Breast Invasive Carcinoma: PARADIGM pathway analysis of mRNA expression data
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
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 67 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
Signaling events regulated by Ret tyrosine kinase 117
Signaling events mediated by Stem cell factor receptor (c-Kit) 113
Wnt signaling 99
FOXM1 transcription factor network 93
Endothelins 88
EGFR-dependent Endothelin signaling events 83
HIF-1-alpha transcription factor network 82
IGF1 pathway 81
Plasma membrane estrogen receptor signaling 80
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 75
Results

The following list describes the columns found in Table 2.

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

  • 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.

Pathway.Name 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
Signaling events regulated by Ret tyrosine kinase 117 9623 82 -0.23 0.018 1000 -1000 -0.057 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 113 8835 78 -0.39 0.17 1000 -1000 -0.043 -1000
Wnt signaling 99 695 7 -0.13 -0.011 1000 -1000 -0.01 -1000
FOXM1 transcription factor network 93 4769 51 -0.43 0.024 1000 -1000 -0.1 -1000
Endothelins 88 8453 96 -0.24 0.018 1000 -1000 -0.038 -1000
EGFR-dependent Endothelin signaling events 83 1747 21 -0.17 0.024 1000 -1000 -0.048 -1000
HIF-1-alpha transcription factor network 82 6258 76 -0.26 0.025 1000 -1000 -0.052 -1000
IGF1 pathway 81 4660 57 -0.14 0.058 1000 -1000 -0.059 -1000
Plasma membrane estrogen receptor signaling 80 6890 86 -0.2 0.19 1000 -1000 -0.054 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 75 5109 68 -0.43 0.22 1000 -1000 -0.082 -1000
Syndecan-1-mediated signaling events 74 2542 34 -0.19 0.018 1000 -1000 -0.02 -1000
IL4-mediated signaling events 74 6813 91 -0.51 0.39 1000 -1000 -0.1 -1000
Glucocorticoid receptor regulatory network 72 8241 114 -0.55 0.28 1000 -1000 -0.046 -1000
TCGA08_retinoblastoma 70 561 8 -0.053 0.026 1000 -1000 -0.005 -1000
FAS signaling pathway (CD95) 69 3266 47 -0.16 0.072 1000 -1000 -0.023 -1000
Noncanonical Wnt signaling pathway 68 1776 26 -0.13 0.018 1000 -1000 -0.034 -1000
IL6-mediated signaling events 68 5156 75 -0.18 0.043 1000 -1000 -0.037 -1000
TCR signaling in naïve CD8+ T cells 65 6069 93 -0.13 0.071 1000 -1000 -0.047 -1000
Fc-epsilon receptor I signaling in mast cells 64 6240 97 -0.15 0.038 1000 -1000 -0.054 -1000
Arf6 signaling events 61 3820 62 -0.15 0.034 1000 -1000 -0.007 -1000
IL23-mediated signaling events 61 3666 60 -0.28 0.017 1000 -1000 -0.085 -1000
IL12-mediated signaling events 60 5293 87 -0.3 0.029 1000 -1000 -0.091 -1000
Osteopontin-mediated events 58 2236 38 -0.15 0.018 1000 -1000 -0.021 -1000
Thromboxane A2 receptor signaling 58 6097 105 -0.14 0.038 1000 -1000 -0.043 -1000
IL27-mediated signaling events 58 2979 51 -0.27 0.17 1000 -1000 -0.06 -1000
Stabilization and expansion of the E-cadherin adherens junction 55 4123 74 -0.14 0.03 1000 -1000 -0.055 -1000
Nongenotropic Androgen signaling 53 2769 52 -0.13 0.063 1000 -1000 -0.034 -1000
PLK2 and PLK4 events 50 150 3 -0.049 0.008 1000 -1000 -0.006 -1000
E-cadherin signaling events 50 250 5 -0.049 0.011 1000 -1000 -0.004 -1000
Signaling events mediated by the Hedgehog family 49 2556 52 -0.16 0.056 1000 -1000 -0.018 -1000
BMP receptor signaling 48 3915 81 -0.23 0.046 1000 -1000 -0.062 -1000
Syndecan-4-mediated signaling events 48 3250 67 -0.079 0.022 1000 -1000 -0.024 -1000
ErbB4 signaling events 43 3033 69 -0.17 0.099 1000 -1000 -0.07 -1000
Ephrin B reverse signaling 42 2059 48 -0.14 0.02 1000 -1000 -0.048 -1000
IL2 signaling events mediated by PI3K 42 2449 58 -0.23 0.018 1000 -1000 -0.048 -1000
BCR signaling pathway 42 4160 99 -0.16 0.043 1000 -1000 -0.055 -1000
Visual signal transduction: Rods 42 2215 52 -0.1 0.026 1000 -1000 -0.052 -1000
amb2 Integrin signaling 41 3385 82 -0.12 0.023 1000 -1000 -0.041 -1000
LPA receptor mediated events 41 4280 102 -0.13 0.018 1000 -1000 -0.054 -1000
Calcium signaling in the CD4+ TCR pathway 40 1257 31 -0.14 0.027 1000 -1000 -0.048 -1000
TCGA08_p53 39 277 7 -0.037 0.029 1000 -1000 -0.007 -1000
Caspase cascade in apoptosis 38 2876 74 -0.086 0.045 1000 -1000 -0.021 -1000
Integrins in angiogenesis 38 3211 84 -0.19 0.031 1000 -1000 -0.056 -1000
Syndecan-2-mediated signaling events 37 2594 69 -0.073 0.022 1000 -1000 -0.023 -1000
Signaling events mediated by PTP1B 37 2847 76 -0.15 0.054 1000 -1000 -0.043 -1000
E-cadherin signaling in keratinocytes 37 1609 43 -0.077 0.018 1000 -1000 -0.014 -1000
Canonical Wnt signaling pathway 36 1882 51 -0.25 0.098 1000 -1000 -0.034 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 35 1595 45 -0.13 0.018 1000 -1000 -0.053 -1000
Ras signaling in the CD4+ TCR pathway 35 603 17 -0.037 0.013 1000 -1000 -0.011 -1000
Coregulation of Androgen receptor activity 34 2596 76 -0.19 0.029 1000 -1000 -0.018 -1000
Glypican 2 network 34 138 4 -0.016 0 1000 -1000 0 -1000
Cellular roles of Anthrax toxin 33 1317 39 -0.14 0.018 1000 -1000 -0.011 -1000
Glypican 1 network 33 1623 48 -0.064 0.017 1000 -1000 -0.017 -1000
TRAIL signaling pathway 33 1607 48 -0.049 0.018 1000 -1000 -0.049 -1000
Signaling mediated by p38-gamma and p38-delta 33 501 15 -0.07 0.014 1000 -1000 -0.007 -1000
E-cadherin signaling in the nascent adherens junction 33 2512 76 -0.079 0.024 1000 -1000 -0.051 -1000
Class IB PI3K non-lipid kinase events 33 99 3 -0.004 -1000 1000 -1000 -0.001 -1000
Presenilin action in Notch and Wnt signaling 32 1952 61 -0.22 0.036 1000 -1000 -0.034 -1000
Nectin adhesion pathway 32 2066 63 -0.11 0.024 1000 -1000 -0.049 -1000
IL1-mediated signaling events 32 2044 62 -0.083 0.051 1000 -1000 -0.05 -1000
Regulation of nuclear SMAD2/3 signaling 31 4243 136 -0.2 0.065 1000 -1000 -0.031 -1000
PDGFR-alpha signaling pathway 29 1295 44 -0.18 0.028 1000 -1000 -0.012 -1000
Syndecan-3-mediated signaling events 29 1026 35 -0.099 0.032 1000 -1000 -0.028 -1000
Visual signal transduction: Cones 28 1092 38 -0.071 0.025 1000 -1000 -0.008 -1000
Class I PI3K signaling events 27 2030 73 -0.089 0.031 1000 -1000 -0.026 -1000
Regulation of Telomerase 27 2844 102 -0.2 0.044 1000 -1000 -0.073 -1000
Insulin Pathway 27 2024 74 -0.16 0.05 1000 -1000 -0.054 -1000
IFN-gamma pathway 26 1786 68 -0.087 0.023 1000 -1000 -0.058 -1000
Ceramide signaling pathway 26 2001 76 -0.14 0.055 1000 -1000 -0.021 -1000
Reelin signaling pathway 26 1509 56 -0.09 0.038 1000 -1000 -0.054 -1000
IL2 signaling events mediated by STAT5 26 573 22 -0.072 0.021 1000 -1000 -0.033 -1000
Aurora B signaling 26 1747 67 -0.096 0.02 1000 -1000 -0.034 -1000
p75(NTR)-mediated signaling 25 3142 125 -0.13 0.036 1000 -1000 -0.056 -1000
TCGA08_rtk_signaling 25 653 26 -0.077 0.039 1000 -1000 -0.006 -1000
RXR and RAR heterodimerization with other nuclear receptor 24 1272 52 -0.12 0.037 1000 -1000 -0.063 -1000
Regulation of Androgen receptor activity 24 1713 70 -0.18 0.026 1000 -1000 -0.042 -1000
Sphingosine 1-phosphate (S1P) pathway 23 670 28 -0.081 0.02 1000 -1000 -0.007 -1000
FOXA2 and FOXA3 transcription factor networks 23 1083 46 -0.2 0.074 1000 -1000 -0.033 -1000
PLK1 signaling events 22 1931 85 -0.1 0.028 1000 -1000 -0.037 -1000
S1P1 pathway 22 819 36 -0.062 0.018 1000 -1000 -0.052 -1000
ErbB2/ErbB3 signaling events 21 1377 65 -0.06 0.024 1000 -1000 -0.043 -1000
Arf6 downstream pathway 21 933 43 -0.022 0.019 1000 -1000 -0.026 -1000
mTOR signaling pathway 20 1099 53 -0.037 0.035 1000 -1000 -0.038 -1000
Atypical NF-kappaB pathway 20 625 31 -0.073 0.028 1000 -1000 -0.006 -1000
Effects of Botulinum toxin 20 543 26 -0.17 0.019 1000 -1000 -0.015 -1000
Angiopoietin receptor Tie2-mediated signaling 20 1847 88 -0.16 0.053 1000 -1000 -0.09 -1000
HIF-2-alpha transcription factor network 19 843 43 -0.084 0.085 1000 -1000 -0.053 -1000
Signaling events mediated by PRL 19 677 34 -0.097 0.026 1000 -1000 -0.015 -1000
JNK signaling in the CD4+ TCR pathway 18 321 17 -0.036 0.029 1000 -1000 -0.014 -1000
Hedgehog signaling events mediated by Gli proteins 18 1225 65 -0.051 0.041 1000 -1000 -0.046 -1000
Aurora A signaling 18 1139 60 -0.037 0.034 1000 -1000 -0.012 -1000
ceramide signaling pathway 18 912 49 -0.12 0.036 1000 -1000 -0.019 -1000
S1P3 pathway 18 787 42 -0.081 0.02 1000 -1000 -0.021 -1000
PDGFR-beta signaling pathway 18 1793 97 -0.081 0.036 1000 -1000 -0.054 -1000
p38 MAPK signaling pathway 18 798 44 -0.079 0.034 1000 -1000 -0.05 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 17 944 54 -0.092 0.031 1000 -1000 -0.059 -1000
Signaling events mediated by HDAC Class III 17 698 40 -0.08 0.034 1000 -1000 -0.014 -1000
Retinoic acid receptors-mediated signaling 17 1008 58 -0.086 0.039 1000 -1000 -0.052 -1000
Signaling mediated by p38-alpha and p38-beta 17 765 44 -0.091 0.024 1000 -1000 -0.011 -1000
EPHB forward signaling 17 1465 85 -0.038 0.036 1000 -1000 -0.063 -1000
Regulation of p38-alpha and p38-beta 17 925 54 -0.073 0.043 1000 -1000 -0.036 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 17 592 33 -0.074 0.049 1000 -1000 -0.016 -1000
Paxillin-independent events mediated by a4b1 and a4b7 16 595 37 -0.024 0.028 1000 -1000 -0.016 -1000
Neurotrophic factor-mediated Trk receptor signaling 16 2016 120 -0.12 0.053 1000 -1000 -0.047 -1000
BARD1 signaling events 15 906 57 -0.039 0.04 1000 -1000 -0.025 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 15 1281 85 -0.14 0.038 1000 -1000 -0.053 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 15 1289 83 -0.12 0.057 1000 -1000 -0.027 -1000
Signaling events mediated by VEGFR1 and VEGFR2 15 1936 125 -0.061 0.055 1000 -1000 -0.072 -1000
VEGFR1 specific signals 15 846 56 -0.034 0.027 1000 -1000 -0.023 -1000
LPA4-mediated signaling events 13 162 12 -0.029 0.015 1000 -1000 -0.014 -1000
a4b1 and a4b7 Integrin signaling 13 68 5 -0.007 0.018 1000 -1000 -0.006 -1000
EPO signaling pathway 13 718 55 -0.15 0.023 1000 -1000 -0.055 -1000
S1P5 pathway 13 227 17 -0.015 0.018 1000 -1000 -0.006 -1000
Signaling events mediated by HDAC Class II 12 951 75 -0.16 0.039 1000 -1000 -0.03 -1000
Paxillin-dependent events mediated by a4b1 12 438 36 -0.033 0.036 1000 -1000 -0.052 -1000
Aurora C signaling 10 72 7 -0.007 0.015 1000 -1000 -0.022 -1000
FoxO family signaling 10 664 64 -0.12 0.067 1000 -1000 -0.018 -1000
S1P4 pathway 10 259 25 -0.015 0.02 1000 -1000 -0.007 -1000
Nephrin/Neph1 signaling in the kidney podocyte 9 320 34 -0.01 0.035 1000 -1000 -0.018 -1000
Canonical NF-kappaB pathway 9 351 39 -0.056 0.06 1000 -1000 -0.057 -1000
Circadian rhythm pathway 9 201 22 -0.045 0.042 1000 -1000 -0.013 -1000
Alternative NF-kappaB pathway 9 117 13 0 0.034 1000 -1000 -0.007 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 8 195 23 -0.031 0.032 1000 -1000 -0.015 -1000
Ephrin A reverse signaling 8 59 7 0 0.016 1000 -1000 -0.008 -1000
Class I PI3K signaling events mediated by Akt 6 415 68 -0.038 0.053 1000 -1000 -0.019 -1000
Arf6 trafficking events 6 459 71 -0.021 0.031 1000 -1000 -0.041 -1000
Insulin-mediated glucose transport 5 173 32 -0.015 0.033 1000 -1000 -0.014 -1000
Signaling events mediated by HDAC Class I 5 538 104 -0.033 0.053 1000 -1000 -0.034 -1000
Rapid glucocorticoid signaling 5 118 20 -0.005 0.02 1000 -1000 -0.008 -1000
Arf1 pathway 3 169 54 -0.001 0.036 1000 -1000 -0.016 -1000
Sumoylation by RanBP2 regulates transcriptional repression 1 39 27 -0.001 0.04 1000 -1000 -0.039 -1000
Total 4488 265945 7203 -16 -990 131000 -131000 -4.6 -131000
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.057 0.13 -9999 0 -0.74 13 13
Crk/p130 Cas/Paxillin -0.17 0.17 -9999 0 -0.4 165 165
JUN -0.17 0.21 -9999 0 -0.42 172 172
HRAS 0.012 0.051 -9999 0 -0.41 7 7
RET51/GFRalpha1/GDNF/GRB10 -0.21 0.22 -9999 0 -0.39 276 276
RAP1A 0.011 0.062 -9999 0 -0.52 7 7
FRS2 0.01 0.047 -9999 0 -0.28 13 13
RAP1A/GDP 0.008 0.045 -9999 0 -0.38 7 7
RET51/GFRalpha1/GDNF/DOK1 -0.21 0.22 -9999 0 -0.39 270 270
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.017 0.023 -9999 0 -0.52 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0.033 -9999 0 -0.52 2 2
RET9/GFRalpha1/GDNF/Enigma -0.1 0.14 -9999 0 -0.28 188 188
RHOA 0.005 0.08 -9999 0 -0.52 12 12
RAP1A/GTP -0.18 0.19 -9999 0 -0.36 246 246
GRB7 -0.017 0.1 -9999 0 -0.29 59 59
RET51/GFRalpha1/GDNF -0.2 0.21 -9999 0 -0.38 264 264
MAPKKK cascade -0.18 0.19 -9999 0 -0.45 147 147
BCAR1 0.017 0.012 -9999 0 -0.26 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.14 0.19 -9999 0 -0.35 199 199
lamellipodium assembly -0.16 0.16 -9999 0 -0.33 217 217
RET51/GFRalpha1/GDNF/SHC -0.2 0.21 -9999 0 -0.38 265 265
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
RET9/GFRalpha1/GDNF/SHC -0.1 0.14 -9999 0 -0.28 189 189
RET9/GFRalpha1/GDNF/Shank3 -0.1 0.14 -9999 0 -0.28 190 190
MAPK3 -0.17 0.18 -9999 0 -0.43 136 136
DOK1 0.002 0.083 -9999 0 -0.41 19 19
DOK6 -0.027 0.14 -9999 0 -0.44 51 51
PXN 0.018 0 -9999 0 -10000 0 0
neurite development -0.16 0.19 -9999 0 -0.41 147 147
DOK5 -0.025 0.13 -9999 0 -0.38 57 57
GFRA1 -0.22 0.24 -9999 0 -0.43 281 281
MAPK8 -0.16 0.2 -9999 0 -0.43 147 147
HRAS/GTP -0.21 0.22 -9999 0 -0.41 242 242
tube development -0.091 0.13 -9999 0 -0.26 193 193
MAPK1 -0.17 0.18 -9999 0 -0.43 136 136
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.079 0.12 -9999 0 -0.24 189 189
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
SRC 0.015 0.035 -9999 0 -0.43 3 3
PDLIM7 0.017 0.012 -9999 0 -0.26 1 1
RET51/GFRalpha1/GDNF/Dok6 -0.2 0.23 -9999 0 -0.39 274 274
SHC1 0.017 0.023 -9999 0 -0.52 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.2 0.21 -9999 0 -0.38 268 268
RET51/GFRalpha1/GDNF/Dok5 -0.22 0.23 -9999 0 -0.41 275 275
PRKCA 0.014 0.034 -9999 0 -0.26 8 8
HRAS/GDP 0.009 0.037 -9999 0 -0.29 7 7
CREB1 -0.14 0.19 -9999 0 -0.38 189 189
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.083 0.14 -9999 0 -0.25 192 192
RET51/GFRalpha1/GDNF/Grb7 -0.22 0.22 -9999 0 -0.4 274 274
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.18 0.23 -9999 0 -0.41 247 247
DOK4 0.013 0.047 -9999 0 -0.37 7 7
JNK cascade -0.16 0.2 -9999 0 -0.41 172 172
RET9/GFRalpha1/GDNF/FRS2 -0.11 0.14 -9999 0 -0.28 190 190
SHANK3 0.016 0.033 -9999 0 -0.52 2 2
RASA1 0.004 0.079 -9999 0 -0.42 16 16
NCK1 0.011 0.046 -9999 0 -0.28 12 12
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.077 0.12 -9999 0 -0.23 189 189
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.16 0.19 -9999 0 -0.43 134 134
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.17 0.21 -9999 0 -0.36 244 244
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.18 0.23 -9999 0 -0.54 132 132
PI3K -0.23 0.28 -9999 0 -0.52 220 220
SOS1 0.017 0.023 -9999 0 -0.52 1 1
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.09 0.14 -9999 0 -0.26 193 193
GRB10 -0.003 0.098 -9999 0 -0.43 24 24
activation of MAPKK activity -0.13 0.16 -9999 0 -0.37 123 123
RET51/GFRalpha1/GDNF/FRS2 -0.2 0.21 -9999 0 -0.38 267 267
GAB1 0.006 0.074 -9999 0 -0.43 14 14
IRS1 -0.048 0.17 -9999 0 -0.49 68 68
IRS2 -0.026 0.13 -9999 0 -0.39 57 57
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.19 0.24 -9999 0 -0.55 138 138
RET51/GFRalpha1/GDNF/PKC alpha -0.2 0.21 -9999 0 -0.39 264 264
GRB2 0.016 0.024 -9999 0 -0.26 4 4
PRKACA 0.018 0 -9999 0 -10000 0 0
GDNF 0.014 0.042 -9999 0 -0.46 4 4
RAC1 0.018 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.23 0.26 -9999 0 -0.44 273 273
Rac1/GTP -0.19 0.2 -9999 0 -0.4 217 217
RET9/GFRalpha1/GDNF -0.12 0.15 -9999 0 -0.32 188 188
GFRalpha1/GDNF -0.15 0.18 -9999 0 -0.37 188 188
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.15 0.21 -10000 0 -0.42 162 162
CRKL -0.16 0.22 -10000 0 -0.45 165 165
HRAS -0.12 0.19 -10000 0 -0.38 142 142
mol:PIP3 -0.15 0.2 -10000 0 -0.42 158 158
SPRED1 -0.002 0.098 -10000 0 -0.47 21 21
SPRED2 -0.003 0.1 -10000 0 -0.5 21 21
GAB1 -0.17 0.23 -10000 0 -0.47 168 168
FOXO3 -0.14 0.2 -10000 0 -0.41 160 160
AKT1 -0.16 0.21 -10000 0 -0.44 164 164
BAD -0.14 0.2 -10000 0 -0.41 154 154
megakaryocyte differentiation -0.17 0.23 -10000 0 -0.47 167 167
GSK3B -0.14 0.2 -10000 0 -0.41 154 154
RAF1 -0.089 0.16 -10000 0 -0.34 85 85
SHC1 0.017 0.023 -10000 0 -0.52 1 1
STAT3 -0.17 0.22 -10000 0 -0.47 163 163
STAT1 -0.37 0.49 -10000 0 -0.92 205 205
HRAS/SPRED1 -0.095 0.17 -10000 0 -0.35 95 95
cell proliferation -0.17 0.22 -10000 0 -0.45 165 165
PIK3CA 0.015 0.029 -10000 0 -0.35 3 3
TEC 0.013 0.052 -10000 0 -0.52 5 5
RPS6KB1 -0.17 0.22 -10000 0 -0.46 170 170
HRAS/SPRED2 -0.096 0.17 -10000 0 -0.36 91 91
LYN/TEC/p62DOK -0.15 0.22 -10000 0 -0.45 163 163
MAPK3 -0.054 0.12 -10000 0 -0.26 53 53
STAP1 -0.19 0.24 -10000 0 -0.48 176 176
GRAP2 0.011 0.044 -10000 0 -0.28 11 11
JAK2 -0.31 0.4 -10000 0 -0.75 213 213
STAT1 (dimer) -0.36 0.47 -10000 0 -0.9 205 205
mol:Gleevec 0.005 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.16 0.23 -10000 0 -0.45 168 168
actin filament polymerization -0.17 0.22 -10000 0 -0.44 182 182
LYN 0.014 0.031 -10000 0 -0.26 7 7
STAP1/STAT5A (dimer) -0.24 0.31 -10000 0 -0.64 167 167
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
CBL/CRKL/GRB2 -0.13 0.2 -10000 0 -0.41 152 152
PI3K -0.16 0.23 -10000 0 -0.45 169 169
PTEN -0.001 0.1 -10000 0 -0.52 19 19
SCF/KIT/EPO/EPOR -0.39 0.54 -10000 0 -1.2 142 142
MAPK8 -0.17 0.22 -10000 0 -0.46 165 165
STAT3 (dimer) -0.17 0.22 -10000 0 -0.46 163 163
positive regulation of transcription -0.042 0.1 -10000 0 -0.21 52 52
mol:GDP -0.12 0.2 -10000 0 -0.4 147 147
PIK3C2B -0.17 0.22 -10000 0 -0.47 164 164
CBL/CRKL -0.14 0.21 -10000 0 -0.43 154 154
FER -0.17 0.22 -10000 0 -0.47 163 163
SH2B3 -0.17 0.22 -10000 0 -0.46 163 163
PDPK1 -0.14 0.18 -10000 0 -0.39 152 152
SNAI2 -0.19 0.25 -10000 0 -0.5 176 176
positive regulation of cell proliferation -0.27 0.36 -10000 0 -0.67 213 213
KITLG -0.096 0.2 -10000 0 -0.45 123 123
cell motility -0.27 0.36 -10000 0 -0.67 213 213
PTPN6 0.023 0.037 -10000 0 -0.43 3 3
EPOR -0.091 0.16 -10000 0 -0.96 2 2
STAT5A (dimer) -0.23 0.3 -10000 0 -0.56 212 212
SOCS1 0.015 0.031 -10000 0 -0.32 4 4
cell migration 0.17 0.22 0.46 170 -10000 0 170
SOS1 0.017 0.023 -10000 0 -0.52 1 1
EPO -0.031 0.1 -10000 0 -0.27 80 80
VAV1 -0.015 0.12 -10000 0 -0.39 42 42
GRB10 -0.18 0.23 -10000 0 -0.48 166 166
PTPN11 0.022 0.024 -10000 0 -0.5 1 1
SCF/KIT -0.18 0.23 -10000 0 -0.47 181 181
GO:0007205 0.008 0.011 -10000 0 -10000 0 0
MAP2K1 -0.063 0.13 -10000 0 -0.28 58 58
CBL 0.017 0.012 -10000 0 -0.26 1 1
KIT -0.33 0.53 -10000 0 -1.3 109 109
MAP2K2 -0.064 0.13 -10000 0 -0.29 59 59
SHC/Grb2/SOS1 -0.14 0.22 -10000 0 -0.43 161 161
STAT5A -0.23 0.31 -10000 0 -0.57 211 211
GRB2 0.016 0.024 -10000 0 -0.26 4 4
response to radiation -0.19 0.24 -10000 0 -0.49 176 176
SHC/GRAP2 0.021 0.035 -10000 0 -0.37 2 2
PTPRO -0.18 0.23 -10000 0 -0.48 167 167
SH2B2 -0.18 0.22 -10000 0 -0.45 182 182
DOK1 0.002 0.083 -10000 0 -0.41 19 19
MATK -0.18 0.23 -10000 0 -0.47 170 170
CREBBP 0.004 0.059 -10000 0 -0.54 2 2
BCL2 -0.33 0.55 -10000 0 -1.3 126 126
Wnt 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
Noncanonical Wnts/FZD -0.13 0.21 -9999 0 -0.34 214 214
FZD6 -0.077 0.2 -9999 0 -0.45 108 108
WNT6 -0.011 0.088 -9999 0 -0.27 54 54
WNT4 -0.063 0.18 -9999 0 -0.45 90 90
FZD3 -0.031 0.15 -9999 0 -0.48 52 52
WNT5A -0.084 0.2 -9999 0 -0.43 120 120
WNT11 -0.013 0.09 -9999 0 -0.27 57 57
FOXM1 transcription factor network

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
NFATC3 -0.24 0.56 -10000 0 -1.1 110 110
PLK1 0.024 0.058 -10000 0 -10000 0 0
BIRC5 -0.092 0.39 -10000 0 -1.4 40 40
HSPA1B -0.24 0.56 -10000 0 -1.1 127 127
MAP2K1 0.018 0.046 -10000 0 -0.3 1 1
BRCA2 -0.26 0.59 -10000 0 -1.1 128 128
FOXM1 -0.4 0.93 -10000 0 -1.7 126 126
XRCC1 -0.24 0.56 -10000 0 -1.1 117 117
FOXM1B/p19 -0.42 0.55 0.46 1 -1.2 142 143
Cyclin D1/CDK4 -0.3 0.57 -10000 0 -1 158 158
CDC2 -0.26 0.61 -10000 0 -1.2 119 119
TGFA -0.29 0.55 -10000 0 -1 149 149
SKP2 -0.24 0.57 -10000 0 -1.1 110 110
CCNE1 -0.019 0.1 -10000 0 -0.29 64 64
CKS1B -0.24 0.57 -10000 0 -1.1 119 119
RB1 -0.22 0.32 -10000 0 -0.87 76 76
FOXM1C/SP1 -0.3 0.66 -10000 0 -1.3 132 132
AURKB 0.012 0.13 -10000 0 -1.4 3 3
CENPF -0.26 0.6 -10000 0 -1.2 113 113
CDK4 0.013 0.032 -10000 0 -0.26 5 5
MYC -0.22 0.52 -10000 0 -0.95 137 137
CHEK2 0.011 0.073 -10000 0 -0.41 9 9
ONECUT1 -0.28 0.57 -10000 0 -1.1 142 142
CDKN2A -0.057 0.15 -10000 0 -0.33 108 108
LAMA4 -0.24 0.57 -10000 0 -1.1 110 110
FOXM1B/HNF6 -0.37 0.71 -10000 0 -1.4 144 144
FOS -0.34 0.64 -10000 0 -1.2 158 158
SP1 0.016 0.024 -10000 0 -0.52 1 1
CDC25B -0.24 0.57 -10000 0 -1.1 110 110
response to radiation 0 0.039 -10000 0 -10000 0 0
CENPB -0.24 0.56 -10000 0 -1.1 112 112
CENPA -0.26 0.6 -10000 0 -1.2 117 117
NEK2 -0.28 0.62 -10000 0 -1.2 138 138
HIST1H2BA -0.24 0.57 -10000 0 -1.1 121 121
CCNA2 -0.025 0.14 -10000 0 -0.41 53 53
EP300 0.014 0.047 -10000 0 -0.52 4 4
CCNB1/CDK1 -0.31 0.7 -10000 0 -1.4 113 113
CCNB2 -0.25 0.58 -10000 0 -1.2 114 114
CCNB1 -0.27 0.62 -10000 0 -1.2 118 118
ETV5 -0.25 0.58 -10000 0 -1.1 114 114
ESR1 -0.43 0.71 -10000 0 -1.2 218 218
CCND1 -0.31 0.6 -10000 0 -1.1 159 159
GSK3A 0.019 0.037 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.013 0.13 -10000 0 -0.35 52 52
CDK2 0.011 0.049 -10000 0 -0.32 10 10
G2/M transition of mitotic cell cycle 0 0.046 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.37 0.53 -10000 0 -1.2 132 132
GAS1 -0.32 0.64 -10000 0 -1.2 150 150
MMP2 -0.27 0.61 -10000 0 -1.2 123 123
RB1/FOXM1C -0.3 0.6 -10000 0 -1.1 160 160
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
Endothelins

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
AKT1 -0.043 0.26 0.28 61 -0.51 80 141
PTK2B 0.017 0.017 -10000 0 -0.26 2 2
mol:Ca2+ -0.072 0.26 -10000 0 -0.65 61 61
EDN1 -0.063 0.24 0.23 56 -0.5 100 156
EDN3 -0.11 0.18 -10000 0 -0.33 194 194
EDN2 -0.13 0.22 -10000 0 -0.41 187 187
HRAS/GDP -0.11 0.24 -10000 0 -0.46 122 122
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.087 0.22 -10000 0 -0.4 131 131
ADCY4 -0.043 0.22 -10000 0 -0.53 58 58
ADCY5 -0.06 0.22 -10000 0 -0.49 74 74
ADCY6 -0.041 0.21 -10000 0 -0.51 60 60
ADCY7 -0.046 0.22 -10000 0 -0.52 61 61
ADCY1 -0.04 0.21 -10000 0 -0.51 58 58
ADCY2 -0.075 0.24 -10000 0 -0.5 89 89
ADCY3 -0.044 0.21 -10000 0 -0.51 64 64
ADCY8 -0.043 0.21 -10000 0 -0.51 59 59
ADCY9 -0.051 0.22 -10000 0 -0.51 68 68
arachidonic acid secretion -0.12 0.26 -10000 0 -0.5 133 133
ETB receptor/Endothelin-1/Gq/GTP -0.08 0.18 -10000 0 -0.33 132 132
GNAO1 0.016 0.024 -10000 0 -0.26 4 4
HRAS 0.011 0.051 -10000 0 -0.41 7 7
ETA receptor/Endothelin-1/G12/GTP -0.002 0.27 0.35 79 -0.51 69 148
ETA receptor/Endothelin-1/Gs/GTP -0.006 0.26 0.34 75 -0.54 59 134
mol:GTP -0.001 0.006 -10000 0 -10000 0 0
COL3A1 -0.047 0.28 -10000 0 -0.67 58 58
EDNRB -0.031 0.13 -10000 0 -0.39 53 53
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.042 0.26 -10000 0 -0.63 57 57
CYSLTR1 -0.075 0.3 -10000 0 -0.65 84 84
SLC9A1 -0.01 0.15 -10000 0 -0.3 55 55
mol:GDP -0.12 0.26 -10000 0 -0.48 132 132
SLC9A3 -0.13 0.34 -10000 0 -0.66 127 127
RAF1 -0.13 0.25 -10000 0 -0.47 139 139
JUN -0.11 0.36 -10000 0 -0.94 67 67
JAK2 -0.043 0.26 0.28 61 -0.5 83 144
mol:IP3 -0.11 0.22 -10000 0 -0.42 135 135
ETA receptor/Endothelin-1 -0.019 0.33 0.42 79 -0.5 114 193
PLCB1 -0.086 0.18 -10000 0 -0.38 138 138
PLCB2 0.014 0.027 -10000 0 -0.39 2 2
ETA receptor/Endothelin-3 -0.082 0.19 -10000 0 -0.39 108 108
FOS -0.18 0.35 -10000 0 -0.86 94 94
Gai/GDP -0.007 0.14 -10000 0 -0.77 12 12
CRK 0.016 0.033 -10000 0 -0.52 2 2
mol:Ca ++ -0.14 0.32 -10000 0 -0.59 133 133
BCAR1 0.017 0.012 -10000 0 -0.26 1 1
PRKCB1 -0.13 0.24 -10000 0 -0.46 140 140
GNAQ -0.001 0.007 -10000 0 -10000 0 0
GNAZ 0.002 0.085 -10000 0 -0.43 18 18
GNAL 0.01 0.052 -10000 0 -0.33 11 11
Gs family/GDP -0.12 0.21 -10000 0 -0.45 119 119
ETA receptor/Endothelin-1/Gq/GTP -0.069 0.23 0.22 22 -0.41 121 143
MAPK14 -0.084 0.17 -10000 0 -0.35 111 111
TRPC6 -0.078 0.28 -10000 0 -0.7 59 59
GNAI2 0.006 0.075 -10000 0 -0.48 12 12
GNAI3 0.017 0.023 -10000 0 -0.52 1 1
GNAI1 -0.015 0.12 -10000 0 -0.38 44 44
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.097 0.18 -10000 0 -0.35 134 134
ETB receptor/Endothelin-2 -0.11 0.18 -10000 0 -0.4 137 137
ETB receptor/Endothelin-3 -0.094 0.16 -10000 0 -0.38 97 97
ETB receptor/Endothelin-1 -0.067 0.21 -10000 0 -0.4 120 120
MAPK3 -0.17 0.34 -10000 0 -0.74 109 109
MAPK1 -0.17 0.34 -10000 0 -0.74 110 110
Rac1/GDP -0.1 0.24 -10000 0 -0.47 116 116
cAMP biosynthetic process -0.048 0.22 0.27 1 -0.5 72 73
MAPK8 -0.09 0.29 -10000 0 -0.62 92 92
SRC 0.015 0.035 -10000 0 -0.43 3 3
ETB receptor/Endothelin-1/Gi/GTP -0.036 0.16 -10000 0 -0.35 69 69
p130Cas/CRK/Src/PYK2 -0.1 0.25 -10000 0 -0.51 114 114
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.1 0.24 -10000 0 -0.46 120 120
COL1A2 -0.12 0.38 -10000 0 -0.76 109 109
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.099 0.22 -10000 0 -0.4 152 152
mol:DAG -0.11 0.22 -10000 0 -0.42 135 135
MAP2K2 -0.15 0.28 -10000 0 -0.58 124 124
MAP2K1 -0.15 0.28 -10000 0 -0.57 124 124
EDNRA -0.003 0.21 0.23 58 -0.55 52 110
positive regulation of muscle contraction -0.031 0.23 0.25 32 -0.52 60 92
Gq family/GDP -0.13 0.21 -10000 0 -0.47 114 114
HRAS/GTP -0.12 0.23 -10000 0 -0.44 133 133
PRKCH -0.1 0.22 -10000 0 -0.43 123 123
RAC1 0.018 0 -10000 0 -10000 0 0
PRKCA -0.098 0.22 -10000 0 -0.43 115 115
PRKCB -0.1 0.21 -10000 0 -0.4 136 136
PRKCE -0.099 0.22 -10000 0 -0.43 117 117
PRKCD -0.099 0.22 -10000 0 -0.42 122 122
PRKCG -0.097 0.22 -10000 0 -0.42 120 120
regulation of vascular smooth muscle contraction -0.21 0.41 -10000 0 -1 93 93
PRKCQ -0.11 0.23 -10000 0 -0.43 132 132
PLA2G4A -0.14 0.28 -10000 0 -0.54 133 133
GNA14 -0.083 0.18 -10000 0 -0.36 141 141
GNA15 0 0.079 -10000 0 -0.33 25 25
GNA12 0.018 0 -10000 0 -10000 0 0
GNA11 0.012 0.047 -10000 0 -0.52 4 4
Rac1/GTP -0.001 0.27 0.35 79 -0.56 57 136
MMP1 -0.24 0.4 0.32 2 -0.89 132 134
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.012 0.051 -9999 0 -0.41 7 7
EGFR -0.077 0.17 -9999 0 -0.35 136 136
EGF/EGFR -0.17 0.21 -9999 0 -0.36 243 243
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.084 0.16 -9999 0 -0.29 168 168
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.032 0.15 -9999 0 -0.5 50 50
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.14 0.23 -9999 0 -0.42 193 193
EGF/EGFR dimer/SHC -0.12 0.18 -9999 0 -0.35 173 173
mol:GDP -0.086 0.15 -9999 0 -0.29 168 168
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.097 0.21 -9999 0 -0.44 134 134
GRB2/SOS1 0.024 0.024 -9999 0 -0.37 1 1
HRAS/GTP -0.1 0.12 -9999 0 -0.34 59 59
SHC1 0.017 0.023 -9999 0 -0.52 1 1
HRAS/GDP -0.08 0.14 -9999 0 -0.35 59 59
FRAP1 -0.078 0.14 -9999 0 -0.35 57 57
EGF/EGFR dimer -0.15 0.2 -9999 0 -0.42 172 172
SOS1 0.017 0.023 -9999 0 -0.52 1 1
GRB2 0.016 0.024 -9999 0 -0.26 4 4
ETA receptor/Endothelin-1 -0.09 0.19 -9999 0 -0.41 121 121
HIF-1-alpha transcription factor network

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
PKM2 -0.16 0.47 -9999 0 -0.91 105 105
HDAC7 0.001 0.006 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.13 0.39 -9999 0 -0.76 93 93
SMAD4 0.01 0.067 -9999 0 -0.49 9 9
ID2 -0.16 0.48 -9999 0 -0.9 111 111
AP1 -0.1 0.19 -9999 0 -0.4 122 122
ABCG2 -0.16 0.48 -9999 0 -0.88 118 118
HIF1A -0.055 0.19 -9999 0 -0.53 58 58
TFF3 -0.23 0.52 -9999 0 -0.92 150 150
GATA2 -0.013 0.096 -9999 0 -0.33 40 40
AKT1 -0.007 0.1 -9999 0 -0.45 8 8
response to hypoxia -0.02 0.083 -9999 0 -0.17 16 16
MCL1 -0.16 0.47 -9999 0 -0.9 109 109
NDRG1 -0.17 0.48 -9999 0 -0.93 111 111
SERPINE1 -0.17 0.48 -9999 0 -0.92 111 111
FECH -0.16 0.48 -9999 0 -0.91 111 111
FURIN -0.16 0.48 -9999 0 -0.92 107 107
NCOA2 0.009 0.063 -9999 0 -0.4 11 11
EP300 0.008 0.12 -9999 0 -0.38 12 12
HMOX1 -0.17 0.49 -9999 0 -0.9 119 119
BHLHE40 -0.17 0.46 -9999 0 -0.87 119 119
BHLHE41 -0.17 0.46 -9999 0 -0.87 119 119
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.009 0.16 -9999 0 -0.36 49 49
ENG 0.007 0.15 -9999 0 -0.37 32 32
JUN -0.037 0.16 -9999 0 -0.47 57 57
RORA -0.17 0.48 -9999 0 -0.91 116 116
ABCB1 -0.099 0.25 -9999 0 -1.1 25 25
TFRC -0.18 0.49 -9999 0 -0.92 114 114
CXCR4 -0.18 0.49 -9999 0 -0.92 118 118
TF -0.16 0.47 -9999 0 -0.91 108 108
CITED2 -0.16 0.48 -9999 0 -0.91 108 108
HIF1A/ARNT -0.2 0.54 -9999 0 -1.1 102 102
LDHA -0.043 0.15 -9999 0 -1.2 8 8
ETS1 -0.16 0.48 -9999 0 -0.87 121 121
PGK1 -0.16 0.47 -9999 0 -0.9 108 108
NOS2 -0.17 0.46 -9999 0 -0.87 119 119
ITGB2 -0.17 0.49 -9999 0 -0.92 116 116
ALDOA -0.16 0.47 -9999 0 -0.9 111 111
Cbp/p300/CITED2 -0.16 0.48 -9999 0 -0.95 100 100
FOS -0.11 0.2 -9999 0 -0.38 171 171
HK2 -0.16 0.47 -9999 0 -0.9 109 109
SP1 0.022 0.031 -9999 0 -0.52 1 1
GCK 0.01 0.2 -9999 0 -1 6 6
HK1 -0.16 0.47 -9999 0 -0.9 108 108
NPM1 -0.16 0.47 -9999 0 -0.9 108 108
EGLN1 -0.16 0.48 -9999 0 -0.91 111 111
CREB1 0.025 0.024 -9999 0 -0.52 1 1
PGM1 -0.16 0.48 -9999 0 -0.9 112 112
SMAD3 0.005 0.079 -9999 0 -0.41 17 17
EDN1 -0.22 0.48 -9999 0 -1.2 98 98
IGFBP1 -0.16 0.47 -9999 0 -0.9 110 110
VEGFA -0.087 0.36 -9999 0 -0.7 85 85
HIF1A/JAB1 -0.038 0.14 -9999 0 -0.38 62 62
CP -0.26 0.5 -9999 0 -0.94 136 136
CXCL12 -0.18 0.51 -9999 0 -0.96 116 116
COPS5 0.009 0.056 -9999 0 -0.36 11 11
SMAD3/SMAD4 0.013 0.074 -9999 0 -0.36 18 18
BNIP3 -0.17 0.48 -9999 0 -0.91 111 111
EGLN3 -0.2 0.5 -9999 0 -0.94 121 121
CA9 -0.17 0.48 -9999 0 -0.92 114 114
TERT -0.16 0.47 -9999 0 -0.9 109 109
ENO1 -0.16 0.47 -9999 0 -0.91 108 108
PFKL -0.16 0.47 -9999 0 -0.9 110 110
NCOA1 0.011 0.057 -9999 0 -0.52 6 6
ADM -0.2 0.51 -9999 0 -0.93 128 128
ARNT 0.003 0.076 -9999 0 -10000 0 0
HNF4A 0.02 0.034 -9999 0 -0.52 2 2
ADFP -0.17 0.49 -9999 0 -0.92 116 116
SLC2A1 -0.086 0.36 -9999 0 -0.69 90 90
LEP -0.19 0.48 -9999 0 -0.89 121 121
HIF1A/ARNT/Cbp/p300 -0.14 0.4 -9999 0 -0.78 92 92
EPO -0.094 0.35 -9999 0 -0.74 61 61
CREBBP 0.01 0.12 -9999 0 -0.33 12 12
HIF1A/ARNT/Cbp/p300/HDAC7 -0.14 0.39 -9999 0 -0.78 89 89
PFKFB3 -0.16 0.48 -9999 0 -0.92 107 107
NT5E -0.16 0.48 -9999 0 -0.91 110 110
IGF1 pathway

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
NCK2 0.015 0.027 -10000 0 -0.26 5 5
PTK2 0.016 0.029 -10000 0 -0.35 3 3
CRKL -0.11 0.19 -10000 0 -0.37 155 155
GRB2/SOS1/SHC 0.034 0.025 -10000 0 -0.3 2 2
HRAS 0.012 0.051 -10000 0 -0.41 7 7
IRS1/Crk -0.1 0.19 -10000 0 -0.37 155 155
IGF-1R heterotetramer/IGF1/PTP1B -0.11 0.19 -10000 0 -0.37 156 156
AKT1 -0.086 0.18 -10000 0 -0.42 86 86
BAD -0.075 0.17 -10000 0 -0.4 84 84
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.1 0.19 -10000 0 -0.36 155 155
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.1 0.19 -10000 0 -0.37 153 153
RAF1 -0.064 0.16 -10000 0 -0.4 69 69
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.089 0.19 -10000 0 -0.35 154 154
YWHAZ 0.017 0.017 -10000 0 -0.26 2 2
IGF-1R heterotetramer/IGF1/IRS1 -0.12 0.21 -10000 0 -0.38 170 170
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
RPS6KB1 -0.087 0.18 -10000 0 -0.42 85 85
GNB2L1 0.015 0.04 -10000 0 -0.52 3 3
positive regulation of MAPKKK cascade -0.058 0.14 -10000 0 -0.34 69 69
PXN 0.018 0 -10000 0 -10000 0 0
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.024 0.024 -10000 0 -0.37 1 1
HRAS/GTP -0.1 0.16 -10000 0 -0.43 72 72
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.061 0.16 -10000 0 -0.35 71 71
IGF-1R heterotetramer -0.11 0.22 -10000 0 -0.51 110 110
IGF-1R heterotetramer/IGF1/IRS/Nck -0.1 0.2 -10000 0 -0.37 153 153
Crk/p130 Cas/Paxillin -0.079 0.18 -10000 0 -0.46 70 70
IGF1R -0.11 0.22 -10000 0 -0.51 110 110
IGF1 -0.12 0.22 -10000 0 -0.44 146 146
IRS2/Crk -0.11 0.2 -10000 0 -0.36 167 167
PI3K -0.1 0.2 -10000 0 -0.36 165 165
apoptosis 0.058 0.15 0.34 84 -10000 0 84
HRAS/GDP 0.009 0.037 -10000 0 -0.29 7 7
PRKCD -0.097 0.21 -10000 0 -0.44 118 118
RAF1/14-3-3 E -0.048 0.14 -10000 0 -0.34 68 68
BAD/14-3-3 -0.061 0.16 -10000 0 -0.37 78 78
PRKCZ -0.091 0.18 -10000 0 -0.32 165 165
Crk/p130 Cas/Paxillin/FAK1 -0.088 0.14 -10000 0 -0.39 67 67
PTPN1 0.002 0.071 -10000 0 -0.29 28 28
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.11 0.22 -10000 0 -0.41 154 154
BCAR1 0.017 0.012 -10000 0 -0.26 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.087 0.17 -10000 0 -0.32 164 164
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.017 0.023 -10000 0 -0.52 1 1
IRS1/NCK2 -0.1 0.19 -10000 0 -0.37 153 153
GRB10 -0.003 0.098 -10000 0 -0.43 24 24
PTPN11 -0.1 0.19 -10000 0 -0.37 153 153
IRS1 -0.12 0.2 -10000 0 -0.38 170 170
IRS2 -0.13 0.21 -10000 0 -0.39 166 166
IGF-1R heterotetramer/IGF1 -0.14 0.23 -10000 0 -0.47 154 154
GRB2 0.016 0.024 -10000 0 -0.26 4 4
PDPK1 -0.094 0.19 -10000 0 -0.33 165 165
YWHAE 0.016 0.029 -10000 0 -0.35 3 3
PRKD1 -0.12 0.23 -10000 0 -0.48 119 119
SHC1 0.017 0.023 -10000 0 -0.52 1 1
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.058 0.13 -10000 0 -0.26 153 153
ER alpha/Gai/GDP/Gbeta gamma -0.089 0.19 -10000 0 -0.35 158 158
AKT1 -0.2 0.35 -10000 0 -0.73 153 153
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.2 0.35 -10000 0 -0.74 153 153
mol:Ca2+ -0.11 0.18 -10000 0 -0.39 115 115
IGF1R -0.083 0.2 -10000 0 -0.47 110 110
E2/ER alpha (dimer)/Striatin -0.09 0.15 -10000 0 -0.32 155 155
SHC1 0.017 0.023 -10000 0 -0.52 1 1
apoptosis 0.19 0.33 0.7 153 -10000 0 153
RhoA/GTP -0.086 0.12 -10000 0 -0.41 27 27
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.12 0.18 -10000 0 -0.38 154 154
regulation of stress fiber formation 0.042 0.12 0.29 41 -10000 0 41
E2/ERA-ERB (dimer) -0.087 0.15 -10000 0 -0.31 149 149
KRAS 0.008 0.069 -10000 0 -0.45 11 11
G13/GTP -0.082 0.14 -10000 0 -0.29 151 151
pseudopodium formation -0.042 0.12 -10000 0 -0.29 41 41
E2/ER alpha (dimer)/PELP1 -0.086 0.15 -10000 0 -0.31 149 149
GRB2 0.016 0.024 -10000 0 -0.26 4 4
GNG2 0.016 0.029 -10000 0 -0.35 3 3
GNAO1 0.016 0.024 -10000 0 -0.26 4 4
HRAS 0.012 0.051 -10000 0 -0.41 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.11 0.22 -10000 0 -0.44 154 154
E2/ER beta (dimer) 0.013 0.008 -10000 0 -0.17 1 1
mol:GDP -0.12 0.17 -10000 0 -0.38 151 151
mol:NADP -0.11 0.22 -10000 0 -0.44 154 154
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
mol:IP3 -0.11 0.19 -10000 0 -0.41 115 115
IGF-1R heterotetramer -0.083 0.2 -10000 0 -0.47 110 110
PLCB1 -0.12 0.19 -10000 0 -0.38 145 145
PLCB2 -0.075 0.17 -10000 0 -0.44 73 73
IGF1 -0.1 0.21 -10000 0 -0.42 146 146
mol:L-citrulline -0.11 0.22 -10000 0 -0.44 154 154
RHOA 0.005 0.08 -10000 0 -0.52 12 12
Gai/GDP -0.008 0.13 -10000 0 -0.71 12 12
JNK cascade 0.013 0.008 -10000 0 -0.17 1 1
BCAR1 0.017 0.012 -10000 0 -0.26 1 1
ESR2 0.017 0.012 -10000 0 -0.26 1 1
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.16 0.24 -10000 0 -0.45 202 202
Gq family/GDP/Gbeta gamma -0.025 0.12 -10000 0 -0.5 19 19
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.044 0.13 -10000 0 -0.63 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.12 0.18 -10000 0 -0.38 155 155
GNAZ 0.002 0.085 -10000 0 -0.43 18 18
E2/ER alpha (dimer) -0.12 0.17 -10000 0 -0.32 202 202
STRN 0.011 0.056 -10000 0 -0.42 8 8
GNAL 0.01 0.052 -10000 0 -0.33 11 11
PELP1 0.018 0 -10000 0 -10000 0 0
MAPK11 0.021 0.007 -10000 0 -10000 0 0
GNAI2 0.006 0.075 -10000 0 -0.48 12 12
GNAI3 0.017 0.023 -10000 0 -0.52 1 1
GNAI1 -0.015 0.12 -10000 0 -0.38 44 44
HBEGF -0.091 0.19 -10000 0 -0.33 166 166
cAMP biosynthetic process -0.082 0.11 -10000 0 -0.25 151 151
SRC -0.078 0.18 -10000 0 -0.33 158 158
PI3K 0.006 0.082 -10000 0 -0.37 21 21
GNB1 0.013 0.052 -10000 0 -0.52 5 5
G13/GDP/Gbeta gamma -0.1 0.15 -10000 0 -0.34 151 151
SOS1 0.017 0.023 -10000 0 -0.52 1 1
IGF-1R heterotetramer/IGF1 -0.16 0.21 -10000 0 -0.44 171 171
Gs family/GTP -0.067 0.13 -10000 0 -0.26 151 151
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.019 0.064 -10000 0 -0.28 20 20
vasodilation -0.1 0.22 -10000 0 -0.42 154 154
mol:DAG -0.11 0.19 -10000 0 -0.41 115 115
Gs family/GDP/Gbeta gamma -0.1 0.15 -10000 0 -0.32 152 152
MSN -0.046 0.13 -10000 0 -0.32 41 41
Gq family/GTP -0.086 0.18 -10000 0 -0.44 82 82
mol:PI-3-4-5-P3 -0.19 0.34 -10000 0 -0.71 153 153
NRAS 0.006 0.072 -10000 0 -0.4 15 15
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.1 0.22 0.42 154 -10000 0 154
GRB2/SOS1 0.024 0.024 -10000 0 -0.37 1 1
RhoA/GDP -0.094 0.18 -10000 0 -0.37 150 150
NOS3 -0.11 0.23 -10000 0 -0.46 154 154
GNA11 0.014 0.047 -10000 0 -0.52 4 4
MAPKKK cascade -0.12 0.26 -10000 0 -0.53 154 154
E2/ER alpha (dimer)/PELP1/Src -0.13 0.18 -10000 0 -0.4 155 155
ruffle organization -0.042 0.12 -10000 0 -0.29 41 41
ROCK2 -0.053 0.13 -10000 0 -0.37 29 29
GNA14 -0.081 0.18 -10000 0 -0.35 141 141
GNA15 0.001 0.078 -10000 0 -0.33 25 25
GNA13 0.009 0.059 -10000 0 -0.38 11 11
MMP9 -0.095 0.18 -10000 0 -0.32 165 165
MMP2 -0.088 0.2 -10000 0 -0.34 168 168
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 0.016 0.037 -10000 0 -0.36 3 3
NFATC2 -0.11 0.26 -10000 0 -0.61 75 75
NFATC3 -0.055 0.11 -10000 0 -0.29 8 8
CD40LG -0.32 0.43 -10000 0 -0.89 153 153
ITCH 0.006 0.085 -10000 0 -10000 0 0
CBLB 0.004 0.092 -10000 0 -0.6 2 2
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.23 0.38 -10000 0 -0.93 84 84
JUNB 0.011 0.055 -10000 0 -0.36 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.008 0.1 -10000 0 -0.27 49 49
T cell anergy -0.033 0.14 -10000 0 -0.39 49 49
TLE4 -0.071 0.23 -10000 0 -0.72 37 37
Jun/NFAT1-c-4/p21SNFT -0.29 0.45 -10000 0 -0.93 137 137
AP-1/NFAT1-c-4 -0.37 0.52 -10000 0 -1 153 153
IKZF1 -0.079 0.23 -10000 0 -0.69 43 43
T-helper 2 cell differentiation -0.22 0.35 -10000 0 -0.76 125 125
AP-1/NFAT1 -0.14 0.24 -10000 0 -0.51 118 118
CALM1 0.002 0.058 -10000 0 -10000 0 0
EGR2 -0.29 0.51 -10000 0 -1.3 85 85
EGR3 -0.37 0.58 -10000 0 -1.3 126 126
NFAT1/FOXP3 -0.064 0.2 -10000 0 -0.55 44 44
EGR1 -0.1 0.2 -10000 0 -0.39 155 155
JUN -0.036 0.15 -10000 0 -0.46 57 57
EGR4 0 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.016 0.06 -10000 0 -10000 0 0
GBP3 -0.14 0.31 -10000 0 -0.74 95 95
FOSL1 0.016 0.024 -10000 0 -0.26 4 4
NFAT1-c-4/MAF/IRF4 -0.27 0.44 -10000 0 -0.91 132 132
DGKA -0.065 0.21 -10000 0 -0.68 34 34
CREM 0.016 0.017 -10000 0 -0.26 2 2
NFAT1-c-4/PPARG -0.3 0.45 -10000 0 -0.93 145 145
CTLA4 -0.051 0.18 -10000 0 -0.54 40 40
NFAT1-c-4 (dimer)/EGR1 -0.33 0.47 -10000 0 -0.99 145 145
NFAT1-c-4 (dimer)/EGR4 -0.28 0.44 -10000 0 -0.88 154 154
FOS -0.11 0.2 -10000 0 -0.37 171 171
IFNG -0.3 0.47 -10000 0 -1.1 98 98
T cell activation -0.17 0.29 -10000 0 -0.82 46 46
MAF -0.012 0.12 -10000 0 -0.44 35 35
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.22 0.38 0.8 110 -10000 0 110
TNF -0.29 0.42 -10000 0 -0.9 137 137
FASLG -0.43 0.65 -10000 0 -1.3 165 165
TBX21 -0.11 0.21 -10000 0 -0.46 137 137
BATF3 0 0.001 -10000 0 -10000 0 0
PRKCQ -0.018 0.11 -10000 0 -0.33 51 51
PTPN1 -0.068 0.2 -10000 0 -0.65 34 34
NFAT1-c-4/ICER1 -0.28 0.44 -10000 0 -0.9 141 141
GATA3 -0.1 0.23 -10000 0 -0.51 124 124
T-helper 1 cell differentiation -0.29 0.44 -10000 0 -1.1 98 98
IL2RA -0.25 0.36 -10000 0 -0.85 98 98
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.058 0.19 -10000 0 -0.61 31 31
E2F1 0.013 0.071 -10000 0 -0.37 16 16
PPARG -0.035 0.13 -10000 0 -0.33 79 79
SLC3A2 -0.059 0.19 -10000 0 -0.57 37 37
IRF4 -0.01 0.086 -10000 0 -0.27 52 52
PTGS2 -0.33 0.44 -10000 0 -0.9 157 157
CSF2 -0.33 0.43 -10000 0 -0.9 155 155
JunB/Fra1/NFAT1-c-4 -0.25 0.43 -10000 0 -0.88 132 132
IL4 -0.24 0.37 -10000 0 -0.8 123 123
IL5 -0.32 0.43 -10000 0 -0.9 148 148
IL2 -0.18 0.29 -10000 0 -0.85 43 43
IL3 -0.04 0.052 -10000 0 -10000 0 0
RNF128 -0.053 0.2 -10000 0 -0.6 47 47
NFATC1 -0.22 0.39 -10000 0 -0.82 108 108
CDK4 0.14 0.22 0.6 36 -10000 0 36
PTPRK -0.12 0.3 -10000 0 -0.76 79 79
IL8 -0.36 0.44 -10000 0 -0.93 157 157
POU2F1 0.027 0 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.017 0.023 -9999 0 -0.52 1 1
CCL5 -0.05 0.18 -9999 0 -0.49 70 70
SDCBP 0.003 0.081 -9999 0 -0.4 19 19
FGFR/FGF2/Syndecan-1 -0.17 0.27 -9999 0 -0.58 116 116
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.16 0.26 -9999 0 -0.58 111 111
Syndecan-1/Syntenin -0.16 0.26 -9999 0 -0.58 112 112
MAPK3 -0.13 0.24 -9999 0 -0.56 94 94
HGF/MET 0.006 0.075 -9999 0 -0.38 14 14
TGFB1/TGF beta receptor Type II 0.017 0.023 -9999 0 -0.52 1 1
BSG 0.016 0.024 -9999 0 -0.26 4 4
keratinocyte migration -0.15 0.25 -9999 0 -0.57 111 111
Syndecan-1/RANTES -0.18 0.28 -9999 0 -0.62 119 119
Syndecan-1/CD147 -0.14 0.25 -9999 0 -0.58 102 102
Syndecan-1/Syntenin/PIP2 -0.15 0.25 -9999 0 -0.56 112 112
LAMA5 0.005 0.075 -9999 0 -0.42 15 15
positive regulation of cell-cell adhesion -0.15 0.24 -9999 0 -0.54 112 112
MMP7 -0.094 0.21 -9999 0 -0.44 128 128
HGF 0.008 0.069 -9999 0 -0.45 11 11
Syndecan-1/CASK -0.16 0.26 -9999 0 -0.56 116 116
Syndecan-1/HGF/MET -0.15 0.25 -9999 0 -0.56 110 110
regulation of cell adhesion -0.12 0.23 -9999 0 -0.53 96 96
HPSE -0.017 0.12 -9999 0 -0.4 44 44
positive regulation of cell migration -0.17 0.27 -9999 0 -0.58 116 116
SDC1 -0.17 0.27 -9999 0 -0.59 116 116
Syndecan-1/Collagen -0.17 0.27 -9999 0 -0.58 116 116
PPIB 0.014 0.044 -9999 0 -0.42 5 5
MET -0.001 0.078 -9999 0 -0.3 31 31
PRKACA 0.018 0 -9999 0 -10000 0 0
MMP9 -0.042 0.17 -9999 0 -0.51 60 60
MAPK1 -0.13 0.24 -9999 0 -0.56 96 96
homophilic cell adhesion -0.16 0.26 -9999 0 -0.58 116 116
MMP1 -0.19 0.22 -9999 0 -0.39 268 268
IL4-mediated signaling events

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
BCL2L1 -0.33 0.62 -10000 0 -1.2 138 138
STAT6 (cleaved dimer) -0.43 0.56 -10000 0 -1.2 148 148
IGHG1 -0.081 0.25 -10000 0 -0.41 93 93
IGHG3 -0.33 0.59 -10000 0 -1.2 143 143
AKT1 -0.11 0.31 -10000 0 -0.65 57 57
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.063 0.24 -10000 0 -0.61 27 27
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.34 -10000 0 -0.68 85 85
THY1 -0.34 0.65 -10000 0 -1.3 140 140
MYB -0.098 0.22 -10000 0 -0.49 121 121
HMGA1 0.014 0.039 -10000 0 -0.36 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.14 0.35 -10000 0 -0.64 99 99
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.12 0.31 -10000 0 -0.62 69 69
SP1 0.021 0.03 -10000 0 -0.53 1 1
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.015 0.055 -10000 0 -0.4 7 7
STAT6 (dimer)/ETS1 -0.33 0.63 -10000 0 -1.2 145 145
SOCS1 -0.18 0.4 -10000 0 -0.74 131 131
SOCS3 -0.11 0.33 -10000 0 -0.9 28 28
FCER2 -0.22 0.46 -10000 0 -0.9 106 106
PARP14 0.006 0.078 -10000 0 -0.43 15 15
CCL17 -0.41 0.71 -10000 0 -1.4 158 158
GRB2 0.016 0.024 -10000 0 -0.26 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.081 0.26 -10000 0 -0.6 32 32
T cell proliferation -0.35 0.65 -10000 0 -1.3 140 140
IL4R/JAK1 -0.34 0.64 -10000 0 -1.3 139 139
EGR2 -0.38 0.69 -10000 0 -1.4 138 138
JAK2 0.001 0.072 -10000 0 -0.35 12 12
JAK3 0.021 0.008 -10000 0 -10000 0 0
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
JAK1 0.012 0.061 -10000 0 -0.52 6 6
COL1A2 -0.22 0.54 -10000 0 -1.5 72 72
CCL26 -0.33 0.63 -10000 0 -1.2 139 139
IL4R -0.37 0.7 -10000 0 -1.4 137 137
PTPN6 0.02 0.038 -10000 0 -0.42 3 3
IL13RA2 -0.38 0.67 -10000 0 -1.3 149 149
IL13RA1 -0.002 0.089 -10000 0 -0.51 11 11
IRF4 -0.037 0.2 -10000 0 -0.83 9 9
ARG1 -0.063 0.27 -10000 0 -1 21 21
CBL -0.13 0.32 -10000 0 -0.61 93 93
GTF3A 0.02 0.032 -10000 0 -0.38 2 2
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
IL13RA1/JAK2 0.004 0.099 -10000 0 -0.36 17 17
IRF4/BCL6 -0.043 0.19 -10000 0 -0.77 9 9
CD40LG 0.012 0.072 -10000 0 -0.32 21 21
MAPK14 -0.13 0.33 -10000 0 -0.63 88 88
mitosis -0.1 0.3 -10000 0 -0.62 57 57
STAT6 -0.43 0.85 -10000 0 -1.6 141 141
SPI1 0.011 0.074 -10000 0 -0.44 12 12
RPS6KB1 -0.097 0.29 -10000 0 -0.6 54 54
STAT6 (dimer) -0.43 0.86 -10000 0 -1.6 141 141
STAT6 (dimer)/PARP14 -0.38 0.7 -10000 0 -1.4 142 142
mast cell activation 0.003 0.019 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.11 0.3 -10000 0 -0.66 53 53
FRAP1 -0.11 0.31 -10000 0 -0.65 57 57
LTA -0.33 0.62 -10000 0 -1.2 138 138
FES 0.011 0.054 -10000 0 -0.38 9 9
T-helper 1 cell differentiation 0.39 0.75 1.4 141 -10000 0 141
CCL11 -0.38 0.65 -10000 0 -1.2 158 158
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.099 0.3 -10000 0 -0.67 36 36
IL2RG 0.001 0.081 -10000 0 -0.29 35 35
IL10 -0.33 0.63 -10000 0 -1.2 137 137
IRS1 -0.048 0.17 -10000 0 -0.49 68 68
IRS2 -0.026 0.13 -10000 0 -0.39 57 57
IL4 -0.038 0.22 -10000 0 -1.4 6 6
IL5 -0.33 0.63 -10000 0 -1.3 128 128
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.24 0.5 -10000 0 -0.92 137 137
COL1A1 -0.22 0.56 -10000 0 -1.5 71 71
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.36 0.67 -10000 0 -1.3 134 134
IL2R gamma/JAK3 0.017 0.059 -10000 0 -0.33 5 5
TFF3 -0.51 0.77 -10000 0 -1.4 205 205
ALOX15 -0.34 0.64 -10000 0 -1.2 141 141
MYBL1 -0.067 0.17 -10000 0 -0.37 116 116
T-helper 2 cell differentiation -0.25 0.49 -10000 0 -0.93 137 137
SHC1 0.017 0.023 -10000 0 -0.52 1 1
CEBPB 0.008 0.075 -10000 0 -0.34 20 20
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.12 0.32 -10000 0 -0.63 71 71
mol:PI-3-4-5-P3 -0.11 0.31 -10000 0 -0.65 57 57
PI3K -0.12 0.33 -10000 0 -0.7 56 56
DOK2 -0.021 0.13 -10000 0 -0.41 48 48
ETS1 0.007 0.067 -10000 0 -0.28 23 23
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.071 0.25 -10000 0 -0.57 29 29
ITGB3 -0.34 0.63 -10000 0 -1.3 133 133
PIGR -0.49 0.76 -10000 0 -1.4 189 189
IGHE 0.022 0.086 0.2 50 -0.25 4 54
MAPKKK cascade -0.069 0.24 -10000 0 -0.56 29 29
BCL6 -0.005 0.1 -10000 0 -0.46 24 24
OPRM1 -0.33 0.63 -10000 0 -1.3 127 127
RETNLB -0.33 0.63 -10000 0 -1.3 129 129
SELP -0.46 0.75 -10000 0 -1.4 171 171
AICDA -0.34 0.61 -10000 0 -1.2 143 143
Glucocorticoid receptor regulatory network

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
PCK2 0.017 0.16 0.34 16 -0.84 11 27
SMARCC2 0.018 0 -10000 0 -10000 0 0
SMARCC1 0.012 0.051 -10000 0 -0.41 7 7
TBX21 -0.2 0.33 -10000 0 -0.72 131 131
SUMO2 0.014 0.022 -10000 0 -0.26 3 3
STAT1 (dimer) -0.024 0.14 -10000 0 -0.35 67 67
FKBP4 0.012 0.055 -10000 0 -0.45 7 7
FKBP5 -0.045 0.16 -10000 0 -0.43 75 75
GR alpha/HSP90/FKBP51/HSP90 0.073 0.16 0.29 79 -0.3 34 113
PRL -0.057 0.14 -10000 0 -0.71 5 5
cortisol/GR alpha (dimer)/TIF2 0.24 0.26 0.52 197 -0.4 2 199
RELA -0.053 0.091 -10000 0 -0.25 25 25
FGG 0.2 0.22 0.48 150 -0.39 2 152
GR beta/TIF2 0.11 0.14 0.3 115 -0.31 14 129
IFNG -0.41 0.43 -10000 0 -0.89 180 180
apoptosis -0.005 0.18 0.48 8 -0.5 8 16
CREB1 0.007 0.057 -10000 0 -0.36 5 5
histone acetylation -0.045 0.14 0.28 2 -0.33 66 68
BGLAP -0.074 0.15 -10000 0 -0.5 19 19
GR/PKAc 0.093 0.14 0.29 65 -0.33 14 79
NF kappa B1 p50/RelA -0.093 0.17 -10000 0 -0.38 83 83
SMARCD1 0.018 0 -10000 0 -10000 0 0
MDM2 0.099 0.1 0.23 141 -10000 0 141
GATA3 -0.093 0.23 -10000 0 -0.5 124 124
AKT1 0.007 0.06 0.21 5 -0.38 9 14
CSF2 -0.074 0.15 -10000 0 -0.68 12 12
GSK3B 0.016 0.008 -10000 0 -10000 0 0
NR1I3 0.008 0.18 0.48 6 -0.91 3 9
CSN2 0.17 0.18 0.4 141 -0.39 5 146
BRG1/BAF155/BAF170/BAF60A 0.041 0.034 -10000 0 -0.27 5 5
NFATC1 -0.004 0.12 -10000 0 -0.42 39 39
POU2F1 0.025 0.012 -10000 0 -0.22 1 1
CDKN1A -0.033 0.27 -10000 0 -1.5 15 15
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.002 0.007 -10000 0 -10000 0 0
SFN -0.015 0.12 -10000 0 -0.45 37 37
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.064 0.16 0.3 60 -0.32 30 90
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.086 0.33 0.46 6 -0.8 79 85
JUN -0.22 0.24 -10000 0 -0.5 172 172
IL4 -0.1 0.2 -10000 0 -0.57 44 44
CDK5R1 0.013 0.032 -10000 0 -0.26 7 7
PRKACA 0.018 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.22 0.28 0.21 47 -0.48 233 280
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.081 0.15 0.3 64 -0.3 23 87
cortisol/GR alpha (monomer) 0.28 0.32 0.62 199 -0.47 2 201
NCOA2 0.009 0.063 -10000 0 -0.4 11 11
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.21 -10000 0 -0.45 171 171
AP-1/NFAT1-c-4 -0.44 0.39 -10000 0 -0.78 253 253
AFP -0.16 0.2 -10000 0 -0.62 38 38
SUV420H1 0.014 0.037 -10000 0 -0.3 7 7
IRF1 0.11 0.25 0.44 61 -0.79 20 81
TP53 -0.014 0.17 -10000 0 -0.54 46 46
PPP5C 0.012 0.052 -10000 0 -0.39 8 8
KRT17 -0.54 0.58 -10000 0 -1.2 196 196
KRT14 -0.32 0.51 -10000 0 -1.1 125 125
TBP 0.028 0.011 -10000 0 -0.24 1 1
CREBBP 0.061 0.1 0.25 86 -0.53 2 88
HDAC1 0.011 0.025 -10000 0 -0.53 1 1
HDAC2 0.008 0.054 -10000 0 -0.29 15 15
AP-1 -0.45 0.4 -10000 0 -0.79 253 253
MAPK14 0.015 0.014 -10000 0 -0.26 1 1
MAPK10 -0.027 0.13 -10000 0 -0.36 59 59
MAPK11 0.016 0.008 -10000 0 -10000 0 0
KRT5 -0.55 0.58 -10000 0 -1.1 222 222
interleukin-1 receptor activity -0.001 0.009 -10000 0 -10000 0 0
NCOA1 0.013 0.059 -10000 0 -0.52 6 6
STAT1 -0.024 0.14 -10000 0 -0.35 67 67
CGA -0.12 0.2 -10000 0 -0.55 52 52
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.12 0.17 0.37 111 -0.35 4 115
MAPK3 0.014 0.027 -10000 0 -0.39 2 2
MAPK1 0.014 0.034 -10000 0 -0.52 2 2
ICAM1 -0.23 0.34 -10000 0 -0.71 127 127
NFKB1 -0.054 0.093 -10000 0 -0.24 38 38
MAPK8 -0.15 0.19 -10000 0 -0.4 150 150
MAPK9 -0.008 0.11 -10000 0 -0.51 24 24
cortisol/GR alpha (dimer) -0.014 0.18 0.48 8 -0.53 8 16
BAX 0.002 0.11 -10000 0 -10000 0 0
POMC -0.13 0.2 -10000 0 -1.1 7 7
EP300 0.059 0.11 0.25 86 -0.53 4 90
cortisol/GR alpha (dimer)/p53 0.21 0.28 0.54 173 -0.48 4 177
proteasomal ubiquitin-dependent protein catabolic process 0.071 0.081 0.21 82 -10000 0 82
SGK1 0.11 0.13 0.32 110 -0.26 4 114
IL13 -0.31 0.29 -10000 0 -0.73 117 117
IL6 -0.29 0.41 -10000 0 -0.92 119 119
PRKACG 0.016 0.033 -10000 0 -0.52 2 2
IL5 -0.27 0.24 -10000 0 -0.67 75 75
IL2 -0.32 0.33 -10000 0 -0.77 129 129
CDK5 0.015 0.027 -10000 0 -0.4 2 2
PRKACB -0.035 0.14 -10000 0 -0.34 78 78
HSP90AA1 0.013 0.045 -10000 0 -0.39 6 6
IL8 -0.27 0.37 -10000 0 -0.75 150 150
CDK5R1/CDK5 0.02 0.03 -10000 0 -0.2 7 7
NF kappa B1 p50/RelA/PKAc -0.064 0.15 -10000 0 -0.35 62 62
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.24 0.51 184 -0.36 1 185
SMARCA4 0.015 0.031 -10000 0 -0.32 4 4
chromatin remodeling 0.16 0.16 0.35 160 -10000 0 160
NF kappa B1 p50/RelA/Cbp -0.019 0.16 0.31 28 -0.37 32 60
JUN (dimer) -0.22 0.24 -10000 0 -0.49 172 172
YWHAH 0.013 0.048 -10000 0 -0.47 5 5
VIPR1 -0.11 0.23 -10000 0 -0.58 76 76
NR3C1 0.16 0.21 0.43 140 -0.45 11 151
NR4A1 0.01 0.064 -10000 0 -0.44 4 4
TIF2/SUV420H1 0.017 0.056 -10000 0 -0.42 6 6
MAPKKK cascade -0.005 0.18 0.48 8 -0.5 8 16
cortisol/GR alpha (dimer)/Src-1 0.24 0.26 0.53 192 -0.43 3 195
PBX1 0.004 0.1 -10000 0 -0.48 23 23
POU1F1 0.023 0.034 -10000 0 -0.3 5 5
SELE -0.36 0.48 -10000 0 -0.93 182 182
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.16 0.16 0.36 157 -10000 0 157
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.24 0.51 184 -0.36 1 185
mol:cortisol 0.16 0.19 0.36 197 -10000 0 197
MMP1 -0.44 0.52 -10000 0 -1.1 167 167
TCGA08_retinoblastoma

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
CDKN2B -0.017 0.12 -10000 0 -0.38 45 45
CDKN2C 0.005 0.085 -10000 0 -0.37 23 23
CDKN2A -0.053 0.15 -10000 0 -0.32 108 108
CCND2 0.019 0.084 0.2 74 -0.15 6 80
RB1 -0.022 0.092 0.15 3 -0.22 77 80
CDK4 0.026 0.095 0.23 77 -10000 0 77
CDK6 0.019 0.093 0.24 61 -0.19 7 68
G1/S progression 0.022 0.092 0.22 77 -0.15 3 80
FAS signaling pathway (CD95)

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
SPTAN1 0.066 0.099 0.24 121 -10000 0 121
RFC1 0.067 0.099 0.24 127 -10000 0 127
PRKDC 0.064 0.1 0.24 123 -0.3 1 124
RIPK1 0.018 0.024 -10000 0 -0.52 1 1
CASP7 -0.013 0.12 0.24 2 -0.68 14 16
FASLG/FAS/FADD/FAF1 -0.013 0.13 0.22 49 -0.3 47 96
MAP2K4 -0.045 0.16 -10000 0 -0.41 47 47
mol:ceramide -0.044 0.14 -10000 0 -0.38 58 58
GSN 0.055 0.11 0.24 122 -0.3 12 134
FASLG/FAS/FADD/FAF1/Caspase 8 -0.013 0.13 -10000 0 -0.36 41 41
FAS -0.026 0.13 -10000 0 -0.42 50 50
BID 0.011 0.065 0.29 15 -0.32 8 23
MAP3K1 -0.017 0.13 0.26 2 -0.37 31 33
MAP3K7 0.015 0.021 -10000 0 -0.26 3 3
RB1 0.054 0.11 0.23 116 -0.29 9 125
CFLAR 0.011 0.064 -10000 0 -0.46 9 9
HGF/MET -0.036 0.14 -10000 0 -0.32 91 91
ARHGDIB 0.044 0.12 0.23 112 -0.29 20 132
FADD -0.002 0.068 -10000 0 -0.26 34 34
actin filament polymerization -0.055 0.11 0.3 12 -0.24 122 134
NFKB1 -0.043 0.08 -10000 0 -0.3 14 14
MAPK8 -0.061 0.19 -10000 0 -0.46 72 72
DFFA 0.066 0.098 0.24 126 -10000 0 126
DNA fragmentation during apoptosis 0.066 0.098 0.23 126 -10000 0 126
FAS/FADD/MET -0.014 0.1 -10000 0 -0.32 39 39
CFLAR/RIP1 0.021 0.05 -10000 0 -0.36 8 8
FAIM3 0 0.096 -10000 0 -0.49 19 19
FAF1 0.013 0.025 -10000 0 -0.52 1 1
PARP1 0.064 0.1 0.24 121 -0.28 5 126
DFFB 0.066 0.098 0.24 126 -10000 0 126
CHUK -0.026 0.092 -10000 0 -0.33 15 15
FASLG -0.066 0.17 -10000 0 -0.38 107 107
FAS/FADD -0.019 0.11 -10000 0 -0.36 36 36
HGF 0.008 0.069 -10000 0 -0.45 11 11
LMNA 0.06 0.095 0.22 112 -0.26 7 119
CASP6 0.062 0.1 0.24 121 -0.27 4 125
CASP10 0.012 0.03 -10000 0 -0.26 6 6
CASP3 0.072 0.12 0.28 127 -10000 0 127
PTPN13 -0.071 0.2 -10000 0 -0.49 93 93
CASP8 0.012 0.066 0.37 17 -10000 0 17
IL6 -0.16 0.4 -10000 0 -1.3 59 59
MET -0.001 0.078 -10000 0 -0.3 31 31
ICAD/CAD 0.066 0.089 0.22 115 -10000 0 115
FASLG/FAS/FADD/FAF1/Caspase 10 -0.045 0.15 -10000 0 -0.38 58 58
activation of caspase activity by cytochrome c 0.011 0.065 0.29 15 -0.32 8 23
PAK2 0.067 0.098 0.24 123 -10000 0 123
BCL2 -0.12 0.22 -10000 0 -0.47 145 145
Noncanonical Wnt signaling 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
NFATC2 0.013 0.048 -9999 0 -0.47 5 5
GNB1/GNG2 -0.11 0.2 -9999 0 -0.42 104 104
mol:DAG -0.094 0.18 -9999 0 -0.44 73 73
PLCG1 -0.097 0.18 -9999 0 -0.46 73 73
YES1 -0.12 0.2 -9999 0 -0.45 106 106
FZD3 -0.031 0.15 -9999 0 -0.48 52 52
FZD6 -0.077 0.2 -9999 0 -0.45 108 108
G protein -0.1 0.19 -9999 0 -0.46 77 77
MAP3K7 -0.069 0.15 -9999 0 -0.39 62 62
mol:Ca2+ -0.091 0.17 -9999 0 -0.43 73 73
mol:IP3 -0.094 0.18 -9999 0 -0.44 73 73
NLK 0.016 0.044 -9999 0 -0.9 1 1
GNB1 0.013 0.052 -9999 0 -0.52 5 5
CAMK2A -0.08 0.16 -9999 0 -0.4 73 73
MAP3K7IP1 0.018 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.13 0.21 -9999 0 -0.34 214 214
CSNK1A1 0.017 0.023 -9999 0 -0.52 1 1
GNAS -0.12 0.2 -9999 0 -0.44 106 106
GO:0007205 -0.093 0.18 -9999 0 -0.43 74 74
WNT6 -0.011 0.088 -9999 0 -0.27 54 54
WNT4 -0.063 0.18 -9999 0 -0.45 90 90
NFAT1/CK1 alpha -0.092 0.19 -9999 0 -0.48 67 67
GNG2 0.016 0.029 -9999 0 -0.35 3 3
WNT5A -0.084 0.2 -9999 0 -0.43 120 120
WNT11 -0.013 0.09 -9999 0 -0.27 57 57
CDC42 -0.11 0.2 -9999 0 -0.42 105 105
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.11 0.3 -10000 0 -0.69 66 66
CRP -0.11 0.3 -10000 0 -0.7 62 62
cell cycle arrest -0.14 0.34 -10000 0 -0.73 97 97
TIMP1 -0.11 0.3 -10000 0 -0.72 71 71
IL6ST -0.11 0.22 -10000 0 -0.46 143 143
Rac1/GDP -0.11 0.22 -10000 0 -0.45 113 113
AP1 -0.05 0.16 -10000 0 -0.43 39 39
GAB2 0.011 0.047 -10000 0 -0.26 16 16
TNFSF11 -0.18 0.41 -10000 0 -0.91 101 101
HSP90B1 0.007 0.11 -10000 0 -0.8 6 6
GAB1 0.007 0.074 -10000 0 -0.42 14 14
MAPK14 -0.11 0.22 -10000 0 -0.48 88 88
AKT1 0.038 0.073 -10000 0 -0.48 3 3
FOXO1 0.036 0.085 -10000 0 -0.45 5 5
MAP2K6 -0.12 0.22 0.27 1 -0.41 149 150
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.11 0.25 -10000 0 -0.52 96 96
MITF -0.11 0.22 0.29 1 -0.4 143 144
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.018 0 -10000 0 -10000 0 0
A2M -0.045 0.28 -10000 0 -1.4 23 23
CEBPB 0.013 0.073 -10000 0 -0.34 20 20
GRB2/SOS1/GAB family/SHP2 -0.018 0.1 -10000 0 -0.41 9 9
STAT3 -0.15 0.37 -10000 0 -0.78 97 97
STAT1 -0.042 0.17 -10000 0 -0.95 16 16
CEBPD -0.16 0.39 -10000 0 -0.91 84 84
PIK3CA 0.017 0.029 -10000 0 -0.34 3 3
PI3K 0.009 0.083 -10000 0 -0.37 21 21
JUN -0.034 0.15 -10000 0 -0.46 57 57
PIAS3/MITF -0.097 0.21 0.27 1 -0.41 118 119
MAPK11 -0.11 0.22 -10000 0 -0.49 85 85
STAT3 (dimer)/FOXO1 -0.085 0.29 -10000 0 -0.61 82 82
GRB2/SOS1/GAB family -0.11 0.18 -10000 0 -0.48 68 68
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.13 0.22 -10000 0 -0.41 149 149
GRB2 0.017 0.024 -10000 0 -0.26 4 4
JAK2 0.01 0.054 -10000 0 -0.32 12 12
LBP -0.1 0.26 -10000 0 -0.59 63 63
PIK3R1 -0.008 0.11 -10000 0 -0.42 32 32
JAK1 0.013 0.058 -10000 0 -0.53 6 6
MYC -0.15 0.37 -10000 0 -0.85 84 84
FGG -0.11 0.3 -10000 0 -0.69 68 68
macrophage differentiation -0.14 0.34 -10000 0 -0.73 97 97
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.13 0.2 -10000 0 -0.37 172 172
JUNB -0.11 0.29 -10000 0 -0.69 64 64
FOS -0.11 0.2 -10000 0 -0.37 171 171
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.12 0.22 0.31 1 -0.42 147 148
STAT1/PIAS1 -0.11 0.22 0.32 1 -0.43 127 128
GRB2/SOS1/GAB family/SHP2/PI3K 0.031 0.067 -10000 0 -0.38 4 4
STAT3 (dimer) -0.15 0.37 -10000 0 -0.77 97 97
PRKCD -0.1 0.27 -10000 0 -0.57 90 90
IL6R 0.002 0.085 -10000 0 -0.38 23 23
SOCS3 -0.1 0.23 -10000 0 -0.68 42 42
gp130 (dimer)/JAK1/JAK1/LMO4 -0.097 0.19 -10000 0 -0.35 171 171
Rac1/GTP -0.11 0.24 -10000 0 -0.47 111 111
HCK -0.005 0.11 -10000 0 -0.47 25 25
MAPKKK cascade 0.008 0.093 -10000 0 -0.55 4 4
bone resorption -0.17 0.38 -10000 0 -0.84 101 101
IRF1 -0.13 0.34 -10000 0 -0.78 73 73
mol:GDP -0.12 0.23 0.29 1 -0.43 138 139
SOS1 0.018 0.024 -10000 0 -0.52 1 1
VAV1 -0.12 0.23 0.29 1 -0.44 138 139
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.12 0.22 -10000 0 -0.5 81 81
PTPN11 0.004 0.058 -10000 0 -1.2 1 1
IL6/IL6RA -0.057 0.14 -10000 0 -0.37 73 73
gp130 (dimer)/TYK2/TYK2/LMO4 -0.096 0.18 -10000 0 -0.34 170 170
gp130 (dimer)/JAK2/JAK2/LMO4 -0.1 0.18 -10000 0 -0.35 175 175
IL6 -0.085 0.18 -10000 0 -0.36 146 146
PIAS3 0.018 0 -10000 0 -10000 0 0
PTPRE 0 0.082 -10000 0 -0.46 15 15
PIAS1 0.017 0.012 -10000 0 -0.26 1 1
RAC1 0.018 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.12 0.18 0.27 1 -0.35 153 154
LMO4 -0.074 0.18 -10000 0 -0.38 124 124
STAT3 (dimer)/PIAS3 -0.14 0.34 -10000 0 -0.72 98 98
MCL1 0.043 0.084 -10000 0 -0.82 2 2
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.058 0.21 -10000 0 -0.46 97 97
FYN -0.085 0.26 -10000 0 -0.55 106 106
LAT/GRAP2/SLP76 -0.099 0.21 -10000 0 -0.47 111 111
IKBKB 0.011 0.047 -10000 0 -0.31 10 10
AKT1 -0.048 0.19 -10000 0 -0.38 111 111
B2M -0.006 0.11 -10000 0 -0.46 26 26
IKBKG 0.002 0.062 -10000 0 -0.13 54 54
MAP3K8 -0.036 0.15 -10000 0 -0.39 69 69
mol:Ca2+ -0.022 0.031 -10000 0 -0.083 67 67
integrin-mediated signaling pathway 0.007 0.067 -10000 0 -0.31 19 19
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.084 0.26 -10000 0 -0.54 112 112
TRPV6 -0.11 0.19 -10000 0 -0.38 159 159
CD28 -0.044 0.16 -10000 0 -0.4 78 78
SHC1 -0.09 0.26 -10000 0 -0.56 103 103
receptor internalization -0.12 0.3 -10000 0 -0.6 123 123
PRF1 -0.081 0.25 -10000 0 -0.76 39 39
KRAS 0.008 0.069 -10000 0 -0.45 11 11
GRB2 0.016 0.024 -10000 0 -0.26 4 4
COT/AKT1 -0.047 0.16 -10000 0 -0.32 109 109
LAT -0.096 0.27 -10000 0 -0.56 112 112
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.028 0.13 -10000 0 -0.35 66 66
CD3E 0.016 0.018 -10000 0 -0.27 2 2
CD3G -0.092 0.2 -10000 0 -0.42 135 135
RASGRP2 -0.002 0.036 -10000 0 -0.15 16 16
RASGRP1 -0.061 0.2 -10000 0 -0.38 126 126
HLA-A -0.013 0.12 -10000 0 -0.44 35 35
RASSF5 -0.002 0.091 -10000 0 -0.38 27 27
RAP1A/GTP/RAPL 0.008 0.067 -10000 0 -0.31 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.004 0.064 -10000 0 -0.12 64 64
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.045 0.078 -10000 0 -0.2 92 92
PRKCA -0.044 0.11 -10000 0 -0.24 96 96
GRAP2 0.011 0.044 -10000 0 -0.28 11 11
mol:IP3 -0.052 0.19 0.22 44 -0.38 100 144
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.081 0.22 -10000 0 -0.46 99 99
ORAI1 0.071 0.11 0.3 68 -0.38 1 69
CSK -0.089 0.26 -10000 0 -0.56 103 103
B7 family/CD28 -0.11 0.3 -10000 0 -0.6 118 118
CHUK 0.005 0.081 -10000 0 -0.5 13 13
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.11 0.3 -10000 0 -0.64 106 106
PTPN6 -0.094 0.26 -10000 0 -0.57 102 102
VAV1 -0.1 0.28 -10000 0 -0.59 107 107
Monovalent TCR/CD3 -0.095 0.22 -10000 0 -0.4 145 145
CBL 0.017 0.012 -10000 0 -0.26 1 1
LCK -0.098 0.28 -10000 0 -0.59 107 107
PAG1 -0.093 0.26 -10000 0 -0.57 104 104
RAP1A 0.011 0.062 -10000 0 -0.52 7 7
TCR/CD3/MHC I/CD8/LCK -0.12 0.3 -10000 0 -0.64 107 107
CD80 0.009 0.049 -10000 0 -0.28 14 14
CD86 -0.009 0.12 -10000 0 -0.5 27 27
PDK1/CARD11/BCL10/MALT1 -0.055 0.095 -10000 0 -0.24 93 93
HRAS 0.012 0.051 -10000 0 -0.41 7 7
GO:0035030 -0.091 0.24 -10000 0 -0.5 118 118
CD8A 0 0.005 -10000 0 -10000 0 0
CD8B 0.001 0.07 -10000 0 -0.28 29 29
PTPRC -0.041 0.16 -10000 0 -0.42 71 71
PDK1/PKC theta -0.061 0.23 -10000 0 -0.47 109 109
CSK/PAG1 -0.08 0.25 -10000 0 -0.54 99 99
SOS1 0.017 0.023 -10000 0 -0.52 1 1
peptide-MHC class I -0.012 0.13 -10000 0 -0.47 33 33
GRAP2/SLP76 -0.086 0.26 -10000 0 -0.55 107 107
STIM1 0.035 0.059 -10000 0 -0.36 2 2
RAS family/GTP -0.002 0.088 -10000 0 -0.17 69 69
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.13 0.33 -10000 0 -0.64 123 123
mol:DAG -0.072 0.15 -10000 0 -0.34 107 107
RAP1A/GDP 0.002 0.032 -10000 0 -0.076 24 24
PLCG1 0.016 0.026 -10000 0 -0.39 2 2
CD247 -0.1 0.21 -10000 0 -0.42 151 151
cytotoxic T cell degranulation -0.077 0.24 -10000 0 -0.69 45 45
RAP1A/GTP -0.005 0.015 -10000 0 -0.076 18 18
mol:PI-3-4-5-P3 -0.064 0.22 -10000 0 -0.45 112 112
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.076 0.23 0.24 39 -0.49 100 139
NRAS 0.006 0.072 -10000 0 -0.4 15 15
ZAP70 0.005 0.061 -10000 0 -0.27 24 24
GRB2/SOS1 0.024 0.024 -10000 0 -0.37 1 1
LAT/GRAP2/SLP76/VAV1 -0.1 0.21 0.16 1 -0.48 110 111
MALT1 0.011 0.054 -10000 0 -0.38 9 9
TRAF6 0.017 0.023 -10000 0 -0.52 1 1
CD8 heterodimer 0.002 0.049 -10000 0 -0.2 29 29
CARD11 0.002 0.078 -10000 0 -0.34 24 24
PRKCB -0.048 0.1 -10000 0 -0.24 107 107
PRKCE -0.045 0.11 -10000 0 -0.24 97 97
PRKCQ -0.079 0.26 -10000 0 -0.53 110 110
LCP2 -0.005 0.1 -10000 0 -0.41 28 28
BCL10 0.017 0.012 -10000 0 -0.26 1 1
regulation of survival gene product expression -0.037 0.16 -10000 0 -0.32 109 109
IKK complex 0.012 0.059 -10000 0 -0.1 51 51
RAS family/GDP -0.008 0.015 -10000 0 -0.064 20 20
MAP3K14 -0.029 0.13 -10000 0 -0.25 91 91
PDPK1 -0.042 0.18 -10000 0 -0.36 107 107
TCR/CD3/MHC I/CD8/Fyn -0.092 0.26 -10000 0 -0.59 93 93
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.007 0.074 -9999 0 -0.5 11 11
LAT2 -0.088 0.18 -9999 0 -0.34 141 141
AP1 -0.14 0.22 -9999 0 -0.48 128 128
mol:PIP3 -0.1 0.22 -9999 0 -0.48 95 95
IKBKB -0.044 0.12 -9999 0 -0.26 85 85
AKT1 -0.067 0.16 -9999 0 -0.4 74 74
IKBKG -0.042 0.12 -9999 0 -0.26 87 87
MS4A2 -0.15 0.23 -9999 0 -0.43 203 203
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.015 0.029 -9999 0 -0.35 3 3
MAP3K1 -0.086 0.2 -9999 0 -0.43 99 99
mol:Ca2+ -0.071 0.16 -9999 0 -0.36 95 95
LYN 0.012 0.033 -9999 0 -0.27 7 7
CBLB -0.086 0.18 -9999 0 -0.34 139 139
SHC1 0.017 0.023 -9999 0 -0.52 1 1
RasGAP/p62DOK -0.013 0.11 -9999 0 -0.3 58 58
positive regulation of cell migration -0.015 0.092 -9999 0 -0.29 48 48
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.088 0.18 -9999 0 -0.39 96 96
PTPN13 -0.12 0.21 -9999 0 -0.55 77 77
PTPN11 0.013 0.027 -9999 0 -0.56 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.046 0.14 -9999 0 -0.32 73 73
SYK -0.024 0.14 -9999 0 -0.49 42 42
GRB2 0.015 0.024 -9999 0 -0.26 4 4
LAT/PLCgamma1/GRB2/SLP76/GADs -0.14 0.2 -9999 0 -0.49 100 100
LAT -0.092 0.18 -9999 0 -0.42 91 91
PAK2 -0.081 0.2 -9999 0 -0.45 88 88
NFATC2 -0.042 0.082 -9999 0 -0.62 5 5
HRAS -0.096 0.21 -9999 0 -0.48 93 93
GAB2 0.009 0.047 -9999 0 -0.26 16 16
PLA2G1B 0.038 0.026 -9999 0 -10000 0 0
Fc epsilon R1 -0.12 0.2 -9999 0 -0.39 168 168
Antigen/IgE/Fc epsilon R1 -0.11 0.19 -9999 0 -0.35 168 168
mol:GDP -0.11 0.22 -9999 0 -0.51 95 95
JUN -0.034 0.15 -9999 0 -0.46 57 57
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 -0.01 0.11 -9999 0 -0.42 32 32
FOS -0.11 0.2 -9999 0 -0.37 171 171
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.097 0.18 -9999 0 -0.36 138 138
CHUK -0.046 0.12 -9999 0 -0.26 93 93
KLRG1 -0.083 0.17 -9999 0 -0.41 75 75
VAV1 -0.1 0.2 -9999 0 -0.45 93 93
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.085 0.18 -9999 0 -0.42 81 81
negative regulation of mast cell degranulation -0.078 0.16 -9999 0 -0.39 75 75
BTK -0.11 0.23 -9999 0 -0.52 93 93
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.13 0.25 -9999 0 -0.47 135 135
GAB2/PI3K/SHP2 -0.1 0.15 -9999 0 -0.44 72 72
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.096 0.2 -9999 0 -0.44 95 95
RAF1 0.029 0.026 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.12 0.21 -9999 0 -0.36 185 185
FCER1G 0.02 0.026 -9999 0 -0.26 4 4
FCER1A -0.074 0.2 -9999 0 -0.51 91 91
Antigen/IgE/Fc epsilon R1/Fyn -0.095 0.18 -9999 0 -0.33 166 166
MAPK3 0.037 0.026 -9999 0 -10000 0 0
MAPK1 0.037 0.026 -9999 0 -10000 0 0
NFKB1 0.017 0.023 -9999 0 -0.52 1 1
MAPK8 -0.02 0.11 -9999 0 -0.48 19 19
DUSP1 -0.038 0.15 -9999 0 -0.41 69 69
NF-kappa-B/RelA -0.039 0.061 -9999 0 -0.18 35 35
actin cytoskeleton reorganization -0.087 0.18 -9999 0 -0.48 65 65
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.091 0.2 -9999 0 -0.45 97 97
FER -0.086 0.18 -9999 0 -0.34 139 139
RELA 0.018 0 -9999 0 -10000 0 0
ITK -0.052 0.13 -9999 0 -0.4 51 51
SOS1 0.017 0.023 -9999 0 -0.52 1 1
PLCG1 -0.1 0.22 -9999 0 -0.51 93 93
cytokine secretion -0.029 0.044 -9999 0 -0.17 3 3
SPHK1 -0.11 0.2 -9999 0 -0.4 121 121
PTK2 -0.091 0.19 -9999 0 -0.5 65 65
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.14 0.21 -9999 0 -0.51 98 98
EDG1 -0.015 0.092 -9999 0 -0.29 48 48
mol:DAG -0.095 0.22 -9999 0 -0.48 98 98
MAP2K2 0.032 0.031 -9999 0 -10000 0 0
MAP2K1 0.033 0.024 -9999 0 -10000 0 0
MAP2K7 0.017 0.023 -9999 0 -0.52 1 1
KLRG1/SHP2 -0.072 0.15 -9999 0 -0.39 70 70
MAP2K4 -0.011 0.16 -9999 0 -0.91 16 16
Fc epsilon R1/FcgammaRIIB -0.12 0.22 -9999 0 -0.38 185 185
mol:Choline -0.086 0.17 -9999 0 -0.39 96 96
SHC/Grb2/SOS1 -0.066 0.17 -9999 0 -0.42 70 70
FYN 0.009 0.063 -9999 0 -0.4 11 11
DOK1 0.002 0.083 -9999 0 -0.41 19 19
PXN -0.078 0.18 -9999 0 -0.46 65 65
HCLS1 -0.095 0.19 -9999 0 -0.43 94 94
PRKCB -0.069 0.16 -9999 0 -0.35 99 99
FCGR2B -0.032 0.15 -9999 0 -0.5 51 51
IGHE -0.003 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.08 0.16 -9999 0 -0.4 75 75
LCP2 -0.005 0.1 -9999 0 -0.41 28 28
PLA2G4A -0.11 0.21 -9999 0 -0.45 110 110
RASA1 0.004 0.079 -9999 0 -0.42 16 16
mol:Phosphatidic acid -0.086 0.17 -9999 0 -0.39 96 96
IKK complex -0.023 0.098 -9999 0 -0.2 72 72
WIPF1 0.005 0.076 -9999 0 -0.41 16 16
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0 0.058 -10000 0 -0.26 23 23
ARNO/beta Arrestin1-2 -0.013 0.09 -10000 0 -0.24 56 56
EGFR -0.077 0.17 -10000 0 -0.35 136 136
EPHA2 0.008 0.06 -10000 0 -0.33 14 14
USP6 0.011 0.041 -10000 0 -0.26 12 12
IQSEC1 0.016 0.026 -10000 0 -0.39 2 2
EGFR/EGFR/EGF/EGF -0.15 0.2 -10000 0 -0.42 172 172
ARRB2 0.011 0.052 -10000 0 -0.32 12 12
mol:GTP 0.006 0.015 0.063 11 -0.093 5 16
ARRB1 0.004 0.075 -10000 0 -0.38 18 18
FBXO8 0.015 0.04 -10000 0 -0.52 3 3
TSHR 0.008 0.071 -10000 0 -0.5 10 10
EGF -0.14 0.23 -10000 0 -0.42 193 193
somatostatin receptor activity 0 0 -10000 0 -0.001 106 106
ARAP2 0 0 -10000 0 0 118 118
mol:GDP -0.054 0.11 -10000 0 -0.25 92 92
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 109 109
ITGA2B 0.016 0.021 -10000 0 -0.26 3 3
ARF6 0.016 0.033 -10000 0 -0.52 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.025 0.071 -10000 0 -0.27 24 24
ADAP1 0 0 -10000 0 0 94 94
KIF13B -0.002 0.095 -10000 0 -0.43 23 23
HGF/MET 0.006 0.075 -10000 0 -0.38 14 14
PXN 0.018 0 -10000 0 -10000 0 0
ARF6/GTP -0.067 0.11 -10000 0 -0.26 106 106
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.12 0.18 -10000 0 -0.35 172 172
ADRB2 -0.045 0.16 -10000 0 -0.4 80 80
receptor agonist activity 0 0 -10000 0 0 106 106
actin filament binding 0 0 -10000 0 0 110 110
SRC 0.015 0.035 -10000 0 -0.43 3 3
ITGB3 0.002 0.076 -10000 0 -0.32 25 25
GNAQ 0 0 -10000 0 -0.001 100 100
EFA6/PI-4-5-P2 0 0 -10000 0 -0.001 97 97
ARF6/GDP -0.003 0.059 -10000 0 -0.24 10 10
ARF6/GDP/GULP/ACAP1 -0.057 0.13 -10000 0 -0.3 94 94
alphaIIb/beta3 Integrin/paxillin/GIT1 0.034 0.048 -10000 0 -0.26 8 8
ACAP1 0 0 -10000 0 0 30 30
ACAP2 0 0 -10000 0 0 117 117
LHCGR/beta Arrestin2 0.009 0.07 -10000 0 -0.44 12 12
EFNA1 0 0.094 -10000 0 -0.49 18 18
HGF 0.008 0.069 -10000 0 -0.45 11 11
CYTH3 0 0 -10000 0 -0.001 108 108
CYTH2 -0.001 0.002 -10000 0 -0.004 112 112
NCK1 0.011 0.046 -10000 0 -0.28 12 12
fibronectin binding 0 0 -10000 0 0 90 90
endosomal lumen acidification 0 0 -10000 0 0 103 103
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.033 0.15 -10000 0 -0.44 59 59
GNAQ/ARNO -0.001 0.003 -10000 0 -0.006 96 96
mol:Phosphatidic acid 0 0 -10000 0 0 117 117
PIP3-E 0.004 0.069 -10000 0 -0.3 23 23
MET -0.001 0.078 -10000 0 -0.3 31 31
GNA14 -0.081 0.18 -10000 0 -0.35 141 141
GNA15 0.001 0.078 -10000 0 -0.33 25 25
GIT1 0.014 0.035 -10000 0 -0.3 6 6
mol:PI-4-5-P2 0 0 -10000 0 -0.001 100 100
GNA11 0.013 0.047 -10000 0 -0.52 4 4
LHCGR 0.003 0.083 -10000 0 -0.46 16 16
AGTR1 -0.15 0.21 -10000 0 -0.36 229 229
desensitization of G-protein coupled receptor protein signaling pathway 0.009 0.07 -10000 0 -0.44 12 12
IPCEF1/ARNO -0.095 0.14 -10000 0 -0.28 178 178
alphaIIb/beta3 Integrin 0.014 0.056 -10000 0 -0.36 7 7
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.24 0.54 -10000 0 -1.2 91 91
IL23A -0.21 0.49 -10000 0 -1.1 82 82
NF kappa B1 p50/RelA/I kappa B alpha -0.22 0.42 -10000 0 -0.99 95 95
positive regulation of T cell mediated cytotoxicity -0.21 0.51 -10000 0 -1.1 94 94
ITGA3 -0.2 0.48 -10000 0 -1.1 84 84
IL17F -0.1 0.32 -10000 0 -0.68 77 77
IL12B 0.003 0.084 -10000 0 -0.36 21 21
STAT1 (dimer) -0.22 0.49 -10000 0 -1.1 95 95
CD4 -0.18 0.44 -10000 0 -1 71 71
IL23 -0.21 0.47 -10000 0 -1.1 84 84
IL23R -0.013 0.18 -10000 0 -1.4 7 7
IL1B -0.24 0.53 -10000 0 -1.2 89 89
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.18 0.44 -10000 0 -1.1 71 71
TYK2 0.013 0.024 -10000 0 -10000 0 0
STAT4 -0.023 0.13 -10000 0 -0.42 49 49
STAT3 0.015 0.041 -10000 0 -0.52 3 3
IL18RAP -0.078 0.19 -10000 0 -0.41 117 117
IL12RB1 0.013 0.024 -10000 0 -10000 0 0
PIK3CA 0.016 0.029 -10000 0 -0.34 3 3
IL12Rbeta1/TYK2 0.017 0.03 -10000 0 -10000 0 0
IL23R/JAK2 -0.014 0.19 -10000 0 -1 10 10
positive regulation of chronic inflammatory response -0.21 0.51 -10000 0 -1.1 94 94
natural killer cell activation 0.002 0.012 0.073 8 -10000 0 8
JAK2 0.01 0.065 -10000 0 -0.34 12 12
PIK3R1 -0.008 0.11 -10000 0 -0.42 32 32
NFKB1 0.016 0.024 -10000 0 -0.52 1 1
RELA 0.017 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.2 0.45 -10000 0 -1 85 85
ALOX12B -0.18 0.44 -10000 0 -1 72 72
CXCL1 -0.27 0.54 -10000 0 -1.1 125 125
T cell proliferation -0.21 0.51 -10000 0 -1.1 94 94
NFKBIA 0.014 0.043 -10000 0 -0.46 4 4
IL17A -0.055 0.26 -10000 0 -0.54 61 61
PI3K -0.19 0.47 -10000 0 -1 94 94
IFNG -0.028 0.05 0.12 2 -0.13 54 56
STAT3 (dimer) -0.21 0.42 -10000 0 -0.97 95 95
IL18R1 -0.014 0.11 -10000 0 -0.41 37 37
IL23/IL23R/JAK2/TYK2/SOCS3 -0.083 0.28 -10000 0 -0.59 65 65
IL18/IL18R -0.085 0.2 -10000 0 -0.41 117 117
macrophage activation -0.015 0.017 -10000 0 -0.043 83 83
TNF -0.21 0.49 -10000 0 -1.2 78 78
STAT3/STAT4 -0.24 0.45 -10000 0 -1 100 100
STAT4 (dimer) -0.22 0.5 -10000 0 -1.1 99 99
IL18 -0.052 0.17 -10000 0 -0.44 78 78
IL19 -0.19 0.44 -10000 0 -1 81 81
STAT5A (dimer) -0.21 0.49 -10000 0 -1.1 94 94
STAT1 -0.02 0.12 -10000 0 -0.33 58 58
SOCS3 0.005 0.074 -10000 0 -0.38 17 17
CXCL9 -0.28 0.56 -10000 0 -1.2 125 125
MPO -0.18 0.44 -10000 0 -1 73 73
positive regulation of humoral immune response -0.21 0.51 -10000 0 -1.1 94 94
IL23/IL23R/JAK2/TYK2 -0.23 0.54 -10000 0 -1.2 94 94
IL6 -0.27 0.55 -10000 0 -1.2 101 101
STAT5A 0.011 0.056 -10000 0 -0.42 8 8
IL2 0.008 0.053 -10000 0 -0.35 10 10
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.012 0.073 8 -10000 0 8
CD3E -0.18 0.44 -10000 0 -1 81 81
keratinocyte proliferation -0.21 0.51 -10000 0 -1.1 94 94
NOS2 -0.18 0.44 -10000 0 -0.96 95 95
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.03 0.12 -10000 0 -0.36 29 29
TBX21 -0.3 0.59 -10000 0 -1.3 124 124
B2M -0.006 0.1 -10000 0 -0.45 26 26
TYK2 0.012 0.022 -10000 0 -10000 0 0
IL12RB1 0.012 0.022 -10000 0 -10000 0 0
GADD45B -0.18 0.44 -10000 0 -1 89 89
IL12RB2 -0.076 0.16 -10000 0 -0.32 141 141
GADD45G -0.18 0.43 -10000 0 -1.1 83 83
natural killer cell activation -0.005 0.024 -10000 0 -10000 0 0
RELB 0.003 0.079 -10000 0 -0.38 19 19
RELA 0.018 0 -10000 0 -10000 0 0
IL18 -0.048 0.17 -10000 0 -0.44 78 78
IL2RA -0.031 0.14 -10000 0 -0.41 61 61
IFNG -0.089 0.17 -10000 0 -0.33 161 161
STAT3 (dimer) -0.14 0.37 -10000 0 -0.78 108 108
HLA-DRB5 -0.004 0.098 -10000 0 -0.51 19 19
FASLG -0.24 0.52 -10000 0 -1.1 110 110
NF kappa B2 p52/RelB -0.24 0.41 -10000 0 -0.89 123 123
CD4 0.015 0.007 -10000 0 -10000 0 0
SOCS1 0.015 0.031 -10000 0 -0.32 4 4
EntrezGene:6955 -0.005 0.012 -10000 0 -10000 0 0
CD3D -0.032 0.13 -10000 0 -0.35 66 66
CD3E 0.013 0.021 -10000 0 -0.28 2 2
CD3G -0.097 0.2 -10000 0 -0.42 135 135
IL12Rbeta2/JAK2 -0.048 0.13 -10000 0 -0.3 79 79
CCL3 -0.2 0.44 -10000 0 -1 95 95
CCL4 -0.2 0.46 -10000 0 -1 102 102
HLA-A -0.013 0.12 -10000 0 -0.43 35 35
IL18/IL18R -0.059 0.22 -10000 0 -0.41 117 117
NOS2 -0.19 0.43 -10000 0 -0.86 124 124
IL12/IL12R/TYK2/JAK2/SPHK2 -0.03 0.12 -10000 0 -0.36 28 28
IL1R1 -0.25 0.51 -10000 0 -1.1 119 119
IL4 0.016 0.063 -10000 0 -0.48 7 7
JAK2 0.004 0.06 -10000 0 -0.34 12 12
EntrezGene:6957 -0.004 0.011 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.13 0.33 -10000 0 -0.66 100 100
RAB7A -0.12 0.34 -10000 0 -0.8 84 84
lysosomal transport -0.12 0.33 -10000 0 -0.75 84 84
FOS -0.29 0.49 -10000 0 -1 139 139
STAT4 (dimer) -0.18 0.43 -10000 0 -0.88 117 117
STAT5A (dimer) -0.27 0.42 -10000 0 -0.9 132 132
GZMA -0.2 0.43 -10000 0 -0.87 125 125
GZMB -0.28 0.57 -10000 0 -1.2 119 119
HLX 0.005 0.079 -10000 0 -0.48 13 13
LCK -0.25 0.52 -10000 0 -1 134 134
TCR/CD3/MHC II/CD4 -0.11 0.23 -10000 0 -0.47 116 116
IL2/IL2R -0.015 0.14 -10000 0 -0.35 61 61
MAPK14 -0.18 0.44 -10000 0 -0.95 102 102
CCR5 -0.19 0.46 -10000 0 -1.1 92 92
IL1B -0.053 0.17 -10000 0 -0.42 81 81
STAT6 -0.067 0.18 -10000 0 -0.35 93 93
STAT4 -0.023 0.13 -10000 0 -0.42 49 49
STAT3 0.015 0.04 -10000 0 -0.52 3 3
STAT1 -0.02 0.12 -10000 0 -0.33 58 58
NFKB1 0.017 0.023 -10000 0 -0.52 1 1
NFKB2 0.015 0.031 -10000 0 -0.32 4 4
IL12B 0 0.078 -10000 0 -0.35 21 21
CD8A -0.001 0.008 -10000 0 -10000 0 0
CD8B 0.001 0.071 -10000 0 -0.28 29 29
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.029 0.12 0.35 29 -10000 0 29
IL2RB -0.017 0.12 -10000 0 -0.44 40 40
proteasomal ubiquitin-dependent protein catabolic process -0.16 0.38 -10000 0 -0.79 116 116
IL2RG -0.003 0.079 -10000 0 -0.29 35 35
IL12 -0.012 0.09 -10000 0 -0.29 26 26
STAT5A 0.011 0.056 -10000 0 -0.42 8 8
CD247 -0.11 0.21 -10000 0 -0.42 151 151
IL2 0.011 0.051 -10000 0 -0.34 10 10
SPHK2 0.016 0.033 -10000 0 -0.52 2 2
FRAP1 0.018 0 -10000 0 -10000 0 0
IL12A -0.02 0.097 -10000 0 -0.28 56 56
IL12/IL12R/TYK2/JAK2 -0.25 0.54 -10000 0 -1.1 124 124
MAP2K3 -0.18 0.44 -10000 0 -0.96 102 102
RIPK2 0.013 0.041 -10000 0 -0.29 9 9
MAP2K6 -0.19 0.45 -10000 0 -0.97 105 105
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.002 0.08 -10000 0 -0.52 12 12
IL18RAP -0.074 0.19 -10000 0 -0.41 117 117
IL12Rbeta1/TYK2 0.018 0.032 -10000 0 -10000 0 0
EOMES -0.057 0.26 -10000 0 -1.3 20 20
STAT1 (dimer) -0.2 0.39 -10000 0 -0.79 126 126
T cell proliferation -0.12 0.31 -10000 0 -0.66 106 106
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.01 0.12 -10000 0 -0.41 37 37
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.2 0.3 -10000 0 -0.72 109 109
ATF2 -0.15 0.4 -10000 0 -0.86 100 100
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.063 0.17 -9999 0 -0.44 49 49
NF kappa B1 p50/RelA/I kappa B alpha -0.044 0.18 -9999 0 -0.49 43 43
alphaV/beta3 Integrin/Osteopontin/Src -0.099 0.19 -9999 0 -0.39 134 134
AP1 -0.15 0.26 -9999 0 -0.58 102 102
ILK -0.065 0.16 -9999 0 -0.42 43 43
bone resorption -0.056 0.17 -9999 0 -0.44 44 44
PTK2B 0.017 0.017 -9999 0 -0.26 2 2
PYK2/p130Cas -0.059 0.17 -9999 0 -0.41 53 53
ITGAV -0.002 0.1 -9999 0 -0.49 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.006 0.082 -9999 0 -0.37 22 22
alphaV/beta3 Integrin/Osteopontin -0.078 0.18 -9999 0 -0.33 145 145
MAP3K1 -0.091 0.18 -9999 0 -0.32 168 168
JUN -0.034 0.15 -9999 0 -0.46 57 57
MAPK3 -0.064 0.17 -9999 0 -0.47 46 46
MAPK1 -0.064 0.17 -9999 0 -0.47 47 47
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
NFKB1 0.017 0.023 -9999 0 -0.52 1 1
MAPK8 -0.081 0.17 -9999 0 -0.41 67 67
ITGB3 0.003 0.078 -9999 0 -0.32 25 25
NFKBIA -0.064 0.19 -9999 0 -0.52 48 48
FOS -0.11 0.2 -9999 0 -0.37 171 171
CD44 -0.004 0.1 -9999 0 -0.43 26 26
CHUK 0.005 0.081 -9999 0 -0.5 13 13
PLAU -0.14 0.37 -9999 0 -1.1 56 56
NF kappa B1 p50/RelA -0.047 0.19 -9999 0 -0.52 45 45
BCAR1 0.017 0.012 -9999 0 -0.26 1 1
RELA 0.018 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.003 0.1 -9999 0 -0.42 23 23
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.086 0.18 -9999 0 -0.32 163 163
VAV3 -0.12 0.2 -9999 0 -0.44 97 97
MAP3K14 -0.07 0.17 -9999 0 -0.31 140 140
ROCK2 0.012 0.053 -9999 0 -0.48 6 6
SPP1 -0.14 0.23 -9999 0 -0.43 188 188
RAC1 0.018 0 -9999 0 -10000 0 0
Rac1/GTP -0.11 0.18 -9999 0 -0.41 89 89
MMP2 -0.13 0.24 -9999 0 -0.54 100 100
Thromboxane A2 receptor 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
TGM2 -0.014 0.11 -10000 0 -0.38 42 42
GNB1/GNG2 -0.058 0.077 -10000 0 -0.18 141 141
AKT1 -0.024 0.12 -10000 0 -0.2 139 139
EGF -0.14 0.23 -10000 0 -0.42 193 193
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.03 0.061 -10000 0 -0.29 5 5
mol:Ca2+ -0.049 0.17 -10000 0 -0.29 142 142
LYN 0.029 0.062 -10000 0 -0.29 5 5
RhoA/GTP -0.041 0.056 -10000 0 -0.12 142 142
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.067 0.19 -10000 0 -0.35 143 143
GNG2 0.016 0.029 -10000 0 -0.35 3 3
ARRB2 0.018 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.005 0.1 -10000 0 -0.39 22 22
G beta5/gamma2 -0.076 0.1 -10000 0 -0.24 140 140
PRKCH -0.063 0.19 -10000 0 -0.35 141 141
DNM1 0.012 0.052 -10000 0 -0.39 8 8
TXA2/TP beta/beta Arrestin3 0.002 0.02 -10000 0 -0.23 2 2
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.002 0.088 -10000 0 -0.35 29 29
G12 family/GTP -0.097 0.13 -10000 0 -0.3 142 142
ADRBK1 0.018 0 -10000 0 -10000 0 0
ADRBK2 0.002 0.088 -10000 0 -0.49 16 16
RhoA/GTP/ROCK1 0.016 0.05 -10000 0 -0.31 12 12
mol:GDP 0.019 0.12 0.32 23 -10000 0 23
mol:NADP 0.017 0.012 -10000 0 -0.26 1 1
RAB11A 0.016 0.029 -10000 0 -0.35 3 3
PRKG1 0.017 0.012 -10000 0 -0.26 1 1
mol:IP3 -0.068 0.2 -10000 0 -0.37 142 142
cell morphogenesis 0.016 0.05 -10000 0 -0.31 12 12
PLCB2 -0.1 0.26 -10000 0 -0.5 142 142
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.016 0.073 -10000 0 -0.31 6 6
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.02 0.085 -10000 0 -0.38 12 12
RHOA 0.005 0.08 -10000 0 -0.52 12 12
PTGIR 0.016 0.033 -10000 0 -0.52 2 2
PRKCB1 -0.082 0.22 -10000 0 -0.4 144 144
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.017 0.012 -10000 0 -0.26 1 1
TXA2/TXA2-R family -0.11 0.27 -10000 0 -0.52 141 141
LCK -0.008 0.11 -10000 0 -0.33 21 21
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.034 0.044 -10000 0 -0.36 2 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.029 0.062 -10000 0 -0.56 5 5
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.034 0.044 -10000 0 -0.36 2 2
MAPK14 -0.034 0.13 -10000 0 -0.23 139 139
TGM2/GTP -0.08 0.23 -10000 0 -0.41 150 150
MAPK11 -0.033 0.14 -10000 0 -0.23 139 139
ARHGEF1 -0.021 0.1 -10000 0 -0.17 138 138
GNAI2 0.006 0.075 -10000 0 -0.48 12 12
JNK cascade -0.07 0.21 -10000 0 -0.38 144 144
RAB11/GDP 0.016 0.028 -10000 0 -0.34 3 3
ICAM1 -0.053 0.17 -10000 0 -0.3 141 141
cAMP biosynthetic process -0.063 0.19 -10000 0 -0.34 149 149
Gq family/GTP/EBP50 -0.039 0.11 -10000 0 -0.25 95 95
actin cytoskeleton reorganization 0.016 0.05 -10000 0 -0.31 12 12
SRC 0.029 0.062 -10000 0 -0.27 6 6
GNB5 0.005 0.081 -10000 0 -0.5 13 13
GNB1 0.013 0.052 -10000 0 -0.52 5 5
EGF/EGFR -0.027 0.11 -10000 0 -0.28 47 47
VCAM1 -0.055 0.17 -10000 0 -0.31 145 145
TP beta/Gq family/GDP/G beta5/gamma2 -0.005 0.1 -10000 0 -0.39 22 22
platelet activation -0.043 0.17 -10000 0 -0.3 141 141
PGI2/IP 0.012 0.024 -10000 0 -0.38 2 2
PRKACA 0.015 0.046 -10000 0 -0.26 12 12
Gq family/GDP/G beta5/gamma2 -0.005 0.096 -10000 0 -0.36 22 22
TXA2/TP beta/beta Arrestin2 -0.006 0.049 -10000 0 -0.54 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.021 0.044 -10000 0 -0.24 12 12
mol:DAG -0.08 0.22 -10000 0 -0.41 142 142
EGFR -0.077 0.17 -10000 0 -0.35 136 136
TXA2/TP alpha -0.092 0.25 -10000 0 -0.46 142 142
Gq family/GTP -0.039 0.079 -10000 0 -0.24 60 60
YES1 0.026 0.07 -10000 0 -0.28 11 11
GNAI2/GTP -0.015 0.055 -10000 0 -0.27 10 10
PGD2/DP -0.001 0.063 -10000 0 -0.24 29 29
SLC9A3R1 -0.044 0.16 -10000 0 -0.44 71 71
FYN 0.027 0.072 -10000 0 -0.33 10 10
mol:NO 0.017 0.012 -10000 0 -0.26 1 1
GNA15 0.001 0.078 -10000 0 -0.33 25 25
PGK/cGMP 0.023 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.006 0.079 -10000 0 -0.51 12 12
TP alpha/TGM2/GDP/G beta/gamma 0.029 0.076 -10000 0 -0.36 6 6
NOS3 0.017 0.012 -10000 0 -0.26 1 1
RAC1 0.018 0 -10000 0 -10000 0 0
PRKCA -0.062 0.19 -10000 0 -0.34 141 141
PRKCB -0.065 0.19 -10000 0 -0.35 142 142
PRKCE -0.063 0.19 -10000 0 -0.35 140 140
PRKCD -0.069 0.2 -10000 0 -0.37 141 141
PRKCG -0.07 0.2 -10000 0 -0.37 142 142
muscle contraction -0.097 0.25 -10000 0 -0.48 143 143
PRKCZ -0.061 0.18 -10000 0 -0.33 144 144
ARR3 0.017 0.012 -10000 0 -0.26 1 1
TXA2/TP beta 0.028 0.059 -10000 0 -0.23 15 15
PRKCQ -0.069 0.2 -10000 0 -0.35 147 147
MAPKKK cascade -0.087 0.23 -10000 0 -0.44 143 143
SELE -0.078 0.2 -10000 0 -0.38 146 146
TP beta/GNAI2/GDP/G beta/gamma 0.038 0.068 -10000 0 -0.37 7 7
ROCK1 0.018 0 -10000 0 -10000 0 0
GNA14 -0.081 0.18 -10000 0 -0.35 141 141
chemotaxis -0.13 0.31 -10000 0 -0.6 141 141
GNA12 0.018 0 -10000 0 -10000 0 0
GNA13 0.009 0.059 -10000 0 -0.38 11 11
GNA11 0.014 0.047 -10000 0 -0.52 4 4
Rac1/GTP 0.013 0.002 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.03 -10000 0 -0.46 2 2
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.17 0.26 0.64 91 -10000 0 91
IL27/IL27R/JAK1 -0.2 0.35 -10000 0 -0.97 65 65
TBX21 -0.22 0.3 -10000 0 -0.62 146 146
IL12B 0.001 0.075 -10000 0 -0.35 21 21
IL12A -0.01 0.066 -10000 0 -0.19 56 56
IL6ST -0.12 0.22 -10000 0 -0.47 143 143
IL27RA/JAK1 -0.11 0.32 -10000 0 -1.2 38 38
IL27 -0.083 0.2 -10000 0 -0.5 99 99
TYK2 0.011 0.011 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.006 0.11 -10000 0 -1.4 1 1
T-helper 2 cell differentiation 0.17 0.26 0.64 91 -10000 0 91
T cell proliferation during immune response 0.17 0.26 0.64 91 -10000 0 91
MAPKKK cascade -0.17 0.26 -10000 0 -0.64 91 91
STAT3 0.015 0.04 -10000 0 -0.52 3 3
STAT2 0.018 0 -10000 0 -10000 0 0
STAT1 -0.021 0.12 -10000 0 -0.33 58 58
IL12RB1 0.017 0.003 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.21 0.28 -10000 0 -0.61 134 134
IL27/IL27R/JAK2/TYK2 -0.17 0.26 -10000 0 -0.65 91 91
positive regulation of T cell mediated cytotoxicity -0.17 0.26 -10000 0 -0.64 91 91
STAT1 (dimer) -0.27 0.39 0.48 7 -0.98 86 93
JAK2 0.004 0.055 -10000 0 -0.34 12 12
JAK1 0.011 0.057 -10000 0 -0.52 6 6
STAT2 (dimer) -0.16 0.25 -10000 0 -0.62 88 88
T cell proliferation -0.2 0.27 -10000 0 -0.66 99 99
IL12/IL12R/TYK2/JAK2 -0.034 0.15 -10000 0 -0.9 8 8
IL17A -0.006 0.11 -10000 0 -1.4 1 1
mast cell activation 0.17 0.26 0.64 91 -10000 0 91
IFNG -0.032 0.047 -10000 0 -0.12 74 74
T cell differentiation -0.01 0.009 0.024 1 -0.023 125 126
STAT3 (dimer) -0.16 0.25 -10000 0 -0.62 89 89
STAT5A (dimer) -0.16 0.26 -10000 0 -0.63 90 90
STAT4 (dimer) -0.17 0.27 -10000 0 -0.62 107 107
STAT4 -0.023 0.13 -10000 0 -0.42 49 49
T cell activation 0.002 0.038 0.12 37 -10000 0 37
IL27R/JAK2/TYK2 -0.16 0.33 -10000 0 -1 50 50
GATA3 -0.25 0.55 -10000 0 -1.3 119 119
IL18 -0.036 0.12 -10000 0 -0.31 78 78
positive regulation of mast cell cytokine production -0.15 0.25 -10000 0 -0.61 89 89
IL27/EBI3 -0.061 0.16 -10000 0 -0.39 92 92
IL27RA -0.12 0.34 -10000 0 -1.3 37 37
IL6 -0.079 0.18 -10000 0 -0.51 60 60
STAT5A 0.011 0.056 -10000 0 -0.42 8 8
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 0.054 0.16 0.49 37 -1.2 3 40
IL1B -0.034 0.12 -10000 0 -0.29 81 81
EBI3 0.001 0.071 -10000 0 -0.44 12 12
TNF -0.003 0.067 -10000 0 -0.25 31 31
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.027 0.13 -10000 0 -0.26 111 111
epithelial cell differentiation -0.007 0.1 -10000 0 -0.26 76 76
CYFIP2 -0.042 0.16 -10000 0 -0.46 65 65
ENAH 0.012 0.097 -10000 0 -0.31 14 14
EGFR -0.077 0.17 -10000 0 -0.35 136 136
EPHA2 0.008 0.06 -10000 0 -0.33 14 14
MYO6 -0.013 0.11 -10000 0 -0.25 92 92
CTNNB1 0.001 0.09 -10000 0 -0.45 19 19
ABI1/Sra1/Nap1 -0.003 0.1 -10000 0 -0.31 52 52
AQP5 -0.086 0.19 -10000 0 -0.46 87 87
CTNND1 0.016 0.029 -10000 0 -0.35 3 3
mol:PI-4-5-P2 -0.005 0.1 -10000 0 -0.24 78 78
regulation of calcium-dependent cell-cell adhesion -0.015 0.1 -10000 0 -0.24 82 82
EGF -0.14 0.23 -10000 0 -0.42 193 193
NCKAP1 0.015 0.031 -10000 0 -0.32 4 4
AQP3 -0.089 0.2 -10000 0 -0.47 98 98
cortical microtubule organization -0.007 0.1 -10000 0 -0.26 76 76
GO:0000145 -0.006 0.095 -10000 0 -0.23 78 78
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.005 0.11 -10000 0 -0.26 76 76
MLLT4 -0.006 0.11 -10000 0 -0.46 26 26
ARF6/GDP -0.04 0.086 -10000 0 -0.39 12 12
ARF6 0.016 0.033 -10000 0 -0.52 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.025 0.071 -10000 0 -0.27 24 24
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.007 0.12 -10000 0 -0.44 15 15
PVRL2 0.002 0.089 -10000 0 -0.52 15 15
ZYX -0.009 0.11 -10000 0 -0.24 84 84
ARF6/GTP 0.03 0.072 -10000 0 -0.27 24 24
CDH1 -0.049 0.17 -10000 0 -0.48 71 71
EGFR/EGFR/EGF/EGF -0.13 0.14 -10000 0 -0.3 185 185
RhoA/GDP -0.01 0.11 -10000 0 -0.25 85 85
actin cytoskeleton organization -0.008 0.11 -10000 0 -0.24 76 76
IGF-1R heterotetramer -0.083 0.2 -10000 0 -0.47 110 110
GIT1 0.014 0.035 -10000 0 -0.3 6 6
IGF1R -0.083 0.2 -10000 0 -0.47 110 110
IGF1 -0.1 0.21 -10000 0 -0.42 146 146
DIAPH1 -0.054 0.18 -10000 0 -0.58 52 52
Wnt receptor signaling pathway 0.007 0.1 0.26 76 -10000 0 76
RHOA 0.005 0.08 -10000 0 -0.52 12 12
RhoA/GTP -0.044 0.089 -10000 0 -0.37 16 16
CTNNA1 0.017 0.023 -10000 0 -0.52 1 1
VCL -0.008 0.11 -10000 0 -0.24 76 76
EFNA1 0 0.094 -10000 0 -0.49 18 18
LPP -0.004 0.1 -10000 0 -0.4 7 7
Ephrin A1/EPHA2 -0.045 0.094 -10000 0 -0.24 91 91
SEC6/SEC8 -0.045 0.092 -10000 0 -0.41 10 10
MGAT3 -0.015 0.11 -10000 0 -0.25 82 82
HGF/MET -0.044 0.089 -10000 0 -0.23 88 88
HGF 0.008 0.069 -10000 0 -0.45 11 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.028 0.13 -10000 0 -0.26 111 111
actin cable formation 0.017 0.1 -10000 0 -0.28 21 21
KIAA1543 0.001 0.1 -10000 0 -0.23 79 79
KIFC3 -0.005 0.1 -10000 0 -0.24 77 77
NCK1 0.011 0.046 -10000 0 -0.28 12 12
EXOC3 0.017 0.012 -10000 0 -0.26 1 1
ACTN1 -0.009 0.11 -10000 0 -0.24 85 85
NCK1/GIT1 0.019 0.042 -10000 0 -0.44 2 2
mol:GDP -0.007 0.1 -10000 0 -0.26 76 76
EXOC4 0.016 0.033 -10000 0 -0.52 2 2
STX4 -0.003 0.1 -10000 0 -0.24 76 76
PIP5K1C -0.005 0.1 -10000 0 -0.24 78 78
LIMA1 -0.025 0.15 -10000 0 -0.52 42 42
ABI1 0.016 0.021 -10000 0 -0.26 3 3
ROCK1 0.009 0.1 -10000 0 -0.32 16 16
adherens junction assembly 0.012 0.1 -10000 0 -0.37 11 11
IGF-1R heterotetramer/IGF1 -0.12 0.16 -10000 0 -0.43 73 73
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.002 0.1 -10000 0 -0.39 33 33
MET -0.001 0.078 -10000 0 -0.3 31 31
PLEKHA7 -0.003 0.099 -10000 0 -0.24 77 77
mol:GTP 0.024 0.071 -10000 0 -0.27 24 24
establishment of epithelial cell apical/basal polarity 0.005 0.11 -10000 0 -0.41 10 10
cortical actin cytoskeleton stabilization -0.027 0.13 -10000 0 -0.26 111 111
regulation of cell-cell adhesion -0.008 0.11 -10000 0 -0.24 76 76
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.028 0.13 -10000 0 -0.26 111 111
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.011 0.02 -10000 0 -0.24 3 3
GNB1/GNG2 -0.031 0.13 -10000 0 -0.28 107 107
regulation of S phase of mitotic cell cycle -0.031 0.12 -10000 0 -0.24 120 120
GNAO1 0.015 0.024 -10000 0 -0.26 4 4
HRAS 0.011 0.051 -10000 0 -0.41 7 7
SHBG/T-DHT 0.012 0 -10000 0 -10000 0 0
PELP1 0.017 0.001 -10000 0 -10000 0 0
AKT1 0.008 0.038 -10000 0 -0.26 9 9
MAP2K1 -0.032 0.12 -10000 0 -0.32 32 32
T-DHT/AR -0.064 0.16 -10000 0 -0.38 104 104
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.005 165 165
GNAI2 0.006 0.075 -10000 0 -0.48 12 12
GNAI3 0.017 0.023 -10000 0 -0.52 1 1
GNAI1 -0.015 0.12 -10000 0 -0.38 44 44
mol:GDP -0.088 0.17 -10000 0 -0.42 108 108
cell proliferation -0.066 0.18 -10000 0 -0.41 82 82
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
FOS -0.13 0.29 -10000 0 -0.78 80 80
mol:Ca2+ -0.014 0.022 -10000 0 -0.06 70 70
MAPK3 -0.05 0.14 -10000 0 -0.42 32 32
MAPK1 -0.029 0.092 -10000 0 -0.27 26 26
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
mol:IP3 -0.001 0.002 -10000 0 -0.003 171 171
cAMP biosynthetic process 0.013 0.021 -10000 0 -10000 0 0
GNG2 0.016 0.029 -10000 0 -0.35 3 3
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.003 171 171
HRAS/GTP -0.036 0.12 -10000 0 -0.26 107 107
actin cytoskeleton reorganization -0.01 0.049 -10000 0 -0.24 21 21
SRC 0.015 0.035 -10000 0 -0.44 3 3
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.003 171 171
PI3K 0.007 0.07 -10000 0 -0.31 21 21
apoptosis 0.063 0.17 0.41 81 -10000 0 81
T-DHT/AR/PELP1 -0.044 0.13 -10000 0 -0.32 103 103
HRAS/GDP -0.063 0.18 -10000 0 -0.4 105 105
CREB1 -0.069 0.18 -10000 0 -0.44 81 81
RAC1-CDC42/GTP 0.02 0.057 -10000 0 -0.24 21 21
AR -0.089 0.21 -10000 0 -0.52 104 104
GNB1 0.013 0.052 -10000 0 -0.52 5 5
RAF1 -0.033 0.12 -10000 0 -0.31 32 32
RAC1-CDC42/GDP -0.047 0.17 -10000 0 -0.38 103 103
T-DHT/AR/PELP1/Src -0.032 0.12 -10000 0 -0.28 105 105
MAP2K2 -0.033 0.12 -10000 0 -0.33 32 32
T-DHT/AR/PELP1/Src/PI3K -0.031 0.12 -10000 0 -0.24 120 120
GNAZ 0.002 0.085 -10000 0 -0.43 18 18
SHBG 0.018 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.002 0.11 -10000 0 -0.41 20 20
mol:T-DHT 0 0.001 0.002 1 -0.003 51 52
RAC1 0.018 0 -10000 0 -10000 0 0
GNRH1 0 0.06 -10000 0 -0.24 27 27
Gi family/GTP -0.022 0.094 -10000 0 -0.23 51 51
CDC42 0.018 0 -10000 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 -0.049 0.17 -9999 0 -0.44 78 78
PLK4 0.008 0.065 -9999 0 -0.38 13 13
regulation of centriole replication -0.03 0.13 -9999 0 -0.37 59 59
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.02 0.13 -9999 0 -0.32 78 78
E-cadherin/beta catenin -0.034 0.14 -9999 0 -0.38 74 74
CTNNB1 0.001 0.09 -9999 0 -0.45 19 19
JUP 0.011 0.056 -9999 0 -0.42 8 8
CDH1 -0.049 0.17 -9999 0 -0.48 71 71
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.099 0.25 -10000 0 -0.62 80 80
IHH -0.013 0.093 -10000 0 -0.48 14 14
SHH Np/Cholesterol/GAS1 -0.057 0.14 -10000 0 -0.29 133 133
LRPAP1 0.016 0.026 -10000 0 -0.39 2 2
dorsoventral neural tube patterning 0.056 0.14 0.29 133 -10000 0 133
SMO/beta Arrestin2 -0.053 0.17 -10000 0 -0.47 47 47
SMO -0.064 0.18 -10000 0 -0.5 47 47
AKT1 -0.027 0.13 -10000 0 -0.52 21 21
ARRB2 0.018 0 -10000 0 -10000 0 0
BOC -0.018 0.12 -10000 0 -0.38 48 48
ADRBK1 0.018 0 -10000 0 -10000 0 0
heart looping -0.063 0.18 -10000 0 -0.49 47 47
STIL -0.052 0.15 -10000 0 -0.37 51 51
DHH N/PTCH2 0.026 0 -10000 0 -10000 0 0
DHH N/PTCH1 -0.027 0.13 -10000 0 -0.37 23 23
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
DHH 0.018 0 -10000 0 -10000 0 0
PTHLH -0.12 0.31 -10000 0 -0.83 64 64
determination of left/right symmetry -0.063 0.18 -10000 0 -0.49 47 47
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
skeletal system development -0.12 0.3 -10000 0 -0.82 64 64
IHH N/Hhip 0.004 0.069 -10000 0 -0.32 17 17
DHH N/Hhip 0.021 0.037 -10000 0 -0.37 3 3
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.063 0.18 -10000 0 -0.49 47 47
pancreas development 0.01 0.052 -10000 0 -0.33 11 11
HHAT -0.045 0.17 -10000 0 -0.51 63 63
PI3K 0.006 0.082 -10000 0 -0.37 21 21
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.072 0.19 -10000 0 -0.47 98 98
somite specification -0.063 0.18 -10000 0 -0.49 47 47
SHH Np/Cholesterol/PTCH1 -0.048 0.14 -10000 0 -0.37 43 43
SHH Np/Cholesterol/PTCH2 -0.007 0.098 -10000 0 -0.28 61 61
SHH Np/Cholesterol/Megalin -0.1 0.18 -10000 0 -0.33 181 181
SHH -0.021 0.13 -10000 0 -0.37 61 61
catabolic process -0.042 0.14 -10000 0 -0.36 46 46
SMO/Vitamin D3 -0.06 0.16 -10000 0 -0.41 55 55
SHH Np/Cholesterol/Hhip -0.01 0.1 -10000 0 -0.28 64 64
LRP2 -0.16 0.24 -10000 0 -0.48 183 183
receptor-mediated endocytosis -0.12 0.2 -10000 0 -0.49 75 75
SHH Np/Cholesterol/BOC -0.026 0.12 -10000 0 -0.28 83 83
SHH Np/Cholesterol/CDO -0.019 0.11 -10000 0 -0.29 74 74
mesenchymal cell differentiation 0.011 0.1 0.28 64 -10000 0 64
mol:Vitamin D3 -0.046 0.14 -10000 0 -0.37 43 43
IHH N/PTCH2 0.01 0.055 -10000 0 -0.32 11 11
CDON -0.004 0.099 -10000 0 -0.41 27 27
IHH N/PTCH1 -0.04 0.14 -10000 0 -0.36 46 46
Megalin/LRPAP1 -0.1 0.18 -10000 0 -0.37 158 158
PTCH2 0.018 0 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.017 0.097 -10000 0 -0.28 61 61
PTCH1 -0.042 0.14 -10000 0 -0.36 46 46
HHIP 0.01 0.052 -10000 0 -0.33 11 11
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.065 0.12 -9999 0 -0.32 61 61
SMAD6-7/SMURF1 0.034 0.021 -9999 0 -0.3 1 1
NOG 0.009 0.056 -9999 0 -0.31 14 14
SMAD9 -0.021 0.11 -9999 0 -0.62 11 11
SMAD4 0.009 0.067 -9999 0 -0.49 9 9
SMAD5 -0.063 0.14 -9999 0 -0.38 54 54
BMP7/USAG1 -0.19 0.19 -9999 0 -0.3 349 349
SMAD5/SKI -0.052 0.14 -9999 0 -0.4 41 41
SMAD1 0.024 0.061 -9999 0 -0.37 7 7
BMP2 -0.018 0.11 -9999 0 -0.32 57 57
SMAD1/SMAD1/SMAD4 -0.01 0.044 -9999 0 -0.33 3 3
BMPR1A 0.01 0.064 -9999 0 -0.46 9 9
BMPR1B -0.11 0.16 -9999 0 -0.3 218 218
BMPR1A-1B/BAMBI -0.13 0.17 -9999 0 -0.37 156 156
AHSG 0.016 0.024 -9999 0 -0.26 4 4
CER1 0.017 0.012 -9999 0 -0.26 1 1
BMP2-4/CER1 -0.052 0.14 -9999 0 -0.34 84 84
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.054 0.14 -9999 0 -0.39 42 42
BMP2-4 (homodimer) -0.075 0.16 -9999 0 -0.41 83 83
RGMB 0.008 0.073 -9999 0 -0.52 10 10
BMP6/BMPR2/BMPR1A-1B -0.043 0.11 -9999 0 -0.3 52 52
RGMA -0.027 0.12 -9999 0 -0.3 74 74
SMURF1 0.018 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.073 0.14 -9999 0 -0.32 98 98
BMP2-4/USAG1 -0.2 0.2 -9999 0 -0.38 249 249
SMAD6/SMURF1/SMAD5 -0.051 0.14 -9999 0 -0.4 41 41
SOSTDC1 -0.23 0.23 -9999 0 -0.4 314 314
BMP7/BMPR2/BMPR1A-1B -0.062 0.12 -9999 0 -0.3 67 67
SKI 0.017 0.017 -9999 0 -0.26 2 2
BMP6 (homodimer) -0.006 0.089 -9999 0 -0.3 39 39
HFE2 0.004 0.08 -9999 0 -0.45 15 15
ZFYVE16 0.015 0.04 -9999 0 -0.52 3 3
MAP3K7 0.016 0.021 -9999 0 -0.26 3 3
BMP2-4/CHRD -0.059 0.16 -9999 0 -0.37 84 84
SMAD5/SMAD5/SMAD4 -0.056 0.14 -9999 0 -0.4 43 43
MAPK1 0.016 0.033 -9999 0 -0.52 2 2
TAK1/TAB family -0.032 0.13 -9999 0 -0.44 24 24
BMP7 (homodimer) -0.042 0.13 -9999 0 -0.29 101 101
NUP214 0.016 0.026 -9999 0 -0.39 2 2
BMP6/FETUA 0.008 0.065 -9999 0 -0.36 8 8
SMAD1/SKI 0.032 0.06 -9999 0 -0.34 7 7
SMAD6 0.016 0.024 -9999 0 -0.26 4 4
CTDSP2 0.014 0.044 -9999 0 -0.42 5 5
BMP2-4/FETUA -0.053 0.14 -9999 0 -0.34 84 84
MAP3K7IP1 0.018 0 -9999 0 -10000 0 0
GREM1 -0.038 0.16 -9999 0 -0.46 62 62
BMPR2 (homodimer) 0.016 0.033 -9999 0 -0.52 2 2
GADD34/PP1CA 0.029 0.042 -9999 0 -0.3 6 6
BMPR1A-1B (homodimer) -0.069 0.12 -9999 0 -0.38 38 38
CHRDL1 -0.013 0.091 -9999 0 -0.27 56 56
ENDOFIN/SMAD1 0.031 0.065 -9999 0 -0.36 8 8
SMAD6-7/SMURF1/SMAD1 0.046 0.058 -9999 0 -0.37 3 3
SMAD6/SMURF1 0.018 0 -9999 0 -10000 0 0
BAMBI -0.13 0.22 -9999 0 -0.41 185 185
SMURF2 0.009 0.058 -9999 0 -0.34 13 13
BMP2-4/CHRDL1 -0.068 0.16 -9999 0 -0.35 97 97
BMP2-4/GREM1 -0.085 0.17 -9999 0 -0.37 120 120
SMAD7 0.016 0.026 -9999 0 -0.39 2 2
SMAD8A/SMAD8A/SMAD4 -0.015 0.11 -9999 0 -0.45 19 19
SMAD1/SMAD6 0.033 0.059 -9999 0 -0.34 7 7
TAK1/SMAD6 0.025 0.014 -9999 0 -10000 0 0
BMP7 -0.042 0.13 -9999 0 -0.29 101 101
BMP6 -0.006 0.089 -9999 0 -0.3 39 39
MAP3K7IP2 0.014 0.047 -9999 0 -0.52 4 4
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.052 0.13 -9999 0 -0.37 39 39
PPM1A 0.016 0.026 -9999 0 -0.39 2 2
SMAD1/SMURF2 0.029 0.067 -9999 0 -0.36 7 7
SMAD7/SMURF1 0.025 0.019 -9999 0 -0.37 1 1
CTDSPL 0.011 0.062 -9999 0 -0.52 7 7
PPP1CA 0.011 0.048 -9999 0 -0.31 11 11
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.016 0.033 -9999 0 -0.52 2 2
PPP1R15A 0.016 0.029 -9999 0 -0.35 3 3
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.081 0.15 -9999 0 -0.35 89 89
CHRD 0.003 0.073 -9999 0 -0.33 22 22
BMPR2 0.016 0.033 -9999 0 -0.52 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.075 0.15 -9999 0 -0.33 98 98
BMP4 -0.092 0.19 -9999 0 -0.39 143 143
FST -0.015 0.1 -9999 0 -0.31 52 52
BMP2-4/NOG -0.056 0.15 -9999 0 -0.35 88 88
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.049 0.11 -9999 0 -0.3 52 52
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.04 0.18 -9999 0 -0.51 64 64
Syndecan-4/Syndesmos -0.043 0.2 -9999 0 -0.51 71 71
positive regulation of JNK cascade -0.072 0.22 -9999 0 -0.5 88 88
Syndecan-4/ADAM12 -0.069 0.24 -9999 0 -0.54 93 93
CCL5 -0.05 0.18 -9999 0 -0.49 70 70
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
DNM2 0.017 0.012 -9999 0 -0.26 1 1
ITGA5 0.014 0.042 -9999 0 -0.46 4 4
SDCBP 0.003 0.081 -9999 0 -0.4 19 19
PLG 0.016 0.033 -9999 0 -0.51 2 2
ADAM12 -0.049 0.17 -9999 0 -0.47 72 72
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.01 0.063 -9999 0 -0.49 8 8
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.006 0.012 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.04 0.2 -9999 0 -0.51 71 71
Syndecan-4/CXCL12/CXCR4 -0.076 0.24 -9999 0 -0.54 88 88
Syndecan-4/Laminin alpha3 -0.079 0.22 -9999 0 -0.54 77 77
MDK -0.016 0.12 -9999 0 -0.37 46 46
Syndecan-4/FZD7 -0.07 0.23 -9999 0 -0.53 84 84
Syndecan-4/Midkine -0.054 0.21 -9999 0 -0.52 76 76
FZD7 -0.05 0.16 -9999 0 -0.4 86 86
Syndecan-4/FGFR1/FGF -0.073 0.21 -9999 0 -0.48 87 87
THBS1 -0.025 0.14 -9999 0 -0.51 43 43
integrin-mediated signaling pathway -0.062 0.22 -9999 0 -0.51 84 84
positive regulation of MAPKKK cascade -0.072 0.22 -9999 0 -0.5 88 88
Syndecan-4/TACI -0.041 0.2 -9999 0 -0.5 72 72
CXCR4 -0.028 0.14 -9999 0 -0.42 55 55
cell adhesion -0.006 0.1 -9999 0 -0.29 54 54
Syndecan-4/Dynamin -0.039 0.2 -9999 0 -0.5 71 71
Syndecan-4/TSP1 -0.059 0.22 -9999 0 -0.52 81 81
Syndecan-4/GIPC -0.041 0.2 -9999 0 -0.5 71 71
Syndecan-4/RANTES -0.071 0.23 -9999 0 -0.54 78 78
ITGB1 0.015 0.037 -9999 0 -0.39 4 4
LAMA1 0.015 0.027 -9999 0 -0.26 5 5
LAMA3 -0.069 0.18 -9999 0 -0.43 102 102
RAC1 0.018 0 -9999 0 -10000 0 0
PRKCA 0.017 0.05 -9999 0 -0.25 6 6
Syndecan-4/alpha-Actinin -0.045 0.21 -9999 0 -0.52 73 73
TFPI 0.005 0.061 -9999 0 -0.27 24 24
F2 0.017 0.007 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0.022 0.041 -9999 0 -0.37 5 5
positive regulation of cell adhesion -0.071 0.22 -9999 0 -0.52 77 77
ACTN1 0.005 0.079 -9999 0 -0.48 13 13
TNC -0.04 0.15 -9999 0 -0.36 81 81
Syndecan-4/CXCL12 -0.066 0.23 -9999 0 -0.53 82 82
FGF6 0.009 0.067 -9999 0 -0.49 9 9
RHOA 0.005 0.08 -9999 0 -0.52 12 12
CXCL12 -0.041 0.16 -9999 0 -0.46 64 64
TNFRSF13B 0.013 0.036 -9999 0 -0.26 9 9
FGF2 -0.064 0.16 -9999 0 -0.34 121 121
FGFR1 -0.011 0.1 -9999 0 -0.35 42 42
Syndecan-4/PI-4-5-P2 -0.05 0.2 -9999 0 -0.51 71 71
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.045 0.16 -9999 0 -0.45 71 71
cell migration 0.001 0.008 -9999 0 -10000 0 0
PRKCD 0.015 0.041 -9999 0 -0.44 4 4
vasculogenesis -0.056 0.21 -9999 0 -0.5 81 81
SDC4 -0.052 0.22 -9999 0 -0.54 71 71
Syndecan-4/Tenascin C -0.065 0.22 -9999 0 -0.53 84 84
Syndecan-4/PI-4-5-P2/PKC alpha -0.005 0.009 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.046 0.21 -9999 0 -0.51 73 73
MMP9 -0.04 0.17 -9999 0 -0.5 60 60
Rac1/GTP -0.007 0.1 -9999 0 -0.3 54 54
cytoskeleton organization -0.04 0.2 -9999 0 -0.49 71 71
GIPC1 0.014 0.042 -9999 0 -0.46 4 4
Syndecan-4/TFPI -0.045 0.2 -9999 0 -0.51 73 73
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.1 0.3 -10000 0 -0.96 49 49
epithelial cell differentiation -0.1 0.23 -10000 0 -0.72 56 56
ITCH 0.019 0.028 -10000 0 -10000 0 0
WWP1 -0.13 0.4 -10000 0 -1.4 44 44
FYN 0.009 0.063 -10000 0 -0.4 11 11
EGFR -0.077 0.17 -10000 0 -0.35 136 136
PRL 0.015 0.031 -10000 0 -0.32 4 4
neuron projection morphogenesis -0.033 0.22 -10000 0 -0.72 45 45
PTPRZ1 -0.027 0.11 -10000 0 -0.29 78 78
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.048 0.25 -10000 0 -0.82 45 45
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.081 0.28 -10000 0 -0.94 45 45
ADAM17 0.017 0.037 -10000 0 -0.26 4 4
ErbB4/ErbB4 -0.11 0.32 -10000 0 -1 52 52
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.1 0.3 -10000 0 -0.89 56 56
NCOR1 0.016 0.033 -10000 0 -0.52 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.073 0.27 -10000 0 -0.88 46 46
GRIN2B -0.074 0.26 -10000 0 -0.82 47 47
ErbB4/ErbB2/betacellulin -0.12 0.28 -10000 0 -0.74 71 71
STAT1 -0.02 0.12 -10000 0 -0.33 58 58
HBEGF 0.006 0.069 -10000 0 -0.35 17 17
PRLR -0.03 0.15 -10000 0 -0.49 50 50
E4ICDs/ETO2 -0.17 0.34 -10000 0 -0.84 82 82
axon guidance -0.08 0.28 -10000 0 -0.91 47 47
NEDD4 0.002 0.099 -10000 0 -0.53 16 16
Prolactin receptor/Prolactin receptor/Prolactin -0.01 0.11 -10000 0 -0.37 45 45
CBFA2T3 -0.13 0.23 -10000 0 -0.45 162 162
ErbB4/ErbB2/HBEGF -0.092 0.27 -10000 0 -0.82 54 54
MAPK3 -0.04 0.23 -10000 0 -0.75 45 45
STAT1 (dimer) -0.11 0.3 -10000 0 -0.91 55 55
MAPK1 -0.041 0.23 -10000 0 -0.75 45 45
JAK2 0.01 0.054 -10000 0 -0.32 12 12
ErbB4/ErbB2/neuregulin 1 beta -0.091 0.27 -10000 0 -0.84 52 52
NRG1 0.019 0.044 -10000 0 -0.26 5 5
NRG3 0 0.082 -10000 0 -0.34 27 27
NRG2 -0.016 0.1 -10000 0 -0.3 57 57
NRG4 0.009 0.051 -10000 0 -0.27 16 16
heart development -0.08 0.28 -10000 0 -0.91 47 47
neural crest cell migration -0.089 0.27 -10000 0 -0.82 52 52
ERBB2 -0.007 0.088 -10000 0 -0.32 22 22
WWOX/E4ICDs -0.1 0.3 -10000 0 -0.92 52 52
SHC1 0.017 0.023 -10000 0 -0.52 1 1
ErbB4/EGFR/neuregulin 4 -0.13 0.31 -10000 0 -0.85 63 63
apoptosis 0.099 0.28 0.9 50 -10000 0 50
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.11 0.31 -10000 0 -0.97 51 51
ErbB4/ErbB2/epiregulin -0.1 0.27 -10000 0 -0.82 55 55
ErbB4/ErbB4/betacellulin/betacellulin -0.13 0.31 -10000 0 -0.89 60 60
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.089 0.29 -10000 0 -0.72 74 74
MDM2 -0.097 0.3 -10000 0 -0.92 52 52
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.063 0.25 -10000 0 -0.85 44 44
STAT5A -0.072 0.27 -10000 0 -0.91 44 44
ErbB4/EGFR/neuregulin 1 beta -0.11 0.29 -10000 0 -0.81 60 60
DLG4 0.018 0 -10000 0 -10000 0 0
GRB2/SHC 0.024 0.024 -10000 0 -0.37 1 1
E4ICDs/TAB2/NCoR1 -0.082 0.28 -10000 0 -0.93 47 47
STAT5A (dimer) -0.11 0.26 -10000 0 -0.84 53 53
MAP3K7IP2 0.014 0.047 -10000 0 -0.52 4 4
STAT5B (dimer) -0.068 0.27 -10000 0 -0.86 48 48
LRIG1 -0.032 0.15 -10000 0 -0.48 53 53
EREG -0.024 0.11 -10000 0 -0.28 74 74
BTC -0.052 0.17 -10000 0 -0.42 84 84
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.081 0.28 -10000 0 -0.93 47 47
ERBB4 -0.11 0.32 -10000 0 -1 52 52
STAT5B 0.016 0.026 -10000 0 -0.39 2 2
YAP1 -0.015 0.1 -10000 0 -0.71 6 6
GRB2 0.016 0.024 -10000 0 -0.26 4 4
ErbB4/ErbB2/neuregulin 4 -0.09 0.27 -10000 0 -0.84 52 52
glial cell differentiation 0.081 0.28 0.92 47 -10000 0 47
WWOX -0.003 0.073 -10000 0 -0.26 40 40
cell proliferation -0.1 0.27 -10000 0 -0.8 56 56
Ephrin B reverse signaling

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
EFNB2 -0.006 0.1 -10000 0 -0.39 31 31
EPHB2 0.008 0.062 -10000 0 -0.32 16 16
EFNB1 0.017 0.053 -10000 0 -0.39 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.084 -10000 0 -0.41 7 7
Ephrin B2/EPHB1-2 -0.005 0.088 -10000 0 -0.28 32 32
neuron projection morphogenesis -0.024 0.063 -10000 0 -0.39 7 7
Ephrin B1/EPHB1-2/Tiam1 0.013 0.09 -10000 0 -0.31 22 22
DNM1 0.012 0.052 -10000 0 -0.39 8 8
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.084 0.23 -10000 0 -0.55 95 95
YES1 -0.13 0.3 -10000 0 -0.84 81 81
Ephrin B1/EPHB1-2/NCK2 0.018 0.081 -10000 0 -0.3 17 17
PI3K -0.081 0.23 -10000 0 -0.55 97 97
mol:GDP 0.012 0.088 -10000 0 -0.3 22 22
ITGA2B 0.016 0.021 -10000 0 -0.26 3 3
endothelial cell proliferation -0.007 0.096 -10000 0 -0.34 35 35
FYN -0.13 0.3 -10000 0 -0.82 82 82
MAP3K7 -0.084 0.23 -10000 0 -0.63 81 81
FGR -0.11 0.3 -10000 0 -0.82 81 81
TIAM1 0.006 0.073 -10000 0 -0.44 13 13
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
RGS3 0.017 0.012 -10000 0 -0.26 1 1
cell adhesion -0.069 0.22 -10000 0 -0.55 85 85
LYN -0.12 0.3 -10000 0 -0.82 81 81
Ephrin B1/EPHB1-2/Src Family Kinases -0.12 0.28 -10000 0 -0.77 81 81
Ephrin B1/EPHB1-2 -0.11 0.25 -10000 0 -0.68 81 81
SRC -0.11 0.3 -10000 0 -0.82 81 81
ITGB3 0.002 0.076 -10000 0 -0.32 25 25
EPHB1 -0.023 0.11 -10000 0 -0.28 73 73
EPHB4 -0.01 0.11 -10000 0 -0.42 33 33
RAC1 0.018 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.007 0.096 -10000 0 -0.34 35 35
alphaIIb/beta3 Integrin 0.014 0.056 -10000 0 -0.36 7 7
BLK -0.13 0.3 -10000 0 -0.83 81 81
HCK -0.13 0.3 -10000 0 -0.82 82 82
regulation of stress fiber formation -0.017 0.08 0.29 17 -10000 0 17
MAPK8 -0.074 0.22 -10000 0 -0.51 97 97
Ephrin B1/EPHB1-2/RGS3 0.019 0.078 -10000 0 -0.29 15 15
endothelial cell migration -0.088 0.21 -10000 0 -0.47 111 111
NCK2 0.015 0.027 -10000 0 -0.26 5 5
PTPN13 -0.089 0.24 -10000 0 -0.59 93 93
regulation of focal adhesion formation -0.017 0.08 0.29 17 -10000 0 17
chemotaxis -0.018 0.077 0.29 15 -10000 0 15
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
Rac1/GTP 0.014 0.08 -10000 0 -0.4 7 7
angiogenesis -0.11 0.24 -10000 0 -0.68 81 81
LCK -0.14 0.31 -10000 0 -0.82 84 84
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.004 0.13 -10000 0 -0.46 25 25
UGCG -0.11 0.27 -10000 0 -0.77 74 74
AKT1/mTOR/p70S6K/Hsp90/TERT -0.07 0.19 -10000 0 -0.38 107 107
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.11 0.27 -10000 0 -0.76 74 74
mol:DAG -0.014 0.12 -10000 0 -0.96 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.14 0.2 -10000 0 -0.41 159 159
FRAP1 -0.12 0.27 -10000 0 -0.48 159 159
FOXO3 -0.064 0.2 -10000 0 -0.41 86 86
AKT1 -0.073 0.21 -10000 0 -0.43 91 91
GAB2 0.008 0.047 -10000 0 -0.26 16 16
SMPD1 -0.004 0.079 -10000 0 -0.8 4 4
SGMS1 -0.01 0.099 -10000 0 -0.74 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 0.069 -10000 0 -0.26 30 30
CALM1 0.018 0 -10000 0 -10000 0 0
cell proliferation -0.088 0.21 -10000 0 -0.42 120 120
EIF3A 0.017 0.012 -10000 0 -0.26 1 1
PI3K 0.006 0.083 -10000 0 -0.31 30 30
RPS6KB1 -0.035 0.1 -10000 0 -0.28 4 4
mol:sphingomyelin -0.014 0.12 -10000 0 -0.96 8 8
natural killer cell activation -0.002 0.004 -10000 0 -0.013 30 30
JAK3 0.018 0.004 -10000 0 -10000 0 0
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
JAK1 0.012 0.057 -10000 0 -0.52 6 6
NFKB1 0.017 0.023 -10000 0 -0.52 1 1
MYC -0.091 0.28 -10000 0 -0.82 50 50
MYB -0.23 0.5 -10000 0 -1.2 108 108
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.043 0.16 -10000 0 -0.39 51 51
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.015 0.099 -10000 0 -0.38 4 4
mol:PI-3-4-5-P3 -0.042 0.16 -10000 0 -0.38 52 52
Rac1/GDP 0.011 0.064 -10000 0 -0.28 21 21
T cell proliferation -0.038 0.15 -10000 0 -0.36 51 51
SHC1 0.015 0.024 -10000 0 -0.52 1 1
RAC1 0.017 0.001 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.009 0.029 -10000 0 -0.061 120 120
PRKCZ -0.041 0.15 -10000 0 -0.37 51 51
NF kappa B1 p50/RelA -0.085 0.23 -10000 0 -0.45 115 115
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.016 0.14 -10000 0 -0.49 28 28
HSP90AA1 0.013 0.045 -10000 0 -0.39 6 6
RELA 0.018 0 -10000 0 -10000 0 0
IL2RA -0.033 0.14 -10000 0 -0.41 61 61
IL2RB -0.016 0.12 -10000 0 -0.43 40 40
TERT 0.013 0.042 -10000 0 -0.33 7 7
E2F1 -0.077 0.19 -10000 0 -0.44 113 113
SOS1 0.015 0.024 -10000 0 -0.53 1 1
RPS6 0.015 0.037 -10000 0 -0.39 4 4
mol:cAMP 0.004 0.014 0.029 121 -10000 0 121
PTPN11 0.015 0.024 -10000 0 -0.52 1 1
IL2RG -0.002 0.079 -10000 0 -0.29 35 35
actin cytoskeleton organization -0.038 0.15 -10000 0 -0.36 51 51
GRB2 0.014 0.024 -10000 0 -0.26 4 4
IL2 0.011 0.051 -10000 0 -0.34 10 10
PIK3CA 0.016 0.03 -10000 0 -0.35 3 3
Rac1/GTP 0.013 0.064 -10000 0 -0.26 21 21
LCK -0.072 0.18 -10000 0 -0.4 115 115
BCL2 -0.19 0.39 -10000 0 -0.83 131 131
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.061 0.16 -10000 0 -0.38 76 76
IKBKB 0.005 0.077 -10000 0 -0.25 11 11
AKT1 -0.017 0.098 0.21 10 -0.22 53 63
IKBKG 0.008 0.078 -10000 0 -0.24 14 14
CALM1 -0.03 0.13 0.21 11 -0.34 50 61
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
MAP3K1 -0.076 0.19 -10000 0 -0.48 69 69
MAP3K7 0.016 0.021 -10000 0 -0.26 3 3
mol:Ca2+ -0.039 0.13 0.21 11 -0.35 56 67
DOK1 0.002 0.083 -10000 0 -0.41 19 19
AP-1 -0.045 0.1 0.17 2 -0.23 77 79
LYN 0.014 0.031 -10000 0 -0.26 7 7
BLNK -0.013 0.12 -10000 0 -0.51 31 31
SHC1 0.017 0.023 -10000 0 -0.52 1 1
BCR complex -0.033 0.13 -10000 0 -0.35 70 70
CD22 -0.056 0.19 -10000 0 -0.47 67 67
CAMK2G -0.021 0.12 0.21 11 -0.33 44 55
CSNK2A1 0.017 0.023 -10000 0 -0.52 1 1
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.057 0.11 -10000 0 -0.44 21 21
GO:0007205 -0.04 0.14 0.21 11 -0.36 56 67
SYK -0.022 0.14 -10000 0 -0.48 42 42
ELK1 -0.032 0.13 0.21 11 -0.36 49 60
NFATC1 -0.041 0.16 -10000 0 -0.38 64 64
B-cell antigen/BCR complex -0.033 0.13 -10000 0 -0.35 70 70
PAG1/CSK 0.008 0.074 -10000 0 -0.37 16 16
NFKBIB 0.014 0.031 0.097 1 -0.11 3 4
HRAS -0.028 0.13 0.19 2 -0.34 49 51
NFKBIA 0.015 0.03 0.097 1 -0.11 2 3
NF-kappa-B/RelA/I kappa B beta 0.02 0.027 0.099 1 -0.16 1 2
RasGAP/Csk -0.026 0.15 -10000 0 -0.31 78 78
mol:GDP -0.038 0.13 0.21 11 -0.34 56 67
PTEN -0.002 0.1 -10000 0 -0.52 19 19
CD79B -0.042 0.15 -10000 0 -0.36 83 83
NF-kappa-B/RelA/I kappa B alpha 0.02 0.027 0.099 1 -0.16 1 2
GRB2 0.016 0.024 -10000 0 -0.26 4 4
PI3K/BCAP/CD19 -0.063 0.18 -10000 0 -0.48 59 59
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
mol:IP3 -0.04 0.14 0.21 11 -0.36 56 67
CSK 0.015 0.031 -10000 0 -0.32 4 4
FOS -0.078 0.15 0.21 8 -0.34 90 98
CHUK 0.001 0.094 -10000 0 -0.28 28 28
IBTK 0.016 0.033 -10000 0 -0.52 2 2
CARD11/BCL10/MALT1/TAK1 -0.022 0.12 0.2 1 -0.36 40 41
PTPN6 -0.047 0.18 -10000 0 -0.46 63 63
RELA 0.018 0 -10000 0 -10000 0 0
BCL2A1 0.013 0.03 -10000 0 -0.094 11 11
VAV2 -0.066 0.19 -10000 0 -0.51 60 60
ubiquitin-dependent protein catabolic process 0.019 0.03 0.1 1 -0.1 3 4
BTK -0.036 0.2 -10000 0 -1.1 18 18
CD19 -0.074 0.2 -10000 0 -0.44 93 93
MAP4K1 0.011 0.041 -10000 0 -0.26 12 12
CD72 -0.031 0.14 -10000 0 -0.38 65 65
PAG1 -0.005 0.097 -10000 0 -0.38 30 30
MAPK14 -0.057 0.17 -10000 0 -0.41 64 64
SH3BP5 -0.005 0.1 -10000 0 -0.44 26 26
PIK3AP1 -0.045 0.16 0.23 11 -0.43 53 64
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.055 0.19 -10000 0 -0.44 70 70
RAF1 -0.019 0.12 -10000 0 -0.36 32 32
RasGAP/p62DOK/SHIP -0.036 0.15 -10000 0 -0.32 80 80
CD79A -0.01 0.085 -10000 0 -0.26 53 53
re-entry into mitotic cell cycle -0.045 0.1 0.17 2 -0.23 76 78
RASA1 0.004 0.079 -10000 0 -0.42 16 16
MAPK3 -0.003 0.1 -10000 0 -0.32 24 24
MAPK1 -0.003 0.1 -10000 0 -0.32 26 26
CD72/SHP1 -0.055 0.19 -10000 0 -0.51 61 61
NFKB1 0.017 0.023 -10000 0 -0.52 1 1
MAPK8 -0.059 0.17 -10000 0 -0.41 67 67
actin cytoskeleton organization -0.049 0.17 -10000 0 -0.47 48 48
NF-kappa-B/RelA 0.043 0.054 0.19 1 -0.23 3 4
Calcineurin -0.023 0.12 -10000 0 -0.34 42 42
PI3K -0.087 0.14 -10000 0 -0.39 72 72
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.043 0.15 0.24 11 -0.41 50 61
SOS1 0.017 0.023 -10000 0 -0.52 1 1
Bam32/HPK1 -0.13 0.31 -10000 0 -0.75 96 96
DAPP1 -0.16 0.35 -10000 0 -0.86 95 95
cytokine secretion -0.037 0.15 -10000 0 -0.35 64 64
mol:DAG -0.04 0.14 0.21 11 -0.36 56 67
PLCG2 -0.017 0.11 -10000 0 -0.32 55 55
MAP2K1 -0.011 0.11 -10000 0 -0.35 27 27
B-cell antigen/BCR complex/FcgammaRIIB -0.045 0.15 -10000 0 -0.32 106 106
mol:PI-3-4-5-P3 -0.058 0.11 0.25 13 -0.29 62 75
ETS1 -0.018 0.12 0.2 10 -0.34 38 48
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.031 0.15 -10000 0 -0.28 123 123
B-cell antigen/BCR complex/LYN -0.077 0.18 -10000 0 -0.5 57 57
MALT1 0.011 0.054 -10000 0 -0.38 9 9
TRAF6 0.017 0.023 -10000 0 -0.52 1 1
RAC1 -0.053 0.18 -10000 0 -0.51 48 48
B-cell antigen/BCR complex/LYN/SYK -0.053 0.19 -10000 0 -0.49 63 63
CARD11 -0.038 0.14 0.21 11 -0.36 60 71
FCGR2B -0.032 0.15 -10000 0 -0.5 51 51
PPP3CA 0.006 0.073 -10000 0 -0.44 13 13
BCL10 0.017 0.012 -10000 0 -0.26 1 1
IKK complex 0.012 0.04 0.11 1 -0.11 8 9
PTPRC -0.04 0.15 -10000 0 -0.41 71 71
PDPK1 -0.017 0.091 0.2 9 -0.21 52 61
PPP3CB 0.016 0.026 -10000 0 -0.39 2 2
PPP3CC -0.001 0.098 -10000 0 -0.51 19 19
POU2F2 0.019 0.021 -10000 0 -0.098 1 1
Visual signal transduction: Rods

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
mol:K + 0.011 0.056 -9999 0 -0.42 8 8
GNAT1/GTP 0.01 0.035 -9999 0 -0.34 5 5
Metarhodopsin II/Arrestin -0.046 0.12 -9999 0 -0.31 64 64
PDE6G/GNAT1/GTP 0.02 0.033 -9999 0 -0.31 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.013 0.048 -9999 0 -0.47 5 5
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel -0.083 0.12 -9999 0 -0.27 139 139
mol:Na + -0.042 0.088 -9999 0 -0.43 13 13
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.055 0.15 -9999 0 -0.34 95 95
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.004 0.11 -9999 0 -0.44 13 13
CNGB1 0.018 0 -9999 0 -10000 0 0
RDH5 -0.003 0.073 -9999 0 -0.26 40 40
SAG -0.099 0.19 -9999 0 -0.36 162 162
mol:Ca2+ -0.001 0.11 -9999 0 -0.39 16 16
Na + (4 Units) -0.04 0.084 -9999 0 -0.38 16 16
RGS9 -0.032 0.13 -9999 0 -0.31 80 80
GNB1/GNGT1 -0.033 0.1 -9999 0 -0.19 148 148
GNAT1/GDP -0.039 0.13 -9999 0 -0.28 98 98
GUCY2D 0.018 0 -9999 0 -10000 0 0
GNGT1 -0.063 0.14 -9999 0 -0.28 143 143
GUCY2F 0.006 0.076 -9999 0 -0.46 13 13
GNB5 0.005 0.081 -9999 0 -0.5 13 13
mol:GMP (4 units) -0.034 0.12 -9999 0 -0.26 119 119
mol:11-cis-retinal -0.003 0.073 -9999 0 -0.26 40 40
mol:cGMP 0.026 0.088 -9999 0 -0.3 31 31
GNB1 0.013 0.052 -9999 0 -0.52 5 5
Rhodopsin 0.012 0.05 -9999 0 -10000 0 0
SLC24A1 0.011 0.056 -9999 0 -0.42 8 8
CNGA1 -0.063 0.16 -9999 0 -0.32 125 125
Metarhodopsin II 0.011 0 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.026 0.076 -9999 0 -0.29 25 25
RGS9BP -0.071 0.18 -9999 0 -0.41 110 110
Metarhodopsin II/Transducin -0.005 0.064 -9999 0 -0.25 22 22
GCAP Family/Ca ++ 0.015 0.075 -9999 0 -0.3 25 25
PDE6A/B -0.067 0.17 -9999 0 -0.37 116 116
mol:Pi -0.055 0.15 -9999 0 -0.33 95 95
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.014 0.084 -9999 0 -0.29 22 22
PDE6B -0.1 0.22 -9999 0 -0.5 123 123
PDE6A 0.011 0.048 -9999 0 -0.31 11 11
PDE6G 0.016 0.024 -9999 0 -0.26 4 4
RHO 0.018 0 -9999 0 -10000 0 0
PDE6 -0.088 0.17 -9999 0 -0.29 188 188
GUCA1A 0.001 0.092 -9999 0 -0.48 18 18
GC2/GCAP Family 0.02 0.093 -9999 0 -0.32 31 31
GUCA1C 0.004 0.081 -9999 0 -0.44 16 16
GUCA1B 0.014 0.035 -9999 0 -0.3 6 6
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.027 0.15 -9999 0 -0.4 60 60
alphaM/beta2 Integrin/GPIbA -0.01 0.11 -9999 0 -0.34 41 41
alphaM/beta2 Integrin/proMMP-9 -0.036 0.15 -9999 0 -0.36 80 80
PLAUR -0.017 0.13 -9999 0 -0.47 37 37
HMGB1 0.011 0.021 -9999 0 -0.27 1 1
alphaM/beta2 Integrin/Talin 0 0.1 -9999 0 -0.36 31 31
AGER 0.01 0.031 -9999 0 -0.4 2 2
RAP1A 0.011 0.062 -9999 0 -0.52 7 7
SELPLG -0.003 0.098 -9999 0 -0.43 24 24
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.013 0.13 -9999 0 -0.37 35 35
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.042 0.17 -9999 0 -0.51 60 60
CYR61 -0.04 0.16 -9999 0 -0.42 70 70
TLN1 0.017 0.023 -9999 0 -0.52 1 1
Rap1/GTP -0.037 0.1 -9999 0 -0.41 28 28
RHOA 0.005 0.08 -9999 0 -0.52 12 12
P-selectin oligomer -0.12 0.22 -9999 0 -0.44 156 156
MYH2 -0.003 0.13 -9999 0 -0.4 31 31
MST1R -0.038 0.16 -9999 0 -0.51 56 56
leukocyte activation during inflammatory response 0.007 0.087 -9999 0 -0.31 30 30
APOB 0.018 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.029 0.15 -9999 0 -0.47 51 51
JAM3 -0.005 0.11 -9999 0 -0.5 23 23
GP1BA -0.002 0.07 -9999 0 -0.26 37 37
alphaM/beta2 Integrin/CTGF -0.03 0.14 -9999 0 -0.4 57 57
alphaM/beta2 Integrin -0.008 0.13 -9999 0 -0.41 33 33
JAM3 homodimer -0.005 0.11 -9999 0 -0.5 23 23
ICAM2 0.007 0.068 -9999 0 -0.4 13 13
ICAM1 -0.021 0.13 -9999 0 -0.4 49 49
phagocytosis triggered by activation of immune response cell surface activating receptor -0.008 0.13 -9999 0 -0.4 33 33
cell adhesion -0.011 0.11 -9999 0 -0.33 41 41
NFKB1 -0.033 0.17 -9999 0 -0.38 77 77
THY1 -0.005 0.11 -9999 0 -0.5 23 23
RhoA/GDP 0.004 0.058 -9999 0 -0.38 12 12
Lipoprotein(a) 0.023 0.016 -9999 0 -0.31 1 1
alphaM/beta2 Integrin/LRP/tPA -0.048 0.14 -9999 0 -0.32 91 91
IL6 -0.088 0.27 -9999 0 -0.71 72 72
ITGB2 -0.022 0.12 -9999 0 -0.43 40 40
elevation of cytosolic calcium ion concentration -0.043 0.18 -9999 0 -0.41 80 80
alphaM/beta2 Integrin/JAM2/JAM3 -0.02 0.15 -9999 0 -0.38 63 63
JAM2 -0.019 0.13 -9999 0 -0.44 43 43
alphaM/beta2 Integrin/ICAM1 -0.029 0.16 -9999 0 -0.33 91 91
alphaM/beta2 Integrin/uPA/Plg -0.026 0.14 -9999 0 -0.34 73 73
RhoA/GTP -0.008 0.14 -9999 0 -0.43 31 31
positive regulation of phagocytosis -0.008 0.16 -9999 0 -0.47 40 40
Ron/MSP -0.016 0.12 -9999 0 -0.37 54 54
alphaM/beta2 Integrin/uPAR/uPA -0.043 0.18 -9999 0 -0.41 80 80
alphaM/beta2 Integrin/uPAR -0.02 0.14 -9999 0 -0.4 52 52
PLAU -0.05 0.17 -9999 0 -0.43 81 81
PLAT -0.092 0.19 -9999 0 -0.37 148 148
actin filament polymerization -0.002 0.13 -9999 0 -0.39 31 31
MST1 0.016 0.021 -9999 0 -0.26 3 3
alphaM/beta2 Integrin/lipoprotein(a) 0.01 0.089 -9999 0 -0.31 30 30
TNF -0.035 0.19 -9999 0 -0.64 29 29
RAP1B 0.013 0.044 -9999 0 -0.32 8 8
alphaM/beta2 Integrin/uPA -0.04 0.15 -9999 0 -0.38 73 73
fibrinolysis -0.027 0.14 -9999 0 -0.34 73 73
HCK -0.005 0.11 -9999 0 -0.47 25 25
dendritic cell antigen processing and presentation -0.008 0.13 -9999 0 -0.4 33 33
VTN 0.016 0.021 -9999 0 -0.26 3 3
alphaM/beta2 Integrin/CYR61 -0.034 0.14 -9999 0 -0.37 68 68
LPA 0.016 0.026 -9999 0 -0.39 2 2
LRP1 0.017 0.023 -9999 0 -0.52 1 1
cell migration -0.05 0.17 -9999 0 -0.36 104 104
FN1 -0.046 0.17 -9999 0 -0.46 71 71
alphaM/beta2 Integrin/Thy1 -0.013 0.12 -9999 0 -0.37 47 47
MPO 0.008 0.051 -9999 0 -0.26 19 19
KNG1 0.017 0.017 -9999 0 -0.26 2 2
RAP1/GDP 0.017 0.046 -9999 0 -0.31 9 9
ROCK1 0 0.13 -9999 0 -0.41 30 30
ELA2 0.017 0.017 -9999 0 -0.26 2 2
PLG 0.016 0.033 -9999 0 -0.52 2 2
CTGF -0.033 0.15 -9999 0 -0.42 61 61
alphaM/beta2 Integrin/Hck -0.012 0.14 -9999 0 -0.43 41 41
ITGAM 0.002 0.071 -9999 0 -0.48 10 10
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.073 0.18 -9999 0 -0.34 132 132
HP 0.013 0.05 -9999 0 -0.43 6 6
leukocyte adhesion -0.033 0.18 -9999 0 -0.55 40 40
SELP -0.12 0.22 -9999 0 -0.44 156 156
LPA receptor mediated events

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
GNB1/GNG2 0.007 0.078 -9999 0 -0.24 45 45
NF kappa B1 p50/RelA/I kappa B alpha 0.003 0.086 -9999 0 -0.27 23 23
AP1 -0.091 0.14 -9999 0 -0.3 131 131
mol:PIP3 -0.065 0.11 -9999 0 -0.28 83 83
AKT1 0.008 0.11 -9999 0 -0.35 25 25
PTK2B -0.008 0.063 -9999 0 -0.2 44 44
RHOA -0.006 0.092 -9999 0 -0.41 17 17
PIK3CB 0.012 0.055 -9999 0 -0.44 7 7
mol:Ca2+ -0.024 0.094 -9999 0 -0.26 60 60
MAGI3 -0.014 0.12 -9999 0 -0.46 35 35
RELA 0.018 0 -9999 0 -10000 0 0
apoptosis -0.003 0.065 -9999 0 -0.22 41 41
HRAS/GDP 0.009 0.037 -9999 0 -0.29 7 7
positive regulation of microtubule depolymerization -0.044 0.12 -9999 0 -0.26 117 117
NF kappa B1 p50/RelA -0.039 0.092 -9999 0 -0.31 31 31
endothelial cell migration -0.032 0.17 -9999 0 -0.55 51 51
ADCY4 -0.004 0.11 -9999 0 -0.31 45 45
ADCY5 -0.012 0.11 -9999 0 -0.3 48 48
ADCY6 -0.002 0.1 -9999 0 -0.29 44 44
ADCY7 -0.006 0.11 -9999 0 -0.32 44 44
ADCY1 -0.001 0.1 -9999 0 -0.29 44 44
ADCY2 -0.023 0.12 -9999 0 -0.34 50 50
ADCY3 -0.004 0.1 -9999 0 -0.29 47 47
ADCY8 -0.003 0.1 -9999 0 -0.29 45 45
ADCY9 -0.009 0.11 -9999 0 -0.3 46 46
GSK3B -0.001 0.06 -9999 0 -0.18 42 42
arachidonic acid secretion 0.003 0.1 -9999 0 -0.28 48 48
GNG2 0.016 0.029 -9999 0 -0.34 3 3
TRIP6 0 0.088 -9999 0 -0.4 23 23
GNAO1 -0.003 0.076 -9999 0 -0.25 41 41
HRAS 0.012 0.051 -9999 0 -0.41 7 7
NFKBIA -0.013 0.091 -9999 0 -0.27 33 33
GAB1 0.006 0.074 -9999 0 -0.43 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly 0.008 0.15 -9999 0 -0.89 14 14
JUN -0.034 0.15 -9999 0 -0.46 57 57
LPA/LPA2/NHERF2 -0.023 0.099 -9999 0 -0.3 52 52
TIAM1 -0.023 0.17 -9999 0 -1 14 14
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
mol:IP3 -0.025 0.095 -9999 0 -0.26 60 60
PLCB3 -0.015 0.094 -9999 0 -0.29 49 49
FOS -0.11 0.2 -9999 0 -0.37 171 171
positive regulation of mitosis 0.003 0.1 -9999 0 -0.28 48 48
LPA/LPA1-2-3 -0.013 0.066 -9999 0 -0.21 51 51
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.017 0.012 -9999 0 -0.26 1 1
stress fiber formation 0.002 0.062 -9999 0 -0.19 42 42
GNAZ -0.011 0.092 -9999 0 -0.28 52 52
EGFR/PI3K-beta/Gab1 -0.067 0.11 -9999 0 -0.29 83 83
positive regulation of dendritic cell cytokine production -0.013 0.066 -9999 0 -0.21 51 51
LPA/LPA2/MAGI-3 -0.013 0.08 -9999 0 -0.28 35 35
ARHGEF1 0.01 0.073 -9999 0 -0.22 44 44
GNAI2 -0.008 0.094 -9999 0 -0.29 47 47
GNAI3 -0.002 0.076 -9999 0 -0.25 42 42
GNAI1 -0.021 0.11 -9999 0 -0.31 55 55
LPA/LPA3 -0.01 0.032 -9999 0 -0.1 51 51
LPA/LPA2 -0.01 0.032 -9999 0 -0.1 51 51
LPA/LPA1 -0.017 0.088 -9999 0 -0.28 51 51
HB-EGF/EGFR -0.068 0.15 -9999 0 -0.34 102 102
HBEGF -0.026 0.13 -9999 0 -0.38 63 63
mol:DAG -0.025 0.095 -9999 0 -0.26 60 60
cAMP biosynthetic process -0.005 0.11 -9999 0 -0.3 48 48
NFKB1 0.017 0.023 -9999 0 -0.52 1 1
SRC 0.015 0.035 -9999 0 -0.43 3 3
GNB1 0.013 0.052 -9999 0 -0.52 5 5
LYN -0.013 0.088 -9999 0 -0.26 30 30
GNAQ -0.005 0.026 -9999 0 -0.081 51 51
LPAR2 0 0.001 -9999 0 -10000 0 0
LPAR3 0 0.001 -9999 0 -10000 0 0
LPAR1 -0.011 0.051 -9999 0 -0.16 51 51
IL8 -0.13 0.19 -9999 0 -0.41 121 121
PTK2 -0.001 0.065 -9999 0 -0.21 42 42
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
CASP3 -0.003 0.066 -9999 0 -0.22 41 41
EGFR -0.077 0.17 -9999 0 -0.35 136 136
PLCG1 -0.014 0.056 -9999 0 -0.14 66 66
PLD2 -0.003 0.069 -9999 0 -0.22 45 45
G12/G13 0.006 0.079 -9999 0 -0.24 44 44
PI3K-beta -0.039 0.098 -9999 0 -0.36 30 30
cell migration 0.017 0.061 -9999 0 -0.25 15 15
SLC9A3R2 -0.032 0.15 -9999 0 -0.49 52 52
PXN 0.002 0.062 -9999 0 -0.2 42 42
HRAS/GTP 0.002 0.1 -9999 0 -0.28 48 48
RAC1 0.018 0 -9999 0 -10000 0 0
MMP9 -0.042 0.17 -9999 0 -0.51 60 60
PRKCE 0.011 0.056 -9999 0 -0.42 8 8
PRKCD -0.019 0.093 -9999 0 -0.26 55 55
Gi(beta/gamma) 0.002 0.1 -9999 0 -0.29 45 45
mol:LPA -0.011 0.051 -9999 0 -0.16 51 51
TRIP6/p130 Cas/FAK1/Paxillin 0.013 0.084 -9999 0 -0.32 15 15
MAPKKK cascade 0.003 0.1 -9999 0 -0.28 48 48
contractile ring contraction involved in cytokinesis -0.006 0.091 -9999 0 -0.4 17 17
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.043 0.097 -9999 0 -0.16 169 169
GNA15 -0.003 0.052 -9999 0 -0.18 25 25
GNA12 0.018 0 -9999 0 -10000 0 0
GNA13 0.009 0.059 -9999 0 -0.38 11 11
MAPT -0.046 0.13 -9999 0 -0.27 117 117
GNA11 0.003 0.038 -9999 0 -0.3 4 4
Rac1/GTP 0.007 0.16 -9999 0 -0.94 14 14
MMP2 -0.032 0.18 -9999 0 -0.55 51 51
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.002 0.077 -9999 0 -0.3 26 26
NFATC2 0.012 0.044 -9999 0 -0.3 5 5
NFATC3 0.015 0.031 -9999 0 -10000 0 0
CD40LG -0.099 0.26 -9999 0 -0.53 99 99
PTGS2 -0.11 0.26 -9999 0 -0.53 106 106
JUNB 0.011 0.055 -9999 0 -0.36 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.019 -9999 0 -10000 0 0
CaM/Ca2+ 0.008 0.019 -9999 0 -10000 0 0
CALM1 0.016 0.009 -9999 0 -10000 0 0
JUN -0.035 0.15 -9999 0 -0.46 57 57
mol:Ca2+ -0.004 0.012 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.01 0.011 -9999 0 -0.15 2 2
FOSL1 0.016 0.024 -9999 0 -0.26 4 4
CREM 0.016 0.017 -9999 0 -0.26 2 2
Jun/NFAT1-c-4/p21SNFT -0.025 0.15 -9999 0 -0.34 58 58
FOS -0.11 0.2 -9999 0 -0.37 171 171
IFNG -0.14 0.3 -9999 0 -0.58 128 128
AP-1/NFAT1-c-4 -0.1 0.31 -9999 0 -0.57 121 121
FASLG -0.13 0.3 -9999 0 -0.6 119 119
NFAT1-c-4/ICER1 0.007 0.095 -9999 0 -0.31 14 14
IL2RA -0.12 0.28 -9999 0 -0.57 107 107
FKBP12/FK506 0.012 0.011 -9999 0 -0.17 2 2
CSF2 -0.1 0.26 -9999 0 -0.52 104 104
JunB/Fra1/NFAT1-c-4 0.015 0.1 -9999 0 -0.32 18 18
IL4 -0.097 0.25 -9999 0 -0.52 99 99
IL2 -0.005 0.1 -9999 0 -1.3 3 3
IL3 0.008 0.021 -9999 0 -10000 0 0
FKBP1A 0.017 0.017 -9999 0 -0.26 2 2
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.027 0 -9999 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.037 0.11 -10000 0 -0.23 108 108
TP53 -0.036 0.1 0.28 2 -0.36 37 39
Senescence -0.036 0.1 0.28 2 -0.36 37 39
Apoptosis -0.036 0.1 0.28 2 -0.36 37 39
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.029 0.072 0.24 31 -0.18 13 44
MDM4 0.013 0.044 -10000 0 -0.32 8 8
Caspase cascade in apoptosis

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
TOP1 -0.002 0.11 0.22 3 -0.27 45 48
ACTA1 -0.03 0.14 0.23 10 -0.34 62 72
NUMA1 -0.005 0.12 0.22 3 -0.26 51 54
SPTAN1 -0.01 0.13 0.24 11 -0.33 54 65
LIMK1 -0.029 0.15 0.23 9 -0.33 77 86
BIRC3 -0.086 0.19 -10000 0 -0.41 129 129
BIRC2 0.016 0.021 -10000 0 -0.26 3 3
BAX 0.016 0.021 -10000 0 -0.26 3 3
CASP10 -0.042 0.14 -10000 0 -0.31 99 99
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.003 0.12 0.2 9 -0.27 52 61
DIABLO 0.018 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.009 0.13 0.23 11 -0.33 54 65
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.009 0.067 -10000 0 -0.49 9 9
GSN -0.02 0.14 0.23 9 -0.34 63 72
MADD 0.018 0 -10000 0 -10000 0 0
TFAP2A -0.009 0.14 -10000 0 -0.56 27 27
BID -0.022 0.09 -10000 0 -0.2 94 94
MAP3K1 -0.03 0.13 -10000 0 -0.42 43 43
TRADD 0.016 0.026 -10000 0 -0.39 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.022 0.041 -10000 0 -0.37 5 5
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.029 0.14 0.23 5 -0.34 68 73
CASP9 0.017 0.023 -10000 0 -0.52 1 1
DNA repair -0.02 0.075 0.29 8 -0.19 37 45
neuron apoptosis -0.025 0.17 -10000 0 -0.64 35 35
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.005 0.13 0.23 9 -0.31 51 60
APAF1 0.012 0.051 -10000 0 -0.41 7 7
CASP6 0.003 0.11 -10000 0 -0.77 6 6
TRAF2 0.014 0.042 -10000 0 -0.46 4 4
ICAD/CAD -0.003 0.13 0.23 11 -0.31 54 65
CASP7 0.045 0.12 0.29 68 -0.4 11 79
KRT18 -0.072 0.21 -10000 0 -0.57 77 77
apoptosis -0.005 0.14 0.26 8 -0.37 22 30
DFFA -0.01 0.13 0.24 11 -0.33 54 65
DFFB -0.01 0.13 0.24 11 -0.33 54 65
PARP1 0.02 0.075 0.19 37 -0.3 8 45
actin filament polymerization 0.026 0.15 0.34 60 -0.22 9 69
TNF -0.004 0.094 -10000 0 -0.36 31 31
CYCS -0.012 0.062 -10000 0 -0.16 38 38
SATB1 -0.018 0.13 -10000 0 -0.47 22 22
SLK -0.01 0.13 0.24 11 -0.33 55 66
p15 BID/BAX -0.011 0.082 -10000 0 -0.28 12 12
CASP2 0.01 0.089 -10000 0 -0.38 11 11
JNK cascade 0.029 0.13 0.41 43 -10000 0 43
CASP3 -0.017 0.14 0.24 14 -0.34 60 74
LMNB2 0.017 0.068 -10000 0 -0.29 7 7
RIPK1 0.017 0.023 -10000 0 -0.52 1 1
CASP4 -0.005 0.11 -10000 0 -0.49 24 24
Mammalian IAPs/DIABLO -0.025 0.11 -10000 0 -0.28 76 76
negative regulation of DNA binding -0.009 0.14 -10000 0 -0.56 27 27
stress fiber formation -0.01 0.13 0.23 11 -0.32 55 66
GZMB -0.058 0.16 -10000 0 -0.38 97 97
CASP1 -0.038 0.16 -10000 0 -0.42 60 60
LMNB1 -0.033 0.12 -10000 0 -0.29 36 36
APP -0.025 0.17 -10000 0 -0.64 35 35
TNFRSF1A 0.016 0.033 -10000 0 -0.52 2 2
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.013 0 -10000 0 -10000 0 0
VIM -0.009 0.14 0.22 31 -0.31 55 86
LMNA 0.014 0.076 -10000 0 -0.3 11 11
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.003 0.095 -10000 0 -0.38 13 13
LRDD 0.018 0 -10000 0 -10000 0 0
SREBF1 -0.036 0.15 0.24 10 -0.33 84 94
APAF-1/Caspase 9 0.015 0.068 -10000 0 -0.57 2 2
nuclear fragmentation during apoptosis -0.005 0.12 0.22 4 -0.26 52 56
CFL2 -0.027 0.15 0.22 9 -0.34 60 69
GAS2 -0.035 0.15 0.24 10 -0.32 82 92
positive regulation of apoptosis -0.003 0.08 -10000 0 -0.26 19 19
PRF1 -0.009 0.093 -10000 0 -0.31 43 43
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.01 0.065 -9999 0 -0.37 9 9
alphaV beta3 Integrin -0.035 0.13 -9999 0 -0.33 63 63
PTK2 -0.008 0.14 -9999 0 -0.47 26 26
IGF1R -0.083 0.2 -9999 0 -0.47 110 110
PI4KB 0.016 0.033 -9999 0 -0.52 2 2
MFGE8 -0.018 0.12 -9999 0 -0.36 50 50
SRC 0.015 0.035 -9999 0 -0.43 3 3
CDKN1B -0.022 0.13 -9999 0 -0.49 30 30
VEGFA 0 0.076 -9999 0 -0.29 31 31
ILK 0.002 0.073 -9999 0 -0.75 2 2
ROCK1 0.018 0 -9999 0 -10000 0 0
AKT1 0.007 0.075 -9999 0 -0.39 8 8
PTK2B 0.012 0.092 -9999 0 -0.32 28 28
alphaV/beta3 Integrin/JAM-A -0.015 0.12 -9999 0 -0.28 61 61
CBL 0.017 0.012 -9999 0 -0.26 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.009 0.09 -9999 0 -0.33 29 29
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.11 0.22 -9999 0 -0.39 170 170
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.02 0.086 -9999 0 -0.38 14 14
alphaV/beta3 Integrin/Syndecan-1 -0.02 0.13 -9999 0 -0.33 67 67
PI4KA 0.018 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.19 0.24 -9999 0 -0.54 131 131
PI4 Kinase 0.025 0.024 -9999 0 -0.37 2 2
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
alphaV/beta3 Integrin/Osteopontin -0.084 0.16 -9999 0 -0.33 144 144
RPS6KB1 -0.15 0.24 -9999 0 -0.49 135 135
TLN1 0.017 0.023 -9999 0 -0.52 1 1
MAPK3 -0.094 0.23 -9999 0 -0.66 59 59
GPR124 0.001 0.092 -9999 0 -0.52 16 16
MAPK1 -0.094 0.23 -9999 0 -0.65 59 59
PXN 0.018 0 -9999 0 -10000 0 0
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
alphaV/beta3 Integrin/Tumstatin 0.011 0.089 -9999 0 -0.34 25 25
cell adhesion -0.01 0.12 -9999 0 -0.31 59 59
ANGPTL3 0.01 0.061 -9999 0 -0.43 9 9
VEGFR2 homodimer/VEGFA homodimer/Src 0.021 0.059 -9999 0 -0.3 11 11
IGF-1R heterotetramer -0.083 0.2 -9999 0 -0.47 110 110
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
TGFBR2 0.012 0.055 -9999 0 -0.45 7 7
ITGB3 0.002 0.076 -9999 0 -0.32 25 25
IGF1 -0.1 0.21 -9999 0 -0.42 146 146
RAC1 0.018 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion 0.004 0.11 -9999 0 -0.38 33 33
apoptosis -0.003 0.1 -9999 0 -0.48 22 22
CD47 -0.005 0.11 -9999 0 -0.47 25 25
alphaV/beta3 Integrin/CD47 -0.001 0.1 -9999 0 -0.32 43 43
VCL 0.016 0.029 -9999 0 -0.35 3 3
alphaV/beta3 Integrin/Del1 -0.066 0.17 -9999 0 -0.36 115 115
CSF1 0.014 0.037 -9999 0 -0.3 7 7
PIK3C2A -0.005 0.1 -9999 0 -0.71 8 8
PI4 Kinase/Pyk2 -0.043 0.093 -9999 0 -0.39 19 19
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.013 0.1 -9999 0 -0.35 28 28
FAK1/Vinculin 0.003 0.11 -9999 0 -0.37 26 26
alphaV beta3/Integrin/ppsTEM5 0.004 0.11 -9999 0 -0.38 33 33
RHOA 0.005 0.08 -9999 0 -0.52 12 12
VTN 0.016 0.021 -9999 0 -0.26 3 3
BCAR1 0.017 0.012 -9999 0 -0.26 1 1
FGF2 -0.064 0.16 -9999 0 -0.34 121 121
F11R -0.037 0.12 -9999 0 -0.37 41 41
alphaV/beta3 Integrin/Lactadherin -0.007 0.12 -9999 0 -0.39 39 39
alphaV/beta3 Integrin/TGFBR2 0.01 0.093 -9999 0 -0.36 27 27
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.031 0.063 -9999 0 -0.27 20 20
HSP90AA1 0.013 0.045 -9999 0 -0.39 6 6
alphaV/beta3 Integrin/Talin 0.013 0.077 -9999 0 -0.3 24 24
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.046 0.17 -9999 0 -0.46 71 71
alphaV/beta3 Integrin/Pyk2 0.017 0.094 -9999 0 -0.32 28 28
SDC1 -0.037 0.16 -9999 0 -0.46 61 61
VAV3 -0.024 0.13 -9999 0 -0.27 91 91
PTPN11 0.017 0.023 -9999 0 -0.52 1 1
IRS1 -0.048 0.17 -9999 0 -0.49 68 68
FAK1/Paxillin 0.004 0.11 -9999 0 -0.38 23 23
cell migration 0.011 0.1 -9999 0 -0.34 23 23
ITGAV -0.003 0.1 -9999 0 -0.48 22 22
PI3K -0.017 0.12 -9999 0 -0.42 21 21
SPP1 -0.14 0.23 -9999 0 -0.43 188 188
KDR 0.013 0.052 -9999 0 -0.52 5 5
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 -0.003 0.1 -9999 0 -0.48 22 22
COL4A3 0.013 0.047 -9999 0 -0.37 7 7
angiogenesis -0.083 0.22 -9999 0 -0.66 57 57
Rac1/GTP -0.013 0.12 -9999 0 -0.42 11 11
EDIL3 -0.11 0.22 -9999 0 -0.44 151 151
cell proliferation 0.01 0.093 -9999 0 -0.35 27 27
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.04 0.15 -9999 0 -0.38 74 74
EPHB2 0.007 0.062 -9999 0 -0.32 16 16
Syndecan-2/TACI -0.006 0.091 -9999 0 -0.3 37 37
LAMA1 0.015 0.027 -9999 0 -0.26 5 5
Syndecan-2/alpha2 ITGB1 -0.061 0.17 -9999 0 -0.31 137 137
HRAS 0.012 0.051 -9999 0 -0.41 7 7
Syndecan-2/CASK -0.016 0.088 -9999 0 -0.31 37 37
ITGA5 0.014 0.042 -9999 0 -0.46 4 4
BAX 0.01 0.085 -9999 0 -10000 0 0
EPB41 0.016 0.026 -9999 0 -0.39 2 2
positive regulation of cell-cell adhesion -0.01 0.093 -9999 0 -0.28 48 48
LAMA3 -0.069 0.18 -9999 0 -0.43 102 102
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.017 0.12 -9999 0 -0.38 46 46
Syndecan-2/MMP2 -0.03 0.14 -9999 0 -0.38 62 62
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.023 0.12 -9999 0 -0.37 56 56
dendrite morphogenesis -0.009 0.095 -9999 0 -0.3 41 41
Syndecan-2/GM-CSF -0.013 0.099 -9999 0 -0.31 42 42
determination of left/right symmetry -0.016 0.11 -9999 0 -0.37 37 37
Syndecan-2/PKC delta -0.005 0.093 -9999 0 -0.3 40 40
GNB2L1 0.015 0.04 -9999 0 -0.52 3 3
MAPK3 -0.004 0.09 -9999 0 -0.27 43 43
MAPK1 -0.005 0.092 -9999 0 -0.28 43 43
Syndecan-2/RACK1 0.004 0.087 -9999 0 -0.26 43 43
NF1 0.015 0.035 -9999 0 -0.43 3 3
FGFR/FGF/Syndecan-2 -0.016 0.11 -9999 0 -0.37 37 37
ITGA2 -0.047 0.17 -9999 0 -0.46 72 72
MAPK8 0.002 0.093 -9999 0 -0.3 40 40
Syndecan-2/alpha2/beta1 Integrin -0.017 0.13 -9999 0 -0.3 82 82
Syndecan-2/Kininogen -0.004 0.09 -9999 0 -0.3 37 37
ITGB1 0.015 0.037 -9999 0 -0.39 4 4
SRC 0.008 0.085 -9999 0 -0.25 44 44
Syndecan-2/CASK/Protein 4.1 -0.003 0.082 -9999 0 -0.27 38 38
extracellular matrix organization -0.004 0.091 -9999 0 -0.3 38 38
actin cytoskeleton reorganization -0.04 0.15 -9999 0 -0.38 74 74
Syndecan-2/Caveolin-2/Ras -0.013 0.12 -9999 0 -0.33 53 53
Syndecan-2/Laminin alpha3 -0.055 0.15 -9999 0 -0.34 98 98
Syndecan-2/RasGAP 0.007 0.093 -9999 0 -0.25 51 51
alpha5/beta1 Integrin 0.022 0.041 -9999 0 -0.37 5 5
PRKCD 0.014 0.042 -9999 0 -0.46 4 4
Syndecan-2 dimer -0.009 0.095 -9999 0 -0.3 41 41
GO:0007205 0.004 0.005 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.012 0.093 -9999 0 -0.41 7 7
RHOA 0.005 0.08 -9999 0 -0.52 12 12
SDCBP 0.003 0.081 -9999 0 -0.4 19 19
TNFRSF13B 0.013 0.036 -9999 0 -0.26 9 9
RASA1 0.004 0.079 -9999 0 -0.42 16 16
alpha2/beta1 Integrin -0.023 0.12 -9999 0 -0.37 56 56
Syndecan-2/Synbindin -0.003 0.09 -9999 0 -0.3 37 37
TGFB1 0.017 0.023 -9999 0 -0.52 1 1
CASP3 0.004 0.084 -9999 0 -0.27 40 40
FN1 -0.046 0.17 -9999 0 -0.46 71 71
Syndecan-2/IL8 -0.055 0.14 -9999 0 -0.33 86 86
SDC2 -0.016 0.11 -9999 0 -0.37 37 37
KNG1 0.017 0.017 -9999 0 -0.26 2 2
Syndecan-2/Neurofibromin -0.005 0.092 -9999 0 -0.3 39 39
TRAPPC4 0.018 0 -9999 0 -10000 0 0
CSF2 -0.001 0.075 -9999 0 -0.28 33 33
Syndecan-2/TGFB1 -0.004 0.091 -9999 0 -0.3 38 38
Syndecan-2/Syntenin/PI-4-5-P2 -0.01 0.094 -9999 0 -0.28 48 48
Syndecan-2/Ezrin -0.009 0.091 -9999 0 -0.28 49 49
PRKACA 0.004 0.083 -9999 0 -0.27 39 39
angiogenesis -0.055 0.14 -9999 0 -0.33 86 86
MMP2 -0.029 0.15 -9999 0 -0.47 51 51
IL8 -0.073 0.17 -9999 0 -0.34 135 135
calcineurin-NFAT signaling pathway -0.006 0.091 -9999 0 -0.3 37 37
Signaling events mediated by PTP1B

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 0.01 0.066 -10000 0 -0.52 8 8
Jak2/Leptin Receptor -0.038 0.12 -10000 0 -0.35 43 43
PTP1B/AKT1 -0.042 0.12 0.29 2 -0.3 59 61
FYN 0.009 0.063 -10000 0 -0.4 11 11
p210 bcr-abl/PTP1B -0.054 0.12 0.32 2 -0.31 67 69
EGFR -0.083 0.18 -10000 0 -0.36 136 136
EGF/EGFR -0.14 0.2 0.18 1 -0.36 193 194
CSF1 0.014 0.037 -10000 0 -0.3 7 7
AKT1 0.011 0.054 -10000 0 -0.38 9 9
INSR 0.015 0.037 -10000 0 -0.39 4 4
PTP1B/N-cadherin -0.064 0.15 0.28 2 -0.35 72 74
Insulin Receptor/Insulin -0.019 0.099 -10000 0 -0.33 26 26
HCK -0.005 0.11 -10000 0 -0.47 25 25
CRK 0.016 0.033 -10000 0 -0.52 2 2
TYK2 -0.044 0.12 0.3 2 -0.32 53 55
EGF -0.15 0.23 -10000 0 -0.43 193 193
YES1 0.007 0.07 -10000 0 -0.43 12 12
CAV1 -0.072 0.14 0.29 2 -0.35 67 69
TXN 0.013 0.017 -10000 0 -0.26 2 2
PTP1B/IRS1/GRB2 -0.066 0.15 -10000 0 -0.36 83 83
cell migration 0.054 0.12 0.31 67 -0.32 2 69
STAT3 0.014 0.041 -10000 0 -0.52 3 3
PRLR -0.027 0.15 -10000 0 -0.49 50 50
ITGA2B 0.015 0.021 -10000 0 -0.26 3 3
CSF1R 0.017 0.017 -10000 0 -0.26 2 2
Prolactin Receptor/Prolactin -0.002 0.12 -10000 0 -0.36 47 47
FGR 0.017 0.017 -10000 0 -0.26 2 2
PTP1B/p130 Cas -0.043 0.12 0.28 2 -0.31 54 56
Crk/p130 Cas -0.034 0.12 -10000 0 -0.34 36 36
DOK1 -0.038 0.13 0.3 2 -0.36 45 47
JAK2 -0.036 0.12 -10000 0 -0.35 41 41
Jak2/Leptin Receptor/Leptin -0.069 0.13 -10000 0 -0.39 41 41
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
PTPN1 -0.055 0.12 0.32 2 -0.31 67 69
LYN 0.014 0.031 -10000 0 -0.26 7 7
CDH2 -0.029 0.13 -10000 0 -0.35 67 67
SRC -0.004 0.07 -10000 0 -0.68 3 3
ITGB3 0.001 0.076 -10000 0 -0.32 25 25
CAT1/PTP1B -0.084 0.17 0.25 2 -0.45 60 62
CAPN1 0.003 0.078 -10000 0 -0.44 15 15
CSK 0.015 0.031 -10000 0 -0.32 4 4
PI3K -0.035 0.1 -10000 0 -0.33 35 35
mol:H2O2 -0.003 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.062 0.12 -10000 0 -0.39 36 36
negative regulation of transcription -0.036 0.11 -10000 0 -0.35 41 41
FCGR2A -0.003 0.099 -10000 0 -0.45 23 23
FER 0.013 0.027 -10000 0 -0.4 2 2
alphaIIb/beta3 Integrin 0.011 0.056 -10000 0 -0.37 7 7
BLK -0.018 0.1 -10000 0 -0.29 61 61
Insulin Receptor/Insulin/Shc 0.032 0.032 -10000 0 -0.31 4 4
RHOA 0.004 0.081 -10000 0 -0.53 12 12
LEPR -0.005 0.091 -10000 0 -0.34 33 33
BCAR1 0.017 0.012 -10000 0 -0.26 1 1
p210 bcr-abl/Grb2 0.016 0.024 -10000 0 -0.26 4 4
mol:NADPH -0.003 0.004 -10000 0 -10000 0 0
TRPV6 -0.059 0.16 -10000 0 -0.47 45 45
PRL 0.018 0.033 -10000 0 -0.32 4 4
SOCS3 -0.005 0.17 -10000 0 -1.3 8 8
SPRY2 -0.034 0.15 -10000 0 -0.43 58 58
Insulin Receptor/Insulin/IRS1 -0.008 0.12 -10000 0 -0.32 62 62
CSF1/CSF1R -0.036 0.12 -10000 0 -0.3 54 54
Ras protein signal transduction 0.029 0.038 -10000 0 -0.2 2 2
IRS1 -0.048 0.17 -10000 0 -0.49 68 68
INS 0.017 0.024 -10000 0 -0.53 1 1
LEP -0.052 0.16 -10000 0 -0.36 99 99
STAT5B -0.042 0.11 0.25 2 -0.28 62 64
STAT5A -0.043 0.11 0.25 2 -0.28 63 65
GRB2 0.016 0.024 -10000 0 -0.26 4 4
PDGFB-D/PDGFRB -0.047 0.13 0.28 2 -0.35 54 56
CSN2 0.019 0.1 -10000 0 -0.88 4 4
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
LAT -0.025 0.12 -10000 0 -0.56 19 19
YBX1 0.007 0.073 -10000 0 -0.33 16 16
LCK -0.073 0.18 -10000 0 -0.4 115 115
SHC1 0.017 0.023 -10000 0 -0.52 1 1
NOX4 -0.057 0.18 -10000 0 -0.49 76 76
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.011 0.088 -10000 0 -0.29 24 24
adherens junction organization -0.013 0.11 -10000 0 -0.25 78 78
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.018 0.11 -10000 0 -0.34 20 20
FMN1 -0.008 0.1 -10000 0 -0.24 78 78
mol:IP3 0.006 0.081 -10000 0 -0.24 25 25
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.008 0.11 -10000 0 -0.25 78 78
CTNNB1 0.002 0.09 -10000 0 -0.45 19 19
AKT1 0.007 0.093 -10000 0 -0.32 12 12
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.018 0.15 -10000 0 -0.38 76 76
CTNND1 0.016 0.029 -10000 0 -0.35 3 3
mol:PI-4-5-P2 0 0.1 -10000 0 -0.23 78 78
VASP -0.007 0.11 -10000 0 -0.24 85 85
ZYX -0.006 0.11 -10000 0 -0.24 86 86
JUB -0.023 0.13 -10000 0 -0.29 50 50
EGFR(dimer) -0.042 0.13 -10000 0 -0.36 31 31
E-cadherin/beta catenin-gamma catenin -0.019 0.12 -10000 0 -0.3 78 78
mol:PI-3-4-5-P3 0.003 0.092 -10000 0 -0.26 28 28
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
PI3K 0.004 0.093 -10000 0 -0.26 28 28
FYN 0.016 0.084 -10000 0 -0.3 14 14
mol:Ca2+ 0.006 0.08 -10000 0 -0.24 25 25
JUP 0.012 0.056 -10000 0 -0.42 8 8
PIK3R1 -0.008 0.11 -10000 0 -0.42 32 32
mol:DAG 0.006 0.081 -10000 0 -0.24 25 25
CDH1 -0.049 0.17 -10000 0 -0.48 71 71
RhoA/GDP -0.024 0.12 -10000 0 -0.35 27 27
establishment of polarity of embryonic epithelium -0.007 0.11 -10000 0 -0.24 85 85
SRC 0.015 0.035 -10000 0 -0.43 3 3
RAC1 0.018 0 -10000 0 -10000 0 0
RHOA 0.005 0.08 -10000 0 -0.52 12 12
EGFR -0.077 0.17 -10000 0 -0.35 136 136
CASR 0.013 0.078 -10000 0 -0.31 7 7
RhoA/GTP 0.008 0.086 -10000 0 -0.32 11 11
AKT2 0.009 0.087 -10000 0 -0.32 7 7
actin cable formation -0.007 0.11 -10000 0 -0.23 85 85
apoptosis -0.006 0.089 0.26 26 -10000 0 26
CTNNA1 0.017 0.024 -10000 0 -0.52 1 1
mol:GDP -0.029 0.12 -10000 0 -0.36 21 21
PIP5K1A -0.001 0.1 -10000 0 -0.23 78 78
PLCG1 0.006 0.082 -10000 0 -0.25 25 25
Rac1/GTP -0.033 0.12 -10000 0 -0.33 30 30
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.035 0.05 0.22 3 -0.53 1 4
AES 0.033 0.037 0.2 3 -10000 0 3
FBXW11 0.015 0.035 -10000 0 -0.43 3 3
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.009 0.076 -10000 0 -0.36 19 19
SMAD4 0.009 0.067 -10000 0 -0.49 9 9
DKK2 -0.025 0.14 -10000 0 -0.43 51 51
TLE1 -0.017 0.16 -10000 0 -0.48 50 50
MACF1 0.016 0.026 -10000 0 -0.39 2 2
CTNNB1 -0.006 0.098 0.28 2 -0.35 15 17
WIF1 -0.025 0.1 -10000 0 -0.26 82 82
beta catenin/RanBP3 0.069 0.19 0.37 120 -0.42 2 122
KREMEN2 -0.19 0.23 -10000 0 -0.41 258 258
DKK1 -0.12 0.19 -10000 0 -0.34 198 198
beta catenin/beta TrCP1 0.005 0.097 0.27 2 -0.35 13 15
FZD1 0.003 0.082 -10000 0 -0.43 17 17
AXIN2 -0.098 0.33 -10000 0 -1.3 31 31
AXIN1 0.017 0.012 -10000 0 -0.26 1 1
RAN 0.018 0.012 -10000 0 -0.26 1 1
Axin1/APC/GSK3/beta catenin 0.034 0.036 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.017 0.16 -10000 0 -0.5 22 22
Axin1/APC/GSK3 0.049 0.042 0.25 4 -10000 0 4
Axin1/APC/GSK3/beta catenin/Macf1 0.037 0.067 -10000 0 -0.3 2 2
HNF1A 0.031 0.046 0.2 1 -0.24 5 6
CTBP1 0.033 0.041 0.21 2 -0.26 1 3
MYC -0.12 0.36 -10000 0 -1.2 48 48
RANBP3 0.018 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.12 0.16 -10000 0 -0.33 186 186
NKD1 0.007 0.068 -10000 0 -0.4 13 13
TCF4 0.01 0.12 0.2 2 -0.49 24 26
TCF3 0.028 0.062 0.21 2 -0.38 6 8
WNT1/LRP6/FZD1/Axin1 0.031 0.062 -10000 0 -0.27 20 20
Ran/GTP 0.014 0.009 -10000 0 -0.17 1 1
CtBP/CBP/TCF/TLE1/AES 0.098 0.25 0.49 123 -0.48 9 132
LEF1 -0.007 0.13 0.2 3 -0.33 58 61
DVL1 0.045 0.042 -10000 0 -0.31 3 3
CSNK2A1 0.017 0.023 -10000 0 -0.52 1 1
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.038 0.17 -10000 0 -0.52 30 30
DKK1/LRP6/Kremen 2 -0.17 0.18 -10000 0 -0.34 248 248
LRP6 0.008 0.065 -10000 0 -0.38 13 13
CSNK1A1 0.035 0.048 0.19 17 -0.45 1 18
NLK 0.008 0.045 -10000 0 -0.28 11 11
CCND1 -0.25 0.54 -10000 0 -1.4 87 87
WNT1 0.016 0.023 -10000 0 -0.52 1 1
GSK3A 0.018 0.001 -10000 0 -10000 0 0
GSK3B 0.017 0.001 -10000 0 -10000 0 0
FRAT1 0.008 0.068 -10000 0 -0.47 10 10
PPP2R5D 0.029 0.039 0.26 8 -10000 0 8
APC 0.026 0.062 -10000 0 -0.24 23 23
WNT1/LRP6/FZD1 0.038 0.06 -10000 0 -0.24 10 10
CREBBP 0.032 0.051 0.21 2 -0.52 2 4
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.002 0.071 -9999 0 -0.29 28 28
Caspase 8 (4 units) -0.033 0.13 -9999 0 -0.4 33 33
NEF -0.015 0.042 -9999 0 -0.18 10 10
NFKBIA -0.004 0.061 -9999 0 -0.52 4 4
BIRC3 -0.065 0.21 -9999 0 -0.54 76 76
CYCS -0.039 0.14 -9999 0 -0.39 39 39
RIPK1 0.017 0.023 -9999 0 -0.52 1 1
CD247 -0.13 0.24 -9999 0 -0.47 151 151
MAP2K7 -0.022 0.13 -9999 0 -0.51 15 15
protein ubiquitination 0.017 0.096 -9999 0 -0.33 14 14
CRADD 0.009 0.067 -9999 0 -0.49 9 9
DAXX 0.017 0.012 -9999 0 -0.26 1 1
FAS -0.023 0.13 -9999 0 -0.42 50 50
BID -0.047 0.14 -9999 0 -0.33 70 70
NF-kappa-B/RelA/I kappa B alpha -0.015 0.12 -9999 0 -0.27 76 76
TRADD 0.016 0.026 -9999 0 -0.39 2 2
MAP3K5 -0.021 0.13 -9999 0 -0.42 46 46
CFLAR 0.01 0.064 -9999 0 -0.46 9 9
FADD 0 0.068 -9999 0 -0.26 34 34
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.015 0.12 -9999 0 -0.27 76 76
MAPK8 -0.015 0.12 -9999 0 -0.5 13 13
APAF1 0.012 0.051 -9999 0 -0.41 7 7
TRAF1 0.013 0.041 -9999 0 -0.29 9 9
TRAF2 0.014 0.042 -9999 0 -0.46 4 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.051 0.14 -9999 0 -0.34 67 67
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.009 0.11 -9999 0 -0.35 19 19
CHUK 0.016 0.1 -9999 0 -0.36 15 15
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.001 0.11 -9999 0 -0.28 54 54
TCRz/NEF -0.11 0.21 -9999 0 -0.44 132 132
TNF -0.004 0.094 -9999 0 -0.36 31 31
FASLG -0.12 0.26 -9999 0 -0.46 157 157
NFKB1 -0.002 0.046 -9999 0 -0.52 1 1
TNFR1A/BAG4/TNF-alpha 0.012 0.074 -9999 0 -0.31 18 18
CASP6 -0.019 0.13 -9999 0 -0.55 17 17
CASP7 -0.072 0.22 -9999 0 -0.54 79 79
RELA -0.001 0.04 -9999 0 -10000 0 0
CASP2 0.018 0 -9999 0 -10000 0 0
CASP3 -0.065 0.22 -9999 0 -0.54 78 78
TNFRSF1A 0.016 0.033 -9999 0 -0.52 2 2
TNFR1A/BAG4 0.014 0.055 -9999 0 -0.37 5 5
CASP8 0.018 0 -9999 0 -10000 0 0
CASP9 0.017 0.023 -9999 0 -0.52 1 1
MAP3K14 0.015 0.1 -9999 0 -0.41 11 11
APAF-1/Caspase 9 -0.097 0.15 -9999 0 -0.39 95 95
BCL2 -0.066 0.15 -9999 0 -0.43 36 36
Ras signaling in the CD4+ TCR pathway

Figure S49.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S49.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.035 0.14 -9999 0 -0.33 75 75
MAP3K8 -0.037 0.15 -9999 0 -0.39 69 69
FOS -0.014 0.092 -9999 0 -0.28 14 14
PRKCA 0.01 0.034 -9999 0 -0.26 8 8
PTPN7 0.006 0.05 -9999 0 -0.28 14 14
HRAS 0.011 0.051 -9999 0 -0.41 7 7
PRKCB -0.003 0.007 -9999 0 -0.013 171 171
NRAS 0.005 0.073 -9999 0 -0.4 15 15
RAS family/GTP 0.013 0.064 -9999 0 -0.28 20 20
MAPK3 0.001 0.057 -9999 0 -0.45 2 2
MAP2K1 -0.005 0.065 -9999 0 -0.22 12 12
ELK1 0.01 0.038 -9999 0 -0.39 4 4
BRAF 0.004 0.06 -9999 0 -0.41 8 8
mol:GTP -0.001 0.002 -9999 0 -0.004 170 170
MAPK1 0.001 0.06 -9999 0 -0.43 3 3
RAF1 0.011 0.029 -9999 0 -10000 0 0
KRAS 0.007 0.069 -9999 0 -0.45 11 11
Coregulation of Androgen receptor activity

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
NRIP1 -0.042 0.16 -9999 0 -0.46 67 67
SVIL -0.004 0.1 -9999 0 -0.44 27 27
ZNF318 0.014 0.005 -9999 0 -10000 0 0
JMJD2C 0.023 0.032 -9999 0 -0.32 4 4
T-DHT/AR/Ubc9 -0.066 0.14 -9999 0 -0.33 103 103
CARM1 0.014 0.039 -9999 0 -0.36 5 5
PRDX1 0.011 0.055 -9999 0 -0.45 7 7
PELP1 0.017 0.001 -9999 0 -10000 0 0
CTNNB1 0.002 0.09 -9999 0 -0.45 19 19
AKT1 0.01 0.054 -9999 0 -0.38 9 9
PTK2B 0.017 0.017 -9999 0 -0.26 2 2
MED1 -0.001 0.068 -9999 0 -0.26 34 34
MAK -0.018 0.096 -9999 0 -0.28 58 58
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.019 0.012 -9999 0 -0.26 1 1
GSN -0.001 0.098 -9999 0 -0.43 24 24
NCOA2 0.009 0.063 -9999 0 -0.4 11 11
NCOA6 0.019 0.012 -9999 0 -0.26 1 1
DNA-PK 0.029 0.029 -9999 0 -0.31 2 2
NCOA4 0.008 0.069 -9999 0 -0.45 11 11
PIAS3 0.019 0.002 -9999 0 -10000 0 0
cell proliferation -0.044 0.092 -9999 0 -0.67 7 7
XRCC5 0.017 0.001 -9999 0 -10000 0 0
UBE3A 0.018 0.033 -9999 0 -0.52 2 2
T-DHT/AR/SNURF -0.077 0.14 -9999 0 -0.29 136 136
FHL2 -0.16 0.35 -9999 0 -0.98 73 73
RANBP9 0.019 0.012 -9999 0 -0.26 1 1
JMJD1A -0.002 0.056 -9999 0 -10000 0 0
CDK6 -0.02 0.11 -9999 0 -0.3 63 63
TGFB1I1 -0.003 0.1 -9999 0 -0.49 23 23
T-DHT/AR/CyclinD1 -0.13 0.21 -9999 0 -0.42 151 151
XRCC6 0.016 0.012 -9999 0 -0.26 1 1
T-DHT/AR -0.087 0.17 -9999 0 -0.33 142 142
CTDSP1 0.016 0.033 -9999 0 -0.52 2 2
CTDSP2 0.011 0.044 -9999 0 -0.42 5 5
BRCA1 0.001 0.094 -9999 0 -0.48 19 19
TCF4 -0.008 0.11 -9999 0 -0.51 24 24
CDKN2A -0.055 0.15 -9999 0 -0.34 108 108
SRF -0.001 0.055 -9999 0 -0.28 4 4
NKX3-1 -0.057 0.11 -9999 0 -0.24 107 107
KLK3 0.022 0.055 -9999 0 -10000 0 0
TMF1 0.018 0.001 -9999 0 -10000 0 0
HNRNPA1 0.015 0.023 -9999 0 -0.52 1 1
AOF2 0.018 0.026 -9999 0 -0.39 2 2
APPL1 0.015 0.054 -9999 0 -0.37 9 9
T-DHT/AR/Caspase 8 -0.067 0.14 -9999 0 -0.34 103 103
AR -0.11 0.22 -9999 0 -0.53 104 104
UBA3 0 0.001 -9999 0 -10000 0 0
PATZ1 0.003 0.084 -9999 0 -0.5 14 14
PAWR 0.001 0.091 -9999 0 -0.44 20 20
PRKDC 0.011 0.046 -9999 0 -0.32 9 9
PA2G4 0.016 0.012 -9999 0 -0.26 1 1
UBE2I 0.018 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.06 0.13 -9999 0 -0.31 103 103
RPS6KA3 0.011 0.057 -9999 0 -0.34 12 12
T-DHT/AR/ARA70 -0.072 0.15 -9999 0 -0.34 110 110
LATS2 0.004 0.078 -9999 0 -0.48 13 13
T-DHT/AR/PRX1 -0.064 0.14 -9999 0 -0.31 108 108
Cyclin D3/CDK11 p58 0.013 0.008 -9999 0 -0.17 1 1
VAV3 -0.082 0.2 -9999 0 -0.48 107 107
KLK2 -0.013 0.076 -9999 0 -0.4 1 1
CASP8 0.017 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.054 0.14 -9999 0 -0.3 111 111
TMPRSS2 -0.19 0.38 -9999 0 -0.91 107 107
CCND1 -0.09 0.2 -9999 0 -0.44 125 125
PIAS1 0.019 0.012 -9999 0 -0.26 1 1
mol:T-DHT -0.019 0.037 -9999 0 -0.077 132 132
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.016 0.05 -9999 0 -0.43 6 6
T-DHT/AR/CDK6 -0.086 0.17 -9999 0 -0.38 118 118
CMTM2 0.016 0.023 -9999 0 -0.52 1 1
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 -0.003 0.05 -9999 0 -0.32 6 6
CCND3 0.017 0.012 -9999 0 -0.26 1 1
TGIF1 0.006 0.073 -9999 0 -0.52 10 10
FKBP4 0.013 0.055 -9999 0 -0.44 7 7
Glypican 2 network

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
MDK -0.016 0.12 -9999 0 -0.37 46 46
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.011 0.083 -9999 0 -0.26 46 46
neuron projection morphogenesis -0.011 0.083 -9999 0 -0.26 46 46
Cellular roles of Anthrax toxin

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
ANTXR1 -0.026 0.14 -10000 0 -0.46 48 48
ANTXR2 0.003 0.087 -10000 0 -0.5 15 15
negative regulation of myeloid dendritic cell antigen processing and presentation -0.007 0.021 -10000 0 -0.073 46 46
monocyte activation -0.021 0.12 -10000 0 -0.41 40 40
MAP2K2 0.007 0.06 -10000 0 -0.77 3 3
MAP2K1 0.005 0.021 -10000 0 -0.096 6 6
MAP2K7 0.005 0.024 -10000 0 -0.27 1 1
MAP2K6 -0.01 0.064 -10000 0 -0.21 37 37
CYAA -0.015 0.091 -10000 0 -0.29 46 46
MAP2K4 -0.006 0.056 -10000 0 -0.21 30 30
IL1B -0.03 0.095 -10000 0 -0.25 69 69
Channel -0.01 0.099 -10000 0 -0.31 46 46
NLRP1 0.002 0.036 -10000 0 -0.32 4 4
CALM1 0.018 0 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.007 0.027 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.007 0.021 0.073 46 -10000 0 46
MAPK3 0.004 0.025 -10000 0 -0.19 2 2
MAPK1 0.004 0.027 -10000 0 -0.27 2 2
PGR -0.14 0.12 -10000 0 -0.21 367 367
PA/Cellular Receptors -0.012 0.11 -10000 0 -0.34 46 46
apoptosis -0.007 0.021 -10000 0 -0.073 46 46
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.008 0.094 -10000 0 -0.3 46 46
macrophage activation 0.011 0.028 -10000 0 -0.25 3 3
TNF -0.004 0.094 -10000 0 -0.36 31 31
VCAM1 -0.021 0.12 -10000 0 -0.42 40 40
platelet activation 0.007 0.027 -10000 0 -10000 0 0
MAPKKK cascade -0.001 0.034 0.12 18 -10000 0 18
IL18 -0.032 0.11 -10000 0 -0.28 70 70
negative regulation of macrophage activation -0.007 0.021 -10000 0 -0.073 46 46
LEF -0.007 0.021 -10000 0 -0.073 46 46
CASP1 -0.006 0.042 -10000 0 -0.15 25 25
mol:cAMP 0.007 0.027 -10000 0 -10000 0 0
necrosis -0.007 0.021 -10000 0 -0.073 46 46
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.008 0.094 -10000 0 -0.3 46 46
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.044 0.14 -10000 0 -0.36 67 67
fibroblast growth factor receptor signaling pathway -0.044 0.14 -10000 0 -0.36 67 67
LAMA1 0.015 0.027 -10000 0 -0.26 5 5
PRNP 0.007 0.07 -10000 0 -0.43 12 12
GPC1/SLIT2 -0.024 0.14 -10000 0 -0.39 59 59
SMAD2 0.011 0.085 -10000 0 -0.28 37 37
GPC1/PrPc/Cu2+ 0.003 0.082 -10000 0 -0.33 29 29
GPC1/Laminin alpha1 0.007 0.082 -10000 0 -0.37 22 22
TDGF1 0.017 0.012 -10000 0 -0.26 1 1
CRIPTO/GPC1 0.009 0.08 -10000 0 -0.37 22 22
APP/GPC1 -0.024 0.13 -10000 0 -0.38 56 56
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.01 0.081 -10000 0 -0.31 30 30
FLT1 0.005 0.077 -10000 0 -0.45 14 14
GPC1/TGFB/TGFBR1/TGFBR2 0.008 0.094 -10000 0 -0.32 36 36
SERPINC1 0.007 0.055 -10000 0 -0.27 19 19
FYN 0.011 0.078 -10000 0 -0.31 28 28
FGR 0.015 0.068 -10000 0 -0.3 22 22
positive regulation of MAPKKK cascade -0.011 0.12 -10000 0 -0.36 41 41
SLIT2 -0.028 0.15 -10000 0 -0.48 49 49
GPC1/NRG 0.003 0.087 -10000 0 -0.38 22 22
NRG1 0.009 0.049 -10000 0 -0.26 17 17
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.003 0.096 -10000 0 -0.32 36 36
LYN 0.014 0.071 -10000 0 -0.31 22 22
mol:Spermine -0.005 0.079 -10000 0 -0.35 25 25
cell growth -0.044 0.14 -10000 0 -0.36 67 67
BMP signaling pathway 0.006 0.11 0.49 25 -10000 0 25
SRC 0.015 0.073 -10000 0 -0.32 23 23
TGFBR1 0.003 0.083 -10000 0 -0.42 18 18
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.057 0.14 -10000 0 -0.3 126 126
GPC1 -0.006 0.11 -10000 0 -0.49 25 25
TGFBR1 (dimer) 0.003 0.082 -10000 0 -0.42 18 18
VEGFA 0 0.076 -10000 0 -0.29 31 31
BLK -0.004 0.092 -10000 0 -0.33 30 30
HCK 0.002 0.095 -10000 0 -0.32 41 41
FGF2 -0.064 0.16 -10000 0 -0.34 121 121
FGFR1 -0.011 0.1 -10000 0 -0.35 42 42
VEGFR1 homodimer 0.005 0.077 -10000 0 -0.44 14 14
TGFBR2 0.012 0.055 -10000 0 -0.45 7 7
cell death -0.024 0.13 -10000 0 -0.38 56 56
ATIII/GPC1 0.002 0.088 -10000 0 -0.38 23 23
PLA2G2A/GPC1 -0.043 0.12 -10000 0 -0.39 41 41
LCK -0.038 0.13 -10000 0 -0.32 81 81
neuron differentiation 0.003 0.087 -10000 0 -0.38 22 22
PrPc/Cu2+ 0.006 0.05 -10000 0 -0.31 12 12
APP -0.028 0.14 -10000 0 -0.42 55 55
TGFBR2 (dimer) 0.012 0.055 -10000 0 -0.44 7 7
TRAIL signaling pathway

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
TNFSF10 -0.042 0.16 -10000 0 -0.46 66 66
positive regulation of NF-kappaB transcription factor activity -0.018 0.12 -10000 0 -0.37 51 51
MAP2K4 -0.013 0.12 -10000 0 -0.38 29 29
IKBKB 0.011 0.047 -10000 0 -0.31 10 10
TNFRSF10B 0.004 0.083 -10000 0 -0.47 15 15
TNFRSF10A -0.003 0.1 -10000 0 -0.46 23 23
SMPD1 -0.008 0.087 -10000 0 -0.23 57 57
IKBKG 0.018 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.015 0.031 -10000 0 -0.32 4 4
TRAIL/TRAILR2 -0.026 0.14 -10000 0 -0.41 56 56
TRAIL/TRAILR3 -0.031 0.13 -10000 0 -0.37 53 53
TRAIL/TRAILR1 -0.031 0.14 -10000 0 -0.4 62 62
TRAIL/TRAILR4 -0.018 0.12 -10000 0 -0.37 51 51
TRAIL/TRAILR1/DAP3/GTP -0.012 0.12 -10000 0 -0.3 63 63
IKK complex -0.028 0.084 -10000 0 -0.43 15 15
RIPK1 0.017 0.023 -10000 0 -0.52 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.012 0.019 -10000 0 -0.28 2 2
MAPK3 -0.018 0.12 -10000 0 -0.37 51 51
MAP3K1 -0.009 0.12 -10000 0 -0.38 27 27
TRAILR4 (trimer) 0.015 0.031 -10000 0 -0.32 4 4
TRADD 0.016 0.026 -10000 0 -0.39 2 2
TRAILR1 (trimer) -0.003 0.1 -10000 0 -0.46 23 23
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.003 0.11 -10000 0 -0.26 65 65
CFLAR 0.01 0.064 -10000 0 -0.46 9 9
MAPK1 -0.019 0.12 -10000 0 -0.37 52 52
TRAIL/TRAILR1/FADD/TRADD/RIP -0.001 0.12 -10000 0 -0.29 62 62
mol:ceramide -0.008 0.086 -10000 0 -0.23 57 57
FADD 0 0.068 -10000 0 -0.26 34 34
MAPK8 -0.007 0.12 -10000 0 -0.39 24 24
TRAF2 0.014 0.042 -10000 0 -0.46 4 4
TRAILR3 (trimer) -0.004 0.075 -10000 0 -0.26 40 40
CHUK 0.005 0.081 -10000 0 -0.5 13 13
TRAIL/TRAILR1/FADD -0.023 0.13 -10000 0 -0.34 63 63
DAP3 0.016 0.026 -10000 0 -0.39 2 2
CASP10 -0.049 0.12 0.26 1 -0.37 53 54
JNK cascade -0.018 0.12 -10000 0 -0.37 51 51
TRAIL (trimer) -0.041 0.16 -10000 0 -0.46 66 66
TNFRSF10C -0.004 0.075 -10000 0 -0.26 40 40
TRAIL/TRAILR1/DAP3/GTP/FADD -0.01 0.12 -10000 0 -0.29 64 64
TRAIL/TRAILR2/FADD -0.019 0.13 -10000 0 -0.35 57 57
cell death -0.008 0.086 -10000 0 -0.23 57 57
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0 0.11 -10000 0 -0.27 58 58
TRAILR2 (trimer) 0.004 0.082 -10000 0 -0.47 15 15
CASP8 0.01 0.042 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.003 0.12 -10000 0 -0.3 55 55
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.018 0.062 -9999 0 -0.31 17 17
SNTA1 0.011 0.058 -9999 0 -0.48 7 7
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.004 0.086 -9999 0 -0.32 31 31
MAPK12 -0.004 0.091 -9999 0 -0.27 46 46
CCND1 -0.07 0.17 -9999 0 -0.42 91 91
p38 gamma/SNTA1 0.003 0.092 -9999 0 -0.26 50 50
MAP2K3 0.014 0.037 -9999 0 -0.3 7 7
PKN1 0.013 0.045 -9999 0 -0.39 6 6
G2/M transition checkpoint -0.003 0.09 -9999 0 -0.27 46 46
MAP2K6 -0.005 0.09 -9999 0 -0.3 42 42
MAPT -0.054 0.15 -9999 0 -0.32 120 120
MAPK13 0.011 0.071 -9999 0 -0.38 16 16
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.004 0.071 -9999 0 -0.33 22 22
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.037 0.17 -9999 0 -0.45 74 74
KLHL20 -0.015 0.1 -9999 0 -0.26 23 23
CYFIP2 -0.042 0.16 -9999 0 -0.46 65 65
Rac1/GDP 0.006 0.11 -9999 0 -0.3 20 20
ENAH -0.036 0.18 -9999 0 -0.45 76 76
AP1M1 0.017 0.023 -9999 0 -0.52 1 1
RAP1B 0.012 0.044 -9999 0 -0.32 8 8
RAP1A 0.011 0.062 -9999 0 -0.52 7 7
CTNNB1 0.001 0.09 -9999 0 -0.45 19 19
CDC42/GTP -0.033 0.07 -9999 0 -0.3 10 10
ABI1/Sra1/Nap1 -0.042 0.054 -9999 0 -0.17 37 37
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.006 0.12 -9999 0 -0.28 79 79
RAPGEF1 -0.015 0.15 -9999 0 -0.38 74 74
CTNND1 0.016 0.029 -9999 0 -0.35 3 3
regulation of calcium-dependent cell-cell adhesion -0.039 0.17 -9999 0 -0.46 74 74
CRK -0.025 0.16 -9999 0 -0.41 75 75
E-cadherin/gamma catenin/alpha catenin -0.011 0.12 -9999 0 -0.31 65 65
alphaE/beta7 Integrin 0.023 0.038 -9999 0 -0.37 5 5
IQGAP1 0.018 0 -9999 0 -10000 0 0
NCKAP1 0.015 0.031 -9999 0 -0.32 4 4
Rap1/GTP/I-afadin 0.014 0.074 -9999 0 -0.28 29 29
DLG1 -0.031 0.17 -9999 0 -0.44 74 74
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.029 0.055 -9999 0 -0.22 15 15
MLLT4 -0.006 0.11 -9999 0 -0.46 26 26
ARF6/GTP/NME1/Tiam1 0.023 0.053 -9999 0 -0.3 10 10
PI3K -0.036 0.07 -9999 0 -0.28 15 15
ARF6 0.016 0.033 -9999 0 -0.52 2 2
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.027 0.13 -9999 0 -0.37 64 64
TIAM1 0.006 0.073 -9999 0 -0.44 13 13
E-cadherin(dimer)/Ca2+ -0.005 0.11 -9999 0 -0.26 76 76
AKT1 -0.022 0.043 -9999 0 -0.17 14 14
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
CDH1 -0.049 0.17 -9999 0 -0.48 71 71
RhoA/GDP 0.002 0.12 -9999 0 -0.31 29 29
actin cytoskeleton organization -0.009 0.075 -9999 0 -0.19 23 23
CDC42/GDP 0.007 0.11 -9999 0 -0.29 24 24
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.008 0.09 -9999 0 -0.24 66 66
ITGB7 0.018 0 -9999 0 -10000 0 0
RAC1 0.018 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.005 0.11 -9999 0 -0.28 76 76
E-cadherin/Ca2+/beta catenin/alpha catenin -0.014 0.1 -9999 0 -0.27 75 75
mol:GDP -0.004 0.13 -9999 0 -0.3 75 75
CDC42/GTP/IQGAP1 0.024 0 -9999 0 -10000 0 0
JUP 0.011 0.056 -9999 0 -0.42 8 8
p120 catenin/RhoA/GDP 0.002 0.12 -9999 0 -0.33 25 25
RAC1/GTP/IQGAP1 0.024 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.023 0.035 -9999 0 -0.37 4 4
RHOA 0.005 0.08 -9999 0 -0.52 12 12
CDC42 0.018 0 -9999 0 -10000 0 0
CTNNA1 0.017 0.023 -9999 0 -0.52 1 1
positive regulation of S phase of mitotic cell cycle -0.028 0.095 -9999 0 -0.2 98 98
NME1 0.012 0.039 -9999 0 -0.26 11 11
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.033 0.17 -9999 0 -0.44 75 75
regulation of cell-cell adhesion -0.029 0.062 -9999 0 -0.26 10 10
WASF2 -0.021 0.031 -9999 0 -0.2 1 1
Rap1/GTP -0.038 0.08 -9999 0 -0.34 10 10
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.009 0.1 -9999 0 -0.25 70 70
CCND1 -0.036 0.12 -9999 0 -0.26 97 97
VAV2 -0.023 0.16 -9999 0 -0.4 74 74
RAP1/GDP 0.004 0.11 -9999 0 -0.36 9 9
adherens junction assembly -0.032 0.17 -9999 0 -0.43 75 75
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.016 0.021 -9999 0 -0.26 3 3
PIP5K1C 0.014 0.042 -9999 0 -0.46 4 4
regulation of heterotypic cell-cell adhesion 0.006 0.11 -9999 0 -0.24 72 72
E-cadherin/beta catenin -0.045 0.11 -9999 0 -0.34 64 64
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.033 0.17 -9999 0 -0.44 75 75
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
Rac1/GTP -0.079 0.12 -9999 0 -0.41 29 29
E-cadherin/beta catenin/alpha catenin -0.017 0.12 -9999 0 -0.31 75 75
ITGAE 0.013 0.052 -9999 0 -0.52 5 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.04 0.18 -9999 0 -0.47 74 74
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process 0.004 0.089 0.33 33 -10000 0 33
PI3K Class IB/PDE3B -0.004 0.089 -10000 0 -0.33 33 33
PDE3B -0.004 0.089 -10000 0 -0.33 33 33
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.025 0.076 -10000 0 -0.64 6 6
HDAC1 0.022 0.03 -10000 0 -0.53 1 1
AES 0.019 0.006 -10000 0 -10000 0 0
FBXW11 0.015 0.035 -10000 0 -0.43 3 3
DTX1 0.012 0.05 -10000 0 -0.35 9 9
LRP6/FZD1 0.009 0.076 -10000 0 -0.36 19 19
TLE1 -0.031 0.15 -10000 0 -0.45 56 56
AP1 -0.051 0.13 -10000 0 -0.3 82 82
NCSTN 0.017 0.023 -10000 0 -0.52 1 1
ADAM10 0.013 0.045 -10000 0 -0.39 6 6
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.041 0.13 -10000 0 -0.44 7 7
NICD/RBPSUH 0.027 0.076 -10000 0 -0.63 6 6
WIF1 -0.025 0.1 -10000 0 -0.26 82 82
NOTCH1 -0.003 0.077 -10000 0 -0.67 6 6
PSENEN 0.017 0.012 -10000 0 -0.26 1 1
KREMEN2 -0.19 0.23 -10000 0 -0.41 258 258
DKK1 -0.12 0.19 -10000 0 -0.34 198 198
beta catenin/beta TrCP1 0.004 0.085 0.24 4 -0.35 17 21
APH1B 0 0.096 -10000 0 -0.51 18 18
APH1A 0.003 0.068 -10000 0 -0.29 25 25
AXIN1 0.006 0.04 0.24 8 -0.21 6 14
CtBP/CBP/TCF1/TLE1/AES 0.036 0.1 0.29 5 -0.27 1 6
PSEN1 0.013 0.052 -10000 0 -0.52 5 5
FOS -0.11 0.2 -10000 0 -0.37 171 171
JUN -0.034 0.15 -10000 0 -0.46 57 57
MAP3K7 0.019 0.022 -10000 0 -0.26 3 3
CTNNB1 -0.005 0.084 0.23 7 -0.38 15 22
MAPK3 0.016 0.026 -10000 0 -0.39 2 2
DKK2/LRP6/Kremen 2 -0.12 0.16 -10000 0 -0.33 186 186
HNF1A 0.016 0.029 -10000 0 -0.25 6 6
CTBP1 0.018 0.018 -10000 0 -0.26 2 2
MYC -0.086 0.34 -10000 0 -1.4 34 34
NKD1 0.008 0.068 -10000 0 -0.4 13 13
FZD1 0.003 0.082 -10000 0 -0.43 17 17
NOTCH1 precursor/Deltex homolog 1 0.024 0.085 -10000 0 -0.69 6 6
apoptosis -0.051 0.13 -10000 0 -0.3 82 82
Delta 1/NOTCHprecursor 0.027 0.076 -10000 0 -0.63 6 6
DLL1 0.017 0.012 -10000 0 -0.26 1 1
PPARD 0.004 0.045 -10000 0 -10000 0 0
Gamma Secretase 0.031 0.071 -10000 0 -0.25 26 26
APC 0.002 0.055 0.24 7 -0.35 7 14
DVL1 0.022 0.038 -10000 0 -0.38 3 3
CSNK2A1 0.016 0.023 -10000 0 -0.52 1 1
MAP3K7IP1 0.02 0.008 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.17 0.18 -10000 0 -0.34 248 248
LRP6 0.008 0.065 -10000 0 -0.38 13 13
CSNK1A1 0.016 0.024 -10000 0 -0.52 1 1
NLK 0.032 0.03 -10000 0 -0.26 1 1
CCND1 -0.22 0.51 -10000 0 -1.4 87 87
WNT1 0.017 0.023 -10000 0 -0.52 1 1
Axin1/APC/beta catenin 0.017 0.075 0.27 5 -0.35 6 11
DKK2 -0.025 0.14 -10000 0 -0.43 51 51
NOTCH1 precursor/DVL1 0.036 0.077 -10000 0 -0.54 7 7
GSK3B 0.018 0.001 -10000 0 -10000 0 0
FRAT1 0.01 0.068 -10000 0 -0.47 10 10
NOTCH/Deltex homolog 1 0.022 0.085 -10000 0 -0.7 6 6
PPP2R5D 0.014 0.039 0.27 7 -10000 0 7
MAPK1 0.016 0.033 -10000 0 -0.52 2 2
WNT1/LRP6/FZD1 0.008 0.08 -10000 0 -0.27 23 23
RBPJ 0.018 0 -10000 0 -10000 0 0
CREBBP 0.013 0.035 -10000 0 -0.52 2 2
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.01 0.066 -9999 0 -0.52 8 8
alphaV beta3 Integrin 0 0.095 -9999 0 -0.4 23 23
PTK2 -0.002 0.15 -9999 0 -0.45 44 44
positive regulation of JNK cascade -0.028 0.086 -9999 0 -0.31 44 44
CDC42/GDP 0.021 0.14 -9999 0 -0.42 42 42
Rac1/GDP 0.023 0.13 -9999 0 -0.41 42 42
RAP1B 0.013 0.044 -9999 0 -0.32 8 8
RAP1A 0.011 0.062 -9999 0 -0.52 7 7
CTNNB1 0.001 0.09 -9999 0 -0.45 19 19
CDC42/GTP -0.033 0.11 -9999 0 -0.38 44 44
nectin-3/I-afadin -0.017 0.12 -9999 0 -0.41 42 42
RAPGEF1 0.009 0.15 -9999 0 -0.47 42 42
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.001 0.17 -9999 0 -0.54 42 42
PDGFB-D/PDGFRB 0.01 0.066 -9999 0 -0.52 8 8
TLN1 0.004 0.098 -9999 0 -0.41 19 19
Rap1/GTP -0.031 0.094 -9999 0 -0.33 43 43
IQGAP1 0.018 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.014 0.074 -9999 0 -0.28 29 29
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.017 0.12 -9999 0 -0.41 42 42
PVR 0.009 0.055 -9999 0 -0.32 13 13
Necl-5(dimer) 0.009 0.055 -9999 0 -0.32 13 13
mol:GDP 0.011 0.16 -9999 0 -0.51 42 42
MLLT4 -0.006 0.11 -9999 0 -0.46 26 26
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
PI3K 0.001 0.13 -9999 0 -0.32 61 61
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.007 0.082 -9999 0 -0.38 21 21
positive regulation of lamellipodium assembly -0.028 0.089 -9999 0 -0.32 42 42
PVRL1 0.014 0.035 -9999 0 -0.3 6 6
PVRL3 -0.02 0.13 -9999 0 -0.4 47 47
PVRL2 0.002 0.089 -9999 0 -0.52 15 15
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
CDH1 -0.049 0.17 -9999 0 -0.48 71 71
CLDN1 -0.11 0.21 -9999 0 -0.4 165 165
JAM-A/CLDN1 -0.066 0.16 -9999 0 -0.32 128 128
SRC -0.011 0.18 -9999 0 -0.6 43 43
ITGB3 0.002 0.076 -9999 0 -0.32 25 25
nectin-1(dimer)/I-afadin/I-afadin 0.007 0.082 -9999 0 -0.38 21 21
FARP2 0.005 0.16 -9999 0 -0.51 44 44
RAC1 0.018 0 -9999 0 -10000 0 0
CTNNA1 0.017 0.023 -9999 0 -0.52 1 1
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.006 0.11 -9999 0 -0.35 44 44
nectin-1/I-afadin 0.007 0.082 -9999 0 -0.38 21 21
nectin-2/I-afadin -0.002 0.1 -9999 0 -0.39 33 33
RAC1/GTP/IQGAP1/filamentous actin 0.024 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.003 0.11 -9999 0 -0.34 44 44
CDC42/GTP/IQGAP1/filamentous actin 0.024 0 -9999 0 -10000 0 0
F11R 0.011 0.055 -9999 0 -0.36 10 10
positive regulation of filopodium formation -0.028 0.086 -9999 0 -0.31 44 44
alphaV/beta3 Integrin/Talin 0.006 0.13 -9999 0 -0.47 21 21
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.002 0.1 -9999 0 -0.39 33 33
nectin-2(dimer)/I-afadin/I-afadin -0.002 0.1 -9999 0 -0.39 33 33
PIP5K1C -0.003 0.1 -9999 0 -0.42 20 20
VAV2 0.006 0.16 -9999 0 -0.52 42 42
RAP1/GDP 0.018 0.13 -9999 0 -0.38 43 43
ITGAV -0.003 0.1 -9999 0 -0.48 22 22
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.01 0.12 -9999 0 -0.35 54 54
nectin-3(dimer)/I-afadin/I-afadin -0.017 0.12 -9999 0 -0.41 42 42
Rac1/GTP -0.033 0.11 -9999 0 -0.39 42 42
PTPRM -0.01 0.11 -9999 0 -0.3 47 47
E-cadherin/beta catenin/alpha catenin -0.012 0.13 -9999 0 -0.25 104 104
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.018 0 -9999 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.012 0.011 -9999 0 -0.17 2 2
PRKCZ 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0.014 0.047 -9999 0 -0.52 4 4
ERC1 0.011 0.056 -9999 0 -0.42 8 8
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.024 0.11 -9999 0 -0.32 41 41
IRAK/TOLLIP 0.029 0.02 -9999 0 -0.24 1 1
IKBKB 0.011 0.047 -9999 0 -0.31 10 10
IKBKG 0.018 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.026 0.12 -9999 0 -0.36 47 47
IL1A 0.006 0.064 -9999 0 -0.32 18 18
IL1B -0.067 0.18 -9999 0 -0.43 86 86
IRAK/TRAF6/p62/Atypical PKCs 0.031 0.054 -9999 0 -0.23 19 19
IL1R2 -0.046 0.15 -9999 0 -0.36 89 89
IL1R1 -0.046 0.16 -9999 0 -0.41 80 80
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.018 0.12 -9999 0 -0.38 25 25
TOLLIP 0.017 0.012 -9999 0 -0.26 1 1
TICAM2 0 0 -9999 0 -10000 0 0
MAP3K3 0.017 0.012 -9999 0 -0.26 1 1
TAK1/TAB1/TAB2 0.033 0.034 -9999 0 -0.34 4 4
IKK complex/ELKS 0.051 0.075 -9999 0 -0.36 7 7
JUN 0.014 0.093 -9999 0 -0.44 4 4
MAP3K7 0.016 0.021 -9999 0 -0.26 3 3
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.059 0.18 -9999 0 -0.35 119 119
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.003 0.1 -9999 0 -0.28 57 57
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.005 0.1 -9999 0 -0.26 57 57
IL1 beta fragment/IL1R1/IL1RAP -0.069 0.18 -9999 0 -0.36 119 119
NFKB1 0.017 0.023 -9999 0 -0.52 1 1
MAPK8 0.032 0.063 -9999 0 -0.37 2 2
IRAK1 0.019 0.019 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.061 0.17 -9999 0 -0.41 87 87
IRAK4 0.014 0.044 -9999 0 -0.42 5 5
PRKCI 0.001 0.088 -9999 0 -0.44 19 19
TRAF6 0.017 0.023 -9999 0 -0.52 1 1
PI3K 0.006 0.082 -9999 0 -0.37 21 21
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.032 0.13 -9999 0 -0.38 42 42
CHUK 0.005 0.081 -9999 0 -0.5 13 13
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.069 0.18 -9999 0 -0.36 119 119
IL1 beta/IL1R2 -0.083 0.18 -9999 0 -0.37 127 127
IRAK/TRAF6/TAK1/TAB1/TAB2 0.048 0.034 -9999 0 -0.33 1 1
NF kappa B1 p50/RelA -0.082 0.14 -9999 0 -0.44 55 55
IRAK3 -0.018 0.1 -9999 0 -0.28 64 64
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.056 0.17 -9999 0 -0.34 109 109
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.004 0.089 -9999 0 -0.38 4 4
IL1 alpha/IL1R1/IL1RAP -0.014 0.11 -9999 0 -0.31 53 53
RELA 0.018 0 -9999 0 -10000 0 0
MAP3K7IP1 0.018 0 -9999 0 -10000 0 0
SQSTM1 0.012 0.053 -9999 0 -0.48 6 6
MYD88 0.013 0.048 -9999 0 -0.47 5 5
IRAK/TRAF6/MEKK3 0.038 0.022 -9999 0 -0.25 1 1
IL1RAP 0.011 0.044 -9999 0 -0.28 11 11
UBE2N 0.017 0.017 -9999 0 -0.26 2 2
IRAK/TRAF6 -0.07 0.12 -9999 0 -0.39 50 50
CASP1 -0.051 0.17 -9999 0 -0.42 83 83
IL1RN/IL1R2 -0.061 0.16 -9999 0 -0.39 83 83
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.057 0.17 -9999 0 -0.35 110 110
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.003 0.1 -9999 0 -0.3 50 50
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
IL1RN -0.043 0.16 -9999 0 -0.41 76 76
TRAF6/TAK1/TAB1/TAB2 0.04 0.031 -9999 0 -0.26 5 5
MAP2K6 0.028 0.063 -9999 0 -0.4 2 2
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.019 0.049 -10000 0 -0.51 4 4
HSPA8 0.001 0.09 -10000 0 -0.52 15 15
SMAD3/SMAD4/ER alpha -0.091 0.2 0.23 5 -0.37 156 161
AKT1 0.01 0.056 -10000 0 -0.37 9 9
GSC -0.2 0.49 -10000 0 -1.4 76 76
NKX2-5 -0.018 0.094 -10000 0 -0.26 67 67
muscle cell differentiation 0.065 0.16 0.47 45 -10000 0 45
SMAD2-3/SMAD4/SP1 -0.004 0.18 -10000 0 -0.43 54 54
SMAD4 -0.015 0.1 -10000 0 -0.35 25 25
CBFB 0.015 0.037 -10000 0 -0.39 4 4
SAP18 0.017 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.014 0.075 -10000 0 -0.29 8 8
SMAD3/SMAD4/VDR 0.027 0.12 -10000 0 -0.36 26 26
MYC -0.024 0.14 -10000 0 -0.44 48 48
CDKN2B -0.044 0.29 -10000 0 -1.4 23 23
AP1 -0.068 0.22 -10000 0 -0.54 76 76
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.037 0.066 -10000 0 -0.28 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.006 0.12 -10000 0 -0.34 34 34
SP3 0.014 0.02 -10000 0 -10000 0 0
CREB1 0.017 0.023 -10000 0 -0.52 1 1
FOXH1 0 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.005 0.13 -10000 0 -0.36 45 45
GATA3 -0.098 0.22 -10000 0 -0.5 124 124
SKI/SIN3/HDAC complex/NCoR1 0.042 0.037 -10000 0 -10000 0 0
MEF2C/TIF2 -0.026 0.17 -10000 0 -0.52 37 37
endothelial cell migration 0.015 0.23 1.3 15 -10000 0 15
MAX 0.018 0.009 -10000 0 -10000 0 0
RBBP7 0.009 0.051 -10000 0 -0.3 13 13
RBBP4 0.016 0.026 -10000 0 -0.39 2 2
RUNX2 0.013 0.05 -10000 0 -0.43 6 6
RUNX3 -0.063 0.18 -10000 0 -0.4 102 102
RUNX1 -0.028 0.14 -10000 0 -0.42 56 56
CTBP1 0.017 0.017 -10000 0 -0.26 2 2
NR3C1 -0.003 0.1 -10000 0 -0.51 21 21
VDR -0.003 0.1 -10000 0 -0.51 21 21
CDKN1A -0.027 0.26 -10000 0 -1.2 20 20
KAT2B 0.001 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.014 0.13 -10000 0 -0.3 60 60
DCP1A 0.017 0.023 -10000 0 -0.52 1 1
SKI 0.016 0.017 -10000 0 -0.26 2 2
SERPINE1 -0.017 0.23 -10000 0 -1.3 15 15
SMAD3/SMAD4/ATF2 0.007 0.1 -10000 0 -0.33 28 28
SMAD3/SMAD4/ATF3 -0.017 0.14 -10000 0 -0.36 51 51
SAP30 0.012 0.053 -10000 0 -0.48 6 6
Cbp/p300/PIAS3 0.047 0.053 -10000 0 -0.28 6 6
JUN -0.07 0.22 -10000 0 -0.53 76 76
SMAD3/SMAD4/IRF7 0.003 0.13 -10000 0 -0.4 29 29
TFE3 0.018 0.026 -10000 0 -10000 0 0
COL1A2 -0.099 0.36 -10000 0 -1 70 70
mesenchymal cell differentiation -0.004 0.11 0.36 31 -10000 0 31
DLX1 -0.009 0.082 -10000 0 -0.26 52 52
TCF3 0.012 0.05 -10000 0 -0.35 9 9
FOS -0.11 0.2 -10000 0 -0.38 171 171
SMAD3/SMAD4/Max 0.008 0.1 -10000 0 -0.33 27 27
Cbp/p300/SNIP1 0.035 0.046 -10000 0 -0.3 9 9
ZBTB17 0.019 0.012 -10000 0 -10000 0 0
LAMC1 0.005 0.14 -10000 0 -0.53 28 28
TGIF2/HDAC complex/SMAD3/SMAD4 0 0.12 -10000 0 -0.35 35 35
IRF7 0.008 0.076 -10000 0 -0.49 11 11
ESR1 -0.15 0.23 -10000 0 -0.46 187 187
HNF4A 0.016 0.033 -10000 0 -0.52 2 2
MEF2C -0.033 0.17 -10000 0 -0.54 39 39
SMAD2-3/SMAD4 -0.007 0.12 -10000 0 -0.34 39 39
Cbp/p300/Src-1 0.036 0.054 -10000 0 -0.28 12 12
IGHV3OR16-13 -0.017 0.039 -10000 0 -0.52 1 1
TGIF2/HDAC complex 0.007 0.071 -10000 0 -0.42 13 13
CREBBP 0.019 0.034 -10000 0 -0.51 2 2
SKIL 0.005 0.071 -10000 0 -0.34 19 19
HDAC1 0.016 0.023 -10000 0 -0.52 1 1
HDAC2 0.008 0.054 -10000 0 -0.29 15 15
SNIP1 0.014 0.04 -10000 0 -0.52 3 3
GCN5L2 0.018 0.044 -10000 0 -0.46 4 4
SMAD3/SMAD4/TFE3 0.015 0.12 -10000 0 -0.37 30 30
MSG1/HSC70 -0.02 0.098 -10000 0 -0.41 16 16
SMAD2 -0.002 0.05 -10000 0 -0.51 1 1
SMAD3 -0.003 0.1 -10000 0 -0.5 15 15
SMAD3/E2F4-5/DP1/p107/SMAD4 0.008 0.097 -10000 0 -0.3 23 23
SMAD2/SMAD2/SMAD4 -0.006 0.054 -10000 0 -0.3 10 10
NCOR1 0.015 0.033 -10000 0 -0.52 2 2
NCOA2 0.009 0.063 -10000 0 -0.4 11 11
NCOA1 0.012 0.057 -10000 0 -0.52 6 6
MYOD/E2A -0.002 0.099 -10000 0 -0.37 32 32
SMAD2-3/SMAD4/SP1/MIZ-1 0.009 0.17 -10000 0 -0.43 44 44
IFNB1 0.006 0.13 -10000 0 -0.45 25 25
SMAD3/SMAD4/MEF2C -0.026 0.2 -10000 0 -0.56 44 44
CITED1 -0.029 0.11 -10000 0 -0.26 88 88
SMAD2-3/SMAD4/ARC105 0.01 0.11 -10000 0 -0.35 24 24
RBL1 0.01 0.049 -10000 0 -0.28 14 14
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.002 0.15 -10000 0 -0.47 33 33
RUNX1-3/PEBPB2 -0.043 0.14 -10000 0 -0.34 86 86
SMAD7 -0.041 0.22 -10000 0 -0.59 48 48
MYC/MIZ-1 -0.003 0.1 -10000 0 -0.37 34 34
SMAD3/SMAD4 0.046 0.14 0.3 41 -0.4 15 56
IL10 -0.046 0.18 -10000 0 -0.41 67 67
PIASy/HDAC complex 0.009 0.051 -10000 0 -0.44 6 6
PIAS3 0.019 0.005 -10000 0 -10000 0 0
CDK2 0.015 0.048 -10000 0 -0.3 10 10
IL5 -0.046 0.18 -10000 0 -0.42 62 62
CDK4 0.019 0.03 -10000 0 -0.26 5 5
PIAS4 0.009 0.051 -10000 0 -0.44 6 6
ATF3 -0.021 0.13 -10000 0 -0.41 48 48
SMAD3/SMAD4/SP1 -0.008 0.17 -10000 0 -0.43 55 55
FOXG1 -0.007 0.083 -10000 0 -0.28 44 44
FOXO3 0.015 0.061 -10000 0 -0.4 8 8
FOXO1 0.008 0.079 -10000 0 -0.37 19 19
FOXO4 0.019 0.047 -10000 0 -0.37 5 5
heart looping -0.033 0.17 -10000 0 -0.53 39 39
CEBPB 0.004 0.073 -10000 0 -0.34 20 20
SMAD3/SMAD4/DLX1 -0.009 0.12 -10000 0 -0.34 33 33
MYOD1 -0.016 0.13 -10000 0 -0.46 37 37
SMAD3/SMAD4/HNF4 0.006 0.11 -10000 0 -0.34 27 27
SMAD3/SMAD4/GATA3 -0.061 0.2 -10000 0 -0.38 125 125
SnoN/SIN3/HDAC complex/NCoR1 0.005 0.071 -10000 0 -0.34 19 19
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.037 0.17 -10000 0 -0.4 64 64
SMAD3/SMAD4/SP1-3 0.001 0.18 -10000 0 -0.49 46 46
MED15 0.018 0 -10000 0 -10000 0 0
SP1 -0.001 0.068 -10000 0 -0.4 3 3
SIN3B 0.017 0.012 -10000 0 -0.26 1 1
SIN3A 0.017 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.019 0.15 -10000 0 -0.38 45 45
ITGB5 -0.03 0.23 -10000 0 -0.65 55 55
TGIF/SIN3/HDAC complex/CtBP 0.041 0.042 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.061 0.19 -10000 0 -0.39 116 116
AR -0.088 0.21 -10000 0 -0.52 104 104
negative regulation of cell growth -0.002 0.12 -10000 0 -0.39 27 27
SMAD3/SMAD4/MYOD -0.015 0.13 -10000 0 -0.32 58 58
E2F5 -0.014 0.12 -10000 0 -0.39 41 41
E2F4 0.017 0.017 -10000 0 -0.26 2 2
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.012 0.11 -10000 0 -0.3 25 25
SMAD2-3/SMAD4/FOXO1-3a-4 0.007 0.12 -10000 0 -0.35 40 40
TFDP1 0.011 0.043 -10000 0 -0.26 13 13
SMAD3/SMAD4/AP1 -0.063 0.23 -10000 0 -0.54 76 76
SMAD3/SMAD4/RUNX2 0.004 0.11 -10000 0 -0.36 31 31
TGIF2 0.007 0.071 -10000 0 -0.42 13 13
TGIF1 0.008 0.073 -10000 0 -0.52 10 10
ATF2 0.018 0 -10000 0 -10000 0 0
PDGFR-alpha signaling 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
PDGFRA -0.025 0.13 -9999 0 -0.5 37 37
PDGF/PDGFRA/CRKL -0.006 0.1 -9999 0 -0.37 36 36
positive regulation of JUN kinase activity 0.019 0.077 -9999 0 -0.26 34 34
CRKL 0.014 0.047 -9999 0 -0.52 4 4
PDGF/PDGFRA/Caveolin-3 -0.005 0.097 -9999 0 -0.37 33 33
AP1 -0.18 0.34 -9999 0 -0.91 83 83
mol:IP3 -0.015 0.1 -9999 0 -0.39 33 33
PLCG1 -0.015 0.1 -9999 0 -0.39 33 33
PDGF/PDGFRA/alphaV Integrin -0.018 0.12 -9999 0 -0.4 48 48
RAPGEF1 0.018 0 -9999 0 -10000 0 0
CRK 0.016 0.033 -9999 0 -0.52 2 2
mol:Ca2+ -0.015 0.1 -9999 0 -0.39 33 33
CAV3 0.016 0.029 -9999 0 -0.35 3 3
CAV1 0 0.081 -9999 0 -0.32 28 28
SHC/Grb2/SOS1 0.02 0.077 -9999 0 -0.26 34 34
PDGF/PDGFRA/Shf -0.009 0.1 -9999 0 -0.37 34 34
FOS -0.17 0.34 -9999 0 -0.89 83 83
JUN -0.051 0.11 -9999 0 -0.38 52 52
oligodendrocyte development -0.018 0.12 -9999 0 -0.39 48 48
GRB2 0.016 0.024 -9999 0 -0.26 4 4
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
mol:DAG -0.015 0.1 -9999 0 -0.39 33 33
PDGF/PDGFRA -0.025 0.13 -9999 0 -0.5 37 37
actin cytoskeleton reorganization -0.01 0.11 -9999 0 -0.39 38 38
SRF 0.028 0.025 -9999 0 -0.35 1 1
SHC1 0.017 0.023 -9999 0 -0.52 1 1
PI3K -0.007 0.11 -9999 0 -0.34 49 49
PDGF/PDGFRA/Crk/C3G 0.01 0.085 -9999 0 -0.31 33 33
JAK1 -0.009 0.1 -9999 0 -0.38 37 37
ELK1/SRF 0.012 0.083 -9999 0 -0.28 36 36
SHB 0.008 0.067 -9999 0 -0.41 12 12
SHF 0.009 0.05 -9999 0 -0.28 15 15
CSNK2A1 0.025 0.029 -9999 0 -0.49 1 1
GO:0007205 -0.018 0.11 -9999 0 -0.42 33 33
SOS1 0.017 0.023 -9999 0 -0.52 1 1
Ras protein signal transduction 0.019 0.077 -9999 0 -0.26 34 34
PDGF/PDGFRA/SHB -0.01 0.11 -9999 0 -0.39 38 38
PDGF/PDGFRA/Caveolin-1 -0.015 0.12 -9999 0 -0.4 37 37
ITGAV -0.003 0.1 -9999 0 -0.48 22 22
ELK1 -0.018 0.1 -9999 0 -0.36 36 36
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
PDGF/PDGFRA/Crk -0.004 0.1 -9999 0 -0.38 33 33
JAK-STAT cascade -0.009 0.1 -9999 0 -0.38 37 37
cell proliferation -0.009 0.1 -9999 0 -0.37 34 34
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.003 0.069 -9999 0 -0.29 26 26
Syndecan-3/Src/Cortactin -0.046 0.16 -9999 0 -0.52 34 34
Syndecan-3/Neurocan -0.007 0.13 -9999 0 -0.57 24 24
POMC 0.001 0.072 -9999 0 -0.28 30 30
EGFR -0.077 0.17 -9999 0 -0.35 136 136
Syndecan-3/EGFR -0.048 0.16 -9999 0 -0.57 30 30
AGRP 0.016 0.029 -9999 0 -0.35 3 3
NCSTN 0.017 0.023 -9999 0 -0.52 1 1
PSENEN 0.017 0.012 -9999 0 -0.26 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0 0.096 -9999 0 -0.51 18 18
APH1A 0.003 0.068 -9999 0 -0.29 25 25
NCAN 0.007 0.054 -9999 0 -0.26 21 21
long-term memory -0.003 0.13 -9999 0 -0.55 25 25
Syndecan-3/IL8 -0.046 0.16 -9999 0 -0.59 29 29
PSEN1 0.013 0.052 -9999 0 -0.52 5 5
Src/Cortactin 0.014 0.054 -9999 0 -0.37 5 5
FYN 0.009 0.063 -9999 0 -0.4 11 11
limb bud formation -0.032 0.12 -9999 0 -0.59 24 24
MC4R 0.014 0.039 -9999 0 -0.36 5 5
SRC 0.015 0.035 -9999 0 -0.43 3 3
PTN -0.099 0.19 -9999 0 -0.38 157 157
FGFR/FGF/Syndecan-3 -0.032 0.12 -9999 0 -0.6 24 24
neuron projection morphogenesis -0.045 0.16 -9999 0 -0.51 34 34
Syndecan-3/AgRP -0.003 0.13 -9999 0 -0.56 25 25
Syndecan-3/AgRP/MC4R 0.005 0.13 -9999 0 -0.56 24 24
Fyn/Cortactin 0.01 0.067 -9999 0 -0.38 9 9
SDC3 -0.032 0.13 -9999 0 -0.61 24 24
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.045 0.15 -9999 0 -0.41 58 58
IL8 -0.073 0.17 -9999 0 -0.34 135 135
Syndecan-3/Fyn/Cortactin -0.003 0.13 -9999 0 -0.56 25 25
Syndecan-3/CASK -0.031 0.12 -9999 0 -0.58 24 24
alpha-MSH/MC4R 0.012 0.057 -9999 0 -0.37 5 5
Gamma Secretase 0.032 0.07 -9999 0 -0.25 26 26
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.019 0.061 -9999 0 -0.27 21 21
RGS9BP -0.071 0.18 -9999 0 -0.41 110 110
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + -0.016 0.089 -9999 0 -0.33 24 24
mol:ADP 0.011 0.025 -9999 0 -0.31 3 3
GNAT2 -0.004 0.1 -9999 0 -0.49 23 23
RGS9-1/Gbeta5/R9AP -0.055 0.15 -9999 0 -0.34 95 95
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.089 -9999 0 -0.33 33 33
GRK7 0.015 0.035 -9999 0 -0.43 3 3
CNGB3 -0.006 0.087 -9999 0 -0.3 39 39
Cone Metarhodopsin II/X-Arrestin 0.013 0.008 -9999 0 -0.17 1 1
mol:Ca2+ -0.01 0.084 -9999 0 -0.3 27 27
Cone PDE6 -0.042 0.14 -9999 0 -0.29 104 104
Cone Metarhodopsin II 0.01 0.019 -9999 0 -0.24 3 3
Na + (4 Units) -0.005 0.086 -9999 0 -0.29 27 27
GNAT2/GDP -0.048 0.14 -9999 0 -0.29 111 111
GNB5 0.005 0.081 -9999 0 -0.5 13 13
mol:GMP (4 units) 0.001 0.091 -9999 0 -0.31 37 37
Cone Transducin 0.02 0.065 -9999 0 -0.29 21 21
SLC24A2 0.014 0.044 -9999 0 -0.42 5 5
GNB3/GNGT2 0.025 0.026 -9999 0 -0.37 2 2
GNB3 0.017 0.012 -9999 0 -0.26 1 1
GNAT2/GTP -0.003 0.076 -9999 0 -0.35 23 23
CNGA3 -0.028 0.12 -9999 0 -0.32 72 72
ARR3 0.017 0.012 -9999 0 -0.26 1 1
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.016 0.09 -9999 0 -0.33 24 24
mol:Pi -0.055 0.15 -9999 0 -0.33 95 95
Cone CNG Channel -0.014 0.11 -9999 0 -0.3 53 53
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.014 0.044 -9999 0 -0.42 5 5
RGS9 -0.032 0.13 -9999 0 -0.31 80 80
PDE6C 0.008 0.065 -9999 0 -0.38 13 13
GNGT2 0.016 0.033 -9999 0 -0.52 2 2
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.001 0.094 -9999 0 -0.45 21 21
Class I PI3K signaling events

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
ARF5/GTP 0.018 0.072 0.24 15 -0.24 23 38
DAPP1 -0.037 0.14 -10000 0 -0.43 41 41
Src family/SYK family/BLNK-LAT/BTK-ITK -0.049 0.22 -10000 0 -0.54 61 61
mol:DAG 0.001 0.1 0.19 9 -0.23 47 56
HRAS 0.012 0.051 -10000 0 -0.41 7 7
RAP1A 0.011 0.062 -10000 0 -0.52 7 7
ARF5/GDP -0.016 0.11 -10000 0 -0.32 30 30
PLCG2 -0.017 0.11 -10000 0 -0.32 55 55
PLCG1 0.016 0.026 -10000 0 -0.39 2 2
ARF5 0.015 0.04 -10000 0 -0.52 3 3
mol:GTP -0.006 0.069 0.22 15 -0.25 26 41
ARF1/GTP -0.006 0.067 0.22 15 -0.24 26 41
RHOA 0.005 0.08 -10000 0 -0.52 12 12
YES1 0.007 0.07 -10000 0 -0.43 12 12
RAP1A/GTP 0.014 0.07 0.22 15 -0.25 26 41
ADAP1 -0.006 0.066 0.21 15 -0.24 26 41
ARAP3 -0.006 0.068 0.22 15 -0.24 26 41
INPPL1 0.012 0.055 -10000 0 -0.45 7 7
PREX1 -0.089 0.2 -10000 0 -0.44 124 124
ARHGEF6 -0.019 0.13 -10000 0 -0.42 45 45
ARHGEF7 0.016 0.021 -10000 0 -0.26 3 3
ARF1 0.017 0.023 -10000 0 -0.52 1 1
NRAS 0.006 0.073 -10000 0 -0.4 15 15
FYN 0.009 0.063 -10000 0 -0.4 11 11
ARF6 0.016 0.033 -10000 0 -0.52 2 2
FGR 0.017 0.017 -10000 0 -0.26 2 2
mol:Ca2+ 0.006 0.054 -10000 0 -0.15 1 1
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.006 0.073 -10000 0 -0.44 13 13
ZAP70 0.005 0.061 -10000 0 -0.27 24 24
mol:IP3 0.004 0.073 -10000 0 -0.18 25 25
LYN 0.014 0.031 -10000 0 -0.26 7 7
ARF1/GDP -0.015 0.1 -10000 0 -0.32 28 28
RhoA/GDP 0.002 0.1 0.23 6 -0.34 26 32
PDK1/Src/Hsp90 0.031 0.039 -10000 0 -0.3 6 6
BLNK -0.013 0.12 -10000 0 -0.51 31 31
actin cytoskeleton reorganization -0.007 0.12 0.23 6 -0.41 24 30
SRC 0.015 0.035 -10000 0 -0.43 3 3
PLEKHA2 0.014 0.041 -10000 0 -0.31 7 7
RAC1 0.018 0 -10000 0 -10000 0 0
PTEN -0.003 0.096 -10000 0 -0.5 19 19
HSP90AA1 0.013 0.045 -10000 0 -0.39 6 6
ARF6/GTP 0.019 0.07 0.24 14 -0.23 27 41
RhoA/GTP 0.015 0.083 0.22 14 -0.27 32 46
Src family/SYK family/BLNK-LAT -0.03 0.17 -10000 0 -0.46 46 46
BLK -0.018 0.1 -10000 0 -0.29 61 61
PDPK1 0.016 0.026 -10000 0 -0.39 2 2
CYTH1 -0.006 0.066 0.21 15 -0.24 26 41
HCK -0.005 0.11 -10000 0 -0.47 25 25
CYTH3 -0.006 0.066 0.21 15 -0.24 26 41
CYTH2 -0.006 0.066 0.21 15 -0.24 26 41
KRAS 0.008 0.069 -10000 0 -0.45 11 11
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.025 0.052 0.18 12 -0.2 10 22
SGK1 -0.004 0.047 0.18 13 -0.21 6 19
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.025 0.11 -10000 0 -0.3 41 41
SOS1 0.017 0.023 -10000 0 -0.52 1 1
SYK -0.022 0.14 -10000 0 -0.48 42 42
ARF6/GDP 0.005 0.085 0.24 6 -0.3 20 26
mol:PI-3-4-5-P3 -0.004 0.075 0.25 19 -0.25 26 45
ARAP3/RAP1A/GTP 0.014 0.071 0.22 15 -0.25 26 41
VAV1 -0.015 0.12 -10000 0 -0.39 42 42
mol:PI-3-4-P2 0.008 0.039 -10000 0 -0.32 7 7
RAS family/GTP/PI3K Class I 0.021 0.07 -10000 0 -0.25 26 26
PLEKHA1 0.012 0.052 -10000 0 -0.32 12 12
Rac1/GDP -0.014 0.1 -10000 0 -0.32 27 27
LAT 0.002 0.069 -10000 0 -0.28 29 29
Rac1/GTP -0.03 0.14 -10000 0 -0.49 25 25
ITK -0.008 0.1 0.22 14 -0.24 62 76
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.008 0.13 0.22 8 -0.32 48 56
LCK -0.073 0.18 -10000 0 -0.4 115 115
BTK 0.006 0.092 0.22 14 -0.27 38 52
Regulation of Telomerase

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
Telomerase catalytic core complex -0.1 0.22 -10000 0 -0.62 46 46
RAD9A 0.018 0 -10000 0 -10000 0 0
AP1 -0.1 0.18 -10000 0 -0.42 107 107
IFNAR2 0.013 0.037 -10000 0 -0.31 6 6
AKT1 -0.053 0.12 -10000 0 -0.28 50 50
ER alpha/Oestrogen -0.12 0.17 -10000 0 -0.33 202 202
NFX1/SIN3/HDAC complex 0.038 0.048 -10000 0 -0.28 3 3
EGF -0.14 0.23 -10000 0 -0.42 193 193
SMG5 0.016 0.029 -10000 0 -0.35 3 3
SMG6 0.017 0.023 -10000 0 -0.52 1 1
SP3/HDAC2 0.018 0.041 -10000 0 -0.28 4 4
TERT/c-Abl -0.089 0.21 -10000 0 -0.59 42 42
SAP18 0.017 0.001 -10000 0 -10000 0 0
MRN complex 0.029 0.047 -10000 0 -0.3 10 10
WT1 -0.1 0.19 -10000 0 -0.35 170 170
WRN 0.012 0.05 -10000 0 -0.35 9 9
SP1 0.016 0.025 -10000 0 -0.53 1 1
SP3 0.017 0.003 -10000 0 -10000 0 0
TERF2IP 0.018 0 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.099 0.17 -10000 0 -0.55 36 36
Mad/Max 0.021 0.024 -10000 0 -10000 0 0
TERT -0.1 0.23 -10000 0 -0.66 41 41
CCND1 -0.2 0.43 -10000 0 -1.1 89 89
MAX 0.017 0.004 -10000 0 -10000 0 0
RBBP7 0.01 0.051 -10000 0 -0.3 13 13
RBBP4 0.016 0.026 -10000 0 -0.39 2 2
TERF2 0.014 0.036 -10000 0 -0.46 3 3
PTGES3 0.016 0.026 -10000 0 -0.39 2 2
SIN3A 0.017 0.001 -10000 0 -10000 0 0
Telomerase/911 0.026 0.046 -10000 0 -0.35 2 2
CDKN1B -0.073 0.19 -10000 0 -0.43 88 88
RAD1 0.016 0.033 -10000 0 -0.52 2 2
XRCC5 0.018 0 -10000 0 -10000 0 0
XRCC6 0.017 0.012 -10000 0 -0.26 1 1
SAP30 0.012 0.053 -10000 0 -0.48 6 6
TRF2/PARP2 0.024 0.03 -10000 0 -0.36 3 3
UBE3A 0.015 0.033 -10000 0 -0.52 2 2
JUN -0.034 0.15 -10000 0 -0.46 57 57
E6 -0.001 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.011 0.025 -10000 0 -0.38 2 2
FOS -0.11 0.2 -10000 0 -0.37 171 171
IFN-gamma/IRF1 -0.077 0.16 -10000 0 -0.37 103 103
PARP2 0.017 0.012 -10000 0 -0.26 1 1
BLM -0.021 0.13 -10000 0 -0.41 48 48
Telomerase 0.025 0.06 -10000 0 -0.36 3 3
IRF1 -0.018 0.12 -10000 0 -0.38 41 41
ESR1 -0.16 0.24 -10000 0 -0.45 202 202
KU/TER 0.026 0.008 -10000 0 -10000 0 0
ATM/TRF2 0.025 0.023 -10000 0 -0.26 3 3
ubiquitin-dependent protein catabolic process 0.043 0.051 -10000 0 -0.35 2 2
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.043 0.052 -10000 0 -0.36 2 2
HDAC1 0.016 0.023 -10000 0 -0.52 1 1
HDAC2 0.008 0.056 -10000 0 -0.3 15 15
ATM 0.001 0.017 0.21 3 -10000 0 3
SMAD3 0.015 0.06 -10000 0 -0.36 11 11
ABL1 0.018 0 -10000 0 -10000 0 0
MXD1 0.013 0.032 -10000 0 -0.26 7 7
MRE11A 0.018 0 -10000 0 -10000 0 0
HUS1 0.016 0.021 -10000 0 -0.26 3 3
RPS6KB1 0.008 0.05 -10000 0 -0.26 18 18
TERT/NF kappa B1/14-3-3 -0.091 0.22 -10000 0 -0.61 44 44
NR2F2 -0.05 0.17 -10000 0 -0.45 78 78
MAPK3 0.019 0.042 -10000 0 -0.37 4 4
MAPK1 0.018 0.044 -10000 0 -0.37 5 5
TGFB1/TGF beta receptor Type II 0.017 0.023 -10000 0 -0.52 1 1
NFKB1 0.017 0.023 -10000 0 -0.52 1 1
HNRNPC 0.018 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.001 0.017 0.21 3 -10000 0 3
NBN 0.015 0.035 -10000 0 -0.43 3 3
EGFR -0.078 0.17 -10000 0 -0.35 136 136
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.15 0.2 -10000 0 -0.42 172 172
MYC -0.027 0.14 -10000 0 -0.43 51 51
IL2 0.01 0.052 -10000 0 -0.34 10 10
KU 0.026 0.008 -10000 0 -10000 0 0
RAD50 0.01 0.066 -10000 0 -0.52 8 8
HSP90AA1 0.013 0.045 -10000 0 -0.39 6 6
TGFB1 0.017 0.024 -10000 0 -0.52 1 1
TRF2/BLM -0.002 0.091 -10000 0 -0.35 30 30
FRAP1 0.018 0 -10000 0 -10000 0 0
KU/TERT -0.08 0.21 -10000 0 -0.61 34 34
SP1/HDAC2 0.019 0.048 -10000 0 -0.34 5 5
PINX1 0.016 0.021 -10000 0 -0.26 3 3
Telomerase/EST1A -0.099 0.17 -10000 0 -0.55 37 37
Smad3/Myc -0.003 0.099 -10000 0 -0.31 46 46
911 complex 0.034 0.024 -10000 0 -0.3 2 2
IFNG -0.093 0.18 -10000 0 -0.33 161 161
Telomerase/PinX1 -0.099 0.17 -10000 0 -0.55 36 36
Telomerase/AKT1/mTOR/p70S6K -0.008 0.092 -10000 0 -0.47 5 5
SIN3B 0.017 0.012 -10000 0 -0.26 1 1
YWHAE 0.016 0.029 -10000 0 -0.35 3 3
Telomerase/EST1B -0.1 0.18 -10000 0 -0.55 37 37
response to DNA damage stimulus 0.004 0.005 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.044 0.049 -10000 0 -0.26 12 12
TRF2/WRN 0.02 0.043 -10000 0 -0.35 6 6
Telomerase/hnRNP C1/C2 -0.099 0.17 -10000 0 -0.55 36 36
E2F1 0.005 0.071 -10000 0 -0.38 16 16
ZNFX1 0.007 0.071 -10000 0 -0.42 13 13
PIF1 0.015 0.027 -10000 0 -0.26 5 5
NCL 0.018 0 -10000 0 -10000 0 0
DKC1 0.016 0.021 -10000 0 -0.26 3 3
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Insulin Pathway

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
CBL/APS/CAP -0.048 0.1 -9999 0 -0.26 87 87
TC10/GTP -0.021 0.061 -9999 0 -0.23 36 36
Insulin Receptor/Insulin/IRS1/Shp2 0.005 0.11 -9999 0 -0.29 63 63
HRAS 0.012 0.051 -9999 0 -0.41 7 7
APS homodimer 0 0 -9999 0 -10000 0 0
GRB14 -0.16 0.21 -9999 0 -0.37 247 247
FOXO3 -0.021 0.065 -9999 0 -0.71 4 4
AKT1 -0.068 0.14 -9999 0 -0.36 45 45
INSR 0.015 0.038 -9999 0 -0.38 4 4
Insulin Receptor/Insulin 0.035 0.08 -9999 0 -0.49 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 -0.003 0.098 -9999 0 -0.43 24 24
SORBS1 -0.032 0.14 -9999 0 -0.39 64 64
CRK 0.016 0.033 -9999 0 -0.52 2 2
PTPN1 0.023 0.076 -9999 0 -0.48 4 4
CAV1 -0.011 0.11 -9999 0 -0.27 68 68
CBL/APS/CAP/Crk-II/C3G 0.015 0.077 -9999 0 -0.25 34 34
Insulin Receptor/Insulin/IRS1/NCK2 0.004 0.11 -9999 0 -0.29 62 62
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.041 0.095 -9999 0 -0.25 80 80
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.013 0.09 -9999 0 -0.46 6 6
RPS6KB1 -0.06 0.13 -9999 0 -0.33 50 50
PARD6A 0.006 0.074 -9999 0 -0.43 14 14
CBL 0.017 0.012 -9999 0 -0.26 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 -0.014 0.11 -9999 0 -0.78 11 11
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.082 0.11 -9999 0 -0.33 51 51
HRAS/GTP -0.028 0.073 -9999 0 -0.35 6 6
Insulin Receptor 0.015 0.038 -9999 0 -0.38 4 4
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.014 0.1 -9999 0 -0.26 63 63
PRKCI -0.032 0.1 -9999 0 -0.52 20 20
Insulin Receptor/Insulin/GRB14/PDK1 -0.099 0.12 -9999 0 -0.37 50 50
SHC1 0.017 0.023 -9999 0 -0.52 1 1
negative regulation of MAPKKK cascade 0.009 0.12 -9999 0 -0.5 20 20
PI3K -0.005 0.11 -9999 0 -0.26 80 80
NCK2 0.015 0.027 -9999 0 -0.26 5 5
RHOQ 0.014 0.042 -9999 0 -0.46 4 4
mol:H2O2 -0.002 0.008 -9999 0 -10000 0 0
HRAS/GDP 0.009 0.037 -9999 0 -0.29 7 7
AKT2 -0.066 0.13 -9999 0 -0.36 42 42
PRKCZ -0.026 0.066 -9999 0 -0.53 7 7
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP -0.002 0.093 -9999 0 -0.25 63 63
F2RL2 -0.072 0.19 -9999 0 -0.44 103 103
TRIP10 0.013 0.048 -9999 0 -0.47 5 5
Insulin Receptor/Insulin/Shc 0.032 0.029 -9999 0 -0.27 4 4
TC10/GTP/CIP4/Exocyst 0.019 0.04 -9999 0 -0.31 7 7
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.05 0.036 -9999 0 -0.38 2 2
RAPGEF1 0.018 0 -9999 0 -10000 0 0
RASA1 0.004 0.079 -9999 0 -0.42 16 16
NCK1 0.011 0.046 -9999 0 -0.28 12 12
CBL/APS/CAP/Crk-II 0.005 0.082 -9999 0 -0.28 34 34
TC10/GDP 0.011 0.03 -9999 0 -0.33 4 4
Insulin Receptor/Insulin/SHC/GRB10 0.032 0.064 -9999 0 -0.27 20 20
INPP5D -0.014 0.096 -9999 0 -0.27 62 62
SOS1 0.017 0.023 -9999 0 -0.52 1 1
SGK1 -0.01 0.012 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.017 0.023 -9999 0 -0.52 1 1
IRS1 -0.048 0.17 -9999 0 -0.49 68 68
p62DOK/RasGAP 0.009 0.12 -9999 0 -0.51 20 20
INS 0.017 0.025 -9999 0 -0.52 1 1
mol:PI-3-4-P2 -0.013 0.095 -9999 0 -0.27 62 62
GRB2 0.016 0.024 -9999 0 -0.26 4 4
EIF4EBP1 -0.068 0.13 -9999 0 -0.34 57 57
PTPRA 0.017 0.028 -9999 0 -0.4 2 2
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
TC10/GTP/CIP4 0.019 0.04 -9999 0 -0.31 7 7
PDPK1 0.016 0.026 -9999 0 -0.39 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.009 0.095 -9999 0 -0.4 6 6
Insulin Receptor/Insulin/IRS1 -0.006 0.11 -9999 0 -0.29 62 62
Insulin Receptor/Insulin/IRS3 0.024 0.034 -9999 0 -0.36 3 3
Par3/Par6 -0.017 0.12 -9999 0 -0.27 84 84
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.013 0.11 -10000 0 -0.26 57 57
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.014 0.047 -10000 0 -0.52 4 4
STAT1 (dimer)/Cbp/p300 -0.012 0.15 -10000 0 -0.46 29 29
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.014 0.063 -10000 0 -0.35 11 11
antigen processing and presentation of peptide antigen via MHC class I -0.056 0.1 -10000 0 -0.29 61 61
CaM/Ca2+ -0.008 0.098 -10000 0 -0.32 17 17
RAP1A 0.011 0.062 -10000 0 -0.52 7 7
STAT1 (dimer)/SHP2 -0.028 0.13 -10000 0 -0.38 34 34
AKT1 -0.012 0.11 -10000 0 -0.35 20 20
MAP2K1 -0.025 0.12 -10000 0 -0.35 35 35
MAP3K11 -0.012 0.099 -10000 0 -0.32 19 19
IFNGR1 0.01 0.04 -10000 0 -0.31 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.029 0.14 -10000 0 -0.39 46 46
Rap1/GTP -0.031 0.07 -10000 0 -0.36 10 10
CRKL/C3G 0.023 0.034 -10000 0 -0.37 4 4
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.01 0.11 -10000 0 -0.34 16 16
CEBPB -0.011 0.16 -10000 0 -0.45 33 33
STAT3 0.015 0.04 -10000 0 -0.52 3 3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0 0.11 -10000 0 -0.67 4 4
STAT1 -0.03 0.13 -10000 0 -0.38 34 34
CALM1 0.018 0 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.087 0.17 -10000 0 -0.33 161 161
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
STAT1 (dimer)/PIAS1 -0.02 0.12 -10000 0 -0.4 25 25
CEBPB/PTGES2/Cbp/p300 -0.044 0.11 -10000 0 -0.4 29 29
mol:Ca2+ -0.015 0.1 -10000 0 -0.26 57 57
MAPK3 -0.017 0.14 -10000 0 -0.5 12 12
STAT1 (dimer) -0.071 0.15 -10000 0 -0.44 55 55
MAPK1 -0.018 0.14 -10000 0 -0.52 14 14
JAK2 0.006 0.057 -10000 0 -0.34 12 12
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
JAK1 0.008 0.059 -10000 0 -0.54 6 6
CAMK2D -0.004 0.098 -10000 0 -0.4 28 28
DAPK1 -0.001 0.14 -10000 0 -0.51 20 20
SMAD7 0.004 0.073 -10000 0 -0.19 19 19
CBL/CRKL/C3G 0.005 0.096 -10000 0 -0.34 12 12
PI3K -0.022 0.11 -10000 0 -0.36 22 22
IFNG -0.087 0.17 -10000 0 -0.33 161 161
apoptosis -0.008 0.12 0.27 2 -0.39 22 24
CAMK2G 0.017 0.017 -10000 0 -0.26 2 2
STAT3 (dimer) 0.015 0.04 -10000 0 -0.52 3 3
CAMK2A 0.017 0.023 -10000 0 -0.52 1 1
CAMK2B -0.079 0.18 -10000 0 -0.37 133 133
FRAP1 -0.005 0.1 -10000 0 -0.35 15 15
PRKCD -0.011 0.11 -10000 0 -0.36 19 19
RAP1B 0.013 0.044 -10000 0 -0.32 8 8
negative regulation of cell growth -0.056 0.1 -10000 0 -0.29 61 61
PTPN2 0.016 0.024 -10000 0 -0.26 4 4
EP300 0.014 0.047 -10000 0 -0.52 4 4
IRF1 -0.009 0.16 -10000 0 -0.48 36 36
STAT1 (dimer)/PIASy -0.025 0.13 -10000 0 -0.42 25 25
SOCS1 0.009 0.064 -10000 0 -1.4 1 1
mol:GDP 0.003 0.092 -10000 0 -0.33 12 12
CASP1 -0.017 0.12 -10000 0 -0.28 67 67
PTGES2 0.017 0.012 -10000 0 -0.26 1 1
IRF9 0.016 0.085 -10000 0 -0.32 19 19
mol:PI-3-4-5-P3 -0.048 0.089 -10000 0 -0.34 24 24
RAP1/GDP -0.032 0.072 -10000 0 -0.37 10 10
CBL -0.011 0.098 -10000 0 -0.33 16 16
MAP3K1 -0.034 0.13 -10000 0 -0.32 55 55
PIAS1 0.017 0.012 -10000 0 -0.26 1 1
PIAS4 0.012 0.05 -10000 0 -0.43 6 6
antigen processing and presentation of peptide antigen via MHC class II -0.056 0.1 -10000 0 -0.29 61 61
PTPN11 -0.02 0.1 -10000 0 -0.26 57 57
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
RAPGEF1 0.018 0 -10000 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.01 0.072 -10000 0 -0.37 17 17
MAP4K4 -0.002 0.11 -10000 0 -0.45 12 12
BAG4 0.002 0.071 -10000 0 -0.29 28 28
PKC zeta/ceramide -0.025 0.04 0.13 9 -0.12 1 10
NFKBIA 0.014 0.042 -10000 0 -0.46 4 4
BIRC3 -0.086 0.19 -10000 0 -0.41 129 129
BAX -0.003 0.022 -10000 0 -10000 0 0
RIPK1 0.017 0.023 -10000 0 -0.52 1 1
AKT1 0.017 0.051 -10000 0 -0.35 9 9
BAD -0.018 0.041 0.15 8 -0.18 1 9
SMPD1 0.008 0.06 -10000 0 -0.24 19 19
RB1 -0.028 0.07 0.15 8 -0.32 20 28
FADD/Caspase 8 0.007 0.1 -10000 0 -0.43 11 11
MAP2K4 -0.043 0.094 0.15 6 -0.28 56 62
NSMAF 0.009 0.065 -10000 0 -0.44 10 10
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.01 0.04 0.15 8 -0.18 1 9
EGF -0.14 0.23 -10000 0 -0.42 193 193
mol:ceramide -0.027 0.044 0.14 11 -0.12 1 12
MADD 0.018 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.027 0.13 -10000 0 -0.38 54 54
ASAH1 -0.037 0.15 -10000 0 -0.42 65 65
negative regulation of cell cycle -0.028 0.069 0.14 9 -0.31 20 29
cell proliferation -0.036 0.097 -10000 0 -0.23 84 84
BID -0.013 0.12 -10000 0 -0.62 13 13
MAP3K1 -0.042 0.085 0.15 7 -0.3 39 46
EIF2A -0.013 0.06 -10000 0 -0.25 17 17
TRADD 0.016 0.026 -10000 0 -0.39 2 2
CRADD 0.009 0.067 -10000 0 -0.49 9 9
MAPK3 0.001 0.039 0.16 1 -0.19 1 2
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.001 0.04 -10000 0 -0.19 1 1
Cathepsin D/ceramide -0.022 0.056 0.14 8 -0.23 12 20
FADD -0.006 0.11 -10000 0 -0.38 19 19
KSR1 -0.018 0.042 0.15 8 -0.2 1 9
MAPK8 -0.031 0.069 0.14 6 -0.19 56 62
PRKRA -0.018 0.041 0.15 8 -10000 0 8
PDGFA -0.001 0.094 -10000 0 -0.44 22 22
TRAF2 0.014 0.042 -10000 0 -0.46 4 4
IGF1 -0.1 0.21 -10000 0 -0.42 146 146
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.027 0.044 0.14 11 -0.12 1 12
CTSD 0.003 0.074 -10000 0 -0.33 23 23
regulation of nitric oxide biosynthetic process 0.026 0.017 -10000 0 -0.37 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.036 0.11 -10000 0 -0.25 84 84
PRKCD 0.014 0.042 -10000 0 -0.46 4 4
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.027 0.13 -10000 0 -0.38 54 54
RelA/NF kappa B1 0.026 0.017 -10000 0 -0.37 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0 0.091 -10000 0 -0.44 20 20
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.006 0.11 -10000 0 -0.45 13 13
TNFR1A/BAG4/TNF-alpha 0.012 0.074 -10000 0 -0.31 18 18
mol:Sphingosine-1-phosphate 0.01 0.072 -10000 0 -0.37 17 17
MAP2K1 -0.002 0.039 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.018 0 -10000 0 -10000 0 0
CYCS 0.027 0.066 0.16 76 -10000 0 76
TNFRSF1A 0.016 0.033 -10000 0 -0.52 2 2
NFKB1 0.017 0.023 -10000 0 -0.52 1 1
TNFR1A/BAG4 0.014 0.055 -10000 0 -0.37 5 5
EIF2AK2 -0.019 0.062 0.15 8 -0.26 18 26
TNF-alpha/TNFR1A/FAN 0.016 0.074 -10000 0 -0.31 21 21
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.062 -10000 0 -0.3 2 2
MAP2K2 -0.004 0.043 -10000 0 -0.27 3 3
SMPD3 0.005 0.072 -10000 0 -0.26 20 20
TNF -0.004 0.094 -10000 0 -0.36 31 31
PKC zeta/PAR4 0.001 0.065 -10000 0 -0.32 20 20
mol:PHOSPHOCHOLINE 0.055 0.1 0.21 133 -10000 0 133
NF kappa B1/RelA/I kappa B alpha 0.03 0.055 -10000 0 -0.25 18 18
AIFM1 0.027 0.066 0.16 76 -10000 0 76
BCL2 -0.12 0.22 -10000 0 -0.47 145 145
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.023 0.029 -9999 0 -0.18 9 9
VLDLR -0.059 0.17 -9999 0 -0.4 98 98
CRKL 0.014 0.047 -9999 0 -0.52 4 4
LRPAP1 0.016 0.026 -9999 0 -0.39 2 2
FYN 0.009 0.063 -9999 0 -0.4 11 11
ITGA3 -0.003 0.096 -9999 0 -0.42 25 25
RELN/VLDLR/Fyn -0.021 0.12 -9999 0 -0.32 61 61
MAPK8IP1/MKK7/MAP3K11/JNK1 0.038 0.061 -9999 0 -0.26 18 18
AKT1 -0.01 0.11 -9999 0 -0.38 18 18
MAP2K7 0.017 0.023 -9999 0 -0.52 1 1
RAPGEF1 0.018 0 -9999 0 -10000 0 0
DAB1 0.018 0 -9999 0 -10000 0 0
RELN/LRP8/DAB1 -0.011 0.094 -9999 0 -0.28 41 41
LRPAP1/LRP8 -0.027 0.11 -9999 0 -0.37 36 36
RELN/LRP8/DAB1/Fyn -0.005 0.093 -9999 0 -0.26 47 47
DAB1/alpha3/beta1 Integrin -0.066 0.1 -9999 0 -0.36 24 24
long-term memory -0.002 0.1 -9999 0 -0.37 5 5
DAB1/LIS1 -0.027 0.12 -9999 0 -0.38 14 14
DAB1/CRLK/C3G -0.058 0.096 -9999 0 -0.37 15 15
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
DAB1/NCK2 -0.028 0.12 -9999 0 -0.36 15 15
ARHGEF2 0.004 0.079 -9999 0 -0.41 17 17
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A 0.017 0.012 -9999 0 -0.26 1 1
CDK5R1 0.014 0.031 -9999 0 -0.26 7 7
RELN 0.009 0.059 -9999 0 -0.38 11 11
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
RELN/LRP8/Fyn -0.019 0.11 -9999 0 -0.31 47 47
GRIN2A/RELN/LRP8/DAB1/Fyn 0.004 0.095 -9999 0 -0.25 46 46
MAPK8 0.015 0.04 -9999 0 -0.52 3 3
RELN/VLDLR/DAB1 -0.013 0.1 -9999 0 -0.28 57 57
ITGB1 0.015 0.037 -9999 0 -0.39 4 4
MAP1B -0.056 0.14 -9999 0 -0.29 109 109
RELN/LRP8 -0.014 0.1 -9999 0 -0.31 42 42
GRIN2B/RELN/LRP8/DAB1/Fyn -0.009 0.11 -9999 0 -0.26 64 64
PI3K 0.006 0.082 -9999 0 -0.37 21 21
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.01 0.077 -9999 0 -0.39 16 16
RAP1A -0.019 0.12 -9999 0 -0.36 16 16
PAFAH1B1 0.017 0.023 -9999 0 -0.52 1 1
MAPK8IP1 0.011 0.048 -9999 0 -0.31 11 11
CRLK/C3G 0.023 0.034 -9999 0 -0.37 4 4
GRIN2B -0.007 0.11 -9999 0 -0.43 29 29
NCK2 0.015 0.027 -9999 0 -0.26 5 5
neuron differentiation 0.012 0.077 -9999 0 -0.3 4 4
neuron adhesion -0.015 0.12 -9999 0 -0.44 8 8
LRP8 -0.057 0.16 -9999 0 -0.34 109 109
GSK3B -0.003 0.1 -9999 0 -0.42 13 13
RELN/VLDLR/DAB1/Fyn -0.007 0.1 -9999 0 -0.27 61 61
MAP3K11 0.015 0.035 -9999 0 -0.43 3 3
RELN/VLDLR/DAB1/P13K -0.015 0.11 -9999 0 -0.26 72 72
CDK5 0.016 0.026 -9999 0 -0.39 2 2
MAPT -0.09 0.2 -9999 0 -0.48 107 107
neuron migration -0.011 0.12 -9999 0 -0.35 25 25
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.012 0.078 -9999 0 -0.31 4 4
RELN/VLDLR -0.043 0.13 -9999 0 -0.28 111 111
IL2 signaling events mediated by STAT5

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
GAB2 0.01 0.047 -9999 0 -0.26 16 16
ELF1 -0.013 0.12 -9999 0 -0.37 44 44
CCNA2 -0.024 0.13 -9999 0 -0.4 53 53
PIK3CA 0.016 0.029 -9999 0 -0.34 3 3
JAK3 0.018 0 -9999 0 -10000 0 0
PIK3R1 -0.008 0.11 -9999 0 -0.42 32 32
JAK1 0.012 0.057 -9999 0 -0.52 6 6
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.01 0.14 -9999 0 -0.46 23 23
SHC1 0.018 0.023 -9999 0 -0.52 1 1
SP1 0.016 0.069 -9999 0 -0.36 15 15
IL2RA -0.036 0.21 -9999 0 -0.68 44 44
IL2RB -0.016 0.12 -9999 0 -0.44 40 40
SOS1 0.017 0.023 -9999 0 -0.52 1 1
IL2RG -0.002 0.079 -9999 0 -0.29 35 35
G1/S transition of mitotic cell cycle -0.024 0.2 -9999 0 -0.56 47 47
PTPN11 0.018 0.023 -9999 0 -0.52 1 1
CCND2 0.011 0.14 -9999 0 -0.77 15 15
LCK -0.072 0.18 -9999 0 -0.4 115 115
GRB2 0.016 0.024 -9999 0 -0.26 4 4
IL2 0.012 0.051 -9999 0 -0.34 10 10
CDK6 -0.02 0.11 -9999 0 -0.3 63 63
CCND3 0.021 0.13 -9999 0 -0.53 5 5
Aurora B signaling

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
Condensin I complex 0.01 0.079 -9999 0 -0.27 27 27
STMN1 0.001 0.089 -9999 0 -0.38 22 22
Aurora B/RasGAP/Survivin -0.012 0.12 -9999 0 -0.34 53 53
Chromosomal passenger complex/Cul3 protein complex -0.054 0.14 -9999 0 -0.36 58 58
BIRC5 -0.039 0.16 -9999 0 -0.43 67 67
DES -0.027 0.13 -9999 0 -0.68 16 16
Aurora C/Aurora B/INCENP 0.014 0.064 -9999 0 -0.29 15 15
Aurora B/TACC1 -0.004 0.086 -9999 0 -0.32 30 30
Aurora B/PP2A 0.019 0.043 -9999 0 -0.39 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.011 0.034 -9999 0 -0.21 9 9
mitotic metaphase/anaphase transition 0 0.005 -9999 0 -10000 0 0
NDC80 -0.015 0.12 -9999 0 -0.4 40 40
Cul3 protein complex -0.049 0.14 -9999 0 -0.33 93 93
KIF2C -0.062 0.24 -9999 0 -0.66 59 59
PEBP1 0.013 0.047 -9999 0 -0.53 4 4
KIF20A -0.027 0.14 -9999 0 -0.47 49 49
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.011 0.07 -9999 0 -0.38 13 13
SEPT1 0.008 0.053 -9999 0 -0.27 17 17
SMC2 0.003 0.079 -9999 0 -0.38 20 20
SMC4 0.014 0.041 -9999 0 -0.35 6 6
NSUN2/NPM1/Nucleolin 0.015 0.082 -9999 0 -0.87 3 3
PSMA3 0.017 0.012 -9999 0 -0.26 1 1
G2/M transition of mitotic cell cycle 0 0.003 -9999 0 -10000 0 0
H3F3B 0.013 0.04 -9999 0 -0.33 5 5
AURKB 0.009 0.058 -9999 0 -0.32 14 14
AURKC 0.008 0.054 -9999 0 -0.27 18 18
CDCA8 -0.018 0.12 -9999 0 -0.41 44 44
cytokinesis -0.05 0.26 -9999 0 -0.74 50 50
Aurora B/Septin1 -0.037 0.24 -9999 0 -0.71 45 45
AURKA -0.012 0.11 -9999 0 -0.42 36 36
INCENP -0.001 0.086 -9999 0 -0.38 23 23
KLHL13 -0.096 0.2 -9999 0 -0.39 147 147
BUB1 -0.051 0.17 -9999 0 -0.44 79 79
hSgo1/Aurora B/Survivin -0.016 0.14 -9999 0 -0.39 52 52
EVI5 0.013 0.047 -9999 0 -0.52 4 4
RhoA/GTP -0.047 0.25 -9999 0 -0.69 54 54
SGOL1 -0.01 0.11 -9999 0 -0.38 37 37
CENPA -0.042 0.22 -9999 0 -0.59 51 51
NCAPG 0 0 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.02 0.041 -9999 0 -0.39 3 3
NCAPD2 0.011 0.041 -9999 0 -0.26 12 12
Aurora B/PP1-gamma 0.018 0.05 -9999 0 -0.38 6 6
RHOA 0.005 0.08 -9999 0 -0.52 12 12
NCAPH -0.007 0.11 -9999 0 -0.46 28 28
NPM1 0.012 0.052 -9999 0 -0.6 3 3
RASA1 0.004 0.079 -9999 0 -0.42 16 16
KLHL9 -0.001 0.096 -9999 0 -0.49 19 19
mitotic prometaphase -0.001 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.041 -9999 0 -0.38 3 3
PPP1CC 0.015 0.04 -9999 0 -0.52 3 3
Centraspindlin -0.054 0.28 -9999 0 -0.71 60 60
RhoA/GDP 0.004 0.058 -9999 0 -0.38 12 12
NSUN2 0.012 0.054 -9999 0 -0.6 3 3
MYLK 0.003 0.068 -9999 0 -0.33 19 19
KIF23 -0.025 0.14 -9999 0 -0.45 48 48
VIM -0.01 0.11 -9999 0 -0.38 34 34
RACGAP1 -0.004 0.1 -9999 0 -0.5 22 22
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.012 0.052 -9999 0 -0.6 3 3
Chromosomal passenger complex -0.047 0.22 -9999 0 -0.59 56 56
Chromosomal passenger complex/EVI5 -0.014 0.15 -9999 0 -0.37 62 62
TACC1 -0.02 0.13 -9999 0 -0.41 47 47
PPP2R5D 0.016 0.021 -9999 0 -0.26 3 3
CUL3 0.01 0.061 -9999 0 -0.43 9 9
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.019 0.05 -10000 0 -0.37 8 8
Necdin/E2F1 -0.026 0.13 -10000 0 -0.38 61 61
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.01 0.11 -10000 0 -0.27 78 78
NGF (dimer)/p75(NTR)/BEX1 -0.016 0.076 -10000 0 -0.29 12 12
NT-4/5 (dimer)/p75(NTR) 0.004 0.046 -10000 0 -0.2 23 23
IKBKB 0.011 0.047 -10000 0 -0.31 10 10
AKT1 0.01 0.072 -10000 0 -0.25 30 30
IKBKG 0.018 0 -10000 0 -10000 0 0
BDNF -0.016 0.092 -10000 0 -0.26 64 64
MGDIs/NGR/p75(NTR)/LINGO1 -0.004 0.087 -10000 0 -0.31 22 22
FURIN 0.003 0.077 -10000 0 -0.36 20 20
proBDNF (dimer)/p75(NTR)/Sortilin 0.003 0.076 -10000 0 -0.33 11 11
LINGO1 -0.02 0.097 -10000 0 -0.26 70 70
Sortilin/TRAF6/NRIF -0.018 0.057 -10000 0 -0.34 5 5
proBDNF (dimer) -0.016 0.092 -10000 0 -0.26 64 64
NTRK1 0.01 0.054 -10000 0 -0.32 12 12
RTN4R 0.001 0.087 -10000 0 -0.41 21 21
neuron apoptosis 0.003 0.1 -10000 0 -0.43 9 9
IRAK1 0.015 0.029 -10000 0 -0.26 6 6
SHC1 0.013 0.041 -10000 0 -0.31 4 4
ARHGDIA 0.016 0.029 -10000 0 -0.35 3 3
RhoA/GTP 0.004 0.058 -10000 0 -0.38 12 12
Gamma Secretase 0.032 0.07 -10000 0 -0.25 26 26
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.002 0.094 -10000 0 -0.3 42 42
MAGEH1 -0.018 0.13 -10000 0 -0.52 35 35
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.012 0.11 -10000 0 -0.3 64 64
Mammalian IAPs/DIABLO -0.024 0.11 -10000 0 -0.28 76 76
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 -0.008 0.11 -10000 0 -0.48 27 27
APP -0.028 0.14 -10000 0 -0.42 55 55
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.013 0.044 -10000 0 -0.32 8 8
RhoA/GDP/RHOGDI 0.017 0.058 -10000 0 -0.27 16 16
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest 0.006 0.055 0.15 3 -0.26 10 13
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.026 0.041 -10000 0 -0.23 9 9
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.016 0.041 -10000 0 -0.31 4 4
NCSTN 0.017 0.023 -10000 0 -0.52 1 1
mol:GTP -0.015 0.089 -10000 0 -0.31 30 30
PSENEN 0.017 0.012 -10000 0 -0.26 1 1
mol:ceramide 0.014 0.056 -10000 0 -0.29 12 12
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.021 0.05 -10000 0 -0.26 1 1
p75(NTR)/beta APP -0.016 0.11 -10000 0 -0.37 38 38
BEX1 -0.04 0.12 -10000 0 -0.26 108 108
mol:GDP 0.002 0.038 -10000 0 -0.32 3 3
NGF (dimer) -0.038 0.13 -10000 0 -0.29 99 99
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.008 0.082 -10000 0 -0.28 23 23
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
RAC1/GTP 0.014 0.033 -10000 0 -0.27 3 3
MYD88 0.013 0.048 -10000 0 -0.47 5 5
CHUK 0.005 0.081 -10000 0 -0.5 13 13
NGF (dimer)/p75(NTR)/PKA -0.015 0.089 -10000 0 -0.31 30 30
RHOB -0.04 0.17 -10000 0 -0.52 57 57
RHOA 0.005 0.08 -10000 0 -0.52 12 12
MAGE-G1/E2F1 0.018 0.051 -10000 0 -0.37 7 7
NT3 (dimer) -0.021 0.1 -10000 0 -0.28 67 67
TP53 -0.001 0.098 -10000 0 -0.26 49 49
PRDM4 0.017 0.049 -10000 0 -0.28 10 10
BDNF (dimer) -0.12 0.2 -10000 0 -0.39 154 154
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
SORT1 0.009 0.065 -10000 0 -0.44 10 10
activation of caspase activity -0.013 0.11 -10000 0 -0.27 78 78
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.022 0.052 -10000 0 -0.28 11 11
RHOC 0.015 0.04 -10000 0 -0.52 3 3
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0 0.096 -10000 0 -0.3 16 16
DIABLO 0.018 0 -10000 0 -10000 0 0
SMPD2 0.014 0.056 -10000 0 -0.3 12 12
APH1B 0 0.096 -10000 0 -0.51 18 18
APH1A 0.003 0.068 -10000 0 -0.29 25 25
proNGF (dimer)/p75(NTR)/Sortilin 0.011 0.055 -10000 0 -0.31 10 10
PSEN1 0.013 0.052 -10000 0 -0.52 5 5
APAF-1/Pro-Caspase 9 0.022 0.041 -10000 0 -0.37 5 5
NT3 (dimer)/p75(NTR) -0.009 0.089 -10000 0 -0.41 12 12
MAPK8 0.014 0.08 -10000 0 -0.28 11 11
MAPK9 0.005 0.097 -10000 0 -0.37 10 10
APAF1 0.012 0.051 -10000 0 -0.41 7 7
NTF3 -0.021 0.1 -10000 0 -0.28 67 67
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.044 0.17 -10000 0 -0.49 64 64
RAC1/GDP 0.013 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.028 0.11 -10000 0 -0.25 95 95
p75 CTF/Sortilin/TRAF6/NRIF 0.036 0.048 -10000 0 -0.27 10 10
RhoA-B-C/GTP -0.015 0.088 -10000 0 -0.31 30 30
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.021 0.07 -10000 0 -0.26 14 14
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.015 0.071 -10000 0 -0.29 12 12
PRKACB -0.035 0.14 -10000 0 -0.34 78 78
proBDNF (dimer)/p75 ECD 0.002 0.065 -10000 0 -0.35 2 2
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.086 0.19 -10000 0 -0.41 129 129
BIRC2 0.016 0.021 -10000 0 -0.26 3 3
neuron projection morphogenesis -0.032 0.11 0.2 2 -0.34 35 37
BAD 0.008 0.091 -10000 0 -0.31 13 13
RIPK2 0.013 0.041 -10000 0 -0.29 9 9
NGFR 0.004 0.066 -10000 0 -0.29 23 23
CYCS 0.009 0.074 -10000 0 -0.25 34 34
ADAM17 0.016 0.024 -10000 0 -0.26 4 4
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.024 0.044 -10000 0 -0.27 6 6
BCL2L11 0.008 0.091 -10000 0 -0.3 15 15
BDNF (dimer)/p75(NTR) -0.006 0.076 -10000 0 -0.4 4 4
PI3K 0.011 0.072 -10000 0 -0.28 25 25
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.022 0.051 -10000 0 -0.28 10 10
NDNL2 0.018 0 -10000 0 -10000 0 0
YWHAE 0.016 0.029 -10000 0 -0.35 3 3
PRKCI 0.001 0.088 -10000 0 -0.44 19 19
NGF (dimer)/p75(NTR) 0.004 0.046 -10000 0 -0.2 23 23
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.008 0.08 -10000 0 -0.28 33 33
TRAF6 0.017 0.023 -10000 0 -0.52 1 1
RAC1 0.018 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.016 0.033 -10000 0 -0.52 2 2
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.005 0.07 -10000 0 -0.28 18 18
SQSTM1 0.012 0.053 -10000 0 -0.48 6 6
NGFRAP1 -0.056 0.18 -10000 0 -0.51 73 73
CASP3 0.01 0.087 -10000 0 -0.29 13 13
E2F1 0.006 0.071 -10000 0 -0.37 16 16
CASP9 0.017 0.023 -10000 0 -0.52 1 1
IKK complex -0.013 0.047 -10000 0 -0.34 3 3
NGF (dimer)/TRKA 0.008 0.038 -10000 0 -0.22 12 12
MMP7 -0.094 0.21 -10000 0 -0.44 128 128
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.028 0.054 -10000 0 -0.25 13 13
MMP3 -0.13 0.22 -10000 0 -0.43 173 173
APAF-1/Caspase 9 -0.046 0.077 -10000 0 -0.31 10 10
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.017 0.13 -10000 0 -0.49 37 37
HRAS 0.012 0.051 -10000 0 -0.41 7 7
EGFR -0.077 0.17 -10000 0 -0.35 136 136
AKT 0.015 0.077 -10000 0 -0.32 15 15
FOXO3 0.011 0.054 -10000 0 -0.38 9 9
AKT1 0.011 0.054 -10000 0 -0.38 9 9
FOXO1 0.001 0.089 -10000 0 -0.46 18 18
AKT3 -0.006 0.082 -10000 0 -0.28 42 42
FOXO4 0.017 0.023 -10000 0 -0.52 1 1
MET -0.001 0.078 -10000 0 -0.3 31 31
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
PIK3CB 0.012 0.055 -10000 0 -0.45 7 7
NRAS 0.006 0.072 -10000 0 -0.4 15 15
PIK3CG -0.007 0.1 -10000 0 -0.41 31 31
PIK3R3 0 0.091 -10000 0 -0.43 21 21
PIK3R2 0.018 0 -10000 0 -10000 0 0
NF1 0.015 0.035 -10000 0 -0.43 3 3
RAS -0.027 0.096 0.21 1 -0.26 50 51
ERBB2 -0.027 0.12 -10000 0 -0.31 72 72
proliferation/survival/translation -0.028 0.057 0.23 10 -0.17 3 13
PI3K -0.019 0.098 0.18 4 -0.23 63 67
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
KRAS 0.008 0.069 -10000 0 -0.45 11 11
FOXO 0.039 0.037 -10000 0 -0.18 2 2
AKT2 0.017 0.012 -10000 0 -0.26 1 1
PTEN -0.002 0.1 -10000 0 -0.52 19 19
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.003 0.062 -9999 0 -1.2 1 1
VDR -0.003 0.1 -9999 0 -0.51 21 21
FAM120B 0.016 0.033 -9999 0 -0.52 2 2
RXRs/LXRs/DNA/9cRA 0.012 0.13 -9999 0 -0.41 22 22
RXRs/LXRs/DNA/Oxysterols 0 0.18 -9999 0 -0.44 68 68
MED1 0 0.068 -9999 0 -0.26 34 34
mol:9cRA -0.001 0.021 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.005 0.11 -9999 0 -0.44 17 17
RXRs/NUR77 0.03 0.077 -9999 0 -0.28 20 20
RXRs/PPAR 0.009 0.09 -9999 0 -0.31 19 19
NCOR2 0.018 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.002 0.075 -9999 0 -0.37 21 21
RARs/VDR/DNA/Vit D3 0.003 0.097 -9999 0 -0.27 50 50
RARA 0.007 0.07 -9999 0 -0.43 12 12
NCOA1 0.012 0.057 -9999 0 -0.52 6 6
VDR/VDR/DNA -0.003 0.1 -9999 0 -0.51 21 21
RARs/RARs/DNA/9cRA 0.004 0.08 -9999 0 -0.27 32 32
RARG 0.017 0.023 -9999 0 -0.52 1 1
RPS6KB1 0.004 0.055 -9999 0 -0.4 1 1
RARs/THRs/DNA/SMRT -0.002 0.11 -9999 0 -0.46 13 13
THRA -0.011 0.11 -9999 0 -0.39 37 37
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.002 0.075 -9999 0 -0.37 21 21
RXRs/PPAR/9cRA/PGJ2/DNA 0.022 0.085 -9999 0 -0.29 19 19
NR1H4 0.015 0.031 -9999 0 -0.32 4 4
RXRs/LXRs/DNA 0.037 0.11 -9999 0 -0.42 10 10
NR1H2 0.018 0.017 -9999 0 -10000 0 0
NR1H3 0.009 0.071 -9999 0 -0.44 11 11
RXRs/VDR/DNA/Vit D3 0.02 0.089 -9999 0 -0.26 38 38
NR4A1 0.009 0.05 -9999 0 -0.28 15 15
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.016 0.064 -9999 0 -0.26 9 9
RXRG 0.003 0.087 -9999 0 -0.47 16 16
RXR alpha/CCPG 0.023 0.041 -9999 0 -0.38 5 5
RXRA 0.014 0.045 -9999 0 -0.54 3 3
RXRB 0.014 0.045 -9999 0 -0.52 3 3
THRB -0.001 0.097 -9999 0 -0.48 20 20
PPARG -0.035 0.13 -9999 0 -0.34 79 79
PPARD 0.017 0.017 -9999 0 -0.26 2 2
TNF -0.01 0.23 -9999 0 -0.8 28 28
mol:Oxysterols 0 0.018 -9999 0 -10000 0 0
cholesterol transport 0 0.18 -9999 0 -0.43 68 68
PPARA 0.013 0.041 -9999 0 -0.29 9 9
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.025 0.13 -9999 0 -0.36 60 60
RXRs/NUR77/BCL2 -0.041 0.12 -9999 0 -0.24 131 131
SREBF1 -0.051 0.33 -9999 0 -1 51 51
RXRs/RXRs/DNA/9cRA 0.022 0.085 -9999 0 -0.29 19 19
ABCA1 -0.008 0.24 -9999 0 -0.82 28 28
RARs/THRs -0.001 0.12 -9999 0 -0.29 59 59
RXRs/FXR 0.033 0.075 -9999 0 -0.28 21 21
BCL2 -0.12 0.22 -9999 0 -0.47 145 145
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 0.025 0.017 -9999 0 -0.37 1 1
SMARCC1 -0.003 0.12 -9999 0 -1.3 4 4
REL 0 0.087 -9999 0 -0.41 21 21
HDAC7 -0.026 0.13 -9999 0 -0.37 36 36
JUN -0.033 0.15 -9999 0 -0.46 57 57
EP300 0.014 0.047 -9999 0 -0.52 4 4
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0 0 -9999 0 -10000 0 0
MAPK14 0.001 0.084 -9999 0 -0.33 26 26
FOXO1 0.002 0.089 -9999 0 -0.46 18 18
T-DHT/AR -0.019 0.15 -9999 0 -0.41 31 31
MAP2K6 -0.013 0.11 -9999 0 -0.4 37 37
BRM/BAF57 0.026 0.023 -9999 0 -0.37 1 1
MAP2K4 -0.007 0.1 -9999 0 -0.39 30 30
SMARCA2 0.017 0.023 -9999 0 -0.52 1 1
PDE9A -0.024 0.15 -9999 0 -0.68 13 13
NCOA2 0.01 0.063 -9999 0 -0.4 11 11
CEBPA 0.004 0.084 -9999 0 -0.5 14 14
EHMT2 0.018 0.001 -9999 0 -10000 0 0
cell proliferation 0.007 0.14 -9999 0 -0.36 25 25
NR0B1 -0.01 0.087 -9999 0 -0.27 50 50
EGR1 -0.1 0.2 -9999 0 -0.39 155 155
RXRs/9cRA 0.024 0.059 -9999 0 -0.28 19 19
AR/RACK1/Src 0.003 0.1 -9999 0 -0.33 23 23
AR/GR -0.039 0.13 -9999 0 -0.29 76 76
GNB2L1 0.015 0.04 -9999 0 -0.52 3 3
PKN1 0.013 0.045 -9999 0 -0.39 6 6
RCHY1 0.002 0.09 -9999 0 -0.5 16 16
epidermal growth factor receptor activity 0 0.001 -9999 0 -0.005 5 5
MAPK8 0.004 0.079 -9999 0 -0.34 22 22
T-DHT/AR/TIF2/CARM1 0 0.11 -9999 0 -0.35 24 24
SRC 0.005 0.09 -9999 0 -0.28 38 38
NR3C1 -0.003 0.1 -9999 0 -0.51 21 21
KLK3 -0.038 0.11 -9999 0 -0.48 5 5
APPBP2 0.009 0.043 -9999 0 -0.26 13 13
TRIM24 0.017 0.024 -9999 0 -0.26 4 4
T-DHT/AR/TIP60 -0.021 0.1 -9999 0 -0.31 43 43
TMPRSS2 -0.18 0.43 -9999 0 -1.1 97 97
RXRG 0.003 0.086 -9999 0 -0.47 16 16
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.015 0.04 -9999 0 -0.52 3 3
RXRB 0.015 0.04 -9999 0 -0.52 3 3
CARM1 0.015 0.039 -9999 0 -0.36 5 5
NR2C2 0.016 0.021 -9999 0 -0.26 3 3
KLK2 0.021 0.095 -9999 0 -0.4 4 4
AR -0.04 0.13 -9999 0 -0.27 116 116
SENP1 0.018 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0.045 -9999 0 -0.39 6 6
MDM2 0.009 0.044 -9999 0 -0.26 14 14
SRY 0.001 0.085 -9999 0 -0.44 18 18
GATA2 -0.008 0.094 -9999 0 -0.32 40 40
MYST2 0.011 0.047 -9999 0 -0.31 10 10
HOXB13 -0.075 0.13 -9999 0 -0.26 182 182
T-DHT/AR/RACK1/Src -0.002 0.11 -9999 0 -0.33 24 24
positive regulation of transcription -0.008 0.093 -9999 0 -0.32 40 40
DNAJA1 0.012 0.043 -9999 0 -0.46 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.06 -9999 0 -0.31 16 16
NCOA1 0.016 0.063 -9999 0 -0.55 6 6
SPDEF -0.081 0.21 -9999 0 -0.52 98 98
T-DHT/AR/TIF2 0.01 0.08 -9999 0 -0.29 12 12
T-DHT/AR/Hsp90 -0.012 0.11 -9999 0 -0.3 43 43
GSK3B 0.018 0.003 -9999 0 -10000 0 0
NR2C1 0.01 0.062 -9999 0 -0.52 7 7
mol:T-DHT -0.002 0.095 -9999 0 -0.3 36 36
SIRT1 0.016 0.029 -9999 0 -0.35 3 3
ZMIZ2 0.016 0.002 -9999 0 -10000 0 0
POU2F1 0.014 0.038 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.022 0.12 -9999 0 -0.3 49 49
CREBBP 0.016 0.033 -9999 0 -0.52 2 2
SMARCE1 0.017 0.021 -9999 0 -0.26 3 3
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.016 0.033 -9999 0 -0.52 2 2
SPHK1 -0.027 0.14 -9999 0 -0.42 54 54
GNAI2 0.006 0.075 -9999 0 -0.48 12 12
mol:S1P -0.001 0.088 -9999 0 -0.3 36 36
GNAO1 0.016 0.024 -9999 0 -0.26 4 4
mol:Sphinganine-1-P -0.008 0.1 -9999 0 -0.38 34 34
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.014 0.076 -9999 0 -0.23 40 40
GNAI3 0.017 0.023 -9999 0 -0.52 1 1
G12/G13 0.02 0.043 -9999 0 -0.37 5 5
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 -0.021 0.13 -9999 0 -0.41 48 48
S1P1/S1P -0.014 0.11 -9999 0 -0.28 61 61
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 -0.015 0.12 -9999 0 -0.38 44 44
S1P/S1P5/G12 0.007 0.07 -9999 0 -0.23 36 36
S1P/S1P3/Gq -0.027 0.11 -9999 0 -0.27 68 68
S1P/S1P4/Gi 0.007 0.09 -9999 0 -0.34 19 19
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.002 0.085 -9999 0 -0.43 18 18
GNA14 -0.081 0.18 -9999 0 -0.35 141 141
GNA15 0.001 0.078 -9999 0 -0.33 25 25
GNA12 0.018 0 -9999 0 -10000 0 0
GNA13 0.009 0.059 -9999 0 -0.38 11 11
GNA11 0.014 0.047 -9999 0 -0.52 4 4
ABCC1 0.012 0.051 -9999 0 -0.41 7 7
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.018 0.27 -9999 0 -0.78 25 25
PCK1 0.018 0.2 -9999 0 -0.95 6 6
HNF4A 0.032 0.27 -9999 0 -0.86 13 13
KCNJ11 -0.016 0.38 -9999 0 -1 48 48
AKT1 0.01 0.17 -9999 0 -0.44 29 29
response to starvation 0.006 0.003 -9999 0 -10000 0 0
DLK1 0.018 0.3 -9999 0 -0.79 27 27
NKX2-1 0.074 0.14 -9999 0 -10000 0 0
ACADM 0.01 0.29 -9999 0 -0.79 32 32
TAT 0.017 0.18 -9999 0 -0.56 6 6
CEBPB 0.01 0.072 -9999 0 -0.33 20 20
CEBPA 0.011 0.085 -9999 0 -0.5 14 14
TTR -0.041 0.28 -9999 0 -0.83 27 27
PKLR 0.022 0.26 -9999 0 -0.75 23 23
APOA1 0.031 0.3 -9999 0 -0.95 12 12
CPT1C -0.001 0.3 -9999 0 -0.86 34 34
ALAS1 0.038 0.19 -9999 0 -1.6 2 2
TFRC -0.045 0.39 -9999 0 -1.2 42 42
FOXF1 -0.003 0.066 -9999 0 -0.32 19 19
NF1 0.023 0.039 -9999 0 -0.46 3 3
HNF1A (dimer) 0.03 0.048 -9999 0 -0.23 12 12
CPT1A 0.005 0.3 -9999 0 -0.87 31 31
HMGCS1 0.017 0.27 -9999 0 -0.74 27 27
NR3C1 0.005 0.11 -9999 0 -0.5 21 21
CPT1B 0.021 0.26 -9999 0 -0.76 23 23
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.02 0.04 -9999 0 -0.3 4 4
GCK 0.016 0.27 -9999 0 -0.74 29 29
CREB1 0.02 0.036 -9999 0 -0.51 1 1
IGFBP1 0.026 0.16 -9999 0 -0.73 4 4
PDX1 0.034 0.26 -9999 0 -1.2 13 13
UCP2 -0.026 0.35 -9999 0 -0.9 51 51
ALDOB 0.023 0.29 -9999 0 -0.79 26 26
AFP -0.049 0.15 -9999 0 -0.51 13 13
BDH1 0.01 0.28 -9999 0 -0.75 34 34
HADH 0.02 0.3 -9999 0 -0.82 27 27
F2 0.031 0.3 -9999 0 -0.92 14 14
HNF1A 0.03 0.048 -9999 0 -0.23 12 12
G6PC 0.035 0.096 -9999 0 -1.3 1 1
SLC2A2 0.042 0.22 -9999 0 -1 6 6
INS 0.002 0.028 -9999 0 -0.53 1 1
FOXA1 -0.081 0.21 -9999 0 -0.5 106 106
FOXA3 -0.015 0.13 -9999 0 -0.38 30 30
FOXA2 0.031 0.35 -9999 0 -0.87 31 31
ABCC8 -0.2 0.52 -9999 0 -0.91 168 168
ALB -0.055 0.17 -9999 0 -0.67 16 16
PLK1 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
regulation of centriole-centriole cohesion 0.001 0.051 0.25 18 -10000 0 18
BUB1B -0.017 0.12 -10000 0 -0.42 39 39
PLK1 0.002 0.041 -10000 0 -0.12 46 46
PLK1S1 0.002 0.019 -10000 0 -0.054 41 41
KIF2A 0.005 0.054 -10000 0 -0.19 23 23
regulation of mitotic centrosome separation 0.002 0.041 -10000 0 -0.12 46 46
GOLGA2 0.016 0.026 -10000 0 -0.39 2 2
Hec1/SPC24 -0.012 0.095 -10000 0 -0.32 38 38
WEE1 -0.003 0.093 -10000 0 -0.35 25 25
cytokinesis -0.026 0.16 -10000 0 -0.55 41 41
PP2A-alpha B56 -0.058 0.27 -10000 0 -0.76 61 61
AURKA -0.002 0.064 -10000 0 -0.28 23 23
PICH/PLK1 -0.024 0.18 -10000 0 -0.52 47 47
CENPE -0.011 0.097 -10000 0 -0.33 38 38
RhoA/GTP 0.004 0.058 -10000 0 -0.38 12 12
positive regulation of microtubule depolymerization 0.005 0.054 -10000 0 -0.19 23 23
PPP2CA 0.011 0.062 -10000 0 -0.52 7 7
FZR1 0.018 0 -10000 0 -10000 0 0
TPX2 -0.013 0.084 -10000 0 -0.29 42 42
PAK1 -0.023 0.13 -10000 0 -0.38 53 53
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.015 0.035 -10000 0 -0.43 3 3
CLSPN 0.002 0.057 -10000 0 -0.35 11 11
GORASP1 0.017 0.023 -10000 0 -0.52 1 1
metaphase 0 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.019 -10000 0 -0.054 41 41
G2 phase of mitotic cell cycle -0.001 0.003 0.016 1 -0.013 21 22
STAG2 0.017 0.023 -10000 0 -0.52 1 1
GRASP65/GM130/RAB1/GTP 0.021 0.04 -10000 0 -0.74 1 1
spindle elongation 0.002 0.041 -10000 0 -0.12 46 46
ODF2 0.016 0.024 -10000 0 -0.53 1 1
BUB1 -0.1 0.28 -10000 0 -0.86 59 59
TPT1 0.009 0.019 -10000 0 -10000 0 0
CDC25C -0.017 0.11 -10000 0 -0.44 34 34
CDC25B 0.003 0.07 -10000 0 -0.31 23 23
SGOL1 -0.001 0.051 -10000 0 -0.25 18 18
RHOA 0.005 0.08 -10000 0 -0.52 12 12
CCNB1/CDK1 -0.013 0.15 -10000 0 -0.48 42 42
CDC14B 0.01 0.03 -10000 0 -0.38 3 3
CDC20 -0.02 0.12 -10000 0 -0.38 51 51
PLK1/PBIP1 -0.011 0.083 -10000 0 -0.29 37 37
mitosis 0.002 0.007 0.034 22 -10000 0 22
FBXO5 0.003 0.054 -10000 0 -0.25 11 11
CDC2 -0.012 0.12 -10000 0 -0.45 34 34
NDC80 -0.03 0.14 -10000 0 -0.42 58 58
metaphase plate congression 0.009 0.023 -10000 0 -10000 0 0
ERCC6L -0.027 0.19 -10000 0 -0.56 47 47
NLP/gamma Tubulin 0.005 0.022 -10000 0 -0.077 4 4
microtubule cytoskeleton organization 0.009 0.019 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.002 0.01 19 -10000 0 19
PPP1R12A 0.015 0.031 -10000 0 -0.32 4 4
interphase 0 0.002 0.01 19 -10000 0 19
PLK1/PRC1-2 -0.018 0.14 -10000 0 -0.42 49 49
GRASP65/GM130/RAB1/GTP/PLK1 0.028 0.039 -10000 0 -0.22 3 3
RAB1A 0.017 0.023 -10000 0 -0.52 1 1
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.006 0.039 -10000 0 -0.15 19 19
mitotic prometaphase 0 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.057 -10000 0 -0.32 6 6
microtubule-based process -0.011 0.1 -10000 0 -0.34 39 39
Golgi organization 0.002 0.041 -10000 0 -0.12 46 46
Cohesin/SA2 0.01 0.036 -10000 0 -0.21 2 2
PPP1CB/MYPT1 0.023 0.026 -10000 0 -0.37 1 1
KIF20A -0.027 0.14 -10000 0 -0.46 49 49
APC/C/CDC20 -0.007 0.089 -10000 0 -0.33 29 29
PPP2R1A 0.017 0.012 -10000 0 -0.26 1 1
chromosome segregation -0.011 0.082 -10000 0 -0.28 37 37
PRC1 -0.02 0.13 -10000 0 -0.43 44 44
ECT2 -0.001 0.07 -10000 0 -0.3 19 19
C13orf34 0.006 0.037 -10000 0 -0.13 14 14
NUDC 0.009 0.023 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.016 0.12 -10000 0 -0.41 39 39
spindle assembly 0.005 0.032 -10000 0 -0.094 27 27
spindle stabilization 0.002 0.019 -10000 0 -0.053 41 41
APC/C/HCDH1 0.02 0.025 -10000 0 -0.32 3 3
MKLP2/PLK1 -0.011 0.1 -10000 0 -0.35 39 39
CCNB1 -0.016 0.13 -10000 0 -0.5 35 35
PPP1CB 0.016 0.021 -10000 0 -0.26 3 3
BTRC 0.009 0.054 -10000 0 -0.29 15 15
ROCK2 0.007 0.057 -10000 0 -0.34 8 8
TUBG1 0.008 0.021 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.046 0.14 -10000 0 -0.48 41 41
MLF1IP -0.018 0.1 -10000 0 -0.32 49 49
INCENP 0 0.085 -10000 0 -0.38 23 23
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.001 0.11 -9999 0 -0.36 32 32
PDGFRB 0.01 0.067 -9999 0 -0.53 8 8
SPHK1 -0.054 0.19 -9999 0 -0.76 33 33
mol:S1P -0.049 0.17 -9999 0 -0.65 35 35
S1P1/S1P/Gi -0.003 0.15 -9999 0 -0.5 26 26
GNAO1 0.016 0.024 -9999 0 -0.26 4 4
PDGFB-D/PDGFRB/PLCgamma1 0.007 0.14 -9999 0 -0.48 24 24
PLCG1 0.003 0.14 -9999 0 -0.47 25 25
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.067 -9999 0 -0.53 8 8
GNAI2 0.007 0.076 -9999 0 -0.48 12 12
GNAI3 0.017 0.024 -9999 0 -0.53 1 1
GNAI1 -0.015 0.12 -9999 0 -0.38 44 44
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.015 0.16 -9999 0 -0.6 32 32
S1P1/S1P -0.029 0.19 -9999 0 -0.52 57 57
negative regulation of cAMP metabolic process -0.002 0.15 -9999 0 -0.48 26 26
MAPK3 0.001 0.16 -9999 0 -0.53 24 24
calcium-dependent phospholipase C activity 0 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
RhoA/GDP 0.004 0.058 -9999 0 -0.38 12 12
KDR 0.005 0.077 -9999 0 -0.65 5 5
PLCB2 -0.017 0.17 -9999 0 -0.45 57 57
RAC1 0.018 0 -9999 0 -10000 0 0
RhoA/GTP -0.062 0.14 -9999 0 -0.42 60 60
receptor internalization -0.026 0.18 -9999 0 -0.48 57 57
PTGS2 -0.002 0.18 -9999 0 -0.6 22 22
Rac1/GTP -0.058 0.14 -9999 0 -0.42 57 57
RHOA 0.005 0.08 -9999 0 -0.52 12 12
VEGFA -0.007 0.086 -9999 0 -0.3 31 31
negative regulation of T cell proliferation -0.002 0.15 -9999 0 -0.48 26 26
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.003 0.085 -9999 0 -0.44 18 18
MAPK1 0 0.16 -9999 0 -0.53 24 24
S1P1/S1P/PDGFB-D/PDGFRB -0.019 0.2 -9999 0 -0.59 40 40
ABCC1 0.012 0.051 -9999 0 -0.41 7 7
ErbB2/ErbB3 signaling events

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
USP8 0.015 0.035 -10000 0 -0.32 4 4
RAS family/GTP 0.002 0.098 -10000 0 -0.3 27 27
NFATC4 0.008 0.079 0.2 1 -0.32 11 12
ERBB2IP 0.016 0.033 -10000 0 -0.52 2 2
HSP90 (dimer) 0.013 0.045 -10000 0 -0.39 6 6
mammary gland morphogenesis -0.009 0.094 0.23 1 -0.28 39 40
JUN 0.02 0.072 -10000 0 -10000 0 0
HRAS 0.012 0.051 -10000 0 -0.41 7 7
DOCK7 -0.002 0.092 0.22 1 -0.3 23 24
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.012 0.1 0.24 1 -0.3 47 48
AKT1 0.008 0.038 -10000 0 -0.26 9 9
BAD 0.016 0.035 -10000 0 -0.31 5 5
MAPK10 0.002 0.069 -10000 0 -0.22 18 18
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.009 0.1 0.25 1 -0.3 38 39
RAF1 0.007 0.1 -10000 0 -0.33 19 19
ErbB2/ErbB3/neuregulin 2 -0.037 0.12 0.24 1 -0.34 56 57
STAT3 0.016 0.095 -10000 0 -0.95 5 5
cell migration 0.009 0.07 0.18 1 -0.21 16 17
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.045 0.24 -10000 0 -0.6 59 59
FOS -0.06 0.22 -10000 0 -0.45 107 107
NRAS 0.006 0.073 -10000 0 -0.4 15 15
mol:Ca2+ -0.009 0.094 0.23 1 -0.28 39 40
MAPK3 -0.021 0.19 -10000 0 -0.47 54 54
MAPK1 -0.021 0.19 -10000 0 -0.47 54 54
JAK2 -0.003 0.096 0.22 1 -0.28 36 37
NF2 0.003 0.01 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.001 0.082 -10000 0 -0.27 38 38
NRG1 0.008 0.049 -10000 0 -0.26 17 17
GRB2/SOS1 0.024 0.024 -10000 0 -0.37 1 1
MAPK8 0 0.089 0.22 1 -0.26 39 40
MAPK9 0.008 0.067 -10000 0 -0.22 17 17
ERBB2 -0.03 0.085 0.38 1 -0.22 71 72
ERBB3 -0.019 0.14 -10000 0 -0.52 36 36
SHC1 0.016 0.023 -10000 0 -0.52 1 1
RAC1 0.018 0 -10000 0 -10000 0 0
apoptosis -0.01 0.041 0.35 5 -10000 0 5
STAT3 (dimer) 0.016 0.093 -10000 0 -0.93 5 5
RNF41 0.021 0.031 -10000 0 -0.28 4 4
FRAP1 0.016 0.032 -10000 0 -0.31 4 4
RAC1-CDC42/GTP -0.022 0.054 -10000 0 -0.27 10 10
ErbB2/ErbB2/HSP90 (dimer) -0.014 0.076 0.26 1 -0.32 18 19
CHRNA1 -0.008 0.16 -10000 0 -0.4 50 50
myelination 0.014 0.079 0.21 1 -0.32 11 12
PPP3CB 0 0.086 0.21 1 -0.28 22 23
KRAS 0.008 0.069 -10000 0 -0.45 11 11
RAC1-CDC42/GDP 0.021 0.074 -10000 0 -0.3 9 9
NRG2 -0.016 0.1 -10000 0 -0.3 57 57
mol:GDP 0.001 0.082 -10000 0 -0.27 38 38
SOS1 0.017 0.023 -10000 0 -0.52 1 1
MAP2K2 0.007 0.11 -10000 0 -0.35 21 21
SRC 0.015 0.035 -10000 0 -0.43 3 3
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 0 0.091 0.22 1 -0.31 18 19
MAP2K1 -0.024 0.17 -10000 0 -0.44 38 38
heart morphogenesis -0.009 0.094 0.23 1 -0.28 39 40
RAS family/GDP 0.013 0.097 -10000 0 -0.31 22 22
GRB2 0.015 0.024 -10000 0 -0.26 4 4
PRKACA -0.001 0.005 -10000 0 -10000 0 0
CHRNE 0.016 0.019 -10000 0 -10000 0 0
HSP90AA1 0.013 0.045 -10000 0 -0.39 6 6
activation of caspase activity -0.008 0.038 0.26 9 -10000 0 9
nervous system development -0.009 0.094 0.23 1 -0.28 39 40
CDC42 0.018 0 -10000 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR -0.022 0.26 -10000 0 -1.1 30 30
regulation of axonogenesis -0.012 0.065 0.33 9 -10000 0 9
myoblast fusion 0.003 0.1 0.4 31 -10000 0 31
mol:GTP -0.002 0.062 -10000 0 -0.24 32 32
regulation of calcium-dependent cell-cell adhesion -0.018 0.082 0.25 39 -10000 0 39
ARF1/GTP 0.012 0.05 -10000 0 -0.26 5 5
mol:GM1 0 0.047 -10000 0 -0.18 32 32
mol:Choline 0.008 0.074 -10000 0 -0.34 15 15
lamellipodium assembly -0.001 0.11 -10000 0 -0.43 32 32
MAPK3 0.009 0.089 -10000 0 -0.33 33 33
ARF6/GTP/NME1/Tiam1 0.018 0.083 -10000 0 -0.25 39 39
ARF1 0.017 0.023 -10000 0 -0.52 1 1
ARF6/GDP -0.003 0.1 -10000 0 -0.4 31 31
ARF1/GDP 0.006 0.097 -10000 0 -0.36 33 33
ARF6 0.007 0.05 -10000 0 -0.62 2 2
RAB11A 0.016 0.029 -10000 0 -0.35 3 3
TIAM1 0.006 0.074 -10000 0 -0.44 13 13
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.009 0.09 -10000 0 -0.33 34 34
actin filament bundle formation 0.002 0.11 0.35 41 -10000 0 41
KALRN -0.022 0.078 -10000 0 -0.3 34 34
RAB11FIP3/RAB11A 0.019 0.05 -10000 0 -0.37 8 8
RhoA/GDP -0.002 0.11 -10000 0 -0.36 41 41
NME1 0.012 0.04 -10000 0 -0.26 11 11
Rac1/GDP 0.004 0.096 -10000 0 -0.36 32 32
substrate adhesion-dependent cell spreading -0.002 0.062 -10000 0 -0.24 32 32
cortical actin cytoskeleton organization -0.002 0.11 -10000 0 -0.43 32 32
RAC1 0.018 0 -10000 0 -10000 0 0
liver development -0.002 0.062 -10000 0 -0.24 32 32
ARF6/GTP -0.002 0.062 -10000 0 -0.24 32 32
RhoA/GTP 0.004 0.073 -10000 0 -0.36 14 14
mol:GDP -0.003 0.1 -10000 0 -0.4 32 32
ARF6/GTP/RAB11FIP3/RAB11A 0.019 0.058 -10000 0 -0.28 10 10
RHOA 0.005 0.08 -10000 0 -0.52 12 12
PLD1 0.001 0.077 -10000 0 -0.38 12 12
RAB11FIP3 0.01 0.063 -10000 0 -0.49 8 8
tube morphogenesis -0.001 0.11 -10000 0 -0.43 32 32
ruffle organization 0.012 0.065 -10000 0 -0.33 9 9
regulation of epithelial cell migration -0.002 0.062 -10000 0 -0.24 32 32
PLD2 0.01 0.06 -10000 0 -0.35 7 7
PIP5K1A 0.012 0.065 -10000 0 -0.34 9 9
mol:Phosphatidic acid 0.008 0.074 -10000 0 -0.34 15 15
Rac1/GTP -0.002 0.11 -10000 0 -0.43 32 32
mTOR signaling pathway

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
GBL 0.015 0.035 -10000 0 -0.43 3 3
MKNK1 0.018 0 -10000 0 -10000 0 0
mol:PIP3 -0.037 0.11 0.25 10 -0.28 70 80
FRAP1 0.015 0.034 -10000 0 -10000 0 0
AKT1 -0.011 0.1 0.22 8 -0.25 71 79
INSR 0.015 0.037 -10000 0 -0.39 4 4
Insulin Receptor/Insulin 0.021 0.027 -10000 0 -0.31 3 3
mol:GTP 0.004 0.085 -10000 0 -0.24 28 28
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.01 0.027 -10000 0 -0.18 1 1
TSC2 0.016 0.026 -10000 0 -0.39 2 2
RHEB/GDP -0.026 0.062 -10000 0 -0.27 15 15
TSC1 0.018 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.022 0.12 -10000 0 -0.33 62 62
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.011 0.031 -10000 0 -0.18 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.017 0.012 -10000 0 -0.26 1 1
RPS6KB1 0.011 0.065 0.19 8 -0.22 10 18
MAP3K5 -0.013 0.088 -10000 0 -0.36 29 29
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
apoptosis -0.013 0.088 -10000 0 -0.36 29 29
mol:LY294002 0 0.001 0.001 1 -0.001 57 58
EIF4B 0.016 0.062 0.18 8 -0.24 7 15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.02 0.057 -10000 0 -0.22 6 6
eIF4E/eIF4G1/eIF4A1 -0.002 0.014 -10000 0 -10000 0 0
KIAA1303 0.015 0.031 -10000 0 -0.32 4 4
PI3K -0.02 0.12 -10000 0 -0.3 79 79
mTOR/RHEB/GTP/Raptor/GBL 0.033 0.054 0.18 8 -0.24 4 12
FKBP1A 0.017 0.017 -10000 0 -0.26 2 2
RHEB/GTP 0.009 0.076 -10000 0 -0.27 15 15
mol:Amino Acids 0 0.001 0.001 1 -0.001 57 58
FKBP12/Rapamycin 0.012 0.012 -10000 0 -0.17 2 2
PDPK1 -0.014 0.1 0.23 8 -0.26 70 78
EIF4E 0.018 0 -10000 0 -10000 0 0
ASK1/PP5C -0.01 0.14 -10000 0 -0.59 29 29
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.035 0.056 -10000 0 -0.56 4 4
TSC1/TSC2 0.009 0.095 0.22 8 -0.26 28 36
tumor necrosis factor receptor activity 0 0.001 0.001 57 -0.001 1 58
RPS6 0.015 0.037 -10000 0 -0.39 4 4
PPP5C 0.012 0.052 -10000 0 -0.39 8 8
EIF4G1 0.014 0.047 -10000 0 -0.52 4 4
IRS1 -0.034 0.12 -10000 0 -0.36 61 61
INS 0.017 0.023 -10000 0 -0.52 1 1
PTEN -0.002 0.1 -10000 0 -0.52 19 19
PDK2 -0.019 0.11 0.23 8 -0.27 76 84
EIF4EBP1 -0.012 0.16 -10000 0 -1.1 10 10
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
PPP2R5D 0.021 0.033 -10000 0 -10000 0 0
peptide biosynthetic process 0.025 0.03 -10000 0 -0.28 5 5
RHEB 0.016 0.026 -10000 0 -0.39 2 2
EIF4A1 0.018 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 15 -0.002 21 36
EEF2 0.025 0.031 -10000 0 -0.28 5 5
eIF4E/4E-BP1 -0.001 0.14 -10000 0 -1 10 10
Atypical NF-kappaB pathway

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
BCL3/RelA 0.02 0.049 -9999 0 -0.37 8 8
FBXW11 0.015 0.035 -9999 0 -0.43 3 3
NF kappa B1 p50/c-Rel 0.018 0.063 -9999 0 -0.31 15 15
NF kappa B1 p50/RelA/I kappa B alpha 0.001 0.11 -9999 0 -0.44 17 17
NFKBIA -0.023 0.12 -9999 0 -0.25 86 86
MAPK14 0.017 0.012 -9999 0 -0.26 1 1
NF kappa B1 p105/p50 0.026 0.038 -9999 0 -0.3 5 5
ARRB2 0.02 0.005 -9999 0 -10000 0 0
REL 0.001 0.087 -9999 0 -0.41 21 21
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.022 0.052 -9999 0 -0.3 11 11
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.028 0.031 -9999 0 -0.3 3 3
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
NF kappa B1 p50 dimer 0.019 0.037 -9999 0 -0.37 3 3
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
NFKB1 0.02 0.037 -9999 0 -0.37 3 3
RELA 0.018 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis -0.013 0.1 -9999 0 -0.24 63 63
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.006 0.11 -9999 0 -0.44 16 16
SRC 0.015 0.035 -9999 0 -0.43 3 3
PI3K 0.006 0.082 -9999 0 -0.37 21 21
NF kappa B1 p50/RelA -0.013 0.1 -9999 0 -0.24 63 63
IKBKB 0.011 0.047 -9999 0 -0.31 10 10
beta TrCP1/SCF ubiquitin ligase complex 0.015 0.035 -9999 0 -0.43 3 3
SYK -0.022 0.14 -9999 0 -0.48 42 42
I kappa B alpha/PIK3R1 -0.026 0.12 -9999 0 -0.37 38 38
cell death 0.006 0.1 -9999 0 -0.42 16 16
NF kappa B1 p105/c-Rel 0.018 0.063 -9999 0 -0.31 15 15
LCK -0.073 0.18 -9999 0 -0.4 115 115
BCL3 0.009 0.067 -9999 0 -0.49 9 9
Effects of Botulinum toxin

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
STX1A 0.009 0.028 -9999 0 -0.17 12 12
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.007 0.062 -9999 0 -0.4 3 3
STXBP1 0.017 0.017 -9999 0 -0.26 2 2
ACh/CHRNA1 0.008 0.046 -9999 0 -0.3 9 9
RAB3GAP2/RIMS1/UNC13B 0.019 0.055 -9999 0 -0.33 4 4
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.004 0.074 -9999 0 -0.26 41 41
mol:ACh 0.002 0.026 -9999 0 -0.1 24 24
RAB3GAP2 0.017 0.023 -9999 0 -0.52 1 1
STX1A/SNAP25/VAMP2 0.018 0.053 -9999 0 -0.25 3 3
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction 0.008 0.046 -9999 0 -0.29 9 9
UNC13B 0.011 0.048 -9999 0 -0.31 11 11
CHRNA1 0.01 0.064 -9999 0 -0.46 9 9
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.1 0.14 -9999 0 -0.31 131 131
SNAP25 -0.008 0.056 -9999 0 -0.29 15 15
VAMP2 0.007 0.011 -9999 0 -0.26 1 1
SYT1 -0.17 0.21 -9999 0 -0.36 264 264
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.019 0.026 -9999 0 -0.27 1 1
STX1A/SNAP25 fragment 1/VAMP2 0.018 0.053 -9999 0 -0.25 3 3
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.042 0.17 -10000 0 -0.9 12 12
NCK1/PAK1/Dok-R -0.032 0.083 -10000 0 -0.46 11 11
NCK1/Dok-R 0.029 0.18 -10000 0 -1.1 11 11
PIK3CA 0.015 0.029 -10000 0 -0.34 3 3
mol:beta2-estradiol -0.009 0.02 0.24 1 -10000 0 1
RELA 0.018 0 -10000 0 -10000 0 0
SHC1 0.017 0.024 -10000 0 -0.52 1 1
Rac/GDP 0.013 0 -10000 0 -10000 0 0
F2 0.006 0.021 0.26 1 -10000 0 1
TNIP2 0.012 0.052 -10000 0 -0.39 8 8
NF kappa B/RelA 0.053 0.15 -10000 0 -0.9 11 11
FN1 -0.046 0.17 -10000 0 -0.46 71 71
PLD2 0.038 0.16 -10000 0 -1 11 11
PTPN11 0.017 0.023 -10000 0 -0.52 1 1
GRB14 -0.16 0.21 -10000 0 -0.37 247 247
ELK1 0.046 0.15 -10000 0 -0.92 11 11
GRB7 -0.017 0.1 -10000 0 -0.29 59 59
PAK1 -0.022 0.13 -10000 0 -0.38 53 53
Tie2/Ang1/alpha5/beta1 Integrin 0.023 0.19 -10000 0 -1 11 11
CDKN1A 0.022 0.2 -10000 0 -0.76 27 27
ITGA5 0.014 0.042 -10000 0 -0.46 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.026 0.18 -10000 0 -1 12 12
CRK 0.016 0.033 -10000 0 -0.52 2 2
mol:NO 0.051 0.14 -10000 0 -0.66 12 12
PLG 0.039 0.16 -10000 0 -1 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.049 0.16 -10000 0 -0.87 11 11
GRB2 0.016 0.024 -10000 0 -0.26 4 4
PIK3R1 -0.008 0.11 -10000 0 -0.42 32 32
ANGPT2 -0.018 0.16 -10000 0 -1 5 5
BMX 0.012 0.19 -10000 0 -1.2 11 11
ANGPT1 0.021 0.085 -10000 0 -1.2 1 1
tube development 0.027 0.17 -10000 0 -0.74 16 16
ANGPT4 0.016 0.035 -10000 0 -0.43 3 3
response to hypoxia 0.003 0.011 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.045 0.19 -10000 0 -1.1 11 11
alpha5/beta1 Integrin 0.022 0.041 -10000 0 -0.37 5 5
FGF2 -0.065 0.16 -10000 0 -0.34 121 121
STAT5A (dimer) 0.027 0.2 -10000 0 -0.8 23 23
mol:L-citrulline 0.051 0.14 -10000 0 -0.66 12 12
AGTR1 -0.15 0.21 -10000 0 -0.36 229 229
MAPK14 0.035 0.18 -10000 0 -1.1 11 11
Tie2/SHP2 0.027 0.16 -10000 0 -1.1 10 10
TEK 0.025 0.18 -10000 0 -1.2 10 10
RPS6KB1 0.041 0.16 -10000 0 -0.88 11 11
Angiotensin II/AT1 -0.099 0.15 -10000 0 -0.25 229 229
Tie2/Ang1/GRB2 0.041 0.16 -10000 0 -1 11 11
MAPK3 0.043 0.15 -10000 0 -0.92 11 11
MAPK1 0.043 0.15 -10000 0 -0.92 11 11
Tie2/Ang1/GRB7 0.025 0.17 -10000 0 -1 11 11
NFKB1 0.017 0.023 -10000 0 -0.52 1 1
MAPK8 0.039 0.16 -10000 0 -1 11 11
PI3K 0.036 0.19 -10000 0 -1.1 11 11
FES 0.032 0.19 -10000 0 -1.1 12 12
Crk/Dok-R 0.031 0.18 -10000 0 -1 11 11
Tie2/Ang1/ABIN2 0.038 0.16 -10000 0 -1 11 11
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.044 0.16 -10000 0 -0.8 12 12
STAT5A 0.011 0.056 -10000 0 -0.42 8 8
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.044 0.16 -10000 0 -0.88 11 11
Tie2/Ang2 0.017 0.21 -10000 0 -1 15 15
Tie2/Ang1 0.035 0.17 -10000 0 -1.1 11 11
FOXO1 0.044 0.17 -10000 0 -0.79 15 15
ELF1 0.017 0.073 -10000 0 -0.49 10 10
ELF2 0.037 0.16 -10000 0 -1 11 11
mol:Choline 0.038 0.16 -10000 0 -0.96 11 11
cell migration -0.023 0.051 -10000 0 -0.23 16 16
FYN 0.024 0.19 -10000 0 -0.85 16 16
DOK2 -0.021 0.13 -10000 0 -0.41 48 48
negative regulation of cell cycle 0.026 0.18 -10000 0 -0.67 27 27
ETS1 0.012 0.072 -10000 0 -0.3 24 24
PXN 0.051 0.14 -10000 0 -0.72 11 11
ITGB1 0.015 0.037 -10000 0 -0.39 4 4
NOS3 0.05 0.15 -10000 0 -0.75 12 12
RAC1 0.018 0 -10000 0 -10000 0 0
TNF 0.004 0.098 -10000 0 -0.36 31 31
MAPKKK cascade 0.038 0.16 -10000 0 -0.96 11 11
RASA1 0.004 0.079 -10000 0 -0.42 16 16
Tie2/Ang1/Shc 0.042 0.16 -10000 0 -1 11 11
NCK1 0.011 0.046 -10000 0 -0.28 12 12
vasculogenesis 0.052 0.13 -10000 0 -0.59 12 12
mol:Phosphatidic acid 0.038 0.16 -10000 0 -0.96 11 11
mol:Angiotensin II 0.002 0.002 -10000 0 -10000 0 0
mol:NADP 0.051 0.14 -10000 0 -0.66 12 12
Rac1/GTP -0.011 0.14 -10000 0 -0.82 11 11
MMP2 0.017 0.19 -10000 0 -1.1 11 11
HIF-2-alpha transcription factor network

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
MMP14 -0.049 0.26 -10000 0 -1.2 26 26
oxygen homeostasis 0.007 0.013 -10000 0 -10000 0 0
TCEB2 0.018 0 -10000 0 -10000 0 0
TCEB1 0.014 0.035 -10000 0 -0.3 6 6
VHL/Elongin B/Elongin C/HIF2A 0.036 0.13 -10000 0 -0.37 22 22
EPO 0.053 0.23 -10000 0 -0.58 25 25
FIH (dimer) 0.024 0.027 -10000 0 -0.52 1 1
APEX1 0.025 0.019 -10000 0 -0.26 1 1
SERPINE1 0.054 0.25 -10000 0 -0.66 33 33
FLT1 -0.019 0.18 -10000 0 -1.1 13 13
ADORA2A 0.042 0.24 -10000 0 -0.63 35 35
germ cell development 0.068 0.22 -10000 0 -0.62 24 24
SLC11A2 0.066 0.23 -10000 0 -0.66 26 26
BHLHE40 0.059 0.23 -10000 0 -0.6 30 30
HIF1AN 0.024 0.027 -10000 0 -0.52 1 1
HIF2A/ARNT/SIRT1 0.041 0.17 -10000 0 -0.43 28 28
ETS1 0.019 0.072 -10000 0 -0.3 23 23
CITED2 -0.013 0.15 -10000 0 -1.1 9 9
KDR -0.008 0.15 -10000 0 -1.1 8 8
PGK1 0.068 0.23 -10000 0 -0.63 26 26
SIRT1 0.015 0.029 -10000 0 -0.35 3 3
response to hypoxia -0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.085 0.27 -10000 0 -0.71 30 30
EPAS1 0.02 0.15 -10000 0 -0.38 33 33
SP1 0.023 0.027 -10000 0 -0.52 1 1
ABCG2 0.06 0.24 -10000 0 -0.65 33 33
EFNA1 0.058 0.24 -10000 0 -0.6 37 37
FXN 0.059 0.22 -10000 0 -0.63 25 25
POU5F1 0.068 0.23 -10000 0 -0.65 24 24
neuron apoptosis -0.084 0.26 0.68 30 -10000 0 30
EP300 0.014 0.047 -10000 0 -0.52 4 4
EGLN3 -0.066 0.19 -10000 0 -0.4 116 116
EGLN2 0.018 0.055 -10000 0 -0.36 9 9
EGLN1 0.009 0.083 -10000 0 -0.36 23 23
VHL/Elongin B/Elongin C 0.032 0.028 -10000 0 -0.3 1 1
VHL 0.014 0.031 -10000 0 -0.26 7 7
ARNT 0.025 0.014 -10000 0 -10000 0 0
SLC2A1 0.053 0.23 -10000 0 -0.64 29 29
TWIST1 0.038 0.27 -10000 0 -0.68 43 43
ELK1 0.022 0.038 -10000 0 -0.39 4 4
HIF2A/ARNT/Cbp/p300 0.054 0.17 -10000 0 -0.44 26 26
VEGFA 0.06 0.24 -10000 0 -0.65 26 26
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
Signaling events mediated by PRL

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
CCNE1 -0.018 0.1 -10000 0 -0.28 64 64
mol:Halofuginone 0.004 0.012 -10000 0 -0.16 1 1
ITGA1 0.001 0.093 -10000 0 -0.51 17 17
CDKN1A -0.017 0.12 -10000 0 -0.46 24 24
PRL-3/alpha Tubulin 0.023 0.026 -10000 0 -0.37 1 1
mol:Ca2+ -0.078 0.14 0.38 1 -0.26 157 158
AGT -0.097 0.19 -10000 0 -0.37 159 159
CCNA2 -0.042 0.13 -10000 0 -0.43 18 18
TUBA1B 0.018 0 -10000 0 -10000 0 0
EGR1 -0.06 0.15 -10000 0 -0.37 81 81
CDK2/Cyclin E1 -0.016 0.12 -10000 0 -0.44 27 27
MAPK3 0.022 0.032 -10000 0 -0.37 2 2
PRL-2 /Rab GGTase beta 0.017 0.056 -10000 0 -0.37 9 9
MAPK1 0.021 0.036 -10000 0 -0.37 3 3
PTP4A1 -0.031 0.12 -10000 0 -0.6 5 5
PTP4A3 0.014 0.037 -10000 0 -0.3 7 7
PTP4A2 0.005 0.075 -10000 0 -0.42 15 15
ITGB1 0.02 0.037 -10000 0 -0.37 3 3
SRC 0.015 0.035 -10000 0 -0.43 3 3
RAC1 0.004 0.066 -10000 0 -0.86 1 1
Rab GGTase beta/Rab GGTase alpha 0.026 0.012 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.022 0.12 -10000 0 -0.56 5 5
RABGGTA 0.018 0 -10000 0 -10000 0 0
BCAR1 0.002 0.023 0.38 1 -10000 0 1
RHOC 0.001 0.075 -10000 0 -0.5 5 5
RHOA -0.006 0.089 -10000 0 -0.42 14 14
cell motility 0.002 0.075 -10000 0 -0.43 4 4
PRL-1/alpha Tubulin -0.02 0.12 -10000 0 -0.61 4 4
PRL-3/alpha1 Integrin 0.011 0.075 -10000 0 -0.39 16 16
ROCK1 0.002 0.075 -10000 0 -0.43 4 4
RABGGTB 0.017 0.017 -10000 0 -0.26 2 2
CDK2 0.011 0.047 -10000 0 -0.31 10 10
mitosis -0.03 0.12 -10000 0 -0.59 5 5
ATF5 0.013 0.041 -10000 0 -0.29 9 9
JNK signaling in the CD4+ TCR pathway

Figure S89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.019 0.091 -9999 0 -0.3 34 34
MAP4K1 0.011 0.041 -9999 0 -0.26 12 12
MAP3K8 -0.036 0.15 -9999 0 -0.39 69 69
PRKCB 0 0 -9999 0 -10000 0 0
DBNL 0.014 0.039 -9999 0 -0.36 5 5
CRKL 0.014 0.047 -9999 0 -0.52 4 4
MAP3K1 0.005 0.1 -9999 0 -0.35 12 12
JUN -0.008 0.092 -9999 0 -0.28 47 47
MAP3K7 0.029 0.067 -9999 0 -0.28 6 6
GRAP2 0.011 0.044 -9999 0 -0.28 11 11
CRK 0.016 0.033 -9999 0 -0.52 2 2
MAP2K4 0.005 0.096 -9999 0 -0.35 16 16
LAT 0.002 0.069 -9999 0 -0.28 29 29
LCP2 -0.005 0.1 -9999 0 -0.41 28 28
MAPK8 0.011 0.052 -9999 0 -0.58 3 3
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.024 0.07 -9999 0 -0.3 6 6
LAT/GRAP2/SLP76/HPK1/HIP-55 0.025 0.089 -9999 0 -0.28 37 37
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.016 0.023 -9999 0 -0.52 1 1
HDAC2 0.009 0.054 -9999 0 -0.29 15 15
GNB1/GNG2 -0.007 0.11 -9999 0 -0.31 53 53
forebrain development 0.007 0.13 -9999 0 -0.53 17 17
GNAO1 0.017 0.024 -9999 0 -0.26 4 4
SMO/beta Arrestin2 -0.017 0.12 -9999 0 -0.37 47 47
SMO -0.046 0.16 -9999 0 -0.41 80 80
ARRB2 0.019 0.001 -9999 0 -10000 0 0
GLI3/SPOP 0.01 0.13 -9999 0 -0.38 28 28
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
GSK3B 0.018 0 -9999 0 -10000 0 0
GNAI2 0.007 0.075 -9999 0 -0.48 12 12
SIN3/HDAC complex 0.041 0.032 -9999 0 -0.27 5 5
GNAI1 -0.014 0.12 -9999 0 -0.38 44 44
XPO1 0.021 0.003 -9999 0 -10000 0 0
GLI1/Su(fu) -0.003 0.16 -9999 0 -0.56 25 25
SAP30 0.012 0.053 -9999 0 -0.48 6 6
mol:GDP -0.045 0.16 -9999 0 -0.41 80 80
MIM/GLI2A -0.023 0.14 -9999 0 -0.4 61 61
IFT88 -0.001 0.097 -9999 0 -0.48 20 20
GNAI3 0.018 0.023 -9999 0 -0.52 1 1
GLI2 0.036 0.054 -9999 0 -0.41 1 1
GLI3 0.003 0.14 -9999 0 -0.3 66 66
CSNK1D 0.018 0 -9999 0 -10000 0 0
CSNK1E 0.017 0.012 -9999 0 -0.26 1 1
SAP18 0.017 0 -9999 0 -10000 0 0
embryonic digit morphogenesis -0.001 0.097 -9999 0 -0.48 20 20
GNG2 0.016 0.029 -9999 0 -0.35 3 3
Gi family/GTP -0.007 0.11 -9999 0 -0.28 59 59
SIN3B 0.017 0.012 -9999 0 -0.26 1 1
SIN3A 0.017 0 -9999 0 -10000 0 0
GLI3/Su(fu) 0.009 0.14 -9999 0 -0.44 35 35
GLI2/Su(fu) 0.027 0.099 -9999 0 -0.45 6 6
FOXA2 -0.051 0.18 -9999 0 -0.73 34 34
neural tube patterning 0.007 0.13 -9999 0 -0.53 17 17
SPOP 0.013 0.042 -9999 0 -0.33 7 7
Su(fu)/PIAS1 0.005 0.092 -9999 0 -0.34 21 21
GNB1 0.013 0.052 -9999 0 -0.52 5 5
CSNK1G2 0.016 0.033 -9999 0 -0.52 2 2
CSNK1G3 0.013 0.052 -9999 0 -0.52 5 5
MTSS1 -0.023 0.14 -9999 0 -0.4 61 61
embryonic limb morphogenesis 0.007 0.13 -9999 0 -0.53 17 17
SUFU -0.005 0.1 -9999 0 -0.38 21 21
LGALS3 -0.041 0.16 -9999 0 -0.48 63 63
catabolic process 0.031 0.12 -9999 0 -0.35 26 26
GLI3A/CBP 0.007 0.069 -9999 0 -0.37 9 9
KIF3A 0.005 0.081 -9999 0 -0.5 13 13
GLI1 0.007 0.13 -9999 0 -0.54 17 17
RAB23 0.009 0.061 -9999 0 -0.37 12 12
CSNK1A1 0.017 0.023 -9999 0 -0.52 1 1
IFT172 0.013 0.05 -9999 0 -0.43 6 6
RBBP7 0.01 0.051 -9999 0 -0.3 13 13
Su(fu)/Galectin3 -0.027 0.14 -9999 0 -0.34 71 71
GNAZ 0.003 0.085 -9999 0 -0.43 18 18
RBBP4 0.016 0.026 -9999 0 -0.39 2 2
CSNK1G1 0.017 0.012 -9999 0 -0.26 1 1
PIAS1 0.017 0.012 -9999 0 -0.26 1 1
PRKACA 0.018 0 -9999 0 -10000 0 0
GLI2/SPOP 0.04 0.057 -9999 0 -0.39 2 2
STK36 0 0.11 -9999 0 -0.52 21 21
Gi family/GNB1/GNG2/GDP 0.001 0.11 -9999 0 -0.37 26 26
PTCH1 0.016 0.12 -9999 0 -0.6 8 8
MIM/GLI1 0.002 0.16 -9999 0 -0.5 24 24
CREBBP 0.007 0.069 -9999 0 -0.37 9 9
Su(fu)/SIN3/HDAC complex 0.036 0.047 -9999 0 -0.26 1 1
Aurora A signaling

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
Aurora A/GADD45A 0.008 0.081 -9999 0 -0.3 23 23
BIRC5 -0.037 0.15 -9999 0 -0.42 67 67
NFKBIA 0.024 0.054 -9999 0 -0.33 3 3
CPEB1 0.004 0.068 -9999 0 -0.31 22 22
AKT1 0.022 0.057 -9999 0 -0.29 5 5
NDEL1 0.018 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.013 0.067 -9999 0 -0.28 16 16
NDEL1/TACC3 0.021 0.079 -9999 0 -0.36 16 16
GADD45A -0.012 0.11 -9999 0 -0.39 38 38
GSK3B 0.021 0.015 -9999 0 -10000 0 0
PAK1/Aurora A 0.002 0.087 -9999 0 -0.3 25 25
MDM2 0.01 0.044 -9999 0 -0.26 14 14
JUB -0.027 0.15 -9999 0 -0.49 47 47
TPX2 -0.01 0.11 -9999 0 -0.37 41 41
TP53 0.004 0.089 -9999 0 -0.29 37 37
DLG7 -0.006 0.11 -9999 0 -0.35 44 44
AURKAIP1 0.016 0.029 -9999 0 -0.35 3 3
ARHGEF7 0.016 0.021 -9999 0 -0.26 3 3
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.022 0.083 -9999 0 -0.38 16 16
G2/M transition of mitotic cell cycle 0.013 0.066 -9999 0 -0.28 16 16
AURKA 0.021 0.058 -9999 0 -0.21 21 21
AURKB -0.007 0.078 -9999 0 -0.22 47 47
CDC25B 0.011 0.069 -9999 0 -0.31 8 8
G2/M transition checkpoint -0.002 0.088 -9999 0 -0.27 42 42
mRNA polyadenylation 0.016 0.053 -9999 0 -0.26 5 5
Aurora A/CPEB 0.016 0.053 -9999 0 -0.26 5 5
Aurora A/TACC1/TRAP/chTOG 0.017 0.092 -9999 0 -0.41 5 5
BRCA1 0 0.094 -9999 0 -0.48 19 19
centrosome duplication 0.002 0.087 -9999 0 -0.3 25 25
regulation of centrosome cycle 0.02 0.078 -9999 0 -0.35 16 16
spindle assembly 0.016 0.09 -9999 0 -0.4 5 5
TDRD7 0.004 0.084 -9999 0 -0.5 14 14
Aurora A/RasGAP/Survivin -0.001 0.12 -9999 0 -0.3 57 57
CENPA -0.016 0.12 -9999 0 -0.36 47 47
Aurora A/PP2A 0.025 0.047 -9999 0 -0.21 1 1
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.008 0.088 -9999 0 -0.34 20 20
negative regulation of DNA binding 0.004 0.089 -9999 0 -0.29 37 37
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.023 0.029 -9999 0 -0.18 9 9
RASA1 0.004 0.079 -9999 0 -0.42 16 16
Ajuba/Aurora A -0.002 0.089 -9999 0 -0.27 42 42
mitotic prometaphase -0.001 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.058 -9999 0 -0.21 21 21
TACC1 -0.02 0.13 -9999 0 -0.41 47 47
TACC3 -0.006 0.11 -9999 0 -0.47 26 26
Aurora A/Antizyme1 0.034 0.044 -9999 0 -0.27 1 1
Aurora A/RasGAP 0.018 0.066 -9999 0 -0.3 11 11
OAZ1 0.018 0 -9999 0 -10000 0 0
RAN 0.017 0.012 -9999 0 -0.26 1 1
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.021 0.015 -9999 0 -10000 0 0
GIT1 0.014 0.035 -9999 0 -0.3 6 6
GIT1/beta-PIX/PAK1 0.009 0.084 -9999 0 -0.32 24 24
Importin alpha/Importin beta/TPX2 -0.01 0.11 -9999 0 -0.37 41 41
PPP2R5D 0.016 0.021 -9999 0 -0.26 3 3
Aurora A/TPX2 0.006 0.1 -9999 0 -0.4 26 26
PAK1 -0.022 0.13 -9999 0 -0.38 53 53
CKAP5 0.017 0.017 -9999 0 -0.26 2 2
ceramide signaling pathway

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.008 0.13 -10000 0 -0.51 12 12
BAG4 0.002 0.071 -10000 0 -0.29 28 28
BAD 0.011 0.045 -10000 0 -0.22 5 5
NFKBIA 0.014 0.042 -10000 0 -0.46 4 4
BIRC3 -0.086 0.19 -10000 0 -0.41 129 129
BAX 0.011 0.045 -10000 0 -0.19 7 7
EnzymeConsortium:3.1.4.12 0.001 0.031 -10000 0 -0.11 12 12
IKBKB -0.003 0.12 -10000 0 -0.44 16 16
MAP2K2 0.022 0.047 -10000 0 -0.24 6 6
MAP2K1 0.023 0.043 -10000 0 -0.23 4 4
SMPD1 0.006 0.039 -10000 0 -0.19 9 9
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.003 0.12 -10000 0 -0.42 19 19
MAP2K4 -0.011 0.09 -10000 0 -0.24 56 56
protein ubiquitination -0.002 0.12 -10000 0 -0.44 15 15
EnzymeConsortium:2.7.1.37 0.02 0.052 -10000 0 -0.24 5 5
response to UV 0 0 -10000 0 -0.002 4 4
RAF1 0.018 0.044 -10000 0 -0.24 3 3
CRADD 0.009 0.067 -10000 0 -0.49 9 9
mol:ceramide 0.005 0.046 -10000 0 -0.17 13 13
I-kappa-B-alpha/RELA/p50/ubiquitin 0.022 0.026 -10000 0 -0.31 3 3
MADD 0.018 0 -10000 0 -10000 0 0
MAP3K1 -0.009 0.084 -10000 0 -0.24 45 45
TRADD 0.016 0.026 -10000 0 -0.39 2 2
RELA/p50 0.018 0 -10000 0 -10000 0 0
MAPK3 0.026 0.044 -10000 0 -0.21 4 4
MAPK1 0.026 0.044 -10000 0 -0.22 3 3
p50/RELA/I-kappa-B-alpha 0.024 0.031 -10000 0 -0.37 3 3
FADD -0.012 0.13 -10000 0 -0.44 19 19
KSR1 0.012 0.045 -10000 0 -0.19 8 8
MAPK8 -0.004 0.087 -10000 0 -0.22 56 56
TRAF2 0.014 0.042 -10000 0 -0.46 4 4
response to radiation 0 0 -10000 0 -0.002 1 1
CHUK -0.006 0.13 -10000 0 -0.44 19 19
TNF R/SODD 0.014 0.055 -10000 0 -0.37 5 5
TNF -0.004 0.094 -10000 0 -0.36 31 31
CYCS 0.036 0.056 0.14 64 -0.17 5 69
IKBKG 0 0.12 -10000 0 -0.47 12 12
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.012 0.13 -10000 0 -0.41 21 21
RELA 0.018 0 -10000 0 -10000 0 0
RIPK1 0.017 0.023 -10000 0 -0.52 1 1
AIFM1 0.036 0.056 0.14 63 -0.19 3 66
TNF/TNF R/SODD 0.012 0.074 -10000 0 -0.31 18 18
TNFRSF1A 0.016 0.033 -10000 0 -0.52 2 2
response to heat 0 0 -10000 0 -0.002 1 1
CASP8 0.021 0.033 -10000 0 -10000 0 0
NSMAF -0.008 0.13 -10000 0 -0.48 14 14
response to hydrogen peroxide 0 0 -10000 0 -0.002 4 4
BCL2 -0.12 0.22 -10000 0 -0.47 145 145
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.01 0.066 -9999 0 -0.52 8 8
mol:S1P 0 0.005 -9999 0 -0.015 42 42
S1P1/S1P/Gi 0 0.1 -9999 0 -0.3 36 36
GNAO1 0.016 0.024 -9999 0 -0.26 4 4
S1P/S1P3/G12/G13 0.02 0.034 -9999 0 -0.28 5 5
AKT1 0.013 0.097 -9999 0 -0.58 12 12
AKT3 0.007 0.13 -9999 0 -1.2 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.066 -9999 0 -0.52 8 8
GNAI2 0.007 0.075 -9999 0 -0.48 12 12
GNAI3 0.017 0.024 -9999 0 -0.52 1 1
GNAI1 -0.015 0.12 -9999 0 -0.38 44 44
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.001 0.005 -9999 0 -0.017 42 42
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 -0.021 0.13 -9999 0 -0.41 48 48
mol:Ca2+ 0.011 0.082 -9999 0 -0.31 14 14
MAPK3 0.017 0.078 -9999 0 -0.37 7 7
MAPK1 0.016 0.079 -9999 0 -0.36 8 8
JAK2 0.007 0.094 -9999 0 -0.34 18 18
CXCR4 -0.005 0.11 -9999 0 -0.31 42 42
FLT1 0.007 0.077 -9999 0 -0.44 14 14
RhoA/GDP 0.004 0.058 -9999 0 -0.38 12 12
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
SRC 0.016 0.081 -9999 0 -0.37 9 9
S1P/S1P3/Gi 0.011 0.082 -9999 0 -0.31 14 14
RAC1 0.018 0 -9999 0 -10000 0 0
RhoA/GTP 0.012 0.087 -9999 0 -0.31 17 17
VEGFA 0.001 0.077 -9999 0 -0.29 31 31
S1P/S1P2/Gi 0.01 0.078 -9999 0 -0.23 40 40
VEGFR1 homodimer/VEGFA homodimer 0.011 0.081 -9999 0 -0.39 14 14
RHOA 0.005 0.08 -9999 0 -0.52 12 12
S1P/S1P3/Gq -0.028 0.095 -9999 0 -0.26 60 60
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.003 0.085 -9999 0 -0.43 18 18
G12/G13 0.02 0.043 -9999 0 -0.37 5 5
GNA14 -0.081 0.18 -9999 0 -0.35 141 141
GNA15 0.001 0.078 -9999 0 -0.33 25 25
GNA12 0.018 0 -9999 0 -10000 0 0
GNA13 0.009 0.059 -9999 0 -0.38 11 11
GNA11 0.014 0.047 -9999 0 -0.52 4 4
Rac1/GTP 0.018 0.075 -9999 0 -0.38 6 6
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.012 0.15 -9999 0 -0.5 25 25
PDGFB-D/PDGFRB/SLAP 0.01 0.074 -9999 0 -0.37 17 17
PDGFB-D/PDGFRB/APS/CBL 0.018 0.042 -9999 0 -0.32 8 8
AKT1 -0.021 0.14 -9999 0 -0.39 34 34
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.006 0.13 -9999 0 -0.57 16 16
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
FGR -0.008 0.065 -9999 0 -0.4 9 9
mol:Ca2+ 0.003 0.11 -9999 0 -0.65 10 10
MYC -0.029 0.22 -9999 0 -0.74 42 42
SHC1 0.017 0.023 -9999 0 -0.52 1 1
HRAS/GDP 0.02 0.069 -9999 0 -0.28 9 9
LRP1/PDGFRB/PDGFB 0.024 0.064 -9999 0 -0.35 13 13
GRB10 -0.003 0.098 -9999 0 -0.43 24 24
PTPN11 0.017 0.023 -9999 0 -0.52 1 1
GO:0007205 0.003 0.11 -9999 0 -0.66 10 10
PTEN -0.002 0.1 -9999 0 -0.52 19 19
GRB2 0.016 0.024 -9999 0 -0.26 4 4
GRB7 -0.017 0.1 -9999 0 -0.29 59 59
PDGFB-D/PDGFRB/SHP2 0.019 0.052 -9999 0 -0.37 9 9
PDGFB-D/PDGFRB/GRB10 0.005 0.086 -9999 0 -0.37 24 24
cell cycle arrest 0.01 0.074 -9999 0 -0.37 17 17
HRAS 0.012 0.051 -9999 0 -0.41 7 7
HIF1A -0.035 0.14 -9999 0 -0.35 46 46
GAB1 -0.011 0.13 -9999 0 -0.63 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.008 0.13 -9999 0 -0.59 14 14
PDGFB-D/PDGFRB 0.019 0.067 -9999 0 -0.35 12 12
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.016 0.062 -9999 0 -0.37 13 13
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.018 0.15 -9999 0 -0.48 32 32
positive regulation of MAPKKK cascade 0.019 0.052 -9999 0 -0.37 9 9
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
mol:IP3 0.003 0.11 -9999 0 -0.67 10 10
E5 0 0.002 -9999 0 -10000 0 0
CSK 0.015 0.031 -9999 0 -0.32 4 4
PDGFB-D/PDGFRB/GRB7 -0.004 0.086 -9999 0 -0.37 16 16
SHB 0.008 0.067 -9999 0 -0.41 12 12
BLK -0.024 0.091 -9999 0 -0.46 17 17
PTPN2 0.015 0.024 -9999 0 -0.26 4 4
PDGFB-D/PDGFRB/SNX15 0.019 0.05 -9999 0 -0.37 8 8
BCAR1 0.017 0.012 -9999 0 -0.26 1 1
VAV2 -0.011 0.14 -9999 0 -0.65 14 14
CBL 0.017 0.012 -9999 0 -0.26 1 1
PDGFB-D/PDGFRB/DEP1 0.015 0.063 -9999 0 -0.37 13 13
LCK -0.081 0.2 -9999 0 -0.57 67 67
PDGFRB 0.009 0.067 -9999 0 -0.53 8 8
ACP1 0.013 0.052 -9999 0 -0.52 5 5
HCK -0.03 0.14 -9999 0 -0.55 27 27
ABL1 -0.005 0.11 -9999 0 -0.58 12 12
PDGFB-D/PDGFRB/CBL -0.01 0.14 -9999 0 -0.79 11 11
PTPN1 0.001 0.071 -9999 0 -0.29 28 28
SNX15 0.017 0.012 -9999 0 -0.26 1 1
STAT3 0.015 0.04 -9999 0 -0.52 3 3
STAT1 -0.02 0.12 -9999 0 -0.33 58 58
cell proliferation -0.022 0.2 -9999 0 -0.65 42 42
SLA 0.004 0.078 -9999 0 -0.39 18 18
actin cytoskeleton reorganization 0.032 0.07 -9999 0 -0.37 7 7
SRC -0.01 0.084 -9999 0 -0.47 11 11
PI3K -0.065 0.12 -9999 0 -0.44 31 31
PDGFB-D/PDGFRB/GRB7/SHC 0.009 0.075 -9999 0 -0.31 17 17
SH2B2 0 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 -0.007 0.14 -9999 0 -0.6 16 16
LYN -0.008 0.066 -9999 0 -0.4 10 10
LRP1 0.017 0.023 -9999 0 -0.52 1 1
SOS1 0.017 0.023 -9999 0 -0.52 1 1
STAT5B 0.016 0.026 -9999 0 -0.39 2 2
STAT5A 0.011 0.056 -9999 0 -0.42 8 8
NCK1-2/p130 Cas 0.033 0.063 -9999 0 -0.38 4 4
SPHK1 -0.027 0.14 -9999 0 -0.42 54 54
EDG1 -0.021 0.13 -9999 0 -0.41 48 48
mol:DAG 0.003 0.11 -9999 0 -0.67 10 10
PLCG1 0.003 0.11 -9999 0 -0.7 10 10
NHERF/PDGFRB -0.038 0.15 -9999 0 -0.35 90 90
YES1 -0.016 0.096 -9999 0 -0.47 18 18
cell migration -0.038 0.15 -9999 0 -0.35 90 90
SHC/Grb2/SOS1 0.036 0.06 -9999 0 -0.35 4 4
SLC9A3R2 -0.032 0.15 -9999 0 -0.49 52 52
SLC9A3R1 -0.044 0.16 -9999 0 -0.44 71 71
NHERF1-2/PDGFRB/PTEN -0.033 0.16 -9999 0 -0.32 102 102
FYN -0.016 0.13 -9999 0 -0.82 10 10
DOK1 0.013 0.074 -9999 0 -0.3 22 22
HRAS/GTP 0.009 0.037 -9999 0 -0.29 7 7
PDGFB 0.008 0.064 -9999 0 -0.39 12 12
RAC1 -0.012 0.16 -9999 0 -0.5 39 39
PRKCD 0.019 0.065 -9999 0 -0.33 13 13
FER 0.02 0.06 -9999 0 -0.31 12 12
MAPKKK cascade -0.007 0.051 -9999 0 -0.34 4 4
RASA1 0.013 0.072 -9999 0 -0.3 21 21
NCK1 0.011 0.046 -9999 0 -0.28 12 12
NCK2 0.015 0.027 -9999 0 -0.26 5 5
p62DOK/Csk 0.023 0.071 -9999 0 -0.28 19 19
PDGFB-D/PDGFRB/SHB 0.013 0.071 -9999 0 -0.4 14 14
chemotaxis -0.004 0.11 -9999 0 -0.56 12 12
STAT1-3-5/STAT1-3-5 -0.022 0.071 -9999 0 -0.4 6 6
Bovine Papilomavirus E5/PDGFRB 0.006 0.049 -9999 0 -0.39 8 8
PTPRJ 0.012 0.055 -9999 0 -0.45 7 7
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.002 0.073 -9999 0 -0.26 33 33
TRAF2/ASK1 -0.002 0.084 -9999 0 -0.31 32 32
ATM 0.017 0.012 -9999 0 -0.26 1 1
MAP2K3 -0.012 0.12 -9999 0 -0.37 39 39
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.016 0.12 -9999 0 -0.32 45 45
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.003 0.083 -9999 0 -0.46 16 16
TXN 0.01 0.008 -9999 0 -10000 0 0
CALM1 0.018 0 -9999 0 -10000 0 0
GADD45A -0.012 0.11 -9999 0 -0.39 38 38
GADD45B -0.002 0.097 -9999 0 -0.44 23 23
MAP3K1 -0.031 0.14 -9999 0 -0.43 58 58
MAP3K6 0.015 0.035 -9999 0 -0.43 3 3
MAP3K7 0.016 0.021 -9999 0 -0.26 3 3
MAP3K4 0.018 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.003 0.098 -9999 0 -0.37 32 32
TAK1/TAB family 0.01 0.039 -9999 0 -0.42 4 4
RAC1/OSM/MEKK3 0.034 0.006 -9999 0 -10000 0 0
TRAF2 0.014 0.042 -9999 0 -0.46 4 4
RAC1/OSM/MEKK3/MKK3 -0.03 0.079 -9999 0 -0.28 38 38
TRAF6 0.017 0.033 -9999 0 -0.32 5 5
RAC1 0.018 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.079 0.18 -9999 0 -0.37 133 133
CCM2 0.018 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.034 0.11 -9999 0 -0.31 55 55
MAPK11 0.018 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.04 0.12 -9999 0 -0.29 86 86
OSM/MEKK3 0.026 0.008 -9999 0 -10000 0 0
TAOK1 0.013 0.041 -9999 0 -0.32 6 6
TAOK2 0.02 0.005 -9999 0 -10000 0 0
TAOK3 0.019 0.016 -9999 0 -0.32 1 1
MAP3K7IP1 0.018 0 -9999 0 -10000 0 0
MAPK14 0.017 0.012 -9999 0 -0.26 1 1
MAP3K7IP2 0.014 0.047 -9999 0 -0.52 4 4
MAP3K5 -0.021 0.13 -9999 0 -0.42 46 46
MAP3K10 -0.001 0.097 -9999 0 -0.48 20 20
MAP3K3 0.017 0.012 -9999 0 -0.26 1 1
TRX/ASK1 -0.003 0.078 -9999 0 -0.31 29 29
GADD45/MTK1/MTK1 0.009 0.097 -9999 0 -0.29 42 42
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.018 0 -9999 0 -10000 0 0
VLDLR -0.059 0.17 -9999 0 -0.4 98 98
LRPAP1 0.016 0.026 -9999 0 -0.39 2 2
NUDC 0.018 0 -9999 0 -10000 0 0
RELN/LRP8 -0.014 0.1 -9999 0 -0.31 42 42
CaM/Ca2+ 0.013 0 -9999 0 -10000 0 0
KATNA1 0.015 0.033 -9999 0 -0.31 5 5
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.008 0.092 -9999 0 -0.28 42 42
IQGAP1/CaM 0.026 0 -9999 0 -10000 0 0
DAB1 0.018 0 -9999 0 -10000 0 0
IQGAP1 0.018 0 -9999 0 -10000 0 0
PLA2G7 -0.092 0.2 -9999 0 -0.41 137 137
CALM1 0.018 0 -9999 0 -10000 0 0
DYNLT1 0.018 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.027 0.11 -9999 0 -0.37 36 36
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.015 0.037 -9999 0 -0.39 4 4
CDK5R1 0.014 0.031 -9999 0 -0.26 7 7
LIS1/Poliovirus Protein 3A 0.018 0.02 -9999 0 -0.31 2 2
CDK5R2 0.017 0.017 -9999 0 -0.26 2 2
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.016 0.11 -9999 0 -0.31 57 57
YWHAE 0.016 0.029 -9999 0 -0.35 3 3
NDEL1/14-3-3 E 0.025 0.079 -9999 0 -0.29 4 4
MAP1B -0.014 0.073 -9999 0 -0.29 32 32
RAC1 0.024 0.01 -9999 0 -10000 0 0
p35/CDK5 0.007 0.085 -9999 0 -0.33 3 3
RELN 0.009 0.059 -9999 0 -0.38 11 11
PAFAH/LIS1 -0.036 0.12 -9999 0 -0.3 80 80
LIS1/CLIP170 0.029 0.031 -9999 0 -0.3 4 4
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.016 0.043 -9999 0 -0.29 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 0.003 0.095 -9999 0 -0.45 3 3
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 0.016 0.08 -9999 0 -0.31 3 3
LIS1/IQGAP1 0.031 0.021 -9999 0 -0.3 2 2
RHOA 0.014 0.067 -9999 0 -0.42 12 12
PAFAH1B1 0.024 0.024 -9999 0 -0.37 2 2
PAFAH1B3 0.009 0.067 -9999 0 -0.49 9 9
PAFAH1B2 0.017 0.012 -9999 0 -0.26 1 1
MAP1B/LIS1/Dynein heavy chain 0.014 0.054 -9999 0 -0.31 2 2
NDEL1/Katanin 60/Dynein heavy chain 0.031 0.078 -9999 0 -0.27 3 3
LRP8 -0.057 0.16 -9999 0 -0.34 109 109
NDEL1/Katanin 60 0.024 0.079 -9999 0 -0.29 3 3
P39/CDK5 0.009 0.084 -9999 0 -0.33 3 3
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.031 0.021 -9999 0 -0.3 2 2
CDK5 -0.001 0.087 -9999 0 -0.25 42 42
PPP2R5D 0.016 0.021 -9999 0 -0.26 3 3
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.025 0.026 -9999 0 -0.26 4 4
CSNK2A1 0.017 0.023 -9999 0 -0.52 1 1
RELN/VLDLR/DAB1/LIS1 0.004 0.1 -9999 0 -0.25 57 57
RELN/VLDLR -0.043 0.13 -9999 0 -0.28 111 111
CDC42 0.024 0.01 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.014 0.047 -10000 0 -0.52 4 4
HDAC4 0.017 0.023 -10000 0 -0.52 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.011 0.026 0.24 3 -0.13 9 12
CDKN1A -0.016 0.12 -10000 0 -0.71 15 15
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.016 0.021 -10000 0 -0.26 3 3
FOXO3 0.001 0.043 0.41 4 -0.25 4 8
FOXO1 0.001 0.089 -10000 0 -0.46 18 18
FOXO4 0.022 0.034 -10000 0 -0.27 7 7
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.017 0.012 -10000 0 -0.26 1 1
TAT -0.007 0.079 -10000 0 -0.26 48 48
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.012 0.091 -10000 0 -0.33 37 37
PPARGC1A -0.012 0.1 -10000 0 -0.31 48 48
FHL2 -0.08 0.19 -10000 0 -0.41 120 120
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.024 0.029 -10000 0 -0.37 1 1
HIST2H4A 0.011 0.026 0.13 9 -0.24 3 12
SIRT1/FOXO3a 0.005 0.041 0.32 4 -0.2 5 9
SIRT1 0.015 0.039 0.2 9 -0.35 3 12
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.034 0.029 -10000 0 -0.31 2 2
SIRT1/Histone H1b 0.004 0.072 -10000 0 -0.23 38 38
apoptosis -0.033 0.028 0.3 1 -10000 0 1
SIRT1/PGC1A 0.005 0.064 -10000 0 -0.31 11 11
p53/SIRT1 -0.017 0.11 0.4 9 -0.37 32 41
SIRT1/FOXO4 0.026 0.037 -10000 0 -0.24 7 7
FOXO1/FHL2/SIRT1 -0.031 0.12 -10000 0 -0.3 81 81
HIST1H1E -0.005 0.08 -10000 0 -0.27 39 39
SIRT1/p300 0.021 0.043 -10000 0 -0.36 5 5
muscle cell differentiation 0.002 0.081 0.31 30 -10000 0 30
TP53 -0.023 0.14 0.2 9 -0.47 43 52
KU70/SIRT1/BAX 0.033 0.028 -10000 0 -0.31 1 1
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
MEF2D 0.018 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.008 0.06 -10000 0 -0.37 1 1
ACSS2 0.023 0.029 -10000 0 -0.37 1 1
SIRT1/PCAF/MYOD -0.002 0.081 -10000 0 -0.31 30 30
Retinoic acid receptors-mediated signaling

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 0.017 0.023 -10000 0 -0.52 1 1
HDAC3 0.018 0 -10000 0 -10000 0 0
VDR -0.003 0.1 -10000 0 -0.51 21 21
Cbp/p300/PCAF 0.02 0.036 -10000 0 -0.31 6 6
EP300 0.014 0.047 -10000 0 -0.52 4 4
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.02 0.062 -10000 0 -0.32 4 4
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.017 0.012 -10000 0 -0.26 1 1
AKT1 0.029 0.093 0.22 53 -0.25 19 72
RAR alpha/9cRA/Cyclin H -0.024 0.063 -10000 0 -0.4 5 5
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.014 0.071 -10000 0 -0.29 9 9
CDC2 -0.012 0.12 -10000 0 -0.44 34 34
response to UV -0.002 0.009 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.014 0.052 -10000 0 -0.36 6 6
NCOR2 0.018 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.002 0.075 -10000 0 -0.37 21 21
RXRs/RARs/NRIP1/9cRA -0.009 0.19 -10000 0 -0.54 54 54
NCOA2 0.009 0.063 -10000 0 -0.4 11 11
NCOA3 0.012 0.052 -10000 0 -0.39 8 8
NCOA1 0.012 0.057 -10000 0 -0.52 6 6
VDR/VDR/DNA -0.003 0.1 -10000 0 -0.51 21 21
RARG 0.016 0.024 -10000 0 -0.52 1 1
RAR gamma1/9cRA 0.022 0.016 -10000 0 -0.31 1 1
MAPK3 0.015 0.027 -10000 0 -0.39 2 2
MAPK1 0.016 0.033 -10000 0 -0.52 2 2
MAPK8 0.013 0.041 -10000 0 -0.52 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.002 0.12 -10000 0 -0.43 12 12
RARA 0.017 0.052 -10000 0 -0.26 11 11
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.013 0.068 -10000 0 -0.26 7 7
PRKCA 0.011 0.038 -10000 0 -0.26 8 8
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.026 0.21 -10000 0 -0.6 54 54
RXRG 0.014 0.065 -10000 0 -0.32 14 14
RXRA 0.011 0.08 -10000 0 -0.3 7 7
RXRB 0.021 0.041 -10000 0 -0.3 3 3
VDR/Vit D3/DNA -0.002 0.075 -10000 0 -0.37 21 21
RBP1 -0.076 0.19 -10000 0 -0.42 112 112
CRBP1/9-cic-RA -0.054 0.14 -10000 0 -0.3 112 112
RARB -0.025 0.13 -10000 0 -0.36 60 60
PRKCG 0.016 0.017 -10000 0 -10000 0 0
MNAT1 0.017 0.012 -10000 0 -0.26 1 1
RAR alpha/RXRs 0.02 0.15 -10000 0 -0.36 43 43
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.022 0.11 -10000 0 -0.37 8 8
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.068 -10000 0 -0.29 6 6
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.026 0.21 -10000 0 -0.6 54 54
positive regulation of DNA binding -0.023 0.06 -10000 0 -0.38 5 5
NRIP1 -0.086 0.38 -10000 0 -1.2 53 53
RXRs/RARs -0.012 0.15 -10000 0 -0.42 56 56
RXRs/RXRs/DNA/9cRA 0.003 0.12 -10000 0 -0.31 51 51
PRKACA 0.018 0 -10000 0 -10000 0 0
CDK7 0.017 0.012 -10000 0 -0.26 1 1
TFIIH 0.033 0.031 -10000 0 -0.3 4 4
RAR alpha/9cRA 0.039 0.044 -10000 0 -0.25 4 4
CCNH 0.014 0.047 -10000 0 -0.52 4 4
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
RAR gamma2/9cRA -0.003 0.022 -10000 0 -0.22 2 2
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.003 0.14 -9999 0 -0.85 7 7
MKNK1 0.018 0 -9999 0 -10000 0 0
MAPK14 0.005 0.055 -9999 0 -0.29 6 6
ATF2/c-Jun -0.028 0.19 -9999 0 -0.6 49 49
MAPK11 0.006 0.053 -9999 0 -0.28 5 5
MITF 0.014 0.071 -9999 0 -0.34 11 11
MAPKAPK5 0.018 0.059 -9999 0 -0.33 5 5
KRT8 -0.005 0.1 -9999 0 -0.34 32 32
MAPKAPK3 0.017 0.017 -9999 0 -0.26 2 2
MAPKAPK2 0.014 0.047 -9999 0 -0.52 4 4
p38alpha-beta/CK2 0.008 0.074 -9999 0 -0.37 7 7
CEBPB 0.011 0.073 -9999 0 -0.32 11 11
SLC9A1 0.018 0.059 -9999 0 -0.33 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.013 0.08 -9999 0 -0.31 6 6
p38alpha-beta/MNK1 0.022 0.059 -9999 0 -0.3 6 6
JUN -0.028 0.19 -9999 0 -0.6 49 49
PPARGC1A 0.002 0.089 -9999 0 -0.28 29 29
USF1 0.005 0.085 -9999 0 -0.34 16 16
RAB5/GDP/GDI1 0.019 0.042 -9999 0 -0.22 6 6
NOS2 0.008 0.059 -9999 0 -0.3 7 7
DDIT3 0.014 0.067 -9999 0 -0.37 6 6
RAB5A 0.018 0 -9999 0 -10000 0 0
HSPB1 -0.013 0.12 -9999 0 -0.33 54 54
p38alpha-beta/HBP1 0.02 0.066 -9999 0 -0.33 9 9
CREB1 0.013 0.076 -9999 0 -0.28 18 18
RAB5/GDP 0.013 0 -9999 0 -10000 0 0
EIF4E 0.024 0.049 -9999 0 -0.27 5 5
RPS6KA4 0.017 0.061 -9999 0 -0.32 6 6
PLA2G4A -0.007 0.1 -9999 0 -0.31 30 30
GDI1 0.017 0.061 -9999 0 -0.32 6 6
TP53 -0.001 0.096 -9999 0 -0.34 21 21
RPS6KA5 0 0.1 -9999 0 -0.35 33 33
ESR1 -0.091 0.17 -9999 0 -0.34 154 154
HBP1 0.015 0.04 -9999 0 -0.52 3 3
MEF2C -0.001 0.1 -9999 0 -0.34 31 31
MEF2A 0.017 0.062 -9999 0 -0.33 6 6
EIF4EBP1 0.008 0.081 -9999 0 -0.28 19 19
KRT19 -0.014 0.12 -9999 0 -0.34 53 53
ELK4 0.015 0.066 -9999 0 -0.31 9 9
ATF6 0.017 0.061 -9999 0 -0.32 6 6
ATF1 0.013 0.077 -9999 0 -0.28 19 19
p38alpha-beta/MAPKAPK2 0.02 0.07 -9999 0 -0.35 9 9
p38alpha-beta/MAPKAPK3 0.022 0.06 -9999 0 -0.32 5 5
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.011 0.056 -10000 0 -0.31 12 12
cell-cell adhesion 0.036 0.083 0.37 18 -10000 0 18
Ephrin B/EPHB2/RasGAP 0.024 0.086 -10000 0 -0.28 30 30
ITSN1 0.015 0.035 -10000 0 -0.43 3 3
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
SHC1 0.017 0.023 -10000 0 -0.52 1 1
Ephrin B1/EPHB3 0.005 0.072 -10000 0 -0.32 21 21
Ephrin B1/EPHB1 -0.004 0.071 -10000 0 -0.31 13 13
HRAS/GDP -0.033 0.079 -10000 0 -0.36 13 13
Ephrin B/EPHB1/GRB7 -0.002 0.096 -10000 0 -0.27 32 32
Endophilin/SYNJ1 0.019 0.063 -10000 0 -0.23 23 23
KRAS 0.008 0.069 -10000 0 -0.45 11 11
Ephrin B/EPHB1/Src 0.014 0.088 -10000 0 -0.28 24 24
endothelial cell migration -0.003 0.1 -10000 0 -0.28 55 55
GRB2 0.016 0.024 -10000 0 -0.26 4 4
GRB7 -0.017 0.1 -10000 0 -0.29 59 59
PAK1 0.003 0.092 -10000 0 -0.35 8 8
HRAS 0.012 0.051 -10000 0 -0.41 7 7
RRAS 0.016 0.074 -10000 0 -0.25 30 30
DNM1 0.012 0.052 -10000 0 -0.39 8 8
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.006 0.078 -10000 0 -0.26 25 25
lamellipodium assembly -0.036 0.083 -10000 0 -0.37 18 18
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.016 0.076 -10000 0 -0.47 5 5
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
EPHB2 0.007 0.062 -10000 0 -0.32 16 16
EPHB3 -0.005 0.1 -10000 0 -0.45 26 26
EPHB1 -0.023 0.11 -10000 0 -0.28 73 73
EPHB4 -0.01 0.11 -10000 0 -0.42 33 33
mol:GDP 0.003 0.098 -10000 0 -0.33 23 23
Ephrin B/EPHB2 0.02 0.069 -10000 0 -0.25 24 24
Ephrin B/EPHB3 0.013 0.085 -10000 0 -0.27 36 36
JNK cascade 0.007 0.081 -10000 0 -0.25 33 33
Ephrin B/EPHB1 0.005 0.083 -10000 0 -0.26 31 31
RAP1/GDP 0.014 0.097 -10000 0 -0.33 15 15
EFNB2 -0.006 0.1 -10000 0 -0.39 31 31
EFNB3 0.018 0 -10000 0 -10000 0 0
EFNB1 0.01 0.051 -10000 0 -0.3 13 13
Ephrin B2/EPHB1-2 -0.006 0.088 -10000 0 -0.28 32 32
RAP1B 0.013 0.044 -10000 0 -0.32 8 8
RAP1A 0.011 0.062 -10000 0 -0.52 7 7
CDC42/GTP -0.03 0.075 -10000 0 -0.39 11 11
Rap1/GTP -0.031 0.079 -10000 0 -0.4 14 14
axon guidance 0.011 0.056 -10000 0 -0.3 12 12
MAPK3 0.028 0.069 -10000 0 -0.42 5 5
MAPK1 0.027 0.07 -10000 0 -0.39 6 6
Rac1/GDP 0.013 0.093 -10000 0 -0.36 9 9
actin cytoskeleton reorganization -0.034 0.073 -10000 0 -0.32 16 16
CDC42/GDP 0.013 0.093 -10000 0 -0.31 21 21
PI3K 0 0.1 -10000 0 -0.28 55 55
EFNA5 0.006 0.069 -10000 0 -0.35 17 17
Ephrin B2/EPHB4 -0.007 0.096 -10000 0 -0.34 35 35
Ephrin B/EPHB2/Intersectin/N-WASP 0.021 0.068 -10000 0 -0.3 3 3
CDC42 0.018 0 -10000 0 -10000 0 0
RAS family/GTP -0.034 0.076 -10000 0 -0.34 17 17
PTK2 0.007 0.034 -10000 0 -0.34 3 3
MAP4K4 0.007 0.082 -10000 0 -0.25 33 33
SRC 0.015 0.035 -10000 0 -0.43 3 3
KALRN 0.006 0.057 -10000 0 -0.27 21 21
Intersectin/N-WASP 0.019 0.054 -10000 0 -0.37 10 10
neuron projection morphogenesis 0.011 0.11 -10000 0 -0.34 21 21
MAP2K1 0.022 0.072 -10000 0 -0.44 5 5
WASL 0.01 0.066 -10000 0 -0.52 8 8
Ephrin B1/EPHB1-2/NCK1 0.011 0.082 -10000 0 -0.27 26 26
cell migration 0.027 0.076 -10000 0 -0.45 5 5
NRAS 0.006 0.072 -10000 0 -0.4 15 15
SYNJ1 0.02 0.064 -10000 0 -0.24 23 23
PXN 0.018 0 -10000 0 -10000 0 0
TF 0.02 0.065 -10000 0 -0.32 1 1
HRAS/GTP 0.004 0.092 -10000 0 -0.38 12 12
Ephrin B1/EPHB1-2 0.003 0.075 -10000 0 -0.27 22 22
cell adhesion mediated by integrin 0.012 0.061 0.26 20 -10000 0 20
RAC1 0.018 0 -10000 0 -10000 0 0
mol:GTP 0.008 0.097 -10000 0 -0.41 11 11
RAC1-CDC42/GTP -0.034 0.08 -10000 0 -0.35 18 18
RASA1 0.004 0.079 -10000 0 -0.42 16 16
RAC1-CDC42/GDP 0.02 0.09 -10000 0 -0.36 7 7
ruffle organization 0.01 0.1 -10000 0 -0.43 11 11
NCK1 0.011 0.046 -10000 0 -0.28 12 12
receptor internalization 0.022 0.067 -10000 0 -0.26 5 5
Ephrin B/EPHB2/KALRN 0.025 0.077 -10000 0 -0.27 22 22
ROCK1 0.012 0.064 -10000 0 -0.28 21 21
RAS family/GDP -0.034 0.075 -10000 0 -0.33 15 15
Rac1/GTP -0.038 0.088 -10000 0 -0.39 18 18
Ephrin B/EPHB1/Src/Paxillin 0.014 0.076 -10000 0 -0.49 4 4
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.023 0.016 -9999 0 -0.31 1 1
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.017 0.023 -9999 0 -0.52 1 1
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.012 0.11 -9999 0 -0.4 37 37
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 -0.005 0.099 -9999 0 -0.39 30 30
RAC1-CDC42/GTP/PAK family -0.001 0.071 -9999 0 -0.22 40 40
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.007 0.07 -9999 0 -0.43 12 12
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.017 0.012 -9999 0 -0.26 1 1
FYN 0.009 0.063 -9999 0 -0.4 11 11
MAP3K12 0.018 0 -9999 0 -10000 0 0
FGR 0.017 0.017 -9999 0 -0.26 2 2
p38 alpha/TAB1 0.011 0.093 -9999 0 -0.28 27 27
PRKG1 0.017 0.012 -9999 0 -0.26 1 1
DUSP8 -0.005 0.11 -9999 0 -0.47 25 25
PGK/cGMP/p38 alpha -0.028 0.07 -9999 0 -0.27 29 29
apoptosis 0.01 0.089 -9999 0 -0.27 28 28
RAL/GTP 0.022 0.029 -9999 0 -0.31 4 4
LYN 0.014 0.031 -9999 0 -0.26 7 7
DUSP1 -0.038 0.15 -9999 0 -0.41 69 69
PAK1 -0.022 0.13 -9999 0 -0.38 53 53
SRC 0.015 0.035 -9999 0 -0.43 3 3
RAC1/OSM/MEKK3/MKK3 0.043 0.022 -9999 0 -0.27 1 1
TRAF6 0.017 0.023 -9999 0 -0.52 1 1
RAC1 0.018 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.018 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.024 0 -9999 0 -10000 0 0
MAPK11 0.003 0.11 -9999 0 -0.33 30 30
BLK -0.018 0.1 -9999 0 -0.29 61 61
HCK -0.005 0.11 -9999 0 -0.47 25 25
MAP2K3 0.014 0.037 -9999 0 -0.3 7 7
DUSP16 0.005 0.078 -9999 0 -0.43 15 15
DUSP10 -0.017 0.12 -9999 0 -0.4 44 44
TRAF6/MEKK3 0.022 0.015 -9999 0 -0.28 1 1
MAP3K7IP1 0.018 0 -9999 0 -10000 0 0
MAPK14 0.004 0.099 -9999 0 -0.3 32 32
positive regulation of innate immune response 0.003 0.12 -9999 0 -0.37 30 30
LCK -0.073 0.18 -9999 0 -0.4 115 115
p38alpha-beta/MKP7 0.006 0.13 -9999 0 -0.36 32 32
p38alpha-beta/MKP5 -0.003 0.13 -9999 0 -0.37 29 29
PGK/cGMP 0.013 0.008 -9999 0 -0.17 1 1
PAK2 0.018 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.012 0.14 -9999 0 -0.38 36 36
CDC42 0.018 0 -9999 0 -10000 0 0
RALB 0.014 0.047 -9999 0 -0.52 4 4
RALA 0.018 0 -9999 0 -10000 0 0
PAK3 -0.033 0.13 -9999 0 -0.32 80 80
Hypoxic and oxygen homeostasis regulation of HIF-1-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
HIF3A 0.015 0.029 -9999 0 -0.26 6 6
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.018 0 -9999 0 -10000 0 0
TCEB1 0.014 0.035 -9999 0 -0.3 6 6
HIF1A/p53 -0.02 0.11 -9999 0 -0.32 37 37
HIF1A -0.011 0.087 -9999 0 -0.32 20 20
COPS5 0.01 0.056 -9999 0 -0.35 11 11
VHL/Elongin B/Elongin C/RBX1/CUL2 0.049 0.026 -9999 0 -0.24 1 1
FIH (dimer) 0.017 0.023 -9999 0 -0.52 1 1
CDKN2A -0.054 0.15 -9999 0 -0.33 108 108
ARNT/IPAS 0.024 0.02 -9999 0 -10000 0 0
HIF1AN 0.017 0.023 -9999 0 -0.52 1 1
GNB2L1 0.015 0.04 -9999 0 -0.52 3 3
HIF1A/ARNT 0 0.084 -9999 0 -0.3 18 18
CUL2 0.017 0.017 -9999 0 -0.26 2 2
OS9 0.014 0.041 -9999 0 -0.35 6 6
RACK1/Elongin B/Elongin C 0.032 0.033 -9999 0 -0.3 4 4
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.002 0.089 -9999 0 -0.32 20 20
PHD1-3/OS9 -0.021 0.12 -9999 0 -0.28 80 80
HIF1A/RACK1/Elongin B/Elongin C 0.012 0.083 -9999 0 -0.34 5 5
VHL 0.014 0.031 -9999 0 -0.26 7 7
HSP90AA1 0.013 0.045 -9999 0 -0.39 6 6
HIF1A/JAB1 -0.004 0.087 -9999 0 -0.3 20 20
EGLN3 -0.074 0.18 -9999 0 -0.4 116 116
EGLN2 0.011 0.054 -9999 0 -0.38 9 9
EGLN1 0.001 0.082 -9999 0 -0.36 23 23
TP53 -0.023 0.14 -9999 0 -0.48 43 43
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.034 0.033 -9999 0 -0.5 1 1
ARNT 0.018 0 -9999 0 -10000 0 0
ARD1A 0.016 0.021 -9999 0 -0.26 3 3
RBX1 0.018 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.032 0.11 -9999 0 -0.32 35 35
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.017 0.078 -9999 0 -0.38 17 17
CRKL 0.014 0.047 -9999 0 -0.52 4 4
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
DOCK1 0.006 0.078 -9999 0 -0.5 12 12
ITGA4 -0.007 0.1 -9999 0 -0.39 32 32
alpha4/beta7 Integrin/MAdCAM1 0.023 0.079 -9999 0 -0.29 27 27
EPO -0.024 0.099 -9999 0 -0.26 80 80
alpha4/beta7 Integrin 0.009 0.074 -9999 0 -0.37 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0.033 -9999 0 -0.52 2 2
alpha4/beta1 Integrin 0.007 0.083 -9999 0 -0.41 16 16
EPO/EPOR (dimer) -0.003 0.069 -9999 0 -0.32 1 1
lamellipodium assembly 0.022 0.069 -9999 0 -0.28 22 22
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
PI3K 0.006 0.082 -9999 0 -0.37 21 21
ARF6 0.016 0.033 -9999 0 -0.52 2 2
JAK2 0.007 0.076 -9999 0 -0.31 18 18
PXN 0.018 0 -9999 0 -10000 0 0
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
MADCAM1 0.014 0.034 -9999 0 -0.26 8 8
cell adhesion 0.021 0.079 -9999 0 -0.29 27 27
CRKL/CBL 0.023 0.035 -9999 0 -0.37 4 4
ITGB1 0.015 0.037 -9999 0 -0.39 4 4
SRC 0 0.1 -9999 0 -0.3 47 47
ITGB7 0.018 0 -9999 0 -10000 0 0
RAC1 0.018 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.004 0.11 -9999 0 -0.34 45 45
p130Cas/Crk/Dock1 0.019 0.099 -9999 0 -0.45 7 7
VCAM1 -0.021 0.13 -9999 0 -0.42 47 47
RHOA 0.005 0.08 -9999 0 -0.52 12 12
alpha4/beta1 Integrin/Paxillin/GIT1 0.028 0.069 -9999 0 -0.3 17 17
BCAR1 0.007 0.097 -9999 0 -0.29 41 41
EPOR 0.017 0.017 -9999 0 -0.26 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.017 0.012 -9999 0 -0.26 1 1
GIT1 0.014 0.035 -9999 0 -0.3 6 6
Rac1/GTP 0.022 0.071 -9999 0 -0.29 22 22
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.014 0.047 -10000 0 -0.52 4 4
RAS family/GTP/Tiam1 0.003 0.08 -10000 0 -0.36 12 12
NT3 (dimer)/TRKC -0.018 0.093 -10000 0 -0.35 16 16
NT3 (dimer)/TRKB -0.015 0.1 -10000 0 -0.32 36 36
SHC/Grb2/SOS1/GAB1/PI3K 0.023 0.065 -10000 0 -0.22 32 32
RAPGEF1 0.018 0 -10000 0 -10000 0 0
BDNF -0.016 0.092 -10000 0 -0.26 64 64
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
DYNLT1 0.018 0 -10000 0 -10000 0 0
NTRK1 0.01 0.054 -10000 0 -0.32 12 12
NTRK2 -0.017 0.11 -10000 0 -0.34 52 52
NTRK3 -0.009 0.082 -10000 0 -0.26 52 52
NT-4/5 (dimer)/TRKB -0.004 0.079 -10000 0 -0.31 23 23
neuron apoptosis 0.036 0.15 0.34 80 -10000 0 80
SHC 2-3/Grb2 -0.04 0.16 -10000 0 -0.37 80 80
SHC1 0.017 0.023 -10000 0 -0.52 1 1
SHC2 -0.062 0.2 0.2 7 -0.5 79 86
SHC3 -0.007 0.11 -10000 0 -0.45 19 19
STAT3 (dimer) -0.045 0.14 -10000 0 -0.34 89 89
NT3 (dimer)/TRKA 0.001 0.083 -10000 0 -0.34 16 16
RIN/GDP 0.048 0.049 -10000 0 -0.31 1 1
GIPC1 0.014 0.042 -10000 0 -0.46 4 4
KRAS 0.008 0.069 -10000 0 -0.45 11 11
DNAJA3 0.017 0.066 0.23 20 -0.26 6 26
RIN/GTP 0.011 0.025 -10000 0 -0.31 3 3
CCND1 -0.12 0.29 -10000 0 -0.75 89 89
MAGED1 -0.008 0.11 -10000 0 -0.48 27 27
PTPN11 0.017 0.023 -10000 0 -0.52 1 1
RICS 0.003 0.083 -10000 0 -0.46 16 16
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.034 0.025 -10000 0 -0.3 2 2
GRB2 0.016 0.024 -10000 0 -0.26 4 4
NGF (dimer)/TRKA/MATK 0.008 0.055 -10000 0 -0.3 7 7
TRKA/NEDD4-2 -0.01 0.11 -10000 0 -0.37 39 39
ELMO1 0.017 0.017 -10000 0 -0.26 2 2
RhoG/GTP/ELMO1/DOCK1 0.016 0.049 -10000 0 -0.31 11 11
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.012 0.051 -10000 0 -0.41 7 7
DOCK1 0.006 0.078 -10000 0 -0.5 12 12
GAB2 0.009 0.047 -10000 0 -0.26 16 16
RIT2 0.015 0.035 -10000 0 -0.43 3 3
RIT1 0.016 0.033 -10000 0 -0.52 2 2
FRS2 0.01 0.047 -10000 0 -0.28 13 13
DNM1 0.012 0.052 -10000 0 -0.39 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0.033 -10000 0 -0.52 2 2
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.018 0.064 0.22 20 -0.25 6 26
mol:GDP 0.053 0.065 -10000 0 -0.4 2 2
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.012 0.011 -10000 0 -0.17 2 2
RIT1/GDP 0.048 0.049 -10000 0 -0.31 1 1
TIAM1 0.006 0.073 -10000 0 -0.44 13 13
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
BDNF (dimer)/TRKB -0.008 0.091 -10000 0 -0.32 24 24
KIDINS220/CRKL/C3G 0.023 0.034 -10000 0 -0.37 4 4
SHC/RasGAP 0.016 0.06 -10000 0 -0.37 11 11
FRS2 family/SHP2 0.031 0.032 -10000 0 -0.3 2 2
SHC/GRB2/SOS1/GAB1 0.037 0.049 -10000 0 -0.26 12 12
RIT1/GTP 0.012 0.024 -10000 0 -0.38 2 2
NT3 (dimer) -0.021 0.1 -10000 0 -0.28 67 67
RAP1/GDP -0.006 0.028 -10000 0 -0.34 1 1
KIDINS220/CRKL 0.014 0.047 -10000 0 -0.52 4 4
BDNF (dimer) -0.016 0.092 -10000 0 -0.26 64 64
ubiquitin-dependent protein catabolic process -0.007 0.091 -10000 0 -0.31 39 39
Schwann cell development -0.008 0.017 -10000 0 -10000 0 0
EHD4 0.013 0.052 -10000 0 -0.52 5 5
FRS2 family/GRB2/SOS1 0.04 0.037 -10000 0 -0.55 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.038 0.037 -10000 0 -0.28 1 1
RAP1B 0.013 0.044 -10000 0 -0.32 8 8
RAP1A 0.011 0.062 -10000 0 -0.52 7 7
CDC42/GTP -0.043 0.077 -10000 0 -0.35 14 14
ABL1 0.018 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.024 0.024 -10000 0 -0.37 1 1
Rap1/GTP 0.029 0.074 -10000 0 -0.39 8 8
STAT3 -0.045 0.14 -10000 0 -0.34 89 89
axon guidance -0.042 0.074 -10000 0 -0.34 14 14
MAPK3 0.013 0.051 -10000 0 -0.27 8 8
MAPK1 0.013 0.052 -10000 0 -0.27 9 9
CDC42/GDP 0.048 0.048 -10000 0 -0.31 1 1
NTF3 -0.021 0.1 -10000 0 -0.28 67 67
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.018 0.036 -10000 0 -0.31 4 4
PI3K 0.006 0.082 -10000 0 -0.37 21 21
FRS3 0.017 0.012 -10000 0 -0.26 1 1
FAIM 0.016 0.029 -10000 0 -0.35 3 3
GAB1 0.006 0.074 -10000 0 -0.43 14 14
RASGRF1 0.006 0.076 0.23 19 -0.27 11 30
SOS1 0.017 0.023 -10000 0 -0.52 1 1
MCF2L -0.008 0.082 -10000 0 -0.3 20 20
RGS19 0.014 0.039 -10000 0 -0.36 5 5
CDC42 0.018 0 -10000 0 -10000 0 0
RAS family/GTP 0.046 0.072 -10000 0 -0.4 5 5
Rac1/GDP 0.048 0.048 -10000 0 -0.31 1 1
NGF (dimer)/TRKA/GRIT 0.011 0.06 -10000 0 -0.31 15 15
neuron projection morphogenesis -0.013 0.13 -10000 0 -0.65 6 6
NGF (dimer)/TRKA/NEDD4-2 -0.007 0.091 -10000 0 -0.31 39 39
MAP2K1 0.034 0.045 -10000 0 -0.24 11 11
NGFR 0.004 0.066 -10000 0 -0.29 23 23
NGF (dimer)/TRKA/GIPC/GAIP 0.027 0.053 -10000 0 -0.31 10 10
RAS family/GTP/PI3K 0.011 0.077 -10000 0 -0.25 39 39
FRS2 family/SHP2/GRB2/SOS1 0.047 0.038 -10000 0 -0.38 2 2
NRAS 0.006 0.072 -10000 0 -0.4 15 15
GRB2/SOS1 0.024 0.024 -10000 0 -0.37 1 1
PRKCI 0.001 0.088 -10000 0 -0.44 19 19
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.018 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.018 0.051 -10000 0 -0.47 4 4
RASA1 0.004 0.079 -10000 0 -0.42 16 16
TRKA/c-Abl 0.021 0.038 -10000 0 -0.37 3 3
SQSTM1 0.012 0.053 -10000 0 -0.48 6 6
BDNF (dimer)/TRKB/GIPC 0.006 0.082 -10000 0 -0.28 22 22
NGF (dimer)/TRKA/p62/Atypical PKCs 0.016 0.061 -10000 0 -0.26 21 21
MATK -0.003 0.076 -10000 0 -0.27 38 38
NEDD4L -0.025 0.14 -10000 0 -0.46 48 48
RAS family/GDP -0.01 0.032 -10000 0 -0.28 1 1
NGF (dimer)/TRKA 0.009 0.071 0.24 21 -0.28 6 27
Rac1/GTP -0.02 0.052 -10000 0 -0.24 15 15
FRS2 family/SHP2/CRK family 0.045 0.043 -10000 0 -0.26 8 8
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.021 0.042 -10000 0 -0.37 5 5
ATM 0.017 0.012 -10000 0 -0.26 1 1
UBE2D3 0.018 0 -10000 0 -10000 0 0
PRKDC 0.012 0.046 -10000 0 -0.32 9 9
ATR 0.017 0.012 -10000 0 -0.26 1 1
UBE2L3 0.018 0 -10000 0 -10000 0 0
FANCD2 0.029 0.012 -10000 0 -10000 0 0
protein ubiquitination 0.016 0.083 -10000 0 -0.28 26 26
XRCC5 0.018 0 -10000 0 -10000 0 0
XRCC6 0.017 0.012 -10000 0 -0.26 1 1
M/R/N Complex 0.029 0.047 -10000 0 -0.3 10 10
MRE11A 0.018 0 -10000 0 -10000 0 0
DNA-PK 0.032 0.028 -10000 0 -0.3 2 2
FA complex/FANCD2/Ubiquitin 0.028 0.075 -10000 0 -0.36 7 7
FANCF 0.012 0.057 -10000 0 -0.52 6 6
BRCA1 0 0.094 -10000 0 -0.48 19 19
CCNE1 -0.018 0.1 -10000 0 -0.28 64 64
CDK2/Cyclin E1 -0.002 0.081 -10000 0 -0.38 11 11
FANCG 0.016 0.024 -10000 0 -0.26 4 4
BRCA1/BACH1/BARD1 0.01 0.076 -10000 0 -0.37 20 20
FANCE 0.006 0.062 -10000 0 -0.3 19 19
FANCC 0.013 0.042 -10000 0 -0.33 7 7
NBN 0.015 0.035 -10000 0 -0.43 3 3
FANCA -0.032 0.13 -10000 0 -0.31 80 80
DNA repair 0.013 0.12 -10000 0 -0.38 24 24
BRCA1/BARD1/ubiquitin 0.01 0.076 -10000 0 -0.37 20 20
BARD1/DNA-PK 0.04 0.038 -10000 0 -0.27 6 6
FANCL 0.014 0.031 -10000 0 -0.26 7 7
mRNA polyadenylation -0.021 0.042 0.37 5 -10000 0 5
BRCA1/BARD1/CTIP/M/R/N Complex 0.026 0.058 -10000 0 -0.32 2 2
BRCA1/BACH1/BARD1/TopBP1 0.022 0.068 -10000 0 -0.31 20 20
BRCA1/BARD1/P53 0.01 0.11 -10000 0 -0.3 51 51
BARD1/CSTF1/BRCA1 0.02 0.069 -10000 0 -0.3 21 21
BRCA1/BACH1 0 0.094 -10000 0 -0.48 19 19
BARD1 0.014 0.047 -10000 0 -0.52 4 4
PCNA 0.009 0.059 -10000 0 -0.38 11 11
BRCA1/BARD1/UbcH5C 0.022 0.066 -10000 0 -0.3 20 20
BRCA1/BARD1/UbcH7 0.022 0.066 -10000 0 -0.3 20 20
BRCA1/BARD1/RAD51/PCNA -0.004 0.12 -10000 0 -0.28 73 73
BARD1/DNA-PK/P53 0.025 0.085 -10000 0 -0.36 2 2
BRCA1/BARD1/Ubiquitin 0.01 0.076 -10000 0 -0.37 20 20
BRCA1/BARD1/CTIP 0.015 0.081 -10000 0 -0.28 32 32
FA complex 0.017 0.074 -10000 0 -0.34 6 6
BARD1/EWS 0.023 0.034 -10000 0 -0.37 4 4
RBBP8 0.007 0.07 -10000 0 -0.37 12 12
TP53 -0.023 0.14 -10000 0 -0.48 43 43
TOPBP1 0.017 0.017 -10000 0 -0.26 2 2
G1/S transition of mitotic cell cycle -0.008 0.11 0.3 51 -10000 0 51
BRCA1/BARD1 0.019 0.085 -10000 0 -0.28 26 26
CSTF1 0.014 0.035 -10000 0 -0.3 6 6
BARD1/EWS-Fli1 0.01 0.034 -10000 0 -0.38 4 4
CDK2 0.011 0.047 -10000 0 -0.31 10 10
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.039 0.16 -10000 0 -0.47 62 62
RAD50 0.01 0.066 -10000 0 -0.52 8 8
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.01 0.076 -10000 0 -0.37 20 20
EWSR1 0.018 0 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.013 0.056 -10000 0 -0.37 5 5
CRKL 0.02 0.086 -10000 0 -0.45 11 11
mol:PIP3 -0.004 0.091 0.47 19 -10000 0 19
AKT1 0.007 0.068 0.34 18 -0.28 4 22
PTK2B 0.017 0.017 -10000 0 -0.26 2 2
RAPGEF1 0.026 0.082 -10000 0 -0.44 10 10
RANBP10 0.018 0 -10000 0 -10000 0 0
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
HGF/MET/SHIP2 0.015 0.072 -10000 0 -0.31 19 19
MAP3K5 0.018 0.1 -10000 0 -0.41 14 14
HGF/MET/CIN85/CBL/ENDOPHILINS 0.021 0.079 -10000 0 -0.29 24 24
AP1 -0.088 0.16 -10000 0 -0.37 110 110
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.017 0.023 -10000 0 -0.52 1 1
apoptosis -0.14 0.3 -10000 0 -0.74 100 100
STAT3 (dimer) 0.029 0.059 -10000 0 -0.29 2 2
GAB1/CRKL/SHP2/PI3K 0.029 0.098 -10000 0 -0.42 13 13
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.03 0.082 -10000 0 -0.46 9 9
PTPN11 0.017 0.023 -10000 0 -0.52 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.016 0.026 -10000 0 -0.39 2 2
PTEN -0.002 0.1 -10000 0 -0.52 19 19
ELK1 -0.005 0.037 0.25 3 -0.17 8 11
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.022 0.045 -10000 0 -0.23 7 7
PAK1 -0.005 0.089 0.32 17 -0.26 29 46
HGF/MET/RANBP10 0.019 0.065 -10000 0 -0.31 14 14
HRAS 0.024 0.081 -10000 0 -0.53 7 7
DOCK1 0.021 0.094 -10000 0 -0.49 10 10
GAB1 0.015 0.087 -10000 0 -0.42 15 15
CRK 0.021 0.085 -10000 0 -0.45 11 11
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.087 -10000 0 -0.49 13 13
JUN -0.034 0.15 -10000 0 -0.46 57 57
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.005 0.052 -10000 0 -0.24 18 18
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
cell morphogenesis 0.038 0.089 -10000 0 -0.36 9 9
GRB2/SHC 0.024 0.05 -10000 0 -0.23 12 12
FOS -0.11 0.2 -10000 0 -0.37 171 171
GLMN -0.001 0.014 -10000 0 -0.25 1 1
cell motility -0.005 0.037 0.25 3 -0.17 8 11
HGF/MET/MUC20 0.007 0.064 -10000 0 -0.32 14 14
cell migration 0.023 0.049 -10000 0 -0.23 12 12
GRB2 0.016 0.024 -10000 0 -0.26 4 4
CBL 0.017 0.012 -10000 0 -0.26 1 1
MET/RANBP10 0.013 0.055 -10000 0 -0.37 5 5
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.025 0.06 -10000 0 -0.3 2 2
MET/MUC20 0 0.054 -10000 0 -0.2 31 31
RAP1B 0.03 0.081 -10000 0 -0.39 12 12
RAP1A 0.029 0.088 -10000 0 -0.44 12 12
HGF/MET/RANBP9 0.019 0.065 -10000 0 -0.31 14 14
RAF1 0.03 0.077 -10000 0 -0.52 6 6
STAT3 0.029 0.06 -10000 0 -0.29 2 2
cell proliferation 0.036 0.072 -10000 0 -0.32 14 14
RPS6KB1 0.009 0.024 -10000 0 -0.15 1 1
MAPK3 -0.011 0.041 0.66 1 -10000 0 1
MAPK1 -0.009 0.055 0.76 2 -10000 0 2
RANBP9 0.017 0.012 -10000 0 -0.26 1 1
MAPK8 0.025 0.093 -10000 0 -0.38 10 10
SRC 0.029 0.059 -10000 0 -0.26 4 4
PI3K 0.011 0.078 -10000 0 -0.26 30 30
MET/Glomulin 0.004 0.049 -10000 0 -0.18 32 32
SOS1 0.017 0.023 -10000 0 -0.52 1 1
MAP2K1 0.036 0.073 -10000 0 -0.51 5 5
MET -0.001 0.078 -10000 0 -0.3 31 31
MAP4K1 0.029 0.082 -10000 0 -0.46 9 9
PTK2 0.016 0.029 -10000 0 -0.35 3 3
MAP2K2 0.035 0.076 -10000 0 -0.5 6 6
BAD 0.013 0.064 0.32 18 -0.26 5 23
MAP2K4 0.015 0.1 -10000 0 -0.36 15 15
SHP2/GRB2/SOS1/GAB1 -0.016 0.068 -10000 0 -0.38 13 13
INPPL1 0.012 0.055 -10000 0 -0.45 7 7
PXN 0.018 0 -10000 0 -10000 0 0
SH3KBP1 0.001 0.083 -10000 0 -0.38 22 22
HGS 0.012 0.049 -10000 0 -0.25 12 12
PLCgamma1/PKC 0.012 0.019 -10000 0 -0.28 2 2
HGF 0.008 0.069 -10000 0 -0.45 11 11
RASA1 0.004 0.079 -10000 0 -0.42 16 16
NCK1 0.011 0.046 -10000 0 -0.28 12 12
PTPRJ 0.012 0.055 -10000 0 -0.45 7 7
NCK/PLCgamma1 0.024 0.056 -10000 0 -0.24 13 13
PDPK1 0.003 0.071 0.38 18 -10000 0 18
HGF/MET/SHIP 0.007 0.064 -10000 0 -0.32 14 14
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.018 0 -10000 0 -10000 0 0
NFATC1 0.033 0.073 -10000 0 -0.26 24 24
NFATC2 0.027 0.041 -10000 0 -0.25 1 1
NFATC3 0.017 0.006 -10000 0 -10000 0 0
YWHAE 0.016 0.029 -10000 0 -0.35 3 3
Calcineurin A alpha-beta B1/CABIN1 0.004 0.092 -10000 0 -0.36 13 13
Exportin 1/Ran/NUP214 0.035 0.018 -10000 0 -0.3 1 1
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.023 0.085 -10000 0 -0.38 9 9
BCL2/BAX -0.071 0.16 -10000 0 -0.37 115 115
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.003 -10000 0 -10000 0 0
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
BAX 0.016 0.021 -10000 0 -0.26 3 3
MAPK14 0.018 0.012 -10000 0 -0.26 1 1
BAD 0.017 0.023 -10000 0 -0.52 1 1
CABIN1/MEF2D 0.013 0.088 -10000 0 -0.38 10 10
Calcineurin A alpha-beta B1/BCL2 -0.12 0.22 -10000 0 -0.47 145 145
FKBP8 0.017 0.012 -10000 0 -0.26 1 1
activation-induced cell death of T cells -0.013 0.087 0.37 10 -10000 0 10
KPNB1 0.013 0.052 -10000 0 -0.52 5 5
KPNA2 -0.002 0.088 -10000 0 -0.35 28 28
XPO1 0.018 0 -10000 0 -10000 0 0
SFN -0.015 0.12 -10000 0 -0.45 37 37
MAP3K8 -0.035 0.15 -10000 0 -0.39 69 69
NFAT4/CK1 alpha 0.01 0.075 -10000 0 -0.24 38 38
MEF2D/NFAT1/Cbp/p300 0.057 0.059 -10000 0 -0.33 3 3
CABIN1 0.004 0.092 -10000 0 -0.37 13 13
CALM1 0.018 0.001 -10000 0 -10000 0 0
RAN 0.017 0.012 -10000 0 -0.26 1 1
MAP3K1 -0.031 0.14 -10000 0 -0.43 58 58
CAMK4 0.011 0.047 -10000 0 -0.31 10 10
mol:Ca2+ 0.001 0.002 -10000 0 -10000 0 0
MAPK3 0.016 0.026 -10000 0 -0.39 2 2
YWHAH 0.013 0.048 -10000 0 -0.47 5 5
Calcineurin A alpha-beta B1/AKAP79/PKA -0.011 0.11 -10000 0 -0.37 40 40
YWHAB 0.015 0.037 -10000 0 -0.39 4 4
MAPK8 0.015 0.04 -10000 0 -0.52 3 3
MAPK9 -0.006 0.11 -10000 0 -0.51 24 24
YWHAG 0.017 0.017 -10000 0 -0.26 2 2
FKBP1A 0.017 0.017 -10000 0 -0.26 2 2
NFAT1-c-4/YWHAQ 0.051 0.067 -10000 0 -0.28 1 1
PRKCH 0.011 0.056 -10000 0 -0.42 8 8
CABIN1/Cbp/p300 0.023 0.042 -10000 0 -0.37 6 6
CASP3 0.018 0.001 -10000 0 -10000 0 0
PIM1 0.013 0.036 -10000 0 -0.26 9 9
Calcineurin A alpha-beta B1/FKBP12/FK506 0.012 0.009 -10000 0 -0.14 2 2
apoptosis -0.026 0.046 -10000 0 -0.32 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.033 0.052 -10000 0 -0.33 1 1
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.011 0.056 -10000 0 -0.42 8 8
JNK2/NFAT4 0.013 0.062 -10000 0 -0.28 23 23
BAD/BCL-XL 0.026 0.017 -10000 0 -0.37 1 1
PRKCD 0.014 0.042 -10000 0 -0.46 4 4
NUP214 0.016 0.026 -10000 0 -0.39 2 2
PRKCZ 0 0.001 -10000 0 -10000 0 0
PRKCA 0.014 0.034 -10000 0 -0.26 8 8
PRKCG 0.018 0 -10000 0 -10000 0 0
PRKCQ -0.014 0.1 -10000 0 -0.32 51 51
FKBP38/BCL2 -0.071 0.16 -10000 0 -0.37 115 115
EP300 0.014 0.047 -10000 0 -0.52 4 4
PRKCB1 -0.051 0.16 -10000 0 -0.39 88 88
CSNK2A1 0.017 0.023 -10000 0 -0.52 1 1
NFATc/JNK1 0.041 0.073 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0.025 0.007 -10000 0 -10000 0 0
FKBP12/FK506 0.012 0.011 -10000 0 -0.17 2 2
CSNK1A1 0.022 0.015 -10000 0 -0.31 1 1
CaM/Ca2+/CAMK IV 0.022 0.028 -10000 0 -0.31 2 2
NFATc/ERK1 0.041 0.073 -10000 0 -0.49 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.02 0.087 -10000 0 -0.39 9 9
NR4A1 0.052 0.066 -10000 0 -0.52 2 2
GSK3B 0.018 0.001 -10000 0 -10000 0 0
positive T cell selection 0.017 0.006 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.027 0.036 -10000 0 -0.25 2 2
RCH1/ KPNB1 0.009 0.074 -10000 0 -0.38 15 15
YWHAQ 0.014 0.039 -10000 0 -0.36 5 5
PRKACA 0.018 0.001 -10000 0 -10000 0 0
AKAP5 -0.035 0.15 -10000 0 -0.42 63 63
MEF2D 0.018 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.017 0.017 -10000 0 -0.26 2 2
NFATc/p38 alpha 0.042 0.07 -10000 0 -0.24 24 24
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
BCL2 -0.12 0.22 -10000 0 -0.47 145 145
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0 0.095 -9999 0 -0.4 23 23
AKT1 0.03 0.15 -9999 0 -0.5 22 22
PTK2B 0.015 0.13 -9999 0 -0.66 11 11
VEGFR2 homodimer/Frs2 0.021 0.095 -9999 0 -0.58 9 9
CAV1 0 0.081 -9999 0 -0.32 28 28
CALM1 0.018 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.02 0.11 -9999 0 -0.57 10 10
endothelial cell proliferation 0.046 0.13 -9999 0 -0.47 17 17
mol:Ca2+ 0.014 0.14 -9999 0 -0.57 17 17
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.033 0.1 -9999 0 -0.55 9 9
RP11-342D11.1 0.004 0.14 -9999 0 -0.58 16 16
CDH5 0.013 0.052 -9999 0 -0.52 5 5
VEGFA homodimer 0.003 0.1 -9999 0 -0.27 52 52
SHC1 0.017 0.023 -9999 0 -0.52 1 1
SHC2 -0.061 0.19 -9999 0 -0.51 78 78
HRAS/GDP -0.036 0.099 -9999 0 -0.51 15 15
SH2D2A -0.038 0.15 -9999 0 -0.38 75 75
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.044 0.12 -9999 0 -0.47 15 15
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.007 0.13 -9999 0 -0.55 13 13
VEGFR1 homodimer 0.005 0.077 -9999 0 -0.44 14 14
SHC/GRB2/SOS1 0.025 0.13 -9999 0 -0.56 15 15
GRB10 0.004 0.17 -9999 0 -0.6 29 29
PTPN11 0.017 0.023 -9999 0 -0.52 1 1
GRB2 0.016 0.024 -9999 0 -0.26 4 4
PAK1 -0.022 0.13 -9999 0 -0.38 53 53
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.029 0.12 -9999 0 -0.56 12 12
HRAS 0.012 0.051 -9999 0 -0.41 7 7
VEGF/Rho/ROCK1/Integrin Complex 0.017 0.12 -9999 0 -0.61 12 12
HIF1A -0.037 0.16 -9999 0 -0.46 61 61
FRS2 0.01 0.047 -9999 0 -0.28 13 13
oxygen and reactive oxygen species metabolic process 0.032 0.1 -9999 0 -0.55 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.018 0 -9999 0 -10000 0 0
Nck/Pak -0.007 0.095 -9999 0 -0.37 25 25
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.019 0.12 -9999 0 -0.62 10 10
mol:GDP -0.038 0.1 -9999 0 -0.54 15 15
mol:NADP 0.042 0.11 -9999 0 -0.4 16 16
eNOS/Hsp90 0.046 0.11 -9999 0 -0.38 16 16
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
mol:IP3 0.014 0.14 -9999 0 -0.58 17 17
HIF1A/ARNT -0.014 0.12 -9999 0 -0.37 47 47
SHB 0.008 0.067 -9999 0 -0.41 12 12
VEGFA -0.002 0.076 -9999 0 -0.29 31 31
VEGFC 0 0.092 -9999 0 -0.47 19 19
FAK1/Vinculin 0.035 0.13 -9999 0 -0.77 8 8
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.005 0.08 -9999 0 -0.52 12 12
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.015 0.14 -9999 0 -0.63 14 14
PTPN6 0.015 0.035 -9999 0 -0.43 3 3
EPAS1 0.013 0.082 -9999 0 -0.45 14 14
mol:L-citrulline 0.042 0.11 -9999 0 -0.4 16 16
ITGAV -0.003 0.1 -9999 0 -0.48 22 22
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.029 0.1 -9999 0 -0.53 10 10
VEGFR2 homodimer/VEGFA homodimer 0.012 0.15 -9999 0 -0.64 16 16
VEGFR2/3 heterodimer 0.025 0.092 -9999 0 -0.58 9 9
VEGFB 0.017 0.023 -9999 0 -0.52 1 1
MAPK11 0.014 0.14 -9999 0 -0.6 16 16
VEGFR2 homodimer 0.02 0.1 -9999 0 -0.57 13 13
FLT1 0.005 0.077 -9999 0 -0.45 14 14
NEDD4 -0.001 0.096 -9999 0 -0.53 16 16
MAPK3 0.016 0.13 -9999 0 -0.54 16 16
MAPK1 0.016 0.13 -9999 0 -0.54 16 16
VEGFA145/NRP2 0.009 0.065 -9999 0 -0.37 8 8
VEGFR1/2 heterodimer 0.018 0.11 -9999 0 -0.59 11 11
KDR 0.02 0.1 -9999 0 -0.57 13 13
VEGFA165/NRP1/VEGFR2 homodimer 0.016 0.15 -9999 0 -0.59 17 17
SRC 0.015 0.035 -9999 0 -0.43 3 3
platelet activating factor biosynthetic process 0.017 0.13 -9999 0 -0.55 16 16
PI3K 0.021 0.16 -9999 0 -0.58 22 22
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.02 0.11 -9999 0 -0.59 9 9
FES 0.011 0.15 -9999 0 -0.62 16 16
GAB1 0.02 0.15 -9999 0 -0.58 17 17
VEGFR2 homodimer/VEGFA homodimer/Src 0.022 0.11 -9999 0 -0.59 9 9
CTNNB1 0.001 0.09 -9999 0 -0.45 19 19
SOS1 0.017 0.023 -9999 0 -0.52 1 1
ARNT 0.018 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.041 0.12 -9999 0 -0.41 18 18
VEGFR2 homodimer/VEGFA homodimer/Yes 0.018 0.11 -9999 0 -0.55 12 12
PI3K/GAB1 0.028 0.16 -9999 0 -0.51 19 19
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.014 0.12 -9999 0 -0.5 12 12
PRKACA 0.018 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.025 0.11 -9999 0 -0.54 14 14
HSP90AA1 0.013 0.045 -9999 0 -0.39 6 6
CDC42 0.014 0.14 -9999 0 -0.6 16 16
actin cytoskeleton reorganization -0.007 0.13 -9999 0 -0.54 13 13
PTK2 0.026 0.14 -9999 0 -0.83 8 8
EDG1 -0.005 0.19 -9999 0 -0.66 31 31
mol:DAG 0.014 0.14 -9999 0 -0.58 17 17
CaM/Ca2+ 0.02 0.13 -9999 0 -0.53 17 17
MAP2K3 0.014 0.14 -9999 0 -0.55 19 19
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.01 0.18 -9999 0 -0.61 29 29
PLCG1 0.013 0.14 -9999 0 -0.59 17 17
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.027 0.11 -9999 0 -0.51 12 12
IQGAP1 0.018 0 -9999 0 -10000 0 0
YES1 0.007 0.07 -9999 0 -0.43 12 12
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.023 0.11 -9999 0 -0.58 10 10
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.022 0.11 -9999 0 -0.59 9 9
cell migration 0.055 0.12 -9999 0 -0.66 8 8
mol:PI-3-4-5-P3 0.022 0.15 -9999 0 -0.53 22 22
FYN 0.009 0.063 -9999 0 -0.4 11 11
VEGFB/NRP1 0.013 0.14 -9999 0 -0.56 16 16
mol:NO 0.042 0.11 -9999 0 -0.4 16 16
PXN 0.018 0 -9999 0 -10000 0 0
HRAS/GTP -0.036 0.099 -9999 0 -0.51 15 15
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.008 0.17 -9999 0 -0.61 29 29
VHL 0.014 0.031 -9999 0 -0.26 7 7
ITGB3 0.002 0.076 -9999 0 -0.32 25 25
NOS3 0.041 0.12 -9999 0 -0.45 16 16
VEGFR2 homodimer/VEGFA homodimer/Sck -0.021 0.15 -9999 0 -0.49 22 22
RAC1 0.018 0 -9999 0 -10000 0 0
PRKCA 0.018 0.14 -9999 0 -0.55 16 16
PRKCB 0.012 0.13 -9999 0 -0.54 17 17
VCL 0.016 0.029 -9999 0 -0.35 3 3
VEGFA165/NRP1 0.008 0.14 -9999 0 -0.59 16 16
VEGFR1/2 heterodimer/VEGFA homodimer 0.017 0.12 -9999 0 -0.59 12 12
VEGFA165/NRP2 0.009 0.065 -9999 0 -0.37 8 8
MAPKKK cascade 0.03 0.15 -9999 0 -0.5 29 29
NRP2 0.01 0.052 -9999 0 -0.33 11 11
VEGFC homodimer 0 0.092 -9999 0 -0.46 19 19
NCK1 0.011 0.046 -9999 0 -0.28 12 12
ROCK1 0.018 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.035 0.13 -9999 0 -0.75 8 8
MAP3K13 0.009 0.15 -9999 0 -0.58 19 19
PDPK1 0.027 0.14 -9999 0 -0.47 22 22
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.008 0.14 -9999 0 -0.7 12 12
VEGFR1 homodimer/NRP1 -0.02 0.14 -9999 0 -0.38 55 55
mol:DAG -0.003 0.13 -9999 0 -0.61 13 13
VEGFR1 homodimer/NRP1/VEGFR 121 -0.016 0.14 -9999 0 -0.64 13 13
CaM/Ca2+ 0.007 0.13 -9999 0 -0.63 11 11
HIF1A -0.034 0.17 -9999 0 -0.47 66 66
GAB1 0.006 0.074 -9999 0 -0.43 14 14
AKT1 0.001 0.14 -9999 0 -0.54 18 18
PLCG1 -0.003 0.13 -9999 0 -0.62 13 13
NOS3 0.019 0.12 -9999 0 -0.56 12 12
CBL 0.017 0.012 -9999 0 -0.26 1 1
mol:NO 0.02 0.12 -9999 0 -0.53 12 12
FLT1 -0.019 0.16 -9999 0 -0.45 55 55
PGF 0.012 0.051 -9999 0 -0.41 7 7
VEGFR1 homodimer/NRP2/VEGFR121 -0.009 0.14 -9999 0 -0.67 13 13
CALM1 0.018 0 -9999 0 -10000 0 0
PIK3CA 0.016 0.029 -9999 0 -0.35 3 3
eNOS/Hsp90 0.027 0.12 -9999 0 -0.52 12 12
endothelial cell proliferation 0.002 0.13 -9999 0 -0.6 13 13
mol:Ca2+ -0.003 0.13 -9999 0 -0.61 13 13
MAPK3 0.008 0.12 -9999 0 -0.57 12 12
MAPK1 0.008 0.12 -9999 0 -0.58 11 11
PIK3R1 -0.009 0.11 -9999 0 -0.42 32 32
PLGF homodimer 0.012 0.051 -9999 0 -0.41 7 7
PRKACA 0.018 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 0 0.081 -9999 0 -0.32 28 28
VEGFA homodimer 0 0.076 -9999 0 -0.29 31 31
VEGFR1 homodimer/VEGFA homodimer -0.018 0.15 -9999 0 -0.69 13 13
platelet activating factor biosynthetic process 0.013 0.12 -9999 0 -0.57 11 11
PI3K -0.003 0.14 -9999 0 -0.61 15 15
PRKCA 0.002 0.12 -9999 0 -0.62 11 11
PRKCB -0.004 0.12 -9999 0 -0.57 13 13
VEGFR1 homodimer/PLGF homodimer -0.011 0.14 -9999 0 -0.7 12 12
VEGFA 0 0.076 -9999 0 -0.29 31 31
VEGFB 0.017 0.023 -9999 0 -0.52 1 1
mol:IP3 -0.003 0.13 -9999 0 -0.61 13 13
RASA1 -0.007 0.14 -9999 0 -0.63 14 14
NRP2 0.01 0.052 -9999 0 -0.33 11 11
VEGFR1 homodimer -0.019 0.16 -9999 0 -0.44 55 55
VEGFB homodimer 0.017 0.023 -9999 0 -0.52 1 1
NCK1 0.011 0.046 -9999 0 -0.28 12 12
eNOS/Caveolin-1 0.021 0.13 -9999 0 -0.56 13 13
PTPN11 0.017 0.023 -9999 0 -0.52 1 1
mol:PI-3-4-5-P3 -0.004 0.14 -9999 0 -0.6 15 15
mol:L-citrulline 0.02 0.12 -9999 0 -0.53 12 12
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.005 0.13 -9999 0 -0.62 12 12
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.008 0.14 -9999 0 -0.65 13 13
CD2AP 0.016 0.029 -9999 0 -0.35 3 3
PI3K/GAB1 0 0.14 -9999 0 -0.56 16 16
PDPK1 -0.002 0.13 -9999 0 -0.56 15 15
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.006 0.14 -9999 0 -0.63 13 13
mol:NADP 0.02 0.12 -9999 0 -0.53 12 12
HSP90AA1 0.013 0.045 -9999 0 -0.39 6 6
ubiquitin-dependent protein catabolic process 0.004 0.13 -9999 0 -0.62 12 12
VEGFR1 homodimer/NRP2 -0.012 0.15 -9999 0 -0.69 13 13
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.012 0.051 -9999 0 -0.31 12 12
ADCY5 -0.01 0.074 -9999 0 -0.32 14 14
ADCY6 0.015 0.04 -9999 0 -0.31 7 7
ADCY7 0.008 0.058 -9999 0 -0.32 13 13
ADCY1 0.015 0.036 -9999 0 -0.31 5 5
ADCY2 -0.029 0.11 -9999 0 -0.32 50 50
ADCY3 0.011 0.052 -9999 0 -0.31 12 12
ADCY8 0.012 0.044 -9999 0 -0.31 6 6
PRKCE 0.008 0.04 -9999 0 -0.3 8 8
ADCY9 0.002 0.075 -9999 0 -0.32 24 24
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.001 0.069 -9999 0 -0.31 11 11
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 0.015 0.037 -9999 0 -0.39 4 4
ITGB7 0.018 0 -9999 0 -10000 0 0
ITGA4 -0.007 0.1 -9999 0 -0.39 32 32
alpha4/beta7 Integrin 0.009 0.074 -9999 0 -0.37 16 16
alpha4/beta1 Integrin 0.007 0.083 -9999 0 -0.41 16 16
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.03 0.17 -10000 0 -0.44 13 13
CRKL 0.006 0.075 -10000 0 -0.33 6 6
mol:DAG 0.006 0.083 -10000 0 -0.28 4 4
HRAS 0.023 0.075 -10000 0 -0.56 1 1
MAPK8 0.009 0.059 -10000 0 -0.28 4 4
RAP1A 0.004 0.079 -10000 0 -0.34 9 9
GAB1 0.002 0.081 -10000 0 -0.34 7 7
MAPK14 0.011 0.054 -10000 0 -0.25 1 1
EPO -0.025 0.099 -10000 0 -0.26 80 80
PLCG1 0.005 0.084 -10000 0 -0.28 4 4
EPOR/TRPC2/IP3 Receptors 0.014 0.02 -10000 0 -0.27 2 2
RAPGEF1 0.018 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0 0.073 -10000 0 -0.33 9 9
GAB1/SHC/GRB2/SOS1 0.019 0.074 -10000 0 -0.43 2 2
EPO/EPOR (dimer) -0.005 0.071 -10000 0 -0.34 1 1
IRS2 -0.014 0.1 -10000 0 -0.34 24 24
STAT1 -0.027 0.14 -10000 0 -0.33 52 52
STAT5B -0.002 0.1 -10000 0 -0.32 3 3
cell proliferation 0.016 0.054 -10000 0 -0.26 4 4
GAB1/SHIP/PIK3R1/SHP2/SHC -0.031 0.067 -10000 0 -0.31 11 11
TEC 0.005 0.075 -10000 0 -0.31 6 6
SOCS3 0.005 0.074 -10000 0 -0.38 17 17
STAT1 (dimer) -0.026 0.14 -10000 0 -0.32 52 52
JAK2 0.008 0.055 -10000 0 -0.33 12 12
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
EPO/EPOR (dimer)/JAK2 0.015 0.083 -10000 0 -0.29 6 6
EPO/EPOR -0.005 0.071 -10000 0 -0.34 1 1
LYN 0.012 0.033 -10000 0 -0.27 7 7
TEC/VAV2 0.014 0.076 -10000 0 -0.31 5 5
elevation of cytosolic calcium ion concentration 0.014 0.02 -10000 0 -0.27 2 2
SHC1 0.017 0.023 -10000 0 -0.52 1 1
EPO/EPOR (dimer)/LYN 0.009 0.066 -10000 0 -0.29 1 1
mol:IP3 0.006 0.083 -10000 0 -0.28 4 4
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.017 0.11 -10000 0 -0.32 36 36
SH2B3 0.015 0.024 -10000 0 -0.52 1 1
NFKB1 0.01 0.056 -10000 0 -0.28 2 2
EPO/EPOR (dimer)/JAK2/SOCS3 -0.005 0.051 0.26 1 -0.23 11 12
PTPN6 0 0.073 -10000 0 -0.29 6 6
TEC/VAV2/GRB2 0.021 0.075 -10000 0 -0.33 3 3
EPOR 0.014 0.02 -10000 0 -0.27 2 2
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.075 -10000 0 -0.44 2 2
SOS1 0.017 0.023 -10000 0 -0.52 1 1
PLCG2 -0.017 0.11 -10000 0 -0.32 55 55
CRKL/CBL/C3G 0.023 0.073 -10000 0 -0.36 3 3
VAV2 0.007 0.071 -10000 0 -0.31 4 4
CBL 0.007 0.07 -10000 0 -0.31 4 4
SHC/Grb2/SOS1 -0.021 0.044 -10000 0 -0.33 2 2
STAT5A -0.005 0.11 -10000 0 -0.36 5 5
GRB2 0.016 0.024 -10000 0 -0.26 4 4
STAT5 (dimer) -0.013 0.15 -10000 0 -0.36 38 38
LYN/PLCgamma2 -0.002 0.081 -10000 0 -0.36 15 15
PTPN11 0.017 0.023 -10000 0 -0.52 1 1
BTK -0.005 0.092 -10000 0 -0.31 22 22
BCL2 -0.15 0.38 -10000 0 -0.86 117 117
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.01 0.08 0.28 22 -10000 0 22
GNAI2 0.006 0.075 -10000 0 -0.48 12 12
S1P/S1P5/G12 0.012 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.016 0.024 -10000 0 -0.26 4 4
RhoA/GTP 0.01 0.082 -10000 0 -0.28 22 22
negative regulation of cAMP metabolic process 0.008 0.075 -10000 0 -0.23 40 40
GNAZ 0.002 0.085 -10000 0 -0.43 18 18
GNAI3 0.017 0.023 -10000 0 -0.52 1 1
GNA12 0.018 0 -10000 0 -10000 0 0
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.008 0.075 -10000 0 -0.23 40 40
RhoA/GDP 0.004 0.058 -10000 0 -0.38 12 12
RHOA 0.005 0.08 -10000 0 -0.52 12 12
GNAI1 -0.015 0.12 -10000 0 -0.38 44 44
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.041 0.037 -10000 0 -0.27 7 7
HDAC3 0.018 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.001 0.011 -10000 0 -0.22 1 1
GATA1/HDAC4 0.026 0.017 -10000 0 -0.37 1 1
GATA1/HDAC5 0.026 0.017 -10000 0 -0.37 1 1
GATA2/HDAC5 0.008 0.068 -10000 0 -0.37 10 10
HDAC5/BCL6/BCoR 0.016 0.078 -10000 0 -0.3 28 28
HDAC9 0.011 0.046 -10000 0 -0.28 12 12
Glucocorticoid receptor/Hsp90/HDAC6 0.02 0.071 -10000 0 -0.3 23 23
HDAC4/ANKRA2 0.013 0.072 -10000 0 -0.37 18 18
HDAC5/YWHAB 0.023 0.032 -10000 0 -0.37 3 3
NPC/RanGAP1/SUMO1/Ubc9 0.023 0.014 -10000 0 -0.2 1 1
GATA2 -0.008 0.094 -10000 0 -0.32 40 40
HDAC4/RFXANK 0.025 0.019 -10000 0 -0.37 1 1
BCOR 0.009 0.07 -10000 0 -0.52 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.015 0.037 -10000 0 -0.39 4 4
HDAC5 0.017 0.023 -10000 0 -0.52 1 1
GNB1/GNG2 0.021 0.043 -10000 0 -0.37 6 6
Histones 0.02 0.07 -10000 0 -0.25 29 29
ADRBK1 0.018 0 -10000 0 -10000 0 0
HDAC4 0.017 0.023 -10000 0 -0.52 1 1
XPO1 0.018 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.013 0.072 -10000 0 -0.37 18 18
HDAC4/Ubc9 0.026 0.017 -10000 0 -0.37 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.024 0.027 -10000 0 -0.37 2 2
TUBA1B 0.018 0 -10000 0 -10000 0 0
HDAC6 0.018 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.025 0.019 -10000 0 -0.37 1 1
CAMK4 0.011 0.047 -10000 0 -0.31 10 10
Tubulin/HDAC6 0.022 0.063 -10000 0 -0.3 17 17
SUMO1 0.018 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.015 0.037 -10000 0 -0.39 4 4
GATA1 0.018 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.016 0.029 -10000 0 -0.35 3 3
NR3C1 -0.003 0.1 -10000 0 -0.51 21 21
SUMO1/HDAC4 0.036 0.02 -10000 0 -0.31 1 1
SRF 0.016 0.024 -10000 0 -0.26 4 4
HDAC4/YWHAB 0.023 0.032 -10000 0 -0.37 3 3
Tubulin 0.01 0.073 -10000 0 -0.37 17 17
HDAC4/14-3-3 E 0.024 0.03 -10000 0 -0.44 2 2
GNB1 0.013 0.052 -10000 0 -0.52 5 5
RANGAP1 0.014 0.037 -10000 0 -0.3 7 7
BCL6/BCoR 0.004 0.089 -10000 0 -0.37 27 27
HDAC4/HDAC3/SMRT (N-CoR2) 0.035 0.015 -10000 0 -0.3 1 1
HDAC4/SRF 0.031 0.035 -10000 0 -0.3 3 3
HDAC4/ER alpha -0.1 0.18 -10000 0 -0.37 150 150
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.02 0.069 -10000 0 -0.25 29 29
cell motility 0.022 0.063 -10000 0 -0.3 17 17
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.018 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0.013 0 -10000 0 -10000 0 0
BCL6 -0.004 0.1 -10000 0 -0.46 24 24
HDAC4/CaMK II delta B 0.017 0.023 -10000 0 -0.52 1 1
Hsp90/HDAC6 0.023 0.033 -10000 0 -0.37 3 3
ESR1 -0.16 0.24 -10000 0 -0.45 202 202
HDAC6/HDAC11 0.004 0.089 -10000 0 -0.37 28 28
Ran/GTP/Exportin 1 0.039 0.014 -10000 0 -10000 0 0
NPC 0.01 0.008 -10000 0 -10000 0 0
MEF2C -0.013 0.12 -10000 0 -0.45 35 35
RAN 0.017 0.012 -10000 0 -0.26 1 1
HDAC4/MEF2C 0.035 0.067 -10000 0 -0.24 27 27
GNG2 0.016 0.029 -10000 0 -0.35 3 3
NCOR2 0.018 0 -10000 0 -10000 0 0
TUBB2A -0.004 0.1 -10000 0 -0.43 26 26
HDAC11 -0.012 0.12 -10000 0 -0.5 31 31
HSP90AA1 0.013 0.045 -10000 0 -0.39 6 6
RANBP2 0.017 0.017 -10000 0 -0.26 2 2
ANKRA2 0 0.095 -10000 0 -0.52 17 17
RFXANK 0.017 0.012 -10000 0 -0.26 1 1
nuclear import -0.032 0.035 0.31 5 -10000 0 5
Paxillin-dependent events mediated by a4b1

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
CRKL 0.014 0.047 -10000 0 -0.52 4 4
Rac1/GDP 0.003 0.012 -10000 0 -10000 0 0
DOCK1 0.006 0.078 -10000 0 -0.5 12 12
ITGA4 -0.007 0.1 -10000 0 -0.39 32 32
RAC1 0.018 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.009 0.074 -10000 0 -0.37 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0.033 -10000 0 -0.52 2 2
alpha4/beta1 Integrin 0.019 0.072 -10000 0 -0.34 16 16
alpha4/beta7 Integrin/Paxillin 0.028 0.058 -10000 0 -0.27 16 16
lamellipodium assembly 0.028 0.091 -10000 0 -0.35 22 22
PIK3CA 0.016 0.029 -10000 0 -0.35 3 3
PI3K 0.006 0.082 -10000 0 -0.37 21 21
ARF6 0.016 0.033 -10000 0 -0.52 2 2
TLN1 0.017 0.023 -10000 0 -0.52 1 1
PXN 0.025 0 -10000 0 -10000 0 0
PIK3R1 -0.009 0.11 -10000 0 -0.42 32 32
ARF6/GTP 0.031 0.06 -10000 0 -0.24 19 19
cell adhesion 0.034 0.063 -10000 0 -0.27 17 17
CRKL/CBL 0.023 0.035 -10000 0 -0.37 4 4
alpha4/beta1 Integrin/Paxillin 0.026 0.066 -10000 0 -0.3 16 16
ITGB1 0.015 0.037 -10000 0 -0.39 4 4
ITGB7 0.018 0 -10000 0 -10000 0 0
ARF6/GDP 0.001 0.034 -10000 0 -0.51 2 2
alpha4/beta1 Integrin/Paxillin/VCAM1 0.016 0.1 -10000 0 -0.29 39 39
p130Cas/Crk/Dock1 0.027 0.054 -10000 0 -0.3 13 13
VCAM1 -0.021 0.13 -10000 0 -0.42 47 47
alpha4/beta1 Integrin/Paxillin/Talin 0.036 0.064 -10000 0 -0.28 17 17
alpha4/beta1 Integrin/Paxillin/GIT1 0.034 0.065 -10000 0 -0.28 17 17
BCAR1 0.017 0.012 -10000 0 -0.26 1 1
mol:GDP -0.033 0.064 0.27 17 -10000 0 17
CBL 0.017 0.012 -10000 0 -0.26 1 1
PRKACA 0.018 0 -10000 0 -10000 0 0
GIT1 0.014 0.035 -10000 0 -0.3 6 6
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.036 0.064 -10000 0 -0.28 17 17
Rac1/GTP -0.019 0.087 -10000 0 -0.38 22 22
Aurora C signaling

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
INCENP 0.001 0.084 -9999 0 -0.37 23 23
Aurora C/Aurora B/INCENP 0.015 0.063 -9999 0 -0.28 15 15
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.007 0.037 -9999 0 -0.52 2 2
AURKB 0.009 0.056 -9999 0 -0.31 14 14
AURKC 0.008 0.054 -9999 0 -0.27 18 18
FoxO family signaling

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
G6PC 0.04 0.081 -9999 0 -1.3 1 1
PLK1 0.029 0.18 -9999 0 -0.68 9 9
CDKN1B 0.062 0.18 -9999 0 -0.48 31 31
FOXO3 0.021 0.19 -9999 0 -0.57 21 21
KAT2B 0.003 0.021 -9999 0 -0.048 24 24
FOXO1/SIRT1 0.036 0.066 -9999 0 -0.37 5 5
CAT 0.023 0.2 -9999 0 -0.86 12 12
CTNNB1 0.001 0.09 -9999 0 -0.45 19 19
AKT1 0.019 0.057 -9999 0 -0.36 9 9
FOXO1 0.036 0.067 -9999 0 -0.3 12 12
MAPK10 0.014 0.074 -9999 0 -0.25 28 28
mol:GTP 0.001 0.003 -9999 0 -10000 0 0
FOXO4 0.06 0.1 -9999 0 -0.38 6 6
response to oxidative stress 0.008 0.022 -9999 0 -0.049 23 23
FOXO3A/SIRT1 0.034 0.16 -9999 0 -0.49 19 19
XPO1 0.018 0.001 -9999 0 -10000 0 0
EP300 0.017 0.047 -9999 0 -0.52 4 4
BCL2L11 0.027 0.038 -9999 0 -10000 0 0
FOXO1/SKP2 0.035 0.071 -9999 0 -0.42 5 5
mol:GDP 0.008 0.022 -9999 0 -0.049 23 23
RAN 0.018 0.012 -9999 0 -0.26 1 1
GADD45A 0.037 0.22 -9999 0 -0.9 21 21
YWHAQ 0.014 0.039 -9999 0 -0.36 5 5
FOXO1/14-3-3 family 0.066 0.061 -9999 0 -0.34 2 2
MST1 0.02 0.031 -9999 0 -0.3 3 3
CSNK1D 0.018 0 -9999 0 -10000 0 0
CSNK1E 0.017 0.012 -9999 0 -0.26 1 1
FOXO4/14-3-3 family 0.04 0.081 -9999 0 -0.42 2 2
YWHAB 0.015 0.037 -9999 0 -0.39 4 4
MAPK8 0.034 0.038 -9999 0 -0.26 7 7
MAPK9 0.023 0.067 -9999 0 -0.25 27 27
YWHAG 0.017 0.017 -9999 0 -0.26 2 2
YWHAE 0.016 0.029 -9999 0 -0.35 3 3
YWHAZ 0.017 0.017 -9999 0 -0.26 2 2
SIRT1 0.018 0.035 -9999 0 -0.35 3 3
SOD2 0.065 0.17 -9999 0 -0.58 12 12
RBL2 0.045 0.16 -9999 0 -0.82 6 6
RAL/GDP 0.031 0.034 -9999 0 -0.31 4 4
CHUK 0.008 0.083 -9999 0 -0.5 13 13
Ran/GTP 0.016 0.009 -9999 0 -0.17 1 1
CSNK1G2 0.016 0.033 -9999 0 -0.52 2 2
RAL/GTP 0.036 0.035 -9999 0 -0.28 4 4
CSNK1G1 0.017 0.012 -9999 0 -0.26 1 1
FASLG -0.12 0.41 -9999 0 -1.4 49 49
SKP2 0.007 0.053 -9999 0 -0.26 20 20
USP7 0.018 0.013 -9999 0 -0.27 1 1
IKBKB 0.015 0.051 -9999 0 -0.31 10 10
CCNB1 -0.021 0.32 -9999 0 -1.1 38 38
FOXO1-3a-4/beta catenin 0.067 0.17 -9999 0 -0.41 23 23
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.07 -9999 0 -0.42 5 5
CSNK1A1 0.017 0.023 -9999 0 -0.52 1 1
SGK1 0.003 0.021 -9999 0 -0.048 24 24
CSNK1G3 0.013 0.052 -9999 0 -0.52 5 5
Ran/GTP/Exportin 1 0.028 0.011 -9999 0 -10000 0 0
ZFAND5 0.066 0.09 -9999 0 -10000 0 0
SFN -0.015 0.12 -9999 0 -0.45 37 37
CDK2 0.015 0.047 -9999 0 -0.31 10 10
FOXO3A/14-3-3 0.043 0.08 -9999 0 -0.35 7 7
CREBBP 0.019 0.033 -9999 0 -0.52 2 2
FBXO32 -0.01 0.3 -9999 0 -1.2 25 25
BCL6 0.015 0.26 -9999 0 -1.1 21 21
RALB 0.015 0.047 -9999 0 -0.52 4 4
RALA 0.019 0.002 -9999 0 -10000 0 0
YWHAH 0.013 0.048 -9999 0 -0.47 5 5
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.016 0.024 -9999 0 -0.26 4 4
CDC42/GTP 0.017 0.069 -9999 0 -0.28 12 12
PLCG1 0.014 0.072 -9999 0 -0.29 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.006 0.075 -9999 0 -0.48 12 12
GNAI3 0.017 0.023 -9999 0 -0.52 1 1
G12/G13 0.02 0.043 -9999 0 -0.37 5 5
cell migration 0.016 0.068 -9999 0 -0.28 12 12
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 0.014 0.072 -9999 0 -0.29 13 13
MAPK1 0.014 0.073 -9999 0 -0.28 14 14
S1P/S1P5/Gi 0.008 0.075 -9999 0 -0.23 40 40
GNAI1 -0.015 0.12 -9999 0 -0.38 44 44
CDC42/GDP 0.013 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0.012 0 -9999 0 -10000 0 0
RHOA 0.016 0.057 -9999 0 -0.3 15 15
S1P/S1P4/Gi 0.008 0.075 -9999 0 -0.23 40 40
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.002 0.085 -9999 0 -0.43 18 18
S1P/S1P4/G12/G13 0.018 0.033 -9999 0 -0.28 5 5
GNA12 0.018 0 -9999 0 -10000 0 0
GNA13 0.009 0.059 -9999 0 -0.38 11 11
CDC42 0.018 0 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.01 0.068 0.39 10 -10000 0 10
KIRREL 0.009 0.071 -10000 0 -0.53 9 9
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.01 0.068 -10000 0 -0.39 10 10
PLCG1 0.016 0.026 -10000 0 -0.39 2 2
ARRB2 0.018 0 -10000 0 -10000 0 0
WASL 0.01 0.066 -10000 0 -0.52 8 8
Nephrin/NEPH1/podocin/CD2AP 0.029 0.058 -10000 0 -0.28 13 13
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.025 0.06 -10000 0 -0.29 5 5
FYN 0.015 0.057 -10000 0 -0.26 17 17
mol:Ca2+ 0.028 0.059 -10000 0 -0.3 12 12
mol:DAG 0.028 0.059 -10000 0 -0.3 12 12
NPHS2 0.015 0.036 -10000 0 -0.43 3 3
mol:IP3 0.028 0.059 -10000 0 -0.3 12 12
regulation of endocytosis 0.028 0.056 -10000 0 -0.26 12 12
Nephrin/NEPH1/podocin/Cholesterol 0.019 0.054 -10000 0 -0.28 12 12
establishment of cell polarity 0.01 0.068 -10000 0 -0.39 10 10
Nephrin/NEPH1/podocin/NCK1-2 0.035 0.059 -10000 0 -0.25 13 13
Nephrin/NEPH1/beta Arrestin2 0.03 0.057 -10000 0 -0.26 12 12
NPHS1 0.004 0.062 -10000 0 -0.27 25 25
Nephrin/NEPH1/podocin 0.021 0.059 -10000 0 -0.26 17 17
TJP1 0.013 0.052 -10000 0 -0.52 5 5
NCK1 0.011 0.046 -10000 0 -0.28 12 12
NCK2 0.015 0.027 -10000 0 -0.26 5 5
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.029 0.06 -10000 0 -0.3 12 12
CD2AP 0.016 0.029 -10000 0 -0.35 3 3
Nephrin/NEPH1/podocin/GRB2 0.029 0.056 -10000 0 -0.27 12 12
GRB2 0.016 0.024 -10000 0 -0.26 4 4
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.012 0.067 -10000 0 -0.27 23 23
cytoskeleton organization 0.03 0.062 -10000 0 -0.31 5 5
Nephrin/NEPH1 0.011 0.048 -10000 0 -0.28 10 10
Nephrin/NEPH1/ZO-1 0.019 0.064 -10000 0 -0.31 15 15
Canonical NF-kappaB 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
FBXW11 0.018 0.036 -9999 0 -0.43 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.06 0.078 -9999 0 -0.32 7 7
ERC1 0.011 0.056 -9999 0 -0.42 8 8
RIP2/NOD2 -0.031 0.13 -9999 0 -0.37 66 66
NFKBIA 0.042 0.051 -9999 0 -0.4 6 6
BIRC2 0.016 0.021 -9999 0 -0.26 3 3
IKBKB 0.011 0.047 -9999 0 -0.31 10 10
RIPK2 0.013 0.041 -9999 0 -0.29 9 9
IKBKG 0.016 0.091 -9999 0 -0.51 5 5
IKK complex/A20 0.026 0.1 -9999 0 -0.44 9 9
NEMO/A20/RIP2 0.012 0.041 -9999 0 -0.29 9 9
XPO1 0.018 0 -9999 0 -10000 0 0
NEMO/ATM 0.024 0.088 -9999 0 -0.48 5 5
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.017 0.012 -9999 0 -0.26 1 1
Exportin 1/RanGTP 0.024 0.007 -9999 0 -10000 0 0
IKK complex/ELKS -0.028 0.077 -9999 0 -0.46 8 8
BCL10/MALT1/TRAF6 0.031 0.041 -9999 0 -0.38 4 4
NOD2 -0.056 0.18 -9999 0 -0.47 81 81
NFKB1 0.019 0.025 -9999 0 -0.52 1 1
RELA 0.02 0.009 -9999 0 -10000 0 0
MALT1 0.011 0.054 -9999 0 -0.38 9 9
cIAP1/UbcH5C 0.025 0.014 -9999 0 -10000 0 0
ATM 0.017 0.012 -9999 0 -0.26 1 1
TNF/TNFR1A 0.009 0.071 -9999 0 -0.37 14 14
TRAF6 0.017 0.023 -9999 0 -0.52 1 1
PRKCA 0.014 0.034 -9999 0 -0.26 8 8
CHUK 0.005 0.081 -9999 0 -0.5 13 13
UBE2D3 0.018 0 -9999 0 -10000 0 0
TNF -0.004 0.094 -9999 0 -0.36 31 31
NF kappa B1 p50/RelA 0.045 0.036 -9999 0 -0.28 6 6
BCL10 0.017 0.012 -9999 0 -0.26 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.051 -9999 0 -0.4 6 6
beta TrCP1/SCF ubiquitin ligase complex 0.018 0.036 -9999 0 -0.43 3 3
TNFRSF1A 0.016 0.033 -9999 0 -0.52 2 2
IKK complex 0.025 0.1 -9999 0 -0.46 9 9
CYLD 0.014 0.044 -9999 0 -0.42 5 5
IKK complex/PKC alpha 0.03 0.1 -9999 0 -0.49 7 7
Circadian rhythm 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
chromatin modification 0.017 0.1 -10000 0 -1.3 1 1
CLOCK 0.02 0.024 -10000 0 -0.52 1 1
TIMELESS/CRY2 0.041 0.06 -10000 0 -1.2 1 1
DEC1/BMAL1 0.015 0.072 -10000 0 -0.39 15 15
ATR 0.017 0.012 -10000 0 -0.26 1 1
NR1D1 0.036 0.045 -10000 0 -10000 0 0
ARNTL 0.009 0.078 -10000 0 -0.49 12 12
TIMELESS 0.036 0.065 -10000 0 -1.3 1 1
NPAS2 -0.003 0.093 -10000 0 -0.32 37 37
CRY2 0.017 0.012 -10000 0 -0.26 1 1
mol:CO -0.014 0.012 0.14 1 -10000 0 1
CHEK1 -0.045 0.15 -10000 0 -0.38 83 83
mol:HEME 0.014 0.012 -10000 0 -0.14 1 1
PER1 0.014 0.037 -10000 0 -0.3 7 7
BMAL/CLOCK/NPAS2 0.03 0.082 -10000 0 -0.32 21 21
BMAL1/CLOCK 0.042 0.077 -10000 0 -0.44 5 5
S phase of mitotic cell cycle 0.017 0.1 -10000 0 -1.3 1 1
TIMELESS/CHEK1/ATR 0.018 0.1 -10000 0 -1.4 1 1
mol:NADPH 0.014 0.012 -10000 0 -0.14 1 1
PER1/TIMELESS 0.039 0.063 -10000 0 -1.2 1 1
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.011 0.057 -10000 0 -0.4 9 9
Alternative 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
IKK alpha homodimer 0.015 0.065 -9999 0 -0.37 14 14
FBXW11 0.015 0.035 -9999 0 -0.43 3 3
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0.035 -9999 0 -0.43 3 3
CHUK 0.005 0.081 -9999 0 -0.5 13 13
NF kappa B2 p100/RelB 0.034 0.074 -9999 0 -0.28 24 24
NFKB1 0.017 0.023 -9999 0 -0.52 1 1
MAP3K14 0.015 0.037 -9999 0 -0.39 4 4
NF kappa B1 p50/RelB 0.015 0.059 -9999 0 -0.37 10 10
RELB 0.003 0.079 -9999 0 -0.38 19 19
NFKB2 0.015 0.031 -9999 0 -0.32 4 4
NF kappa B2 p52/RelB 0.014 0.052 -9999 0 -0.31 11 11
regulation of B cell activation 0.014 0.052 -9999 0 -0.31 11 11
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.009 0.067 -10000 0 -0.49 9 9
SMAD2 0.021 0.048 0.24 1 -0.23 9 10
SMAD3 0.032 0.056 -10000 0 -0.39 2 2
SMAD3/SMAD4 0.032 0.071 -10000 0 -0.34 11 11
SMAD4/Ubc9/PIASy 0.027 0.052 -10000 0 -0.3 12 12
SMAD2/SMAD2/SMAD4 0.03 0.062 -10000 0 -0.27 1 1
PPM1A 0.016 0.026 -10000 0 -0.39 2 2
CALM1 0.018 0 -10000 0 -10000 0 0
SMAD2/SMAD4 0.024 0.056 0.2 1 -0.23 17 18
MAP3K1 -0.031 0.14 -10000 0 -0.43 58 58
TRAP-1/SMAD4 0.02 0.05 -10000 0 -0.37 8 8
MAPK3 0.016 0.026 -10000 0 -0.39 2 2
MAPK1 0.016 0.033 -10000 0 -0.52 2 2
NUP214 0.016 0.026 -10000 0 -0.39 2 2
CTDSP1 0.016 0.033 -10000 0 -0.52 2 2
CTDSP2 0.014 0.044 -10000 0 -0.42 5 5
CTDSPL 0.011 0.062 -10000 0 -0.52 7 7
KPNB1 0.013 0.052 -10000 0 -0.52 5 5
TGFBRAP1 0.017 0.012 -10000 0 -0.26 1 1
UBE2I 0.018 0 -10000 0 -10000 0 0
NUP153 0.016 0.024 -10000 0 -0.26 4 4
KPNA2 -0.002 0.088 -10000 0 -0.35 28 28
PIAS4 0.013 0.05 -10000 0 -0.43 6 6
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.015 0.047 -9999 0 -0.31 8 8
EFNA5 0.006 0.069 -9999 0 -0.35 17 17
FYN 0.016 0.054 -9999 0 -0.28 14 14
neuron projection morphogenesis 0.015 0.047 -9999 0 -0.31 8 8
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0.015 0.047 -9999 0 -0.31 8 8
EPHA5 0.015 0.037 -9999 0 -0.39 4 4
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.025 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.04 0.016 -10000 0 -0.27 1 1
CDKN1B 0.021 0.079 -10000 0 -0.37 8 8
CDKN1A 0.026 0.071 -10000 0 -0.44 6 6
FRAP1 0.018 0 -10000 0 -10000 0 0
PRKDC 0.012 0.046 -10000 0 -0.32 9 9
FOXO3 0.033 0.062 -10000 0 -0.46 6 6
AKT1 0.03 0.054 -10000 0 -0.43 6 6
BAD 0.017 0.023 -10000 0 -0.52 1 1
AKT3 0.008 0.044 -10000 0 -0.32 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.035 0.053 -10000 0 -0.39 7 7
AKT1/ASK1 0.018 0.081 -10000 0 -0.36 10 10
BAD/YWHAZ 0.035 0.018 -10000 0 -0.3 1 1
RICTOR 0.018 0 -10000 0 -10000 0 0
RAF1 0.017 0.012 -10000 0 -0.26 1 1
JNK cascade -0.017 0.078 0.35 10 -10000 0 10
TSC1 0.036 0.051 -10000 0 -0.4 6 6
YWHAZ 0.017 0.017 -10000 0 -0.26 2 2
AKT1/RAF1 0.038 0.052 -10000 0 -0.4 6 6
EP300 0.014 0.047 -10000 0 -0.52 4 4
mol:GDP 0.03 0.053 -10000 0 -0.42 6 6
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.035 0.056 -10000 0 -0.44 6 6
YWHAQ 0.014 0.039 -10000 0 -0.36 5 5
TBC1D4 0.011 0.064 -10000 0 -0.3 19 19
MAP3K5 -0.021 0.13 -10000 0 -0.42 46 46
MAPKAP1 0.016 0.026 -10000 0 -0.39 2 2
negative regulation of cell cycle -0.034 0.049 0.24 3 -10000 0 3
YWHAH 0.013 0.048 -10000 0 -0.47 5 5
AKT1S1 0.032 0.063 -10000 0 -0.4 9 9
CASP9 0.035 0.053 -10000 0 -0.39 7 7
YWHAB 0.015 0.037 -10000 0 -0.39 4 4
p27Kip1/KPNA1 0.03 0.076 -10000 0 -0.36 7 7
GBL 0.015 0.035 -10000 0 -0.43 3 3
PDK1/Src/Hsp90 0.031 0.039 -10000 0 -0.3 6 6
YWHAE 0.016 0.029 -10000 0 -0.35 3 3
SRC 0.015 0.035 -10000 0 -0.43 3 3
AKT2/p21CIP1 0.03 0.067 -10000 0 -0.39 6 6
KIAA1303 0.015 0.031 -10000 0 -0.32 4 4
mTOR/RHEB/GTP/Raptor/GBL 0.038 0.041 -10000 0 -0.39 4 4
CHUK 0.03 0.068 -10000 0 -0.42 7 7
BAD/BCL-XL 0.053 0.051 -10000 0 -0.37 6 6
mTORC2 0.043 0.025 -10000 0 -0.27 3 3
AKT2 0.019 0.017 -10000 0 -0.32 1 1
FOXO1-3a-4/14-3-3 family 0.046 0.064 -10000 0 -0.28 5 5
PDPK1 0.016 0.026 -10000 0 -0.39 2 2
MDM2 0.033 0.054 -10000 0 -0.4 6 6
MAPKKK cascade -0.038 0.051 0.39 6 -10000 0 6
MDM2/Cbp/p300 0.047 0.061 -10000 0 -0.4 6 6
TSC1/TSC2 0.041 0.055 -10000 0 -0.42 6 6
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.058 -10000 0 -0.38 6 6
glucose import 0.011 0.064 -10000 0 -0.26 21 21
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.044 0.053 -10000 0 -0.38 5 5
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.011 0.064 -10000 0 -0.26 21 21
GSK3A 0.036 0.051 -10000 0 -0.4 6 6
FOXO1 0.028 0.067 -10000 0 -0.39 7 7
GSK3B 0.036 0.051 -10000 0 -0.4 6 6
SFN -0.015 0.12 -10000 0 -0.45 37 37
G1/S transition of mitotic cell cycle 0.042 0.05 -10000 0 -0.38 6 6
p27Kip1/14-3-3 family 0.034 0.063 -10000 0 -0.37 4 4
PRKACA 0.018 0 -10000 0 -10000 0 0
KPNA1 0.018 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0.045 -10000 0 -0.39 6 6
YWHAG 0.017 0.017 -10000 0 -0.26 2 2
RHEB 0.016 0.026 -10000 0 -0.39 2 2
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
Arf6 trafficking events

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
SLC2A4 0.005 0.061 -10000 0 -0.27 24 24
CLTC 0.024 0.05 -10000 0 -0.42 4 4
calcium ion-dependent exocytosis 0.022 0.039 -10000 0 -0.28 4 4
Dynamin 2/GTP 0.025 0.028 -10000 0 -0.28 2 2
EXOC4 0.016 0.033 -10000 0 -0.52 2 2
CD59 0.021 0.05 -10000 0 -0.42 4 4
CPE -0.021 0.11 -10000 0 -0.32 53 53
CTNNB1 0.001 0.09 -10000 0 -0.45 19 19
membrane fusion 0.021 0.04 -10000 0 -0.29 4 4
CTNND1 0.029 0.029 -10000 0 -0.25 3 3
DNM2 0.017 0.012 -10000 0 -0.26 1 1
mol:PI-4-5-P2 0.028 0.039 -10000 0 -0.28 6 6
TSHR 0.014 0.048 -10000 0 -0.31 11 11
INS 0.02 0.026 -10000 0 -0.51 1 1
BIN1 0.014 0.041 -10000 0 -0.35 6 6
mol:Choline 0.021 0.04 -10000 0 -0.29 4 4
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.03 -10000 0 -0.31 2 2
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.016 0.033 -10000 0 -0.52 2 2
mol:Ca2+ 0.025 0.028 -10000 0 -0.27 2 2
JUP 0.023 0.046 -10000 0 -0.42 4 4
ASAP2/amphiphysin II 0.019 0.029 -10000 0 -0.28 4 4
ARF6/GTP 0.012 0.024 -10000 0 -0.38 2 2
CDH1 0 0.078 -10000 0 -0.46 3 3
clathrin-independent pinocytosis 0.012 0.024 -10000 0 -0.38 2 2
MAPK8IP3 0.006 0.075 -10000 0 -0.48 12 12
positive regulation of endocytosis 0.012 0.024 -10000 0 -0.38 2 2
EXOC2 -0.004 0.086 -10000 0 -0.31 35 35
substrate adhesion-dependent cell spreading 0.022 0.078 -10000 0 -0.24 38 38
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.014 0.035 -10000 0 -0.3 6 6
regulation of calcium-dependent cell-cell adhesion -0.011 0.077 0.44 4 -10000 0 4
positive regulation of phagocytosis 0.018 0.032 -10000 0 -0.31 5 5
ARF6/GTP/JIP3 0.016 0.051 -10000 0 -0.31 12 12
ACAP1 0.019 0.034 -10000 0 -0.26 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.016 0.046 -10000 0 -0.52 2 2
clathrin heavy chain/ACAP1 0.028 0.048 -10000 0 -0.46 3 3
JIP4/KLC1 0.031 0.027 -10000 0 -0.28 3 3
EXOC1 0.018 0 -10000 0 -10000 0 0
exocyst 0.022 0.079 -10000 0 -0.25 38 38
RALA/GTP 0.013 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.021 0.029 -10000 0 -0.31 3 3
receptor recycling 0.012 0.024 -10000 0 -0.38 2 2
CTNNA1 0.03 0.028 -10000 0 -0.25 3 3
NME1 0.017 0.03 -10000 0 -0.31 2 2
clathrin coat assembly 0.024 0.05 -10000 0 -0.41 4 4
IL2RA 0.008 0.069 -10000 0 -0.33 8 8
VAMP3 0.018 0.032 -10000 0 -0.31 5 5
GLUT4/clathrin heavy chain/ACAP1 -0.008 0.04 -10000 0 -0.43 3 3
EXOC6 -0.013 0.12 -10000 0 -0.5 31 31
PLD1 0.016 0.049 -10000 0 -0.3 10 10
PLD2 0.021 0.033 -10000 0 -0.26 6 6
EXOC5 0.016 0.033 -10000 0 -0.52 2 2
PIP5K1C 0.028 0.039 -10000 0 -0.29 6 6
SDC1 0.005 0.071 -10000 0 -0.36 5 5
ARF6/GDP 0.018 0.03 -10000 0 -0.31 2 2
EXOC7 0.018 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.013 0.08 -10000 0 -0.46 4 4
mol:Phosphatidic acid 0.021 0.04 -10000 0 -0.29 4 4
endocytosis -0.019 0.029 0.28 4 -10000 0 4
SCAMP2 0.015 0.035 -10000 0 -0.43 3 3
ADRB2 0.001 0.096 -10000 0 -0.39 11 11
EXOC3 0.017 0.012 -10000 0 -0.26 1 1
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.027 0.028 -10000 0 -0.27 2 2
KLC1 0.018 0 -10000 0 -10000 0 0
AVPR2 0.03 0.049 -10000 0 -0.45 3 3
RALA 0.018 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.019 0.06 -10000 0 -0.58 2 2
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.038 0.061 -9999 0 -0.39 3 3
CaM/Ca2+ 0.013 0 -9999 0 -10000 0 0
AKT1 0.011 0.054 -9999 0 -0.38 9 9
AKT2 0.017 0.012 -9999 0 -0.26 1 1
STXBP4 0.008 0.061 -9999 0 -0.33 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose 0.033 0.054 -9999 0 -0.29 2 2
YWHAZ 0.017 0.017 -9999 0 -0.26 2 2
CALM1 0.018 0 -9999 0 -10000 0 0
YWHAQ 0.014 0.039 -9999 0 -0.36 5 5
TBC1D4 0.004 0.086 -9999 0 -0.38 21 21
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.013 0.048 -9999 0 -0.47 5 5
YWHAB 0.015 0.037 -9999 0 -0.39 4 4
SNARE/Synip 0.029 0.042 -9999 0 -0.3 6 6
YWHAG 0.017 0.017 -9999 0 -0.26 2 2
ASIP 0 0 -9999 0 -10000 0 0
PRKCI 0.001 0.088 -9999 0 -0.44 19 19
AS160/CaM/Ca2+ 0.013 0 -9999 0 -10000 0 0
RHOQ 0.014 0.042 -9999 0 -0.46 4 4
GYS1 0.031 0.027 -9999 0 -0.26 4 4
PRKCZ 0 0 -9999 0 -10000 0 0
TRIP10 0.013 0.048 -9999 0 -0.47 5 5
TC10/GTP/CIP4/Exocyst 0.019 0.04 -9999 0 -0.31 7 7
AS160/14-3-3 0.025 0.066 -9999 0 -0.31 2 2
VAMP2 0.017 0.023 -9999 0 -0.52 1 1
SLC2A4 0.033 0.057 -9999 0 -0.32 2 2
STX4 0.017 0.023 -9999 0 -0.52 1 1
GSK3B 0.026 0.032 -9999 0 -0.31 4 4
SFN -0.015 0.12 -9999 0 -0.45 37 37
LNPEP 0.01 0.061 -9999 0 -0.43 9 9
YWHAE 0.016 0.029 -9999 0 -0.35 3 3
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.033 0.064 -10000 0 -0.29 16 16
Ran/GTP/Exportin 1/HDAC1 -0.001 0.011 -10000 0 -0.22 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.039 0.064 -10000 0 -0.27 16 16
SUMO1 0.018 0 -10000 0 -10000 0 0
ZFPM1 0.009 0.068 -10000 0 -0.47 10 10
NPC/RanGAP1/SUMO1/Ubc9 0.023 0.014 -10000 0 -0.2 1 1
FKBP3 0.013 0.048 -10000 0 -0.47 5 5
Histones 0.043 0.051 -10000 0 -0.28 2 2
YY1/LSF 0.021 0.055 -10000 0 -0.26 19 19
SMG5 0.016 0.029 -10000 0 -0.35 3 3
RAN 0.017 0.012 -10000 0 -0.26 1 1
I kappa B alpha/HDAC3 0.025 0.056 -10000 0 -0.24 19 19
I kappa B alpha/HDAC1 0.027 0.051 -10000 0 -0.31 6 6
SAP18 0.018 0 -10000 0 -10000 0 0
RELA 0.03 0.051 -10000 0 -0.21 14 14
HDAC1/Smad7 0.035 0.022 -10000 0 -0.3 2 2
RANGAP1 0.014 0.037 -10000 0 -0.3 7 7
HDAC3/TR2 0.026 0.053 -10000 0 -0.28 9 9
NuRD/MBD3 Complex 0.045 0.038 -10000 0 -0.27 2 2
NF kappa B1 p50/RelA 0.035 0.049 -10000 0 -0.24 1 1
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.008 0.094 -10000 0 -0.32 40 40
GATA1 0.018 0 -10000 0 -10000 0 0
Mad/Max 0.024 0.021 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.053 0.054 -10000 0 -0.48 2 2
RBBP7 0.01 0.051 -10000 0 -0.3 13 13
NPC 0.01 0.008 -10000 0 -10000 0 0
RBBP4 0.016 0.026 -10000 0 -0.39 2 2
MAX 0.018 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.015 0.035 -10000 0 -0.43 3 3
NFKBIA 0.02 0.054 -10000 0 -0.36 5 5
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.041 0.036 -10000 0 -10000 0 0
SIN3 complex 0.042 0.032 -10000 0 -0.27 5 5
SMURF1 0.018 0 -10000 0 -10000 0 0
CHD3 0.015 0.037 -10000 0 -0.39 4 4
SAP30 0.012 0.053 -10000 0 -0.48 6 6
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.016 0.033 -10000 0 -0.52 2 2
YY1/HDAC3 0.033 0.045 -10000 0 -0.29 2 2
YY1/HDAC2 0.023 0.044 -10000 0 -0.25 10 10
YY1/HDAC1 0.027 0.034 -10000 0 -0.23 9 9
NuRD/MBD2 Complex (MeCP1) 0.044 0.038 -10000 0 -0.27 2 2
PPARG 0.007 0.095 -10000 0 -0.3 37 37
HDAC8/hEST1B 0.034 0.027 -10000 0 -0.3 3 3
UBE2I 0.018 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.015 0.035 -10000 0 -0.43 3 3
TNFRSF1A 0.016 0.033 -10000 0 -0.52 2 2
HDAC3/SMRT (N-CoR2) 0.03 0.041 -10000 0 -0.32 2 2
MBD3L2 0.007 0.072 -10000 0 -0.46 12 12
ubiquitin-dependent protein catabolic process 0.034 0.022 -10000 0 -0.3 2 2
CREBBP 0.016 0.033 -10000 0 -0.52 2 2
NuRD/MBD3/MBD3L2 Complex 0.049 0.052 -10000 0 -0.33 2 2
HDAC1 0.017 0.023 -10000 0 -0.52 1 1
HDAC3 0.023 0.045 -10000 0 -0.36 2 2
HDAC2 0.009 0.054 -10000 0 -0.29 15 15
YY1 0.021 0.036 -10000 0 -0.27 8 8
HDAC8 0.016 0.033 -10000 0 -0.52 2 2
SMAD7 0.016 0.026 -10000 0 -0.39 2 2
NCOR2 0.018 0 -10000 0 -10000 0 0
MXD1 0.014 0.031 -10000 0 -0.26 7 7
STAT3 0.024 0.044 -10000 0 -0.31 9 9
NFKB1 0.017 0.023 -10000 0 -0.52 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.017 0.017 -10000 0 -0.26 2 2
YY1/LSF/HDAC1 0.03 0.053 -10000 0 -0.26 12 12
YY1/SAP30/HDAC1 0.033 0.046 -10000 0 -0.3 6 6
EP300 0.014 0.047 -10000 0 -0.52 4 4
STAT3 (dimer non-phopshorylated) 0.024 0.044 -10000 0 -0.31 9 9
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.054 -10000 0 -0.36 5 5
histone deacetylation 0.044 0.038 -10000 0 -0.27 2 2
STAT3 (dimer non-phopshorylated)/HDAC3 0.035 0.051 -10000 0 -0.32 3 3
nuclear export -0.033 0.027 0.3 3 -10000 0 3
PRKACA 0.018 0 -10000 0 -10000 0 0
GATAD2B 0.017 0.023 -10000 0 -0.52 1 1
GATAD2A 0.014 0.037 -10000 0 -0.3 7 7
GATA2/HDAC3 0.017 0.069 -10000 0 -0.32 12 12
GATA1/HDAC1 0.026 0.017 -10000 0 -0.37 1 1
GATA1/HDAC3 0.03 0.041 -10000 0 -0.32 2 2
CHD4 0.017 0.023 -10000 0 -0.52 1 1
TNF-alpha/TNFR1A 0.009 0.071 -10000 0 -0.37 14 14
SIN3/HDAC complex/Mad/Max 0.046 0.033 -10000 0 -10000 0 0
NuRD Complex 0.052 0.044 -10000 0 -0.33 2 2
positive regulation of chromatin silencing 0.04 0.049 -10000 0 -0.27 2 2
SIN3B 0.017 0.012 -10000 0 -0.26 1 1
MTA2 0.014 0.044 -10000 0 -0.42 5 5
SIN3A 0.018 0 -10000 0 -10000 0 0
XPO1 0.018 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0.036 0.018 -10000 0 -0.24 1 1
HDAC complex 0.035 0.046 -10000 0 -0.26 7 7
GATA1/Fog1 0.02 0.05 -10000 0 -0.37 8 8
FKBP25/HDAC1/HDAC2 0.027 0.047 -10000 0 -0.3 8 8
TNF -0.004 0.094 -10000 0 -0.36 31 31
negative regulation of cell growth 0.046 0.033 -10000 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.044 0.038 -10000 0 -0.27 2 2
Ran/GTP/Exportin 1 0.039 0.014 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.031 0.065 -10000 0 -0.29 16 16
SIN3/HDAC complex/NCoR1 0.043 0.035 -10000 0 -10000 0 0
TFCP2 0.006 0.077 -10000 0 -0.52 11 11
NR2C1 0.011 0.062 -10000 0 -0.52 7 7
MBD3 0.018 0 -10000 0 -10000 0 0
MBD2 0.017 0.017 -10000 0 -0.26 2 2
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.024 0.045 -10000 0 -0.29 8 8
MAPK9 -0.005 0.07 -10000 0 -0.33 23 23
adrenocorticotropin secretion 0.005 0.042 -10000 0 -0.21 18 18
GNB1/GNG2 0.02 0.037 -10000 0 -0.31 6 6
GNB1 0.013 0.052 -10000 0 -0.52 5 5
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 0.01 0.005 -10000 0 -0.11 1 1
Gs family/GTP 0.008 0.028 -10000 0 -0.17 11 11
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 0.007 0.048 11 -10000 0 11
GNAL 0.01 0.052 -10000 0 -0.33 11 11
GNG2 0.016 0.029 -10000 0 -0.35 3 3
CRH 0.007 0.061 -10000 0 -0.3 18 18
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.008 0.026 -10000 0 -0.33 3 3
MAPK11 0.01 0 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.022 0.018 -10000 0 -0.2 2 2
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.02 0.019 -10000 0 -0.27 1 1
AP2 0.021 0.041 -10000 0 -0.36 5 5
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.019 0.041 -10000 0 -0.31 8 8
CLTB 0.015 0.035 -10000 0 -0.43 3 3
coatomer protein complex/ARF1/GTP/ER cargo protein 0.027 0.02 -10000 0 -0.24 3 3
CD4 0.018 0 -10000 0 -10000 0 0
CLTA 0.018 0 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.012 0.014 -10000 0 -0.17 3 3
mol:PI-4-5-P2 0.012 0.025 0.15 8 -0.18 4 12
ARF1/GTP -0.001 0.015 -10000 0 -0.29 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.028 0.015 -10000 0 -0.2 1 1
mol:Choline 0.011 0.025 0.15 8 -0.19 4 12
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.016 0.024 -10000 0 -0.53 1 1
DDEF1 0.012 0.025 0.15 8 -0.19 4 12
ARF1/GDP 0.008 0.013 -10000 0 -0.12 3 3
AP2M1 0.013 0.05 -10000 0 -0.43 6 6
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.017 0.013 -10000 0 -0.28 1 1
Rac/GTP 0.014 0.001 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.028 0.021 -10000 0 -0.26 2 2
ARFIP2 0.008 0.063 -10000 0 -0.47 9 9
COPA 0.018 0 -10000 0 -10000 0 0
RAC1 0.018 0 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.026 0.017 -10000 0 -0.2 2 2
ARF1/GTP/ARHGAP10 0.01 0.014 -10000 0 -0.32 1 1
GGA3 0.016 0.026 -10000 0 -0.39 2 2
ARF1/GTP/Membrin 0.017 0.015 -10000 0 -0.27 1 1
AP2A1 0.016 0.024 -10000 0 -0.26 4 4
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.028 0.021 -10000 0 -0.23 3 3
ARF1/GDP/Membrin 0.019 0.015 -10000 0 -0.26 1 1
Arfaptin 2/Rac/GDP 0.018 0.041 -10000 0 -0.31 8 8
CYTH2 0.001 0.002 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.021 0.022 -10000 0 -0.32 2 2
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.013 0 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.036 0.036 -10000 0 -0.45 2 2
PLD2 0.011 0.026 0.15 8 -0.19 4 12
ARF-GAP1/v-SNARE 0.012 0.014 -10000 0 -0.17 3 3
PIP5K1A 0.012 0.025 0.15 8 -0.18 4 12
ARF1/GTP/Membrin/GBF1/p115 0.018 0.016 -10000 0 -0.26 1 1
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.011 0.025 0.15 8 -0.19 4 12
KDEL Receptor/Ligand/ARF-GAP1 0.012 0.014 -10000 0 -0.17 3 3
GOSR2 0.015 0.014 -10000 0 -10000 0 0
USO1 0.015 0.013 -10000 0 -10000 0 0
GBF1 0.014 0.023 -10000 0 -0.41 1 1
ARF1/GTP/Arfaptin 2 0.018 0.044 -10000 0 -0.31 9 9
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.032 0.035 -10000 0 -0.3 5 5
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.017 0.023 -9999 0 -0.52 1 1
Ran/GTP/Exportin 1/HDAC4 -0.001 0.013 -9999 0 -0.25 1 1
MDM2/SUMO1 0.033 0.024 -9999 0 -10000 0 0
HDAC4 0.017 0.023 -9999 0 -0.52 1 1
Ran/GTP/Exportin 1/HDAC1 -0.001 0.011 -9999 0 -0.2 1 1
SUMO1 0.018 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.018 0.016 -9999 0 -0.24 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.029 0.013 -9999 0 -0.18 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.017 0.012 -9999 0 -0.26 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.017 0.017 -9999 0 -0.26 2 2
SUMO1/HDAC4 0.036 0.02 -9999 0 -0.31 1 1
SUMO1/HDAC1 0.036 0.018 -9999 0 -0.24 1 1
RANGAP1 0.014 0.037 -9999 0 -0.3 7 7
MDM2/SUMO1/SUMO1 0.04 0.032 -9999 0 -0.27 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.023 0.014 -9999 0 -0.2 1 1
Ran/GTP 0.031 0.014 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.01 0.044 -9999 0 -0.26 14 14
UBE2I 0.018 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.037 0.013 -9999 0 -10000 0 0
NPC 0.01 0.008 -9999 0 -10000 0 0
PIAS2 0.015 0.035 -9999 0 -0.43 3 3
PIAS1 0.017 0.012 -9999 0 -0.26 1 1
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Methods & Data
Input

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

  • Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA/1708440/2.GDAC_MergeDataFiles.Finished/BRCA.transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.data.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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