 339
PRKCG 0.17 0.13 0.26 339 -10000 0 339
muscle contraction 0.18 0.14 0.28 339 -10000 0 339
PRKCZ 0.16 0.13 0.25 340 -10000 0 340
ARR3 -0.014 0 -10000 0 -10000 0 0
TXA2/TP beta 0.005 0.019 0.099 2 -10000 0 2
PRKCQ 0.17 0.13 0.25 340 -10000 0 340
MAPKKK cascade 0.18 0.14 0.26 339 -10000 0 339
SELE 0.15 0.12 0.23 353 -10000 0 353
TP beta/GNAI2/GDP/G beta/gamma -0.023 0.003 -10000 0 -10000 0 0
ROCK1 -0.014 0 -10000 0 -10000 0 0
GNA14 -0.014 0.001 0 2 -10000 0 2
chemotaxis 0.2 0.15 0.62 16 -10000 0 16
GNA12 -0.014 0.001 0 4 -10000 0 4
GNA13 -0.014 0.001 0 2 -10000 0 2
GNA11 -0.014 0 -10000 0 -10000 0 0
Rac1/GTP 0.003 0.009 0.009 353 -10000 0 353
Syndecan-1-mediated signaling events

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
TGFB1 -0.013 0.003 0 27 -9999 0 27
CCL5 -0.013 0.003 0 28 -9999 0 28
SDCBP -0.014 0 -10000 0 -9999 0 0
FGFR/FGF2/Syndecan-1 0.043 0.072 0.099 256 -9999 0 256
mol:PI-4-5-P2 0 0 -10000 0 -9999 0 0
RP11-540L11.1 0 0 -10000 0 -9999 0 0
Syndecan-1/Laminin-5 0.035 0.065 0.099 208 -9999 0 208
Syndecan-1/Syntenin 0.037 0.067 0.1 218 -9999 0 218
MAPK3 0.003 0.026 0.11 21 -9999 0 21
HGF/MET -0.017 0.003 0 12 -9999 0 12
TGFB1/TGF beta receptor Type II -0.013 0.003 0 27 -9999 0 27
BSG -0.014 0 -10000 0 -9999 0 0
keratinocyte migration 0.034 0.064 0.098 208 -9999 0 208
Syndecan-1/RANTES 0.03 0.059 0.091 196 -9999 0 196
Syndecan-1/CD147 0.006 0.03 0.084 52 -9999 0 52
Syndecan-1/Syntenin/PIP2 0.027 0.051 0.082 201 -9999 0 201
LAMA5 -0.014 0.002 0 14 -9999 0 14
positive regulation of cell-cell adhesion 0.026 0.049 0.079 199 -9999 0 199
MMP7 -0.012 0.005 0 78 -9999 0 78
HGF -0.014 0.001 0 2 -9999 0 2
Syndecan-1/CASK 0.01 0.026 0.052 118 -9999 0 118
Syndecan-1/HGF/MET 0.033 0.066 0.099 210 -9999 0 210
regulation of cell adhesion 0.085 0.079 0.12 386 -9999 0 386
HPSE -0.013 0.004 0 44 -9999 0 44
positive regulation of cell migration 0.043 0.072 0.099 256 -9999 0 256
SDC1 0.025 0.047 0.075 214 -9999 0 214
Syndecan-1/Collagen 0.043 0.072 0.099 256 -9999 0 256
PPIB -0.004 0.006 0 373 -9999 0 373
MET -0.014 0.002 0 10 -9999 0 10
PRKACA -0.014 0 -10000 0 -9999 0 0
MMP9 -0.009 0.007 0 179 -9999 0 179
MAPK1 0.003 0.026 0.11 21 -9999 0 21
homophilic cell adhesion 0.043 0.073 0.11 218 -9999 0 218
MMP1 -0.013 0.004 0 43 -9999 0 43
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.004 0.007 0.01 51 -10000 0 51
NF kappa B1 p50/RelA/I kappa B alpha 0.029 0.05 0.11 59 -10000 0 59
AP1 0 0.022 0.078 36 -10000 0 36
mol:PIP3 -0.007 0.01 -10000 0 -10000 0 0
AKT1 0.041 0.064 0.11 247 -0.16 1 248
PTK2B 0.047 0.054 0.1 250 -10000 0 250
RHOA 0.04 0.053 0.095 247 -0.25 2 249
PIK3CB -0.015 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.016 0.031 0.061 60 -10000 0 60
MAGI3 0 0 -10000 0 -0.002 6 6
RELA -0.014 0.001 -10000 0 -10000 0 0
apoptosis -0.003 0.004 0 320 -10000 0 320
HRAS/GDP -0.009 0.001 0 2 -10000 0 2
positive regulation of microtubule depolymerization 0.041 0.057 0.097 250 -10000 0 250
NF kappa B1 p50/RelA -0.003 0.034 0.086 57 -10000 0 57
endothelial cell migration -0.006 0.005 0 250 -10000 0 250
ADCY4 0.003 0.022 0.13 16 -10000 0 16
ADCY5 0.003 0.022 0.13 16 -10000 0 16
ADCY6 0.003 0.022 0.13 16 -10000 0 16
ADCY7 0.003 0.022 0.13 16 -10000 0 16
ADCY1 0.003 0.022 0.13 16 -10000 0 16
ADCY2 0.003 0.022 0.13 16 -10000 0 16
ADCY3 0.003 0.022 0.13 16 -10000 0 16
ADCY8 0.003 0.022 0.13 16 -10000 0 16
ADCY9 0.003 0.022 0.13 16 -10000 0 16
GSK3B 0.039 0.051 0.092 250 -10000 0 250
arachidonic acid secretion 0.003 0.021 0.12 16 -10000 0 16
GNG2 -0.001 0.001 -10000 0 -0.002 33 33
TRIP6 0.006 0.017 0.041 96 -10000 0 96
GNAO1 0.004 0.027 0.16 16 -10000 0 16
HRAS -0.014 0.001 0 2 -10000 0 2
NFKBIA 0.027 0.045 0.073 250 -10000 0 250
GAB1 -0.014 0.001 0 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.016 0.16 -10000 0 -0.79 21 21
JUN -0.013 0.002 0.008 5 -10000 0 5
LPA/LPA2/NHERF2 -0.003 0.006 0.002 303 -10000 0 303
TIAM1 -0.03 0.18 -10000 0 -0.9 21 21
PIK3R1 -0.014 0.004 0 36 -10000 0 36
mol:IP3 0.016 0.031 0.061 60 -10000 0 60
PLCB3 0.023 0.038 0.062 250 -10000 0 250
FOS -0.01 0.006 0 127 -10000 0 127
positive regulation of mitosis 0.003 0.021 0.12 16 -10000 0 16
LPA/LPA1-2-3 -0.001 0.006 0.015 57 -10000 0 57
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 0.002 81 -10000 0 81
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation 0.055 0.061 0.12 250 -0.11 2 252
GNAZ 0.059 0.082 0.16 215 -10000 0 215
EGFR/PI3K-beta/Gab1 -0.006 0.011 0.013 16 -10000 0 16
positive regulation of dendritic cell cytokine production -0.001 0.006 0.014 57 -10000 0 57
LPA/LPA2/MAGI-3 -0.001 0.002 0.003 50 -0.006 8 58
ARHGEF1 0.053 0.078 0.14 251 -10000 0 251
GNAI2 0.068 0.084 0.16 250 -10000 0 250
GNAI3 0.059 0.082 0.16 216 -10000 0 216
GNAI1 0.061 0.082 0.16 221 -10000 0 221
LPA/LPA3 -0.001 0.002 0.001 306 -10000 0 306
LPA/LPA2 -0.001 0.002 0.001 303 -0.007 1 304
LPA/LPA1 -0.003 0.004 0.001 300 -0.013 1 301
HB-EGF/EGFR -0.007 0.01 0.001 338 -10000 0 338
HBEGF -0.011 0.008 0 179 -10000 0 179
mol:DAG 0.016 0.031 0.061 60 -10000 0 60
cAMP biosynthetic process 0.068 0.072 0.14 251 -10000 0 251
NFKB1 -0.014 0.001 0 4 -10000 0 4
SRC -0.014 0 -10000 0 -10000 0 0
GNB1 -0.015 0.002 0 6 -10000 0 6
LYN 0.036 0.053 0.083 258 -10000 0 258
GNAQ 0.03 0.035 0.066 250 -10000 0 250
LPAR2 0 0.001 0.002 108 -0.002 2 110
LPAR3 0 0.001 0.002 115 -10000 0 115
LPAR1 -0.002 0.002 0 266 -0.008 1 267
IL8 0.15 0.16 0.3 221 -10000 0 221
PTK2 0.064 0.075 0.14 250 -10000 0 250
Rac1/GDP -0.009 0 -10000 0 -10000 0 0
CASP3 -0.003 0.004 0 320 -10000 0 320
EGFR -0.006 0.009 0.003 253 -10000 0 253
PLCG1 0.03 0.034 0.065 250 -10000 0 250
PLD2 0.064 0.075 0.14 250 -10000 0 250
G12/G13 -0.006 0.01 0.015 50 -10000 0 50
PI3K-beta -0.009 0.012 -10000 0 -0.17 1 1
cell migration 0.009 0.054 -10000 0 -0.22 21 21
SLC9A3R2 -0.014 0 -10000 0 -10000 0 0
PXN 0.055 0.061 0.12 250 -0.11 2 252
HRAS/GTP 0.003 0.021 0.12 16 -10000 0 16
RAC1 -0.014 0 -10000 0 -10000 0 0
MMP9 -0.009 0.007 0.001 190 -10000 0 190
PRKCE -0.015 0.001 -10000 0 -10000 0 0
PRKCD 0.012 0.03 0.075 11 -10000 0 11
Gi(beta/gamma) 0.003 0.023 0.13 16 -10000 0 16
mol:LPA -0.002 0.002 0 266 -0.008 1 267
TRIP6/p130 Cas/FAK1/Paxillin 0.018 0.046 0.11 96 -0.12 1 97
MAPKKK cascade 0.003 0.021 0.12 16 -10000 0 16
contractile ring contraction involved in cytokinesis 0.041 0.054 0.095 250 -0.24 2 252
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.03 0.035 0.066 250 -10000 0 250
GNA15 0.029 0.035 0.066 243 -10000 0 243
GNA12 -0.014 0.001 0 4 -10000 0 4
GNA13 -0.014 0.001 0 2 -10000 0 2
MAPT 0.041 0.057 0.098 250 -10000 0 250
GNA11 0.03 0.035 0.066 250 -10000 0 250
Rac1/GTP -0.018 0.17 -10000 0 -0.83 21 21
MMP2 -0.006 0.005 0 250 -10000 0 250
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.006 0.033 -10000 0 -0.17 15 15
MAP3K8 -0.007 0.013 0.019 107 -10000 0 107
FOS 0.041 0.089 0.19 125 -0.17 15 140
PRKCA -0.003 0.021 0.034 125 -10000 0 125
PTPN7 0.001 0.029 0.053 125 -10000 0 125
HRAS -0.008 0.011 0.012 127 -10000 0 127
PRKCB 0.006 0.011 0.025 125 -10000 0 125
NRAS -0.006 0.01 0.005 233 -10000 0 233
RAS family/GTP 0 0.026 0.053 97 -10000 0 97
MAPK3 0.033 0.051 0.16 5 -10000 0 5
MAP2K1 0.026 0.047 0.1 135 -10000 0 135
ELK1 -0.007 0.015 0.02 125 -10000 0 125
BRAF 0.012 0.03 0.064 125 -10000 0 125
mol:GTP 0.001 0.002 0.004 125 -10000 0 125
MAPK1 0.022 0.084 -10000 0 -0.34 17 17
RAF1 0.012 0.03 0.064 125 -10000 0 125
KRAS -0.008 0.011 0.011 134 -10000 0 134
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.016 0.028 -10000 0 -10000 0 0
PLK1 0.15 0.14 0.4 51 -10000 0 51
CDKN1B 0.19 0.14 0.34 202 -10000 0 202
FOXO3 0.16 0.14 0.3 182 -10000 0 182
KAT2B 0.025 0.023 0.043 301 -10000 0 301
FOXO1/SIRT1 0.025 0.038 0.16 7 -10000 0 7
CAT 0.14 0.12 0.39 33 -10000 0 33
CTNNB1 -0.014 0 -10000 0 -10000 0 0
AKT1 0.034 0.031 0.057 301 -10000 0 301
FOXO1 0.02 0.032 0.17 6 -10000 0 6
MAPK10 0.016 0.036 0.1 56 -10000 0 56
mol:GTP 0.003 0.005 0.015 49 -10000 0 49
FOXO4 0.055 0.1 0.25 72 -10000 0 72
response to oxidative stress 0.031 0.026 0.059 184 -10000 0 184
FOXO3A/SIRT1 0.16 0.13 0.3 184 -10000 0 184
XPO1 -0.011 0.008 0.014 48 -10000 0 48
EP300 0 0.014 0.014 174 -10000 0 174
BCL2L11 0.028 0.031 -10000 0 -10000 0 0
FOXO1/SKP2 0.016 0.029 0.14 5 -10000 0 5
mol:GDP 0.031 0.026 0.059 184 -10000 0 184
RAN -0.004 0.013 0.014 189 -10000 0 189
GADD45A 0.14 0.14 0.44 56 -10000 0 56
YWHAQ -0.014 0 -10000 0 -10000 0 0
FOXO1/14-3-3 family -0.045 0.051 0.11 1 -0.19 7 8
MST1 0.029 0.029 0.051 301 -10000 0 301
CSNK1D -0.014 0.001 0 2 -10000 0 2
CSNK1E -0.014 0.001 0 1 -10000 0 1
FOXO4/14-3-3 family -0.068 0.088 0.098 2 -0.15 233 235
YWHAB -0.014 0.001 0 2 -10000 0 2
MAPK8 0.03 0.045 0.11 93 -10000 0 93
MAPK9 0.029 0.043 0.11 94 -10000 0 94
YWHAG 0 0 -10000 0 -10000 0 0
YWHAE -0.014 0.001 0 2 -10000 0 2
YWHAZ -0.014 0.002 0 6 -10000 0 6
SIRT1 0.003 0.019 0.044 45 -10000 0 45
SOD2 0.24 0.18 0.38 304 -10000 0 304
RBL2 0.13 0.11 0.33 52 -10000 0 52
RAL/GDP 0.031 0.031 0.066 173 -10000 0 173
CHUK 0.03 0.029 0.051 305 -10000 0 305
Ran/GTP 0.006 0.015 0.021 189 -10000 0 189
CSNK1G2 -0.014 0 -10000 0 -10000 0 0
RAL/GTP 0.041 0.042 0.087 174 -10000 0 174
CSNK1G1 -0.014 0 -10000 0 -10000 0 0
FASLG 0.028 0.031 -10000 0 -10000 0 0
SKP2 -0.014 0.001 0 2 -10000 0 2
USP7 -0.004 0.013 0.014 189 -10000 0 189
IKBKB 0.03 0.029 0.051 305 -10000 0 305
CCNB1 0.2 0.17 0.34 284 -10000 0 284
FOXO1-3a-4/beta catenin 0.17 0.15 0.33 205 -10000 0 205
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.029 0.14 5 -10000 0 5
CSNK1A1 -0.014 0 -10000 0 -10000 0 0
SGK1 0.025 0.023 0.043 301 -10000 0 301
CSNK1G3 -0.014 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.011 0.025 0.035 189 -10000 0 189
ZFAND5 0.053 0.093 0.28 41 -10000 0 41
SFN -0.013 0.003 0 33 -10000 0 33
CDK2 0 0.015 -10000 0 -10000 0 0
FOXO3A/14-3-3 -0.015 0.079 0.11 38 -0.15 55 93
CREBBP 0 0.015 -10000 0 -10000 0 0
FBXO32 0.14 0.12 0.27 180 -10000 0 180
BCL6 0.13 0.12 0.36 57 -10000 0 57
RALB 0 0.014 0.012 292 -10000 0 292
RALA 0 0.013 0.012 261 -10000 0 261
YWHAH -0.007 0.007 0 284 -10000 0 284
Effects of Botulinum toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0 0.001 0 512 -10000 0 512
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.017 0.001 0 1 -10000 0 1
STXBP1 -0.001 0.004 0 479 -10000 0 479
ACh/CHRNA1 -0.021 0.014 -10000 0 -0.052 51 51
RAB3GAP2/RIMS1/UNC13B -0.02 0.001 0 1 -10000 0 1
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 -0.014 0 -10000 0 -10000 0 0
mol:ACh -0.019 0.016 -10000 0 -0.061 51 51
RAB3GAP2 -0.014 0 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.001 0.005 -10000 0 -0.057 2 2
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.021 0.014 -10000 0 -0.052 51 51
UNC13B -0.014 0.001 0 1 -10000 0 1
CHRNA1 -0.014 0.001 0 3 -10000 0 3
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0 0.004 0.018 16 -10000 0 16
SNAP25 0 0 0 483 -10000 0 483
VAMP2 -0.001 0 0 49 -10000 0 49
SYT1 -0.001 0.003 0 495 -10000 0 495
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0 0.002 0 514 -10000 0 514
STX1A/SNAP25 fragment 1/VAMP2 -0.001 0.005 -10000 0 -0.057 2 2
PLK2 and PLK4 events

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
PLK2 -0.01 0.006 0 155 -9999 0 155
PLK4 -0.014 0 -9999 0 -9999 0 0
regulation of centriole replication -0.012 0.008 0 155 -9999 0 155
EGFR-dependent Endothelin signaling events

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
HRAS -0.014 0.001 0 2 -9999 0 2
EGFR -0.009 0.007 0 194 -9999 0 194
EGF/EGFR -0.009 0.01 0 304 -9999 0 304
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.012 0.011 0 241 -9999 0 241
mol:GTP 0 0 -10000 0 -9999 0 0
EDNRA -0.01 0.006 0 154 -9999 0 154
response to oxidative stress 0 0 -10000 0 -9999 0 0
EGF -0.014 0.001 0 2 -9999 0 2
EGF/EGFR dimer/SHC -0.011 0.01 0 237 -9999 0 237
mol:GDP -0.012 0.011 0 241 -9999 0 241
mol:Ca2+ 0 0 -10000 0 -9999 0 0
EDN1 -0.014 0.002 0 9 -9999 0 9
GRB2/SOS1 -0.008 0.001 0 5 -9999 0 5
HRAS/GTP -0.013 0.012 -10000 0 -9999 0 0
SHC1 -0.013 0.004 0 46 -9999 0 46
HRAS/GDP -0.014 0.013 -10000 0 -9999 0 0
FRAP1 0.025 0.056 0.087 235 -9999 0 235
EGF/EGFR dimer -0.011 0.008 0 196 -9999 0 196
SOS1 0 0 -10000 0 -9999 0 0
GRB2 -0.014 0.001 0 5 -9999 0 5
ETA receptor/Endothelin-1 -0.012 0.008 0 158 -9999 0 158
HIF-2-alpha transcription factor network

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
MMP14 -0.005 0.016 0.3 1 -10000 0 1
oxygen homeostasis 0.024 0.032 0.059 191 -10000 0 191
TCEB2 -0.014 0 -10000 0 -10000 0 0
TCEB1 -0.014 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.064 0.094 0.19 148 -10000 0 148
EPO 0.16 0.21 0.4 185 -10000 0 185
FIH (dimer) 0.026 0.039 0.069 186 -10000 0 186
APEX1 0.018 0.03 0.05 181 -10000 0 181
SERPINE1 0.022 0.12 0.39 16 -10000 0 16
FLT1 -0.006 0.012 -10000 0 -10000 0 0
ADORA2A 0.17 0.22 0.43 184 -10000 0 184
germ cell development 0.17 0.22 0.43 183 -10000 0 183
SLC11A2 0.18 0.23 0.44 187 -10000 0 187
BHLHE40 0.17 0.22 0.44 183 -10000 0 183
HIF1AN 0.026 0.039 0.069 186 -10000 0 186
HIF2A/ARNT/SIRT1 0.018 0.076 0.2 7 -10000 0 7
ETS1 -0.012 0.025 0.13 17 -10000 0 17
CITED2 -0.005 0.015 0.28 1 -10000 0 1
KDR -0.005 0.021 0.3 2 -10000 0 2
PGK1 0.18 0.23 0.44 187 -10000 0 187
SIRT1 -0.015 0 -10000 0 -10000 0 0
response to hypoxia -0.001 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.035 0.12 0.32 7 -10000 0 7
EPAS1 0.12 0.16 0.3 191 -10000 0 191
SP1 -0.015 0.009 0.13 2 -10000 0 2
ABCG2 0.18 0.23 0.44 185 -10000 0 185
EFNA1 0.16 0.22 0.43 174 -10000 0 174
FXN 0.17 0.22 0.43 187 -10000 0 187
POU5F1 0.17 0.22 0.44 183 -10000 0 183
neuron apoptosis -0.034 0.12 -10000 0 -0.32 7 7
EP300 -0.014 0 -10000 0 -10000 0 0
EGLN3 0.026 0.039 0.068 183 -10000 0 183
EGLN2 0.026 0.039 0.068 186 -10000 0 186
EGLN1 0.026 0.039 0.069 186 -10000 0 186
VHL/Elongin B/Elongin C -0.014 0 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.018 0.03 0.05 181 -10000 0 181
SLC2A1 0.16 0.22 0.43 179 -10000 0 179
TWIST1 0.13 0.21 0.41 150 -10000 0 150
ELK1 -0.012 0.023 0.13 14 -10000 0 14
HIF2A/ARNT/Cbp/p300 0.02 0.08 0.21 7 -10000 0 7
VEGFA 0.002 0.11 0.44 17 -10000 0 17
CREBBP -0.014 0 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.004 0.021 0.034 112 -10000 0 112
PDGF/PDGFRA/CRKL -0.006 0.02 0.031 112 -10000 0 112
positive regulation of JUN kinase activity -0.005 0.019 0.031 99 -10000 0 99
CRKL -0.014 0 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.006 0.02 0.031 112 -10000 0 112
AP1 -0.014 0.031 -10000 0 -0.26 2 2
mol:IP3 0.002 0.039 0.066 124 -10000 0 124
PLCG1 0.002 0.039 0.066 124 -10000 0 124
PDGF/PDGFRA/alphaV Integrin -0.006 0.02 0.031 107 -10000 0 107
RAPGEF1 -0.014 0 -10000 0 -10000 0 0
CRK -0.014 0 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.039 0.066 124 -10000 0 124
CAV3 -0.014 0 -10000 0 -10000 0 0
CAV1 -0.005 0.007 0 324 -10000 0 324
SHC/Grb2/SOS1 -0.005 0.019 0.032 99 -10000 0 99
PDGF/PDGFRA/Shf -0.001 0.014 0.025 112 -10000 0 112
FOS 0.051 0.13 0.3 112 -10000 0 112
JUN 0.001 0.028 0.051 124 -0.045 2 126
oligodendrocyte development -0.006 0.02 0.031 107 -10000 0 107
GRB2 -0.014 0.001 0 5 -10000 0 5
PIK3R1 -0.013 0.004 0 36 -10000 0 36
mol:DAG 0.002 0.039 0.066 124 -10000 0 124
PDGF/PDGFRA -0.004 0.021 0.035 112 -10000 0 112
actin cytoskeleton reorganization -0.006 0.02 0.031 112 -10000 0 112
SRF -0.02 0.006 0.015 2 -0.034 14 16
SHC1 -0.013 0.004 0 46 -10000 0 46
PI3K -0.006 0.021 0.034 104 -10000 0 104
PDGF/PDGFRA/Crk/C3G -0.007 0.022 0.034 112 -10000 0 112
JAK1 -0.008 0.015 0.019 112 -10000 0 112
ELK1/SRF -0.013 0.027 0.072 39 -10000 0 39
SHB -0.014 0 -10000 0 -10000 0 0
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 -0.019 0.009 0.03 2 -0.034 125 127
GO:0007205 0.014 0.051 0.082 163 -10000 0 163
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction -0.005 0.019 0.031 99 -10000 0 99
PDGF/PDGFRA/SHB -0.006 0.02 0.031 112 -10000 0 112
PDGF/PDGFRA/Caveolin-1 -0.004 0.011 0.031 25 -10000 0 25
ITGAV -0.014 0.002 0 16 -10000 0 16
ELK1 0.01 0.047 0.084 151 -10000 0 151
PIK3CA -0.014 0.003 0 25 -10000 0 25
PDGF/PDGFRA/Crk -0.006 0.02 0.031 112 -10000 0 112
JAK-STAT cascade -0.008 0.015 0.019 112 -10000 0 112
cell proliferation -0.001 0.014 0.025 112 -10000 0 112
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.008 0.001 0 2 -10000 0 2
GNB1/GNG2 -0.005 0.011 0.015 122 -10000 0 122
regulation of S phase of mitotic cell cycle -0.004 0.008 0.009 114 -10000 0 114
GNAO1 -0.001 0.004 0 481 -10000 0 481
HRAS -0.008 0.011 0.012 127 -10000 0 127
SHBG/T-DHT -0.007 0.001 0.006 3 -10000 0 3
PELP1 -0.008 0.011 0.012 125 -10000 0 125
AKT1 -0.009 0.001 0 4 -10000 0 4
MAP2K1 0.001 0.054 0.094 125 -0.14 2 127
T-DHT/AR -0.004 0.008 0.01 130 -10000 0 130
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 0.004 125 -0.006 2 127
GNAI2 -0.014 0.001 0 1 -10000 0 1
GNAI3 -0.012 0.005 0 65 -10000 0 65
GNAI1 -0.012 0.005 0 81 -10000 0 81
mol:GDP -0.009 0.007 -10000 0 -10000 0 0
cell proliferation 0.017 0.1 0.19 125 -0.37 2 127
PIK3CA -0.014 0.003 0 25 -10000 0 25
FOS 0.046 0.14 0.28 125 -0.51 2 127
mol:Ca2+ 0 0.003 0.019 15 -10000 0 15
MAPK3 0.01 0.079 0.15 125 -0.26 2 127
MAPK1 0.011 0.094 0.19 3 -0.34 19 22
PIK3R1 -0.013 0.004 0 36 -10000 0 36
mol:IP3 0.001 0.002 0.005 125 -0.004 2 127
cAMP biosynthetic process 0 0.001 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0.001 0.002 0.005 125 -0.004 2 127
HRAS/GTP 0.002 0.041 0.076 122 -0.068 2 124
actin cytoskeleton reorganization -0.017 0.007 0.016 2 -10000 0 2
SRC -0.008 0.011 0.012 125 -10000 0 125
voltage-gated calcium channel activity 0.001 0.002 0.005 125 -0.004 2 127
PI3K -0.012 0.004 0 60 -10000 0 60
apoptosis -0.028 0.11 0.36 2 -0.21 125 127
T-DHT/AR/PELP1 -0.005 0.015 0.021 122 -10000 0 122
HRAS/GDP -0.009 0.016 0.065 5 -10000 0 5
CREB1 -0.021 0.044 0.28 3 -0.38 2 5
RAC1-CDC42/GTP -0.01 0.017 0.019 116 -10000 0 116
AR -0.008 0.011 0.011 130 -10000 0 130
GNB1 -0.014 0.002 0 6 -10000 0 6
RAF1 0 0.046 0.079 111 -0.1 2 113
RAC1-CDC42/GDP -0.01 0.022 0.056 30 -10000 0 30
T-DHT/AR/PELP1/Src -0.006 0.022 0.035 122 -0.037 2 124
MAP2K2 0.001 0.054 0.094 125 -0.14 2 127
T-DHT/AR/PELP1/Src/PI3K -0.004 0.008 0.009 114 -10000 0 114
GNAZ -0.012 0.005 0 72 -10000 0 72
SHBG -0.014 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.13 0.072 -10000 0 -0.15 444 444
mol:T-DHT 0 0 -10000 0 -10000 0 0
RAC1 -0.014 0 -10000 0 -10000 0 0
GNRH1 -0.008 0 -10000 0 -10000 0 0
Gi family/GTP 0 0.006 0.05 5 -0.069 1 6
CDC42 -0.014 0 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 -0.013 0.007 0 125 -9999 0 125
ATM -0.014 0.003 0 25 -9999 0 25
UBE2D3 -0.014 0.001 0 1 -9999 0 1
PRKDC -0.014 0.003 0 23 -9999 0 23
ATR -0.014 0 -10000 0 -9999 0 0
UBE2L3 -0.014 0 -10000 0 -9999 0 0
FANCD2 -0.005 0.001 -10000 0 -9999 0 0
protein ubiquitination -0.019 0.012 -10000 0 -9999 0 0
XRCC5 -0.014 0 -10000 0 -9999 0 0
XRCC6 -0.014 0 -10000 0 -9999 0 0
M/R/N Complex -0.02 0 -10000 0 -9999 0 0
MRE11A -0.014 0 -10000 0 -9999 0 0
DNA-PK -0.019 0.004 0 23 -9999 0 23
FA complex/FANCD2/Ubiquitin -0.005 0.007 -10000 0 -9999 0 0
FANCF -0.014 0.001 0 2 -9999 0 2
BRCA1 -0.014 0.001 0 5 -9999 0 5
CCNE1 -0.014 0.002 0 7 -9999 0 7
CDK2/Cyclin E1 -0.016 0.004 0 30 -9999 0 30
FANCG -0.012 0.005 0 66 -9999 0 66
BRCA1/BACH1/BARD1 -0.013 0.007 0 126 -9999 0 126
FANCE -0.014 0.001 0 1 -9999 0 1
FANCC -0.014 0 -10000 0 -9999 0 0
NBN -0.014 0 -10000 0 -9999 0 0
FANCA -0.014 0 -10000 0 -9999 0 0
DNA repair 0.062 0.076 0.17 133 -9999 0 133
BRCA1/BARD1/ubiquitin -0.013 0.007 0 126 -9999 0 126
BARD1/DNA-PK -0.017 0.01 0 138 -9999 0 138
FANCL 0 0 -10000 0 -9999 0 0
mRNA polyadenylation 0.013 0.007 -10000 0 0 125 125
BRCA1/BARD1/CTIP/M/R/N Complex 0.029 0.034 0.057 297 -9999 0 297
BRCA1/BACH1/BARD1/TopBP1 -0.015 0.009 0 126 -9999 0 126
BRCA1/BARD1/P53 -0.016 0.011 0 166 -9999 0 166
BARD1/CSTF1/BRCA1 -0.015 0.009 0 126 -9999 0 126
BRCA1/BACH1 -0.014 0.001 0 5 -9999 0 5
BARD1 -0.011 0.006 0 125 -9999 0 125
PCNA -0.005 0.007 0 342 -9999 0 342
BRCA1/BARD1/UbcH5C -0.015 0.009 0 127 -9999 0 127
BRCA1/BARD1/UbcH7 -0.015 0.009 0 126 -9999 0 126
BRCA1/BARD1/RAD51/PCNA -0.008 0.011 0 359 -9999 0 359
BARD1/DNA-PK/P53 -0.018 0.013 -10000 0 -9999 0 0
BRCA1/BARD1/Ubiquitin -0.013 0.007 0 126 -9999 0 126
BRCA1/BARD1/CTIP -0.005 0.009 0 423 -9999 0 423
FA complex -0.008 0.004 0.05 1 -9999 0 1
BARD1/EWS -0.013 0.007 0 125 -9999 0 125
RBBP8 -0.004 0.007 0 411 -9999 0 411
TP53 -0.012 0.005 0 69 -9999 0 69
TOPBP1 -0.014 0.001 0 1 -9999 0 1
G1/S transition of mitotic cell cycle 0.016 0.011 -10000 0 0 166 166
BRCA1/BARD1 -0.02 0.012 -10000 0 -9999 0 0
CSTF1 -0.014 0 -10000 0 -9999 0 0
BARD1/EWS-Fli1 -0.007 0.004 0 125 -9999 0 125
CDK2 -0.013 0.003 0 27 -9999 0 27
UniProt:Q9BZD1 0 0 -10000 0 -9999 0 0
RAD51 -0.014 0 -10000 0 -9999 0 0
RAD50 -0.014 0 -10000 0 -9999 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.013 0.007 0 126 -9999 0 126
EWSR1 -0.014 0 -10000 0 -9999 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.007 0.03 0.051 162 -10000 0 162
mol:DAG 0.012 0.042 0.06 208 -10000 0 208
PLCG1 0.013 0.043 0.061 208 -10000 0 208
YES1 0.004 0.027 0.049 135 -10000 0 135
FZD3 -0.014 0.002 0 16 -10000 0 16
FZD6 -0.012 0.006 0 100 -10000 0 100
G protein 0.011 0.04 0.099 42 -10000 0 42
MAP3K7 0.001 0.036 0.085 45 -10000 0 45
mol:Ca2+ 0.012 0.041 0.059 208 -10000 0 208
mol:IP3 0.012 0.042 0.06 208 -10000 0 208
NLK 0.006 0.054 -10000 0 -0.71 3 3
GNB1 -0.014 0.002 0 6 -10000 0 6
CAMK2A 0.006 0.038 0.095 45 -10000 0 45
MAP3K7IP1 -0.014 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.006 0.005 -10000 0 -10000 0 0
CSNK1A1 -0.014 0 -10000 0 -10000 0 0
GNAS 0.006 0.029 0.049 163 -10000 0 163
GO:0007205 0.013 0.04 0.1 46 -10000 0 46
WNT6 -0.014 0 -10000 0 -10000 0 0
WNT4 -0.014 0.001 0 2 -10000 0 2
NFAT1/CK1 alpha 0.009 0.045 0.11 59 -10000 0 59
GNG2 0 0 -10000 0 -10000 0 0
WNT5A -0.01 0.007 0 168 -10000 0 168
WNT11 -0.014 0.001 0 2 -10000 0 2
CDC42 0.005 0.032 0.084 30 -10000 0 30
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.005 0.01 -10000 0 -0.021 111 111
BUB1B 0.055 0.063 0.11 269 -10000 0 269
PLK1 0.004 0.024 0.083 38 -10000 0 38
PLK1S1 0.01 0.016 0.036 112 -10000 0 112
KIF2A 0.009 0.023 0.071 36 -10000 0 36
regulation of mitotic centrosome separation 0.016 0.027 0.057 112 -10000 0 112
GOLGA2 -0.014 0 -10000 0 -10000 0 0
Hec1/SPC24 0.003 0.013 0.043 15 -10000 0 15
WEE1 0.05 0.049 0.13 105 -10000 0 105
cytokinesis 0.059 0.074 0.15 198 -10000 0 198
PP2A-alpha B56 0.033 0.017 -10000 0 -10000 0 0
AURKA 0.014 0.022 0.087 25 -10000 0 25
PICH/PLK1 0.007 0.031 0.058 131 -10000 0 131
CENPE 0.024 0.058 0.15 77 -10000 0 77
RhoA/GTP -0.009 0.001 0 2 -10000 0 2
positive regulation of microtubule depolymerization 0.009 0.023 0.074 33 -10000 0 33
PPP2CA -0.014 0.001 0 4 -10000 0 4
FZR1 -0.014 0 -10000 0 -10000 0 0
TPX2 0.033 0.032 0.066 208 -10000 0 208
PAK1 -0.008 0.011 0.013 108 -10000 0 108
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 -0.014 0 -10000 0 -10000 0 0
CLSPN 0.011 0.016 0.077 7 -10000 0 7
GORASP1 -0.014 0 -10000 0 -10000 0 0
metaphase 0.001 0.002 0.009 22 -10000 0 22
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.01 0.016 0.036 112 -10000 0 112
G2 phase of mitotic cell cycle 0.001 0.002 0.006 26 -10000 0 26
STAG2 -0.013 0.003 0 27 -10000 0 27
GRASP65/GM130/RAB1/GTP 0.003 0.006 -10000 0 -10000 0 0
spindle elongation 0.016 0.027 0.057 112 -10000 0 112
ODF2 -0.008 0.011 0.013 108 -10000 0 108
BUB1 0.002 0.004 -10000 0 -10000 0 0
TPT1 0.011 0.016 0.072 13 -10000 0 13
CDC25C 0.011 0.015 0.079 5 -10000 0 5
CDC25B 0.005 0.014 0.015 352 -10000 0 352
SGOL1 0.005 0.01 0.021 111 -10000 0 111
RHOA -0.014 0.001 0 2 -10000 0 2
CCNB1/CDK1 0.005 0.008 -10000 0 -10000 0 0
CDC14B -0.008 0.001 -10000 0 -10000 0 0
CDC20 -0.006 0.007 0 303 -10000 0 303
PLK1/PBIP1 -0.001 0.003 -10000 0 -10000 0 0
mitosis 0.002 0.004 0.013 19 -10000 0 19
FBXO5 0.049 0.06 0.1 257 -10000 0 257
CDC2 -0.001 0.011 0.012 174 -10000 0 174
NDC80 -0.009 0.007 0 183 -10000 0 183
metaphase plate congression 0.012 0.017 0.086 5 -10000 0 5
ERCC6L 0.003 0.025 0.061 71 -10000 0 71
NLP/gamma Tubulin 0.012 0.019 0.042 109 -10000 0 109
microtubule cytoskeleton organization 0.011 0.016 0.072 13 -10000 0 13
G2/M transition DNA damage checkpoint 0.001 0.002 0.005 19 -10000 0 19
PPP1R12A -0.013 0.003 0.011 8 -10000 0 8
interphase 0.001 0.002 0.005 19 -10000 0 19
PLK1/PRC1-2 0 0.014 0.042 6 -10000 0 6
GRASP65/GM130/RAB1/GTP/PLK1 0.015 0.027 0.05 112 -10000 0 112
RAB1A -0.014 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.013 0.035 0.13 31 -10000 0 31
mitotic prometaphase 0.001 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.002 0.003 -10000 0 -10000 0 0
microtubule-based process 0.003 0.014 0.042 18 -10000 0 18
Golgi organization 0.016 0.027 0.057 112 -10000 0 112
Cohesin/SA2 0.013 0.022 0.048 98 -10000 0 98
PPP1CB/MYPT1 -0.01 0.013 0.016 108 -10000 0 108
KIF20A -0.009 0.007 0 186 -10000 0 186
APC/C/CDC20 -0.001 0.009 0.041 2 -10000 0 2
PPP2R1A -0.014 0.002 0 16 -10000 0 16
chromosome segregation -0.001 0.003 -10000 0 -10000 0 0
PRC1 -0.008 0.007 0 224 -10000 0 224
ECT2 0.051 0.074 0.15 184 -10000 0 184
C13orf34 0.013 0.036 0.12 36 -10000 0 36
NUDC 0.012 0.017 0.086 5 -10000 0 5
regulation of attachment of spindle microtubules to kinetochore 0.055 0.063 0.11 269 -10000 0 269
spindle assembly 0.013 0.024 0.05 112 -10000 0 112
spindle stabilization 0.01 0.016 0.036 112 -10000 0 112
APC/C/HCDH1 -0.013 0.001 -10000 0 -10000 0 0
MKLP2/PLK1 0.003 0.014 0.042 18 -10000 0 18
CCNB1 -0.003 0.009 0.011 71 -10000 0 71
PPP1CB -0.013 0.003 0.011 7 -10000 0 7
BTRC -0.014 0 -10000 0 -10000 0 0
ROCK2 0.012 0.019 0.093 5 -0.1 2 7
TUBG1 0.011 0.018 0.072 22 -10000 0 22
G2/M transition of mitotic cell cycle 0.011 0.031 0.063 131 -10000 0 131
MLF1IP -0.001 0.003 0 449 -10000 0 449
INCENP -0.009 0.009 0.011 90 -10000 0 90
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.003 0.028 0.19 1 -10000 0 1
UGCG 0.017 0.028 -10000 0 -10000 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT 0.037 0.087 0.18 124 -10000 0 124
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide 0.017 0.028 -10000 0 -10000 0 0
mol:DAG 0.004 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.016 0.077 0.18 88 -10000 0 88
FRAP1 0.041 0.11 0.22 129 -10000 0 129
FOXO3 0.041 0.1 0.22 128 -0.21 2 130
AKT1 0.001 0.062 0.28 20 -0.22 2 22
GAB2 -0.006 0.014 0.018 135 -10000 0 135
SMPD1 0.017 0.028 -10000 0 -10000 0 0
SGMS1 0.016 0.028 -10000 0 -10000 0 0
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 -0.006 0.012 0.016 108 -10000 0 108
CALM1 -0.013 0.003 0 27 -10000 0 27
cell proliferation 0.042 0.079 0.18 128 -10000 0 128
EIF3A -0.014 0 -10000 0 -10000 0 0
PI3K -0.005 0.021 0.035 108 -10000 0 108
RPS6KB1 0.013 0.027 0.24 1 -10000 0 1
mol:sphingomyelin 0.004 0.003 -10000 0 -10000 0 0
natural killer cell activation 0.002 0.004 0.009 137 -10000 0 137
JAK3 -0.006 0.015 0.018 137 -10000 0 137
PIK3R1 -0.006 0.014 0.02 117 -10000 0 117
JAK1 -0.006 0.014 0.018 136 -10000 0 136
NFKB1 -0.014 0.001 0 4 -10000 0 4
MYC 0.066 0.14 0.3 133 -10000 0 133
MYB 0.008 0.038 0.32 4 -10000 0 4
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.033 0.084 0.17 127 -0.2 2 129
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.021 0.024 0.21 1 -10000 0 1
mol:PI-3-4-5-P3 0.032 0.084 0.17 127 -0.2 2 129
Rac1/GDP -0.006 0.023 0.031 117 -10000 0 117
T cell proliferation 0.031 0.079 0.16 128 -0.19 2 130
SHC1 -0.006 0.013 0.018 115 -10000 0 115
RAC1 -0.014 0.001 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.011 0.093 8 -10000 0 8
PRKCZ 0.031 0.08 0.16 128 -0.19 2 130
NF kappa B1 p50/RelA 0.031 0.099 0.2 126 -10000 0 126
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.001 0.026 0.15 3 -10000 0 3
HSP90AA1 -0.014 0 -10000 0 -10000 0 0
RELA -0.014 0 -10000 0 -10000 0 0
IL2RA -0.006 0.014 0.018 135 -10000 0 135
IL2RB -0.006 0.014 0.018 133 -10000 0 133
TERT -0.014 0 -10000 0 -10000 0 0
E2F1 0.009 0.031 0.25 8 -10000 0 8
SOS1 0.003 0.005 0.01 137 -10000 0 137
RPS6 -0.014 0 -10000 0 -10000 0 0
mol:cAMP 0 0.006 -10000 0 -0.05 8 8
PTPN11 -0.006 0.015 0.02 137 -10000 0 137
IL2RG -0.006 0.015 0.019 128 -10000 0 128
actin cytoskeleton organization 0.031 0.079 0.16 128 -0.19 2 130
GRB2 -0.006 0.014 0.019 136 -10000 0 136
IL2 -0.006 0.015 0.019 137 -10000 0 137
PIK3CA -0.006 0.015 0.019 127 -10000 0 127
Rac1/GTP 0.013 0.053 0.11 117 -10000 0 117
LCK -0.006 0.015 0.019 134 -10000 0 134
BCL2 0.037 0.098 0.24 33 -10000 0 33
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.013 0.007 0 116 -10000 0 116
VLDLR -0.014 0.001 0 3 -10000 0 3
CRKL -0.014 0 -10000 0 -10000 0 0
LRPAP1 -0.014 0 -10000 0 -10000 0 0
FYN -0.014 0.003 0 21 -10000 0 21
ITGA3 -0.014 0.003 0 19 -10000 0 19
RELN/VLDLR/Fyn -0.009 0.01 0 295 -10000 0 295
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.027 0 -10000 0 -10000 0 0
AKT1 -0.006 0.007 -10000 0 -10000 0 0
MAP2K7 -0.014 0 -10000 0 -10000 0 0
RAPGEF1 -0.014 0 -10000 0 -10000 0 0
DAB1 -0.014 0 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.008 0.009 0 282 -10000 0 282
LRPAP1/LRP8 -0.017 0 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.01 0.011 0 294 -10000 0 294
DAB1/alpha3/beta1 Integrin -0.016 0.017 -10000 0 -10000 0 0
long-term memory -0.01 0.015 -10000 0 -10000 0 0
DAB1/LIS1 -0.014 0.015 -10000 0 -10000 0 0
DAB1/CRLK/C3G -0.016 0.017 -10000 0 -10000 0 0
PIK3CA -0.014 0.003 0 25 -10000 0 25
DAB1/NCK2 -0.014 0.015 -10000 0 -10000 0 0
ARHGEF2 -0.014 0 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.01 0.007 0 174 -10000 0 174
CDK5R1 -0.011 0.006 0 101 -10000 0 101
RELN -0.007 0.007 0 282 -10000 0 282
PIK3R1 -0.013 0.004 0 36 -10000 0 36
RELN/LRP8/Fyn -0.009 0.01 0 294 -10000 0 294
GRIN2A/RELN/LRP8/DAB1/Fyn -0.009 0.013 -10000 0 -10000 0 0
MAPK8 -0.014 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.008 0.009 0 283 -10000 0 283
ITGB1 -0.014 0 -10000 0 -10000 0 0
MAP1B -0.01 0.013 0.079 2 -10000 0 2
RELN/LRP8 -0.009 0.01 0 282 -10000 0 282
GRIN2B/RELN/LRP8/DAB1/Fyn -0.012 0.014 -10000 0 -10000 0 0
PI3K -0.015 0.005 0 60 -10000 0 60
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin -0.016 0.003 0 19 -10000 0 19
RAP1A -0.004 0.033 0.12 2 -10000 0 2
PAFAH1B1 -0.014 0.002 0 6 -10000 0 6
MAPK8IP1 -0.014 0 -10000 0 -10000 0 0
CRLK/C3G -0.017 0 -10000 0 -10000 0 0
GRIN2B -0.014 0 -10000 0 -10000 0 0
NCK2 -0.014 0.001 0 1 -10000 0 1
neuron differentiation -0.044 0.034 -10000 0 -0.075 282 282
neuron adhesion -0.01 0.037 0.11 19 -10000 0 19
LRP8 -0.014 0 -10000 0 -10000 0 0
GSK3B -0.006 0.013 0.085 1 -10000 0 1
RELN/VLDLR/DAB1/Fyn -0.01 0.011 -10000 0 -10000 0 0
MAP3K11 -0.014 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.004 0.005 -10000 0 -10000 0 0
CDK5 -0.013 0.003 0 33 -10000 0 33
MAPT -0.004 0.005 -10000 0 -10000 0 0
neuron migration -0.051 0.051 0.09 1 -0.12 182 183
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.044 0.034 -10000 0 -0.076 282 282
RELN/VLDLR -0.011 0.012 0 283 -10000 0 283
Regulation of nuclear SMAD2/3 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
EP300 0.005 0.023 0.033 215 -10000 0 215
HSPA8 -0.017 0.004 0 3 -10000 0 3
SMAD3/SMAD4/ER alpha -0.011 0.038 0.096 36 -10000 0 36
AKT1 -0.012 0.009 0.015 6 -10000 0 6
GSC -0.007 0.014 0.049 1 -0.044 33 34
NKX2-5 -0.012 0.012 0.015 86 -10000 0 86
muscle cell differentiation -0.015 0.05 -10000 0 -0.15 27 27
SMAD2-3/SMAD4/SP1 0.019 0.082 0.25 41 -10000 0 41
SMAD4 0.008 0.046 0.092 59 -10000 0 59
CBFB -0.014 0.001 0 4 -10000 0 4
SAP18 -0.015 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.012 0.039 0.061 203 -10000 0 203
SMAD3/SMAD4/VDR 0.023 0.061 0.12 129 -10000 0 129
MYC -0.01 0.006 -10000 0 -10000 0 0
CDKN2B -0.012 0.037 -10000 0 -10000 0 0
AP1 0.018 0.06 0.12 75 -10000 0 75
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.005 0.024 0.07 17 -10000 0 17
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.002 0.03 -10000 0 -10000 0 0
SP3 -0.014 0.012 0.076 7 -10000 0 7
CREB1 -0.014 0 -10000 0 -10000 0 0
FOXH1 -0.012 0.012 0.015 86 -10000 0 86
SMAD3/SMAD4/GR -0.015 0.042 0.091 19 -0.13 18 37
GATA3 -0.024 0.003 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 -0.003 0.021 0.041 74 -10000 0 74
MEF2C/TIF2 0.005 0.045 0.08 65 -10000 0 65
endothelial cell migration -0.13 0.15 -10000 0 -0.32 214 214
MAX -0.038 0.031 -10000 0 -0.075 215 215
RBBP7 -0.015 0.001 -10000 0 -10000 0 0
RBBP4 -0.012 0.006 0 100 -10000 0 100
RUNX2 -0.014 0 -10000 0 -10000 0 0
RUNX3 -0.014 0.001 0 3 -10000 0 3
RUNX1 -0.014 0 -10000 0 -10000 0 0
CTBP1 -0.014 0.002 0 7 -10000 0 7
NR3C1 -0.038 0.031 -10000 0 -0.075 215 215
VDR -0.014 0 -10000 0 -10000 0 0
CDKN1A 0.089 0.14 0.42 51 -10000 0 51
KAT2B 0.003 0.004 0.008 215 -10000 0 215
SMAD2/SMAD2/SMAD4/FOXH1 0.002 0.036 0.068 57 -10000 0 57
DCP1A -0.014 0 -10000 0 -10000 0 0
SKI -0.015 0.001 -10000 0 -10000 0 0
SERPINE1 0.13 0.15 0.32 212 -10000 0 212
SMAD3/SMAD4/ATF2 -0.006 0.038 0.094 43 -10000 0 43
SMAD3/SMAD4/ATF3 -0.006 0.034 0.09 34 -10000 0 34
SAP30 -0.015 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.021 0.051 0.083 214 -10000 0 214
JUN 0.048 0.08 0.15 144 -10000 0 144
SMAD3/SMAD4/IRF7 -0.004 0.045 0.1 52 -10000 0 52
TFE3 0.034 0.056 0.081 285 -10000 0 285
COL1A2 0.035 0.095 0.25 84 -10000 0 84
mesenchymal cell differentiation 0.006 0.038 -10000 0 -0.093 43 43
DLX1 0 0 -10000 0 -10000 0 0
TCF3 -0.014 0 -10000 0 -10000 0 0
FOS -0.001 0.019 0.037 11 -10000 0 11
SMAD3/SMAD4/Max -0.015 0.042 0.091 20 -0.13 18 38
Cbp/p300/SNIP1 0.003 0.029 0.038 215 -10000 0 215
ZBTB17 -0.014 0 -10000 0 -10000 0 0
LAMC1 0 0.038 0.096 25 -10000 0 25
TGIF2/HDAC complex/SMAD3/SMAD4 -0.006 0.038 0.094 43 -10000 0 43
IRF7 -0.019 0.003 -10000 0 -10000 0 0
ESR1 -0.022 0.013 0.11 4 -10000 0 4
HNF4A -0.014 0 -10000 0 -10000 0 0
MEF2C 0.005 0.043 0.081 65 -10000 0 65
SMAD2-3/SMAD4 -0.007 0.038 0.1 17 -10000 0 17
Cbp/p300/Src-1 0.01 0.037 0.055 211 -10000 0 211
IGHV3OR16-13 -0.004 0.007 -10000 0 -10000 0 0
TGIF2/HDAC complex -0.014 0.002 0 8 -10000 0 8
CREBBP 0.002 0.019 0.025 215 -10000 0 215
SKIL -0.014 0 -10000 0 -10000 0 0
HDAC1 -0.013 0.005 0 65 -10000 0 65
HDAC2 -0.015 0.002 0 5 -10000 0 5
SNIP1 -0.016 0.003 -10000 0 -10000 0 0
GCN5L2 0.003 0.02 0.027 215 -10000 0 215
SMAD3/SMAD4/TFE3 0.005 0.048 0.13 28 -10000 0 28
MSG1/HSC70 -0.019 0.005 -10000 0 -10000 0 0
SMAD2 -0.013 0.012 0.035 1 -10000 0 1
SMAD3 0.017 0.056 0.085 169 -10000 0 169
SMAD3/E2F4-5/DP1/p107/SMAD4 0.013 0.04 0.077 125 -10000 0 125
SMAD2/SMAD2/SMAD4 0.027 0.036 0.084 79 -10000 0 79
NCOR1 -0.015 0.001 -10000 0 -10000 0 0
NCOA2 -0.014 0 -10000 0 -10000 0 0
NCOA1 -0.014 0.002 0 14 -10000 0 14
MYOD/E2A -0.017 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.035 0.09 0.19 95 -10000 0 95
IFNB1 0.037 0.076 0.12 187 -10000 0 187
SMAD3/SMAD4/MEF2C -0.002 0.048 0.13 22 -10000 0 22
CITED1 -0.013 0.003 0 25 -10000 0 25
SMAD2-3/SMAD4/ARC105 -0.001 0.048 0.13 37 -10000 0 37
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.006 0.029 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.02 0.002 0 7 -10000 0 7
SMAD7 0.04 0.084 0.18 121 -10000 0 121
MYC/MIZ-1 -0.012 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4 0.1 0.1 0.22 206 -10000 0 206
IL10 0.033 0.077 0.14 128 -10000 0 128
PIASy/HDAC complex -0.022 0.01 -10000 0 -0.033 215 215
PIAS3 -0.002 0.015 0.016 214 -10000 0 214
CDK2 0.002 0.019 0.024 208 -10000 0 208
IL5 0.033 0.077 0.13 139 -10000 0 139
CDK4 0.002 0.012 0.027 88 -10000 0 88
PIAS4 -0.022 0.01 -10000 0 -0.033 215 215
ATF3 -0.011 0.006 0 108 -10000 0 108
SMAD3/SMAD4/SP1 0.018 0.083 0.26 38 -10000 0 38
FOXG1 -0.015 0.009 -10000 0 -0.038 48 48
FOXO3 -0.015 0.007 -10000 0 -10000 0 0
FOXO1 -0.016 0.005 -10000 0 -10000 0 0
FOXO4 -0.016 0.005 -10000 0 -10000 0 0
heart looping 0.005 0.043 0.08 65 -10000 0 65
CEBPB -0.014 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.006 0.032 0.091 32 -10000 0 32
MYOD1 -0.014 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.006 0.038 0.094 43 -10000 0 43
SMAD3/SMAD4/GATA3 -0.005 0.052 0.11 62 -10000 0 62
SnoN/SIN3/HDAC complex/NCoR1 -0.014 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.011 0.055 0.098 117 -10000 0 117
SMAD3/SMAD4/SP1-3 0.02 0.081 0.25 38 -10000 0 38
MED15 -0.014 0 -10000 0 -10000 0 0
SP1 0.031 0.053 0.078 279 -10000 0 279
SIN3B -0.015 0.001 -10000 0 -10000 0 0
SIN3A -0.001 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.001 0.039 0.071 57 -10000 0 57
ITGB5 0.074 0.11 0.19 204 -10000 0 204
TGIF/SIN3/HDAC complex/CtBP 0.016 0.021 0.041 124 -10000 0 124
SMAD3/SMAD4/AR -0.006 0.038 0.094 43 -10000 0 43
AR -0.014 0.002 0 8 -10000 0 8
negative regulation of cell growth 0.019 0.045 0.13 47 -10000 0 47
SMAD3/SMAD4/MYOD -0.006 0.038 0.094 43 -10000 0 43
E2F5 -0.014 0 -10000 0 -10000 0 0
E2F4 -0.014 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.01 0.043 0.083 96 -10000 0 96
SMAD2-3/SMAD4/FOXO1-3a-4 0.003 0.026 -10000 0 -10000 0 0
TFDP1 -0.014 0.002 0 15 -10000 0 15
SMAD3/SMAD4/AP1 0 0.046 0.13 22 -10000 0 22
SMAD3/SMAD4/RUNX2 -0.006 0.038 0.094 43 -10000 0 43
TGIF2 -0.014 0.002 0 8 -10000 0 8
TGIF1 -0.004 0.006 0 371 -10000 0 371
ATF2 -0.014 0 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.15 0.16 0.49 57 -10000 0 57
CRP 0.15 0.16 0.49 58 -10000 0 58
cell cycle arrest 0.16 0.17 0.46 87 -10000 0 87
TIMP1 0.26 0.2 0.5 151 -10000 0 151
IL6ST 0.016 0.022 0.045 128 -10000 0 128
Rac1/GDP 0.067 0.088 0.2 123 -10000 0 123
AP1 0.13 0.11 0.24 139 -0.26 2 141
GAB2 -0.012 0.008 0.021 24 -10000 0 24
TNFSF11 0.15 0.16 0.49 58 -10000 0 58
HSP90B1 0.052 0.071 0.42 3 -0.5 1 4
GAB1 -0.013 0.006 0.02 16 -10000 0 16
MAPK14 0.01 0.036 0.2 2 -10000 0 2
AKT1 0.013 0.035 0.29 4 -10000 0 4
FOXO1 0.01 0.038 0.27 5 -10000 0 5
MAP2K6 0.038 0.06 0.19 43 -10000 0 43
mol:GTP 0.002 0.002 0.009 40 -10000 0 40
MAP2K4 0.09 0.12 0.26 127 -10000 0 127
MITF 0.056 0.079 0.18 120 -10000 0 120
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 -0.014 0.001 0 1 -10000 0 1
A2M -0.005 0.12 0.3 23 -0.88 7 30
CEBPB -0.014 0.008 0.14 1 -10000 0 1
GRB2/SOS1/GAB family/SHP2 0.042 0.052 0.19 25 -10000 0 25
STAT3 0.15 0.17 0.42 118 -10000 0 118
STAT1 0.031 0.036 0.26 1 -10000 0 1
CEBPD 0.15 0.16 0.49 58 -10000 0 58
PIK3CA -0.013 0.005 0.03 5 -10000 0 5
PI3K -0.014 0.009 0.028 14 -10000 0 14
JUN -0.012 0.006 0.012 33 -10000 0 33
PIAS3/MITF 0.053 0.074 0.16 120 -10000 0 120
MAPK11 0.01 0.036 0.2 2 -10000 0 2
STAT3 (dimer)/FOXO1 0.14 0.16 0.39 117 -10000 0 117
GRB2/SOS1/GAB family 0.034 0.049 0.14 41 -10000 0 41
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.03 0.053 0.12 108 -10000 0 108
GRB2 -0.013 0.006 0.02 16 -10000 0 16
JAK2 -0.014 0 -10000 0 -10000 0 0
LBP 0.14 0.15 0.46 62 -10000 0 62
PIK3R1 -0.012 0.006 0.024 8 -10000 0 8
JAK1 0.008 0.015 0.032 45 -10000 0 45
MYC 0.17 0.19 0.5 102 -10000 0 102
FGG 0.15 0.17 0.5 59 -10000 0 59
macrophage differentiation 0.16 0.17 0.46 87 -10000 0 87
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.027 0.041 0.086 91 -10000 0 91
JUNB 0.15 0.16 0.48 58 -10000 0 58
FOS -0.009 0.007 0.001 139 -10000 0 139
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.068 0.085 0.2 123 -10000 0 123
STAT1/PIAS1 0.091 0.1 0.24 125 -10000 0 125
GRB2/SOS1/GAB family/SHP2/PI3K 0.019 0.03 0.23 4 -10000 0 4
STAT3 (dimer) 0.15 0.17 0.42 118 -10000 0 118
PRKCD 0.11 0.14 0.32 125 -10000 0 125
IL6R 0.008 0.015 0.033 44 -10000 0 44
SOCS3 -0.011 0.021 -10000 0 -10000 0 0
gp130 (dimer)/JAK1/JAK1/LMO4 0.033 0.041 0.09 121 -10000 0 121
Rac1/GTP 0.077 0.097 0.22 123 -10000 0 123
HCK -0.011 0.006 0.001 93 -10000 0 93
MAPKKK cascade 0.05 0.061 0.25 13 -0.27 2 15
bone resorption 0.15 0.16 0.48 58 -10000 0 58
IRF1 0.16 0.18 0.5 85 -10000 0 85
mol:GDP 0.061 0.085 0.19 118 -10000 0 118
SOS1 0.001 0.004 0.021 10 -10000 0 10
VAV1 0.062 0.085 0.19 118 -10000 0 118
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.007 0.02 -10000 0 -0.22 3 3
PTPN11 0.031 0.035 0.25 1 -10000 0 1
IL6/IL6RA 0.017 0.026 0.055 96 -10000 0 96
gp130 (dimer)/TYK2/TYK2/LMO4 0.025 0.032 0.067 121 -10000 0 121
gp130 (dimer)/JAK2/JAK2/LMO4 0.025 0.032 0.067 123 -10000 0 123
IL6 0.012 0.02 0.042 101 -10000 0 101
PIAS3 -0.014 0.001 0 2 -10000 0 2
PTPRE -0.031 0.022 -10000 0 -0.08 55 55
PIAS1 -0.014 0 -10000 0 -10000 0 0
RAC1 -0.004 0.013 0.013 185 -10000 0 185
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.034 0.05 0.11 122 -10000 0 122
LMO4 0.015 0.022 0.044 121 -10000 0 121
STAT3 (dimer)/PIAS3 0.14 0.16 0.39 117 -10000 0 117
MCL1 0.011 0.039 0.36 4 -10000 0 4
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.017 0.059 0.11 68 -0.34 5 73
Syndecan-4/Syndesmos 0 0.057 0.13 1 -0.19 32 33
positive regulation of JNK cascade -0.006 0.052 0.13 15 -0.19 25 40
Syndecan-4/ADAM12 0.016 0.076 0.14 68 -0.19 32 100
CCL5 -0.013 0.003 0 28 -10000 0 28
Rac1/GDP -0.009 0 -10000 0 -10000 0 0
DNM2 -0.014 0 -10000 0 -10000 0 0
ITGA5 -0.012 0.005 0 74 -10000 0 74
SDCBP -0.014 0 -10000 0 -10000 0 0
PLG -0.017 0.007 -10000 0 -0.032 71 71
ADAM12 -0.014 0.001 0 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.015 0.013 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0 0.057 0.13 1 -0.19 32 33
Syndecan-4/CXCL12/CXCR4 -0.006 0.054 0.13 15 -0.2 25 40
Syndecan-4/Laminin alpha3 0.014 0.075 0.14 66 -0.19 32 98
MDK -0.006 0.007 0 299 -10000 0 299
Syndecan-4/FZD7 0 0.062 0.14 27 -0.19 30 57
Syndecan-4/Midkine -0.002 0.056 0.14 24 -0.19 23 47
FZD7 -0.008 0.007 0 244 -10000 0 244
Syndecan-4/FGFR1/FGF 0.01 0.075 0.12 69 -0.19 31 100
THBS1 -0.013 0.004 0 43 -10000 0 43
integrin-mediated signaling pathway -0.006 0.029 0.13 2 -0.21 4 6
positive regulation of MAPKKK cascade -0.006 0.052 0.13 15 -0.19 25 40
Syndecan-4/TACI 0.016 0.076 0.14 69 -0.19 32 101
CXCR4 -0.007 0.007 0 275 -10000 0 275
cell adhesion -0.01 0.006 -10000 0 -10000 0 0
Syndecan-4/Dynamin 0.016 0.076 0.14 69 -0.19 32 101
Syndecan-4/TSP1 0.01 0.072 0.14 51 -0.19 32 83
Syndecan-4/GIPC 0.016 0.076 0.14 69 -0.19 32 101
Syndecan-4/RANTES 0.012 0.073 0.14 58 -0.19 32 90
ITGB1 -0.014 0 -10000 0 -10000 0 0
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 -0.014 0.002 0 15 -10000 0 15
RAC1 -0.014 0 -10000 0 -10000 0 0
PRKCA -0.013 0.012 -10000 0 -10000 0 0
Syndecan-4/alpha-Actinin 0.012 0.074 0.14 61 -0.19 32 93
TFPI -0.011 0.006 0 117 -10000 0 117
F2 -0.005 0.015 0.016 168 -0.033 33 201
alpha5/beta1 Integrin -0.015 0.006 0 74 -10000 0 74
positive regulation of cell adhesion 0.012 0.071 0.13 66 -0.19 32 98
ACTN1 -0.013 0.004 0 43 -10000 0 43
TNC -0.001 0.003 0 504 -10000 0 504
Syndecan-4/CXCL12 0.014 0.073 0.14 61 -0.19 30 91
FGF6 -0.014 0 -10000 0 -10000 0 0
RHOA -0.014 0.001 0 2 -10000 0 2
CXCL12 -0.014 0.002 0 15 -10000 0 15
TNFRSF13B -0.014 0 -10000 0 -10000 0 0
FGF2 -0.014 0.001 0 2 -10000 0 2
FGFR1 -0.014 0.001 0 2 -10000 0 2
Syndecan-4/PI-4-5-P2 0 0.057 0.13 1 -0.19 32 33
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.011 0.006 0 104 -10000 0 104
cell migration -0.008 0.007 -10000 0 -10000 0 0
PRKCD -0.017 0.007 -10000 0 -0.032 71 71
vasculogenesis 0.009 0.07 0.13 51 -0.19 32 83
SDC4 0.023 0.071 0.14 69 -0.21 22 91
Syndecan-4/Tenascin C -0.006 0.03 0.14 2 -0.22 4 6
Syndecan-4/PI-4-5-P2/PKC alpha -0.012 0.011 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.016 0.076 0.14 69 -0.19 32 101
MMP9 -0.01 0.008 0.016 2 -0.03 22 24
Rac1/GTP -0.01 0.007 -10000 0 -10000 0 0
cytoskeleton organization 0 0.056 -10000 0 -0.18 32 32
GIPC1 -0.014 0 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.009 0.067 0.14 48 -0.19 25 73
Angiopoietin receptor Tie2-mediated 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
AKT1 0.15 0.16 0.4 84 -10000 0 84
NCK1/PAK1/Dok-R -0.009 0.016 -10000 0 -10000 0 0
NCK1/Dok-R 0.043 0.065 0.19 44 -10000 0 44
PIK3CA -0.013 0.003 0 25 -10000 0 25
mol:beta2-estradiol -0.016 0.035 -10000 0 -0.099 78 78
RELA -0.014 0 -10000 0 -10000 0 0
SHC1 0.001 0.013 0.011 304 -10000 0 304
Rac/GDP -0.009 0 -10000 0 -10000 0 0
F2 -0.047 0.052 -10000 0 -0.12 114 114
TNIP2 -0.014 0.002 0 11 -10000 0 11
NF kappa B/RelA 0.042 0.068 0.24 5 -10000 0 5
FN1 -0.011 0.006 0 104 -10000 0 104
PLD2 0.041 0.068 0.27 4 -10000 0 4
PTPN11 -0.014 0 -10000 0 -10000 0 0
GRB14 -0.014 0.003 0 18 -10000 0 18
ELK1 0.034 0.063 0.24 5 -10000 0 5
GRB7 -0.014 0.001 0 1 -10000 0 1
PAK1 -0.014 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.028 0.063 0.24 5 -10000 0 5
CDKN1A 0.17 0.18 0.46 92 -10000 0 92
ITGA5 -0.012 0.005 0 74 -10000 0 74
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.043 0.065 0.19 44 -10000 0 44
CRK -0.014 0 -10000 0 -10000 0 0
mol:NO 0.14 0.15 0.37 86 -10000 0 86
PLG 0.041 0.068 0.24 8 -10000 0 8
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.11 0.13 0.34 65 -10000 0 65
GRB2 -0.014 0.001 0 5 -10000 0 5
PIK3R1 0.001 0.013 0.012 318 -10000 0 318
ANGPT2 0.18 0.17 0.33 279 -10000 0 279
BMX 0.041 0.068 0.24 8 -10000 0 8
ANGPT1 0.052 0.088 0.25 78 -10000 0 78
tube development 0.17 0.17 0.4 102 -10000 0 102
ANGPT4 0.006 0.019 0.024 288 -10000 0 288
response to hypoxia 0.006 0.008 0.025 39 -10000 0 39
Tie2/Ang1/GRB14 0.046 0.069 0.26 4 -10000 0 4
alpha5/beta1 Integrin -0.015 0.006 0 74 -10000 0 74
FGF2 -0.023 0.008 -10000 0 -0.03 278 278
STAT5A (dimer) 0.18 0.19 0.48 87 -10000 0 87
mol:L-citrulline 0.14 0.15 0.37 86 -10000 0 86
AGTR1 0.014 0.026 0.037 293 -10000 0 293
MAPK14 0.1 0.1 0.33 17 -10000 0 17
Tie2/SHP2 0.025 0.037 0.15 4 -10000 0 4
TEK 0.03 0.042 0.19 4 -10000 0 4
RPS6KB1 0.13 0.14 0.37 81 -10000 0 81
Angiotensin II/AT1 0.038 0.044 0.079 279 -10000 0 279
Tie2/Ang1/GRB2 0.047 0.069 0.26 5 -10000 0 5
MAPK3 0.034 0.065 0.25 5 -10000 0 5
MAPK1 0.034 0.064 0.25 5 -10000 0 5
Tie2/Ang1/GRB7 0.047 0.07 0.26 5 -10000 0 5
NFKB1 -0.014 0.001 0 4 -10000 0 4
MAPK8 0.041 0.068 0.24 8 -10000 0 8
PI3K 0.14 0.15 0.39 81 -10000 0 81
FES 0.1 0.1 0.33 17 -10000 0 17
Crk/Dok-R 0.044 0.065 0.19 44 -10000 0 44
Tie2/Ang1/ABIN2 0.046 0.069 0.26 5 -10000 0 5
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.15 0.15 0.39 84 -10000 0 84
STAT5A -0.011 0.01 0.018 55 -10000 0 55
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.13 0.14 0.37 81 -10000 0 81
Tie2/Ang2 0.18 0.18 0.46 84 -10000 0 84
Tie2/Ang1 0.05 0.073 0.22 44 -10000 0 44
FOXO1 0.16 0.16 0.42 84 -10000 0 84
ELF1 0.003 0.016 -10000 0 -10000 0 0
ELF2 0.048 0.071 0.21 44 -10000 0 44
mol:Choline 0.041 0.068 0.26 5 -10000 0 5
cell migration -0.007 0.011 -10000 0 -10000 0 0
FYN 0.17 0.17 0.43 86 -10000 0 86
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle 0.17 0.18 0.45 93 -10000 0 93
ETS1 -0.001 0.043 0.1 78 -10000 0 78
PXN 0.12 0.14 0.35 82 -10000 0 82
ITGB1 -0.014 0 -10000 0 -10000 0 0
NOS3 0.14 0.15 0.38 84 -10000 0 84
RAC1 -0.014 0 -10000 0 -10000 0 0
TNF 0.016 0.041 0.11 78 -10000 0 78
MAPKKK cascade 0.041 0.068 0.26 5 -10000 0 5
RASA1 -0.014 0.002 0 8 -10000 0 8
Tie2/Ang1/Shc 0.05 0.073 0.26 9 -10000 0 9
NCK1 -0.014 0.002 0 11 -10000 0 11
vasculogenesis 0.13 0.14 0.34 100 -10000 0 100
mol:Phosphatidic acid 0.041 0.068 0.26 5 -10000 0 5
mol:Angiotensin II 0.016 0.015 0.03 279 -10000 0 279
mol:NADP 0.14 0.15 0.37 86 -10000 0 86
Rac1/GTP 0.06 0.095 -10000 0 -10000 0 0
MMP2 0.09 0.091 0.26 64 -10000 0 64
S1P5 pathway

Figure S29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S29.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.061 0.038 0.12 126 -0.046 3 129
GNAI2 -0.014 0.001 0 1 -10000 0 1
S1P/S1P5/G12 -0.007 0.001 0 4 -10000 0 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.001 0.004 0 481 -10000 0 481
RhoA/GTP -0.062 0.039 0.048 3 -0.12 126 129
negative regulation of cAMP metabolic process 0 0.005 0.05 3 -0.068 1 4
GNAZ -0.012 0.005 0 72 -10000 0 72
GNAI3 -0.012 0.005 0 65 -10000 0 65
GNA12 -0.014 0.001 0 4 -10000 0 4
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0 0.005 0.05 3 -0.069 1 4
RhoA/GDP -0.009 0.001 0 2 -10000 0 2
RHOA -0.014 0.001 0 2 -10000 0 2
GNAI1 -0.012 0.005 0 81 -10000 0 81
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.016 0.002 0 6 -10000 0 6
ER alpha/Gai/GDP/Gbeta gamma -0.13 0.065 -10000 0 -0.16 406 406
AKT1 -0.019 0.013 -10000 0 -10000 0 0
PIK3CA -0.014 0.003 0 25 -10000 0 25
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.018 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.016 0.008 -10000 0 -10000 0 0
IGF1R -0.014 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.014 0 -10000 0 -10000 0 0
SHC1 -0.013 0.004 0 46 -10000 0 46
apoptosis 0.019 0.013 -10000 0 -10000 0 0
RhoA/GTP -0.021 0.013 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.11 0.046 -10000 0 -0.12 422 422
regulation of stress fiber formation 0.002 0.024 -10000 0 -0.099 4 4
E2/ERA-ERB (dimer) -0.014 0 -10000 0 -10000 0 0
KRAS -0.014 0.002 0 9 -10000 0 9
G13/GTP -0.012 0.001 0 2 -10000 0 2
pseudopodium formation -0.002 0.024 0.099 4 -10000 0 4
E2/ER alpha (dimer)/PELP1 -0.014 0 -10000 0 -10000 0 0
GRB2 -0.014 0.001 0 5 -10000 0 5
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 -0.001 0.004 0 481 -10000 0 481
HRAS -0.014 0.001 0 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.079 0.039 -10000 0 -0.18 20 20
E2/ER beta (dimer) -0.009 0 -10000 0 -10000 0 0
mol:GDP -0.012 0.008 0.065 1 -10000 0 1
mol:NADP -0.079 0.039 -10000 0 -0.18 20 20
PIK3R1 -0.013 0.004 0 36 -10000 0 36
mol:IP3 -0.017 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer -0.014 0 -10000 0 -10000 0 0
PLCB1 -0.013 0.007 -10000 0 -10000 0 0
PLCB2 -0.013 0.007 -10000 0 -10000 0 0
IGF1 -0.014 0.001 0 4 -10000 0 4
mol:L-citrulline -0.079 0.039 -10000 0 -0.18 20 20
RHOA -0.014 0.001 0 2 -10000 0 2
Gai/GDP -0.47 0.15 -10000 0 -0.52 481 481
JNK cascade -0.009 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 -0.014 0 -10000 0 -10000 0 0
GNAQ -0.014 0 -10000 0 -10000 0 0
ESR1 -0.014 0 -10000 0 -10000 0 0
Gq family/GDP/Gbeta gamma -0.003 0.021 -10000 0 -0.18 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.025 0.061 -10000 0 -0.63 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.1 0.051 -10000 0 -0.13 343 343
GNAZ -0.012 0.005 0 72 -10000 0 72
E2/ER alpha (dimer) -0.009 0 -10000 0 -10000 0 0
STRN -0.014 0 -10000 0 -10000 0 0
GNAL -0.014 0 -10000 0 -10000 0 0
PELP1 -0.014 0 -10000 0 -10000 0 0
MAPK11 -0.014 0 -10000 0 -10000 0 0
GNAI2 -0.014 0.001 0 1 -10000 0 1
GNAI3 -0.012 0.005 0 65 -10000 0 65
GNAI1 -0.012 0.005 0 81 -10000 0 81
HBEGF -0.086 0.074 0.12 5 -0.16 216 221
cAMP biosynthetic process -0.015 0 -10000 0 -10000 0 0
SRC -0.13 0.062 -10000 0 -0.16 406 406
PI3K -0.015 0.005 0 60 -10000 0 60
GNB1 -0.014 0.002 0 6 -10000 0 6
G13/GDP/Gbeta gamma -0.016 0.01 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.096 0.043 -10000 0 -0.12 391 391
Gs family/GTP -0.016 0 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.013 0.008 0 143 -10000 0 143
vasodilation -0.076 0.038 -10000 0 -0.16 31 31
mol:DAG -0.017 0.008 -10000 0 -10000 0 0
Gs family/GDP/Gbeta gamma -0.017 0.011 -10000 0 -10000 0 0
MSN -0.002 0.025 0.1 4 -10000 0 4
Gq family/GTP -0.009 0.001 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.018 0.014 -10000 0 -10000 0 0
NRAS -0.011 0.006 0 136 -10000 0 136
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.076 0.038 0.16 31 -10000 0 31
GRB2/SOS1 -0.008 0.001 0 5 -10000 0 5
RhoA/GDP -0.015 0.01 0.066 1 -10000 0 1
NOS3 -0.081 0.04 -10000 0 -0.19 20 20
GNA11 -0.014 0 -10000 0 -10000 0 0
MAPKKK cascade -0.054 0.04 -10000 0 -0.35 5 5
E2/ER alpha (dimer)/PELP1/Src -0.11 0.048 -10000 0 -0.13 366 366
ruffle organization -0.002 0.024 0.099 4 -10000 0 4
ROCK2 -0.004 0.046 0.12 6 -10000 0 6
GNA14 -0.014 0.001 0 2 -10000 0 2
GNA15 -0.014 0.002 0 7 -10000 0 7
GNA13 -0.014 0.001 0 2 -10000 0 2
MMP9 -0.096 0.077 0.11 3 -0.16 273 276
MMP2 -0.081 0.08 0.14 1 -0.16 223 224
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.022 0.052 0.11 125 -10000 0 125
PDGFB-D/PDGFRB/SLAP -0.007 0.016 0.021 121 -10000 0 121
PDGFB-D/PDGFRB/APS/CBL -0.005 0.014 0.019 138 -10000 0 138
AKT1 -0.026 0.032 0.15 4 -10000 0 4
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.019 0.043 0.11 50 -10000 0 50
PIK3CA -0.014 0.003 0 25 -10000 0 25
FGR 0.012 0.029 0.14 3 -10000 0 3
mol:Ca2+ 0.02 0.037 0.12 16 -10000 0 16
MYC 0.077 0.14 0.3 137 -10000 0 137
SHC1 -0.013 0.004 0 46 -10000 0 46
HRAS/GDP -0.013 0.021 0.092 4 -10000 0 4
LRP1/PDGFRB/PDGFB -0.008 0.02 0.025 134 -10000 0 134
GRB10 -0.014 0.002 0 16 -10000 0 16
PTPN11 -0.014 0 -10000 0 -10000 0 0
GO:0007205 0.02 0.037 0.12 16 -10000 0 16
PTEN -0.014 0.001 0 2 -10000 0 2
GRB2 -0.014 0.001 0 5 -10000 0 5
GRB7 -0.014 0.001 0 1 -10000 0 1
PDGFB-D/PDGFRB/SHP2 -0.007 0.017 0.021 136 -10000 0 136
PDGFB-D/PDGFRB/GRB10 -0.007 0.017 0.021 131 -10000 0 131
cell cycle arrest -0.007 0.016 0.021 121 -10000 0 121
HRAS -0.014 0.001 0 2 -10000 0 2
HIF1A -0.028 0.029 0.14 4 -10000 0 4
GAB1 0.036 0.06 0.13 129 -10000 0 129
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.031 0.061 0.13 130 -10000 0 130
PDGFB-D/PDGFRB 0.006 0.043 0.078 135 -10000 0 135
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.007 0.017 0.021 136 -10000 0 136
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.027 0.072 0.15 122 -10000 0 122
positive regulation of MAPKKK cascade -0.007 0.017 0.021 136 -10000 0 136
PIK3R1 -0.013 0.004 0 36 -10000 0 36
mol:IP3 0.02 0.037 0.12 16 -10000 0 16
E5 0 0.001 -10000 0 -10000 0 0
CSK -0.015 0.003 -10000 0 -0.023 2 2
PDGFB-D/PDGFRB/GRB7 -0.007 0.017 0.021 136 -10000 0 136
SHB -0.014 0 -10000 0 -10000 0 0
BLK 0.009 0.025 0.15 2 -10000 0 2
PTPN2 -0.006 0.014 0.018 139 -10000 0 139
PDGFB-D/PDGFRB/SNX15 -0.007 0.017 0.021 136 -10000 0 136
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 0.025 0.067 0.21 56 -10000 0 56
CBL -0.014 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.007 0.017 0.021 136 -10000 0 136
LCK 0.01 0.026 0.15 2 -10000 0 2
PDGFRB -0.005 0.015 0.021 136 -10000 0 136
ACP1 -0.014 0.001 0 2 -10000 0 2
HCK 0.009 0.027 0.15 2 -10000 0 2
ABL1 0.028 0.047 0.1 128 -10000 0 128
PDGFB-D/PDGFRB/CBL 0.038 0.057 0.15 59 -10000 0 59
PTPN1 -0.006 0.014 0.018 139 -10000 0 139
SNX15 -0.014 0 -10000 0 -10000 0 0
STAT3 -0.014 0.002 0 10 -10000 0 10
STAT1 -0.014 0.003 0 18 -10000 0 18
cell proliferation 0.076 0.13 0.3 137 -10000 0 137
SLA -0.013 0.004 0 35 -10000 0 35
actin cytoskeleton reorganization -0.015 0.027 0.1 12 -10000 0 12
SRC 0.009 0.025 0.15 2 -10000 0 2
PI3K -0.03 0.013 0.013 2 -10000 0 2
PDGFB-D/PDGFRB/GRB7/SHC -0.009 0.019 0.025 114 -10000 0 114
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.019 0.043 0.11 50 -10000 0 50
LYN 0.01 0.028 0.16 2 -10000 0 2
LRP1 -0.014 0.003 0 18 -10000 0 18
SOS1 0 0 -10000 0 -10000 0 0
STAT5B -0.014 0 -10000 0 -10000 0 0
STAT5A -0.014 0.001 0 1 -10000 0 1
NCK1-2/p130 Cas -0.002 0.039 0.064 131 -10000 0 131
SPHK1 -0.008 0.011 0.011 144 -10000 0 144
EDG1 -0.008 0.012 0.012 139 -10000 0 139
mol:DAG 0.02 0.037 0.12 16 -10000 0 16
PLCG1 0.021 0.037 0.12 15 -10000 0 15
NHERF/PDGFRB -0.009 0.02 0.025 134 -10000 0 134
YES1 0.008 0.026 0.17 2 -10000 0 2
cell migration -0.009 0.019 0.025 134 -10000 0 134
SHC/Grb2/SOS1 -0.003 0.037 0.064 119 -10000 0 119
SLC9A3R2 -0.014 0 -10000 0 -10000 0 0
SLC9A3R1 -0.014 0.001 0 2 -10000 0 2
NHERF1-2/PDGFRB/PTEN -0.01 0.023 0.029 133 -10000 0 133
FYN 0.004 0.042 0.15 2 -0.31 6 8
DOK1 -0.019 0.012 0.096 4 -10000 0 4
HRAS/GTP -0.009 0.001 0 2 -10000 0 2
PDGFB -0.014 0 -10000 0 -10000 0 0
RAC1 0.013 0.067 0.29 27 -10000 0 27
PRKCD -0.013 0.019 0.1 4 -10000 0 4
FER -0.013 0.019 0.1 4 -10000 0 4
MAPKKK cascade -0.011 0.035 0.094 48 -10000 0 48
RASA1 -0.012 0.019 0.1 4 -10000 0 4
NCK1 -0.014 0.002 0 11 -10000 0 11
NCK2 -0.014 0.001 0 1 -10000 0 1
p62DOK/Csk -0.026 0.009 0.081 4 -10000 0 4
PDGFB-D/PDGFRB/SHB -0.007 0.017 0.021 136 -10000 0 136
chemotaxis 0.028 0.047 0.1 129 -10000 0 129
STAT1-3-5/STAT1-3-5 -0.012 0.036 0.052 124 -10000 0 124
Bovine Papilomavirus E5/PDGFRB -0.001 0.012 0.018 134 -10000 0 134
PTPRJ -0.014 0 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.015 0.002 0 6 -9999 0 6
CRKL -0.014 0 -10000 0 -9999 0 0
Rac1/GDP -0.009 0 -10000 0 -9999 0 0
DOCK1 -0.014 0 -10000 0 -9999 0 0
ITGA4 -0.014 0.001 0 5 -9999 0 5
alpha4/beta7 Integrin/MAdCAM1 -0.023 0.003 0 7 -9999 0 7
EPO -0.014 0 -10000 0 -9999 0 0
alpha4/beta7 Integrin -0.017 0.002 0 5 -9999 0 5
mol:GTP 0 0 -10000 0 -9999 0 0
CRK -0.014 0 -10000 0 -9999 0 0
alpha4/beta1 Integrin -0.017 0.002 0 5 -9999 0 5
EPO/EPOR (dimer) -0.017 0 -10000 0 -9999 0 0
lamellipodium assembly 0.002 0.021 0.083 16 -9999 0 16
PIK3CA -0.014 0.003 0 25 -9999 0 25
PI3K -0.015 0.005 0 60 -9999 0 60
ARF6 -0.014 0 -10000 0 -9999 0 0
JAK2 -0.013 0.001 -10000 0 -9999 0 0
PXN -0.014 0 -10000 0 -9999 0 0
PIK3R1 -0.013 0.004 0 36 -9999 0 36
MADCAM1 -0.014 0 -10000 0 -9999 0 0
cell adhesion -0.023 0.003 0 7 -9999 0 7
CRKL/CBL -0.017 0 -10000 0 -9999 0 0
ITGB1 -0.014 0 -10000 0 -9999 0 0
SRC 0.055 0.056 0.093 353 -9999 0 353
ITGB7 -0.014 0.001 0 2 -9999 0 2
RAC1 -0.014 0 -10000 0 -9999 0 0
alpha4/beta1 Integrin/VCAM1 -0.007 0.01 0 353 -9999 0 353
p130Cas/Crk/Dock1 0.049 0.056 0.088 353 -9999 0 353
VCAM1 -0.005 0.007 0 351 -9999 0 351
RHOA -0.014 0.001 0 2 -9999 0 2
alpha4/beta1 Integrin/Paxillin/GIT1 -0.023 0.002 0 5 -9999 0 5
BCAR1 0.052 0.053 0.089 353 -9999 0 353
EPOR -0.014 0 -10000 0 -9999 0 0
mol:GDP 0 0 -10000 0 -9999 0 0
CBL -0.014 0 -10000 0 -9999 0 0
GIT1 -0.014 0 -10000 0 -9999 0 0
Rac1/GTP 0.002 0.022 0.083 16 -9999 0 16
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.005 0.049 0.12 67 -10000 0 67
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL -0.014 0 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.033 0.022 0.072 11 -10000 0 11
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.014 0.023 0.045 68 -10000 0 68
antigen processing and presentation of peptide antigen via MHC class I -0.038 0.032 -10000 0 -10000 0 0
CaM/Ca2+ 0.002 0.047 0.11 62 -10000 0 62
RAP1A -0.014 0 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.007 0.053 0.12 69 -10000 0 69
AKT1 -0.009 0.044 0.089 58 -10000 0 58
MAP2K1 -0.015 0.038 0.076 65 -10000 0 65
MAP3K11 -0.01 0.041 0.084 81 -10000 0 81
IFNGR1 -0.012 0.012 0.018 68 -10000 0 68
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.1 0.096 -10000 0 -0.17 323 323
Rap1/GTP -0.03 0.014 -10000 0 -10000 0 0
CRKL/C3G -0.017 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.003 0.037 0.069 67 -10000 0 67
CEBPB -0.016 0.062 0.21 2 -0.28 15 17
STAT3 -0.014 0.002 0 10 -10000 0 10
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.01 0.034 -10000 0 -10000 0 0
STAT1 -0.007 0.051 0.12 65 -10000 0 65
CALM1 -0.013 0.003 0 27 -10000 0 27
IFN-gamma (dimer) -0.012 0.013 0.018 80 -10000 0 80
PIK3CA -0.013 0.003 0 25 -10000 0 25
STAT1 (dimer)/PIAS1 -0.011 0.051 0.12 65 -10000 0 65
CEBPB/PTGES2/Cbp/p300 -0.037 0.037 -10000 0 -0.22 15 15
mol:Ca2+ 0.004 0.047 0.11 67 -10000 0 67
MAPK3 -0.004 0.039 -10000 0 -10000 0 0
STAT1 (dimer) -0.031 0.079 0.2 44 -10000 0 44
MAPK1 -0.025 0.12 -10000 0 -0.67 17 17
JAK2 -0.012 0.013 0.018 81 -10000 0 81
PIK3R1 -0.013 0.004 0 36 -10000 0 36
JAK1 -0.012 0.013 0.018 81 -10000 0 81
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 -0.012 0.046 0.18 2 -0.19 15 17
SMAD7 0.02 0.086 0.14 165 -10000 0 165
CBL/CRKL/C3G -0.017 0.044 0.084 81 -10000 0 81
PI3K -0.002 0.045 0.098 57 -10000 0 57
IFNG -0.012 0.013 0.018 80 -10000 0 80
apoptosis -0.001 0.048 0.18 2 -10000 0 2
CAMK2G -0.007 0.007 0 266 -10000 0 266
STAT3 (dimer) -0.014 0.002 0 10 -10000 0 10
CAMK2A -0.013 0.003 0 24 -10000 0 24
CAMK2B -0.002 0.005 0 451 -10000 0 451
FRAP1 -0.011 0.046 0.1 33 -10000 0 33
PRKCD -0.004 0.052 0.1 70 -10000 0 70
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.038 0.032 -10000 0 -10000 0 0
PTPN2 -0.014 0.001 0 1 -10000 0 1
EP300 -0.011 0.011 0.017 70 -10000 0 70
IRF1 -0.033 0.02 -10000 0 -10000 0 0
STAT1 (dimer)/PIASy -0.01 0.052 0.13 58 -10000 0 58
SOCS1 -0.003 0.001 -10000 0 -10000 0 0
mol:GDP -0.017 0.041 0.077 81 -10000 0 81
CASP1 -0.024 0.022 0.13 1 -10000 0 1
PTGES2 -0.014 0 -10000 0 -10000 0 0
IRF9 -0.012 0.037 0.078 57 -0.1 15 72
mol:PI-3-4-5-P3 -0.011 0.03 0.059 34 -10000 0 34
RAP1/GDP -0.029 0.018 0.041 16 -10000 0 16
CBL -0.01 0.041 0.084 81 -10000 0 81
MAP3K1 -0.01 0.041 0.085 77 -10000 0 77
PIAS1 -0.014 0 -10000 0 -10000 0 0
PIAS4 -0.014 0 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.038 0.032 -10000 0 -10000 0 0
PTPN11 -0.006 0.042 0.091 81 -10000 0 81
CREBBP -0.011 0.011 0.017 70 -10000 0 70
RAPGEF1 -0.014 0 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.001 0.043 0.075 131 -10000 0 131
DAPP1 0.012 0.041 0.1 66 -10000 0 66
Src family/SYK family/BLNK-LAT/BTK-ITK 0.027 0.059 0.16 60 -10000 0 60
mol:DAG 0.016 0.05 0.11 88 -10000 0 88
HRAS -0.008 0.013 0.014 136 -10000 0 136
RAP1A -0.008 0.013 0.014 137 -10000 0 137
ARF5/GDP -0.007 0.047 -10000 0 -0.21 21 21
PLCG2 -0.014 0.002 0 10 -10000 0 10
PLCG1 -0.014 0 -10000 0 -10000 0 0
ARF5 -0.014 0 -10000 0 -10000 0 0
mol:GTP 0.004 0.042 0.075 135 -10000 0 135
ARF1/GTP 0.007 0.038 0.072 135 -10000 0 135
RHOA -0.014 0.001 0 2 -10000 0 2
YES1 -0.012 0.005 0 79 -10000 0 79
RAP1A/GTP 0.006 0.045 0.082 135 -10000 0 135
ADAP1 0.003 0.039 0.07 131 -10000 0 131
ARAP3 0.004 0.042 0.074 135 -10000 0 135
INPPL1 -0.014 0 -10000 0 -10000 0 0
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 -0.014 0.003 0 19 -10000 0 19
ARHGEF7 -0.014 0.001 0 1 -10000 0 1
ARF1 -0.014 0.001 0 2 -10000 0 2
NRAS -0.012 0.007 0.014 1 -10000 0 1
FYN -0.014 0.003 0 21 -10000 0 21
ARF6 -0.014 0 -10000 0 -10000 0 0
FGR -0.014 0.003 0 17 -10000 0 17
mol:Ca2+ 0.006 0.031 0.081 52 -10000 0 52
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.014 0.003 0 21 -10000 0 21
ZAP70 -0.014 0 -10000 0 -10000 0 0
mol:IP3 0.007 0.039 0.098 52 -10000 0 52
LYN -0.012 0.005 0 64 -10000 0 64
ARF1/GDP -0.007 0.047 -10000 0 -0.21 21 21
RhoA/GDP 0.002 0.045 0.079 127 -0.096 4 131
PDK1/Src/Hsp90 -0.02 0 -10000 0 -10000 0 0
BLNK -0.012 0.005 0 68 -10000 0 68
actin cytoskeleton reorganization 0.001 0.038 0.098 7 -0.11 6 13
SRC -0.014 0 -10000 0 -10000 0 0
PLEKHA2 -0.013 0.001 0 1 -10000 0 1
RAC1 -0.014 0 -10000 0 -10000 0 0
PTEN -0.015 0.003 0 2 -0.025 4 6
HSP90AA1 -0.014 0 -10000 0 -10000 0 0
ARF6/GTP 0.001 0.043 0.075 131 -10000 0 131
RhoA/GTP 0.002 0.044 0.076 135 -10000 0 135
Src family/SYK family/BLNK-LAT -0.002 0.021 -10000 0 -10000 0 0
BLK -0.014 0 -10000 0 -10000 0 0
PDPK1 -0.014 0 -10000 0 -10000 0 0
CYTH1 0.003 0.039 0.07 131 -10000 0 131
HCK -0.012 0.005 0 86 -10000 0 86
CYTH3 0.003 0.039 0.07 131 -10000 0 131
CYTH2 0.003 0.039 0.07 131 -10000 0 131
KRAS -0.008 0.013 0.014 133 -10000 0 133
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.001 0.024 -10000 0 -10000 0 0
SGK1 0.006 0.025 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.004 0.047 -10000 0 -0.21 21 21
SOS1 0 0 -10000 0 -10000 0 0
SYK -0.013 0.004 0 36 -10000 0 36
ARF6/GDP 0 0.042 0.072 127 -0.096 4 131
mol:PI-3-4-5-P3 0.004 0.042 0.076 131 -10000 0 131
ARAP3/RAP1A/GTP 0.006 0.045 0.083 135 -10000 0 135
VAV1 -0.014 0.001 0 1 -10000 0 1
mol:PI-3-4-P2 -0.009 0 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I -0.015 0.009 -10000 0 -10000 0 0
PLEKHA1 -0.012 0.004 0 63 -10000 0 63
Rac1/GDP -0.007 0.047 -10000 0 -0.21 21 21
LAT -0.014 0.001 0 1 -10000 0 1
Rac1/GTP -0.009 0.046 -10000 0 -0.2 23 23
ITK -0.001 0.04 0.068 128 -10000 0 128
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.017 0.058 0.12 87 -10000 0 87
LCK -0.014 0.001 0 4 -10000 0 4
BTK -0.001 0.04 0.068 131 -10000 0 131
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 -0.014 0.002 0 11 -10000 0 11
VLDLR -0.014 0.001 0 3 -10000 0 3
LRPAP1 -0.014 0 -10000 0 -10000 0 0
NUDC -0.014 0 -10000 0 -10000 0 0
RELN/LRP8 -0.009 0.01 0 282 -10000 0 282
CaM/Ca2+ -0.008 0.002 0 27 -10000 0 27
KATNA1 -0.014 0.002 0 6 -10000 0 6
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.011 0.013 0.092 2 -10000 0 2
IQGAP1/CaM -0.012 0.008 0 145 -10000 0 145
DAB1 -0.014 0 -10000 0 -10000 0 0
IQGAP1 -0.011 0.006 0 127 -10000 0 127
PLA2G7 -0.014 0.002 0 8 -10000 0 8
CALM1 -0.013 0.003 0 27 -10000 0 27
DYNLT1 -0.012 0.005 0 75 -10000 0 75
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 -0.017 0 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 -0.014 0 -10000 0 -10000 0 0
CDK5R1 -0.011 0.006 0 101 -10000 0 101
LIS1/Poliovirus Protein 3A -0.013 0.001 0 6 -10000 0 6
CDK5R2 -0.005 0.007 0 325 -10000 0 325
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.009 0.01 0 283 -10000 0 283
YWHAE -0.014 0.001 0 2 -10000 0 2
NDEL1/14-3-3 E -0.014 0.03 0.094 2 -10000 0 2
MAP1B -0.002 0.001 -10000 0 -10000 0 0
RAC1 -0.006 0.003 0 133 -10000 0 133
p35/CDK5 -0.001 0.026 0.084 1 -10000 0 1
RELN -0.007 0.007 0 282 -10000 0 282
PAFAH/LIS1 -0.02 0.003 0 14 -10000 0 14
LIS1/CLIP170 -0.02 0.002 0 6 -10000 0 6
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.023 0.028 0.046 1 -10000 0 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.005 0.006 -10000 0 -10000 0 0
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.002 0.016 0.075 1 -10000 0 1
LIS1/IQGAP1 -0.015 0.009 0 133 -10000 0 133
RHOA -0.005 0.003 0 134 -10000 0 134
PAFAH1B1 -0.017 0.002 0 6 -10000 0 6
PAFAH1B3 -0.014 0.001 0 1 -10000 0 1
PAFAH1B2 -0.014 0 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.018 0.01 -10000 0 -0.054 39 39
NDEL1/Katanin 60/Dynein heavy chain -0.019 0.03 0.093 2 -10000 0 2
LRP8 -0.014 0 -10000 0 -10000 0 0
NDEL1/Katanin 60 -0.013 0.029 0.094 2 -10000 0 2
P39/CDK5 -0.002 0.018 0.084 1 -10000 0 1
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.02 0.002 0 6 -10000 0 6
CDK5 -0.011 0.015 0.086 2 -10000 0 2
PPP2R5D -0.014 0 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.016 0.002 0 6 -10000 0 6
CSNK2A1 -0.014 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.012 0.014 -10000 0 -10000 0 0
RELN/VLDLR -0.011 0.012 0 283 -10000 0 283
CDC42 -0.006 0.003 0 133 -10000 0 133
IL23-mediated signaling events

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
CCL2 0.12 0.3 0.62 85 -0.79 15 100
IL23A 0.094 0.23 0.66 41 -10000 0 41
NF kappa B1 p50/RelA/I kappa B alpha 0.033 0.15 0.39 1 -10000 0 1
positive regulation of T cell mediated cytotoxicity 0.11 0.25 0.73 43 -10000 0 43
ITGA3 0.097 0.23 0.62 50 -10000 0 50
IL17F 0.056 0.17 0.39 75 -10000 0 75
IL12B 0.025 0.067 0.15 92 -10000 0 92
STAT1 (dimer) 0.086 0.21 0.59 42 -10000 0 42
CD4 0.1 0.24 0.67 46 -10000 0 46
IL23 0.085 0.22 0.6 41 -10000 0 41
IL23R 0.054 0.12 0.27 92 -10000 0 92
IL1B 0.099 0.24 0.67 44 -10000 0 44
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.099 0.23 0.66 40 -10000 0 40
TYK2 0.012 0.045 0.093 92 -10000 0 92
STAT4 -0.008 0.007 0 219 -10000 0 219
STAT3 -0.014 0.002 0 10 -10000 0 10
IL18RAP -0.016 0.004 0.031 1 -0.033 1 2
IL12RB1 0.012 0.045 0.093 92 -10000 0 92
PIK3CA -0.014 0.003 0 25 -10000 0 25
IL12Rbeta1/TYK2 0.013 0.051 0.1 92 -10000 0 92
IL23R/JAK2 0.069 0.14 0.33 92 -10000 0 92
positive regulation of chronic inflammatory response 0.11 0.25 0.73 43 -10000 0 43
natural killer cell activation -0.004 0.009 -10000 0 -0.021 92 92
JAK2 0.025 0.067 0.15 92 -10000 0 92
PIK3R1 -0.013 0.004 0 36 -10000 0 36
NFKB1 -0.003 0.015 0.019 90 -10000 0 90
RELA -0.003 0.015 0.019 92 -10000 0 92
positive regulation of dendritic cell antigen processing and presentation 0.085 0.21 0.58 44 -10000 0 44
ALOX12B 0.099 0.23 0.66 40 -10000 0 40
CXCL1 0.1 0.24 0.69 47 -10000 0 47
T cell proliferation 0.11 0.25 0.73 43 -10000 0 43
NFKBIA -0.003 0.015 0.019 91 -10000 0 91
IL17A 0.056 0.17 0.37 86 -10000 0 86
PI3K 0.032 0.14 0.38 3 -10000 0 3
IFNG 0.009 0.022 0.08 28 -10000 0 28
STAT3 (dimer) 0.024 0.14 -10000 0 -10000 0 0
IL18R1 -0.016 0.004 0.031 1 -0.033 1 2
IL23/IL23R/JAK2/TYK2/SOCS3 0.083 0.19 0.43 92 -10000 0 92
IL18/IL18R -0.02 0.013 0.14 1 -10000 0 1
macrophage activation -0.001 0.007 -10000 0 -10000 0 0
TNF 0.098 0.23 0.67 41 -10000 0 41
STAT3/STAT4 0.026 0.13 0.38 2 -10000 0 2
STAT4 (dimer) 0.069 0.2 0.59 37 -10000 0 37
IL18 -0.014 0.005 0.031 1 -10000 0 1
IL19 0.099 0.22 0.66 40 -10000 0 40
STAT5A (dimer) 0.089 0.22 0.59 43 -10000 0 43
STAT1 -0.014 0.003 0 18 -10000 0 18
SOCS3 -0.014 0 -10000 0 -10000 0 0
CXCL9 0.11 0.24 0.64 58 -10000 0 58
MPO 0.099 0.22 0.66 40 -10000 0 40
positive regulation of humoral immune response 0.11 0.25 0.73 43 -10000 0 43
IL23/IL23R/JAK2/TYK2 0.11 0.25 0.73 43 -10000 0 43
IL6 0.1 0.24 0.66 54 -10000 0 54
STAT5A -0.014 0.001 0 1 -10000 0 1
IL2 -0.018 0.01 0.066 1 -0.05 12 13
positive regulation of tyrosine phosphorylation of STAT protein -0.004 0.009 -10000 0 -0.021 92 92
CD3E 0.099 0.23 0.66 40 -10000 0 40
keratinocyte proliferation 0.11 0.25 0.73 43 -10000 0 43
NOS2 0.1 0.22 0.64 43 -10000 0 43
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.008 0.008 0 292 -9999 0 292
alphaV beta3 Integrin -0.02 0.004 0 18 -9999 0 18
PTK2 0.022 0.042 0.12 29 -9999 0 29
IGF1R -0.014 0 -10000 0 -9999 0 0
PI4KB -0.014 0.001 0 1 -9999 0 1
MFGE8 -0.014 0.001 0 3 -9999 0 3
SRC -0.014 0 -10000 0 -9999 0 0
CDKN1B -0.008 0.002 -10000 0 -9999 0 0
VEGFA -0.006 0.007 0 287 -9999 0 287
ILK -0.008 0.002 -10000 0 -9999 0 0
ROCK1 -0.014 0 -10000 0 -9999 0 0
AKT1 -0.012 0.01 0.099 4 -9999 0 4
PTK2B 0.041 0.064 0.094 298 -9999 0 298
alphaV/beta3 Integrin/JAM-A -0.019 0.029 0.087 36 -9999 0 36
CBL -0.014 0 -10000 0 -9999 0 0
mol:GTP 0 0 -10000 0 -9999 0 0
alphaV beta3 Integrin/ANGPTL3 -0.02 0.003 0 16 -9999 0 16
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.023 0.003 0 9 -9999 0 9
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.021 0.028 0.048 279 -9999 0 279
alphaV/beta3 Integrin/Syndecan-1 -0.018 0.006 0 59 -9999 0 59
PI4KA -0.005 0.007 0 338 -9999 0 338
IGF-1R heterotetramer/IGF1/IRS1 -0.027 0.014 -10000 0 -9999 0 0
PI4 Kinase -0.006 0.008 0 338 -9999 0 338
PIK3CA -0.014 0.003 0 25 -9999 0 25
alphaV/beta3 Integrin/Osteopontin -0.013 0.01 0 191 -9999 0 191
RPS6KB1 -0.013 0.051 0.18 12 -9999 0 12
TLN1 -0.013 0.004 0 46 -9999 0 46
MAPK3 -0.004 0.028 0.1 5 -9999 0 5
GPR124 -0.014 0.001 0 4 -9999 0 4
MAPK1 -0.004 0.027 0.1 5 -9999 0 5
PXN -0.014 0 -10000 0 -9999 0 0
PIK3R1 -0.013 0.004 0 36 -9999 0 36
alphaV/beta3 Integrin/Tumstatin -0.02 0.003 0 16 -9999 0 16
cell adhesion -0.021 0.004 -10000 0 -9999 0 0
ANGPTL3 -0.014 0 -10000 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.009 0.01 0 292 -9999 0 292
IGF-1R heterotetramer -0.014 0 -10000 0 -9999 0 0
Rac1/GDP -0.009 0 -10000 0 -9999 0 0
TGFBR2 -0.014 0.002 0 8 -9999 0 8
ITGB3 -0.014 0 -10000 0 -9999 0 0
IGF1 -0.014 0.001 0 4 -9999 0 4
RAC1 -0.014 0 -10000 0 -9999 0 0
regulation of cell-matrix adhesion -0.019 0.004 0 20 -9999 0 20
apoptosis -0.014 0.002 0 16 -9999 0 16
CD47 -0.014 0.001 0 2 -9999 0 2
alphaV/beta3 Integrin/CD47 -0.02 0.004 0 18 -9999 0 18
VCL -0.014 0 -10000 0 -9999 0 0
alphaV/beta3 Integrin/Del1 -0.02 0.003 0 16 -9999 0 16
CSF1 -0.014 0 -10000 0 -9999 0 0
PIK3C2A -0.008 0.002 -10000 0 -9999 0 0
PI4 Kinase/Pyk2 -0.007 0.016 -10000 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.01 0.012 0 298 -9999 0 298
FAK1/Vinculin 0.02 0.041 0.12 29 -9999 0 29
alphaV beta3/Integrin/ppsTEM5 -0.019 0.004 0 20 -9999 0 20
RHOA -0.014 0.001 0 2 -9999 0 2
VTN -0.014 0.001 0 2 -9999 0 2
BCAR1 0 0 -10000 0 -9999 0 0
FGF2 -0.014 0.001 0 2 -9999 0 2
F11R -0.016 0.004 0 36 -9999 0 36
alphaV/beta3 Integrin/Lactadherin -0.02 0.004 0 19 -9999 0 19
alphaV/beta3 Integrin/TGFBR2 -0.019 0.004 0 24 -9999 0 24
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.017 0.003 0 16 -9999 0 16
HSP90AA1 -0.014 0 -10000 0 -9999 0 0
alphaV/beta3 Integrin/Talin -0.016 0.006 0 57 -9999 0 57
mol:GDP 0 0 -10000 0 -9999 0 0
FN1 -0.011 0.006 0 104 -9999 0 104
alphaV/beta3 Integrin/Pyk2 0.034 0.058 0.09 271 -9999 0 271
SDC1 -0.013 0.004 0 47 -9999 0 47
VAV3 -0.018 0.017 0.091 12 -9999 0 12
PTPN11 -0.014 0 -10000 0 -9999 0 0
IRS1 -0.014 0.001 0 5 -9999 0 5
FAK1/Paxillin 0.02 0.041 0.12 29 -9999 0 29
cell migration 0.015 0.039 0.11 29 -9999 0 29
ITGAV -0.014 0.002 0 16 -9999 0 16
PI3K -0.027 0.02 0.073 12 -9999 0 12
SPP1 -0.009 0.007 0 187 -9999 0 187
KDR -0.014 0.003 0 17 -9999 0 17
mol:PI-4-5-P2 0 0 -10000 0 -9999 0 0
alphaV/beta3 Integrin/Caspase 8 -0.014 0.002 0 16 -9999 0 16
COL4A3 -0.014 0 -10000 0 -9999 0 0
angiogenesis -0.002 0.032 0.12 10 -9999 0 10
Rac1/GTP -0.021 0.017 0.085 12 -9999 0 12
EDIL3 -0.014 0 -10000 0 -9999 0 0
cell proliferation -0.019 0.004 0 24 -9999 0 24
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.046 0.096 0.15 9 -0.33 52 61
CRKL -0.043 0.1 0.16 9 -0.34 52 61
HRAS -0.04 0.084 0.15 9 -0.28 52 61
mol:PIP3 -0.03 0.097 0.16 9 -0.31 52 61
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 -0.014 0 -10000 0 -10000 0 0
GAB1 -0.039 0.11 0.18 9 -0.35 52 61
FOXO3 -0.034 0.092 -10000 0 -0.3 52 52
AKT1 -0.031 0.098 -10000 0 -0.32 52 52
BAD -0.034 0.092 -10000 0 -0.3 52 52
megakaryocyte differentiation -0.038 0.1 0.18 9 -0.34 52 61
GSK3B -0.034 0.093 0.21 1 -0.3 52 53
RAF1 -0.035 0.073 0.13 9 -0.24 52 61
SHC1 -0.013 0.004 0 46 -10000 0 46
STAT3 -0.039 0.11 0.18 9 -0.35 52 61
STAT1 -0.074 0.21 -10000 0 -0.7 52 52
HRAS/SPRED1 -0.034 0.071 0.13 9 -0.24 52 61
cell proliferation -0.039 0.1 0.18 9 -0.34 52 61
PIK3CA -0.014 0.003 0 25 -10000 0 25
TEC -0.014 0 -10000 0 -10000 0 0
RPS6KB1 -0.031 0.11 0.18 9 -0.34 52 61
HRAS/SPRED2 -0.034 0.074 0.13 9 -0.24 52 61
LYN/TEC/p62DOK -0.044 0.1 0.17 9 -0.34 52 61
MAPK3 -0.028 0.055 0.12 1 -0.18 52 53
STAP1 -0.039 0.1 0.18 9 -0.35 52 61
GRAP2 -0.014 0 -10000 0 -10000 0 0
JAK2 -0.064 0.19 -10000 0 -0.62 52 52
STAT1 (dimer) -0.073 0.21 -10000 0 -0.69 52 52
mol:Gleevec 0.002 0.004 0.014 52 -0.011 9 61
GRB2/SOCS1/VAV1 -0.047 0.1 0.17 9 -0.34 52 61
actin filament polymerization -0.034 0.1 0.18 9 -0.34 52 61
LYN -0.012 0.005 0 64 -10000 0 64
STAP1/STAT5A (dimer) -0.055 0.14 -10000 0 -0.47 52 52
PIK3R1 -0.013 0.004 0 36 -10000 0 36
CBL/CRKL/GRB2 -0.048 0.095 0.16 9 -0.32 52 61
PI3K -0.038 0.1 0.17 7 -0.33 52 59
PTEN -0.014 0.001 0 2 -10000 0 2
SCF/KIT/EPO/EPOR -0.087 0.24 -10000 0 -0.79 52 52
MAPK8 -0.04 0.11 0.18 9 -0.35 52 61
STAT3 (dimer) -0.037 0.11 0.18 9 -0.34 52 61
positive regulation of transcription -0.023 0.046 0.11 1 -0.15 52 53
mol:GDP -0.043 0.087 0.15 9 -0.29 52 61
PIK3C2B -0.039 0.11 0.18 9 -0.35 52 61
CBL/CRKL -0.045 0.097 0.16 9 -0.33 52 61
FER -0.04 0.11 0.18 9 -0.35 52 61
SH2B3 -0.039 0.1 0.18 9 -0.34 52 61
PDPK1 -0.032 0.091 0.15 9 -0.29 52 61
SNAI2 -0.034 0.1 0.19 9 -0.32 52 61
positive regulation of cell proliferation -0.06 0.17 -10000 0 -0.57 52 52
KITLG -0.016 0.012 0.035 9 -0.043 1 10
cell motility -0.06 0.17 -10000 0 -0.57 52 52
PTPN6 -0.01 0.013 0.028 52 -10000 0 52
EPOR -0.026 0.077 -10000 0 -10000 0 0
STAT5A (dimer) -0.05 0.14 -10000 0 -0.48 52 52
SOCS1 -0.014 0 -10000 0 -10000 0 0
cell migration 0.039 0.1 0.34 52 -0.18 9 61
SOS1 0 0 -10000 0 -10000 0 0
EPO -0.015 0.008 0.016 25 -10000 0 25
VAV1 -0.014 0.001 0 1 -10000 0 1
GRB10 -0.038 0.1 0.18 9 -0.34 52 61
PTPN11 -0.01 0.011 0.022 52 -10000 0 52
SCF/KIT -0.036 0.11 0.2 9 -0.36 52 61
GO:0007205 0.003 0.006 0.02 52 -0.014 9 61
MAP2K1 -0.032 0.06 0.11 8 -0.2 52 60
CBL -0.014 0 -10000 0 -10000 0 0
KIT -0.081 0.25 0.31 9 -0.84 52 61
MAP2K2 -0.032 0.06 0.11 9 -0.2 52 61
SHC/Grb2/SOS1 -0.04 0.096 0.16 9 -0.32 52 61
STAT5A -0.052 0.15 -10000 0 -0.49 52 52
GRB2 -0.014 0.001 0 5 -10000 0 5
response to radiation -0.016 0.11 0.19 9 -0.32 52 61
SHC/GRAP2 -0.016 0.005 0 46 -10000 0 46
PTPRO -0.039 0.1 0.18 9 -0.35 52 61
SH2B2 -0.035 0.11 0.18 9 -0.35 52 61
DOK1 -0.014 0 -10000 0 -10000 0 0
MATK -0.04 0.11 0.18 9 -0.35 52 61
CREBBP -0.023 0.034 0.14 9 -10000 0 9
BCL2 -0.025 0.075 -10000 0 -10000 0 0
Aurora B 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
Condensin I complex -0.002 0.005 0.05 2 -10000 0 2
STMN1 -0.015 0.004 0 28 -10000 0 28
Aurora B/RasGAP/Survivin -0.011 0.012 -10000 0 -10000 0 0
Chromosomal passenger complex/Cul3 protein complex -0.004 0.007 -10000 0 -0.065 6 6
BIRC5 -0.008 0.008 0.012 9 -10000 0 9
DES 0.005 0.005 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.002 0.018 0.025 21 -10000 0 21
Aurora B/TACC1 -0.006 0.011 0.014 71 -10000 0 71
Aurora B/PP2A -0.01 0.012 0.014 99 -10000 0 99
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.002 0.001 0.003 1 -0.007 1 2
mitotic metaphase/anaphase transition 0 0.001 -10000 0 -10000 0 0
NDC80 -0.011 0.008 0 184 -10000 0 184
Cul3 protein complex -0.013 0.002 0 12 -10000 0 12
KIF2C 0 0.006 -10000 0 -10000 0 0
PEBP1 -0.006 0.013 0.014 161 -10000 0 161
KIF20A -0.009 0.007 0.011 4 -10000 0 4
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP -0.01 0.012 0.014 99 -10000 0 99
SEPT1 0 0 -10000 0 -10000 0 0
SMC2 -0.013 0.005 0 61 -10000 0 61
SMC4 -0.003 0.006 0 401 -10000 0 401
NSUN2/NPM1/Nucleolin 0.006 0.018 -10000 0 -10000 0 0
PSMA3 -0.014 0.001 0 2 -10000 0 2
G2/M transition of mitotic cell cycle 0 0.001 0.004 1 -0.005 1 2
H3F3B -0.004 0.002 0.003 22 -10000 0 22
AURKB -0.008 0.01 0.011 103 -10000 0 103
AURKC -0.014 0.001 0 2 -10000 0 2
CDCA8 -0.004 0.014 0.015 175 -10000 0 175
cytokinesis 0.002 0.024 0.062 47 -10000 0 47
Aurora B/Septin1 0.006 0.032 0.086 47 -10000 0 47
AURKA -0.012 0.005 0.011 19 -10000 0 19
INCENP -0.003 0.015 0.016 192 -10000 0 192
KLHL13 0 0 -10000 0 -10000 0 0
BUB1 -0.013 0.005 0.01 17 -10000 0 17
hSgo1/Aurora B/Survivin -0.006 0.008 -10000 0 -10000 0 0
EVI5 -0.007 0.012 0.012 153 -10000 0 153
RhoA/GTP -0.003 0.024 0.063 30 -10000 0 30
SGOL1 0 0 -10000 0 -10000 0 0
CENPA 0.004 0.017 0.086 11 -10000 0 11
NCAPG -0.011 0.006 0 116 -10000 0 116
Aurora B/HC8 Proteasome -0.01 0.012 0.014 99 -10000 0 99
NCAPD2 -0.011 0.006 0 105 -10000 0 105
Aurora B/PP1-gamma -0.01 0.012 0.014 99 -10000 0 99
RHOA -0.014 0.001 0 2 -10000 0 2
NCAPH -0.014 0.002 0 16 -10000 0 16
NPM1 0 0.005 -10000 0 -10000 0 0
RASA1 -0.014 0.002 0 8 -10000 0 8
KLHL9 -0.014 0.002 0 12 -10000 0 12
mitotic prometaphase 0.001 0.003 0.007 93 -10000 0 93
proteasomal ubiquitin-dependent protein catabolic process -0.01 0.012 0.014 99 -10000 0 99
PPP1CC -0.014 0.001 0 1 -10000 0 1
Centraspindlin -0.001 0.024 0.069 30 -10000 0 30
RhoA/GDP -0.009 0.001 0 2 -10000 0 2
NSUN2 0 0.002 -10000 0 -10000 0 0
MYLK -0.004 0.002 0.003 22 -10000 0 22
KIF23 -0.008 0.01 0.006 164 -10000 0 164
VIM -0.014 0.005 0 47 -10000 0 47
RACGAP1 -0.009 0.008 0.001 179 -10000 0 179
mitosis 0 0 -10000 0 -10000 0 0
NCL 0 0.002 -10000 0 -10000 0 0
Chromosomal passenger complex -0.001 0.01 0.047 9 -10000 0 9
Chromosomal passenger complex/EVI5 -0.014 0.016 -10000 0 -10000 0 0
TACC1 -0.014 0.001 0 3 -10000 0 3
PPP2R5D -0.014 0 -10000 0 -10000 0 0
CUL3 -0.014 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.017 0 -10000 0 -10000 0 0
Necdin/E2F1 -0.011 0.008 0 200 -10000 0 200
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.021 0.005 0 29 -10000 0 29
NGF (dimer)/p75(NTR)/BEX1 -0.009 0.006 0 175 -10000 0 175
NT-4/5 (dimer)/p75(NTR) -0.008 0.002 0 22 -10000 0 22
IKBKB -0.014 0 -10000 0 -10000 0 0
AKT1 -0.01 0.034 0.098 43 -10000 0 43
IKBKG -0.014 0 -10000 0 -10000 0 0
BDNF -0.004 0.006 0 376 -10000 0 376
MGDIs/NGR/p75(NTR)/LINGO1 -0.006 0.001 0 22 -10000 0 22
FURIN -0.014 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.005 0.009 0 386 -10000 0 386
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.035 0.011 -10000 0 -10000 0 0
proBDNF (dimer) -0.004 0.006 0 376 -10000 0 376
NTRK1 -0.014 0.001 0 2 -10000 0 2
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis 0.009 0.029 0.14 10 -10000 0 10
IRAK1 -0.014 0.001 0 1 -10000 0 1
SHC1 -0.012 0.004 0 66 -10000 0 66
ARHGDIA -0.014 0 -10000 0 -10000 0 0
RhoA/GTP -0.009 0.001 0 2 -10000 0 2
Gamma Secretase -0.025 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.016 0.006 0 61 -10000 0 61
MAGEH1 -0.013 0.004 0 41 -10000 0 41
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.011 0.009 0 215 -10000 0 215
Mammalian IAPs/DIABLO -0.017 0.004 0 33 -10000 0 33
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 -0.014 0.001 0 3 -10000 0 3
APP -0.014 0.001 0 1 -10000 0 1
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 -0.014 0.002 0 6 -10000 0 6
RhoA/GDP/RHOGDI -0.012 0.022 0.091 22 -10000 0 22
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.009 0.022 0.1 17 -10000 0 17
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.008 0.004 -10000 0 -10000 0 0
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.013 0.003 0 22 -10000 0 22
NCSTN -0.013 0.003 0 30 -10000 0 30
mol:GTP -0.012 0.004 0 67 -10000 0 67
PSENEN -0.014 0.001 0 1 -10000 0 1
mol:ceramide -0.013 0.023 0.096 22 -10000 0 22
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.007 0.002 -10000 0 -10000 0 0
p75(NTR)/beta APP -0.016 0.003 0 23 -10000 0 23
BEX1 -0.01 0.007 0 158 -10000 0 158
mol:GDP -0.006 0.001 0 22 -10000 0 22
NGF (dimer) -0.015 0.006 0 78 -10000 0 78
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.011 0.002 0 22 -10000 0 22
PIK3R1 -0.013 0.004 0 36 -10000 0 36
RAC1/GTP -0.01 0.002 0 22 -10000 0 22
MYD88 -0.012 0.005 0 71 -10000 0 71
CHUK -0.014 0.001 0 1 -10000 0 1
NGF (dimer)/p75(NTR)/PKA -0.012 0.004 0 67 -10000 0 67
RHOB -0.014 0.003 0 21 -10000 0 21
RHOA -0.014 0.001 0 2 -10000 0 2
MAGE-G1/E2F1 -0.009 0 -10000 0 -10000 0 0
NT3 (dimer) -0.014 0 -10000 0 -10000 0 0
TP53 -0.005 0.018 0.08 11 -10000 0 11
PRDM4 -0.013 0.023 0.097 22 -10000 0 22
BDNF (dimer) -0.005 0.01 0 406 -10000 0 406
PIK3CA -0.014 0.003 0 25 -10000 0 25
SORT1 -0.014 0 -10000 0 -10000 0 0
activation of caspase activity -0.021 0.005 0 29 -10000 0 29
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.017 0.004 0 22 -10000 0 22
RHOC -0.01 0.007 0 163 -10000 0 163
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.003 0.019 0.088 12 -10000 0 12
DIABLO -0.014 0 -10000 0 -10000 0 0
SMPD2 -0.013 0.023 0.097 22 -10000 0 22
APH1B -0.014 0 -10000 0 -10000 0 0
APH1A -0.014 0.002 0 10 -10000 0 10
proNGF (dimer)/p75(NTR)/Sortilin -0.013 0.003 0 22 -10000 0 22
PSEN1 -0.014 0.001 0 1 -10000 0 1
APAF-1/Pro-Caspase 9 -0.017 0.001 0 4 -10000 0 4
NT3 (dimer)/p75(NTR) -0.016 0.003 0 22 -10000 0 22
MAPK8 0.004 0.023 0.089 15 -10000 0 15
MAPK9 0.004 0.023 0.089 15 -10000 0 15
APAF1 -0.014 0 -10000 0 -10000 0 0
NTF3 -0.014 0 -10000 0 -10000 0 0
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.009 0.007 0 200 -10000 0 200
RAC1/GDP -0.009 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.015 0.012 -10000 0 -10000 0 0
p75 CTF/Sortilin/TRAF6/NRIF -0.023 0.003 0 11 -10000 0 11
RhoA-B-C/GTP -0.012 0.004 0 67 -10000 0 67
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.007 0.012 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.006 0.01 0 386 -10000 0 386
PRKACB -0.013 0.004 0 46 -10000 0 46
proBDNF (dimer)/p75 ECD -0.005 0.008 0 379 -10000 0 379
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.013 0.003 0 33 -10000 0 33
BIRC2 -0.014 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.005 0.015 0.087 10 -10000 0 10
BAD -0.008 0.025 0.083 12 -10000 0 12
RIPK2 -0.014 0.001 0 1 -10000 0 1
NGFR -0.014 0.003 0 22 -10000 0 22
CYCS -0.017 0.022 0.091 22 -10000 0 22
ADAM17 -0.014 0.001 0 5 -10000 0 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.017 0.004 0 23 -10000 0 23
BCL2L11 -0.008 0.025 0.083 12 -10000 0 12
BDNF (dimer)/p75(NTR) -0.005 0.008 0 386 -10000 0 386
PI3K -0.015 0.006 0 79 -10000 0 79
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.011 0.002 0 22 -10000 0 22
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE -0.014 0.001 0 2 -10000 0 2
PRKCI -0.014 0.001 0 1 -10000 0 1
NGF (dimer)/p75(NTR) -0.008 0.002 0 22 -10000 0 22
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.017 0.004 0 25 -10000 0 25
TRAF6 -0.014 0 -10000 0 -10000 0 0
RAC1 -0.014 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG -0.014 0 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.003 0.014 0.082 9 -10000 0 9
SQSTM1 -0.014 0.001 0 1 -10000 0 1
NGFRAP1 -0.014 0.001 0 5 -10000 0 5
CASP3 -0.007 0.024 0.08 12 -10000 0 12
E2F1 -0.014 0 -10000 0 -10000 0 0
CASP9 -0.014 0.001 0 4 -10000 0 4
IKK complex -0.023 0.014 0.042 24 -0.077 1 25
NGF (dimer)/TRKA -0.009 0.001 0 2 -10000 0 2
MMP7 -0.012 0.005 0 78 -10000 0 78
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.021 0.005 0 28 -10000 0 28
MMP3 -0.014 0.002 0 7 -10000 0 7
APAF-1/Caspase 9 -0.035 0.013 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 -0.02 0.014 -10000 0 -0.052 32 32
AES -0.022 0.012 -10000 0 -0.047 43 43
FBXW11 -0.014 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.016 0.004 0.004 15 -10000 0 15
SMAD4 -0.011 0.006 0 126 -10000 0 126
DKK2 -0.014 0.002 0 10 -10000 0 10
TLE1 -0.022 0.012 -10000 0 -0.047 42 42
MACF1 -0.014 0.001 0 2 -10000 0 2
CTNNB1 0.034 0.024 0.12 9 -10000 0 9
WIF1 -0.002 0.005 0 462 -10000 0 462
beta catenin/RanBP3 -0.009 0.065 -10000 0 -0.2 7 7
KREMEN2 -0.014 0 -10000 0 -10000 0 0
DKK1 -0.011 0.006 0 116 -10000 0 116
beta catenin/beta TrCP1 0.036 0.024 0.11 10 -10000 0 10
FZD1 -0.013 0.002 0 10 -10000 0 10
AXIN2 0.028 0.039 0.11 44 -10000 0 44
AXIN1 -0.014 0 -10000 0 -10000 0 0
RAN -0.015 0.001 0 3 -10000 0 3
Axin1/APC/GSK3/beta catenin 0.008 0.039 -10000 0 -0.43 4 4
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.021 0.029 0.11 1 -10000 0 1
Axin1/APC/GSK3 0.018 0.015 0.073 8 -10000 0 8
Axin1/APC/GSK3/beta catenin/Macf1 0.005 0.035 0.1 9 -0.14 18 27
HNF1A -0.022 0.012 -10000 0 -0.048 42 42
CTBP1 -0.022 0.012 -10000 0 -0.048 42 42
MYC 0.09 0.14 0.33 137 -10000 0 137
RANBP3 -0.015 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.02 0.003 0 11 -10000 0 11
NKD1 0 0 -10000 0 -10000 0 0
TCF4 -0.022 0.012 -10000 0 -0.048 40 40
TCF3 -0.022 0.012 -10000 0 -0.048 42 42
WNT1/LRP6/FZD1/Axin1 -0.004 0.021 0.022 216 -10000 0 216
Ran/GTP -0.009 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.088 0.13 -10000 0 -0.26 173 173
LEF1 -0.022 0.012 -10000 0 -0.048 42 42
DVL1 -0.001 0.004 -10000 0 -10000 0 0
CSNK2A1 -0.014 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.035 0.034 0.11 35 -0.16 1 36
DKK1/LRP6/Kremen 2 -0.016 0.008 0 117 -10000 0 117
LRP6 -0.014 0.001 0 1 -10000 0 1
CSNK1A1 -0.023 0.014 -10000 0 -0.052 43 43
NLK -0.004 0.013 0.013 193 -10000 0 193
CCND1 0.072 0.13 0.34 99 -10000 0 99
WNT1 -0.014 0 -10000 0 -10000 0 0
GSK3A -0.014 0 -10000 0 -10000 0 0
GSK3B -0.013 0.004 0.008 15 -10000 0 15
FRAT1 -0.014 0.001 0 1 -10000 0 1
PPP2R5D 0 0.002 -10000 0 -10000 0 0
APC -0.022 0.017 0.086 11 -10000 0 11
WNT1/LRP6/FZD1 -0.001 0.004 -10000 0 -10000 0 0
CREBBP -0.022 0.012 -10000 0 -0.048 42 42
Circadian rhythm pathway

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
chromatin modification 0.004 0.067 0.24 2 -10000 0 2
CLOCK -0.006 0.019 0.034 96 -10000 0 96
TIMELESS/CRY2 0.032 0.097 0.26 3 -10000 0 3
DEC1/BMAL1 -0.009 0.019 0.031 98 -10000 0 98
ATR -0.014 0 -10000 0 -10000 0 0
NR1D1 0.024 0.072 -10000 0 -10000 0 0
ARNTL -0.006 0.019 0.034 98 -10000 0 98
TIMELESS 0.048 0.12 0.3 98 -10000 0 98
NPAS2 -0.006 0.019 0.034 99 -10000 0 99
CRY2 -0.014 0 -10000 0 -10000 0 0
mol:CO -0.017 0.04 -10000 0 -0.1 99 99
CHEK1 -0.013 0.005 0 61 -10000 0 61
mol:HEME 0.017 0.04 0.1 99 -10000 0 99
PER1 -0.014 0.001 0 3 -10000 0 3
BMAL/CLOCK/NPAS2 0.006 0.06 0.13 95 -10000 0 95
BMAL1/CLOCK 0.024 0.075 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.004 0.067 0.24 2 -10000 0 2
TIMELESS/CHEK1/ATR 0.004 0.068 0.24 2 -10000 0 2
mol:NADPH 0.017 0.04 0.1 99 -10000 0 99
PER1/TIMELESS 0.031 0.097 0.26 3 -10000 0 3
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.014 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.013 0.01 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 -0.016 0.006 0 68 -9999 0 68
NF kappa B1 p50/RelA/I kappa B alpha 0.011 0.037 0.062 184 -9999 0 184
SUMO1 -0.014 0 -10000 0 -9999 0 0
ZFPM1 0 0 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1/Ubc9 -0.005 0 -10000 0 -9999 0 0
FKBP3 -0.014 0.001 0 2 -9999 0 2
Histones 0.006 0.031 0.051 164 -9999 0 164
YY1/LSF -0.011 0 -10000 0 -9999 0 0
SMG5 -0.014 0 -10000 0 -9999 0 0
RAN -0.014 0.001 0 3 -9999 0 3
I kappa B alpha/HDAC3 -0.009 0.006 -10000 0 -9999 0 0
I kappa B alpha/HDAC1 0.008 0.03 0.052 165 -9999 0 165
SAP18 -0.014 0 -10000 0 -9999 0 0
RELA 0.019 0.034 0.066 185 -9999 0 185
HDAC1/Smad7 -0.018 0.007 0 65 -9999 0 65
RANGAP1 -0.014 0 -10000 0 -9999 0 0
HDAC3/TR2 0.009 0.032 0.052 185 -9999 0 185
NuRD/MBD3 Complex 0.006 0.021 0.041 137 -9999 0 137
NF kappa B1 p50/RelA 0.014 0.034 -10000 0 -9999 0 0
EntrezGene:23225 0 0 -10000 0 -9999 0 0
GATA2 -0.014 0.001 0 1 -9999 0 1
GATA1 -0.014 0 -10000 0 -9999 0 0
Mad/Max -0.017 0 -10000 0 -9999 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.003 0.023 -10000 0 -9999 0 0
RBBP7 -0.014 0 -10000 0 -9999 0 0
NPC -0.005 0 -10000 0 -9999 0 0
RBBP4 -0.012 0.006 0 100 -9999 0 100
MAX -0.014 0 -10000 0 -9999 0 0
EntrezGene:9972 0 0 -10000 0 -9999 0 0
FBXW11 -0.014 0 -10000 0 -9999 0 0
NFKBIA -0.006 0.004 0 186 -9999 0 186
KAT2B 0 0 -10000 0 -9999 0 0
mol:GTP 0 0 -10000 0 -9999 0 0
SIN3/HDAC complex -0.006 0.005 0.048 2 -9999 0 2
SIN3 complex -0.018 0 -10000 0 -9999 0 0
SMURF1 -0.014 0 -10000 0 -9999 0 0
CHD3 -0.014 0 -10000 0 -9999 0 0
SAP30 -0.014 0 -10000 0 -9999 0 0
EntrezGene:23636 0 0 -10000 0 -9999 0 0
NCOR1 -0.014 0 -10000 0 -9999 0 0
YY1/HDAC3 -0.007 0.005 -10000 0 -9999 0 0
YY1/HDAC2 -0.011 0.001 -10000 0 -9999 0 0
YY1/HDAC1 -0.009 0.004 -10000 0 -9999 0 0
NuRD/MBD2 Complex (MeCP1) 0.006 0.021 0.041 137 -9999 0 137
PPARG 0.021 0.04 0.075 184 -9999 0 184
HDAC8/hEST1B -0.014 0 -10000 0 -9999 0 0
UBE2I -0.014 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex -0.014 0 -10000 0 -9999 0 0
TNFRSF1A -0.009 0.007 0 183 -9999 0 183
HDAC3/SMRT (N-CoR2) 0.009 0.032 0.052 185 -9999 0 185
MBD3L2 0 0 -10000 0 -9999 0 0
ubiquitin-dependent protein catabolic process -0.018 0.007 0 65 -9999 0 65
CREBBP -0.014 0 -10000 0 -9999 0 0
NuRD/MBD3/MBD3L2 Complex 0.004 0.027 0.091 16 -9999 0 16
HDAC1 -0.012 0.005 0 65 -9999 0 65
HDAC3 -0.006 0.004 0 185 -9999 0 185
HDAC2 -0.014 0.001 0 5 -9999 0 5
YY1 -0.005 0 -10000 0 -9999 0 0
HDAC8 0 0 -10000 0 -9999 0 0
SMAD7 -0.014 0.001 0 1 -9999 0 1
NCOR2 -0.014 0 -10000 0 -9999 0 0
MXD1 -0.014 0 -10000 0 -9999 0 0
STAT3 -0.008 0.001 0 10 -9999 0 10
NFKB1 -0.014 0.001 0 4 -9999 0 4
EntrezGene:8021 0 0 -10000 0 -9999 0 0
RANBP2 -0.014 0.001 0 1 -9999 0 1
YY1/LSF/HDAC1 -0.013 0.005 -10000 0 -9999 0 0
YY1/SAP30/HDAC1 -0.013 0.005 -10000 0 -9999 0 0
EP300 -0.014 0 -10000 0 -9999 0 0
STAT3 (dimer non-phopshorylated) -0.008 0.001 0 10 -9999 0 10
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.004 0 186 -9999 0 186
histone deacetylation 0.006 0.021 0.041 137 -9999 0 137
STAT3 (dimer non-phopshorylated)/HDAC3 0.007 0.027 0.046 175 -9999 0 175
nuclear export 0.013 0 -10000 0 -9999 0 0
PRKACA -0.014 0 -10000 0 -9999 0 0
GATAD2B 0 0 -10000 0 -9999 0 0
GATAD2A -0.013 0.004 0 49 -9999 0 49
GATA2/HDAC3 0.009 0.032 0.052 185 -9999 0 185
GATA1/HDAC1 -0.015 0.006 0 65 -9999 0 65
GATA1/HDAC3 0.009 0.032 0.052 185 -9999 0 185
CHD4 -0.014 0 -10000 0 -9999 0 0
TNF-alpha/TNFR1A -0.011 0.008 0 185 -9999 0 185
SIN3/HDAC complex/Mad/Max 0.005 0.021 0.041 129 -9999 0 129
NuRD Complex 0.003 0.027 0.09 16 -9999 0 16
positive regulation of chromatin silencing 0.005 0.03 0.049 164 -9999 0 164
SIN3B -0.014 0 -10000 0 -9999 0 0
MTA2 -0.014 0 -10000 0 -9999 0 0
SIN3A 0 0 -10000 0 -9999 0 0
XPO1 -0.014 0 -10000 0 -9999 0 0
SUMO1/HDAC1 -0.01 0.004 -10000 0 -9999 0 0
HDAC complex -0.017 0.011 0 149 -9999 0 149
GATA1/Fog1 -0.009 0 -10000 0 -9999 0 0
FKBP25/HDAC1/HDAC2 -0.018 0.007 0 70 -9999 0 70
TNF -0.014 0.001 0 2 -9999 0 2
negative regulation of cell growth 0.005 0.021 0.041 129 -9999 0 129
NuRD/MBD2/PRMT5 Complex 0.006 0.021 0.041 137 -9999 0 137
Ran/GTP/Exportin 1 -0.014 0.003 0.05 1 -9999 0 1
NF kappa B/RelA/I kappa B alpha -0.007 0.005 -10000 0 -9999 0 0
SIN3/HDAC complex/NCoR1 -0.002 0.014 -10000 0 -9999 0 0
TFCP2 -0.014 0 -10000 0 -9999 0 0
NR2C1 -0.014 0 -10000 0 -9999 0 0
MBD3 -0.014 0 -10000 0 -9999 0 0
MBD2 -0.014 0 -10000 0 -9999 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.013 0.005 0 61 -10000 0 61
HRAS -0.014 0.001 0 2 -10000 0 2
EGFR -0.009 0.007 0 194 -10000 0 194
AKT 0.008 0.046 0.074 62 -0.1 3 65
FOXO3 -0.014 0 -10000 0 -10000 0 0
AKT1 -0.014 0.001 0 4 -10000 0 4
FOXO1 -0.014 0.002 0 11 -10000 0 11
AKT3 -0.014 0.001 0 1 -10000 0 1
FOXO4 -0.014 0 -10000 0 -10000 0 0
MET -0.014 0.002 0 10 -10000 0 10
PIK3CA -0.014 0.003 0 25 -10000 0 25
PIK3CB -0.014 0 -10000 0 -10000 0 0
NRAS -0.011 0.006 0 136 -10000 0 136
PIK3CG -0.014 0 -10000 0 -10000 0 0
PIK3R3 -0.014 0.001 0 1 -10000 0 1
PIK3R2 -0.014 0 -10000 0 -10000 0 0
NF1 -0.014 0 -10000 0 -10000 0 0
RAS 0.023 0.03 0.049 274 -10000 0 274
ERBB2 -0.014 0 -10000 0 -10000 0 0
proliferation/survival/translation -0.006 0.013 -10000 0 -10000 0 0
PI3K 0.024 0.032 0.059 204 -10000 0 204
PIK3R1 -0.013 0.004 0 36 -10000 0 36
KRAS -0.014 0.002 0 9 -10000 0 9
FOXO 0.02 0.04 0.073 76 -10000 0 76
AKT2 -0.014 0 -10000 0 -10000 0 0
PTEN -0.014 0.001 0 2 -10000 0 2
Regulation of Telomerase

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
Telomerase catalytic core complex 0.057 0.096 0.3 12 -10000 0 12
RAD9A -0.014 0.001 0 1 -10000 0 1
AP1 -0.006 0.018 0.034 75 -10000 0 75
IFNAR2 -0.007 0.016 0.026 99 -10000 0 99
AKT1 0 0.017 0.036 97 -10000 0 97
ER alpha/Oestrogen -0.004 0.01 0.017 99 -10000 0 99
NFX1/SIN3/HDAC complex 0.013 0.03 0.054 146 -10000 0 146
EGF -0.009 0.012 0.016 99 -10000 0 99
SMG5 -0.014 0 -10000 0 -10000 0 0
SMG6 -0.014 0 -10000 0 -10000 0 0
SP3/HDAC2 -0.007 0.021 0.044 71 -10000 0 71
TERT/c-Abl 0.026 0.056 0.27 12 -10000 0 12
SAP18 -0.009 0.01 0.011 99 -10000 0 99
MRN complex -0.02 0 -10000 0 -10000 0 0
WT1 -0.007 0.016 0.026 96 -10000 0 96
WRN -0.014 0.001 0 5 -10000 0 5
SP1 -0.006 0.019 0.035 99 -10000 0 99
SP3 -0.008 0.011 0.017 72 -10000 0 72
TERF2IP -0.013 0.004 0 44 -10000 0 44
Telomerase/Nucleolin 0.008 0.029 -10000 0 -10000 0 0
Mad/Max -0.008 0.02 0.034 99 -10000 0 99
TERT 0.035 0.078 0.3 17 -10000 0 17
CCND1 0.07 0.13 0.33 82 -10000 0 82
MAX -0.009 0.012 0.017 99 -10000 0 99
RBBP7 -0.009 0.01 0.012 99 -10000 0 99
RBBP4 -0.008 0.01 0.005 173 -10000 0 173
TERF2 -0.015 0.006 -10000 0 -10000 0 0
PTGES3 -0.014 0.001 0 1 -10000 0 1
SIN3A 0.001 0.001 -10000 0 -10000 0 0
Telomerase/911 0.012 0.027 0.12 4 -10000 0 4
CDKN1B -0.007 0.042 0.099 71 -10000 0 71
RAD1 -0.014 0.001 0 2 -10000 0 2
XRCC5 -0.014 0 -10000 0 -10000 0 0
XRCC6 -0.014 0 -10000 0 -10000 0 0
SAP30 -0.009 0.01 0.012 99 -10000 0 99
TRF2/PARP2 -0.017 0.006 -10000 0 -10000 0 0
UBE3A -0.009 0.012 0.016 99 -10000 0 99
JUN -0.008 0.012 0.017 99 -10000 0 99
E6 0.001 0.003 0.008 99 -10000 0 99
HPV-16 E6/E6AP -0.002 0.013 0.025 99 -10000 0 99
FOS -0.007 0.011 0.017 75 -10000 0 75
IFN-gamma/IRF1 -0.012 0.022 0.035 87 -10000 0 87
PARP2 -0.014 0.001 0 3 -10000 0 3
BLM -0.011 0.006 0 124 -10000 0 124
Telomerase 0.012 0.028 0.11 3 -10000 0 3
IRF1 -0.011 0.014 0.016 87 -10000 0 87
ESR1 -0.009 0.011 0.013 99 -10000 0 99
KU/TER -0.017 0 -10000 0 -10000 0 0
ATM/TRF2 -0.015 0.006 0 76 -10000 0 76
ubiquitin-dependent protein catabolic process 0.011 0.031 0.081 48 -10000 0 48
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.009 0.028 0.078 34 -10000 0 34
HDAC1 -0.008 0.01 0.006 150 -10000 0 150
HDAC2 -0.006 0.017 0.031 95 -10000 0 95
ATM 0.007 0.009 0.035 51 -10000 0 51
SMAD3 -0.018 0.006 0 27 -0.03 4 31
ABL1 -0.014 0.001 0 4 -10000 0 4
MXD1 -0.009 0.012 0.017 99 -10000 0 99
MRE11A -0.014 0 -10000 0 -10000 0 0
HUS1 -0.014 0 -10000 0 -10000 0 0
RPS6KB1 -0.014 0.001 0 1 -10000 0 1
TERT/NF kappa B1/14-3-3 0.05 0.085 0.28 3 -10000 0 3
NR2F2 -0.017 0.007 -10000 0 -0.033 2 2
MAPK3 -0.012 0.012 0.012 99 -10000 0 99
MAPK1 -0.011 0.012 0.012 99 -10000 0 99
TGFB1/TGF beta receptor Type II -0.015 0.004 -10000 0 -10000 0 0
NFKB1 -0.014 0.001 0 4 -10000 0 4
HNRNPC -0.014 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.007 0.009 0.035 51 -10000 0 51
NBN -0.014 0 -10000 0 -10000 0 0
EGFR -0.005 0.011 0.015 74 -10000 0 74
mol:Oestrogen 0.001 0.002 0.005 2 -10000 0 2
EGF/EGFR -0.005 0.016 0.029 74 -10000 0 74
MYC -0.007 0.011 0.019 56 -10000 0 56
IL2 -0.006 0.019 0.035 99 -10000 0 99
KU -0.017 0 -10000 0 -10000 0 0
RAD50 -0.014 0 -10000 0 -10000 0 0
HSP90AA1 -0.014 0 -10000 0 -10000 0 0
TGFB1 -0.015 0.004 -10000 0 -10000 0 0
TRF2/BLM -0.013 0.009 -10000 0 -10000 0 0
FRAP1 -0.014 0.001 0 1 -10000 0 1
KU/TERT 0.055 0.088 0.28 10 -10000 0 10
SP1/HDAC2 -0.003 0.031 0.064 95 -10000 0 95
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.008 0.029 -10000 0 -10000 0 0
Smad3/Myc -0.015 0.01 -10000 0 -10000 0 0
911 complex -0.02 0.002 0 3 -10000 0 3
IFNG -0.013 0.014 0.016 99 -10000 0 99
Telomerase/PinX1 0.008 0.026 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.019 0.042 0.14 9 -10000 0 9
SIN3B -0.009 0.01 0.012 99 -10000 0 99
YWHAE -0.014 0.001 0 2 -10000 0 2
Telomerase/EST1B 0.008 0.029 -10000 0 -10000 0 0
response to DNA damage stimulus 0.003 0.009 0.044 25 -10000 0 25
MRN complex/TRF2/Rap1 -0.026 0.01 -10000 0 -10000 0 0
TRF2/WRN -0.017 0.006 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.008 0.029 -10000 0 -10000 0 0
E2F1 -0.007 0.016 0.026 99 -10000 0 99
ZNFX1 0.001 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL -0.014 0 -10000 0 -10000 0 0
DKC1 -0.014 0.002 0 7 -10000 0 7
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.006 0.005 -9999 0 -9999 0 0
FZD6 -0.012 0.006 0 100 -9999 0 100
WNT6 -0.014 0 -9999 0 -9999 0 0
WNT4 -0.014 0.001 0 2 -9999 0 2
FZD3 -0.014 0.002 0 16 -9999 0 16
WNT5A -0.01 0.007 0 168 -9999 0 168
WNT11 -0.014 0.001 0 2 -9999 0 2
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.001 0.004 0 481 -10000 0 481
CDC42/GTP -0.062 0.039 0.048 3 -0.12 127 130
PLCG1 -0.001 0.006 0.043 3 -0.069 1 4
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 -0.014 0.001 0 1 -10000 0 1
GNAI3 -0.012 0.005 0 65 -10000 0 65
G12/G13 -0.017 0.002 0 6 -10000 0 6
cell migration -0.062 0.038 0.046 3 -0.12 127 130
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.001 0.006 0.043 3 -0.069 1 4
MAPK1 -0.001 0.006 0.043 3 -0.069 1 4
S1P/S1P5/Gi 0 0.005 0.05 3 -0.069 1 4
GNAI1 -0.012 0.005 0 81 -10000 0 81
CDC42/GDP -0.009 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.007 0.001 0 4 -10000 0 4
RHOA -0.015 0.012 0.095 6 -10000 0 6
S1P/S1P4/Gi 0 0.005 0.05 3 -0.069 1 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.012 0.005 0 72 -10000 0 72
S1P/S1P4/G12/G13 -0.012 0.001 0 6 -10000 0 6
GNA12 -0.014 0.001 0 4 -10000 0 4
GNA13 -0.014 0.001 0 2 -10000 0 2
CDC42 -0.014 0 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.005 0.003 -10000 0 -10000 0 0
HDAC1 -0.02 0.015 -10000 0 -0.059 32 32
AES -0.016 0.003 -10000 0 -10000 0 0
FBXW11 -0.014 0 -10000 0 -10000 0 0
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 -0.016 0.002 0 11 -10000 0 11
TLE1 -0.017 0.004 -10000 0 -0.029 11 11
AP1 -0.005 0.004 -10000 0 -10000 0 0
NCSTN -0.013 0.003 0 30 -10000 0 30
ADAM10 -0.014 0.003 0 18 -10000 0 18
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.047 0.07 0.22 43 -10000 0 43
NICD/RBPSUH -0.004 0.014 -10000 0 -10000 0 0
WIF1 -0.002 0.005 0 462 -10000 0 462
NOTCH1 -0.003 0.001 -10000 0 -10000 0 0
PSENEN -0.014 0.001 0 1 -10000 0 1
KREMEN2 -0.014 0 -10000 0 -10000 0 0
DKK1 -0.011 0.006 0 116 -10000 0 116
beta catenin/beta TrCP1 0.014 0.031 0.1 8 -10000 0 8
APH1B -0.014 0 -10000 0 -10000 0 0
APH1A -0.014 0.002 0 10 -10000 0 10
AXIN1 0.009 0.018 0.18 4 -0.15 1 5
CtBP/CBP/TCF1/TLE1/AES -0.043 0.053 -10000 0 -0.12 170 170
PSEN1 -0.014 0.001 0 1 -10000 0 1
FOS -0.011 0.006 0 127 -10000 0 127
JUN -0.014 0.001 0 1 -10000 0 1
MAP3K7 -0.019 0.007 -10000 0 -0.036 43 43
CTNNB1 0.016 0.028 0.11 8 -10000 0 8
MAPK3 -0.014 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.02 0.003 0 11 -10000 0 11
HNF1A -0.016 0.003 -10000 0 -10000 0 0
CTBP1 -0.016 0.004 -10000 0 -10000 0 0
MYC 0.084 0.14 0.32 135 -10000 0 135
NKD1 -0.002 0.002 -10000 0 -0.008 43 43
FZD1 -0.014 0.002 0 10 -10000 0 10
NOTCH1 precursor/Deltex homolog 1 -0.003 0.001 -10000 0 -10000 0 0
apoptosis -0.005 0.004 -10000 0 -10000 0 0
Delta 1/NOTCHprecursor -0.003 0.001 -10000 0 -10000 0 0
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.014 0.03 -10000 0 -10000 0 0
Gamma Secretase -0.007 0.026 0.03 169 -10000 0 169
APC -0.006 0.063 0.18 1 -0.28 25 26
DVL1 0.001 0.006 0.022 39 -10000 0 39
CSNK2A1 -0.011 0.008 0.014 43 -10000 0 43
MAP3K7IP1 -0.019 0.007 -10000 0 -0.036 43 43
DKK1/LRP6/Kremen 2 -0.016 0.008 0 117 -10000 0 117
LRP6 -0.014 0.001 0 1 -10000 0 1
CSNK1A1 -0.011 0.008 0.014 43 -10000 0 43
NLK -0.018 0.016 -10000 0 -0.037 190 190
CCND1 0.065 0.13 0.33 99 -10000 0 99
WNT1 -0.014 0 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.013 0.038 0.14 6 -10000 0 6
DKK2 -0.014 0.002 0 10 -10000 0 10
NOTCH1 precursor/DVL1 0.005 0.009 -10000 0 -10000 0 0
GSK3B -0.015 0.001 0 4 -10000 0 4
FRAT1 -0.016 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.005 0.003 -10000 0 -10000 0 0
PPP2R5D 0.008 0.008 -10000 0 -10000 0 0
MAPK1 -0.014 0.003 0 17 -10000 0 17
WNT1/LRP6/FZD1 -0.001 0.008 0.026 19 -10000 0 19
RBPJ -0.014 0 -10000 0 -10000 0 0
CREBBP 0.002 0.023 0.031 193 -10000 0 193
p38 MAPK signaling pathway

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
TRAF6/ASK1 -0.009 0.001 -9999 0 -10000 0 0
TRAF2/ASK1 -0.013 0.001 0 4 -10000 0 4
ATM -0.014 0.003 0 25 -10000 0 25
MAP2K3 0 0.012 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0 0.014 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G -0.014 0.002 0 13 -10000 0 13
TXN -0.003 0 0 1 -10000 0 1
CALM1 -0.013 0.003 0 27 -10000 0 27
GADD45A -0.013 0.004 0 46 -10000 0 46
GADD45B -0.014 0.002 0 9 -10000 0 9
MAP3K1 -0.014 0.001 0 1 -10000 0 1
MAP3K6 -0.014 0.001 0 3 -10000 0 3
MAP3K7 -0.014 0.001 0 1 -10000 0 1
MAP3K4 -0.014 0.001 0 1 -10000 0 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.017 0.002 0 7 -10000 0 7
TAK1/TAB family 0.003 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 -0.012 0 -9999 0 -10000 0 0
TRAF2 -0.014 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.007 0.012 -9999 0 -10000 0 0
TRAF6 -0.005 0 -9999 0 -10000 0 0
RAC1 -0.014 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.002 0.005 0 451 -10000 0 451
CCM2 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.002 0.005 0 451 -10000 0 451
MAPK11 -0.014 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.003 0.006 0 451 -10000 0 451
OSM/MEKK3 -0.009 0 -9999 0 -10000 0 0
TAOK1 -0.003 0.001 0 25 -10000 0 25
TAOK2 -0.005 0.001 0 25 -10000 0 25
TAOK3 -0.005 0.001 0 25 -10000 0 25
MAP3K7IP1 -0.014 0 -9999 0 -10000 0 0
MAPK14 -0.014 0.001 0 2 -10000 0 2
MAP3K7IP2 -0.014 0 -9999 0 -10000 0 0
MAP3K5 -0.014 0.001 0 4 -10000 0 4
MAP3K10 -0.014 0 -9999 0 -10000 0 0
MAP3K3 -0.014 0 -9999 0 -10000 0 0
TRX/ASK1 -0.009 0.003 -9999 0 -0.065 1 1
GADD45/MTK1/MTK1 -0.019 0.007 0 67 -10000 0 67
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.02 0.003 0 12 -9999 0 12
fibroblast growth factor receptor signaling pathway -0.02 0.003 0 12 -9999 0 12
LAMA1 0 0 -10000 0 -9999 0 0
PRNP -0.013 0.003 0 33 -9999 0 33
GPC1/SLIT2 -0.011 0.008 0 189 -9999 0 189
SMAD2 -0.02 0.02 0.092 16 -9999 0 16
GPC1/PrPc/Cu2+ -0.012 0.004 0 41 -9999 0 41
GPC1/Laminin alpha1 -0.008 0.001 0 8 -9999 0 8
TDGF1 -0.014 0.001 0 2 -9999 0 2
CRIPTO/GPC1 -0.017 0.002 0 10 -9999 0 10
APP/GPC1 -0.017 0.002 0 9 -9999 0 9
mol:NO 0 0 -10000 0 -9999 0 0
YES1 -0.016 0.014 0.099 6 -9999 0 6
FLT1 -0.014 0 -10000 0 -9999 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.02 0.003 0 16 -9999 0 16
SERPINC1 -0.014 0.001 0 1 -9999 0 1
FYN -0.017 0.017 0.099 10 -9999 0 10
FGR -0.017 0.017 0.099 10 -9999 0 10
positive regulation of MAPKKK cascade 0.007 0.046 0.1 74 -9999 0 74
SLIT2 -0.009 0.007 0 186 -9999 0 186
GPC1/NRG -0.017 0.002 0 8 -9999 0 8
NRG1 -0.014 0 -10000 0 -9999 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.009 0.01 0 290 -9999 0 290
LYN -0.016 0.017 0.099 9 -9999 0 9
mol:Spermine -0.008 0.001 0 8 -9999 0 8
cell growth -0.02 0.003 0 12 -9999 0 12
BMP signaling pathway 0.014 0.002 -10000 0 0 8 8
SRC -0.018 0.016 0.099 10 -9999 0 10
TGFBR1 -0.014 0 -10000 0 -9999 0 0
mol:Cu2+ 0 0 -10000 0 -9999 0 0
PLA2G2A -0.009 0.007 0 191 -9999 0 191
GPC1 -0.014 0.002 0 8 -9999 0 8
TGFBR1 (dimer) -0.014 0 -10000 0 -9999 0 0
VEGFA -0.006 0.007 0 287 -9999 0 287
BLK -0.018 0.016 0.099 10 -9999 0 10
HCK -0.015 0.017 0.099 9 -9999 0 9
FGF2 -0.014 0.001 0 2 -9999 0 2
FGFR1 -0.014 0.001 0 2 -9999 0 2
VEGFR1 homodimer -0.014 0 -10000 0 -9999 0 0
TGFBR2 -0.014 0.002 0 8 -9999 0 8
cell death -0.017 0.002 0 9 -9999 0 9
ATIII/GPC1 -0.017 0.002 0 9 -9999 0 9
PLA2G2A/GPC1 -0.011 0.008 0 196 -9999 0 196
LCK -0.018 0.016 0.099 9 -9999 0 9
neuron differentiation -0.017 0.002 0 8 -9999 0 8
PrPc/Cu2+ -0.008 0.002 0 33 -9999 0 33
APP -0.014 0.001 0 1 -9999 0 1
TGFBR2 (dimer) -0.014 0.002 0 8 -9999 0 8
BCR 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
JUN 0.015 0.045 0.14 39 -10000 0 39
IKBKB 0.019 0.038 0.15 23 -10000 0 23
AKT1 0.014 0.058 0.14 63 -10000 0 63
IKBKG 0.016 0.037 0.14 27 -10000 0 27
CALM1 0.014 0.035 0.12 41 -10000 0 41
PIK3CA -0.014 0.003 0 25 -10000 0 25
MAP3K1 0.021 0.053 0.15 50 -10000 0 50
MAP3K7 -0.014 0.001 0 1 -10000 0 1
mol:Ca2+ 0.022 0.04 0.13 47 -10000 0 47
DOK1 -0.014 0 -10000 0 -10000 0 0
AP-1 0.028 0.051 0.14 58 -10000 0 58
LYN -0.012 0.005 0 64 -10000 0 64
BLNK -0.012 0.005 0 68 -10000 0 68
SHC1 -0.013 0.004 0 46 -10000 0 46
BCR complex -0.017 0.001 0 2 -10000 0 2
CD22 -0.003 0.02 -10000 0 -10000 0 0
CAMK2G 0.007 0.031 0.12 26 -10000 0 26
CSNK2A1 -0.014 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.025 0.015 -10000 0 -10000 0 0
GO:0007205 0.022 0.04 0.13 45 -10000 0 45
SYK -0.013 0.004 0 36 -10000 0 36
ELK1 0.016 0.039 0.12 43 -10000 0 43
NFATC1 0.017 0.055 0.14 63 -10000 0 63
B-cell antigen/BCR complex -0.017 0.001 0 2 -10000 0 2
PAG1/CSK -0.009 0 -10000 0 -10000 0 0
NFKBIB 0.011 0.018 0.079 18 -10000 0 18
HRAS 0.016 0.047 0.13 54 -10000 0 54
NFKBIA 0.011 0.018 0.079 17 -10000 0 17
NF-kappa-B/RelA/I kappa B beta 0.01 0.019 0.064 36 -10000 0 36
RasGAP/Csk -0.02 0.012 0 133 -10000 0 133
mol:GDP 0.021 0.039 0.12 45 -10000 0 45
PTEN -0.014 0.001 0 2 -10000 0 2
CD79B -0.014 0.001 0 1 -10000 0 1
NF-kappa-B/RelA/I kappa B alpha 0.01 0.019 0.062 38 -10000 0 38
GRB2 -0.014 0.001 0 5 -10000 0 5
PI3K/BCAP/CD19 0.02 0.072 0.21 32 -0.17 10 42
PIK3R1 -0.013 0.004 0 36 -10000 0 36
mol:IP3 0.022 0.04 0.13 46 -10000 0 46
CSK -0.014 0 -10000 0 -10000 0 0
FOS 0.034 0.059 0.12 135 -10000 0 135
CHUK 0.016 0.037 0.14 27 -10000 0 27
IBTK -0.014 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.027 0.026 0.13 17 -10000 0 17
PTPN6 -0.001 0.029 0.081 34 -10000 0 34
RELA -0.014 0 -10000 0 -10000 0 0
BCL2A1 0.01 0.024 0.064 75 -10000 0 75
VAV2 0.002 0.029 0.087 37 -10000 0 37
ubiquitin-dependent protein catabolic process 0.011 0.018 0.077 19 -10000 0 19
BTK 0.005 0.002 -10000 0 -10000 0 0
CD19 -0.003 0.02 -10000 0 -10000 0 0
MAP4K1 -0.014 0.001 0 1 -10000 0 1
CD72 -0.014 0 -10000 0 -10000 0 0
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 0.015 0.05 0.14 52 -10000 0 52
SH3BP5 -0.013 0.004 0 49 -10000 0 49
PIK3AP1 0.022 0.038 0.13 43 -10000 0 43
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.002 0.02 0.12 7 -10000 0 7
RAF1 0.011 0.046 0.13 51 -10000 0 51
RasGAP/p62DOK/SHIP -0.019 0.011 0 133 -10000 0 133
CD79A -0.014 0.001 0 2 -10000 0 2
re-entry into mitotic cell cycle 0.028 0.051 0.14 58 -10000 0 58
RASA1 -0.014 0.002 0 8 -10000 0 8
MAPK3 0.002 0.042 0.12 43 -10000 0 43
MAPK1 0.002 0.042 0.12 42 -10000 0 42
CD72/SHP1 0.013 0.057 0.12 92 -10000 0 92
NFKB1 -0.014 0.001 0 4 -10000 0 4
MAPK8 0.015 0.05 0.14 50 -10000 0 50
actin cytoskeleton organization 0.019 0.061 0.16 64 -10000 0 64
NF-kappa-B/RelA 0.02 0.036 0.14 27 -10000 0 27
Calcineurin 0.003 0.033 0.099 33 -10000 0 33
PI3K -0.019 0.02 -10000 0 -10000 0 0
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.013 0.026 0.1 23 -10000 0 23
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 0.033 0.04 -10000 0 -10000 0 0
DAPP1 0.021 0.034 -10000 0 -10000 0 0
cytokine secretion 0.017 0.054 0.14 63 -10000 0 63
mol:DAG 0.022 0.04 0.13 46 -10000 0 46
PLCG2 -0.014 0.002 0 10 -10000 0 10
MAP2K1 0.006 0.044 0.13 43 -10000 0 43
B-cell antigen/BCR complex/FcgammaRIIB -0.015 0.009 0 128 -10000 0 128
mol:PI-3-4-5-P3 -0.003 0.042 0.1 49 -10000 0 49
ETS1 0.019 0.049 0.13 58 -10000 0 58
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.022 0.011 -10000 0 -10000 0 0
B-cell antigen/BCR complex/LYN -0.006 0.005 -10000 0 -10000 0 0
MALT1 -0.014 0.003 0 24 -10000 0 24
TRAF6 -0.014 0 -10000 0 -10000 0 0
RAC1 0.018 0.059 0.16 63 -10000 0 63
B-cell antigen/BCR complex/LYN/SYK -0.015 0.02 -10000 0 -10000 0 0
CARD11 0.021 0.038 0.12 46 -10000 0 46
FCGR2B -0.011 0.006 0 128 -10000 0 128
PPP3CA -0.011 0.006 0 101 -10000 0 101
BCL10 -0.014 0.001 0 4 -10000 0 4
IKK complex 0.01 0.024 0.086 30 -10000 0 30
PTPRC -0.011 0.006 0 127 -10000 0 127
PDPK1 0.007 0.055 0.12 75 -10000 0 75
PPP3CB -0.014 0.002 0 8 -10000 0 8
PPP3CC -0.014 0 -10000 0 -10000 0 0
POU2F2 0.004 0.013 0.052 18 -10000 0 18
Arf6 downstream 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
PLAUR 0.014 0.086 0.29 47 -10000 0 47
regulation of axonogenesis 0.002 0.027 -10000 0 -0.084 47 47
myoblast fusion -0.011 0.05 -10000 0 -0.17 47 47
mol:GTP 0.015 0.027 0.1 45 -10000 0 45
regulation of calcium-dependent cell-cell adhesion -0.003 0.043 -10000 0 -0.14 45 45
ARF1/GTP 0.018 0.024 0.094 45 -10000 0 45
mol:GM1 0.006 0.028 0.095 47 -10000 0 47
mol:Choline -0.007 0.027 0.079 47 -10000 0 47
lamellipodium assembly 0.008 0.05 0.17 45 -10000 0 45
MAPK3 0.004 0.056 0.18 47 -10000 0 47
ARF6/GTP/NME1/Tiam1 0.003 0.043 0.14 45 -10000 0 45
ARF1 -0.014 0.001 0 2 -10000 0 2
ARF6/GDP 0.011 0.05 0.17 47 -10000 0 47
ARF1/GDP 0.005 0.046 0.15 47 -10000 0 47
ARF6 -0.006 0.024 0.069 47 -10000 0 47
RAB11A -0.014 0.001 0 1 -10000 0 1
TIAM1 -0.011 0.011 0.023 45 -10000 0 45
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.005 0.056 0.18 47 -10000 0 47
actin filament bundle formation 0.006 0.014 -10000 0 -0.17 2 2
KALRN -0.006 0.002 -10000 0 -10000 0 0
RAB11FIP3/RAB11A -0.017 0.001 0 1 -10000 0 1
RhoA/GDP 0.006 0.046 0.15 47 -10000 0 47
NME1 0 0.005 0.015 45 -10000 0 45
Rac1/GDP 0.006 0.046 0.15 47 -10000 0 47
substrate adhesion-dependent cell spreading 0.015 0.027 0.1 45 -10000 0 45
cortical actin cytoskeleton organization -0.006 0.006 -10000 0 -10000 0 0
RAC1 -0.014 0 -10000 0 -10000 0 0
liver development 0.015 0.027 0.1 45 -10000 0 45
ARF6/GTP 0.015 0.027 0.1 45 -10000 0 45
RhoA/GTP 0.018 0.024 0.094 45 -10000 0 45
mol:GDP -0.004 0.001 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.022 0.024 0.093 47 -10000 0 47
RHOA -0.014 0.001 0 2 -10000 0 2
PLD1 -0.001 0.03 0.095 47 -10000 0 47
RAB11FIP3 -0.014 0 -10000 0 -10000 0 0
tube morphogenesis 0.008 0.05 0.17 45 -10000 0 45
ruffle organization -0.002 0.027 0.084 47 -10000 0 47
regulation of epithelial cell migration 0.015 0.027 0.1 45 -10000 0 45
PLD2 -0.001 0.03 0.095 47 -10000 0 47
PIP5K1A -0.002 0.027 0.084 47 -10000 0 47
mol:Phosphatidic acid -0.007 0.027 0.079 47 -10000 0 47
Rac1/GTP -0.006 0.006 -10000 0 -10000 0 0
amb2 Integrin signaling

Figure S53.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S53.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.006 0.015 0.064 11 -10000 0 11
alphaM/beta2 Integrin/GPIbA -0.011 0.017 0.063 15 -10000 0 15
alphaM/beta2 Integrin/proMMP-9 -0.008 0.015 0.064 9 -10000 0 9
PLAUR -0.013 0.004 0 47 -10000 0 47
HMGB1 -0.011 0.018 0.043 53 -10000 0 53
alphaM/beta2 Integrin/Talin -0.01 0.017 0.063 15 -10000 0 15
AGER -0.011 0.017 0.042 50 -10000 0 50
RAP1A -0.014 0 -10000 0 -10000 0 0
SELPLG -0.014 0 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.017 0.015 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.009 0.007 0 179 -10000 0 179
CYR61 -0.01 0.007 0 163 -10000 0 163
TLN1 -0.013 0.004 0 46 -10000 0 46
Rap1/GTP 0.003 0.018 -10000 0 -10000 0 0
RHOA -0.014 0.001 0 2 -10000 0 2
P-selectin oligomer -0.014 0.001 0 1 -10000 0 1
MYH2 0.017 0.043 0.13 41 -0.098 1 42
MST1R -0.014 0.001 0 2 -10000 0 2
leukocyte activation during inflammatory response -0.011 0.017 0.058 16 -10000 0 16
APOB -0.014 0.001 0 3 -10000 0 3
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.007 0.007 0 250 -10000 0 250
JAM3 -0.014 0.003 0 19 -10000 0 19
GP1BA -0.014 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.01 0.017 0.063 14 -10000 0 14
alphaM/beta2 Integrin 0.009 0.023 0.065 16 -10000 0 16
JAM3 homodimer -0.014 0.003 0 19 -10000 0 19
ICAM2 -0.014 0.001 0 3 -10000 0 3
ICAM1 -0.014 0.003 0 17 -10000 0 17
phagocytosis triggered by activation of immune response cell surface activating receptor 0.009 0.023 0.065 16 -10000 0 16
cell adhesion -0.011 0.017 0.063 15 -10000 0 15
NFKB1 0.007 0.056 0.083 181 -10000 0 181
THY1 -0.01 0.006 0 142 -10000 0 142
RhoA/GDP -0.009 0.001 0 2 -10000 0 2
Lipoprotein(a) -0.013 0.001 0 3 -10000 0 3
alphaM/beta2 Integrin/LRP/tPA -0.006 0.017 0.07 12 -10000 0 12
IL6 0.003 0.051 0.072 181 -10000 0 181
ITGB2 -0.008 0.012 0.04 16 -10000 0 16
elevation of cytosolic calcium ion concentration -0.012 0.016 0.064 9 -10000 0 9
alphaM/beta2 Integrin/JAM2/JAM3 -0.01 0.017 0.066 11 -10000 0 11
JAM2 -0.012 0.005 0 81 -10000 0 81
alphaM/beta2 Integrin/ICAM1 -0.014 0.02 0.069 15 -10000 0 15
alphaM/beta2 Integrin/uPA/Plg -0.012 0.016 0.066 9 -10000 0 9
RhoA/GTP 0 0.011 -10000 0 -10000 0 0
positive regulation of phagocytosis -0.006 0.019 0.062 15 -10000 0 15
Ron/MSP -0.017 0.002 0 8 -10000 0 8
alphaM/beta2 Integrin/uPAR/uPA -0.012 0.016 0.066 9 -10000 0 9
alphaM/beta2 Integrin/uPAR -0.011 0.016 0.063 13 -10000 0 13
PLAU -0.011 0.006 0 123 -10000 0 123
PLAT -0.008 0.007 0 244 -10000 0 244
actin filament polymerization 0.018 0.045 0.13 44 -10000 0 44
MST1 -0.014 0.002 0 6 -10000 0 6
alphaM/beta2 Integrin/lipoprotein(a) -0.011 0.018 0.064 16 -10000 0 16
TNF 0.028 0.093 0.26 51 -10000 0 51
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.01 0.015 0.064 9 -10000 0 9
fibrinolysis -0.012 0.016 0.064 9 -10000 0 9
HCK -0.012 0.005 0 86 -10000 0 86
dendritic cell antigen processing and presentation 0.009 0.023 0.065 16 -10000 0 16
VTN -0.014 0.001 0 2 -10000 0 2
alphaM/beta2 Integrin/CYR61 -0.009 0.014 0.063 7 -10000 0 7
LPA -0.014 0 -10000 0 -10000 0 0
LRP1 -0.014 0.003 0 18 -10000 0 18
cell migration -0.005 0.014 0.062 9 -10000 0 9
FN1 -0.011 0.006 0 104 -10000 0 104
alphaM/beta2 Integrin/Thy1 -0.008 0.013 0.063 6 -10000 0 6
MPO -0.014 0 -10000 0 -10000 0 0
KNG1 -0.014 0.001 0 1 -10000 0 1
RAP1/GDP -0.007 0 -10000 0 -10000 0 0
ROCK1 0.017 0.043 0.12 46 -0.098 1 47
ELA2 -0.014 0 -10000 0 -10000 0 0
PLG -0.014 0 -10000 0 -10000 0 0
CTGF -0.013 0.004 0 43 -10000 0 43
alphaM/beta2 Integrin/Hck -0.011 0.017 0.063 14 -10000 0 14
ITGAM -0.011 0.018 0.043 53 -10000 0 53
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.012 0.019 0.069 16 -10000 0 16
HP -0.012 0.005 0 84 -10000 0 84
leukocyte adhesion -0.007 0.026 0.068 33 -10000 0 33
SELP -0.014 0.001 0 1 -10000 0 1
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.006 0.011 -10000 0 -10000 0 0
KLHL20 0.022 0.087 0.2 97 -10000 0 97
CYFIP2 -0.008 0.007 0 225 -10000 0 225
Rac1/GDP -0.011 0.025 0.089 6 -10000 0 6
ENAH -0.007 0.009 -10000 0 -10000 0 0
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 0 99 -10000 0 99
RAP1A -0.014 0 -10000 0 -10000 0 0
CTNNB1 -0.014 0.001 -10000 0 -10000 0 0
CDC42/GTP -0.022 0.018 0.032 9 -10000 0 9
ABI1/Sra1/Nap1 -0.008 0.01 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.015 0.019 0.025 95 -10000 0 95
RAPGEF1 -0.013 0.014 -10000 0 -10000 0 0
CTNND1 -0.014 0.002 0 10 -10000 0 10
regulation of calcium-dependent cell-cell adhesion -0.002 0.008 -10000 0 -10000 0 0
CRK -0.009 0.015 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin -0.013 0.015 0.019 90 -10000 0 90
alphaE/beta7 Integrin -0.017 0.001 0 4 -10000 0 4
IQGAP1 -0.011 0.006 0 127 -10000 0 127
NCKAP1 -0.014 0 -10000 0 -10000 0 0
Rap1/GTP/I-afadin -0.007 0.01 0.015 99 -10000 0 99
DLG1 -0.006 0.011 -10000 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.02 0.017 0.015 70 -10000 0 70
MLLT4 -0.014 0 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.007 0.01 0.014 93 -10000 0 93
PI3K -0.024 0.023 0.026 70 -10000 0 70
ARF6 -0.014 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0 0 0.001 99 -10000 0 99
E-cadherin/gamma catenin -0.016 0.003 0 19 -10000 0 19
TIAM1 -0.013 0.003 0 21 -10000 0 21
E-cadherin(dimer)/Ca2+ -0.013 0.019 0.029 90 -10000 0 90
AKT1 -0.018 0.017 0.046 12 -10000 0 12
PIK3R1 -0.013 0.004 0 36 -10000 0 36
CDH1 -0.014 0.002 0 8 -10000 0 8
RhoA/GDP -0.013 0.02 -10000 0 -10000 0 0
actin cytoskeleton organization 0.02 0.073 0.17 99 -10000 0 99
CDC42/GDP -0.013 0.02 -10000 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.007 0.002 -10000 0 -10000 0 0
ITGB7 -0.014 0.001 0 2 -10000 0 2
RAC1 -0.014 0.001 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.014 0.021 0.031 90 -10000 0 90
E-cadherin/Ca2+/beta catenin/alpha catenin -0.01 0.014 0.021 95 -10000 0 95
mol:GDP -0.012 0.018 -10000 0 -10000 0 0
CDC42/GTP/IQGAP1 -0.01 0.006 0 127 -10000 0 127
JUP -0.014 0.002 0 16 -10000 0 16
p120 catenin/RhoA/GDP -0.015 0.02 0.078 4 -10000 0 4
RAC1/GTP/IQGAP1 -0.006 0.01 0.005 207 -10000 0 207
PIP5K1C/AP1M1 -0.008 0.002 0 20 -10000 0 20
RHOA -0.014 0.001 0 2 -10000 0 2
CDC42 -0.014 0 -10000 0 -10000 0 0
CTNNA1 -0.014 0 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.01 0.006 -10000 0 -10000 0 0
NME1 0 0 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.006 0.011 -10000 0 -10000 0 0
regulation of cell-cell adhesion -0.021 0.014 0.017 5 -10000 0 5
WASF2 -0.005 0.006 -10000 0 -10000 0 0
Rap1/GTP -0.02 0.018 0.056 5 -10000 0 5
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.017 0.02 0.027 90 -10000 0 90
CCND1 -0.012 0.007 -10000 0 -10000 0 0
VAV2 0.007 0.026 -10000 0 -10000 0 0
RAP1/GDP -0.016 0.018 0.065 7 -10000 0 7
adherens junction assembly -0.006 0.012 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 -0.014 0 -10000 0 -10000 0 0
PIP5K1C -0.014 0.003 0 20 -10000 0 20
regulation of heterotypic cell-cell adhesion -0.028 0.018 0.091 11 -10000 0 11
E-cadherin/beta catenin -0.01 0.01 -10000 0 -0.029 121 121
mol:GTP 0 0 0.001 99 -10000 0 99
SRC -0.004 0.015 -10000 0 -10000 0 0
PIK3CA -0.014 0.003 0 25 -10000 0 25
Rac1/GTP -0.019 0.01 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin -0.012 0.017 0.024 95 -10000 0 95
ITGAE -0.014 0.001 0 2 -10000 0 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.002 0.008 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.014 0.001 0 3 -10000 0 3
LAT2 -0.007 0.012 0.052 8 -10000 0 8
AP1 0.01 0.035 -10000 0 -10000 0 0
mol:PIP3 0.016 0.056 0.17 40 -0.12 2 42
IKBKB 0.009 0.04 0.12 40 -0.08 2 42
AKT1 0.02 0.058 0.14 32 -10000 0 32
IKBKG 0.009 0.04 0.12 41 -0.08 2 43
MS4A2 -0.01 0.009 0.01 44 -10000 0 44
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA -0.013 0.003 0 26 -10000 0 26
MAP3K1 0.013 0.045 0.12 49 -0.11 1 50
mol:Ca2+ 0.015 0.049 0.15 40 -0.098 2 42
LYN -0.003 0.013 0.012 200 -10000 0 200
CBLB -0.006 0.013 0.056 9 -10000 0 9
SHC1 -0.013 0.004 0 46 -10000 0 46
RasGAP/p62DOK -0.017 0.004 0 26 -10000 0 26
positive regulation of cell migration -0.009 0.001 0 4 -10000 0 4
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 0.028 0.057 0.084 259 -10000 0 259
PTPN13 0.025 0.057 0.2 4 -0.58 2 6
PTPN11 -0.002 0.014 0.018 68 -10000 0 68
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.012 0.047 0.14 10 -0.28 2 12
SYK -0.002 0.014 0.013 231 -10000 0 231
GRB2 -0.014 0.002 0.002 6 -10000 0 6
LAT/PLCgamma1/GRB2/SLP76/GADs -0.014 0.016 -10000 0 -0.11 2 2
LAT -0.006 0.013 0.056 9 -10000 0 9
PAK2 0.018 0.047 0.12 56 -0.11 1 57
NFATC2 -0.004 0.004 0.001 1 -10000 0 1
HRAS 0.019 0.042 0.12 47 -0.12 2 49
GAB2 -0.014 0.001 0 4 -10000 0 4
PLA2G1B -0.006 0.014 -10000 0 -10000 0 0
Fc epsilon R1 -0.011 0.012 0.021 2 -10000 0 2
Antigen/IgE/Fc epsilon R1 -0.009 0.012 -10000 0 -10000 0 0
mol:GDP 0.02 0.039 0.13 29 -0.15 2 31
JUN -0.014 0.001 0 1 -10000 0 1
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 -0.013 0.004 0 37 -10000 0 37
FOS -0.011 0.006 0 127 -10000 0 127
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.005 0.01 0.046 12 -10000 0 12
CHUK 0.009 0.04 0.12 41 -10000 0 41
KLRG1 -0.006 0.013 0.058 10 -10000 0 10
VAV1 -0.007 0.013 0.075 5 -10000 0 5
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.006 0.013 0.056 9 -10000 0 9
negative regulation of mast cell degranulation -0.006 0.012 0.052 10 -10000 0 10
BTK 0.018 0.034 0.13 18 -0.15 2 20
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK 0.008 0.026 0.048 147 -0.066 7 154
GAB2/PI3K/SHP2 -0.017 0.02 -10000 0 -10000 0 0
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.006 0.008 0.046 5 -10000 0 5
RAF1 0 0.011 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.011 0.012 -10000 0 -10000 0 0
FCER1G -0.008 0.008 0.011 4 -10000 0 4
FCER1A -0.001 0.014 0.013 253 -10000 0 253
Antigen/IgE/Fc epsilon R1/Fyn -0.012 0.013 -10000 0 -10000 0 0
MAPK3 -0.005 0.012 -10000 0 -10000 0 0
MAPK1 -0.009 0.023 -10000 0 -10000 0 0
NFKB1 -0.014 0.001 0 4 -10000 0 4
MAPK8 0.005 0.079 -10000 0 -0.38 21 21
DUSP1 -0.014 0.003 0 18 -10000 0 18
NF-kappa-B/RelA -0.001 0.022 0.055 18 -0.059 2 20
actin cytoskeleton reorganization 0.025 0.054 0.19 1 -0.59 2 3
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.013 0.041 0.11 40 -0.11 2 42
FER -0.006 0.013 0.056 9 -10000 0 9
RELA -0.014 0 -10000 0 -10000 0 0
ITK -0.001 0.006 0.067 3 -10000 0 3
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 0.017 0.043 0.12 37 -0.15 2 39
cytokine secretion -0.003 0.014 0.026 5 -0.044 2 7
SPHK1 -0.007 0.011 0.069 3 -10000 0 3
PTK2 0.025 0.055 -10000 0 -0.62 2 2
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.012 0.015 -10000 0 -0.11 2 2
EDG1 -0.009 0.001 0 4 -10000 0 4
mol:DAG 0.017 0.055 0.16 41 -0.12 2 43
MAP2K2 -0.006 0.01 -10000 0 -10000 0 0
MAP2K1 -0.006 0.01 -10000 0 -10000 0 0
MAP2K7 -0.014 0 -10000 0 -10000 0 0
KLRG1/SHP2 -0.007 0.014 0.08 5 -10000 0 5
MAP2K4 -0.02 0.16 -10000 0 -0.8 21 21
Fc epsilon R1/FcgammaRIIB -0.012 0.013 -10000 0 -10000 0 0
mol:Choline 0.028 0.056 0.083 259 -10000 0 259
SHC/Grb2/SOS1 0.011 0.033 0.08 31 -10000 0 31
FYN -0.014 0.003 0 21 -10000 0 21
DOK1 -0.014 0 -10000 0 -10000 0 0
PXN 0.019 0.052 -10000 0 -0.58 2 2
HCLS1 -0.007 0.012 0.052 8 -10000 0 8
PRKCB 0.014 0.048 0.14 41 -0.098 2 43
FCGR2B -0.011 0.006 0 128 -10000 0 128
IGHE 0.001 0.003 0.006 61 -10000 0 61
KLRG1/SHIP -0.006 0.012 0.053 10 -10000 0 10
LCP2 -0.013 0.003 0 30 -10000 0 30
PLA2G4A -0.005 0.009 -10000 0 -10000 0 0
RASA1 -0.014 0.002 0 8 -10000 0 8
mol:Phosphatidic acid 0.028 0.056 0.083 259 -10000 0 259
IKK complex 0.003 0.035 0.11 35 -10000 0 35
WIPF1 -0.014 0.002 0 11 -10000 0 11
IL12-mediated signaling events

Figure S56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.008 0.064 0.17 31 -0.13 2 33
TBX21 -0.023 0.18 0.49 16 -0.52 2 18
B2M -0.014 0 -10000 0 -10000 0 0
TYK2 -0.007 0.03 0.073 31 -10000 0 31
IL12RB1 -0.007 0.03 0.073 31 -10000 0 31
GADD45B -0.012 0.16 0.48 16 -10000 0 16
IL12RB2 -0.007 0.03 0.076 31 -10000 0 31
GADD45G -0.01 0.16 0.48 12 -10000 0 12
natural killer cell activation 0.001 0.022 0.067 31 -10000 0 31
RELB -0.014 0.001 0 1 -10000 0 1
RELA -0.014 0 -10000 0 -10000 0 0
IL18 -0.011 0.013 0.034 26 -10000 0 26
IL2RA -0.014 0.002 0 6 -10000 0 6
IFNG -0.014 0.001 0 1 -10000 0 1
STAT3 (dimer) -0.02 0.16 0.41 20 -0.44 2 22
HLA-DRB5 0.005 0.009 0.021 125 -0.014 2 127
FASLG -0.023 0.18 0.48 17 -0.52 2 19
NF kappa B2 p52/RelB -0.047 0.15 -10000 0 -0.52 2 2
CD4 -0.005 0.018 0.029 113 -10000 0 113
SOCS1 -0.014 0 -10000 0 -10000 0 0
EntrezGene:6955 0.005 0.01 0.023 125 -0.019 2 127
CD3D -0.004 0.019 0.032 119 -0.034 2 121
CD3E -0.004 0.019 0.03 125 -10000 0 125
CD3G -0.004 0.02 0.032 125 -0.034 2 127
IL12Rbeta2/JAK2 -0.005 0.046 0.12 31 -10000 0 31
CCL3 -0.021 0.18 0.44 23 -0.52 2 25
CCL4 -0.09 0.32 0.49 19 -0.77 85 104
HLA-A -0.014 0.001 0 1 -10000 0 1
IL18/IL18R -0.001 0.051 0.18 32 -10000 0 32
NOS2 -0.016 0.17 0.43 24 -0.45 2 26
IL12/IL12R/TYK2/JAK2/SPHK2 -0.008 0.064 0.17 31 -10000 0 31
IL1R1 -0.022 0.18 0.5 17 -0.52 2 19
IL4 -0.012 0.028 -10000 0 -0.092 23 23
JAK2 -0.007 0.03 0.073 31 -10000 0 31
EntrezGene:6957 0.005 0.009 0.021 125 -0.014 2 127
TCR/CD3/MHC I/CD8 0.007 0.024 0.06 24 -0.048 2 26
RAB7A -0.009 0.15 0.46 11 -10000 0 11
lysosomal transport -0.008 0.14 0.46 11 -10000 0 11
FOS 0.062 0.19 0.37 93 -0.99 2 95
STAT4 (dimer) -0.041 0.17 0.42 18 -0.46 1 19
STAT5A (dimer) -0.047 0.15 -10000 0 -0.52 2 2
GZMA -0.02 0.19 0.56 17 -0.52 2 19
GZMB -0.022 0.18 0.54 17 -0.52 2 19
HLX -0.014 0.001 0 5 -10000 0 5
LCK -0.027 0.19 0.45 23 -0.54 2 25
TCR/CD3/MHC II/CD4 0.04 0.081 0.18 124 -10000 0 124
IL2/IL2R -0.023 0.004 0 15 -10000 0 15
MAPK14 -0.01 0.16 0.44 17 -10000 0 17
CCR5 -0.011 0.16 0.53 14 -10000 0 14
IL1B -0.007 0.029 0.074 29 -10000 0 29
STAT6 0.002 0.084 0.27 20 -10000 0 20
STAT4 -0.008 0.007 0 219 -10000 0 219
STAT3 -0.014 0.002 0 10 -10000 0 10
STAT1 -0.014 0.003 0 18 -10000 0 18
NFKB1 -0.014 0.001 0 4 -10000 0 4
NFKB2 -0.014 0 -10000 0 -10000 0 0
IL12B -0.007 0.03 0.076 31 -10000 0 31
CD8A 0 0 -10000 0 -10000 0 0
CD8B -0.014 0.001 0 2 -10000 0 2
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.008 0.063 0.13 2 -0.17 31 33
IL2RB -0.014 0.001 0 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process -0.038 0.16 0.41 19 -0.44 1 20
IL2RG -0.014 0.002 0 9 -10000 0 9
IL12 -0.005 0.046 0.12 31 -10000 0 31
STAT5A -0.014 0.001 0 1 -10000 0 1
CD247 -0.004 0.019 0.03 124 -10000 0 124
IL2 -0.014 0 -10000 0 -10000 0 0
SPHK2 -0.014 0 -10000 0 -10000 0 0
FRAP1 -0.014 0.001 0 1 -10000 0 1
IL12A -0.007 0.03 0.073 31 -10000 0 31
IL12/IL12R/TYK2/JAK2 -0.022 0.2 0.49 23 -0.56 2 25
MAP2K3 -0.01 0.16 0.5 11 -10000 0 11
RIPK2 -0.014 0.001 0 1 -10000 0 1
MAP2K6 -0.01 0.16 0.44 18 -10000 0 18
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.003 0.011 0.03 35 -10000 0 35
IL18RAP -0.011 0.014 0.036 32 -10000 0 32
IL12Rbeta1/TYK2 -0.007 0.04 0.1 31 -10000 0 31
EOMES 0 0.032 0.089 1 -0.11 22 23
STAT1 (dimer) -0.021 0.16 0.4 18 -0.43 2 20
T cell proliferation -0.038 0.14 0.36 22 -10000 0 22
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.011 0.014 0.036 32 -10000 0 32
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.071 0.1 -10000 0 -10000 0 0
ATF2 -0.014 0.15 0.47 11 -10000 0 11
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 -0.014 0 -10000 0 -10000 0 0
SPHK1 -0.014 0.003 0 19 -10000 0 19
GNAI2 -0.014 0.001 0 1 -10000 0 1
mol:S1P -0.005 0.001 -10000 0 -10000 0 0
GNAO1 -0.001 0.004 0 481 -10000 0 481
mol:Sphinganine-1-P -0.016 0.003 0 19 -10000 0 19
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 -0.011 0.015 0.057 25 -10000 0 25
GNAI3 -0.012 0.005 0 65 -10000 0 65
G12/G13 -0.017 0.002 0 6 -10000 0 6
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 -0.014 0.001 0 4 -10000 0 4
S1P1/S1P -0.007 0.015 0.061 25 -10000 0 25
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 -0.012 0.005 0 81 -10000 0 81
S1P/S1P5/G12 -0.007 0.013 0.051 24 -10000 0 24
S1P/S1P3/Gq -0.002 0.008 -10000 0 -10000 0 0
S1P/S1P4/Gi -0.008 0.043 0.049 3 -0.26 15 18
GNAQ -0.014 0 -10000 0 -10000 0 0
GNAZ -0.012 0.005 0 72 -10000 0 72
GNA14 -0.014 0.001 0 2 -10000 0 2
GNA15 -0.014 0.002 0 7 -10000 0 7
GNA12 -0.014 0.001 0 4 -10000 0 4
GNA13 -0.014 0.001 0 2 -10000 0 2
GNA11 -0.014 0 -10000 0 -10000 0 0
ABCC1 -0.014 0.002 0 9 -10000 0 9
IL1-mediated signaling events

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
UBC13/UEV1A -0.009 0 0 1 -9999 0 1
PRKCZ 0 0 -10000 0 -9999 0 0
MAP3K7IP2 -0.014 0 -10000 0 -9999 0 0
ERC1 -0.014 0.001 0 1 -9999 0 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.003 0.012 0.049 22 -9999 0 22
IRAK/TOLLIP -0.018 0.001 -10000 0 -9999 0 0
IKBKB -0.014 0 -10000 0 -9999 0 0
IKBKG -0.014 0 -10000 0 -9999 0 0
IL1 alpha/IL1R2 -0.016 0.005 0 43 -9999 0 43
IL1A -0.014 0.001 0 3 -9999 0 3
IL1B -0.011 0.008 0 179 -9999 0 179
IRAK/TRAF6/p62/Atypical PKCs -0.025 0.002 -10000 0 -9999 0 0
IL1R2 -0.013 0.004 0 40 -9999 0 40
IL1R1 -0.014 0.001 0 3 -9999 0 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.007 0.024 -10000 0 -9999 0 0
TOLLIP -0.014 0 -10000 0 -9999 0 0
TICAM2 0 0 -10000 0 -9999 0 0
MAP3K3 -0.014 0 -10000 0 -9999 0 0
TAK1/TAB1/TAB2 -0.02 0.001 0 1 -9999 0 1
IKK complex/ELKS -0.021 0.004 -10000 0 -9999 0 0
JUN -0.036 0.005 0.06 1 -9999 0 1
MAP3K7 -0.014 0.001 0 1 -9999 0 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.003 0.048 0.085 127 -9999 0 127
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.019 0.01 0 111 -9999 0 111
PIK3R1 -0.013 0.004 0 36 -9999 0 36
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.021 0.011 -10000 0 -9999 0 0
IL1 beta fragment/IL1R1/IL1RAP -0.015 0.011 0 199 -9999 0 199
NFKB1 -0.014 0.001 0 4 -9999 0 4
MAPK8 -0.033 0.005 0.069 1 -9999 0 1
IRAK1 -0.013 0.001 0 2 -9999 0 2
IL1RN/IL1R1 -0.017 0.001 0 3 -9999 0 3
IRAK4 -0.014 0.001 0 1 -9999 0 1
PRKCI -0.014 0.001 0 1 -9999 0 1
TRAF6 -0.014 0 -10000 0 -9999 0 0
PI3K -0.015 0.005 0 60 -9999 0 60
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.009 0.029 0.06 108 -9999 0 108
CHUK -0.014 0.001 0 1 -9999 0 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.015 0.011 0 199 -9999 0 199
IL1 beta/IL1R2 -0.011 0.016 0.11 5 -9999 0 5
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.03 0.002 -10000 0 -9999 0 0
NF kappa B1 p50/RelA -0.022 0.019 -10000 0 -9999 0 0
IRAK3 -0.014 0.001 0 2 -9999 0 2
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.006 0.046 0.08 146 -9999 0 146
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.009 0.005 -10000 0 -9999 0 0
IL1 alpha/IL1R1/IL1RAP -0.018 0.006 0 50 -9999 0 50
RELA -0.014 0 -10000 0 -9999 0 0
MAP3K7IP1 -0.014 0 -10000 0 -9999 0 0
SQSTM1 -0.014 0.001 0 1 -9999 0 1
MYD88 -0.012 0.005 0 71 -9999 0 71
IRAK/TRAF6/MEKK3 -0.022 0.001 -10000 0 -9999 0 0
IL1RAP -0.013 0.004 0 45 -9999 0 45
UBE2N -0.014 0.001 0 1 -9999 0 1
IRAK/TRAF6 -0.023 0.018 -10000 0 -9999 0 0
CASP1 -0.01 0.007 0 173 -9999 0 173
IL1RN/IL1R2 -0.016 0.005 0 40 -9999 0 40
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.002 0.044 0.087 109 -9999 0 109
TMEM189-UBE2V1 0 0 -10000 0 -9999 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.003 0.014 -10000 0 -9999 0 0
PIK3CA -0.014 0.003 0 25 -9999 0 25
IL1RN -0.014 0 -10000 0 -9999 0 0
TRAF6/TAK1/TAB1/TAB2 -0.026 0.002 -10000 0 -9999 0 0
MAP2K6 -0.029 0.005 0.078 1 -9999 0 1
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.034 0.028 -10000 0 -0.11 11 11
CaM/Ca2+ -0.008 0.002 0 27 -10000 0 27
AKT1 -0.014 0.001 0 4 -10000 0 4
AKT2 -0.014 0 -10000 0 -10000 0 0
STXBP4 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.034 0.034 -10000 0 -0.1 37 37
YWHAZ -0.014 0.002 0 6 -10000 0 6
CALM1 -0.013 0.003 0 27 -10000 0 27
YWHAQ -0.014 0 -10000 0 -10000 0 0
TBC1D4 -0.017 0.001 0 4 -10000 0 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH -0.007 0.007 0 284 -10000 0 284
YWHAB -0.014 0.001 0 2 -10000 0 2
SNARE/Synip -0.012 0.004 0 49 -10000 0 49
YWHAG 0 0 -10000 0 -10000 0 0
ASIP -0.014 0 -10000 0 -10000 0 0
PRKCI -0.014 0.001 0 1 -10000 0 1
AS160/CaM/Ca2+ -0.008 0.002 0 27 -10000 0 27
RHOQ -0.014 0 -10000 0 -10000 0 0
GYS1 -0.003 0.034 0.12 36 -10000 0 36
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 -0.014 0.002 0 6 -10000 0 6
TC10/GTP/CIP4/Exocyst -0.013 0.001 0 6 -10000 0 6
AS160/14-3-3 -0.048 0.042 0.049 2 -0.089 257 259
VAMP2 -0.013 0.004 0 49 -10000 0 49
SLC2A4 -0.037 0.036 -10000 0 -0.11 37 37
STX4 -0.014 0 -10000 0 -10000 0 0
GSK3B -0.008 0.001 0 8 -10000 0 8
SFN -0.013 0.003 0 33 -10000 0 33
LNPEP -0.014 0.001 0 1 -10000 0 1
YWHAE -0.014 0.001 0 2 -10000 0 2
FAS signaling pathway (CD95)

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
SPTAN1 -0.005 0.007 0.077 3 -10000 0 3
RFC1 -0.006 0.007 0.077 3 -10000 0 3
PRKDC -0.002 0.021 0.11 17 -10000 0 17
RIPK1 -0.016 0.006 0 9 -0.032 51 60
CASP7 0.008 0.02 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.002 0.029 0.074 49 -0.067 25 74
MAP2K4 0.014 0.058 0.18 50 -0.13 1 51
mol:ceramide 0.008 0.051 0.15 50 -10000 0 50
GSN -0.003 0.02 0.12 14 -10000 0 14
FASLG/FAS/FADD/FAF1/Caspase 8 0.002 0.041 0.1 51 -0.072 24 75
FAS -0.01 0.01 0.026 33 -10000 0 33
BID -0.015 0.012 0.026 18 -10000 0 18
MAP3K1 0.017 0.046 0.15 36 -10000 0 36
MAP3K7 -0.011 0.009 0.016 53 -10000 0 53
RB1 -0.006 0.007 0.077 3 -10000 0 3
CFLAR -0.016 0.005 0 5 -0.032 50 55
HGF/MET -0.019 0.005 0 41 -10000 0 41
ARHGDIB 0.003 0.032 0.12 35 -10000 0 35
FADD -0.01 0.012 0.026 52 -10000 0 52
actin filament polymerization 0.002 0.023 -10000 0 -0.11 20 20
NFKB1 0.023 0.045 0.18 16 -10000 0 16
MAPK8 0.013 0.071 0.22 50 -10000 0 50
DFFA -0.006 0.007 0.077 3 -10000 0 3
DNA fragmentation during apoptosis -0.005 0.011 0.072 9 -10000 0 9
FAS/FADD/MET -0.014 0.016 0.043 31 -10000 0 31
CFLAR/RIP1 -0.019 0.009 -10000 0 -0.044 49 49
FAIM3 -0.015 0.001 0 1 -10000 0 1
FAF1 -0.01 0.015 0.035 50 -10000 0 50
PARP1 -0.006 0.007 0.077 3 -10000 0 3
DFFB -0.006 0.007 0.077 3 -10000 0 3
CHUK 0.013 0.04 -10000 0 -10000 0 0
FASLG -0.01 0.015 0.035 52 -10000 0 52
FAS/FADD -0.011 0.015 0.041 33 -10000 0 33
HGF -0.014 0.001 0 2 -10000 0 2
LMNA -0.004 0.026 0.1 27 -10000 0 27
CASP6 -0.002 0.023 0.11 19 -10000 0 19
CASP10 -0.01 0.012 0.026 52 -10000 0 52
CASP3 -0.001 0.003 -10000 0 -10000 0 0
PTPN13 -0.013 0.003 0 30 -10000 0 30
CASP8 -0.011 0.006 0.006 58 -10000 0 58
IL6 0.032 0.095 0.32 52 -10000 0 52
MET -0.014 0.002 0 10 -10000 0 10
ICAD/CAD -0.01 0.005 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 0.004 0.049 0.15 50 -10000 0 50
activation of caspase activity by cytochrome c -0.015 0.012 0.026 18 -10000 0 18
PAK2 -0.002 0.021 0.11 16 -10000 0 16
BCL2 -0.014 0.001 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.02 0.001 0 2 -9999 0 2
VEGFR1 homodimer/NRP1 -0.014 0.001 0 2 -9999 0 2
mol:DAG -0.022 0.009 0.095 2 -9999 0 2
VEGFR1 homodimer/NRP1/VEGFR 121 -0.008 0.009 -10000 0 -9999 0 0
CaM/Ca2+ -0.025 0.011 0.09 2 -9999 0 2
HIF1A -0.02 0.001 0 2 -9999 0 2
GAB1 -0.014 0.001 0 4 -9999 0 4
AKT1 -0.02 0.028 0.12 4 -9999 0 4
PLCG1 -0.022 0.009 0.095 2 -9999 0 2
NOS3 -0.019 0.026 0.11 2 -9999 0 2
CBL -0.014 0 -10000 0 -9999 0 0
mol:NO -0.018 0.026 0.11 2 -9999 0 2
FLT1 -0.017 0.001 0 2 -9999 0 2
PGF -0.014 0.003 0 21 -9999 0 21
VEGFR1 homodimer/NRP2/VEGFR121 -0.011 0.012 -10000 0 -9999 0 0
CALM1 -0.013 0.003 0 27 -9999 0 27
PIK3CA -0.014 0.003 0 25 -9999 0 25
eNOS/Hsp90 -0.022 0.028 0.11 2 -9999 0 2
endothelial cell proliferation -0.015 0.02 0.089 2 -9999 0 2
mol:Ca2+ -0.022 0.009 0.095 2 -9999 0 2
MAPK3 -0.026 0.021 0.073 23 -9999 0 23
MAPK1 -0.025 0.022 0.073 23 -9999 0 23
PIK3R1 -0.013 0.004 0 36 -9999 0 36
PLGF homodimer -0.014 0.003 0 21 -9999 0 21
PRKACA -0.014 0 -10000 0 -9999 0 0
RP11-342D11.1 0 0 -10000 0 -9999 0 0
CAV1 -0.005 0.007 0 324 -9999 0 324
VEGFA homodimer -0.006 0.007 0 287 -9999 0 287
VEGFR1 homodimer/VEGFA homodimer -0.009 0.01 0 289 -9999 0 289
platelet activating factor biosynthetic process -0.029 0.021 -10000 0 -9999 0 0
PI3K -0.023 0.012 0.088 2 -9999 0 2
PRKCA -0.023 0.022 0.08 23 -9999 0 23
PRKCB -0.02 0.008 0.089 2 -9999 0 2
VEGFR1 homodimer/PLGF homodimer -0.02 0.004 0 23 -9999 0 23
VEGFA -0.006 0.007 0 287 -9999 0 287
VEGFB -0.014 0 -10000 0 -9999 0 0
mol:IP3 -0.022 0.009 0.095 2 -9999 0 2
RASA1 -0.023 0.008 0.095 2 -9999 0 2
NRP2 -0.014 0.001 0 1 -9999 0 1
VEGFR1 homodimer -0.017 0.001 0 2 -9999 0 2
VEGFB homodimer -0.014 0 -10000 0 -9999 0 0
NCK1 -0.014 0.002 0 11 -9999 0 11
eNOS/Caveolin-1 -0.009 0.021 -10000 0 -9999 0 0
PTPN11 -0.014 0 -10000 0 -9999 0 0
mol:PI-3-4-5-P3 -0.023 0.012 0.085 2 -9999 0 2
mol:L-citrulline -0.018 0.026 0.11 2 -9999 0 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.011 0.014 -10000 0 -9999 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.01 0.012 -10000 0 -9999 0 0
CD2AP -0.013 0.004 0 49 -9999 0 49
PI3K/GAB1 -0.026 0.013 0.086 2 -9999 0 2
PDPK1 -0.02 0.031 0.13 4 -9999 0 4
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.011 0.012 -10000 0 -9999 0 0
mol:NADP -0.018 0.026 0.11 2 -9999 0 2
HSP90AA1 -0.014 0 -10000 0 -9999 0 0
ubiquitin-dependent protein catabolic process -0.011 0.013 -10000 0 -9999 0 0
VEGFR1 homodimer/NRP2 -0.02 0.002 0 3 -9999 0 3
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.013 0.008 0.056 1 -0.074 4 5
BIRC5 -0.009 0.007 0 211 -10000 0 211
NFKBIA -0.014 0.007 0.12 1 -10000 0 1
CPEB1 -0.011 0.006 0 136 -10000 0 136
AKT1 -0.013 0.013 0.12 4 -10000 0 4
NDEL1 -0.014 0.003 0 25 -10000 0 25
Aurora A/BRCA1 -0.013 0.005 -10000 0 -0.065 4 4
NDEL1/TACC3 -0.014 0.009 0.047 1 -0.066 3 4
GADD45A -0.013 0.004 0 46 -10000 0 46
GSK3B -0.015 0.002 -10000 0 -10000 0 0
PAK1/Aurora A -0.015 0.007 0.056 1 -0.074 4 5
MDM2 -0.014 0.003 0 18 -10000 0 18
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.007 0.008 0 298 -10000 0 298
TP53 -0.003 0.002 -10000 0 -10000 0 0
DLG7 0.027 0.062 0.12 150 -10000 0 150
AURKAIP1 -0.014 0 -10000 0 -10000 0 0
ARHGEF7 -0.014 0.001 0 1 -10000 0 1
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.015 0.009 0.049 1 -0.071 3 4
G2/M transition of mitotic cell cycle -0.013 0.005 -10000 0 -0.065 4 4
AURKA -0.01 0.003 -10000 0 -10000 0 0
AURKB 0.001 0.001 -10000 0 -10000 0 0
CDC25B -0.005 0.002 -10000 0 -10000 0 0
G2/M transition checkpoint -0.007 0.005 -10000 0 -0.059 4 4
mRNA polyadenylation -0.009 0.006 -10000 0 -0.065 1 1
Aurora A/CPEB -0.01 0.006 -10000 0 -0.065 1 1
Aurora A/TACC1/TRAP/chTOG -0.021 0.015 0.054 18 -0.071 4 22
BRCA1 -0.014 0.001 0 5 -10000 0 5
centrosome duplication -0.015 0.007 0.056 1 -0.074 4 5
regulation of centrosome cycle -0.014 0.009 0.045 1 -0.066 3 4
spindle assembly -0.02 0.014 0.052 18 -0.071 4 22
TDRD7 -0.014 0.001 0 1 -10000 0 1
Aurora A/RasGAP/Survivin -0.013 0.012 0.048 1 -0.068 3 4
CENPA 0.001 0.001 -10000 0 -10000 0 0
Aurora A/PP2A -0.015 0.007 0.056 1 -0.074 4 5
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.016 0.04 0.075 161 -10000 0 161
negative regulation of DNA binding -0.003 0.002 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX -0.017 0.001 0 1 -10000 0 1
RASA1 -0.014 0.002 0 8 -10000 0 8
Ajuba/Aurora A -0.007 0.005 -10000 0 -0.06 4 4
mitotic prometaphase -0.002 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.01 0.003 -10000 0 -10000 0 0
TACC1 -0.014 0.001 0 3 -10000 0 3
TACC3 -0.012 0.005 0 96 -10000 0 96
Aurora A/Antizyme1 -0.017 0.014 0.051 19 -0.071 4 23
Aurora A/RasGAP -0.014 0.007 0.056 1 -0.074 4 5
OAZ1 -0.014 0 -10000 0 -10000 0 0
RAN -0.014 0.001 0 3 -10000 0 3
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.015 0.001 -10000 0 -10000 0 0
GIT1 -0.014 0 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.02 0.001 0 1 -10000 0 1
Importin alpha/Importin beta/TPX2 -0.007 0.008 0 298 -10000 0 298
PPP2R5D -0.014 0 -10000 0 -10000 0 0
Aurora A/TPX2 -0.008 0.01 0.046 1 -0.071 2 3
PAK1 -0.014 0 -10000 0 -10000 0 0
CKAP5 -0.014 0 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.011 0 -10000 0 -9999 0 0
RGS9BP 0 0 -10000 0 -9999 0 0
mol:GTP 0 0 -10000 0 -9999 0 0
GRK1 0 0 -10000 0 -9999 0 0
mol:Na + -0.009 0.006 0 184 -9999 0 184
mol:ADP 0 0 -10000 0 -9999 0 0
GNAT2 -0.014 0 -10000 0 -9999 0 0
RGS9-1/Gbeta5/R9AP -0.013 0.002 0 7 -9999 0 7
mol:GDP 0 0 -10000 0 -9999 0 0
PDE6H/GNAT2/GTP -0.014 0 -10000 0 -9999 0 0
GRK7 0 0 -10000 0 -9999 0 0
CNGB3 -0.014 0 -10000 0 -9999 0 0
Cone Metarhodopsin II/X-Arrestin -0.009 0 -10000 0 -9999 0 0
mol:Ca2+ 0.022 0.055 0.097 184 -9999 0 184
Cone PDE6 -0.022 0.002 0 7 -9999 0 7
Cone Metarhodopsin II 0 0 -10000 0 -9999 0 0
Na + (4 Units) -0.012 0.008 0 184 -9999 0 184
GNAT2/GDP -0.016 0.002 0 7 -9999 0 7
GNB5 -0.014 0.002 0 7 -9999 0 7
mol:GMP (4 units) -0.018 0 -10000 0 -9999 0 0
Cone Transducin -0.012 0 -10000 0 -9999 0 0
SLC24A2 -0.014 0 -10000 0 -9999 0 0
GNB3/GNGT2 -0.009 0 -10000 0 -9999 0 0
GNB3 -0.014 0 -10000 0 -9999 0 0
GNAT2/GTP -0.009 0 -10000 0 -9999 0 0
CNGA3 -0.009 0.007 0 184 -9999 0 184
ARR3 -0.014 0 -10000 0 -9999 0 0
absorption of light 0 0 -10000 0 -9999 0 0
cGMP/Cone CNG Channel -0.009 0.006 0 184 -9999 0 184
mol:Pi -0.013 0.002 0 7 -9999 0 7
Cone CNG Channel -0.017 0.012 -10000 0 -9999 0 0
mol:all-trans-retinal 0 0 -10000 0 -9999 0 0
mol:K + -0.014 0 -10000 0 -9999 0 0
RGS9 -0.014 0 -10000 0 -9999 0 0
PDE6C -0.014 0 -10000 0 -9999 0 0
GNGT2 0 0 -10000 0 -9999 0 0
mol:cGMP (4 units) 0 0 -10000 0 -9999 0 0
PDE6H -0.014 0 -10000 0 -9999 0 0
Ceramide signaling pathway

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
SPHK2 -0.016 0.003 0 19 -10000 0 19
MAP4K4 0.005 0.025 0.04 178 -10000 0 178
BAG4 -0.014 0 -10000 0 -10000 0 0
PKC zeta/ceramide 0.004 0.014 -10000 0 -0.084 11 11
NFKBIA -0.014 0.001 0 1 -10000 0 1
BIRC3 -0.013 0.003 0 33 -10000 0 33
BAX 0.005 0.008 -10000 0 -10000 0 0
RIPK1 -0.014 0.002 0 9 -10000 0 9
AKT1 -0.011 0.026 0.28 4 -10000 0 4
BAD -0.001 0.014 -10000 0 -0.089 11 11
SMPD1 0.013 0.028 0.051 185 -10000 0 185
RB1 -0.001 0.014 -10000 0 -0.089 11 11
FADD/Caspase 8 0.005 0.028 0.084 18 -10000 0 18
MAP2K4 -0.006 0.014 0.1 1 -0.09 11 12
NSMAF -0.014 0.001 0 2 -10000 0 2
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.006 0.014 0.1 1 -0.09 11 12
EGF -0.014 0.001 0 2 -10000 0 2
mol:ceramide 0.004 0.015 -10000 0 -0.09 11 11
MADD -0.014 0.001 0 4 -10000 0 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.016 0.003 0 20 -10000 0 20
ASAH1 -0.014 0.001 0 1 -10000 0 1
negative regulation of cell cycle -0.001 0.014 -10000 0 -0.089 11 11
cell proliferation -0.017 0.015 0.084 1 -0.091 11 12
BID 0.017 0.022 -10000 0 -10000 0 0
MAP3K1 -0.001 0.015 0.11 1 -0.089 11 12
EIF2A -0.006 0.013 -10000 0 -0.086 11 11
TRADD -0.014 0 -10000 0 -10000 0 0
CRADD -0.014 0 -10000 0 -10000 0 0
MAPK3 -0.01 0.014 0.09 1 -0.089 11 12
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.013 0.024 0.09 1 -0.12 19 20
Cathepsin D/ceramide 0.008 0.016 -10000 0 -0.089 11 11
FADD 0.005 0.026 0.04 180 -10000 0 180
KSR1 -0.001 0.014 -10000 0 -0.089 11 11
MAPK8 -0.001 0.015 -10000 0 -0.085 11 11
PRKRA -0.001 0.014 -10000 0 -0.089 11 11
PDGFA -0.014 0.003 0 19 -10000 0 19
TRAF2 -0.014 0 -10000 0 -10000 0 0
IGF1 -0.014 0.001 0 4 -10000 0 4
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.004 0.015 -10000 0 -0.09 11 11
CTSD -0.014 0.002 0 16 -10000 0 16
regulation of nitric oxide biosynthetic process -0.017 0.001 0 4 -10000 0 4
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.018 0.016 0.091 1 -0.096 11 12
PRKCD -0.014 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.016 0.003 0 20 -10000 0 20
RelA/NF kappa B1 -0.017 0.001 0 4 -10000 0 4
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR -0.014 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.01 0.027 0.048 179 -10000 0 179
TNFR1A/BAG4/TNF-alpha -0.013 0.01 0 185 -10000 0 185
mol:Sphingosine-1-phosphate -0.016 0.003 0 19 -10000 0 19
MAP2K1 -0.011 0.014 0.091 1 -0.091 11 12
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA -0.014 0 -10000 0 -10000 0 0
CYCS 0.001 0.01 -10000 0 -10000 0 0
TNFRSF1A -0.009 0.007 0 183 -10000 0 183
NFKB1 -0.014 0.001 0 4 -10000 0 4
TNFR1A/BAG4 -0.011 0.008 0 183 -10000 0 183
EIF2AK2 -0.006 0.014 -10000 0 -0.09 11 11
TNF-alpha/TNFR1A/FAN -0.013 0.01 0 187 -10000 0 187
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.01 0.016 -10000 0 -10000 0 0
MAP2K2 -0.011 0.014 0.091 1 -0.091 11 12
SMPD3 0.016 0.029 0.075 24 -10000 0 24
TNF -0.014 0.001 0 2 -10000 0 2
PKC zeta/PAR4 -0.009 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.01 0.013 -10000 0 -0.066 9 9
NF kappa B1/RelA/I kappa B alpha -0.022 0.002 0 5 -10000 0 5
AIFM1 0.002 0.013 0.087 1 -10000 0 1
BCL2 -0.014 0 -10000 0 -10000 0 0
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 -0.001 0.003 -10000 0 -10000 0 0
epithelial cell differentiation -0.021 0.004 0 18 -10000 0 18
CYFIP2 -0.008 0.007 0 225 -10000 0 225
ENAH -0.03 0.036 0.14 15 -10000 0 15
EGFR -0.009 0.007 0 194 -10000 0 194
EPHA2 -0.014 0.002 0 13 -10000 0 13
MYO6 -0.022 0.02 0.084 18 -10000 0 18
CTNNB1 -0.014 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.012 0.01 0 225 -10000 0 225
AQP5 -0.018 0.018 -10000 0 -10000 0 0
CTNND1 -0.014 0.002 0 10 -10000 0 10
mol:PI-4-5-P2 -0.021 0.02 0.084 17 -10000 0 17
regulation of calcium-dependent cell-cell adhesion -0.022 0.02 0.084 18 -10000 0 18
EGF -0.014 0.001 0 2 -10000 0 2
NCKAP1 -0.014 0 -10000 0 -10000 0 0
AQP3 -0.019 0.017 -10000 0 -10000 0 0
cortical microtubule organization -0.021 0.004 0 18 -10000 0 18
GO:0000145 -0.02 0.018 0.077 17 -10000 0 17
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.021 0.004 0 18 -10000 0 18
MLLT4 -0.014 0 -10000 0 -10000 0 0
ARF6/GDP -0.037 0.012 -10000 0 -10000 0 0
ARF6 -0.014 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.022 0.006 0 38 -10000 0 38
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.015 0.017 0.076 10 -10000 0 10
PVRL2 -0.014 0 -10000 0 -10000 0 0
ZYX -0.017 0.018 0.084 11 -10000 0 11
ARF6/GTP -0.025 0.007 -10000 0 -10000 0 0
CDH1 -0.014 0.002 0 8 -10000 0 8
EGFR/EGFR/EGF/EGF -0.018 0.015 -10000 0 -10000 0 0
RhoA/GDP -0.025 0.005 -10000 0 -10000 0 0
actin cytoskeleton organization -0.024 0.019 0.075 18 -10000 0 18
IGF-1R heterotetramer -0.014 0 -10000 0 -10000 0 0
GIT1 -0.014 0 -10000 0 -10000 0 0
IGF1R -0.014 0 -10000 0 -10000 0 0
IGF1 -0.014 0.001 0 4 -10000 0 4
DIAPH1 -0.18 0.22 -10000 0 -0.44 222 222
Wnt receptor signaling pathway 0.021 0.004 -10000 0 0 18 18
RHOA -0.014 0.001 0 2 -10000 0 2
RhoA/GTP -0.037 0.012 -10000 0 -10000 0 0
CTNNA1 -0.014 0 -10000 0 -10000 0 0
VCL -0.025 0.019 0.076 18 -10000 0 18
EFNA1 -0.014 0.003 0 24 -10000 0 24
LPP -0.025 0.017 0.076 12 -10000 0 12
Ephrin A1/EPHA2 -0.027 0.008 -10000 0 -10000 0 0
SEC6/SEC8 -0.032 0.006 -10000 0 -10000 0 0
MGAT3 -0.022 0.02 0.084 18 -10000 0 18
HGF/MET -0.028 0.007 -10000 0 -10000 0 0
HGF -0.014 0.001 0 2 -10000 0 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.001 0.003 -10000 0 -10000 0 0
actin cable formation -0.03 0.042 0.14 11 -10000 0 11
KIAA1543 -0.016 0.018 0.079 18 -10000 0 18
KIFC3 -0.022 0.02 0.084 18 -10000 0 18
NCK1 -0.014 0.002 0 11 -10000 0 11
EXOC3 -0.014 0 -10000 0 -10000 0 0
ACTN1 -0.021 0.018 0.084 12 -10000 0 12
NCK1/GIT1 -0.017 0.002 0 11 -10000 0 11
mol:GDP -0.021 0.004 0 18 -10000 0 18
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.022 0.02 0.084 18 -10000 0 18
PIP5K1C -0.021 0.02 0.084 17 -10000 0 17
LIMA1 -0.002 0.005 0 453 -10000 0 453
ABI1 -0.014 0 -10000 0 -10000 0 0
ROCK1 -0.031 0.039 0.15 15 -10000 0 15
adherens junction assembly -0.026 0.028 0.079 1 -0.14 19 20
IGF-1R heterotetramer/IGF1 -0.029 0.006 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.017 0 -10000 0 -10000 0 0
MET -0.014 0.002 0 10 -10000 0 10
PLEKHA7 -0.02 0.004 0 18 -10000 0 18
mol:GTP -0.022 0.006 0 38 -10000 0 38
establishment of epithelial cell apical/basal polarity -0.033 0.018 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.001 0.003 -10000 0 -10000 0 0
regulation of cell-cell adhesion -0.024 0.019 0.075 18 -10000 0 18
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.001 0.003 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.01 0.021 0.073 25 -10000 0 25
adherens junction organization -0.004 0.019 0.097 10 -10000 0 10
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.053 0.081 205 -10000 0 205
FMN1 -0.005 0.014 0.063 10 -10000 0 10
mol:IP3 -0.011 0.022 0.079 24 -10000 0 24
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.006 0.014 0.062 9 -10000 0 9
CTNNB1 -0.015 0.001 -10000 0 -10000 0 0
AKT1 -0.017 0.011 0.047 7 -10000 0 7
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.006 0.006 -10000 0 -10000 0 0
CTNND1 -0.013 0.006 0.012 27 -10000 0 27
mol:PI-4-5-P2 -0.009 0.017 0.098 6 -10000 0 6
VASP -0.009 0.017 0.073 13 -10000 0 13
ZYX -0.007 0.016 0.071 14 -10000 0 14
JUB -0.005 0.014 0.063 10 -10000 0 10
EGFR(dimer) -0.004 0.018 0.1 7 -10000 0 7
E-cadherin/beta catenin-gamma catenin -0.021 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.013 0.011 0.054 7 -10000 0 7
PIK3CA -0.014 0.004 0.009 6 -10000 0 6
PI3K -0.013 0.011 0.055 7 -10000 0 7
FYN -0.013 0.02 0.068 25 -10000 0 25
mol:Ca2+ -0.011 0.022 0.078 24 -10000 0 24
JUP -0.014 0.003 -10000 0 -10000 0 0
PIK3R1 -0.013 0.007 0.012 25 -10000 0 25
mol:DAG -0.011 0.022 0.079 24 -10000 0 24
CDH1 -0.014 0.002 0 8 -10000 0 8
RhoA/GDP 0.018 0.053 0.081 205 -10000 0 205
establishment of polarity of embryonic epithelium -0.009 0.017 0.098 6 -10000 0 6
SRC -0.014 0 -10000 0 -10000 0 0
RAC1 -0.014 0 -10000 0 -10000 0 0
RHOA -0.014 0.001 0 2 -10000 0 2
EGFR -0.009 0.007 0 194 -10000 0 194
CASR -0.015 0.022 0.072 25 -10000 0 25
RhoA/GTP -0.014 0.022 0.068 30 -10000 0 30
AKT2 -0.017 0.011 0.047 7 -10000 0 7
actin cable formation -0.009 0.016 0.097 6 -10000 0 6
apoptosis 0.009 0.021 -10000 0 -0.077 25 25
CTNNA1 -0.013 0.006 0.012 31 -10000 0 31
mol:GDP -0.01 0.018 0.075 12 -10000 0 12
PIP5K1A -0.009 0.017 0.071 14 -10000 0 14
PLCG1 -0.012 0.022 0.08 24 -10000 0 24
Rac1/GTP -0.006 0.018 0.091 7 -10000 0 7
homophilic cell adhesion -0.001 0.001 0.007 1 -10000 0 1
ErbB2/ErbB3 signaling events

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
USP8 -0.014 0.002 0 4 -10000 0 4
RAS family/GTP 0.001 0.038 0.1 11 -10000 0 11
NFATC4 -0.023 0.021 -10000 0 -10000 0 0
ERBB2IP -0.013 0.003 0 31 -10000 0 31
HSP90 (dimer) -0.014 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.007 0.037 0.063 106 -10000 0 106
JUN 0.013 0.063 0.12 103 -10000 0 103
HRAS -0.013 0.003 0.008 6 -10000 0 6
DOCK7 -0.016 0.02 0.069 7 -10000 0 7
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.012 0.021 -10000 0 -10000 0 0
AKT1 -0.009 0.001 0 4 -10000 0 4
BAD -0.014 0.001 0 4 -10000 0 4
MAPK10 -0.01 0.016 -10000 0 -10000 0 0
mol:GTP 0 0.001 0.004 4 -0.003 1 5
ErbB2/ErbB3/neuregulin 1 beta -0.007 0.04 0.069 106 -10000 0 106
RAF1 0.022 0.063 0.15 51 -10000 0 51
ErbB2/ErbB3/neuregulin 2 -0.019 0.009 -10000 0 -10000 0 0
STAT3 0.009 0.004 -10000 0 -10000 0 0
cell migration -0.01 0.017 -10000 0 -0.074 1 1
mol:PI-3-4-5-P3 -0.001 0 -10000 0 -10000 0 0
cell proliferation 0.037 0.12 0.37 5 -0.51 5 10
FOS 0.052 0.13 0.28 118 -0.3 7 125
NRAS -0.01 0.006 0 139 -10000 0 139
mol:Ca2+ -0.007 0.037 0.063 106 -10000 0 106
MAPK3 0.036 0.089 0.32 5 -10000 0 5
MAPK1 0.025 0.12 0.32 5 -0.44 15 20
JAK2 -0.017 0.026 0.071 7 -10000 0 7
NF2 -0.003 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.008 0.008 -10000 0 -0.05 5 5
NRG1 -0.014 0.003 0.012 6 -10000 0 6
GRB2/SOS1 -0.005 0.007 0.008 128 -10000 0 128
MAPK8 -0.02 0.044 0.074 1 -0.13 55 56
MAPK9 -0.02 0.016 -10000 0 -10000 0 0
ERBB2 -0.013 0.003 0 31 -10000 0 31
ERBB3 -0.012 0.006 0.014 2 -10000 0 2
SHC1 -0.013 0.004 0.001 49 -10000 0 49
RAC1 -0.014 0 -10000 0 -10000 0 0
apoptosis 0.009 0.01 -10000 0 -0.12 3 3
STAT3 (dimer) 0.01 0.006 -10000 0 -10000 0 0
RNF41 -0.018 0.002 0 4 -10000 0 4
FRAP1 -0.014 0.002 0 5 -10000 0 5
RAC1-CDC42/GTP -0.021 0.018 0.021 1 -0.055 1 2
ErbB2/ErbB2/HSP90 (dimer) -0.019 0.005 -10000 0 -0.037 31 31
CHRNA1 0.032 0.091 0.27 10 -0.29 5 15
myelination -0.027 0.02 -10000 0 -10000 0 0
PPP3CB -0.016 0.025 0.067 7 -10000 0 7
KRAS -0.013 0.003 0.004 13 -10000 0 13
RAC1-CDC42/GDP -0.013 0.031 0.055 63 -10000 0 63
NRG2 -0.014 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.008 -10000 0 -0.05 5 5
SOS1 0 0.001 0.006 1 -10000 0 1
MAP2K2 0.019 0.064 0.16 37 -10000 0 37
SRC -0.014 0 -10000 0 -10000 0 0
mol:cAMP -0.001 0 -10000 0 -10000 0 0
PTPN11 -0.021 0.023 0.072 4 -10000 0 4
MAP2K1 0.023 0.13 0.31 5 -0.56 13 18
heart morphogenesis -0.007 0.037 0.063 106 -10000 0 106
RAS family/GDP -0.004 0.033 0.082 10 -10000 0 10
GRB2 -0.014 0.002 0.002 6 -10000 0 6
PRKACA 0.003 0.002 -10000 0 -10000 0 0
CHRNE 0.001 0.018 0.04 33 -10000 0 33
HSP90AA1 -0.014 0 -10000 0 -10000 0 0
activation of caspase activity 0.009 0.001 -10000 0 0 4 4
nervous system development -0.007 0.037 0.063 106 -10000 0 106
CDC42 -0.014 0 -10000 0 -10000 0 0
IL4-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
BCL2L1 0.053 0.25 0.6 10 -10000 0 10
STAT6 (cleaved dimer) -0.034 0.16 -10000 0 -10000 0 0
IGHG1 0.05 0.15 0.36 43 -0.44 1 44
IGHG3 0.047 0.23 0.53 11 -10000 0 11
AKT1 0.025 0.17 0.4 13 -0.64 3 16
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.034 0.13 0.36 14 -10000 0 14
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 0.039 0.17 0.39 17 -0.57 3 20
THY1 -0.079 0.43 0.6 9 -0.89 55 64
MYB -0.014 0.002 0 8 -10000 0 8
HMGA1 -0.014 0.001 0 1 -10000 0 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 0.047 0.19 0.41 42 -10000 0 42
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP 0.039 0.17 0.4 16 -0.57 3 19
SP1 0.06 0.078 0.14 261 -0.12 4 265
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 -0.011 0.024 -10000 0 -0.053 22 22
STAT6 (dimer)/ETS1 0.031 0.22 0.49 9 -10000 0 9
SOCS1 0.026 0.19 0.37 31 -10000 0 31
SOCS3 0.033 0.16 0.42 8 -10000 0 8
FCER2 0.051 0.22 0.55 15 -10000 0 15
PARP14 0 0.001 0.022 1 -10000 0 1
CCL17 0.053 0.25 0.6 10 -10000 0 10
GRB2 -0.014 0.001 0 5 -10000 0 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.04 0.15 0.35 33 -10000 0 33
T cell proliferation 0.036 0.23 0.53 9 -10000 0 9
IL4R/JAK1 0.04 0.24 0.53 12 -10000 0 12
EGR2 0.057 0.26 0.65 15 -10000 0 15
JAK2 0.014 0.047 0.1 45 -10000 0 45
JAK3 -0.015 0.006 0.051 1 -10000 0 1
PIK3R1 -0.013 0.004 0 36 -10000 0 36
JAK1 0.007 0.026 0.058 44 -10000 0 44
COL1A2 0.12 0.21 0.38 128 -0.9 4 132
CCL26 0.055 0.25 0.56 15 -10000 0 15
IL4R 0.062 0.27 0.67 15 -10000 0 15
PTPN6 -0.013 0.019 -10000 0 -0.051 11 11
IL13RA2 0.1 0.28 0.63 34 -10000 0 34
IL13RA1 0.008 0.043 0.082 72 -10000 0 72
IRF4 0.03 0.093 0.35 2 -10000 0 2
ARG1 0.039 0.13 0.42 13 -10000 0 13
CBL 0.037 0.17 0.37 30 -10000 0 30
GTF3A 0.004 0.051 0.14 66 -10000 0 66
PIK3CA -0.014 0.003 0 25 -10000 0 25
IL13RA1/JAK2 0.021 0.066 0.14 75 -10000 0 75
IRF4/BCL6 0.024 0.082 -10000 0 -10000 0 0
CD40LG -0.015 0.008 0.16 1 -10000 0 1
MAPK14 0.036 0.17 0.41 16 -10000 0 16
mitosis 0.025 0.16 0.39 14 -0.61 3 17
STAT6 0.079 0.28 0.63 30 -10000 0 30
SPI1 -0.015 0.002 -10000 0 -10000 0 0
RPS6KB1 0.02 0.16 0.38 13 -0.59 3 16
STAT6 (dimer) 0.079 0.27 0.63 30 -10000 0 30
STAT6 (dimer)/PARP14 -0.056 0.16 -10000 0 -10000 0 0
mast cell activation -0.004 0.013 -10000 0 -0.033 44 44
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 0.037 0.16 0.39 14 -10000 0 14
FRAP1 0.024 0.17 0.4 13 -0.64 3 16
LTA 0.053 0.25 0.6 10 -10000 0 10
FES -0.014 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation -0.069 0.28 -10000 0 -0.6 42 42
CCL11 0.047 0.23 0.54 11 -10000 0 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.038 0.16 0.39 14 -10000 0 14
IL2RG -0.015 0.006 -10000 0 -10000 0 0
IL10 0.053 0.25 0.59 11 -10000 0 11
IRS1 -0.014 0.001 0 5 -10000 0 5
IRS2 -0.014 0.002 0 11 -10000 0 11
IL4 0.045 0.13 0.42 11 -10000 0 11
IL5 0.053 0.25 0.6 10 -10000 0 10
IL4/IL4R/JAK1/IL13RA1/JAK2 0.067 0.25 0.55 42 -10000 0 42
COL1A1 0.073 0.19 0.49 62 -10000 0 62
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 0.036 0.23 0.53 8 -10000 0 8
IL2R gamma/JAK3 -0.017 0.005 -10000 0 -10000 0 0
TFF3 0.055 0.25 0.63 11 -10000 0 11
ALOX15 0.053 0.25 0.59 11 -10000 0 11
MYBL1 -0.012 0.005 0 80 -10000 0 80
T-helper 2 cell differentiation 0.048 0.23 0.51 17 -10000 0 17
SHC1 -0.013 0.004 0 46 -10000 0 46
CEBPB -0.015 0.002 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 0.035 0.16 0.35 31 -0.58 3 34
mol:PI-3-4-5-P3 0.025 0.17 0.4 13 -0.64 3 16
PI3K 0.024 0.17 0.4 13 -0.67 3 16
DOK2 0 0 -10000 0 -10000 0 0
ETS1 -0.015 0.028 -10000 0 -0.067 45 45
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.036 0.15 0.34 33 -10000 0 33
ITGB3 0.053 0.25 0.6 10 -10000 0 10
PIGR 0.053 0.25 0.61 11 -10000 0 11
IGHE -0.028 0.048 -10000 0 -0.11 70 70
MAPKKK cascade 0.037 0.14 0.32 44 -10000 0 44
BCL6 -0.014 0.003 -10000 0 -0.054 1 1
OPRM1 0.053 0.25 0.6 10 -10000 0 10
RETNLB 0.055 0.25 0.56 15 -10000 0 15
SELP 0.053 0.25 0.61 10 -10000 0 10
AICDA 0.046 0.23 0.55 8 -10000 0 8
Ephrin B reverse 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
EFNB2 -0.014 0.003 0 22 -9999 0 22
EPHB2 -0.013 0.006 0.011 32 -9999 0 32
EFNB1 -0.003 0.007 0 433 -9999 0 433
mol:GTP 0 0 -10000 0 -9999 0 0
Rac1/GDP -0.005 0.012 -10000 0 -9999 0 0
Ephrin B2/EPHB1-2 -0.013 0.012 0.02 54 -9999 0 54
neuron projection morphogenesis -0.005 0.011 0.018 2 -9999 0 2
Ephrin B1/EPHB1-2/Tiam1 -0.004 0.011 -10000 0 -9999 0 0
DNM1 -0.002 0.006 0 439 -9999 0 439
cell-cell signaling 0 0.001 0.007 2 -9999 0 2
MAP2K4 -0.005 0.01 -10000 0 -9999 0 0
YES1 0.004 0.004 -10000 0 -9999 0 0
Ephrin B1/EPHB1-2/NCK2 -0.004 0.011 -10000 0 -9999 0 0
PI3K 0.013 0.014 -10000 0 -9999 0 0
mol:GDP -0.004 0.011 -10000 0 -9999 0 0
ITGA2B -0.014 0 -10000 0 -9999 0 0
endothelial cell proliferation -0.011 0.008 0.013 43 -9999 0 43
FYN 0.004 0.004 -10000 0 -9999 0 0
MAP3K7 -0.002 0.006 0.12 1 -9999 0 1
FGR 0.001 0.004 -10000 0 -9999 0 0
TIAM1 -0.014 0.003 0 21 -9999 0 21
PIK3R1 -0.013 0.004 0 36 -9999 0 36
RGS3 -0.014 0.001 0 1 -9999 0 1
cell adhesion -0.01 0.015 -10000 0 -9999 0 0
LYN 0.004 0.004 -10000 0 -9999 0 0
Ephrin B1/EPHB1-2/Src Family Kinases 0.002 0.003 -10000 0 -9999 0 0
Ephrin B1/EPHB1-2 0.001 0.001 -10000 0 -9999 0 0
SRC 0.001 0.004 -10000 0 -9999 0 0
ITGB3 -0.014 0 -10000 0 -9999 0 0
EPHB1 -0.013 0.005 0.007 31 -9999 0 31
EPHB4 -0.014 0 -10000 0 -9999 0 0
RAC1 -0.014 0 -10000 0 -9999 0 0
Ephrin B2/EPHB4 -0.011 0.008 0.013 43 -9999 0 43
alphaIIb/beta3 Integrin -0.017 0 -10000 0 -9999 0 0
BLK 0.004 0.004 -10000 0 -9999 0 0
HCK 0.004 0.004 -10000 0 -9999 0 0
regulation of stress fiber formation 0.004 0.011 -10000 0 -9999 0 0
MAPK8 -0.008 0.012 -10000 0 -9999 0 0
Ephrin B1/EPHB1-2/RGS3 -0.004 0.011 -10000 0 -9999 0 0
endothelial cell migration -0.005 0.01 -10000 0 -9999 0 0
NCK2 -0.014 0.001 0 1 -9999 0 1
PTPN13 -0.01 0.004 -10000 0 -9999 0 0
regulation of focal adhesion formation 0.004 0.011 -10000 0 -9999 0 0
chemotaxis 0.004 0.011 -10000 0 -9999 0 0
PIK3CA -0.014 0.003 0 25 -9999 0 25
Rac1/GTP -0.005 0.012 0.022 4 -9999 0 4
angiogenesis 0.001 0.004 -10000 0 -9999 0 0
LCK 0.001 0.004 -10000 0 -9999 0 0
S1P1 pathway

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.01 0.012 0.031 7 -10000 0 7
PDGFRB -0.014 0.007 0.012 30 -10000 0 30
SPHK1 -0.006 0.009 -10000 0 -10000 0 0
mol:S1P -0.008 0.023 0.18 1 -10000 0 1
S1P1/S1P/Gi -0.042 0.059 0.16 13 -0.27 3 16
GNAO1 -0.001 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.059 0.062 0.16 16 -0.18 3 19
PLCG1 -0.051 0.064 0.16 15 -0.16 47 62
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.014 0.007 0.012 30 -10000 0 30
GNAI2 -0.012 0.011 0.03 34 -10000 0 34
GNAI3 -0.011 0.009 0.021 26 -10000 0 26
GNAI1 -0.011 0.009 0.021 28 -10000 0 28
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.045 0.062 0.1 280 -10000 0 280
S1P1/S1P 0.032 0.057 0.17 28 -10000 0 28
negative regulation of cAMP metabolic process -0.041 0.061 0.16 15 -0.2 7 22
MAPK3 -0.055 0.072 0.21 15 -0.24 3 18
calcium-dependent phospholipase C activity 0 0.002 0.009 28 -10000 0 28
Rac1/GDP -0.009 0 -10000 0 -10000 0 0
RhoA/GDP -0.009 0.001 0 2 -10000 0 2
KDR -0.016 0.008 -10000 0 -10000 0 0
PLCB2 0.033 0.06 0.17 36 -10000 0 36
RAC1 -0.014 0 -10000 0 -10000 0 0
RhoA/GTP -0.01 0.018 0.075 2 -10000 0 2
receptor internalization 0.029 0.054 0.16 25 -10000 0 25
PTGS2 -0.066 0.078 0.26 15 -10000 0 15
Rac1/GTP -0.01 0.018 0.075 2 -10000 0 2
RHOA -0.014 0.001 0 2 -10000 0 2
VEGFA -0.008 0.009 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.041 0.061 0.16 15 -0.2 7 22
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.011 0.008 0.022 19 -10000 0 19
MAPK1 -0.052 0.071 0.21 15 -0.24 3 18
S1P1/S1P/PDGFB-D/PDGFRB 0.038 0.068 0.15 69 -10000 0 69
ABCC1 -0.014 0.007 0.01 37 -10000 0 37
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 -0.011 0.006 0 126 -10000 0 126
SMAD2 -0.011 0.018 -10000 0 -0.11 6 6
SMAD3 -0.005 0.018 0.06 38 -10000 0 38
SMAD3/SMAD4 -0.002 0.009 -10000 0 -10000 0 0
SMAD4/Ubc9/PIASy -0.015 0.009 0 126 -10000 0 126
SMAD2/SMAD2/SMAD4 -0.022 0.018 -10000 0 -0.1 5 5
PPM1A -0.014 0 -10000 0 -10000 0 0
CALM1 -0.013 0.003 0 27 -10000 0 27
SMAD2/SMAD4 -0.012 0.016 -10000 0 -0.1 5 5
MAP3K1 -0.014 0.001 0 1 -10000 0 1
TRAP-1/SMAD4 -0.013 0.007 0 126 -10000 0 126
MAPK3 -0.014 0 -10000 0 -10000 0 0
MAPK1 -0.014 0.003 0 17 -10000 0 17
NUP214 -0.014 0 -10000 0 -10000 0 0
CTDSP1 -0.014 0.001 0 3 -10000 0 3
CTDSP2 -0.013 0.004 0 37 -10000 0 37
CTDSPL -0.014 0 -10000 0 -10000 0 0
KPNB1 -0.014 0 -10000 0 -10000 0 0
TGFBRAP1 -0.014 0 -10000 0 -10000 0 0
UBE2I -0.014 0 -10000 0 -10000 0 0
NUP153 -0.014 0.001 0 3 -10000 0 3
KPNA2 -0.014 0.002 0 12 -10000 0 12
PIAS4 -0.014 0 -10000 0 -10000 0 0
Signaling mediated by 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
PTGS2 0.002 0.062 0.26 29 -9999 0 29
MKNK1 -0.014 0 -10000 0 -9999 0 0
MAPK14 -0.014 0.029 0.11 30 -9999 0 30
ATF2/c-Jun -0.011 0.02 0.071 29 -9999 0 29
MAPK11 -0.014 0.029 0.11 30 -9999 0 30
MITF -0.005 0.032 0.12 30 -9999 0 30
MAPKAPK5 -0.005 0.032 0.12 30 -9999 0 30
KRT8 -0.004 0.036 0.14 30 -9999 0 30
MAPKAPK3 -0.014 0.001 0 2 -9999 0 2
MAPKAPK2 -0.014 0 -10000 0 -9999 0 0
p38alpha-beta/CK2 -0.015 0.044 0.16 30 -9999 0 30
CEBPB -0.004 0.037 0.14 30 -9999 0 30
SLC9A1 -0.005 0.032 0.12 30 -9999 0 30
mol:GDP 0 0 -10000 0 -9999 0 0
ATF2 -0.007 0.034 0.13 30 -9999 0 30
p38alpha-beta/MNK1 -0.016 0.04 0.15 30 -9999 0 30
JUN -0.011 0.02 0.07 29 -9999 0 29
PPARGC1A -0.005 0.033 0.13 30 -9999 0 30
USF1 -0.002 0.031 0.12 30 -9999 0 30
RAB5/GDP/GDI1 -0.012 0.02 0.073 22 -9999 0 22
NOS2 -0.002 0.031 0.12 30 -9999 0 30
DDIT3 -0.003 0.036 0.14 30 -9999 0 30
RAB5A -0.014 0 -10000 0 -9999 0 0
HSPB1 -0.008 0.032 0.1 39 -9999 0 39
p38alpha-beta/HBP1 -0.016 0.04 0.15 30 -9999 0 30
CREB1 0.001 0.031 0.13 29 -9999 0 29
RAB5/GDP -0.009 0 -10000 0 -9999 0 0
EIF4E -0.02 0.028 0.092 31 -9999 0 31
RPS6KA4 -0.005 0.032 0.12 30 -9999 0 30
PLA2G4A -0.018 0.021 0.091 12 -9999 0 12
GDI1 -0.006 0.027 0.12 22 -9999 0 22
TP53 -0.008 0.04 0.15 30 -9999 0 30
RPS6KA5 -0.005 0.032 0.12 30 -9999 0 30
ESR1 -0.005 0.032 0.12 30 -9999 0 30
HBP1 -0.014 0 -10000 0 -9999 0 0
MEF2C -0.005 0.027 0.12 21 -9999 0 21
MEF2A -0.005 0.032 0.12 30 -9999 0 30
EIF4EBP1 -0.001 0.017 0.13 8 -9999 0 8
KRT19 -0.004 0.036 0.14 30 -9999 0 30
ELK4 -0.005 0.032 0.12 30 -9999 0 30
ATF6 -0.005 0.032 0.12 30 -9999 0 30
ATF1 0 0.028 0.13 24 -9999 0 24
p38alpha-beta/MAPKAPK2 -0.016 0.04 0.15 30 -9999 0 30
p38alpha-beta/MAPKAPK3 -0.016 0.04 0.15 30 -9999 0 30
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.014 0 -10000 0 -10000 0 0
Caspase 8 (4 units) -0.01 0.024 0.052 64 -0.068 4 68
NEF -0.005 0 -10000 0 -10000 0 0
NFKBIA -0.013 0.021 0.069 32 -10000 0 32
BIRC3 -0.028 0.011 0.087 3 -10000 0 3
CYCS -0.012 0.025 0.09 12 -10000 0 12
RIPK1 -0.014 0.002 0 9 -10000 0 9
CD247 -0.019 0.001 -10000 0 -10000 0 0
MAP2K7 0.008 0.024 -10000 0 -10000 0 0
protein ubiquitination 0 0.035 0.12 23 -10000 0 23
CRADD -0.014 0 -10000 0 -10000 0 0
DAXX -0.014 0.001 0 1 -10000 0 1
FAS -0.012 0.005 0 68 -10000 0 68
BID -0.015 0.008 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha -0.027 0.007 0 36 -10000 0 36
TRADD -0.014 0 -10000 0 -10000 0 0
MAP3K5 -0.014 0.001 0 4 -10000 0 4
CFLAR -0.014 0.001 0 5 -10000 0 5
FADD -0.014 0.001 0 2 -10000 0 2
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.027 0.007 0 36 -10000 0 36
MAPK8 0.003 0.023 -10000 0 -10000 0 0
APAF1 -0.014 0 -10000 0 -10000 0 0
TRAF1 -0.014 0.001 0 1 -10000 0 1
TRAF2 -0.014 0 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.011 0.008 -10000 0 -10000 0 0
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.004 0.029 0.089 18 -10000 0 18
CHUK 0 0.036 0.12 23 -10000 0 23
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.023 0.01 -10000 0 -10000 0 0
TCRz/NEF -0.016 0.001 0 2 -10000 0 2
TNF -0.014 0.001 0 2 -10000 0 2
FASLG -0.018 0.001 0 2 -10000 0 2
NFKB1 -0.012 0.021 0.069 32 -10000 0 32
TNFR1A/BAG4/TNF-alpha -0.013 0.01 0 185 -10000 0 185
CASP6 0.002 0.018 -10000 0 -10000 0 0
CASP7 -0.002 0.071 0.24 36 -10000 0 36
RELA -0.012 0.021 0.069 33 -10000 0 33
CASP2 -0.014 0.001 0 1 -10000 0 1
CASP3 0 0.07 0.24 35 -10000 0 35
TNFRSF1A -0.009 0.007 0 183 -10000 0 183
TNFR1A/BAG4 -0.011 0.008 0 183 -10000 0 183
CASP8 -0.014 0.002 0 10 -10000 0 10
CASP9 -0.014 0.001 0 4 -10000 0 4
MAP3K14 0.005 0.038 0.12 27 -10000 0 27
APAF-1/Caspase 9 -0.034 0.024 0.047 2 -10000 0 2
BCL2 -0.002 0.022 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 -0.013 0.002 0 9 -10000 0 9
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 -0.014 0.002 0 9 -10000 0 9
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 -0.014 0.003 0 21 -10000 0 21
RAC1-CDC42/GTP/PAK family -0.001 0.002 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 -0.012 0.005 0 79 -10000 0 79
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 -0.014 0 -10000 0 -10000 0 0
FYN -0.014 0.003 0 21 -10000 0 21
MAP3K12 -0.014 0 -10000 0 -10000 0 0
FGR -0.014 0.003 0 17 -10000 0 17
p38 alpha/TAB1 -0.02 0.043 0.087 6 -0.15 16 22
PRKG1 -0.014 0 -10000 0 -10000 0 0
DUSP8 -0.011 0.006 0 130 -10000 0 130
PGK/cGMP/p38 alpha -0.021 0.04 0.073 4 -0.15 16 20
apoptosis -0.02 0.041 0.083 6 -0.15 16 22
RAL/GTP -0.012 0.004 0 46 -10000 0 46
LYN -0.012 0.005 0 64 -10000 0 64
DUSP1 -0.014 0.003 0 18 -10000 0 18
PAK1 -0.014 0 -10000 0 -10000 0 0
SRC -0.014 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.018 0 -10000 0 -10000 0 0
TRAF6 -0.014 0 -10000 0 -10000 0 0
RAC1 -0.014 0 -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 0 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.014 0 -10000 0 -10000 0 0
MAPK11 -0.021 0.041 0.096 8 -0.14 14 22
BLK -0.014 0 -10000 0 -10000 0 0
HCK -0.012 0.005 0 86 -10000 0 86
MAP2K3 -0.014 0 -10000 0 -10000 0 0
DUSP16 0 0 -10000 0 -10000 0 0
DUSP10 -0.014 0.002 0 7 -10000 0 7
TRAF6/MEKK3 -0.012 0 -10000 0 -10000 0 0
MAP3K7IP1 -0.014 0 -10000 0 -10000 0 0
MAPK14 -0.019 0.044 0.093 6 -0.16 16 22
positive regulation of innate immune response -0.027 0.05 0.11 7 -0.16 20 27
LCK -0.014 0.001 0 4 -10000 0 4
p38alpha-beta/MKP7 -0.028 0.047 0.1 7 -0.16 20 27
p38alpha-beta/MKP5 -0.029 0.051 0.11 7 -0.16 20 27
PGK/cGMP -0.009 0 -10000 0 -10000 0 0
PAK2 -0.014 0.003 0 24 -10000 0 24
p38alpha-beta/MKP1 -0.029 0.05 0.1 6 -0.16 20 26
CDC42 -0.014 0 -10000 0 -10000 0 0
RALB -0.014 0.001 0 1 -10000 0 1
RALA -0.013 0.004 0 45 -10000 0 45
PAK3 -0.002 0.005 0 450 -10000 0 450
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL -0.014 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.008 0.005 -10000 0 -10000 0 0
NT3 (dimer)/TRKC -0.017 0.003 0 8 -10000 0 8
NT3 (dimer)/TRKB -0.017 0.007 0 38 -10000 0 38
SHC/Grb2/SOS1/GAB1/PI3K -0.007 0.004 -10000 0 -10000 0 0
RAPGEF1 -0.014 0 -10000 0 -10000 0 0
BDNF -0.004 0.006 0 192 -10000 0 192
PIK3CA -0.014 0.003 0 11 -10000 0 11
DYNLT1 -0.012 0.005 0 34 -10000 0 34
NTRK1 -0.014 0.001 0 1 -10000 0 1
NTRK2 -0.013 0.005 0 31 -10000 0 31
NTRK3 -0.014 0.002 0 8 -10000 0 8
NT-4/5 (dimer)/TRKB -0.012 0.005 0 38 -10000 0 38
neuron apoptosis 0.059 0.046 0.14 38 -0.085 2 40
SHC 2-3/Grb2 -0.062 0.049 0.089 2 -0.15 38 40
SHC1 -0.013 0.004 0 25 -10000 0 25
SHC2 -0.047 0.043 -10000 0 -10000 0 0
SHC3 -0.045 0.051 -10000 0 -0.3 3 3
STAT3 (dimer) -0.016 0.008 0 52 -10000 0 52
NT3 (dimer)/TRKA -0.02 0.004 0 9 -10000 0 9
RIN/GDP -0.012 0.023 0.061 1 -0.17 3 4
GIPC1 -0.014 0 -10000 0 -10000 0 0
KRAS -0.014 0.002 0 4 -10000 0 4
DNAJA3 -0.008 0.011 0.046 10 -10000 0 10
RIN/GTP -0.005 0.004 0 116 -10000 0 116
CCND1 -0.014 0.007 0 52 -10000 0 52
MAGED1 -0.014 0.001 0 2 -10000 0 2
PTPN11 -0.014 0 -10000 0 -10000 0 0
RICS -0.01 0.006 0 78 -10000 0 78
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.012 0.004 0 28 -10000 0 28
GRB2 -0.014 0.001 0 3 -10000 0 3
NGF (dimer)/TRKA/MATK -0.013 0.001 0 1 -10000 0 1
TRKA/NEDD4-2 -0.017 0.001 0 1 -10000 0 1
ELMO1 -0.009 0.007 0 97 -10000 0 97
RhoG/GTP/ELMO1/DOCK1 -0.009 0.006 0 97 -10000 0 97
NGF 0 0 -10000 0 -10000 0 0
HRAS -0.014 0 -10000 0 -10000 0 0
DOCK1 -0.014 0 -10000 0 -10000 0 0
GAB2 -0.014 0.001 0 2 -10000 0 2
RIT2 -0.008 0.007 0 116 -10000 0 116
RIT1 -0.01 0.006 0 79 -10000 0 79
FRS2 -0.014 0.001 0 3 -10000 0 3
DNM1 -0.002 0.005 0 225 -10000 0 225
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.014 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.004 0.014 0.052 14 -10000 0 14
mol:GDP -0.026 0.041 0.076 2 -0.16 11 13
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP -0.005 0.004 0 97 -10000 0 97
RIT1/GDP -0.018 0.027 -10000 0 -0.14 6 6
TIAM1 -0.014 0.003 0 12 -10000 0 12
PIK3R1 -0.013 0.004 0 22 -10000 0 22
BDNF (dimer)/TRKB -0.004 0.008 0 214 -10000 0 214
KIDINS220/CRKL/C3G -0.017 0 -10000 0 -10000 0 0
SHC/RasGAP -0.015 0.005 0 30 -10000 0 30
FRS2 family/SHP2 -0.02 0.002 0 3 -10000 0 3
SHC/GRB2/SOS1/GAB1 -0.016 0.006 0 30 -10000 0 30
RIT1/GTP -0.006 0.004 0 79 -10000 0 79
NT3 (dimer) -0.014 0 -10000 0 -10000 0 0
RAP1/GDP -0.021 0.024 -10000 0 -0.1 12 12
KIDINS220/CRKL -0.014 0 -10000 0 -10000 0 0
BDNF (dimer) -0.004 0.006 0 192 -10000 0 192
ubiquitin-dependent protein catabolic process -0.013 0.001 0 1 -10000 0 1
Schwann cell development -0.002 0.004 -10000 0 -10000 0 0
EHD4 -0.013 0.004 0 21 -10000 0 21
FRS2 family/GRB2/SOS1 -0.017 0.003 0 6 -10000 0 6
FRS2 family/SHP2/CRK family/C3G/GAB2 -0.01 0.008 0.049 4 -0.072 1 5
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A -0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.005 0.012 -10000 0 -10000 0 0
ABL1 -0.014 0.001 0 2 -10000 0 2
SH2B family/GRB2/SOS1 -0.008 0.001 0 3 -10000 0 3
Rap1/GTP -0.002 0.005 -10000 0 -10000 0 0
STAT3 -0.016 0.008 0 52 -10000 0 52
axon guidance -0.005 0.012 -10000 0 -10000 0 0
MAPK3 -0.017 0.007 0.097 1 -10000 0 1
MAPK1 -0.017 0.008 0.097 1 -10000 0 1
CDC42/GDP -0.022 0.031 0.061 2 -0.12 11 13
NTF3 -0.014 0 -10000 0 -10000 0 0
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM -0.013 0.002 0 5 -10000 0 5
PI3K -0.015 0.006 0 32 -10000 0 32
FRS3 -0.014 0 -10000 0 -10000 0 0
FAIM -0.014 0.002 0 4 -10000 0 4
GAB1 -0.014 0.001 0 2 -10000 0 2
RASGRF1 -0.008 0.011 0.046 10 -10000 0 10
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.017 0.007 -10000 0 -10000 0 0
RGS19 -0.014 0 -10000 0 -10000 0 0
CDC42 -0.014 0 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.044 0.11 2 -0.28 4 6
Rac1/GDP -0.022 0.031 0.059 3 -0.12 11 14
NGF (dimer)/TRKA/GRIT -0.01 0.006 0 79 -10000 0 79
neuron projection morphogenesis 0.011 0.026 -10000 0 -10000 0 0
NGF (dimer)/TRKA/NEDD4-2 -0.013 0.001 0 1 -10000 0 1
MAP2K1 -0.01 0.034 0.091 27 -10000 0 27
NGFR -0.014 0.002 0 8 -10000 0 8
NGF (dimer)/TRKA/GIPC/GAIP -0.001 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K -0.006 0.004 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.021 0.003 0 6 -10000 0 6
NRAS -0.011 0.006 0 67 -10000 0 67
GRB2/SOS1 -0.008 0.001 0 3 -10000 0 3
PRKCI -0.014 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 -0.014 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0 0.007 -10000 0 -10000 0 0
RASA1 -0.014 0.002 0 5 -10000 0 5
TRKA/c-Abl -0.017 0.002 0 3 -10000 0 3
SQSTM1 -0.014 0.001 0 1 -10000 0 1
BDNF (dimer)/TRKB/GIPC -0.005 0.01 0 212 -10000 0 212
NGF (dimer)/TRKA/p62/Atypical PKCs -0.016 0.001 0 2 -10000 0 2
MATK -0.014 0 -10000 0 -10000 0 0
NEDD4L -0.014 0 -10000 0 -10000 0 0
RAS family/GDP -0.02 0.02 -10000 0 -0.071 25 25
NGF (dimer)/TRKA -0.006 0.002 -10000 0 -10000 0 0
Rac1/GTP -0.012 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family -0.027 0.003 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.014 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.023 0.054 -9999 0 -0.29 18 18
Syndecan-3/Neurocan -0.016 0.053 -9999 0 -0.29 18 18
POMC -0.014 0 -9999 0 -10000 0 0
EGFR -0.009 0.007 0 194 -10000 0 194
Syndecan-3/EGFR -0.016 0.062 -9999 0 -0.33 19 19
AGRP -0.014 0 -9999 0 -10000 0 0
NCSTN -0.013 0.003 0 30 -10000 0 30
PSENEN -0.014 0.001 0 1 -10000 0 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B -0.014 0 -9999 0 -10000 0 0
APH1A -0.014 0.002 0 10 -10000 0 10
NCAN -0.012 0.005 0 91 -10000 0 91
long-term memory -0.021 0.055 -9999 0 -0.29 19 19
Syndecan-3/IL8 -0.016 0.058 -9999 0 -0.3 19 19
PSEN1 -0.014 0.001 0 1 -10000 0 1
Src/Cortactin -0.017 0 -9999 0 -10000 0 0
FYN -0.014 0.003 0 21 -10000 0 21
limb bud formation -0.015 0.06 -9999 0 -0.37 15 15
MC4R -0.014 0.001 0 1 -10000 0 1
SRC -0.014 0 -9999 0 -10000 0 0
PTN -0.014 0.003 0 26 -10000 0 26
FGFR/FGF/Syndecan-3 -0.015 0.061 -9999 0 -0.37 15 15
neuron projection morphogenesis -0.025 0.043 -9999 0 -0.24 18 18
Syndecan-3/AgRP -0.019 0.063 -9999 0 -0.34 19 19
Syndecan-3/AgRP/MC4R -0.021 0.062 -9999 0 -0.33 19 19
Fyn/Cortactin -0.016 0.003 0 21 -10000 0 21
SDC3 -0.015 0.061 -9999 0 -0.37 15 15
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.016 0.057 -9999 0 -0.3 19 19
IL8 -0.011 0.006 0 115 -10000 0 115
Syndecan-3/Fyn/Cortactin -0.02 0.057 -9999 0 -0.31 18 18
Syndecan-3/CASK -0.016 0.061 -9999 0 -0.33 19 19
alpha-MSH/MC4R -0.017 0.001 0 1 -10000 0 1
Gamma Secretase -0.025 0.007 -9999 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.007 0 0 2 -10000 0 2
ARNO/beta Arrestin1-2 -0.013 0.001 0 1 -10000 0 1
EGFR -0.009 0.007 0 194 -10000 0 194
EPHA2 -0.014 0.002 0 13 -10000 0 13
USP6 -0.014 0 -10000 0 -10000 0 0
IQSEC1 -0.014 0.002 0 9 -10000 0 9
EGFR/EGFR/EGF/EGF -0.011 0.008 0 196 -10000 0 196
ARRB2 -0.005 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.004 0.032 2 -0.027 2 4
ARRB1 -0.014 0 -10000 0 -10000 0 0
FBXO8 0 0 -10000 0 -10000 0 0
TSHR -0.014 0.001 0 4 -10000 0 4
EGF -0.014 0.001 0 2 -10000 0 2
somatostatin receptor activity 0 0 0 1 -10000 0 1
ARAP2 0 0 0 1 -10000 0 1
mol:GDP 0.004 0.012 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 0 1 -10000 0 1
ITGA2B -0.014 0 -10000 0 -10000 0 0
ARF6 -0.014 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.022 0.006 0 38 -10000 0 38
ADAP1 0 0 -10000 0 -10000 0 0
KIF13B -0.014 0.001 0 2 -10000 0 2
HGF/MET -0.017 0.003 0 12 -10000 0 12
PXN -0.014 0 -10000 0 -10000 0 0
ARF6/GTP 0.005 0.018 0.072 1 -10000 0 1
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.012 0.01 0 203 -10000 0 203
ADRB2 -0.014 0.001 0 1 -10000 0 1
receptor agonist activity 0 0 0 1 -10000 0 1
actin filament binding 0 0 0 1 -10000 0 1
SRC -0.014 0 -10000 0 -10000 0 0
ITGB3 -0.014 0 -10000 0 -10000 0 0
GNAQ -0.014 0 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 0 2 -10000 0 2
ARF6/GDP 0 0.016 0.095 8 -10000 0 8
ARF6/GDP/GULP/ACAP1 0.002 0.018 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.024 0 -10000 0 -10000 0 0
ACAP1 0 0 -10000 0 -10000 0 0
ACAP2 0 0 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.008 0 -10000 0 -10000 0 0
EFNA1 -0.014 0.003 0 24 -10000 0 24
HGF -0.014 0.001 0 2 -10000 0 2
CYTH3 0 0 0 1 -10000 0 1
CYTH2 0 0 -10000 0 -10000 0 0
NCK1 -0.014 0.002 0 11 -10000 0 11
fibronectin binding 0 0 0 1 -10000 0 1
endosomal lumen acidification 0 0 0 1 -10000 0 1
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.014 0.001 0 4 -10000 0 4
GNAQ/ARNO 0 0.006 -10000 0 -10000 0 0
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E -0.001 0.003 0 502 -10000 0 502
MET -0.014 0.002 0 10 -10000 0 10
GNA14 -0.014 0.001 0 2 -10000 0 2
GNA15 -0.014 0.002 0 7 -10000 0 7
GIT1 -0.014 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0 1 -10000 0 1
GNA11 -0.014 0 -10000 0 -10000 0 0
LHCGR -0.014 0 -10000 0 -10000 0 0
AGTR1 -0.014 0.001 0 2 -10000 0 2
desensitization of G-protein coupled receptor protein signaling pathway -0.008 0 -10000 0 -10000 0 0
IPCEF1/ARNO -0.001 0.003 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.017 0 -10000 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 -0.013 0.004 0 46 -9999 0 46
positive regulation of NF-kappaB transcription factor activity -0.016 0.005 0 46 -9999 0 46
MAP2K4 -0.004 0.017 -10000 0 -9999 0 0
IKBKB -0.014 0 -10000 0 -9999 0 0
TNFRSF10B -0.014 0.002 0 8 -9999 0 8
TNFRSF10A 0 0 -10000 0 -9999 0 0
SMPD1 -0.007 0.002 0 52 -9999 0 52
IKBKG -0.014 0 -10000 0 -9999 0 0
mol:GTP 0 0 -10000 0 -9999 0 0
TNFRSF10D -0.014 0 -10000 0 -9999 0 0
TRAIL/TRAILR2 -0.015 0.005 0 52 -9999 0 52
TRAIL/TRAILR3 -0.016 0.005 0 46 -9999 0 46
TRAIL/TRAILR1 -0.008 0.002 0 46 -9999 0 46
TRAIL/TRAILR4 -0.016 0.005 0 46 -9999 0 46
TRAIL/TRAILR1/DAP3/GTP -0.011 0.003 0 46 -9999 0 46
IKK complex -0.013 0.006 -10000 0 -9999 0 0
RIPK1 -0.014 0.002 0 9 -9999 0 9
response to oxidative stress 0 0 -10000 0 -9999 0 0
DAP3/GTP -0.009 0 -10000 0 -9999 0 0
MAPK3 -0.016 0.005 0 46 -9999 0 46
MAP3K1 -0.004 0.005 0.058 1 -9999 0 1
TRAILR4 (trimer) -0.014 0 -10000 0 -9999 0 0
TRADD -0.014 0 -10000 0 -9999 0 0
TRAILR1 (trimer) 0 0 -10000 0 -9999 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.008 0.003 -10000 0 -9999 0 0
CFLAR -0.014 0.001 0 5 -9999 0 5
MAPK1 -0.015 0.005 0 58 -9999 0 58
TRAIL/TRAILR1/FADD/TRADD/RIP -0.02 0.007 0 54 -9999 0 54
mol:ceramide -0.007 0.002 0 52 -9999 0 52
FADD -0.014 0.001 0 2 -9999 0 2
MAPK8 -0.008 0.018 0.09 4 -9999 0 4
TRAF2 -0.014 0 -10000 0 -9999 0 0
TRAILR3 (trimer) -0.014 0 -10000 0 -9999 0 0
CHUK -0.014 0.001 0 1 -9999 0 1
TRAIL/TRAILR1/FADD -0.012 0.004 0 47 -9999 0 47
DAP3 -0.014 0 -10000 0 -9999 0 0
CASP10 -0.003 0.03 0.087 51 -9999 0 51
JNK cascade -0.016 0.005 0 46 -9999 0 46
TRAIL (trimer) -0.013 0.004 0 46 -9999 0 46
TNFRSF10C -0.014 0 -10000 0 -9999 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD -0.015 0.005 0 47 -9999 0 47
TRAIL/TRAILR2/FADD -0.018 0.006 0 53 -9999 0 53
cell death -0.007 0.002 0 52 -9999 0 52
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.01 0.004 -10000 0 -9999 0 0
TRAILR2 (trimer) -0.014 0.002 0 8 -9999 0 8
CASP8 0.002 0.013 -10000 0 -9999 0 0
negative regulation of caspase activity 0 0 -10000 0 -9999 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.024 0.009 -10000 0 -9999 0 0
Caspase cascade in apoptosis

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
TOP1 0.001 0.025 0.12 3 -10000 0 3
ACTA1 -0.009 0.03 0.1 10 -0.097 20 30
NUMA1 0.001 0.025 0.13 2 -10000 0 2
SPTAN1 -0.009 0.031 0.12 11 -0.098 15 26
LIMK1 -0.012 0.029 0.11 5 -0.099 18 23
BIRC3 -0.013 0.003 0 33 -10000 0 33
BIRC2 -0.014 0 -10000 0 -10000 0 0
BAX -0.014 0.002 0 7 -10000 0 7
CASP10 -0.019 0.004 0 22 -10000 0 22
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0 0.029 0.12 3 -0.24 2 5
DIABLO -0.014 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.009 0.031 0.12 11 -0.097 15 26
response to UV 0 0 -10000 0 -10000 0 0
CRADD -0.014 0 -10000 0 -10000 0 0
GSN -0.009 0.033 0.11 13 -0.098 20 33
MADD -0.014 0.001 0 4 -10000 0 4
TFAP2A 0.01 0.008 -10000 0 -10000 0 0
BID -0.009 0.002 0 36 -10000 0 36
MAP3K1 0 0.014 -10000 0 -10000 0 0
TRADD -0.014 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.017 0.001 0 4 -10000 0 4
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.002 0.042 0.13 30 -0.094 17 47
CASP9 -0.014 0.001 0 4 -10000 0 4
DNA repair 0.001 0.022 0.086 4 -10000 0 4
neuron apoptosis 0.005 0.028 -10000 0 -0.58 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.006 0.028 0.12 3 -10000 0 3
APAF1 -0.014 0 -10000 0 -10000 0 0
CASP6 0.006 0.019 -10000 0 -10000 0 0
TRAF2 -0.014 0 -10000 0 -10000 0 0
ICAD/CAD -0.016 0.028 0.1 5 -0.1 15 20
CASP7 0.002 0.039 -10000 0 -0.13 30 30
KRT18 0.008 0.012 -10000 0 -10000 0 0
apoptosis -0.008 0.035 0.13 3 -10000 0 3
DFFA -0.012 0.029 0.11 5 -0.096 22 27
DFFB -0.012 0.029 0.11 5 -0.099 18 23
PARP1 -0.001 0.022 -10000 0 -0.087 4 4
actin filament polymerization 0.011 0.027 0.093 18 -0.11 5 23
TNF -0.014 0.001 0 2 -10000 0 2
CYCS -0.004 0.019 0.08 14 -0.18 1 15
SATB1 0.001 0.019 -10000 0 -10000 0 0
SLK -0.012 0.029 0.11 5 -0.099 18 23
p15 BID/BAX -0.009 0.02 0.064 35 -10000 0 35
CASP2 0.006 0.026 0.078 23 -10000 0 23
JNK cascade 0 0.014 -10000 0 -10000 0 0
CASP3 -0.007 0.031 0.11 8 -0.097 22 30
LMNB2 0.011 0.021 -10000 0 -10000 0 0
RIPK1 -0.014 0.002 0 9 -10000 0 9
CASP4 -0.011 0.006 0 107 -10000 0 107
Mammalian IAPs/DIABLO -0.017 0.004 0 33 -10000 0 33
negative regulation of DNA binding 0.01 0.008 -10000 0 -10000 0 0
stress fiber formation -0.012 0.029 0.11 5 -0.098 18 23
GZMB -0.016 0.003 0 22 -10000 0 22
CASP1 -0.003 0.003 0 195 -10000 0 195
LMNB1 0.013 0.021 -10000 0 -10000 0 0
APP 0.005 0.028 -10000 0 -0.59 1 1
TNFRSF1A -0.009 0.007 0 183 -10000 0 183
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.008 0.001 0 10 -10000 0 10
VIM -0.003 0.036 0.13 4 -10000 0 4
LMNA 0.01 0.02 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.012 0.028 0.087 22 -10000 0 22
LRDD -0.014 0 -10000 0 -10000 0 0
SREBF1 -0.012 0.029 0.11 5 -0.099 18 23
APAF-1/Caspase 9 0.011 0.008 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.001 0.025 0.13 2 -10000 0 2
CFL2 -0.011 0.028 0.11 5 -0.094 18 23
GAS2 -0.003 0.042 0.11 38 -0.097 20 58
positive regulation of apoptosis 0.014 0.021 -10000 0 -10000 0 0
PRF1 -0.014 0.002 0 12 -10000 0 12
Syndecan-2-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
Syndecan-2/Fibronectin -0.011 0.01 0.097 3 -9999 0 3
EPHB2 -0.014 0.001 0 2 -9999 0 2
Syndecan-2/TACI -0.014 0.011 0.097 5 -9999 0 5
LAMA1 0 0 -10000 0 -9999 0 0
Syndecan-2/alpha2 ITGB1 -0.017 0.017 0.09 9 -9999 0 9
HRAS -0.014 0.001 0 2 -9999 0 2
Syndecan-2/CASK -0.008 0.002 -10000 0 -9999 0 0
ITGA5 -0.012 0.005 0 74 -9999 0 74
BAX -0.015 0.014 -10000 0 -9999 0 0
EPB41 -0.014 0 -10000 0 -9999 0 0
positive regulation of cell-cell adhesion -0.013 0.002 -10000 0 -9999 0 0
LAMA3 -0.014 0.002 0 15 -9999 0 15
EZR 0 0 -10000 0 -9999 0 0
mol:PI-4-5-P2 0 0 -10000 0 -9999 0 0
CAV2 -0.012 0.005 0 72 -9999 0 72
Syndecan-2/MMP2 -0.007 0.01 0.097 2 -9999 0 2
RP11-540L11.1 0 0 -10000 0 -9999 0 0
alpha2 ITGB1 -0.014 0.007 0 93 -9999 0 93
dendrite morphogenesis -0.014 0.011 0.097 5 -9999 0 5
Syndecan-2/GM-CSF -0.014 0.011 0.097 5 -9999 0 5
determination of left/right symmetry -0.009 0.013 0.13 5 -9999 0 5
Syndecan-2/PKC delta -0.014 0.011 0.097 5 -9999 0 5
GNB2L1 -0.014 0 -10000 0 -9999 0 0
MAPK3 -0.016 0.019 0.1 13 -9999 0 13
MAPK1 -0.016 0.019 0.1 13 -9999 0 13
Syndecan-2/RACK1 -0.016 0.011 0.089 5 -9999 0 5
NF1 -0.014 0 -10000 0 -9999 0 0
FGFR/FGF/Syndecan-2 -0.009 0.013 0.13 5 -9999 0 5
ITGA2 -0.012 0.005 0 93 -9999 0 93
MAPK8 -0.015 0.021 0.2 5 -9999 0 5
Syndecan-2/alpha2/beta1 Integrin -0.013 0.012 0.089 5 -9999 0 5
Syndecan-2/Kininogen -0.014 0.011 0.097 5 -9999 0 5
ITGB1 -0.014 0 -10000 0 -9999 0 0
SRC -0.019 0.018 0.09 14 -9999 0 14
Syndecan-2/CASK/Protein 4.1 -0.013 0.002 -10000 0 -9999 0 0
extracellular matrix organization -0.013 0.011 0.097 5 -9999 0 5
actin cytoskeleton reorganization -0.011 0.01 0.097 3 -9999 0 3
Syndecan-2/Caveolin-2/Ras -0.015 0.012 0.094 4 -9999 0 4
Syndecan-2/Laminin alpha3 -0.014 0.01 0.097 4 -9999 0 4
Syndecan-2/RasGAP -0.02 0.011 0.087 5 -9999 0 5
alpha5/beta1 Integrin -0.015 0.006 0 74 -9999 0 74
PRKCD -0.014 0 -10000 0 -9999 0 0
Syndecan-2 dimer -0.014 0.011 0.097 5 -9999 0 5
GO:0007205 -0.001 0 -10000 0 -9999 0 0
DNA mediated transformation 0 0 -10000 0 -9999 0 0
Syndecan-2/RasGAP/Src -0.024 0.012 0.081 6 -9999 0 6
RHOA -0.014 0.001 0 2 -9999 0 2
SDCBP -0.014 0 -10000 0 -9999 0 0
TNFRSF13B -0.014 0 -10000 0 -9999 0 0
RASA1 -0.014 0.002 0 8 -9999 0 8
alpha2/beta1 Integrin -0.014 0.007 0 93 -9999 0 93
Syndecan-2/Synbindin -0.014 0.011 0.097 5 -9999 0 5
TGFB1 -0.013 0.003 0 27 -9999 0 27
CASP3 -0.013 0.018 0.1 10 -9999 0 10
FN1 -0.011 0.006 0 104 -9999 0 104
Syndecan-2/IL8 -0.011 0.012 0.097 5 -9999 0 5
SDC2 -0.009 0.013 0.13 5 -9999 0 5
KNG1 -0.014 0.001 0 1 -9999 0 1
Syndecan-2/Neurofibromin -0.014 0.011 0.097 5 -9999 0 5
TRAPPC4 -0.014 0.001 0 1 -9999 0 1
CSF2 -0.014 0 -10000 0 -9999 0 0
Syndecan-2/TGFB1 -0.013 0.012 0.097 5 -9999 0 5
Syndecan-2/Syntenin/PI-4-5-P2 -0.013 0.002 -10000 0 -9999 0 0
Syndecan-2/Ezrin -0.013 0.003 -10000 0 -9999 0 0
PRKACA -0.016 0.019 0.1 13 -9999 0 13
angiogenesis -0.011 0.012 0.097 5 -9999 0 5
MMP2 -0.007 0.007 0 250 -9999 0 250
IL8 -0.011 0.006 0 115 -9999 0 115
calcineurin-NFAT signaling pathway -0.014 0.011 0.097 5 -9999 0 5
TCGA08_p53

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
CDKN2A -0.008 0.003 0 59 -10000 0 59
TP53 0.002 0.015 -10000 0 -0.097 12 12
Senescence 0.002 0.015 -10000 0 -0.097 12 12
Apoptosis 0.002 0.015 -10000 0 -0.097 12 12
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.003 0.025 0.16 12 -10000 0 12
MDM4 -0.014 0.002 0 13 -10000 0 13
Paxillin-dependent events mediated by a4b1

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
CRKL -0.014 0 -9999 0 -10000 0 0
Rac1/GDP -0.014 0 -9999 0 -10000 0 0
DOCK1 -0.014 0 -9999 0 -10000 0 0
ITGA4 -0.014 0.001 0 5 -10000 0 5
RAC1 -0.014 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin -0.017 0.002 0 5 -10000 0 5
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.02 0.002 0 5 -10000 0 5
alpha4/beta7 Integrin/Paxillin -0.023 0.002 0 5 -10000 0 5
lamellipodium assembly -0.021 0.048 -9999 0 -0.19 36 36
PIK3CA -0.014 0.003 0 25 -10000 0 25
PI3K -0.015 0.005 0 60 -10000 0 60
ARF6 -0.014 0 -9999 0 -10000 0 0
TLN1 -0.013 0.004 0 46 -10000 0 46
PXN -0.017 0 -9999 0 -10000 0 0
PIK3R1 -0.013 0.004 0 36 -10000 0 36
ARF6/GTP -0.029 0.003 -9999 0 -10000 0 0
cell adhesion -0.025 0.008 -9999 0 -10000 0 0
CRKL/CBL -0.017 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.023 0.002 0 5 -10000 0 5
ITGB1 -0.014 0 -9999 0 -10000 0 0
ITGB7 -0.014 0.001 0 2 -10000 0 2
ARF6/GDP -0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.009 0.013 -9999 0 -10000 0 0
p130Cas/Crk/Dock1 -0.014 0 -9999 0 -10000 0 0
VCAM1 -0.005 0.007 0 351 -10000 0 351
alpha4/beta1 Integrin/Paxillin/Talin -0.025 0.008 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.027 0.003 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
mol:GDP 0.027 0.003 -9999 0 -10000 0 0
CBL -0.014 0 -9999 0 -10000 0 0
PRKACA -0.014 0 -9999 0 -10000 0 0
GIT1 -0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.025 0.008 -9999 0 -10000 0 0
Rac1/GTP -0.023 0.052 -9999 0 -0.21 36 36
IL2 signaling events mediated by STAT5

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
GAB2 -0.014 0.002 0.022 1 -10000 0 1
ELF1 -0.02 0.004 0.001 14 -10000 0 14
CCNA2 -0.01 0.006 0 139 -10000 0 139
PIK3CA -0.014 0.003 0.001 26 -10000 0 26
JAK3 -0.014 0.002 0.021 1 -10000 0 1
PIK3R1 -0.013 0.004 0.001 37 -10000 0 37
JAK1 -0.014 0.002 0.004 6 -10000 0 6
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.012 0.031 0.22 1 -0.21 2 3
SHC1 -0.013 0.004 0 47 -10000 0 47
SP1 -0.019 0.004 0 27 -10000 0 27
IL2RA -0.017 0.003 0.001 14 -10000 0 14
IL2RB -0.014 0.002 0.004 5 -10000 0 5
SOS1 0 0.001 0.013 1 -10000 0 1
IL2RG -0.014 0.002 0.022 1 -10000 0 1
G1/S transition of mitotic cell cycle 0.008 0.067 0.18 14 -0.31 13 27
PTPN11 -0.014 0.002 0.022 1 -10000 0 1
CCND2 -0.017 0.004 0 27 -10000 0 27
LCK -0.014 0.002 0.004 5 -10000 0 5
GRB2 -0.014 0.002 0.004 6 -10000 0 6
IL2 -0.014 0.002 0.022 1 -10000 0 1
CDK6 -0.014 0 -10000 0 -10000 0 0
CCND3 -0.012 0.032 0.3 1 -10000 0 1
Signaling events mediated by PRL

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 -0.014 0.002 0 7 -10000 0 7
mol:Halofuginone -0.003 0 -10000 0 -10000 0 0
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A -0.003 0.016 -10000 0 -0.31 1 1
PRL-3/alpha Tubulin -0.016 0.004 0 31 -10000 0 31
mol:Ca2+ -0.012 0.005 0 74 -10000 0 74
AGT -0.013 0.004 0 44 -10000 0 44
CCNA2 0.008 0.049 0.09 140 -10000 0 140
TUBA1B -0.014 0 -10000 0 -10000 0 0
EGR1 -0.012 0.008 0.17 1 -10000 0 1
CDK2/Cyclin E1 -0.005 0.025 0.13 3 -0.28 1 4
MAPK3 -0.016 0.004 0 31 -10000 0 31
PRL-2 /Rab GGTase beta -0.017 0.001 0 1 -10000 0 1
MAPK1 -0.016 0.005 0 48 -10000 0 48
PTP4A1 -0.017 0.003 0 21 -10000 0 21
PTP4A3 -0.013 0.003 0 31 -10000 0 31
PTP4A2 -0.014 0.001 0 1 -10000 0 1
ITGB1 -0.016 0.004 0 31 -10000 0 31
SRC -0.014 0 -10000 0 -10000 0 0
RAC1 -0.002 0.009 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha -0.017 0 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.018 0.021 0.21 1 -10000 0 1
RABGGTA -0.014 0 -10000 0 -10000 0 0
BCAR1 -0.005 0.001 0 31 -10000 0 31
RHOC -0.001 0.009 -10000 0 -10000 0 0
RHOA -0.003 0.021 -10000 0 -0.31 2 2
cell motility 0.011 0.026 0.16 5 -10000 0 5
PRL-1/alpha Tubulin -0.018 0.021 0.21 1 -10000 0 1
PRL-3/alpha1 Integrin -0.008 0.002 0 31 -10000 0 31
ROCK1 0.01 0.023 0.14 2 -10000 0 2
RABGGTB -0.014 0 -10000 0 -10000 0 0
CDK2 -0.013 0.003 0 27 -10000 0 27
mitosis -0.014 0.02 0.1 15 -10000 0 15
ATF5 -0.014 0.001 0 1 -10000 0 1
BMP receptor signaling

Figure S85.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.026 0.006 -10000 0 -10000 0 0
SMAD6-7/SMURF1 -0.02 0.001 0 1 -10000 0 1
NOG 0 0 -10000 0 -10000 0 0
SMAD9 0.006 0.008 -10000 0 -10000 0 0
SMAD4 -0.011 0.006 0 126 -10000 0 126
SMAD5 -0.004 0.016 0.086 8 -10000 0 8
BMP7/USAG1 -0.017 0.002 0 9 -10000 0 9
SMAD5/SKI -0.008 0.018 0.092 6 -10000 0 6
SMAD1 0 0.04 0.13 5 -0.15 16 21
BMP2 -0.013 0.004 0 54 -10000 0 54
SMAD1/SMAD1/SMAD4 -0.019 0.032 -10000 0 -0.15 14 14
BMPR1A -0.014 0.002 0 6 -10000 0 6
BMPR1B -0.014 0.001 0 1 -10000 0 1
BMPR1A-1B/BAMBI -0.019 0.005 0 41 -10000 0 41
AHSG -0.014 0.001 0 2 -10000 0 2
CER1 -0.014 0 -10000 0 -10000 0 0
BMP2-4/CER1 -0.018 0.007 0 62 -10000 0 62
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.004 0.016 -10000 0 -10000 0 0
BMP2-4 (homodimer) -0.015 0.005 0 62 -10000 0 62
RGMB 0 0 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.023 0.003 0 9 -10000 0 9
RGMA 0 0 -10000 0 -10000 0 0
SMURF1 -0.014 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0 0.014 0.043 53 -10000 0 53
BMP2-4/USAG1 -0.018 0.007 0 66 -10000 0 66
SMAD6/SMURF1/SMAD5 -0.008 0.018 0.092 6 -10000 0 6
SOSTDC1 -0.014 0.002 0 7 -10000 0 7
BMP7/BMPR2/BMPR1A-1B -0.023 0.003 0 9 -10000 0 9
SKI -0.014 0 -10000 0 -10000 0 0
BMP6 (homodimer) -0.014 0.001 0 2 -10000 0 2
HFE2 0 0 -10000 0 -10000 0 0
ZFYVE16 -0.014 0.001 0 5 -10000 0 5
MAP3K7 -0.014 0.001 0 1 -10000 0 1
BMP2-4/CHRD -0.018 0.007 0 62 -10000 0 62
SMAD5/SMAD5/SMAD4 -0.007 0.013 0.084 2 -10000 0 2
MAPK1 -0.014 0.003 0 17 -10000 0 17
TAK1/TAB family -0.014 0.024 0.05 64 -10000 0 64
BMP7 (homodimer) -0.014 0.001 0 2 -10000 0 2
NUP214 -0.014 0 -10000 0 -10000 0 0
BMP6/FETUA -0.017 0.001 0 4 -10000 0 4
SMAD1/SKI -0.003 0.041 0.13 5 -0.15 16 21
SMAD6 -0.014 0 -10000 0 -10000 0 0
CTDSP2 -0.013 0.004 0 37 -10000 0 37
BMP2-4/FETUA -0.018 0.007 0 63 -10000 0 63
MAP3K7IP1 -0.014 0 -10000 0 -10000 0 0
GREM1 -0.014 0.003 0 23 -10000 0 23
BMPR2 (homodimer) -0.014 0 -10000 0 -10000 0 0
GADD34/PP1CA -0.02 0.002 0 6 -10000 0 6
BMPR1A-1B (homodimer) -0.017 0.002 0 7 -10000 0 7
CHRDL1 0 0 -10000 0 -10000 0 0
ENDOFIN/SMAD1 -0.003 0.041 0.13 5 -0.15 16 21
SMAD6-7/SMURF1/SMAD1 -0.009 0.044 0.12 5 -0.15 16 21
SMAD6/SMURF1 -0.014 0 -10000 0 -10000 0 0
BAMBI -0.013 0.004 0 36 -10000 0 36
SMURF2 -0.014 0.001 0 2 -10000 0 2
BMP2-4/CHRDL1 -0.012 0.004 0 62 -10000 0 62
BMP2-4/GREM1 -0.017 0.007 0 82 -10000 0 82
SMAD7 -0.014 0.001 0 1 -10000 0 1
SMAD8A/SMAD8A/SMAD4 0.008 0.007 -10000 0 -10000 0 0
SMAD1/SMAD6 -0.003 0.041 0.13 5 -0.15 16 21
TAK1/SMAD6 -0.017 0.001 0 1 -10000 0 1
BMP7 -0.014 0.001 0 2 -10000 0 2
BMP6 -0.014 0.001 0 2 -10000 0 2
MAP3K7IP2 -0.014 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0 0.015 0.043 60 -10000 0 60
PPM1A -0.014 0 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.003 0.041 0.13 5 -0.15 16 21
SMAD7/SMURF1 -0.017 0.001 0 1 -10000 0 1
CTDSPL -0.014 0 -10000 0 -10000 0 0
PPP1CA -0.014 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 -0.014 0.001 0 3 -10000 0 3
PPP1R15A -0.014 0.001 0 1 -10000 0 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.001 0.014 0.043 49 -10000 0 49
CHRD -0.014 0 -10000 0 -10000 0 0
BMPR2 -0.014 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.005 0.002 -10000 0 -10000 0 0
BMP4 -0.014 0.002 0 8 -10000 0 8
FST -0.014 0.002 0 16 -10000 0 16
BMP2-4/NOG -0.012 0.004 0 62 -10000 0 62
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.027 0.004 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 -0.006 0.027 0.23 3 -0.14 5 8
SMARCC2 -0.014 0.001 0 1 -10000 0 1
SMARCC1 -0.014 0.003 0 18 -10000 0 18
TBX21 -0.002 0.023 0.14 4 -10000 0 4
SUMO2 -0.014 0.005 0.021 10 -10000 0 10
STAT1 (dimer) -0.003 0.039 0.11 58 -10000 0 58
FKBP4 -0.014 0 -10000 0 -10000 0 0
FKBP5 -0.014 0.003 0 26 -10000 0 26
GR alpha/HSP90/FKBP51/HSP90 -0.009 0.023 -10000 0 -0.13 2 2
PRL -0.052 0.069 0.3 3 -10000 0 3
cortisol/GR alpha (dimer)/TIF2 0.007 0.05 -10000 0 -0.29 3 3
RELA 0.007 0.057 0.096 137 -10000 0 137
FGG 0.093 0.14 0.31 26 -0.29 3 29
GR beta/TIF2 -0.01 0.024 -10000 0 -0.14 3 3
IFNG -0.081 0.11 0.34 4 -0.29 3 7
apoptosis -0.016 0.087 -10000 0 -0.4 4 4
CREB1 -0.016 0.015 0.11 7 -10000 0 7
histone acetylation 0.003 0.016 -10000 0 -10000 0 0
BGLAP 0.001 0.02 0.15 1 -10000 0 1
GR/PKAc 0.032 0.06 0.13 22 -10000 0 22
NF kappa B1 p50/RelA 0.004 0.071 0.14 103 -10000 0 103
SMARCD1 -0.014 0 -10000 0 -10000 0 0
MDM2 0.037 0.054 0.13 23 -0.1 2 25
GATA3 -0.017 0.002 -10000 0 -10000 0 0
AKT1 -0.016 0.015 -10000 0 -0.12 10 10
CSF2 -0.067 0.074 -10000 0 -10000 0 0
GSK3B -0.014 0.006 0.021 10 -10000 0 10
NR1I3 -0.011 0.087 -10000 0 -0.4 2 2
CSN2 0.1 0.14 0.29 28 -0.26 3 31
BRG1/BAF155/BAF170/BAF60A -0.023 0.005 0 21 -10000 0 21
NFATC1 -0.018 0 -10000 0 -10000 0 0
POU2F1 -0.014 0.013 0.11 6 -10000 0 6
CDKN1A 0.042 0.1 0.33 51 -10000 0 51
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.003 0.016 1 -0.014 1 2
SFN -0.013 0.003 0 33 -10000 0 33
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.033 0.06 0.13 18 -10000 0 18
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.011 0.093 0.38 4 -0.48 4 8
JUN -0.004 0.055 0.36 9 -10000 0 9
IL4 0 0.019 0.15 1 -10000 0 1
CDK5R1 -0.011 0.007 0.015 9 -10000 0 9
PRKACA -0.014 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.022 0.04 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.032 0.062 0.13 16 -0.13 1 17
cortisol/GR alpha (monomer) 0.006 0.054 -10000 0 -0.34 3 3
NCOA2 -0.014 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.011 0.029 0.16 10 -10000 0 10
AP-1/NFAT1-c-4 -0.036 0.071 0.43 8 -10000 0 8
AFP -0.073 0.068 0.5 1 -10000 0 1
SUV420H1 -0.014 0.001 0 2 -10000 0 2
IRF1 -0.005 0.042 0.28 8 -0.18 3 11
TP53 -0.001 0.048 0.26 4 -10000 0 4
PPP5C -0.014 0 -10000 0 -10000 0 0
KRT17 -0.079 0.11 0.49 4 -0.29 3 7
KRT14 0.006 0.04 0.36 6 -10000 0 6
TBP -0.018 0.001 -10000 0 -10000 0 0
CREBBP -0.014 0.013 -10000 0 -0.12 8 8
HDAC1 -0.011 0.004 -10000 0 -10000 0 0
HDAC2 -0.014 0.001 -10000 0 -10000 0 0
AP-1 -0.036 0.071 0.43 8 -10000 0 8
MAPK14 -0.014 0.005 0.02 10 -10000 0 10
MAPK10 -0.008 0.008 0.022 8 -10000 0 8
MAPK11 -0.014 0.005 0.021 10 -10000 0 10
KRT5 -0.08 0.11 0.45 4 -0.3 2 6
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 -0.015 0.009 0.052 9 -10000 0 9
STAT1 -0.003 0.039 0.11 58 -10000 0 58
CGA 0.001 0.022 0.21 2 -10000 0 2
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.054 0.072 0.25 1 -0.2 1 2
MAPK3 -0.014 0.006 0.022 10 -10000 0 10
MAPK1 -0.014 0.006 0.02 9 -10000 0 9
ICAM1 -0.062 0.087 0.21 5 -0.2 25 30
NFKB1 0.006 0.055 0.095 136 -10000 0 136
MAPK8 -0.003 0.042 0.27 8 -10000 0 8
MAPK9 -0.014 0.005 0.02 10 -10000 0 10
cortisol/GR alpha (dimer) -0.019 0.088 -10000 0 -0.38 6 6
BAX 0.023 0.064 0.39 7 -10000 0 7
POMC -0.087 0.08 -10000 0 -10000 0 0
EP300 -0.014 0.013 -10000 0 -0.12 8 8
cortisol/GR alpha (dimer)/p53 0.008 0.052 0.32 1 -0.29 3 4
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.032 0.11 13 -0.086 2 15
SGK1 0.024 0.029 -10000 0 -0.15 6 6
IL13 -0.066 0.086 0.29 3 -10000 0 3
IL6 -0.06 0.095 0.32 8 -0.2 25 33
PRKACG -0.014 0 -10000 0 -10000 0 0
IL5 -0.068 0.084 -10000 0 -10000 0 0
IL2 -0.081 0.11 0.34 4 -0.3 2 6
CDK5 -0.013 0.005 0.015 9 -10000 0 9
PRKACB -0.013 0.004 0 46 -10000 0 46
HSP90AA1 -0.014 0 -10000 0 -10000 0 0
IL8 -0.054 0.11 0.29 27 -0.2 25 52
CDK5R1/CDK5 -0.013 0.01 0.028 9 -10000 0 9
NF kappa B1 p50/RelA/PKAc 0.005 0.076 0.14 112 -10000 0 112
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.008 0.049 -10000 0 -0.27 3 3
SMARCA4 -0.014 0.001 0 2 -10000 0 2
chromatin remodeling 0.055 0.084 0.19 26 -0.19 3 29
NF kappa B1 p50/RelA/Cbp 0.012 0.084 0.18 59 -10000 0 59
JUN (dimer) -0.004 0.055 0.36 9 -10000 0 9
YWHAH -0.007 0.007 0 284 -10000 0 284
VIPR1 -0.002 0.023 0.14 4 -10000 0 4
NR3C1 -0.003 0.053 0.18 20 -0.2 3 23
NR4A1 -0.016 0 -10000 0 -10000 0 0
TIF2/SUV420H1 -0.017 0.001 0 2 -10000 0 2
MAPKKK cascade -0.016 0.087 -10000 0 -0.4 4 4
cortisol/GR alpha (dimer)/Src-1 0.007 0.049 -10000 0 -0.32 2 2
PBX1 -0.014 0.013 0.11 6 -10000 0 6
POU1F1 -0.014 0.013 0.11 6 -10000 0 6
SELE -0.062 0.087 0.21 5 -0.2 25 30
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.055 0.085 0.19 26 -0.19 3 29
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.008 0.049 -10000 0 -0.27 3 3
mol:cortisol -0.008 0.026 -10000 0 -0.19 3 3
MMP1 0.005 0.05 0.32 12 -10000 0 12
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.005 0.031 0.097 22 -10000 0 22
FYN 0.001 0.045 0.18 19 -10000 0 19
LAT/GRAP2/SLP76 -0.014 0.027 0.13 9 -10000 0 9
IKBKB -0.014 0 -10000 0 -10000 0 0
AKT1 -0.006 0.037 0.15 18 -10000 0 18
B2M -0.013 0.007 0.028 15 -10000 0 15
IKBKG -0.01 0.014 0.043 16 -10000 0 16
MAP3K8 -0.013 0.004 0 42 -10000 0 42
mol:Ca2+ -0.011 0.003 -10000 0 -10000 0 0
integrin-mediated signaling pathway -0.007 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.005 0.043 0.18 18 -10000 0 18
TRPV6 -0.01 0.001 -10000 0 -10000 0 0
CD28 -0.014 0.004 0.013 12 -10000 0 12
SHC1 0.003 0.048 0.15 38 -10000 0 38
receptor internalization -0.002 0.029 0.16 12 -10000 0 12
PRF1 0.001 0.053 0.34 12 -10000 0 12
KRAS -0.014 0.002 0 9 -10000 0 9
GRB2 -0.014 0.001 0 5 -10000 0 5
COT/AKT1 -0.011 0.024 0.12 9 -10000 0 9
LAT -0.005 0.037 0.18 14 -10000 0 14
EntrezGene:6955 0 0.003 0.023 12 -10000 0 12
CD3D -0.013 0.006 0.029 9 -10000 0 9
CD3E -0.013 0.008 0.028 17 -10000 0 17
CD3G -0.014 0.007 0.031 11 -10000 0 11
RASGRP2 -0.002 0.006 0.042 2 -10000 0 2
RASGRP1 -0.061 0.073 0.16 10 -0.15 184 194
HLA-A -0.013 0.008 0.027 18 -10000 0 18
RASSF5 0 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL -0.007 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.017 0.029 0.08 16 -0.097 5 21
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.017 0.009 -10000 0 -10000 0 0
PRKCA -0.017 0.023 0.07 21 -10000 0 21
GRAP2 -0.014 0 -10000 0 -10000 0 0
mol:IP3 -0.02 0.019 -10000 0 -10000 0 0
EntrezGene:6957 0 0.004 0.024 12 -10000 0 12
TCR/CD3/MHC I/CD8 -0.002 0.028 0.17 12 -10000 0 12
ORAI1 0.001 0 -10000 0 -10000 0 0
CSK -0.004 0.036 0.17 14 -10000 0 14
B7 family/CD28 -0.006 0.051 0.29 12 -10000 0 12
CHUK -0.014 0.001 0 1 -10000 0 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.001 0.037 0.17 16 -10000 0 16
PTPN6 -0.002 0.044 0.19 20 -10000 0 20
VAV1 -0.005 0.037 0.17 15 -10000 0 15
Monovalent TCR/CD3 -0.006 0.014 0.089 10 -10000 0 10
CBL -0.014 0 -10000 0 -10000 0 0
LCK 0.003 0.046 0.18 22 -10000 0 22
PAG1 -0.001 0.036 0.18 14 -10000 0 14
RAP1A -0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.001 0.039 0.18 16 -10000 0 16
CD80 -0.014 0.004 0.012 13 -10000 0 13
CD86 -0.013 0.005 0.003 34 -10000 0 34
PDK1/CARD11/BCL10/MALT1 -0.016 0.01 -10000 0 -10000 0 0
HRAS -0.014 0.001 0 2 -10000 0 2
GO:0035030 -0.01 0.04 0.23 12 -10000 0 12
CD8A 0 0.004 0.025 12 -10000 0 12
CD8B -0.013 0.008 0.028 17 -10000 0 17
PTPRC -0.011 0.006 0 128 -10000 0 128
PDK1/PKC theta -0.012 0.042 0.18 14 -10000 0 14
CSK/PAG1 -0.005 0.035 0.17 14 -10000 0 14
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I -0.015 0.012 0.038 24 -10000 0 24
GRAP2/SLP76 -0.009 0.032 0.16 10 -10000 0 10
STIM1 -0.01 0.002 -10000 0 -10000 0 0
RAS family/GTP -0.011 0.037 0.11 17 -0.14 11 28
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.002 0.03 0.16 13 -10000 0 13
mol:DAG -0.023 0.011 -10000 0 -10000 0 0
RAP1A/GDP -0.01 0.014 0.036 15 -0.047 5 20
PLCG1 -0.014 0 -10000 0 -10000 0 0
CD247 -0.014 0.006 0.031 10 -10000 0 10
cytotoxic T cell degranulation 0.001 0.052 0.33 12 -10000 0 12
RAP1A/GTP -0.003 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.041 0.17 18 -10000 0 18
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.023 0.024 -10000 0 -10000 0 0
NRAS -0.011 0.006 0 136 -10000 0 136
ZAP70 -0.014 0 -10000 0 -10000 0 0
GRB2/SOS1 -0.008 0.001 0 5 -10000 0 5
LAT/GRAP2/SLP76/VAV1 -0.022 0.018 0.086 2 -10000 0 2
MALT1 -0.014 0.003 0 24 -10000 0 24
TRAF6 -0.014 0 -10000 0 -10000 0 0
CD8 heterodimer -0.007 0.01 0.053 12 -10000 0 12
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.018 0.009 -10000 0 -10000 0 0
PRKCE -0.017 0.023 0.07 21 -10000 0 21
PRKCQ -0.009 0.043 0.19 15 -10000 0 15
LCP2 -0.013 0.003 0 30 -10000 0 30
BCL10 -0.014 0.001 0 4 -10000 0 4
regulation of survival gene product expression -0.005 0.035 0.15 18 -10000 0 18
IKK complex -0.004 0.02 0.087 15 -10000 0 15
RAS family/GDP -0.007 0.007 -10000 0 -0.018 108 108
MAP3K14 -0.011 0.03 0.14 14 -10000 0 14
PDPK1 -0.008 0.037 0.15 18 -10000 0 18
TCR/CD3/MHC I/CD8/Fyn -0.004 0.019 0.13 8 -10000 0 8
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.013 0.001 0 2 -10000 0 2
cell-cell adhesion 0.033 0.01 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP -0.025 0.007 -10000 0 -10000 0 0
ITSN1 -0.014 0 -10000 0 -10000 0 0
PIK3CA -0.014 0.003 0 25 -10000 0 25
SHC1 -0.013 0.004 0 46 -10000 0 46
Ephrin B1/EPHB3 -0.013 0.002 0 13 -10000 0 13
Ephrin B1/EPHB1 -0.013 0.002 0 12 -10000 0 12
HRAS/GDP -0.03 0.012 -10000 0 -0.093 13 13
Ephrin B/EPHB1/GRB7 -0.025 0.007 -10000 0 -10000 0 0
Endophilin/SYNJ1 -0.023 0.01 0.084 2 -10000 0 2
KRAS -0.014 0.002 0 9 -10000 0 9
Ephrin B/EPHB1/Src -0.025 0.007 -10000 0 -10000 0 0
endothelial cell migration -0.019 0.007 0 71 -10000 0 71
GRB2 -0.014 0.001 0 5 -10000 0 5
GRB7 -0.014 0.001 0 1 -10000 0 1
PAK1 -0.029 0.009 0.08 2 -10000 0 2
HRAS -0.014 0.001 0 2 -10000 0 2
RRAS -0.023 0.01 0.084 2 -10000 0 2
DNM1 -0.003 0.005 0 432 -10000 0 432
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.022 0.017 0.084 11 -10000 0 11
lamellipodium assembly -0.033 0.01 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.01 0.007 -10000 0 -0.072 5 5
PIK3R1 -0.013 0.004 0 36 -10000 0 36
EPHB2 -0.014 0.001 0 2 -10000 0 2
EPHB3 -0.014 0.002 0 13 -10000 0 13
EPHB1 -0.014 0.002 0 12 -10000 0 12
EPHB4 -0.014 0 -10000 0 -10000 0 0
mol:GDP -0.02 0.018 0.07 11 -0.091 13 24
Ephrin B/EPHB2 -0.021 0.005 0 28 -10000 0 28
Ephrin B/EPHB3 -0.02 0.006 0 39 -10000 0 39
JNK cascade -0.022 0.024 0.086 25 -10000 0 25
Ephrin B/EPHB1 -0.02 0.006 0 37 -10000 0 37
RAP1/GDP -0.026 0.019 0.065 11 -0.088 13 24
EFNB2 -0.014 0.003 0 22 -10000 0 22
EFNB3 -0.014 0.001 0 4 -10000 0 4
EFNB1 -0.014 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.017 0.004 0 35 -10000 0 35
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A -0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.031 0.015 0.063 11 -10000 0 11
Rap1/GTP -0.034 0.01 -10000 0 -10000 0 0
axon guidance -0.013 0.001 0 2 -10000 0 2
MAPK3 -0.013 0.019 -10000 0 -0.074 3 3
MAPK1 -0.012 0.019 -10000 0 -10000 0 0
Rac1/GDP -0.026 0.02 0.07 11 -0.091 13 24
actin cytoskeleton reorganization -0.029 0.019 -10000 0 -0.08 8 8
CDC42/GDP -0.026 0.02 0.07 11 -0.091 13 24
PI3K -0.019 0.007 0 71 -10000 0 71
EFNA5 -0.014 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.013 0.003 0 22 -10000 0 22
Ephrin B/EPHB2/Intersectin/N-WASP -0.01 0.002 -10000 0 -10000 0 0
CDC42 -0.014 0 -10000 0 -10000 0 0
RAS family/GTP -0.028 0.019 -10000 0 -10000 0 0
PTK2 -0.014 0.002 -10000 0 -10000 0 0
MAP4K4 -0.022 0.024 0.086 25 -10000 0 25
SRC -0.014 0 -10000 0 -10000 0 0
KALRN -0.014 0 -10000 0 -10000 0 0
Intersectin/N-WASP -0.017 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.038 0.015 -10000 0 -10000 0 0
MAP2K1 -0.013 0.007 -10000 0 -0.072 3 3
WASL -0.014 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.023 0.005 0 25 -10000 0 25
cell migration -0.013 0.025 0.11 1 -0.11 2 3
NRAS -0.011 0.006 0 136 -10000 0 136
SYNJ1 -0.023 0.01 0.084 2 -10000 0 2
PXN -0.014 0 -10000 0 -10000 0 0
TF -0.015 0.016 -10000 0 -10000 0 0
HRAS/GTP -0.03 0.01 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2 -0.017 0.003 0 14 -10000 0 14
cell adhesion mediated by integrin 0.015 0.016 -10000 0 -10000 0 0
RAC1 -0.014 0 -10000 0 -10000 0 0
mol:GTP -0.026 0.017 0.072 13 -10000 0 13
RAC1-CDC42/GTP -0.037 0.013 -10000 0 -10000 0 0
RASA1 -0.014 0.002 0 8 -10000 0 8
RAC1-CDC42/GDP -0.03 0.02 0.069 11 -0.093 13 24
ruffle organization -0.036 0.019 -10000 0 -10000 0 0
NCK1 -0.014 0.002 0 11 -10000 0 11
receptor internalization -0.005 0.012 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN -0.026 0.006 -10000 0 -10000 0 0
ROCK1 -0.015 0.018 0.097 13 -10000 0 13
RAS family/GDP -0.029 0.02 -10000 0 -0.086 8 8
Rac1/GTP -0.035 0.011 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/Paxillin -0.01 0.003 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.017 0.003 0 16 -9999 0 16
AKT1 0.014 0.059 0.2 29 -9999 0 29
PTK2B 0.033 0.073 0.2 42 -9999 0 42
VEGFR2 homodimer/Frs2 -0.022 0.021 0.098 15 -9999 0 15
CAV1 -0.005 0.007 0 324 -9999 0 324
CALM1 -0.013 0.003 0 27 -9999 0 27
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.015 0.017 -10000 0 -9999 0 0
endothelial cell proliferation 0.015 0.061 0.21 29 -9999 0 29
mol:Ca2+ 0.028 0.076 0.25 30 -9999 0 30
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.014 0.018 -10000 0 -9999 0 0
RP11-342D11.1 -0.015 0.023 0.14 4 -9999 0 4
CDH5 -0.013 0.003 0 29 -9999 0 29
VEGFA homodimer -0.009 0.01 -10000 0 -9999 0 0
SHC1 -0.013 0.004 0 46 -9999 0 46
SHC2 -0.014 0 -10000 0 -9999 0 0
HRAS/GDP -0.018 0.022 -10000 0 -9999 0 0
SH2D2A -0.014 0 -10000 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.015 0.02 -10000 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.015 0.017 -10000 0 -9999 0 0
VEGFR1 homodimer -0.014 0 -10000 0 -9999 0 0
SHC/GRB2/SOS1 -0.017 0.021 -10000 0 -9999 0 0
GRB10 0.021 0.063 0.22 15 -9999 0 15
PTPN11 -0.014 0 -10000 0 -9999 0 0
GRB2 -0.014 0.001 0 5 -9999 0 5
PAK1 -0.014 0 -10000 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.015 0.019 -10000 0 -9999 0 0
HRAS -0.014 0.001 0 2 -9999 0 2
VEGF/Rho/ROCK1/Integrin Complex 0.018 0.033 0.13 15 -9999 0 15
HIF1A -0.014 0.001 0 2 -9999 0 2
FRS2 -0.014 0.001 0 3 -9999 0 3
oxygen and reactive oxygen species metabolic process -0.014 0.017 -10000 0 -9999 0 0
mol:GTP 0 0 -10000 0 -9999 0 0
FLT4 -0.014 0 -10000 0 -9999 0 0
Nck/Pak -0.017 0.002 0 11 -9999 0 11
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.014 0.016 -10000 0 -9999 0 0
mol:GDP -0.017 0.021 -10000 0 -9999 0 0
mol:NADP 0.024 0.063 0.22 30 -9999 0 30
eNOS/Hsp90 0.023 0.063 0.21 30 -9999 0 30
PIK3R1 -0.013 0.004 0 36 -9999 0 36
mol:IP3 0.028 0.076 0.25 30 -9999 0 30
HIF1A/ARNT -0.017 0.001 0 2 -9999 0 2
SHB -0.014 0 -10000 0 -9999 0 0
VEGFA -0.009 0.009 -10000 0 -9999 0 0
VEGFC -0.014 0.002 0 13 -9999 0 13
FAK1/Vinculin 0.028 0.062 0.18 40 -9999 0 40
mol:Ca ++ 0 0 -10000 0 -9999 0 0
RHOA -0.014 0.001 0 2 -9999 0 2
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.016 0.018 -10000 0 -9999 0 0
PTPN6 -0.014 0.002 0 11 -9999 0 11
EPAS1 -0.022 0.016 0.064 15 -9999 0 15
mol:L-citrulline 0.024 0.063 0.22 30 -9999 0 30
ITGAV -0.014 0.002 0 16 -9999 0 16
PIK3CA -0.014 0.003 0 25 -9999 0 25
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.016 0.018 -10000 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer -0.018 0.02 -10000 0 -9999 0 0
VEGFR2/3 heterodimer -0.022 0.021 0.098 15 -9999 0 15
VEGFB -0.014 0 -10000 0 -9999 0 0
MAPK11 0.036 0.081 0.25 40 -9999 0 40
VEGFR2 homodimer -0.02 0.026 0.13 15 -9999 0 15
FLT1 -0.014 0 -10000 0 -9999 0 0
NEDD4 -0.017 0.014 0.058 16 -9999 0 16
MAPK3 0.031 0.08 0.25 36 -9999 0 36
MAPK1 0.031 0.079 0.25 36 -9999 0 36
VEGFA145/NRP2 -0.009 0.01 -10000 0 -9999 0 0
VEGFR1/2 heterodimer -0.022 0.021 0.098 15 -9999 0 15
KDR -0.02 0.026 0.13 15 -9999 0 15
VEGFA165/NRP1/VEGFR2 homodimer -0.017 0.021 0.074 3 -9999 0 3
SRC -0.014 0 -10000 0 -9999 0 0
platelet activating factor biosynthetic process 0.031 0.08 0.25 36 -9999 0 36
PI3K 0.003 0.038 0.14 5 -9999 0 5
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.014 0.016 -10000 0 -9999 0 0
FES 0.028 0.077 0.25 30 -9999 0 30
GAB1 0.009 0.037 0.13 3 -9999 0 3
VEGFR2 homodimer/VEGFA homodimer/Src -0.015 0.017 -10000 0 -9999 0 0
CTNNB1 -0.014 0 -10000 0 -9999 0 0
SOS1 0 0 -10000 0 -9999 0 0
ARNT -0.014 0 -10000 0 -9999 0 0
eNOS/Caveolin-1 0.002 0.035 0.2 6 -9999 0 6
VEGFR2 homodimer/VEGFA homodimer/Yes -0.013 0.016 -10000 0 -9999 0 0
PI3K/GAB1 0.008 0.055 0.19 21 -9999 0 21
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.017 0.02 -10000 0 -9999 0 0
PRKACA -0.014 0 -10000 0 -9999 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.024 0.021 0.094 14 -9999 0 14
HSP90AA1 -0.014 0 -10000 0 -9999 0 0
CDC42 0.028 0.077 0.25 30 -9999 0 30
actin cytoskeleton reorganization -0.015 0.016 -10000 0 -9999 0 0
PTK2 0.03 0.061 0.18 40 -9999 0 40
EDG1 0.029 0.076 0.25 30 -9999 0 30
mol:DAG 0.028 0.076 0.25 30 -9999 0 30
CaM/Ca2+ 0.014 0.051 0.13 4 -9999 0 4
MAP2K3 0.028 0.08 0.24 39 -9999 0 39
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.018 0.021 -10000 0 -9999 0 0
PLCG1 0.028 0.077 0.25 30 -9999 0 30
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.016 0.018 -10000 0 -9999 0 0
IQGAP1 -0.011 0.006 0 127 -9999 0 127
YES1 -0.012 0.005 0 79 -9999 0 79
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.015 0.017 -10000 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.014 0.016 -10000 0 -9999 0 0
cell migration 0.037 0.074 0.15 108 -9999 0 108
mol:PI-3-4-5-P3 0.003 0.037 0.13 5 -9999 0 5
FYN -0.014 0.003 0 21 -9999 0 21
VEGFB/NRP1 0.015 0.051 0.14 4 -9999 0 4
mol:NO 0.024 0.063 0.22 30 -9999 0 30
PXN -0.014 0 -10000 0 -9999 0 0
HRAS/GTP -0.018 0.022 -10000 0 -9999 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.018 0.022 0.073 3 -9999 0 3
VHL 0 0 -10000 0 -9999 0 0
ITGB3 -0.014 0 -10000 0 -9999 0 0
NOS3 0.025 0.065 0.23 28 -9999 0 28
VEGFR2 homodimer/VEGFA homodimer/Sck -0.015 0.017 -10000 0 -9999 0 0
RAC1 -0.014 0 -10000 0 -9999 0 0
PRKCA 0.028 0.079 0.23 39 -9999 0 39
PRKCB 0.031 0.078 0.24 39 -9999 0 39
VCL -0.014 0 -10000 0 -9999 0 0
VEGFA165/NRP1 -0.015 0.023 0.15 4 -9999 0 4
VEGFR1/2 heterodimer/VEGFA homodimer -0.015 0.017 -10000 0 -9999 0 0
VEGFA165/NRP2 -0.009 0.01 -10000 0 -9999 0 0
MAPKKK cascade -0.016 0.03 0.085 1 -9999 0 1
NRP2 -0.014 0.001 0 1 -9999 0 1
VEGFC homodimer -0.014 0.002 0 13 -9999 0 13
NCK1 -0.014 0.002 0 11 -9999 0 11
ROCK1 -0.014 0 -10000 0 -9999 0 0
FAK1/Paxillin 0.028 0.062 0.18 40 -9999 0 40
MAP3K13 0.028 0.077 0.25 30 -9999 0 30
PDPK1 0.01 0.056 0.17 35 -9999 0 35
Signaling events mediated by PTP1B

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
PDGFRB -0.014 0.001 0 3 -10000 0 3
Jak2/Leptin Receptor 0.009 0.021 -10000 0 -10000 0 0
PTP1B/AKT1 0.007 0.026 -10000 0 -0.15 1 1
FYN -0.014 0.003 0 21 -10000 0 21
p210 bcr-abl/PTP1B 0.009 0.025 -10000 0 -0.15 1 1
EGFR -0.009 0.007 0.012 6 -10000 0 6
EGF/EGFR -0.004 0.018 -10000 0 -0.13 1 1
CSF1 -0.014 0 -10000 0 -10000 0 0
AKT1 -0.014 0.001 0 4 -10000 0 4
INSR -0.014 0.001 0.011 1 -10000 0 1
PTP1B/N-cadherin 0.008 0.026 -10000 0 -0.15 1 1
Insulin Receptor/Insulin 0.003 0.026 -10000 0 -0.15 1 1
HCK -0.012 0.005 0 86 -10000 0 86
CRK -0.014 0 -10000 0 -10000 0 0
TYK2 0.003 0.024 0.12 1 -0.15 1 2
EGF -0.004 0.013 0.012 198 -10000 0 198
YES1 -0.012 0.005 0 79 -10000 0 79
CAV1 0.038 0.034 0.11 18 -10000 0 18
TXN -0.012 0.006 0.011 37 -10000 0 37
PTP1B/IRS1/GRB2 0.007 0.03 -10000 0 -10000 0 0
cell migration -0.009 0.025 0.15 1 -10000 0 1
STAT3 -0.014 0.002 0 10 -10000 0 10
PRLR -0.015 0 -10000 0 -10000 0 0
ITGA2B -0.014 0 -10000 0 -10000 0 0
CSF1R -0.013 0.004 0 41 -10000 0 41
Prolactin Receptor/Prolactin -0.018 0.002 -10000 0 -10000 0 0
FGR -0.014 0.003 0 17 -10000 0 17
PTP1B/p130 Cas 0.008 0.023 0.092 2 -0.14 1 3
Crk/p130 Cas 0.007 0.026 -10000 0 -0.14 1 1
DOK1 0.003 0.022 -10000 0 -0.14 1 1
JAK2 0.009 0.017 -10000 0 -10000 0 0
Jak2/Leptin Receptor/Leptin -0.008 0.032 -10000 0 -0.14 1 1
PIK3R1 -0.013 0.004 0 36 -10000 0 36
PTPN1 0.009 0.025 -10000 0 -0.15 1 1
LYN -0.012 0.005 0 64 -10000 0 64
CDH2 -0.014 0.002 0 16 -10000 0 16
SRC 0.01 0.011 -10000 0 -10000 0 0
ITGB3 -0.014 0 -10000 0 -10000 0 0
CAT1/PTP1B 0.02 0.046 0.13 41 -10000 0 41
CAPN1 -0.014 0.002 0.012 4 -10000 0 4
CSK -0.014 0 -10000 0 -10000 0 0
PI3K 0 0.027 -10000 0 -10000 0 0
mol:H2O2 0 0.001 -10000 0 -10000 0 0
STAT3 (dimer) -0.008 0.029 -10000 0 -0.13 1 1
negative regulation of transcription 0.009 0.016 -10000 0 -10000 0 0
FCGR2A -0.007 0.007 0 265 -10000 0 265
FER -0.012 0.006 0.011 37 -10000 0 37
alphaIIb/beta3 Integrin -0.017 0.004 -10000 0 -10000 0 0
BLK -0.014 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.018 0.007 0.02 4 -10000 0 4
RHOA -0.014 0.002 0.012 4 -10000 0 4
LEPR -0.014 0.001 0 3 -10000 0 3
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 -0.014 0.001 0 5 -10000 0 5
mol:NADPH 0.001 0.001 -10000 0 -10000 0 0
TRPV6 0.019 0.048 0.12 66 -0.12 3 69
PRL -0.015 0.002 -10000 0 -10000 0 0
SOCS3 -0.005 0.001 -10000 0 -10000 0 0
SPRY2 -0.013 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.02 0.004 0.02 4 -10000 0 4
CSF1/CSF1R 0.007 0.03 -10000 0 -0.15 1 1
Ras protein signal transduction -0.014 0.012 0.18 1 -10000 0 1
IRS1 -0.014 0.001 0 5 -10000 0 5
INS -0.014 0.001 0.011 1 -10000 0 1
LEP -0.014 0 -10000 0 -10000 0 0
STAT5B 0.01 0.022 -10000 0 -10000 0 0
STAT5A 0.01 0.022 -10000 0 -10000 0 0
GRB2 -0.014 0.001 0 5 -10000 0 5
PDGFB-D/PDGFRB 0.008 0.027 -10000 0 -0.15 1 1
CSN2 -0.008 0.009 -10000 0 -10000 0 0
PIK3CA -0.014 0.003 0 25 -10000 0 25
LAT 0.03 0.024 -10000 0 -10000 0 0
YBX1 -0.019 0.003 -10000 0 -10000 0 0
LCK -0.014 0.001 0 4 -10000 0 4
SHC1 -0.013 0.004 0 46 -10000 0 46
NOX4 -0.011 0.006 0.013 1 -10000 0 1
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.01 0.029 0.092 24 -10000 0 24
BAG4 -0.014 0 -10000 0 -10000 0 0
BAD -0.003 0.012 -10000 0 -10000 0 0
NFKBIA -0.014 0.001 0 1 -10000 0 1
BIRC3 -0.013 0.003 0 33 -10000 0 33
BAX -0.001 0.018 0.11 7 -10000 0 7
EnzymeConsortium:3.1.4.12 0.003 0.009 0.029 24 -10000 0 24
IKBKB 0.005 0.028 0.13 1 -10000 0 1
MAP2K2 -0.012 0.013 0.074 1 -10000 0 1
MAP2K1 -0.011 0.013 0.074 1 -10000 0 1
SMPD1 0.002 0.009 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.01 0.029 0.12 1 -10000 0 1
MAP2K4 -0.007 0.012 0.08 1 -10000 0 1
protein ubiquitination 0.004 0.029 0.13 2 -10000 0 2
EnzymeConsortium:2.7.1.37 -0.014 0.015 0.07 1 -10000 0 1
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.008 0.013 0.081 1 -10000 0 1
CRADD -0.014 0 -10000 0 -10000 0 0
mol:ceramide 0.002 0.013 0.04 3 -10000 0 3
I-kappa-B-alpha/RELA/p50/ubiquitin -0.013 0.001 0 1 -10000 0 1
MADD -0.014 0.001 0 4 -10000 0 4
MAP3K1 -0.003 0.013 0.088 1 -10000 0 1
TRADD -0.014 0 -10000 0 -10000 0 0
RELA/p50 -0.014 0 -10000 0 -10000 0 0
MAPK3 -0.011 0.013 0.073 1 -10000 0 1
MAPK1 -0.013 0.02 0.073 1 -0.11 12 13
p50/RELA/I-kappa-B-alpha -0.017 0.001 0 1 -10000 0 1
FADD 0.011 0.029 0.089 25 -10000 0 25
KSR1 -0.003 0.013 -10000 0 -10000 0 0
MAPK8 -0.011 0.014 0.072 2 -10000 0 2
TRAF2 -0.014 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.005 0.028 0.13 1 -10000 0 1
TNF R/SODD -0.011 0.008 0 183 -10000 0 183
TNF -0.014 0.001 0 2 -10000 0 2
CYCS -0.004 0.015 0.076 5 -10000 0 5
IKBKG 0.005 0.028 0.13 1 -10000 0 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.016 0.03 0.099 22 -10000 0 22
RELA -0.014 0 -10000 0 -10000 0 0
RIPK1 -0.014 0.002 0 9 -10000 0 9
AIFM1 -0.003 0.016 0.079 7 -10000 0 7
TNF/TNF R/SODD -0.013 0.01 0 185 -10000 0 185
TNFRSF1A -0.009 0.007 0 183 -10000 0 183
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.014 0.011 -10000 0 -10000 0 0
NSMAF 0.01 0.029 0.088 26 -10000 0 26
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
BCL2 -0.014 0 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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 -0.012 0.005 0 65 -9999 0 65
HDAC3 -0.014 0 -10000 0 -9999 0 0
VDR -0.014 0 -10000 0 -9999 0 0
Cbp/p300/PCAF -0.014 0 -10000 0 -9999 0 0
EP300 -0.014 0 -10000 0 -9999 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.006 0.005 -10000 0 -9999 0 0
KAT2B 0 0 -10000 0 -9999 0 0
MAPK14 -0.014 0.001 0 2 -9999 0 2
AKT1 -0.028 0.034 0.083 11 -9999 0 11
RAR alpha/9cRA/Cyclin H -0.001 0.031 -10000 0 -9999 0 0
mol:9cRA 0 0 -10000 0 -9999 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.007 0.004 0.051 3 -9999 0 3
CDC2 -0.009 0.007 0 193 -9999 0 193
response to UV 0 0.002 0.022 3 -9999 0 3
RAR alpha/Jnk1 -0.008 0.005 0.061 3 -9999 0 3
NCOR2 -0.014 0 -10000 0 -9999 0 0
VDR/VDR/Vit D3 -0.009 0 -10000 0 -9999 0 0
RXRs/RARs/NRIP1/9cRA -0.007 0.025 0.25 3 -9999 0 3
NCOA2 -0.014 0 -10000 0 -9999 0 0
NCOA3 -0.014 0.001 0 3 -9999 0 3
NCOA1 -0.014 0.002 0 14 -9999 0 14
VDR/VDR/DNA -0.014 0 -10000 0 -9999 0 0
RARG -0.014 0.003 0.028 3 -9999 0 3
RAR gamma1/9cRA -0.013 0.003 0.025 3 -9999 0 3
MAPK3 -0.014 0.003 0.023 3 -9999 0 3
MAPK1 -0.014 0.003 0 17 -9999 0 17
MAPK8 -0.014 0.003 0.03 3 -9999 0 3
mol:Vit D3 0 0 -10000 0 -9999 0 0
RXRs/VDR/DNA/Vit D3 0.006 0.031 0.21 3 -9999 0 3
RARA -0.005 0.006 0.081 3 -9999 0 3
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -9999 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.007 0.004 0.051 3 -9999 0 3
PRKCA -0.014 0.007 0.072 3 -9999 0 3
RXRs/RARs/NRIP1/9cRA/HDAC1 0.007 0.028 0.29 3 -9999 0 3
RXRG -0.008 0.007 0.089 3 -9999 0 3
RXRA 0.012 0.031 0.18 3 -9999 0 3
RXRB -0.008 0.007 0.084 3 -9999 0 3
VDR/Vit D3/DNA -0.009 0 -10000 0 -9999 0 0
RBP1 -0.008 0.007 0 248 -9999 0 248
CRBP1/9-cic-RA -0.005 0.004 0 248 -9999 0 248
RARB -0.014 0.005 0.051 3 -9999 0 3
PRKCG -0.014 0.006 0.069 3 -9999 0 3
MNAT1 -0.014 0.001 0 1 -9999 0 1
RAR alpha/RXRs -0.016 0.039 0.19 3 -9999 0 3
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.01 0.02 0.16 3 -9999 0 3
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.007 0.069 3 -9999 0 3
RXRs/RARs/NRIP1/9cRA/HDAC3 0.003 0.025 0.28 3 -9999 0 3
positive regulation of DNA binding -0.003 0.027 -10000 0 -9999 0 0
NRIP1 0.004 0.027 0.33 3 -9999 0 3
RXRs/RARs 0.006 0.022 0.25 3 -9999 0 3
RXRs/RXRs/DNA/9cRA 0.007 0.028 0.22 3 -9999 0 3
PRKACA -0.014 0 -10000 0 -9999 0 0
CDK7 -0.014 0.001 0 2 -9999 0 2
TFIIH -0.02 0.002 0 5 -9999 0 5
RAR alpha/9cRA -0.022 0.006 0.054 3 -9999 0 3
CCNH -0.014 0.001 0 2 -9999 0 2
CREBBP -0.014 0 -10000 0 -9999 0 0
RAR gamma2/9cRA -0.03 0.003 -10000 0 -9999 0 0
S1P3 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
PDGFRB -0.014 0.001 0 3 -10000 0 3
mol:S1P 0 0.001 0.025 1 -10000 0 1
S1P1/S1P/Gi -0.041 0.035 -10000 0 -0.071 294 294
GNAO1 -0.001 0.004 -10000 0 -10000 0 0
S1P/S1P3/G12/G13 -0.012 0.003 0.057 1 -10000 0 1
AKT1 0 0.003 -10000 0 -10000 0 0
AKT3 0.001 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.014 0.001 0 3 -10000 0 3
GNAI2 -0.015 0.002 0.04 1 -10000 0 1
GNAI3 -0.013 0.005 -10000 0 -10000 0 0
GNAI1 -0.012 0.006 0.033 1 -10000 0 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0 0.001 0.031 1 -10000 0 1
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 -0.014 0.001 0 4 -10000 0 4
mol:Ca2+ -0.001 0.005 -10000 0 -10000 0 0
MAPK3 -0.001 0.006 -10000 0 -10000 0 0
MAPK1 -0.001 0.006 -10000 0 -10000 0 0
JAK2 -0.015 0.05 0.11 2 -0.14 62 64
CXCR4 -0.001 0.005 -10000 0 -10000 0 0
FLT1 -0.015 0.003 0.06 1 -10000 0 1
RhoA/GDP -0.009 0.001 0 2 -10000 0 2
Rac1/GDP -0.009 0 -10000 0 -10000 0 0
SRC -0.001 0.006 -10000 0 -10000 0 0
S1P/S1P3/Gi -0.001 0.005 -10000 0 -10000 0 0
RAC1 -0.014 0 -10000 0 -10000 0 0
RhoA/GTP -0.065 0.038 -10000 0 -0.12 122 122
VEGFA -0.007 0.008 0.06 1 -10000 0 1
S1P/S1P2/Gi -0.001 0.005 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.008 0.011 0.14 1 -10000 0 1
RHOA -0.014 0.001 0 2 -10000 0 2
S1P/S1P3/Gq -0.008 0.002 0.025 1 -10000 0 1
GNAQ -0.014 0 -10000 0 -10000 0 0
GNAZ -0.012 0.005 0.033 1 -10000 0 1
G12/G13 -0.017 0.002 0 6 -10000 0 6
GNA14 -0.014 0.001 0 2 -10000 0 2
GNA15 -0.014 0.002 0 7 -10000 0 7
GNA12 -0.014 0.001 0 4 -10000 0 4
GNA13 -0.014 0.001 0 2 -10000 0 2
GNA11 -0.014 0 -10000 0 -10000 0 0
Rac1/GTP -0.065 0.038 -10000 0 -0.12 123 123
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 -0.018 0.004 0.068 1 -9999 0 1
mol:GTP 0 0 -10000 0 -9999 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.017 0.014 0.11 3 -9999 0 3
ERC1 -0.014 0.001 0 1 -9999 0 1
RIP2/NOD2 -0.017 0.002 0 9 -9999 0 9
NFKBIA -0.029 0.011 0.094 4 -9999 0 4
BIRC2 -0.014 0 -10000 0 -9999 0 0
IKBKB -0.014 0 -10000 0 -9999 0 0
RIPK2 -0.014 0.001 0 1 -9999 0 1
IKBKG -0.005 0.011 0.038 33 -9999 0 33
IKK complex/A20 -0.013 0.014 -10000 0 -9999 0 0
NEMO/A20/RIP2 -0.014 0.001 0 1 -9999 0 1
XPO1 -0.014 0 -10000 0 -9999 0 0
NEMO/ATM -0.009 0.014 0.086 1 -9999 0 1
tumor necrosis factor receptor activity 0 0 -10000 0 -9999 0 0
RAN -0.014 0.001 0 3 -9999 0 3
Exportin 1/RanGTP -0.013 0.001 0 3 -9999 0 3
IKK complex/ELKS -0.017 0.015 -10000 0 -9999 0 0
BCL10/MALT1/TRAF6 -0.019 0.004 0 27 -9999 0 27
NOD2 -0.014 0.002 0 8 -9999 0 8
NFKB1 -0.018 0.004 0.069 1 -9999 0 1
RELA -0.018 0.004 0.069 1 -9999 0 1
MALT1 -0.014 0.003 0 24 -9999 0 24
cIAP1/UbcH5C -0.017 0.001 0 1 -9999 0 1
ATM -0.014 0.003 0 25 -9999 0 25
TNF/TNFR1A -0.011 0.008 0 185 -9999 0 185
TRAF6 -0.014 0 -10000 0 -9999 0 0
PRKCA -0.014 0 -10000 0 -9999 0 0
CHUK -0.014 0.001 0 1 -9999 0 1
UBE2D3 -0.014 0.001 0 1 -9999 0 1
TNF -0.014 0.001 0 2 -9999 0 2
NF kappa B1 p50/RelA -0.028 0.003 0 5 -9999 0 5
BCL10 -0.014 0.001 0 4 -9999 0 4
proteasomal ubiquitin-dependent protein catabolic process -0.029 0.011 0.094 4 -9999 0 4
beta TrCP1/SCF ubiquitin ligase complex -0.018 0.004 0.069 1 -9999 0 1
TNFRSF1A -0.009 0.007 0 183 -9999 0 183
IKK complex -0.013 0.016 0.087 1 -9999 0 1
CYLD -0.014 0 -10000 0 -9999 0 0
IKK complex/PKC alpha -0.017 0.018 0.083 2 -9999 0 2
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.017 0.014 -10000 0 -0.054 21 21
KIRREL -0.015 0.009 0.027 22 -10000 0 22
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.017 0.014 0.054 21 -10000 0 21
PLCG1 -0.014 0 -10000 0 -10000 0 0
ARRB2 -0.014 0 -10000 0 -10000 0 0
WASL -0.014 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.02 0.016 0.092 8 -10000 0 8
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.01 0.014 0.051 20 -10000 0 20
FYN -0.017 0.007 0.075 2 -10000 0 2
mol:Ca2+ -0.019 0.023 0.094 21 -10000 0 21
mol:DAG -0.019 0.024 0.096 21 -10000 0 21
NPHS2 -0.015 0.009 0.027 23 -10000 0 23
mol:IP3 -0.019 0.024 0.096 21 -10000 0 21
regulation of endocytosis -0.021 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/Cholesterol -0.013 0.022 0.093 21 -10000 0 21
establishment of cell polarity -0.017 0.014 0.054 21 -10000 0 21
Nephrin/NEPH1/podocin/NCK1-2 -0.022 0.026 0.11 20 -10000 0 20
Nephrin/NEPH1/beta Arrestin2 -0.021 0.007 0.071 2 -10000 0 2
NPHS1 -0.015 0.009 0.027 22 -10000 0 22
Nephrin/NEPH1/podocin -0.017 0.008 0.093 2 -10000 0 2
TJP1 -0.014 0 -10000 0 -10000 0 0
NCK1 -0.014 0.002 0 11 -10000 0 11
NCK2 -0.014 0.001 0 1 -10000 0 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.019 0.024 0.098 21 -10000 0 21
CD2AP -0.013 0.004 0 49 -10000 0 49
Nephrin/NEPH1/podocin/GRB2 -0.02 0.022 0.098 18 -10000 0 18
GRB2 -0.014 0.001 0 5 -10000 0 5
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.019 0.01 0.074 2 -10000 0 2
cytoskeleton organization -0.019 0.017 0.08 12 -10000 0 12
Nephrin/NEPH1 -0.01 0.011 0.045 21 -10000 0 21
Nephrin/NEPH1/ZO-1 -0.019 0.015 0.053 21 -10000 0 21
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.02 0.043 0.23 15 -10000 0 15
IHH -0.019 0.022 0.084 22 -10000 0 22
SHH Np/Cholesterol/GAS1 -0.016 0.006 0 58 -10000 0 58
LRPAP1 -0.014 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.016 0.006 -10000 0 0 58 58
SMO/beta Arrestin2 -0.013 0.035 0.16 22 -10000 0 22
SMO -0.009 0.037 0.17 22 -10000 0 22
AKT1 -0.01 0.052 -10000 0 -0.21 29 29
ARRB2 -0.014 0 -10000 0 -10000 0 0
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 -0.014 0 -10000 0 -10000 0 0
heart looping -0.009 0.036 0.16 22 -10000 0 22
STIL -0.022 0.033 0.14 18 -10000 0 18
DHH N/PTCH2 -0.009 0 -10000 0 -10000 0 0
DHH N/PTCH1 -0.018 0.022 0.16 8 -10000 0 8
PIK3CA -0.014 0.003 0 25 -10000 0 25
DHH 0 0 -10000 0 -10000 0 0
PTHLH -0.017 0.028 0.22 7 -10000 0 7
determination of left/right symmetry -0.009 0.036 0.16 22 -10000 0 22
PIK3R1 -0.013 0.004 0 36 -10000 0 36
skeletal system development -0.017 0.028 0.22 7 -10000 0 7
IHH N/Hhip -0.008 0.013 0.054 22 -10000 0 22
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.009 0.036 0.16 22 -10000 0 22
pancreas development 0 0 -10000 0 -10000 0 0
HHAT -0.014 0 -10000 0 -10000 0 0
PI3K -0.015 0.005 0 60 -10000 0 60
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.013 0.004 0 58 -10000 0 58
somite specification -0.009 0.036 0.16 22 -10000 0 22
SHH Np/Cholesterol/PTCH1 -0.025 0.021 0.14 8 -10000 0 8
SHH Np/Cholesterol/PTCH2 -0.018 0 -10000 0 -10000 0 0
SHH Np/Cholesterol/Megalin -0.018 0.001 0 1 -10000 0 1
SHH -0.017 0 -10000 0 -10000 0 0
catabolic process -0.019 0.035 0.19 15 -10000 0 15
SMO/Vitamin D3 -0.023 0.023 0.16 8 -10000 0 8
SHH Np/Cholesterol/Hhip -0.012 0 -10000 0 -10000 0 0
LRP2 -0.014 0.001 0 1 -10000 0 1
receptor-mediated endocytosis -0.021 0.033 0.14 22 -10000 0 22
SHH Np/Cholesterol/BOC -0.012 0 -10000 0 -10000 0 0
SHH Np/Cholesterol/CDO -0.018 0 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.012 0 -10000 0 -10000 0 0
mol:Vitamin D3 -0.025 0.024 0.16 8 -10000 0 8
IHH N/PTCH2 -0.017 0.016 0.06 22 -10000 0 22
CDON -0.014 0 -10000 0 -10000 0 0
IHH N/PTCH1 -0.021 0.029 0.22 8 -10000 0 8
Megalin/LRPAP1 -0.017 0.001 0 1 -10000 0 1
PTCH2 -0.014 0 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.012 0 -10000 0 -10000 0 0
PTCH1 -0.019 0.035 0.19 15 -10000 0 15
HHIP 0 0 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP -0.014 0 -9999 0 -9999 0 0
Aurora C/Aurora B/INCENP -0.017 0.004 0 29 -9999 0 29
metaphase 0 0 -9999 0 -9999 0 0
mitosis 0 0 -9999 0 -9999 0 0
H3F3B -0.005 0.001 0 29 -9999 0 29
AURKB -0.013 0.003 0 27 -9999 0 27
AURKC -0.014 0.001 0 2 -9999 0 2
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.013 0.002 0 15 -10000 0 15
SNTA1 -0.014 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.02 0.003 0 16 -10000 0 16
MAPK12 -0.015 0.002 -10000 0 -10000 0 0
CCND1 -0.004 0.002 -10000 0 -10000 0 0
p38 gamma/SNTA1 -0.018 0.01 0.053 10 -10000 0 10
MAP2K3 -0.014 0 -10000 0 -10000 0 0
PKN1 -0.014 0.002 0 10 -10000 0 10
G2/M transition checkpoint -0.015 0.002 -10000 0 -10000 0 0
MAP2K6 -0.011 0.001 -10000 0 -10000 0 0
MAPT -0.034 0.044 0.066 1 -0.12 115 116
MAPK13 -0.017 0.003 0 15 -10000 0 15
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK -0.005 0.001 0 10 -10000 0 10
Atypical NF-kappaB 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
BCL3/RelA -0.017 0 -10000 0 -9999 0 0
FBXW11 -0.014 0 -10000 0 -9999 0 0
NF kappa B1 p50/c-Rel -0.02 0.002 0 4 -9999 0 4
NF kappa B1 p50/RelA/I kappa B alpha -0.016 0.018 0.048 37 -9999 0 37
NFKBIA -0.003 0.015 0.051 37 -9999 0 37
MAPK14 -0.014 0.001 0 2 -9999 0 2
NF kappa B1 p105/p50 -0.02 0.002 0 4 -9999 0 4
ARRB2 -0.005 0 -10000 0 -9999 0 0
REL -0.014 0 -10000 0 -9999 0 0
response to oxidative stress 0 0 -10000 0 -9999 0 0
BCL3/NF kappa B1 p50 -0.02 0.002 0 4 -9999 0 4
response to UV 0 0 -10000 0 -9999 0 0
NF kappa B1 p105/RelA -0.02 0.002 0 4 -9999 0 4
PIK3CA -0.014 0.003 0 25 -9999 0 25
NF kappa B1 p50 dimer -0.016 0.013 0.13 4 -9999 0 4
PIK3R1 -0.013 0.004 0 36 -9999 0 36
NFKB1 -0.017 0.001 0 4 -9999 0 4
RELA -0.014 0 -10000 0 -9999 0 0
positive regulation of anti-apoptosis -0.009 0.005 0.047 4 -9999 0 4
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.018 0.018 0.047 37 -9999 0 37
SRC -0.014 0 -10000 0 -9999 0 0
PI3K -0.015 0.005 0 60 -9999 0 60
NF kappa B1 p50/RelA -0.009 0.005 0.047 4 -9999 0 4
IKBKB -0.014 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex -0.014 0 -10000 0 -9999 0 0
SYK -0.013 0.004 0 36 -9999 0 36
I kappa B alpha/PIK3R1 -0.007 0.016 0.054 32 -9999 0 32
cell death -0.017 0.018 0.046 37 -9999 0 37
NF kappa B1 p105/c-Rel -0.02 0.002 0 4 -9999 0 4
LCK -0.014 0.001 0 4 -9999 0 4
BCL3 -0.014 0 -10000 0 -9999 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 -0.014 0.001 0 4 -10000 0 4
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0 0 4 -10000 0 4
monocyte activation 0.001 0.002 -10000 0 -10000 0 0
MAP2K2 0.004 0 -10000 0 -10000 0 0
MAP2K1 -0.007 0.001 0 17 -10000 0 17
MAP2K7 -0.007 0.001 0 4 -10000 0 4
MAP2K6 -0.007 0.001 0 4 -10000 0 4
CYAA -0.005 0 0 4 -10000 0 4
MAP2K4 -0.006 0.001 0 25 -10000 0 25
IL1B -0.005 0.012 0.1 6 -10000 0 6
Channel -0.006 0.001 0 4 -10000 0 4
NLRP1 -0.007 0.001 0 4 -10000 0 4
CALM1 -0.013 0.003 0 27 -10000 0 27
negative regulation of phagocytosis -0.017 0.08 -10000 0 -0.36 27 27
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0 -10000 0 0 4 4
MAPK3 -0.007 0.001 0 4 -10000 0 4
MAPK1 -0.007 0.001 0 21 -10000 0 21
PGR -0.007 0.001 0 4 -10000 0 4
PA/Cellular Receptors -0.007 0.001 0 4 -10000 0 4
apoptosis -0.001 0 0 4 -10000 0 4
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.005 0 -10000 0 0 4 4
macrophage activation -0.011 0.002 -10000 0 -10000 0 0
TNF -0.014 0.001 0 2 -10000 0 2
VCAM1 0.001 0.002 -10000 0 -10000 0 0
platelet activation -0.017 0.08 -10000 0 -0.36 27 27
MAPKKK cascade 0.007 0.003 -10000 0 -10000 0 0
IL18 -0.003 0.016 0.1 12 -10000 0 12
negative regulation of macrophage activation -0.001 0 0 4 -10000 0 4
LEF -0.001 0 0 4 -10000 0 4
CASP1 -0.002 0.002 0 174 -10000 0 174
mol:cAMP -0.017 0.08 -10000 0 -0.36 27 27
necrosis -0.001 0 0 4 -10000 0 4
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.005 0 0 4 -10000 0 4
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Nectin adhesion 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 -0.014 0.001 0 3 -10000 0 3
alphaV beta3 Integrin -0.017 0.003 0 16 -10000 0 16
PTK2 -0.006 0.018 -10000 0 -10000 0 0
positive regulation of JNK cascade 0.006 0.007 -10000 0 -10000 0 0
CDC42/GDP 0.009 0.012 -10000 0 -10000 0 0
Rac1/GDP 0.008 0.012 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A -0.014 0 -10000 0 -10000 0 0
CTNNB1 -0.014 0 -10000 0 -10000 0 0
CDC42/GTP 0.009 0.01 -10000 0 -10000 0 0
nectin-3/I-afadin -0.017 0.001 0 2 -10000 0 2
RAPGEF1 -0.005 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.014 0.001 0 3 -10000 0 3
TLN1 -0.006 0.031 0.094 46 -10000 0 46
Rap1/GTP -0.008 0.009 -10000 0 -10000 0 0
IQGAP1 -0.011 0.006 0 127 -10000 0 127
Rap1/GTP/I-afadin -0.012 0 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.017 0.001 0 2 -10000 0 2
PVR -0.014 0 -10000 0 -10000 0 0
Necl-5(dimer) -0.014 0 -10000 0 -10000 0 0
mol:GDP 0.004 0.013 -10000 0 -10000 0 0
MLLT4 -0.014 0 -10000 0 -10000 0 0
PIK3CA -0.014 0.003 0 25 -10000 0 25
PI3K -0.024 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.017 0 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.008 0.008 -10000 0 -10000 0 0
PVRL1 -0.014 0 -10000 0 -10000 0 0
PVRL3 -0.014 0.001 0 2 -10000 0 2
PVRL2 -0.014 0 -10000 0 -10000 0 0
PIK3R1 -0.013 0.004 0 36 -10000 0 36
CDH1 -0.014 0.002 0 8 -10000 0 8
CLDN1 -0.014 0.002 0 9 -10000 0 9
JAM-A/CLDN1 -0.022 0.006 0 36 -10000 0 36
SRC 0.007 0.009 -10000 0 -10000 0 0
ITGB3 -0.014 0 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin -0.017 0 -10000 0 -10000 0 0
FARP2 0.008 0.013 -10000 0 -10000 0 0
RAC1 -0.014 0 -10000 0 -10000 0 0
CTNNA1 -0.014 0 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.02 0.001 0 2 -10000 0 2
nectin-1/I-afadin -0.017 0 -10000 0 -10000 0 0
nectin-2/I-afadin -0.017 0 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin -0.01 0.006 0 127 -10000 0 127
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.02 0.001 0 2 -10000 0 2
CDC42/GTP/IQGAP1/filamentous actin -0.01 0.006 0 127 -10000 0 127
F11R -0.013 0.003 0 34 -10000 0 34
positive regulation of filopodium formation 0.006 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.015 0.035 0.09 41 -0.1 10 51
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.017 0 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin -0.017 0 -10000 0 -10000 0 0
PIP5K1C -0.012 0.003 0 32 -10000 0 32
VAV2 0.009 0.013 -10000 0 -10000 0 0
RAP1/GDP -0.002 0.012 -10000 0 -10000 0 0
ITGAV -0.014 0.002 0 16 -10000 0 16
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.02 0.001 0 2 -10000 0 2
nectin-3(dimer)/I-afadin/I-afadin -0.017 0.001 0 2 -10000 0 2
Rac1/GTP 0.01 0.011 -10000 0 -10000 0 0
PTPRM -0.007 0.001 0 12 -10000 0 12
E-cadherin/beta catenin/alpha catenin -0.031 0.004 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 -0.014 0 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.021 0.02 0.13 3 -9999 0 3
NFATC2 -0.015 0.018 0.066 14 -9999 0 14
NFATC3 -0.021 0.02 0.13 3 -9999 0 3
CD40LG -0.047 0.083 0.24 30 -9999 0 30
PTGS2 -0.059 0.05 0.2 4 -9999 0 4
JUNB -0.014 0.002 0 8 -9999 0 8
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.014 0.011 0.029 27 -9999 0 27
CaM/Ca2+ -0.014 0.011 0.029 27 -9999 0 27
CALM1 -0.016 0.011 0.045 3 -9999 0 3
JUN -0.017 0.011 0.044 3 -9999 0 3
mol:Ca2+ -0.005 0.004 0.012 30 -9999 0 30
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.008 0.006 0.029 3 -9999 0 3
FOSL1 -0.014 0.002 0 13 -9999 0 13
CREM -0.014 0 -10000 0 -9999 0 0
Jun/NFAT1-c-4/p21SNFT -0.051 0.047 0.14 27 -9999 0 27
FOS -0.013 0.011 0.042 2 -9999 0 2
IFNG -0.047 0.083 0.24 29 -9999 0 29
AP-1/NFAT1-c-4 -0.056 0.065 0.2 16 -9999 0 16
FASLG -0.047 0.083 0.3 14 -9999 0 14
NFAT1-c-4/ICER1 -0.038 0.039 0.13 13 -9999 0 13
IL2RA -0.05 0.072 0.26 10 -9999 0 10
FKBP12/FK506 -0.009 0 0 1 -9999 0 1
CSF2 -0.047 0.083 0.24 30 -9999 0 30
JunB/Fra1/NFAT1-c-4 -0.04 0.037 0.11 24 -9999 0 24
IL4 -0.047 0.083 0.24 30 -9999 0 30
IL2 -0.006 0.005 -10000 0 -9999 0 0
IL3 -0.009 0.007 -10000 0 -9999 0 0
FKBP1A -0.014 0.001 0 1 -9999 0 1
BATF3 0 0 -10000 0 -9999 0 0
mol:FK506 0 0 -10000 0 -9999 0 0
POU2F1 -0.015 0 -10000 0 -9999 0 0
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.014 0 -10000 0 -9999 0 0
CLTC 0.001 0.007 -10000 0 -9999 0 0
calcium ion-dependent exocytosis 0 0.016 0.098 1 -9999 0 1
Dynamin 2/GTP -0.012 0 -10000 0 -9999 0 0
EXOC4 0 0 -10000 0 -9999 0 0
CD59 -0.001 0.009 -10000 0 -9999 0 0
CPE -0.012 0.004 0 45 -9999 0 45
CTNNB1 -0.014 0 -10000 0 -9999 0 0
membrane fusion -0.001 0.017 0.055 44 -9999 0 44
CTNND1 -0.016 0.002 -10000 0 -9999 0 0
DNM2 -0.014 0 -10000 0 -9999 0 0
mol:PI-4-5-P2 -0.003 0.011 0.063 1 -9999 0 1
TSHR -0.013 0.001 0 4 -9999 0 4
INS 0.002 0.006 -10000 0 -9999 0 0
BIN1 -0.013 0.004 0 41 -9999 0 41
mol:Choline -0.001 0.017 0.055 44 -9999 0 44
growth hormone secretagogue receptor activity 0 0 -10000 0 -9999 0 0
mol:GDP -0.007 0 -10000 0 -9999 0 0
membrane depolarization 0 0 -10000 0 -9999 0 0
ARF6 -0.014 0 -10000 0 -9999 0 0
mol:Ca2+ -0.012 0 -10000 0 -9999 0 0
JUP 0 0.013 -10000 0 -9999 0 0
ASAP2/amphiphysin II -0.011 0.003 0 41 -9999 0 41
ARF6/GTP -0.009 0 -10000 0 -9999 0 0
CDH1 -0.001 0.012 -10000 0 -9999 0 0
clathrin-independent pinocytosis -0.009 0 -10000 0 -9999 0 0
MAPK8IP3 -0.014 0 -10000 0 -9999 0 0
positive regulation of endocytosis -0.009 0 -10000 0 -9999 0 0
EXOC2 -0.014 0 -10000 0 -9999 0 0
substrate adhesion-dependent cell spreading -0.007 0.002 -10000 0 -9999 0 0
insulin receptor binding 0 0 -10000 0 -9999 0 0
SPAG9 -0.014 0.001 0 1 -9999 0 1
regulation of calcium-dependent cell-cell adhesion 0.009 0.012 -10000 0 -9999 0 0
positive regulation of phagocytosis -0.013 0.001 0 1 -9999 0 1
ARF6/GTP/JIP3 -0.014 0 -10000 0 -9999 0 0
ACAP1 0.001 0.016 0.052 44 -9999 0 44
mol:GTP 0 0 -10000 0 -9999 0 0
CHRM2 -0.001 0.009 -10000 0 -9999 0 0
clathrin heavy chain/ACAP1 -0.002 0.014 -10000 0 -9999 0 0
JIP4/KLC1 -0.013 0.008 0 139 -9999 0 139
EXOC1 -0.014 0.002 0 8 -9999 0 8
exocyst -0.007 0.002 -10000 0 -9999 0 0
RALA/GTP -0.008 0.002 0 45 -9999 0 45
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex -0.013 0.001 0 1 -9999 0 1
receptor recycling -0.009 0 -10000 0 -9999 0 0
CTNNA1 -0.016 0 -10000 0 -9999 0 0
NME1 -0.007 0 -10000 0 -9999 0 0
clathrin coat assembly 0 0.009 -10000 0 -9999 0 0
IL2RA -0.001 0.011 -10000 0 -9999 0 0
VAMP3 -0.013 0.001 0 1 -9999 0 1
GLUT4/clathrin heavy chain/ACAP1 -0.006 0.015 -10000 0 -9999 0 0
EXOC6 0 0 -10000 0 -9999 0 0
PLD1 -0.004 0.001 -10000 0 -9999 0 0
PLD2 -0.004 0.001 0 45 -9999 0 45
EXOC5 -0.014 0.003 0 17 -9999 0 17
PIP5K1C -0.003 0.011 -10000 0 -9999 0 0
SDC1 0.003 0.018 -10000 0 -9999 0 0
ARF6/GDP -0.007 0 -10000 0 -9999 0 0
EXOC7 -0.014 0 -10000 0 -9999 0 0
E-cadherin/beta catenin -0.009 0.013 -10000 0 -9999 0 0
mol:Phosphatidic acid -0.001 0.017 0.055 44 -9999 0 44
endocytosis 0.011 0.003 -10000 0 0 41 41
SCAMP2 -0.014 0 -10000 0 -9999 0 0
ADRB2 -0.005 0.01 -10000 0 -9999 0 0
EXOC3 -0.014 0 -10000 0 -9999 0 0
ASAP2 0 0 -10000 0 -9999 0 0
Dynamin 2/GDP -0.012 0 -10000 0 -9999 0 0
KLC1 -0.01 0.006 0 138 -9999 0 138
AVPR2 -0.005 0.008 -10000 0 -9999 0 0
RALA -0.013 0.004 0 45 -9999 0 45
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.016 0.019 0.087 10 -9999 0 10
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 -0.012 0.005 0 65 -10000 0 65
HDAC2 -0.014 0.001 0 5 -10000 0 5
GNB1/GNG2 -0.013 0.005 0.023 11 -10000 0 11
forebrain development -0.036 0.044 0.27 7 -10000 0 7
GNAO1 -0.001 0.004 0.018 1 -10000 0 1
SMO/beta Arrestin2 -0.016 0.009 0.046 11 -10000 0 11
SMO -0.014 0.006 0.026 11 -10000 0 11
ARRB2 -0.014 0.005 0.019 11 -10000 0 11
GLI3/SPOP -0.015 0.038 -10000 0 -0.13 47 47
mol:GTP 0 0.001 0.008 11 -10000 0 11
GSK3B -0.014 0.001 0 4 -10000 0 4
GNAI2 -0.014 0.005 0.018 11 -10000 0 11
SIN3/HDAC complex -0.018 0.001 -10000 0 -10000 0 0
GNAI1 -0.012 0.007 0.017 11 -10000 0 11
XPO1 -0.014 0.009 0.045 11 -10000 0 11
GLI1/Su(fu) -0.027 0.027 0.2 3 -10000 0 3
SAP30 -0.014 0 -10000 0 -10000 0 0
mol:GDP -0.014 0.006 0.026 11 -10000 0 11
MIM/GLI2A -0.014 0.013 0.14 4 -10000 0 4
IFT88 -0.014 0 -10000 0 -10000 0 0
GNAI3 -0.012 0.006 0.016 7 -10000 0 7
GLI2 -0.009 0.008 -10000 0 -0.14 1 1
GLI3 -0.012 0.038 -10000 0 -0.13 47 47
CSNK1D -0.014 0.001 0 2 -10000 0 2
CSNK1E -0.014 0.001 0 1 -10000 0 1
SAP18 -0.014 0 -10000 0 -10000 0 0
embryonic digit morphogenesis -0.014 0 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
Gi family/GTP -0.001 0.006 0.052 4 -0.072 1 5
SIN3B -0.014 0 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
GLI3/Su(fu) -0.015 0.028 -10000 0 -0.099 44 44
GLI2/Su(fu) -0.012 0.008 -10000 0 -0.12 1 1
FOXA2 -0.009 0.027 0.3 4 -10000 0 4
neural tube patterning -0.036 0.044 0.27 7 -10000 0 7
SPOP -0.014 0 -10000 0 -10000 0 0
Su(fu)/PIAS1 -0.01 0.006 0.033 8 -10000 0 8
GNB1 -0.014 0.002 0 6 -10000 0 6
CSNK1G2 -0.014 0 -10000 0 -10000 0 0
CSNK1G3 -0.014 0 -10000 0 -10000 0 0
MTSS1 -0.014 0.013 0.14 4 -10000 0 4
embryonic limb morphogenesis -0.036 0.044 0.27 7 -10000 0 7
SUFU -0.006 0.005 0.025 11 -10000 0 11
LGALS3 -0.012 0.005 0 72 -10000 0 72
catabolic process -0.02 0.036 -10000 0 -0.19 6 6
GLI3A/CBP -0.02 0.006 0.024 7 -10000 0 7
KIF3A -0.013 0.004 0 49 -10000 0 49
GLI1 -0.039 0.039 0.32 4 -10000 0 4
RAB23 -0.014 0.001 0 5 -10000 0 5
CSNK1A1 -0.014 0 -10000 0 -10000 0 0
IFT172 0 0 -10000 0 -10000 0 0
RBBP7 -0.014 0 -10000 0 -10000 0 0
Su(fu)/Galectin3 -0.009 0.006 0.03 5 -10000 0 5
GNAZ -0.012 0.006 0.018 7 -10000 0 7
RBBP4 -0.012 0.006 0 100 -10000 0 100
CSNK1G1 -0.014 0 -10000 0 -10000 0 0
PIAS1 -0.014 0 -10000 0 -10000 0 0
PRKACA -0.014 0 -10000 0 -10000 0 0
GLI2/SPOP -0.014 0.008 -10000 0 -0.13 1 1
STK36 0 0.005 0.036 11 -10000 0 11
Gi family/GNB1/GNG2/GDP -0.001 0.003 -10000 0 -10000 0 0
PTCH1 -0.034 0.05 0.34 7 -10000 0 7
MIM/GLI1 -0.042 0.046 0.24 10 -10000 0 10
CREBBP -0.02 0.006 0.024 7 -10000 0 7
Su(fu)/SIN3/HDAC complex 0.008 0.025 0.09 17 -10000 0 17
EPO 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
BCL2L1 -0.011 0.031 0.18 2 -9999 0 2
CRKL -0.025 0.02 0.086 11 -9999 0 11
mol:DAG -0.013 0.026 -10000 0 -9999 0 0
HRAS -0.025 0.036 0.14 8 -9999 0 8
MAPK8 -0.011 0.04 0.096 64 -9999 0 64
RAP1A -0.025 0.02 0.086 11 -9999 0 11
GAB1 -0.025 0.02 0.086 11 -9999 0 11
MAPK14 -0.011 0.04 0.096 64 -9999 0 64
EPO -0.016 0.007 0.026 2 -9999 0 2
PLCG1 -0.013 0.026 -10000 0 -9999 0 0
EPOR/TRPC2/IP3 Receptors -0.016 0.007 0.026 2 -9999 0 2
RAPGEF1 -0.014 0 -10000 0 -9999 0 0
EPO/EPOR (dimer)/SOCS3 -0.021 0.01 0.045 2 -9999 0 2
GAB1/SHC/GRB2/SOS1 -0.03 0.017 0.061 9 -9999 0 9
EPO/EPOR (dimer) -0.019 0.009 0.044 2 -9999 0 2
IRS2 -0.025 0.02 0.088 10 -9999 0 10
STAT1 -0.015 0.025 -10000 0 -9999 0 0
STAT5B -0.014 0.026 -10000 0 -9999 0 0
cell proliferation -0.014 0.039 0.09 64 -9999 0 64
GAB1/SHIP/PIK3R1/SHP2/SHC -0.032 0.017 0.046 6 -9999 0 6
TEC -0.025 0.02 0.086 11 -9999 0 11
SOCS3 -0.014 0 -10000 0 -9999 0 0
STAT1 (dimer) -0.015 0.025 -10000 0 -9999 0 0
JAK2 -0.016 0.007 0.017 19 -9999 0 19
PIK3R1 -0.013 0.004 0 36 -9999 0 36
EPO/EPOR (dimer)/JAK2 -0.023 0.016 -10000 0 -9999 0 0
EPO/EPOR -0.019 0.009 0.044 2 -9999 0 2
LYN -0.013 0.005 -10000 0 -9999 0 0
TEC/VAV2 -0.029 0.021 0.086 11 -9999 0 11
elevation of cytosolic calcium ion concentration -0.016 0.007 0.026 2 -9999 0 2
SHC1 -0.013 0.004 0 46 -9999 0 46
EPO/EPOR (dimer)/LYN -0.02 0.009 -10000 0 -9999 0 0
mol:IP3 -0.013 0.026 -10000 0 -9999 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.027 0.02 0.083 9 -9999 0 9
SH2B3 -0.017 0.005 0.017 9 -9999 0 9
NFKB1 -0.011 0.039 0.096 62 -9999 0 62
EPO/EPOR (dimer)/JAK2/SOCS3 -0.006 0.001 -10000 0 -9999 0 0
PTPN6 -0.023 0.012 0.073 8 -9999 0 8
TEC/VAV2/GRB2 -0.033 0.022 0.086 11 -9999 0 11
EPOR -0.016 0.007 0.026 2 -9999 0 2
INPP5D 0 0 -10000 0 -9999 0 0
mol:GDP -0.03 0.017 0.061 9 -9999 0 9
SOS1 0 0 -10000 0 -9999 0 0
PLCG2 -0.014 0.002 0 10 -9999 0 10
CRKL/CBL/C3G -0.033 0.021 0.086 11 -9999 0 11
VAV2 -0.025 0.02 0.086 11 -9999 0 11
CBL -0.025 0.02 0.086 11 -9999 0 11
SHC/Grb2/SOS1 -0.028 0.01 -10000 0 -9999 0 0
STAT5A -0.014 0.026 -10000 0 -9999 0 0
GRB2 -0.014 0.001 0 5 -9999 0 5
STAT5 (dimer) -0.022 0.028 -10000 0 -9999 0 0
LYN/PLCgamma2 -0.015 0.006 -10000 0 -9999 0 0
PTPN11 -0.014 0 -10000 0 -9999 0 0
BTK -0.025 0.02 0.088 10 -9999 0 10
BCL2 -0.011 0.031 0.18 2 -9999 0 2
Signaling events mediated by HDAC Class III

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
EP300 -0.014 0 -10000 0 -9999 0 0
HDAC4 -0.014 0 -10000 0 -9999 0 0
induction of apoptosis 0 0 -10000 0 -9999 0 0
regulation of S phase of mitotic cell cycle 0.009 0.003 -10000 0 -9999 0 0
CDKN1A -0.006 0.003 0 112 -9999 0 112
KAT2B 0 0 -10000 0 -9999 0 0
BAX -0.014 0.002 0 7 -9999 0 7
FOXO3 0.004 0.001 -10000 0 -9999 0 0
FOXO1 -0.014 0.002 0 11 -9999 0 11
FOXO4 -0.005 0 -10000 0 -9999 0 0
response to UV 0 0 -10000 0 -9999 0 0
XRCC6 -0.014 0 -10000 0 -9999 0 0
TAT -0.014 0 -10000 0 -9999 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -9999 0 0
MYOD1 -0.009 0 -10000 0 -9999 0 0
PPARGC1A -0.014 0.001 0 3 -9999 0 3
FHL2 -0.014 0.003 0 26 -9999 0 26
response to nutrient levels 0 0 -10000 0 -9999 0 0
KU70/SIRT1 -0.019 0.001 -10000 0 -9999 0 0
HIST2H4A -0.009 0.003 -10000 0 -9999 0 0
SIRT1/FOXO3a -0.009 0.003 -10000 0 -9999 0 0
SIRT1 -0.015 0.005 -10000 0 -9999 0 0
response to hypoxia 0 0 -10000 0 -9999 0 0
SIRT1/MEF2D/HDAC4 -0.022 0 -10000 0 -9999 0 0
SIRT1/Histone H1b -0.011 0.005 0.057 1 -9999 0 1
apoptosis 0.021 0.003 -10000 0 0 7 7
SIRT1/PGC1A -0.015 0.001 0 3 -9999 0 3
p53/SIRT1 -0.017 0.009 0 112 -9999 0 112
SIRT1/FOXO4 -0.011 0.004 -10000 0 -9999 0 0
FOXO1/FHL2/SIRT1 -0.018 0.005 0 37 -9999 0 37
HIST1H1E -0.005 0 0 1 -9999 0 1
SIRT1/p300 -0.019 0.001 -10000 0 -9999 0 0
muscle cell differentiation 0.015 0 -10000 0 -9999 0 0
TP53 -0.013 0.007 0 112 -9999 0 112
KU70/SIRT1/BAX -0.021 0.003 0 7 -9999 0 7
CREBBP -0.014 0 -10000 0 -9999 0 0
MEF2D -0.014 0 -10000 0 -9999 0 0
HIV-1 Tat/SIRT1 -0.019 0.001 -10000 0 -9999 0 0
ACSS2 -0.009 0.003 -10000 0 -9999 0 0
SIRT1/PCAF/MYOD -0.015 0 -10000 0 -9999 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 -0.014 0 -10000 0 -10000 0 0
NFATC1 -0.01 0.011 -10000 0 -10000 0 0
NFATC2 -0.002 0.016 -10000 0 -0.084 3 3
NFATC3 -0.005 0.001 -10000 0 -10000 0 0
YWHAE -0.014 0.001 0 2 -10000 0 2
Calcineurin A alpha-beta B1/CABIN1 -0.065 0.015 -10000 0 -10000 0 0
Exportin 1/Ran/NUP214 -0.02 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.068 0.017 -10000 0 -10000 0 0
BCL2/BAX -0.017 0.002 0 7 -10000 0 7
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.009 0.002 -10000 0 -10000 0 0
CaM/Ca2+ -0.009 0.002 -10000 0 -10000 0 0
BAX -0.014 0.002 0 7 -10000 0 7
MAPK14 -0.014 0.001 -10000 0 -10000 0 0
BAD -0.014 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.067 0.014 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/BCL2 -0.014 0 -10000 0 -10000 0 0
FKBP8 -0.014 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.066 0.014 -10000 0 -10000 0 0
KPNB1 -0.014 0 -10000 0 -10000 0 0
KPNA2 -0.014 0.002 0 12 -10000 0 12
XPO1 -0.014 0 -10000 0 -10000 0 0
SFN -0.013 0.003 0 33 -10000 0 33
MAP3K8 -0.013 0.004 -10000 0 -10000 0 0
NFAT4/CK1 alpha -0.018 0.004 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.014 0.028 0.057 6 -0.093 3 9
CABIN1 -0.065 0.015 -10000 0 -10000 0 0
CALM1 -0.014 0.003 -10000 0 -10000 0 0
RAN -0.014 0.001 0 3 -10000 0 3
MAP3K1 -0.014 0.001 0 1 -10000 0 1
CAMK4 -0.014 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0 -10000 0 -10000 0 0
MAPK3 -0.014 0 -10000 0 -10000 0 0
YWHAH -0.007 0.007 0 284 -10000 0 284
Calcineurin A alpha-beta B1/AKAP79/PKA -0.017 0 -10000 0 -10000 0 0
YWHAB -0.014 0.001 0 2 -10000 0 2
MAPK8 -0.015 0 -10000 0 -10000 0 0
MAPK9 -0.014 0.001 0 3 -10000 0 3
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A -0.014 0.001 0 1 -10000 0 1
NFAT1-c-4/YWHAQ -0.016 0.023 -10000 0 -0.15 3 3
PRKCH -0.014 0.001 0 2 -10000 0 2
CABIN1/Cbp/p300 -0.018 0 -10000 0 -10000 0 0
CASP3 -0.012 0.006 -10000 0 -10000 0 0
PIM1 -0.014 0.001 0 2 -10000 0 2
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.007 0 -10000 0 -10000 0 0
apoptosis -0.01 0.001 0 7 -10000 0 7
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.002 0.006 0.042 7 -10000 0 7
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE -0.014 0 -10000 0 -10000 0 0
JNK2/NFAT4 -0.011 0.002 -10000 0 -10000 0 0
BAD/BCL-XL -0.017 0 -10000 0 -10000 0 0
PRKCD -0.014 0 -10000 0 -10000 0 0
NUP214 -0.014 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA -0.014 0 -10000 0 -10000 0 0
PRKCG -0.014 0 -10000 0 -10000 0 0
PRKCQ -0.014 0 -10000 0 -10000 0 0
FKBP38/BCL2 -0.017 0 -10000 0 -10000 0 0
EP300 -0.015 0 -10000 0 -10000 0 0
PRKCB1 -0.001 0.003 0 498 -10000 0 498
CSNK2A1 -0.014 0 -10000 0 -10000 0 0
NFATc/JNK1 -0.014 0.012 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 -0.013 0.003 -10000 0 -10000 0 0
FKBP12/FK506 -0.009 0 0 1 -10000 0 1
CSNK1A1 -0.014 0.003 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.013 0.003 -10000 0 -10000 0 0
NFATc/ERK1 -0.014 0.012 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.067 0.017 -10000 0 -10000 0 0
NR4A1 -0.025 0.014 -10000 0 -0.089 3 3
GSK3B -0.014 0.001 -10000 0 -10000 0 0
positive T cell selection -0.005 0.001 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.007 0.012 -10000 0 -10000 0 0
RCH1/ KPNB1 -0.017 0.003 0 12 -10000 0 12
YWHAQ -0.014 0 -10000 0 -10000 0 0
PRKACA -0.014 0 -10000 0 -10000 0 0
AKAP5 -0.014 0 -10000 0 -10000 0 0
MEF2D -0.015 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ -0.014 0.002 0 6 -10000 0 6
NFATc/p38 alpha -0.014 0.011 -10000 0 -10000 0 0
CREBBP -0.015 0 -10000 0 -10000 0 0
BCL2 -0.014 0 -10000 0 -10000 0 0
IGF1 pathway

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
NCK2 -0.014 0.001 0 1 -10000 0 1
PTK2 -0.014 0.001 0 2 -10000 0 2
CRKL -0.016 0.011 0.069 9 -10000 0 9
GRB2/SOS1/SHC -0.012 0.004 0 51 -10000 0 51
HRAS -0.014 0.001 0 2 -10000 0 2
IRS1/Crk -0.017 0.002 0 9 -10000 0 9
IGF-1R heterotetramer/IGF1/PTP1B -0.02 0.007 0.053 5 -10000 0 5
AKT1 -0.021 0.026 0.079 28 -10000 0 28
BAD -0.023 0.027 0.07 28 -10000 0 28
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.016 0.011 0.069 9 -10000 0 9
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.017 0.009 0.076 5 -10000 0 5
RAF1 -0.011 0.026 0.12 2 -10000 0 2
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.015 0.009 0.079 5 -10000 0 5
YWHAZ -0.014 0.002 0 6 -10000 0 6
IGF-1R heterotetramer/IGF1/IRS1 -0.012 0.009 0.083 5 -10000 0 5
PIK3CA -0.014 0.003 0 25 -10000 0 25
RPS6KB1 -0.021 0.026 0.079 28 -10000 0 28
GNB2L1 -0.014 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.012 0.027 0.16 3 -10000 0 3
PXN -0.014 0 -10000 0 -10000 0 0
PIK3R1 -0.013 0.004 0 36 -10000 0 36
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 -0.008 0.001 0 5 -10000 0 5
HRAS/GTP -0.022 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.019 0.008 0.052 2 -10000 0 2
IGF-1R heterotetramer -0.016 0.006 0.027 9 -10000 0 9
IGF-1R heterotetramer/IGF1/IRS/Nck -0.016 0.01 0.083 5 -10000 0 5
Crk/p130 Cas/Paxillin -0.02 0.009 0.071 5 -10000 0 5
IGF1R -0.016 0.006 0.027 9 -10000 0 9
IGF1 -0.016 0.005 0.032 5 -10000 0 5
IRS2/Crk -0.02 0.01 0.074 5 -10000 0 5
PI3K -0.019 0.01 0.083 3 -10000 0 3
apoptosis 0.024 0.028 -10000 0 -0.095 4 4
HRAS/GDP -0.009 0.001 0 2 -10000 0 2
PRKCD -0.007 0.014 -10000 0 -10000 0 0
RAF1/14-3-3 E -0.013 0.027 0.11 2 -10000 0 2
BAD/14-3-3 -0.025 0.029 0.099 4 -10000 0 4
PRKCZ -0.017 0.023 0.074 27 -10000 0 27
Crk/p130 Cas/Paxillin/FAK1 -0.031 0.024 0.048 27 -10000 0 27
PTPN1 -0.014 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.005 0.005 0.046 5 -10000 0 5
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.02 0.009 0.055 2 -10000 0 2
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.017 0.008 0.067 4 -10000 0 4
GRB10 -0.014 0.002 0 16 -10000 0 16
PTPN11 -0.016 0.011 0.069 9 -10000 0 9
IRS1 -0.012 0.007 0.069 4 -10000 0 4
IRS2 -0.016 0.011 0.069 9 -10000 0 9
IGF-1R heterotetramer/IGF1 -0.018 0.007 0.054 5 -10000 0 5
GRB2 -0.014 0.001 0 5 -10000 0 5
PDPK1 -0.018 0.024 0.08 27 -10000 0 27
YWHAE -0.014 0.001 0 2 -10000 0 2
PRKD1 0.017 0.044 0.095 119 -10000 0 119
SHC1 -0.013 0.004 0 46 -10000 0 46
E-cadherin 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
E-cadherin/beta catenin-gamma catenin -0.02 0.004 0 19 -9999 0 19
E-cadherin/beta catenin -0.017 0.002 0 8 -9999 0 8
CTNNB1 -0.014 0 -9999 0 -9999 0 0
JUP -0.014 0.002 0 16 -9999 0 16
CDH1 -0.014 0.002 0 8 -9999 0 8
JNK signaling in the CD4+ TCR pathway

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.022 0.006 0 32 -9999 0 32
MAP4K1 -0.014 0.001 0 1 -9999 0 1
MAP3K8 -0.013 0.004 0 42 -9999 0 42
PRKCB 0 0 -10000 0 -9999 0 0
DBNL 0 0 -10000 0 -9999 0 0
CRKL -0.014 0 -10000 0 -9999 0 0
MAP3K1 -0.013 0.007 0.059 3 -9999 0 3
JUN -0.004 0.008 -10000 0 -9999 0 0
MAP3K7 -0.013 0.007 0.059 3 -9999 0 3
GRAP2 -0.014 0 -10000 0 -9999 0 0
CRK -0.014 0 -10000 0 -9999 0 0
MAP2K4 -0.007 0.022 0.09 15 -9999 0 15
LAT -0.014 0.001 0 1 -9999 0 1
LCP2 -0.013 0.003 0 30 -9999 0 30
MAPK8 0.001 0.007 -10000 0 -9999 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.008 0.004 0.05 2 -9999 0 2
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.021 0.005 0 32 -9999 0 32
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.017 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ -0.023 0.003 0 6 -10000 0 6
CDKN1B -0.009 0.012 -10000 0 -10000 0 0
CDKN1A 0.002 0.033 0.095 54 -10000 0 54
FRAP1 -0.014 0.001 0 1 -10000 0 1
PRKDC -0.014 0.003 0 23 -10000 0 23
FOXO3 -0.009 0.012 -10000 0 -10000 0 0
AKT1 -0.006 0.001 -10000 0 -10000 0 0
BAD -0.014 0 -10000 0 -10000 0 0
AKT3 -0.005 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.009 0.012 -10000 0 -10000 0 0
AKT1/ASK1 -0.008 0.014 -10000 0 -10000 0 0
BAD/YWHAZ -0.02 0.002 0 6 -10000 0 6
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 -0.014 0.001 0 1 -10000 0 1
JNK cascade 0.008 0.013 -10000 0 -10000 0 0
TSC1 -0.008 0.013 0.094 1 -10000 0 1
YWHAZ -0.014 0.002 0 6 -10000 0 6
AKT1/RAF1 -0.008 0.014 -10000 0 -10000 0 0
EP300 -0.014 0 -10000 0 -10000 0 0
mol:GDP -0.006 0.001 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.009 0.012 -10000 0 -10000 0 0
YWHAQ -0.014 0 -10000 0 -10000 0 0
TBC1D4 -0.011 0 -10000 0 -10000 0 0
MAP3K5 -0.014 0.001 0 4 -10000 0 4
MAPKAP1 -0.014 0 -10000 0 -10000 0 0
negative regulation of cell cycle 0.03 0.033 0.16 7 -10000 0 7
YWHAH -0.007 0.007 0 284 -10000 0 284
AKT1S1 -0.003 0.012 -10000 0 -10000 0 0
CASP9 -0.008 0.016 0.13 3 -10000 0 3
YWHAB -0.014 0.001 0 2 -10000 0 2
p27Kip1/KPNA1 -0.013 0.014 -10000 0 -10000 0 0
GBL -0.014 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 -0.02 0 -10000 0 -10000 0 0
YWHAE -0.014 0.001 0 2 -10000 0 2
SRC -0.014 0 -10000 0 -10000 0 0
AKT2/p21CIP1 0 0.033 0.091 54 -10000 0 54
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.004 0.005 -10000 0 -10000 0 0
CHUK -0.008 0.013 -10000 0 -10000 0 0
BAD/BCL-XL -0.017 0.015 -10000 0 -10000 0 0
mTORC2 -0.018 0.001 0 1 -10000 0 1
AKT2 -0.005 0 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.043 0.041 -10000 0 -0.19 7 7
PDPK1 -0.014 0 -10000 0 -10000 0 0
MDM2 -0.005 0.023 0.15 1 -10000 0 1
MAPKKK cascade 0.008 0.014 -10000 0 -10000 0 0
MDM2/Cbp/p300 -0.013 0.025 0.14 1 -10000 0 1
TSC1/TSC2 -0.013 0.012 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.013 0.024 0.14 1 -10000 0 1
glucose import -0.015 0 -10000 0 -10000 0 0
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0 0.01 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.015 0 -10000 0 -10000 0 0
GSK3A -0.009 0.012 -10000 0 -10000 0 0
FOXO1 -0.006 0.019 0.099 11 -10000 0 11
GSK3B -0.009 0.012 -10000 0 -10000 0 0
SFN -0.013 0.003 0 33 -10000 0 33
G1/S transition of mitotic cell cycle -0.013 0.012 -10000 0 -10000 0 0
p27Kip1/14-3-3 family -0.003 0.01 -10000 0 -0.22 1 1
PRKACA -0.014 0 -10000 0 -10000 0 0
KPNA1 -0.014 0 -10000 0 -10000 0 0
HSP90AA1 -0.014 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB -0.014 0 -10000 0 -10000 0 0
CREBBP -0.014 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.018 0.002 0 6 -9999 0 6
HDAC3 -0.014 0 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 -0.019 0.002 0 4 -9999 0 4
GATA1/HDAC4 -0.017 0 -10000 0 -9999 0 0
GATA1/HDAC5 -0.017 0 -10000 0 -9999 0 0
GATA2/HDAC5 -0.017 0.001 0 1 -9999 0 1
HDAC5/BCL6/BCoR -0.019 0.004 0 21 -9999 0 21
HDAC9 -0.014 0.001 0 2 -9999 0 2
Glucocorticoid receptor/Hsp90/HDAC6 -0.02 0 -10000 0 -9999 0 0
HDAC4/ANKRA2 -0.017 0.001 0 1 -9999 0 1
HDAC5/YWHAB -0.017 0.001 0 2 -9999 0 2
NPC/RanGAP1/SUMO1/Ubc9 -0.005 0 0 1 -9999 0 1
GATA2 -0.014 0.001 0 1 -9999 0 1
HDAC4/RFXANK -0.015 0.005 0 53 -9999 0 53
BCOR -0.014 0.001 0 5 -9999 0 5
mol:GTP 0 0 -10000 0 -9999 0 0
HDAC10 0 0 -10000 0 -9999 0 0
HDAC5 -0.014 0 -10000 0 -9999 0 0
GNB1/GNG2 -0.008 0.001 0 6 -9999 0 6
Histones -0.007 0.004 0.05 2 -9999 0 2
ADRBK1 -0.014 0 -10000 0 -9999 0 0
HDAC4 -0.014 0 -10000 0 -9999 0 0
XPO1 -0.014 0 -10000 0 -9999 0 0
HDAC5/ANKRA2 -0.017 0.001 0 1 -9999 0 1
HDAC4/Ubc9 -0.017 0 -10000 0 -9999 0 0
HDAC7 0 0 -10000 0 -9999 0 0
HDAC5/14-3-3 E -0.017 0.001 0 2 -9999 0 2
TUBA1B -0.014 0 -10000 0 -9999 0 0
HDAC6 -0.014 0 -10000 0 -9999 0 0
HDAC5/RFXANK -0.015 0.005 0 53 -9999 0 53
CAMK4 -0.014 0 -10000 0 -9999 0 0
Tubulin/HDAC6 -0.019 0.005 0 34 -9999 0 34
SUMO1 -0.014 0 -10000 0 -9999 0 0
EntrezGene:9972 0 0 -10000 0 -9999 0 0
YWHAB -0.014 0.001 0 2 -9999 0 2
GATA1 -0.014 0 -10000 0 -9999 0 0
EntrezGene:8021 0 0 -10000 0 -9999 0 0
YWHAE -0.014 0.001 0 2 -9999 0 2
NR3C1 -0.014 0 -10000 0 -9999 0 0
SUMO1/HDAC4 -0.012 0.003 0.048 1 -9999 0 1
SRF -0.014 0 -10000 0 -9999 0 0
HDAC4/YWHAB -0.017 0.001 0 2 -9999 0 2
Tubulin -0.016 0.004 0 34 -9999 0 34
HDAC4/14-3-3 E -0.017 0.001 0 2 -9999 0 2
GNB1 -0.014 0.002 0 6 -9999 0 6
RANGAP1 -0.014 0 -10000 0 -9999 0 0
BCL6/BCoR -0.016 0.003 0 21 -9999 0 21
HDAC4/HDAC3/SMRT (N-CoR2) -0.02 0 -10000 0 -9999 0 0
HDAC4/SRF -0.02 0 -10000 0 -9999 0 0
HDAC4/ER alpha -0.017 0 -10000 0 -9999 0 0
EntrezGene:23225 0 0 -10000 0 -9999 0 0
positive regulation of chromatin silencing -0.007 0.004 0.05 2 -9999 0 2
cell motility -0.019 0.005 0 34 -9999 0 34
EntrezGene:23636 0 0 -10000 0 -9999 0 0
UBE2I -0.014 0 -10000 0 -9999 0 0
HDAC7/HDAC3 -0.009 0 -10000 0 -9999 0 0
BCL6 -0.014 0.002 0 16 -9999 0 16
HDAC4/CaMK II delta B -0.014 0 -10000 0 -9999 0 0
Hsp90/HDAC6 -0.017 0 -10000 0 -9999 0 0
ESR1 -0.014 0 -10000 0 -9999 0 0
HDAC6/HDAC11 -0.017 0 -10000 0 -9999 0 0
Ran/GTP/Exportin 1 -0.014 0.003 0.05 1 -9999 0 1
NPC -0.005 0 0 1 -9999 0 1
MEF2C -0.012 0.005 0 86 -9999 0 86
RAN -0.014 0.001 0 3 -9999 0 3
HDAC4/MEF2C -0.023 0.01 -10000 0 -9999 0 0
GNG2 0 0 -10000 0 -9999 0 0
NCOR2 -0.014 0 -10000 0 -9999 0 0
TUBB2A -0.013 0.003 0 34 -9999 0 34
HDAC11 -0.014 0 -10000 0 -9999 0 0
HSP90AA1 -0.014 0 -10000 0 -9999 0 0
RANBP2 -0.014 0.001 0 1 -9999 0 1
ANKRA2 -0.014 0.001 0 1 -9999 0 1
RFXANK -0.013 0.004 0 53 -9999 0 53
nuclear import 0.013 0.001 -10000 0 0 3 3
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.012 0.017 0.19 1 -10000 0 1
epithelial cell differentiation -0.022 0.021 -10000 0 -10000 0 0
ITCH -0.014 0.009 0.064 1 -10000 0 1
WWP1 -0.006 0.014 0.3 1 -10000 0 1
FYN -0.014 0.003 0 21 -10000 0 21
EGFR -0.009 0.007 0 194 -10000 0 194
PRL -0.014 0.002 0 6 -10000 0 6
neuron projection morphogenesis -0.024 0.031 0.12 1 -10000 0 1
PTPRZ1 -0.013 0.004 0 55 -10000 0 55
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.023 0.017 0.15 1 -10000 0 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.014 0.013 0.18 1 -10000 0 1
ADAM17 -0.014 0.009 0.064 1 -10000 0 1
ErbB4/ErbB4 -0.005 0.012 0.28 1 -10000 0 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.007 0.012 -10000 0 -10000 0 0
NCOR1 -0.014 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.018 0.012 0.16 1 -10000 0 1
GRIN2B -0.021 0.013 0.15 1 -10000 0 1
ErbB4/ErbB2/betacellulin -0.018 0.013 0.16 1 -10000 0 1
STAT1 -0.014 0.003 0 18 -10000 0 18
HBEGF -0.014 0.001 0 2 -10000 0 2
PRLR -0.014 0 -10000 0 -10000 0 0
E4ICDs/ETO2 -0.012 0.017 0.19 1 -10000 0 1
axon guidance -0.002 0.019 0.21 1 -10000 0 1
NEDD4 -0.013 0.009 0.064 1 -10000 0 1
Prolactin receptor/Prolactin receptor/Prolactin -0.017 0.002 0 6 -10000 0 6
CBFA2T3 -0.014 0 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF -0.018 0.013 0.16 1 -10000 0 1
MAPK3 -0.021 0.032 0.13 1 -10000 0 1
STAT1 (dimer) -0.011 0.017 0.19 1 -10000 0 1
MAPK1 -0.02 0.032 0.13 1 -10000 0 1
JAK2 -0.014 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.018 0.012 0.16 1 -10000 0 1
NRG1 -0.017 0.006 0.033 1 -10000 0 1
NRG3 0 0 -10000 0 -10000 0 0
NRG2 -0.014 0 -10000 0 -10000 0 0
NRG4 0 0 -10000 0 -10000 0 0
heart development -0.002 0.019 0.21 1 -10000 0 1
neural crest cell migration -0.018 0.012 0.16 1 -10000 0 1
ERBB2 -0.017 0.006 0.033 1 -10000 0 1
WWOX/E4ICDs -0.012 0.017 0.19 1 -10000 0 1
SHC1 -0.013 0.004 0 46 -10000 0 46
ErbB4/EGFR/neuregulin 4 -0.007 0.013 -10000 0 -10000 0 0
apoptosis 0.008 0.014 -10000 0 -0.19 1 1
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.012 0.017 0.19 1 -10000 0 1
ErbB4/ErbB2/epiregulin -0.018 0.012 0.16 1 -10000 0 1
ErbB4/ErbB4/betacellulin/betacellulin -0.012 0.017 0.19 1 -10000 0 1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.024 0.018 0.16 1 -10000 0 1
MDM2 -0.006 0.026 0.21 1 -10000 0 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.017 0.006 -10000 0 -10000 0 0
STAT5A -0.007 0.019 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.012 0.013 -10000 0 -10000 0 0
DLG4 -0.014 0 -10000 0 -10000 0 0
GRB2/SHC -0.015 0.005 0 51 -10000 0 51
E4ICDs/TAB2/NCoR1 -0.016 0.017 0.17 1 -10000 0 1
STAT5A (dimer) -0.021 0.026 -10000 0 -10000 0 0
MAP3K7IP2 -0.014 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.006 0.023 -10000 0 -10000 0 0
LRIG1 -0.013 0.003 0 29 -10000 0 29
EREG -0.014 0.002 0 10 -10000 0 10
BTC -0.014 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.003 0.017 0.21 1 -10000 0 1
ERBB4 -0.005 0.012 0.28 1 -10000 0 1
STAT5B -0.014 0 -10000 0 -10000 0 0
YAP1 0.007 0.016 -10000 0 -10000 0 0
GRB2 -0.014 0.001 0 5 -10000 0 5
ErbB4/ErbB2/neuregulin 4 -0.013 0.009 -10000 0 -10000 0 0
glial cell differentiation 0.016 0.017 -10000 0 -0.17 1 1
WWOX -0.014 0 -10000 0 -10000 0 0
cell proliferation -0.012 0.011 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.017 0.002 0 11 -10000 0 11
CRKL -0.006 0.009 -10000 0 -10000 0 0
mol:PIP3 0.01 0.02 -10000 0 -0.32 2 2
AKT1 -0.003 0.019 0.11 4 -0.27 2 6
PTK2B -0.014 0 -10000 0 -10000 0 0
RAPGEF1 -0.01 0.009 -10000 0 -10000 0 0
RANBP10 -0.014 0 -10000 0 -10000 0 0
PIK3CA -0.014 0.003 0 25 -10000 0 25
HGF/MET/SHIP2 -0.02 0.003 0 12 -10000 0 12
MAP3K5 -0.01 0.008 -10000 0 -10000 0 0
HGF/MET/CIN85/CBL/ENDOPHILINS -0.017 0.003 0 12 -10000 0 12
AP1 -0.012 0.019 0.062 25 -10000 0 25
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 -0.013 0.004 0 46 -10000 0 46
apoptosis 0.011 0.045 -10000 0 -0.68 2 2
STAT3 (dimer) -0.01 0.015 -10000 0 -0.095 9 9
GAB1/CRKL/SHP2/PI3K -0.017 0.011 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.01 0.01 -10000 0 -10000 0 0
PTPN11 -0.014 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 -0.014 0 -10000 0 -10000 0 0
PTEN -0.014 0.001 0 2 -10000 0 2
ELK1 -0.002 0.044 0.22 17 -10000 0 17
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.005 0.002 -10000 0 -10000 0 0
PAK1 -0.008 0.018 -10000 0 -0.26 2 2
HGF/MET/RANBP10 -0.02 0.003 0 12 -10000 0 12
HRAS -0.001 0.009 -10000 0 -10000 0 0
DOCK1 -0.01 0.009 -10000 0 -10000 0 0
GAB1 0 0.009 -10000 0 -10000 0 0
CRK -0.006 0.009 -10000 0 -10000 0 0
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.004 0.008 -10000 0 -10000 0 0
JUN -0.014 0.001 0 1 -10000 0 1
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.004 0.004 0.052 2 -10000 0 2
PIK3R1 -0.013 0.004 0 36 -10000 0 36
cell morphogenesis -0.016 0.026 0.12 1 -10000 0 1
GRB2/SHC -0.012 0.01 0.058 8 -10000 0 8
FOS -0.011 0.006 0 127 -10000 0 127
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.002 0.044 0.22 17 -10000 0 17
HGF/MET/MUC20 -0.013 0.002 0 12 -10000 0 12
cell migration -0.012 0.01 0.057 8 -10000 0 8
GRB2 -0.014 0.001 0 5 -10000 0 5
CBL -0.014 0 -10000 0 -10000 0 0
MET/RANBP10 -0.017 0.002 0 10 -10000 0 10
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.011 0.002 -10000 0 -10000 0 0
MET/MUC20 -0.008 0.001 0 10 -10000 0 10
RAP1B -0.01 0.008 -10000 0 -10000 0 0
RAP1A -0.015 0.008 -10000 0 -10000 0 0
HGF/MET/RANBP9 -0.02 0.003 0 13 -10000 0 13
RAF1 -0.006 0.016 -10000 0 -0.31 1 1
STAT3 -0.008 0.009 0.051 12 -10000 0 12
cell proliferation -0.008 0.031 0.11 9 -10000 0 9
RPS6KB1 0.002 0.005 -10000 0 -10000 0 0
MAPK3 -0.01 0.017 -10000 0 -10000 0 0
MAPK1 0.011 0.12 0.65 17 -10000 0 17
RANBP9 -0.014 0.001 0 1 -10000 0 1
MAPK8 -0.011 0.013 -10000 0 -10000 0 0
SRC -0.014 0.01 0.049 12 -10000 0 12
PI3K -0.012 0.01 0.058 8 -10000 0 8
MET/Glomulin -0.007 0.001 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 -0.01 0.009 -10000 0 -10000 0 0
MET -0.014 0.002 0 10 -10000 0 10
MAP4K1 -0.006 0.009 -10000 0 -10000 0 0
PTK2 -0.014 0.001 0 2 -10000 0 2
MAP2K2 -0.01 0.016 -10000 0 -0.3 1 1
BAD -0.008 0.018 -10000 0 -0.26 2 2
MAP2K4 -0.013 0.01 -10000 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 -0.012 0.005 -10000 0 -10000 0 0
INPPL1 -0.014 0 -10000 0 -10000 0 0
PXN -0.014 0 -10000 0 -10000 0 0
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.009 0.004 0.043 2 -10000 0 2
PLCgamma1/PKC -0.009 0 -10000 0 -10000 0 0
HGF -0.014 0.001 0 2 -10000 0 2
RASA1 -0.014 0.002 0 8 -10000 0 8
NCK1 -0.014 0.002 0 11 -10000 0 11
PTPRJ -0.014 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.014 0.011 0.057 12 -10000 0 12
PDPK1 0.002 0.018 -10000 0 -0.29 2 2
HGF/MET/SHIP -0.013 0.002 0 12 -10000 0 12
Signaling events regulated by Ret tyrosine kinase

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 -0.006 0.001 -10000 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.025 0.01 -10000 0 -10000 0 0
JUN -0.018 0.011 0.045 15 -10000 0 15
HRAS -0.014 0.001 0 2 -10000 0 2
RET51/GFRalpha1/GDNF/GRB10 -0.023 0.004 0 19 -10000 0 19
RAP1A -0.014 0 -10000 0 -10000 0 0
FRS2 -0.014 0.001 0 3 -10000 0 3
RAP1A/GDP -0.009 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.024 0.002 0 3 -10000 0 3
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 -0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.014 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.018 0.001 0 2 -10000 0 2
RHOA -0.014 0.001 0 2 -10000 0 2
RAP1A/GTP -0.026 0.002 -10000 0 -10000 0 0
GRB7 -0.014 0.001 0 1 -10000 0 1
RET51/GFRalpha1/GDNF -0.024 0.002 0 3 -10000 0 3
MAPKKK cascade -0.027 0.007 0.014 6 -10000 0 6
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.018 0.002 0 7 -10000 0 7
lamellipodium assembly -0.016 0.015 0.038 1 -10000 0 1
RET51/GFRalpha1/GDNF/SHC -0.022 0.007 0 47 -10000 0 47
PIK3CA -0.014 0.003 0 25 -10000 0 25
RET9/GFRalpha1/GDNF/SHC -0.016 0.005 0 46 -10000 0 46
RET9/GFRalpha1/GDNF/Shank3 -0.012 0.001 0 2 -10000 0 2
MAPK3 -0.029 0.008 0.078 3 -10000 0 3
DOK1 -0.014 0 -10000 0 -10000 0 0
DOK6 0 0 -10000 0 -10000 0 0
PXN -0.014 0 -10000 0 -10000 0 0
neurite development -0.027 0.009 0.069 3 -10000 0 3
DOK5 -0.013 0.004 0 36 -10000 0 36
GFRA1 -0.014 0.001 0 2 -10000 0 2
MAPK8 -0.014 0.01 0.049 14 -10000 0 14
HRAS/GTP -0.025 0.007 0.02 8 -10000 0 8
tube development -0.016 0.007 0.058 5 -10000 0 5
MAPK1 -0.028 0.01 0.078 3 -10000 0 3
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.009 0.001 -10000 0 -10000 0 0
Rac1/GDP -0.009 0 -10000 0 -10000 0 0
SRC -0.014 0 -10000 0 -10000 0 0
PDLIM7 -0.014 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.022 0.002 0 3 -10000 0 3
SHC1 -0.013 0.004 0 46 -10000 0 46
RET51/GFRalpha1/GDNF/Dok4 -0.024 0.002 0 3 -10000 0 3
RET51/GFRalpha1/GDNF/Dok5 -0.022 0.006 0 39 -10000 0 39
PRKCA -0.014 0 -10000 0 -10000 0 0
HRAS/GDP -0.009 0.001 0 2 -10000 0 2
CREB1 -0.003 0.001 -10000 0 -10000 0 0
PIK3R1 -0.013 0.004 0 36 -10000 0 36
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.008 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Grb7 -0.023 0.002 0 4 -10000 0 4
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.014 0.001 0 1 -10000 0 1
DOK4 -0.014 0 -10000 0 -10000 0 0
JNK cascade -0.018 0.011 0.084 1 -10000 0 1
RET9/GFRalpha1/GDNF/FRS2 -0.018 0.002 0 5 -10000 0 5
SHANK3 0 0 -10000 0 -10000 0 0
RASA1 -0.014 0.002 0 8 -10000 0 8
NCK1 -0.014 0.002 0 11 -10000 0 11
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.007 0.002 0 51 -10000 0 51
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.011 0.002 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.011 0.002 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.008 0.003 -10000 0 -10000 0 0
PI3K -0.012 0.023 0.089 11 -10000 0 11
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.016 0.002 0 7 -10000 0 7
GRB10 -0.014 0.002 0 16 -10000 0 16
activation of MAPKK activity -0.011 0.009 0.05 1 -0.098 5 6
RET51/GFRalpha1/GDNF/FRS2 -0.023 0.003 0 6 -10000 0 6
GAB1 -0.014 0.001 0 4 -10000 0 4
IRS1 -0.014 0.001 0 5 -10000 0 5
IRS2 -0.014 0.002 0 11 -10000 0 11
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.01 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/PKC alpha -0.024 0.002 0 3 -10000 0 3
GRB2 -0.014 0.001 0 5 -10000 0 5
PRKACA -0.014 0 -10000 0 -10000 0 0
GDNF -0.014 0 -10000 0 -10000 0 0
RAC1 -0.014 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.023 0.003 0 8 -10000 0 8
Rac1/GTP -0.017 0.019 0.059 7 -10000 0 7
RET9/GFRalpha1/GDNF -0.013 0.001 0 2 -10000 0 2
GFRalpha1/GDNF -0.017 0.001 0 2 -10000 0 2
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.014 0 -9999 0 -9999 0 0
oxygen homeostasis 0 0 -9999 0 -9999 0 0
TCEB2 -0.014 0 -9999 0 -9999 0 0
TCEB1 -0.014 0 -9999 0 -9999 0 0
HIF1A/p53 -0.009 0.013 -9999 0 -9999 0 0
HIF1A -0.006 0.011 -9999 0 -9999 0 0
COPS5 -0.014 0 -9999 0 -9999 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.022 0 -9999 0 -9999 0 0
FIH (dimer) -0.014 0 -9999 0 -9999 0 0
CDKN2A -0.013 0.004 0 59 -9999 0 59
ARNT/IPAS -0.017 0 -9999 0 -9999 0 0
HIF1AN -0.014 0 -9999 0 -9999 0 0
GNB2L1 -0.014 0 -9999 0 -9999 0 0
HIF1A/ARNT -0.01 0.014 -9999 0 -9999 0 0
CUL2 -0.014 0 -9999 0 -9999 0 0
OS9 -0.013 0.004 0 43 -9999 0 43
RACK1/Elongin B/Elongin C -0.02 0 -9999 0 -9999 0 0
response to hypoxia 0 0 -9999 0 -9999 0 0
HIF1A/Hsp90 -0.01 0.014 -9999 0 -9999 0 0
PHD1-3/OS9 -0.021 0.007 0 48 -9999 0 48
HIF1A/RACK1/Elongin B/Elongin C -0.017 0.018 -9999 0 -9999 0 0
VHL 0 0 -9999 0 -9999 0 0
HSP90AA1 -0.014 0 -9999 0 -9999 0 0
HIF1A/JAB1 -0.01 0.014 -9999 0 -9999 0 0
EGLN3 -0.014 0.001 0 4 -9999 0 4
EGLN2 -0.014 0 -9999 0 -9999 0 0
EGLN1 -0.014 0.001 0 1 -9999 0 1
TP53 -0.012 0.005 0 69 -9999 0 69
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.002 0.004 -9999 0 -9999 0 0
ARNT -0.014 0 -9999 0 -9999 0 0
ARD1A -0.014 0.001 0 1 -9999 0 1
RBX1 -0.014 0 -9999 0 -9999 0 0
HIF1A/p19ARF -0.01 0.012 -9999 0 -9999 0 0
Regulation of Androgen receptor activity

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
HDAC1 -0.008 0.003 0 65 -10000 0 65
SMARCC1 0.002 0.057 0.3 18 -10000 0 18
REL -0.014 0 -10000 0 -10000 0 0
HDAC7 -0.03 0.027 0.11 7 -10000 0 7
JUN -0.014 0.001 0 1 -10000 0 1
EP300 -0.014 0 -10000 0 -10000 0 0
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.018 0.007 0.019 9 -10000 0 9
FOXO1 -0.014 0.002 0 11 -10000 0 11
T-DHT/AR -0.03 0.035 0.16 8 -10000 0 8
MAP2K6 -0.014 0.008 0.014 39 -10000 0 39
BRM/BAF57 -0.017 0 -10000 0 -10000 0 0
MAP2K4 -0.014 0.008 0.015 32 -10000 0 32
SMARCA2 -0.014 0 -10000 0 -10000 0 0
PDE9A -0.01 0.03 0.31 4 -10000 0 4
NCOA2 -0.014 0 -10000 0 -10000 0 0
CEBPA -0.014 0.002 0 16 -10000 0 16
EHMT2 -0.014 0 -10000 0 -10000 0 0
cell proliferation -0.033 0.022 0.15 1 -10000 0 1
NR0B1 -0.013 0.004 0 49 -10000 0 49
EGR1 -0.014 0.003 -10000 0 -10000 0 0
RXRs/9cRA -0.018 0.001 -10000 0 -10000 0 0
AR/RACK1/Src -0.031 0.017 -10000 0 -10000 0 0
AR/GR -0.018 0.014 0.066 1 -0.093 2 3
GNB2L1 -0.014 0 -10000 0 -10000 0 0
PKN1 -0.014 0.002 0 10 -10000 0 10
RCHY1 -0.014 0 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.017 0.008 0.021 7 -10000 0 7
T-DHT/AR/TIF2/CARM1 -0.03 0.02 -10000 0 -10000 0 0
SRC -0.028 0.013 0.078 2 -10000 0 2
NR3C1 -0.014 0 -10000 0 -10000 0 0
KLK3 -0.011 0.016 -10000 0 -10000 0 0
APPBP2 -0.014 0.008 0.014 39 -10000 0 39
TRIM24 -0.014 0.002 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.022 0.013 0.045 7 -10000 0 7
TMPRSS2 -0.011 0.024 0.28 3 -10000 0 3
RXRG -0.014 0.001 0 3 -10000 0 3
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA -0.014 0 -10000 0 -10000 0 0
RXRB -0.014 0 -10000 0 -10000 0 0
CARM1 -0.014 0 -10000 0 -10000 0 0
NR2C2 -0.014 0 -10000 0 -10000 0 0
KLK2 -0.03 0.014 -10000 0 -10000 0 0
AR -0.014 0.013 0.058 10 -10000 0 10
SENP1 0 0 -10000 0 -10000 0 0
HSP90AA1 -0.014 0 -10000 0 -10000 0 0
MDM2 -0.013 0.003 -10000 0 -10000 0 0
SRY -0.014 0.001 -10000 0 -10000 0 0
GATA2 -0.014 0.001 0 1 -10000 0 1
MYST2 -0.014 0 -10000 0 -10000 0 0
HOXB13 -0.015 0 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.031 0.017 -10000 0 -10000 0 0
positive regulation of transcription -0.014 0.001 0 1 -10000 0 1
DNAJA1 -0.014 0.008 0.014 38 -10000 0 38
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.001 -10000 0 -10000 0 0
NCOA1 -0.01 0.02 0.097 18 -10000 0 18
SPDEF -0.014 0 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.017 0.012 -10000 0 -10000 0 0
T-DHT/AR/Hsp90 -0.026 0.017 0.076 2 -10000 0 2
GSK3B -0.014 0.004 0.013 8 -10000 0 8
NR2C1 -0.014 0 -10000 0 -10000 0 0
mol:T-DHT -0.025 0.012 -10000 0 -10000 0 0
SIRT1 -0.014 0 -10000 0 -10000 0 0
ZMIZ2 -0.014 0 -10000 0 -10000 0 0
POU2F1 -0.014 0.017 0.13 7 -10000 0 7
T-DHT/AR/DAX-1 -0.024 0.018 0.076 2 -10000 0 2
CREBBP -0.014 0 -10000 0 -10000 0 0
SMARCE1 -0.014 0 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.025 0.096 0.37 7 -10000 0 7
PCK1 -0.01 0.068 0.4 5 -10000 0 5
HNF4A -0.027 0.1 0.66 3 -10000 0 3
KCNJ11 -0.023 0.1 0.41 5 -10000 0 5
AKT1 -0.027 0.072 0.3 3 -10000 0 3
response to starvation -0.002 0.001 -10000 0 -10000 0 0
DLK1 -0.013 0.13 0.44 13 -10000 0 13
NKX2-1 -0.011 0.064 0.34 1 -10000 0 1
ACADM -0.025 0.096 0.36 8 -10000 0 8
TAT -0.011 0.066 0.56 2 -10000 0 2
CEBPB -0.014 0.007 0.06 4 -10000 0 4
CEBPA -0.014 0.007 0.07 3 -10000 0 3
TTR -0.011 0.067 0.6 3 -10000 0 3
PKLR -0.025 0.095 0.37 6 -10000 0 6
APOA1 -0.012 0.11 0.74 3 -10000 0 3
CPT1C -0.023 0.094 0.38 6 -10000 0 6
ALAS1 -0.009 0.075 0.43 2 -0.84 1 3
TFRC -0.013 0.1 0.41 6 -0.73 3 9
FOXF1 -0.012 0.006 -10000 0 -0.12 1 1
NF1 -0.016 0.006 -10000 0 -0.16 1 1
HNF1A (dimer) -0.018 0.006 0.13 1 -10000 0 1
CPT1A -0.025 0.095 0.37 6 -10000 0 6
HMGCS1 -0.025 0.095 0.37 6 -10000 0 6
NR3C1 -0.014 0.02 0.11 13 -10000 0 13
CPT1B -0.025 0.095 0.43 4 -10000 0 4
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 -0.016 0 -10000 0 -10000 0 0
GCK -0.025 0.095 0.37 6 -10000 0 6
CREB1 -0.015 0.013 0.11 5 -10000 0 5
IGFBP1 -0.005 0.073 0.47 4 -10000 0 4
PDX1 -0.012 0.065 0.4 2 -10000 0 2
UCP2 -0.011 0.12 0.37 20 -10000 0 20
ALDOB -0.026 0.11 0.41 5 -10000 0 5
AFP -0.007 0.02 0.24 2 -0.081 3 5
BDH1 -0.026 0.098 0.37 6 -0.42 3 9
HADH -0.025 0.11 0.4 6 -10000 0 6
F2 -0.012 0.11 0.89 2 -10000 0 2
HNF1A -0.018 0.006 0.13 1 -10000 0 1
G6PC -0.011 0.023 -10000 0 -10000 0 0
SLC2A2 -0.011 0.078 0.55 2 -10000 0 2
INS -0.014 0.018 0.16 1 -0.12 13 14
FOXA1 -0.004 0.017 0.16 3 -0.11 3 6
FOXA3 -0.008 0.025 0.14 8 -0.14 3 11
FOXA2 -0.028 0.13 0.52 6 -10000 0 6
ABCC8 -0.026 0.11 0.41 5 -10000 0 5
ALB -0.007 0.02 0.24 2 -0.081 3 5
mTOR signaling pathway

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
GBL -0.014 0 -10000 0 -10000 0 0
MKNK1 -0.014 0 -10000 0 -10000 0 0
mol:PIP3 -0.011 0.008 0.059 4 -10000 0 4
FRAP1 0.004 0.011 -10000 0 -10000 0 0
AKT1 -0.01 0.02 0.08 24 -10000 0 24
INSR -0.014 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin -0.014 0 -10000 0 -10000 0 0
mol:GTP -0.015 0.024 0.073 26 -10000 0 26
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.017 0.008 -10000 0 -10000 0 0
TSC2 -0.014 0 -10000 0 -10000 0 0
RHEB/GDP -0.022 0.013 0.04 2 -10000 0 2
TSC1 -0.014 0.002 0 8 -10000 0 8
Insulin Receptor/IRS1 0.006 0.005 0.059 5 -10000 0 5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.014 0.013 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A -0.014 0 -10000 0 -10000 0 0
RPS6KB1 -0.001 0.017 0.12 1 -10000 0 1
MAP3K5 -0.003 0.012 -10000 0 -0.14 4 4
PIK3R1 -0.013 0.004 0 36 -10000 0 36
apoptosis -0.003 0.012 -10000 0 -0.14 4 4
mol:LY294002 0 0 -10000 0 0 1 1
EIF4B -0.005 0.016 0.11 1 -10000 0 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.007 0.019 0.11 1 -10000 0 1
eIF4E/eIF4G1/eIF4A1 -0.014 0.01 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.009 0.007 0.058 3 -10000 0 3
mTOR/RHEB/GTP/Raptor/GBL -0.011 0.017 0.1 2 -10000 0 2
FKBP1A -0.014 0.001 0 1 -10000 0 1
RHEB/GTP -0.018 0.023 0.064 26 -10000 0 26
mol:Amino Acids 0 0 -10000 0 0 1 1
FKBP12/Rapamycin -0.008 0.004 0.009 24 -10000 0 24
PDPK1 -0.012 0.021 0.081 24 -10000 0 24
EIF4E -0.014 0.001 0 5 -10000 0 5
ASK1/PP5C 0.012 0.049 -10000 0 -0.55 4 4
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.001 0.006 -10000 0 -10000 0 0
TSC1/TSC2 -0.016 0.026 0.081 24 -10000 0 24
tumor necrosis factor receptor activity 0 0 0 1 -10000 0 1
RPS6 -0.014 0 -10000 0 -10000 0 0
PPP5C -0.014 0 -10000 0 -10000 0 0
EIF4G1 -0.014 0.001 0 4 -10000 0 4
IRS1 0.001 0.006 0.063 5 -10000 0 5
INS -0.014 0 -10000 0 -10000 0 0
PTEN -0.014 0.001 0 2 -10000 0 2
PDK2 -0.012 0.021 0.081 24 -10000 0 24
EIF4EBP1 0.029 0.021 -10000 0 -10000 0 0
PIK3CA -0.014 0.003 0 25 -10000 0 25
PPP2R5D -0.001 0.011 -10000 0 -10000 0 0
peptide biosynthetic process -0.018 0 -10000 0 -10000 0 0
RHEB -0.014 0 -10000 0 -10000 0 0
EIF4A1 -0.014 0.002 0 10 -10000 0 10
mol:Rapamycin 0 0 0.002 2 -10000 0 2
EEF2 -0.018 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.027 0.015 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.015 0.004 -10000 0 -9999 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -9999 0 0
cytokine production during immune response 0.008 0.007 -10000 0 -9999 0 0
IL27/IL27R/JAK1 -0.028 0.008 -10000 0 -9999 0 0
TBX21 -0.039 0.019 -10000 0 -9999 0 0
IL12B -0.014 0.002 0.029 1 -9999 0 1
IL12A -0.009 0.001 0.01 1 -9999 0 1
IL6ST -0.016 0.002 -10000 0 -9999 0 0
IL27RA/JAK1 -0.012 0.003 -10000 0 -9999 0 0
IL27 -0.002 0.001 -10000 0 -9999 0 0
TYK2 -0.015 0.003 0.049 1 -9999 0 1
T-helper cell lineage commitment 0.009 0.043 -10000 0 -9999 0 0
T-helper 2 cell differentiation 0.008 0.007 -10000 0 -9999 0 0
T cell proliferation during immune response 0.008 0.007 -10000 0 -9999 0 0
MAPKKK cascade -0.008 0.007 -10000 0 -9999 0 0
STAT3 -0.014 0.002 0 10 -9999 0 10
STAT2 -0.014 0 -10000 0 -9999 0 0
STAT1 -0.015 0.003 -10000 0 -9999 0 0
IL12RB1 -0.014 0.001 0.018 1 -9999 0 1
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -9999 0 0
IL12RB2 -0.039 0.019 -10000 0 -9999 0 0
IL27/IL27R/JAK2/TYK2 -0.009 0.008 -10000 0 -9999 0 0
positive regulation of T cell mediated cytotoxicity -0.008 0.007 -10000 0 -9999 0 0
STAT1 (dimer) -0.043 0.014 -10000 0 -9999 0 0
JAK2 -0.015 0.002 0.04 1 -9999 0 1
JAK1 -0.015 0.002 -10000 0 -9999 0 0
STAT2 (dimer) -0.013 0.008 -10000 0 -9999 0 0
T cell proliferation -0.012 0.012 -10000 0 -9999 0 0
IL12/IL12R/TYK2/JAK2 0.004 0.008 -10000 0 -9999 0 0
IL17A 0.009 0.044 -10000 0 -9999 0 0
mast cell activation 0.008 0.007 -10000 0 -9999 0 0
IFNG -0.001 0.005 0.1 1 -9999 0 1
T cell differentiation -0.002 0.001 0.009 1 -9999 0 1
STAT3 (dimer) -0.013 0.008 -10000 0 -9999 0 0
STAT5A (dimer) -0.013 0.008 -10000 0 -9999 0 0
STAT4 (dimer) -0.007 0.01 -10000 0 -9999 0 0
STAT4 -0.008 0.007 0 219 -9999 0 219
T cell activation 0.001 0 -10000 0 -9999 0 0
IL27R/JAK2/TYK2 -0.021 0.009 -10000 0 -9999 0 0
GATA3 0.001 0.022 -10000 0 -9999 0 0
IL18 -0.008 0.002 0 45 -9999 0 45
positive regulation of mast cell cytokine production -0.013 0.008 -10000 0 -9999 0 0
IL27/EBI3 -0.011 0.003 -10000 0 -9999 0 0
IL27RA -0.005 0.002 -10000 0 -9999 0 0
IL6 -0.014 0.005 -10000 0 -9999 0 0
STAT5A -0.014 0.001 0 1 -9999 0 1
monocyte differentiation 0 0 0.005 1 -9999 0 1
IL2 0.001 0.002 -10000 0 -9999 0 0
IL1B -0.008 0.001 0 14 -9999 0 14
EBI3 -0.016 0.002 -10000 0 -9999 0 0
TNF -0.009 0.001 -0.001 3 -9999 0 3
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 -0.012 0.005 0 65 -9999 0 65
Ran/GTP/Exportin 1/HDAC4 -0.022 0.002 -10000 0 -9999 0 0
MDM2/SUMO1 -0.011 0.003 0.048 1 -9999 0 1
HDAC4 -0.014 0 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 -0.019 0.007 -10000 0 -9999 0 0
SUMO1 -0.014 0 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1 -0.004 0 -10000 0 -9999 0 0
mol:GTP 0 0 -10000 0 -9999 0 0
XPO1 -0.01 0 -10000 0 -9999 0 0
EntrezGene:23636 0 0 -10000 0 -9999 0 0
RAN -0.014 0.001 0 3 -9999 0 3
EntrezGene:8021 0 0 -10000 0 -9999 0 0
RANBP2 -0.014 0.001 0 1 -9999 0 1
SUMO1/HDAC4 -0.012 0.003 0.048 1 -9999 0 1
SUMO1/HDAC1 -0.01 0.004 -10000 0 -9999 0 0
RANGAP1 -0.014 0 -10000 0 -9999 0 0
MDM2/SUMO1/SUMO1 -0.023 0.004 0 18 -9999 0 18
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 -0.005 0 0 1 -9999 0 1
Ran/GTP -0.009 0.003 0.048 1 -9999 0 1
EntrezGene:23225 0 0 -10000 0 -9999 0 0
MDM2 -0.014 0.003 0 18 -9999 0 18
UBE2I -0.014 0 -10000 0 -9999 0 0
Ran/GTP/Exportin 1 -0.014 0.003 -10000 0 -9999 0 0
NPC -0.005 0 0 1 -9999 0 1
PIAS2 -0.014 0 -10000 0 -9999 0 0
PIAS1 -0.014 0 -10000 0 -9999 0 0
EntrezGene:9972 0 0 -10000 0 -9999 0 0
a4b1 and a4b7 Integrin signaling

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 -0.014 0 -9999 0 -9999 0 0
ITGB7 -0.014 0.001 0 2 -9999 0 2
ITGA4 -0.014 0.001 0 5 -9999 0 5
alpha4/beta7 Integrin -0.017 0.002 0 5 -9999 0 5
alpha4/beta1 Integrin -0.017 0.002 0 5 -9999 0 5
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.026 0.003 -10000 0 -10000 0 0
TC10/GTP -0.025 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 -0.025 0.003 -10000 0 -10000 0 0
HRAS -0.014 0.001 0 2 -10000 0 2
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 -0.014 0.003 0 18 -10000 0 18
FOXO3 -0.002 0.008 -10000 0 -10000 0 0
AKT1 -0.024 0.034 0.12 5 -10000 0 5
INSR -0.018 0.001 -10000 0 -10000 0 0
Insulin Receptor/Insulin -0.026 0.003 0 8 -10000 0 8
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 -0.014 0.002 0 16 -10000 0 16
SORBS1 -0.014 0 -10000 0 -10000 0 0
CRK -0.014 0 -10000 0 -10000 0 0
PTPN1 -0.026 0.003 -10000 0 -10000 0 0
CAV1 -0.009 0.011 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II/C3G -0.022 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 -0.025 0.003 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.024 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.012 0.02 -10000 0 -0.21 5 5
RPS6KB1 -0.028 0.032 0.12 5 -10000 0 5
PARD6A -0.014 0 -10000 0 -10000 0 0
CBL -0.014 0 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.007 0.003 -10000 0 -10000 0 0
PIK3R1 -0.013 0.004 0 36 -10000 0 36
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.032 0.031 0.055 39 -10000 0 39
HRAS/GTP -0.026 0.009 -10000 0 -10000 0 0
Insulin Receptor -0.018 0.001 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.026 0.009 -10000 0 -10000 0 0
PRKCI -0.006 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.03 0.012 -10000 0 -10000 0 0
SHC1 -0.013 0.004 0 46 -10000 0 46
negative regulation of MAPKKK cascade 0.014 0.008 -10000 0 -10000 0 0
PI3K -0.024 0.009 -10000 0 -10000 0 0
NCK2 -0.014 0.001 0 1 -10000 0 1
RHOQ -0.014 0 -10000 0 -10000 0 0
mol:H2O2 -0.004 0.001 0.004 8 -10000 0 8
HRAS/GDP -0.009 0.001 0 2 -10000 0 2
AKT2 -0.025 0.034 0.12 5 -10000 0 5
PRKCZ -0.008 0.005 -10000 0 -10000 0 0
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.019 0.009 0.085 2 -10000 0 2
F2RL2 -0.014 0 -10000 0 -10000 0 0
TRIP10 -0.014 0.002 0 6 -10000 0 6
Insulin Receptor/Insulin/Shc -0.018 0.006 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst -0.013 0.001 0 6 -10000 0 6
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.021 0.007 -10000 0 -10000 0 0
RAPGEF1 -0.014 0 -10000 0 -10000 0 0
RASA1 -0.014 0.002 0 8 -10000 0 8
NCK1 -0.014 0.002 0 11 -10000 0 11
CBL/APS/CAP/Crk-II -0.018 0 -10000 0 -10000 0 0
TC10/GDP -0.009 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.023 0.008 -10000 0 -10000 0 0
INPP5D -0.017 0.002 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
SGK1 -0.004 0.002 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 -0.014 0 -10000 0 -10000 0 0
IRS1 -0.014 0.001 0 5 -10000 0 5
p62DOK/RasGAP 0.014 0.008 -10000 0 -10000 0 0
INS -0.018 0.001 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.017 0.002 -10000 0 -10000 0 0
GRB2 -0.014 0.001 0 5 -10000 0 5
EIF4EBP1 -0.014 0.026 0.13 2 -10000 0 2
PTPRA -0.018 0.002 -10000 0 -10000 0 0
PIK3CA -0.014 0.003 0 25 -10000 0 25
TC10/GTP/CIP4 -0.013 0.001 0 6 -10000 0 6
PDPK1 -0.014 0 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.01 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.019 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 -0.021 0.001 -10000 0 -10000 0 0
Par3/Par6 -0.022 0.002 0 6 -10000 0 6
LPA4-mediated signaling events

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
ADCY4 -0.007 0 -9999 0 -9999 0 0
ADCY5 -0.007 0 -9999 0 -9999 0 0
ADCY6 -0.014 0 -9999 0 -9999 0 0
ADCY7 -0.013 0.001 0 5 -9999 0 5
ADCY1 -0.014 0 -9999 0 -9999 0 0
ADCY2 -0.014 0 -9999 0 -9999 0 0
ADCY3 -0.007 0 -9999 0 -9999 0 0
ADCY8 -0.013 0.002 0 7 -9999 0 7
PRKCE -0.009 0 -9999 0 -9999 0 0
ADCY9 -0.014 0 -9999 0 -9999 0 0
mol:DAG 0 0 -9999 0 -9999 0 0
cAMP biosynthetic process -0.014 0.008 -9999 0 -9999 0 0
Coregulation of Androgen receptor activity

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
NRIP1 -0.014 0.001 -10000 0 -9999 0 0
SVIL -0.014 0.003 -10000 0 -9999 0 0
ZNF318 -0.014 0 -10000 0 -9999 0 0
JMJD2C -0.016 0 -10000 0 -9999 0 0
T-DHT/AR/Ubc9 -0.019 0.011 0.074 7 -9999 0 7
CARM1 -0.014 0 -10000 0 -9999 0 0
PRDX1 -0.014 0.001 -10000 0 -9999 0 0
PELP1 -0.014 0 -10000 0 -9999 0 0
CTNNB1 -0.014 0 -10000 0 -9999 0 0
AKT1 -0.014 0.001 -10000 0 -9999 0 0
PTK2B -0.014 0 -10000 0 -9999 0 0
MED1 -0.014 0 -10000 0 -9999 0 0
MAK -0.013 0.002 -10000 0 -9999 0 0
response to oxidative stress 0 0 -10000 0 -9999 0 0
HIP1 -0.013 0.004 -10000 0 -9999 0 0
GSN -0.014 0.002 -10000 0 -9999 0 0
NCOA2 -0.014 0 -10000 0 -9999 0 0
NCOA6 -0.014 0.001 -10000 0 -9999 0 0
DNA-PK -0.019 0.004 -10000 0 -9999 0 0
NCOA4 -0.014 0.001 0 1 -9999 0 1
PIAS3 -0.014 0.001 -10000 0 -9999 0 0
cell proliferation -0.006 0.003 -10000 0 -9999 0 0
XRCC5 -0.014 0 -10000 0 -9999 0 0
UBE3A -0.015 0 -10000 0 -9999 0 0
T-DHT/AR/SNURF -0.013 0.009 0.07 6 -9999 0 6
FHL2 -0.014 0.007 0.049 3 -9999 0 3
RANBP9 -0.014 0.001 -10000 0 -9999 0 0
JMJD1A -0.017 0.011 0.12 3 -9999 0 3
CDK6 -0.014 0 -10000 0 -9999 0 0
TGFB1I1 -0.002 0.005 -10000 0 -9999 0 0
T-DHT/AR/CyclinD1 -0.016 0.01 0.075 2 -9999 0 2
XRCC6 -0.014 0 -10000 0 -9999 0 0
T-DHT/AR -0.024 0.02 0.15 6 -9999 0 6
CTDSP1 -0.014 0.001 -10000 0 -9999 0 0
CTDSP2 -0.013 0.004 -10000 0 -9999 0 0
BRCA1 -0.014 0.001 -10000 0 -9999 0 0
TCF4 -0.014 0.002 -10000 0 -9999 0 0
CDKN2A -0.012 0.004 -10000 0 -9999 0 0
SRF -0.014 0.012 0.12 4 -9999 0 4
NKX3-1 -0.016 0.014 0.089 6 -9999 0 6
KLK3 0.003 0.017 -10000 0 -9999 0 0
TMF1 -0.014 0.001 0 4 -9999 0 4
HNRNPA1 -0.014 0 -10000 0 -9999 0 0
AOF2 -0.014 0.002 -10000 0 -9999 0 0
APPL1 -0.017 0.001 -10000 0 -9999 0 0
T-DHT/AR/Caspase 8 -0.019 0.01 0.074 5 -9999 0 5
AR -0.019 0.008 0.044 7 -9999 0 7
UBA3 0 0 -10000 0 -9999 0 0
PATZ1 -0.014 0 -10000 0 -9999 0 0
PAWR -0.014 0 -10000 0 -9999 0 0
PRKDC -0.013 0.003 -10000 0 -9999 0 0
PA2G4 -0.014 0.001 -10000 0 -9999 0 0
UBE2I -0.014 0 -10000 0 -9999 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.017 0.011 0.071 7 -9999 0 7
RPS6KA3 -0.014 0.001 -10000 0 -9999 0 0
T-DHT/AR/ARA70 -0.019 0.011 0.074 7 -9999 0 7
LATS2 0 0 -10000 0 -9999 0 0
T-DHT/AR/PRX1 -0.017 0.011 0.071 7 -9999 0 7
Cyclin D3/CDK11 p58 -0.008 0 -10000 0 -9999 0 0
VAV3 -0.013 0.004 -10000 0 -9999 0 0
KLK2 -0.015 0.009 0.049 6 -9999 0 6
CASP8 -0.014 0.002 -10000 0 -9999 0 0
T-DHT/AR/TIF2/CARM1 -0.023 0.012 0.075 7 -9999 0 7
TMPRSS2 -0.017 0.008 0.047 3 -9999 0 3
CCND1 -0.012 0.006 -10000 0 -9999 0 0
PIAS1 -0.015 0 -10000 0 -9999 0 0
mol:T-DHT -0.006 0.005 0.035 7 -9999 0 7
CDC2L1 0 0 -10000 0 -9999 0 0
PIAS4 -0.015 0 -10000 0 -9999 0 0
T-DHT/AR/CDK6 -0.019 0.011 0.074 7 -9999 0 7
CMTM2 0 0 -10000 0 -9999 0 0
SNURF 0 0 -10000 0 -9999 0 0
ZMIZ1 -0.019 0.008 0.044 6 -9999 0 6
CCND3 -0.014 0.001 0 1 -9999 0 1
TGIF1 -0.004 0.006 -10000 0 -9999 0 0
FKBP4 -0.014 0 -10000 0 -9999 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.011 0.001 0 6 -9999 0 6
MAPK9 -0.003 0 0 3 -9999 0 3
adrenocorticotropin secretion -0.009 0 0 1 -9999 0 1
GNB1/GNG2 -0.007 0.001 0 6 -9999 0 6
GNB1 -0.014 0.002 0 6 -9999 0 6
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -9999 0 0
mol:GDP 0 0 -9999 0 -9999 0 0
MAPK14 -0.003 0 0 2 -9999 0 2
Gs family/GTP -0.006 0 -9999 0 -9999 0 0
EntrezGene:2778 0 0 -9999 0 -9999 0 0
vasopressin secretion 0 0 -9999 0 -9999 0 0
G-protein coupled receptor activity 0 0 -9999 0 -9999 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -9999 0 0
glutamate secretion 0.002 0 -9999 0 -9999 0 0
GNAL -0.014 0 -9999 0 -9999 0 0
GNG2 0 0 -9999 0 -9999 0 0
CRH -0.014 0.001 0 1 -9999 0 1
mol:cortisol 0 0 -9999 0 -9999 0 0
MAPK8 -0.003 0 -9999 0 -9999 0 0
MAPK11 -0.003 0 -9999 0 -9999 0 0
Visual signal transduction: Rods

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
mol:K + -0.014 0 -9999 0 -9999 0 0
GNAT1/GTP -0.009 0 -9999 0 -9999 0 0
Metarhodopsin II/Arrestin -0.013 0.001 0 1 -9999 0 1
PDE6G/GNAT1/GTP -0.014 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
absorption of light 0 0 -9999 0 -9999 0 0
GNAT1 -0.014 0 -9999 0 -9999 0 0
GRK1 0 0 -9999 0 -9999 0 0
CNG Channel -0.03 0 -9999 0 -9999 0 0
mol:Na + -0.024 0 -9999 0 -9999 0 0
mol:ADP 0 0 -9999 0 -9999 0 0
RGS9-1/Gbeta5/R9AP -0.013 0.002 0 7 -9999 0 7
mol:GDP 0 0 -9999 0 -9999 0 0
cGMP/CNG Channel -0.025 0 -9999 0 -9999 0 0
CNGB1 -0.014 0 -9999 0 -9999 0 0
RDH5 -0.014 0.001 0 1 -9999 0 1
SAG -0.014 0.001 0 1 -9999 0 1
mol:Ca2+ -0.029 0 -9999 0 -9999 0 0
Na + (4 Units) -0.028 0 -9999 0 -9999 0 0
RGS9 -0.014 0 -9999 0 -9999 0 0
GNB1/GNGT1 -0.017 0.002 0 6 -9999 0 6
GNAT1/GDP -0.016 0.002 0 7 -9999 0 7
GUCY2D -0.014 0 -9999 0 -9999 0 0
GNGT1 -0.014 0 -9999 0 -9999 0 0
GUCY2F -0.014 0 -9999 0 -9999 0 0
GNB5 -0.014 0.002 0 7 -9999 0 7
mol:GMP (4 units) -0.022 0 -9999 0 -9999 0 0
mol:11-cis-retinal -0.014 0.001 0 1 -9999 0 1
mol:cGMP -0.016 0 -9999 0 -9999 0 0
GNB1 -0.014 0.002 0 6 -9999 0 6
Rhodopsin -0.017 0.001 0 1 -9999 0 1
SLC24A1 -0.014 0 -9999 0 -9999 0 0
CNGA1 -0.014 0 -9999 0 -9999 0 0
Metarhodopsin II -0.006 0 -9999 0 -9999 0 0
mol:Ca ++ 0 0 -9999 0 -9999 0 0
GC1/GCAP Family -0.012 0 -9999 0 -9999 0 0
RGS9BP 0 0 -9999 0 -9999 0 0
Metarhodopsin II/Transducin -0.007 0.001 0 6 -9999 0 6
GCAP Family/Ca ++ -0.006 0 -9999 0 -9999 0 0
PDE6A/B -0.017 0 -9999 0 -9999 0 0
mol:Pi -0.013 0.002 0 7 -9999 0 7
mol:all-trans-retinal 0 0 -9999 0 -9999 0 0
Transducin -0.018 0.002 0 6 -9999 0 6
PDE6B -0.014 0 -9999 0 -9999 0 0
PDE6A -0.014 0 -9999 0 -9999 0 0
PDE6G -0.014 0 -9999 0 -9999 0 0
RHO -0.014 0 -9999 0 -9999 0 0
PDE6 -0.026 0.003 -9999 0 -9999 0 0
GUCA1A 0 0 -9999 0 -9999 0 0
GC2/GCAP Family -0.012 0 -9999 0 -9999 0 0
GUCA1C 0 0 -9999 0 -9999 0 0
GUCA1B -0.014 0 -9999 0 -9999 0 0
Arf1 pathway

Figure S128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex -0.008 0.003 0.043 2 -10000 0 2
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A -0.001 0.008 -10000 0 -0.12 2 2
AP2 -0.008 0.001 0 11 -10000 0 11
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP -0.015 0 -10000 0 -10000 0 0
CLTB -0.014 0.001 0 2 -10000 0 2
coatomer protein complex/ARF1/GTP/ER cargo protein -0.008 0.001 -10000 0 -10000 0 0
CD4 -0.014 0.003 0 20 -10000 0 20
CLTA -0.014 0 -10000 0 -10000 0 0
mol:GTP -0.002 0 -10000 0 -10000 0 0
ARFGAP1 -0.009 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.004 0 -10000 0 -10000 0 0
ARF1/GTP -0.011 0.001 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.01 0.001 -10000 0 -10000 0 0
mol:Choline -0.005 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 -0.015 0.002 0.012 1 -10000 0 1
DDEF1 -0.004 0 -10000 0 -10000 0 0
ARF1/GDP -0.003 0.001 -10000 0 -10000 0 0
AP2M1 -0.014 0.002 0 11 -10000 0 11
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.013 0.001 0.004 1 -10000 0 1
Rac/GTP -0.01 0.001 0.008 1 -10000 0 1
ARF1/GTP/GGA3/ARF-GAP1 -0.017 0.002 0.01 1 -10000 0 1
ARFIP2 -0.015 0 -10000 0 -10000 0 0
COPA -0.014 0 -10000 0 -10000 0 0
RAC1 -0.014 0 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex -0.004 0.001 -10000 0 -10000 0 0
ARF1/GTP/ARHGAP10 -0.008 0.001 -10000 0 -10000 0 0
GGA3 -0.014 0 -10000 0 -10000 0 0
ARF1/GTP/Membrin -0.006 0 -10000 0 -10000 0 0
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.007 0.001 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.006 0.001 -10000 0 -10000 0 0
Arfaptin 2/Rac/GDP -0.014 0 -10000 0 -10000 0 0
CYTH2 -0.002 0 -10000 0 -10000 0 0
ARF1/GTP/GGA3 -0.015 0.001 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP -0.009 0 -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 -0.006 0.002 -10000 0 -10000 0 0
PLD2 -0.005 0 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.009 0 -10000 0 -10000 0 0
PIP5K1A -0.004 0 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 -0.009 0.001 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.005 0 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.009 0 -10000 0 -10000 0 0
GOSR2 0.001 0 -10000 0 -10000 0 0
USO1 0.001 0 -10000 0 -10000 0 0
GBF1 0.001 0 -10000 0 -10000 0 0
ARF1/GTP/Arfaptin 2 -0.016 0.001 0.005 1 -10000 0 1
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.013 0.003 0 31 -10000 0 31
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.017 0.001 0 3 -9999 0 3
FBXW11 -0.014 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex -0.014 0 -9999 0 -9999 0 0
CHUK -0.014 0.001 0 1 -9999 0 1
NF kappa B2 p100/RelB -0.027 0.002 -9999 0 -9999 0 0
NFKB1 -0.014 0.001 0 4 -9999 0 4
MAP3K14 -0.014 0.001 0 2 -9999 0 2
NF kappa B1 p50/RelB -0.017 0.002 0 5 -9999 0 5
RELB -0.014 0.001 0 1 -9999 0 1
NFKB2 -0.014 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB -0.013 0.001 0 1 -9999 0 1
regulation of B cell activation -0.013 0.001 0 1 -9999 0 1
Ephrin A reverse signaling

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
MAPKKK cascade -0.013 0 -9999 0 -9999 0 0
EFNA5 -0.014 0 -9999 0 -9999 0 0
FYN -0.017 0.003 -9999 0 -9999 0 0
neuron projection morphogenesis -0.013 0 -9999 0 -9999 0 0
cell-cell signaling 0 0 -9999 0 -9999 0 0
Ephrin A5/EPHA5 -0.014 0 -9999 0 -9999 0 0
EPHA5 -0.014 0 -9999 0 -9999 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.014 0 -9999 0 -9999 0 0
PI3K Class IB/PDE3B -0.014 0 -9999 0 -9999 0 0
PDE3B -0.014 0 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 528 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.87.5896 TCGA.81.5910 TCGA.76.6285 TCGA.76.6282
109_MAP3K5 0.01 -0.011 -0.011 -0.011
47_PPARGC1A -0.014 -0.014 -0.014 -0.014
105_BMP4 -0.014 -0.014 -0.014 -0.014
105_BMP6 -0.014 -0.014 -0.014 -0.014
105_BMP7 -0.014 -0.014 -0.014 -0.014
105_BMP2 -0.014 -0.014 0 -0.014
131_RELN/VLDLR -0.024 0 -0.024 0
30_TGFB1/TGF beta receptor Type II 0 -0.014 -0.022 0
84_STAT5B 0.096 0.06 -0.004 0.06
84_STAT5A 0.096 0.06 -0.004 0.06
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM-TP/19076708/GDAC_MergeDataFiles_12184161/GBM-TP.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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