PARADIGM pathway analysis of mRNASeq expression and copy number data
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 69 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
Glypican 2 network 169
FOXM1 transcription factor network 160
Plasma membrane estrogen receptor signaling 96
PDGFR-alpha signaling pathway 88
Signaling mediated by p38-alpha and p38-beta 85
Signaling events regulated by Ret tyrosine kinase 83
Nongenotropic Androgen signaling 78
Aurora B signaling 77
Ephrin A reverse signaling 74
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 73
Results
Summary Table

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 371 . 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 ( 371 ).

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
Glypican 2 network 0.4555 169 676 4 0.067 0.18 1000 -1000 0.015 -1000
FOXM1 transcription factor network 0.4313 160 8164 51 0.005 1.1 1000 -1000 0.009 -1000
Plasma membrane estrogen receptor signaling 0.2588 96 8301 86 -0.53 0.49 1000 -1000 -0.042 -1000
PDGFR-alpha signaling pathway 0.2372 88 3890 44 -0.6 0.05 1000 -1000 -0.03 -1000
Signaling mediated by p38-alpha and p38-beta 0.2291 85 3772 44 -0.32 0.026 1000 -1000 -0.017 -1000
Signaling events regulated by Ret tyrosine kinase 0.2237 83 6809 82 -0.31 0.034 1000 -1000 -0.054 -1000
Nongenotropic Androgen signaling 0.2102 78 4068 52 -0.42 0.24 1000 -1000 -0.027 -1000
Aurora B signaling 0.2075 77 5188 67 -0.01 0.32 1000 -1000 -0.028 -1000
Ephrin A reverse signaling 0.1995 74 519 7 -0.09 0.028 1000 -1000 0 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1968 73 5005 68 -0.58 0.24 1000 -1000 -0.036 -1000
EPO signaling pathway 0.1914 71 3940 55 -0.19 0.026 1000 -1000 -0.02 -1000
FOXA2 and FOXA3 transcription factor networks 0.1887 70 3247 46 -0.68 0.039 1000 -1000 -0.016 -1000
PLK1 signaling events 0.1860 69 5866 85 -0.068 0.29 1000 -1000 -0.023 -1000
Ephrin B reverse signaling 0.1860 69 3331 48 -0.29 0.085 1000 -1000 -0.022 -1000
p75(NTR)-mediated signaling 0.1833 68 8565 125 -0.35 0.21 1000 -1000 -0.068 -1000
IGF1 pathway 0.1833 68 3895 57 -0.23 0.075 1000 -1000 -0.028 -1000
HIF-1-alpha transcription factor network 0.1779 66 5047 76 -0.45 0.046 1000 -1000 -0.025 -1000
TCGA08_retinoblastoma 0.1752 65 525 8 -0.11 0.23 1000 -1000 -0.003 -1000
IL4-mediated signaling events 0.1698 63 5741 91 -0.93 0.48 1000 -1000 -0.069 -1000
Reelin signaling pathway 0.1617 60 3401 56 -0.18 0.13 1000 -1000 -0.027 -1000
IL6-mediated signaling events 0.1617 60 4506 75 -0.47 0.057 1000 -1000 -0.024 -1000
LPA receptor mediated events 0.1563 58 6015 102 -0.28 0.067 1000 -1000 -0.059 -1000
Noncanonical Wnt signaling pathway 0.1536 57 1490 26 -0.16 0.044 1000 -1000 -0.023 -1000
Wnt signaling 0.1536 57 405 7 -0.15 0.044 1000 -1000 -0.01 -1000
Endothelins 0.1482 55 5343 96 -0.55 0.16 1000 -1000 -0.015 -1000
EPHB forward signaling 0.1482 55 4740 85 -0.14 0.15 1000 -1000 -0.055 -1000
Signaling events mediated by the Hedgehog family 0.1321 49 2556 52 -0.27 0.14 1000 -1000 -0.017 -1000
Glypican 1 network 0.1321 49 2397 48 -0.22 0.059 1000 -1000 -0.013 -1000
Calcium signaling in the CD4+ TCR pathway 0.1321 49 1540 31 -0.3 0.026 1000 -1000 -0.036 -1000
IL23-mediated signaling events 0.1267 47 2837 60 -0.31 0.034 1000 -1000 -0.009 -1000
Syndecan-1-mediated signaling events 0.1186 44 1503 34 -0.32 0.094 1000 -1000 -0.023 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.1186 44 3740 85 -0.43 0.033 1000 -1000 -0.036 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1132 42 3728 88 -0.21 0.037 1000 -1000 -0.06 -1000
S1P1 pathway 0.1105 41 1488 36 -0.39 0.16 1000 -1000 -0.025 -1000
S1P5 pathway 0.1078 40 682 17 -0.26 0.16 1000 -1000 -0.006 -1000
PLK2 and PLK4 events 0.1051 39 118 3 0.024 0.074 1000 -1000 -0.008 -1000
ErbB2/ErbB3 signaling events 0.1024 38 2515 65 -0.25 0.089 1000 -1000 -0.059 -1000
IL12-mediated signaling events 0.1024 38 3349 87 -0.64 0.038 1000 -1000 -0.051 -1000
Thromboxane A2 receptor signaling 0.0997 37 3885 105 -0.15 0.093 1000 -1000 -0.036 -1000
S1P4 pathway 0.0997 37 931 25 -0.26 0.16 1000 -1000 -0.013 -1000
Glucocorticoid receptor regulatory network 0.0916 34 3879 114 -0.62 0.2 1000 -1000 -0.054 -1000
TCGA08_p53 0.0916 34 238 7 -0.094 0.036 1000 -1000 -0.005 -1000
FoxO family signaling 0.0916 34 2215 64 -0.2 0.41 1000 -1000 -0.019 -1000
Osteopontin-mediated events 0.0863 32 1242 38 -0.27 0.1 1000 -1000 -0.015 -1000
S1P3 pathway 0.0836 31 1340 42 -0.26 0.17 1000 -1000 -0.014 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0809 30 1657 54 -0.18 0.055 1000 -1000 -0.025 -1000
amb2 Integrin signaling 0.0809 30 2530 82 -0.26 0.1 1000 -1000 -0.019 -1000
Syndecan-4-mediated signaling events 0.0809 30 2063 67 -0.24 0.2 1000 -1000 -0.025 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0809 30 3615 120 -0.37 0.11 1000 -1000 -0.041 -1000
BCR signaling pathway 0.0755 28 2841 99 -0.2 0.028 1000 -1000 -0.05 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0728 27 760 28 -0.26 0.16 1000 -1000 -0.006 -1000
Arf6 signaling events 0.0701 26 1650 62 -0.32 0.093 1000 -1000 -0.02 -1000
TCR signaling in naïve CD8+ T cells 0.0701 26 2438 93 -0.17 0.074 1000 -1000 -0.041 -1000
Integrins in angiogenesis 0.0647 24 2059 84 -0.23 0.094 1000 -1000 -0.026 -1000
Signaling events mediated by PRL 0.0647 24 845 34 -0.2 0.048 1000 -1000 -0.029 -1000
Ras signaling in the CD4+ TCR pathway 0.0647 24 424 17 -0.16 0.025 1000 -1000 -0.017 -1000
LPA4-mediated signaling events 0.0620 23 283 12 -0.15 0.018 1000 -1000 -0.015 -1000
Coregulation of Androgen receptor activity 0.0620 23 1776 76 -0.15 0.23 1000 -1000 -0.011 -1000
Aurora C signaling 0.0620 23 164 7 0 0.16 1000 -1000 -0.014 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0620 23 1737 74 -0.32 0.093 1000 -1000 -0.058 -1000
Fc-epsilon receptor I signaling in mast cells 0.0593 22 2207 97 -0.27 0.04 1000 -1000 -0.051 -1000
Nectin adhesion pathway 0.0593 22 1422 63 -0.094 0.043 1000 -1000 -0.038 -1000
IL1-mediated signaling events 0.0593 22 1375 62 -0.078 0.042 1000 -1000 -0.026 -1000
p38 MAPK signaling pathway 0.0593 22 996 44 -0.28 0.048 1000 -1000 -0.009 -1000
BMP receptor signaling 0.0566 21 1739 81 -0.099 0.091 1000 -1000 -0.038 -1000
FAS signaling pathway (CD95) 0.0539 20 951 47 -0.32 0.035 1000 -1000 -0.027 -1000
ErbB4 signaling events 0.0512 19 1365 69 -0.16 0.093 1000 -1000 -0.026 -1000
Presenilin action in Notch and Wnt signaling 0.0512 19 1166 61 -0.27 0.13 1000 -1000 -0.032 -1000
Regulation of Telomerase 0.0512 19 1963 102 -0.3 0.23 1000 -1000 -0.03 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0485 18 636 34 -0.016 0.06 1000 -1000 -0.022 -1000
IL27-mediated signaling events 0.0485 18 924 51 -0.14 0.095 1000 -1000 -0.035 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0458 17 629 37 -0.2 0.056 1000 -1000 -0.022 -1000
Canonical Wnt signaling pathway 0.0458 17 905 51 -0.053 0.15 1000 -1000 -0.033 -1000
Visual signal transduction: Rods 0.0458 17 903 52 -0.13 0.06 1000 -1000 -0.02 -1000
JNK signaling in the CD4+ TCR pathway 0.0431 16 286 17 -0.093 0.052 1000 -1000 -0.013 -1000
Regulation of Androgen receptor activity 0.0431 16 1170 70 -0.19 0.084 1000 -1000 -0.034 -1000
Regulation of nuclear SMAD2/3 signaling 0.0404 15 2096 136 -0.37 0.36 1000 -1000 -0.028 -1000
HIF-2-alpha transcription factor network 0.0404 15 665 43 -0.18 0.039 1000 -1000 -0.07 -1000
Syndecan-3-mediated signaling events 0.0404 15 544 35 -0.1 0.053 1000 -1000 -0.019 -1000
Syndecan-2-mediated signaling events 0.0377 14 969 69 -0.1 0.1 1000 -1000 -0.033 -1000
Aurora A signaling 0.0377 14 880 60 -0.009 0.22 1000 -1000 -0.009 -1000
Signaling events mediated by HDAC Class III 0.0377 14 587 40 -0.22 0.048 1000 -1000 -0.026 -1000
IL2 signaling events mediated by PI3K 0.0377 14 835 58 -0.049 0.16 1000 -1000 -0.022 -1000
IL2 signaling events mediated by STAT5 0.0377 14 325 22 -0.022 0.17 1000 -1000 -0.015 -1000
Signaling events mediated by PTP1B 0.0350 13 995 76 -0.18 0.14 1000 -1000 -0.027 -1000
Effects of Botulinum toxin 0.0350 13 346 26 -0.056 0.038 1000 -1000 -0.003 -1000
E-cadherin signaling events 0.0350 13 66 5 -0.015 0.026 1000 -1000 0.015 -1000
Ceramide signaling pathway 0.0323 12 913 76 -0.23 0.093 1000 -1000 -0.021 -1000
Signaling mediated by p38-gamma and p38-delta 0.0323 12 187 15 -0.002 0.083 1000 -1000 -0.024 -1000
E-cadherin signaling in the nascent adherens junction 0.0323 12 919 76 -0.035 0.043 1000 -1000 -0.048 -1000
EGFR-dependent Endothelin signaling events 0.0323 12 257 21 0 0.093 1000 -1000 -0.031 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0323 12 398 33 0 0.23 1000 -1000 -0.027 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0323 12 949 78 -0.2 0.033 1000 -1000 -0.031 -1000
Caspase cascade in apoptosis 0.0296 11 858 74 -0.084 0.069 1000 -1000 -0.028 -1000
Cellular roles of Anthrax toxin 0.0296 11 461 39 -0.06 0.025 1000 -1000 -0.02 -1000
Class IB PI3K non-lipid kinase events 0.0296 11 33 3 -0.007 0.007 1000 -1000 -0.013 -1000
BARD1 signaling events 0.0270 10 588 57 -0.059 0.13 1000 -1000 -0.029 -1000
Hedgehog signaling events mediated by Gli proteins 0.0270 10 656 65 -0.26 0.16 1000 -1000 -0.029 -1000
Insulin-mediated glucose transport 0.0270 10 326 32 -0.02 0.2 1000 -1000 -0.017 -1000
E-cadherin signaling in keratinocytes 0.0270 10 455 43 -0.054 0.03 1000 -1000 -0.016 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0243 9 511 52 -0.072 0.063 1000 -1000 -0.019 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0243 9 444 45 -0.041 0.06 1000 -1000 -0.034 -1000
Regulation of p38-alpha and p38-beta 0.0243 9 517 54 -0.069 0.06 1000 -1000 -0.042 -1000
TCGA08_rtk_signaling 0.0243 9 259 26 -0.22 0.028 1000 -1000 -0.016 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0216 8 728 83 -0.074 0.2 1000 -1000 -0.009 -1000
Signaling events mediated by HDAC Class II 0.0189 7 526 75 -0.31 0.07 1000 -1000 -0.028 -1000
mTOR signaling pathway 0.0189 7 393 53 -0.15 0.037 1000 -1000 -0.034 -1000
Retinoic acid receptors-mediated signaling 0.0189 7 439 58 -0.093 0.05 1000 -1000 -0.015 -1000
Rapid glucocorticoid signaling 0.0189 7 159 20 -0.012 0.075 1000 -1000 -0.004 -1000
PDGFR-beta signaling pathway 0.0189 7 717 97 -0.13 0.071 1000 -1000 -0.047 -1000
a4b1 and a4b7 Integrin signaling 0.0162 6 34 5 0.015 0.028 1000 -1000 0.011 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0162 6 806 125 -0.024 0.048 1000 -1000 -0.042 -1000
Class I PI3K signaling events 0.0162 6 452 73 -0.069 0.05 1000 -1000 -0.026 -1000
Arf6 downstream pathway 0.0135 5 241 43 -0.026 0.044 1000 -1000 -0.023 -1000
IFN-gamma pathway 0.0135 5 385 68 -0.28 0.073 1000 -1000 -0.045 -1000
Class I PI3K signaling events mediated by Akt 0.0135 5 392 68 -0.061 0.2 1000 -1000 -0.024 -1000
Visual signal transduction: Cones 0.0108 4 170 38 -0.015 0.066 1000 -1000 -0.002 -1000
Paxillin-dependent events mediated by a4b1 0.0108 4 172 36 -0.046 0.048 1000 -1000 -0.02 -1000
Canonical NF-kappaB pathway 0.0081 3 130 39 0 0.052 1000 -1000 -0.014 -1000
TRAIL signaling pathway 0.0081 3 190 48 -0.004 0.044 1000 -1000 -0.023 -1000
ceramide signaling pathway 0.0081 3 186 49 -0.001 0.037 1000 -1000 -0.026 -1000
Atypical NF-kappaB pathway 0.0081 3 106 31 0 0.034 1000 -1000 -0.007 -1000
Insulin Pathway 0.0081 3 239 74 -0.064 0.065 1000 -1000 -0.046 -1000
Signaling events mediated by HDAC Class I 0.0054 2 254 104 -0.039 0.059 1000 -1000 -0.025 -1000
Arf6 trafficking events 0.0054 2 158 71 -0.046 0.048 1000 -1000 -0.026 -1000
VEGFR1 specific signals 0.0054 2 126 56 -0.029 0.059 1000 -1000 -0.032 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0027 1 45 23 -0.008 0.047 1000 -1000 -0.015 -1000
Arf1 pathway 0.0027 1 89 54 -0.027 0.038 1000 -1000 -0.011 -1000
Circadian rhythm pathway 0.0000 0 15 22 -0.007 0.055 1000 -1000 -0.011 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 8 27 0 0.063 1000 -1000 -0.031 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.07 1000 -1000 0 -1000
Total NA 3891 220310 7203 -24 14 131000 -131000 -3.3 -131000
Glypican 2 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
MDK 0.2 0.16 0.34 201 -9999 0 201
GPC2 0.067 0.11 0.34 49 -9999 0 49
GPC2/Midkine 0.18 0.14 0.28 213 -9999 0 213
neuron projection morphogenesis 0.18 0.14 0.28 213 -9999 0 213
FOXM1 transcription factor 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
NFATC3 0.74 0.64 1.2 193 -0.92 7 200
PLK1 0.56 0.44 0.92 200 -10000 0 200
BIRC5 0.6 0.42 0.9 221 -10000 0 221
HSPA1B 0.77 0.67 1.3 194 -0.89 7 201
MAP2K1 0.26 0.2 0.44 186 -10000 0 186
BRCA2 0.75 0.68 1.3 194 -1 10 204
FOXM1 1.1 0.98 1.8 201 -1 9 210
XRCC1 0.74 0.65 1.3 190 -0.92 7 197
FOXM1B/p19 0.05 0.34 1 15 -0.97 9 24
Cyclin D1/CDK4 0.52 0.58 1 153 -0.89 12 165
CDC2 0.88 0.76 1.5 201 -0.92 9 210
TGFA 0.44 0.68 1.1 157 -0.96 30 187
SKP2 0.76 0.66 1.3 193 -0.91 7 200
CCNE1 0.17 0.16 0.4 122 -10000 0 122
CKS1B 0.74 0.64 1.2 200 -0.88 9 209
RB1 0.36 0.45 0.88 134 -0.76 3 137
FOXM1C/SP1 0.55 0.6 1.1 172 -0.96 11 183
AURKB 0.47 0.5 0.9 175 -0.97 10 185
CENPF 0.97 0.81 1.6 208 -0.92 5 213
CDK4 0.1 0.077 0.24 18 -10000 0 18
MYC 0.39 0.59 1.1 131 -0.88 11 142
CHEK2 0.26 0.2 0.44 186 -10000 0 186
ONECUT1 0.5 0.64 1.1 157 -0.94 13 170
CDKN2A 0.014 0.21 0.32 78 -0.37 41 119
LAMA4 0.75 0.65 1.3 192 -0.92 7 199
FOXM1B/HNF6 0.5 0.66 1.1 154 -1.1 13 167
FOS 0.19 0.84 1.3 104 -1.1 49 153
SP1 0.005 0.08 -10000 0 -0.31 19 19
CDC25B 0.74 0.65 1.3 196 -0.92 7 203
response to radiation 0.16 0.12 0.27 167 -10000 0 167
CENPB 0.74 0.65 1.2 196 -0.92 7 203
CENPA 0.92 0.78 1.5 201 -0.94 6 207
NEK2 1 0.8 1.6 218 -0.96 3 221
HIST1H2BA 0.76 0.66 1.3 193 -0.89 7 200
CCNA2 0.2 0.18 0.4 172 -10000 0 172
EP300 0.026 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.84 0.75 1.4 198 -0.98 9 207
CCNB2 0.94 0.78 1.5 210 -0.92 7 217
CCNB1 0.96 0.84 1.6 200 -0.96 7 207
ETV5 0.74 0.64 1.2 194 -0.92 7 201
ESR1 0.083 0.7 1.3 67 -1.2 32 99
CCND1 0.56 0.64 1.2 159 -0.91 12 171
GSK3A 0.18 0.13 0.32 119 -10000 0 119
Cyclin A-E1/CDK1-2 0.31 0.25 0.55 174 -10000 0 174
CDK2 0.079 0.051 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.24 0.19 0.39 207 -10000 0 207
FOXM1B/Cbp/p300 0.052 0.32 0.74 6 -0.91 10 16
GAS1 0.54 0.8 1.3 166 -1.2 24 190
MMP2 0.7 0.7 1.3 189 -1.1 12 201
RB1/FOXM1C 0.48 0.6 1.1 144 -0.91 11 155
CREBBP 0.025 0.006 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.15 0.2 -10000 0 -0.34 176 176
ER alpha/Gai/GDP/Gbeta gamma -0.41 0.41 -10000 0 -0.66 229 229
AKT1 -0.52 0.46 -10000 0 -0.9 214 214
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.53 0.48 -10000 0 -0.92 214 214
mol:Ca2+ -0.15 0.23 -10000 0 -0.58 71 71
IGF1R 0.015 0.1 0.34 4 -0.62 8 12
E2/ER alpha (dimer)/Striatin -0.2 0.21 -10000 0 -0.38 207 207
SHC1 0.02 0.011 -10000 0 -10000 0 0
apoptosis 0.49 0.44 0.84 214 -10000 0 214
RhoA/GTP -0.14 0.16 -10000 0 -0.31 167 167
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.35 0.33 -10000 0 -0.61 207 207
regulation of stress fiber formation 0.14 0.13 0.36 13 -10000 0 13
E2/ERA-ERB (dimer) -0.19 0.21 0.22 2 -0.37 197 199
KRAS 0.026 0.004 -10000 0 -10000 0 0
G13/GTP -0.17 0.19 -10000 0 -0.33 197 197
pseudopodium formation -0.14 0.13 -10000 0 -0.36 13 13
E2/ER alpha (dimer)/PELP1 -0.19 0.2 -10000 0 -0.38 190 190
GRB2 0.025 0.005 -10000 0 -10000 0 0
GNG2 0.022 0.048 -10000 0 -0.62 2 2
GNAO1 -0.26 0.31 -10000 0 -0.58 174 174
HRAS 0.027 0.017 0.34 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.39 0.36 -10000 0 -0.67 212 212
E2/ER beta (dimer) 0.019 0.016 0.23 2 -10000 0 2
mol:GDP -0.23 0.23 -10000 0 -0.44 195 195
mol:NADP -0.39 0.36 -10000 0 -0.67 212 212
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
mol:IP3 -0.15 0.25 -10000 0 -0.61 71 71
IGF-1R heterotetramer 0.015 0.1 0.34 4 -0.62 8 12
PLCB1 -0.15 0.25 -10000 0 -0.64 67 67
PLCB2 -0.16 0.26 -10000 0 -0.64 71 71
IGF1 -0.23 0.31 -10000 0 -0.61 144 144
mol:L-citrulline -0.39 0.36 -10000 0 -0.67 212 212
RHOA 0.026 0.003 -10000 0 -10000 0 0
Gai/GDP -0.39 0.46 -10000 0 -0.84 181 181
JNK cascade 0.019 0.016 0.22 2 -10000 0 2
BCAR1 0.024 0.007 -10000 0 -10000 0 0
ESR2 0.026 0.024 0.34 2 -10000 0 2
GNAQ 0.025 0.017 -10000 0 -0.3 1 1
ESR1 -0.31 0.31 -10000 0 -0.58 198 198
Gq family/GDP/Gbeta gamma -0.094 0.22 -10000 0 -0.67 32 32
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.16 0.17 -10000 0 -0.44 22 22
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.33 0.32 -10000 0 -0.59 196 196
GNAZ 0.16 0.16 0.34 165 -0.62 1 166
E2/ER alpha (dimer) -0.23 0.23 -10000 0 -0.43 198 198
STRN 0.005 0.12 -10000 0 -0.62 12 12
GNAL 0.075 0.11 0.34 57 -10000 0 57
PELP1 0.022 0.01 -10000 0 -10000 0 0
MAPK11 0.02 0.036 0.2 12 -10000 0 12
GNAI2 0.026 0.003 -10000 0 -10000 0 0
GNAI3 0.025 0.005 -10000 0 -10000 0 0
GNAI1 0.022 0.048 -10000 0 -0.62 2 2
HBEGF -0.34 0.34 0.34 2 -0.66 172 174
cAMP biosynthetic process -0.13 0.17 -10000 0 -0.3 177 177
SRC -0.39 0.38 -10000 0 -0.73 173 173
PI3K 0.034 0.052 -10000 0 -0.64 2 2
GNB1 0.024 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.19 0.22 -10000 0 -0.4 192 192
SOS1 0.026 0.001 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.34 0.27 -10000 0 -0.55 213 213
Gs family/GTP -0.13 0.18 -10000 0 -0.31 177 177
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.048 0.016 -10000 0 -10000 0 0
vasodilation -0.37 0.34 -10000 0 -0.63 212 212
mol:DAG -0.15 0.25 -10000 0 -0.61 71 71
Gs family/GDP/Gbeta gamma -0.18 0.2 -10000 0 -0.37 189 189
MSN -0.15 0.14 -10000 0 -0.39 13 13
Gq family/GTP -0.16 0.26 -10000 0 -0.65 71 71
mol:PI-3-4-5-P3 -0.5 0.46 -10000 0 -0.87 214 214
NRAS 0.025 0.004 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.37 0.34 0.63 212 -10000 0 212
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
RhoA/GDP -0.21 0.23 -10000 0 -0.42 194 194
NOS3 -0.42 0.4 -10000 0 -0.72 212 212
GNA11 0.009 0.1 -10000 0 -0.58 10 10
MAPKKK cascade -0.4 0.36 -10000 0 -0.68 218 218
E2/ER alpha (dimer)/PELP1/Src -0.37 0.35 -10000 0 -0.64 207 207
ruffle organization -0.14 0.13 -10000 0 -0.36 13 13
ROCK2 -0.16 0.15 -10000 0 -0.31 165 165
GNA14 -0.078 0.24 -10000 0 -0.6 60 60
GNA15 0.026 0.041 0.34 2 -0.62 1 3
GNA13 0.025 0.005 -10000 0 -10000 0 0
MMP9 -0.35 0.35 0.37 1 -0.68 169 170
MMP2 -0.37 0.35 -10000 0 -0.69 177 177
PDGFR-alpha signaling pathway

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
PDGFRA -0.25 0.31 -10000 0 -0.62 143 143
PDGF/PDGFRA/CRKL -0.17 0.23 -10000 0 -0.45 145 145
positive regulation of JUN kinase activity -0.085 0.18 -10000 0 -0.37 85 85
CRKL 0.025 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.18 0.23 -10000 0 -0.46 142 142
AP1 -0.6 0.54 -10000 0 -1.1 177 177
mol:IP3 -0.2 0.23 -10000 0 -0.48 140 140
PLCG1 -0.2 0.23 -10000 0 -0.48 140 140
PDGF/PDGFRA/alphaV Integrin -0.17 0.23 -10000 0 -0.45 145 145
RAPGEF1 0.026 0.004 -10000 0 -10000 0 0
CRK 0.022 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.2 0.23 -10000 0 -0.48 140 140
CAV3 0.019 0.003 -10000 0 -10000 0 0
CAV1 0.025 0.005 -10000 0 -10000 0 0
SHC/Grb2/SOS1 -0.084 0.18 -10000 0 -0.37 85 85
PDGF/PDGFRA/Shf -0.19 0.25 -10000 0 -0.47 157 157
FOS -0.58 0.53 -10000 0 -1.1 177 177
JUN -0.059 0.067 -10000 0 -0.5 6 6
oligodendrocyte development -0.17 0.23 -10000 0 -0.45 145 145
GRB2 0.025 0.005 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
mol:DAG -0.2 0.23 -10000 0 -0.48 140 140
PDGF/PDGFRA -0.25 0.31 -10000 0 -0.62 143 143
actin cytoskeleton reorganization -0.17 0.23 -10000 0 -0.46 142 142
SRF 0.023 0.014 -10000 0 -10000 0 0
SHC1 0.02 0.011 -10000 0 -10000 0 0
PI3K -0.13 0.22 -10000 0 -0.41 133 133
PDGF/PDGFRA/Crk/C3G -0.13 0.21 -10000 0 -0.4 133 133
JAK1 -0.18 0.22 -10000 0 -0.46 141 141
ELK1/SRF -0.15 0.18 -10000 0 -0.39 111 111
SHB 0.024 0.034 -10000 0 -0.62 1 1
SHF -0.007 0.14 -10000 0 -0.6 19 19
CSNK2A1 0.05 0.023 -10000 0 -10000 0 0
GO:0007205 -0.21 0.24 -10000 0 -0.5 144 144
SOS1 0.026 0.001 -10000 0 -10000 0 0
Ras protein signal transduction -0.085 0.18 -10000 0 -0.37 85 85
PDGF/PDGFRA/SHB -0.17 0.23 -10000 0 -0.46 142 142
PDGF/PDGFRA/Caveolin-1 -0.17 0.23 -10000 0 -0.45 142 142
ITGAV 0.027 0.017 0.34 1 -10000 0 1
ELK1 -0.21 0.22 -10000 0 -0.47 142 142
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
PDGF/PDGFRA/Crk -0.17 0.23 -10000 0 -0.45 143 143
JAK-STAT cascade -0.18 0.22 -10000 0 -0.45 141 141
cell proliferation -0.19 0.25 -10000 0 -0.47 157 157
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.31 0.52 0.44 1 -1 121 122
MKNK1 0.025 0.006 -10000 0 -10000 0 0
MAPK14 -0.073 0.2 -10000 0 -0.36 102 102
ATF2/c-Jun -0.079 0.2 -10000 0 -0.52 34 34
MAPK11 -0.07 0.22 0.35 11 -0.38 107 118
MITF -0.085 0.23 0.37 1 -0.43 101 102
MAPKAPK5 -0.086 0.22 0.37 1 -0.42 101 102
KRT8 -0.09 0.22 0.37 1 -0.42 105 106
MAPKAPK3 0.026 0.003 -10000 0 -10000 0 0
MAPKAPK2 0.021 0.011 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.12 0.32 0.44 1 -0.59 102 103
CEBPB -0.085 0.22 0.37 1 -0.42 101 102
SLC9A1 -0.095 0.24 0.37 1 -0.45 103 104
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.087 0.24 0.36 3 -0.43 101 104
p38alpha-beta/MNK1 -0.09 0.28 0.38 1 -0.5 97 98
JUN -0.076 0.2 -10000 0 -0.51 34 34
PPARGC1A -0.14 0.29 0.37 1 -0.49 126 127
USF1 -0.072 0.21 0.37 4 -0.4 92 96
RAB5/GDP/GDI1 -0.067 0.17 -10000 0 -0.32 100 100
NOS2 -0.06 0.25 0.49 23 -0.54 30 53
DDIT3 -0.086 0.22 0.37 1 -0.42 102 103
RAB5A 0.026 0.002 -10000 0 -10000 0 0
HSPB1 -0.069 0.18 0.28 2 -0.36 85 87
p38alpha-beta/HBP1 -0.085 0.28 0.38 1 -0.5 94 95
CREB1 -0.11 0.25 0.34 2 -0.47 103 105
RAB5/GDP 0.019 0.002 -10000 0 -10000 0 0
EIF4E -0.098 0.24 0.36 1 -0.46 93 94
RPS6KA4 -0.088 0.23 0.37 1 -0.42 103 104
PLA2G4A -0.1 0.23 0.36 1 -0.45 100 101
GDI1 -0.086 0.22 0.37 2 -0.42 102 104
TP53 -0.13 0.3 0.39 1 -0.58 95 96
RPS6KA5 -0.1 0.26 0.37 2 -0.46 102 104
ESR1 -0.32 0.36 0.37 1 -0.55 209 210
HBP1 0.025 0.004 -10000 0 -10000 0 0
MEF2C -0.086 0.22 0.37 2 -0.42 102 104
MEF2A -0.088 0.23 0.37 1 -0.43 101 102
EIF4EBP1 -0.12 0.27 0.34 2 -0.52 102 104
KRT19 -0.22 0.37 0.38 5 -0.57 160 165
ELK4 -0.076 0.21 0.38 3 -0.41 94 97
ATF6 -0.073 0.21 0.37 4 -0.4 93 97
ATF1 -0.11 0.25 0.34 2 -0.47 103 105
p38alpha-beta/MAPKAPK2 -0.076 0.24 -10000 0 -0.44 92 92
p38alpha-beta/MAPKAPK3 -0.086 0.28 0.38 1 -0.5 95 96
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.057 0.067 -10000 0 -0.41 1 1
Crk/p130 Cas/Paxillin -0.19 0.17 -10000 0 -0.4 96 96
JUN -0.21 0.2 -10000 0 -0.5 84 84
HRAS 0.027 0.017 0.34 1 -10000 0 1
RET51/GFRalpha1/GDNF/GRB10 -0.26 0.27 -10000 0 -0.45 224 224
RAP1A 0.025 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.003 -10000 0 -10000 0 0
RAP1A/GDP 0.019 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.26 0.27 -10000 0 -0.45 228 228
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.009 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.062 0.18 -10000 0 -0.36 95 95
RHOA 0.026 0.003 -10000 0 -10000 0 0
RAP1A/GTP -0.24 0.25 -10000 0 -0.41 220 220
GRB7 0.024 0.078 0.34 6 -0.62 4 10
RET51/GFRalpha1/GDNF -0.26 0.27 -10000 0 -0.45 227 227
MAPKKK cascade -0.24 0.23 -10000 0 -0.41 209 209
BCAR1 0.024 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.065 0.19 -10000 0 -0.36 98 98
lamellipodium assembly -0.16 0.16 -10000 0 -0.37 98 98
RET51/GFRalpha1/GDNF/SHC -0.23 0.26 -10000 0 -0.46 178 178
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
RET9/GFRalpha1/GDNF/SHC -0.063 0.17 -10000 0 -0.34 91 91
RET9/GFRalpha1/GDNF/Shank3 -0.065 0.18 -10000 0 -0.36 97 97
MAPK3 -0.24 0.21 -10000 0 -0.4 214 214
DOK1 0.026 0.001 -10000 0 -10000 0 0
DOK6 -0.065 0.22 0.34 3 -0.59 55 58
PXN 0.026 0.003 -10000 0 -10000 0 0
neurite development -0.25 0.22 -10000 0 -0.53 91 91
DOK5 0.023 0.088 0.34 8 -0.62 5 13
GFRA1 -0.16 0.29 -10000 0 -0.6 107 107
MAPK8 -0.22 0.21 -10000 0 -0.4 148 148
HRAS/GTP -0.26 0.27 -10000 0 -0.45 222 222
tube development -0.057 0.18 -10000 0 -0.34 91 91
MAPK1 -0.24 0.21 -10000 0 -0.4 213 213
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.058 0.14 -10000 0 -0.28 89 89
Rac1/GDP 0.019 0.003 -10000 0 -10000 0 0
SRC 0.03 0.037 0.34 5 -10000 0 5
PDLIM7 0.028 0.029 0.34 3 -10000 0 3
RET51/GFRalpha1/GDNF/Dok6 -0.29 0.3 -10000 0 -0.48 227 227
SHC1 0.02 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.26 0.27 -10000 0 -0.45 228 228
RET51/GFRalpha1/GDNF/Dok5 -0.26 0.28 -10000 0 -0.45 225 225
PRKCA 0.025 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.011 0.23 1 -10000 0 1
CREB1 -0.14 0.19 -10000 0 -0.44 90 90
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.058 0.13 -10000 0 -0.3 72 72
RET51/GFRalpha1/GDNF/Grb7 -0.26 0.27 -10000 0 -0.45 227 227
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.31 0.32 0.34 2 -0.61 195 197
DOK4 0.024 0.007 -10000 0 -10000 0 0
JNK cascade -0.21 0.2 -10000 0 -0.49 84 84
RET9/GFRalpha1/GDNF/FRS2 -0.064 0.19 -10000 0 -0.36 97 97
SHANK3 0.026 0.017 0.34 1 -10000 0 1
RASA1 0.022 0.048 -10000 0 -0.62 2 2
NCK1 0.026 0.001 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.056 0.13 -10000 0 -0.28 71 71
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.21 0.2 -10000 0 -0.35 217 217
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.21 0.21 -10000 0 -0.35 224 224
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.22 0.26 -10000 0 -0.43 173 173
PI3K -0.24 0.26 -10000 0 -0.58 99 99
SOS1 0.026 0.001 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.051 0.18 -10000 0 -0.34 91 91
GRB10 0.026 0.004 -10000 0 -10000 0 0
activation of MAPKK activity -0.15 0.17 -10000 0 -0.43 65 65
RET51/GFRalpha1/GDNF/FRS2 -0.26 0.27 -10000 0 -0.45 226 226
GAB1 0.024 0.007 -10000 0 -10000 0 0
IRS1 0.026 0.002 -10000 0 -10000 0 0
IRS2 0.012 0.088 -10000 0 -0.62 7 7
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.23 0.26 -10000 0 -0.44 179 179
RET51/GFRalpha1/GDNF/PKC alpha -0.25 0.27 -10000 0 -0.45 221 221
GRB2 0.025 0.005 -10000 0 -10000 0 0
PRKACA 0.026 0.004 -10000 0 -10000 0 0
GDNF 0.034 0.061 0.34 14 -10000 0 14
RAC1 0.026 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.26 0.27 -10000 0 -0.45 228 228
Rac1/GTP -0.19 0.2 -10000 0 -0.45 97 97
RET9/GFRalpha1/GDNF -0.083 0.19 0.22 10 -0.38 106 116
GFRalpha1/GDNF -0.099 0.22 0.25 10 -0.44 106 116
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.005 0.004 -10000 0 -10000 0 0
GNB1/GNG2 -0.069 0.18 -10000 0 -0.36 100 100
regulation of S phase of mitotic cell cycle -0.066 0.14 -10000 0 -0.29 97 97
GNAO1 -0.26 0.31 -10000 0 -0.58 174 174
HRAS 0.025 0.017 0.34 1 -10000 0 1
SHBG/T-DHT -0.12 0.18 -10000 0 -0.34 140 140
PELP1 0.021 0.009 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 -0.14 0.15 -10000 0 -0.36 94 94
T-DHT/AR -0.11 0.21 -10000 0 -0.46 98 98
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.003 0.003 -10000 0 -0.007 142 142
GNAI2 0.026 0.003 -10000 0 -10000 0 0
GNAI3 0.025 0.005 -10000 0 -10000 0 0
GNAI1 0.022 0.048 -10000 0 -0.62 2 2
mol:GDP -0.14 0.22 -10000 0 -0.5 99 99
cell proliferation -0.26 0.24 -10000 0 -0.48 173 173
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
FOS -0.42 0.42 -10000 0 -0.84 177 177
mol:Ca2+ -0.037 0.05 -10000 0 -0.088 152 152
MAPK3 -0.2 0.2 -10000 0 -0.49 76 76
MAPK1 -0.12 0.14 -10000 0 -0.33 61 61
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
mol:IP3 -0.002 0.002 -10000 0 -0.004 169 169
cAMP biosynthetic process -0.1 0.17 -10000 0 -0.33 127 127
GNG2 0.022 0.048 -10000 0 -0.62 2 2
potassium channel inhibitor activity -0.002 0.002 -10000 0 -0.004 169 169
HRAS/GTP -0.094 0.16 -10000 0 -0.36 95 95
actin cytoskeleton reorganization 0.033 0.041 -10000 0 -0.48 2 2
SRC 0.029 0.037 0.34 5 -10000 0 5
voltage-gated calcium channel activity -0.002 0.002 -10000 0 -0.004 169 169
PI3K 0.031 0.047 -10000 0 -0.57 2 2
apoptosis 0.24 0.24 0.47 176 -10000 0 176
T-DHT/AR/PELP1 -0.09 0.19 -10000 0 -0.4 98 98
HRAS/GDP -0.13 0.22 -10000 0 -0.48 99 99
CREB1 -0.26 0.26 -10000 0 -0.5 176 176
RAC1-CDC42/GTP 0.042 0.044 -10000 0 -0.49 2 2
AR -0.15 0.28 -10000 0 -0.62 98 98
GNB1 0.024 0.008 -10000 0 -10000 0 0
RAF1 -0.12 0.16 -10000 0 -0.36 94 94
RAC1-CDC42/GDP -0.1 0.22 -10000 0 -0.46 99 99
T-DHT/AR/PELP1/Src -0.076 0.18 -10000 0 -0.37 96 96
MAP2K2 -0.14 0.15 -10000 0 -0.36 93 93
T-DHT/AR/PELP1/Src/PI3K -0.066 0.14 -10000 0 -0.29 97 97
GNAZ 0.16 0.16 0.34 165 -0.62 1 166
SHBG -0.2 0.29 -10000 0 -0.55 140 140
Gi family/GNB1/GNG2/GDP -0.19 0.27 -10000 0 -0.44 167 167
mol:T-DHT -0.001 0.001 -10000 0 -0.005 10 10
RAC1 0.026 0.004 -10000 0 -10000 0 0
GNRH1 0.006 0.016 0.21 2 -10000 0 2
Gi family/GTP -0.13 0.2 -10000 0 -0.36 126 126
CDC42 0.025 0.006 -10000 0 -10000 0 0
Aurora B signaling

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
Condensin I complex 0.17 0.14 0.32 150 -10000 0 150
STMN1 0.1 0.12 0.25 112 -10000 0 112
Aurora B/RasGAP/Survivin 0.2 0.18 0.41 146 -10000 0 146
Chromosomal passenger complex/Cul3 protein complex 0.14 0.13 0.27 157 -0.24 5 162
BIRC5 0.22 0.16 0.35 226 -10000 0 226
DES -0.003 0.25 0.48 2 -0.59 39 41
Aurora C/Aurora B/INCENP 0.11 0.096 0.28 9 -10000 0 9
Aurora B/TACC1 0.09 0.093 0.21 111 -10000 0 111
Aurora B/PP2A 0.11 0.1 0.25 29 -10000 0 29
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.04 0.039 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.01 0.009 -10000 0 -10000 0 0
NDC80 0.22 0.21 0.42 179 -10000 0 179
Cul3 protein complex 0.038 0.069 -10000 0 -0.4 8 8
KIF2C 0.23 0.17 0.35 229 -10000 0 229
PEBP1 0.023 0.075 -10000 0 -0.61 5 5
KIF20A 0.23 0.14 0.33 249 -10000 0 249
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.11 0.11 0.24 47 -0.35 2 49
SEPT1 0.026 0.017 0.34 1 -10000 0 1
SMC2 0.027 0.017 0.34 1 -10000 0 1
SMC4 0.029 0.028 0.34 3 -10000 0 3
NSUN2/NPM1/Nucleolin 0.13 0.21 0.35 108 -0.43 22 130
PSMA3 0.025 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.008 -10000 0 -10000 0 0
H3F3B 0.084 0.086 0.18 102 -10000 0 102
AURKB 0.15 0.15 0.32 160 -10000 0 160
AURKC 0.025 0.005 -10000 0 -10000 0 0
CDCA8 0.18 0.16 0.35 167 -10000 0 167
cytokinesis 0.23 0.23 0.46 165 -0.32 1 166
Aurora B/Septin1 0.24 0.24 0.5 153 -10000 0 153
AURKA 0.1 0.14 0.33 93 -10000 0 93
INCENP 0.038 0.025 0.35 2 -10000 0 2
KLHL13 0.012 0.094 -10000 0 -0.62 8 8
BUB1 0.23 0.14 0.33 248 -10000 0 248
hSgo1/Aurora B/Survivin 0.25 0.23 0.49 158 -10000 0 158
EVI5 0.031 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.28 0.22 0.48 172 -10000 0 172
SGOL1 0.15 0.15 0.34 142 -10000 0 142
CENPA 0.24 0.2 0.39 203 -10000 0 203
NCAPG 0.22 0.15 0.34 230 -10000 0 230
Aurora B/HC8 Proteasome 0.12 0.1 0.25 14 -10000 0 14
NCAPD2 0.029 0.037 0.34 5 -10000 0 5
Aurora B/PP1-gamma 0.12 0.1 -10000 0 -10000 0 0
RHOA 0.026 0.003 -10000 0 -10000 0 0
NCAPH 0.18 0.16 0.34 173 -10000 0 173
NPM1 0.1 0.14 0.29 33 -0.29 1 34
RASA1 0.022 0.048 -10000 0 -0.62 2 2
KLHL9 0.022 0.03 -10000 0 -0.3 3 3
mitotic prometaphase 0.006 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.11 0.1 0.25 14 -10000 0 14
PPP1CC 0.026 0.003 -10000 0 -10000 0 0
Centraspindlin 0.32 0.24 0.52 189 -10000 0 189
RhoA/GDP 0.019 0.002 -10000 0 -10000 0 0
NSUN2 0.097 0.15 0.27 93 -0.55 2 95
MYLK 0.075 0.094 0.19 3 -0.25 7 10
KIF23 0.17 0.16 0.35 163 -10000 0 163
VIM 0.1 0.11 0.22 158 -10000 0 158
RACGAP1 0.078 0.11 0.36 47 -10000 0 47
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.098 0.15 0.27 64 -0.42 4 68
Chromosomal passenger complex 0.26 0.2 0.41 215 -10000 0 215
Chromosomal passenger complex/EVI5 0.24 0.22 0.48 154 -10000 0 154
TACC1 0.022 0.01 -10000 0 -10000 0 0
PPP2R5D 0.024 0.008 -10000 0 -10000 0 0
CUL3 0.026 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Ephrin A reverse 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
MAPKKK cascade -0.044 0.19 0.24 30 -0.39 78 108
EFNA5 -0.09 0.28 0.34 25 -0.62 78 103
FYN -0.057 0.16 0.26 4 -0.36 78 82
neuron projection morphogenesis -0.044 0.19 0.24 30 -0.39 78 108
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.044 0.19 0.24 30 -0.4 78 108
EPHA5 0.028 0.053 0.34 10 -10000 0 10
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

Figure S10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 0.045 0.13 0.34 26 -0.57 9 35
NFATC2 -0.12 0.32 0.57 6 -0.64 78 84
NFATC3 -0.042 0.13 0.3 1 -0.29 57 58
CD40LG -0.48 0.58 0.79 5 -1.1 144 149
ITCH 0.022 0.035 -10000 0 -10000 0 0
CBLB 0.023 0.035 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.27 0.51 0.87 11 -1 77 88
JUNB -0.006 0.14 -10000 0 -0.58 19 19
CaM/Ca2+/Calcineurin A alpha-beta B1 0.028 0.042 -10000 0 -0.32 5 5
T cell anergy -0.004 0.076 -10000 0 -0.44 5 5
TLE4 -0.088 0.23 0.42 1 -0.53 52 53
Jun/NFAT1-c-4/p21SNFT -0.3 0.55 0.78 4 -1 119 123
AP-1/NFAT1-c-4 -0.58 0.78 0.93 7 -1.4 143 150
IKZF1 -0.093 0.25 0.79 1 -0.59 47 48
T-helper 2 cell differentiation -0.23 0.38 0.58 2 -0.85 78 80
AP-1/NFAT1 -0.25 0.34 0.57 7 -0.55 172 179
CALM1 0.029 0.027 -10000 0 -10000 0 0
EGR2 -0.49 0.78 0.82 3 -1.6 118 121
EGR3 -0.43 0.72 0.81 3 -1.3 124 127
NFAT1/FOXP3 -0.053 0.28 0.53 15 -0.51 72 87
EGR1 -0.19 0.3 -10000 0 -0.62 121 121
JUN 0.008 0.088 0.25 1 -0.62 6 7
EGR4 0.025 0.031 0.34 3 -10000 0 3
mol:Ca2+ 0.005 0.022 -10000 0 -10000 0 0
GBP3 -0.11 0.29 0.42 1 -0.59 77 78
FOSL1 0.001 0.13 0.34 3 -0.6 16 19
NFAT1-c-4/MAF/IRF4 -0.34 0.56 0.75 3 -1 133 136
DGKA -0.084 0.23 0.63 2 -0.52 50 52
CREM 0.025 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.32 0.55 0.64 3 -1 124 127
CTLA4 -0.039 0.28 0.53 33 -0.55 42 75
NFAT1-c-4 (dimer)/EGR1 -0.42 0.62 0.74 1 -1.2 132 133
NFAT1-c-4 (dimer)/EGR4 -0.32 0.56 0.65 3 -1 123 126
FOS -0.28 0.32 0.25 1 -0.6 175 176
IFNG -0.14 0.32 0.62 9 -0.74 49 58
T cell activation -0.28 0.37 0.62 2 -0.82 96 98
MAF 0.022 0.034 -10000 0 -0.62 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.24 0.41 0.76 121 -0.71 3 124
TNF -0.38 0.52 0.6 1 -1 133 134
FASLG -0.52 0.79 0.96 3 -1.5 130 133
TBX21 0.02 0.11 0.22 13 -0.62 9 22
BATF3 0.018 0.051 0.34 1 -0.62 2 3
PRKCQ 0.004 0.12 0.37 2 -0.6 14 16
PTPN1 -0.085 0.22 0.42 1 -0.48 69 70
NFAT1-c-4/ICER1 -0.32 0.55 0.64 3 -1 124 127
GATA3 -0.018 0.16 0.34 1 -0.62 25 26
T-helper 1 cell differentiation -0.14 0.31 0.62 9 -0.72 50 59
IL2RA -0.27 0.48 0.82 11 -0.91 93 104
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.081 0.22 -10000 0 -0.53 46 46
E2F1 0.22 0.15 0.34 217 -10000 0 217
PPARG 0.027 0.017 0.34 1 -10000 0 1
SLC3A2 -0.084 0.22 0.45 2 -0.51 50 52
IRF4 -0.076 0.25 0.34 9 -0.62 61 70
PTGS2 -0.53 0.63 0.73 4 -1.2 146 150
CSF2 -0.48 0.57 0.73 4 -1.1 142 146
JunB/Fra1/NFAT1-c-4 -0.32 0.57 0.69 3 -1 127 130
IL4 -0.24 0.4 0.58 2 -0.93 72 74
IL5 -0.48 0.57 0.69 5 -1.1 142 147
IL2 -0.29 0.38 0.62 2 -0.84 96 98
IL3 -0.063 0.098 -10000 0 -0.78 2 2
RNF128 0.017 0.086 -10000 0 -0.71 5 5
NFATC1 -0.24 0.42 0.71 3 -0.76 121 124
CDK4 0.24 0.3 0.65 94 -0.86 1 95
PTPRK -0.081 0.22 0.42 1 -0.52 46 47
IL8 -0.53 0.62 0.72 7 -1.2 155 162
POU2F1 0.021 0.011 -10000 0 -10000 0 0
EPO signaling pathway

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
BCL2L1 -0.075 0.19 -10000 0 -0.44 1 1
CRKL -0.092 0.16 0.26 1 -0.31 126 127
mol:DAG -0.1 0.19 -10000 0 -0.37 110 110
HRAS -0.051 0.15 0.36 2 -10000 0 2
MAPK8 -0.098 0.2 0.32 1 -0.36 122 123
RAP1A -0.091 0.16 0.26 1 -0.31 125 126
GAB1 -0.091 0.16 -10000 0 -0.31 123 123
MAPK14 -0.082 0.18 0.32 1 -0.34 105 106
EPO -0.19 0.32 0.33 12 -0.62 130 142
PLCG1 -0.11 0.19 -10000 0 -0.38 110 110
EPOR/TRPC2/IP3 Receptors 0.003 0.035 -10000 0 -10000 0 0
RAPGEF1 0.026 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.15 0.25 -10000 0 -0.42 152 152
GAB1/SHC/GRB2/SOS1 -0.055 0.14 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.13 0.25 0.26 2 -0.46 130 132
IRS2 -0.096 0.16 0.26 1 -0.31 126 127
STAT1 -0.1 0.19 0.37 1 -0.37 111 112
STAT5B -0.1 0.19 -10000 0 -0.38 109 109
cell proliferation -0.1 0.18 0.34 3 -0.34 114 117
GAB1/SHIP/PIK3R1/SHP2/SHC -0.06 0.14 -10000 0 -10000 0 0
TEC -0.095 0.16 0.26 1 -0.31 128 129
SOCS3 -0.053 0.21 -10000 0 -0.62 44 44
STAT1 (dimer) -0.098 0.19 0.37 1 -0.37 111 112
JAK2 0.002 0.035 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
EPO/EPOR (dimer)/JAK2 -0.064 0.19 0.37 1 -0.32 126 127
EPO/EPOR -0.13 0.25 0.26 2 -0.46 130 132
LYN 0.022 0.01 -10000 0 -10000 0 0
TEC/VAV2 -0.083 0.17 -10000 0 -0.3 126 126
elevation of cytosolic calcium ion concentration 0.003 0.035 -10000 0 -10000 0 0
SHC1 0.02 0.011 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.093 0.2 -10000 0 -0.38 113 113
mol:IP3 -0.1 0.19 -10000 0 -0.37 110 110
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.075 0.17 -10000 0 -0.42 6 6
SH2B3 0.002 0.035 -10000 0 -10000 0 0
NFKB1 -0.08 0.19 0.32 1 -0.34 113 114
EPO/EPOR (dimer)/JAK2/SOCS3 -0.13 0.18 -10000 0 -0.33 142 142
PTPN6 -0.094 0.17 -10000 0 -0.32 126 126
TEC/VAV2/GRB2 -0.074 0.17 -10000 0 -0.3 113 113
EPOR 0.003 0.036 -10000 0 -10000 0 0
INPP5D 0.026 0.003 -10000 0 -10000 0 0
mol:GDP -0.057 0.14 -10000 0 -10000 0 0
SOS1 0.026 0.001 -10000 0 -10000 0 0
PLCG2 0.012 0.083 -10000 0 -0.57 7 7
CRKL/CBL/C3G -0.071 0.16 -10000 0 -0.29 121 121
VAV2 -0.091 0.16 0.26 1 -0.31 125 126
CBL -0.091 0.16 0.26 1 -0.31 126 127
SHC/Grb2/SOS1 -0.062 0.14 -10000 0 -0.29 87 87
STAT5A -0.1 0.19 -10000 0 -0.38 109 109
GRB2 0.025 0.005 -10000 0 -10000 0 0
STAT5 (dimer) -0.078 0.18 0.38 1 -0.34 104 105
LYN/PLCgamma2 0.021 0.066 -10000 0 -0.42 7 7
PTPN11 0.026 0.003 -10000 0 -10000 0 0
BTK -0.097 0.17 0.26 1 -0.31 131 132
BCL2 -0.078 0.2 -10000 0 -0.58 4 4
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.33 0.53 -10000 0 -1 103 103
PCK1 -0.67 0.78 -10000 0 -1.5 167 167
HNF4A -0.39 0.65 -10000 0 -1.3 94 94
KCNJ11 -0.32 0.57 0.74 2 -1.1 96 98
AKT1 -0.13 0.23 0.44 1 -0.45 63 64
response to starvation -0.006 0.025 -10000 0 -0.2 2 2
DLK1 -0.3 0.58 0.81 5 -1.2 81 86
NKX2-1 -0.096 0.23 0.52 6 -0.43 63 69
ACADM -0.34 0.55 -10000 0 -1.1 100 100
TAT -0.68 0.79 -10000 0 -1.5 160 160
CEBPB 0.003 0.042 -10000 0 -10000 0 0
CEBPA -0.002 0.074 0.34 1 -0.65 3 4
TTR -0.4 0.64 -10000 0 -1.4 103 103
PKLR -0.32 0.58 -10000 0 -1.2 92 92
APOA1 -0.47 0.74 -10000 0 -1.5 98 98
CPT1C -0.32 0.54 0.68 1 -1.1 100 101
ALAS1 -0.14 0.3 -10000 0 -1.6 6 6
TFRC -0.27 0.46 -10000 0 -0.93 78 78
FOXF1 -0.035 0.18 -10000 0 -0.54 38 38
NF1 0.027 0.016 -10000 0 -10000 0 0
HNF1A (dimer) 0.01 0.12 -10000 0 -0.42 10 10
CPT1A -0.32 0.54 -10000 0 -1.1 97 97
HMGCS1 -0.33 0.54 -10000 0 -1.1 100 100
NR3C1 -0.078 0.12 -10000 0 -0.28 65 65
CPT1B -0.33 0.54 -10000 0 -1 104 104
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.039 0.082 -10000 0 -0.24 7 7
GCK -0.51 0.68 0.64 3 -1.2 168 171
CREB1 -0.056 0.11 -10000 0 -0.26 40 40
IGFBP1 -0.44 0.65 -10000 0 -1.5 94 94
PDX1 -0.16 0.48 0.74 5 -1.2 41 46
UCP2 -0.33 0.54 -10000 0 -1.1 102 102
ALDOB -0.44 0.69 -10000 0 -1.4 113 113
AFP -0.058 0.3 -10000 0 -0.89 27 27
BDH1 -0.35 0.58 -10000 0 -1.1 102 102
HADH -0.32 0.55 -10000 0 -1.1 97 97
F2 -0.4 0.67 -10000 0 -1.3 93 93
HNF1A 0.01 0.12 -10000 0 -0.42 10 10
G6PC -0.29 0.55 -10000 0 -1.5 61 61
SLC2A2 -0.26 0.57 0.63 1 -1.6 46 47
INS 0.035 0.097 0.31 16 -10000 0 16
FOXA1 0.02 0.16 0.28 1 -0.36 33 34
FOXA3 -0.13 0.25 -10000 0 -0.49 90 90
FOXA2 -0.37 0.66 1 1 -1.2 103 104
ABCC8 -0.3 0.57 0.81 5 -1.1 91 96
ALB -0.18 0.43 -10000 0 -1.1 58 58
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.068 0.075 0.16 1 -0.16 144 145
BUB1B 0.13 0.098 0.22 198 -10000 0 198
PLK1 0.061 0.047 0.12 87 -10000 0 87
PLK1S1 0.037 0.032 0.16 5 -0.15 3 8
KIF2A 0.052 0.044 0.2 3 -10000 0 3
regulation of mitotic centrosome separation 0.061 0.047 0.12 87 -10000 0 87
GOLGA2 0.026 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.28 0.18 0.39 249 -10000 0 249
WEE1 0.073 0.061 0.2 1 -0.51 1 2
cytokinesis 0.19 0.13 0.29 201 -10000 0 201
PP2A-alpha B56 0.16 0.12 -10000 0 -0.49 3 3
AURKA 0.066 0.064 0.16 95 -0.18 1 96
PICH/PLK1 0.16 0.14 0.31 141 -0.21 1 142
CENPE 0.11 0.095 0.21 154 -10000 0 154
RhoA/GTP 0.019 0.002 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.052 0.043 0.23 2 -10000 0 2
PPP2CA 0.025 0.004 -10000 0 -10000 0 0
FZR1 0.026 0.004 -10000 0 -10000 0 0
TPX2 0.053 0.055 0.18 49 -10000 0 49
PAK1 0.024 0.004 -10000 0 -10000 0 0
SPC24 0.17 0.16 0.34 171 -10000 0 171
FBXW11 0.025 0.004 -10000 0 -10000 0 0
CLSPN 0.07 0.1 0.19 114 -0.21 18 132
GORASP1 0.026 0.002 -10000 0 -10000 0 0
metaphase 0 0.003 0.016 6 -0.011 2 8
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.03 0.024 0.054 145 -10000 0 145
G2 phase of mitotic cell cycle 0 0.004 0.016 5 -10000 0 5
STAG2 0.026 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.033 0.031 -10000 0 -0.47 1 1
spindle elongation 0.061 0.047 0.12 87 -10000 0 87
ODF2 0.027 0.005 -10000 0 -10000 0 0
BUB1 0.16 0.13 0.46 1 -0.52 3 4
TPT1 0.019 0.057 -10000 0 -0.17 12 12
CDC25C 0.16 0.084 0.2 265 -0.17 1 266
CDC25B 0.033 0.018 0.35 1 -10000 0 1
SGOL1 0.068 0.075 0.16 144 -0.16 1 145
RHOA 0.026 0.003 -10000 0 -10000 0 0
CCNB1/CDK1 0.12 0.098 0.23 157 -0.27 1 158
CDC14B -0.008 0.078 -10000 0 -0.44 11 11
CDC20 0.24 0.15 0.34 246 -10000 0 246
PLK1/PBIP1 0.053 0.06 0.21 36 -10000 0 36
mitosis -0.001 0.003 0.024 3 -10000 0 3
FBXO5 0.044 0.044 0.14 3 -10000 0 3
CDC2 0.007 0.006 0.014 162 -10000 0 162
NDC80 0.23 0.15 0.34 242 -10000 0 242
metaphase plate congression 0.034 0.066 -10000 0 -0.22 17 17
ERCC6L 0.15 0.13 0.31 127 -0.26 1 128
NLP/gamma Tubulin 0.035 0.026 0.089 13 -10000 0 13
microtubule cytoskeleton organization 0.019 0.057 -10000 0 -0.17 12 12
G2/M transition DNA damage checkpoint -0.002 0.002 0.014 4 -10000 0 4
PPP1R12A 0.027 0.003 -10000 0 -10000 0 0
interphase -0.002 0.002 0.014 4 -10000 0 4
PLK1/PRC1-2 0.29 0.19 0.41 242 -10000 0 242
GRASP65/GM130/RAB1/GTP/PLK1 0.082 0.033 -10000 0 -10000 0 0
RAB1A 0.026 0.002 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.047 0.041 0.11 90 -10000 0 90
mitotic prometaphase 0.003 0.005 0.022 22 -10000 0 22
proteasomal ubiquitin-dependent protein catabolic process 0.082 0.061 -10000 0 -10000 0 0
microtubule-based process 0.2 0.12 0.28 249 -10000 0 249
Golgi organization 0.061 0.047 0.12 87 -10000 0 87
Cohesin/SA2 0.064 0.037 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.039 0.006 -10000 0 -10000 0 0
KIF20A 0.24 0.15 0.34 249 -10000 0 249
APC/C/CDC20 0.2 0.13 0.29 246 -10000 0 246
PPP2R1A 0.025 0.004 -10000 0 -10000 0 0
chromosome segregation 0.041 0.06 0.2 36 -10000 0 36
PRC1 0.18 0.16 0.34 177 -10000 0 177
ECT2 0.081 0.083 0.22 82 -10000 0 82
C13orf34 0.048 0.038 0.1 86 -10000 0 86
NUDC 0.034 0.066 -10000 0 -0.22 17 17
regulation of attachment of spindle microtubules to kinetochore 0.13 0.098 0.21 198 -10000 0 198
spindle assembly 0.048 0.037 0.097 75 -10000 0 75
spindle stabilization 0.037 0.032 0.16 5 -0.15 3 8
APC/C/HCDH1 0.011 0.07 -10000 0 -0.4 10 10
MKLP2/PLK1 0.2 0.12 0.28 249 -10000 0 249
CCNB1 0.17 0.16 0.34 167 -10000 0 167
PPP1CB 0.027 0.002 -10000 0 -10000 0 0
BTRC 0.025 0.005 -10000 0 -10000 0 0
ROCK2 0.039 0.088 -10000 0 -0.4 12 12
TUBG1 0.037 0.028 0.15 2 -0.15 1 3
G2/M transition of mitotic cell cycle 0.089 0.08 0.19 80 -0.27 1 81
MLF1IP 0.027 0.064 0.22 36 -10000 0 36
INCENP 0.028 0.023 0.34 2 -10000 0 2
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.025 0.006 -10000 0 -10000 0 0
EPHB2 0.085 0.13 0.34 72 -0.62 1 73
EFNB1 0.015 0.083 0.22 21 -0.46 7 28
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.012 0.2 0.33 8 -0.35 76 84
Ephrin B2/EPHB1-2 -0.008 0.18 0.23 53 -0.32 79 132
neuron projection morphogenesis -0.029 0.18 0.25 8 -0.32 83 91
Ephrin B1/EPHB1-2/Tiam1 -0.021 0.22 0.35 8 -0.35 93 101
DNM1 0.034 0.11 0.34 21 -0.62 6 27
cell-cell signaling 0.001 0.004 -10000 0 -10000 0 0
MAP2K4 -0.19 0.31 -10000 0 -0.64 111 111
YES1 -0.26 0.42 -10000 0 -0.88 111 111
Ephrin B1/EPHB1-2/NCK2 0 0.2 0.38 8 -0.33 81 89
PI3K -0.17 0.33 -10000 0 -0.66 111 111
mol:GDP -0.022 0.21 0.34 8 -0.35 93 101
ITGA2B 0.031 0.046 0.34 8 -10000 0 8
endothelial cell proliferation 0.033 0.01 -10000 0 -10000 0 0
FYN -0.26 0.42 -10000 0 -0.88 111 111
MAP3K7 -0.2 0.32 -10000 0 -0.68 110 110
FGR -0.26 0.42 -10000 0 -0.88 111 111
TIAM1 -0.009 0.14 -10000 0 -0.6 20 20
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
RGS3 0.025 0.004 -10000 0 -10000 0 0
cell adhesion -0.18 0.32 -10000 0 -0.63 118 118
LYN -0.26 0.42 -10000 0 -0.87 111 111
Ephrin B1/EPHB1-2/Src Family Kinases -0.24 0.39 -10000 0 -0.82 111 111
Ephrin B1/EPHB1-2 -0.22 0.35 -10000 0 -0.73 110 110
SRC -0.25 0.42 -10000 0 -0.88 111 111
ITGB3 -0.024 0.17 -10000 0 -0.62 28 28
EPHB1 -0.11 0.26 -10000 0 -0.61 79 79
EPHB4 0.026 0.017 0.34 1 -10000 0 1
RAC1 0.026 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.033 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.003 0.14 0.25 8 -0.46 28 36
BLK -0.29 0.43 -10000 0 -0.92 111 111
HCK -0.26 0.42 -10000 0 -0.88 111 111
regulation of stress fiber formation 0.002 0.19 0.33 81 -0.37 8 89
MAPK8 -0.2 0.3 -10000 0 -0.61 120 120
Ephrin B1/EPHB1-2/RGS3 0.001 0.19 0.35 8 -0.33 80 88
endothelial cell migration -0.17 0.28 -10000 0 -0.57 111 111
NCK2 0.025 0.037 0.34 1 -0.62 1 2
PTPN13 -0.14 0.32 0.33 2 -0.72 84 86
regulation of focal adhesion formation 0.002 0.19 0.33 81 -0.37 8 89
chemotaxis 0 0.19 0.32 80 -0.34 8 88
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
Rac1/GTP -0.019 0.19 0.3 8 -0.34 79 87
angiogenesis -0.22 0.34 -10000 0 -0.73 111 111
LCK -0.26 0.43 -10000 0 -0.89 111 111
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.042 0.045 0.25 11 -0.46 1 12
Necdin/E2F1 0.15 0.14 0.26 210 -0.37 8 218
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.11 0.24 -10000 0 -0.39 138 138
NGF (dimer)/p75(NTR)/BEX1 -0.24 0.31 -10000 0 -0.49 201 201
NT-4/5 (dimer)/p75(NTR) -0.15 0.24 0.25 3 -0.46 136 139
IKBKB 0.023 0.009 -10000 0 -10000 0 0
AKT1 -0.14 0.2 -10000 0 -0.38 136 136
IKBKG 0.026 0.004 -10000 0 -10000 0 0
BDNF 0.036 0.056 0.34 12 -10000 0 12
MGDIs/NGR/p75(NTR)/LINGO1 -0.094 0.24 -10000 0 -0.39 137 137
FURIN 0.014 0.083 -10000 0 -0.57 7 7
proBDNF (dimer)/p75(NTR)/Sortilin -0.11 0.22 0.43 1 -0.39 134 135
LINGO1 0.075 0.12 0.34 59 -0.62 1 60
Sortilin/TRAF6/NRIF 0.025 0.023 -10000 0 -10000 0 0
proBDNF (dimer) 0.036 0.056 0.34 12 -10000 0 12
NTRK1 0.02 0.026 0.34 2 -10000 0 2
RTN4R 0.018 0.067 -10000 0 -0.62 4 4
neuron apoptosis -0.086 0.24 0.49 1 -0.53 45 46
IRAK1 0.026 0.004 -10000 0 -10000 0 0
SHC1 -0.14 0.21 -10000 0 -0.43 107 107
ARHGDIA 0.025 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.019 0.002 -10000 0 -10000 0 0
Gamma Secretase 0.053 0.036 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.11 0.24 -10000 0 -0.4 137 137
MAGEH1 0.017 0.075 -10000 0 -0.62 5 5
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.11 0.25 0.42 1 -0.4 138 139
Mammalian IAPs/DIABLO 0.069 0.046 -10000 0 -0.36 1 1
proNGF (dimer) -0.005 0.14 -10000 0 -0.62 17 17
MAGED1 0.021 0.058 -10000 0 -0.62 3 3
APP 0.018 0.067 -10000 0 -0.62 4 4
NT-4/5 (dimer) 0.021 0.029 0.34 3 -10000 0 3
ZNF274 0.025 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.11 0.2 -10000 0 -0.37 129 129
NGF -0.005 0.14 -10000 0 -0.62 17 17
cell cycle arrest -0.11 0.2 0.36 2 -0.35 134 136
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.093 0.16 -10000 0 -0.31 108 108
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.12 0.22 -10000 0 -0.4 137 137
NCSTN 0.02 0.011 -10000 0 -10000 0 0
mol:GTP -0.13 0.24 -10000 0 -0.43 137 137
PSENEN 0.026 0.004 -10000 0 -10000 0 0
mol:ceramide -0.14 0.21 -10000 0 -0.39 136 136
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.094 0.16 -10000 0 -0.45 36 36
p75(NTR)/beta APP -0.15 0.24 -10000 0 -0.46 139 139
BEX1 -0.15 0.32 0.34 29 -0.62 111 140
mol:GDP -0.16 0.21 -10000 0 -0.42 139 139
NGF (dimer) -0.11 0.24 -10000 0 -0.4 135 135
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.072 0.23 -10000 0 -0.36 129 129
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
RAC1/GTP -0.11 0.21 -10000 0 -0.37 139 139
MYD88 0.026 0.002 -10000 0 -10000 0 0
CHUK 0.025 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.13 0.24 -10000 0 -0.43 137 137
RHOB -0.006 0.14 -10000 0 -0.62 18 18
RHOA 0.026 0.003 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.16 0.1 0.25 215 -10000 0 215
NT3 (dimer) -0.28 0.32 -10000 0 -0.6 179 179
TP53 -0.12 0.16 0.47 1 -0.33 126 127
PRDM4 -0.14 0.21 -10000 0 -0.4 135 135
BDNF (dimer) -0.075 0.22 0.47 4 -0.36 124 128
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
SORT1 0.035 0.054 0.34 11 -10000 0 11
activation of caspase activity -0.11 0.24 -10000 0 -0.39 138 138
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.11 0.24 -10000 0 -0.4 136 136
RHOC 0.025 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.003 -10000 0 -10000 0 0
MAPK10 -0.15 0.22 0.35 2 -0.43 124 126
DIABLO 0.026 0.003 -10000 0 -10000 0 0
SMPD2 -0.14 0.21 -10000 0 -0.39 136 136
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.02 0.011 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.13 0.25 -10000 0 -0.43 137 137
PSEN1 0.025 0.006 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.036 0.01 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.35 0.36 -10000 0 -0.62 212 212
MAPK8 -0.14 0.21 0.4 1 -0.4 126 127
MAPK9 -0.13 0.2 0.4 1 -0.39 123 124
APAF1 0.026 0.003 -10000 0 -10000 0 0
NTF3 -0.28 0.32 -10000 0 -0.6 179 179
NTF4 0.021 0.029 0.34 3 -10000 0 3
NDN 0.02 0.11 0.34 10 -0.62 8 18
RAC1/GDP 0.019 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.11 0.23 -10000 0 -0.38 139 139
p75 CTF/Sortilin/TRAF6/NRIF 0.066 0.043 -10000 0 -0.36 1 1
RhoA-B-C/GTP -0.13 0.24 -10000 0 -0.43 137 137
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.074 0.21 0.41 1 -0.34 131 132
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.087 0.21 0.42 1 -0.36 134 135
PRKACB 0.024 0.018 -10000 0 -0.3 1 1
proBDNF (dimer)/p75 ECD 0.044 0.036 0.25 11 -10000 0 11
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.035 0.072 0.34 14 -0.46 2 16
BIRC2 0.025 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis -0.11 0.23 0.26 3 -0.38 135 138
BAD -0.15 0.21 0.4 1 -0.41 125 126
RIPK2 0.02 0.011 -10000 0 -10000 0 0
NGFR -0.21 0.31 -10000 0 -0.62 136 136
CYCS -0.13 0.2 -10000 0 -0.38 134 134
ADAM17 0.026 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.1 0.21 -10000 0 -0.4 108 108
BCL2L11 -0.15 0.21 0.4 1 -0.41 125 126
BDNF (dimer)/p75(NTR) -0.14 0.24 0.25 8 -0.46 136 144
PI3K -0.11 0.24 -10000 0 -0.4 137 137
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.1 0.24 -10000 0 -0.4 136 136
NDNL2 0.026 0.003 -10000 0 -10000 0 0
YWHAE 0.022 0.009 -10000 0 -10000 0 0
PRKCI 0.026 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.16 0.27 -10000 0 -0.49 139 139
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.11 0.24 -10000 0 -0.4 138 138
TRAF6 0.024 0.034 -10000 0 -0.62 1 1
RAC1 0.026 0.004 -10000 0 -10000 0 0
PRKCZ -0.001 0.12 -10000 0 -0.52 17 17
PLG -0.071 0.22 -10000 0 -0.58 57 57
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.13 0.22 0.28 2 -0.41 136 138
SQSTM1 0.028 0.029 0.34 3 -10000 0 3
NGFRAP1 -0.001 0.13 0.34 1 -0.62 16 17
CASP3 -0.14 0.2 0.38 1 -0.4 123 124
E2F1 0.21 0.15 0.34 217 -10000 0 217
CASP9 0.025 0.006 -10000 0 -10000 0 0
IKK complex -0.052 0.16 -10000 0 -0.43 31 31
NGF (dimer)/TRKA 0.009 0.095 0.25 2 -0.4 17 19
MMP7 -0.095 0.29 0.34 30 -0.59 86 116
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.092 0.23 -10000 0 -0.38 134 134
MMP3 0.039 0.074 0.34 21 -10000 0 21
APAF-1/Caspase 9 -0.1 0.16 -10000 0 -0.51 15 15
IGF1 pathway

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
NCK2 0.025 0.037 0.34 1 -0.62 1 2
PTK2 0.019 0.012 -10000 0 -10000 0 0
CRKL -0.13 0.17 -10000 0 -0.34 145 145
GRB2/SOS1/SHC 0.038 0.024 -10000 0 -10000 0 0
HRAS 0.027 0.017 0.34 1 -10000 0 1
IRS1/Crk -0.12 0.18 -10000 0 -0.33 144 144
IGF-1R heterotetramer/IGF1/PTP1B -0.12 0.21 -10000 0 -0.38 140 140
AKT1 -0.12 0.15 -10000 0 -0.3 138 138
BAD -0.12 0.14 -10000 0 -0.29 113 113
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.12 0.17 -10000 0 -0.33 144 144
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.12 0.18 -10000 0 -0.34 145 145
RAF1 -0.098 0.14 -10000 0 -0.5 7 7
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.092 0.18 -10000 0 -0.32 140 140
YWHAZ 0.019 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.12 0.2 -10000 0 -0.36 147 147
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
RPS6KB1 -0.12 0.15 -10000 0 -0.3 134 134
GNB2L1 0.025 0.005 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.068 0.13 0.28 1 -0.41 4 5
PXN 0.026 0.003 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
HRAS/GTP -0.082 0.14 -10000 0 -0.3 96 96
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.066 0.16 -10000 0 -0.31 97 97
IGF-1R heterotetramer -0.03 0.12 0.28 4 -0.66 8 12
IGF-1R heterotetramer/IGF1/IRS/Nck -0.11 0.19 -10000 0 -0.34 145 145
Crk/p130 Cas/Paxillin -0.091 0.18 -10000 0 -0.31 141 141
IGF1R -0.03 0.12 0.28 4 -0.66 8 12
IGF1 -0.23 0.32 -10000 0 -0.63 142 142
IRS2/Crk -0.12 0.17 -10000 0 -0.33 139 139
PI3K -0.096 0.19 -10000 0 -0.33 144 144
apoptosis 0.075 0.12 0.4 5 -0.29 1 6
HRAS/GDP 0.02 0.011 0.23 1 -10000 0 1
PRKCD -0.14 0.2 -10000 0 -0.39 138 138
RAF1/14-3-3 E -0.076 0.13 -10000 0 -0.41 7 7
BAD/14-3-3 -0.079 0.12 0.3 1 -0.43 5 6
PRKCZ -0.13 0.16 -10000 0 -0.32 138 138
Crk/p130 Cas/Paxillin/FAK1 -0.075 0.13 -10000 0 -0.43 4 4
PTPN1 0.025 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.15 0.21 -10000 0 -0.4 145 145
BCAR1 0.024 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.082 0.17 -10000 0 -0.34 102 102
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.026 0.001 -10000 0 -10000 0 0
IRS1/NCK2 -0.12 0.18 -10000 0 -0.34 145 145
GRB10 0.026 0.004 -10000 0 -10000 0 0
PTPN11 -0.12 0.17 -10000 0 -0.34 145 145
IRS1 -0.14 0.19 -10000 0 -0.36 147 147
IRS2 -0.13 0.18 -10000 0 -0.34 142 142
IGF-1R heterotetramer/IGF1 -0.17 0.26 -10000 0 -0.48 149 149
GRB2 0.025 0.005 -10000 0 -10000 0 0
PDPK1 -0.12 0.17 -10000 0 -0.31 141 141
YWHAE 0.022 0.009 -10000 0 -10000 0 0
PRKD1 -0.14 0.2 -10000 0 -0.39 143 143
SHC1 0.02 0.011 -10000 0 -10000 0 0
HIF-1-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
PKM2 -0.17 0.43 0.76 9 -0.85 68 77
HDAC7 0.029 0.02 0.34 1 -10000 0 1
HIF1A/ARNT/Cbp/p300/Src-1 -0.26 0.47 0.85 8 -0.82 111 119
SMAD4 0.026 0.005 -10000 0 -10000 0 0
ID2 -0.13 0.47 0.84 3 -0.87 67 70
AP1 -0.2 0.25 -10000 0 -0.45 175 175
ABCG2 -0.18 0.47 0.79 1 -0.9 75 76
HIF1A -0.005 0.12 0.4 2 -0.29 3 5
TFF3 -0.12 0.49 0.97 9 -0.86 69 78
GATA2 0.024 0.054 0.34 2 -0.62 2 4
AKT1 -0.021 0.15 0.4 6 -0.26 27 33
response to hypoxia -0.035 0.14 0.3 18 -0.22 83 101
MCL1 -0.13 0.44 0.84 3 -0.84 63 66
NDRG1 -0.13 0.44 0.88 5 -0.85 62 67
SERPINE1 -0.22 0.53 0.84 3 -0.92 93 96
FECH -0.13 0.47 0.84 3 -0.85 68 71
FURIN -0.14 0.47 0.87 2 -0.87 67 69
NCOA2 -0.051 0.18 -10000 0 -0.62 33 33
EP300 -0.058 0.26 0.54 17 -0.35 110 127
HMOX1 -0.14 0.47 0.85 2 -0.86 71 73
BHLHE40 -0.13 0.47 0.87 2 -0.87 67 69
BHLHE41 -0.13 0.48 0.89 4 -0.87 68 72
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.029 0.13 -10000 0 -10000 0 0
ENG 0.046 0.13 -10000 0 -10000 0 0
JUN 0.014 0.082 -10000 0 -0.62 6 6
RORA -0.13 0.46 0.84 3 -0.85 68 71
ABCB1 -0.17 0.38 -10000 0 -1.1 46 46
TFRC -0.13 0.46 0.84 3 -0.85 67 70
CXCR4 -0.13 0.47 0.87 2 -0.87 67 69
TF -0.15 0.48 0.84 3 -0.87 73 76
CITED2 -0.14 0.46 0.85 2 -0.86 67 69
HIF1A/ARNT -0.21 0.47 0.97 5 -1 59 64
LDHA -0.043 0.077 -10000 0 -0.58 4 4
ETS1 -0.13 0.47 0.84 3 -0.87 64 67
PGK1 -0.13 0.47 0.84 3 -0.87 64 67
NOS2 -0.1 0.48 0.88 8 -0.86 64 72
ITGB2 -0.13 0.47 0.87 2 -0.86 68 70
ALDOA -0.12 0.47 0.87 4 -0.85 67 71
Cbp/p300/CITED2 -0.28 0.55 0.87 6 -0.96 106 112
FOS -0.27 0.31 -10000 0 -0.59 176 176
HK2 -0.11 0.5 0.92 10 -0.88 65 75
SP1 0.012 0.054 -10000 0 -0.25 3 3
GCK -0.45 0.78 0.85 11 -1.4 143 154
HK1 -0.13 0.46 0.83 4 -0.85 67 71
NPM1 -0.13 0.46 0.84 3 -0.86 66 69
EGLN1 -0.13 0.44 0.84 3 -0.84 63 66
CREB1 0.03 0.003 -10000 0 -10000 0 0
PGM1 -0.13 0.47 0.84 3 -0.86 67 70
SMAD3 0.026 0.005 -10000 0 -10000 0 0
EDN1 -0.22 0.35 -10000 0 -0.74 67 67
IGFBP1 -0.21 0.5 0.84 3 -0.91 88 91
VEGFA -0.17 0.42 0.78 9 -0.71 90 99
HIF1A/JAB1 0.004 0.092 0.38 4 -10000 0 4
CP -0.16 0.5 0.84 3 -0.9 80 83
CXCL12 -0.27 0.5 -10000 0 -0.91 101 101
COPS5 0.007 0.032 -10000 0 -10000 0 0
SMAD3/SMAD4 0.038 0.01 -10000 0 -10000 0 0
BNIP3 -0.13 0.46 0.84 3 -0.86 66 69
EGLN3 -0.11 0.51 0.95 14 -0.87 69 83
CA9 -0.18 0.55 0.93 18 -0.89 95 113
TERT -0.049 0.52 0.94 21 -0.86 60 81
ENO1 -0.13 0.46 0.84 3 -0.86 66 69
PFKL -0.13 0.46 0.84 3 -0.85 67 70
NCOA1 0.02 0.02 -10000 0 -10000 0 0
ADM -0.13 0.47 0.84 3 -0.86 66 69
ARNT 0.008 0.095 0.33 2 -10000 0 2
HNF4A -0.022 0.12 -10000 0 -0.33 24 24
ADFP -0.17 0.43 0.76 9 -0.85 68 77
SLC2A1 -0.16 0.44 0.87 10 -0.7 101 111
LEP -0.12 0.48 0.93 11 -0.85 67 78
HIF1A/ARNT/Cbp/p300 -0.26 0.47 0.86 8 -0.85 102 110
EPO -0.42 0.61 0.91 9 -1 156 165
CREBBP -0.063 0.26 0.53 18 -0.36 113 131
HIF1A/ARNT/Cbp/p300/HDAC7 -0.24 0.46 0.84 8 -0.83 100 108
PFKFB3 -0.14 0.47 0.84 3 -0.87 67 70
NT5E -0.14 0.47 0.85 2 -0.87 70 72
TCGA08_retinoblastoma

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
CDKN2B 0.04 0.069 0.35 16 -10000 0 16
CDKN2C 0.005 0.096 0.32 27 -10000 0 27
CDKN2A 0.23 0.15 0.34 238 -10000 0 238
CCND2 -0.097 0.095 -10000 0 -0.26 53 53
RB1 0.11 0.1 0.3 49 -10000 0 49
CDK4 -0.11 0.1 -10000 0 -0.32 37 37
CDK6 -0.11 0.11 -10000 0 -0.33 49 49
G1/S progression -0.1 0.11 0.18 7 -0.3 49 56
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.43 0.72 0.97 2 -1.3 108 110
STAT6 (cleaved dimer) -0.54 0.69 -10000 0 -1.3 130 130
IGHG1 -0.1 0.3 0.65 10 -0.56 17 27
IGHG3 -0.43 0.68 0.81 1 -1.2 126 127
AKT1 -0.2 0.42 0.88 1 -0.8 67 68
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.14 0.36 0.84 1 -0.76 44 45
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.18 0.43 0.8 2 -0.95 36 38
THY1 -0.39 0.78 1.1 15 -1.3 107 122
MYB 0.055 0.094 0.34 36 -10000 0 36
HMGA1 0.04 0.07 0.34 19 -10000 0 19
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.28 0.57 0.82 12 -0.94 105 117
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.18 0.43 0.94 1 -0.97 34 35
SP1 0.038 0.044 0.26 1 -10000 0 1
INPP5D 0.026 0.003 -10000 0 -10000 0 0
SOCS5 0.025 0.05 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.48 0.74 0.9 1 -1.3 124 125
SOCS1 -0.26 0.46 0.79 1 -0.79 110 111
SOCS3 -0.3 0.57 0.86 1 -1.2 78 79
FCER2 -0.37 0.66 1.2 5 -1.2 108 113
PARP14 0.027 0.038 -10000 0 -0.62 1 1
CCL17 -0.43 0.74 1.2 6 -1.3 107 113
GRB2 0.025 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.11 0.33 0.73 3 -0.7 23 26
T cell proliferation -0.47 0.74 1 1 -1.3 121 122
IL4R/JAK1 -0.45 0.72 -10000 0 -1.3 117 117
EGR2 -0.6 0.88 1.1 4 -1.6 140 144
JAK2 0.001 0.085 -10000 0 -0.31 1 1
JAK3 0.018 0.057 0.38 4 -0.6 1 5
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
JAK1 0.011 0.046 -10000 0 -10000 0 0
COL1A2 -0.073 0.32 0.71 7 -1.3 7 14
CCL26 -0.41 0.75 1.2 6 -1.3 104 110
IL4R -0.46 0.8 1.2 8 -1.4 110 118
PTPN6 0.021 0.036 -10000 0 -10000 0 0
IL13RA2 -0.93 0.79 0.96 1 -1.5 216 217
IL13RA1 0.001 0.084 -10000 0 -10000 0 0
IRF4 -0.29 0.66 0.9 4 -1.5 77 81
ARG1 -0.3 0.6 0.66 1 -1.4 69 70
CBL -0.26 0.51 0.75 5 -0.88 104 109
GTF3A 0.045 0.065 0.24 15 -10000 0 15
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
IL13RA1/JAK2 0.011 0.12 0.36 5 -10000 0 5
IRF4/BCL6 -0.28 0.6 0.55 2 -1.4 77 79
CD40LG -0.011 0.14 0.31 6 -0.63 14 20
MAPK14 -0.28 0.56 0.77 4 -0.99 98 102
mitosis -0.18 0.4 0.88 1 -0.75 66 67
STAT6 -0.53 0.99 1.3 13 -1.7 116 129
SPI1 -0.01 0.098 -10000 0 -0.34 18 18
RPS6KB1 -0.17 0.38 0.83 1 -0.72 63 64
STAT6 (dimer) -0.54 0.99 1.3 13 -1.7 116 129
STAT6 (dimer)/PARP14 -0.5 0.79 0.89 4 -1.4 121 125
mast cell activation 0.004 0.026 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.2 0.43 0.79 2 -0.78 74 76
FRAP1 -0.2 0.42 0.88 1 -0.8 69 70
LTA -0.42 0.74 1.2 5 -1.3 101 106
FES 0.017 0.075 -10000 0 -0.62 5 5
T-helper 1 cell differentiation 0.48 0.9 1.5 116 -1.3 13 129
CCL11 -0.41 0.7 0.94 6 -1.3 110 116
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.18 0.41 0.79 2 -0.78 59 61
IL2RG 0.013 0.089 0.34 6 -0.61 5 11
IL10 -0.46 0.79 1.2 4 -1.4 115 119
IRS1 0.026 0.002 -10000 0 -10000 0 0
IRS2 0.012 0.088 -10000 0 -0.62 7 7
IL4 -0.034 0.27 0.82 8 -1.2 2 10
IL5 -0.44 0.72 0.96 2 -1.3 107 109
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.29 0.61 1 13 -1 99 112
COL1A1 -0.11 0.49 0.94 15 -1.3 28 43
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.47 0.74 -10000 0 -1.4 104 104
IL2R gamma/JAK3 0.023 0.09 0.31 7 -0.53 5 12
TFF3 -0.44 0.74 0.97 2 -1.4 105 107
ALOX15 -0.43 0.73 1.2 2 -1.3 106 108
MYBL1 0.025 0.038 0.34 5 -10000 0 5
T-helper 2 cell differentiation -0.34 0.61 0.87 7 -1 117 124
SHC1 0.02 0.011 -10000 0 -10000 0 0
CEBPB -0.005 0.08 -10000 0 -0.28 17 17
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.18 0.42 0.78 2 -0.92 40 42
mol:PI-3-4-5-P3 -0.2 0.42 0.89 1 -0.8 67 68
PI3K -0.21 0.45 0.89 1 -0.87 68 69
DOK2 0.014 0.056 -10000 0 -0.43 5 5
ETS1 0.016 0.056 -10000 0 -0.58 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.097 0.31 0.65 5 -0.68 20 25
ITGB3 -0.48 0.77 0.97 2 -1.4 115 117
PIGR -0.53 0.81 1.2 3 -1.4 129 132
IGHE -0.008 0.1 0.2 10 -0.29 17 27
MAPKKK cascade -0.094 0.31 0.64 5 -0.66 20 25
BCL6 0.024 0.013 -10000 0 -10000 0 0
OPRM1 -0.44 0.72 0.96 2 -1.3 106 108
RETNLB -0.44 0.72 -10000 0 -1.3 104 104
SELP -0.57 0.87 1.2 5 -1.5 140 145
AICDA -0.43 0.68 0.98 3 -1.3 112 115
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.039 0.024 0.25 4 -10000 0 4
VLDLR 0.01 0.2 0.34 40 -0.57 30 70
CRKL 0.025 0.004 -10000 0 -10000 0 0
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
FYN 0.024 0.007 -10000 0 -10000 0 0
ITGA3 0.046 0.088 0.34 26 -0.62 1 27
RELN/VLDLR/Fyn -0.11 0.25 -10000 0 -0.43 129 129
MAPK8IP1/MKK7/MAP3K11/JNK1 0.036 0.098 -10000 0 -0.37 16 16
AKT1 -0.13 0.19 -10000 0 -0.33 149 149
MAP2K7 0.026 0.003 -10000 0 -10000 0 0
RAPGEF1 0.026 0.004 -10000 0 -10000 0 0
DAB1 -0.069 0.22 0.34 1 -0.6 54 55
RELN/LRP8/DAB1 -0.13 0.22 -10000 0 -0.37 156 156
LRPAP1/LRP8 0.055 0.062 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.12 0.22 -10000 0 -0.35 155 155
DAB1/alpha3/beta1 Integrin -0.12 0.23 0.33 6 -0.39 124 130
long-term memory -0.1 0.21 0.35 3 -0.36 119 122
DAB1/LIS1 -0.12 0.24 0.37 3 -0.39 133 136
DAB1/CRLK/C3G -0.12 0.23 0.29 4 -0.39 133 137
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
DAB1/NCK2 -0.12 0.25 0.37 4 -0.4 134 138
ARHGEF2 0.021 0.026 0.34 2 -10000 0 2
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.071 0.11 0.34 55 -10000 0 55
CDK5R1 0.029 0.033 0.34 4 -10000 0 4
RELN -0.18 0.3 0.34 3 -0.61 122 125
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
RELN/LRP8/Fyn -0.085 0.22 -10000 0 -0.38 119 119
GRIN2A/RELN/LRP8/DAB1/Fyn -0.096 0.23 0.41 3 -0.35 145 148
MAPK8 -0.006 0.14 -10000 0 -0.62 18 18
RELN/VLDLR/DAB1 -0.15 0.26 -10000 0 -0.4 169 169
ITGB1 0.025 0.005 -10000 0 -10000 0 0
MAP1B -0.15 0.23 0.26 1 -0.39 155 156
RELN/LRP8 -0.083 0.22 -10000 0 -0.38 117 117
GRIN2B/RELN/LRP8/DAB1/Fyn -0.12 0.22 -10000 0 -0.36 148 148
PI3K 0.034 0.052 -10000 0 -0.64 2 2
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.05 0.06 -10000 0 -0.46 1 1
RAP1A -0.14 0.2 0.34 1 -0.54 34 35
PAFAH1B1 0.022 0.009 -10000 0 -10000 0 0
MAPK8IP1 0.019 0.067 -10000 0 -0.62 4 4
CRLK/C3G 0.037 0.008 -10000 0 -10000 0 0
GRIN2B 0.021 0.006 -10000 0 -10000 0 0
NCK2 0.025 0.037 0.34 1 -0.62 1 2
neuron differentiation -0.081 0.16 -10000 0 -0.4 45 45
neuron adhesion -0.13 0.19 0.37 2 -0.52 31 33
LRP8 0.053 0.09 0.34 33 -10000 0 33
GSK3B -0.13 0.18 -10000 0 -0.47 43 43
RELN/VLDLR/DAB1/Fyn -0.14 0.25 -10000 0 -0.39 164 164
MAP3K11 0.026 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.13 0.2 0.21 1 -0.35 150 151
CDK5 0.025 0.005 -10000 0 -10000 0 0
MAPT 0.13 0.18 0.37 107 -10000 0 107
neuron migration -0.15 0.21 0.37 1 -0.4 119 120
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.081 0.16 -10000 0 -0.4 45 45
RELN/VLDLR -0.075 0.25 0.42 6 -0.39 122 128
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.34 0.39 -10000 0 -0.84 108 108
CRP -0.47 0.55 -10000 0 -1.1 150 150
cell cycle arrest -0.42 0.49 -10000 0 -0.96 134 134
TIMP1 -0.29 0.35 -10000 0 -0.75 101 101
IL6ST -0.16 0.27 -10000 0 -0.63 89 89
Rac1/GDP -0.18 0.25 -10000 0 -0.51 103 103
AP1 -0.13 0.21 -10000 0 -0.57 24 24
GAB2 0.029 0.009 -10000 0 -10000 0 0
TNFSF11 -0.45 0.49 -10000 0 -1 140 140
HSP90B1 -0.021 0.11 -10000 0 -0.89 4 4
GAB1 0.026 0.009 -10000 0 -10000 0 0
MAPK14 -0.17 0.3 -10000 0 -0.75 59 59
AKT1 0.021 0.067 -10000 0 -0.54 3 3
FOXO1 0.018 0.069 -10000 0 -0.51 3 3
MAP2K6 -0.18 0.27 -10000 0 -0.56 89 89
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.22 0.28 -10000 0 -0.59 103 103
MITF -0.16 0.23 -10000 0 -0.49 94 94
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.026 0.004 -10000 0 -10000 0 0
A2M -0.21 0.56 -10000 0 -1.5 59 59
CEBPB 0.029 0.007 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.02 0.14 -10000 0 -0.55 11 11
STAT3 -0.46 0.55 -10000 0 -1.1 134 134
STAT1 -0.002 0.069 -10000 0 -1.1 1 1
CEBPD -0.33 0.41 -10000 0 -0.86 102 102
PIK3CA 0.025 0.034 -10000 0 -0.62 1 1
PI3K 0.036 0.052 -10000 0 -0.64 2 2
JUN 0.015 0.082 -10000 0 -0.62 6 6
PIAS3/MITF -0.14 0.22 -10000 0 -0.48 79 79
MAPK11 -0.18 0.32 -10000 0 -0.83 58 58
STAT3 (dimer)/FOXO1 -0.32 0.38 -10000 0 -0.77 122 122
GRB2/SOS1/GAB family -0.075 0.21 -10000 0 -0.5 41 41
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.14 0.22 -10000 0 -0.45 87 87
GRB2 0.027 0.008 -10000 0 -10000 0 0
JAK2 0.024 0.018 -10000 0 -0.3 1 1
LBP -0.29 0.35 -10000 0 -0.76 95 95
PIK3R1 0.023 0.048 -10000 0 -0.62 2 2
JAK1 0.009 0.029 -10000 0 -10000 0 0
MYC -0.36 0.47 -10000 0 -0.95 113 113
FGG -0.39 0.44 -10000 0 -0.94 118 118
macrophage differentiation -0.42 0.49 -10000 0 -0.96 134 134
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.11 0.22 -10000 0 -0.42 99 99
JUNB -0.35 0.4 -10000 0 -0.87 106 106
FOS -0.27 0.31 -10000 0 -0.59 176 176
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.18 0.24 -10000 0 -0.5 100 100
STAT1/PIAS1 -0.17 0.23 -10000 0 -0.5 84 84
GRB2/SOS1/GAB family/SHP2/PI3K 0.022 0.074 -10000 0 -0.57 3 3
STAT3 (dimer) -0.46 0.55 -10000 0 -1.1 134 134
PRKCD -0.28 0.33 -10000 0 -0.69 106 106
IL6R 0 0.084 -10000 0 -0.62 6 6
SOCS3 -0.2 0.43 -10000 0 -1.2 53 53
gp130 (dimer)/JAK1/JAK1/LMO4 -0.11 0.19 -10000 0 -0.42 91 91
Rac1/GTP -0.2 0.27 -10000 0 -0.55 104 104
HCK 0.005 0.12 -10000 0 -0.62 12 12
MAPKKK cascade 0.003 0.13 -10000 0 -0.65 8 8
bone resorption -0.41 0.44 -10000 0 -0.91 140 140
IRF1 -0.34 0.39 -10000 0 -0.85 104 104
mol:GDP -0.19 0.25 -10000 0 -0.52 103 103
SOS1 0.029 0.008 -10000 0 -10000 0 0
VAV1 -0.19 0.26 -10000 0 -0.53 103 103
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.15 0.3 -10000 0 -0.71 60 60
PTPN11 -0.006 0.088 -10000 0 -0.91 3 3
IL6/IL6RA -0.056 0.17 -10000 0 -0.44 55 55
gp130 (dimer)/TYK2/TYK2/LMO4 -0.088 0.19 -10000 0 -0.41 90 90
gp130 (dimer)/JAK2/JAK2/LMO4 -0.087 0.19 -10000 0 -0.42 89 89
IL6 -0.081 0.22 0.34 7 -0.63 49 56
PIAS3 0.02 0.011 -10000 0 -10000 0 0
PTPRE 0.034 0.058 0.35 2 -0.61 2 4
PIAS1 0.026 0.004 -10000 0 -10000 0 0
RAC1 0.025 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.12 0.19 -10000 0 -0.37 112 112
LMO4 -0.004 0.05 -10000 0 -0.51 2 2
STAT3 (dimer)/PIAS3 -0.4 0.45 -10000 0 -0.92 132 132
MCL1 0.057 0.094 -10000 0 -0.57 1 1
LPA receptor mediated 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
GNB1/GNG2 -0.057 0.2 0.39 2 -0.38 93 95
NF kappa B1 p50/RelA/I kappa B alpha -0.016 0.12 -10000 0 -0.42 7 7
AP1 -0.2 0.27 0.28 6 -0.43 191 197
mol:PIP3 -0.08 0.15 -10000 0 -0.34 83 83
AKT1 -0.044 0.13 -10000 0 -0.41 14 14
PTK2B -0.09 0.18 0.27 2 -0.33 95 97
RHOA -0.008 0.063 -10000 0 -0.37 2 2
PIK3CB 0.026 0.002 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.085 0.26 1 -0.41 5 6
MAGI3 0.025 0.005 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
apoptosis -0.068 0.18 0.3 6 -0.36 89 95
HRAS/GDP 0.02 0.011 0.23 1 -10000 0 1
positive regulation of microtubule depolymerization -0.05 0.16 0.28 3 -0.38 41 44
NF kappa B1 p50/RelA -0.068 0.18 0.26 6 -0.38 56 62
endothelial cell migration -0.098 0.24 0.48 6 -0.46 93 99
ADCY4 -0.17 0.25 0.28 2 -0.5 110 112
ADCY5 -0.23 0.32 0.28 2 -0.52 161 163
ADCY6 -0.18 0.25 0.28 2 -0.52 101 103
ADCY7 -0.18 0.26 0.28 2 -0.43 149 151
ADCY1 -0.28 0.33 0.28 1 -0.54 185 186
ADCY2 -0.17 0.25 0.34 3 -0.42 146 149
ADCY3 -0.17 0.25 0.28 3 -0.42 147 150
ADCY8 -0.16 0.25 0.28 2 -0.46 120 122
ADCY9 -0.18 0.26 0.28 2 -0.53 103 105
GSK3B -0.088 0.17 0.25 2 -0.39 57 59
arachidonic acid secretion -0.19 0.25 0.26 2 -0.43 152 154
GNG2 0.022 0.047 -10000 0 -0.61 2 2
TRIP6 0.022 0.045 -10000 0 -0.34 3 3
GNAO1 -0.26 0.27 0.22 4 -0.47 209 213
HRAS 0.027 0.017 0.34 1 -10000 0 1
NFKBIA -0.034 0.12 0.3 1 -0.48 7 8
GAB1 0.024 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.044 0.28 -10000 0 -0.91 35 35
JUN 0.014 0.082 -10000 0 -0.62 6 6
LPA/LPA2/NHERF2 0.035 0.061 0.22 15 -0.39 3 18
TIAM1 -0.071 0.34 -10000 0 -1.1 35 35
PIK3R1 0.023 0.047 -10000 0 -0.62 2 2
mol:IP3 -0.005 0.083 0.26 1 -0.42 4 5
PLCB3 0.018 0.053 -10000 0 -0.36 3 3
FOS -0.27 0.31 -10000 0 -0.59 176 176
positive regulation of mitosis -0.19 0.25 0.26 2 -0.43 152 154
LPA/LPA1-2-3 -0.037 0.22 0.43 7 -0.38 89 96
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.024 0.007 -10000 0 -10000 0 0
stress fiber formation -0.067 0.18 0.27 5 -0.36 74 79
GNAZ -0.011 0.23 0.22 124 -0.37 90 214
EGFR/PI3K-beta/Gab1 -0.071 0.17 -10000 0 -0.35 83 83
positive regulation of dendritic cell cytokine production -0.038 0.22 0.42 7 -0.38 89 96
LPA/LPA2/MAGI-3 0.039 0.05 0.22 14 -0.39 1 15
ARHGEF1 -0.065 0.17 0.26 2 -0.37 77 79
GNAI2 -0.087 0.2 0.26 6 -0.41 92 98
GNAI3 -0.087 0.2 0.26 6 -0.41 93 99
GNAI1 -0.089 0.2 0.26 6 -0.41 94 100
LPA/LPA3 0.031 0.066 0.24 29 -10000 0 29
LPA/LPA2 0.026 0.055 0.23 15 -0.46 1 16
LPA/LPA1 -0.099 0.23 0.29 8 -0.46 96 104
HB-EGF/EGFR 0.028 0.12 -10000 0 -0.38 21 21
HBEGF 0.035 0.12 0.22 70 -0.46 12 82
mol:DAG -0.005 0.083 0.26 1 -0.42 4 5
cAMP biosynthetic process -0.23 0.28 0.26 2 -0.45 190 192
NFKB1 0.024 0.008 -10000 0 -10000 0 0
SRC 0.03 0.037 0.34 5 -10000 0 5
GNB1 0.024 0.008 -10000 0 -10000 0 0
LYN -0.023 0.13 0.3 1 -0.49 8 9
GNAQ 0.026 0.054 0.25 7 -0.33 1 8
LPAR2 0.037 0.071 0.34 15 -0.62 1 16
LPAR3 0.046 0.088 0.34 30 -10000 0 30
LPAR1 -0.13 0.29 0.39 4 -0.6 93 97
IL8 -0.17 0.28 0.5 7 -0.5 129 136
PTK2 -0.059 0.17 0.3 4 -0.37 67 71
Rac1/GDP 0.019 0.003 -10000 0 -10000 0 0
CASP3 -0.069 0.18 0.32 5 -0.37 89 94
EGFR 0.009 0.1 -10000 0 -0.62 9 9
PLCG1 0.003 0.086 0.26 6 -0.28 9 15
PLD2 -0.064 0.18 0.3 4 -0.36 85 89
G12/G13 -0.047 0.19 0.39 2 -0.38 80 82
PI3K-beta -0.057 0.14 -10000 0 -0.42 19 19
cell migration -0.027 0.11 0.22 4 -0.28 34 38
SLC9A3R2 0.02 0.051 -10000 0 -0.51 3 3
PXN -0.069 0.18 0.27 5 -0.37 74 79
HRAS/GTP -0.2 0.26 0.26 2 -0.45 152 154
RAC1 0.026 0.004 -10000 0 -10000 0 0
MMP9 0.067 0.17 0.34 69 -0.62 10 79
PRKCE 0.025 0.037 0.34 1 -0.62 1 2
PRKCD -0.009 0.083 -10000 0 -0.4 5 5
Gi(beta/gamma) -0.18 0.26 0.28 2 -0.43 149 151
mol:LPA -0.001 0.033 -10000 0 -0.19 6 6
TRIP6/p130 Cas/FAK1/Paxillin -0.059 0.19 0.33 4 -0.4 63 67
MAPKKK cascade -0.19 0.25 0.26 2 -0.43 152 154
contractile ring contraction involved in cytokinesis -0.007 0.064 -10000 0 -0.36 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.029 0.14 0.24 6 -0.33 58 64
GNA15 0.027 0.058 0.26 9 -0.27 2 11
GNA12 0.026 0.004 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
MAPT -0.052 0.16 0.31 2 -0.39 41 43
GNA11 0.018 0.079 0.25 7 -0.32 11 18
Rac1/GTP -0.048 0.3 -10000 0 -0.97 35 35
MMP2 -0.098 0.24 0.48 6 -0.47 93 99
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.088 0.24 -10000 0 -0.62 64 64
GNB1/GNG2 -0.12 0.25 0.3 1 -0.51 75 76
mol:DAG -0.12 0.22 0.28 2 -0.47 73 75
PLCG1 -0.12 0.23 0.28 2 -0.48 73 75
YES1 -0.14 0.24 0.27 2 -0.42 123 125
FZD3 0.008 0.082 -10000 0 -0.48 9 9
FZD6 0.017 0.035 -10000 0 -0.62 1 1
G protein -0.11 0.24 -10000 0 -0.48 73 73
MAP3K7 -0.094 0.18 0.35 1 -0.42 56 57
mol:Ca2+ -0.11 0.22 0.27 2 -0.45 73 75
mol:IP3 -0.12 0.22 0.28 2 -0.47 73 75
NLK 0.009 0.017 -10000 0 -10000 0 0
GNB1 0.024 0.008 -10000 0 -10000 0 0
CAMK2A -0.098 0.2 0.32 2 -0.45 58 60
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.15 0.25 0.29 2 -0.44 126 128
CSNK1A1 0.025 0.004 -10000 0 -10000 0 0
GNAS -0.14 0.24 0.27 2 -0.52 74 76
GO:0007205 -0.12 0.22 0.27 2 -0.46 73 75
WNT6 0.044 0.075 0.34 22 -10000 0 22
WNT4 -0.051 0.26 0.34 36 -0.58 64 100
NFAT1/CK1 alpha -0.16 0.26 0.36 1 -0.5 103 104
GNG2 0.022 0.048 -10000 0 -0.62 2 2
WNT5A -0.036 0.2 0.34 5 -0.61 38 43
WNT11 -0.15 0.29 -10000 0 -0.61 102 102
CDC42 -0.13 0.23 0.28 1 -0.5 72 73
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.15 0.25 0.29 2 -0.44 126 128
FZD6 0.017 0.035 -10000 0 -0.62 1 1
WNT6 0.044 0.075 0.34 22 -10000 0 22
WNT4 -0.051 0.26 0.34 36 -0.58 64 100
FZD3 0.008 0.082 -10000 0 -0.48 9 9
WNT5A -0.036 0.2 0.34 5 -0.61 38 43
WNT11 -0.15 0.29 -10000 0 -0.61 102 102
Endothelins

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
AKT1 -0.02 0.14 0.41 5 -0.47 17 22
PTK2B 0.021 0.011 -10000 0 -10000 0 0
mol:Ca2+ -0.053 0.29 0.56 20 -0.7 27 47
EDN1 -0.01 0.13 0.36 4 -0.58 12 16
EDN3 0.026 0.044 0.34 7 -10000 0 7
EDN2 -0.025 0.18 0.34 5 -0.6 31 36
HRAS/GDP -0.13 0.26 0.43 3 -0.57 68 71
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.067 0.21 0.35 5 -0.43 65 70
ADCY4 0.015 0.13 0.39 2 -0.4 14 16
ADCY5 -0.045 0.19 0.36 3 -0.4 60 63
ADCY6 0.014 0.13 0.36 3 -0.41 14 17
ADCY7 0.012 0.13 0.36 3 -0.4 15 18
ADCY1 -0.11 0.22 0.36 3 -0.39 112 115
ADCY2 0.013 0.13 0.41 5 -0.42 14 19
ADCY3 0.015 0.13 0.36 3 -0.41 15 18
ADCY8 0.011 0.12 0.33 7 -0.4 11 18
ADCY9 0.012 0.13 0.36 3 -0.4 15 18
arachidonic acid secretion -0.23 0.35 0.44 8 -0.55 160 168
ETB receptor/Endothelin-1/Gq/GTP -0.069 0.23 0.3 6 -0.45 72 78
GNAO1 -0.26 0.31 -10000 0 -0.58 174 174
HRAS 0.025 0.017 0.34 1 -10000 0 1
ETA receptor/Endothelin-1/G12/GTP 0 0.14 0.49 5 -0.43 16 21
ETA receptor/Endothelin-1/Gs/GTP 0.017 0.14 0.48 4 -0.42 15 19
mol:GTP 0 0.011 -10000 0 -10000 0 0
COL3A1 -0.035 0.21 0.57 7 -0.61 28 35
EDNRB -0.012 0.16 -10000 0 -0.58 25 25
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.025 0.16 0.41 5 -0.52 22 27
CYSLTR1 -0.031 0.17 0.41 5 -0.58 23 28
SLC9A1 -0.015 0.1 0.3 5 -0.37 15 20
mol:GDP -0.14 0.28 0.42 4 -0.58 77 81
SLC9A3 -0.038 0.32 0.52 10 -0.79 41 51
RAF1 -0.21 0.31 0.38 3 -0.6 103 106
JUN -0.077 0.31 0.57 5 -0.8 33 38
JAK2 -0.022 0.14 0.41 5 -0.47 17 22
mol:IP3 -0.096 0.25 0.38 4 -0.5 77 81
ETA receptor/Endothelin-1 -0.016 0.17 0.57 5 -0.49 22 27
PLCB1 0.031 0.049 0.34 9 -10000 0 9
PLCB2 0.002 0.091 -10000 0 -0.58 8 8
ETA receptor/Endothelin-3 0.009 0.092 0.34 2 -0.38 8 10
FOS -0.46 0.51 -10000 0 -0.97 179 179
Gai/GDP -0.33 0.42 -10000 0 -0.74 179 179
CRK 0.023 0.01 -10000 0 -10000 0 0
mol:Ca ++ -0.097 0.27 0.44 7 -0.63 50 57
BCAR1 0.025 0.008 -10000 0 -10000 0 0
PRKCB1 -0.098 0.24 0.37 4 -0.49 75 79
GNAQ 0.018 0.028 -10000 0 -0.3 1 1
GNAZ 0.16 0.16 0.34 165 -0.62 1 166
GNAL 0.075 0.11 0.34 57 -10000 0 57
Gs family/GDP -0.1 0.26 0.4 6 -0.54 67 73
ETA receptor/Endothelin-1/Gq/GTP -0.057 0.21 0.4 6 -0.42 66 72
MAPK14 -0.066 0.2 0.3 7 -0.46 54 61
TRPC6 -0.058 0.3 0.57 20 -0.76 25 45
GNAI2 0.026 0.003 -10000 0 -10000 0 0
GNAI3 0.025 0.005 -10000 0 -10000 0 0
GNAI1 0.022 0.048 -10000 0 -0.62 2 2
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.072 0.22 0.31 3 -0.44 68 71
ETB receptor/Endothelin-2 -0.031 0.18 0.34 1 -0.47 50 51
ETB receptor/Endothelin-3 0.008 0.13 0.25 7 -0.43 25 32
ETB receptor/Endothelin-1 -0.015 0.18 0.36 9 -0.54 28 37
MAPK3 -0.4 0.46 0.39 1 -0.83 182 183
MAPK1 -0.4 0.46 0.39 1 -0.83 182 183
Rac1/GDP -0.13 0.26 0.43 3 -0.55 72 75
cAMP biosynthetic process -0.062 0.19 0.38 3 -0.44 45 48
MAPK8 -0.091 0.34 0.48 20 -0.76 51 71
SRC 0.03 0.036 0.34 5 -10000 0 5
ETB receptor/Endothelin-1/Gi/GTP -0.082 0.19 0.25 7 -0.34 82 89
p130Cas/CRK/Src/PYK2 -0.12 0.3 0.43 18 -0.62 68 86
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.13 0.26 0.43 3 -0.55 72 75
COL1A2 -0.031 0.22 0.55 14 -0.64 25 39
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.028 0.16 0.39 3 -0.46 36 39
mol:DAG -0.096 0.25 0.38 4 -0.5 77 81
MAP2K2 -0.29 0.36 0.39 1 -0.63 174 175
MAP2K1 -0.3 0.36 0.39 1 -0.63 176 177
EDNRA -0.006 0.12 0.44 4 -0.44 12 16
positive regulation of muscle contraction -0.016 0.12 0.35 5 -0.41 16 21
Gq family/GDP -0.14 0.28 -10000 0 -0.57 85 85
HRAS/GTP -0.15 0.28 0.38 4 -0.56 84 88
PRKCH -0.096 0.24 0.36 5 -0.5 69 74
RAC1 0.026 0.004 -10000 0 -10000 0 0
PRKCA -0.094 0.24 0.36 5 -0.49 70 75
PRKCB -0.12 0.27 0.38 5 -0.54 84 89
PRKCE -0.1 0.24 0.36 4 -0.5 72 76
PRKCD -0.1 0.24 0.37 4 -0.51 70 74
PRKCG -0.099 0.24 0.37 4 -0.51 69 73
regulation of vascular smooth muscle contraction -0.55 0.6 -10000 0 -1.1 178 178
PRKCQ -0.11 0.26 0.36 4 -0.53 72 76
PLA2G4A -0.25 0.38 0.44 8 -0.61 162 170
GNA14 -0.084 0.24 -10000 0 -0.61 60 60
GNA15 0.026 0.043 0.34 2 -0.62 1 3
GNA12 0.026 0.004 -10000 0 -10000 0 0
GNA11 0.009 0.1 -10000 0 -0.59 10 10
Rac1/GTP 0 0.14 0.49 5 -0.43 16 21
MMP1 0.078 0.17 0.41 65 -0.34 1 66
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.014 0.2 0.23 74 -0.37 79 153
cell-cell adhesion 0.12 0.16 0.37 94 -10000 0 94
Ephrin B/EPHB2/RasGAP -0.012 0.18 0.41 1 -0.32 73 74
ITSN1 0.025 0.004 -10000 0 -10000 0 0
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
SHC1 0.02 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.005 0.14 0.22 9 -0.4 38 47
Ephrin B1/EPHB1 -0.059 0.18 -10000 0 -0.4 79 79
HRAS/GDP -0.12 0.2 -10000 0 -0.4 104 104
Ephrin B/EPHB1/GRB7 -0.11 0.24 -10000 0 -0.42 127 127
Endophilin/SYNJ1 -0.046 0.14 -10000 0 -0.32 51 51
KRAS 0.026 0.004 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.11 0.24 -10000 0 -0.42 122 122
endothelial cell migration 0.049 0.039 -10000 0 -0.42 2 2
GRB2 0.025 0.005 -10000 0 -10000 0 0
GRB7 0.024 0.078 0.34 6 -0.62 4 10
PAK1 -0.057 0.14 -10000 0 -0.34 50 50
HRAS 0.027 0.017 0.34 1 -10000 0 1
RRAS -0.045 0.14 -10000 0 -0.33 49 49
DNM1 0.033 0.11 0.34 21 -0.62 6 27
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.13 0.21 -10000 0 -0.4 123 123
lamellipodium assembly -0.12 0.16 -10000 0 -0.37 94 94
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.093 0.16 -10000 0 -0.37 71 71
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
EPHB2 0.085 0.13 0.34 72 -0.62 1 73
EPHB3 -0.032 0.2 0.34 9 -0.62 37 46
EPHB1 -0.11 0.26 -10000 0 -0.62 79 79
EPHB4 0.026 0.017 0.34 1 -10000 0 1
mol:GDP -0.12 0.19 -10000 0 -0.4 92 92
Ephrin B/EPHB2 -0.017 0.17 0.4 1 -0.32 72 73
Ephrin B/EPHB3 -0.074 0.21 0.4 1 -0.4 95 96
JNK cascade -0.044 0.15 0.35 1 -0.34 62 63
Ephrin B/EPHB1 -0.12 0.24 -10000 0 -0.42 124 124
RAP1/GDP -0.096 0.18 -10000 0 -0.38 72 72
EFNB2 0.025 0.006 -10000 0 -10000 0 0
EFNB3 -0.13 0.26 0.34 1 -0.52 105 106
EFNB1 0.024 0.034 -10000 0 -0.62 1 1
Ephrin B2/EPHB1-2 -0.01 0.18 0.23 54 -0.33 80 134
RAP1B 0.026 0.003 -10000 0 -10000 0 0
RAP1A 0.025 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.1 0.22 0.31 1 -0.42 99 100
Rap1/GTP -0.11 0.18 -10000 0 -0.38 95 95
axon guidance -0.015 0.2 0.23 74 -0.37 79 153
MAPK3 -0.089 0.15 -10000 0 -0.4 42 42
MAPK1 -0.089 0.15 -10000 0 -0.4 42 42
Rac1/GDP -0.11 0.18 -10000 0 -0.38 83 83
actin cytoskeleton reorganization -0.1 0.15 -10000 0 -0.34 74 74
CDC42/GDP -0.11 0.18 -10000 0 -0.39 83 83
PI3K 0.054 0.04 -10000 0 -0.42 2 2
EFNA5 -0.09 0.28 0.34 25 -0.62 78 103
Ephrin B2/EPHB4 0.033 0.009 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.038 0.14 0.27 1 -0.29 58 59
CDC42 0.025 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.11 0.18 -10000 0 -0.37 98 98
PTK2 0.15 0.25 0.57 92 -10000 0 92
MAP4K4 -0.045 0.16 0.36 1 -0.35 62 63
SRC 0.03 0.037 0.34 5 -10000 0 5
KALRN 0.023 0.047 -10000 0 -0.62 2 2
Intersectin/N-WASP 0.036 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.091 0.17 0.36 1 -0.4 46 47
MAP2K1 -0.091 0.15 -10000 0 -0.36 66 66
WASL 0.025 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0 0.2 -10000 0 -0.34 80 80
cell migration -0.099 0.19 -10000 0 -0.47 44 44
NRAS 0.025 0.004 -10000 0 -10000 0 0
SYNJ1 -0.047 0.14 -10000 0 -0.33 51 51
PXN 0.026 0.003 -10000 0 -10000 0 0
TF -0.079 0.14 -10000 0 -0.33 63 63
HRAS/GTP -0.092 0.21 0.28 1 -0.39 99 100
Ephrin B1/EPHB1-2 -0.012 0.19 -10000 0 -0.34 80 80
cell adhesion mediated by integrin 0.083 0.15 0.34 81 -0.22 3 84
RAC1 0.026 0.004 -10000 0 -10000 0 0
mol:GTP -0.095 0.22 0.34 1 -0.41 99 100
RAC1-CDC42/GTP -0.14 0.2 -10000 0 -0.41 115 115
RASA1 0.022 0.048 -10000 0 -0.62 2 2
RAC1-CDC42/GDP -0.096 0.18 -10000 0 -0.38 74 74
ruffle organization -0.11 0.18 0.32 1 -0.47 42 43
NCK1 0.026 0.001 -10000 0 -10000 0 0
receptor internalization -0.053 0.14 0.34 1 -0.33 51 52
Ephrin B/EPHB2/KALRN -0.01 0.18 0.41 1 -0.32 73 74
ROCK1 -0.021 0.12 -10000 0 -0.36 38 38
RAS family/GDP -0.11 0.14 -10000 0 -0.34 72 72
Rac1/GTP -0.12 0.18 -10000 0 -0.39 94 94
Ephrin B/EPHB1/Src/Paxillin -0.12 0.19 -10000 0 -0.36 124 124
Signaling events mediated by the Hedgehog family

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
TGFB2 0.087 0.28 0.51 78 -0.63 21 99
IHH 0.054 0.16 0.34 29 -0.6 10 39
SHH Np/Cholesterol/GAS1 -0.053 0.16 0.21 1 -0.39 54 55
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.053 0.15 0.39 54 -0.21 1 55
SMO/beta Arrestin2 0.046 0.23 0.41 11 -0.62 27 38
SMO 0.033 0.24 0.4 29 -0.66 27 56
AKT1 0.035 0.17 0.31 7 -0.68 8 15
ARRB2 0.022 0.01 -10000 0 -10000 0 0
BOC 0.036 0.054 0.34 11 -10000 0 11
ADRBK1 0.025 0.004 -10000 0 -10000 0 0
heart looping 0.034 0.24 0.4 29 -0.65 27 56
STIL 0.074 0.21 0.42 36 -0.55 18 54
DHH N/PTCH2 0.035 0.042 -10000 0 -0.46 2 2
DHH N/PTCH1 0.057 0.21 0.44 17 -0.55 26 43
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
DHH 0.026 0.017 0.34 1 -10000 0 1
PTHLH 0.098 0.31 0.58 72 -0.67 21 93
determination of left/right symmetry 0.034 0.24 0.4 29 -0.65 27 56
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
skeletal system development 0.098 0.31 0.58 72 -0.67 21 93
IHH N/Hhip -0.2 0.28 0.28 2 -0.49 170 172
DHH N/Hhip -0.19 0.24 0.25 2 -0.45 167 169
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.034 0.24 0.4 29 -0.65 27 56
pancreas development -0.26 0.31 0.34 1 -0.6 167 168
HHAT 0.019 0.035 -10000 0 -0.62 1 1
PI3K 0.034 0.052 -10000 0 -0.64 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.093 0.25 0.34 1 -0.61 69 70
somite specification 0.034 0.24 0.4 29 -0.65 27 56
SHH Np/Cholesterol/PTCH1 0.02 0.19 0.39 11 -0.51 26 37
SHH Np/Cholesterol/PTCH2 0.006 0.077 -10000 0 -0.39 11 11
SHH Np/Cholesterol/Megalin -0.027 0.15 0.32 4 -0.37 50 54
SHH -0.004 0.09 0.25 2 -0.49 11 13
catabolic process 0.06 0.24 0.5 27 -0.58 28 55
SMO/Vitamin D3 0.064 0.24 0.44 28 -0.6 25 53
SHH Np/Cholesterol/Hhip -0.15 0.18 0.21 1 -0.37 130 131
LRP2 -0.043 0.24 0.34 24 -0.61 50 74
receptor-mediated endocytosis 0.007 0.24 0.4 20 -0.65 24 44
SHH Np/Cholesterol/BOC 0.012 0.081 0.22 10 -0.35 13 23
SHH Np/Cholesterol/CDO 0.006 0.074 -10000 0 -0.39 11 11
mesenchymal cell differentiation 0.14 0.18 0.37 130 -0.21 1 131
mol:Vitamin D3 0.073 0.22 0.45 27 -0.51 26 53
IHH N/PTCH2 0.046 0.11 0.27 4 -0.42 11 15
CDON 0.025 0.005 -10000 0 -10000 0 0
IHH N/PTCH1 0.076 0.26 0.43 71 -0.59 28 99
Megalin/LRPAP1 -0.018 0.18 -10000 0 -0.46 49 49
PTCH2 0.023 0.053 0.34 2 -0.62 2 4
SHH Np/Cholesterol -0.001 0.072 -10000 0 -0.36 13 13
PTCH1 0.06 0.25 0.5 27 -0.58 28 55
HHIP -0.27 0.32 0.34 1 -0.6 167 168
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.014 0.17 0.43 1 -0.44 45 46
fibroblast growth factor receptor signaling pathway -0.014 0.17 0.43 1 -0.44 45 46
LAMA1 -0.035 0.22 0.34 20 -0.61 44 64
PRNP -0.015 0.16 -10000 0 -0.62 23 23
GPC1/SLIT2 -0.034 0.2 0.26 13 -0.49 53 66
SMAD2 -0.011 0.097 -10000 0 -0.36 25 25
GPC1/PrPc/Cu2+ -0.021 0.16 0.22 1 -0.45 41 42
GPC1/Laminin alpha1 -0.045 0.21 0.26 18 -0.48 65 83
TDGF1 0.059 0.22 0.34 84 -0.62 22 106
CRIPTO/GPC1 0.02 0.2 0.25 75 -0.44 46 121
APP/GPC1 -0.003 0.14 -10000 0 -0.46 29 29
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.006 0.16 -10000 0 -0.38 46 46
FLT1 0.024 0.007 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.02 0.11 -10000 0 -0.4 25 25
SERPINC1 -0.054 0.2 -10000 0 -0.62 42 42
FYN -0.009 0.15 -10000 0 -0.38 46 46
FGR -0.009 0.16 -10000 0 -0.38 48 48
positive regulation of MAPKKK cascade -0.054 0.2 0.33 1 -0.48 54 55
SLIT2 -0.023 0.2 0.34 13 -0.59 35 48
GPC1/NRG -0.18 0.25 0.25 1 -0.43 164 165
NRG1 -0.22 0.29 -10000 0 -0.54 152 152
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.015 0.11 -10000 0 -0.4 20 20
LYN -0.011 0.15 -10000 0 -0.39 41 41
mol:Spermine -0.025 0.12 0.21 1 -0.45 26 27
cell growth -0.014 0.17 0.43 1 -0.44 45 46
BMP signaling pathway 0.018 0.16 0.6 26 -0.34 1 27
SRC -0.002 0.16 0.36 1 -0.38 43 44
TGFBR1 0.026 0.004 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.2 0.34 0.34 33 -0.58 150 183
GPC1 -0.018 0.16 0.34 1 -0.6 26 27
TGFBR1 (dimer) 0.026 0.004 -10000 0 -10000 0 0
VEGFA 0.023 0.009 -10000 0 -10000 0 0
BLK -0.063 0.2 -10000 0 -0.41 78 78
HCK -0.017 0.17 -10000 0 -0.39 54 54
FGF2 -0.007 0.15 0.34 5 -0.6 21 26
FGFR1 0.015 0.082 0.34 3 -0.56 6 9
VEGFR1 homodimer 0.024 0.007 -10000 0 -10000 0 0
TGFBR2 0.026 0.003 -10000 0 -10000 0 0
cell death -0.003 0.14 -10000 0 -0.46 29 29
ATIII/GPC1 -0.058 0.18 -10000 0 -0.44 68 68
PLA2G2A/GPC1 -0.17 0.28 0.25 32 -0.46 162 194
LCK -0.018 0.17 -10000 0 -0.39 54 54
neuron differentiation -0.18 0.25 0.25 1 -0.43 164 165
PrPc/Cu2+ -0.011 0.12 -10000 0 -0.46 23 23
APP 0.018 0.067 -10000 0 -0.62 4 4
TGFBR2 (dimer) 0.026 0.003 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR 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
NFATC1 0.003 0.067 0.4 3 -0.42 4 7
NFATC2 -0.063 0.16 0.3 6 -0.41 63 69
NFATC3 0.008 0.05 0.3 6 -10000 0 6
CD40LG -0.25 0.34 0.82 6 -0.66 117 123
PTGS2 -0.3 0.39 0.76 6 -0.75 130 136
JUNB -0.006 0.14 -10000 0 -0.58 19 19
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.033 0.25 3 -10000 0 3
CaM/Ca2+ 0.012 0.033 0.25 3 -10000 0 3
CALM1 0.021 0.022 -10000 0 -10000 0 0
JUN 0.01 0.086 0.22 1 -0.62 6 7
mol:Ca2+ -0.002 0.016 0.17 1 -10000 0 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.016 0.013 -10000 0 -10000 0 0
FOSL1 0.001 0.13 0.34 3 -0.6 16 19
CREM 0.025 0.005 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.041 0.2 0.67 6 -0.43 34 40
FOS -0.27 0.32 -10000 0 -0.6 174 174
IFNG -0.24 0.34 0.74 10 -0.63 116 126
AP-1/NFAT1-c-4 -0.28 0.42 0.94 6 -0.76 119 125
FASLG -0.23 0.33 0.86 6 -0.62 113 119
NFAT1-c-4/ICER1 -0.051 0.18 0.5 6 -0.37 62 68
IL2RA -0.24 0.35 0.77 10 -0.64 117 127
FKBP12/FK506 0.019 0.003 -10000 0 -10000 0 0
CSF2 -0.25 0.32 0.76 6 -0.63 118 124
JunB/Fra1/NFAT1-c-4 -0.068 0.22 0.52 6 -0.39 85 91
IL4 -0.25 0.32 0.75 6 -0.63 116 122
IL2 -0.069 0.28 -10000 0 -1.1 25 25
IL3 -0.017 0.076 -10000 0 -0.74 3 3
FKBP1A 0.026 0.004 -10000 0 -10000 0 0
BATF3 0.018 0.051 0.34 1 -0.62 2 3
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.021 0.011 -10000 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.18 0.65 1 11 -1.3 69 80
IL23A -0.17 0.63 1.1 10 -1.3 58 68
NF kappa B1 p50/RelA/I kappa B alpha -0.19 0.54 -10000 0 -1.1 70 70
positive regulation of T cell mediated cytotoxicity -0.17 0.69 1.2 13 -1.4 62 75
ITGA3 -0.14 0.6 1.2 11 -1.2 56 67
IL17F -0.083 0.39 0.74 12 -0.73 57 69
IL12B 0.033 0.1 0.43 11 -10000 0 11
STAT1 (dimer) -0.17 0.63 0.87 13 -1.2 68 81
CD4 -0.17 0.63 1 12 -1.3 64 76
IL23 -0.17 0.59 0.94 9 -1.2 58 67
IL23R 0.02 0.27 0.77 10 -1 12 22
IL1B -0.23 0.71 1.1 12 -1.4 77 89
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.1 0.58 1.1 13 -1.1 54 67
TYK2 0.023 0.067 0.29 3 -10000 0 3
STAT4 0 0.13 0.34 1 -0.62 15 16
STAT3 0.026 0.004 -10000 0 -10000 0 0
IL18RAP -0.012 0.15 -10000 0 -0.61 22 22
IL12RB1 0.003 0.14 0.29 3 -0.65 12 15
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
IL12Rbeta1/TYK2 0.015 0.12 0.3 4 -0.5 12 16
IL23R/JAK2 0.029 0.27 0.71 9 -0.96 12 21
positive regulation of chronic inflammatory response -0.17 0.69 1.2 13 -1.4 62 75
natural killer cell activation -0.003 0.017 -10000 0 -0.066 11 11
JAK2 0.034 0.094 0.39 8 -0.33 1 9
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
NFKB1 0.026 0.012 -10000 0 -10000 0 0
RELA 0.028 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.16 0.56 0.94 9 -1.1 58 67
ALOX12B -0.14 0.58 1 13 -1.1 57 70
CXCL1 -0.31 0.75 1.1 14 -1.3 119 133
T cell proliferation -0.17 0.69 1.2 13 -1.4 62 75
NFKBIA 0.028 0.009 -10000 0 -10000 0 0
IL17A -0.039 0.33 0.71 14 -0.59 37 51
PI3K -0.19 0.57 -10000 0 -1.2 70 70
IFNG 0.003 0.075 0.26 16 -0.13 5 21
STAT3 (dimer) -0.17 0.55 -10000 0 -1.1 65 65
IL18R1 -0.072 0.23 -10000 0 -0.61 57 57
IL23/IL23R/JAK2/TYK2/SOCS3 -0.081 0.46 0.84 16 -0.89 52 68
IL18/IL18R -0.042 0.22 -10000 0 -0.46 71 71
macrophage activation -0.005 0.034 0.086 22 -10000 0 22
TNF -0.17 0.64 1.1 13 -1.3 55 68
STAT3/STAT4 -0.19 0.58 -10000 0 -1.2 70 70
STAT4 (dimer) -0.18 0.64 0.88 12 -1.2 70 82
IL18 0.017 0.093 0.33 3 -0.61 7 10
IL19 -0.11 0.57 1 12 -1.1 54 66
STAT5A (dimer) -0.17 0.63 0.88 12 -1.2 68 80
STAT1 0.028 0.023 0.34 2 -10000 0 2
SOCS3 -0.053 0.21 -10000 0 -0.62 44 44
CXCL9 -0.13 0.6 1.1 15 -1.2 57 72
MPO -0.15 0.59 1 11 -1.2 59 70
positive regulation of humoral immune response -0.17 0.69 1.2 13 -1.4 62 75
IL23/IL23R/JAK2/TYK2 -0.2 0.78 1.2 13 -1.5 62 75
IL6 -0.23 0.68 1 10 -1.3 83 93
STAT5A 0.027 0.017 0.34 1 -10000 0 1
IL2 0.016 0.034 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.003 0.017 -10000 0 -0.066 11 11
CD3E -0.15 0.6 1 12 -1.2 57 69
keratinocyte proliferation -0.17 0.69 1.2 13 -1.4 62 75
NOS2 -0.12 0.58 1 15 -1.1 56 71
Syndecan-1-mediated signaling events

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
TGFB1 0.029 0.033 0.34 4 -10000 0 4
CCL5 0.013 0.097 0.34 2 -0.62 8 10
SDCBP 0.021 0.01 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.017 0.19 0.34 13 -0.46 29 42
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.008 0.19 0.32 16 -0.49 23 39
Syndecan-1/Syntenin -0.013 0.18 0.31 12 -0.47 23 35
MAPK3 -0.012 0.17 0.29 12 -0.45 23 35
HGF/MET -0.23 0.25 0.25 1 -0.46 194 195
TGFB1/TGF beta receptor Type II 0.029 0.033 0.34 4 -10000 0 4
BSG 0.026 0.017 0.34 1 -10000 0 1
keratinocyte migration -0.008 0.19 0.32 16 -0.48 23 39
Syndecan-1/RANTES -0.015 0.2 0.32 14 -0.47 34 48
Syndecan-1/CD147 -0.002 0.19 0.31 11 -0.47 23 34
Syndecan-1/Syntenin/PIP2 -0.015 0.17 0.29 12 -0.46 23 35
LAMA5 0.03 0.037 0.34 5 -10000 0 5
positive regulation of cell-cell adhesion -0.015 0.17 0.28 12 -0.44 24 36
MMP7 -0.095 0.29 0.34 30 -0.59 86 116
HGF -0.32 0.32 0.34 1 -0.62 194 195
Syndecan-1/CASK -0.026 0.18 0.28 12 -0.44 29 41
Syndecan-1/HGF/MET -0.18 0.28 0.32 10 -0.44 161 171
regulation of cell adhesion -0.018 0.17 0.28 12 -0.44 22 34
HPSE -0.008 0.14 0.34 1 -0.56 21 22
positive regulation of cell migration -0.017 0.19 0.34 13 -0.46 29 42
SDC1 -0.011 0.19 0.34 13 -0.46 26 39
Syndecan-1/Collagen -0.017 0.19 0.34 13 -0.46 29 42
PPIB 0.026 0.003 -10000 0 -10000 0 0
MET 0.023 0.034 -10000 0 -0.62 1 1
PRKACA 0.026 0.004 -10000 0 -10000 0 0
MMP9 0.067 0.17 0.34 69 -0.62 10 79
MAPK1 -0.013 0.17 0.28 13 -0.45 23 36
homophilic cell adhesion -0.017 0.19 0.34 13 -0.46 29 42
MMP1 0.094 0.13 0.34 81 -10000 0 81
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.033 0.029 -10000 0 -0.46 1 1
CRKL -0.13 0.2 -10000 0 -0.67 27 27
mol:PIP3 0.011 0.025 -10000 0 -10000 0 0
AKT1 0.006 0.027 -10000 0 -10000 0 0
PTK2B 0.02 0.011 -10000 0 -10000 0 0
RAPGEF1 -0.13 0.19 -10000 0 -0.63 27 27
RANBP10 0.024 0.007 -10000 0 -10000 0 0
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
HGF/MET/SHIP2 -0.19 0.22 -10000 0 -0.4 193 193
MAP3K5 -0.15 0.22 -10000 0 -0.57 55 55
HGF/MET/CIN85/CBL/ENDOPHILINS -0.16 0.22 -10000 0 -0.37 193 193
AP1 -0.18 0.22 -10000 0 -0.4 169 169
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.02 0.011 -10000 0 -10000 0 0
apoptosis -0.43 0.46 -10000 0 -0.87 184 184
STAT3 (dimer) -0.13 0.17 -10000 0 -0.37 59 59
GAB1/CRKL/SHP2/PI3K -0.11 0.2 -10000 0 -0.61 27 27
INPP5D 0.026 0.003 -10000 0 -10000 0 0
CBL/CRK -0.12 0.19 -10000 0 -0.62 27 27
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.026 0.004 -10000 0 -10000 0 0
PTEN 0.023 0.025 -10000 0 -0.3 2 2
ELK1 0.008 0.11 0.35 21 -0.24 1 22
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.081 0.1 -10000 0 -0.29 25 25
PAK1 0.006 0.032 -10000 0 -10000 0 0
HGF/MET/RANBP10 -0.19 0.22 -10000 0 -0.4 194 194
HRAS -0.15 0.18 -10000 0 -0.49 19 19
DOCK1 -0.14 0.2 -10000 0 -0.63 31 31
GAB1 -0.14 0.21 -10000 0 -0.68 29 29
CRK -0.13 0.2 -10000 0 -0.66 27 27
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.25 0.27 -10000 0 -0.5 190 190
JUN 0.015 0.082 -10000 0 -0.62 6 6
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.11 0.12 -10000 0 -0.22 193 193
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
cell morphogenesis -0.15 0.19 -10000 0 -0.44 56 56
GRB2/SHC -0.059 0.11 -10000 0 -0.31 5 5
FOS -0.27 0.31 -10000 0 -0.59 176 176
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.008 0.11 0.34 21 -0.23 1 22
HGF/MET/MUC20 -0.2 0.22 0.22 1 -0.4 194 195
cell migration -0.056 0.11 -10000 0 -0.3 5 5
GRB2 0.025 0.005 -10000 0 -10000 0 0
CBL 0.025 0.006 -10000 0 -10000 0 0
MET/RANBP10 0.033 0.029 -10000 0 -0.46 1 1
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.14 0.16 -10000 0 -0.31 145 145
MET/MUC20 0.017 0.025 -10000 0 -0.46 1 1
RAP1B -0.12 0.18 -10000 0 -0.59 26 26
RAP1A -0.12 0.18 -10000 0 -0.6 26 26
HGF/MET/RANBP9 -0.18 0.22 -10000 0 -0.37 194 194
RAF1 -0.14 0.18 -10000 0 -0.54 10 10
STAT3 -0.13 0.17 -10000 0 -0.37 59 59
cell proliferation -0.14 0.22 0.34 2 -0.4 102 104
RPS6KB1 -0.031 0.048 -10000 0 -10000 0 0
MAPK3 0.013 0.16 0.78 12 -10000 0 12
MAPK1 0.005 0.14 0.76 9 -10000 0 9
RANBP9 0.024 0.007 -10000 0 -10000 0 0
MAPK8 -0.13 0.21 -10000 0 -0.54 54 54
SRC -0.13 0.15 -10000 0 -0.36 47 47
PI3K -0.085 0.13 -10000 0 -0.31 10 10
MET/Glomulin 0.016 0.031 -10000 0 -0.4 1 1
SOS1 0.026 0.001 -10000 0 -10000 0 0
MAP2K1 -0.14 0.17 -10000 0 -0.51 9 9
MET 0.023 0.034 -10000 0 -0.62 1 1
MAP4K1 -0.13 0.21 -10000 0 -0.66 30 30
PTK2 0.019 0.012 -10000 0 -10000 0 0
MAP2K2 -0.13 0.17 -10000 0 -0.53 8 8
BAD 0.004 0.025 -10000 0 -10000 0 0
MAP2K4 -0.13 0.2 -10000 0 -0.52 53 53
SHP2/GRB2/SOS1/GAB1 -0.11 0.18 -10000 0 -0.59 26 26
INPPL1 0.025 0.004 -10000 0 -10000 0 0
PXN 0.026 0.003 -10000 0 -10000 0 0
SH3KBP1 0.024 0.034 -10000 0 -0.62 1 1
HGS -0.098 0.11 -10000 0 -0.21 177 177
PLCgamma1/PKC 0.019 0.003 -10000 0 -10000 0 0
HGF -0.32 0.32 0.34 1 -0.62 194 195
RASA1 0.022 0.048 -10000 0 -0.62 2 2
NCK1 0.026 0.001 -10000 0 -10000 0 0
PTPRJ 0.026 0.002 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.095 0.14 -10000 0 -0.23 185 185
PDPK1 0.007 0.023 -10000 0 -10000 0 0
HGF/MET/SHIP -0.19 0.22 -10000 0 -0.4 192 192
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.12 0.42 -10000 0 -0.93 72 72
NCK1/PAK1/Dok-R -0.092 0.17 -10000 0 -0.43 73 73
NCK1/Dok-R -0.14 0.43 -10000 0 -1 71 71
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
mol:beta2-estradiol 0.002 0.031 0.27 3 -0.14 2 5
RELA 0.026 0.004 -10000 0 -10000 0 0
SHC1 0.02 0.012 -10000 0 -10000 0 0
Rac/GDP 0.019 0.003 -10000 0 -10000 0 0
F2 -0.029 0.16 0.3 3 -0.61 24 27
TNIP2 0.025 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.12 0.41 -10000 0 -0.94 71 71
FN1 0.024 0.034 -10000 0 -0.62 1 1
PLD2 -0.16 0.44 -10000 0 -1 71 71
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GRB14 0.015 0.082 -10000 0 -0.62 6 6
ELK1 -0.15 0.41 -10000 0 -0.96 73 73
GRB7 0.024 0.078 0.34 6 -0.62 4 10
PAK1 0.025 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.12 0.43 -10000 0 -0.97 71 71
CDKN1A -0.083 0.32 -10000 0 -0.68 72 72
ITGA5 0.026 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.15 0.43 -10000 0 -1 71 71
CRK 0.022 0.009 -10000 0 -10000 0 0
mol:NO -0.071 0.32 0.53 2 -0.68 72 74
PLG -0.21 0.45 -10000 0 -1.1 72 72
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.13 0.38 -10000 0 -0.87 73 73
GRB2 0.025 0.005 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
ANGPT2 -0.043 0.23 0.5 12 -0.74 11 23
BMX -0.19 0.47 -10000 0 -1.1 72 72
ANGPT1 -0.001 0.15 0.49 1 -1.3 3 4
tube development -0.099 0.34 0.52 1 -0.74 70 71
ANGPT4 0.023 0.048 0.34 7 -10000 0 7
response to hypoxia -0.011 0.027 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.16 0.45 -10000 0 -1 71 71
alpha5/beta1 Integrin 0.037 0.007 -10000 0 -10000 0 0
FGF2 -0.009 0.15 0.34 5 -0.62 20 25
STAT5A (dimer) -0.11 0.39 -10000 0 -0.86 70 70
mol:L-citrulline -0.071 0.32 0.53 2 -0.68 72 74
AGTR1 -0.027 0.18 -10000 0 -0.61 32 32
MAPK14 -0.19 0.51 -10000 0 -1.2 73 73
Tie2/SHP2 -0.18 0.46 -10000 0 -1.1 72 72
TEK -0.2 0.5 -10000 0 -1.2 72 72
RPS6KB1 -0.11 0.4 -10000 0 -0.88 73 73
Angiotensin II/AT1 -0.015 0.14 -10000 0 -0.45 32 32
Tie2/Ang1/GRB2 -0.15 0.45 -10000 0 -1 71 71
MAPK3 -0.15 0.4 -10000 0 -0.96 71 71
MAPK1 -0.15 0.4 -10000 0 -0.96 71 71
Tie2/Ang1/GRB7 -0.15 0.45 -10000 0 -1 71 71
NFKB1 0.024 0.008 -10000 0 -10000 0 0
MAPK8 -0.18 0.45 -10000 0 -1.1 71 71
PI3K -0.15 0.48 -10000 0 -1.1 73 73
FES -0.19 0.51 -10000 0 -1.2 74 74
Crk/Dok-R -0.14 0.43 -10000 0 -0.99 71 71
Tie2/Ang1/ABIN2 -0.16 0.45 -10000 0 -1.1 71 71
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.098 0.38 -10000 0 -0.82 72 72
STAT5A 0.027 0.017 0.34 1 -10000 0 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.079 0.41 0.62 2 -0.87 72 74
Tie2/Ang2 -0.16 0.46 -10000 0 -1 70 70
Tie2/Ang1 -0.17 0.47 -10000 0 -1.1 71 71
FOXO1 -0.099 0.38 -10000 0 -0.84 70 70
ELF1 0.005 0.071 -10000 0 -0.65 2 2
ELF2 -0.16 0.44 -10000 0 -1 71 71
mol:Choline -0.15 0.42 -10000 0 -0.99 71 71
cell migration -0.046 0.097 -10000 0 -0.24 73 73
FYN -0.12 0.38 -10000 0 -0.86 70 70
DOK2 0.014 0.056 -10000 0 -0.43 5 5
negative regulation of cell cycle -0.069 0.29 0.51 1 -0.61 72 73
ETS1 0.015 0.053 -10000 0 -0.37 4 4
PXN -0.053 0.35 0.59 2 -0.71 71 73
ITGB1 0.025 0.005 -10000 0 -10000 0 0
NOS3 -0.092 0.36 0.59 1 -0.78 72 73
RAC1 0.026 0.004 -10000 0 -10000 0 0
TNF -0.002 0.12 0.34 2 -0.56 15 17
MAPKKK cascade -0.15 0.42 -10000 0 -0.99 71 71
RASA1 0.022 0.048 -10000 0 -0.62 2 2
Tie2/Ang1/Shc -0.16 0.43 -10000 0 -1 71 71
NCK1 0.026 0.001 -10000 0 -10000 0 0
vasculogenesis -0.057 0.29 0.52 2 -0.6 72 74
mol:Phosphatidic acid -0.15 0.42 -10000 0 -0.99 71 71
mol:Angiotensin II 0.003 0.011 -10000 0 -10000 0 0
mol:NADP -0.071 0.32 0.53 2 -0.68 72 74
Rac1/GTP -0.1 0.37 -10000 0 -0.83 73 73
MMP2 -0.17 0.46 -10000 0 -1.1 71 71
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.015 0.071 -10000 0 -0.41 8 8
PDGFRB 0.03 0.046 0.34 8 -10000 0 8
SPHK1 0.001 0.15 -10000 0 -0.94 6 6
mol:S1P -0.005 0.14 0.28 5 -0.86 6 11
S1P1/S1P/Gi -0.18 0.26 -10000 0 -0.47 131 131
GNAO1 -0.27 0.31 -10000 0 -0.6 166 166
PDGFB-D/PDGFRB/PLCgamma1 -0.15 0.23 0.3 3 -0.45 102 105
PLCG1 -0.17 0.24 -10000 0 -0.44 130 130
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.03 0.046 0.34 8 -10000 0 8
GNAI2 0.012 0.023 -10000 0 -10000 0 0
GNAI3 0.011 0.021 -10000 0 -10000 0 0
GNAI1 0.008 0.051 -10000 0 -0.62 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.01 0.056 -10000 0 -0.38 7 7
S1P1/S1P -0.016 0.13 0.24 4 -0.5 12 16
negative regulation of cAMP metabolic process -0.18 0.26 -10000 0 -0.46 131 131
MAPK3 -0.25 0.33 -10000 0 -0.65 127 127
calcium-dependent phospholipase C activity -0.004 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.002 -10000 0 -10000 0 0
KDR 0.005 0.092 -10000 0 -0.55 9 9
PLCB2 -0.004 0.14 0.29 3 -0.43 16 19
RAC1 0.026 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.03 0.096 -10000 0 -0.43 11 11
receptor internalization -0.016 0.12 0.23 3 -0.46 12 15
PTGS2 -0.39 0.52 -10000 0 -1.1 125 125
Rac1/GTP -0.03 0.095 -10000 0 -0.42 11 11
RHOA 0.026 0.003 -10000 0 -10000 0 0
VEGFA 0.017 0.016 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.18 0.26 -10000 0 -0.46 131 131
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.16 0.17 0.34 165 -0.63 1 166
MAPK1 -0.25 0.33 -10000 0 -0.66 124 124
S1P1/S1P/PDGFB-D/PDGFRB -0.011 0.14 0.3 1 -0.49 12 13
ABCC1 0.03 0.046 0.34 8 -10000 0 8
S1P5 pathway

Figure S35.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S35.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.068 0.15 0.27 79 -10000 0 79
GNAI2 0.026 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.029 0.051 0.22 1 -0.4 5 6
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.26 0.31 -10000 0 -0.58 174 174
RhoA/GTP -0.069 0.15 -10000 0 -0.27 79 79
negative regulation of cAMP metabolic process -0.076 0.16 -10000 0 -0.29 85 85
GNAZ 0.16 0.16 0.34 165 -0.62 1 166
GNAI3 0.025 0.005 -10000 0 -10000 0 0
GNA12 0.026 0.004 -10000 0 -10000 0 0
S1PR5 0.018 0.077 0.34 1 -0.62 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.077 0.16 -10000 0 -0.29 85 85
RhoA/GDP 0.019 0.002 -10000 0 -10000 0 0
RHOA 0.026 0.003 -10000 0 -10000 0 0
GNAI1 0.022 0.048 -10000 0 -0.62 2 2
PLK2 and PLK4 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
PLK2 0.024 0.034 -10000 0 -0.62 1 1
PLK4 0.074 0.12 0.34 58 -10000 0 58
regulation of centriole replication 0.044 0.08 0.22 58 -0.46 1 59
ErbB2/ErbB3 signaling events

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
USP8 -0.01 0.008 -10000 0 -10000 0 0
RAS family/GTP -0.084 0.14 -10000 0 -0.3 31 31
NFATC4 -0.11 0.12 0.3 2 -0.28 43 45
ERBB2IP 0.029 0.004 -10000 0 -10000 0 0
HSP90 (dimer) 0.025 0.006 -10000 0 -10000 0 0
mammary gland morphogenesis -0.13 0.16 -10000 0 -0.34 122 122
JUN -0.065 0.085 0.26 1 -0.46 7 8
HRAS 0.026 0.017 0.34 1 -10000 0 1
DOCK7 -0.14 0.14 -10000 0 -0.32 118 118
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.1 0.17 -10000 0 -0.37 95 95
AKT1 -0.002 0.009 -10000 0 -10000 0 0
BAD -0.007 0.005 -10000 0 -10000 0 0
MAPK10 -0.082 0.096 0.18 1 -0.28 22 23
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.14 0.17 -10000 0 -0.36 122 122
RAF1 -0.087 0.13 -10000 0 -0.31 30 30
ErbB2/ErbB3/neuregulin 2 0.037 0.1 0.32 1 -0.35 8 9
STAT3 0.026 0.072 -10000 0 -0.87 2 2
cell migration -0.085 0.09 -10000 0 -0.24 27 27
mol:PI-3-4-5-P3 -0.003 0.003 -10000 0 -10000 0 0
cell proliferation -0.19 0.22 0.47 2 -0.52 51 53
FOS -0.25 0.27 0.41 2 -0.51 177 179
NRAS 0.025 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.13 0.16 -10000 0 -0.34 122 122
MAPK3 -0.14 0.19 0.43 2 -0.59 17 19
MAPK1 -0.14 0.18 0.43 2 -0.58 14 16
JAK2 -0.14 0.14 -10000 0 -0.32 117 117
NF2 -0.004 0.054 -10000 0 -0.7 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.083 0.14 -10000 0 -0.3 96 96
NRG1 -0.2 0.29 -10000 0 -0.57 136 136
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
MAPK8 -0.15 0.15 -10000 0 -0.32 135 135
MAPK9 -0.074 0.081 0.18 1 -0.25 4 5
ERBB2 -0.03 0.058 -10000 0 -0.48 6 6
ERBB3 0.018 0.058 -10000 0 -0.62 3 3
SHC1 0.019 0.011 -10000 0 -10000 0 0
RAC1 0.026 0.004 -10000 0 -10000 0 0
apoptosis 0.002 0.01 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.07 -10000 0 -0.85 2 2
RNF41 -0.014 0.01 -10000 0 -10000 0 0
FRAP1 -0.005 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.1 0.11 -10000 0 -0.24 114 114
ErbB2/ErbB2/HSP90 (dimer) -0.016 0.054 -10000 0 -0.41 6 6
CHRNA1 -0.097 0.15 0.47 3 -0.4 6 9
myelination -0.1 0.12 0.3 3 -0.38 4 7
PPP3CB -0.13 0.13 -10000 0 -0.3 117 117
KRAS 0.025 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.073 0.14 -10000 0 -0.27 88 88
NRG2 0.089 0.13 0.34 74 -10000 0 74
mol:GDP -0.083 0.14 -10000 0 -0.3 96 96
SOS1 0.026 0.002 -10000 0 -10000 0 0
MAP2K2 -0.089 0.13 0.32 3 -0.31 28 31
SRC 0.03 0.037 0.34 5 -10000 0 5
mol:cAMP -0.002 0.002 -10000 0 -10000 0 0
PTPN11 -0.14 0.14 -10000 0 -0.32 121 121
MAP2K1 -0.17 0.19 -10000 0 -0.48 39 39
heart morphogenesis -0.13 0.16 -10000 0 -0.34 122 122
RAS family/GDP -0.071 0.14 -10000 0 -0.3 31 31
GRB2 0.025 0.005 -10000 0 -10000 0 0
PRKACA -0.002 0.057 -10000 0 -0.74 2 2
CHRNE -0.011 0.033 -10000 0 -0.22 7 7
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
activation of caspase activity 0.002 0.009 -10000 0 -10000 0 0
nervous system development -0.13 0.16 -10000 0 -0.34 122 122
CDC42 0.025 0.006 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.013 0.14 0.49 1 -0.46 16 17
TBX21 -0.18 0.42 0.94 1 -1.1 43 44
B2M 0.019 0.024 -10000 0 -10000 0 0
TYK2 0.005 0.042 -10000 0 -10000 0 0
IL12RB1 -0.016 0.12 -10000 0 -0.65 12 12
GADD45B -0.28 0.55 0.82 1 -1.2 86 87
IL12RB2 -0.004 0.13 0.32 13 -0.6 12 25
GADD45G -0.28 0.53 0.82 1 -1.1 87 88
natural killer cell activation -0.005 0.026 0.21 1 -10000 0 1
RELB 0.026 0.004 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
IL18 0.006 0.1 0.34 3 -0.53 10 13
IL2RA 0.022 0.1 0.34 11 -0.62 7 18
IFNG 0.038 0.065 0.34 16 -10000 0 16
STAT3 (dimer) -0.16 0.36 0.76 1 -0.77 63 64
HLA-DRB5 -0.009 0.011 -10000 0 -0.024 92 92
FASLG -0.15 0.44 1.2 1 -1.2 37 38
NF kappa B2 p52/RelB -0.17 0.4 -10000 0 -0.87 64 64
CD4 -0.047 0.17 -10000 0 -0.61 30 30
SOCS1 0.025 0.058 0.34 4 -0.62 2 6
EntrezGene:6955 -0.014 0.019 -10000 0 -0.032 157 157
CD3D -0.007 0.13 0.33 16 -0.55 12 28
CD3E -0.024 0.12 0.34 1 -0.57 15 16
CD3G -0.014 0.12 0.33 7 -0.58 11 18
IL12Rbeta2/JAK2 0.004 0.11 0.34 2 -0.43 13 15
CCL3 -0.22 0.51 0.94 1 -1.3 50 51
CCL4 -0.2 0.47 0.94 1 -1.3 39 40
HLA-A -0.004 0.015 -10000 0 -0.049 31 31
IL18/IL18R -0.048 0.24 -10000 0 -0.48 71 71
NOS2 -0.15 0.4 0.95 1 -1 36 37
IL12/IL12R/TYK2/JAK2/SPHK2 -0.013 0.13 0.49 1 -0.42 15 16
IL1R1 -0.17 0.41 0.94 1 -1.1 37 38
IL4 0.008 0.039 -10000 0 -10000 0 0
JAK2 0.004 0.045 -10000 0 -0.33 1 1
EntrezGene:6957 -0.013 0.018 -10000 0 -0.032 121 121
TCR/CD3/MHC I/CD8 -0.15 0.43 0.42 4 -1.1 51 55
RAB7A -0.2 0.39 0.74 1 -0.78 84 85
lysosomal transport -0.19 0.37 0.73 1 -0.74 84 85
FOS -0.64 0.72 0.71 1 -1.3 182 183
STAT4 (dimer) -0.17 0.41 0.76 1 -0.82 75 76
STAT5A (dimer) -0.16 0.41 0.64 4 -0.88 62 66
GZMA -0.18 0.43 1.1 1 -1.1 40 41
GZMB -0.18 0.43 1.1 1 -1 54 55
HLX 0.021 0.011 -10000 0 -10000 0 0
LCK -0.19 0.46 0.94 1 -1 61 62
TCR/CD3/MHC II/CD4 -0.11 0.22 0.26 5 -0.46 65 70
IL2/IL2R 0.023 0.15 0.42 2 -0.44 31 33
MAPK14 -0.26 0.5 0.8 1 -0.92 108 109
CCR5 -0.17 0.4 0.81 1 -1.1 38 39
IL1B -0.1 0.25 -10000 0 -0.63 63 63
STAT6 -0.029 0.15 0.65 1 -0.68 5 6
STAT4 0 0.13 0.34 1 -0.62 15 16
STAT3 0.026 0.004 -10000 0 -10000 0 0
STAT1 0.028 0.023 0.34 2 -10000 0 2
NFKB1 0.024 0.008 -10000 0 -10000 0 0
NFKB2 0.025 0.004 -10000 0 -10000 0 0
IL12B 0.003 0.052 0.36 3 -10000 0 3
CD8A -0.016 0.16 0.34 4 -0.63 22 26
CD8B -0.002 0.16 0.34 12 -0.63 18 30
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.013 0.14 0.46 16 -0.49 1 17
IL2RB -0.022 0.17 -10000 0 -0.59 28 28
proteasomal ubiquitin-dependent protein catabolic process -0.15 0.37 0.75 1 -0.76 68 69
IL2RG 0.022 0.085 0.34 6 -0.62 5 11
IL12 0.016 0.076 0.35 2 -10000 0 2
STAT5A 0.027 0.017 0.34 1 -10000 0 1
CD247 -0.002 0.057 0.34 1 -0.63 2 3
IL2 0.019 0.006 -10000 0 -10000 0 0
SPHK2 0.026 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.014 0.072 0.33 12 -10000 0 12
IL12/IL12R/TYK2/JAK2 -0.21 0.53 1.2 1 -1.1 61 62
MAP2K3 -0.28 0.52 0.8 1 -0.99 99 100
RIPK2 0.02 0.011 -10000 0 -10000 0 0
MAP2K6 -0.26 0.5 0.8 1 -0.96 94 95
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.01 0.013 -10000 0 -0.026 124 124
IL18RAP -0.021 0.16 -10000 0 -0.61 23 23
IL12Rbeta1/TYK2 -0.005 0.11 0.29 1 -0.51 12 13
EOMES -0.13 0.44 -10000 0 -1.4 41 41
STAT1 (dimer) -0.14 0.35 0.75 2 -0.78 55 57
T cell proliferation -0.14 0.32 0.67 1 -0.62 76 77
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.08 0.23 -10000 0 -0.62 56 56
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.21 0.34 -10000 0 -0.68 100 100
ATF2 -0.24 0.44 0.74 1 -0.87 97 98
Thromboxane A2 receptor 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
TGM2 0.018 0.067 -10000 0 -0.62 4 4
GNB1/GNG2 -0.065 0.087 -10000 0 -0.19 109 109
AKT1 -0.047 0.14 0.34 7 -0.37 14 21
EGF 0.093 0.13 0.34 83 -10000 0 83
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.031 0.12 -10000 0 -0.36 21 21
mol:Ca2+ -0.062 0.17 0.4 7 -0.34 44 51
LYN -0.028 0.11 -10000 0 -0.38 15 15
RhoA/GTP -0.027 0.069 -10000 0 -0.15 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.077 0.19 0.41 7 -0.36 87 94
GNG2 0.022 0.048 -10000 0 -0.62 2 2
ARRB2 0.022 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.046 0.15 -10000 0 -0.46 28 28
G beta5/gamma2 -0.077 0.12 -10000 0 -0.26 107 107
PRKCH -0.078 0.19 0.41 7 -0.37 87 94
DNM1 0.033 0.11 0.34 21 -0.62 6 27
TXA2/TP beta/beta Arrestin3 0.011 0.061 -10000 0 -0.43 2 2
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.007 0.14 -10000 0 -0.55 20 20
G12 family/GTP -0.072 0.15 -10000 0 -0.31 101 101
ADRBK1 0.025 0.004 -10000 0 -10000 0 0
ADRBK2 0.034 0.066 0.34 12 -0.62 1 13
RhoA/GTP/ROCK1 0.034 0.006 -10000 0 -10000 0 0
mol:GDP 0.048 0.15 0.37 37 -0.3 2 39
mol:NADP 0.022 0.048 -10000 0 -0.62 2 2
RAB11A 0.026 0.003 -10000 0 -10000 0 0
PRKG1 -0.004 0.14 0.34 1 -0.62 17 18
mol:IP3 -0.084 0.21 0.43 7 -0.42 54 61
cell morphogenesis 0.034 0.006 -10000 0 -10000 0 0
PLCB2 -0.12 0.28 0.48 2 -0.53 101 103
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.063 0.15 -10000 0 -0.35 58 58
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.038 0.13 -10000 0 -0.37 27 27
RHOA 0.026 0.003 -10000 0 -10000 0 0
PTGIR -0.033 0.18 -10000 0 -0.6 34 34
PRKCB1 -0.083 0.2 0.42 7 -0.38 101 108
GNAQ 0.025 0.017 -10000 0 -0.3 1 1
mol:L-citrulline 0.022 0.048 -10000 0 -0.62 2 2
TXA2/TXA2-R family -0.13 0.28 0.49 2 -0.54 105 107
LCK -0.037 0.12 -10000 0 -0.37 25 25
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.029 0.14 -10000 0 -0.32 53 53
TXA2-R family/G12 family/GDP/G beta/gamma -0.026 0.14 -10000 0 -0.44 32 32
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.026 0.14 -10000 0 -0.4 22 22
MAPK14 -0.039 0.13 0.36 7 -0.27 8 15
TGM2/GTP -0.096 0.23 0.45 7 -0.47 49 56
MAPK11 -0.044 0.13 0.36 7 -0.28 6 13
ARHGEF1 -0.035 0.1 0.28 7 -10000 0 7
GNAI2 0.026 0.003 -10000 0 -10000 0 0
JNK cascade -0.086 0.21 0.44 7 -0.39 105 112
RAB11/GDP 0.026 0.004 -10000 0 -10000 0 0
ICAM1 -0.057 0.16 0.38 7 -0.3 17 24
cAMP biosynthetic process -0.08 0.19 0.4 7 -0.39 49 56
Gq family/GTP/EBP50 -0.03 0.11 -10000 0 -0.24 62 62
actin cytoskeleton reorganization 0.034 0.006 -10000 0 -10000 0 0
SRC -0.027 0.11 -10000 0 -0.36 18 18
GNB5 0.026 0.004 -10000 0 -10000 0 0
GNB1 0.024 0.008 -10000 0 -10000 0 0
EGF/EGFR -0.034 0.12 -10000 0 -0.31 34 34
VCAM1 -0.065 0.18 0.42 7 -0.37 38 45
TP beta/Gq family/GDP/G beta5/gamma2 -0.046 0.15 -10000 0 -0.46 28 28
platelet activation -0.056 0.17 0.43 7 -0.34 19 26
PGI2/IP -0.024 0.14 -10000 0 -0.44 34 34
PRKACA -0.029 0.12 -10000 0 -0.34 44 44
Gq family/GDP/G beta5/gamma2 -0.04 0.13 -10000 0 -0.4 28 28
TXA2/TP beta/beta Arrestin2 -0.008 0.11 0.23 8 -0.51 10 18
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.049 0.14 -10000 0 -0.35 57 57
mol:DAG -0.096 0.23 0.44 7 -0.44 101 108
EGFR 0.01 0.1 -10000 0 -0.62 9 9
TXA2/TP alpha -0.11 0.26 0.48 2 -0.5 90 92
Gq family/GTP -0.042 0.11 -10000 0 -0.26 74 74
YES1 -0.03 0.11 -10000 0 -0.35 19 19
GNAI2/GTP -0.026 0.13 -10000 0 -0.3 52 52
PGD2/DP -0.005 0.1 -10000 0 -0.41 20 20
SLC9A3R1 0.023 0.034 -10000 0 -0.62 1 1
FYN -0.03 0.11 -10000 0 -0.35 19 19
mol:NO 0.022 0.048 -10000 0 -0.62 2 2
GNA15 0.026 0.041 0.34 2 -0.62 1 3
PGK/cGMP 0.011 0.095 -10000 0 -0.4 18 18
RhoA/GDP 0.026 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.016 0.16 -10000 0 -0.44 24 24
NOS3 0.022 0.048 -10000 0 -0.62 2 2
RAC1 0.026 0.004 -10000 0 -10000 0 0
PRKCA -0.073 0.19 0.41 7 -0.36 82 89
PRKCB -0.093 0.21 0.41 7 -0.4 101 108
PRKCE -0.077 0.2 0.41 7 -0.37 82 89
PRKCD -0.086 0.21 0.42 7 -0.39 101 108
PRKCG -0.086 0.21 0.42 7 -0.4 98 105
muscle contraction -0.12 0.26 0.46 7 -0.5 105 112
PRKCZ -0.082 0.19 0.41 7 -0.36 86 93
ARR3 0.02 0.017 0.34 1 -10000 0 1
TXA2/TP beta -0.018 0.15 -10000 0 -0.33 53 53
PRKCQ -0.082 0.2 0.41 7 -0.38 91 98
MAPKKK cascade -0.11 0.24 0.44 6 -0.47 100 106
SELE -0.089 0.21 0.4 7 -0.41 98 105
TP beta/GNAI2/GDP/G beta/gamma -0.013 0.15 -10000 0 -0.36 36 36
ROCK1 0.026 0.003 -10000 0 -10000 0 0
GNA14 -0.078 0.24 -10000 0 -0.6 60 60
chemotaxis -0.15 0.31 0.52 2 -0.62 105 107
GNA12 0.026 0.004 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
GNA11 0.009 0.1 -10000 0 -0.58 10 10
Rac1/GTP 0.019 0.003 -10000 0 -10000 0 0
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.26 0.31 -10000 0 -0.58 174 174
CDC42/GTP -0.066 0.15 -10000 0 -0.26 83 83
PLCG1 -0.07 0.14 0.29 1 -0.27 80 81
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.026 0.003 -10000 0 -10000 0 0
GNAI3 0.025 0.005 -10000 0 -10000 0 0
G12/G13 0.037 0.009 -10000 0 -10000 0 0
cell migration -0.065 0.14 -10000 0 -0.26 83 83
S1PR5 0.018 0.077 0.34 1 -0.62 5 6
S1PR4 0.026 0.024 0.34 1 -0.3 1 2
MAPK3 -0.069 0.14 -10000 0 -0.27 79 79
MAPK1 -0.072 0.15 -10000 0 -0.28 80 80
S1P/S1P5/Gi -0.077 0.16 -10000 0 -0.29 85 85
GNAI1 0.022 0.048 -10000 0 -0.62 2 2
CDC42/GDP 0.018 0.005 -10000 0 -10000 0 0
S1P/S1P5/G12 0.029 0.051 0.22 1 -0.4 5 6
RHOA 0.022 0.041 0.36 1 -10000 0 1
S1P/S1P4/Gi -0.073 0.16 0.2 1 -0.29 82 83
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.16 0.16 0.34 165 -0.62 1 166
S1P/S1P4/G12/G13 0.047 0.019 -10000 0 -10000 0 0
GNA12 0.026 0.004 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
CDC42 0.025 0.006 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 -0.061 0.33 -10000 0 -1.1 33 33
SMARCC2 0.024 0.018 -10000 0 -10000 0 0
SMARCC1 0.024 0.018 -10000 0 -10000 0 0
TBX21 -0.068 0.21 -10000 0 -0.6 25 25
SUMO2 0.013 0.026 -10000 0 -10000 0 0
STAT1 (dimer) 0.032 0.023 0.34 2 -10000 0 2
FKBP4 0.025 0.005 -10000 0 -10000 0 0
FKBP5 0.023 0.008 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.059 0.12 0.31 5 -10000 0 5
PRL -0.016 0.15 0.69 3 -0.64 2 5
cortisol/GR alpha (dimer)/TIF2 0.042 0.31 0.54 51 -0.56 25 76
RELA -0.064 0.13 -10000 0 -0.28 48 48
FGG 0.003 0.32 0.46 28 -0.65 45 73
GR beta/TIF2 0.003 0.19 0.31 22 -0.45 31 53
IFNG -0.066 0.29 0.64 19 -0.6 19 38
apoptosis -0.16 0.37 0.67 6 -0.81 55 61
CREB1 0.042 0.049 -10000 0 -10000 0 0
histone acetylation -0.061 0.14 -10000 0 -0.35 32 32
BGLAP -0.006 0.14 0.52 1 -0.43 5 6
GR/PKAc 0.069 0.12 0.35 5 -10000 0 5
NF kappa B1 p50/RelA -0.12 0.24 0.44 1 -0.41 114 115
SMARCD1 0.024 0.018 -10000 0 -10000 0 0
MDM2 0.041 0.097 0.23 32 -10000 0 32
GATA3 -0.011 0.16 0.35 1 -0.6 25 26
AKT1 0.033 0.042 -10000 0 -10000 0 0
CSF2 -0.05 0.11 -10000 0 -0.48 3 3
GSK3B 0.013 0.027 -10000 0 -10000 0 0
NR1I3 -0.18 0.44 0.62 10 -0.89 79 89
CSN2 0.028 0.21 0.38 21 -0.48 17 38
BRG1/BAF155/BAF170/BAF60A 0.061 0.049 -10000 0 -0.28 2 2
NFATC1 0.018 0.067 -10000 0 -0.62 4 4
POU2F1 0.021 0.015 -10000 0 -10000 0 0
CDKN1A -0.028 0.27 -10000 0 -1.5 10 10
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.013 -10000 0 -10000 0 0
SFN 0.2 0.16 0.34 202 -0.3 2 204
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.15 0.15 0.37 67 -10000 0 67
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.3 0.46 0.67 4 -0.84 140 144
JUN 0.051 0.26 0.56 38 -0.48 19 57
IL4 -0.046 0.15 -10000 0 -0.61 5 5
CDK5R1 0.025 0.035 0.33 4 -10000 0 4
PRKACA 0.026 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.14 0.17 -10000 0 -0.4 77 77
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.066 0.12 0.32 3 -10000 0 3
cortisol/GR alpha (monomer) 0.13 0.35 0.62 70 -0.56 23 93
NCOA2 -0.038 0.18 -10000 0 -0.62 33 33
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.22 0.34 0.32 15 -0.56 167 182
AP-1/NFAT1-c-4 -0.088 0.35 0.61 30 -0.58 50 80
AFP 0.039 0.37 0.67 22 -1.3 13 35
SUV420H1 0.025 0.005 -10000 0 -10000 0 0
IRF1 0.07 0.16 0.5 3 -10000 0 3
TP53 0.021 0.071 -10000 0 -0.48 7 7
PPP5C 0.026 0.004 -10000 0 -10000 0 0
KRT17 -0.052 0.4 0.68 33 -1 21 54
KRT14 0.004 0.2 0.54 30 -0.47 1 31
TBP 0.029 0.017 -10000 0 -10000 0 0
CREBBP 0 0.073 -10000 0 -0.26 12 12
HDAC1 0.024 0.006 -10000 0 -10000 0 0
HDAC2 0.024 0.007 -10000 0 -10000 0 0
AP-1 -0.087 0.35 0.62 30 -0.58 50 80
MAPK14 0.012 0.024 -10000 0 -10000 0 0
MAPK10 -0.018 0.15 0.33 7 -0.53 23 30
MAPK11 0.025 0.064 0.33 13 -10000 0 13
KRT5 -0.045 0.33 0.65 32 -0.62 22 54
interleukin-1 receptor activity 0 0.001 -10000 0 -10000 0 0
NCOA1 0.018 0.032 -10000 0 -10000 0 0
STAT1 0.032 0.023 0.34 2 -10000 0 2
CGA -0.012 0.17 0.53 10 -0.46 4 14
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.02 0.16 0.34 1 -0.45 17 18
MAPK3 0.011 0.025 -10000 0 -10000 0 0
MAPK1 0.012 0.025 -10000 0 -10000 0 0
ICAM1 -0.14 0.25 -10000 0 -0.57 56 56
NFKB1 -0.059 0.13 -10000 0 -0.28 47 47
MAPK8 -0.005 0.25 0.49 32 -0.42 43 75
MAPK9 0.011 0.024 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.18 0.4 0.67 6 -0.88 56 62
BAX -0.008 0.091 -10000 0 -10000 0 0
POMC -0.096 0.25 -10000 0 -0.96 9 9
EP300 0.002 0.073 -10000 0 -0.26 11 11
cortisol/GR alpha (dimer)/p53 0.073 0.28 0.52 46 -0.53 14 60
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.09 0.29 14 -10000 0 14
SGK1 -0.039 0.28 -10000 0 -1.4 12 12
IL13 -0.081 0.28 0.72 2 -0.77 21 23
IL6 -0.25 0.48 0.57 5 -1.1 68 73
PRKACG 0.019 0.004 -10000 0 -10000 0 0
IL5 -0.071 0.24 0.53 2 -0.71 17 19
IL2 -0.1 0.3 0.58 10 -0.73 23 33
CDK5 0.021 0.013 -10000 0 -10000 0 0
PRKACB 0.024 0.018 -10000 0 -0.3 1 1
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
IL8 -0.33 0.55 0.61 8 -1.1 103 111
CDK5R1/CDK5 0.03 0.033 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.068 0.2 0.38 1 -0.41 47 48
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.11 0.28 0.51 62 -0.48 16 78
SMARCA4 0.023 0.02 -10000 0 -10000 0 0
chromatin remodeling 0.062 0.18 0.38 24 -0.43 6 30
NF kappa B1 p50/RelA/Cbp -0.11 0.21 0.39 1 -0.45 56 57
JUN (dimer) 0.051 0.26 0.56 38 -0.48 19 57
YWHAH 0.025 0.004 -10000 0 -10000 0 0
VIPR1 -0.62 0.48 -10000 0 -0.97 237 237
NR3C1 0.072 0.2 0.39 54 -0.37 1 55
NR4A1 -0.07 0.23 -10000 0 -0.6 58 58
TIF2/SUV420H1 -0.016 0.14 -10000 0 -0.46 33 33
MAPKKK cascade -0.16 0.37 0.67 6 -0.81 55 61
cortisol/GR alpha (dimer)/Src-1 0.11 0.32 0.54 65 -0.53 23 88
PBX1 -0.017 0.15 -10000 0 -0.62 22 22
POU1F1 0.021 0.021 0.34 1 -10000 0 1
SELE -0.32 0.53 0.48 2 -1.1 97 99
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.062 0.18 0.38 24 -0.43 6 30
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.11 0.28 0.51 62 -0.48 16 78
mol:cortisol 0.062 0.19 0.34 70 -0.28 23 93
MMP1 0.069 0.28 0.53 55 -0.84 10 65
TCGA08_p53

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
CDKN2A 0.14 0.099 0.21 238 -9999 0 238
TP53 0.036 0.038 -10000 0 -9999 0 0
Senescence 0.036 0.038 -10000 0 -9999 0 0
Apoptosis 0.036 0.038 -10000 0 -9999 0 0
Activated_Oncogenes 0 0 -10000 0 -9999 0 0
MDM2 -0.094 0.066 -10000 0 -9999 0 0
MDM4 0.021 0.011 -10000 0 -9999 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.2 0.51 -10000 0 -1.3 61 61
PLK1 0.43 0.38 0.84 140 -0.6 1 141
CDKN1B 0.21 0.22 0.53 77 -10000 0 77
FOXO3 0.36 0.37 0.78 135 -0.53 6 141
KAT2B 0.1 0.096 0.28 8 -0.58 3 11
FOXO1/SIRT1 -0.058 0.16 0.33 1 -0.39 62 63
CAT 0.29 0.4 0.68 120 -1 16 136
CTNNB1 0.026 0.002 -10000 0 -10000 0 0
AKT1 0.093 0.076 0.28 6 -10000 0 6
FOXO1 -0.042 0.17 -10000 0 -0.4 62 62
MAPK10 0.031 0.088 0.26 2 -0.32 17 19
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
FOXO4 0.054 0.12 -10000 0 -0.5 6 6
response to oxidative stress 0.077 0.071 0.17 111 -10000 0 111
FOXO3A/SIRT1 0.31 0.29 0.61 141 -0.57 5 146
XPO1 0.026 0.002 -10000 0 -10000 0 0
EP300 0.014 0.034 -10000 0 -10000 0 0
BCL2L11 0.12 0.12 -10000 0 -0.63 1 1
FOXO1/SKP2 -0.03 0.16 -10000 0 -0.37 58 58
mol:GDP 0.077 0.071 0.17 110 -10000 0 110
RAN 0.026 0.004 -10000 0 -10000 0 0
GADD45A 0.2 0.27 0.6 14 -0.77 11 25
YWHAQ 0.026 0.002 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.068 0.1 0.3 1 -0.36 4 5
MST1 0.063 0.18 0.28 8 -0.53 25 33
CSNK1D 0.025 0.006 -10000 0 -10000 0 0
CSNK1E 0.025 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.078 0.13 -10000 0 -0.38 12 12
YWHAB 0.026 0.004 -10000 0 -10000 0 0
MAPK8 0.031 0.09 -10000 0 -0.34 17 17
MAPK9 0.047 0.036 -10000 0 -10000 0 0
YWHAG 0.026 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.009 -10000 0 -10000 0 0
YWHAZ 0.019 0.012 -10000 0 -10000 0 0
SIRT1 0.006 0.064 0.4 2 -0.61 2 4
SOD2 0.2 0.25 0.54 65 -0.65 7 72
RBL2 0.21 0.37 0.61 68 -1 12 80
RAL/GDP 0.085 0.05 -10000 0 -10000 0 0
CHUK 0.1 0.076 0.29 9 -10000 0 9
Ran/GTP 0.02 0.007 -10000 0 -10000 0 0
CSNK1G2 0.026 0.004 -10000 0 -10000 0 0
RAL/GTP 0.084 0.049 -10000 0 -10000 0 0
CSNK1G1 0.026 0.003 -10000 0 -10000 0 0
FASLG 0.078 0.3 0.55 3 -1.3 14 17
SKP2 0.025 0.005 -10000 0 -10000 0 0
USP7 0.025 0.007 -10000 0 -10000 0 0
IKBKB 0.095 0.077 0.28 7 -10000 0 7
CCNB1 0.41 0.38 0.83 140 -0.6 1 141
FOXO1-3a-4/beta catenin 0.18 0.22 0.51 61 -0.43 3 64
proteasomal ubiquitin-dependent protein catabolic process -0.029 0.16 -10000 0 -0.37 58 58
CSNK1A1 0.025 0.004 -10000 0 -10000 0 0
SGK1 0.082 0.13 0.28 8 -0.55 10 18
CSNK1G3 0.026 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.037 0.01 -10000 0 -10000 0 0
ZFAND5 0.051 0.11 -10000 0 -0.61 3 3
SFN 0.2 0.16 0.34 202 -0.3 2 204
CDK2 0.002 0.049 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.17 0.14 0.35 88 -0.34 2 90
CREBBP 0.001 0.049 -10000 0 -10000 0 0
FBXO32 0.4 0.37 0.78 136 -1.4 1 137
BCL6 0.29 0.26 0.61 70 -10000 0 70
RALB 0.026 0.003 -10000 0 -10000 0 0
RALA 0.026 0.004 -10000 0 -10000 0 0
YWHAH 0.025 0.004 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.027 0.15 0.33 5 -0.35 34 39
NF kappa B1 p50/RelA/I kappa B alpha 0.036 0.14 0.4 7 -0.47 3 10
alphaV/beta3 Integrin/Osteopontin/Src 0.084 0.16 0.25 121 -0.38 24 145
AP1 -0.14 0.28 0.57 5 -0.63 50 55
ILK 0.017 0.15 0.34 1 -0.37 34 35
bone resorption 0.004 0.16 0.38 2 -0.47 13 15
PTK2B 0.02 0.011 -10000 0 -10000 0 0
PYK2/p130Cas 0.055 0.17 0.37 3 -0.35 34 37
ITGAV 0.03 0.018 0.34 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.024 0.1 0.25 8 -0.46 14 22
alphaV/beta3 Integrin/Osteopontin 0.061 0.19 0.38 5 -0.38 44 49
MAP3K1 0.017 0.15 0.31 3 -0.37 36 39
JUN 0.015 0.082 -10000 0 -0.62 6 6
MAPK3 0.012 0.14 0.39 6 -0.35 34 40
MAPK1 0.011 0.15 0.39 6 -0.35 34 40
Rac1/GDP 0.019 0.003 -10000 0 -10000 0 0
NFKB1 0.024 0.008 -10000 0 -10000 0 0
MAPK8 -0.006 0.17 0.32 3 -0.41 41 44
ITGB3 -0.021 0.17 -10000 0 -0.61 28 28
NFKBIA 0.014 0.14 0.4 7 -0.34 33 40
FOS -0.27 0.31 -10000 0 -0.59 176 176
CD44 0.029 0.066 0.34 8 -0.62 2 10
CHUK 0.025 0.005 -10000 0 -10000 0 0
PLAU 0.004 0.16 0.59 6 -0.54 2 8
NF kappa B1 p50/RelA 0.041 0.14 0.43 6 -0.45 3 9
BCAR1 0.024 0.007 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.006 0.14 0.25 1 -0.46 28 29
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.014 0.16 0.3 2 -0.38 37 39
VAV3 0.008 0.15 0.29 8 -0.37 36 44
MAP3K14 0.018 0.16 0.35 5 -0.37 35 40
ROCK2 0.005 0.12 -10000 0 -0.62 12 12
SPP1 0.1 0.22 0.34 123 -0.61 17 140
RAC1 0.026 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.016 0.14 0.27 1 -0.34 34 35
MMP2 -0.13 0.24 0.57 6 -0.57 49 55
S1P3 pathway

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
PDGFRB 0.032 0.046 0.34 8 -10000 0 8
mol:S1P 0.001 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.053 0.14 -10000 0 -0.24 82 82
GNAO1 -0.26 0.31 -10000 0 -0.59 165 165
S1P/S1P3/G12/G13 0.038 0.066 -10000 0 -0.37 8 8
AKT1 -0.031 0.14 -10000 0 -0.5 22 22
AKT3 -0.033 0.16 -10000 0 -0.86 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.032 0.046 0.34 8 -10000 0 8
GNAI2 0.027 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.006 -10000 0 -10000 0 0
GNAI1 0.023 0.048 -10000 0 -0.62 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.01 0.1 0.34 1 -0.56 11 12
S1PR2 0.02 0.058 -10000 0 -0.62 3 3
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.079 0.18 -10000 0 -0.32 86 86
MAPK3 -0.073 0.16 -10000 0 -0.3 79 79
MAPK1 -0.078 0.17 -10000 0 -0.31 82 82
JAK2 -0.084 0.18 -10000 0 -0.51 23 23
CXCR4 -0.08 0.17 -10000 0 -0.31 85 85
FLT1 0.025 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.003 -10000 0 -10000 0 0
SRC -0.076 0.17 0.3 1 -0.3 80 81
S1P/S1P3/Gi -0.079 0.18 -10000 0 -0.32 86 86
RAC1 0.026 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.071 0.17 -10000 0 -0.47 18 18
VEGFA 0.024 0.012 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.073 0.16 -10000 0 -0.3 83 83
VEGFR1 homodimer/VEGFA homodimer 0.034 0.023 0.26 1 -10000 0 1
RHOA 0.026 0.003 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.044 0.14 -10000 0 -0.31 77 77
GNAQ 0.025 0.017 -10000 0 -0.3 1 1
GNAZ 0.17 0.16 0.34 165 -0.62 1 166
G12/G13 0.037 0.009 -10000 0 -10000 0 0
GNA14 -0.078 0.24 -10000 0 -0.6 60 60
GNA15 0.026 0.041 0.34 2 -0.62 1 3
GNA12 0.026 0.004 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
GNA11 0.009 0.1 -10000 0 -0.58 10 10
Rac1/GTP -0.072 0.17 -10000 0 -0.3 82 82
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.025 0.006 -10000 0 -10000 0 0
VLDLR 0.01 0.2 0.34 40 -0.57 30 70
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
NUDC 0.025 0.006 -10000 0 -10000 0 0
RELN/LRP8 -0.083 0.22 -10000 0 -0.38 117 117
CaM/Ca2+ 0.018 0.004 -10000 0 -10000 0 0
KATNA1 0.024 0.008 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.095 0.18 -10000 0 -0.35 117 117
IQGAP1/CaM 0.036 0.01 -10000 0 -10000 0 0
DAB1 -0.069 0.22 0.34 1 -0.6 54 55
IQGAP1 0.025 0.004 -10000 0 -10000 0 0
PLA2G7 0.033 0.068 0.34 13 -0.62 1 14
CALM1 0.025 0.006 -10000 0 -10000 0 0
DYNLT1 0.024 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.055 0.062 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.003 -10000 0 -10000 0 0
CDK5R1 0.029 0.033 0.34 4 -10000 0 4
LIS1/Poliovirus Protein 3A 0.008 0.004 -10000 0 -10000 0 0
CDK5R2 0.029 0.052 0.34 10 -10000 0 10
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.17 0.28 -10000 0 -0.44 169 169
YWHAE 0.022 0.009 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.067 0.16 0.35 3 -0.34 24 27
MAP1B 0.008 0.019 -10000 0 -10000 0 0
RAC1 0.012 0.006 -10000 0 -10000 0 0
p35/CDK5 -0.08 0.16 -10000 0 -0.33 99 99
RELN -0.18 0.3 0.34 3 -0.61 122 125
PAFAH/LIS1 0.027 0.043 0.24 10 -0.4 1 11
LIS1/CLIP170 0.025 0.011 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.059 0.13 -10000 0 -0.3 11 11
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.14 0.23 0.24 1 -0.38 136 137
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.082 0.16 0.43 1 -0.33 73 74
LIS1/IQGAP1 0.024 0.011 -10000 0 -10000 0 0
RHOA 0.012 0.006 -10000 0 -10000 0 0
PAFAH1B1 0.011 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.051 0.095 0.34 32 -0.62 1 33
PAFAH1B2 0.022 0.038 -10000 0 -0.46 2 2
MAP1B/LIS1/Dynein heavy chain 0.017 0.028 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.064 0.16 0.41 1 -0.34 24 25
LRP8 0.053 0.09 0.34 33 -10000 0 33
NDEL1/Katanin 60 -0.072 0.16 0.36 2 -0.35 24 26
P39/CDK5 -0.081 0.17 0.31 3 -0.33 101 104
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.024 0.012 -10000 0 -10000 0 0
CDK5 -0.1 0.16 -10000 0 -0.34 102 102
PPP2R5D 0.024 0.008 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.021 0.009 -10000 0 -10000 0 0
CSNK2A1 0.026 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.14 0.24 -10000 0 -0.39 164 164
RELN/VLDLR -0.075 0.25 0.42 6 -0.39 122 128
CDC42 0.011 0.006 -10000 0 -10000 0 0
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.008 0.13 -10000 0 -0.47 20 20
alphaM/beta2 Integrin/GPIbA 0.017 0.1 -10000 0 -0.44 11 11
alphaM/beta2 Integrin/proMMP-9 0.048 0.15 0.36 3 -0.45 17 20
PLAUR 0.025 0.056 0.34 3 -0.62 2 5
HMGB1 0.015 0.032 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.024 0.093 -10000 0 -0.47 8 8
AGER 0.018 0.047 0.35 4 -10000 0 4
RAP1A 0.025 0.005 -10000 0 -10000 0 0
SELPLG 0.022 0.048 -10000 0 -0.62 2 2
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.023 0.13 0.4 2 -0.42 11 13
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.067 0.17 0.34 69 -0.62 10 79
CYR61 -0.04 0.19 -10000 0 -0.55 41 41
TLN1 0.025 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.061 0.16 -10000 0 -0.43 38 38
RHOA 0.026 0.003 -10000 0 -10000 0 0
P-selectin oligomer -0.12 0.26 -10000 0 -0.61 80 80
MYH2 -0.11 0.23 -10000 0 -0.61 43 43
MST1R 0.056 0.14 0.34 50 -0.62 7 57
leukocyte activation during inflammatory response -0.16 0.21 -10000 0 -0.37 162 162
APOB -0.002 0.13 -10000 0 -0.62 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.002 0.13 0.34 6 -0.56 17 23
JAM3 0.026 0.017 0.34 1 -10000 0 1
GP1BA 0.018 0.071 0.34 4 -0.49 5 9
alphaM/beta2 Integrin/CTGF 0.014 0.12 -10000 0 -0.5 13 13
alphaM/beta2 Integrin -0.086 0.17 -10000 0 -0.47 42 42
JAM3 homodimer 0.026 0.017 0.34 1 -10000 0 1
ICAM2 0.026 0.017 0.34 1 -10000 0 1
ICAM1 0.026 0.004 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.085 0.17 -10000 0 -0.47 42 42
cell adhesion 0.017 0.1 -10000 0 -0.44 11 11
NFKB1 -0.03 0.19 0.38 10 -0.44 48 58
THY1 0.1 0.14 0.34 92 -10000 0 92
RhoA/GDP 0.019 0.002 -10000 0 -10000 0 0
Lipoprotein(a) -0.18 0.22 -10000 0 -0.38 183 183
alphaM/beta2 Integrin/LRP/tPA 0.027 0.1 -10000 0 -0.44 11 11
IL6 -0.09 0.31 0.48 8 -0.82 50 58
ITGB2 0.008 0.077 0.34 1 -0.63 4 5
elevation of cytosolic calcium ion concentration 0.033 0.1 0.36 2 -0.42 10 12
alphaM/beta2 Integrin/JAM2/JAM3 0.024 0.12 0.42 1 -0.41 18 19
JAM2 0.005 0.11 0.34 1 -0.57 13 14
alphaM/beta2 Integrin/ICAM1 0.03 0.15 0.32 1 -0.36 28 29
alphaM/beta2 Integrin/uPA/Plg -0.026 0.16 -10000 0 -0.37 56 56
RhoA/GTP -0.12 0.24 -10000 0 -0.64 41 41
positive regulation of phagocytosis -0.062 0.17 -10000 0 -0.49 32 32
Ron/MSP 0.02 0.15 -10000 0 -0.41 32 32
alphaM/beta2 Integrin/uPAR/uPA 0.035 0.1 0.37 2 -0.42 10 12
alphaM/beta2 Integrin/uPAR 0.022 0.1 0.32 1 -0.46 10 11
PLAU 0.029 0.037 0.34 5 -10000 0 5
PLAT 0.018 0.077 0.34 4 -0.55 5 9
actin filament polymerization -0.11 0.21 -10000 0 -0.57 43 43
MST1 -0.018 0.16 -10000 0 -0.62 25 25
alphaM/beta2 Integrin/lipoprotein(a) -0.16 0.21 -10000 0 -0.37 162 162
TNF -0.053 0.22 0.48 3 -0.86 16 19
RAP1B 0.026 0.003 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.025 0.096 -10000 0 -0.44 9 9
fibrinolysis -0.027 0.16 -10000 0 -0.36 56 56
HCK 0.005 0.12 -10000 0 -0.62 12 12
dendritic cell antigen processing and presentation -0.085 0.17 -10000 0 -0.47 42 42
VTN 0.003 0.12 -10000 0 -0.62 13 13
alphaM/beta2 Integrin/CYR61 -0.018 0.16 -10000 0 -0.43 41 41
LPA -0.26 0.31 -10000 0 -0.57 177 177
LRP1 0.024 0.034 -10000 0 -0.62 1 1
cell migration 0.018 0.15 0.31 3 -0.42 28 31
FN1 0.024 0.034 -10000 0 -0.62 1 1
alphaM/beta2 Integrin/Thy1 0.07 0.13 0.36 5 -0.47 8 13
MPO 0.009 0.1 0.34 1 -0.62 9 10
KNG1 -0.025 0.17 -10000 0 -0.62 29 29
RAP1/GDP 0.033 0.008 -10000 0 -10000 0 0
ROCK1 -0.11 0.22 -10000 0 -0.61 39 39
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.071 0.22 -10000 0 -0.58 57 57
CTGF 0.01 0.091 -10000 0 -0.55 9 9
alphaM/beta2 Integrin/Hck 0.012 0.14 -10000 0 -0.61 14 14
ITGAM 0.007 0.087 0.33 2 -0.64 5 7
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.058 0.2 -10000 0 -0.4 81 81
HP -0.16 0.28 -10000 0 -0.57 115 115
leukocyte adhesion 0.038 0.16 0.36 6 -0.39 17 23
SELP -0.12 0.26 -10000 0 -0.61 80 80
Syndecan-4-mediated signaling events

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
PTK2 0.03 0.08 -10000 0 -0.65 2 2
Syndecan-4/Syndesmos -0.036 0.24 -10000 0 -0.66 38 38
positive regulation of JNK cascade -0.15 0.26 -10000 0 -0.6 59 59
Syndecan-4/ADAM12 -0.021 0.25 0.37 10 -0.64 38 48
CCL5 0.013 0.097 0.34 2 -0.62 8 10
Rac1/GDP 0.019 0.003 -10000 0 -10000 0 0
DNM2 0.026 0.003 -10000 0 -10000 0 0
ITGA5 0.026 0.002 -10000 0 -10000 0 0
SDCBP 0.021 0.01 -10000 0 -10000 0 0
PLG -0.073 0.22 -10000 0 -0.56 57 57
ADAM12 0.056 0.1 0.34 38 -0.62 1 39
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.025 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.032 0.023 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.068 0.26 0.37 1 -0.64 41 42
Syndecan-4/CXCL12/CXCR4 -0.16 0.28 -10000 0 -0.64 59 59
Syndecan-4/Laminin alpha3 -0.013 0.26 0.37 7 -0.66 38 45
MDK 0.2 0.16 0.34 201 -10000 0 201
Syndecan-4/FZD7 -0.04 0.25 -10000 0 -0.66 38 38
Syndecan-4/Midkine 0.057 0.28 0.37 41 -0.63 37 78
FZD7 0.017 0.094 0.34 4 -0.62 7 11
Syndecan-4/FGFR1/FGF -0.05 0.24 -10000 0 -0.6 46 46
THBS1 -0.065 0.22 -10000 0 -0.61 52 52
integrin-mediated signaling pathway -0.055 0.25 0.37 2 -0.64 41 43
positive regulation of MAPKKK cascade -0.15 0.26 -10000 0 -0.6 59 59
Syndecan-4/TACI -0.038 0.25 0.37 3 -0.67 38 41
CXCR4 0.021 0.058 -10000 0 -0.62 3 3
cell adhesion 0.025 0.038 0.2 13 -0.31 1 14
Syndecan-4/Dynamin -0.036 0.24 -10000 0 -0.67 38 38
Syndecan-4/TSP1 -0.081 0.27 -10000 0 -0.67 44 44
Syndecan-4/GIPC -0.035 0.24 -10000 0 -0.67 37 37
Syndecan-4/RANTES -0.042 0.25 0.37 1 -0.67 39 40
ITGB1 0.025 0.005 -10000 0 -10000 0 0
LAMA1 -0.035 0.22 0.34 20 -0.61 44 64
LAMA3 0.066 0.13 0.34 55 -0.62 4 59
RAC1 0.026 0.004 -10000 0 -10000 0 0
PRKCA 0.035 0.16 0.78 16 -10000 0 16
Syndecan-4/alpha-Actinin -0.036 0.24 -10000 0 -0.66 38 38
TFPI 0 0.13 -10000 0 -0.62 15 15
F2 -0.014 0.16 -10000 0 -0.6 24 24
alpha5/beta1 Integrin 0.037 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.058 0.25 -10000 0 -0.62 41 41
ACTN1 0.025 0.006 -10000 0 -10000 0 0
TNC -0.022 0.18 0.34 5 -0.58 31 36
Syndecan-4/CXCL12 -0.17 0.28 -10000 0 -0.65 59 59
FGF6 0.017 0.004 -10000 0 -10000 0 0
RHOA 0.026 0.003 -10000 0 -10000 0 0
CXCL12 -0.24 0.31 -10000 0 -0.6 153 153
TNFRSF13B 0.023 0.061 0.34 5 -0.62 2 7
FGF2 -0.007 0.15 0.34 5 -0.6 21 26
FGFR1 0.015 0.082 0.34 3 -0.56 6 9
Syndecan-4/PI-4-5-P2 -0.052 0.24 -10000 0 -0.66 38 38
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.022 0.036 -10000 0 -0.57 1 1
cell migration -0.015 0.01 -10000 0 -10000 0 0
PRKCD 0.024 0.017 -10000 0 -10000 0 0
vasculogenesis -0.076 0.26 -10000 0 -0.64 44 44
SDC4 -0.049 0.26 -10000 0 -0.71 38 38
Syndecan-4/Tenascin C -0.059 0.26 0.37 2 -0.67 41 43
Syndecan-4/PI-4-5-P2/PKC alpha -0.026 0.018 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.044 0.24 -10000 0 -0.67 37 37
MMP9 0.067 0.17 0.34 69 -0.61 10 79
Rac1/GTP 0.025 0.039 0.2 13 -0.32 1 14
cytoskeleton organization -0.033 0.23 -10000 0 -0.63 38 38
GIPC1 0.026 0.004 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.047 0.26 -10000 0 -0.7 40 40
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.025 0.004 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.11 0.14 -10000 0 -0.37 42 42
NT3 (dimer)/TRKC -0.22 0.26 -10000 0 -0.47 179 179
NT3 (dimer)/TRKB -0.37 0.4 -10000 0 -0.66 216 216
SHC/Grb2/SOS1/GAB1/PI3K 0.018 0.032 -10000 0 -0.36 2 2
RAPGEF1 0.026 0.004 -10000 0 -10000 0 0
BDNF 0.036 0.056 0.34 12 -10000 0 12
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
DYNLT1 0.024 0.008 -10000 0 -10000 0 0
NTRK1 0.02 0.026 0.34 2 -10000 0 2
NTRK2 -0.11 0.27 0.34 9 -0.61 82 91
NTRK3 -0.002 0.14 0.34 4 -0.62 17 21
NT-4/5 (dimer)/TRKB -0.2 0.3 -10000 0 -0.51 161 161
neuron apoptosis 0.11 0.22 0.47 77 -0.39 1 78
SHC 2-3/Grb2 -0.12 0.24 0.4 1 -0.51 77 78
SHC1 0.02 0.011 -10000 0 -10000 0 0
SHC2 -0.14 0.25 -10000 0 -0.55 81 81
SHC3 -0.11 0.23 0.31 4 -0.52 71 75
STAT3 (dimer) 0.017 0.075 0.29 1 -0.37 13 14
NT3 (dimer)/TRKA -0.28 0.31 -10000 0 -0.56 185 185
RIN/GDP -0.047 0.12 0.23 1 -0.26 14 15
GIPC1 0.026 0.004 -10000 0 -10000 0 0
KRAS 0.026 0.004 -10000 0 -10000 0 0
DNAJA3 -0.13 0.19 0.27 2 -0.36 135 137
RIN/GTP 0.014 0.003 -10000 0 -10000 0 0
CCND1 -0.015 0.17 0.54 1 -0.83 14 15
MAGED1 0.021 0.058 -10000 0 -0.62 3 3
PTPN11 0.026 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.021 0.029 0.34 3 -10000 0 3
SHC/GRB2/SOS1 0.038 0.024 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.02 0.091 -10000 0 -0.4 13 13
TRKA/NEDD4-2 0.028 0.023 0.25 2 -10000 0 2
ELMO1 0.024 0.034 -10000 0 -0.62 1 1
RhoG/GTP/ELMO1/DOCK1 0.022 0.072 -10000 0 -0.44 8 8
NGF -0.005 0.14 -10000 0 -0.62 17 17
HRAS 0.027 0.017 0.34 1 -10000 0 1
DOCK1 0.011 0.094 -10000 0 -0.62 8 8
GAB2 0.025 0.004 -10000 0 -10000 0 0
RIT2 0.019 0.004 -10000 0 -10000 0 0
RIT1 0.02 0.011 -10000 0 -10000 0 0
FRS2 0.026 0.003 -10000 0 -10000 0 0
DNM1 0.033 0.11 0.34 21 -0.62 6 27
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.009 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.12 0.2 0.27 2 -0.36 135 137
mol:GDP -0.077 0.17 -10000 0 -0.37 25 25
NGF (dimer) -0.005 0.14 -10000 0 -0.62 17 17
RhoG/GDP 0.018 0.025 -10000 0 -0.46 1 1
RIT1/GDP -0.051 0.1 -10000 0 -0.26 17 17
TIAM1 -0.009 0.14 -10000 0 -0.6 20 20
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
BDNF (dimer)/TRKB -0.04 0.2 0.43 2 -0.4 80 82
KIDINS220/CRKL/C3G 0.037 0.008 -10000 0 -10000 0 0
SHC/RasGAP 0.027 0.034 -10000 0 -0.35 2 2
FRS2 family/SHP2 0.048 0.017 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.046 0.032 -10000 0 -10000 0 0
RIT1/GTP 0.015 0.008 -10000 0 -10000 0 0
NT3 (dimer) -0.28 0.32 -10000 0 -0.6 179 179
RAP1/GDP -0.046 0.098 -10000 0 -0.22 14 14
KIDINS220/CRKL 0.025 0.004 -10000 0 -10000 0 0
BDNF (dimer) 0.036 0.056 0.34 12 -10000 0 12
ubiquitin-dependent protein catabolic process 0.021 0.086 -10000 0 -0.4 12 12
Schwann cell development -0.046 0.04 -10000 0 -10000 0 0
EHD4 0.026 0.003 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.059 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.013 0.049 -10000 0 -0.3 2 2
RAP1B 0.026 0.003 -10000 0 -10000 0 0
RAP1A 0.025 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.2 0.25 0.31 2 -0.41 186 188
ABL1 0.026 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.014 0.11 -10000 0 -0.43 8 8
STAT3 0.017 0.075 0.29 1 -0.37 13 14
axon guidance -0.19 0.23 0.24 2 -0.4 186 188
MAPK3 0.027 0.11 0.31 1 -0.36 13 14
MAPK1 0.027 0.11 0.31 1 -0.36 13 14
CDC42/GDP -0.046 0.12 0.23 1 -0.26 18 19
NTF3 -0.28 0.32 -10000 0 -0.6 179 179
NTF4 0.021 0.029 0.34 3 -10000 0 3
NGF (dimer)/TRKA/FAIM 0.022 0.085 -10000 0 -0.39 12 12
PI3K 0.034 0.052 -10000 0 -0.64 2 2
FRS3 0.024 0.007 -10000 0 -10000 0 0
FAIM 0.027 0.016 0.34 1 -10000 0 1
GAB1 0.024 0.007 -10000 0 -10000 0 0
RASGRF1 -0.11 0.2 0.28 3 -0.36 129 132
SOS1 0.026 0.001 -10000 0 -10000 0 0
MCF2L -0.19 0.21 -10000 0 -0.41 170 170
RGS19 0.025 0.004 -10000 0 -10000 0 0
CDC42 0.025 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.1 -10000 0 -0.43 4 4
Rac1/GDP -0.046 0.12 0.23 1 -0.26 14 15
NGF (dimer)/TRKA/GRIT 0.009 0.082 0.22 2 -0.34 17 19
neuron projection morphogenesis -0.11 0.22 -10000 0 -0.62 24 24
NGF (dimer)/TRKA/NEDD4-2 0.021 0.087 -10000 0 -0.4 12 12
MAP2K1 0.058 0.082 0.36 7 -10000 0 7
NGFR -0.21 0.31 -10000 0 -0.62 136 136
NGF (dimer)/TRKA/GIPC/GAIP 0.007 0.085 0.25 1 -0.32 16 17
RAS family/GTP/PI3K 0.022 0.029 -10000 0 -0.35 2 2
FRS2 family/SHP2/GRB2/SOS1 0.068 0.027 -10000 0 -10000 0 0
NRAS 0.025 0.004 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
PRKCI 0.026 0.002 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.004 -10000 0 -10000 0 0
PRKCZ -0.001 0.12 -10000 0 -0.52 17 17
MAPKKK cascade -0.049 0.18 -10000 0 -0.66 24 24
RASA1 0.022 0.048 -10000 0 -0.62 2 2
TRKA/c-Abl 0.029 0.023 0.25 2 -10000 0 2
SQSTM1 0.028 0.029 0.34 3 -10000 0 3
BDNF (dimer)/TRKB/GIPC -0.026 0.19 0.42 2 -0.36 80 82
NGF (dimer)/TRKA/p62/Atypical PKCs 0.024 0.1 -10000 0 -0.36 18 18
MATK 0.024 0.058 0.34 3 -0.51 3 6
NEDD4L 0.025 0.005 -10000 0 -10000 0 0
RAS family/GDP -0.064 0.068 -10000 0 -0.22 6 6
NGF (dimer)/TRKA -0.13 0.2 0.29 2 -0.38 137 139
Rac1/GTP -0.12 0.14 -10000 0 -0.3 126 126
FRS2 family/SHP2/CRK family 0.06 0.033 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN -0.044 0.16 0.35 3 -0.4 23 26
IKBKB -0.035 0.12 0.3 4 -0.31 26 30
AKT1 -0.028 0.12 0.29 10 -0.25 16 26
IKBKG -0.004 0.086 0.27 3 -0.3 4 7
CALM1 -0.031 0.12 -10000 0 -0.38 18 18
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
MAP3K1 -0.063 0.21 0.41 3 -0.52 32 35
MAP3K7 0.024 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.034 0.12 -10000 0 -0.37 23 23
DOK1 0.026 0.001 -10000 0 -10000 0 0
AP-1 -0.081 0.11 0.28 2 -0.25 50 52
LYN 0.022 0.01 -10000 0 -10000 0 0
BLNK 0.009 0.1 -10000 0 -0.62 9 9
SHC1 0.02 0.011 -10000 0 -10000 0 0
BCR complex -0.066 0.21 0.47 2 -0.45 82 84
CD22 -0.12 0.21 0.47 2 -0.47 71 73
CAMK2G -0.029 0.11 -10000 0 -0.38 14 14
CSNK2A1 0.026 0.004 -10000 0 -10000 0 0
INPP5D 0.026 0.003 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.043 0.13 -10000 0 -0.33 53 53
GO:0007205 -0.035 0.13 -10000 0 -0.38 23 23
SYK 0.02 0.058 -10000 0 -0.62 3 3
ELK1 -0.035 0.12 -10000 0 -0.38 19 19
NFATC1 -0.038 0.17 0.3 5 -0.41 29 34
B-cell antigen/BCR complex -0.066 0.21 0.47 2 -0.45 82 84
PAG1/CSK 0.027 0.043 -10000 0 -0.46 2 2
NFKBIB -0.001 0.057 0.16 3 -0.13 15 18
HRAS -0.019 0.12 0.26 1 -0.36 19 20
NFKBIA -0.001 0.057 0.16 3 -0.13 19 22
NF-kappa-B/RelA/I kappa B beta 0.006 0.048 0.16 3 -10000 0 3
RasGAP/Csk -0.15 0.25 0.41 2 -0.42 140 142
mol:GDP -0.028 0.12 -10000 0 -0.36 22 22
PTEN 0.023 0.025 -10000 0 -0.3 2 2
CD79B 0.028 0.029 0.34 3 -10000 0 3
NF-kappa-B/RelA/I kappa B alpha 0.006 0.048 0.16 3 -10000 0 3
GRB2 0.025 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.065 0.2 0.42 3 -0.45 45 48
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
mol:IP3 -0.033 0.13 -10000 0 -0.39 22 22
CSK 0.026 0.004 -10000 0 -10000 0 0
FOS -0.17 0.2 -10000 0 -0.44 85 85
CHUK -0.01 0.099 0.27 3 -0.32 14 17
IBTK 0.025 0.006 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.014 0.14 0.33 1 -0.41 19 20
PTPN6 -0.11 0.2 0.42 2 -0.48 58 60
RELA 0.026 0.004 -10000 0 -10000 0 0
BCL2A1 0.001 0.045 -10000 0 -0.13 8 8
VAV2 -0.075 0.2 0.43 2 -0.46 46 48
ubiquitin-dependent protein catabolic process 0.001 0.057 0.16 3 -0.12 34 37
BTK -0.005 0.17 -10000 0 -1.1 8 8
CD19 -0.085 0.18 0.35 6 -0.41 63 69
MAP4K1 0.016 0.093 0.34 3 -0.62 7 10
CD72 0.021 0.073 0.34 3 -0.62 4 7
PAG1 0.018 0.054 0.34 2 -0.62 2 4
MAPK14 -0.04 0.18 0.35 8 -0.42 31 39
SH3BP5 0.022 0.048 -10000 0 -0.62 2 2
PIK3AP1 -0.029 0.13 -10000 0 -0.39 23 23
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.067 0.21 0.34 1 -0.43 70 71
RAF1 -0.018 0.12 0.26 2 -0.36 15 17
RasGAP/p62DOK/SHIP -0.14 0.24 0.37 2 -0.41 140 142
CD79A -0.11 0.28 0.34 9 -0.61 83 92
re-entry into mitotic cell cycle -0.08 0.11 0.27 2 -0.25 48 50
RASA1 0.022 0.048 -10000 0 -0.62 2 2
MAPK3 -0.016 0.1 -10000 0 -0.33 11 11
MAPK1 -0.016 0.1 -10000 0 -0.34 9 9
CD72/SHP1 -0.086 0.22 0.44 3 -0.49 53 56
NFKB1 0.024 0.008 -10000 0 -10000 0 0
MAPK8 -0.066 0.19 0.39 3 -0.43 38 41
actin cytoskeleton organization -0.051 0.19 0.36 4 -0.41 42 46
NF-kappa-B/RelA 0.014 0.095 0.29 3 -10000 0 3
Calcineurin -0.011 0.11 -10000 0 -0.37 10 10
PI3K -0.099 0.16 -10000 0 -0.42 54 54
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.024 0.13 0.25 1 -0.4 21 22
SOS1 0.026 0.001 -10000 0 -10000 0 0
Bam32/HPK1 -0.12 0.3 0.76 1 -0.82 41 42
DAPP1 -0.15 0.32 0.6 1 -0.94 40 41
cytokine secretion -0.034 0.16 0.28 6 -0.38 29 35
mol:DAG -0.033 0.13 -10000 0 -0.39 22 22
PLCG2 0.012 0.083 -10000 0 -0.57 7 7
MAP2K1 -0.016 0.11 -10000 0 -0.36 12 12
B-cell antigen/BCR complex/FcgammaRIIB -0.18 0.27 0.43 2 -0.45 159 161
mol:PI-3-4-5-P3 -0.058 0.13 0.31 3 -0.3 44 47
ETS1 -0.029 0.1 -10000 0 -0.37 12 12
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.031 0.18 0.41 2 -0.36 74 76
B-cell antigen/BCR complex/LYN -0.1 0.18 0.39 2 -0.43 63 65
MALT1 0.025 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.034 -10000 0 -0.62 1 1
RAC1 -0.064 0.19 0.38 3 -0.43 42 45
B-cell antigen/BCR complex/LYN/SYK -0.1 0.22 0.48 2 -0.5 65 67
CARD11 -0.039 0.14 0.31 3 -0.44 23 26
FCGR2B -0.2 0.3 0.34 2 -0.62 124 126
PPP3CA 0.024 0.007 -10000 0 -10000 0 0
BCL10 0.025 0.005 -10000 0 -10000 0 0
IKK complex -0.001 0.052 0.19 6 -0.14 2 8
PTPRC -0.014 0.15 0.34 1 -0.62 20 21
PDPK1 -0.028 0.11 0.25 12 -0.24 20 32
PPP3CB 0.025 0.005 -10000 0 -10000 0 0
PPP3CC 0.02 0.011 -10000 0 -10000 0 0
POU2F2 0.003 0.042 0.18 2 -0.13 7 9
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.026 0.004 -10000 0 -10000 0 0
SPHK1 0.071 0.14 0.34 64 -0.62 5 69
GNAI2 0.026 0.003 -10000 0 -10000 0 0
mol:S1P 0.037 0.084 0.3 10 -0.38 5 15
GNAO1 -0.26 0.31 -10000 0 -0.58 174 174
mol:Sphinganine-1-P 0.044 0.1 0.23 64 -0.46 5 69
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.06 0.076 -10000 0 -0.35 7 7
GNAI3 0.025 0.005 -10000 0 -10000 0 0
G12/G13 0.037 0.009 -10000 0 -10000 0 0
S1PR3 0.009 0.1 0.34 1 -0.56 11 12
S1PR2 0.02 0.058 -10000 0 -0.62 3 3
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.019 0.062 0.2 7 -0.33 5 12
S1PR5 0.018 0.077 0.34 1 -0.62 5 6
S1PR4 0.026 0.024 0.34 1 -0.3 1 2
GNAI1 0.022 0.048 -10000 0 -0.62 2 2
S1P/S1P5/G12 0.049 0.083 -10000 0 -0.35 9 9
S1P/S1P3/Gq -0.028 0.15 -10000 0 -0.32 56 56
S1P/S1P4/Gi -0.056 0.15 0.26 2 -0.28 74 76
GNAQ 0.025 0.017 -10000 0 -0.3 1 1
GNAZ 0.16 0.16 0.34 165 -0.62 1 166
GNA14 -0.078 0.24 -10000 0 -0.6 60 60
GNA15 0.026 0.041 0.34 2 -0.62 1 3
GNA12 0.026 0.004 -10000 0 -10000 0 0
GNA13 0.025 0.005 -10000 0 -10000 0 0
GNA11 0.009 0.1 -10000 0 -0.58 10 10
ABCC1 0.032 0.046 0.34 8 -10000 0 8
Arf6 signaling events

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
CENTA1/KIF3B 0.022 0.069 0.22 8 -0.39 8 16
ARNO/beta Arrestin1-2 -0.02 0.15 -10000 0 -0.87 5 5
EGFR 0.01 0.1 -10000 0 -0.62 9 9
EPHA2 -0.009 0.14 -10000 0 -0.56 21 21
USP6 0.02 0.035 -10000 0 -0.62 1 1
IQSEC1 0.026 0.002 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.066 0.12 0.25 78 -0.42 9 87
ARRB2 0.008 0.004 -10000 0 -10000 0 0
mol:GTP 0.002 0.053 0.17 2 -0.18 12 14
ARRB1 0.018 0.069 -10000 0 -0.55 5 5
FBXO8 0.024 0.008 -10000 0 -10000 0 0
TSHR 0.023 0.006 -10000 0 -10000 0 0
EGF 0.093 0.13 0.34 83 -10000 0 83
somatostatin receptor activity 0 0 0.001 2 -0.001 57 59
ARAP2 0.004 0.12 -10000 0 -0.62 12 12
mol:GDP -0.057 0.12 0.2 1 -0.3 48 49
mol:PI-3-4-5-P3 0 0 0.001 1 -0.001 35 36
ITGA2B 0.031 0.046 0.34 8 -10000 0 8
ARF6 0.025 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.028 0.087 -10000 0 -0.36 12 12
ADAP1 0.022 0.11 0.34 12 -0.62 8 20
KIF13B 0.02 0.011 -10000 0 -10000 0 0
HGF/MET -0.23 0.25 0.25 1 -0.46 194 195
PXN 0.026 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.065 0.13 0.25 1 -0.29 59 60
EGFR/EGFR/EGF/EGF/ARFGEP100 0.076 0.1 -10000 0 -0.34 9 9
ADRB2 -0.049 0.2 -10000 0 -0.62 42 42
receptor agonist activity 0 0 -10000 0 0 50 50
actin filament binding 0 0 0 2 -0.001 60 62
SRC 0.03 0.037 0.34 5 -10000 0 5
ITGB3 -0.024 0.17 -10000 0 -0.62 28 28
GNAQ 0.025 0.017 -10000 0 -0.3 1 1
EFA6/PI-4-5-P2 0 0 0.002 3 -0.001 25 28
ARF6/GDP -0.051 0.17 -10000 0 -0.43 42 42
ARF6/GDP/GULP/ACAP1 -0.048 0.17 0.27 2 -0.36 55 57
alphaIIb/beta3 Integrin/paxillin/GIT1 0.035 0.12 -10000 0 -0.37 27 27
ACAP1 0.012 0.088 0.34 3 -0.46 10 13
ACAP2 0.026 0.003 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.007 0.027 -10000 0 -10000 0 0
EFNA1 0.014 0.059 -10000 0 -0.62 3 3
HGF -0.32 0.32 0.34 1 -0.62 194 195
CYTH3 0.008 0.015 0.21 2 -10000 0 2
CYTH2 0.003 0.12 -10000 0 -1 5 5
NCK1 0.026 0.001 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 1 0 60 61
endosomal lumen acidification 0 0 0 3 0 47 50
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.01 0.22 0.34 50 -0.61 34 84
GNAQ/ARNO 0.018 0.12 -10000 0 -0.96 5 5
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 2 2
MET 0.023 0.034 -10000 0 -0.62 1 1
GNA14 -0.078 0.24 -10000 0 -0.61 60 60
GNA15 0.025 0.041 0.34 2 -0.62 1 3
GIT1 0.026 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 2 -0.001 38 40
GNA11 0.009 0.1 -10000 0 -0.58 10 10
LHCGR 0.018 0.001 -10000 0 -10000 0 0
AGTR1 -0.03 0.18 -10000 0 -0.62 32 32
desensitization of G-protein coupled receptor protein signaling pathway 0.007 0.027 -10000 0 -10000 0 0
IPCEF1/ARNO 0.052 0.14 -10000 0 -0.86 5 5
alphaIIb/beta3 Integrin 0.003 0.14 0.25 8 -0.46 28 36
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.049 0.2 0.33 23 -0.53 27 50
FYN -0.003 0.26 0.39 8 -0.73 31 39
LAT/GRAP2/SLP76 0.012 0.21 0.48 5 -0.62 27 32
IKBKB 0.023 0.009 -10000 0 -10000 0 0
AKT1 0.004 0.17 0.43 5 -0.46 30 35
B2M 0.026 0.008 -10000 0 -10000 0 0
IKBKG 0.008 0.059 0.22 5 -0.16 16 21
MAP3K8 0.022 0.048 -10000 0 -0.62 2 2
mol:Ca2+ -0.034 0.043 0.051 8 -0.097 104 112
integrin-mediated signaling pathway 0.023 0.041 -10000 0 -0.39 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.008 0.24 0.48 5 -0.69 30 35
TRPV6 -0.17 0.33 1 6 -0.61 109 115
CD28 0.025 0.038 0.34 1 -0.61 1 2
SHC1 0.029 0.25 0.32 60 -0.64 32 92
receptor internalization -0.011 0.24 0.45 5 -0.61 39 44
PRF1 -0.025 0.28 0.51 1 -0.94 24 25
KRAS 0.026 0.004 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
COT/AKT1 0.018 0.14 0.4 5 -0.38 28 33
LAT -0.009 0.24 0.49 5 -0.65 34 39
EntrezGene:6955 0 0.002 -10000 0 -10000 0 0
CD3D 0.021 0.12 0.34 16 -0.54 12 28
CD3E 0.004 0.12 0.35 1 -0.56 15 16
CD3G 0.012 0.11 0.34 7 -0.56 11 18
RASGRP2 0.007 0.04 0.16 6 -0.17 8 14
RASGRP1 0.009 0.18 0.5 5 -0.48 29 34
HLA-A 0.001 0.005 -10000 0 -10000 0 0
RASSF5 0.015 0.059 -10000 0 -0.62 3 3
RAP1A/GTP/RAPL 0.024 0.041 -10000 0 -0.4 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.046 0.081 0.19 40 -0.13 15 55
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.021 0.072 -10000 0 -0.24 29 29
PRKCA 0.013 0.1 0.26 10 -0.27 27 37
GRAP2 0.016 0.1 0.34 6 -0.58 9 15
mol:IP3 0.037 0.19 0.27 88 -0.44 29 117
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.027 0.21 0.43 4 -0.68 26 30
ORAI1 0.074 0.19 -10000 0 -0.84 6 6
CSK -0.008 0.24 0.39 7 -0.7 31 38
B7 family/CD28 0.007 0.25 0.43 4 -0.7 30 34
CHUK 0.025 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.017 0.28 0.41 7 -0.74 36 43
PTPN6 -0.016 0.24 0.39 6 -0.72 30 36
VAV1 -0.019 0.26 0.44 5 -0.68 37 42
Monovalent TCR/CD3 -0.007 0.14 0.29 6 -0.45 23 29
CBL 0.025 0.006 -10000 0 -10000 0 0
LCK -0.013 0.27 0.38 8 -0.76 33 41
PAG1 0.011 0.26 0.34 20 -0.69 32 52
RAP1A 0.025 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.019 0.27 0.39 7 -0.76 34 41
CD80 0.002 0.12 0.34 1 -0.62 14 15
CD86 0.009 0.11 -10000 0 -0.62 10 10
PDK1/CARD11/BCL10/MALT1 -0.011 0.093 0.15 1 -0.29 29 30
HRAS 0.027 0.017 0.34 1 -10000 0 1
GO:0035030 -0.013 0.2 0.39 4 -0.55 32 36
CD8A -0.009 0.16 0.34 4 -0.62 22 26
CD8B 0.005 0.15 0.34 12 -0.62 18 30
PTPRC -0.014 0.15 0.35 1 -0.62 20 21
PDK1/PKC theta -0.001 0.2 0.48 5 -0.57 31 36
CSK/PAG1 0.013 0.25 0.34 19 -0.7 29 48
SOS1 0.026 0.001 -10000 0 -10000 0 0
peptide-MHC class I 0.02 0.011 -10000 0 -10000 0 0
GRAP2/SLP76 0.009 0.24 0.47 5 -0.71 29 34
STIM1 0.046 0.12 1.1 3 -10000 0 3
RAS family/GTP 0.043 0.095 0.25 15 -0.19 18 33
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.015 0.26 0.46 5 -0.65 39 44
mol:DAG -0.013 0.13 0.14 20 -0.38 32 52
RAP1A/GDP 0.023 0.04 0.12 15 -10000 0 15
PLCG1 0.026 0.004 -10000 0 -10000 0 0
CD247 0.017 0.052 0.34 1 -0.62 2 3
cytotoxic T cell degranulation -0.021 0.26 0.5 1 -0.87 25 26
RAP1A/GTP 0.002 0.012 -10000 0 -0.065 8 8
mol:PI-3-4-5-P3 0.003 0.2 0.47 5 -0.56 29 34
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.039 0.24 0.3 81 -0.58 29 110
NRAS 0.025 0.004 -10000 0 -10000 0 0
ZAP70 0.024 0.077 0.34 5 -0.62 4 9
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.001 0.2 0.49 4 -0.6 29 33
MALT1 0.025 0.005 -10000 0 -10000 0 0
TRAF6 0.024 0.034 -10000 0 -0.62 1 1
CD8 heterodimer -0.002 0.19 0.48 4 -0.56 32 36
CARD11 0.012 0.11 0.34 5 -0.62 10 15
PRKCB -0.004 0.14 0.29 7 -0.34 37 44
PRKCE 0.011 0.11 0.26 10 -0.28 28 38
PRKCQ -0.007 0.23 0.49 5 -0.66 31 36
LCP2 0.015 0.082 -10000 0 -0.62 6 6
BCL10 0.025 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression 0.009 0.15 0.39 6 -0.39 30 36
IKK complex 0.016 0.067 0.2 12 -0.13 18 30
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.015 0.11 0.36 5 -0.29 25 30
PDPK1 0.009 0.16 0.4 6 -0.44 28 34
TCR/CD3/MHC I/CD8/Fyn -0.046 0.29 0.51 4 -0.89 31 35
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.023 0.068 -10000 0 -0.4 8 8
alphaV beta3 Integrin -0.006 0.16 -10000 0 -0.43 43 43
PTK2 0.022 0.17 0.36 3 -0.54 16 19
IGF1R 0.015 0.1 0.34 4 -0.62 8 12
PI4KB 0.02 0.011 -10000 0 -10000 0 0
MFGE8 0.03 0.037 0.34 5 -10000 0 5
SRC 0.03 0.037 0.34 5 -10000 0 5
CDKN1B -0.018 0.12 -10000 0 -0.54 14 14
VEGFA 0.023 0.009 -10000 0 -10000 0 0
ILK -0.016 0.12 -10000 0 -0.53 14 14
ROCK1 0.026 0.003 -10000 0 -10000 0 0
AKT1 -0.021 0.11 -10000 0 -0.49 14 14
PTK2B -0.006 0.12 0.36 1 -0.39 26 27
alphaV/beta3 Integrin/JAM-A -0.01 0.14 -10000 0 -0.39 38 38
CBL 0.025 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.029 0.18 -10000 0 -0.42 60 60
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.11 0.22 -10000 0 -0.37 145 145
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.01 0.093 -10000 0 -0.38 9 9
alphaV/beta3 Integrin/Syndecan-1 0.012 0.13 -10000 0 -0.4 32 32
PI4KA 0.025 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.24 -10000 0 -0.39 153 153
PI4 Kinase 0.029 0.017 -10000 0 -10000 0 0
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
alphaV/beta3 Integrin/Osteopontin 0.051 0.19 0.43 1 -0.38 44 45
RPS6KB1 -0.16 0.19 -10000 0 -0.38 136 136
TLN1 0.025 0.004 -10000 0 -10000 0 0
MAPK3 -0.1 0.23 -10000 0 -0.64 50 50
GPR124 0.017 0.051 -10000 0 -0.51 3 3
MAPK1 -0.1 0.23 -10000 0 -0.63 51 51
PXN 0.026 0.003 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
alphaV/beta3 Integrin/Tumstatin 0.006 0.17 -10000 0 -0.44 40 40
cell adhesion -0.025 0.16 -10000 0 -0.38 56 56
ANGPTL3 -0.041 0.19 -10000 0 -0.61 38 38
VEGFR2 homodimer/VEGFA homodimer/Src 0.038 0.067 -10000 0 -0.4 6 6
IGF-1R heterotetramer 0.015 0.1 0.34 4 -0.62 8 12
Rac1/GDP 0.019 0.003 -10000 0 -10000 0 0
TGFBR2 0.026 0.003 -10000 0 -10000 0 0
ITGB3 -0.024 0.17 -10000 0 -0.62 28 28
IGF1 -0.23 0.31 -10000 0 -0.61 144 144
RAC1 0.026 0.004 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.009 0.12 -10000 0 -0.38 30 30
apoptosis 0.027 0.017 0.34 1 -10000 0 1
CD47 0.024 0.034 -10000 0 -0.62 1 1
alphaV/beta3 Integrin/CD47 0.016 0.12 -10000 0 -0.4 29 29
VCL 0.025 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.056 0.15 0.43 1 -0.4 28 29
CSF1 0.02 0.071 0.34 2 -0.62 4 6
PIK3C2A -0.016 0.12 -10000 0 -0.53 14 14
PI4 Kinase/Pyk2 -0.023 0.13 -10000 0 -0.39 30 30
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.019 0.13 -10000 0 -0.42 27 27
FAK1/Vinculin 0.043 0.15 0.32 8 -0.42 16 24
alphaV beta3/Integrin/ppsTEM5 0.009 0.12 -10000 0 -0.39 30 30
RHOA 0.026 0.003 -10000 0 -10000 0 0
VTN 0.003 0.12 -10000 0 -0.62 13 13
BCAR1 0.024 0.007 -10000 0 -10000 0 0
FGF2 -0.007 0.15 0.34 5 -0.6 21 26
F11R -0.006 0.1 0.27 5 -0.46 15 20
alphaV/beta3 Integrin/Lactadherin 0.02 0.12 -10000 0 -0.39 28 28
alphaV/beta3 Integrin/TGFBR2 0.019 0.12 -10000 0 -0.38 28 28
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.056 0.049 -10000 0 -0.36 3 3
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.017 0.11 -10000 0 -0.36 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.024 0.034 -10000 0 -0.62 1 1
alphaV/beta3 Integrin/Pyk2 0.014 0.13 -10000 0 -0.39 26 26
SDC1 0.019 0.067 -10000 0 -0.62 4 4
VAV3 0.01 0.045 -10000 0 -0.34 4 4
PTPN11 0.026 0.003 -10000 0 -10000 0 0
IRS1 0.026 0.002 -10000 0 -10000 0 0
FAK1/Paxillin 0.043 0.15 0.32 8 -0.42 16 24
cell migration 0.039 0.14 0.31 9 -0.38 16 25
ITGAV 0.027 0.017 0.34 1 -10000 0 1
PI3K -0.004 0.15 -10000 0 -0.38 38 38
SPP1 0.094 0.22 0.34 123 -0.52 24 147
KDR 0.011 0.091 -10000 0 -0.55 9 9
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.027 0.017 0.34 1 -10000 0 1
COL4A3 0.009 0.16 0.34 18 -0.62 18 36
angiogenesis -0.081 0.25 -10000 0 -0.61 56 56
Rac1/GTP 0.025 0.039 -10000 0 -0.31 3 3
EDIL3 0.093 0.13 0.34 79 -10000 0 79
cell proliferation 0.019 0.12 -10000 0 -0.38 28 28
Signaling events mediated by PRL

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
CCNE1 0.13 0.15 0.34 122 -10000 0 122
mol:Halofuginone 0.002 0.005 -10000 0 -10000 0 0
ITGA1 0.022 0.047 -10000 0 -0.62 2 2
CDKN1A -0.057 0.15 -10000 0 -0.51 27 27
PRL-3/alpha Tubulin 0.047 0.064 0.25 32 -10000 0 32
mol:Ca2+ -0.031 0.072 -10000 0 -0.27 28 28
AGT 0.014 0.067 -10000 0 -0.62 4 4
CCNA2 -0.044 0.18 -10000 0 -1 1 1
TUBA1B 0.026 0.002 -10000 0 -10000 0 0
EGR1 -0.14 0.22 -10000 0 -0.46 121 121
CDK2/Cyclin E1 0.031 0.18 0.34 1 -0.55 15 16
MAPK3 0.048 0.085 0.24 61 -10000 0 61
PRL-2 /Rab GGTase beta 0.036 0.01 -10000 0 -10000 0 0
MAPK1 0.047 0.084 0.24 60 -10000 0 60
PTP4A1 -0.11 0.18 -10000 0 -1.2 1 1
PTP4A3 0.047 0.091 0.34 32 -10000 0 32
PTP4A2 0.025 0.006 -10000 0 -10000 0 0
ITGB1 0.048 0.086 0.24 60 -10000 0 60
SRC 0.03 0.037 0.34 5 -10000 0 5
RAC1 0.002 0.085 -10000 0 -0.31 2 2
Rab GGTase beta/Rab GGTase alpha 0.037 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.2 0.24 -10000 0 -0.64 46 46
RABGGTA 0.026 0.003 -10000 0 -10000 0 0
BCAR1 -0.031 0.063 -10000 0 -0.24 31 31
RHOC -0.009 0.11 -10000 0 -0.4 10 10
RHOA -0.003 0.096 -10000 0 -0.54 2 2
cell motility -0.004 0.12 0.32 2 -0.38 8 10
PRL-1/alpha Tubulin -0.088 0.18 -10000 0 -1.1 1 1
PRL-3/alpha1 Integrin 0.044 0.074 0.25 32 -0.46 2 34
ROCK1 -0.004 0.12 0.28 1 -0.38 8 9
RABGGTB 0.025 0.005 -10000 0 -10000 0 0
CDK2 0.026 0.003 -10000 0 -10000 0 0
mitosis -0.11 0.17 -10000 0 -1.2 1 1
ATF5 -0.2 0.3 -10000 0 -0.61 127 127
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.16 0.25 -10000 0 -0.61 43 43
MAP3K8 0.014 0.049 -10000 0 -0.62 2 2
FOS -0.09 0.18 -10000 0 -0.5 35 35
PRKCA 0.005 0.024 -10000 0 -10000 0 0
PTPN7 0 0.063 0.34 4 -0.62 2 6
HRAS 0.025 0.017 0.34 1 -10000 0 1
PRKCB -0.049 0.18 -10000 0 -0.61 31 31
NRAS 0.024 0.004 -10000 0 -10000 0 0
RAS family/GTP 0.017 0.038 -10000 0 -10000 0 0
MAPK3 -0.047 0.15 -10000 0 -0.66 15 15
MAP2K1 -0.063 0.16 -10000 0 -0.47 40 40
ELK1 -0.002 0.031 -10000 0 -10000 0 0
BRAF -0.046 0.14 -10000 0 -0.48 31 31
mol:GTP -0.003 0.003 -10000 0 -0.005 175 175
MAPK1 -0.042 0.13 -10000 0 -0.59 12 12
RAF1 -0.045 0.14 -10000 0 -0.47 33 33
KRAS 0.024 0.004 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 -0.006 0.022 -10000 0 -0.4 1 1
ADCY5 -0.075 0.15 -10000 0 -0.4 66 66
ADCY6 -0.005 0.008 0.16 1 -10000 0 1
ADCY7 -0.006 0.022 0.16 1 -0.4 1 2
ADCY1 -0.15 0.19 0.16 2 -0.4 134 136
ADCY2 -0.004 0.024 0.16 8 -10000 0 8
ADCY3 -0.005 0.025 0.16 3 -0.4 1 4
ADCY8 0.018 0.067 0.2 42 -10000 0 42
PRKCE 0.006 0.027 0.21 1 -0.46 1 2
ADCY9 -0.006 0.022 0.16 1 -0.4 1 2
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.012 0.078 0.2 3 -0.2 16 19
Coregulation of Androgen receptor activity

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
NRIP1 0.024 0.037 -10000 0 -0.62 1 1
SVIL 0.022 0.049 -10000 0 -0.6 2 2
ZNF318 0.022 0.031 -10000 0 -10000 0 0
JMJD2C 0.019 0.057 0.21 30 -10000 0 30
T-DHT/AR/Ubc9 -0.087 0.2 -10000 0 -0.41 98 98
CARM1 0.025 0.006 -10000 0 -10000 0 0
PRDX1 0.025 0.006 -10000 0 -10000 0 0
PELP1 0.021 0.012 -10000 0 -10000 0 0
CTNNB1 0.026 0.014 -10000 0 -10000 0 0
AKT1 0.022 0.015 -10000 0 -10000 0 0
PTK2B 0.021 0.013 -10000 0 -10000 0 0
MED1 0.024 0.013 -10000 0 -10000 0 0
MAK 0.021 0.031 0.2 5 -10000 0 5
response to oxidative stress 0 0.002 -10000 0 -10000 0 0
HIP1 0.015 0.083 -10000 0 -0.61 6 6
GSN 0.026 0.024 0.37 1 -10000 0 1
NCOA2 -0.038 0.18 -10000 0 -0.62 33 33
NCOA6 0.026 0.014 -10000 0 -10000 0 0
DNA-PK 0.04 0.036 -10000 0 -10000 0 0
NCOA4 0.026 0.005 -10000 0 -10000 0 0
PIAS3 0.02 0.015 -10000 0 -10000 0 0
cell proliferation -0.007 0.048 -10000 0 -0.42 1 1
XRCC5 0.024 0.014 -10000 0 -10000 0 0
UBE3A 0.026 0.02 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.091 0.21 -10000 0 -0.41 103 103
FHL2 -0.12 0.34 -10000 0 -1.1 39 39
RANBP9 0.024 0.016 -10000 0 -10000 0 0
JMJD1A -0.002 0.027 -10000 0 -0.12 17 17
CDK6 -0.016 0.16 -10000 0 -0.6 24 24
TGFB1I1 0.025 0.016 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.098 0.21 -10000 0 -0.41 107 107
XRCC6 0.023 0.013 -10000 0 -10000 0 0
T-DHT/AR -0.085 0.23 0.28 17 -0.42 101 118
CTDSP1 0.025 0.008 -10000 0 -10000 0 0
CTDSP2 0.023 0.02 -10000 0 -10000 0 0
BRCA1 0.025 0.016 -10000 0 -10000 0 0
TCF4 0.023 0.017 -10000 0 -10000 0 0
CDKN2A 0.23 0.15 0.34 238 -10000 0 238
SRF 0.011 0.049 -10000 0 -10000 0 0
NKX3-1 -0.053 0.096 -10000 0 -0.19 98 98
KLK3 -0.014 0.22 0.47 16 -1.5 6 22
TMF1 0.026 0.006 -10000 0 -10000 0 0
HNRNPA1 0.024 0.015 -10000 0 -10000 0 0
AOF2 0.001 0.012 0.056 1 -0.07 6 7
APPL1 0.01 0.018 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.085 0.2 -10000 0 -0.41 97 97
AR -0.15 0.29 -10000 0 -0.62 98 98
UBA3 0.026 0.008 -10000 0 -10000 0 0
PATZ1 0.024 0.015 -10000 0 -10000 0 0
PAWR 0.026 0.006 -10000 0 -10000 0 0
PRKDC 0.02 0.015 -10000 0 -10000 0 0
PA2G4 0.024 0.017 -10000 0 -10000 0 0
UBE2I 0.025 0.006 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.076 0.18 -10000 0 -0.37 95 95
RPS6KA3 0.022 0.044 -10000 0 -0.4 3 3
T-DHT/AR/ARA70 -0.086 0.2 -10000 0 -0.4 99 99
LATS2 0.023 0.015 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.078 0.18 0.23 1 -0.37 98 99
Cyclin D3/CDK11 p58 0.018 0.006 -10000 0 -10000 0 0
VAV3 0.028 0.051 0.34 5 -0.62 1 6
KLK2 -0.005 0.15 0.46 21 -0.53 1 22
CASP8 0.024 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.092 0.22 -10000 0 -0.44 90 90
TMPRSS2 -0.082 0.26 -10000 0 -1.1 19 19
CCND1 0 0.12 -10000 0 -0.59 14 14
PIAS1 0.026 0.02 -10000 0 -10000 0 0
mol:T-DHT -0.002 0.027 0.06 18 -0.073 30 48
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.025 0.031 -10000 0 -0.22 1 1
T-DHT/AR/CDK6 -0.11 0.22 -10000 0 -0.41 117 117
CMTM2 0.024 0.025 0.34 2 -10000 0 2
SNURF 0.018 0.1 0.34 8 -0.58 8 16
ZMIZ1 0.02 0.035 -10000 0 -10000 0 0
CCND3 0.024 0.008 -10000 0 -10000 0 0
TGIF1 0.023 0.015 -10000 0 -10000 0 0
FKBP4 0.025 0.015 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.027 0.024 0.34 2 -9999 0 2
Aurora C/Aurora B/INCENP 0.12 0.099 0.4 2 -9999 0 2
metaphase 0 0 -10000 0 -9999 0 0
mitosis 0 0 -10000 0 -9999 0 0
H3F3B 0.005 0.007 -10000 0 -9999 0 0
AURKB 0.16 0.16 0.34 160 -9999 0 160
AURKC 0.025 0.005 -10000 0 -9999 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.005 0.071 -10000 0 -0.27 22 22
epithelial cell differentiation 0.026 0.095 -10000 0 -0.34 22 22
CYFIP2 -0.01 0.15 -10000 0 -0.62 20 20
ENAH -0.015 0.083 0.31 3 -0.4 3 6
EGFR 0.01 0.1 -10000 0 -0.62 9 9
EPHA2 -0.009 0.14 -10000 0 -0.56 21 21
MYO6 -0.008 0.094 -10000 0 -0.36 22 22
CTNNB1 0.026 0.002 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.028 0.097 -10000 0 -0.37 20 20
AQP5 0.005 0.083 -10000 0 -10000 0 0
CTNND1 0.026 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.005 0.085 -10000 0 -0.32 22 22
regulation of calcium-dependent cell-cell adhesion 0.004 0.099 -10000 0 -0.33 23 23
EGF 0.093 0.13 0.34 83 -10000 0 83
NCKAP1 0.026 0.002 -10000 0 -10000 0 0
AQP3 -0.047 0.17 -10000 0 -0.56 29 29
cortical microtubule organization 0.026 0.095 -10000 0 -0.34 22 22
GO:0000145 -0.022 0.078 -10000 0 -0.31 22 22
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.031 0.097 -10000 0 -0.34 22 22
MLLT4 0.023 0.008 -10000 0 -10000 0 0
ARF6/GDP -0.039 0.092 -10000 0 -0.35 26 26
ARF6 0.025 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.028 0.087 -10000 0 -0.36 12 12
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.01 0.077 -10000 0 -0.3 22 22
PVRL2 0.026 0.004 -10000 0 -10000 0 0
ZYX -0.005 0.086 -10000 0 -0.33 22 22
ARF6/GTP 0.033 0.085 -10000 0 -0.34 12 12
CDH1 -0.015 0.15 -10000 0 -0.62 22 22
EGFR/EGFR/EGF/EGF 0.034 0.12 -10000 0 -0.37 21 21
RhoA/GDP 0.028 0.092 -10000 0 -0.33 22 22
actin cytoskeleton organization -0.025 0.086 -10000 0 -0.35 21 21
IGF-1R heterotetramer 0.015 0.1 0.34 4 -0.62 8 12
GIT1 0.026 0.003 -10000 0 -10000 0 0
IGF1R 0.015 0.1 0.34 4 -0.62 8 12
IGF1 -0.23 0.31 -10000 0 -0.61 144 144
DIAPH1 -0.006 0.17 -10000 0 -0.64 22 22
Wnt receptor signaling pathway -0.026 0.095 0.34 22 -10000 0 22
RHOA 0.026 0.003 -10000 0 -10000 0 0
RhoA/GTP -0.039 0.092 -10000 0 -0.35 25 25
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
VCL -0.025 0.088 -10000 0 -0.36 21 21
EFNA1 0.014 0.059 -10000 0 -0.62 3 3
LPP -0.025 0.078 -10000 0 -0.32 22 22
Ephrin A1/EPHA2 0 0.12 -10000 0 -0.38 26 26
SEC6/SEC8 -0.008 0.076 -10000 0 -0.31 22 22
MGAT3 0.004 0.1 -10000 0 -0.33 23 23
HGF/MET -0.17 0.21 -10000 0 -0.35 189 189
HGF -0.32 0.32 0.34 1 -0.62 194 195
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.005 0.072 -10000 0 -0.28 22 22
actin cable formation 0.031 0.11 0.33 8 -0.31 6 14
KIAA1543 -0.025 0.083 -10000 0 -0.32 25 25
KIFC3 -0.006 0.086 -10000 0 -0.33 22 22
NCK1 0.026 0.001 -10000 0 -10000 0 0
EXOC3 0.025 0.006 -10000 0 -10000 0 0
ACTN1 -0.007 0.085 -10000 0 -0.33 22 22
NCK1/GIT1 0.038 0.005 -10000 0 -10000 0 0
mol:GDP 0.026 0.095 -10000 0 -0.34 22 22
EXOC4 0.025 0.006 -10000 0 -10000 0 0
STX4 -0.005 0.086 -10000 0 -0.33 22 22
PIP5K1C -0.005 0.086 -10000 0 -0.33 22 22
LIMA1 0.026 0.002 -10000 0 -10000 0 0
ABI1 0.025 0.004 -10000 0 -10000 0 0
ROCK1 0.003 0.12 0.33 5 -0.42 7 12
adherens junction assembly -0.024 0.1 -10000 0 -0.41 7 7
IGF-1R heterotetramer/IGF1 -0.12 0.19 -10000 0 -0.34 155 155
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.034 0.013 -10000 0 -10000 0 0
MET 0.023 0.034 -10000 0 -0.62 1 1
PLEKHA7 -0.008 0.091 -10000 0 -0.33 25 25
mol:GTP 0.027 0.086 -10000 0 -0.36 12 12
establishment of epithelial cell apical/basal polarity -0.006 0.099 0.33 6 -10000 0 6
cortical actin cytoskeleton stabilization 0.005 0.071 -10000 0 -0.27 22 22
regulation of cell-cell adhesion -0.025 0.086 -10000 0 -0.35 21 21
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.005 0.072 -10000 0 -0.28 22 22
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.026 0.003 -10000 0 -10000 0 0
LAT2 -0.002 0.084 -10000 0 -0.4 5 5
AP1 -0.11 0.22 -10000 0 -0.53 49 49
mol:PIP3 0.035 0.17 0.37 9 -0.38 32 41
IKBKB 0.027 0.12 0.31 12 -0.29 19 31
AKT1 0.034 0.16 0.3 64 -0.41 3 67
IKBKG 0.027 0.12 0.29 15 -0.3 19 34
MS4A2 0.026 0.046 0.33 7 -10000 0 7
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.025 0.034 -10000 0 -0.62 1 1
MAP3K1 0.031 0.13 0.28 1 -0.45 10 11
mol:Ca2+ 0.037 0.14 0.3 16 -0.29 32 48
LYN 0.024 0.014 -10000 0 -10000 0 0
CBLB -0.003 0.085 -10000 0 -0.37 7 7
SHC1 0.019 0.011 -10000 0 -10000 0 0
RasGAP/p62DOK 0.008 0.13 -10000 0 -0.37 35 35
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.026 0.003 -10000 0 -10000 0 0
PLD2 0.036 0.17 0.33 69 -0.33 31 100
PTPN13 -0.05 0.17 -10000 0 -0.54 19 19
PTPN11 0.025 0.018 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.032 0.12 0.32 3 -0.33 4 7
SYK 0.023 0.06 -10000 0 -0.62 3 3
GRB2 0.025 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.022 0.13 -10000 0 -0.38 34 34
LAT -0.003 0.086 -10000 0 -0.37 7 7
PAK2 0.032 0.14 -10000 0 -0.5 10 10
NFATC2 -0.091 0.21 -10000 0 -0.53 62 62
HRAS 0.03 0.15 -10000 0 -0.53 11 11
GAB2 0.025 0.004 -10000 0 -10000 0 0
PLA2G1B 0.024 0.073 -10000 0 -0.98 1 1
Fc epsilon R1 0.002 0.13 -10000 0 -0.41 32 32
Antigen/IgE/Fc epsilon R1 0.003 0.12 -10000 0 -0.37 32 32
mol:GDP -0.009 0.13 -10000 0 -0.58 12 12
JUN 0.015 0.082 -10000 0 -0.62 6 6
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.023 0.048 -10000 0 -0.62 2 2
FOS -0.27 0.31 -10000 0 -0.59 176 176
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.001 0.091 -10000 0 -0.37 8 8
CHUK 0.024 0.12 0.29 11 -0.29 19 30
KLRG1 -0.005 0.088 -10000 0 -0.35 9 9
VAV1 -0.012 0.11 -10000 0 -0.45 13 13
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.003 0.084 -10000 0 -0.37 7 7
negative regulation of mast cell degranulation 0.007 0.09 -10000 0 -0.37 6 6
BTK -0.006 0.14 -10000 0 -0.6 12 12
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.11 0.21 -10000 0 -0.35 126 126
GAB2/PI3K/SHP2 -0.025 0.099 -10000 0 -0.33 33 33
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.009 0.084 -10000 0 -0.27 30 30
RAF1 0.021 0.073 -10000 0 -0.96 1 1
Fc epsilon R1/FcgammaRIIB/SHIP -0.12 0.23 -10000 0 -0.41 131 131
FCER1G 0.012 0.061 0.33 1 -0.61 3 4
FCER1A -0.032 0.18 0.33 1 -0.63 29 30
Antigen/IgE/Fc epsilon R1/Fyn 0.009 0.12 -10000 0 -0.35 32 32
MAPK3 0.018 0.075 -10000 0 -1 1 1
MAPK1 0.019 0.071 -10000 0 -0.88 1 1
NFKB1 0.024 0.008 -10000 0 -10000 0 0
MAPK8 -0.051 0.24 -10000 0 -0.62 41 41
DUSP1 -0.035 0.19 -10000 0 -0.62 34 34
NF-kappa-B/RelA 0.016 0.069 -10000 0 -0.2 12 12
actin cytoskeleton reorganization 0.024 0.12 -10000 0 -0.62 5 5
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.004 0.13 -10000 0 -0.52 10 10
FER -0.003 0.085 -10000 0 -0.37 7 7
RELA 0.026 0.004 -10000 0 -10000 0 0
ITK -0.015 0.1 0.16 1 -0.46 18 19
SOS1 0.026 0.001 -10000 0 -10000 0 0
PLCG1 0.021 0.15 -10000 0 -0.54 13 13
cytokine secretion -0.002 0.04 -10000 0 -10000 0 0
SPHK1 0.016 0.11 0.26 13 -0.38 9 22
PTK2 0.024 0.12 -10000 0 -0.72 4 4
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.013 0.14 -10000 0 -0.4 33 33
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.04 0.17 0.36 11 -0.37 31 42
MAP2K2 0.017 0.07 -10000 0 -0.9 1 1
MAP2K1 0.016 0.068 -10000 0 -0.9 1 1
MAP2K7 0.026 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 0.001 0.089 0.24 1 -0.41 5 6
MAP2K4 -0.09 0.32 -10000 0 -0.86 53 53
Fc epsilon R1/FcgammaRIIB -0.13 0.24 -10000 0 -0.43 131 131
mol:Choline 0.036 0.17 0.33 69 -0.32 31 100
SHC/Grb2/SOS1 0.026 0.097 -10000 0 -0.36 7 7
FYN 0.024 0.007 -10000 0 -10000 0 0
DOK1 0.026 0.001 -10000 0 -10000 0 0
PXN 0.023 0.12 -10000 0 -0.66 4 4
HCLS1 -0.005 0.09 -10000 0 -0.37 9 9
PRKCB 0.022 0.16 0.32 11 -0.41 21 32
FCGR2B -0.2 0.3 0.34 2 -0.62 124 126
IGHE 0.002 0.007 -10000 0 -10000 0 0
KLRG1/SHIP 0.007 0.092 -10000 0 -0.38 6 6
LCP2 0.015 0.082 -10000 0 -0.62 6 6
PLA2G4A -0.021 0.12 0.24 1 -0.39 27 28
RASA1 0.022 0.048 -10000 0 -0.62 2 2
mol:Phosphatidic acid 0.036 0.17 0.33 69 -0.32 31 100
IKK complex 0.031 0.11 0.28 16 -0.24 13 29
WIPF1 0.026 0.003 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.032 0.046 0.34 8 -10000 0 8
alphaV beta3 Integrin 0 0.13 0.25 1 -0.46 28 29
PTK2 -0.066 0.19 -10000 0 -0.5 46 46
positive regulation of JNK cascade -0.04 0.14 -10000 0 -0.33 49 49
CDC42/GDP -0.044 0.19 -10000 0 -0.45 48 48
Rac1/GDP -0.043 0.19 -10000 0 -0.44 48 48
RAP1B 0.026 0.003 -10000 0 -10000 0 0
RAP1A 0.025 0.005 -10000 0 -10000 0 0
CTNNB1 0.026 0.002 -10000 0 -10000 0 0
CDC42/GTP -0.046 0.18 -10000 0 -0.41 48 48
nectin-3/I-afadin -0.028 0.16 -10000 0 -0.46 46 46
RAPGEF1 -0.063 0.2 -10000 0 -0.49 46 46
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.083 0.21 -10000 0 -0.56 46 46
PDGFB-D/PDGFRB 0.032 0.046 0.34 8 -10000 0 8
TLN1 -0.025 0.08 -10000 0 -0.52 3 3
Rap1/GTP -0.042 0.14 -10000 0 -0.35 45 45
IQGAP1 0.025 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.043 0.018 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.028 0.16 -10000 0 -0.46 46 46
PVR 0.026 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.026 0.004 -10000 0 -10000 0 0
mol:GDP -0.069 0.22 -10000 0 -0.55 49 49
MLLT4 0.023 0.008 -10000 0 -10000 0 0
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
PI3K 0.014 0.15 -10000 0 -0.36 47 47
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.034 0.018 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly -0.04 0.15 -10000 0 -0.34 49 49
PVRL1 0.026 0.017 0.34 1 -10000 0 1
PVRL3 -0.055 0.21 -10000 0 -0.62 46 46
PVRL2 0.026 0.004 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
CDH1 -0.015 0.15 -10000 0 -0.62 22 22
CLDN1 0.017 0.075 -10000 0 -0.62 5 5
JAM-A/CLDN1 -0.007 0.14 -10000 0 -0.37 39 39
SRC -0.094 0.24 -10000 0 -0.62 48 48
ITGB3 -0.024 0.17 -10000 0 -0.62 28 28
nectin-1(dimer)/I-afadin/I-afadin 0.034 0.018 -10000 0 -10000 0 0
FARP2 -0.068 0.23 -10000 0 -0.54 49 49
RAC1 0.026 0.004 -10000 0 -10000 0 0
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.011 0.15 -10000 0 -0.4 46 46
nectin-1/I-afadin 0.034 0.018 -10000 0 -10000 0 0
nectin-2/I-afadin 0.034 0.013 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.034 0.008 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.011 0.15 -10000 0 -0.4 46 46
CDC42/GTP/IQGAP1/filamentous actin 0.032 0.01 -10000 0 -10000 0 0
F11R 0.02 0.011 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.04 0.14 -10000 0 -0.33 49 49
alphaV/beta3 Integrin/Talin -0.026 0.14 0.35 1 -0.44 29 30
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.034 0.013 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.034 0.013 -10000 0 -10000 0 0
PIP5K1C -0.024 0.087 -10000 0 -0.23 46 46
VAV2 -0.07 0.23 -10000 0 -0.56 47 47
RAP1/GDP -0.039 0.18 -10000 0 -0.42 46 46
ITGAV 0.027 0.017 0.34 1 -10000 0 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.011 0.15 -10000 0 -0.4 46 46
nectin-3(dimer)/I-afadin/I-afadin -0.028 0.16 -10000 0 -0.46 46 46
Rac1/GTP -0.047 0.18 -10000 0 -0.42 49 49
PTPRM -0.022 0.096 -10000 0 -0.26 46 46
E-cadherin/beta catenin/alpha catenin 0.038 0.1 -10000 0 -0.33 22 22
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.025 0.006 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.019 0.002 -10000 0 -10000 0 0
PRKCZ -0.001 0.12 -10000 0 -0.52 17 17
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.025 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.05 0.15 -10000 0 -0.35 46 46
IRAK/TOLLIP 0.029 0.007 -10000 0 -10000 0 0
IKBKB 0.023 0.009 -10000 0 -10000 0 0
IKBKG 0.026 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.036 0.032 0.25 2 -0.46 1 3
IL1A 0.024 0.024 0.34 2 -10000 0 2
IL1B -0.069 0.18 -10000 0 -0.47 62 62
IRAK/TRAF6/p62/Atypical PKCs 0.042 0.078 -10000 0 -0.33 12 12
IL1R2 0.025 0.037 0.34 1 -0.62 1 2
IL1R1 0.021 0.058 -10000 0 -0.62 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.043 0.12 0.25 1 -0.44 14 15
TOLLIP 0.026 0.003 -10000 0 -10000 0 0
TICAM2 0.024 0.034 -10000 0 -0.62 1 1
MAP3K3 0.025 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.017 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.008 0.082 0.34 1 -0.45 1 2
JUN -0.03 0.093 -10000 0 -0.33 28 28
MAP3K7 0.024 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.053 0.21 -10000 0 -0.38 96 96
IL1 alpha/IL1R1/IL1RAP/MYD88 0.01 0.15 -10000 0 -0.39 43 43
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.022 0.15 -10000 0 -0.37 43 43
IL1 beta fragment/IL1R1/IL1RAP -0.078 0.21 -10000 0 -0.4 98 98
NFKB1 0.024 0.008 -10000 0 -10000 0 0
MAPK8 -0.024 0.084 -10000 0 -0.32 24 24
IRAK1 0.014 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.023 0.16 -10000 0 -0.46 45 45
IRAK4 0.026 0.002 -10000 0 -10000 0 0
PRKCI 0.026 0.002 -10000 0 -10000 0 0
TRAF6 0.024 0.034 -10000 0 -0.62 1 1
PI3K 0.034 0.052 -10000 0 -0.64 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.056 0.16 -10000 0 -0.37 48 48
CHUK 0.025 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.078 0.21 -10000 0 -0.4 98 98
IL1 beta/IL1R2 -0.041 0.17 -10000 0 -0.41 62 62
IRAK/TRAF6/TAK1/TAB1/TAB2 0.033 0.022 -10000 0 -0.32 1 1
NF kappa B1 p50/RelA -0.059 0.19 -10000 0 -0.36 94 94
IRAK3 0.011 0.1 0.34 1 -0.62 9 10
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.051 0.2 -10000 0 -0.37 94 94
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.01 0.11 -10000 0 -0.3 43 43
IL1 alpha/IL1R1/IL1RAP -0.006 0.16 -10000 0 -0.42 44 44
RELA 0.026 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.028 0.029 0.34 3 -10000 0 3
MYD88 0.026 0.002 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.042 0.026 -10000 0 -0.34 1 1
IL1RAP -0.052 0.21 -10000 0 -0.62 44 44
UBE2N 0.026 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.06 0.17 -10000 0 -0.33 88 88
CASP1 0.023 0.038 -10000 0 -0.46 2 2
IL1RN/IL1R2 -0.019 0.16 0.25 1 -0.47 42 43
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.062 0.21 -10000 0 -0.39 97 97
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.003 0.094 -10000 0 -0.44 5 5
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
IL1RN -0.048 0.2 -10000 0 -0.62 42 42
TRAF6/TAK1/TAB1/TAB2 0.034 0.022 -10000 0 -0.33 1 1
MAP2K6 0.009 0.061 -10000 0 -0.36 7 7
p38 MAPK 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
TRAF6/ASK1 -0.017 0.1 -10000 0 -0.33 34 34
TRAF2/ASK1 -0.011 0.12 -10000 0 -0.35 41 41
ATM 0.025 0.005 -10000 0 -10000 0 0
MAP2K3 -0.059 0.099 -10000 0 -0.35 11 11
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.07 0.14 -10000 0 -0.39 43 43
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.054 0.21 -10000 0 -0.58 48 48
TXN 0.007 0.001 -10000 0 -10000 0 0
CALM1 0.025 0.006 -10000 0 -10000 0 0
GADD45A 0.018 0.063 -10000 0 -0.49 5 5
GADD45B -0.068 0.22 -10000 0 -0.59 55 55
MAP3K1 0.026 0.002 -10000 0 -10000 0 0
MAP3K6 0.025 0.018 0.34 1 -10000 0 1
MAP3K7 0.024 0.007 -10000 0 -10000 0 0
MAP3K4 0.023 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.014 0.14 0.25 1 -0.43 37 38
TAK1/TAB family -0.007 0.032 -10000 0 -0.2 4 4
RAC1/OSM/MEKK3 0.048 0.012 -10000 0 -10000 0 0
TRAF2 0.026 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.041 0.09 -10000 0 -0.32 6 6
TRAF6 0.006 0.02 -10000 0 -0.37 1 1
RAC1 0.026 0.004 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.28 0.32 -10000 0 -0.62 175 175
CCM2 0.026 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.17 0.21 -10000 0 -0.4 175 175
MAPK11 0.036 0.058 0.34 13 -10000 0 13
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.19 0.23 -10000 0 -0.4 191 191
OSM/MEKK3 0.037 0.009 -10000 0 -10000 0 0
TAOK1 0.011 0.028 -10000 0 -0.37 2 2
TAOK2 0.013 0.004 -10000 0 -10000 0 0
TAOK3 0.014 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.024 0.008 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 -0.041 0.19 -10000 0 -0.55 41 41
MAP3K10 0.026 0.004 -10000 0 -10000 0 0
MAP3K3 0.025 0.005 -10000 0 -10000 0 0
TRX/ASK1 -0.016 0.12 -10000 0 -0.39 33 33
GADD45/MTK1/MTK1 -0.052 0.2 -10000 0 -0.41 79 79
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.027 0.2 0.41 1 -0.36 80 81
SMAD6-7/SMURF1 0.033 0.082 -10000 0 -0.4 12 12
NOG 0.025 0.037 0.34 5 -10000 0 5
SMAD9 -0.044 0.18 -10000 0 -0.5 42 42
SMAD4 0.025 0.005 -10000 0 -10000 0 0
SMAD5 -0.036 0.14 -10000 0 -0.42 16 16
BMP7/USAG1 0.091 0.11 0.27 89 -10000 0 89
SMAD5/SKI -0.028 0.15 0.34 1 -0.41 17 18
SMAD1 -0.005 0.087 -10000 0 -0.44 7 7
BMP2 0.021 0.065 0.34 2 -0.54 4 6
SMAD1/SMAD1/SMAD4 -0.002 0.1 -10000 0 -0.47 6 6
BMPR1A 0.025 0.005 -10000 0 -10000 0 0
BMPR1B -0.099 0.25 0.34 4 -0.57 76 80
BMPR1A-1B/BAMBI -0.065 0.21 -10000 0 -0.43 81 81
AHSG -0.076 0.24 -10000 0 -0.62 58 58
CER1 0.021 0.034 0.34 4 -10000 0 4
BMP2-4/CER1 0.056 0.067 -10000 0 -0.36 3 3
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.032 0.13 -10000 0 -0.42 12 12
BMP2-4 (homodimer) 0.049 0.073 0.25 29 -0.42 3 32
RGMB 0.023 0.05 0.34 1 -0.62 2 3
BMP6/BMPR2/BMPR1A-1B -0.022 0.17 -10000 0 -0.37 61 61
RGMA 0.054 0.09 0.34 33 -10000 0 33
SMURF1 0.025 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.042 0.13 -10000 0 -0.41 14 14
BMP2-4/USAG1 0.089 0.099 0.43 6 -0.36 3 9
SMAD6/SMURF1/SMAD5 -0.028 0.15 0.34 1 -0.42 16 17
SOSTDC1 0.076 0.12 0.34 60 -10000 0 60
BMP7/BMPR2/BMPR1A-1B -0.003 0.18 0.42 1 -0.36 63 64
SKI 0.024 0.008 -10000 0 -10000 0 0
BMP6 (homodimer) 0.017 0.078 0.34 2 -0.62 5 7
HFE2 -0.04 0.18 -10000 0 -0.62 34 34
ZFYVE16 0.026 0.002 -10000 0 -10000 0 0
MAP3K7 0.024 0.007 -10000 0 -10000 0 0
BMP2-4/CHRD 0.053 0.09 -10000 0 -0.37 10 10
SMAD5/SMAD5/SMAD4 -0.027 0.15 0.34 1 -0.42 16 17
MAPK1 0.026 0.004 -10000 0 -10000 0 0
TAK1/TAB family -0.025 0.12 -10000 0 -0.35 15 15
BMP7 (homodimer) 0.058 0.1 0.34 42 -10000 0 42
NUP214 0.026 0.003 -10000 0 -10000 0 0
BMP6/FETUA -0.05 0.18 -10000 0 -0.45 63 63
SMAD1/SKI 0.004 0.089 -10000 0 -0.42 7 7
SMAD6 0.005 0.11 -10000 0 -0.59 12 12
CTDSP2 0.026 0.004 -10000 0 -10000 0 0
BMP2-4/FETUA -0.011 0.18 -10000 0 -0.39 60 60
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.01 0.21 0.34 30 -0.61 35 65
BMPR2 (homodimer) 0.026 0.002 -10000 0 -10000 0 0
GADD34/PP1CA 0.05 0.016 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.06 0.19 -10000 0 -0.43 74 74
CHRDL1 -0.08 0.25 0.34 10 -0.62 64 74
ENDOFIN/SMAD1 0.004 0.091 -10000 0 -0.42 7 7
SMAD6-7/SMURF1/SMAD1 0.01 0.12 -10000 0 -0.49 7 7
SMAD6/SMURF1 0.025 0.005 -10000 0 -10000 0 0
BAMBI -0.019 0.16 -10000 0 -0.62 25 25
SMURF2 0.025 0.005 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.012 0.18 -10000 0 -0.39 63 63
BMP2-4/GREM1 0.031 0.16 0.43 1 -0.38 37 38
SMAD7 0.022 0.048 -10000 0 -0.62 2 2
SMAD8A/SMAD8A/SMAD4 -0.045 0.19 -10000 0 -0.48 47 47
SMAD1/SMAD6 0.003 0.089 -10000 0 -0.41 6 6
TAK1/SMAD6 0.035 0.012 -10000 0 -10000 0 0
BMP7 0.058 0.1 0.34 42 -10000 0 42
BMP6 0.017 0.079 0.34 2 -0.62 5 7
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.023 0.13 -10000 0 -0.38 15 15
PPM1A 0.025 0.006 -10000 0 -10000 0 0
SMAD1/SMURF2 0.003 0.091 -10000 0 -0.42 7 7
SMAD7/SMURF1 0.034 0.031 -10000 0 -0.35 2 2
CTDSPL 0.026 0.002 -10000 0 -10000 0 0
PPP1CA 0.025 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.003 -10000 0 -10000 0 0
CTDSP1 0.026 0.003 -10000 0 -10000 0 0
PPP1R15A 0.026 0.017 0.34 1 -10000 0 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.044 0.16 -10000 0 -0.42 30 30
CHRD 0.015 0.09 0.34 1 -0.62 7 8
BMPR2 0.026 0.002 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.038 0.14 -10000 0 -0.42 14 14
BMP4 0.049 0.084 0.34 28 -10000 0 28
FST -0.028 0.18 0.34 1 -0.62 31 32
BMP2-4/NOG 0.061 0.066 -10000 0 -0.34 2 2
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.004 0.18 0.41 1 -0.34 62 63
FAS signaling pathway (CD95)

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
SPTAN1 -0.006 0.027 0.26 1 -0.27 1 2
RFC1 -0.003 0.037 0.22 6 -0.27 1 7
PRKDC 0.018 0.073 0.22 40 -10000 0 40
RIPK1 0.023 0.012 -10000 0 -10000 0 0
CASP7 -0.01 0.13 -10000 0 -0.69 11 11
FASLG/FAS/FADD/FAF1 0.027 0.11 0.32 7 -0.33 11 18
MAP2K4 -0.03 0.17 0.35 2 -0.47 31 33
mol:ceramide -0.003 0.11 0.3 4 -0.43 11 15
GSN -0.005 0.028 0.26 1 -0.27 1 2
FASLG/FAS/FADD/FAF1/Caspase 8 0.023 0.097 0.27 1 -0.37 7 8
FAS 0 0.11 -10000 0 -0.59 12 12
BID -0.012 0.029 0.28 3 -10000 0 3
MAP3K1 -0.02 0.13 0.26 1 -0.49 16 17
MAP3K7 0.023 0.01 -10000 0 -10000 0 0
RB1 -0.005 0.027 0.26 1 -0.27 1 2
CFLAR 0.026 0.009 -10000 0 -10000 0 0
HGF/MET -0.27 0.3 -10000 0 -0.51 206 206
ARHGDIB -0.006 0.027 0.26 1 -0.27 1 2
FADD 0.02 0.019 -10000 0 -10000 0 0
actin filament polymerization 0.012 0.044 0.27 1 -0.26 1 2
NFKB1 -0.053 0.21 -10000 0 -0.66 31 31
MAPK8 -0.067 0.22 0.37 6 -0.5 61 67
DFFA -0.006 0.027 0.22 1 -0.27 1 2
DNA fragmentation during apoptosis -0.012 0.048 0.24 2 -0.32 2 4
FAS/FADD/MET 0.028 0.08 -10000 0 -0.4 10 10
CFLAR/RIP1 0.035 0.018 -10000 0 -10000 0 0
FAIM3 0.016 0.061 0.34 1 -0.62 3 4
FAF1 0.02 0.021 -10000 0 -10000 0 0
PARP1 -0.006 0.028 0.26 1 -0.27 1 2
DFFB -0.006 0.036 0.24 2 -0.32 2 4
CHUK -0.051 0.2 -10000 0 -0.66 28 28
FASLG 0.004 0.1 0.34 3 -0.62 8 11
FAS/FADD 0.014 0.089 -10000 0 -0.46 11 11
HGF -0.32 0.32 0.34 1 -0.62 194 195
LMNA -0.001 0.049 0.23 1 -10000 0 1
CASP6 -0.005 0.023 0.26 1 -0.27 1 2
CASP10 0.02 0.019 -10000 0 -10000 0 0
CASP3 -0.003 0.025 0.33 1 -0.3 1 2
PTPN13 -0.13 0.27 0.34 2 -0.55 98 100
CASP8 -0.012 0.039 0.39 3 -0.24 1 4
IL6 -0.18 0.49 0.51 6 -1.2 60 66
MET 0.023 0.034 -10000 0 -0.62 1 1
ICAD/CAD -0.006 0.034 0.41 1 -0.3 2 3
FASLG/FAS/FADD/FAF1/Caspase 10 -0.003 0.11 0.3 3 -0.43 11 14
activation of caspase activity by cytochrome c -0.012 0.029 0.28 3 -10000 0 3
PAK2 -0.005 0.035 0.23 4 -0.27 1 5
BCL2 0.024 0.034 -10000 0 -0.62 1 1
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF 0.048 0.046 -10000 0 -0.32 1 1
epithelial cell differentiation -0.005 0.087 -10000 0 -0.37 3 3
ITCH 0.026 0.01 -10000 0 -10000 0 0
WWP1 0.06 0.084 -10000 0 -10000 0 0
FYN 0.024 0.007 -10000 0 -10000 0 0
EGFR 0.01 0.1 -10000 0 -0.62 9 9
PRL 0.019 0.024 0.34 2 -10000 0 2
neuron projection morphogenesis -0.034 0.17 0.37 7 -10000 0 7
PTPRZ1 0.033 0.057 0.34 12 -10000 0 12
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.064 0.15 -10000 0 -0.34 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.09 0.17 -10000 0 -0.35 85 85
ADAM17 0.026 0.01 -10000 0 -10000 0 0
ErbB4/ErbB4 0.017 0.022 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.009 0.15 0.34 3 -0.37 38 41
NCOR1 0.021 0.025 -10000 0 -0.3 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.09 0.16 -10000 0 -0.33 82 82
GRIN2B -0.09 0.15 -10000 0 -0.32 77 77
ErbB4/ErbB2/betacellulin 0.04 0.059 -10000 0 -0.33 5 5
STAT1 0.028 0.023 0.34 2 -10000 0 2
HBEGF 0.022 0.048 -10000 0 -0.62 2 2
PRLR 0.006 0.11 -10000 0 -0.62 11 11
E4ICDs/ETO2 0.007 0.12 -10000 0 -0.36 24 24
axon guidance -0.015 0.08 -10000 0 -10000 0 0
NEDD4 0.022 0.048 -10000 0 -0.61 2 2
Prolactin receptor/Prolactin receptor/Prolactin 0.015 0.084 0.25 1 -0.45 11 12
CBFA2T3 -0.056 0.2 -10000 0 -0.52 54 54
ErbB4/ErbB2/HBEGF 0.04 0.059 -10000 0 -0.33 5 5
MAPK3 -0.053 0.15 0.39 2 -10000 0 2
STAT1 (dimer) 0.053 0.04 0.32 1 -10000 0 1
MAPK1 -0.053 0.15 0.39 2 -10000 0 2
JAK2 0.024 0.018 -10000 0 -0.3 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.1 0.16 -10000 0 -0.34 85 85
NRG1 -0.16 0.22 -10000 0 -0.42 139 139
NRG3 -0.073 0.24 0.34 6 -0.6 59 65
NRG2 0.089 0.13 0.34 74 -10000 0 74
NRG4 -0.067 0.22 0.34 1 -0.61 53 54
heart development -0.015 0.08 -10000 0 -10000 0 0
neural crest cell migration -0.1 0.16 -10000 0 -0.34 85 85
ERBB2 0.005 0.062 -10000 0 -0.47 6 6
WWOX/E4ICDs 0.048 0.038 -10000 0 -10000 0 0
SHC1 0.02 0.011 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.002 0.15 -10000 0 -0.36 38 38
apoptosis 0.017 0.17 0.41 37 -0.31 3 40
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.093 0.096 0.32 21 -10000 0 21
ErbB4/ErbB2/epiregulin 0.055 0.08 -10000 0 -0.33 5 5
ErbB4/ErbB4/betacellulin/betacellulin 0.049 0.045 0.33 2 -10000 0 2
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.055 0.079 -10000 0 -10000 0 0
MDM2 0.037 0.045 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.099 0.16 -10000 0 -0.33 105 105
STAT5A -0.012 0.079 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.098 0.17 -10000 0 -0.34 85 85
DLG4 0.022 0.01 -10000 0 -10000 0 0
GRB2/SHC 0.028 0.017 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.041 0.036 -10000 0 -10000 0 0
STAT5A (dimer) 0.002 0.099 -10000 0 -0.39 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.003 0.084 -10000 0 -10000 0 0
LRIG1 0.026 0.004 -10000 0 -10000 0 0
EREG 0.049 0.089 0.34 31 -10000 0 31
BTC 0.025 0.029 0.34 3 -10000 0 3
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.016 0.079 -10000 0 -10000 0 0
ERBB4 0.017 0.022 -10000 0 -10000 0 0
STAT5B 0.026 0.004 -10000 0 -10000 0 0
YAP1 0.01 0.07 -10000 0 -0.36 11 11
GRB2 0.025 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.009 0.13 -10000 0 -0.33 39 39
glial cell differentiation -0.04 0.036 -10000 0 -10000 0 0
WWOX 0.023 0.008 -10000 0 -10000 0 0
cell proliferation -0.12 0.18 -10000 0 -0.45 29 29
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.018 0.096 -10000 0 -0.45 11 11
HDAC1 0.028 0.017 -10000 0 -10000 0 0
AES 0.027 0.008 -10000 0 -10000 0 0
FBXW11 0.025 0.004 -10000 0 -10000 0 0
DTX1 -0.15 0.28 -10000 0 -0.61 98 98
LRP6/FZD1 0.026 0.074 -10000 0 -0.46 8 8
TLE1 0.025 0.034 -10000 0 -0.62 1 1
AP1 -0.14 0.21 -10000 0 -0.37 135 135
NCSTN 0.02 0.011 -10000 0 -10000 0 0
ADAM10 0.024 0.034 -10000 0 -0.62 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.033 0.19 -10000 0 -0.67 20 20
NICD/RBPSUH 0.023 0.079 -10000 0 -0.4 10 10
WIF1 0.052 0.097 0.34 37 -10000 0 37
NOTCH1 0.009 0.072 -10000 0 -0.41 10 10
PSENEN 0.026 0.004 -10000 0 -10000 0 0
KREMEN2 0.057 0.098 0.34 39 -10000 0 39
DKK1 0.13 0.15 0.34 123 -10000 0 123
beta catenin/beta TrCP1 0.013 0.082 -10000 0 -10000 0 0
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.02 0.011 -10000 0 -10000 0 0
AXIN1 0.002 0.1 0.31 1 -0.45 12 13
CtBP/CBP/TCF1/TLE1/AES 0.029 0.063 0.29 3 -0.37 3 6
PSEN1 0.025 0.006 -10000 0 -10000 0 0
FOS -0.27 0.31 -10000 0 -0.59 176 176
JUN 0.015 0.082 -10000 0 -0.62 6 6
MAP3K7 0.026 0.01 -10000 0 -10000 0 0
CTNNB1 0.004 0.081 0.26 2 -10000 0 2
MAPK3 0.025 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.087 0.088 0.43 4 -10000 0 4
HNF1A 0.02 0.067 -10000 0 -0.61 4 4
CTBP1 0.026 0.008 -10000 0 -10000 0 0
MYC -0.15 0.47 -10000 0 -1.4 43 43
NKD1 0.065 0.19 0.34 79 -0.6 16 95
FZD1 0.012 0.096 0.34 1 -0.62 8 9
NOTCH1 precursor/Deltex homolog 1 -0.061 0.17 -10000 0 -0.52 12 12
apoptosis -0.14 0.21 -10000 0 -0.36 135 135
Delta 1/NOTCHprecursor 0.018 0.096 -10000 0 -0.45 11 11
DLL1 0.015 0.079 0.34 2 -0.46 8 10
PPARD 0.005 0.11 -10000 0 -1.1 3 3
Gamma Secretase 0.053 0.036 -10000 0 -10000 0 0
APC 0.018 0.058 0.31 1 -0.32 3 4
DVL1 0.017 0.027 -10000 0 -0.29 1 1
CSNK2A1 0.025 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0.001 0.006 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.12 0.12 0.43 21 -10000 0 21
LRP6 0.025 0.005 -10000 0 -10000 0 0
CSNK1A1 0.025 0.005 -10000 0 -10000 0 0
NLK 0.016 0.015 -10000 0 -10000 0 0
CCND1 -0.044 0.3 -10000 0 -1.4 16 16
WNT1 0.027 0.033 0.34 4 -10000 0 4
Axin1/APC/beta catenin 0.027 0.1 0.32 2 -0.38 5 7
DKK2 0.064 0.11 0.34 47 -10000 0 47
NOTCH1 precursor/DVL1 0.01 0.086 -10000 0 -0.46 5 5
GSK3B 0.027 0.001 -10000 0 -10000 0 0
FRAT1 0.024 0.034 -10000 0 -0.62 1 1
NOTCH/Deltex homolog 1 -0.062 0.17 -10000 0 -0.52 12 12
PPP2R5D -0.008 0.1 0.3 11 -0.29 7 18
MAPK1 0.026 0.004 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.065 0.087 -10000 0 -0.36 8 8
RBPJ 0.025 0.005 -10000 0 -10000 0 0
CREBBP 0.023 0.011 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex 0.2 0.27 0.56 87 -0.58 3 90
RAD9A 0.025 0.005 -10000 0 -10000 0 0
AP1 -0.18 0.26 -10000 0 -0.45 167 167
IFNAR2 0.045 0.026 -10000 0 -10000 0 0
AKT1 -0.092 0.16 -10000 0 -0.45 28 28
ER alpha/Oestrogen -0.22 0.23 -10000 0 -0.42 198 198
NFX1/SIN3/HDAC complex 0.039 0.078 -10000 0 -0.31 9 9
EGF 0.1 0.13 0.35 83 -10000 0 83
SMG5 0.02 0.011 -10000 0 -10000 0 0
SMG6 0.022 0.009 -10000 0 -10000 0 0
SP3/HDAC2 0.066 0.042 -10000 0 -10000 0 0
TERT/c-Abl 0.13 0.21 0.47 45 -0.55 3 48
SAP18 0.028 0.008 -10000 0 -10000 0 0
MRN complex 0.037 0.025 -10000 0 -10000 0 0
WT1 0.067 0.087 0.36 28 -10000 0 28
WRN 0.021 0.011 -10000 0 -10000 0 0
SP1 0.055 0.036 -10000 0 -10000 0 0
SP3 0.035 0.012 -10000 0 -10000 0 0
TERF2IP 0.024 0.007 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.017 0.1 -10000 0 -0.51 3 3
Mad/Max 0.061 0.035 0.31 1 -10000 0 1
TERT 0.2 0.27 0.57 80 -0.59 3 83
CCND1 0.16 0.34 0.63 33 -1 14 47
MAX 0.035 0.015 -10000 0 -10000 0 0
RBBP7 0.029 0.006 -10000 0 -10000 0 0
RBBP4 0.028 0.008 -10000 0 -10000 0 0
TERF2 0.021 0.01 -10000 0 -10000 0 0
PTGES3 0.026 0.003 -10000 0 -10000 0 0
SIN3A 0.029 0.006 -10000 0 -10000 0 0
Telomerase/911 0.088 0.076 -10000 0 -10000 0 0
CDKN1B 0.039 0.037 -10000 0 -10000 0 0
RAD1 0.025 0.005 -10000 0 -10000 0 0
XRCC5 0.026 0.003 -10000 0 -10000 0 0
XRCC6 0.026 0.004 -10000 0 -10000 0 0
SAP30 0.027 0.009 -10000 0 -10000 0 0
TRF2/PARP2 0.034 0.012 -10000 0 -10000 0 0
UBE3A 0.035 0.012 -10000 0 -10000 0 0
JUN 0.021 0.083 -10000 0 -0.61 6 6
E6 0.009 0.011 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.041 0.027 -10000 0 -10000 0 0
FOS -0.25 0.32 -10000 0 -0.59 167 167
IFN-gamma/IRF1 0.073 0.056 0.31 9 -10000 0 9
PARP2 0.026 0.003 -10000 0 -10000 0 0
BLM 0.12 0.15 0.34 116 -10000 0 116
Telomerase 0.082 0.12 0.29 23 -0.46 2 25
IRF1 0.038 0.015 -10000 0 -10000 0 0
ESR1 -0.3 0.31 -10000 0 -0.59 191 191
KU/TER 0.038 0.007 -10000 0 -10000 0 0
ATM/TRF2 0.035 0.012 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.038 0.082 -10000 0 -0.32 5 5
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.038 0.083 -10000 0 -0.33 5 5
HDAC1 0.028 0.008 -10000 0 -10000 0 0
HDAC2 0.047 0.031 -10000 0 -10000 0 0
ATM 0.014 0.016 -10000 0 -10000 0 0
SMAD3 -0.003 0.036 0.22 5 -10000 0 5
ABL1 0.026 0.004 -10000 0 -10000 0 0
MXD1 0.037 0.021 0.36 1 -10000 0 1
MRE11A 0.025 0.005 -10000 0 -10000 0 0
HUS1 0.026 0.004 -10000 0 -10000 0 0
RPS6KB1 0.025 0.006 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.086 0.25 0.52 24 -0.6 8 32
NR2F2 -0.005 0.037 -10000 0 -10000 0 0
MAPK3 0.018 0.03 -10000 0 -10000 0 0
MAPK1 0.017 0.03 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.011 0.042 0.34 4 -10000 0 4
NFKB1 0.024 0.008 -10000 0 -10000 0 0
HNRNPC 0.026 0.003 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.014 0.016 -10000 0 -10000 0 0
NBN 0.02 0.011 -10000 0 -10000 0 0
EGFR 0.018 0.099 -10000 0 -0.6 9 9
mol:Oestrogen 0.003 0.005 -10000 0 -10000 0 0
EGF/EGFR 0.082 0.12 0.26 77 -0.4 9 86
MYC -0.041 0.2 -10000 0 -0.6 39 39
IL2 0.046 0.037 -10000 0 -10000 0 0
KU 0.038 0.007 -10000 0 -10000 0 0
RAD50 0.025 0.005 -10000 0 -10000 0 0
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
TGFB1 0.011 0.042 0.34 4 -10000 0 4
TRF2/BLM 0.088 0.092 0.28 3 -10000 0 3
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.18 0.24 0.52 62 -0.54 3 65
SP1/HDAC2 0.086 0.066 -10000 0 -10000 0 0
PINX1 0.02 0.011 -10000 0 -10000 0 0
Telomerase/EST1A 0.014 0.097 -10000 0 -0.51 3 3
Smad3/Myc -0.037 0.12 -10000 0 -0.4 36 36
911 complex 0.049 0.015 -10000 0 -10000 0 0
IFNG 0.051 0.066 0.35 16 -10000 0 16
Telomerase/PinX1 0.013 0.097 -10000 0 -0.5 3 3
Telomerase/AKT1/mTOR/p70S6K 0.052 0.17 0.33 12 -0.41 15 27
SIN3B 0.029 0.006 -10000 0 -10000 0 0
YWHAE 0.022 0.009 -10000 0 -10000 0 0
Telomerase/EST1B 0.015 0.089 -10000 0 -0.54 2 2
response to DNA damage stimulus 0.004 0.018 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.048 0.036 -10000 0 -10000 0 0
TRF2/WRN 0.028 0.017 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.017 0.1 -10000 0 -0.51 3 3
E2F1 0.23 0.16 0.36 217 -10000 0 217
ZNFX1 0.029 0.006 -10000 0 -10000 0 0
PIF1 0.11 0.14 0.34 99 -10000 0 99
NCL 0.026 0.002 -10000 0 -10000 0 0
DKC1 0.026 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.007 0.13 0.45 22 -0.24 13 35
KIRREL -0.016 0.15 0.32 1 -0.62 22 23
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.007 0.13 0.24 13 -0.45 22 35
PLCG1 0.026 0.004 -10000 0 -10000 0 0
ARRB2 0.022 0.01 -10000 0 -10000 0 0
WASL 0.025 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.027 0.1 -10000 0 -0.35 19 19
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.006 0.086 -10000 0 -0.32 18 18
FYN 0.035 0.14 0.28 61 -0.33 21 82
mol:Ca2+ 0.029 0.11 -10000 0 -0.35 21 21
mol:DAG 0.03 0.11 -10000 0 -0.35 21 21
NPHS2 0.017 0.043 0.32 5 -10000 0 5
mol:IP3 0.03 0.11 -10000 0 -0.35 21 21
regulation of endocytosis 0.016 0.088 -10000 0 -0.31 21 21
Nephrin/NEPH1/podocin/Cholesterol 0.019 0.1 0.27 4 -0.34 22 26
establishment of cell polarity 0.007 0.13 0.24 13 -0.45 22 35
Nephrin/NEPH1/podocin/NCK1-2 0.041 0.11 -10000 0 -0.35 19 19
Nephrin/NEPH1/beta Arrestin2 0.018 0.09 -10000 0 -0.32 20 20
NPHS1 0.043 0.076 0.33 21 -10000 0 21
Nephrin/NEPH1/podocin 0.019 0.097 -10000 0 -0.33 21 21
TJP1 0.026 0.003 -10000 0 -10000 0 0
NCK1 0.026 0.001 -10000 0 -10000 0 0
NCK2 0.025 0.037 0.34 1 -0.62 1 2
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.031 0.11 -10000 0 -0.35 21 21
CD2AP 0.024 0.007 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.031 0.1 0.28 4 -0.35 18 22
GRB2 0.025 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.06 0.16 0.31 64 -0.31 21 85
cytoskeleton organization 0.001 0.096 -10000 0 -0.38 16 16
Nephrin/NEPH1 0.009 0.093 0.22 4 -0.32 22 26
Nephrin/NEPH1/ZO-1 0.02 0.11 -10000 0 -0.38 21 21
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.031 0.034 0.34 4 -10000 0 4
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.095 0.2 0.68 22 -10000 0 22
IL27/IL27R/JAK1 -0.087 0.23 0.57 2 -0.63 17 19
TBX21 -0.095 0.2 0.45 3 -0.54 24 27
IL12B 0.027 0.033 0.38 3 -10000 0 3
IL12A 0.013 0.038 0.22 12 -10000 0 12
IL6ST -0.13 0.28 -10000 0 -0.62 89 89
IL27RA/JAK1 0.014 0.045 -10000 0 -10000 0 0
IL27 -0.074 0.24 -10000 0 -0.62 57 57
TYK2 0.028 0.018 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.009 0.13 0.67 1 -10000 0 1
T-helper 2 cell differentiation 0.095 0.2 0.68 22 -10000 0 22
T cell proliferation during immune response 0.095 0.2 0.68 22 -10000 0 22
MAPKKK cascade -0.095 0.2 -10000 0 -0.68 22 22
STAT3 0.026 0.004 -10000 0 -10000 0 0
STAT2 0.026 0.003 -10000 0 -10000 0 0
STAT1 0.028 0.024 0.34 2 -10000 0 2
IL12RB1 0.006 0.12 -10000 0 -0.62 12 12
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.091 0.21 0.45 9 -0.58 24 33
IL27/IL27R/JAK2/TYK2 -0.096 0.21 -10000 0 -0.69 22 22
positive regulation of T cell mediated cytotoxicity -0.095 0.2 -10000 0 -0.68 22 22
STAT1 (dimer) -0.082 0.28 0.59 14 -0.73 18 32
JAK2 0.027 0.021 -10000 0 -0.31 1 1
JAK1 0.026 0.007 -10000 0 -10000 0 0
STAT2 (dimer) -0.084 0.2 -10000 0 -0.67 21 21
T cell proliferation -0.14 0.22 -10000 0 -0.65 33 33
IL12/IL12R/TYK2/JAK2 0.027 0.16 0.5 3 -0.88 7 10
IL17A -0.009 0.13 0.67 1 -10000 0 1
mast cell activation 0.095 0.2 0.68 22 -10000 0 22
IFNG -0.002 0.044 0.17 8 -0.11 8 16
T cell differentiation -0.004 0.007 0.02 4 -0.022 13 17
STAT3 (dimer) -0.083 0.2 -10000 0 -0.66 22 22
STAT5A (dimer) -0.083 0.2 -10000 0 -0.66 22 22
STAT4 (dimer) -0.097 0.22 -10000 0 -0.66 28 28
STAT4 0 0.13 0.34 1 -0.62 15 16
T cell activation -0.01 0.012 -10000 0 -0.2 1 1
IL27R/JAK2/TYK2 -0.031 0.18 -10000 0 -0.55 1 1
GATA3 -0.066 0.37 0.75 6 -1.4 25 31
IL18 -0.002 0.069 0.21 3 -0.38 10 13
positive regulation of mast cell cytokine production -0.081 0.2 -10000 0 -0.64 22 22
IL27/EBI3 -0.061 0.2 -10000 0 -0.45 73 73
IL27RA 0.002 0.044 -10000 0 -10000 0 0
IL6 -0.054 0.23 0.34 7 -0.62 49 56
STAT5A 0.027 0.017 0.34 1 -10000 0 1
monocyte differentiation 0.001 0.002 -10000 0 -10000 0 0
IL2 -0.008 0.028 -10000 0 -10000 0 0
IL1B -0.073 0.18 -10000 0 -0.46 63 63
EBI3 -0.001 0.13 -10000 0 -0.57 17 17
TNF -0.008 0.085 0.21 2 -0.46 12 14
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.004 0.075 -10000 0 -0.39 12 12
CRKL 0.025 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.003 -10000 0 -10000 0 0
DOCK1 0.011 0.094 -10000 0 -0.62 8 8
ITGA4 0.015 0.09 0.34 1 -0.62 7 8
alpha4/beta7 Integrin/MAdCAM1 0.055 0.084 0.42 1 -0.36 12 13
EPO -0.2 0.32 0.34 12 -0.62 130 142
alpha4/beta7 Integrin 0.023 0.089 0.25 1 -0.46 12 13
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.028 0.069 0.25 1 -0.46 7 8
EPO/EPOR (dimer) -0.13 0.24 0.25 12 -0.46 130 142
lamellipodium assembly 0.013 0.061 -10000 0 -0.51 2 2
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
PI3K 0.034 0.052 -10000 0 -0.64 2 2
ARF6 0.025 0.005 -10000 0 -10000 0 0
JAK2 -0.095 0.17 -10000 0 -0.32 126 126
PXN 0.026 0.003 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
MADCAM1 0.032 0.046 0.34 8 -10000 0 8
cell adhesion 0.052 0.083 0.41 1 -0.36 12 13
CRKL/CBL 0.036 0.01 -10000 0 -10000 0 0
ITGB1 0.025 0.005 -10000 0 -10000 0 0
SRC -0.002 0.11 -10000 0 -0.39 21 21
ITGB7 0.017 0.075 -10000 0 -0.62 5 5
RAC1 0.026 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.02 0.12 -10000 0 -0.43 23 23
p130Cas/Crk/Dock1 0.007 0.12 -10000 0 -0.38 25 25
VCAM1 -0.006 0.15 0.34 5 -0.62 20 25
RHOA 0.026 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.056 0.061 -10000 0 -0.36 7 7
BCAR1 -0.023 0.097 -10000 0 -0.37 21 21
EPOR 0.026 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.006 -10000 0 -10000 0 0
GIT1 0.026 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.063 -10000 0 -0.53 2 2
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.03 0.055 0.27 6 -10000 0 6
AES 0.03 0.048 0.24 6 -10000 0 6
FBXW11 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.026 0.074 -10000 0 -0.46 8 8
SMAD4 0.025 0.005 -10000 0 -10000 0 0
DKK2 0.064 0.11 0.34 47 -10000 0 47
TLE1 0.027 0.058 0.26 2 -0.62 1 3
MACF1 0.025 0.006 -10000 0 -10000 0 0
CTNNB1 0.027 0.087 0.33 2 -0.33 2 4
WIF1 0.052 0.096 0.34 37 -10000 0 37
beta catenin/RanBP3 0.049 0.19 0.45 49 -0.5 1 50
KREMEN2 0.057 0.098 0.34 39 -10000 0 39
DKK1 0.13 0.15 0.34 123 -10000 0 123
beta catenin/beta TrCP1 0.037 0.087 0.33 2 -10000 0 2
FZD1 0.012 0.096 0.34 1 -0.62 8 9
AXIN2 -0.034 0.4 0.62 11 -1.4 21 32
AXIN1 0.025 0.006 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.015 0.11 -10000 0 -0.52 7 7
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.051 0.13 0.33 2 -0.59 7 9
Axin1/APC/GSK3 0.004 0.068 0.26 1 -0.38 1 2
Axin1/APC/GSK3/beta catenin/Macf1 0.024 0.073 0.4 1 -0.37 5 6
HNF1A 0.021 0.08 0.26 3 -0.6 4 7
CTBP1 0.028 0.049 0.26 4 -10000 0 4
MYC -0.033 0.59 0.62 49 -1.5 42 91
RANBP3 0.026 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.088 0.088 0.43 4 -10000 0 4
NKD1 0.064 0.19 0.34 79 -0.58 17 96
TCF4 0.028 0.047 0.3 2 -10000 0 2
TCF3 0.029 0.048 0.27 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.052 0.069 -10000 0 -0.36 8 8
Ran/GTP 0.02 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.056 0.26 0.62 39 -0.49 5 44
LEF1 0.15 0.15 0.33 144 -10000 0 144
DVL1 0.012 0.055 0.27 1 -0.42 2 3
CSNK2A1 0.026 0.004 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.037 0.16 -10000 0 -0.51 10 10
DKK1/LRP6/Kremen 2 0.12 0.12 0.43 21 -10000 0 21
LRP6 0.025 0.005 -10000 0 -10000 0 0
CSNK1A1 0.031 0.055 0.25 11 -10000 0 11
NLK 0.021 0.017 -10000 0 -10000 0 0
CCND1 -0.053 0.36 0.78 7 -1.5 17 24
WNT1 0.026 0.034 0.34 4 -10000 0 4
GSK3A 0.026 0.003 -10000 0 -10000 0 0
GSK3B 0.026 0.001 -10000 0 -10000 0 0
FRAT1 0.023 0.034 -10000 0 -0.62 1 1
PPP2R5D -0.01 0.11 0.31 12 -0.27 7 19
APC 0.003 0.064 0.36 1 -0.34 8 9
WNT1/LRP6/FZD1 0.003 0.07 -10000 0 -0.29 7 7
CREBBP 0.028 0.048 0.25 4 -10000 0 4
Visual signal transduction: Rods

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
mol:K + 0.026 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.02 0.019 0.23 3 -10000 0 3
Metarhodopsin II/Arrestin 0.038 0.041 0.22 18 -10000 0 18
PDE6G/GNAT1/GTP 0.02 0.079 0.22 3 -0.39 12 15
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.028 0.029 0.34 3 -10000 0 3
GRK1 0.017 0.004 -10000 0 -10000 0 0
CNG Channel -0.048 0.16 -10000 0 -0.34 71 71
mol:Na + -0.039 0.16 -10000 0 -0.34 66 66
mol:ADP 0.017 0.004 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.047 0.089 0.43 1 -0.4 10 11
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.032 0.16 -10000 0 -0.34 66 66
CNGB1 0.031 0.057 0.34 12 -10000 0 12
RDH5 -0.062 0.22 -10000 0 -0.62 50 50
SAG 0.02 0.017 0.34 1 -10000 0 1
mol:Ca2+ -0.052 0.16 0.32 20 -0.59 2 22
Na + (4 Units) -0.042 0.14 -10000 0 -0.32 65 65
RGS9 0.02 0.12 0.34 14 -0.62 10 24
GNB1/GNGT1 0.055 0.071 -10000 0 -10000 0 0
GNAT1/GDP 0.055 0.081 0.39 1 -0.34 10 11
GUCY2D 0.057 0.1 0.34 43 -10000 0 43
GNGT1 0.06 0.11 0.34 46 -10000 0 46
GUCY2F 0.02 0.003 -10000 0 -10000 0 0
GNB5 0.026 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.023 0.083 0.32 2 -0.34 12 14
mol:11-cis-retinal -0.062 0.22 -10000 0 -0.62 50 50
mol:cGMP 0.042 0.075 0.35 1 -0.35 7 8
GNB1 0.024 0.008 -10000 0 -10000 0 0
Rhodopsin -0.023 0.17 0.25 12 -0.45 50 62
SLC24A1 0.026 0.003 -10000 0 -10000 0 0
CNGA1 -0.13 0.27 -10000 0 -0.6 90 90
Metarhodopsin II 0.033 0.037 0.2 16 -10000 0 16
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.057 0.091 0.42 1 -0.37 7 8
RGS9BP 0.032 0.049 0.34 9 -10000 0 9
Metarhodopsin II/Transducin 0.034 0.046 0.22 3 -10000 0 3
GCAP Family/Ca ++ 0.031 0.059 -10000 0 -0.37 7 7
PDE6A/B 0.048 0.068 -10000 0 -0.46 2 2
mol:Pi 0.046 0.088 0.43 1 -0.4 10 11
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.062 0.062 -10000 0 -10000 0 0
PDE6B 0.036 0.082 0.34 17 -0.62 2 19
PDE6A 0.033 0.054 0.34 11 -10000 0 11
PDE6G 0.004 0.12 -10000 0 -0.62 12 12
RHO 0.038 0.067 0.34 17 -10000 0 17
PDE6 0.058 0.12 0.37 1 -0.35 20 21
GUCA1A 0.02 0.025 0.34 2 -10000 0 2
GC2/GCAP Family 0.042 0.062 -10000 0 -0.37 7 7
GUCA1C 0.018 0 -10000 0 -10000 0 0
GUCA1B 0.012 0.088 -10000 0 -0.62 7 7
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.044 0.12 0.6 1 -0.44 16 17
MAP4K1 0.016 0.093 0.34 3 -0.62 7 10
MAP3K8 0.022 0.048 -10000 0 -0.62 2 2
PRKCB -0.028 0.18 -10000 0 -0.61 31 31
DBNL 0.026 0.004 -10000 0 -10000 0 0
CRKL 0.025 0.004 -10000 0 -10000 0 0
MAP3K1 -0.006 0.11 0.31 1 -0.47 13 14
JUN -0.093 0.27 -10000 0 -0.64 65 65
MAP3K7 -0.004 0.11 0.31 1 -0.47 13 14
GRAP2 0.016 0.1 0.34 6 -0.58 9 15
CRK 0.022 0.009 -10000 0 -10000 0 0
MAP2K4 -0.007 0.12 0.29 1 -0.54 12 13
LAT 0.027 0.024 0.34 2 -10000 0 2
LCP2 0.015 0.082 -10000 0 -0.62 6 6
MAPK8 -0.091 0.28 -10000 0 -0.66 65 65
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.001 0.12 0.34 1 -0.48 14 15
LAT/GRAP2/SLP76/HPK1/HIP-55 0.052 0.12 0.59 1 -0.42 16 17
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0.006 -10000 0 -10000 0 0
SMARCC1 0.013 0.016 -10000 0 -10000 0 0
REL 0.001 0.12 -10000 0 -0.62 12 12
HDAC7 -0.048 0.14 -10000 0 -0.45 19 19
JUN 0.015 0.082 -10000 0 -0.62 6 6
EP300 0.026 0.004 -10000 0 -10000 0 0
KAT2B 0.021 0.058 -10000 0 -0.61 3 3
KAT5 0.025 0.004 -10000 0 -10000 0 0
MAPK14 0.003 0.076 0.26 6 -0.46 7 13
FOXO1 0.02 0.045 -10000 0 -0.38 4 4
T-DHT/AR -0.034 0.16 -10000 0 -0.42 30 30
MAP2K6 0.014 0.099 0.34 6 -0.62 7 13
BRM/BAF57 0.028 0.072 -10000 0 -0.36 10 10
MAP2K4 0.019 0.018 -10000 0 -10000 0 0
SMARCA2 0.012 0.089 -10000 0 -0.49 10 10
PDE9A -0.096 0.32 -10000 0 -1.1 34 34
NCOA2 -0.037 0.18 -10000 0 -0.61 33 33
CEBPA 0.02 0.061 0.34 1 -0.62 3 4
EHMT2 0.024 0.009 -10000 0 -10000 0 0
cell proliferation 0.009 0.16 0.43 4 -0.47 11 15
NR0B1 0.073 0.12 0.34 61 -10000 0 61
EGR1 -0.19 0.3 -10000 0 -0.61 121 121
RXRs/9cRA 0.046 0.076 0.23 29 -0.36 5 34
AR/RACK1/Src -0.009 0.15 0.37 16 -0.4 20 36
AR/GR -0.064 0.16 -10000 0 -0.31 84 84
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
PKN1 0.026 0.004 -10000 0 -10000 0 0
RCHY1 0.024 0.007 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0.001 0.005 0.022 11 -10000 0 11
MAPK8 -0.014 0.1 -10000 0 -0.46 18 18
T-DHT/AR/TIF2/CARM1 -0.039 0.18 0.36 8 -0.45 38 46
SRC -0.021 0.096 0.3 3 -0.35 21 24
NR3C1 0.026 0.004 -10000 0 -10000 0 0
KLK3 0.008 0.21 0.53 17 -1.2 6 23
APPBP2 0.019 0.019 -10000 0 -10000 0 0
TRIM24 0.027 0.012 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.031 0.13 0.29 1 -0.42 24 25
TMPRSS2 -0.061 0.27 -10000 0 -1.2 19 19
RXRG 0.04 0.11 0.34 32 -0.62 4 36
mol:9cRA 0 0.002 -10000 0 -10000 0 0
RXRA 0.024 0.034 -10000 0 -0.62 1 1
RXRB 0.024 0.007 -10000 0 -10000 0 0
CARM1 0.027 0.006 -10000 0 -10000 0 0
NR2C2 0.018 0.074 -10000 0 -0.61 5 5
KLK2 -0.008 0.17 0.51 20 -0.46 10 30
AR -0.084 0.16 0.27 1 -0.33 95 96
SENP1 0.026 0.003 -10000 0 -10000 0 0
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
MDM2 0.021 0.02 -10000 0 -10000 0 0
SRY -0.003 0.013 0.031 6 -0.053 20 26
GATA2 0.024 0.053 0.34 2 -0.62 2 4
MYST2 -0.001 0.003 -10000 0 -10000 0 0
HOXB13 0.084 0.13 0.35 71 -10000 0 71
T-DHT/AR/RACK1/Src -0.02 0.14 0.36 4 -0.42 20 24
positive regulation of transcription 0.024 0.053 0.34 2 -0.62 2 4
DNAJA1 0.019 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.008 -10000 0 -10000 0 0
NCOA1 0.031 0.017 -10000 0 -10000 0 0
SPDEF 0.069 0.12 0.35 52 -10000 0 52
T-DHT/AR/TIF2 -0.029 0.15 0.29 2 -0.43 30 32
T-DHT/AR/Hsp90 -0.03 0.13 0.29 1 -0.41 24 25
GSK3B 0.026 0.008 -10000 0 -10000 0 0
NR2C1 0.024 0.011 -10000 0 -10000 0 0
mol:T-DHT -0.027 0.098 0.29 2 -0.36 24 26
SIRT1 0.022 0.048 -10000 0 -0.62 2 2
ZMIZ2 0.021 0.02 -10000 0 -10000 0 0
POU2F1 0.012 0.044 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.001 0.15 0.35 5 -0.42 23 28
CREBBP 0.025 0.006 -10000 0 -10000 0 0
SMARCE1 0.027 0.01 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.003 0.032 -10000 0 -10000 0 0
HSPA8 0.026 0.034 -10000 0 -0.61 1 1
SMAD3/SMAD4/ER alpha -0.22 0.23 -10000 0 -0.43 182 182
AKT1 0.028 0.015 -10000 0 -10000 0 0
GSC 0.045 0.14 0.54 15 -10000 0 15
NKX2-5 0.001 0 -10000 0 -10000 0 0
muscle cell differentiation -0.003 0.075 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.053 0.11 0.42 2 -0.42 2 4
SMAD4 -0.003 0.065 -10000 0 -0.27 1 1
CBFB 0.024 0.007 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.024 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR 0.013 0.1 0.39 1 -0.39 8 9
MYC -0.055 0.2 -10000 0 -0.61 40 40
CDKN2B -0.002 0.16 0.54 7 -0.53 2 9
AP1 -0.13 0.21 -10000 0 -0.37 108 108
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.006 0.1 -10000 0 -0.37 13 13
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.018 0.063 0.29 3 -0.32 3 6
SP3 0.027 0.003 -10000 0 -10000 0 0
CREB1 0.026 0.003 -10000 0 -10000 0 0
FOXH1 0.037 0.072 0.35 18 -10000 0 18
SMAD3/SMAD4/GR 0.032 0.09 -10000 0 -0.27 4 4
GATA3 -0.036 0.18 0.34 1 -0.53 36 37
SKI/SIN3/HDAC complex/NCoR1 0 0.099 -10000 0 -0.34 21 21
MEF2C/TIF2 0.007 0.11 -10000 0 -0.34 18 18
endothelial cell migration 0.36 0.62 1.4 100 -10000 0 100
MAX 0.036 0.023 -10000 0 -10000 0 0
RBBP7 0.027 0.004 -10000 0 -10000 0 0
RBBP4 0.026 0.006 -10000 0 -10000 0 0
RUNX2 0.016 0.09 0.34 4 -0.57 7 11
RUNX3 0.01 0.094 -10000 0 -0.62 8 8
RUNX1 0.024 0.034 -10000 0 -0.62 1 1
CTBP1 0.025 0.004 -10000 0 -10000 0 0
NR3C1 0.037 0.023 -10000 0 -10000 0 0
VDR 0.023 0.1 0.34 11 -0.62 7 18
CDKN1A -0.021 0.23 -10000 0 -1.3 10 10
KAT2B 0.006 0.062 -10000 0 -0.62 3 3
SMAD2/SMAD2/SMAD4/FOXH1 0.046 0.074 0.41 3 -10000 0 3
DCP1A 0.026 0.003 -10000 0 -10000 0 0
SKI 0.025 0.008 -10000 0 -10000 0 0
SERPINE1 -0.37 0.64 -10000 0 -1.4 100 100
SMAD3/SMAD4/ATF2 0.005 0.096 -10000 0 -0.38 7 7
SMAD3/SMAD4/ATF3 -0.002 0.11 -10000 0 -0.47 13 13
SAP30 0.025 0.008 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.012 0.047 -10000 0 -10000 0 0
JUN -0.13 0.2 -10000 0 -0.36 104 104
SMAD3/SMAD4/IRF7 0.006 0.099 -10000 0 -0.44 6 6
TFE3 0.006 0.043 -10000 0 -10000 0 0
COL1A2 0.097 0.17 0.55 17 -1.1 4 21
mesenchymal cell differentiation -0.006 0.1 0.41 9 -0.35 4 13
DLX1 0.048 0.086 0.34 29 -10000 0 29
TCF3 0.026 0.004 -10000 0 -10000 0 0
FOS -0.26 0.32 -10000 0 -0.62 161 161
SMAD3/SMAD4/Max 0.033 0.091 -10000 0 -0.28 1 1
Cbp/p300/SNIP1 0.025 0.04 -10000 0 -10000 0 0
ZBTB17 0.019 0.026 -10000 0 -10000 0 0
LAMC1 -0.007 0.062 0.42 2 -10000 0 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.011 0.082 -10000 0 -0.34 1 1
IRF7 0.017 0.075 -10000 0 -0.62 5 5
ESR1 -0.31 0.31 -10000 0 -0.59 198 198
HNF4A 0.015 0.082 -10000 0 -0.62 6 6
MEF2C 0.064 0.087 -10000 0 -10000 0 0
SMAD2-3/SMAD4 0.02 0.088 -10000 0 -0.34 1 1
Cbp/p300/Src-1 0.019 0.045 -10000 0 -10000 0 0
IGHV3OR16-13 0.005 0.033 -10000 0 -0.34 2 2
TGIF2/HDAC complex 0.026 0.003 -10000 0 -10000 0 0
CREBBP 0.006 0.027 -10000 0 -10000 0 0
SKIL 0.026 0.002 -10000 0 -10000 0 0
HDAC1 0.026 0.006 -10000 0 -10000 0 0
HDAC2 0.025 0.007 -10000 0 -10000 0 0
SNIP1 0.027 0.007 -10000 0 -10000 0 0
GCN5L2 -0.009 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.001 0.094 0.34 1 -0.39 1 2
MSG1/HSC70 0.047 0.044 0.25 12 -0.32 1 13
SMAD2 0.033 0.018 -10000 0 -10000 0 0
SMAD3 -0.005 0.064 -10000 0 -0.28 1 1
SMAD3/E2F4-5/DP1/p107/SMAD4 0.011 0.054 -10000 0 -0.3 1 1
SMAD2/SMAD2/SMAD4 0.003 0.054 -10000 0 -0.35 3 3
NCOR1 0.023 0.01 -10000 0 -10000 0 0
NCOA2 -0.038 0.18 -10000 0 -0.62 33 33
NCOA1 0.026 0.002 -10000 0 -10000 0 0
MYOD/E2A 0.032 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.068 0.1 0.43 2 -0.39 2 4
IFNB1 -0.011 0.076 -10000 0 -0.41 5 5
SMAD3/SMAD4/MEF2C 0.054 0.099 0.37 2 -10000 0 2
CITED1 0.037 0.058 0.34 13 -10000 0 13
SMAD2-3/SMAD4/ARC105 0.031 0.087 -10000 0 -0.3 1 1
RBL1 0.037 0.058 0.34 13 -10000 0 13
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.023 0.065 0.31 8 -10000 0 8
RUNX1-3/PEBPB2 0.036 0.075 -10000 0 -0.44 8 8
SMAD7 -0.11 0.2 -10000 0 -0.68 11 11
MYC/MIZ-1 -0.034 0.15 -10000 0 -0.47 39 39
SMAD3/SMAD4 -0.13 0.22 -10000 0 -0.47 97 97
IL10 -0.068 0.22 0.5 1 -0.58 47 48
PIASy/HDAC complex 0.034 0.014 -10000 0 -10000 0 0
PIAS3 0.01 0.019 -10000 0 -10000 0 0
CDK2 0.007 0.026 -10000 0 -10000 0 0
IL5 -0.051 0.17 -10000 0 -0.46 40 40
CDK4 0.007 0.027 -10000 0 -10000 0 0
PIAS4 0.034 0.014 -10000 0 -10000 0 0
ATF3 -0.002 0.12 -10000 0 -0.62 13 13
SMAD3/SMAD4/SP1 0.022 0.1 0.37 1 -0.47 2 3
FOXG1 0.027 0.053 0.34 10 -10000 0 10
FOXO3 0.016 0.02 -10000 0 -10000 0 0
FOXO1 0.014 0.033 -10000 0 -0.46 1 1
FOXO4 0.018 0.019 -10000 0 -10000 0 0
heart looping 0.063 0.087 -10000 0 -10000 0 0
CEBPB 0.028 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.024 0.098 0.36 3 -0.29 3 6
MYOD1 0.018 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.004 0.096 -10000 0 -0.36 10 10
SMAD3/SMAD4/GATA3 -0.039 0.2 0.37 1 -0.49 46 47
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.02 0.11 -10000 0 -0.46 8 8
SMAD3/SMAD4/SP1-3 0.04 0.1 -10000 0 -0.42 2 2
MED15 0.025 0.004 -10000 0 -10000 0 0
SP1 0.03 0.032 -10000 0 -10000 0 0
SIN3B 0.027 0.004 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.046 0.07 0.43 2 -10000 0 2
ITGB5 0.005 0.074 -10000 0 -0.38 2 2
TGIF/SIN3/HDAC complex/CtBP 0.014 0.067 -10000 0 -0.29 11 11
SMAD3/SMAD4/AR -0.11 0.21 -10000 0 -0.43 99 99
AR -0.15 0.28 -10000 0 -0.62 98 98
negative regulation of cell growth 0.011 0.07 -10000 0 -0.31 3 3
SMAD3/SMAD4/MYOD 0.006 0.082 -10000 0 -0.34 1 1
E2F5 0.022 0.048 0.34 4 -0.62 1 5
E2F4 0.024 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.054 0.074 0.41 2 -10000 0 2
SMAD2-3/SMAD4/FOXO1-3a-4 0.02 0.057 0.29 2 -10000 0 2
TFDP1 0.025 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.12 0.22 -10000 0 -0.37 101 101
SMAD3/SMAD4/RUNX2 0.006 0.11 0.35 4 -0.42 9 13
TGIF2 0.026 0.003 -10000 0 -10000 0 0
TGIF1 0.026 0.004 -10000 0 -10000 0 0
ATF2 0.017 0.075 -10000 0 -0.62 5 5
HIF-2-alpha transcription factor network

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
MMP14 0.022 0.12 0.57 9 -0.68 3 12
oxygen homeostasis 0.001 0.028 0.23 1 -10000 0 1
TCEB2 0.026 0.017 0.34 1 -10000 0 1
TCEB1 0.02 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.035 0.13 0.43 6 -0.39 5 11
EPO -0.18 0.41 0.88 9 -0.69 108 117
FIH (dimer) 0.016 0.037 -10000 0 -10000 0 0
APEX1 0.014 0.044 0.36 1 -10000 0 1
SERPINE1 -0.1 0.36 0.79 7 -0.67 72 79
FLT1 -0.033 0.18 -10000 0 -0.76 15 15
ADORA2A -0.013 0.27 0.74 9 -0.59 12 21
germ cell development 0.022 0.28 0.84 14 -0.63 6 20
SLC11A2 -0.006 0.25 0.79 7 -0.61 10 17
BHLHE40 -0.011 0.27 0.75 9 -0.68 13 22
HIF1AN 0.016 0.037 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.019 0.21 0.75 7 -0.55 6 13
ETS1 0.027 0.042 -10000 0 -0.62 1 1
CITED2 -0.037 0.18 -10000 0 -0.72 20 20
KDR -0.045 0.24 -10000 0 -0.92 21 21
PGK1 -0.006 0.25 0.75 9 -0.68 6 15
SIRT1 0.011 0.051 -10000 0 -0.62 2 2
response to hypoxia -0.004 0.01 -10000 0 -10000 0 0
HIF2A/ARNT -0.011 0.28 0.88 8 -0.7 10 18
EPAS1 0.018 0.16 0.55 11 -0.4 8 19
SP1 0.035 0.034 0.25 6 -10000 0 6
ABCG2 -0.054 0.28 0.74 8 -0.68 26 34
EFNA1 -0.014 0.24 0.82 5 -0.61 10 15
FXN -0.011 0.27 0.72 10 -0.59 12 22
POU5F1 0.021 0.28 0.84 14 -0.66 6 20
neuron apoptosis 0.011 0.28 0.68 10 -0.87 8 18
EP300 0.026 0.004 -10000 0 -10000 0 0
EGLN3 0.026 0.15 0.37 32 -0.6 11 43
EGLN2 0.017 0.039 0.26 1 -10000 0 1
EGLN1 0.015 0.033 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.039 0.024 -10000 0 -10000 0 0
VHL 0.026 0.002 -10000 0 -10000 0 0
ARNT 0.011 0.039 0.36 1 -10000 0 1
SLC2A1 -0.007 0.28 0.7 17 -0.6 14 31
TWIST1 -0.009 0.27 0.71 12 -0.6 11 23
ELK1 0.029 0.009 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.017 0.18 0.63 7 -0.5 4 11
VEGFA -0.007 0.24 0.74 8 -0.66 6 14
CREBBP 0.025 0.006 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.025 0.005 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.004 0.16 -10000 0 -0.35 49 49
Syndecan-3/Neurocan 0.011 0.082 -10000 0 -0.38 13 13
POMC 0.024 0.067 0.34 4 -0.62 3 7
EGFR 0.01 0.1 -10000 0 -0.62 9 9
Syndecan-3/EGFR 0.002 0.093 -10000 0 -0.36 20 20
AGRP 0.032 0.06 0.34 13 -10000 0 13
NCSTN 0.02 0.011 -10000 0 -10000 0 0
PSENEN 0.026 0.004 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.026 0.003 -10000 0 -10000 0 0
APH1A 0.02 0.011 -10000 0 -10000 0 0
NCAN 0.027 0.037 0.34 5 -10000 0 5
long-term memory 0.039 0.086 -10000 0 -0.36 13 13
Syndecan-3/IL8 -0.05 0.16 0.31 2 -0.37 62 64
PSEN1 0.025 0.006 -10000 0 -10000 0 0
Src/Cortactin 0.04 0.026 0.25 5 -10000 0 5
FYN 0.024 0.007 -10000 0 -10000 0 0
limb bud formation -0.004 0.075 -10000 0 -0.39 13 13
MC4R 0.019 0.017 0.34 1 -10000 0 1
SRC 0.03 0.037 0.34 5 -10000 0 5
PTN -0.066 0.23 0.34 3 -0.62 53 56
FGFR/FGF/Syndecan-3 -0.004 0.076 -10000 0 -0.4 13 13
neuron projection morphogenesis -0.03 0.14 0.34 2 -0.45 14 16
Syndecan-3/AgRP 0.018 0.09 0.31 7 -0.37 13 20
Syndecan-3/AgRP/MC4R 0.042 0.095 0.3 7 -0.36 12 19
Fyn/Cortactin 0.035 0.012 -10000 0 -10000 0 0
SDC3 -0.004 0.076 -10000 0 -0.4 13 13
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.049 0.16 0.31 2 -0.36 62 64
IL8 -0.1 0.26 0.34 9 -0.57 83 92
Syndecan-3/Fyn/Cortactin 0.04 0.088 -10000 0 -0.37 13 13
Syndecan-3/CASK -0.006 0.073 -10000 0 -0.38 13 13
alpha-MSH/MC4R 0.031 0.052 0.24 5 -0.46 3 8
Gamma Secretase 0.053 0.036 -10000 0 -10000 0 0
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 0.019 0.025 -10000 0 -0.39 1 1
EPHB2 0.085 0.13 0.34 72 -0.62 1 73
Syndecan-2/TACI 0.018 0.042 0.23 5 -0.39 2 7
LAMA1 -0.035 0.22 0.34 20 -0.61 44 64
Syndecan-2/alpha2 ITGB1 0.1 0.14 0.41 39 -0.34 2 41
HRAS 0.027 0.017 0.34 1 -10000 0 1
Syndecan-2/CASK 0.006 0.004 -10000 0 -10000 0 0
ITGA5 0.026 0.002 -10000 0 -10000 0 0
BAX -0.004 0.052 -10000 0 -10000 0 0
EPB41 0.025 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.018 0.011 -10000 0 -10000 0 0
LAMA3 0.066 0.13 0.34 55 -0.62 4 59
EZR 0.022 0.034 -10000 0 -0.62 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.008 0.1 -10000 0 -0.62 10 10
Syndecan-2/MMP2 0.008 0.075 0.23 6 -0.39 8 14
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.073 0.08 -10000 0 -10000 0 0
dendrite morphogenesis 0.068 0.11 0.27 72 -0.39 1 73
Syndecan-2/GM-CSF 0.018 0.011 -10000 0 -10000 0 0
determination of left/right symmetry 0.008 0.005 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.02 0.012 -10000 0 -10000 0 0
GNB2L1 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.053 0.075 -10000 0 -10000 0 0
MAPK1 0.053 0.075 -10000 0 -10000 0 0
Syndecan-2/RACK1 0.03 0.024 0.32 1 -10000 0 1
NF1 0.025 0.017 -10000 0 -0.3 1 1
FGFR/FGF/Syndecan-2 0.008 0.005 -10000 0 -10000 0 0
ITGA2 0.081 0.12 0.34 64 -10000 0 64
MAPK8 -0.003 0.062 -10000 0 -0.39 9 9
Syndecan-2/alpha2/beta1 Integrin 0.045 0.15 0.36 17 -0.32 26 43
Syndecan-2/Kininogen -0.009 0.1 -10000 0 -0.39 23 23
ITGB1 0.025 0.005 -10000 0 -10000 0 0
SRC 0.063 0.083 0.34 9 -10000 0 9
Syndecan-2/CASK/Protein 4.1 0.018 0.012 -10000 0 -10000 0 0
extracellular matrix organization 0.023 0.029 0.26 4 -10000 0 4
actin cytoskeleton reorganization 0.019 0.025 -10000 0 -0.39 1 1
Syndecan-2/Caveolin-2/Ras 0.023 0.055 -10000 0 -0.36 5 5
Syndecan-2/Laminin alpha3 0.055 0.1 0.27 55 -0.29 4 59
Syndecan-2/RasGAP 0.037 0.031 -10000 0 -0.33 1 1
alpha5/beta1 Integrin 0.037 0.007 -10000 0 -10000 0 0
PRKCD 0.026 0.003 -10000 0 -10000 0 0
Syndecan-2 dimer 0.068 0.11 0.27 72 -0.39 1 73
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.029 0.036 0.3 1 -0.32 1 2
RHOA 0.026 0.003 -10000 0 -10000 0 0
SDCBP 0.021 0.01 -10000 0 -10000 0 0
TNFRSF13B 0.023 0.061 0.34 5 -0.62 2 7
RASA1 0.022 0.048 -10000 0 -0.62 2 2
alpha2/beta1 Integrin 0.073 0.08 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.02 0.013 -10000 0 -10000 0 0
TGFB1 0.029 0.033 0.34 4 -10000 0 4
CASP3 0.054 0.075 -10000 0 -10000 0 0
FN1 0.024 0.034 -10000 0 -0.62 1 1
Syndecan-2/IL8 -0.052 0.16 0.26 9 -0.34 71 80
SDC2 0.008 0.005 -10000 0 -10000 0 0
KNG1 -0.025 0.17 -10000 0 -0.62 29 29
Syndecan-2/Neurofibromin 0.02 0.016 -10000 0 -10000 0 0
TRAPPC4 0.025 0.005 -10000 0 -10000 0 0
CSF2 0.021 0.005 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.023 0.029 0.27 4 -10000 0 4
Syndecan-2/Syntenin/PI-4-5-P2 0.019 0.011 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.028 0.029 -10000 0 -0.36 1 1
PRKACA 0.056 0.077 -10000 0 -10000 0 0
angiogenesis -0.052 0.16 0.26 9 -0.34 71 80
MMP2 0.002 0.13 0.34 6 -0.56 17 23
IL8 -0.1 0.26 0.34 9 -0.57 83 92
calcineurin-NFAT signaling pathway 0.018 0.041 0.23 5 -0.39 2 7
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.021 0.07 -10000 0 -0.34 4 4
BIRC5 0.22 0.15 0.34 226 -10000 0 226
NFKBIA 0.013 0.059 0.31 3 -10000 0 3
CPEB1 0.031 0.057 0.34 12 -10000 0 12
AKT1 0.012 0.054 0.25 2 -10000 0 2
NDEL1 0.022 0.01 -10000 0 -10000 0 0
Aurora A/BRCA1 0.019 0.051 -10000 0 -10000 0 0
NDEL1/TACC3 0.046 0.082 0.28 23 -10000 0 23
GADD45A 0.018 0.063 -10000 0 -0.49 5 5
GSK3B -0.009 0.03 -10000 0 -10000 0 0
PAK1/Aurora A 0.025 0.059 -10000 0 -10000 0 0
MDM2 0.026 0.004 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.041 0.073 0.23 48 -10000 0 48
TP53 0.008 0.07 -10000 0 -10000 0 0
DLG7 0.013 0.053 -10000 0 -10000 0 0
AURKAIP1 0.024 0.008 -10000 0 -10000 0 0
ARHGEF7 0.025 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.049 0.087 0.3 23 -10000 0 23
G2/M transition of mitotic cell cycle 0.019 0.05 -10000 0 -10000 0 0
AURKA 0.021 0.069 -10000 0 -10000 0 0
AURKB 0.1 0.1 0.22 144 -10000 0 144
CDC25B 0.02 0.049 0.25 1 -10000 0 1
G2/M transition checkpoint 0.01 0.043 -10000 0 -10000 0 0
mRNA polyadenylation 0.023 0.062 0.25 8 -10000 0 8
Aurora A/CPEB 0.023 0.062 0.25 8 -10000 0 8
Aurora A/TACC1/TRAP/chTOG 0.034 0.062 -10000 0 -10000 0 0
BRCA1 0.026 0.004 -10000 0 -10000 0 0
centrosome duplication 0.025 0.059 -10000 0 -10000 0 0
regulation of centrosome cycle 0.045 0.08 0.27 23 -10000 0 23
spindle assembly 0.033 0.06 -10000 0 -10000 0 0
TDRD7 0.026 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.16 0.1 0.28 76 -0.26 1 77
CENPA 0.11 0.1 0.23 143 -10000 0 143
Aurora A/PP2A 0.024 0.058 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.023 0.05 -10000 0 -10000 0 0
negative regulation of DNA binding 0.008 0.069 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.036 0.01 -10000 0 -10000 0 0
RASA1 0.022 0.048 -10000 0 -0.62 2 2
Ajuba/Aurora A 0.01 0.043 -10000 0 -10000 0 0
mitotic prometaphase -0.005 0.034 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.069 -10000 0 -10000 0 0
TACC1 0.022 0.01 -10000 0 -10000 0 0
TACC3 0.063 0.1 0.34 44 -10000 0 44
Aurora A/Antizyme1 0.03 0.058 -10000 0 -10000 0 0
Aurora A/RasGAP 0.024 0.067 -10000 0 -0.38 2 2
OAZ1 0.025 0.004 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.008 0.029 -10000 0 -10000 0 0
GIT1 0.026 0.003 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.048 0.016 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.041 0.073 0.22 48 -10000 0 48
PPP2R5D 0.024 0.008 -10000 0 -10000 0 0
Aurora A/TPX2 0.039 0.084 0.24 34 -10000 0 34
PAK1 0.025 0.004 -10000 0 -10000 0 0
CKAP5 0.026 0.002 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.026 0.004 -10000 0 -10000 0 0
HDAC4 0.027 0.017 0.34 1 -10000 0 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.028 0.069 0.3 2 -0.24 30 32
CDKN1A -0.027 0.12 -10000 0 -0.77 10 10
KAT2B 0.021 0.058 -10000 0 -0.62 3 3
BAX 0.026 0.004 -10000 0 -10000 0 0
FOXO3 -0.005 0.01 -10000 0 -10000 0 0
FOXO1 0.02 0.045 -10000 0 -0.38 4 4
FOXO4 0.015 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.026 0.004 -10000 0 -10000 0 0
TAT -0.22 0.3 -10000 0 -0.58 149 149
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.016 0.041 -10000 0 -0.46 3 3
PPARGC1A -0.055 0.21 -10000 0 -0.61 46 46
FHL2 -0.041 0.2 -10000 0 -0.62 38 38
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.036 0.039 -10000 0 -0.41 2 2
HIST2H4A 0.028 0.069 0.24 30 -0.3 2 32
SIRT1/FOXO3a 0.014 0.037 -10000 0 -0.34 2 2
SIRT1 0.024 0.05 -10000 0 -0.56 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.038 0.036 -10000 0 -0.3 1 1
SIRT1/Histone H1b 0.032 0.049 -10000 0 -0.28 3 3
apoptosis -0.048 0.036 0.35 2 -10000 0 2
SIRT1/PGC1A -0.022 0.14 -10000 0 -0.39 47 47
p53/SIRT1 0.03 0.06 0.42 6 -0.38 2 8
SIRT1/FOXO4 0.021 0.045 -10000 0 -0.29 3 3
FOXO1/FHL2/SIRT1 -0.001 0.13 -10000 0 -0.36 40 40
HIST1H1E 0.019 0.03 -10000 0 -10000 0 0
SIRT1/p300 0.036 0.039 -10000 0 -0.41 2 2
muscle cell differentiation -0.027 0.055 0.51 3 -10000 0 3
TP53 0.023 0.026 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.048 0.036 -10000 0 -0.36 2 2
CREBBP 0.025 0.006 -10000 0 -10000 0 0
MEF2D 0.02 0.011 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.16 0.24 -10000 0 -0.44 146 146
ACSS2 0.012 0.039 0.35 1 -0.41 2 3
SIRT1/PCAF/MYOD 0.027 0.055 -10000 0 -0.52 3 3
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.013 0.14 -10000 0 -0.63 12 12
UGCG -0.049 0.23 -10000 0 -0.71 36 36
AKT1/mTOR/p70S6K/Hsp90/TERT 0.055 0.17 0.37 6 -0.46 15 21
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.048 0.22 -10000 0 -0.7 36 36
mol:DAG -0.008 0.13 -10000 0 -0.85 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.18 0.43 1 -0.5 23 24
FRAP1 -0.005 0.21 0.48 1 -0.6 23 24
FOXO3 -0.014 0.21 0.43 1 -0.51 37 38
AKT1 -0.015 0.22 0.45 1 -0.54 41 42
GAB2 0.023 0.011 -10000 0 -10000 0 0
SMPD1 0.019 0.059 -10000 0 -0.61 2 2
SGMS1 0.008 0.11 -10000 0 -0.64 8 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.002 0.045 -10000 0 -0.56 2 2
CALM1 0.025 0.006 -10000 0 -10000 0 0
cell proliferation -0.02 0.23 -10000 0 -0.66 24 24
EIF3A 0.025 0.006 -10000 0 -10000 0 0
PI3K 0.033 0.055 -10000 0 -0.64 2 2
RPS6KB1 0.043 0.068 -10000 0 -10000 0 0
mol:sphingomyelin -0.008 0.13 -10000 0 -0.85 8 8
natural killer cell activation -0.001 0.004 -10000 0 -10000 0 0
JAK3 0.028 0.048 0.34 4 -0.62 1 5
PIK3R1 0.021 0.048 -10000 0 -0.61 2 2
JAK1 0.025 0.009 -10000 0 -10000 0 0
NFKB1 0.024 0.008 -10000 0 -10000 0 0
MYC -0.031 0.37 -10000 0 -0.98 44 44
MYB 0.15 0.15 0.57 36 -10000 0 36
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.011 0.17 0.45 1 -0.56 18 19
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.063 0.06 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.011 0.17 0.44 1 -0.54 18 19
Rac1/GDP 0.017 0.044 -10000 0 -0.52 2 2
T cell proliferation 0 0.16 0.42 1 -0.53 17 18
SHC1 0.018 0.014 -10000 0 -10000 0 0
RAC1 0.026 0.004 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.022 0.058 0.2 36 -10000 0 36
PRKCZ -0.001 0.17 0.42 1 -0.54 18 19
NF kappa B1 p50/RelA 0.016 0.19 0.45 1 -0.5 22 23
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.012 0.16 0.36 1 -0.58 20 21
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
IL2RA 0.02 0.1 0.34 11 -0.62 7 18
IL2RB -0.022 0.17 -10000 0 -0.59 28 28
TERT 0.14 0.15 0.34 131 -10000 0 131
E2F1 0.16 0.15 0.54 36 -10000 0 36
SOS1 0.024 0.011 -10000 0 -10000 0 0
RPS6 0.025 0.005 -10000 0 -10000 0 0
mol:cAMP -0.01 0.026 -10000 0 -0.09 36 36
PTPN11 0.023 0.012 -10000 0 -10000 0 0
IL2RG 0.021 0.086 0.34 6 -0.62 5 11
actin cytoskeleton organization 0 0.16 0.42 1 -0.53 17 18
GRB2 0.023 0.011 -10000 0 -10000 0 0
IL2 0.017 0.014 -10000 0 -10000 0 0
PIK3CA 0.023 0.035 -10000 0 -0.61 1 1
Rac1/GTP 0.043 0.05 -10000 0 -0.49 2 2
LCK 0.006 0.11 0.35 1 -0.59 11 12
BCL2 0.005 0.17 0.44 1 -0.57 10 11
IL2 signaling events mediated by STAT5

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
GAB2 0.026 0.005 -10000 0 -10000 0 0
ELF1 0.025 0.075 -10000 0 -0.44 7 7
CCNA2 0.17 0.16 0.34 172 -10000 0 172
PIK3CA 0.025 0.034 -10000 0 -0.62 1 1
JAK3 0.028 0.047 0.34 4 -0.62 1 5
PIK3R1 0.023 0.048 -10000 0 -0.62 2 2
JAK1 0.025 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.024 0.15 0.42 1 -0.56 16 17
SHC1 0.02 0.012 -10000 0 -10000 0 0
SP1 0.033 0.023 -10000 0 -10000 0 0
IL2RA 0.01 0.14 0.43 11 -0.72 9 20
IL2RB -0.022 0.17 -10000 0 -0.59 28 28
SOS1 0.027 0.001 -10000 0 -10000 0 0
IL2RG 0.023 0.085 0.34 6 -0.62 5 11
G1/S transition of mitotic cell cycle 0.049 0.2 0.42 3 -0.78 12 15
PTPN11 0.026 0.003 -10000 0 -10000 0 0
CCND2 0.023 0.048 0.43 5 -10000 0 5
LCK 0.008 0.11 0.34 1 -0.59 11 12
GRB2 0.025 0.005 -10000 0 -10000 0 0
IL2 0.019 0.006 -10000 0 -10000 0 0
CDK6 -0.016 0.16 -10000 0 -0.6 24 24
CCND3 0.034 0.14 -10000 0 -0.6 6 6
Signaling events mediated by PTP1B

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
PDGFRB 0.032 0.046 0.34 8 -10000 0 8
Jak2/Leptin Receptor 0.007 0.16 0.29 1 -0.42 18 19
PTP1B/AKT1 0.05 0.081 -10000 0 -0.34 5 5
FYN 0.024 0.007 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.046 0.086 0.27 1 -0.35 6 7
EGFR 0.012 0.1 -10000 0 -0.62 9 9
EGF/EGFR 0.077 0.12 0.27 30 -0.33 8 38
CSF1 0.02 0.071 0.34 2 -0.62 4 6
AKT1 0.025 0.007 -10000 0 -10000 0 0
INSR 0.026 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.047 0.099 0.25 1 -0.34 11 12
Insulin Receptor/Insulin 0.057 0.078 0.36 1 -0.38 2 3
HCK 0.005 0.12 -10000 0 -0.62 12 12
CRK 0.022 0.009 -10000 0 -10000 0 0
TYK2 0.042 0.083 0.29 2 -0.36 5 7
EGF 0.093 0.13 0.34 83 -10000 0 83
YES1 0.026 0.004 -10000 0 -10000 0 0
CAV1 0.052 0.093 0.26 4 -0.34 5 9
TXN 0.027 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.062 0.086 -10000 0 -0.35 5 5
cell migration -0.046 0.086 0.35 6 -0.27 1 7
STAT3 0.026 0.004 -10000 0 -10000 0 0
PRLR 0.007 0.11 -10000 0 -0.62 11 11
ITGA2B 0.03 0.047 0.34 8 -10000 0 8
CSF1R 0.01 0.1 -10000 0 -0.62 9 9
Prolactin Receptor/Prolactin 0.019 0.086 -10000 0 -0.45 11 11
FGR 0.021 0.048 -10000 0 -0.62 2 2
PTP1B/p130 Cas 0.055 0.081 -10000 0 -0.35 5 5
Crk/p130 Cas 0.059 0.083 -10000 0 -0.32 5 5
DOK1 0.048 0.083 -10000 0 -0.36 5 5
JAK2 0.039 0.1 -10000 0 -0.42 7 7
Jak2/Leptin Receptor/Leptin -0.012 0.19 0.31 1 -0.48 43 44
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
PTPN1 0.046 0.087 0.27 1 -0.35 6 7
LYN 0.022 0.01 -10000 0 -10000 0 0
CDH2 0.008 0.1 -10000 0 -0.56 11 11
SRC 0.04 0.073 -10000 0 -0.44 4 4
ITGB3 -0.023 0.17 -10000 0 -0.62 28 28
CAT1/PTP1B -0.054 0.19 -10000 0 -0.47 36 36
CAPN1 0.027 0.005 -10000 0 -10000 0 0
CSK 0.026 0.004 -10000 0 -10000 0 0
PI3K 0.059 0.085 0.32 1 -0.47 3 4
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.019 0.2 -10000 0 -0.51 44 44
negative regulation of transcription 0.04 0.1 -10000 0 -0.41 7 7
FCGR2A 0.022 0.026 0.34 2 -10000 0 2
FER 0.027 0.004 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.004 0.14 0.25 8 -0.46 28 36
BLK -0.069 0.21 0.34 2 -0.5 64 66
Insulin Receptor/Insulin/Shc 0.037 0.029 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
LEPR -0.073 0.23 -10000 0 -0.6 57 57
BCAR1 0.024 0.007 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.025 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.12 0.22 -10000 0 -0.5 65 65
PRL 0.02 0.025 0.34 2 -10000 0 2
SOCS3 -0.18 0.48 -10000 0 -1.3 52 52
SPRY2 0.017 0.068 -10000 0 -0.62 4 4
Insulin Receptor/Insulin/IRS1 0.05 0.024 -10000 0 -10000 0 0
CSF1/CSF1R 0.052 0.11 0.31 2 -0.36 11 13
Ras protein signal transduction 0 0.11 0.49 16 -10000 0 16
IRS1 0.026 0.002 -10000 0 -10000 0 0
INS 0.02 0.039 0.34 5 -10000 0 5
LEP 0.027 0.059 0.34 12 -10000 0 12
STAT5B 0.051 0.084 0.24 1 -0.33 6 7
STAT5A 0.051 0.084 0.23 2 -0.33 6 8
GRB2 0.025 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.056 0.092 0.3 8 -0.36 5 13
CSN2 -0.013 0.07 -10000 0 -10000 0 0
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
LAT 0.037 0.095 0.38 1 -0.5 8 9
YBX1 0.03 0.007 -10000 0 -10000 0 0
LCK 0.007 0.11 0.34 1 -0.59 11 12
SHC1 0.02 0.011 -10000 0 -10000 0 0
NOX4 0.14 0.15 0.34 135 -10000 0 135
Effects of Botulinum toxin

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
STX1A 0.014 0.039 0.21 13 -10000 0 13
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.034 0.025 0.24 4 -10000 0 4
STXBP1 0.022 0.048 -10000 0 -0.62 2 2
ACh/CHRNA1 0.016 0.069 0.28 14 -0.16 6 20
RAB3GAP2/RIMS1/UNC13B 0.038 0.031 -10000 0 -10000 0 0
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 0.022 0.03 0.34 3 -10000 0 3
mol:ACh -0.006 0.053 0.1 11 -0.15 27 38
RAB3GAP2 0.021 0.011 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.018 0.074 -10000 0 -0.34 4 4
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.016 0.069 0.28 14 -0.16 6 20
UNC13B 0.026 0.017 0.34 1 -10000 0 1
CHRNA1 0.035 0.061 0.34 14 -10000 0 14
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.043 0.18 0.25 19 -0.41 60 79
SNAP25 -0.005 0.1 0.15 36 -0.32 28 64
VAMP2 0.004 0.002 -10000 0 -10000 0 0
SYT1 -0.056 0.25 0.34 21 -0.61 57 78
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.026 0.042 -10000 0 -0.4 2 2
STX1A/SNAP25 fragment 1/VAMP2 0.018 0.074 -10000 0 -0.34 4 4
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.021 0.11 -9999 0 -0.4 22 22
E-cadherin/beta catenin 0.005 0.12 -9999 0 -0.46 22 22
CTNNB1 0.026 0.002 -9999 0 -10000 0 0
JUP 0.026 0.003 -9999 0 -10000 0 0
CDH1 -0.015 0.15 -9999 0 -0.62 22 22
Ceramide signaling pathway

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
SPHK2 0.026 0.052 0.22 24 -10000 0 24
MAP4K4 0.007 0.06 -10000 0 -10000 0 0
BAG4 0.008 0.085 -10000 0 -0.44 11 11
PKC zeta/ceramide 0.005 0.077 -10000 0 -0.26 22 22
NFKBIA 0.026 0.004 -10000 0 -10000 0 0
BIRC3 0.035 0.072 0.34 14 -0.46 2 16
BAX 0.009 0.046 -10000 0 -0.33 5 5
RIPK1 0.024 0.008 -10000 0 -10000 0 0
AKT1 -0.001 0.054 0.7 2 -10000 0 2
BAD 0.002 0.043 -10000 0 -0.18 5 5
SMPD1 0.027 0.073 0.23 13 -0.22 10 23
RB1 0.001 0.042 -10000 0 -0.18 5 5
FADD/Caspase 8 0.014 0.066 0.29 1 -10000 0 1
MAP2K4 0 0.042 0.23 1 -10000 0 1
NSMAF 0.021 0.01 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.004 0.05 0.29 2 -10000 0 2
EGF 0.093 0.13 0.34 83 -10000 0 83
mol:ceramide 0.004 0.046 -10000 0 -0.19 10 10
MADD 0.026 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.02 0.049 0.23 17 -10000 0 17
ASAH1 0.021 0.02 0.34 1 -10000 0 1
negative regulation of cell cycle 0.001 0.043 -10000 0 -0.18 5 5
cell proliferation -0.091 0.16 -10000 0 -0.3 103 103
BID 0.012 0.13 -10000 0 -0.57 13 13
MAP3K1 0.003 0.045 0.24 1 -0.18 6 7
EIF2A 0.001 0.045 -10000 0 -10000 0 0
TRADD 0.023 0.018 -10000 0 -0.3 1 1
CRADD 0.024 0.034 -10000 0 -0.62 1 1
MAPK3 0.004 0.053 0.35 1 -10000 0 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.005 0.052 0.28 2 -10000 0 2
Cathepsin D/ceramide 0.019 0.048 -10000 0 -0.18 6 6
FADD 0.009 0.061 0.3 1 -10000 0 1
KSR1 0.005 0.048 0.2 4 -10000 0 4
MAPK8 -0.027 0.11 -10000 0 -0.31 29 29
PRKRA 0.004 0.046 0.2 3 -0.18 10 13
PDGFA 0.045 0.076 0.34 23 -10000 0 23
TRAF2 0.026 0.004 -10000 0 -10000 0 0
IGF1 -0.23 0.31 -10000 0 -0.61 144 144
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.004 0.046 -10000 0 -0.19 10 10
CTSD 0.026 0.003 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.035 0.012 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.096 0.17 -10000 0 -0.32 102 102
PRKCD 0.026 0.003 -10000 0 -10000 0 0
PRKCZ -0.001 0.12 -10000 0 -0.52 17 17
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.02 0.049 0.23 17 -10000 0 17
RelA/NF kappa B1 0.035 0.012 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.026 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.013 0.058 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.019 0.098 -10000 0 -0.4 17 17
mol:Sphingosine-1-phosphate 0.026 0.051 0.22 24 -10000 0 24
MAP2K1 0.002 0.048 0.35 1 -10000 0 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
CYCS 0.01 0.035 0.18 1 -10000 0 1
TNFRSF1A 0.025 0.006 -10000 0 -10000 0 0
NFKB1 0.024 0.008 -10000 0 -10000 0 0
TNFR1A/BAG4 0.021 0.065 -10000 0 -0.35 9 9
EIF2AK2 0.002 0.045 0.22 1 -10000 0 1
TNF-alpha/TNFR1A/FAN 0.027 0.076 -10000 0 -0.4 9 9
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.009 0.086 -10000 0 -0.35 8 8
MAP2K2 0.004 0.051 0.35 1 -10000 0 1
SMPD3 -0.017 0.14 0.22 9 -0.35 46 55
TNF 0.004 0.12 0.34 2 -0.62 12 14
PKC zeta/PAR4 0.016 0.093 -10000 0 -0.38 17 17
mol:PHOSPHOCHOLINE -0.04 0.075 -10000 0 -0.22 14 14
NF kappa B1/RelA/I kappa B alpha 0.048 0.082 -10000 0 -0.34 12 12
AIFM1 0.01 0.039 0.18 1 -0.18 1 2
BCL2 0.024 0.034 -10000 0 -0.62 1 1
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.017 0.074 0.28 4 -0.4 3 7
SNTA1 0.027 0.023 0.34 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.028 0.091 0.32 14 -0.4 3 17
MAPK12 0.014 0.072 0.29 5 -0.32 7 12
CCND1 0.003 0.094 0.2 3 -0.42 14 17
p38 gamma/SNTA1 0.037 0.073 0.3 3 -0.3 7 10
MAP2K3 0.024 0.007 -10000 0 -10000 0 0
PKN1 0.026 0.004 -10000 0 -10000 0 0
G2/M transition checkpoint 0.014 0.072 0.29 5 -0.32 7 12
MAP2K6 -0.002 0.056 -10000 0 -0.38 7 7
MAPT 0.083 0.094 0.26 39 -0.26 2 41
MAPK13 0.042 0.092 0.23 59 -0.46 3 62
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.001 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.028 0.14 -10000 0 -0.51 22 22
KLHL20 -0.005 0.077 0.34 1 -0.28 7 8
CYFIP2 -0.01 0.15 -10000 0 -0.62 20 20
Rac1/GDP -0.002 0.098 -10000 0 -0.32 21 21
ENAH -0.02 0.13 -10000 0 -0.43 25 25
AP1M1 0.026 0.004 -10000 0 -10000 0 0
RAP1B 0.026 0.003 -10000 0 -10000 0 0
RAP1A 0.025 0.005 -10000 0 -10000 0 0
CTNNB1 0.026 0.002 -10000 0 -10000 0 0
CDC42/GTP 0.006 0.071 -10000 0 -0.26 22 22
ABI1/Sra1/Nap1 -0.029 0.056 -10000 0 -0.18 24 24
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.025 0.12 -10000 0 -0.36 27 27
RAPGEF1 -0.027 0.13 -10000 0 -0.45 22 22
CTNND1 0.026 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.027 0.15 -10000 0 -0.5 26 26
CRK -0.023 0.13 -10000 0 -0.48 22 22
E-cadherin/gamma catenin/alpha catenin 0.02 0.11 -10000 0 -0.4 22 22
alphaE/beta7 Integrin 0.03 0.064 0.25 6 -0.45 5 11
IQGAP1 0.025 0.004 -10000 0 -10000 0 0
NCKAP1 0.026 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.043 0.018 -10000 0 -10000 0 0
DLG1 -0.03 0.14 -10000 0 -0.5 24 24
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.01 0.05 -10000 0 -0.19 23 23
MLLT4 0.023 0.008 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.026 0.092 -10000 0 -0.36 18 18
PI3K -0.009 0.066 -10000 0 -0.27 3 3
ARF6 0.025 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.005 0.12 -10000 0 -0.46 22 22
TIAM1 -0.009 0.14 -10000 0 -0.6 20 20
E-cadherin(dimer)/Ca2+ 0.031 0.097 -10000 0 -0.34 22 22
AKT1 -0.003 0.042 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
CDH1 -0.015 0.15 -10000 0 -0.62 22 22
RhoA/GDP -0.001 0.098 -10000 0 -0.32 22 22
actin cytoskeleton organization -0.002 0.058 0.29 1 -0.2 7 8
CDC42/GDP 0 0.097 -10000 0 -0.32 22 22
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0 0.072 -10000 0 -0.28 22 22
ITGB7 0.017 0.075 -10000 0 -0.62 5 5
RAC1 0.026 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.034 0.1 -10000 0 -0.36 22 22
E-cadherin/Ca2+/beta catenin/alpha catenin 0.018 0.093 -10000 0 -0.34 22 22
mol:GDP -0.017 0.11 -10000 0 -0.36 22 22
CDC42/GTP/IQGAP1 0.032 0.01 -10000 0 -10000 0 0
JUP 0.026 0.003 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.004 0.1 -10000 0 -0.32 21 21
RAC1/GTP/IQGAP1 0.034 0.008 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.038 0.007 -10000 0 -10000 0 0
RHOA 0.026 0.003 -10000 0 -10000 0 0
CDC42 0.025 0.006 -10000 0 -10000 0 0
CTNNA1 0.026 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.004 0.062 0.27 2 -0.24 14 16
NME1 0.027 0.023 0.34 2 -10000 0 2
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.03 0.14 -10000 0 -0.5 24 24
regulation of cell-cell adhesion 0 0.06 -10000 0 -0.22 22 22
WASF2 -0.005 0.037 -10000 0 -0.12 5 5
Rap1/GTP 0.008 0.081 -10000 0 -0.3 2 2
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.033 0.11 -10000 0 -0.34 27 27
CCND1 -0.006 0.076 0.3 2 -0.3 14 16
VAV2 -0.029 0.17 -10000 0 -0.5 33 33
RAP1/GDP 0.008 0.087 -10000 0 -0.3 2 2
adherens junction assembly -0.029 0.14 -10000 0 -0.48 24 24
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.025 0.004 -10000 0 -10000 0 0
PIP5K1C 0.026 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.023 0.11 -10000 0 -0.33 27 27
E-cadherin/beta catenin -0.013 0.1 -10000 0 -0.41 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.03 0.15 -10000 0 -0.5 24 24
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
Rac1/GTP -0.035 0.12 0.49 1 -0.38 23 24
E-cadherin/beta catenin/alpha catenin 0.02 0.11 -10000 0 -0.4 22 22
ITGAE 0.027 0.041 0.34 6 -10000 0 6
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.028 0.15 -10000 0 -0.51 26 26
EGFR-dependent Endothelin signaling events

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
HRAS 0.027 0.017 0.34 1 -10000 0 1
EGFR 0.01 0.1 -10000 0 -0.62 9 9
EGF/EGFR 0.054 0.11 0.34 1 -0.32 17 18
EGF/EGFR dimer/SHC/GRB2/SOS1 0.065 0.092 -10000 0 -0.31 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.024 0.056 0.34 3 -0.62 2 5
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.093 0.13 0.34 83 -10000 0 83
EGF/EGFR dimer/SHC 0.054 0.096 -10000 0 -0.34 7 7
mol:GDP 0.059 0.087 -10000 0 -0.31 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.009 0.1 0.34 1 -0.62 9 10
GRB2/SOS1 0.037 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.039 0.065 -10000 0 -0.32 4 4
SHC1 0.02 0.011 -10000 0 -10000 0 0
HRAS/GDP 0.055 0.079 -10000 0 -0.33 4 4
FRAP1 0.002 0.054 -10000 0 -0.3 6 6
EGF/EGFR dimer 0.066 0.12 0.25 78 -0.42 9 87
SOS1 0.026 0.001 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 0.021 0.089 -10000 0 -0.46 11 11
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.012 0.13 0.34 9 -0.62 12 21
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.026 0.017 0.34 1 -10000 0 1
TCEB1 0.02 0.011 -10000 0 -10000 0 0
HIF1A/p53 0.026 0.061 -10000 0 -0.39 2 2
HIF1A 0.015 0.056 -10000 0 -0.3 7 7
COPS5 0.021 0.01 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.054 0.036 -10000 0 -10000 0 0
FIH (dimer) 0.025 0.005 -10000 0 -10000 0 0
CDKN2A 0.23 0.15 0.34 238 -10000 0 238
ARNT/IPAS 0.018 0.09 0.25 8 -0.42 12 20
HIF1AN 0.025 0.005 -10000 0 -10000 0 0
GNB2L1 0.025 0.005 -10000 0 -10000 0 0
HIF1A/ARNT 0.017 0.055 -10000 0 -0.3 7 7
CUL2 0.025 0.005 -10000 0 -10000 0 0
OS9 0.026 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.038 0.024 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.029 0.063 -10000 0 -0.3 7 7
PHD1-3/OS9 0.056 0.084 -10000 0 -0.36 6 6
HIF1A/RACK1/Elongin B/Elongin C 0.034 0.066 -10000 0 -0.38 2 2
VHL 0.026 0.002 -10000 0 -10000 0 0
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
HIF1A/JAB1 0.022 0.064 -10000 0 -0.4 2 2
EGLN3 0.035 0.14 0.34 32 -0.59 11 43
EGLN2 0.026 0.004 -10000 0 -10000 0 0
EGLN1 0.021 0.011 -10000 0 -10000 0 0
TP53 0.022 0.01 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.033 0.065 -10000 0 -0.64 3 3
ARNT 0.02 0.011 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.026 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF 0.14 0.11 0.29 38 -0.41 1 39
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.012 0.094 -10000 0 -0.41 11 11
CRKL -0.01 0.084 -10000 0 -0.41 10 10
HRAS -0.004 0.1 0.39 1 -0.44 8 9
mol:PIP3 0.021 0.1 0.32 1 -0.4 8 9
SPRED1 0.024 0.034 -10000 0 -0.62 1 1
SPRED2 0.026 0.003 -10000 0 -10000 0 0
GAB1 -0.009 0.088 0.3 3 -0.42 10 13
FOXO3 -0.009 0.12 -10000 0 -0.44 13 13
AKT1 -0.009 0.13 -10000 0 -0.47 14 14
BAD -0.009 0.12 -10000 0 -0.44 13 13
megakaryocyte differentiation -0.028 0.12 0.3 3 -0.37 28 31
GSK3B -0.009 0.12 -10000 0 -0.44 13 13
RAF1 0.018 0.1 0.35 2 -0.4 5 7
SHC1 0.02 0.011 -10000 0 -10000 0 0
STAT3 -0.013 0.092 0.3 3 -0.42 11 14
STAT1 -0.055 0.22 -10000 0 -1.1 12 12
HRAS/SPRED1 0.021 0.1 0.36 1 -0.4 5 6
cell proliferation -0.027 0.12 0.3 3 -0.39 24 27
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
TEC 0.014 0.082 -10000 0 -0.62 6 6
RPS6KB1 0 0.1 0.31 3 -0.44 11 14
HRAS/SPRED2 0.022 0.1 0.36 1 -0.4 5 6
LYN/TEC/p62DOK 0.009 0.1 -10000 0 -0.39 11 11
MAPK3 0.02 0.089 0.28 5 -0.29 5 10
STAP1 -0.008 0.088 0.3 3 -0.43 10 13
GRAP2 0.016 0.1 0.34 6 -0.58 9 15
JAK2 -0.047 0.2 -10000 0 -0.83 16 16
STAT1 (dimer) -0.052 0.21 -10000 0 -1 12 12
mol:Gleevec 0 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.007 0.12 -10000 0 -0.39 17 17
actin filament polymerization -0.012 0.09 0.3 3 -0.4 11 14
LYN 0.022 0.01 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.019 0.13 -10000 0 -0.6 12 12
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
CBL/CRKL/GRB2 0.006 0.089 -10000 0 -0.38 9 9
PI3K 0.023 0.11 -10000 0 -0.45 12 12
PTEN 0.023 0.025 -10000 0 -0.3 2 2
SCF/KIT/EPO/EPOR -0.13 0.31 -10000 0 -1.4 11 11
MAPK8 -0.028 0.12 0.3 3 -0.4 24 27
STAT3 (dimer) -0.013 0.09 0.3 3 -0.41 11 14
positive regulation of transcription 0.02 0.078 0.26 5 -0.23 5 10
mol:GDP -0.005 0.11 0.42 1 -0.45 10 11
PIK3C2B -0.009 0.087 0.3 3 -0.42 9 12
CBL/CRKL 0 0.088 -10000 0 -0.39 10 10
FER -0.013 0.09 0.3 3 -0.42 11 14
SH2B3 -0.011 0.089 0.3 3 -0.43 10 13
PDPK1 0.02 0.096 0.3 1 -0.37 8 9
SNAI2 -0.011 0.092 0.3 3 -0.42 9 12
positive regulation of cell proliferation -0.028 0.16 -10000 0 -0.72 13 13
KITLG 0.015 0.041 0.33 4 -10000 0 4
cell motility -0.028 0.16 -10000 0 -0.72 13 13
PTPN6 0.025 0.01 -10000 0 -10000 0 0
EPOR -0.014 0.17 -10000 0 -0.75 11 11
STAT5A (dimer) -0.02 0.13 0.36 3 -0.59 13 16
SOCS1 0.025 0.058 0.34 4 -0.62 2 6
cell migration 0.013 0.097 0.43 13 -0.3 3 16
SOS1 0.026 0.001 -10000 0 -10000 0 0
EPO -0.2 0.32 0.34 12 -0.62 130 142
VAV1 -0.002 0.13 -10000 0 -0.58 17 17
GRB10 -0.013 0.091 0.3 3 -0.42 11 14
PTPN11 0.025 0.007 -10000 0 -10000 0 0
SCF/KIT -0.011 0.097 0.32 3 -0.44 11 14
GO:0007205 0.001 0.005 -10000 0 -10000 0 0
MAP2K1 0.018 0.087 0.32 2 -0.32 4 6
CBL 0.025 0.006 -10000 0 -10000 0 0
KIT -0.045 0.29 0.52 3 -1 22 25
MAP2K2 0.019 0.09 0.31 5 -0.32 4 9
SHC/Grb2/SOS1 0.012 0.093 -10000 0 -0.4 8 8
STAT5A -0.021 0.14 0.36 3 -0.6 13 16
GRB2 0.025 0.005 -10000 0 -10000 0 0
response to radiation -0.01 0.091 0.3 3 -0.41 9 12
SHC/GRAP2 0.022 0.07 0.25 5 -0.36 9 14
PTPRO -0.028 0.12 0.3 3 -0.38 28 31
SH2B2 -0.012 0.091 0.3 3 -0.41 11 14
DOK1 0.026 0.001 -10000 0 -10000 0 0
MATK -0.014 0.099 0.3 3 -0.44 13 16
CREBBP 0.033 0.036 -10000 0 -10000 0 0
BCL2 -0.021 0.2 -10000 0 -0.82 14 14
Caspase cascade in apoptosis

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
TOP1 -0.025 0.14 -10000 0 -0.4 33 33
ACTA1 -0.013 0.11 -10000 0 -0.45 14 14
NUMA1 -0.03 0.16 -10000 0 -0.44 34 34
SPTAN1 -0.029 0.11 -10000 0 -0.45 15 15
LIMK1 -0.024 0.11 -10000 0 -0.45 15 15
BIRC3 0.035 0.072 0.34 14 -0.46 2 16
BIRC2 0.025 0.005 -10000 0 -10000 0 0
BAX 0.026 0.004 -10000 0 -10000 0 0
CASP10 -0.022 0.083 -10000 0 -0.42 14 14
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.026 0.003 -10000 0 -10000 0 0
PTK2 -0.03 0.13 -10000 0 -0.38 33 33
DIABLO 0.026 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.028 0.1 -10000 0 -0.44 15 15
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.024 0.034 -10000 0 -0.62 1 1
GSN -0.029 0.11 -10000 0 -0.45 15 15
MADD 0.026 0.002 -10000 0 -10000 0 0
TFAP2A 0.019 0.18 0.41 2 -0.69 15 17
BID -0.002 0.049 -10000 0 -0.23 14 14
MAP3K1 0.003 0.038 -10000 0 -0.23 1 1
TRADD 0.023 0.018 -10000 0 -0.3 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.036 0.01 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.029 0.11 -10000 0 -0.45 15 15
CASP9 0.025 0.006 -10000 0 -10000 0 0
DNA repair 0.001 0.059 0.31 6 -0.19 1 7
neuron apoptosis -0.018 0.16 -10000 0 -0.71 17 17
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.034 0.15 -10000 0 -0.43 32 32
APAF1 0.026 0.003 -10000 0 -10000 0 0
CASP6 -0.055 0.26 -10000 0 -0.91 29 29
TRAF2 0.026 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.028 0.11 0.36 1 -0.44 15 16
CASP7 -0.019 0.081 0.27 2 -0.64 2 4
KRT18 0.004 0.081 -10000 0 -0.88 2 2
apoptosis -0.04 0.15 -10000 0 -0.41 40 40
DFFA -0.027 0.11 -10000 0 -0.45 15 15
DFFB -0.028 0.11 -10000 0 -0.44 16 16
PARP1 -0.002 0.059 0.19 1 -0.31 6 7
actin filament polymerization 0.025 0.11 0.42 16 -0.32 1 17
TNF 0.004 0.12 0.34 2 -0.62 12 14
CYCS 0.006 0.041 0.17 2 -0.22 2 4
SATB1 -0.084 0.27 -10000 0 -0.88 31 31
SLK -0.028 0.11 -10000 0 -0.45 15 15
p15 BID/BAX 0.011 0.055 -10000 0 -0.28 2 2
CASP2 0.008 0.063 -10000 0 -0.34 1 1
JNK cascade -0.003 0.038 0.23 1 -10000 0 1
CASP3 -0.028 0.11 -10000 0 -0.47 15 15
LMNB2 -0.001 0.13 -10000 0 -0.41 22 22
RIPK1 0.024 0.008 -10000 0 -10000 0 0
CASP4 0.023 0.034 -10000 0 -0.62 1 1
Mammalian IAPs/DIABLO 0.069 0.046 -10000 0 -0.37 1 1
negative regulation of DNA binding 0.023 0.18 0.41 2 -0.68 15 17
stress fiber formation -0.028 0.1 -10000 0 -0.44 15 15
GZMB -0.004 0.1 0.22 4 -0.49 14 18
CASP1 0.012 0.028 -10000 0 -0.37 2 2
LMNB1 0.002 0.12 -10000 0 -0.37 21 21
APP -0.019 0.17 -10000 0 -0.72 17 17
TNFRSF1A 0.025 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0.001 -10000 0 -10000 0 0
VIM -0.04 0.15 -10000 0 -0.42 40 40
LMNA -0.002 0.11 -10000 0 -0.37 21 21
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.008 0.067 -10000 0 -0.36 1 1
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.028 0.11 0.3 1 -0.44 16 17
APAF-1/Caspase 9 -0.016 0.14 -10000 0 -0.61 18 18
nuclear fragmentation during apoptosis -0.029 0.16 -10000 0 -0.43 34 34
CFL2 -0.025 0.11 0.32 1 -0.43 16 17
GAS2 -0.04 0.12 -10000 0 -0.4 27 27
positive regulation of apoptosis 0.001 0.13 -10000 0 -0.39 24 24
PRF1 0.013 0.088 -10000 0 -0.62 7 7
Cellular roles of Anthrax toxin

Figure S95.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S95.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.015 0.09 0.34 1 -0.62 7 8
ANTXR2 0.016 0.069 -10000 0 -0.55 5 5
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.014 -10000 0 -0.078 12 12
monocyte activation -0.029 0.16 -10000 0 -0.44 40 40
MAP2K2 0.002 0.088 -10000 0 -0.58 8 8
MAP2K1 -0.005 0.013 -10000 0 -10000 0 0
MAP2K7 -0.005 0.013 -10000 0 -10000 0 0
MAP2K6 -0.008 0.051 0.11 8 -0.34 7 15
CYAA -0.014 0.058 -10000 0 -0.34 11 11
MAP2K4 -0.004 0.012 -10000 0 -10000 0 0
IL1B -0.06 0.13 -10000 0 -0.34 62 62
Channel 0.019 0.069 0.21 1 -0.34 12 13
NLRP1 -0.004 0.013 0.11 1 -10000 0 1
CALM1 0.025 0.006 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.013 0.1 -10000 0 -0.43 19 19
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.014 0.078 12 -10000 0 12
MAPK3 -0.005 0.013 -10000 0 -10000 0 0
MAPK1 -0.005 0.013 -10000 0 -10000 0 0
PGR -0.059 0.13 0.11 4 -0.35 59 63
PA/Cellular Receptors 0.02 0.075 0.22 1 -0.38 12 13
apoptosis -0.003 0.014 -10000 0 -0.078 12 12
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.019 0.065 0.2 1 -0.32 12 13
macrophage activation -0.007 0.012 -10000 0 -10000 0 0
TNF 0.004 0.12 0.34 2 -0.62 12 14
VCAM1 -0.029 0.16 -10000 0 -0.44 40 40
platelet activation -0.013 0.1 -10000 0 -0.43 19 19
MAPKKK cascade 0.002 0.022 -10000 0 -10000 0 0
IL18 -0.008 0.05 -10000 0 -0.35 7 7
negative regulation of macrophage activation -0.003 0.014 -10000 0 -0.078 12 12
LEF -0.003 0.014 -10000 0 -0.078 12 12
CASP1 0 0.012 0.07 1 -0.074 5 6
mol:cAMP -0.013 0.1 -10000 0 -0.43 19 19
necrosis -0.003 0.014 -10000 0 -0.078 12 12
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.019 0.065 0.2 1 -0.32 12 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.007 0.11 0.58 11 -10000 0 11
PI3K Class IB/PDE3B 0.007 0.11 -10000 0 -0.59 11 11
PDE3B 0.007 0.11 -10000 0 -0.59 11 11
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.048 0.048 0.25 20 -10000 0 20
ATM 0.025 0.005 -10000 0 -10000 0 0
UBE2D3 0.024 0.008 -10000 0 -10000 0 0
PRKDC 0.022 0.01 -10000 0 -10000 0 0
ATR 0.026 0.002 -10000 0 -10000 0 0
UBE2L3 0.025 0.004 -10000 0 -10000 0 0
FANCD2 0.063 0.075 0.31 2 -10000 0 2
protein ubiquitination 0.12 0.092 0.39 13 -10000 0 13
XRCC5 0.026 0.003 -10000 0 -10000 0 0
XRCC6 0.026 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.037 0.025 -10000 0 -10000 0 0
MRE11A 0.025 0.005 -10000 0 -10000 0 0
DNA-PK 0.043 0.021 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.039 0.086 -10000 0 -0.5 5 5
FANCF 0.026 0.002 -10000 0 -10000 0 0
BRCA1 0.026 0.004 -10000 0 -10000 0 0
CCNE1 0.13 0.15 0.34 122 -10000 0 122
CDK2/Cyclin E1 0.11 0.099 0.25 120 -10000 0 120
FANCG 0.026 0.017 0.34 1 -10000 0 1
BRCA1/BACH1/BARD1 0.048 0.047 0.25 19 -10000 0 19
FANCE 0.032 0.049 0.34 9 -10000 0 9
FANCC 0.024 0.034 -10000 0 -0.62 1 1
NBN 0.02 0.011 -10000 0 -10000 0 0
FANCA 0.024 0.008 -10000 0 -10000 0 0
DNA repair 0.072 0.11 0.36 9 -0.43 1 10
BRCA1/BARD1/ubiquitin 0.048 0.047 0.25 19 -10000 0 19
BARD1/DNA-PK 0.062 0.047 -10000 0 -10000 0 0
FANCL 0.026 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.048 0.048 -10000 0 -0.25 20 20
BRCA1/BARD1/CTIP/M/R/N Complex 0.037 0.054 -10000 0 -0.28 1 1
BRCA1/BACH1/BARD1/TopBP1 0.06 0.043 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.061 0.044 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.059 0.044 -10000 0 -10000 0 0
BRCA1/BACH1 0.026 0.004 -10000 0 -10000 0 0
BARD1 0.043 0.071 0.34 20 -10000 0 20
PCNA 0.025 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.054 0.041 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.058 0.041 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.12 0.1 0.42 14 -10000 0 14
BARD1/DNA-PK/P53 0.059 0.051 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.048 0.047 0.25 19 -10000 0 19
BRCA1/BARD1/CTIP 0.05 0.043 -10000 0 -10000 0 0
FA complex 0.026 0.027 -10000 0 -10000 0 0
BARD1/EWS 0.046 0.044 0.25 16 -10000 0 16
RBBP8 0.013 0.003 -10000 0 -10000 0 0
TP53 0.022 0.01 -10000 0 -10000 0 0
TOPBP1 0.026 0.002 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.059 0.042 -10000 0 -10000 0 0
BRCA1/BARD1 0.13 0.099 0.4 14 -10000 0 14
CSTF1 0.025 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.03 0.047 0.23 20 -10000 0 20
CDK2 0.026 0.003 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.12 0.14 0.34 104 -10000 0 104
RAD50 0.025 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.048 0.047 0.25 19 -10000 0 19
EWSR1 0.025 0.005 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.025 0.006 -10000 0 -10000 0 0
HDAC2 0.024 0.007 -10000 0 -10000 0 0
GNB1/GNG2 0.038 0.059 -10000 0 -0.4 6 6
forebrain development -0.02 0.14 -10000 0 -0.5 16 16
GNAO1 -0.26 0.31 -10000 0 -0.58 174 174
SMO/beta Arrestin2 0.026 0.055 -10000 0 -0.46 4 4
SMO 0.017 0.068 -10000 0 -0.62 4 4
ARRB2 0.022 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.039 0.058 0.29 1 -0.39 1 2
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.026 0 -10000 0 -10000 0 0
GNAI2 0.024 0.009 -10000 0 -10000 0 0
SIN3/HDAC complex 0.058 0.024 -10000 0 -10000 0 0
GNAI1 0.022 0.048 -10000 0 -0.62 2 2
XPO1 0.025 0.013 -10000 0 -10000 0 0
GLI1/Su(fu) -0.014 0.14 -10000 0 -0.54 12 12
SAP30 0.024 0.007 -10000 0 -10000 0 0
mol:GDP 0.017 0.068 -10000 0 -0.62 4 4
MIM/GLI2A 0.021 0.017 -10000 0 -10000 0 0
IFT88 0.025 0.006 -10000 0 -10000 0 0
GNAI3 0.025 0.007 -10000 0 -10000 0 0
GLI2 0.012 0.07 -10000 0 -0.3 2 2
GLI3 0.027 0.059 0.3 1 -0.41 1 2
CSNK1D 0.025 0.006 -10000 0 -10000 0 0
CSNK1E 0.025 0.004 -10000 0 -10000 0 0
SAP18 0.025 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.025 0.006 -10000 0 -10000 0 0
GNG2 0.022 0.048 -10000 0 -0.62 2 2
Gi family/GTP -0.078 0.16 -10000 0 -0.29 92 92
SIN3B 0.026 0.003 -10000 0 -10000 0 0
SIN3A 0.026 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.028 0.063 -10000 0 -0.38 2 2
GLI2/Su(fu) 0.017 0.075 -10000 0 -0.36 3 3
FOXA2 0.01 0.11 -10000 0 -0.91 4 4
neural tube patterning -0.02 0.14 -10000 0 -0.5 16 16
SPOP 0.026 0.003 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.021 0.047 -10000 0 -10000 0 0
GNB1 0.024 0.008 -10000 0 -10000 0 0
CSNK1G2 0.026 0.004 -10000 0 -10000 0 0
CSNK1G3 0.026 0.004 -10000 0 -10000 0 0
MTSS1 0.021 0.017 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.02 0.14 -10000 0 -0.5 16 16
SUFU 0.017 0.029 -10000 0 -10000 0 0
LGALS3 0.048 0.082 0.34 27 -10000 0 27
catabolic process 0.045 0.08 -10000 0 -0.41 2 2
GLI3A/CBP 0.037 0.044 0.3 1 -10000 0 1
KIF3A 0.025 0.005 -10000 0 -10000 0 0
GLI1 -0.021 0.14 -10000 0 -0.52 16 16
RAB23 0.024 0.007 -10000 0 -10000 0 0
CSNK1A1 0.025 0.004 -10000 0 -10000 0 0
IFT172 0.026 0.002 -10000 0 -10000 0 0
RBBP7 0.026 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.035 0.07 -10000 0 -10000 0 0
GNAZ 0.16 0.16 0.34 165 -0.62 1 166
RBBP4 0.025 0.006 -10000 0 -10000 0 0
CSNK1G1 0.026 0.003 -10000 0 -10000 0 0
PIAS1 0.026 0.004 -10000 0 -10000 0 0
PRKACA 0.026 0.004 -10000 0 -10000 0 0
GLI2/SPOP 0.025 0.07 -10000 0 -0.31 1 1
STK36 0.025 0.013 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.068 0.16 -10000 0 -0.37 34 34
PTCH1 -0.055 0.27 -10000 0 -1.2 18 18
MIM/GLI1 -0.013 0.13 -10000 0 -0.49 9 9
CREBBP 0.037 0.044 0.3 1 -10000 0 1
Su(fu)/SIN3/HDAC complex -0.002 0.1 -10000 0 -0.39 18 18
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.002 0.16 -10000 0 -0.4 25 25
CaM/Ca2+ 0.018 0.004 -10000 0 -10000 0 0
AKT1 0.024 0.007 -10000 0 -10000 0 0
AKT2 0.026 0.004 -10000 0 -10000 0 0
STXBP4 0.028 0.029 0.34 3 -10000 0 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.015 0.17 -10000 0 -0.4 35 35
YWHAZ 0.019 0.012 -10000 0 -10000 0 0
CALM1 0.025 0.006 -10000 0 -10000 0 0
YWHAQ 0.026 0.002 -10000 0 -10000 0 0
TBC1D4 0.008 0.043 -10000 0 -0.46 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.025 0.004 -10000 0 -10000 0 0
YWHAB 0.026 0.004 -10000 0 -10000 0 0
SNARE/Synip 0.044 0.028 -10000 0 -10000 0 0
YWHAG 0.026 0.004 -10000 0 -10000 0 0
ASIP 0.025 0.017 0.34 1 -10000 0 1
PRKCI 0.026 0.002 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.018 0.004 -10000 0 -10000 0 0
RHOQ 0.026 0.002 -10000 0 -10000 0 0
GYS1 0.011 0.008 -10000 0 -10000 0 0
PRKCZ -0.001 0.12 -10000 0 -0.52 17 17
TRIP10 0.026 0.003 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.035 0.006 -10000 0 -10000 0 0
AS160/14-3-3 0.076 0.086 -10000 0 -0.3 3 3
VAMP2 0.022 0.01 -10000 0 -10000 0 0
SLC2A4 -0.02 0.18 -10000 0 -0.45 35 35
STX4 0.025 0.004 -10000 0 -10000 0 0
GSK3B 0.02 0.006 -10000 0 -10000 0 0
SFN 0.2 0.16 0.34 202 -0.3 2 204
LNPEP 0.026 0.003 -10000 0 -10000 0 0
YWHAE 0.022 0.009 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.005 0.059 -10000 0 -0.45 2 2
adherens junction organization -0.007 0.08 -10000 0 -0.27 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.009 0.087 -10000 0 -0.4 9 9
FMN1 -0.005 0.081 -10000 0 -0.27 21 21
mol:IP3 0.004 0.059 -10000 0 -0.57 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.005 0.082 -10000 0 -0.28 22 22
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.005 0.066 -10000 0 -0.57 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.018 0.13 -10000 0 -0.44 22 22
CTNND1 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.004 0.062 -10000 0 -0.27 14 14
VASP -0.008 0.077 -10000 0 -0.27 22 22
ZYX -0.009 0.077 -10000 0 -0.27 22 22
JUB -0.007 0.078 -10000 0 -0.27 22 22
EGFR(dimer) -0.001 0.1 -10000 0 -0.33 25 25
E-cadherin/beta catenin-gamma catenin 0.021 0.1 -10000 0 -0.38 22 22
mol:PI-3-4-5-P3 0.021 0.076 -10000 0 -0.42 2 2
PIK3CA 0.025 0.035 -10000 0 -0.63 1 1
PI3K 0.021 0.077 -10000 0 -0.43 2 2
FYN -0.048 0.12 0.25 1 -0.38 13 14
mol:Ca2+ 0.004 0.057 -10000 0 -0.56 1 1
JUP 0.027 0.004 -10000 0 -10000 0 0
PIK3R1 0.023 0.048 -10000 0 -0.62 2 2
mol:DAG 0.004 0.059 -10000 0 -0.57 1 1
CDH1 -0.015 0.15 -10000 0 -0.62 22 22
RhoA/GDP 0.011 0.086 -10000 0 -0.39 9 9
establishment of polarity of embryonic epithelium -0.008 0.076 -10000 0 -0.27 22 22
SRC 0.03 0.037 0.34 5 -10000 0 5
RAC1 0.026 0.004 -10000 0 -10000 0 0
RHOA 0.026 0.003 -10000 0 -10000 0 0
EGFR 0.01 0.1 -10000 0 -0.62 9 9
CASR -0.054 0.13 0.25 2 -0.32 62 64
RhoA/GTP 0.016 0.058 -10000 0 -0.51 1 1
AKT2 0.005 0.066 -10000 0 -0.57 1 1
actin cable formation -0.008 0.077 -10000 0 -0.27 21 21
apoptosis -0.005 0.064 0.41 2 -0.23 1 3
CTNNA1 0.026 0.005 -10000 0 -10000 0 0
mol:GDP -0.007 0.083 -10000 0 -0.43 9 9
PIP5K1A -0.004 0.063 -10000 0 -0.27 14 14
PLCG1 0.004 0.06 -10000 0 -0.59 1 1
Rac1/GTP 0.01 0.1 -10000 0 -0.31 25 25
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.016 0.081 0.52 5 -10000 0 5
VDR 0.023 0.1 0.34 11 -0.62 7 18
FAM120B 0.023 0.019 -10000 0 -0.3 1 1
RXRs/LXRs/DNA/9cRA 0.026 0.086 0.32 1 -0.41 3 4
RXRs/LXRs/DNA/Oxysterols 0.033 0.12 0.4 1 -0.48 11 12
MED1 0.026 0.004 -10000 0 -10000 0 0
mol:9cRA 0.001 0.015 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.014 0.066 -10000 0 -0.27 17 17
RXRs/NUR77 -0.002 0.16 -10000 0 -0.35 50 50
RXRs/PPAR 0.03 0.061 -10000 0 -0.3 5 5
NCOR2 0.026 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.016 0.075 0.23 11 -0.46 7 18
RARs/VDR/DNA/Vit D3 0.041 0.1 -10000 0 -0.34 21 21
RARA 0.026 0.003 -10000 0 -10000 0 0
NCOA1 0.026 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.023 0.1 0.34 11 -0.62 7 18
RARs/RARs/DNA/9cRA 0.028 0.079 -10000 0 -0.34 15 15
RARG 0.026 0.002 -10000 0 -10000 0 0
RPS6KB1 0.026 0.098 0.47 16 -10000 0 16
RARs/THRs/DNA/SMRT 0.014 0.069 -10000 0 -0.28 17 17
THRA 0.026 0.003 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.016 0.075 0.23 11 -0.46 7 18
RXRs/PPAR/9cRA/PGJ2/DNA 0.046 0.083 0.31 1 -0.35 5 6
NR1H4 0.008 0.1 -10000 0 -0.62 10 10
RXRs/LXRs/DNA 0.063 0.094 -10000 0 -0.33 5 5
NR1H2 0.025 0.019 -10000 0 -10000 0 0
NR1H3 0.026 0.021 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.049 0.093 0.4 1 -0.32 10 11
NR4A1 -0.072 0.23 -10000 0 -0.61 56 56
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.015 0.076 -10000 0 -0.3 13 13
RXRG 0.04 0.12 0.34 32 -0.61 4 36
RXR alpha/CCPG 0.031 0.034 -10000 0 -0.46 1 1
RXRA 0.023 0.038 -10000 0 -0.61 1 1
RXRB 0.024 0.02 -10000 0 -10000 0 0
THRB 0.021 0.058 -10000 0 -0.62 3 3
PPARG 0.027 0.017 0.34 1 -10000 0 1
PPARD 0.024 0.008 -10000 0 -10000 0 0
TNF 0.005 0.22 0.5 1 -1 14 15
mol:Oxysterols 0.001 0.012 -10000 0 -10000 0 0
cholesterol transport 0.033 0.12 0.4 1 -0.47 11 12
PPARA 0.025 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.001 0.13 -10000 0 -0.62 15 15
RXRs/NUR77/BCL2 -0.018 0.12 -10000 0 -0.3 45 45
SREBF1 0.021 0.12 -10000 0 -0.86 3 3
RXRs/RXRs/DNA/9cRA 0.046 0.083 0.31 1 -0.35 5 6
ABCA1 0.022 0.14 -10000 0 -0.91 5 5
RARs/THRs 0.054 0.093 -10000 0 -0.35 18 18
RXRs/FXR 0.045 0.11 -10000 0 -0.38 13 13
BCL2 0.024 0.034 -10000 0 -0.62 1 1
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.008 0.085 -10000 0 -0.44 11 11
Caspase 8 (4 units) -0.006 0.13 -10000 0 -0.49 13 13
NEF -0.008 0.068 -10000 0 -0.33 13 13
NFKBIA 0.03 0.019 -10000 0 -10000 0 0
BIRC3 0.034 0.094 0.46 14 -0.66 1 15
CYCS -0.003 0.13 0.28 1 -0.5 12 13
RIPK1 0.024 0.008 -10000 0 -10000 0 0
CD247 0.016 0.066 0.44 1 -0.7 2 3
MAP2K7 -0.001 0.18 -10000 0 -0.67 16 16
protein ubiquitination -0.001 0.11 0.31 2 -0.37 10 12
CRADD 0.024 0.034 -10000 0 -0.62 1 1
DAXX 0.024 0.007 -10000 0 -10000 0 0
FAS 0.005 0.11 -10000 0 -0.59 12 12
BID 0.001 0.14 0.28 2 -0.51 13 15
NF-kappa-B/RelA/I kappa B alpha 0.06 0.055 0.32 12 -0.32 1 13
TRADD 0.023 0.018 -10000 0 -0.3 1 1
MAP3K5 -0.041 0.19 -10000 0 -0.55 41 41
CFLAR 0.026 0.002 -10000 0 -10000 0 0
FADD 0.025 0.006 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.06 0.056 0.32 12 -0.32 1 13
MAPK8 -0.015 0.18 -10000 0 -0.6 20 20
APAF1 0.026 0.003 -10000 0 -10000 0 0
TRAF1 0.026 0.017 0.34 1 -10000 0 1
TRAF2 0.026 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.018 0.13 0.3 2 -0.54 13 15
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.012 0.12 -10000 0 -0.45 13 13
CHUK -0.002 0.11 0.32 2 -0.4 10 12
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.015 0.14 -10000 0 -0.39 34 34
TCRz/NEF 0.01 0.074 0.31 3 -0.4 8 11
TNF 0.004 0.12 0.34 2 -0.62 12 14
FASLG 0.001 0.12 0.48 3 -0.68 9 12
NFKB1 0.028 0.02 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.019 0.098 -10000 0 -0.4 17 17
CASP6 -0.007 0.18 -10000 0 -0.59 15 15
CASP7 0.023 0.15 0.46 5 -0.47 9 14
RELA 0.029 0.02 -10000 0 -10000 0 0
CASP2 0.025 0.005 -10000 0 -10000 0 0
CASP3 0.015 0.16 0.44 5 -0.48 13 18
TNFRSF1A 0.025 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.021 0.065 -10000 0 -0.35 9 9
CASP8 0.026 0.003 -10000 0 -10000 0 0
CASP9 0.025 0.006 -10000 0 -10000 0 0
MAP3K14 -0.007 0.12 -10000 0 -0.45 10 10
APAF-1/Caspase 9 0.017 0.11 0.32 11 -0.41 7 18
BCL2 -0.014 0.17 -10000 0 -0.56 19 19
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.031 0.012 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.024 0.008 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.018 0.097 0.34 6 -0.62 7 13
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.009 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.025 0.031 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.026 0.004 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.025 0.005 -10000 0 -10000 0 0
FYN 0.024 0.007 -10000 0 -10000 0 0
MAP3K12 0.028 0.023 0.34 2 -10000 0 2
FGR 0.021 0.048 -10000 0 -0.62 2 2
p38 alpha/TAB1 -0.057 0.11 -10000 0 -0.33 37 37
PRKG1 -0.004 0.14 0.34 1 -0.62 17 18
DUSP8 0.023 0.05 0.34 1 -0.62 2 3
PGK/cGMP/p38 alpha -0.031 0.14 0.26 1 -0.37 36 37
apoptosis -0.055 0.1 -10000 0 -0.32 35 35
RAL/GTP 0.035 0.006 -10000 0 -10000 0 0
LYN 0.022 0.01 -10000 0 -10000 0 0
DUSP1 -0.035 0.19 -10000 0 -0.62 34 34
PAK1 0.025 0.004 -10000 0 -10000 0 0
SRC 0.03 0.037 0.34 5 -10000 0 5
RAC1/OSM/MEKK3/MKK3 0.06 0.022 -10000 0 -10000 0 0
TRAF6 0.024 0.034 -10000 0 -0.62 1 1
RAC1 0.026 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.026 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.033 0.01 -10000 0 -10000 0 0
MAPK11 -0.028 0.14 0.45 1 -0.41 24 25
BLK -0.069 0.21 0.34 2 -0.5 64 66
HCK 0.005 0.12 -10000 0 -0.62 12 12
MAP2K3 0.024 0.007 -10000 0 -10000 0 0
DUSP16 0.023 0.034 -10000 0 -0.62 1 1
DUSP10 0.014 0.067 -10000 0 -0.62 4 4
TRAF6/MEKK3 0.031 0.022 -10000 0 -0.36 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.023 0.14 0.36 1 -0.36 35 36
positive regulation of innate immune response -0.029 0.17 0.48 1 -0.46 27 28
LCK 0.007 0.11 0.34 1 -0.59 11 12
p38alpha-beta/MKP7 -0.02 0.16 0.47 1 -0.44 27 28
p38alpha-beta/MKP5 -0.02 0.15 -10000 0 -0.45 24 24
PGK/cGMP -0.003 0.1 0.23 1 -0.46 17 18
PAK2 0.026 0.003 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.047 0.19 0.47 1 -0.47 37 38
CDC42 0.025 0.006 -10000 0 -10000 0 0
RALB 0.026 0.003 -10000 0 -10000 0 0
RALA 0.026 0.003 -10000 0 -10000 0 0
PAK3 0.054 0.096 0.34 37 -10000 0 37
TCGA08_rtk_signaling

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
PDGFRA -0.22 0.31 -10000 0 -0.59 145 145
HRAS 0.027 0.017 0.34 1 -10000 0 1
EGFR 0.01 0.1 -10000 0 -0.62 9 9
AKT -0.007 0.085 0.24 1 -0.31 7 8
FOXO3 0.024 0.007 -10000 0 -10000 0 0
AKT1 0.024 0.007 -10000 0 -10000 0 0
FOXO1 0.02 0.045 -10000 0 -0.38 4 4
AKT3 0.018 0.051 0.34 1 -0.62 2 3
FOXO4 0.026 0.001 -10000 0 -10000 0 0
MET 0.023 0.034 -10000 0 -0.62 1 1
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
PIK3CB 0.026 0.001 -10000 0 -10000 0 0
NRAS 0.025 0.004 -10000 0 -10000 0 0
PIK3CG 0.004 0.12 0.34 2 -0.62 13 15
PIK3R3 0.026 0.017 0.34 1 -10000 0 1
PIK3R2 0.026 0.017 0.34 1 -10000 0 1
NF1 0.025 0.017 -10000 0 -0.3 1 1
RAS -0.049 0.097 -10000 0 -0.28 19 19
ERBB2 0.015 0.082 -10000 0 -0.62 6 6
proliferation/survival/translation -0.016 0.079 0.26 16 -10000 0 16
PI3K -0.036 0.095 0.23 2 -0.25 20 22
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
KRAS 0.026 0.004 -10000 0 -10000 0 0
FOXO 0.028 0.052 0.24 1 -0.15 1 2
AKT2 0.026 0.004 -10000 0 -10000 0 0
PTEN 0.023 0.025 -10000 0 -0.3 2 2
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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 0.026 0.003 -10000 0 -10000 0 0
NFATC1 0.006 0.095 -10000 0 -0.42 4 4
NFATC2 -0.044 0.1 -10000 0 -0.28 36 36
NFATC3 -0.003 0.086 -10000 0 -0.4 16 16
YWHAE 0.022 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.01 0.1 -10000 0 -0.4 13 13
Exportin 1/Ran/NUP214 0.05 0.011 -10000 0 -10000 0 0
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.008 0.12 -10000 0 -0.37 24 24
BCL2/BAX 0.035 0.027 -10000 0 -0.46 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.013 0.016 -10000 0 -10000 0 0
CaM/Ca2+ 0.013 0.016 -10000 0 -10000 0 0
BAX 0.026 0.004 -10000 0 -10000 0 0
MAPK14 0.023 0.008 -10000 0 -10000 0 0
BAD 0.026 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D 0.003 0.09 -10000 0 -0.39 10 10
Calcineurin A alpha-beta B1/BCL2 0.023 0.034 -10000 0 -0.62 1 1
FKBP8 0.026 0.004 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.003 0.089 0.39 10 -10000 0 10
KPNB1 0.026 0.003 -10000 0 -10000 0 0
KPNA2 0.027 0.024 0.34 2 -10000 0 2
XPO1 0.026 0.002 -10000 0 -10000 0 0
SFN 0.2 0.16 0.34 202 -0.3 2 204
MAP3K8 0.021 0.048 -10000 0 -0.62 2 2
NFAT4/CK1 alpha 0.005 0.062 -10000 0 -0.28 12 12
MEF2D/NFAT1/Cbp/p300 -0.045 0.15 -10000 0 -0.36 46 46
CABIN1 -0.01 0.1 -10000 0 -0.4 13 13
CALM1 0.023 0.01 -10000 0 -10000 0 0
RAN 0.025 0.004 -10000 0 -10000 0 0
MAP3K1 0.026 0.002 -10000 0 -10000 0 0
CAMK4 -0.022 0.17 0.34 1 -0.62 27 28
mol:Ca2+ -0.002 0.006 -10000 0 -10000 0 0
MAPK3 0.025 0.004 -10000 0 -10000 0 0
YWHAH 0.025 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.036 0.019 0.25 2 -10000 0 2
YWHAB 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.008 0.14 -10000 0 -0.62 18 18
MAPK9 0.025 0.006 -10000 0 -10000 0 0
YWHAG 0.026 0.004 -10000 0 -10000 0 0
FKBP1A 0.026 0.004 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.012 0.12 -10000 0 -0.38 21 21
PRKCH 0.024 0.018 -10000 0 -0.3 1 1
CABIN1/Cbp/p300 0.027 0.027 -10000 0 -10000 0 0
CASP3 0.022 0.019 -10000 0 -0.3 1 1
PIM1 0.024 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.01 -10000 0 -10000 0 0
apoptosis 0.019 0.014 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.064 0.084 -10000 0 -0.28 4 4
PRKCB -0.028 0.18 -10000 0 -0.61 31 31
PRKCE 0.025 0.037 0.34 1 -0.62 1 2
JNK2/NFAT4 -0.009 0.098 -10000 0 -0.36 17 17
BAD/BCL-XL 0.038 0.007 -10000 0 -10000 0 0
PRKCD 0.026 0.003 -10000 0 -10000 0 0
NUP214 0.026 0.003 -10000 0 -10000 0 0
PRKCZ -0.003 0.12 -10000 0 -0.52 17 17
PRKCA 0.025 0.005 -10000 0 -10000 0 0
PRKCG 0.023 0.034 0.34 4 -10000 0 4
PRKCQ 0.003 0.12 0.34 2 -0.59 14 16
FKBP38/BCL2 0.035 0.028 -10000 0 -0.46 1 1
EP300 0.019 0.018 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.026 0.004 -10000 0 -10000 0 0
NFATc/JNK1 0.002 0.12 -10000 0 -0.45 10 10
CaM/Ca2+/FKBP38 0.025 0.021 -10000 0 -10000 0 0
FKBP12/FK506 0.019 0.003 -10000 0 -10000 0 0
CSNK1A1 0.007 0.015 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.006 0.11 0.22 1 -0.4 27 28
NFATc/ERK1 0.02 0.095 -10000 0 -0.43 3 3
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.006 0.13 0.27 1 -0.35 31 32
NR4A1 -0.074 0.24 -10000 0 -0.6 56 56
GSK3B 0.024 0.007 -10000 0 -10000 0 0
positive T cell selection -0.003 0.086 -10000 0 -0.4 16 16
NFAT1/CK1 alpha -0.032 0.081 -10000 0 -0.27 17 17
RCH1/ KPNB1 0.038 0.018 0.25 2 -10000 0 2
YWHAQ 0.026 0.002 -10000 0 -10000 0 0
PRKACA 0.025 0.005 -10000 0 -10000 0 0
AKAP5 0.026 0.024 0.34 2 -10000 0 2
MEF2D 0.014 0.018 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.012 -10000 0 -10000 0 0
NFATc/p38 alpha 0.011 0.09 -10000 0 -0.4 4 4
CREBBP 0.018 0.018 -10000 0 -10000 0 0
BCL2 0.024 0.034 -10000 0 -0.62 1 1
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.054 0.04 -10000 0 -0.36 2 2
HDAC3 0.026 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.007 0.002 -10000 0 -10000 0 0
GATA1/HDAC4 0.037 0.023 0.25 4 -10000 0 4
GATA1/HDAC5 0.036 0.02 0.25 3 -10000 0 3
GATA2/HDAC5 0.036 0.04 0.25 2 -0.46 2 4
HDAC5/BCL6/BCoR 0.05 0.016 -10000 0 -10000 0 0
HDAC9 -0.006 0.14 -10000 0 -0.62 18 18
Glucocorticoid receptor/Hsp90/HDAC6 0.049 0.014 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.037 0.029 0.25 1 -0.46 1 2
HDAC5/YWHAB 0.037 0.008 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.014 0.004 -10000 0 -10000 0 0
GATA2 0.024 0.053 0.34 2 -0.62 2 4
HDAC4/RFXANK 0.039 0.02 -10000 0 -10000 0 0
BCOR 0.025 0.017 -10000 0 -0.3 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.025 0.005 -10000 0 -10000 0 0
HDAC5 0.026 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.032 0.039 -10000 0 -0.46 2 2
Histones 0.016 0.065 -10000 0 -0.34 2 2
ADRBK1 0.025 0.004 -10000 0 -10000 0 0
HDAC4 0.027 0.017 0.34 1 -10000 0 1
XPO1 0.026 0.002 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.036 0.027 -10000 0 -0.46 1 1
HDAC4/Ubc9 0.037 0.015 0.25 1 -10000 0 1
HDAC7 0.027 0.017 0.34 1 -10000 0 1
HDAC5/14-3-3 E 0.033 0.014 -10000 0 -10000 0 0
TUBA1B 0.026 0.002 -10000 0 -10000 0 0
HDAC6 0.026 0.002 -10000 0 -10000 0 0
HDAC5/RFXANK 0.038 0.014 0.25 1 -10000 0 1
CAMK4 -0.022 0.17 0.34 1 -0.62 27 28
Tubulin/HDAC6 0.048 0.017 -10000 0 -10000 0 0
SUMO1 0.026 0.002 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.026 0.004 -10000 0 -10000 0 0
GATA1 0.024 0.029 0.34 3 -10000 0 3
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.009 -10000 0 -10000 0 0
NR3C1 0.026 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.034 0.037 -10000 0 -0.32 1 1
SRF 0.024 0.008 -10000 0 -10000 0 0
HDAC4/YWHAB 0.038 0.013 0.25 1 -10000 0 1
Tubulin 0.035 0.012 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.033 0.014 -10000 0 -10000 0 0
GNB1 0.024 0.008 -10000 0 -10000 0 0
RANGAP1 0.025 0.004 -10000 0 -10000 0 0
BCL6/BCoR 0.037 0.014 -10000 0 -0.21 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.05 0.016 -10000 0 -10000 0 0
HDAC4/SRF 0.017 0.11 -10000 0 -0.4 22 22
HDAC4/ER alpha -0.22 0.24 0.25 1 -0.43 198 199
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.016 0.065 -10000 0 -0.34 2 2
cell motility 0.047 0.016 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.025 0.006 -10000 0 -10000 0 0
HDAC7/HDAC3 0.038 0.013 0.25 1 -10000 0 1
BCL6 0.026 0.003 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.027 0.017 0.34 1 -10000 0 1
Hsp90/HDAC6 0.037 0.009 -10000 0 -10000 0 0
ESR1 -0.31 0.31 -10000 0 -0.58 198 198
HDAC6/HDAC11 0.043 0.031 0.25 8 -10000 0 8
Ran/GTP/Exportin 1 0.035 0.037 -10000 0 -0.33 1 1
NPC 0.015 0.001 -10000 0 -10000 0 0
MEF2C 0.026 0.003 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
HDAC4/MEF2C 0.07 0.026 -10000 0 -10000 0 0
GNG2 0.022 0.048 -10000 0 -0.62 2 2
NCOR2 0.026 0.004 -10000 0 -10000 0 0
TUBB2A 0.024 0.008 -10000 0 -10000 0 0
HDAC11 0.033 0.046 0.34 8 -10000 0 8
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
RANBP2 0.026 0.002 -10000 0 -10000 0 0
ANKRA2 0.024 0.034 -10000 0 -0.62 1 1
RFXANK 0.027 0.023 0.34 2 -10000 0 2
nuclear import -0.029 0.014 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.025 0.006 -10000 0 -10000 0 0
mol:PIP3 0.004 0.041 0.2 1 -0.46 2 3
FRAP1 0.006 0.061 -10000 0 -0.46 5 5
AKT1 0.004 0.049 -10000 0 -0.44 2 2
INSR 0.026 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.032 0.023 0.22 5 -10000 0 5
mol:GTP 0.024 0.055 -10000 0 -0.37 2 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.009 0.025 -10000 0 -0.19 1 1
TSC2 0.023 0.025 -10000 0 -0.3 2 2
RHEB/GDP 0.013 0.042 -10000 0 -0.35 2 2
TSC1 0.026 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.023 0.02 -10000 0 -0.19 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.022 0.034 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.025 0.006 -10000 0 -10000 0 0
RPS6KB1 0.021 0.056 -10000 0 -0.27 4 4
MAP3K5 -0.048 0.13 -10000 0 -0.32 61 61
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
apoptosis -0.048 0.13 -10000 0 -0.31 61 61
mol:LY294002 0 0 0.001 1 -0.001 3 4
EIF4B 0.019 0.052 0.24 1 -0.29 1 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.05 -10000 0 -0.27 1 1
eIF4E/eIF4G1/eIF4A1 0.01 0.038 -10000 0 -0.27 5 5
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.035 0.045 -10000 0 -0.48 2 2
mTOR/RHEB/GTP/Raptor/GBL 0.006 0.035 -10000 0 -0.24 1 1
FKBP1A 0.026 0.004 -10000 0 -10000 0 0
RHEB/GTP 0.028 0.051 -10000 0 -0.34 2 2
mol:Amino Acids 0 0 0.001 1 -0.001 3 4
FKBP12/Rapamycin 0.019 0.004 -10000 0 -10000 0 0
PDPK1 -0.009 0.037 0.2 1 -0.44 2 3
EIF4E 0.024 0.007 -10000 0 -10000 0 0
ASK1/PP5C -0.074 0.24 -10000 0 -0.59 66 66
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.008 0.082 -10000 0 -0.82 1 1
TSC1/TSC2 0.027 0.059 -10000 0 -0.4 2 2
tumor necrosis factor receptor activity 0 0 0.001 3 -0.001 1 4
RPS6 0.025 0.005 -10000 0 -10000 0 0
PPP5C 0.026 0.004 -10000 0 -10000 0 0
EIF4G1 0.026 0.002 -10000 0 -10000 0 0
IRS1 0.006 0.019 -10000 0 -0.2 3 3
INS 0.023 0.037 0.34 5 -10000 0 5
PTEN 0.023 0.025 -10000 0 -0.3 2 2
PDK2 -0.01 0.041 0.2 1 -0.4 3 4
EIF4EBP1 -0.15 0.39 -10000 0 -1 59 59
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
PPP2R5D 0.02 0.075 0.24 1 -0.41 5 6
peptide biosynthetic process 0.013 0.017 -10000 0 -10000 0 0
RHEB 0.025 0.005 -10000 0 -10000 0 0
EIF4A1 0.022 0.01 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 5 -0.004 1 6
EEF2 0.013 0.017 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.13 0.37 -10000 0 -0.96 59 59
Retinoic acid receptors-mediated signaling

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
HDAC1 0.025 0.006 -10000 0 -10000 0 0
HDAC3 0.026 0.004 -10000 0 -10000 0 0
VDR 0.023 0.1 0.34 11 -0.62 7 18
Cbp/p300/PCAF 0.046 0.043 -10000 0 -0.4 3 3
EP300 0.026 0.004 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.018 0.068 -10000 0 -0.32 5 5
KAT2B 0.021 0.058 -10000 0 -0.62 3 3
MAPK14 0.024 0.008 -10000 0 -10000 0 0
AKT1 0.029 0.1 0.23 20 -0.28 13 33
RAR alpha/9cRA/Cyclin H 0.031 0.077 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.005 0.074 -10000 0 -0.34 7 7
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.004 0.12 -10000 0 -0.49 18 18
NCOR2 0.026 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.016 0.075 0.23 11 -0.46 7 18
RXRs/RARs/NRIP1/9cRA 0.034 0.088 -10000 0 -0.5 2 2
NCOA2 -0.038 0.18 -10000 0 -0.62 33 33
NCOA3 0.026 0.004 -10000 0 -10000 0 0
NCOA1 0.026 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.023 0.1 0.34 11 -0.62 7 18
RARG 0.026 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.035 0.006 -10000 0 -10000 0 0
MAPK3 0.026 0.005 -10000 0 -10000 0 0
MAPK1 0.026 0.004 -10000 0 -10000 0 0
MAPK8 -0.006 0.14 -10000 0 -0.62 18 18
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.037 0.085 -10000 0 -10000 0 0
RARA 0.006 0.06 -10000 0 -0.26 16 16
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.021 0.11 -10000 0 -0.4 18 18
PRKCA 0.026 0.008 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.032 0.085 -10000 0 -0.53 1 1
RXRG 0.028 0.07 0.31 3 -0.36 4 7
RXRA 0.007 0.062 0.22 1 -0.24 17 18
RXRB 0.019 0.02 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.016 0.075 0.23 11 -0.46 7 18
RBP1 -0.093 0.26 0.34 7 -0.62 71 78
CRBP1/9-cic-RA -0.07 0.19 0.23 7 -0.46 71 78
RARB 0 0.13 -10000 0 -0.62 15 15
PRKCG 0.025 0.034 0.34 4 -10000 0 4
MNAT1 0.025 0.006 -10000 0 -10000 0 0
RAR alpha/RXRs 0.021 0.088 0.42 1 -10000 0 1
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.033 0.084 -10000 0 -0.55 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.08 -10000 0 -0.39 4 4
RXRs/RARs/NRIP1/9cRA/HDAC3 0.034 0.085 -10000 0 -0.53 1 1
positive regulation of DNA binding 0.022 0.069 -10000 0 -10000 0 0
NRIP1 0.032 0.1 -10000 0 -1.2 1 1
RXRs/RARs 0.037 0.082 -10000 0 -0.34 2 2
RXRs/RXRs/DNA/9cRA 0.009 0.056 -10000 0 -10000 0 0
PRKACA 0.026 0.004 -10000 0 -10000 0 0
CDK7 0.026 0.003 -10000 0 -10000 0 0
TFIIH 0.05 0.013 -10000 0 -10000 0 0
RAR alpha/9cRA 0.045 0.06 -10000 0 -10000 0 0
CCNH 0.026 0.003 -10000 0 -10000 0 0
CREBBP 0.025 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.044 0.02 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.063 0.07 -10000 0 -0.34 2 2
MAPK9 0.007 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.002 0.024 0.21 4 -10000 0 4
GNB1/GNG2 0.029 0.034 -10000 0 -0.4 2 2
GNB1 0.024 0.008 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.002 -10000 0 -10000 0 0
Gs family/GTP 0.044 0.064 0.19 57 -10000 0 57
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.001 0 -10000 0 -10000 0 0
GNAL 0.075 0.11 0.34 57 -10000 0 57
GNG2 0.022 0.048 -10000 0 -0.62 2 2
CRH 0.019 0.035 0.34 4 -10000 0 4
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 -0.012 0.083 -10000 0 -0.37 18 18
MAPK11 0.013 0.032 0.18 13 -10000 0 13
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.037 0.11 0.35 4 -0.39 6 10
PDGFB-D/PDGFRB/SLAP 0.02 0.081 0.24 7 -0.47 8 15
PDGFB-D/PDGFRB/APS/CBL 0.054 0.04 0.43 1 -10000 0 1
AKT1 0.001 0.068 0.3 3 -0.53 1 4
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.043 0.12 0.36 4 -0.38 7 11
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
FGR -0.008 0.12 -10000 0 -0.47 18 18
mol:Ca2+ 0.013 0.078 -10000 0 -0.35 6 6
MYC -0.021 0.3 -10000 0 -0.83 41 41
SHC1 0.02 0.011 -10000 0 -10000 0 0
HRAS/GDP 0.032 0.045 -10000 0 -0.33 1 1
LRP1/PDGFRB/PDGFB 0.053 0.04 -10000 0 -0.4 1 1
GRB10 0.026 0.004 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GO:0007205 0.013 0.078 -10000 0 -0.36 6 6
PTEN 0.023 0.025 -10000 0 -0.3 2 2
GRB2 0.025 0.005 -10000 0 -10000 0 0
GRB7 0.024 0.078 0.34 6 -0.62 4 10
PDGFB-D/PDGFRB/SHP2 0.042 0.031 0.24 8 -10000 0 8
PDGFB-D/PDGFRB/GRB10 0.042 0.031 0.24 8 -10000 0 8
cell cycle arrest 0.02 0.081 0.24 7 -0.47 8 15
HRAS 0.027 0.017 0.34 1 -10000 0 1
HIF1A -0.001 0.062 0.28 3 -0.47 1 4
GAB1 0.006 0.1 -10000 0 -0.43 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.007 0.1 -10000 0 -0.42 5 5
PDGFB-D/PDGFRB 0.047 0.04 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.042 0.031 0.24 8 -10000 0 8
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.035 0.13 0.36 4 -0.42 7 11
positive regulation of MAPKKK cascade 0.042 0.031 0.24 8 -10000 0 8
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
mol:IP3 0.013 0.079 -10000 0 -0.36 6 6
E5 0 0.002 -10000 0 -10000 0 0
CSK 0.025 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.039 0.064 0.24 13 -0.44 4 17
SHB 0.024 0.034 -10000 0 -0.62 1 1
BLK -0.13 0.24 -10000 0 -0.48 106 106
PTPN2 0.025 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.041 0.032 0.24 8 -10000 0 8
BCAR1 0.024 0.007 -10000 0 -10000 0 0
VAV2 -0.001 0.14 -10000 0 -0.48 11 11
CBL 0.025 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.042 0.031 0.24 8 -10000 0 8
LCK -0.017 0.15 -10000 0 -0.5 25 25
PDGFRB 0.03 0.048 0.34 8 -10000 0 8
ACP1 0.026 0.002 -10000 0 -10000 0 0
HCK 0.003 0.12 -10000 0 -0.57 12 12
ABL1 -0.003 0.1 -10000 0 -0.39 10 10
PDGFB-D/PDGFRB/CBL 0.002 0.11 -10000 0 -0.45 7 7
PTPN1 0.025 0.007 -10000 0 -10000 0 0
SNX15 0.026 0.004 -10000 0 -10000 0 0
STAT3 0.026 0.004 -10000 0 -10000 0 0
STAT1 0.028 0.023 0.34 2 -10000 0 2
cell proliferation -0.01 0.27 -10000 0 -0.72 41 41
SLA 0.005 0.094 -10000 0 -0.62 8 8
actin cytoskeleton reorganization 0.029 0.05 0.32 2 -0.32 1 3
SRC 0.022 0.047 -10000 0 -10000 0 0
PI3K -0.002 0.048 -10000 0 -0.38 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.041 0.054 -10000 0 -0.27 4 4
SH2B2 0.029 0.033 0.34 4 -10000 0 4
PLCgamma1/SPHK1 0.044 0.12 0.36 4 -0.39 7 11
LYN 0.011 0.062 -10000 0 -0.42 4 4
LRP1 0.024 0.034 -10000 0 -0.62 1 1
SOS1 0.026 0.001 -10000 0 -10000 0 0
STAT5B 0.026 0.004 -10000 0 -10000 0 0
STAT5A 0.027 0.017 0.34 1 -10000 0 1
NCK1-2/p130 Cas 0.068 0.048 0.39 1 -0.33 1 2
SPHK1 0.071 0.14 0.34 64 -0.62 5 69
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.013 0.079 -10000 0 -0.36 6 6
PLCG1 0.013 0.08 -10000 0 -0.37 6 6
NHERF/PDGFRB 0.047 0.054 -10000 0 -0.4 3 3
YES1 0.012 0.086 -10000 0 -0.62 5 5
cell migration 0.046 0.053 -10000 0 -0.4 3 3
SHC/Grb2/SOS1 0.055 0.045 -10000 0 -10000 0 0
SLC9A3R2 0.02 0.051 -10000 0 -0.51 3 3
SLC9A3R1 0.023 0.034 -10000 0 -0.62 1 1
NHERF1-2/PDGFRB/PTEN 0.055 0.056 -10000 0 -0.36 3 3
FYN -0.008 0.12 -10000 0 -0.41 23 23
DOK1 0.023 0.042 -10000 0 -10000 0 0
HRAS/GTP 0.02 0.011 0.23 1 -10000 0 1
PDGFB 0.026 0.017 0.34 1 -10000 0 1
RAC1 -0.019 0.18 -10000 0 -0.48 40 40
PRKCD 0.023 0.044 -10000 0 -10000 0 0
FER 0.021 0.041 -10000 0 -10000 0 0
MAPKKK cascade 0.05 0.1 0.35 16 -10000 0 16
RASA1 0.019 0.05 -10000 0 -0.36 2 2
NCK1 0.026 0.001 -10000 0 -10000 0 0
NCK2 0.025 0.037 0.34 1 -0.62 1 2
p62DOK/Csk 0.041 0.037 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.04 0.036 0.24 7 -0.34 1 8
chemotaxis -0.002 0.1 -10000 0 -0.38 10 10
STAT1-3-5/STAT1-3-5 0.06 0.031 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.021 0.032 0.22 8 -10000 0 8
PTPRJ 0.026 0.002 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.025 0.005 -10000 0 -10000 0 0
ITGB7 0.017 0.075 -10000 0 -0.62 5 5
ITGA4 0.015 0.09 0.34 1 -0.62 7 8
alpha4/beta7 Integrin 0.023 0.089 0.25 1 -0.46 12 13
alpha4/beta1 Integrin 0.028 0.069 0.25 1 -0.46 7 8
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0 0.13 0.25 1 -0.46 28 29
AKT1 0.018 0.12 -10000 0 -0.6 9 9
PTK2B -0.011 0.15 0.34 1 -0.74 8 9
VEGFR2 homodimer/Frs2 0.015 0.12 -10000 0 -0.7 9 9
CAV1 0.025 0.005 -10000 0 -10000 0 0
CALM1 0.025 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.026 0.11 -10000 0 -0.64 9 9
endothelial cell proliferation 0.013 0.12 -10000 0 -0.55 9 9
mol:Ca2+ 0.001 0.11 -10000 0 -0.63 9 9
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.036 0.11 -10000 0 -0.61 9 9
RP11-342D11.1 -0.008 0.1 -10000 0 -0.6 10 10
CDH5 0.022 0.034 -10000 0 -0.62 1 1
VEGFA homodimer 0.044 0.033 -10000 0 -10000 0 0
SHC1 0.02 0.011 -10000 0 -10000 0 0
SHC2 0.012 0.09 -10000 0 -0.58 8 8
HRAS/GDP 0.018 0.084 -10000 0 -0.54 6 6
SH2D2A 0.011 0.095 0.34 4 -0.62 7 11
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.026 0.12 -10000 0 -0.61 8 8
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.013 0.12 -10000 0 -0.55 13 13
VEGFR1 homodimer 0.024 0.007 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.033 0.1 -10000 0 -0.61 6 6
GRB10 0.002 0.1 -10000 0 -0.61 9 9
PTPN11 0.026 0.003 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
PAK1 0.025 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.043 0.11 -10000 0 -0.62 9 9
HRAS 0.027 0.017 0.34 1 -10000 0 1
VEGF/Rho/ROCK1/Integrin Complex -0.003 0.099 -10000 0 -0.5 8 8
HIF1A 0.025 0.006 -10000 0 -10000 0 0
FRS2 0.026 0.003 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.035 0.1 -10000 0 -0.6 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.023 0.034 -10000 0 -0.62 1 1
Nck/Pak 0.038 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.024 0.11 -10000 0 -0.65 9 9
mol:GDP 0.024 0.093 -10000 0 -0.59 6 6
mol:NADP 0.026 0.11 -10000 0 -0.52 8 8
eNOS/Hsp90 0.038 0.1 -10000 0 -0.51 7 7
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
mol:IP3 0.001 0.11 -10000 0 -0.64 9 9
HIF1A/ARNT 0.029 0.017 -10000 0 -10000 0 0
SHB 0.024 0.034 -10000 0 -0.62 1 1
VEGFA 0.024 0.009 -10000 0 -10000 0 0
VEGFC 0.024 0.018 0.34 1 -10000 0 1
FAK1/Vinculin 0.013 0.16 -10000 0 -0.76 9 9
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.026 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.011 0.16 -10000 0 -0.46 30 30
PTPN6 0.025 0.005 -10000 0 -10000 0 0
EPAS1 0.022 0.061 -10000 0 -0.36 9 9
mol:L-citrulline 0.026 0.11 -10000 0 -0.52 8 8
ITGAV 0.027 0.017 0.34 1 -10000 0 1
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.038 0.1 -10000 0 -0.57 9 9
VEGFR2 homodimer/VEGFA homodimer 0.026 0.12 -10000 0 -0.65 10 10
VEGFR2/3 heterodimer 0.013 0.12 -10000 0 -0.74 9 9
VEGFB 0.012 0.1 0.34 2 -0.62 9 11
MAPK11 0.014 0.13 0.38 1 -0.62 10 11
VEGFR2 homodimer -0.001 0.13 -10000 0 -0.8 9 9
FLT1 0.024 0.007 -10000 0 -10000 0 0
NEDD4 0.023 0.048 -10000 0 -0.62 2 2
MAPK3 0.004 0.12 0.36 1 -0.58 9 10
MAPK1 0.004 0.12 0.36 1 -0.57 9 10
VEGFA145/NRP2 0.031 0.048 0.25 1 -0.45 3 4
VEGFR1/2 heterodimer 0.013 0.12 -10000 0 -0.72 9 9
KDR -0.001 0.13 -10000 0 -0.81 9 9
VEGFA165/NRP1/VEGFR2 homodimer 0.026 0.12 -10000 0 -0.65 9 9
SRC 0.03 0.037 0.34 5 -10000 0 5
platelet activating factor biosynthetic process 0.005 0.12 0.37 1 -0.59 9 10
PI3K 0.011 0.13 -10000 0 -0.72 9 9
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.026 0.11 -10000 0 -0.65 9 9
FES -0.003 0.12 -10000 0 -0.65 9 9
GAB1 0.024 0.11 -10000 0 -0.62 8 8
VEGFR2 homodimer/VEGFA homodimer/Src 0.028 0.11 -10000 0 -0.65 9 9
CTNNB1 0.026 0.002 -10000 0 -10000 0 0
SOS1 0.026 0.001 -10000 0 -10000 0 0
ARNT 0.02 0.011 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.035 0.1 -10000 0 -0.5 7 7
VEGFR2 homodimer/VEGFA homodimer/Yes 0.024 0.11 -10000 0 -0.65 9 9
PI3K/GAB1 0.029 0.12 -10000 0 -0.58 9 9
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.047 0.11 -10000 0 -0.59 9 9
PRKACA 0.026 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.024 0.12 -10000 0 -0.69 9 9
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
CDC42 0 0.11 -10000 0 -0.65 9 9
actin cytoskeleton reorganization 0.013 0.12 -10000 0 -0.54 13 13
PTK2 -0.012 0.15 -10000 0 -0.83 9 9
EDG1 -0.008 0.1 -10000 0 -0.6 10 10
mol:DAG 0.001 0.11 -10000 0 -0.64 9 9
CaM/Ca2+ 0.03 0.11 -10000 0 -0.59 9 9
MAP2K3 0.011 0.12 0.35 1 -0.58 9 10
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.027 0.11 -10000 0 -0.64 9 9
PLCG1 0.001 0.11 -10000 0 -0.65 9 9
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.038 0.11 -10000 0 -0.6 10 10
IQGAP1 0.025 0.004 -10000 0 -10000 0 0
YES1 0.026 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.026 0.11 -10000 0 -0.63 9 9
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.025 0.11 -10000 0 -0.65 9 9
cell migration 0.018 0.14 0.36 1 -0.68 8 9
mol:PI-3-4-5-P3 0.012 0.12 -10000 0 -0.65 9 9
FYN 0.024 0.007 -10000 0 -10000 0 0
VEGFB/NRP1 0.001 0.11 -10000 0 -0.52 13 13
mol:NO 0.026 0.11 -10000 0 -0.52 8 8
PXN 0.026 0.003 -10000 0 -10000 0 0
HRAS/GTP 0.006 0.08 -10000 0 -0.54 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.019 0.11 -10000 0 -0.64 9 9
VHL 0.026 0.002 -10000 0 -10000 0 0
ITGB3 -0.024 0.17 -10000 0 -0.62 28 28
NOS3 0.024 0.12 -10000 0 -0.61 8 8
VEGFR2 homodimer/VEGFA homodimer/Sck 0.018 0.12 -10000 0 -0.55 14 14
RAC1 0.026 0.004 -10000 0 -10000 0 0
PRKCA 0.014 0.11 0.35 1 -0.56 9 10
PRKCB -0.01 0.14 0.35 1 -0.61 9 10
VCL 0.025 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.009 0.11 -10000 0 -0.6 10 10
VEGFR1/2 heterodimer/VEGFA homodimer 0.023 0.11 -10000 0 -0.65 9 9
VEGFA165/NRP2 0.031 0.048 0.25 1 -0.45 3 4
MAPKKK cascade 0.048 0.11 -10000 0 -0.57 5 5
NRP2 0.022 0.06 0.34 1 -0.62 3 4
VEGFC homodimer 0.024 0.018 0.34 1 -10000 0 1
NCK1 0.026 0.001 -10000 0 -10000 0 0
ROCK1 0.026 0.003 -10000 0 -10000 0 0
FAK1/Paxillin 0.013 0.16 -10000 0 -0.8 8 8
MAP3K13 0 0.11 0.35 1 -0.65 9 10
PDPK1 0.011 0.1 -10000 0 -0.56 9 9
Class I PI3K 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
ARF5/GTP -0.011 0.033 0.29 1 -10000 0 1
DAPP1 -0.054 0.17 0.3 1 -0.46 34 35
Src family/SYK family/BLNK-LAT/BTK-ITK -0.069 0.22 0.42 1 -0.63 34 35
mol:DAG -0.019 0.092 0.32 1 -0.27 19 20
HRAS 0.028 0.017 0.33 1 -10000 0 1
RAP1A 0.026 0.006 -10000 0 -10000 0 0
ARF5/GDP 0.014 0.082 -10000 0 -0.32 6 6
PLCG2 0.012 0.083 -10000 0 -0.57 7 7
PLCG1 0.026 0.004 -10000 0 -10000 0 0
ARF5 0.026 0.004 -10000 0 -10000 0 0
mol:GTP -0.012 0.025 0.3 1 -10000 0 1
ARF1/GTP -0.002 0.024 0.28 1 -10000 0 1
RHOA 0.026 0.003 -10000 0 -10000 0 0
YES1 0.026 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.013 0.021 -10000 0 -10000 0 0
ADAP1 -0.011 0.058 0.29 2 -0.33 6 8
ARAP3 -0.012 0.025 0.3 1 -10000 0 1
INPPL1 0.025 0.004 -10000 0 -10000 0 0
PREX1 0.025 0.004 -10000 0 -10000 0 0
ARHGEF6 0.026 0.003 -10000 0 -10000 0 0
ARHGEF7 0.025 0.006 -10000 0 -10000 0 0
ARF1 0.021 0.01 -10000 0 -10000 0 0
NRAS 0.026 0.006 -10000 0 -10000 0 0
FYN 0.024 0.007 -10000 0 -10000 0 0
ARF6 0.025 0.005 -10000 0 -10000 0 0
FGR 0.021 0.048 -10000 0 -0.62 2 2
mol:Ca2+ -0.008 0.049 0.22 1 -10000 0 1
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.009 0.14 -10000 0 -0.6 20 20
ZAP70 0.023 0.077 0.34 5 -0.62 4 9
mol:IP3 -0.013 0.065 0.26 1 -0.2 12 13
LYN 0.022 0.01 -10000 0 -10000 0 0
ARF1/GDP 0.012 0.075 -10000 0 -0.32 6 6
RhoA/GDP 0.026 0.046 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.05 0.028 -10000 0 -10000 0 0
BLNK 0.009 0.1 -10000 0 -0.62 9 9
actin cytoskeleton reorganization 0.009 0.07 0.32 1 -0.42 1 2
SRC 0.03 0.037 0.34 5 -10000 0 5
PLEKHA2 -0.007 0.009 -10000 0 -10000 0 0
RAC1 0.026 0.004 -10000 0 -10000 0 0
PTEN 0.024 0.018 -10000 0 -0.28 1 1
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.012 0.03 0.29 1 -10000 0 1
RhoA/GTP -0.012 0.027 0.3 1 -10000 0 1
Src family/SYK family/BLNK-LAT -0.045 0.18 0.38 1 -0.53 29 30
BLK -0.069 0.21 0.34 2 -0.5 64 66
PDPK1 0.025 0.006 -10000 0 -10000 0 0
CYTH1 -0.01 0.034 0.29 2 -10000 0 2
HCK 0.005 0.12 -10000 0 -0.62 12 12
CYTH3 -0.01 0.035 0.29 2 -10000 0 2
CYTH2 -0.011 0.034 0.29 2 -10000 0 2
KRAS 0.026 0.006 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.006 0.1 -10000 0 -0.49 12 12
SGK1 -0.019 0.13 -10000 0 -0.4 31 31
INPP5D 0.026 0.003 -10000 0 -10000 0 0
mol:GDP 0 0.083 -10000 0 -0.35 7 7
SOS1 0.026 0.001 -10000 0 -10000 0 0
SYK 0.02 0.058 -10000 0 -0.62 3 3
ARF6/GDP 0.014 0.043 0.32 1 -10000 0 1
mol:PI-3-4-5-P3 -0.01 0.034 0.29 2 -10000 0 2
ARAP3/RAP1A/GTP -0.013 0.021 -10000 0 -10000 0 0
VAV1 -0.002 0.13 -10000 0 -0.58 17 17
mol:PI-3-4-P2 0.013 0.003 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.046 0.04 0.32 1 -10000 0 1
PLEKHA1 -0.007 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.083 -10000 0 -0.33 7 7
LAT 0.027 0.024 0.34 2 -10000 0 2
Rac1/GTP -0.002 0.092 -10000 0 -0.34 13 13
ITK -0.026 0.066 0.28 1 -0.33 14 15
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.031 0.12 0.36 1 -0.38 21 22
LCK 0.007 0.11 0.34 1 -0.59 11 12
BTK -0.015 0.05 0.29 2 -0.33 5 7
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.016 0.1 0.49 3 -1.2 2 5
regulation of axonogenesis -0.002 0.048 0.32 1 -10000 0 1
myoblast fusion -0.022 0.046 0.41 2 -0.28 3 5
mol:GTP 0.016 0.036 -10000 0 -0.23 2 2
regulation of calcium-dependent cell-cell adhesion -0.026 0.1 0.36 22 -0.26 3 25
ARF1/GTP 0.027 0.028 -10000 0 -10000 0 0
mol:GM1 0.007 0.027 -10000 0 -10000 0 0
mol:Choline -0.013 0.092 -10000 0 -0.38 21 21
lamellipodium assembly 0.014 0.064 0.28 3 -0.38 7 10
MAPK3 0.019 0.043 0.32 3 -0.35 2 5
ARF6/GTP/NME1/Tiam1 0.027 0.1 0.27 3 -0.36 22 25
ARF1 0.021 0.01 -10000 0 -10000 0 0
ARF6/GDP 0.022 0.047 0.28 3 -0.41 2 5
ARF1/GDP 0.022 0.047 0.25 3 -0.38 1 4
ARF6 0.031 0.017 -10000 0 -10000 0 0
RAB11A 0.026 0.003 -10000 0 -10000 0 0
TIAM1 -0.009 0.14 -10000 0 -0.6 20 20
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.019 0.043 0.32 3 -0.35 2 5
actin filament bundle formation -0.026 0.052 0.38 2 -0.25 3 5
KALRN 0.013 0.041 -10000 0 -0.34 4 4
RAB11FIP3/RAB11A 0.036 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.027 0.052 0.25 3 -0.38 2 5
NME1 0.027 0.024 0.34 2 -10000 0 2
Rac1/GDP 0.028 0.05 0.25 3 -0.38 2 5
substrate adhesion-dependent cell spreading 0.016 0.036 -10000 0 -0.23 2 2
cortical actin cytoskeleton organization 0.014 0.065 0.28 3 -0.38 7 10
RAC1 0.026 0.004 -10000 0 -10000 0 0
liver development 0.016 0.036 -10000 0 -0.23 2 2
ARF6/GTP 0.016 0.036 -10000 0 -0.23 2 2
RhoA/GTP 0.032 0.031 -10000 0 -10000 0 0
mol:GDP 0.014 0.055 0.31 3 -0.41 2 5
ARF6/GTP/RAB11FIP3/RAB11A 0.044 0.032 -10000 0 -10000 0 0
RHOA 0.026 0.003 -10000 0 -10000 0 0
PLD1 -0.009 0.11 -10000 0 -0.43 21 21
RAB11FIP3 0.025 0.006 -10000 0 -10000 0 0
tube morphogenesis 0.014 0.064 0.28 3 -0.38 7 10
ruffle organization 0.002 0.048 -10000 0 -0.32 1 1
regulation of epithelial cell migration 0.016 0.036 -10000 0 -0.23 2 2
PLD2 0.016 0.026 -10000 0 -10000 0 0
PIP5K1A 0.002 0.048 -10000 0 -0.32 1 1
mol:Phosphatidic acid -0.013 0.092 -10000 0 -0.38 21 21
Rac1/GTP 0.013 0.065 0.28 3 -0.38 7 10
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.062 0.046 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.025 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.053 0.036 -10000 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.048 0.025 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.046 0.084 -10000 0 -0.4 4 4
CaM/Ca2+ 0.061 0.044 -10000 0 -10000 0 0
RAP1A 0.025 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.034 0.036 0.29 1 -10000 0 1
AKT1 0.012 0.054 -10000 0 -0.68 1 1
MAP2K1 0.002 0.04 0.28 3 -10000 0 3
MAP3K11 0.019 0.035 0.28 2 -10000 0 2
IFNGR1 0.026 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.14 0.2 -10000 0 -0.46 36 36
Rap1/GTP 0.017 0.014 -10000 0 -10000 0 0
CRKL/C3G 0.037 0.008 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.073 0.047 -10000 0 -10000 0 0
CEBPB 0.021 0.086 0.39 1 -0.5 3 4
STAT3 0.026 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.042 0.18 -10000 0 -0.76 16 16
STAT1 0.019 0.037 0.28 2 -10000 0 2
CALM1 0.025 0.006 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.038 0.062 0.33 16 -10000 0 16
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
STAT1 (dimer)/PIAS1 0.034 0.039 -10000 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 0.034 0.057 -10000 0 -0.4 1 1
mol:Ca2+ 0.058 0.044 -10000 0 -10000 0 0
MAPK3 0.004 0.14 -10000 0 -0.74 11 11
STAT1 (dimer) -0.056 0.12 -10000 0 -0.61 4 4
MAPK1 0.011 0.11 -10000 0 -0.67 8 8
JAK2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
JAK1 0.026 0.007 -10000 0 -10000 0 0
CAMK2D 0.024 0.007 -10000 0 -10000 0 0
DAPK1 0.019 0.074 0.34 1 -0.54 3 4
SMAD7 -0.02 0.057 0.26 1 -0.36 2 3
CBL/CRKL/C3G 0.044 0.036 -10000 0 -10000 0 0
PI3K 0.056 0.059 -10000 0 -0.74 1 1
IFNG 0.038 0.062 0.33 16 -10000 0 16
apoptosis 0.008 0.075 -10000 0 -0.41 7 7
CAMK2G 0.025 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.004 -10000 0 -10000 0 0
CAMK2A 0.048 0.084 0.34 28 -10000 0 28
CAMK2B -0.28 0.32 -10000 0 -0.62 175 175
FRAP1 -0.001 0.05 0.26 1 -0.62 1 2
PRKCD 0.012 0.054 -10000 0 -0.69 1 1
RAP1B 0.026 0.003 -10000 0 -10000 0 0
negative regulation of cell growth -0.046 0.084 -10000 0 -0.4 4 4
PTPN2 0.026 0.004 -10000 0 -10000 0 0
EP300 0.026 0.004 -10000 0 -10000 0 0
IRF1 0.013 0.046 0.4 1 -10000 0 1
STAT1 (dimer)/PIASy 0.031 0.044 -10000 0 -10000 0 0
SOCS1 -0.017 0.24 -10000 0 -1.1 16 16
mol:GDP 0.041 0.033 -10000 0 -10000 0 0
CASP1 -0.021 0.057 0.26 1 -0.3 3 4
PTGES2 0.027 0.017 0.34 1 -10000 0 1
IRF9 0.022 0.032 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.041 0.051 -10000 0 -0.71 1 1
RAP1/GDP 0.038 0.024 -10000 0 -10000 0 0
CBL 0.018 0.035 0.28 2 -10000 0 2
MAP3K1 0.019 0.035 0.28 2 -10000 0 2
PIAS1 0.026 0.004 -10000 0 -10000 0 0
PIAS4 0.025 0.007 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.046 0.084 -10000 0 -0.4 4 4
PTPN11 0.019 0.034 0.3 1 -10000 0 1
CREBBP 0.025 0.006 -10000 0 -10000 0 0
RAPGEF1 0.026 0.004 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.013 0.002 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.031 0.021 -10000 0 -10000 0 0
CDKN1B -0.005 0.08 -10000 0 -0.62 1 1
CDKN1A -0.009 0.1 -10000 0 -0.43 4 4
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.022 0.01 -10000 0 -10000 0 0
FOXO3 -0.005 0.08 -10000 0 -0.62 1 1
AKT1 -0.008 0.087 -10000 0 -0.32 17 17
BAD 0.026 0.003 -10000 0 -10000 0 0
AKT3 0.009 0.038 0.18 1 -0.46 2 3
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 -0.007 0.084 -10000 0 -0.62 1 1
AKT1/ASK1 -0.018 0.13 -10000 0 -0.47 7 7
BAD/YWHAZ 0.037 0.024 -10000 0 -10000 0 0
RICTOR 0.025 0.004 -10000 0 -10000 0 0
RAF1 0.026 0.003 -10000 0 -10000 0 0
JNK cascade 0.018 0.13 0.46 7 -10000 0 7
TSC1 -0.007 0.084 -10000 0 -0.62 1 1
YWHAZ 0.019 0.012 -10000 0 -10000 0 0
AKT1/RAF1 0.017 0.096 -10000 0 -0.62 1 1
EP300 0.026 0.004 -10000 0 -10000 0 0
mol:GDP -0.007 0.088 -10000 0 -0.32 18 18
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.006 0.082 -10000 0 -0.52 2 2
YWHAQ 0.026 0.002 -10000 0 -10000 0 0
TBC1D4 0.003 0.035 -10000 0 -0.38 3 3
MAP3K5 -0.041 0.19 -10000 0 -0.55 41 41
MAPKAP1 0.026 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.061 0.092 0.3 9 -0.24 2 11
YWHAH 0.025 0.004 -10000 0 -10000 0 0
AKT1S1 -0.006 0.084 -10000 0 -0.62 1 1
CASP9 -0.003 0.078 -10000 0 -0.62 1 1
YWHAB 0.026 0.004 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.016 0.093 -10000 0 -0.59 1 1
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.05 0.028 -10000 0 -10000 0 0
YWHAE 0.022 0.009 -10000 0 -10000 0 0
SRC 0.03 0.037 0.34 5 -10000 0 5
AKT2/p21CIP1 0.008 0.11 -10000 0 -0.39 8 8
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.001 0.06 -10000 0 -0.39 6 6
CHUK -0.003 0.073 -10000 0 -10000 0 0
BAD/BCL-XL 0.021 0.094 -10000 0 -0.58 1 1
mTORC2 0.032 0.007 -10000 0 -10000 0 0
AKT2 0.013 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.06 0.12 0.3 1 -0.42 9 10
PDPK1 0.025 0.006 -10000 0 -10000 0 0
MDM2 -0.005 0.089 -10000 0 -0.62 1 1
MAPKKK cascade -0.017 0.094 0.6 1 -10000 0 1
MDM2/Cbp/p300 0.03 0.097 -10000 0 -0.57 1 1
TSC1/TSC2 -0.008 0.082 -10000 0 -0.5 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.093 -10000 0 -0.54 1 1
glucose import -0.002 0.062 0.21 2 -0.35 9 11
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.001 0.065 -10000 0 -0.49 2 2
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.002 0.062 0.21 2 -0.35 9 11
GSK3A -0.008 0.086 -10000 0 -0.62 1 1
FOXO1 -0.002 0.075 -10000 0 -0.52 2 2
GSK3B -0.008 0.085 -10000 0 -0.62 1 1
SFN 0.2 0.16 0.34 202 -0.3 2 204
G1/S transition of mitotic cell cycle 0 0.09 -10000 0 -0.6 1 1
p27Kip1/14-3-3 family 0.046 0.067 0.27 1 -0.45 1 2
PRKACA 0.026 0.004 -10000 0 -10000 0 0
KPNA1 0.026 0 -10000 0 -10000 0 0
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
YWHAG 0.026 0.004 -10000 0 -10000 0 0
RHEB 0.025 0.005 -10000 0 -10000 0 0
CREBBP 0.025 0.006 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.041 0.049 -10000 0 -0.34 4 4
RGS9BP 0.032 0.049 0.34 9 -10000 0 9
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.017 0.004 -10000 0 -10000 0 0
mol:Na + 0.034 0.054 0.41 1 -10000 0 1
mol:ADP -0.015 0.005 -10000 0 -10000 0 0
GNAT2 0.024 0.006 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.047 0.089 0.43 1 -0.4 10 11
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.008 -10000 0 -10000 0 0
GRK7 0.02 0.004 -10000 0 -10000 0 0
CNGB3 0.038 0.084 0.34 26 -10000 0 26
Cone Metarhodopsin II/X-Arrestin 0.015 0.011 0.23 1 -10000 0 1
mol:Ca2+ 0.002 0.048 0.26 1 -10000 0 1
Cone PDE6 0.066 0.09 0.4 1 -0.35 10 11
Cone Metarhodopsin II 0.023 0.006 -10000 0 -10000 0 0
Na + (4 Units) 0.038 0.052 0.39 1 -10000 0 1
GNAT2/GDP 0.052 0.081 0.39 1 -0.34 10 11
GNB5 0.026 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.009 0.046 -10000 0 -10000 0 0
Cone Transducin 0.044 0.052 -10000 0 -0.36 4 4
SLC24A2 0.017 0.004 -10000 0 -10000 0 0
GNB3/GNGT2 0.035 0.061 0.25 8 -0.46 4 12
GNB3 0.031 0.047 0.34 8 -10000 0 8
GNAT2/GTP 0.018 0.004 -10000 0 -10000 0 0
CNGA3 0.021 0.024 0.34 2 -10000 0 2
ARR3 0.02 0.017 0.34 1 -10000 0 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.034 0.055 0.25 7 -10000 0 7
mol:Pi 0.046 0.088 0.43 1 -0.4 10 11
Cone CNG Channel 0.05 0.058 0.35 2 -10000 0 2
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.017 0.004 -10000 0 -10000 0 0
RGS9 0.02 0.12 0.34 14 -0.62 10 24
PDE6C 0.038 0.071 0.34 19 -10000 0 19
GNGT2 0.019 0.067 -10000 0 -0.62 4 4
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.018 0.004 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.025 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.025 0.01 -10000 0 -10000 0 0
DOCK1 0.011 0.094 -10000 0 -0.62 8 8
ITGA4 0.015 0.09 0.34 1 -0.62 7 8
RAC1 0.026 0.004 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.023 0.089 0.25 1 -0.46 12 13
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.042 0.063 -10000 0 -0.4 7 7
alpha4/beta7 Integrin/Paxillin 0.03 0.073 -10000 0 -0.36 12 12
lamellipodium assembly 0.006 0.082 -10000 0 -0.47 6 6
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
PI3K 0.034 0.052 -10000 0 -0.64 2 2
ARF6 0.025 0.005 -10000 0 -10000 0 0
TLN1 0.025 0.004 -10000 0 -10000 0 0
PXN 0.013 0.002 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
ARF6/GTP 0.045 0.052 -10000 0 -0.32 6 6
cell adhesion 0.045 0.057 -10000 0 -0.34 7 7
CRKL/CBL 0.036 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.034 0.057 -10000 0 -0.36 7 7
ITGB1 0.025 0.005 -10000 0 -10000 0 0
ITGB7 0.017 0.075 -10000 0 -0.62 5 5
ARF6/GDP 0.025 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.029 0.11 -10000 0 -0.38 21 21
p130Cas/Crk/Dock1 0.034 0.064 -10000 0 -0.37 8 8
VCAM1 -0.006 0.15 0.34 5 -0.62 20 25
alpha4/beta1 Integrin/Paxillin/Talin 0.047 0.058 -10000 0 -0.34 7 7
alpha4/beta1 Integrin/Paxillin/GIT1 0.048 0.058 -10000 0 -0.34 7 7
BCAR1 0.024 0.007 -10000 0 -10000 0 0
mol:GDP -0.046 0.057 0.34 7 -10000 0 7
CBL 0.025 0.006 -10000 0 -10000 0 0
PRKACA 0.026 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.047 0.058 -10000 0 -0.34 7 7
Rac1/GTP 0.005 0.093 -10000 0 -0.54 6 6
Canonical NF-kappaB 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
FBXW11 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.021 0.11 -10000 0 -0.35 10 10
ERC1 0.025 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.022 0.054 -10000 0 -0.46 4 4
NFKBIA 0.013 0.012 -10000 0 -10000 0 0
BIRC2 0.025 0.005 -10000 0 -10000 0 0
IKBKB 0.023 0.009 -10000 0 -10000 0 0
RIPK2 0.02 0.011 -10000 0 -10000 0 0
IKBKG 0.012 0.038 -10000 0 -0.36 1 1
IKK complex/A20 0.025 0.13 -10000 0 -0.42 13 13
NEMO/A20/RIP2 0.02 0.011 -10000 0 -10000 0 0
XPO1 0.026 0.002 -10000 0 -10000 0 0
NEMO/ATM 0.027 0.12 -10000 0 -0.4 18 18
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.035 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.024 0.11 -10000 0 -0.38 17 17
BCL10/MALT1/TRAF6 0.048 0.027 -10000 0 -0.4 1 1
NOD2 0.017 0.067 -10000 0 -0.62 4 4
NFKB1 0.025 0.008 -10000 0 -10000 0 0
RELA 0.027 0.004 -10000 0 -10000 0 0
MALT1 0.025 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.035 0.012 -10000 0 -10000 0 0
ATM 0.025 0.005 -10000 0 -10000 0 0
TNF/TNFR1A 0.018 0.091 0.25 2 -0.46 12 14
TRAF6 0.024 0.034 -10000 0 -0.62 1 1
PRKCA 0.025 0.005 -10000 0 -10000 0 0
CHUK 0.025 0.005 -10000 0 -10000 0 0
UBE2D3 0.024 0.008 -10000 0 -10000 0 0
TNF 0.004 0.12 0.34 2 -0.62 12 14
NF kappa B1 p50/RelA 0.052 0.02 -10000 0 -10000 0 0
BCL10 0.025 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.012 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.025 0.006 -10000 0 -10000 0 0
IKK complex 0.029 0.12 -10000 0 -0.4 17 17
CYLD 0.025 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.036 0.12 -10000 0 -0.4 16 16
TRAIL signaling pathway

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
TNFSF10 0.017 0.075 -10000 0 -0.62 5 5
positive regulation of NF-kappaB transcription factor activity 0.021 0.064 -10000 0 -0.46 6 6
MAP2K4 0.01 0.045 -10000 0 -0.26 4 4
IKBKB 0.023 0.009 -10000 0 -10000 0 0
TNFRSF10B 0.02 0.011 -10000 0 -10000 0 0
TNFRSF10A 0.013 0.063 -10000 0 -0.49 5 5
SMPD1 0.008 0.029 -10000 0 -0.23 5 5
IKBKG 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.019 0.035 -10000 0 -0.62 1 1
TRAIL/TRAILR2 0.023 0.059 -10000 0 -0.46 5 5
TRAIL/TRAILR3 0.024 0.065 0.25 4 -0.46 5 9
TRAIL/TRAILR1 0.017 0.075 -10000 0 -0.41 10 10
TRAIL/TRAILR4 0.021 0.065 -10000 0 -0.46 6 6
TRAIL/TRAILR1/DAP3/GTP 0.021 0.062 -10000 0 -0.36 7 7
IKK complex 0.001 0.063 -10000 0 -10000 0 0
RIPK1 0.024 0.008 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.015 0.008 -10000 0 -10000 0 0
MAPK3 0.006 0.055 -10000 0 -0.46 5 5
MAP3K1 0.012 0.052 -10000 0 -0.26 6 6
TRAILR4 (trimer) 0.019 0.035 -10000 0 -0.62 1 1
TRADD 0.023 0.018 -10000 0 -0.3 1 1
TRAILR1 (trimer) 0.013 0.063 -10000 0 -0.49 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.012 0.049 -10000 0 -0.27 8 8
CFLAR 0.026 0.002 -10000 0 -10000 0 0
MAPK1 0.006 0.055 -10000 0 -0.46 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP 0.04 0.07 -10000 0 -0.35 8 8
mol:ceramide 0.008 0.029 -10000 0 -0.23 5 5
FADD 0.025 0.006 -10000 0 -10000 0 0
MAPK8 -0.004 0.094 -10000 0 -0.35 19 19
TRAF2 0.026 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.023 0.039 0.34 4 -0.3 1 5
CHUK 0.025 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.028 0.07 -10000 0 -0.4 8 8
DAP3 0.02 0.011 -10000 0 -10000 0 0
CASP10 0.006 0.062 0.25 1 -0.4 5 6
JNK cascade 0.021 0.064 -10000 0 -0.46 6 6
TRAIL (trimer) 0.017 0.075 -10000 0 -0.62 5 5
TNFRSF10C 0.023 0.039 0.34 4 -0.3 1 5
TRAIL/TRAILR1/DAP3/GTP/FADD 0.027 0.063 -10000 0 -0.34 7 7
TRAIL/TRAILR2/FADD 0.033 0.056 -10000 0 -0.4 5 5
cell death 0.008 0.029 -10000 0 -0.23 5 5
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.015 0.04 -10000 0 -0.27 5 5
TRAILR2 (trimer) 0.02 0.011 -10000 0 -10000 0 0
CASP8 0.019 0.05 -10000 0 -0.6 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.044 0.06 -10000 0 -0.35 5 5
ceramide signaling pathway

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
MAP4K4 0.01 0.078 -10000 0 -0.51 1 1
BAG4 0.008 0.085 -10000 0 -0.44 11 11
BAD 0.015 0.04 -10000 0 -10000 0 0
NFKBIA 0.026 0.004 -10000 0 -10000 0 0
BIRC3 0.035 0.072 0.34 14 -0.46 2 16
BAX 0.016 0.043 0.2 2 -10000 0 2
EnzymeConsortium:3.1.4.12 0.007 0.027 0.08 2 -0.11 1 3
IKBKB 0.017 0.088 0.34 5 -0.48 1 6
MAP2K2 0.017 0.054 0.28 5 -10000 0 5
MAP2K1 0.015 0.051 0.27 4 -10000 0 4
SMPD1 0.01 0.029 -10000 0 -0.13 1 1
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.026 0.093 0.32 2 -0.5 1 3
MAP2K4 0.016 0.04 0.28 1 -10000 0 1
protein ubiquitination 0.02 0.09 -10000 0 -0.5 1 1
EnzymeConsortium:2.7.1.37 0.016 0.056 0.28 4 -10000 0 4
response to UV 0 0.001 0.003 6 -10000 0 6
RAF1 0.016 0.051 0.28 4 -10000 0 4
CRADD 0.024 0.034 -10000 0 -0.62 1 1
mol:ceramide 0.016 0.043 0.12 12 -0.16 1 13
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.007 -10000 0 -10000 0 0
MADD 0.026 0.002 -10000 0 -10000 0 0
MAP3K1 0.015 0.045 0.24 2 -10000 0 2
TRADD 0.024 0.007 -10000 0 -10000 0 0
RELA/p50 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.016 0.058 0.28 4 -0.25 1 5
MAPK1 0.017 0.055 0.28 4 -10000 0 4
p50/RELA/I-kappa-B-alpha 0.037 0.008 -10000 0 -10000 0 0
FADD 0.015 0.082 0.33 1 -0.51 1 2
KSR1 0.017 0.048 0.25 4 -10000 0 4
MAPK8 -0.001 0.073 0.27 1 -0.28 17 18
TRAF2 0.025 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.003 1 -10000 0 1
CHUK 0.019 0.079 -10000 0 -0.48 1 1
TNF R/SODD 0.021 0.065 -10000 0 -0.35 9 9
TNF 0.004 0.12 0.34 2 -0.62 12 14
CYCS 0.017 0.04 -10000 0 -10000 0 0
IKBKG 0.02 0.09 0.32 3 -0.48 1 4
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.011 0.082 -10000 0 -0.53 1 1
RELA 0.026 0.004 -10000 0 -10000 0 0
RIPK1 0.024 0.008 -10000 0 -10000 0 0
AIFM1 0.017 0.041 0.15 1 -10000 0 1
TNF/TNF R/SODD 0.019 0.098 -10000 0 -0.39 17 17
TNFRSF1A 0.025 0.006 -10000 0 -10000 0 0
response to heat 0 0 0.003 1 -10000 0 1
CASP8 0.013 0.1 -10000 0 -0.57 10 10
NSMAF 0.032 0.1 0.31 2 -0.5 1 3
response to hydrogen peroxide 0 0.001 0.003 6 -10000 0 6
BCL2 0.024 0.034 -10000 0 -0.62 1 1
Atypical NF-kappaB pathway

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
BCL3/RelA 0.037 0.008 -10000 0 -10000 0 0
FBXW11 0.025 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.01 0.073 -10000 0 -0.39 11 11
NF kappa B1 p50/RelA/I kappa B alpha 0.02 0.065 -10000 0 -0.42 3 3
NFKBIA 0.013 0.067 -10000 0 -0.31 10 10
MAPK14 0.024 0.008 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.023 0.012 -10000 0 -10000 0 0
ARRB2 0.011 0.006 -10000 0 -10000 0 0
REL 0.005 0.12 -10000 0 -0.62 12 12
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.023 0.012 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.023 0.012 -10000 0 -10000 0 0
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
NF kappa B1 p50 dimer 0.019 0.009 -10000 0 -10000 0 0
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
NFKB1 0.01 0.005 -10000 0 -10000 0 0
RELA 0.026 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.006 0.063 -10000 0 -0.32 10 10
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.017 0.069 -10000 0 -0.39 4 4
SRC 0.03 0.037 0.34 5 -10000 0 5
PI3K 0.034 0.052 -10000 0 -0.64 2 2
NF kappa B1 p50/RelA 0.006 0.064 -10000 0 -0.32 10 10
IKBKB 0.023 0.009 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
SYK 0.02 0.058 -10000 0 -0.62 3 3
I kappa B alpha/PIK3R1 0.02 0.076 -10000 0 -0.38 6 6
cell death 0.016 0.066 -10000 0 -0.38 4 4
NF kappa B1 p105/c-Rel 0.01 0.073 -10000 0 -0.39 11 11
LCK 0.007 0.11 0.34 1 -0.59 11 12
BCL3 0.026 0.004 -10000 0 -10000 0 0
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 0.05 0.034 -10000 0 -0.33 1 1
TC10/GTP 0.04 0.033 -10000 0 -0.32 1 1
Insulin Receptor/Insulin/IRS1/Shp2 0.065 0.025 -10000 0 -10000 0 0
HRAS 0.027 0.017 0.34 1 -10000 0 1
APS homodimer 0.029 0.033 0.34 4 -10000 0 4
GRB14 0.015 0.082 -10000 0 -0.62 6 6
FOXO3 -0.043 0.2 -10000 0 -0.65 36 36
AKT1 -0.014 0.058 -10000 0 -0.56 1 1
INSR 0.028 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.057 0.033 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.026 0.004 -10000 0 -10000 0 0
SORBS1 0.022 0.048 -10000 0 -0.62 2 2
CRK 0.022 0.009 -10000 0 -10000 0 0
PTPN1 0.007 0.018 -10000 0 -10000 0 0
CAV1 0.014 0.014 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II/C3G 0.062 0.044 -10000 0 -0.3 2 2
Insulin Receptor/Insulin/IRS1/NCK2 0.064 0.035 -10000 0 -0.38 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.049 0.046 -10000 0 -0.49 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.022 0.042 -10000 0 -10000 0 0
RPS6KB1 -0.016 0.052 -10000 0 -0.51 1 1
PARD6A 0.025 0.018 0.34 1 -10000 0 1
CBL 0.025 0.006 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.014 0.033 -10000 0 -0.58 1 1
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.03 0.056 -10000 0 -0.51 1 1
HRAS/GTP 0.014 0.01 -10000 0 -10000 0 0
Insulin Receptor 0.028 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.055 0.039 -10000 0 -10000 0 0
PRKCI 0.027 0.05 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 0.023 0.06 -10000 0 -0.36 8 8
SHC1 0.02 0.011 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.041 0.043 -10000 0 -0.39 3 3
PI3K 0.061 0.049 -10000 0 -0.5 2 2
NCK2 0.025 0.037 0.34 1 -0.62 1 2
RHOQ 0.026 0.002 -10000 0 -10000 0 0
mol:H2O2 0 0.002 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.011 0.23 1 -10000 0 1
AKT2 -0.013 0.06 -10000 0 -0.34 8 8
PRKCZ -0.024 0.15 -10000 0 -0.57 16 16
SH2B2 0.029 0.033 0.34 4 -10000 0 4
SHC/SHIP 0.022 0.016 -10000 0 -10000 0 0
F2RL2 -0.031 0.2 0.34 8 -0.62 36 44
TRIP10 0.026 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.036 0.027 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.035 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.055 0.039 -10000 0 -10000 0 0
RAPGEF1 0.026 0.004 -10000 0 -10000 0 0
RASA1 0.022 0.048 -10000 0 -0.62 2 2
NCK1 0.026 0.001 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.054 0.042 -10000 0 -0.31 2 2
TC10/GDP 0.019 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.048 0.034 -10000 0 -10000 0 0
INPP5D 0.014 0.015 -10000 0 -10000 0 0
SOS1 0.026 0.001 -10000 0 -10000 0 0
SGK1 -0.064 0.24 -10000 0 -0.75 38 38
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.003 -10000 0 -10000 0 0
IRS1 0.026 0.002 -10000 0 -10000 0 0
p62DOK/RasGAP 0.042 0.043 -10000 0 -0.39 3 3
INS 0.025 0.036 0.33 5 -10000 0 5
mol:PI-3-4-P2 0.014 0.015 -10000 0 -10000 0 0
GRB2 0.025 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.014 0.052 -10000 0 -0.51 1 1
PTPRA 0.028 0.005 -10000 0 -10000 0 0
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
TC10/GTP/CIP4 0.035 0.006 -10000 0 -10000 0 0
PDPK1 0.025 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.022 0.02 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.049 0.023 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.039 0.026 -10000 0 -10000 0 0
Par3/Par6 0.021 0.12 -10000 0 -0.34 36 36
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.034 0.092 -10000 0 -0.4 12 12
Ran/GTP/Exportin 1/HDAC1 -0.007 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.025 0.085 -10000 0 -0.36 12 12
SUMO1 0.026 0.002 -10000 0 -10000 0 0
ZFPM1 0.02 0.048 -10000 0 -0.62 2 2
NPC/RanGAP1/SUMO1/Ubc9 0.014 0.004 -10000 0 -10000 0 0
FKBP3 0.026 0.004 -10000 0 -10000 0 0
Histones 0.052 0.056 -10000 0 -10000 0 0
YY1/LSF 0.015 0.061 -10000 0 -0.32 5 5
SMG5 0.02 0.011 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.013 0.058 -10000 0 -0.29 12 12
I kappa B alpha/HDAC1 0.029 0.051 -10000 0 -10000 0 0
SAP18 0.025 0.006 -10000 0 -10000 0 0
RELA 0.02 0.064 -10000 0 -0.27 12 12
HDAC1/Smad7 0.045 0.032 -10000 0 -0.4 1 1
RANGAP1 0.025 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.032 0.052 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.022 0.064 -10000 0 -0.25 8 8
NF kappa B1 p50/RelA 0.026 0.076 -10000 0 -0.36 3 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.024 0.053 0.34 2 -0.62 2 4
GATA1 0.024 0.029 0.34 3 -10000 0 3
Mad/Max 0.037 0.014 0.25 1 -10000 0 1
NuRD/MBD3 Complex/GATA1/Fog1 0.018 0.086 -10000 0 -0.34 7 7
RBBP7 0.026 0.003 -10000 0 -10000 0 0
NPC 0.015 0.001 -10000 0 -10000 0 0
RBBP4 0.025 0.006 -10000 0 -10000 0 0
MAX 0.025 0.006 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.025 0.004 -10000 0 -10000 0 0
NFKBIA 0.012 0.045 -10000 0 -10000 0 0
KAT2B 0.021 0.058 -10000 0 -0.62 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.018 0.036 -10000 0 -0.36 1 1
SIN3 complex 0.058 0.024 -10000 0 -10000 0 0
SMURF1 0.025 0.005 -10000 0 -10000 0 0
CHD3 0.028 0.045 0.34 7 -10000 0 7
SAP30 0.024 0.007 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.021 0.025 -10000 0 -0.3 2 2
YY1/HDAC3 0.011 0.057 -10000 0 -10000 0 0
YY1/HDAC2 0.018 0.05 -10000 0 -0.26 3 3
YY1/HDAC1 0.02 0.05 -10000 0 -0.26 3 3
NuRD/MBD2 Complex (MeCP1) 0.023 0.06 -10000 0 -0.25 5 5
PPARG 0.016 0.089 -10000 0 -0.42 11 11
HDAC8/hEST1B 0.04 0.023 -10000 0 -10000 0 0
UBE2I 0.025 0.006 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.025 0.006 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.032 0.05 -10000 0 -10000 0 0
MBD3L2 0.018 0.003 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.031 -10000 0 -0.4 1 1
CREBBP 0.025 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.021 0.077 -10000 0 -0.32 5 5
HDAC1 0.025 0.006 -10000 0 -10000 0 0
HDAC3 0.013 0.045 -10000 0 -10000 0 0
HDAC2 0.024 0.007 -10000 0 -10000 0 0
YY1 0.016 0.03 -10000 0 -0.3 3 3
HDAC8 0.026 0.002 -10000 0 -10000 0 0
SMAD7 0.022 0.048 -10000 0 -0.62 2 2
NCOR2 0.026 0.004 -10000 0 -10000 0 0
MXD1 0.027 0.016 0.34 1 -10000 0 1
STAT3 0.02 0.006 -10000 0 -10000 0 0
NFKB1 0.024 0.008 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.026 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.029 0.061 -10000 0 -0.38 2 2
YY1/SAP30/HDAC1 0.03 0.051 -10000 0 -10000 0 0
EP300 0.026 0.004 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.02 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.045 -10000 0 -10000 0 0
histone deacetylation 0.023 0.06 -10000 0 -0.25 5 5
STAT3 (dimer non-phopshorylated)/HDAC3 0.018 0.045 -10000 0 -10000 0 0
nuclear export -0.039 0.023 -10000 0 -10000 0 0
PRKACA 0.026 0.004 -10000 0 -10000 0 0
GATAD2B 0.02 0.011 -10000 0 -10000 0 0
GATAD2A 0.026 0.004 -10000 0 -10000 0 0
GATA2/HDAC3 0.031 0.061 -10000 0 -0.35 2 2
GATA1/HDAC1 0.035 0.021 0.25 3 -10000 0 3
GATA1/HDAC3 0.031 0.055 -10000 0 -10000 0 0
CHD4 0.025 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.018 0.091 0.25 2 -0.46 12 14
SIN3/HDAC complex/Mad/Max 0.006 0.075 -10000 0 -0.27 17 17
NuRD Complex 0.021 0.078 -10000 0 -0.34 3 3
positive regulation of chromatin silencing 0.05 0.054 -10000 0 -10000 0 0
SIN3B 0.026 0.003 -10000 0 -10000 0 0
MTA2 0.026 0.004 -10000 0 -10000 0 0
SIN3A 0.026 0.004 -10000 0 -10000 0 0
XPO1 0.026 0.002 -10000 0 -10000 0 0
SUMO1/HDAC1 0.036 0.033 -10000 0 -0.33 1 1
HDAC complex 0.059 0.023 -10000 0 -10000 0 0
GATA1/Fog1 0.031 0.043 0.25 3 -0.46 2 5
FKBP25/HDAC1/HDAC2 0.046 0.018 -10000 0 -10000 0 0
TNF 0.004 0.12 0.34 2 -0.62 12 14
negative regulation of cell growth 0.006 0.074 -10000 0 -0.27 17 17
NuRD/MBD2/PRMT5 Complex 0.023 0.06 -10000 0 -0.25 5 5
Ran/GTP/Exportin 1 0.035 0.037 -10000 0 -0.33 1 1
NF kappa B/RelA/I kappa B alpha 0.004 0.081 -10000 0 -0.36 13 13
SIN3/HDAC complex/NCoR1 -0.006 0.088 -10000 0 -0.3 21 21
TFCP2 0.022 0.047 -10000 0 -0.62 2 2
NR2C1 0.026 0.003 -10000 0 -10000 0 0
MBD3 0.026 0.004 -10000 0 -10000 0 0
MBD2 0.025 0.005 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 0.021 0.1 0.34 12 -0.57 7 19
CLTC 0.011 0.061 -10000 0 -0.38 7 7
calcium ion-dependent exocytosis 0 0.053 -10000 0 -0.33 2 2
Dynamin 2/GTP 0.026 0.012 -10000 0 -10000 0 0
EXOC4 0.025 0.006 -10000 0 -10000 0 0
CD59 0.006 0.05 -10000 0 -0.32 7 7
CPE 0.017 0.038 0.2 10 -0.4 1 11
CTNNB1 0.026 0.002 -10000 0 -10000 0 0
membrane fusion 0.005 0.04 -10000 0 -10000 0 0
CTNND1 0.017 0.03 -10000 0 -10000 0 0
DNM2 0.026 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.007 0.041 -10000 0 -0.28 1 1
TSHR 0.008 0.01 -10000 0 -10000 0 0
INS 0.009 0.049 -10000 0 -0.46 3 3
BIN1 0.024 0.034 -10000 0 -0.62 1 1
mol:Choline 0.005 0.04 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.014 0.2 2 -10000 0 2
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.025 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.025 0.012 -10000 0 -10000 0 0
JUP 0.006 0.05 -10000 0 -0.32 7 7
ASAP2/amphiphysin II 0.048 0.028 -10000 0 -0.36 1 1
ARF6/GTP 0.019 0.003 -10000 0 -10000 0 0
CDH1 -0.007 0.077 -10000 0 -0.32 13 13
clathrin-independent pinocytosis 0.019 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.025 0.006 -10000 0 -10000 0 0
positive regulation of endocytosis 0.019 0.003 -10000 0 -10000 0 0
EXOC2 0.024 0.008 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.019 0.028 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.019 0.08 0.38 1 -10000 0 1
positive regulation of phagocytosis 0.012 0.005 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.032 0.01 -10000 0 -10000 0 0
ACAP1 0.008 0.046 -10000 0 -0.3 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.001 0.058 -10000 0 -0.32 9 9
clathrin heavy chain/ACAP1 0.009 0.057 0.26 1 -0.34 4 5
JIP4/KLC1 0.045 0.016 -10000 0 -10000 0 0
EXOC1 0.025 0.005 -10000 0 -10000 0 0
exocyst 0.019 0.028 -10000 0 -10000 0 0
RALA/GTP 0.019 0.002 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.033 0.008 -10000 0 -10000 0 0
receptor recycling 0.019 0.003 -10000 0 -10000 0 0
CTNNA1 0.016 0.029 -10000 0 -10000 0 0
NME1 0.014 0.014 0.2 2 -10000 0 2
clathrin coat assembly 0.014 0.063 -10000 0 -0.37 7 7
IL2RA 0.008 0.061 -10000 0 -0.32 8 8
VAMP3 0.012 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.016 0.078 -10000 0 -0.41 1 1
EXOC6 0.025 0.005 -10000 0 -10000 0 0
PLD1 -0.005 0.075 -10000 0 -0.3 21 21
PLD2 0.012 0.008 -10000 0 -10000 0 0
EXOC5 0.025 0.005 -10000 0 -10000 0 0
PIP5K1C 0.007 0.038 -10000 0 -0.28 1 1
SDC1 0.004 0.057 -10000 0 -0.32 7 7
ARF6/GDP 0.024 0.012 -10000 0 -10000 0 0
EXOC7 0.025 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.022 0.083 -10000 0 -0.39 1 1
mol:Phosphatidic acid 0.005 0.04 -10000 0 -10000 0 0
endocytosis -0.046 0.027 0.36 1 -10000 0 1
SCAMP2 0.026 0.004 -10000 0 -10000 0 0
ADRB2 -0.023 0.12 -10000 0 -0.5 6 6
EXOC3 0.025 0.006 -10000 0 -10000 0 0
ASAP2 0.028 0.023 0.34 2 -10000 0 2
Dynamin 2/GDP 0.029 0.014 -10000 0 -10000 0 0
KLC1 0.024 0.007 -10000 0 -10000 0 0
AVPR2 0.021 0.072 0.37 1 -0.36 7 8
RALA 0.026 0.003 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.017 0.079 -10000 0 -0.37 1 1
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.019 0.069 -10000 0 -0.4 9 9
VEGFR1 homodimer/NRP1 0.012 0.004 -10000 0 -10000 0 0
mol:DAG 0.015 0.022 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.023 0.012 -10000 0 -10000 0 0
CaM/Ca2+ 0.03 0.021 -10000 0 -10000 0 0
HIF1A 0.029 0.007 -10000 0 -10000 0 0
GAB1 0.024 0.007 -10000 0 -10000 0 0
AKT1 0.011 0.046 -10000 0 -0.64 1 1
PLCG1 0.015 0.022 -10000 0 -10000 0 0
NOS3 0.015 0.061 -10000 0 -0.59 2 2
CBL 0.025 0.006 -10000 0 -10000 0 0
mol:NO 0.016 0.071 0.55 1 -0.52 3 4
FLT1 0.016 0.006 -10000 0 -10000 0 0
PGF 0.03 0.04 0.34 6 -10000 0 6
VEGFR1 homodimer/NRP2/VEGFR121 0.034 0.041 -10000 0 -0.35 3 3
CALM1 0.025 0.006 -10000 0 -10000 0 0
PIK3CA 0.024 0.034 -10000 0 -0.62 1 1
eNOS/Hsp90 0.027 0.066 -10000 0 -0.55 2 2
endothelial cell proliferation -0.007 0.083 -10000 0 -0.38 3 3
mol:Ca2+ 0.015 0.022 -10000 0 -10000 0 0
MAPK3 -0.004 0.025 0.35 1 -10000 0 1
MAPK1 -0.004 0.025 0.35 1 -10000 0 1
PIK3R1 0.022 0.048 -10000 0 -0.62 2 2
PLGF homodimer 0.03 0.04 0.34 6 -10000 0 6
PRKACA 0.026 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.025 0.005 -10000 0 -10000 0 0
VEGFA homodimer 0.023 0.009 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.026 0.014 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.006 0.024 0.33 1 -10000 0 1
PI3K 0.052 0.053 -10000 0 -0.5 2 2
PRKCA -0.004 0.018 -10000 0 -10000 0 0
PRKCB -0.029 0.092 -10000 0 -0.34 25 25
VEGFR1 homodimer/PLGF homodimer 0.031 0.027 -10000 0 -10000 0 0
VEGFA 0.023 0.009 -10000 0 -10000 0 0
VEGFB 0.012 0.1 0.34 2 -0.62 9 11
mol:IP3 0.015 0.022 -10000 0 -10000 0 0
RASA1 0.003 0.067 -10000 0 -0.36 11 11
NRP2 0.022 0.06 0.34 1 -0.62 3 4
VEGFR1 homodimer 0.016 0.006 -10000 0 -10000 0 0
VEGFB homodimer 0.012 0.1 0.34 2 -0.62 9 11
NCK1 0.026 0.001 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.022 0.076 0.52 1 -0.5 3 4
PTPN11 0.026 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.051 0.052 -10000 0 -0.5 2 2
mol:L-citrulline 0.016 0.071 0.55 1 -0.52 3 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.047 0.027 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.037 0.02 -10000 0 -10000 0 0
CD2AP 0.024 0.007 -10000 0 -10000 0 0
PI3K/GAB1 0.059 0.054 -10000 0 -0.49 2 2
PDPK1 0.014 0.045 -10000 0 -0.62 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.037 0.02 -10000 0 -10000 0 0
mol:NADP 0.016 0.071 0.55 1 -0.52 3 4
HSP90AA1 0.025 0.006 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.026 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.026 0.04 -10000 0 -0.38 3 3
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.025 0.005 -10000 0 -10000 0 0
SMAD2 -0.001 0.037 -10000 0 -0.26 1 1
SMAD3 0.02 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4 0.036 0.041 -10000 0 -0.39 2 2
SMAD4/Ubc9/PIASy 0.047 0.017 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.044 0.048 -10000 0 -10000 0 0
PPM1A 0.025 0.006 -10000 0 -10000 0 0
CALM1 0.025 0.006 -10000 0 -10000 0 0
SMAD2/SMAD4 0.013 0.037 -10000 0 -0.24 1 1
MAP3K1 0.026 0.002 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.011 0.11 -10000 0 -0.46 19 19
MAPK3 0.025 0.004 -10000 0 -10000 0 0
MAPK1 0.026 0.004 -10000 0 -10000 0 0
NUP214 0.026 0.003 -10000 0 -10000 0 0
CTDSP1 0.026 0.003 -10000 0 -10000 0 0
CTDSP2 0.026 0.004 -10000 0 -10000 0 0
CTDSPL 0.026 0.002 -10000 0 -10000 0 0
KPNB1 0.026 0.003 -10000 0 -10000 0 0
TGFBRAP1 -0.008 0.14 -10000 0 -0.6 20 20
UBE2I 0.025 0.006 -10000 0 -10000 0 0
NUP153 0.024 0.008 -10000 0 -10000 0 0
KPNA2 0.027 0.024 0.34 2 -10000 0 2
PIAS4 0.025 0.004 -10000 0 -10000 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 0.021 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.024 0.056 0.2 1 -0.22 4 5
AP2 0.038 0.007 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.031 0.013 -10000 0 -10000 0 0
CLTB 0.025 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.015 0.01 -10000 0 -10000 0 0
CD4 -0.027 0.17 -10000 0 -0.6 30 30
CLTA 0.025 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.007 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.006 0.012 -10000 0 -10000 0 0
ARF1/GTP 0.024 0.019 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.009 0.008 -10000 0 -10000 0 0
mol:Choline 0.006 0.012 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.022 0.012 -10000 0 -10000 0 0
DDEF1 0.005 0.012 -10000 0 -10000 0 0
ARF1/GDP 0 0.019 -10000 0 -10000 0 0
AP2M1 0.026 0.003 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.011 0.008 -10000 0 -10000 0 0
Rac/GTP 0.023 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.03 0.018 -10000 0 -10000 0 0
ARFIP2 0.011 0.021 -10000 0 -10000 0 0
COPA 0.02 0.011 -10000 0 -10000 0 0
RAC1 0.026 0.004 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.024 -10000 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.015 0.009 -10000 0 -10000 0 0
GGA3 0.025 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.018 0.014 -10000 0 -10000 0 0
AP2A1 0.026 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.013 0.009 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.019 0.019 -10000 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.028 0.015 -10000 0 -10000 0 0
CYTH2 0.031 0.011 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.028 0.017 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 0.003 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.005 0.062 -10000 0 -0.23 18 18
PLD2 0.006 0.012 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.007 0.001 -10000 0 -10000 0 0
PIP5K1A 0.006 0.012 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.009 0.027 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.006 0.012 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.007 0.001 -10000 0 -10000 0 0
GOSR2 0.01 0.009 -10000 0 -10000 0 0
USO1 0.004 0.046 -10000 0 -0.32 7 7
GBF1 0.01 0.009 -10000 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.028 0.017 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.013 0.12 -10000 0 -0.4 29 29
Circadian rhythm 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
chromatin modification 0.049 0.035 -10000 0 -10000 0 0
CLOCK 0.025 0.034 -10000 0 -0.61 1 1
TIMELESS/CRY2 0.034 0.025 -10000 0 -10000 0 0
DEC1/BMAL1 0.033 0.007 -10000 0 -10000 0 0
ATR 0.026 0.002 -10000 0 -10000 0 0
NR1D1 0.015 0.072 -10000 0 -1.4 1 1
ARNTL 0.027 0.005 -10000 0 -10000 0 0
TIMELESS 0.018 0.023 -10000 0 -10000 0 0
NPAS2 0.026 0.034 -10000 0 -0.61 1 1
CRY2 0.026 0.002 -10000 0 -10000 0 0
mol:CO -0.007 0.008 0.14 1 -10000 0 1
CHEK1 0.03 0.04 0.34 6 -10000 0 6
mol:HEME 0.007 0.008 -10000 0 -0.14 1 1
PER1 0.022 0.01 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.055 0.038 -10000 0 -0.39 2 2
BMAL1/CLOCK 0.013 0.075 -10000 0 -0.86 1 1
S phase of mitotic cell cycle 0.049 0.035 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.05 0.035 -10000 0 -10000 0 0
mol:NADPH 0.007 0.008 -10000 0 -0.14 1 1
PER1/TIMELESS 0.029 0.026 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.018 0.003 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.025 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.005 0.011 -10000 0 -10000 0 0
MDM2/SUMO1 0.034 0.037 -10000 0 -0.33 1 1
HDAC4 0.027 0.017 0.34 1 -10000 0 1
Ran/GTP/Exportin 1/HDAC1 0.005 0.01 -10000 0 -10000 0 0
SUMO1 0.026 0.002 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.011 0.016 -10000 0 -0.27 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.009 0.021 -10000 0 -0.35 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.026 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.034 0.037 -10000 0 -0.32 1 1
SUMO1/HDAC1 0.036 0.033 -10000 0 -0.33 1 1
RANGAP1 0.025 0.004 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.063 0.017 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.014 0.004 -10000 0 -10000 0 0
Ran/GTP 0.023 0.034 -10000 0 -0.34 1 1
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.026 0.004 -10000 0 -10000 0 0
UBE2I 0.025 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.021 0.033 -10000 0 -0.33 1 1
NPC 0.015 0.001 -10000 0 -10000 0 0
PIAS2 0.025 0.005 -10000 0 -10000 0 0
PIAS1 0.026 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.037 0.008 -9999 0 -9999 0 0
FBXW11 0.025 0.004 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -9999 0 -9999 0 0
CHUK 0.025 0.005 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.07 0.023 -9999 0 -9999 0 0
NFKB1 0.024 0.008 -9999 0 -9999 0 0
MAP3K14 0.026 0.004 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.035 0.012 -9999 0 -9999 0 0
RELB 0.026 0.004 -9999 0 -9999 0 0
NFKB2 0.025 0.004 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.034 0.008 -9999 0 -9999 0 0
regulation of B cell activation 0.033 0.008 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 364 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZS.A9CG TCGA.ZS.A9CF TCGA.ZS.A9CE TCGA.ZS.A9CD
109_MAP3K5 -0.16 -0.34 -0.21 0.063
47_PPARGC1A 0.026 0 0.026 0.026
105_BMP4 0.026 0.026 0.026 0.026
105_BMP6 0.026 0.026 0.026 0.026
105_BMP7 0.026 0.026 0.026 0.018
105_BMP2 0.026 0.026 0.026 0.026
131_RELN/VLDLR 0.24 -0.48 0.062 0.067
30_TGFB1/TGF beta receptor Type II 0.026 0.021 -0.023 0.026
84_STAT5B 0.1 0.13 0.033 0.032
84_STAT5A 0.1 0.13 0.033 0.032
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LIHC-TP/14527201/LIHC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/LIHC-TP/15082962/Gistic2_Analysis_15082974/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

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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