Breast Invasive Carcinoma: PARADIGM pathway analysis of mRNA expression and copy number 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 50 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 94
Signaling events mediated by Stem cell factor receptor (c-Kit) 89
Endothelins 80
FOXM1 transcription factor network 73
IGF1 pathway 71
Osteopontin-mediated events 68
Plasma membrane estrogen receptor signaling 66
Syndecan-1-mediated signaling events 62
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 61
EGFR-dependent Endothelin signaling events 61
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 94 7743 82 -0.16 0.036 1000 -1000 -0.042 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 89 6943 78 -0.31 0.13 1000 -1000 -0.023 -1000
Endothelins 80 7772 96 -0.18 0.035 1000 -1000 -0.031 -1000
FOXM1 transcription factor network 73 3765 51 -0.43 0.033 1000 -1000 -0.033 -1000
IGF1 pathway 71 4052 57 -0.08 0.051 1000 -1000 -0.024 -1000
Osteopontin-mediated events 68 2616 38 -0.14 0.038 1000 -1000 -0.016 -1000
Plasma membrane estrogen receptor signaling 66 5698 86 -0.22 0.21 1000 -1000 -0.042 -1000
Syndecan-1-mediated signaling events 62 2109 34 -0.13 0.041 1000 -1000 -0.015 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 61 4172 68 -0.34 0.15 1000 -1000 -0.055 -1000
EGFR-dependent Endothelin signaling events 61 1293 21 -0.073 0.047 1000 -1000 -0.019 -1000
IL4-mediated signaling events 59 5456 91 -0.53 0.42 1000 -1000 -0.081 -1000
HIF-1-alpha transcription factor network 56 4312 76 -0.18 0.049 1000 -1000 -0.004 -1000
Glucocorticoid receptor regulatory network 56 6459 114 -0.39 0.19 1000 -1000 -0.039 -1000
Signaling events mediated by the Hedgehog family 53 2758 52 -0.097 0.051 1000 -1000 -0.011 -1000
Noncanonical Wnt signaling pathway 53 1380 26 -0.068 0.035 1000 -1000 -0.036 -1000
Wnt signaling 49 347 7 -0.068 0.03 1000 -1000 0 -1000
Thromboxane A2 receptor signaling 48 5083 105 -0.11 0.06 1000 -1000 -0.031 -1000
TCR signaling in naïve CD8+ T cells 48 4537 93 -0.074 0.047 1000 -1000 -0.034 -1000
FAS signaling pathway (CD95) 47 2221 47 -0.1 0.048 1000 -1000 -0.029 -1000
IL12-mediated signaling events 46 4040 87 -0.26 0.042 1000 -1000 -0.031 -1000
Fc-epsilon receptor I signaling in mast cells 45 4457 97 -0.096 0.035 1000 -1000 -0.055 -1000
Stabilization and expansion of the E-cadherin adherens junction 45 3359 74 -0.095 0.058 1000 -1000 -0.046 -1000
IL23-mediated signaling events 45 2712 60 -0.2 0.036 1000 -1000 -0.055 -1000
Nongenotropic Androgen signaling 44 2291 52 -0.11 0.062 1000 -1000 -0.021 -1000
IL27-mediated signaling events 44 2286 51 -0.2 0.1 1000 -1000 -0.053 -1000
IL6-mediated signaling events 42 3157 75 -0.14 0.037 1000 -1000 -0.028 -1000
Syndecan-4-mediated signaling events 39 2644 67 -0.06 0.089 1000 -1000 -0.028 -1000
E-cadherin signaling in keratinocytes 39 1682 43 -0.061 0.036 1000 -1000 -0.014 -1000
Arf6 signaling events 38 2357 62 -0.069 0.079 1000 -1000 -0.005 -1000
Signaling mediated by p38-gamma and p38-delta 38 570 15 -0.056 0.033 1000 -1000 -0.029 -1000
LPA receptor mediated events 38 3883 102 -0.077 0.035 1000 -1000 -0.061 -1000
IL2 signaling events mediated by PI3K 36 2136 58 -0.23 0.035 1000 -1000 -0.021 -1000
E-cadherin signaling in the nascent adherens junction 36 2800 76 -0.081 0.056 1000 -1000 -0.038 -1000
Ephrin B reverse signaling 35 1713 48 -0.12 0.071 1000 -1000 -0.038 -1000
TCGA08_p53 34 240 7 -0.029 0.026 1000 -1000 -0.002 -1000
E-cadherin signaling events 34 173 5 -0.012 0.028 1000 -1000 0.023 -1000
ErbB4 signaling events 33 2308 69 -0.11 0.06 1000 -1000 -0.032 -1000
PLK2 and PLK4 events 32 97 3 -0.015 0.03 1000 -1000 0.006 -1000
Canonical Wnt signaling pathway 32 1680 51 -0.15 0.09 1000 -1000 -0.032 -1000
Coregulation of Androgen receptor activity 31 2384 76 -0.15 0.054 1000 -1000 -0.017 -1000
Signaling events mediated by PTP1B 31 2398 76 -0.089 0.06 1000 -1000 -0.028 -1000
Integrins in angiogenesis 31 2634 84 -0.12 0.058 1000 -1000 -0.021 -1000
Syndecan-2-mediated signaling events 30 2125 69 -0.019 0.047 1000 -1000 -0.036 -1000
Cellular roles of Anthrax toxin 29 1161 39 -0.074 0.035 1000 -1000 -0.017 -1000
Caspase cascade in apoptosis 28 2095 74 -0.067 0.047 1000 -1000 -0.026 -1000
amb2 Integrin signaling 28 2376 82 -0.05 0.046 1000 -1000 -0.025 -1000
TCGA08_retinoblastoma 28 228 8 -0.011 0.023 1000 -1000 -0.007 -1000
BMP receptor signaling 27 2212 81 -0.11 0.067 1000 -1000 -0.015 -1000
Nectin adhesion pathway 27 1715 63 -0.048 0.052 1000 -1000 -0.026 -1000
Visual signal transduction: Rods 27 1446 52 -0.066 0.065 1000 -1000 -0.014 -1000
Regulation of nuclear SMAD2/3 signaling 26 3592 136 -0.19 0.066 1000 -1000 -0.039 -1000
BCR signaling pathway 26 2588 99 -0.1 0.064 1000 -1000 -0.038 -1000
mTOR signaling pathway 25 1362 53 -0.067 0.044 1000 -1000 -0.033 -1000
Reelin signaling pathway 25 1403 56 -0.071 0.068 1000 -1000 -0.024 -1000
IL1-mediated signaling events 25 1573 62 -0.028 0.075 1000 -1000 -0.028 -1000
VEGFR1 specific signals 24 1399 56 -0.028 0.036 1000 -1000 -0.028 -1000
Aurora B signaling 24 1631 67 -0.064 0.052 1000 -1000 -0.029 -1000
Arf6 downstream pathway 23 1009 43 -0.047 0.048 1000 -1000 -0.035 -1000
PDGFR-alpha signaling pathway 23 1048 44 -0.14 0.049 1000 -1000 -0.029 -1000
FOXA2 and FOXA3 transcription factor networks 22 1039 46 -0.2 0.043 1000 -1000 -0.042 -1000
PLK1 signaling events 22 1912 85 -0.073 0.051 1000 -1000 -0.031 -1000
Visual signal transduction: Cones 21 824 38 -0.022 0.05 1000 -1000 0 -1000
Presenilin action in Notch and Wnt signaling 21 1315 61 -0.2 0.07 1000 -1000 -0.04 -1000
Glypican 1 network 21 1029 48 -0.023 0.049 1000 -1000 -0.019 -1000
IFN-gamma pathway 21 1441 68 -0.058 0.059 1000 -1000 -0.029 -1000
S1P1 pathway 21 772 36 -0.034 0.036 1000 -1000 -0.025 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 21 968 45 -0.042 0.055 1000 -1000 -0.028 -1000
Calcium signaling in the CD4+ TCR pathway 21 670 31 -0.035 0.045 1000 -1000 -0.034 -1000
PDGFR-beta signaling pathway 21 2061 97 -0.066 0.066 1000 -1000 -0.031 -1000
TRAIL signaling pathway 20 999 48 -0.024 0.036 1000 -1000 -0.018 -1000
Class I PI3K signaling events 20 1471 73 -0.06 0.045 1000 -1000 -0.021 -1000
Insulin Pathway 20 1544 74 -0.063 0.079 1000 -1000 -0.021 -1000
Ceramide signaling pathway 19 1492 76 -0.069 0.068 1000 -1000 -0.028 -1000
Regulation of Telomerase 19 1990 102 -0.15 0.062 1000 -1000 -0.025 -1000
ErbB2/ErbB3 signaling events 18 1220 65 -0.047 0.047 1000 -1000 -0.058 -1000
ceramide signaling pathway 18 892 49 -0.057 0.048 1000 -1000 -0.021 -1000
EPHB forward signaling 18 1601 85 -0.046 0.11 1000 -1000 -0.05 -1000
Ras signaling in the CD4+ TCR pathway 18 311 17 -0.002 0.05 1000 -1000 -0.013 -1000
RXR and RAR heterodimerization with other nuclear receptor 17 931 52 -0.057 0.061 1000 -1000 -0.029 -1000
Atypical NF-kappaB pathway 17 548 31 -0.018 0.035 1000 -1000 -0.004 -1000
p75(NTR)-mediated signaling 16 2006 125 -0.047 0.086 1000 -1000 -0.043 -1000
Syndecan-3-mediated signaling events 16 581 35 -0.031 0.068 1000 -1000 -0.025 -1000
Hedgehog signaling events mediated by Gli proteins 15 980 65 -0.024 0.076 1000 -1000 -0.022 -1000
EPO signaling pathway 15 834 55 -0.11 0.046 1000 -1000 -0.019 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 14 804 54 -0.036 0.049 1000 -1000 -0.026 -1000
Aurora A signaling 14 844 60 -0.011 0.05 1000 -1000 -0.007 -1000
HIF-2-alpha transcription factor network 14 641 43 -0.11 0.11 1000 -1000 -0.038 -1000
Regulation of p38-alpha and p38-beta 14 771 54 -0.018 0.072 1000 -1000 -0.018 -1000
Neurotrophic factor-mediated Trk receptor signaling 14 1721 120 -0.079 0.088 1000 -1000 -0.035 -1000
Regulation of Androgen receptor activity 14 1034 70 -0.14 0.047 1000 -1000 -0.045 -1000
LPA4-mediated signaling events 13 163 12 -0.028 0.022 1000 -1000 -0.019 -1000
Sphingosine 1-phosphate (S1P) pathway 13 380 28 -0.01 0.043 1000 -1000 -0.007 -1000
Signaling mediated by p38-alpha and p38-beta 13 586 44 -0.054 0.056 1000 -1000 -0.014 -1000
Glypican 2 network 13 54 4 0 0.013 1000 -1000 0 -1000
IL2 signaling events mediated by STAT5 13 303 22 -0.025 0.036 1000 -1000 -0.021 -1000
p38 MAPK signaling pathway 13 593 44 -0.05 0.058 1000 -1000 -0.012 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 12 1058 85 -0.14 0.064 1000 -1000 -0.049 -1000
FoxO family signaling 12 816 64 -0.092 0.048 1000 -1000 -0.026 -1000
Retinoic acid receptors-mediated signaling 12 718 58 -0.071 0.067 1000 -1000 -0.038 -1000
S1P3 pathway 12 505 42 -0.017 0.043 1000 -1000 -0.024 -1000
S1P4 pathway 12 313 25 -0.008 0.043 1000 -1000 -0.014 -1000
S1P5 pathway 11 195 17 -0.001 0.035 1000 -1000 -0.007 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 11 920 83 -0.057 0.069 1000 -1000 -0.019 -1000
Effects of Botulinum toxin 11 302 26 -0.063 0.051 1000 -1000 -0.001 -1000
Signaling events mediated by VEGFR1 and VEGFR2 11 1488 125 -0.026 0.044 1000 -1000 -0.025 -1000
Angiopoietin receptor Tie2-mediated signaling 11 1044 88 -0.063 0.063 1000 -1000 -0.053 -1000
Nephrin/Neph1 signaling in the kidney podocyte 10 354 34 -0.039 0.076 1000 -1000 -0.031 -1000
BARD1 signaling events 10 571 57 -0.047 0.069 1000 -1000 -0.04 -1000
Paxillin-independent events mediated by a4b1 and a4b7 10 404 37 -0.024 0.073 1000 -1000 -0.025 -1000
Paxillin-dependent events mediated by a4b1 10 370 36 -0.061 0.064 1000 -1000 -0.033 -1000
TCGA08_rtk_signaling 10 273 26 -0.026 0.042 1000 -1000 -0.013 -1000
Signaling events mediated by PRL 10 361 34 -0.037 0.05 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class II 9 689 75 -0.088 0.076 1000 -1000 -0.026 -1000
a4b1 and a4b7 Integrin signaling 9 47 5 0.021 0.041 1000 -1000 0.019 -1000
Signaling events mediated by HDAC Class III 9 377 40 -0.063 0.064 1000 -1000 -0.034 -1000
Class IB PI3K non-lipid kinase events 9 27 3 -0.025 0.025 1000 -1000 -0.024 -1000
Insulin-mediated glucose transport 8 270 32 0 0.043 1000 -1000 -0.009 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 8 282 33 -0.016 0.071 1000 -1000 -0.039 -1000
JNK signaling in the CD4+ TCR pathway 7 124 17 -0.01 0.078 1000 -1000 -0.018 -1000
Class I PI3K signaling events mediated by Akt 7 508 68 -0.053 0.075 1000 -1000 -0.017 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 6 142 23 0 0.054 1000 -1000 -0.012 -1000
Ephrin A reverse signaling 6 43 7 0 0.041 1000 -1000 0 -1000
Arf6 trafficking events 6 427 71 -0.04 0.042 1000 -1000 -0.03 -1000
Alternative NF-kappaB pathway 5 74 13 0 0.082 1000 -1000 0 -1000
Canonical NF-kappaB pathway 4 192 39 0 0.074 1000 -1000 -0.009 -1000
Circadian rhythm pathway 4 101 22 -0.01 0.066 1000 -1000 -0.024 -1000
Aurora C signaling 3 24 7 0 0.052 1000 -1000 -0.004 -1000
Signaling events mediated by HDAC Class I 3 395 104 -0.046 0.08 1000 -1000 -0.031 -1000
Arf1 pathway 3 197 54 -0.001 0.06 1000 -1000 -0.011 -1000
Rapid glucocorticoid signaling 2 56 20 -0.002 0.044 1000 -1000 -0.002 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 25 27 0 0.08 1000 -1000 -0.021 -1000
Total 3430 210697 7203 -11 7.9 131000 -131000 -3.3 -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 -0.038 0.13 -10000 0 -0.52 29 29
Crk/p130 Cas/Paxillin -0.13 0.16 -10000 0 -0.33 165 165
JUN -0.13 0.18 0.19 2 -0.41 111 113
HRAS 0.032 0.036 -10000 0 -0.42 3 3
RET51/GFRalpha1/GDNF/GRB10 -0.1 0.2 -10000 0 -0.31 229 229
RAP1A 0.03 0.05 -10000 0 -0.42 6 6
FRS2 0.033 0.022 -10000 0 -0.42 1 1
RAP1A/GDP 0.022 0.035 -10000 0 -0.3 6 6
RET51/GFRalpha1/GDNF/DOK1 -0.099 0.21 -10000 0 -0.32 221 221
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.036 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.023 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/Enigma -0.042 0.14 -10000 0 -0.23 171 171
RHOA 0.026 0.061 -10000 0 -0.42 9 9
RAP1A/GTP -0.095 0.18 -10000 0 -0.28 223 223
GRB7 0.023 0.058 -10000 0 -0.42 8 8
RET51/GFRalpha1/GDNF -0.094 0.2 -10000 0 -0.31 218 218
MAPKKK cascade -0.11 0.19 -10000 0 -0.33 203 203
BCAR1 0.029 0.014 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.064 0.17 -10000 0 -0.28 181 181
lamellipodium assembly -0.11 0.16 -10000 0 -0.31 166 166
RET51/GFRalpha1/GDNF/SHC -0.082 0.18 -10000 0 -0.3 195 195
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/SHC -0.029 0.12 -10000 0 -0.24 123 123
RET9/GFRalpha1/GDNF/Shank3 -0.043 0.14 -10000 0 -0.23 174 174
MAPK3 -0.12 0.15 0.34 1 -0.38 91 92
DOK1 0.027 0.061 -10000 0 -0.42 9 9
DOK6 0.006 0.11 -10000 0 -0.42 30 30
PXN 0.036 0.004 -10000 0 -10000 0 0
neurite development -0.11 0.16 0.28 2 -0.37 103 105
DOK5 0.014 0.082 -10000 0 -0.42 17 17
GFRA1 -0.13 0.21 -10000 0 -0.42 177 177
MAPK8 -0.12 0.18 -10000 0 -0.42 104 104
HRAS/GTP -0.12 0.22 -10000 0 -0.35 217 217
tube development -0.031 0.14 0.22 21 -0.22 163 184
MAPK1 -0.12 0.16 0.34 1 -0.38 91 92
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.054 0.12 -10000 0 -0.22 157 157
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
SRC 0.032 0.03 -10000 0 -0.42 2 2
PDLIM7 0.035 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.095 0.21 -10000 0 -0.32 219 219
SHC1 0.027 0.025 -10000 0 -0.42 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.1 0.2 -10000 0 -0.31 221 221
RET51/GFRalpha1/GDNF/Dok5 -0.1 0.2 -10000 0 -0.32 212 212
PRKCA 0.031 0.012 -10000 0 -10000 0 0
HRAS/GDP 0.023 0.025 -10000 0 -0.3 3 3
CREB1 -0.087 0.17 -10000 0 -0.4 88 88
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.039 0.11 -10000 0 -0.23 115 115
RET51/GFRalpha1/GDNF/Grb7 -0.097 0.2 -10000 0 -0.32 213 213
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.096 0.2 -10000 0 -0.42 138 138
DOK4 0.027 0.032 -10000 0 -0.42 2 2
JNK cascade -0.13 0.17 0.19 2 -0.4 111 113
RET9/GFRalpha1/GDNF/FRS2 -0.043 0.14 -10000 0 -0.24 169 169
SHANK3 0.034 0.029 -10000 0 -0.42 2 2
RASA1 0.028 0.054 -10000 0 -0.42 7 7
NCK1 0.034 0.021 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.037 0.1 -10000 0 -0.22 114 114
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.11 0.18 -10000 0 -0.3 205 205
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.12 0.2 -10000 0 -0.32 221 221
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.11 0.2 -10000 0 -0.34 181 181
PI3K -0.16 0.25 -10000 0 -0.46 168 168
SOS1 0.034 0.021 -10000 0 -0.42 1 1
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.029 0.14 -10000 0 -0.22 163 163
GRB10 0.022 0.075 -10000 0 -0.42 14 14
activation of MAPKK activity -0.082 0.15 -10000 0 -0.34 93 93
RET51/GFRalpha1/GDNF/FRS2 -0.097 0.2 -10000 0 -0.32 217 217
GAB1 0.027 0.061 -10000 0 -0.42 9 9
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
IRS2 0.008 0.099 -10000 0 -0.42 25 25
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.12 0.2 -10000 0 -0.35 186 186
RET51/GFRalpha1/GDNF/PKC alpha -0.091 0.2 -10000 0 -0.32 201 201
GRB2 0.033 0.01 -10000 0 -10000 0 0
PRKACA 0.035 0.004 -10000 0 -10000 0 0
GDNF 0.032 0.036 -10000 0 -0.42 3 3
RAC1 0.035 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.12 0.23 -10000 0 -0.35 226 226
Rac1/GTP -0.12 0.2 -10000 0 -0.37 165 165
RET9/GFRalpha1/GDNF -0.061 0.14 -10000 0 -0.26 172 172
GFRalpha1/GDNF -0.075 0.16 -10000 0 -0.3 172 172
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 -0.12 0.19 0.38 1 -0.41 132 133
CRKL -0.13 0.2 -10000 0 -0.43 137 137
HRAS -0.077 0.17 -10000 0 -0.36 86 86
mol:PIP3 -0.088 0.2 0.28 2 -0.41 101 103
SPRED1 0.02 0.08 -10000 0 -0.42 16 16
SPRED2 0.02 0.082 -10000 0 -0.42 17 17
GAB1 -0.14 0.21 -10000 0 -0.45 136 136
FOXO3 -0.1 0.2 -10000 0 -0.39 129 129
AKT1 -0.11 0.21 -10000 0 -0.42 129 129
BAD -0.1 0.2 -10000 0 -0.4 125 125
megakaryocyte differentiation -0.13 0.21 -10000 0 -0.44 133 133
GSK3B -0.1 0.2 0.34 1 -0.4 126 127
RAF1 -0.055 0.15 0.26 6 -0.31 73 79
SHC1 0.027 0.025 -10000 0 -0.42 1 1
STAT3 -0.12 0.21 -10000 0 -0.43 132 132
STAT1 -0.31 0.48 -10000 0 -0.88 184 184
HRAS/SPRED1 -0.055 0.16 0.26 1 -0.33 78 79
cell proliferation -0.13 0.2 -10000 0 -0.43 134 134
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
TEC 0.031 0.045 -10000 0 -0.42 5 5
RPS6KB1 -0.12 0.22 -10000 0 -0.45 135 135
HRAS/SPRED2 -0.053 0.16 0.26 1 -0.32 79 80
LYN/TEC/p62DOK -0.094 0.22 -10000 0 -0.42 126 126
MAPK3 -0.033 0.12 0.25 10 -0.25 29 39
STAP1 -0.13 0.21 -10000 0 -0.44 134 134
GRAP2 0.032 0.023 -10000 0 -0.42 1 1
JAK2 -0.26 0.41 -10000 0 -0.74 188 188
STAT1 (dimer) -0.3 0.46 -10000 0 -0.86 184 184
mol:Gleevec 0.005 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.099 0.22 -10000 0 -0.42 122 122
actin filament polymerization -0.13 0.2 -10000 0 -0.43 134 134
LYN 0.03 0.013 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.19 0.3 -10000 0 -0.55 182 182
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
CBL/CRKL/GRB2 -0.1 0.2 -10000 0 -0.4 124 124
PI3K -0.1 0.23 -10000 0 -0.45 125 125
PTEN 0.027 0.061 -10000 0 -0.42 9 9
SCF/KIT/EPO/EPOR -0.3 0.53 -10000 0 -1.1 128 128
MAPK8 -0.13 0.21 -10000 0 -0.44 134 134
STAT3 (dimer) -0.12 0.2 -10000 0 -0.42 132 132
positive regulation of transcription -0.024 0.1 0.23 11 -0.21 26 37
mol:GDP -0.084 0.17 -10000 0 -0.38 84 84
PIK3C2B -0.12 0.2 -10000 0 -0.42 127 127
CBL/CRKL -0.12 0.2 -10000 0 -0.41 133 133
FER -0.13 0.21 -10000 0 -0.45 132 132
SH2B3 -0.13 0.21 -10000 0 -0.44 134 134
PDPK1 -0.07 0.2 0.3 14 -0.38 92 106
SNAI2 -0.14 0.22 -10000 0 -0.46 136 136
positive regulation of cell proliferation -0.22 0.36 -10000 0 -0.68 167 167
KITLG -0.052 0.16 -10000 0 -0.45 72 72
cell motility -0.22 0.36 -10000 0 -0.68 167 167
PTPN6 0.038 0.032 -10000 0 -0.41 2 2
EPOR -0.069 0.18 -10000 0 -0.95 6 6
STAT5A (dimer) -0.19 0.3 -10000 0 -0.56 179 179
SOCS1 0.031 0.023 -10000 0 -0.42 1 1
cell migration 0.13 0.2 0.44 133 -10000 0 133
SOS1 0.034 0.021 -10000 0 -0.42 1 1
EPO 0.012 0.029 -10000 0 -10000 0 0
VAV1 0.018 0.082 -10000 0 -0.42 17 17
GRB10 -0.14 0.21 -10000 0 -0.45 133 133
PTPN11 0.04 0.009 -10000 0 -10000 0 0
SCF/KIT -0.14 0.22 -10000 0 -0.46 134 134
GO:0007205 0.007 0.011 -10000 0 -10000 0 0
MAP2K1 -0.041 0.13 0.26 9 -0.26 48 57
CBL 0.031 0.012 -10000 0 -10000 0 0
KIT -0.27 0.53 -10000 0 -1.3 101 101
MAP2K2 -0.041 0.13 0.26 9 -0.27 45 54
SHC/Grb2/SOS1 -0.081 0.2 -10000 0 -0.42 94 94
STAT5A -0.2 0.31 -10000 0 -0.58 179 179
GRB2 0.033 0.01 -10000 0 -10000 0 0
response to radiation -0.14 0.22 -10000 0 -0.45 136 136
SHC/GRAP2 0.038 0.032 -10000 0 -0.3 2 2
PTPRO -0.14 0.21 -10000 0 -0.46 132 132
SH2B2 -0.13 0.21 -10000 0 -0.44 134 134
DOK1 0.027 0.061 -10000 0 -0.42 9 9
MATK -0.13 0.21 -10000 0 -0.45 133 133
CREBBP -0.009 0.08 -10000 0 -0.18 16 16
BCL2 -0.3 0.56 -10000 0 -1.3 115 115
Endothelins

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
AKT1 -0.012 0.2 0.27 74 -0.32 104 178
PTK2B 0.028 0.015 -10000 0 -10000 0 0
mol:Ca2+ -0.057 0.26 -10000 0 -0.68 49 49
EDN1 -0.01 0.19 0.23 69 -0.37 87 156
EDN3 -0.014 0.12 -10000 0 -0.42 40 40
EDN2 -0.055 0.18 -10000 0 -0.42 94 94
HRAS/GDP -0.065 0.24 0.28 5 -0.44 106 111
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.06 0.2 0.18 11 -0.39 106 117
ADCY4 -0.013 0.17 0.25 9 -0.4 45 54
ADCY5 -0.016 0.16 0.23 5 -0.39 46 51
ADCY6 -0.011 0.16 0.24 7 -0.39 44 51
ADCY7 -0.015 0.16 0.24 5 -0.38 43 48
ADCY1 -0.01 0.16 0.25 8 -0.38 44 52
ADCY2 -0.028 0.18 0.24 6 -0.41 55 61
ADCY3 -0.012 0.16 0.24 10 -0.39 47 57
ADCY8 -0.007 0.14 0.26 4 -0.38 35 39
ADCY9 -0.015 0.16 0.23 8 -0.39 45 53
arachidonic acid secretion -0.089 0.25 0.27 1 -0.5 111 112
ETB receptor/Endothelin-1/Gq/GTP -0.05 0.16 -10000 0 -0.29 127 127
GNAO1 0.03 0.014 -10000 0 -10000 0 0
HRAS 0.031 0.036 -10000 0 -0.42 3 3
ETA receptor/Endothelin-1/G12/GTP 0.03 0.22 0.37 75 -0.3 105 180
ETA receptor/Endothelin-1/Gs/GTP 0.025 0.2 0.35 74 -0.29 99 173
mol:GTP -0.001 0.006 -10000 0 -10000 0 0
COL3A1 -0.018 0.21 0.27 74 -0.51 47 121
EDNRB 0.002 0.099 -10000 0 -0.36 27 27
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.01 0.2 0.27 72 -0.38 73 145
CYSLTR1 -0.028 0.23 0.27 74 -0.52 61 135
SLC9A1 -0.005 0.13 0.19 74 -0.3 40 114
mol:GDP -0.081 0.24 0.26 6 -0.46 113 119
SLC9A3 -0.12 0.35 -10000 0 -0.68 118 118
RAF1 -0.094 0.24 -10000 0 -0.48 111 111
JUN -0.098 0.35 -10000 0 -0.96 60 60
JAK2 -0.01 0.19 0.27 74 -0.32 100 174
mol:IP3 -0.073 0.21 0.23 1 -0.41 110 111
ETA receptor/Endothelin-1 0.014 0.26 0.42 75 -0.37 107 182
PLCB1 -0.021 0.14 -10000 0 -0.42 56 56
PLCB2 0.032 0.023 -10000 0 -0.43 1 1
ETA receptor/Endothelin-3 -0.003 0.15 -10000 0 -0.32 77 77
FOS -0.14 0.36 -10000 0 -0.88 84 84
Gai/GDP -0.11 0.32 -10000 0 -0.72 101 101
CRK 0.031 0.023 -10000 0 -0.42 1 1
mol:Ca ++ -0.088 0.27 0.24 26 -0.48 123 149
BCAR1 0.029 0.014 -10000 0 -10000 0 0
PRKCB1 -0.076 0.22 0.26 13 -0.43 108 121
GNAQ -0.001 0.007 -10000 0 -10000 0 0
GNAZ 0.023 0.067 -10000 0 -0.42 11 11
GNAL 0.031 0.036 -10000 0 -0.42 3 3
Gs family/GDP -0.064 0.22 0.26 4 -0.43 103 107
ETA receptor/Endothelin-1/Gq/GTP -0.042 0.2 0.2 67 -0.37 102 169
MAPK14 -0.068 0.17 0.23 1 -0.35 100 101
TRPC6 -0.062 0.27 -10000 0 -0.73 48 48
GNAI2 0.027 0.057 -10000 0 -0.42 8 8
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNAI1 0.017 0.085 -10000 0 -0.42 18 18
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.066 0.18 -10000 0 -0.36 106 106
ETB receptor/Endothelin-2 -0.041 0.15 -10000 0 -0.31 115 115
ETB receptor/Endothelin-3 -0.011 0.11 -10000 0 -0.31 57 57
ETB receptor/Endothelin-1 -0.012 0.17 -10000 0 -0.3 109 109
MAPK3 -0.14 0.34 -10000 0 -0.76 98 98
MAPK1 -0.14 0.34 -10000 0 -0.78 96 96
Rac1/GDP -0.063 0.23 0.28 5 -0.45 103 108
cAMP biosynthetic process -0.005 0.17 0.26 23 -0.4 45 68
MAPK8 -0.072 0.3 -10000 0 -0.68 71 71
SRC 0.032 0.03 -10000 0 -0.42 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.043 0.16 -10000 0 -0.34 82 82
p130Cas/CRK/Src/PYK2 -0.099 0.26 0.31 1 -0.54 102 103
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.062 0.23 0.27 6 -0.44 106 112
COL1A2 -0.073 0.3 0.31 4 -0.54 117 121
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.033 0.18 -10000 0 -0.32 127 127
mol:DAG -0.073 0.21 0.23 1 -0.41 110 111
MAP2K2 -0.12 0.28 0.32 1 -0.59 105 106
MAP2K1 -0.11 0.28 0.29 2 -0.59 105 107
EDNRA 0.015 0.17 0.23 74 -0.37 62 136
positive regulation of muscle contraction -0.014 0.17 0.22 75 -0.31 80 155
Gq family/GDP -0.059 0.22 -10000 0 -0.42 101 101
HRAS/GTP -0.081 0.23 -10000 0 -0.45 104 104
PRKCH -0.074 0.21 0.23 4 -0.42 101 105
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCA -0.06 0.21 0.23 23 -0.41 97 120
PRKCB -0.073 0.2 0.22 1 -0.4 110 111
PRKCE -0.076 0.2 0.21 1 -0.41 102 103
PRKCD -0.074 0.2 0.22 1 -0.42 99 100
PRKCG -0.078 0.2 0.22 1 -0.43 99 100
regulation of vascular smooth muscle contraction -0.18 0.42 -10000 0 -1.1 84 84
PRKCQ -0.068 0.2 0.23 6 -0.42 96 102
PLA2G4A -0.1 0.28 -10000 0 -0.55 111 111
GNA14 -0.014 0.13 -10000 0 -0.43 44 44
GNA15 0.026 0.048 -10000 0 -0.42 5 5
GNA12 0.035 0.006 -10000 0 -10000 0 0
GNA11 0.029 0.039 -10000 0 -0.42 3 3
Rac1/GTP 0.029 0.22 0.37 74 -0.3 103 177
MMP1 -0.17 0.35 0.23 14 -0.78 120 134
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 0.51 -9999 0 -1.1 97 97
PLK1 0.017 0.098 -9999 0 -1.1 3 3
BIRC5 -0.086 0.39 -9999 0 -1.4 41 41
HSPA1B -0.24 0.51 -9999 0 -1.1 101 101
MAP2K1 0.005 0.057 -9999 0 -10000 0 0
BRCA2 -0.26 0.54 -9999 0 -1.1 105 105
FOXM1 -0.38 0.86 -9999 0 -1.8 101 101
XRCC1 -0.24 0.51 -9999 0 -1.2 83 83
FOXM1B/p19 -0.29 0.57 -9999 0 -1.3 100 100
Cyclin D1/CDK4 -0.29 0.52 -9999 0 -1 139 139
CDC2 -0.27 0.56 -9999 0 -1.2 95 95
TGFA -0.28 0.5 -9999 0 -1 118 118
SKP2 -0.24 0.51 -9999 0 -1.1 95 95
CCNE1 0.023 0.05 -9999 0 -0.44 5 5
CKS1B -0.22 0.52 -9999 0 -1.2 86 86
RB1 -0.15 0.39 -9999 0 -1 65 65
FOXM1C/SP1 -0.3 0.62 -9999 0 -1.3 108 108
AURKB -0.082 0.32 -9999 0 -0.94 53 53
CENPF -0.23 0.56 -9999 0 -1.2 95 95
CDK4 0.016 0.037 -9999 0 -10000 0 0
MYC -0.23 0.44 -9999 0 -0.95 106 106
CHEK2 0.001 0.065 -9999 0 -0.45 3 3
ONECUT1 -0.27 0.52 -9999 0 -1.1 105 105
CDKN2A 0.014 0.075 -9999 0 -0.42 14 14
LAMA4 -0.25 0.52 -9999 0 -1.1 96 96
FOXM1B/HNF6 -0.34 0.65 -9999 0 -1.4 106 106
FOS -0.33 0.6 -9999 0 -1.2 133 133
SP1 0.033 0.024 -9999 0 -0.42 1 1
CDC25B -0.24 0.52 -9999 0 -1.1 94 94
response to radiation -0.004 0.031 -9999 0 -10000 0 0
CENPB -0.24 0.51 -9999 0 -1.1 96 96
CENPA -0.27 0.54 -9999 0 -1.2 95 95
NEK2 -0.26 0.58 -9999 0 -1.2 110 110
HIST1H2BA -0.24 0.52 -9999 0 -1.2 85 85
CCNA2 0.004 0.11 -9999 0 -0.43 28 28
EP300 0.033 0.022 -9999 0 -0.42 1 1
CCNB1/CDK1 -0.31 0.64 -9999 0 -1.5 85 85
CCNB2 -0.25 0.53 -9999 0 -1.2 85 85
CCNB1 -0.27 0.56 -9999 0 -1.2 95 95
ETV5 -0.25 0.52 -9999 0 -1.1 95 95
ESR1 -0.43 0.65 -9999 0 -1.2 205 205
CCND1 -0.32 0.52 -9999 0 -1 140 140
GSK3A 0.008 0.052 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.021 0.11 -9999 0 -0.33 29 29
CDK2 0.028 0.034 -9999 0 -0.43 2 2
G2/M transition of mitotic cell cycle -0.006 0.036 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.27 0.57 -9999 0 -1.2 101 101
GAS1 -0.32 0.59 -9999 0 -1.2 129 129
MMP2 -0.27 0.56 -9999 0 -1.3 96 96
RB1/FOXM1C -0.29 0.55 -9999 0 -1.1 140 140
CREBBP 0.032 0.011 -9999 0 -10000 0 0
IGF1 pathway

Figure S5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.035 0.004 -10000 0 -10000 0 0
PTK2 0.027 0.015 -10000 0 -10000 0 0
CRKL -0.073 0.15 0.17 2 -0.3 137 139
GRB2/SOS1/SHC 0.051 0.036 -10000 0 -0.26 1 1
HRAS 0.032 0.036 -10000 0 -0.42 3 3
IRS1/Crk -0.066 0.16 -10000 0 -0.3 143 143
IGF-1R heterotetramer/IGF1/PTP1B -0.037 0.16 -10000 0 -0.29 131 131
AKT1 -0.08 0.14 0.17 12 -0.29 115 127
BAD -0.078 0.13 0.15 12 -0.36 59 71
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.069 0.15 0.17 2 -0.3 131 133
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.061 0.16 0.22 1 -0.3 143 144
RAF1 -0.041 0.14 0.29 3 -0.48 16 19
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.027 0.17 -10000 0 -0.29 130 130
YWHAZ 0.026 0.016 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.065 0.17 -10000 0 -0.3 154 154
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
RPS6KB1 -0.073 0.13 0.17 2 -0.38 56 58
GNB2L1 0.033 0.035 -10000 0 -0.42 3 3
positive regulation of MAPKKK cascade -0.027 0.14 0.32 7 -0.42 13 20
PXN 0.036 0.004 -10000 0 -10000 0 0
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.047 0.022 -10000 0 -0.3 1 1
HRAS/GTP -0.042 0.13 -10000 0 -0.26 114 114
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.001 0.14 -10000 0 -0.24 104 104
IGF-1R heterotetramer -0.062 0.18 -10000 0 -0.47 84 84
IGF-1R heterotetramer/IGF1/IRS/Nck -0.045 0.17 -10000 0 -0.28 153 153
Crk/p130 Cas/Paxillin -0.04 0.16 -10000 0 -0.28 138 138
IGF1R -0.062 0.18 -10000 0 -0.47 84 84
IGF1 -0.063 0.18 -10000 0 -0.46 81 81
IRS2/Crk -0.072 0.16 -10000 0 -0.29 151 151
PI3K -0.04 0.18 -10000 0 -0.29 147 147
apoptosis 0.051 0.12 0.31 46 -0.29 5 51
HRAS/GDP 0.023 0.025 -10000 0 -0.3 3 3
PRKCD -0.065 0.18 -10000 0 -0.34 130 130
RAF1/14-3-3 E -0.021 0.14 0.29 3 -0.41 16 19
BAD/14-3-3 -0.054 0.12 0.3 5 -0.33 46 51
PRKCZ -0.078 0.14 0.16 3 -0.28 130 133
Crk/p130 Cas/Paxillin/FAK1 -0.036 0.12 -10000 0 -0.34 44 44
PTPN1 0.029 0.031 -10000 0 -0.42 2 2
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.078 0.18 -10000 0 -0.35 132 132
BCAR1 0.029 0.014 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.02 0.15 -10000 0 -0.26 123 123
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.034 0.021 -10000 0 -0.42 1 1
IRS1/NCK2 -0.056 0.16 -10000 0 -0.28 153 153
GRB10 0.022 0.075 -10000 0 -0.42 14 14
PTPN11 -0.074 0.15 0.17 2 -0.3 143 145
IRS1 -0.077 0.16 -10000 0 -0.3 153 153
IRS2 -0.08 0.16 0.17 2 -0.31 143 145
IGF-1R heterotetramer/IGF1 -0.074 0.19 -10000 0 -0.37 141 141
GRB2 0.033 0.01 -10000 0 -10000 0 0
PDPK1 -0.077 0.14 -10000 0 -0.29 127 127
YWHAE 0.032 0.011 -10000 0 -10000 0 0
PRKD1 -0.075 0.2 0.21 4 -0.37 129 133
SHC1 0.027 0.025 -10000 0 -0.42 1 1
Osteopontin-mediated 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
IKK alpha homodimer -0.037 0.15 0.36 1 -0.27 130 131
NF kappa B1 p50/RelA/I kappa B alpha -0.034 0.17 0.33 1 -0.39 58 59
alphaV/beta3 Integrin/Osteopontin/Src -0.045 0.17 -10000 0 -0.32 127 127
AP1 -0.085 0.23 -10000 0 -0.49 83 83
ILK -0.047 0.14 0.38 1 -0.26 122 123
bone resorption -0.054 0.14 0.32 1 -0.35 45 46
PTK2B 0.028 0.015 -10000 0 -10000 0 0
PYK2/p130Cas -0.028 0.16 -10000 0 -0.27 111 111
ITGAV 0.017 0.084 -10000 0 -0.43 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.038 0.066 -10000 0 -0.3 18 18
alphaV/beta3 Integrin/Osteopontin -0.023 0.16 -10000 0 -0.28 128 128
MAP3K1 -0.06 0.14 0.38 1 -0.27 145 146
JUN -0.002 0.12 -10000 0 -0.42 39 39
MAPK3 -0.06 0.14 0.3 2 -0.27 131 133
MAPK1 -0.064 0.15 0.3 2 -0.28 140 142
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
NFKB1 0.035 0.005 -10000 0 -10000 0 0
MAPK8 -0.065 0.13 0.26 3 -0.25 144 147
ITGB3 0.024 0.051 -10000 0 -0.43 5 5
NFKBIA -0.069 0.16 0.35 2 -0.41 61 63
FOS -0.032 0.15 -10000 0 -0.42 66 66
CD44 0.022 0.075 -10000 0 -0.42 14 14
CHUK 0.025 0.067 -10000 0 -0.42 11 11
PLAU -0.14 0.36 -10000 0 -1.2 51 51
NF kappa B1 p50/RelA -0.022 0.19 -10000 0 -0.45 55 55
BCAR1 0.029 0.014 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.03 0.082 -10000 0 -0.32 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.061 0.15 0.38 1 -0.28 148 149
VAV3 -0.1 0.15 0.29 2 -0.27 201 203
MAP3K14 -0.05 0.14 0.39 1 -0.28 128 129
ROCK2 0.032 0.041 -10000 0 -0.42 4 4
SPP1 -0.077 0.19 -10000 0 -0.43 116 116
RAC1 0.035 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.083 0.15 -10000 0 -0.25 195 195
MMP2 -0.1 0.19 -10000 0 -0.45 85 85
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.007 0.13 -10000 0 -0.22 132 132
ER alpha/Gai/GDP/Gbeta gamma -0.12 0.21 -10000 0 -0.37 156 156
AKT1 -0.22 0.37 -10000 0 -0.74 164 164
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.22 0.38 -10000 0 -0.75 164 164
mol:Ca2+ -0.07 0.15 0.17 1 -0.4 65 66
IGF1R -0.043 0.17 -10000 0 -0.42 84 84
E2/ER alpha (dimer)/Striatin -0.037 0.13 -10000 0 -0.25 133 133
SHC1 0.027 0.025 -10000 0 -0.42 1 1
apoptosis 0.21 0.35 0.7 164 -10000 0 164
RhoA/GTP -0.039 0.11 -10000 0 -0.21 129 129
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.1 0.21 -10000 0 -0.38 148 148
regulation of stress fiber formation 0.04 0.1 0.33 7 -0.23 2 9
E2/ERA-ERB (dimer) -0.036 0.13 -10000 0 -0.25 130 130
KRAS 0.027 0.057 -10000 0 -0.42 8 8
G13/GTP -0.033 0.12 -10000 0 -0.23 125 125
pseudopodium formation -0.04 0.1 0.23 2 -0.33 7 9
E2/ER alpha (dimer)/PELP1 -0.038 0.13 -10000 0 -0.25 129 129
GRB2 0.033 0.01 -10000 0 -10000 0 0
GNG2 0.034 0.021 -10000 0 -0.42 1 1
GNAO1 0.03 0.014 -10000 0 -10000 0 0
HRAS 0.032 0.036 -10000 0 -0.42 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.14 0.24 0.24 1 -0.45 162 163
E2/ER beta (dimer) 0.025 0.006 -10000 0 -10000 0 0
mol:GDP -0.075 0.17 -10000 0 -0.34 136 136
mol:NADP -0.14 0.24 0.24 1 -0.45 162 163
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
mol:IP3 -0.073 0.15 -10000 0 -0.39 72 72
IGF-1R heterotetramer -0.043 0.17 -10000 0 -0.42 84 84
PLCB1 -0.071 0.16 -10000 0 -0.34 99 99
PLCB2 -0.052 0.15 -10000 0 -0.42 58 58
IGF1 -0.041 0.17 -10000 0 -0.42 81 81
mol:L-citrulline -0.14 0.24 0.24 1 -0.45 162 163
RHOA 0.026 0.061 -10000 0 -0.42 9 9
Gai/GDP -0.1 0.28 -10000 0 -0.62 103 103
JNK cascade 0.025 0.006 -10000 0 -10000 0 0
BCAR1 0.029 0.014 -10000 0 -10000 0 0
ESR2 0.034 0.007 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.088 0.2 -10000 0 -0.42 130 130
Gq family/GDP/Gbeta gamma -0.018 0.17 -10000 0 -0.69 22 22
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.033 0.13 -10000 0 -0.6 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.088 0.19 -10000 0 -0.38 121 121
GNAZ 0.023 0.067 -10000 0 -0.42 11 11
E2/ER alpha (dimer) -0.061 0.14 -10000 0 -0.3 130 130
STRN 0.031 0.045 -10000 0 -0.42 5 5
GNAL 0.031 0.036 -10000 0 -0.42 3 3
PELP1 0.032 0.011 -10000 0 -10000 0 0
MAPK11 0.016 0.006 -10000 0 -10000 0 0
GNAI2 0.027 0.057 -10000 0 -0.42 8 8
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNAI1 0.017 0.085 -10000 0 -0.42 18 18
HBEGF -0.11 0.21 0.32 9 -0.48 63 72
cAMP biosynthetic process -0.028 0.1 -10000 0 -0.2 127 127
SRC -0.1 0.2 0.28 1 -0.36 140 141
PI3K 0.035 0.067 -10000 0 -0.3 18 18
GNB1 0.031 0.045 -10000 0 -0.42 5 5
G13/GDP/Gbeta gamma -0.05 0.17 -10000 0 -0.32 119 119
SOS1 0.034 0.021 -10000 0 -0.42 1 1
IGF-1R heterotetramer/IGF1 -0.13 0.19 -10000 0 -0.4 144 144
Gs family/GTP -0.022 0.11 -10000 0 -0.21 127 127
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.053 0.054 -10000 0 -0.23 15 15
vasodilation -0.13 0.22 0.24 1 -0.43 162 163
mol:DAG -0.073 0.15 -10000 0 -0.39 72 72
Gs family/GDP/Gbeta gamma -0.064 0.15 -10000 0 -0.32 112 112
MSN -0.043 0.11 0.24 2 -0.35 7 9
Gq family/GTP -0.053 0.15 -10000 0 -0.43 60 60
mol:PI-3-4-5-P3 -0.21 0.36 -10000 0 -0.72 164 164
NRAS 0.029 0.05 -10000 0 -0.42 6 6
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.13 0.22 0.43 162 -0.24 1 163
GRB2/SOS1 0.047 0.022 -10000 0 -0.3 1 1
RhoA/GDP -0.06 0.17 -10000 0 -0.32 142 142
NOS3 -0.14 0.25 -10000 0 -0.47 162 162
GNA11 0.032 0.036 -10000 0 -0.42 3 3
MAPKKK cascade -0.14 0.27 -10000 0 -0.52 156 156
E2/ER alpha (dimer)/PELP1/Src -0.11 0.21 -10000 0 -0.39 150 150
ruffle organization -0.04 0.1 0.23 2 -0.33 7 9
ROCK2 -0.041 0.12 0.26 2 -0.33 10 12
GNA14 -0.01 0.13 -10000 0 -0.42 44 44
GNA15 0.029 0.046 -10000 0 -0.42 5 5
GNA13 0.028 0.042 -10000 0 -0.42 4 4
MMP9 -0.12 0.21 0.38 9 -0.47 64 73
MMP2 -0.11 0.2 0.26 3 -0.48 58 61
Syndecan-1-mediated signaling events

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
TGFB1 0.035 0.021 -10000 0 -0.42 1 1
CCL5 -0.013 0.14 -10000 0 -0.42 51 51
SDCBP 0.022 0.061 -10000 0 -0.42 9 9
FGFR/FGF2/Syndecan-1 -0.11 0.23 0.22 6 -0.49 102 108
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.11 0.22 -10000 0 -0.51 89 89
Syndecan-1/Syntenin -0.11 0.22 0.26 1 -0.49 93 94
MAPK3 -0.097 0.2 0.24 1 -0.46 89 90
HGF/MET 0.041 0.057 -10000 0 -0.3 13 13
TGFB1/TGF beta receptor Type II 0.034 0.021 -10000 0 -0.42 1 1
BSG 0.034 0.008 -10000 0 -10000 0 0
keratinocyte migration -0.11 0.22 -10000 0 -0.5 89 89
Syndecan-1/RANTES -0.13 0.24 0.26 1 -0.5 112 113
Syndecan-1/CD147 -0.096 0.23 0.27 1 -0.5 91 92
Syndecan-1/Syntenin/PIP2 -0.1 0.21 0.25 1 -0.47 93 94
LAMA5 0.026 0.05 -10000 0 -0.42 6 6
positive regulation of cell-cell adhesion -0.1 0.21 0.24 1 -0.46 93 94
MMP7 -0.033 0.16 -10000 0 -0.42 69 69
HGF 0.028 0.057 -10000 0 -0.42 8 8
Syndecan-1/CASK -0.12 0.21 -10000 0 -0.37 158 158
Syndecan-1/HGF/MET -0.1 0.23 0.27 1 -0.49 94 95
regulation of cell adhesion -0.1 0.19 0.23 1 -0.45 89 90
HPSE 0.014 0.093 -10000 0 -0.42 22 22
positive regulation of cell migration -0.11 0.23 0.22 6 -0.49 102 108
SDC1 -0.11 0.23 0.28 1 -0.4 152 153
Syndecan-1/Collagen -0.11 0.23 0.22 6 -0.49 102 108
PPIB 0.033 0.029 -10000 0 -0.42 2 2
MET 0.028 0.046 -10000 0 -0.42 5 5
PRKACA 0.035 0.004 -10000 0 -10000 0 0
MMP9 -0.014 0.14 -10000 0 -0.42 52 52
MAPK1 -0.1 0.21 0.24 1 -0.47 91 92
homophilic cell adhesion -0.12 0.22 0.22 6 -0.53 88 94
MMP1 -0.076 0.18 -10000 0 -0.42 109 109
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.034 0.034 -10000 0 -0.26 4 4
NFATC2 -0.051 0.21 -10000 0 -0.5 53 53
NFATC3 -0.018 0.12 -10000 0 -0.26 77 77
CD40LG -0.19 0.38 -10000 0 -0.76 126 126
ITCH 0.012 0.071 -10000 0 -0.22 42 42
CBLB 0.013 0.074 -10000 0 -0.22 42 42
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.14 0.33 -10000 0 -0.79 74 74
JUNB 0.032 0.041 -10000 0 -0.42 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.087 -10000 0 -0.26 45 45
T cell anergy -0.015 0.12 0.26 2 -0.36 45 47
TLE4 -0.044 0.17 -10000 0 -0.48 41 41
Jun/NFAT1-c-4/p21SNFT -0.17 0.39 -10000 0 -0.79 116 116
AP-1/NFAT1-c-4 -0.19 0.45 -10000 0 -0.86 123 123
IKZF1 -0.038 0.14 -10000 0 -0.34 53 53
T-helper 2 cell differentiation -0.17 0.3 -10000 0 -0.79 67 67
AP-1/NFAT1 -0.045 0.2 -10000 0 -0.4 82 82
CALM1 0.027 0.058 -10000 0 -0.16 2 2
EGR2 -0.22 0.48 -10000 0 -1.1 82 82
EGR3 -0.29 0.55 -10000 0 -1.1 131 131
NFAT1/FOXP3 -0.017 0.16 -10000 0 -0.38 45 45
EGR1 -0.038 0.16 -10000 0 -0.42 75 75
JUN -0.003 0.12 -10000 0 -0.42 39 39
EGR4 0 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.046 -10000 0 -0.15 46 46
GBP3 -0.088 0.25 -10000 0 -0.63 75 75
FOSL1 0.035 0.007 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.15 0.39 -10000 0 -0.78 114 114
DGKA -0.04 0.16 -10000 0 -0.42 43 43
CREM 0.034 0.008 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.18 0.4 -10000 0 -0.81 120 120
CTLA4 -0.026 0.14 -10000 0 -0.37 37 37
NFAT1-c-4 (dimer)/EGR1 -0.19 0.42 -10000 0 -0.84 127 127
NFAT1-c-4 (dimer)/EGR4 -0.17 0.39 -10000 0 -0.79 120 120
FOS -0.034 0.15 -10000 0 -0.42 66 66
IFNG -0.19 0.43 -10000 0 -1 85 85
T cell activation -0.1 0.26 -10000 0 -0.71 38 38
MAF 0.015 0.075 -10000 0 -0.42 14 14
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.15 0.34 0.74 91 -10000 0 91
TNF -0.19 0.37 -10000 0 -0.77 128 128
FASLG -0.34 0.64 -10000 0 -1.2 147 147
TBX21 -0.045 0.17 -10000 0 -0.43 85 85
BATF3 0 0.001 -10000 0 -10000 0 0
PRKCQ 0.021 0.061 -10000 0 -0.44 7 7
PTPN1 -0.037 0.15 -10000 0 -0.41 40 40
NFAT1-c-4/ICER1 -0.16 0.39 -10000 0 -0.79 117 117
GATA3 -0.047 0.17 -10000 0 -0.42 90 90
T-helper 1 cell differentiation -0.19 0.41 -10000 0 -0.96 87 87
IL2RA -0.14 0.33 -10000 0 -0.76 77 77
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.035 0.14 -10000 0 -0.39 37 37
E2F1 0.032 0.054 -10000 0 -0.42 7 7
PPARG 0.012 0.091 -10000 0 -0.42 21 21
SLC3A2 -0.034 0.14 -10000 0 -0.37 43 43
IRF4 0.031 0.031 -10000 0 -0.42 2 2
PTGS2 -0.18 0.36 -10000 0 -0.78 106 106
CSF2 -0.19 0.38 -10000 0 -0.76 125 125
JunB/Fra1/NFAT1-c-4 -0.15 0.39 -10000 0 -0.78 114 114
IL4 -0.17 0.32 -10000 0 -0.83 66 66
IL5 -0.19 0.38 -10000 0 -0.76 126 126
IL2 -0.1 0.26 -10000 0 -0.75 34 34
IL3 -0.013 0.14 -10000 0 -0.88 9 9
RNF128 -0.017 0.16 -10000 0 -0.52 44 44
NFATC1 -0.16 0.34 -10000 0 -0.75 89 89
CDK4 0.1 0.21 0.56 40 -10000 0 40
PTPRK -0.067 0.22 -10000 0 -0.6 61 61
IL8 -0.2 0.38 -10000 0 -0.78 124 124
POU2F1 0.033 0.017 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.032 0.036 -10000 0 -0.42 3 3
EGFR -0.013 0.13 -10000 0 -0.42 47 47
EGF/EGFR -0.073 0.18 -10000 0 -0.27 200 200
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.002 0.13 -10000 0 -0.23 104 104
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.004 0.13 -10000 0 -0.42 43 43
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.069 0.19 -10000 0 -0.42 110 110
EGF/EGFR dimer/SHC -0.029 0.14 -10000 0 -0.26 120 120
mol:GDP -0.006 0.12 -10000 0 -0.23 104 104
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.038 0.16 -10000 0 -0.42 77 77
GRB2/SOS1 0.047 0.022 -10000 0 -0.3 1 1
HRAS/GTP -0.017 0.11 -10000 0 -0.21 106 106
SHC1 0.027 0.025 -10000 0 -0.42 1 1
HRAS/GDP -0.007 0.12 -10000 0 -0.22 106 106
FRAP1 -0.016 0.14 0.37 11 -0.4 4 15
EGF/EGFR dimer -0.061 0.16 -10000 0 -0.3 151 151
SOS1 0.034 0.021 -10000 0 -0.42 1 1
GRB2 0.033 0.01 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.03 0.16 -10000 0 -0.33 104 104
IL4-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
BCL2L1 -0.36 0.64 -10000 0 -1.3 119 119
STAT6 (cleaved dimer) -0.38 0.65 -10000 0 -1.3 135 135
IGHG1 -0.082 0.24 -10000 0 -0.61 21 21
IGHG3 -0.35 0.61 -10000 0 -1.2 136 136
AKT1 -0.12 0.33 -10000 0 -0.88 34 34
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.066 0.26 -10000 0 -0.91 19 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.36 -10000 0 -0.9 48 48
THY1 -0.37 0.66 -10000 0 -1.4 119 119
MYB -0.056 0.18 -10000 0 -0.42 98 98
HMGA1 0.033 0.029 -10000 0 -0.42 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.14 0.35 -10000 0 -0.78 48 48
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.12 0.33 -10000 0 -0.99 28 28
SP1 0.023 0.051 -10000 0 -0.21 5 5
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.019 0.056 -10000 0 -0.42 4 4
STAT6 (dimer)/ETS1 -0.37 0.64 -10000 0 -1.3 128 128
SOCS1 -0.2 0.38 -10000 0 -0.78 110 110
SOCS3 -0.12 0.32 -10000 0 -0.99 22 22
FCER2 -0.23 0.46 -10000 0 -0.94 95 95
PARP14 0.03 0.051 -10000 0 -0.42 6 6
CCL17 -0.42 0.71 -10000 0 -1.4 138 138
GRB2 0.033 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.075 0.26 -10000 0 -0.74 27 27
T cell proliferation -0.37 0.67 -10000 0 -1.4 126 126
IL4R/JAK1 -0.37 0.65 -10000 0 -1.4 124 124
EGR2 -0.41 0.69 -10000 0 -1.4 136 136
JAK2 -0.005 0.069 -10000 0 -0.46 2 2
JAK3 0.038 0.014 -10000 0 -10000 0 0
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
JAK1 0.018 0.048 -10000 0 -0.42 3 3
COL1A2 -0.22 0.53 -10000 0 -1.5 70 70
CCL26 -0.36 0.64 -10000 0 -1.3 121 121
IL4R -0.39 0.71 -10000 0 -1.5 123 123
PTPN6 0.021 0.045 -10000 0 -0.41 2 2
IL13RA2 -0.4 0.67 -10000 0 -1.4 134 134
IL13RA1 -0.009 0.086 -10000 0 -0.46 8 8
IRF4 -0.005 0.16 -10000 0 -1 5 5
ARG1 -0.065 0.26 -10000 0 -1.1 17 17
CBL -0.14 0.32 -10000 0 -0.75 43 43
GTF3A 0.024 0.045 -10000 0 -0.17 2 2
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
IL13RA1/JAK2 -0.002 0.1 -10000 0 -0.36 8 8
IRF4/BCL6 -0.005 0.16 -10000 0 -0.97 5 5
CD40LG 0.038 0.038 -10000 0 -0.42 3 3
MAPK14 -0.14 0.33 -10000 0 -0.87 32 32
mitosis -0.11 0.31 -10000 0 -0.81 35 35
STAT6 -0.47 0.88 -10000 0 -1.7 133 133
SPI1 0.032 0.055 -10000 0 -0.34 9 9
RPS6KB1 -0.092 0.3 -10000 0 -0.8 32 32
STAT6 (dimer) -0.47 0.88 -10000 0 -1.7 133 133
STAT6 (dimer)/PARP14 -0.41 0.73 -10000 0 -1.5 134 134
mast cell activation 0.005 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.14 0.35 -10000 0 -0.91 40 40
FRAP1 -0.12 0.33 -10000 0 -0.88 34 34
LTA -0.36 0.64 -10000 0 -1.4 115 115
FES 0.03 0.041 -10000 0 -0.42 4 4
T-helper 1 cell differentiation 0.42 0.78 1.5 133 -10000 0 133
CCL11 -0.39 0.66 -10000 0 -1.3 137 137
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.1 0.31 -10000 0 -0.91 27 27
IL2RG 0.033 0.042 -10000 0 -0.41 4 4
IL10 -0.33 0.65 -10000 0 -1.3 118 118
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
IRS2 0.008 0.099 -10000 0 -0.42 25 25
IL4 -0.064 0.29 -10000 0 -1.3 19 19
IL5 -0.36 0.64 -10000 0 -1.4 118 118
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.26 0.51 -10000 0 -0.98 121 121
COL1A1 -0.26 0.59 -10000 0 -1.4 88 88
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.39 0.69 -10000 0 -1.5 115 115
IL2R gamma/JAK3 0.053 0.035 -10000 0 -0.29 4 4
TFF3 -0.53 0.76 -10000 0 -1.4 188 188
ALOX15 -0.37 0.65 -10000 0 -1.4 109 109
MYBL1 -0.012 0.13 -10000 0 -0.42 43 43
T-helper 2 cell differentiation -0.27 0.52 -10000 0 -1 115 115
SHC1 0.027 0.025 -10000 0 -0.42 1 1
CEBPB 0.028 0.056 -10000 0 -0.3 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.13 0.33 -10000 0 -0.88 38 38
mol:PI-3-4-5-P3 -0.12 0.33 -10000 0 -0.88 34 34
PI3K -0.13 0.35 -10000 0 -0.97 34 34
DOK2 0.01 0.084 -10000 0 -0.42 18 18
ETS1 0.014 0.043 -10000 0 -0.38 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.061 0.25 -10000 0 -0.7 22 22
ITGB3 -0.36 0.64 -10000 0 -1.4 121 121
PIGR -0.45 0.77 -10000 0 -1.4 168 168
IGHE 0.012 0.089 0.21 35 -0.22 10 45
MAPKKK cascade -0.059 0.24 -10000 0 -0.68 22 22
BCL6 0.017 0.085 -10000 0 -0.42 18 18
OPRM1 -0.36 0.64 -10000 0 -1.3 120 120
RETNLB -0.36 0.64 -10000 0 -1.3 120 120
SELP -0.42 0.75 -10000 0 -1.5 148 148
AICDA -0.36 0.62 -10000 0 -1.3 124 124
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.058 0.35 -10000 0 -0.72 76 76
HDAC7 0 0.003 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.011 0.34 -10000 0 -0.7 57 57
SMAD4 0.029 0.054 -10000 0 -0.42 7 7
ID2 -0.059 0.35 -10000 0 -0.72 77 77
AP1 -0.035 0.16 -10000 0 -0.35 89 89
ABCG2 -0.061 0.35 -10000 0 -0.72 79 79
HIF1A -0.023 0.16 -10000 0 -0.45 49 49
TFF3 -0.11 0.37 -10000 0 -0.74 87 87
GATA2 0.018 0.054 -10000 0 -0.42 5 5
AKT1 0.009 0.093 -10000 0 -0.26 13 13
response to hypoxia -0.008 0.065 -10000 0 -0.15 32 32
MCL1 -0.061 0.35 -10000 0 -0.72 76 76
NDRG1 -0.068 0.33 -10000 0 -0.74 67 67
SERPINE1 -0.065 0.36 -10000 0 -0.74 76 76
FECH -0.065 0.35 -10000 0 -0.72 80 80
FURIN -0.061 0.35 -10000 0 -0.72 77 77
NCOA2 0.026 0.047 -10000 0 -0.42 5 5
EP300 0.007 0.11 -10000 0 -0.3 27 27
HMOX1 -0.07 0.36 -10000 0 -0.72 81 81
BHLHE40 -0.08 0.34 -10000 0 -0.7 79 79
BHLHE41 -0.08 0.34 -10000 0 -0.7 79 79
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.049 0.17 -10000 0 -0.32 44 44
ENG -0.008 0.13 -10000 0 -0.31 41 41
JUN -0.009 0.12 -10000 0 -0.43 39 39
RORA -0.068 0.36 -10000 0 -0.73 78 78
ABCB1 -0.029 0.25 -10000 0 -0.95 28 28
TFRC -0.075 0.36 -10000 0 -0.73 82 82
CXCR4 -0.071 0.37 -10000 0 -0.74 81 81
TF -0.059 0.35 -10000 0 -0.72 75 75
CITED2 -0.062 0.35 -10000 0 -0.72 75 75
HIF1A/ARNT -0.039 0.42 -10000 0 -0.87 61 61
LDHA 0.01 0.18 -10000 0 -0.86 17 17
ETS1 -0.069 0.34 -10000 0 -0.72 76 76
PGK1 -0.057 0.35 -10000 0 -0.72 76 76
NOS2 -0.08 0.34 -10000 0 -0.7 79 79
ITGB2 -0.068 0.36 -10000 0 -0.74 79 79
ALDOA -0.055 0.34 -10000 0 -0.72 72 72
Cbp/p300/CITED2 -0.058 0.36 -10000 0 -0.8 62 62
FOS -0.039 0.15 -10000 0 -0.43 66 66
HK2 -0.058 0.35 -10000 0 -0.71 78 78
SP1 0.035 0.039 -10000 0 -0.18 8 8
GCK 0.013 0.18 -10000 0 -1.2 4 4
HK1 -0.057 0.35 -10000 0 -0.72 76 76
NPM1 -0.056 0.35 -10000 0 -0.71 76 76
EGLN1 -0.068 0.33 -10000 0 -0.72 70 70
CREB1 0.039 0.026 -10000 0 -0.42 1 1
PGM1 -0.063 0.35 -10000 0 -0.72 77 77
SMAD3 0.027 0.061 -10000 0 -0.42 9 9
EDN1 -0.18 0.47 -10000 0 -1.2 88 88
IGFBP1 -0.057 0.35 -10000 0 -0.71 78 78
VEGFA -0.044 0.27 0.44 1 -0.58 64 65
HIF1A/JAB1 0.002 0.12 -10000 0 -0.34 42 42
CP -0.12 0.38 -10000 0 -0.77 89 89
CXCL12 -0.074 0.37 -10000 0 -0.75 84 84
COPS5 0.027 0.042 -10000 0 -0.42 4 4
SMAD3/SMAD4 0.04 0.063 -10000 0 -0.3 16 16
BNIP3 -0.064 0.36 -10000 0 -0.72 79 79
EGLN3 -0.083 0.37 -10000 0 -0.75 86 86
CA9 -0.063 0.35 -10000 0 -0.72 76 76
TERT -0.058 0.35 -10000 0 -0.72 74 74
ENO1 -0.06 0.35 -10000 0 -0.72 75 75
PFKL -0.059 0.35 -10000 0 -0.73 75 75
NCOA1 0.031 0.045 -10000 0 -0.42 5 5
ADM -0.082 0.38 -10000 0 -0.76 85 85
ARNT 0.014 0.077 -10000 0 -10000 0 0
HNF4A 0.034 0.033 -10000 0 -0.28 4 4
ADFP -0.067 0.36 -10000 0 -0.74 80 80
SLC2A1 -0.033 0.28 -10000 0 -0.6 59 59
LEP -0.076 0.36 -10000 0 -0.73 78 78
HIF1A/ARNT/Cbp/p300 -0.025 0.34 -10000 0 -0.71 58 58
EPO -0.029 0.27 -10000 0 -0.69 41 41
CREBBP 0.015 0.097 -10000 0 -0.29 16 16
HIF1A/ARNT/Cbp/p300/HDAC7 -0.023 0.33 -10000 0 -0.69 58 58
PFKFB3 -0.061 0.35 -10000 0 -0.74 73 73
NT5E -0.06 0.35 -10000 0 -0.73 76 76
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 0.054 0.16 0.32 5 -0.84 9 14
SMARCC2 0.035 0.004 -10000 0 -10000 0 0
SMARCC1 0.032 0.03 -10000 0 -0.42 2 2
TBX21 -0.15 0.28 0.36 1 -0.72 89 90
SUMO2 0.028 0.02 -10000 0 -10000 0 0
STAT1 (dimer) 0.019 0.093 -10000 0 -0.38 24 24
FKBP4 0.029 0.046 -10000 0 -0.42 5 5
FKBP5 -0.005 0.13 -10000 0 -0.42 42 42
GR alpha/HSP90/FKBP51/HSP90 0.06 0.14 0.26 102 -0.25 27 129
PRL -0.036 0.13 0.42 1 -0.64 5 6
cortisol/GR alpha (dimer)/TIF2 0.13 0.24 0.53 108 -0.34 1 109
RELA -0.021 0.11 -10000 0 -0.21 94 94
FGG 0.14 0.22 0.45 137 -0.36 2 139
GR beta/TIF2 0.069 0.14 0.3 84 -0.29 8 92
IFNG -0.26 0.4 -10000 0 -0.82 137 137
apoptosis -0.003 0.17 0.5 5 -0.54 7 12
CREB1 0.038 0.042 -10000 0 -0.37 5 5
histone acetylation -0.025 0.11 0.3 4 -0.32 35 39
BGLAP -0.048 0.14 -10000 0 -0.49 15 15
GR/PKAc 0.11 0.12 0.32 54 -0.27 13 67
NF kappa B1 p50/RelA -0.043 0.19 -10000 0 -0.34 121 121
SMARCD1 0.036 0.004 -10000 0 -10000 0 0
MDM2 0.072 0.1 0.22 126 -10000 0 126
GATA3 -0.039 0.18 -10000 0 -0.42 90 90
AKT1 0.029 0.041 0.18 9 -0.43 3 12
CSF2 -0.05 0.13 -10000 0 -0.86 5 5
GSK3B 0.029 0.02 -10000 0 -10000 0 0
NR1I3 0.029 0.18 0.61 3 -0.89 3 6
CSN2 0.12 0.19 0.38 132 -0.35 5 137
BRG1/BAF155/BAF170/BAF60A 0.083 0.036 -10000 0 -0.24 3 3
NFATC1 0.022 0.09 -10000 0 -0.4 21 21
POU2F1 0.033 0.021 -10000 0 -0.25 1 1
CDKN1A -0.046 0.26 -10000 0 -1.5 13 13
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.006 -10000 0 -10000 0 0
SFN 0.011 0.099 -10000 0 -0.42 25 25
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.068 0.14 0.29 60 -0.24 41 101
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.079 0.31 0.47 3 -0.78 77 80
JUN -0.16 0.23 0.36 4 -0.46 145 149
IL4 -0.087 0.19 -10000 0 -0.6 30 30
CDK5R1 0.033 0.01 -10000 0 -10000 0 0
PRKACA 0.035 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.096 0.21 0.21 72 -0.37 149 221
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.085 0.13 0.29 68 -0.22 32 100
cortisol/GR alpha (monomer) 0.19 0.31 0.6 147 -0.38 2 149
NCOA2 0.024 0.047 -10000 0 -0.42 5 5
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.083 0.16 -10000 0 -0.41 78 78
AP-1/NFAT1-c-4 -0.27 0.37 -10000 0 -0.7 182 182
AFP -0.12 0.2 -10000 0 -0.74 11 11
SUV420H1 0.032 0.022 -10000 0 -0.42 1 1
IRF1 0.093 0.21 0.4 68 -0.67 15 83
TP53 0.015 0.12 -10000 0 -0.45 31 31
PPP5C 0.031 0.041 -10000 0 -0.42 4 4
KRT17 -0.39 0.56 -10000 0 -1.2 151 151
KRT14 -0.26 0.49 -10000 0 -1.2 97 97
TBP 0.04 0.018 -10000 0 -0.28 1 1
CREBBP 0.065 0.096 0.28 79 -10000 0 79
HDAC1 0.03 0.021 -10000 0 -0.43 1 1
HDAC2 0.03 0.023 -10000 0 -0.42 1 1
AP-1 -0.28 0.37 -10000 0 -0.71 181 181
MAPK14 0.031 0.015 -10000 0 -10000 0 0
MAPK10 0.008 0.091 -10000 0 -0.42 21 21
MAPK11 0.027 0.02 -10000 0 -10000 0 0
KRT5 -0.39 0.57 -10000 0 -1.2 150 150
interleukin-1 receptor activity -0.001 0.007 -10000 0 -10000 0 0
NCOA1 0.031 0.048 -10000 0 -0.37 6 6
STAT1 0.019 0.093 -10000 0 -0.38 24 24
CGA -0.072 0.17 -10000 0 -0.55 29 29
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.083 0.16 0.37 89 -0.36 3 92
MAPK3 0.026 0.028 -10000 0 -0.42 1 1
MAPK1 0.029 0.026 -10000 0 -0.42 1 1
ICAM1 -0.16 0.31 -10000 0 -0.74 85 85
NFKB1 -0.023 0.11 -10000 0 -0.22 79 79
MAPK8 -0.11 0.19 0.48 2 -0.38 131 133
MAPK9 0.014 0.087 -10000 0 -0.42 19 19
cortisol/GR alpha (dimer) -0.006 0.18 0.5 5 -0.56 7 12
BAX -0.011 0.1 -10000 0 -10000 0 0
POMC -0.091 0.2 -10000 0 -1.2 5 5
EP300 0.066 0.097 0.28 83 -0.43 1 84
cortisol/GR alpha (dimer)/p53 0.12 0.25 0.52 105 -10000 0 105
proteasomal ubiquitin-dependent protein catabolic process 0.053 0.11 0.28 64 -10000 0 64
SGK1 0.081 0.14 0.34 93 -0.42 2 95
IL13 -0.22 0.26 -10000 0 -0.66 85 85
IL6 -0.2 0.38 -10000 0 -0.9 94 94
PRKACG 0.034 0.029 -10000 0 -0.42 2 2
IL5 -0.18 0.22 -10000 0 -0.64 40 40
IL2 -0.22 0.33 -10000 0 -0.72 120 120
CDK5 0.034 0.007 -10000 0 -10000 0 0
PRKACB 0.009 0.097 -10000 0 -0.42 24 24
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.18 0.34 -10000 0 -0.81 93 93
CDK5R1/CDK5 0.047 0.017 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.003 0.18 -10000 0 -0.35 63 63
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.16 0.24 0.49 141 -10000 0 141
SMARCA4 0.034 0.021 -10000 0 -0.42 1 1
chromatin remodeling 0.11 0.16 0.34 128 -10000 0 128
NF kappa B1 p50/RelA/Cbp 0.023 0.18 0.35 40 -0.36 39 79
JUN (dimer) -0.15 0.23 0.36 4 -0.46 145 149
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
VIPR1 -0.1 0.21 -10000 0 -0.5 82 82
NR3C1 0.12 0.21 0.4 135 -0.39 8 143
NR4A1 0.037 0.045 -10000 0 -0.44 4 4
TIF2/SUV420H1 0.036 0.046 -10000 0 -0.35 5 5
MAPKKK cascade -0.003 0.17 0.5 5 -0.54 7 12
cortisol/GR alpha (dimer)/Src-1 0.18 0.26 0.53 145 -0.36 1 146
PBX1 0.019 0.077 -10000 0 -0.41 15 15
POU1F1 0.039 0.025 -10000 0 -0.33 2 2
SELE -0.24 0.42 -10000 0 -0.93 124 124
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.11 0.16 0.34 126 -10000 0 126
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.16 0.24 0.49 141 -10000 0 141
mol:cortisol 0.11 0.18 0.35 150 -10000 0 150
MMP1 -0.37 0.54 -10000 0 -1.1 165 165
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.038 0.19 -10000 0 -0.59 51 51
IHH 0.017 0.087 -10000 0 -0.27 26 26
SHH Np/Cholesterol/GAS1 -0.026 0.1 -10000 0 -0.24 98 98
LRPAP1 0.034 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.026 0.1 0.23 98 -10000 0 98
SMO/beta Arrestin2 -0.019 0.17 -10000 0 -0.35 85 85
SMO -0.035 0.16 -10000 0 -0.36 86 86
AKT1 -0.013 0.16 -10000 0 -0.54 29 29
ARRB2 0.032 0.011 -10000 0 -10000 0 0
BOC 0.015 0.089 -10000 0 -0.42 20 20
ADRBK1 0.033 0.009 -10000 0 -10000 0 0
heart looping -0.034 0.16 -10000 0 -0.35 86 86
STIL -0.004 0.13 0.2 70 -0.25 63 133
DHH N/PTCH2 0.051 0.011 -10000 0 -10000 0 0
DHH N/PTCH1 0 0.12 -10000 0 -0.29 67 67
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
DHH 0.035 0.004 -10000 0 -10000 0 0
PTHLH -0.062 0.25 -10000 0 -0.73 54 54
determination of left/right symmetry -0.034 0.16 -10000 0 -0.35 86 86
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
skeletal system development -0.061 0.24 -10000 0 -0.72 54 54
IHH N/Hhip 0.034 0.064 -10000 0 -0.29 12 12
DHH N/Hhip 0.049 0.029 -10000 0 -0.3 3 3
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.034 0.16 -10000 0 -0.35 86 86
pancreas development 0.032 0.036 -10000 0 -0.42 3 3
HHAT -0.016 0.13 -10000 0 -0.42 49 49
PI3K 0.035 0.067 -10000 0 -0.3 18 18
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.03 0.16 -10000 0 -0.42 71 71
somite specification -0.034 0.16 -10000 0 -0.35 86 86
SHH Np/Cholesterol/PTCH1 -0.029 0.11 -10000 0 -0.23 99 99
SHH Np/Cholesterol/PTCH2 0.003 0.073 -10000 0 -0.23 43 43
SHH Np/Cholesterol/Megalin -0.055 0.14 -10000 0 -0.27 133 133
SHH -0.016 0.089 -10000 0 -0.3 45 45
catabolic process -0.023 0.12 -10000 0 -0.32 68 68
SMO/Vitamin D3 -0.016 0.15 0.2 36 -0.33 60 96
SHH Np/Cholesterol/Hhip 0.002 0.074 -10000 0 -0.23 44 44
LRP2 -0.097 0.21 -10000 0 -0.42 145 145
receptor-mediated endocytosis -0.069 0.17 -10000 0 -0.36 95 95
SHH Np/Cholesterol/BOC -0.007 0.084 -10000 0 -0.23 61 61
SHH Np/Cholesterol/CDO -0.007 0.082 -10000 0 -0.24 55 55
mesenchymal cell differentiation -0.002 0.073 0.23 44 -10000 0 44
mol:Vitamin D3 -0.005 0.13 0.2 62 -0.23 99 161
IHH N/PTCH2 0.037 0.059 -10000 0 -0.27 10 10
CDON 0.02 0.067 -10000 0 -0.42 11 11
IHH N/PTCH1 -0.004 0.13 -10000 0 -0.32 68 68
Megalin/LRPAP1 -0.051 0.16 -10000 0 -0.3 145 145
PTCH2 0.035 0.006 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.006 0.07 -10000 0 -0.23 45 45
PTCH1 -0.023 0.12 -10000 0 -0.32 68 68
HHIP 0.032 0.036 -10000 0 -0.42 3 3
Noncanonical Wnt signaling pathway

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
NFATC2 0.029 0.037 -10000 0 -0.42 3 3
GNB1/GNG2 -0.049 0.17 -10000 0 -0.38 65 65
mol:DAG -0.058 0.15 0.19 2 -0.34 64 66
PLCG1 -0.06 0.15 0.2 2 -0.36 64 66
YES1 -0.067 0.15 -10000 0 -0.28 134 134
FZD3 0.006 0.096 -10000 0 -0.42 24 24
FZD6 -0.029 0.14 -10000 0 -0.42 60 60
G protein -0.034 0.17 0.29 12 -0.36 62 74
MAP3K7 -0.057 0.12 0.18 7 -0.32 56 63
mol:Ca2+ -0.056 0.14 0.19 2 -0.34 64 66
mol:IP3 -0.058 0.15 0.19 2 -0.34 64 66
NLK -0.036 0.25 -10000 0 -0.82 45 45
GNB1 0.031 0.045 -10000 0 -0.42 5 5
CAMK2A -0.057 0.14 0.22 4 -0.32 62 66
MAP3K7IP1 0.033 0.009 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.068 0.15 -10000 0 -0.29 137 137
CSNK1A1 0.035 0.005 -10000 0 -10000 0 0
GNAS -0.065 0.14 -10000 0 -0.28 131 131
GO:0007205 -0.06 0.14 0.22 4 -0.34 64 68
WNT6 0.03 0.031 -10000 0 -0.42 2 2
WNT4 -0.019 0.14 -10000 0 -0.42 58 58
NFAT1/CK1 alpha -0.049 0.16 0.29 2 -0.38 55 57
GNG2 0.034 0.021 -10000 0 -0.42 1 1
WNT5A -0.027 0.15 -10000 0 -0.42 64 64
WNT11 0.027 0.032 -10000 0 -0.42 2 2
CDC42 -0.064 0.15 0.19 2 -0.39 55 57
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.068 0.15 -9999 0 -0.29 137 137
FZD6 -0.029 0.14 -9999 0 -0.42 60 60
WNT6 0.03 0.031 -9999 0 -0.42 2 2
WNT4 -0.019 0.14 -9999 0 -0.42 58 58
FZD3 0.006 0.096 -9999 0 -0.42 24 24
WNT5A -0.027 0.15 -9999 0 -0.42 64 64
WNT11 0.027 0.032 -9999 0 -0.42 2 2
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.016 0.085 -10000 0 -0.42 18 18
GNB1/GNG2 -0.05 0.08 -10000 0 -0.18 128 128
AKT1 -0.014 0.12 0.23 4 -0.24 40 44
EGF -0.069 0.19 -10000 0 -0.42 110 110
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.016 0.065 0.25 5 -0.26 3 8
mol:Ca2+ -0.037 0.17 -10000 0 -0.3 127 127
LYN 0.014 0.058 0.26 4 -0.28 2 6
RhoA/GTP -0.015 0.075 -10000 0 -0.13 113 113
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.056 0.19 -10000 0 -0.35 130 130
GNG2 0.034 0.021 -10000 0 -0.42 1 1
ARRB2 0.032 0.011 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.013 0.14 -10000 0 -0.45 34 34
G beta5/gamma2 -0.054 0.11 -10000 0 -0.24 123 123
PRKCH -0.053 0.19 0.3 3 -0.36 129 132
DNM1 0.032 0.041 -10000 0 -0.42 4 4
TXA2/TP beta/beta Arrestin3 0.028 0.027 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.027 0.054 -10000 0 -0.42 7 7
G12 family/GTP -0.05 0.16 -10000 0 -0.3 119 119
ADRBK1 0.033 0.009 -10000 0 -10000 0 0
ADRBK2 0.023 0.067 -10000 0 -0.42 11 11
RhoA/GTP/ROCK1 0.04 0.04 -10000 0 -0.25 8 8
mol:GDP 0.023 0.14 0.42 31 -0.23 2 33
mol:NADP 0.035 0.007 -10000 0 -10000 0 0
RAB11A 0.034 0.021 -10000 0 -0.42 1 1
PRKG1 0.035 0.005 -10000 0 -10000 0 0
mol:IP3 -0.054 0.21 -10000 0 -0.38 127 127
cell morphogenesis 0.04 0.039 -10000 0 -0.25 8 8
PLCB2 -0.088 0.27 -10000 0 -0.52 127 127
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.007 0.06 0.25 4 -0.24 4 8
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.009 0.076 0.25 5 -0.32 8 13
RHOA 0.026 0.061 -10000 0 -0.42 9 9
PTGIR 0.033 0.029 -10000 0 -0.42 2 2
PRKCB1 -0.057 0.21 -10000 0 -0.4 121 121
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.035 0.007 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.088 0.27 -10000 0 -0.52 129 129
LCK -0.005 0.092 0.25 5 -0.31 13 18
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.049 0.047 0.23 1 -0.2 9 10
TXA2-R family/G12 family/GDP/G beta/gamma 0.034 0.094 -10000 0 -0.48 13 13
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.044 0.047 0.23 1 -0.2 9 10
MAPK14 -0.033 0.13 0.22 3 -0.23 128 131
TGM2/GTP -0.065 0.22 -10000 0 -0.42 122 122
MAPK11 -0.034 0.13 0.25 3 -0.24 125 128
ARHGEF1 -0.014 0.11 0.24 4 -0.18 113 117
GNAI2 0.027 0.057 -10000 0 -0.42 8 8
JNK cascade -0.055 0.21 -10000 0 -0.38 129 129
RAB11/GDP 0.034 0.021 -10000 0 -0.42 1 1
ICAM1 -0.038 0.16 -10000 0 -0.3 128 128
cAMP biosynthetic process -0.05 0.19 -10000 0 -0.35 119 119
Gq family/GTP/EBP50 -0.022 0.096 -10000 0 -0.23 80 80
actin cytoskeleton reorganization 0.04 0.039 -10000 0 -0.25 8 8
SRC 0.015 0.064 0.24 6 -0.27 2 8
GNB5 0.024 0.067 -10000 0 -0.42 11 11
GNB1 0.031 0.045 -10000 0 -0.42 5 5
EGF/EGFR -0.032 0.11 0.24 10 -0.3 38 48
VCAM1 -0.042 0.17 -10000 0 -0.31 129 129
TP beta/Gq family/GDP/G beta5/gamma2 -0.013 0.14 -10000 0 -0.45 34 34
platelet activation -0.041 0.17 0.31 1 -0.3 127 128
PGI2/IP 0.024 0.021 -10000 0 -0.3 2 2
PRKACA 0.018 0.035 -10000 0 -0.23 9 9
Gq family/GDP/G beta5/gamma2 -0.008 0.12 -10000 0 -0.39 34 34
TXA2/TP beta/beta Arrestin2 0.008 0.069 -10000 0 -0.44 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.008 0.029 -10000 0 -0.21 8 8
mol:DAG -0.065 0.23 -10000 0 -0.43 130 130
EGFR -0.013 0.13 -10000 0 -0.42 47 47
TXA2/TP alpha -0.076 0.25 -10000 0 -0.48 119 119
Gq family/GTP -0.017 0.078 0.22 2 -0.22 59 61
YES1 0.013 0.07 0.25 5 -0.29 6 11
GNAI2/GTP 0.02 0.054 -10000 0 -0.21 18 18
PGD2/DP 0.02 0.038 -10000 0 -0.3 7 7
SLC9A3R1 -0.009 0.13 -10000 0 -0.42 46 46
FYN 0.011 0.068 0.25 4 -0.29 7 11
mol:NO 0.035 0.007 -10000 0 -10000 0 0
GNA15 0.029 0.046 -10000 0 -0.42 5 5
PGK/cGMP 0.046 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.026 0.06 -10000 0 -0.42 9 9
TP alpha/TGM2/GDP/G beta/gamma 0.053 0.073 0.29 1 -0.32 4 5
NOS3 0.035 0.007 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCA -0.042 0.19 0.3 3 -0.35 113 116
PRKCB -0.053 0.19 -10000 0 -0.36 130 130
PRKCE -0.053 0.2 0.3 1 -0.36 128 129
PRKCD -0.06 0.2 -10000 0 -0.39 129 129
PRKCG -0.059 0.21 -10000 0 -0.39 128 128
muscle contraction -0.082 0.25 -10000 0 -0.49 129 129
PRKCZ -0.047 0.18 -10000 0 -0.34 129 129
ARR3 0.036 0.002 -10000 0 -10000 0 0
TXA2/TP beta 0.04 0.056 -10000 0 -0.21 15 15
PRKCQ -0.049 0.2 0.3 1 -0.37 121 122
MAPKKK cascade -0.072 0.24 -10000 0 -0.45 128 128
SELE -0.057 0.19 -10000 0 -0.37 129 129
TP beta/GNAI2/GDP/G beta/gamma 0.06 0.068 0.29 1 -0.4 3 4
ROCK1 0.035 0.005 -10000 0 -10000 0 0
GNA14 -0.01 0.13 -10000 0 -0.42 44 44
chemotaxis -0.11 0.31 -10000 0 -0.61 129 129
GNA12 0.035 0.006 -10000 0 -10000 0 0
GNA13 0.028 0.042 -10000 0 -0.42 4 4
GNA11 0.032 0.036 -10000 0 -0.42 3 3
Rac1/GTP 0.026 0.005 -10000 0 -10000 0 0
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 0.003 0.17 0.24 41 -0.34 70 111
FYN -0.038 0.2 0.28 5 -0.42 77 82
LAT/GRAP2/SLP76 -0.021 0.17 0.24 11 -0.36 75 86
IKBKB 0.029 0.014 -10000 0 -10000 0 0
AKT1 -0.027 0.15 0.25 16 -0.31 82 98
B2M 0.025 0.065 -10000 0 -0.43 10 10
IKBKG 0 0.056 0.13 20 -0.13 28 48
MAP3K8 0.003 0.11 -10000 0 -0.42 32 32
mol:Ca2+ -0.017 0.02 0.09 1 -0.058 70 71
integrin-mediated signaling pathway 0.029 0.048 -10000 0 -0.25 12 12
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.053 0.2 0.26 2 -0.43 87 89
TRPV6 -0.03 0.22 1.2 9 -0.62 1 10
CD28 -0.001 0.12 -10000 0 -0.42 37 37
SHC1 -0.022 0.2 0.24 48 -0.39 84 132
receptor internalization -0.07 0.2 0.17 1 -0.4 125 126
PRF1 -0.052 0.22 -10000 0 -0.88 22 22
KRAS 0.027 0.057 -10000 0 -0.42 8 8
GRB2 0.033 0.01 -10000 0 -10000 0 0
COT/AKT1 -0.016 0.14 0.24 15 -0.28 75 90
LAT -0.043 0.19 0.24 17 -0.38 95 112
EntrezGene:6955 0 0.003 -10000 0 -0.016 8 8
CD3D 0.016 0.074 -10000 0 -0.43 13 13
CD3E 0.031 0.015 -10000 0 -10000 0 0
CD3G -0.022 0.14 -10000 0 -0.42 54 54
RASGRP2 -0.001 0.044 -10000 0 -0.17 28 28
RASGRP1 -0.043 0.17 0.24 7 -0.34 90 97
HLA-A 0.017 0.088 -10000 0 -0.43 19 19
RASSF5 0.019 0.061 -10000 0 -0.42 9 9
RAP1A/GTP/RAPL 0.03 0.048 -10000 0 -0.25 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.067 0.13 53 -0.12 30 83
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.022 0.071 -10000 0 -0.18 58 58
PRKCA -0.01 0.091 0.17 23 -0.22 46 69
GRAP2 0.032 0.023 -10000 0 -0.42 1 1
mol:IP3 -0.021 0.14 0.21 32 -0.32 60 92
EntrezGene:6957 0 0.004 0.011 2 -0.021 8 10
TCR/CD3/MHC I/CD8 -0.032 0.15 -10000 0 -0.34 70 70
ORAI1 0.007 0.16 0.59 1 -1 9 10
CSK -0.047 0.18 0.26 2 -0.4 86 88
B7 family/CD28 -0.03 0.22 0.29 1 -0.47 76 77
CHUK 0.025 0.067 -10000 0 -0.42 11 11
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.061 0.21 0.26 1 -0.42 104 105
PTPN6 -0.055 0.19 0.24 4 -0.4 89 93
VAV1 -0.06 0.2 0.26 2 -0.41 101 103
Monovalent TCR/CD3 -0.018 0.11 -10000 0 -0.3 61 61
CBL 0.031 0.012 -10000 0 -10000 0 0
LCK -0.048 0.21 0.25 5 -0.44 86 91
PAG1 -0.032 0.19 0.23 14 -0.39 86 100
RAP1A 0.03 0.05 -10000 0 -0.42 6 6
TCR/CD3/MHC I/CD8/LCK -0.063 0.21 0.28 1 -0.42 105 106
CD80 0.033 0.022 -10000 0 -0.42 1 1
CD86 0.016 0.092 -10000 0 -0.42 21 21
PDK1/CARD11/BCL10/MALT1 -0.015 0.091 -10000 0 -0.21 61 61
HRAS 0.032 0.036 -10000 0 -0.42 3 3
GO:0035030 -0.054 0.17 0.25 1 -0.4 77 78
CD8A 0 0.003 0.011 2 -0.018 8 10
CD8B 0 0.004 0.011 3 -0.014 20 23
PTPRC 0.006 0.095 -10000 0 -0.43 23 23
PDK1/PKC theta -0.028 0.18 0.31 22 -0.37 79 101
CSK/PAG1 -0.026 0.18 0.23 11 -0.4 69 80
SOS1 0.034 0.021 -10000 0 -0.42 1 1
peptide-MHC class I 0.03 0.091 -10000 0 -0.35 25 25
GRAP2/SLP76 -0.035 0.2 0.29 1 -0.38 98 99
STIM1 0.006 0.092 1.3 2 -10000 0 2
RAS family/GTP 0.012 0.086 0.16 12 -0.18 35 47
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.074 0.21 -10000 0 -0.41 125 125
mol:DAG -0.042 0.11 0.11 3 -0.26 78 81
RAP1A/GDP 0.011 0.035 0.074 20 -0.068 20 40
PLCG1 0.033 0.009 -10000 0 -10000 0 0
CD247 0 0.003 -10000 0 -0.016 8 8
cytotoxic T cell degranulation -0.049 0.21 -10000 0 -0.83 22 22
RAP1A/GTP 0 0.018 -10000 0 -0.065 33 33
mol:PI-3-4-5-P3 -0.041 0.17 0.22 5 -0.36 86 91
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.021 0.17 0.24 28 -0.39 64 92
NRAS 0.029 0.05 -10000 0 -0.42 6 6
ZAP70 0.033 0.022 -10000 0 -0.42 1 1
GRB2/SOS1 0.047 0.022 -10000 0 -0.3 1 1
LAT/GRAP2/SLP76/VAV1 -0.031 0.17 0.22 10 -0.38 72 82
MALT1 0.031 0.041 -10000 0 -0.42 4 4
TRAF6 0.034 0.021 -10000 0 -0.42 1 1
CD8 heterodimer 0.001 0.006 0.02 3 -0.022 13 16
CARD11 0.027 0.054 -10000 0 -0.42 7 7
PRKCB -0.033 0.077 0.11 4 -0.18 81 85
PRKCE -0.011 0.098 0.17 24 -0.22 49 73
PRKCQ -0.046 0.19 0.27 5 -0.41 84 89
LCP2 0.023 0.07 -10000 0 -0.42 12 12
BCL10 0.034 0.007 -10000 0 -10000 0 0
regulation of survival gene product expression -0.02 0.13 0.23 18 -0.27 81 99
IKK complex 0.014 0.063 0.16 37 -0.11 14 51
RAS family/GDP -0.004 0.015 -10000 0 -0.049 19 19
MAP3K14 -0.015 0.11 0.19 17 -0.22 71 88
PDPK1 -0.022 0.15 0.27 22 -0.31 69 91
TCR/CD3/MHC I/CD8/Fyn -0.062 0.2 -10000 0 -0.43 95 95
FAS signaling pathway (CD95)

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
SPTAN1 0.024 0.084 0.2 85 -0.19 8 93
RFC1 0.02 0.076 0.19 72 -0.19 5 77
PRKDC 0.044 0.1 0.22 120 -0.2 5 125
RIPK1 0.035 0.008 -10000 0 -10000 0 0
CASP7 -0.007 0.14 -10000 0 -0.68 18 18
FASLG/FAS/FADD/FAF1 0.003 0.092 0.2 38 -0.26 28 66
MAP2K4 -0.025 0.17 0.44 2 -0.44 46 48
mol:ceramide -0.013 0.11 -10000 0 -0.36 33 33
GSN 0.018 0.088 0.19 81 -0.22 16 97
FASLG/FAS/FADD/FAF1/Caspase 8 0.007 0.11 0.23 4 -0.33 28 32
FAS 0.003 0.1 -10000 0 -0.42 28 28
BID -0.017 0.053 0.26 12 -0.27 7 19
MAP3K1 -0.01 0.14 0.3 4 -0.48 22 26
MAP3K7 0.032 0.01 -10000 0 -10000 0 0
RB1 0.019 0.073 0.19 70 -0.2 5 75
CFLAR 0.032 0.046 -10000 0 -0.42 5 5
HGF/MET 0.015 0.12 -10000 0 -0.27 78 78
ARHGDIB 0.016 0.091 0.2 73 -0.23 18 91
FADD 0.025 0.021 -10000 0 -10000 0 0
actin filament polymerization -0.017 0.089 0.22 17 -0.19 81 98
NFKB1 0.003 0.1 -10000 0 -0.63 8 8
MAPK8 -0.044 0.21 0.51 2 -0.5 69 71
DFFA 0.022 0.08 0.19 77 -0.19 6 83
DNA fragmentation during apoptosis 0.022 0.081 0.19 80 -0.19 6 86
FAS/FADD/MET 0.032 0.079 -10000 0 -0.26 29 29
CFLAR/RIP1 0.048 0.038 -10000 0 -0.3 5 5
FAIM3 0.015 0.078 -10000 0 -0.42 15 15
FAF1 0.028 0.03 -10000 0 -0.42 1 1
PARP1 0.028 0.096 0.21 84 -0.21 8 92
DFFB 0.022 0.081 0.19 80 -0.19 6 86
CHUK -0.007 0.1 -10000 0 -0.55 10 10
FASLG -0.009 0.11 -10000 0 -0.42 34 34
FAS/FADD 0.019 0.078 -10000 0 -0.3 24 24
HGF 0.028 0.057 -10000 0 -0.42 8 8
LMNA 0.023 0.096 0.32 26 -0.22 6 32
CASP6 0.019 0.081 0.19 78 -0.21 9 87
CASP10 0.029 0.02 -10000 0 -10000 0 0
CASP3 0.032 0.093 0.24 81 -0.22 6 87
PTPN13 -0.031 0.16 -10000 0 -0.42 72 72
CASP8 -0.012 0.057 0.33 13 -10000 0 13
IL6 -0.1 0.41 -10000 0 -1.2 61 61
MET 0.028 0.046 -10000 0 -0.42 5 5
ICAD/CAD 0.019 0.073 0.18 69 -10000 0 69
FASLG/FAS/FADD/FAF1/Caspase 10 -0.014 0.11 -10000 0 -0.36 33 33
activation of caspase activity by cytochrome c -0.017 0.053 0.26 12 -0.27 7 19
PAK2 0.021 0.078 0.19 77 -0.19 6 83
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
IL12-mediated 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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.005 0.1 -10000 0 -0.33 19 19
TBX21 -0.26 0.57 -10000 0 -1.3 103 103
B2M 0.023 0.066 -10000 0 -0.42 10 10
TYK2 0.013 0.042 -10000 0 -10000 0 0
IL12RB1 0.013 0.042 -10000 0 -10000 0 0
GADD45B -0.18 0.44 -10000 0 -1.1 84 84
IL12RB2 -0.01 0.1 -10000 0 -0.43 25 25
GADD45G -0.17 0.42 -10000 0 -1 88 88
natural killer cell activation -0.005 0.022 -10000 0 -0.04 114 114
RELB 0.029 0.05 -10000 0 -0.42 6 6
RELA 0.035 0.006 -10000 0 -10000 0 0
IL18 0 0.11 -10000 0 -0.43 31 31
IL2RA 0.004 0.11 -10000 0 -0.42 31 31
IFNG -0.007 0.12 -10000 0 -0.42 37 37
STAT3 (dimer) -0.14 0.36 -10000 0 -0.81 96 96
HLA-DRB5 0.014 0.082 -10000 0 -0.42 16 16
FASLG -0.18 0.49 -10000 0 -1.2 81 81
NF kappa B2 p52/RelB -0.16 0.44 -10000 0 -0.96 98 98
CD4 0.028 0.021 -10000 0 -10000 0 0
SOCS1 0.031 0.023 -10000 0 -0.42 1 1
EntrezGene:6955 -0.003 0.012 -10000 0 -0.028 76 76
CD3D 0.009 0.076 -10000 0 -0.43 13 13
CD3E 0.024 0.026 -10000 0 -10000 0 0
CD3G -0.028 0.14 -10000 0 -0.43 54 54
IL12Rbeta2/JAK2 0.004 0.094 -10000 0 -0.33 25 25
CCL3 -0.17 0.43 -10000 0 -1 86 86
CCL4 -0.18 0.45 -10000 0 -1 87 87
HLA-A 0.016 0.088 -10000 0 -0.42 19 19
IL18/IL18R -0.002 0.17 -10000 0 -0.35 83 83
NOS2 -0.18 0.43 -10000 0 -0.88 112 112
IL12/IL12R/TYK2/JAK2/SPHK2 -0.01 0.11 -10000 0 -0.35 18 18
IL1R1 -0.22 0.5 -10000 0 -1.1 104 104
IL4 0.034 0.052 -10000 0 -0.42 5 5
JAK2 0.011 0.051 -10000 0 -0.46 2 2
EntrezGene:6957 -0.003 0.012 -10000 0 -0.029 68 68
TCR/CD3/MHC I/CD8 -0.071 0.27 -10000 0 -0.75 51 51
RAB7A -0.13 0.34 -10000 0 -0.74 104 104
lysosomal transport -0.12 0.32 -10000 0 -0.69 104 104
FOS -0.24 0.5 -10000 0 -1.1 105 105
STAT4 (dimer) -0.15 0.41 -10000 0 -0.9 98 98
STAT5A (dimer) -0.18 0.44 -10000 0 -0.96 100 100
GZMA -0.18 0.42 -10000 0 -0.93 101 101
GZMB -0.26 0.56 -10000 0 -1.3 104 104
HLX 0 0 -10000 0 -10000 0 0
LCK -0.21 0.5 -10000 0 -1.1 104 104
TCR/CD3/MHC II/CD4 -0.058 0.17 -10000 0 -0.36 91 91
IL2/IL2R 0.042 0.11 -10000 0 -0.29 45 45
MAPK14 -0.18 0.44 -10000 0 -0.98 99 99
CCR5 -0.17 0.4 -10000 0 -0.82 112 112
IL1B -0.022 0.13 -10000 0 -0.45 40 40
STAT6 -0.056 0.2 -10000 0 -0.59 35 35
STAT4 0.01 0.1 -10000 0 -0.42 26 26
STAT3 0.028 0.031 -10000 0 -0.42 2 2
STAT1 0.02 0.075 -10000 0 -0.42 14 14
NFKB1 0.035 0.005 -10000 0 -10000 0 0
NFKB2 0.034 0.021 -10000 0 -0.42 1 1
IL12B 0.009 0.063 -10000 0 -0.42 6 6
CD8A 0 0.008 -10000 0 -0.038 18 18
CD8B 0 0.009 -10000 0 -0.043 20 20
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.005 0.1 0.32 19 -10000 0 19
IL2RB 0.012 0.095 -10000 0 -0.42 23 23
proteasomal ubiquitin-dependent protein catabolic process -0.13 0.37 -10000 0 -0.8 98 98
IL2RG 0.03 0.041 -10000 0 -0.42 4 4
IL12 0.014 0.076 -10000 0 -0.33 10 10
STAT5A 0.028 0.037 -10000 0 -0.42 3 3
CD247 -0.002 0.011 -10000 0 -0.027 67 67
IL2 0.032 0.036 -10000 0 -0.42 3 3
SPHK2 0.034 0.021 -10000 0 -0.42 1 1
FRAP1 0.034 0.007 -10000 0 -10000 0 0
IL12A 0.005 0.059 -10000 0 -0.42 5 5
IL12/IL12R/TYK2/JAK2 -0.22 0.53 -10000 0 -1.1 101 101
MAP2K3 -0.19 0.46 -10000 0 -1 100 100
RIPK2 0.028 0.015 -10000 0 -10000 0 0
MAP2K6 -0.18 0.44 -10000 0 -0.96 104 104
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.019 0.064 -10000 0 -0.42 9 9
IL18RAP -0.024 0.15 -10000 0 -0.43 60 60
IL12Rbeta1/TYK2 0.026 0.056 -10000 0 -10000 0 0
EOMES -0.046 0.27 -10000 0 -1.1 28 28
STAT1 (dimer) -0.15 0.38 -10000 0 -0.82 102 102
T cell proliferation -0.11 0.3 -10000 0 -0.63 103 103
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.016 0.091 -10000 0 -0.43 20 20
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.11 0.33 -10000 0 -0.67 109 109
ATF2 -0.16 0.4 -10000 0 -0.88 99 99
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.029 0.05 -10000 0 -0.42 6 6
LAT2 -0.048 0.14 -10000 0 -0.31 85 85
AP1 -0.059 0.21 -10000 0 -0.48 66 66
mol:PIP3 -0.024 0.19 0.3 21 -0.44 46 67
IKBKB 0.011 0.13 0.25 51 -0.24 42 93
AKT1 0.013 0.18 0.33 77 -0.36 26 103
IKBKG -0.008 0.12 0.22 25 -0.24 45 70
MS4A2 -0.076 0.19 -10000 0 -0.41 120 120
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
MAP3K1 -0.039 0.16 0.25 10 -0.39 57 67
mol:Ca2+ -0.012 0.16 0.26 27 -0.33 46 73
LYN 0.031 0.017 -10000 0 -10000 0 0
CBLB -0.047 0.13 -10000 0 -0.31 83 83
SHC1 0.027 0.025 -10000 0 -0.42 1 1
RasGAP/p62DOK 0.034 0.095 -10000 0 -0.25 47 47
positive regulation of cell migration -0.007 0.066 -10000 0 -0.3 25 25
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.003 0.18 0.32 75 -0.31 57 132
PTPN13 -0.068 0.2 -10000 0 -0.62 29 29
PTPN11 0.033 0.024 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.004 0.15 0.32 20 -0.33 24 44
SYK 0.007 0.12 -10000 0 -0.43 33 33
GRB2 0.033 0.01 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.056 0.16 -10000 0 -0.38 73 73
LAT -0.045 0.13 -10000 0 -0.3 82 82
PAK2 -0.033 0.17 0.26 10 -0.42 48 58
NFATC2 -0.012 0.066 -10000 0 -0.36 8 8
HRAS -0.034 0.18 0.26 12 -0.44 50 62
GAB2 0.031 0.013 -10000 0 -10000 0 0
PLA2G1B 0.008 0.12 -10000 0 -0.92 7 7
Fc epsilon R1 -0.03 0.16 -10000 0 -0.3 110 110
Antigen/IgE/Fc epsilon R1 -0.025 0.14 -10000 0 -0.27 110 110
mol:GDP -0.051 0.18 0.25 1 -0.48 50 51
JUN -0.001 0.12 -10000 0 -0.42 39 39
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
FOS -0.031 0.15 -10000 0 -0.42 66 66
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.043 0.14 -10000 0 -0.32 84 84
CHUK -0.01 0.12 0.21 26 -0.25 49 75
KLRG1 -0.038 0.12 0.16 1 -0.36 39 40
VAV1 -0.051 0.14 -10000 0 -0.32 86 86
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.045 0.13 -10000 0 -0.31 81 81
negative regulation of mast cell degranulation -0.041 0.11 -10000 0 -0.34 38 38
BTK -0.057 0.18 -10000 0 -0.52 47 47
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.064 0.18 -10000 0 -0.36 110 110
GAB2/PI3K/SHP2 -0.053 0.1 -10000 0 -0.3 52 52
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.048 0.13 -10000 0 -0.31 74 74
RAF1 0.01 0.13 -10000 0 -1 7 7
Fc epsilon R1/FcgammaRIIB/SHIP -0.026 0.16 -10000 0 -0.29 117 117
FCER1G 0.032 0.019 -10000 0 -10000 0 0
FCER1A -0.024 0.14 -10000 0 -0.43 56 56
Antigen/IgE/Fc epsilon R1/Fyn -0.016 0.14 -10000 0 -0.26 107 107
MAPK3 0.009 0.12 -10000 0 -0.95 7 7
MAPK1 0.004 0.12 -10000 0 -0.92 7 7
NFKB1 0.035 0.005 -10000 0 -10000 0 0
MAPK8 -0.039 0.22 -10000 0 -0.66 41 41
DUSP1 0.001 0.12 -10000 0 -0.42 35 35
NF-kappa-B/RelA 0.012 0.084 0.16 31 -0.16 31 62
actin cytoskeleton reorganization -0.042 0.18 -10000 0 -0.67 15 15
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.027 0.18 0.26 1 -0.42 49 50
FER -0.045 0.13 -10000 0 -0.3 83 83
RELA 0.035 0.006 -10000 0 -10000 0 0
ITK -0.032 0.11 -10000 0 -0.39 39 39
SOS1 0.034 0.021 -10000 0 -0.42 1 1
PLCG1 -0.039 0.18 0.27 5 -0.48 47 52
cytokine secretion -0.003 0.051 -10000 0 -0.12 15 15
SPHK1 -0.054 0.14 -10000 0 -0.32 84 84
PTK2 -0.045 0.19 -10000 0 -0.73 14 14
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.057 0.17 -10000 0 -0.39 81 81
EDG1 -0.007 0.066 -10000 0 -0.3 25 25
mol:DAG -0.03 0.19 0.3 17 -0.43 52 69
MAP2K2 0.004 0.12 -10000 0 -0.94 7 7
MAP2K1 0.005 0.12 -10000 0 -0.94 7 7
MAP2K7 0.034 0.021 -10000 0 -0.42 1 1
KLRG1/SHP2 -0.025 0.12 0.21 3 -0.35 33 36
MAP2K4 -0.096 0.35 -10000 0 -0.93 74 74
Fc epsilon R1/FcgammaRIIB -0.027 0.17 -10000 0 -0.31 117 117
mol:Choline -0.003 0.18 0.31 75 -0.3 57 132
SHC/Grb2/SOS1 -0.011 0.14 -10000 0 -0.38 32 32
FYN 0.027 0.05 -10000 0 -0.42 6 6
DOK1 0.027 0.061 -10000 0 -0.42 9 9
PXN -0.044 0.18 -10000 0 -0.66 14 14
HCLS1 -0.05 0.14 -10000 0 -0.32 86 86
PRKCB -0.016 0.15 0.25 26 -0.33 47 73
FCGR2B 0.001 0.11 -10000 0 -0.42 30 30
IGHE 0.001 0.009 -10000 0 -10000 0 0
KLRG1/SHIP -0.042 0.12 -10000 0 -0.35 38 38
LCP2 0.023 0.07 -10000 0 -0.42 12 12
PLA2G4A -0.052 0.14 -10000 0 -0.32 88 88
RASA1 0.028 0.054 -10000 0 -0.42 7 7
mol:Phosphatidic acid -0.003 0.18 0.31 75 -0.3 57 132
IKK complex 0.011 0.11 0.23 46 -0.2 28 74
WIPF1 0 0 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.013 0.082 -10000 0 -0.22 66 66
epithelial cell differentiation 0.026 0.093 -10000 0 -0.22 56 56
CYFIP2 -0.006 0.13 -10000 0 -0.42 44 44
ENAH -0.027 0.077 0.37 2 -0.31 8 10
EGFR -0.013 0.13 -10000 0 -0.42 47 47
EPHA2 0.031 0.036 -10000 0 -0.42 3 3
MYO6 -0.037 0.077 0.18 7 -0.22 67 74
CTNNB1 0.024 0.067 -10000 0 -0.42 11 11
ABI1/Sra1/Nap1 0.041 0.089 -10000 0 -0.26 39 39
AQP5 -0.094 0.17 -10000 0 -0.45 83 83
CTNND1 0.033 0.022 -10000 0 -0.42 1 1
mol:PI-4-5-P2 -0.031 0.069 0.18 6 -0.21 57 63
regulation of calcium-dependent cell-cell adhesion -0.032 0.068 0.18 5 -0.21 58 63
EGF -0.069 0.19 -10000 0 -0.42 110 110
NCKAP1 0.034 0.021 -10000 0 -0.42 1 1
AQP3 -0.095 0.17 -10000 0 -0.45 84 84
cortical microtubule organization 0.026 0.093 -10000 0 -0.22 56 56
GO:0000145 -0.033 0.064 0.16 6 -0.2 57 63
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.03 0.096 -10000 0 -0.22 56 56
MLLT4 0.02 0.075 -10000 0 -0.42 14 14
ARF6/GDP -0.041 0.068 -10000 0 -0.22 52 52
ARF6 0.033 0.029 -10000 0 -0.42 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.053 0.071 -10000 0 -0.23 20 20
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.026 0.093 -10000 0 -0.34 18 18
PVRL2 0.026 0.064 -10000 0 -0.42 10 10
ZYX -0.033 0.074 0.18 8 -0.22 63 71
ARF6/GTP 0.058 0.077 -10000 0 -0.24 20 20
CDH1 -0.012 0.13 -10000 0 -0.42 45 45
EGFR/EGFR/EGF/EGF -0.057 0.14 -10000 0 -0.22 190 190
RhoA/GDP 0.023 0.098 -10000 0 -0.22 63 63
actin cytoskeleton organization -0.04 0.074 -10000 0 -0.22 54 54
IGF-1R heterotetramer -0.043 0.17 -10000 0 -0.42 84 84
GIT1 0.033 0.022 -10000 0 -0.42 1 1
IGF1R -0.043 0.17 -10000 0 -0.42 84 84
IGF1 -0.041 0.17 -10000 0 -0.42 81 81
DIAPH1 0.002 0.2 -10000 0 -0.57 44 44
Wnt receptor signaling pathway -0.026 0.093 0.22 56 -10000 0 56
RHOA 0.026 0.061 -10000 0 -0.42 9 9
RhoA/GTP -0.043 0.068 -10000 0 -0.22 60 60
CTNNA1 0.035 0.006 -10000 0 -10000 0 0
VCL -0.041 0.075 -10000 0 -0.22 66 66
EFNA1 0.014 0.08 -10000 0 -0.42 16 16
LPP -0.038 0.071 0.17 8 -0.21 59 67
Ephrin A1/EPHA2 0.009 0.092 -10000 0 -0.22 57 57
SEC6/SEC8 -0.048 0.068 -10000 0 -0.21 73 73
MGAT3 -0.032 0.069 0.18 5 -0.21 58 63
HGF/MET 0.015 0.093 -10000 0 -0.21 66 66
HGF 0.028 0.057 -10000 0 -0.42 8 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.013 0.083 -10000 0 -0.22 66 66
actin cable formation 0.015 0.11 0.27 11 -0.29 10 21
KIAA1543 -0.037 0.068 0.17 7 -0.21 54 61
KIFC3 -0.031 0.067 0.18 6 -0.21 51 57
NCK1 0.034 0.021 -10000 0 -0.42 1 1
EXOC3 0.036 0.002 -10000 0 -10000 0 0
ACTN1 -0.034 0.074 0.18 8 -0.21 63 71
NCK1/GIT1 0.048 0.025 -10000 0 -0.3 2 2
mol:GDP 0.026 0.093 -10000 0 -0.22 56 56
EXOC4 0.034 0.021 -10000 0 -0.42 1 1
STX4 -0.033 0.062 -10000 0 -0.21 56 56
PIP5K1C -0.032 0.07 0.18 6 -0.22 57 63
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0.034 0.007 -10000 0 -10000 0 0
ROCK1 -0.008 0.1 0.34 5 -0.32 7 12
adherens junction assembly -0.045 0.12 0.26 1 -0.46 16 17
IGF-1R heterotetramer/IGF1 -0.057 0.15 -10000 0 -0.24 177 177
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.074 -10000 0 -0.3 23 23
MET 0.028 0.046 -10000 0 -0.42 5 5
PLEKHA7 -0.03 0.07 0.18 8 -0.21 55 63
mol:GTP 0.05 0.07 -10000 0 -0.23 20 20
establishment of epithelial cell apical/basal polarity -0.043 0.072 0.14 14 -0.2 63 77
cortical actin cytoskeleton stabilization -0.013 0.082 -10000 0 -0.22 66 66
regulation of cell-cell adhesion -0.04 0.074 -10000 0 -0.22 54 54
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.013 0.083 -10000 0 -0.22 66 66
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.16 0.54 -10000 0 -1.3 79 79
IL23A -0.14 0.49 -10000 0 -1.2 63 63
NF kappa B1 p50/RelA/I kappa B alpha -0.1 0.48 -10000 0 -1.1 70 70
positive regulation of T cell mediated cytotoxicity -0.14 0.52 -10000 0 -1.2 70 70
ITGA3 -0.14 0.48 -10000 0 -1.1 73 73
IL17F -0.053 0.33 -10000 0 -0.69 71 71
IL12B 0.019 0.075 -10000 0 -0.44 6 6
STAT1 (dimer) -0.15 0.5 -10000 0 -1.2 70 70
CD4 -0.11 0.45 -10000 0 -1.1 51 51
IL23 -0.13 0.47 -10000 0 -1.2 63 63
IL23R -0.002 0.22 -10000 0 -1.3 11 11
IL1B -0.16 0.53 -10000 0 -1.3 71 71
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.082 0.46 -10000 0 -1.1 58 58
TYK2 0.02 0.046 -10000 0 -10000 0 0
STAT4 0.01 0.1 -10000 0 -0.42 26 26
STAT3 0.028 0.031 -10000 0 -0.42 2 2
IL18RAP -0.024 0.15 -10000 0 -0.42 60 60
IL12RB1 0.02 0.046 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
IL12Rbeta1/TYK2 0.029 0.058 -10000 0 -10000 0 0
IL23R/JAK2 0.01 0.22 -10000 0 -1.2 11 11
positive regulation of chronic inflammatory response -0.14 0.52 -10000 0 -1.2 70 70
natural killer cell activation 0 0.012 0.081 7 -10000 0 7
JAK2 0.022 0.063 -10000 0 -0.46 2 2
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
NFKB1 0.036 0.007 -10000 0 -10000 0 0
RELA 0.036 0.007 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.12 0.45 -10000 0 -1.1 63 63
ALOX12B -0.12 0.45 -10000 0 -1.1 57 57
CXCL1 -0.18 0.55 -10000 0 -1.2 98 98
T cell proliferation -0.14 0.52 -10000 0 -1.2 70 70
NFKBIA 0.033 0.03 -10000 0 -0.42 2 2
IL17A -0.03 0.26 -10000 0 -0.53 69 69
PI3K -0.12 0.49 -10000 0 -1.1 73 73
IFNG -0.007 0.049 0.15 5 -0.13 45 50
STAT3 (dimer) -0.12 0.46 -10000 0 -1.1 71 71
IL18R1 0.015 0.09 -10000 0 -0.42 20 20
IL23/IL23R/JAK2/TYK2/SOCS3 -0.039 0.29 0.51 1 -0.68 44 45
IL18/IL18R -0.01 0.16 -10000 0 -0.34 83 83
macrophage activation -0.007 0.021 -10000 0 -0.044 58 58
TNF -0.13 0.48 -10000 0 -1.2 66 66
STAT3/STAT4 -0.14 0.49 -10000 0 -1.2 71 71
STAT4 (dimer) -0.14 0.52 -10000 0 -1.2 73 73
IL18 0 0.11 -10000 0 -0.42 31 31
IL19 -0.082 0.46 -10000 0 -1.1 58 58
STAT5A (dimer) -0.15 0.49 -10000 0 -1.2 69 69
STAT1 0.02 0.075 -10000 0 -0.42 14 14
SOCS3 0.028 0.046 -10000 0 -0.42 5 5
CXCL9 -0.2 0.57 -10000 0 -1.2 108 108
MPO -0.1 0.45 -10000 0 -1.1 60 60
positive regulation of humoral immune response -0.14 0.52 -10000 0 -1.2 70 70
IL23/IL23R/JAK2/TYK2 -0.15 0.56 -10000 0 -1.3 70 70
IL6 -0.18 0.56 -10000 0 -1.3 90 90
STAT5A 0.028 0.037 -10000 0 -0.42 3 3
IL2 0.029 0.039 -10000 0 -0.42 3 3
positive regulation of tyrosine phosphorylation of STAT protein 0 0.012 0.081 7 -10000 0 7
CD3E -0.11 0.45 -10000 0 -1.1 63 63
keratinocyte proliferation -0.14 0.52 -10000 0 -1.2 70 70
NOS2 -0.12 0.45 -10000 0 -1 70 70
Nongenotropic Androgen 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
PTK2 0.007 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.006 0.12 -10000 0 -0.24 102 102
regulation of S phase of mitotic cell cycle -0.028 0.11 -10000 0 -0.23 102 102
GNAO1 0.029 0.014 -10000 0 -10000 0 0
HRAS 0.031 0.036 -10000 0 -0.42 3 3
SHBG/T-DHT 0.021 0.008 -10000 0 -10000 0 0
PELP1 0.032 0.011 -10000 0 -10000 0 0
AKT1 0.007 0.024 -10000 0 -0.3 3 3
MAP2K1 -0.054 0.097 0.17 18 -0.32 21 39
T-DHT/AR -0.037 0.13 -10000 0 -0.3 99 99
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.006 72 72
GNAI2 0.027 0.057 -10000 0 -0.42 8 8
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNAI1 0.017 0.085 -10000 0 -0.42 18 18
mol:GDP -0.072 0.15 -10000 0 -0.38 97 97
cell proliferation -0.074 0.17 0.24 2 -0.43 77 79
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
FOS -0.11 0.28 -10000 0 -0.78 74 74
mol:Ca2+ -0.009 0.023 -10000 0 -0.063 56 56
MAPK3 -0.059 0.14 0.26 3 -0.34 69 72
MAPK1 -0.044 0.12 -10000 0 -0.33 54 54
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
mol:IP3 0 0.002 -10000 0 -0.004 72 72
cAMP biosynthetic process 0.003 0.017 -10000 0 -10000 0 0
GNG2 0.034 0.021 -10000 0 -0.42 1 1
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 72 72
HRAS/GTP -0.007 0.12 -10000 0 -0.22 97 97
actin cytoskeleton reorganization 0.038 0.052 -10000 0 -0.21 18 18
SRC 0.032 0.03 -10000 0 -0.42 2 2
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 72 72
PI3K 0.032 0.057 -10000 0 -0.25 18 18
apoptosis 0.062 0.17 0.43 77 -10000 0 77
T-DHT/AR/PELP1 -0.016 0.12 -10000 0 -0.25 99 99
HRAS/GDP -0.051 0.16 -10000 0 -0.36 98 98
CREB1 -0.07 0.18 -10000 0 -0.46 77 77
RAC1-CDC42/GTP 0.049 0.056 -10000 0 -0.21 18 18
AR -0.054 0.18 -10000 0 -0.42 99 99
GNB1 0.031 0.045 -10000 0 -0.42 5 5
RAF1 -0.038 0.1 0.19 4 -0.22 92 96
RAC1-CDC42/GDP -0.03 0.16 -10000 0 -0.35 95 95
T-DHT/AR/PELP1/Src 0.001 0.12 -10000 0 -0.24 96 96
MAP2K2 -0.055 0.099 0.17 19 -0.31 24 43
T-DHT/AR/PELP1/Src/PI3K -0.028 0.11 -10000 0 -0.24 102 102
GNAZ 0.023 0.067 -10000 0 -0.42 11 11
SHBG 0.032 0.012 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.038 0.14 -10000 0 -0.43 36 36
mol:T-DHT 0 0.001 0.002 2 -0.003 42 44
RAC1 0.035 0.006 -10000 0 -10000 0 0
GNRH1 0.005 0.019 -10000 0 -0.3 2 2
Gi family/GTP -0.029 0.086 -10000 0 -0.24 45 45
CDC42 0.034 0.007 -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 0.035 0.021 -10000 0 -0.42 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.1 0.25 0.63 68 -0.52 2 70
IL27/IL27R/JAK1 -0.09 0.34 0.88 2 -1.1 37 39
TBX21 -0.096 0.3 0.61 23 -0.59 94 117
IL12B 0.026 0.052 -10000 0 -0.42 6 6
IL12A 0.003 0.031 -10000 0 -0.3 5 5
IL6ST -0.05 0.16 -10000 0 -0.4 87 87
IL27RA/JAK1 -0.062 0.33 0.43 2 -1.2 35 37
IL27 -0.037 0.16 0.15 3 -0.42 74 77
TYK2 0.028 0.029 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.014 0.086 0.2 11 -0.25 54 65
T-helper 2 cell differentiation 0.1 0.25 0.63 68 -0.52 2 70
T cell proliferation during immune response 0.1 0.25 0.63 68 -0.52 2 70
MAPKKK cascade -0.1 0.25 0.52 2 -0.63 68 70
STAT3 0.028 0.031 -10000 0 -0.42 2 2
STAT2 0.035 0.005 -10000 0 -10000 0 0
STAT1 0.022 0.077 -10000 0 -0.42 14 14
IL12RB1 0.035 0.006 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.08 0.29 0.64 22 -0.6 75 97
IL27/IL27R/JAK2/TYK2 -0.1 0.26 0.52 2 -0.64 68 70
positive regulation of T cell mediated cytotoxicity -0.1 0.25 0.52 2 -0.63 68 70
STAT1 (dimer) -0.1 0.39 0.56 32 -0.96 58 90
JAK2 0.024 0.037 -10000 0 -0.43 2 2
JAK1 0.034 0.036 -10000 0 -0.39 3 3
STAT2 (dimer) -0.087 0.25 0.46 2 -0.61 68 70
T cell proliferation -0.12 0.26 0.47 2 -0.62 76 78
IL12/IL12R/TYK2/JAK2 -0.002 0.2 -10000 0 -0.92 18 18
IL17A -0.014 0.086 0.2 11 -0.25 54 65
mast cell activation 0.1 0.25 0.63 68 -0.52 2 70
IFNG -0.01 0.05 0.13 6 -0.12 54 60
T cell differentiation -0.005 0.011 0.029 13 -0.023 87 100
STAT3 (dimer) -0.078 0.24 0.46 2 -0.61 64 66
STAT5A (dimer) -0.079 0.24 0.46 2 -0.62 64 66
STAT4 (dimer) -0.097 0.26 0.46 2 -0.61 74 76
STAT4 0.01 0.1 -10000 0 -0.42 26 26
T cell activation -0.002 0.032 0.12 31 -10000 0 31
IL27R/JAK2/TYK2 -0.08 0.32 -10000 0 -1.1 36 36
GATA3 -0.2 0.52 0.78 8 -1.3 90 98
IL18 -0.012 0.073 -10000 0 -0.3 31 31
positive regulation of mast cell cytokine production -0.076 0.24 0.46 2 -0.59 64 66
IL27/EBI3 -0.01 0.13 0.22 6 -0.31 77 83
IL27RA -0.091 0.33 -10000 0 -1.3 35 35
IL6 -0.019 0.14 -10000 0 -0.42 53 53
STAT5A 0.028 0.037 -10000 0 -0.42 3 3
monocyte differentiation 0 0.002 -10000 0 -0.015 1 1
IL2 0.023 0.15 0.47 35 -1.2 3 38
IL1B -0.017 0.082 -10000 0 -0.3 40 40
EBI3 0.026 0.053 -10000 0 -0.43 5 5
TNF 0.002 0.041 -10000 0 -0.3 9 9
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.075 0.28 -10000 0 -0.77 42 42
CRP -0.045 0.3 0.65 1 -0.75 44 45
cell cycle arrest -0.097 0.34 0.49 1 -0.8 66 67
TIMP1 -0.07 0.3 0.46 1 -0.78 53 54
IL6ST -0.049 0.17 -10000 0 -0.42 88 88
Rac1/GDP -0.052 0.19 0.28 1 -0.43 62 63
AP1 0.012 0.18 -10000 0 -0.51 27 27
GAB2 0.032 0.014 -10000 0 -10000 0 0
TNFSF11 -0.14 0.4 -10000 0 -0.95 83 83
HSP90B1 -0.001 0.12 -10000 0 -0.83 8 8
GAB1 0.028 0.061 -10000 0 -0.42 9 9
MAPK14 -0.048 0.17 -10000 0 -0.52 33 33
AKT1 0.029 0.08 0.28 1 -0.39 7 8
FOXO1 0.036 0.079 -10000 0 -0.37 7 7
MAP2K6 -0.054 0.16 0.24 1 -0.42 56 57
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.061 0.21 0.33 2 -0.47 68 70
MITF -0.055 0.17 -10000 0 -0.41 63 63
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.035 0.005 -10000 0 -10000 0 0
A2M -0.056 0.33 -10000 0 -1.3 33 33
CEBPB 0.027 0.05 -10000 0 -0.42 6 6
GRB2/SOS1/GAB family/SHP2 0.004 0.12 0.3 1 -0.43 19 20
STAT3 -0.11 0.37 0.5 1 -0.88 66 67
STAT1 -0.011 0.17 -10000 0 -0.88 17 17
CEBPD -0.1 0.37 -10000 0 -0.94 63 63
PIK3CA 0.034 0.022 -10000 0 -0.42 1 1
PI3K 0.037 0.067 -10000 0 -0.3 18 18
JUN -0.001 0.12 -10000 0 -0.42 39 39
PIAS3/MITF -0.047 0.17 -10000 0 -0.41 55 55
MAPK11 -0.046 0.16 -10000 0 -0.52 33 33
STAT3 (dimer)/FOXO1 -0.055 0.28 0.47 1 -0.65 54 55
GRB2/SOS1/GAB family -0.018 0.17 0.29 1 -0.44 35 36
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.063 0.17 -10000 0 -0.4 70 70
GRB2 0.034 0.011 -10000 0 -10000 0 0
JAK2 0.031 0.03 -10000 0 -0.42 2 2
LBP -0.033 0.23 0.45 1 -0.6 39 40
PIK3R1 0.019 0.083 -10000 0 -0.42 17 17
JAK1 0.031 0.039 -10000 0 -0.42 3 3
MYC -0.068 0.36 0.59 2 -0.9 60 62
FGG -0.078 0.29 -10000 0 -0.74 49 49
macrophage differentiation -0.097 0.34 0.49 1 -0.8 66 67
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.025 0.16 -10000 0 -0.25 135 135
JUNB -0.077 0.28 -10000 0 -0.77 40 40
FOS -0.031 0.15 -10000 0 -0.42 66 66
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.062 0.17 -10000 0 -0.4 70 70
STAT1/PIAS1 -0.048 0.19 0.3 1 -0.41 69 70
GRB2/SOS1/GAB family/SHP2/PI3K 0.03 0.08 -10000 0 -0.36 10 10
STAT3 (dimer) -0.11 0.37 0.49 1 -0.86 66 67
PRKCD -0.073 0.24 0.36 1 -0.56 68 69
IL6R 0.02 0.06 -10000 0 -0.43 8 8
SOCS3 -0.045 0.19 0.43 1 -0.73 19 20
gp130 (dimer)/JAK1/JAK1/LMO4 -0.028 0.15 -10000 0 -0.26 136 136
Rac1/GTP -0.055 0.2 -10000 0 -0.44 68 68
HCK 0.017 0.087 -10000 0 -0.42 19 19
MAPKKK cascade 0.02 0.14 -10000 0 -0.52 24 24
bone resorption -0.13 0.37 0.46 1 -0.87 83 84
IRF1 -0.093 0.32 -10000 0 -0.83 55 55
mol:GDP -0.058 0.18 -10000 0 -0.42 66 66
SOS1 0.036 0.022 -10000 0 -0.42 1 1
VAV1 -0.059 0.18 -10000 0 -0.42 66 66
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.045 0.18 -10000 0 -0.54 37 37
PTPN11 0.017 0.084 -10000 0 -1.2 2 2
IL6/IL6RA 0.004 0.1 -10000 0 -0.3 47 47
gp130 (dimer)/TYK2/TYK2/LMO4 -0.024 0.14 -10000 0 -0.26 134 134
gp130 (dimer)/JAK2/JAK2/LMO4 -0.026 0.15 -10000 0 -0.26 135 135
IL6 -0.022 0.14 -10000 0 -0.42 53 53
PIAS3 0.035 0.006 -10000 0 -10000 0 0
PTPRE 0.021 0.064 -10000 0 -0.41 10 10
PIAS1 0.035 0.006 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.056 0.13 -10000 0 -0.32 69 69
LMO4 -0.02 0.14 -10000 0 -0.42 54 54
STAT3 (dimer)/PIAS3 -0.092 0.34 -10000 0 -0.81 63 63
MCL1 0.037 0.093 -10000 0 -0.78 2 2
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.025 0.18 -10000 0 -0.46 59 59
Syndecan-4/Syndesmos -0.031 0.2 -10000 0 -0.5 61 61
positive regulation of JNK cascade -0.044 0.22 -10000 0 -0.48 76 76
Syndecan-4/ADAM12 -0.049 0.23 -10000 0 -0.51 80 80
CCL5 -0.013 0.14 -10000 0 -0.42 51 51
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
DNM2 0.035 0.005 -10000 0 -10000 0 0
ITGA5 0.033 0.035 -10000 0 -0.42 3 3
SDCBP 0.022 0.061 -10000 0 -0.42 9 9
PLG 0.021 0.04 -10000 0 -0.4 2 2
ADAM12 -0.012 0.14 -10000 0 -0.42 51 51
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.028 0.046 -10000 0 -0.42 5 5
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.032 0.02 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.032 0.21 -10000 0 -0.5 66 66
Syndecan-4/CXCL12/CXCR4 -0.047 0.23 -10000 0 -0.52 72 72
Syndecan-4/Laminin alpha3 -0.053 0.22 -10000 0 -0.51 68 68
MDK 0.017 0.085 -10000 0 -0.42 18 18
Syndecan-4/FZD7 -0.048 0.22 -10000 0 -0.51 74 74
Syndecan-4/Midkine -0.038 0.21 -10000 0 -0.5 67 67
FZD7 -0.007 0.13 -10000 0 -0.42 44 44
Syndecan-4/FGFR1/FGF -0.033 0.2 -10000 0 -0.47 60 60
THBS1 0.001 0.12 -10000 0 -0.42 37 37
integrin-mediated signaling pathway -0.039 0.21 -10000 0 -0.48 75 75
positive regulation of MAPKKK cascade -0.044 0.22 -10000 0 -0.48 76 76
Syndecan-4/TACI -0.033 0.21 -10000 0 -0.5 66 66
CXCR4 0.006 0.11 -10000 0 -0.42 31 31
cell adhesion 0.012 0.098 0.2 44 -0.27 40 84
Syndecan-4/Dynamin -0.03 0.21 -10000 0 -0.5 66 66
Syndecan-4/TSP1 -0.044 0.22 -10000 0 -0.5 73 73
Syndecan-4/GIPC -0.03 0.21 -10000 0 -0.49 66 66
Syndecan-4/RANTES -0.05 0.22 -10000 0 -0.51 70 70
ITGB1 0.033 0.029 -10000 0 -0.42 2 2
LAMA1 0.034 0.009 -10000 0 -10000 0 0
LAMA3 -0.019 0.14 -10000 0 -0.42 57 57
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCA 0.089 0.26 0.79 58 -10000 0 58
Syndecan-4/alpha-Actinin -0.033 0.22 -10000 0 -0.51 67 67
TFPI 0.034 0.008 -10000 0 -10000 0 0
F2 0.031 0.025 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.047 0.037 -10000 0 -0.3 5 5
positive regulation of cell adhesion -0.06 0.2 -10000 0 -0.5 68 68
ACTN1 0.026 0.061 -10000 0 -0.42 9 9
TNC 0.004 0.11 -10000 0 -0.42 31 31
Syndecan-4/CXCL12 -0.048 0.22 -10000 0 -0.51 74 74
FGF6 0.026 0.057 -10000 0 -0.42 8 8
RHOA 0.026 0.061 -10000 0 -0.42 9 9
CXCL12 -0.007 0.13 -10000 0 -0.42 46 46
TNFRSF13B 0.032 0.012 -10000 0 -10000 0 0
FGF2 -0.001 0.11 -10000 0 -0.42 34 34
FGFR1 0.021 0.061 -10000 0 -0.42 9 9
Syndecan-4/PI-4-5-P2 -0.059 0.19 -10000 0 -0.49 66 66
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.018 0.13 -10000 0 -0.41 48 48
cell migration -0.015 0.015 -10000 0 -10000 0 0
PRKCD 0.022 0.04 -10000 0 -0.3 3 3
vasculogenesis -0.041 0.21 -10000 0 -0.48 73 73
SDC4 -0.058 0.21 -10000 0 -0.52 66 66
Syndecan-4/Tenascin C -0.041 0.22 -10000 0 -0.5 75 75
Syndecan-4/PI-4-5-P2/PKC alpha -0.025 0.016 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.034 0.2 -10000 0 -0.5 60 60
MMP9 -0.014 0.14 -10000 0 -0.42 52 52
Rac1/GTP 0.012 0.1 0.2 44 -0.27 40 84
cytoskeleton organization -0.029 0.2 -10000 0 -0.48 61 61
GIPC1 0.033 0.035 -10000 0 -0.42 3 3
Syndecan-4/TFPI -0.032 0.21 -10000 0 -0.5 66 66
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.013 0.089 0.22 1 -0.27 24 25
adherens junction organization -0.045 0.13 -10000 0 -0.28 85 85
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.017 0.1 0.23 1 -0.27 27 28
FMN1 -0.034 0.12 -10000 0 -0.26 87 87
mol:IP3 -0.016 0.076 -10000 0 -0.23 24 24
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.033 0.13 -10000 0 -0.27 87 87
CTNNB1 0.026 0.067 -10000 0 -0.42 11 11
AKT1 -0.016 0.094 0.18 2 -0.28 22 24
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.061 0.19 -10000 0 -0.43 75 75
CTNND1 0.034 0.022 -10000 0 -0.43 1 1
mol:PI-4-5-P2 -0.031 0.12 0.22 1 -0.25 79 80
VASP -0.038 0.12 -10000 0 -0.27 83 83
ZYX -0.037 0.12 -10000 0 -0.26 85 85
JUB -0.048 0.13 -10000 0 -0.28 87 87
EGFR(dimer) -0.04 0.14 0.23 1 -0.27 102 103
E-cadherin/beta catenin-gamma catenin 0.016 0.099 -10000 0 -0.24 58 58
mol:PI-3-4-5-P3 0 0.11 0.22 2 -0.26 28 30
PIK3CA 0.034 0.022 -10000 0 -0.42 1 1
PI3K 0 0.11 0.23 2 -0.26 28 30
FYN -0.018 0.091 0.22 1 -0.29 23 24
mol:Ca2+ -0.015 0.075 -10000 0 -0.23 24 24
JUP 0.03 0.042 -10000 0 -0.42 4 4
PIK3R1 0.019 0.083 -10000 0 -0.42 17 17
mol:DAG -0.016 0.076 -10000 0 -0.23 24 24
CDH1 -0.012 0.13 -10000 0 -0.42 45 45
RhoA/GDP -0.019 0.11 0.23 1 -0.28 31 32
establishment of polarity of embryonic epithelium -0.036 0.12 0.22 1 -0.26 83 84
SRC 0.032 0.03 -10000 0 -0.42 2 2
RAC1 0.035 0.006 -10000 0 -10000 0 0
RHOA 0.026 0.061 -10000 0 -0.42 9 9
EGFR -0.013 0.13 -10000 0 -0.42 47 47
CASR -0.014 0.077 0.22 1 -0.25 16 17
RhoA/GTP -0.002 0.089 0.21 1 -0.25 18 19
AKT2 -0.016 0.094 0.19 2 -0.28 20 22
actin cable formation -0.036 0.12 0.2 5 -0.26 83 88
apoptosis 0.009 0.1 0.27 27 -0.24 5 32
CTNNA1 0.036 0.007 -10000 0 -10000 0 0
mol:GDP -0.029 0.098 0.22 1 -0.27 33 34
PIP5K1A -0.033 0.12 -10000 0 -0.26 79 79
PLCG1 -0.016 0.077 -10000 0 -0.24 23 23
Rac1/GTP -0.029 0.14 -10000 0 -0.31 52 52
homophilic cell adhesion 0 0.004 -10000 0 -10000 0 0
Arf6 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
CENTA1/KIF3B 0.015 0.032 -10000 0 -0.25 6 6
ARNO/beta Arrestin1-2 0.013 0.069 -10000 0 -0.19 42 42
EGFR -0.013 0.13 -10000 0 -0.42 47 47
EPHA2 0.031 0.036 -10000 0 -0.42 3 3
USP6 0.031 0.012 -10000 0 -10000 0 0
IQSEC1 0.034 0.021 -10000 0 -0.42 1 1
EGFR/EGFR/EGF/EGF -0.061 0.16 -10000 0 -0.3 151 151
ARRB2 0.011 0.043 -10000 0 -0.3 9 9
mol:GTP 0.006 0.019 0.11 5 -0.11 2 7
ARRB1 0.026 0.05 -10000 0 -0.42 6 6
FBXO8 0.035 0.007 -10000 0 -10000 0 0
TSHR 0.029 0.05 -10000 0 -0.42 6 6
EGF -0.069 0.19 -10000 0 -0.42 110 110
somatostatin receptor activity 0 0 0 2 -0.001 78 80
ARAP2 0 0 0 1 0 71 72
mol:GDP -0.029 0.1 -10000 0 -0.25 61 61
mol:PI-3-4-5-P3 0 0 0 2 -0.001 78 80
ITGA2B 0.033 0.009 -10000 0 -10000 0 0
ARF6 0.033 0.029 -10000 0 -0.42 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.052 0.071 -10000 0 -0.23 20 20
ADAP1 0 0 0 1 0 45 46
KIF13B 0.022 0.051 -10000 0 -0.42 6 6
HGF/MET 0.041 0.057 -10000 0 -0.3 13 13
PXN 0.036 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.035 0.1 0.15 2 -0.24 77 79
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.035 0.15 -10000 0 -0.26 150 150
ADRB2 0.003 0.11 -10000 0 -0.42 33 33
receptor agonist activity 0 0 0 2 0 71 73
actin filament binding 0 0 0 2 0 80 82
SRC 0.032 0.03 -10000 0 -0.42 2 2
ITGB3 0.028 0.046 -10000 0 -0.42 5 5
GNAQ 0 0 0.001 3 -0.001 58 61
EFA6/PI-4-5-P2 0 0 0.001 4 -0.001 57 61
ARF6/GDP 0.004 0.074 0.2 2 -0.25 16 18
ARF6/GDP/GULP/ACAP1 -0.017 0.12 -10000 0 -0.28 69 69
alphaIIb/beta3 Integrin/paxillin/GIT1 0.079 0.042 -10000 0 -0.24 5 5
ACAP1 0 0 0 1 0 1 2
ACAP2 0 0 0 1 0 76 77
LHCGR/beta Arrestin2 0.018 0.06 -10000 0 -0.38 9 9
EFNA1 0.014 0.08 -10000 0 -0.42 16 16
HGF 0.028 0.057 -10000 0 -0.42 8 8
CYTH3 0 0 0.001 3 -0.001 74 77
CYTH2 -0.001 0.002 -10000 0 -0.004 81 81
NCK1 0.034 0.021 -10000 0 -0.42 1 1
fibronectin binding 0 0 0 2 0 57 59
endosomal lumen acidification 0 0 0 2 0 65 67
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.001 0.12 -10000 0 -0.42 37 37
GNAQ/ARNO -0.001 0.003 0.006 4 -0.006 54 58
mol:Phosphatidic acid 0 0 0 1 0 76 77
PIP3-E 0.028 0.042 -10000 0 -0.42 4 4
MET 0.028 0.046 -10000 0 -0.42 5 5
GNA14 -0.01 0.13 -10000 0 -0.42 44 44
GNA15 0.029 0.046 -10000 0 -0.42 5 5
GIT1 0.033 0.022 -10000 0 -0.42 1 1
mol:PI-4-5-P2 0 0 0.001 2 -0.001 68 70
GNA11 0.032 0.036 -10000 0 -0.42 3 3
LHCGR 0.027 0.061 -10000 0 -0.42 9 9
AGTR1 -0.046 0.16 -10000 0 -0.42 79 79
desensitization of G-protein coupled receptor protein signaling pathway 0.018 0.06 -10000 0 -0.38 9 9
IPCEF1/ARNO -0.024 0.12 -10000 0 -0.2 149 149
alphaIIb/beta3 Integrin 0.046 0.034 -10000 0 -0.3 4 4
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.016 0.036 -10000 0 -0.26 11 11
SNTA1 0.031 0.041 -10000 0 -0.42 4 4
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.022 0.05 -10000 0 -0.26 22 22
MAPK12 0.003 0.083 0.21 39 -0.23 33 72
CCND1 -0.056 0.16 -10000 0 -0.42 81 81
p38 gamma/SNTA1 0.026 0.087 0.21 46 -0.22 35 81
MAP2K3 0.032 0.023 -10000 0 -0.42 1 1
PKN1 0.033 0.035 -10000 0 -0.42 3 3
G2/M transition checkpoint 0.003 0.083 0.21 39 -0.23 33 72
MAP2K6 0.013 0.094 0.24 44 -0.24 33 77
MAPT -0.055 0.13 0.28 5 -0.28 105 110
MAPK13 0.006 0.052 -10000 0 -0.3 14 14
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.005 0.062 -10000 0 -0.29 22 22
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.032 0.071 -10000 0 -0.22 32 32
NF kappa B1 p50/RelA/I kappa B alpha 0.021 0.095 0.27 6 -0.24 19 25
AP1 -0.034 0.12 -10000 0 -0.25 100 100
mol:PIP3 -0.03 0.09 -10000 0 -0.22 86 86
AKT1 -0.006 0.1 0.25 3 -0.31 28 31
PTK2B -0.041 0.1 0.14 1 -0.21 114 115
RHOA -0.015 0.1 -10000 0 -0.34 33 33
PIK3CB 0.031 0.045 -10000 0 -0.42 5 5
mol:Ca2+ -0.009 0.092 0.18 46 -0.2 54 100
MAGI3 0.012 0.099 -10000 0 -0.42 25 25
RELA 0.035 0.006 -10000 0 -10000 0 0
apoptosis 0.004 0.052 -10000 0 -0.18 36 36
HRAS/GDP 0.023 0.025 -10000 0 -0.3 3 3
positive regulation of microtubule depolymerization -0.075 0.12 0.18 3 -0.24 128 131
NF kappa B1 p50/RelA -0.02 0.082 -10000 0 -0.21 59 59
endothelial cell migration -0.008 0.12 -10000 0 -0.52 25 25
ADCY4 -0.014 0.086 -10000 0 -0.28 37 37
ADCY5 -0.014 0.083 -10000 0 -0.28 33 33
ADCY6 -0.012 0.08 -10000 0 -0.26 35 35
ADCY7 -0.012 0.085 -10000 0 -0.29 32 32
ADCY1 -0.012 0.081 -10000 0 -0.27 36 36
ADCY2 -0.024 0.097 -10000 0 -0.3 40 40
ADCY3 -0.013 0.081 -10000 0 -0.27 34 34
ADCY8 -0.011 0.072 -10000 0 -0.27 27 27
ADCY9 -0.015 0.08 -10000 0 -0.26 33 33
GSK3B -0.041 0.097 0.16 1 -0.21 107 108
arachidonic acid secretion -0.017 0.088 -10000 0 -0.27 43 43
GNG2 0.034 0.021 -10000 0 -0.42 1 1
TRIP6 0.008 0.071 -10000 0 -0.36 17 17
GNAO1 0.006 0.053 -10000 0 -0.22 25 25
HRAS 0.032 0.036 -10000 0 -0.42 3 3
NFKBIA -0.008 0.091 0.21 14 -0.25 22 36
GAB1 0.027 0.061 -10000 0 -0.42 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.023 0.2 -10000 0 -0.92 21 21
JUN -0.001 0.12 -10000 0 -0.42 39 39
LPA/LPA2/NHERF2 -0.004 0.077 -10000 0 -0.19 62 62
TIAM1 0.002 0.23 -10000 0 -1.1 21 21
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
mol:IP3 -0.008 0.091 0.18 46 -0.2 51 97
PLCB3 0.01 0.091 0.19 47 -0.23 42 89
FOS -0.031 0.15 -10000 0 -0.42 66 66
positive regulation of mitosis -0.017 0.088 -10000 0 -0.27 43 43
LPA/LPA1-2-3 -0.006 0.049 -10000 0 -0.17 39 39
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.029 0.014 -10000 0 -10000 0 0
stress fiber formation -0.006 0.081 -10000 0 -0.28 21 21
GNAZ 0 0.069 -10000 0 -0.21 46 46
EGFR/PI3K-beta/Gab1 -0.022 0.097 -10000 0 -0.22 86 86
positive regulation of dendritic cell cytokine production -0.006 0.048 -10000 0 -0.17 39 39
LPA/LPA2/MAGI-3 0.005 0.064 -10000 0 -0.17 48 48
ARHGEF1 0.026 0.076 0.19 50 -0.21 22 72
GNAI2 0.002 0.07 -10000 0 -0.22 41 41
GNAI3 0.007 0.056 -10000 0 -0.19 35 35
GNAI1 -0.004 0.08 -10000 0 -0.23 51 51
LPA/LPA3 -0.004 0.025 -10000 0 -0.086 39 39
LPA/LPA2 -0.004 0.024 -10000 0 -0.085 39 39
LPA/LPA1 -0.009 0.065 -10000 0 -0.23 39 39
HB-EGF/EGFR -0.025 0.12 -10000 0 -0.28 89 89
HBEGF -0.02 0.098 -10000 0 -0.3 55 55
mol:DAG -0.008 0.091 0.18 46 -0.2 51 97
cAMP biosynthetic process -0.019 0.088 0.2 3 -0.27 37 40
NFKB1 0.035 0.005 -10000 0 -10000 0 0
SRC 0.032 0.03 -10000 0 -0.42 2 2
GNB1 0.032 0.045 -10000 0 -0.42 5 5
LYN 0.006 0.095 0.23 25 -0.24 17 42
GNAQ -0.003 0.02 -10000 0 -0.07 39 39
LPAR2 0 0.001 -10000 0 -10000 0 0
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.007 0.038 -10000 0 -0.14 39 39
IL8 -0.069 0.18 -10000 0 -0.43 78 78
PTK2 0.011 0.042 -10000 0 -0.16 25 25
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
CASP3 0.004 0.052 -10000 0 -0.18 36 36
EGFR -0.013 0.13 -10000 0 -0.42 47 47
PLCG1 -0.003 0.043 -10000 0 -0.12 48 48
PLD2 0.01 0.052 -10000 0 -0.17 36 36
G12/G13 0.031 0.062 -10000 0 -0.18 34 34
PI3K-beta -0.019 0.1 -10000 0 -0.34 29 29
cell migration 0.009 0.067 -10000 0 -0.25 21 21
SLC9A3R2 -0.005 0.12 -10000 0 -0.42 40 40
PXN -0.006 0.082 -10000 0 -0.28 21 21
HRAS/GTP -0.017 0.09 -10000 0 -0.28 43 43
RAC1 0.035 0.006 -10000 0 -10000 0 0
MMP9 -0.014 0.14 -10000 0 -0.42 52 52
PRKCE 0.031 0.046 -10000 0 -0.42 5 5
PRKCD -0.011 0.089 0.18 42 -0.21 42 84
Gi(beta/gamma) -0.007 0.085 -10000 0 -0.26 37 37
mol:LPA -0.007 0.038 -10000 0 -0.14 39 39
TRIP6/p130 Cas/FAK1/Paxillin 0.01 0.08 -10000 0 -0.29 17 17
MAPKKK cascade -0.017 0.088 -10000 0 -0.27 43 43
contractile ring contraction involved in cytokinesis -0.016 0.1 -10000 0 -0.33 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.015 0.075 -10000 0 -0.2 63 63
GNA15 0.007 0.035 -10000 0 -0.11 27 27
GNA12 0.035 0.006 -10000 0 -10000 0 0
GNA13 0.028 0.042 -10000 0 -0.42 4 4
MAPT -0.077 0.12 0.18 3 -0.24 131 134
GNA11 0.008 0.03 -10000 0 -0.099 26 26
Rac1/GTP 0.022 0.21 -10000 0 -0.98 21 21
MMP2 -0.008 0.12 -10000 0 -0.52 25 25
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.012 0.12 -10000 0 -0.52 5 5
UGCG -0.091 0.27 -10000 0 -0.72 74 74
AKT1/mTOR/p70S6K/Hsp90/TERT -0.063 0.19 0.31 1 -0.37 106 107
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.089 0.26 -10000 0 -0.71 74 74
mol:DAG -0.006 0.028 0.17 11 -10000 0 11
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.08 0.23 0.34 1 -0.42 126 127
FRAP1 -0.1 0.26 0.36 1 -0.48 129 130
FOXO3 -0.05 0.2 0.36 1 -0.45 66 67
AKT1 -0.056 0.22 0.38 1 -0.49 66 67
GAB2 0.028 0.015 -10000 0 -10000 0 0
SMPD1 -0.004 0.13 -10000 0 -0.69 15 15
SGMS1 -0.004 0.034 0.058 1 -0.075 55 56
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 -0.009 0.049 -10000 0 -0.25 18 18
CALM1 0.035 0.007 -10000 0 -10000 0 0
cell proliferation -0.042 0.18 0.26 4 -0.37 95 99
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.033 0.068 -10000 0 -0.3 18 18
RPS6KB1 -0.043 0.16 -10000 0 -0.84 13 13
mol:sphingomyelin -0.006 0.028 0.17 11 -10000 0 11
natural killer cell activation -0.002 0.004 -10000 0 -0.013 37 37
JAK3 0.035 0.008 -10000 0 -10000 0 0
PIK3R1 0.017 0.083 -10000 0 -0.42 17 17
JAK1 0.031 0.036 -10000 0 -0.42 3 3
NFKB1 0.035 0.005 -10000 0 -10000 0 0
MYC -0.028 0.29 0.46 2 -0.93 36 38
MYB -0.23 0.5 -10000 0 -1.2 104 104
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.022 0.15 -10000 0 -0.36 55 55
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.026 0.16 -10000 0 -0.72 14 14
mol:PI-3-4-5-P3 -0.02 0.15 0.24 1 -0.35 55 56
Rac1/GDP 0.008 0.052 -10000 0 -0.23 18 18
T cell proliferation -0.018 0.14 0.28 3 -0.33 55 58
SHC1 0.025 0.026 -10000 0 -0.42 1 1
RAC1 0.035 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.01 0.028 -10000 0 -0.065 103 103
PRKCZ -0.021 0.15 0.23 1 -0.34 55 56
NF kappa B1 p50/RelA -0.07 0.24 0.36 1 -0.43 123 124
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.012 0.13 -10000 0 -0.42 31 31
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
IL2RA 0.001 0.11 -10000 0 -0.42 31 31
IL2RB 0.011 0.095 -10000 0 -0.42 23 23
TERT 0.032 0.03 -10000 0 -0.42 2 2
E2F1 -0.073 0.2 -10000 0 -0.43 113 113
SOS1 0.032 0.023 -10000 0 -0.43 1 1
RPS6 0.034 0.022 -10000 0 -0.42 1 1
mol:cAMP 0.004 0.013 0.031 100 -10000 0 100
PTPN11 0.032 0.012 -10000 0 -10000 0 0
IL2RG 0.028 0.042 -10000 0 -0.42 4 4
actin cytoskeleton organization -0.018 0.14 0.28 3 -0.33 55 58
GRB2 0.03 0.013 -10000 0 -10000 0 0
IL2 0.03 0.037 -10000 0 -0.42 3 3
PIK3CA 0.032 0.024 -10000 0 -0.43 1 1
Rac1/GTP 0.032 0.065 -10000 0 -0.22 18 18
LCK -0.019 0.14 -10000 0 -0.42 54 54
BCL2 -0.18 0.38 0.35 1 -0.82 119 120
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.069 0.16 -10000 0 -0.34 126 126
KLHL20 -0.025 0.09 0.25 1 -0.24 22 23
CYFIP2 -0.006 0.13 -10000 0 -0.42 44 44
Rac1/GDP -0.033 0.12 0.26 5 -0.26 60 65
ENAH -0.064 0.16 -10000 0 -0.35 102 102
AP1M1 0.034 0.021 -10000 0 -0.42 1 1
RAP1B 0.032 0.03 -10000 0 -0.42 2 2
RAP1A 0.03 0.05 -10000 0 -0.42 6 6
CTNNB1 0.024 0.067 -10000 0 -0.42 11 11
CDC42/GTP -0.012 0.083 -10000 0 -0.25 8 8
ABI1/Sra1/Nap1 -0.046 0.054 -10000 0 -0.16 41 41
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.03 0.1 -10000 0 -0.23 58 58
RAPGEF1 -0.07 0.15 0.24 3 -0.37 77 80
CTNND1 0.033 0.022 -10000 0 -0.42 1 1
regulation of calcium-dependent cell-cell adhesion -0.073 0.18 -10000 0 -0.35 143 143
CRK -0.067 0.16 -10000 0 -0.38 82 82
E-cadherin/gamma catenin/alpha catenin 0.019 0.098 -10000 0 -0.26 48 48
alphaE/beta7 Integrin 0.044 0.038 -10000 0 -0.3 5 5
IQGAP1 0.034 0.008 -10000 0 -10000 0 0
NCKAP1 0.034 0.021 -10000 0 -0.42 1 1
Rap1/GTP/I-afadin 0.047 0.063 -10000 0 -0.23 21 21
DLG1 -0.081 0.18 -10000 0 -0.35 144 144
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.03 0.056 -10000 0 -0.17 19 19
MLLT4 0.02 0.075 -10000 0 -0.42 14 14
ARF6/GTP/NME1/Tiam1 0.056 0.045 -10000 0 -0.24 9 9
PI3K -0.035 0.074 -10000 0 -0.22 19 19
ARF6 0.033 0.029 -10000 0 -0.42 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.004 0.1 -10000 0 -0.31 48 48
TIAM1 0.028 0.057 -10000 0 -0.42 8 8
E-cadherin(dimer)/Ca2+ 0.03 0.096 -10000 0 -0.22 56 56
AKT1 -0.024 0.053 0.18 4 -0.17 6 10
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
CDH1 -0.012 0.13 -10000 0 -0.42 45 45
RhoA/GDP -0.033 0.12 0.26 5 -0.27 62 67
actin cytoskeleton organization -0.017 0.068 0.17 2 -0.18 21 23
CDC42/GDP -0.031 0.12 0.26 5 -0.26 62 67
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.01 0.077 -10000 0 -0.22 55 55
ITGB7 0.035 0.004 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.033 0.1 -10000 0 -0.23 56 56
E-cadherin/Ca2+/beta catenin/alpha catenin 0.018 0.087 -10000 0 -0.22 55 55
mol:GDP -0.052 0.12 0.26 5 -0.3 65 70
CDC42/GTP/IQGAP1 0.045 0.013 -10000 0 -10000 0 0
JUP 0.028 0.042 -10000 0 -0.42 4 4
p120 catenin/RhoA/GDP -0.029 0.13 0.28 4 -0.28 60 64
RAC1/GTP/IQGAP1 0.045 0.012 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.048 0.033 -10000 0 -0.3 4 4
RHOA 0.026 0.061 -10000 0 -0.42 9 9
CDC42 0.034 0.007 -10000 0 -10000 0 0
CTNNA1 0.035 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.03 0.077 0.14 2 -0.18 82 84
NME1 0.033 0.01 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.078 0.17 -10000 0 -0.35 136 136
regulation of cell-cell adhesion -0.018 0.069 -10000 0 -0.2 13 13
WASF2 -0.016 0.041 0.11 3 -0.11 15 18
Rap1/GTP -0.014 0.093 0.25 2 -0.25 13 15
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.037 0.1 -10000 0 -0.23 52 52
CCND1 -0.038 0.095 0.16 2 -0.23 82 84
VAV2 -0.066 0.19 -10000 0 -0.5 26 26
RAP1/GDP -0.018 0.1 0.27 2 -0.27 13 15
adherens junction assembly -0.077 0.17 -10000 0 -0.34 137 137
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.034 0.007 -10000 0 -10000 0 0
PIP5K1C 0.032 0.036 -10000 0 -0.42 3 3
regulation of heterotypic cell-cell adhesion 0.028 0.1 -10000 0 -0.22 61 61
E-cadherin/beta catenin -0.024 0.1 -10000 0 -0.29 63 63
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.079 0.17 -10000 0 -0.36 122 122
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
Rac1/GTP -0.076 0.13 -10000 0 -0.37 34 34
E-cadherin/beta catenin/alpha catenin 0.02 0.1 -10000 0 -0.26 55 55
ITGAE 0.028 0.046 -10000 0 -0.42 5 5
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.074 0.19 -10000 0 -0.36 143 143
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 0.019 0.075 -10000 0 -0.42 14 14
EPHB2 0.032 0.03 -10000 0 -0.42 2 2
EFNB1 0.014 0.032 -10000 0 -0.3 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.071 0.067 -10000 0 -0.24 17 17
Ephrin B2/EPHB1-2 0.045 0.065 -10000 0 -0.24 21 21
neuron projection morphogenesis 0.047 0.057 -10000 0 -0.23 17 17
Ephrin B1/EPHB1-2/Tiam1 0.062 0.066 -10000 0 -0.25 17 17
DNM1 0.032 0.041 -10000 0 -0.42 4 4
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.08 0.2 0.22 2 -0.55 78 80
YES1 -0.11 0.3 -10000 0 -0.8 79 79
Ephrin B1/EPHB1-2/NCK2 0.067 0.053 -10000 0 -0.24 12 12
PI3K -0.048 0.23 -10000 0 -0.56 79 79
mol:GDP 0.06 0.065 -10000 0 -0.25 17 17
ITGA2B 0.033 0.009 -10000 0 -10000 0 0
endothelial cell proliferation 0.022 0.077 -10000 0 -0.27 31 31
FYN -0.11 0.3 -10000 0 -0.8 79 79
MAP3K7 -0.08 0.21 0.23 2 -0.59 75 77
FGR -0.1 0.29 -10000 0 -0.78 79 79
TIAM1 0.028 0.057 -10000 0 -0.42 8 8
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
RGS3 0.035 0.005 -10000 0 -10000 0 0
cell adhesion -0.056 0.21 -10000 0 -0.52 78 78
LYN -0.1 0.29 -10000 0 -0.78 79 79
Ephrin B1/EPHB1-2/Src Family Kinases -0.1 0.27 -10000 0 -0.73 79 79
Ephrin B1/EPHB1-2 -0.086 0.23 -10000 0 -0.64 75 75
SRC -0.099 0.29 -10000 0 -0.78 78 78
ITGB3 0.028 0.046 -10000 0 -0.42 5 5
EPHB1 0.026 0.05 -10000 0 -0.42 6 6
EPHB4 0.017 0.087 -10000 0 -0.42 19 19
RAC1 0.035 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.023 0.077 -10000 0 -0.27 31 31
alphaIIb/beta3 Integrin 0.046 0.034 -10000 0 -0.3 4 4
BLK -0.12 0.29 -10000 0 -0.8 78 78
HCK -0.11 0.29 -10000 0 -0.78 78 78
regulation of stress fiber formation -0.065 0.052 0.23 12 -10000 0 12
MAPK8 -0.079 0.2 -10000 0 -0.53 78 78
Ephrin B1/EPHB1-2/RGS3 0.067 0.053 -10000 0 -0.24 12 12
endothelial cell migration -0.076 0.19 0.2 1 -0.51 74 75
NCK2 0.035 0.004 -10000 0 -10000 0 0
PTPN13 -0.046 0.2 -10000 0 -0.54 72 72
regulation of focal adhesion formation -0.065 0.052 0.23 12 -10000 0 12
chemotaxis -0.065 0.052 0.23 12 -10000 0 12
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
Rac1/GTP 0.06 0.063 -10000 0 -0.24 17 17
angiogenesis -0.088 0.23 -10000 0 -0.63 78 78
LCK -0.12 0.3 -10000 0 -0.8 79 79
TCGA08_p53

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
CDKN2A -0.002 0.05 -10000 0 -0.3 14 14
TP53 -0.026 0.091 0.26 1 -0.26 60 61
Senescence -0.029 0.093 0.25 1 -0.25 68 69
Apoptosis -0.029 0.093 0.25 1 -0.25 68 69
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.004 0.061 0.26 25 -10000 0 25
MDM4 0.026 0.032 -10000 0 -0.42 2 2
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.014 0.1 -9999 0 -0.26 58 58
E-cadherin/beta catenin 0.004 0.11 -9999 0 -0.3 55 55
CTNNB1 0.024 0.067 -9999 0 -0.42 11 11
JUP 0.028 0.042 -9999 0 -0.42 4 4
CDH1 -0.012 0.13 -9999 0 -0.42 45 45
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.06 0.29 -10000 0 -0.93 46 46
epithelial cell differentiation -0.028 0.25 -10000 0 -0.72 48 48
ITCH 0.034 0.038 -10000 0 -10000 0 0
WWP1 -0.087 0.39 -10000 0 -1.3 42 42
FYN 0.027 0.05 -10000 0 -0.42 6 6
EGFR -0.013 0.13 -10000 0 -0.42 47 47
PRL 0.033 0.022 -10000 0 -0.42 1 1
neuron projection morphogenesis -0.019 0.22 0.34 10 -0.65 43 53
PTPRZ1 0.023 0.058 -10000 0 -0.42 8 8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.03 0.23 -10000 0 -0.72 43 43
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.064 0.26 -10000 0 -0.88 43 43
ADAM17 0.035 0.037 -10000 0 -0.11 6 6
ErbB4/ErbB4 -0.08 0.3 -10000 0 -1 45 45
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.063 0.29 -10000 0 -0.91 47 47
NCOR1 0.032 0.011 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.053 0.25 -10000 0 -0.82 43 43
GRIN2B -0.061 0.22 0.25 1 -0.75 43 44
ErbB4/ErbB2/betacellulin -0.071 0.26 -10000 0 -0.73 56 56
STAT1 0.02 0.075 -10000 0 -0.42 14 14
HBEGF 0.03 0.046 -10000 0 -0.42 5 5
PRLR -0.002 0.12 -10000 0 -0.42 40 40
E4ICDs/ETO2 -0.11 0.32 -10000 0 -0.85 61 61
axon guidance -0.069 0.28 -10000 0 -0.91 45 45
NEDD4 0.024 0.079 -10000 0 -0.43 12 12
Prolactin receptor/Prolactin receptor/Prolactin 0.022 0.094 -10000 0 -0.3 39 39
CBFA2T3 -0.047 0.16 -10000 0 -0.42 81 81
ErbB4/ErbB2/HBEGF -0.051 0.26 -10000 0 -0.78 50 50
MAPK3 -0.016 0.22 0.35 9 -0.67 43 52
STAT1 (dimer) -0.064 0.29 -10000 0 -0.91 47 47
MAPK1 -0.016 0.22 0.35 9 -0.67 43 52
JAK2 0.031 0.03 -10000 0 -0.42 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.064 0.25 -10000 0 -0.77 50 50
NRG1 0.012 0.021 -10000 0 -10000 0 0
NRG3 0.028 0.054 -10000 0 -0.42 7 7
NRG2 0.025 0.058 -10000 0 -0.42 8 8
NRG4 0.033 0.022 -10000 0 -0.42 1 1
heart development -0.069 0.28 -10000 0 -0.91 45 45
neural crest cell migration -0.063 0.25 -10000 0 -0.76 50 50
ERBB2 0.006 0.058 -10000 0 -0.3 15 15
WWOX/E4ICDs -0.071 0.29 -10000 0 -0.92 46 46
SHC1 0.027 0.025 -10000 0 -0.42 1 1
ErbB4/EGFR/neuregulin 4 -0.065 0.28 -10000 0 -0.88 45 45
apoptosis 0.06 0.28 0.84 50 -10000 0 50
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.062 0.29 -10000 0 -0.92 47 47
ErbB4/ErbB2/epiregulin -0.054 0.26 -10000 0 -0.78 50 50
ErbB4/ErbB4/betacellulin/betacellulin -0.081 0.3 -10000 0 -0.89 50 50
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.034 0.28 -10000 0 -0.72 58 58
MDM2 -0.069 0.29 0.29 13 -0.93 45 58
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.046 0.23 -10000 0 -0.78 43 43
STAT5A -0.043 0.28 0.33 6 -0.89 43 49
ErbB4/EGFR/neuregulin 1 beta -0.07 0.25 -10000 0 -0.81 45 45
DLG4 0.032 0.012 -10000 0 -10000 0 0
GRB2/SHC 0.038 0.028 -10000 0 -0.3 1 1
E4ICDs/TAB2/NCoR1 -0.048 0.28 -10000 0 -0.86 46 46
STAT5A (dimer) -0.022 0.28 -10000 0 -0.81 48 48
MAP3K7IP2 0.031 0.03 -10000 0 -0.42 2 2
STAT5B (dimer) -0.045 0.28 -10000 0 -0.87 46 46
LRIG1 0.005 0.11 -10000 0 -0.42 32 32
EREG 0.025 0.051 -10000 0 -0.42 6 6
BTC -0.011 0.14 -10000 0 -0.42 49 49
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.071 0.28 -10000 0 -0.92 45 45
ERBB4 -0.081 0.31 -10000 0 -1 45 45
STAT5B 0.03 0.024 -10000 0 -0.42 1 1
YAP1 -0.023 0.15 -10000 0 -0.41 46 46
GRB2 0.033 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.049 0.26 -10000 0 -0.77 50 50
glial cell differentiation 0.047 0.27 0.85 46 -10000 0 46
WWOX 0.027 0.016 -10000 0 -10000 0 0
cell proliferation -0.079 0.26 0.33 1 -0.81 48 49
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.007 0.13 -9999 0 -0.42 43 43
PLK4 0.03 0.05 -9999 0 -0.42 6 6
regulation of centriole replication -0.015 0.093 -9999 0 -0.3 48 48
Canonical Wnt signaling pathway

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
HDAC1 0.052 0.052 0.23 20 -0.42 1 21
AES 0.051 0.042 0.2 21 -10000 0 21
FBXW11 0.034 0.021 -10000 0 -0.42 1 1
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.04 0.053 -10000 0 -0.3 11 11
SMAD4 0.028 0.054 -10000 0 -0.42 7 7
DKK2 0.006 0.11 -10000 0 -0.42 31 31
TLE1 0.021 0.12 0.22 20 -0.42 33 53
MACF1 0.034 0.021 -10000 0 -0.42 1 1
CTNNB1 -0.001 0.1 0.28 4 -0.35 13 17
WIF1 0.03 0.014 -10000 0 -10000 0 0
beta catenin/RanBP3 0.073 0.2 0.41 114 -0.36 7 121
KREMEN2 -0.091 0.19 -10000 0 -0.42 129 129
DKK1 -0.028 0.15 -10000 0 -0.42 61 61
beta catenin/beta TrCP1 0.012 0.11 0.29 3 -0.35 12 15
FZD1 0.028 0.054 -10000 0 -0.42 7 7
AXIN2 -0.05 0.39 0.6 50 -1.2 34 84
AXIN1 0.036 0.002 -10000 0 -10000 0 0
RAN 0.036 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.044 0.065 -10000 0 -0.59 4 4
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.007 0.17 0.3 7 -0.44 42 49
Axin1/APC/GSK3 0.034 0.049 -10000 0 -0.27 2 2
Axin1/APC/GSK3/beta catenin/Macf1 0.021 0.08 0.34 3 -0.36 5 8
HNF1A 0.017 0.046 0.19 22 -10000 0 22
CTBP1 0.049 0.045 0.24 16 -10000 0 16
MYC 0.029 0.46 0.59 113 -1.3 37 150
RANBP3 0.035 0.007 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.044 0.15 -10000 0 -0.26 153 153
NKD1 0.026 0.037 -10000 0 -0.42 3 3
TCF4 0.033 0.099 0.22 20 -0.4 20 40
TCF3 0.047 0.056 0.22 18 -0.42 3 21
WNT1/LRP6/FZD1/Axin1 0.076 0.056 -10000 0 -0.24 12 12
Ran/GTP 0.028 0.005 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.09 0.26 0.51 109 -0.44 15 124
LEF1 0.037 0.085 0.22 20 -0.4 13 33
DVL1 0.032 0.048 0.2 1 -0.27 4 5
CSNK2A1 0.034 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.044 0.18 -10000 0 -0.5 43 43
DKK1/LRP6/Kremen 2 -0.062 0.16 -10000 0 -0.28 169 169
LRP6 0.029 0.046 -10000 0 -0.42 5 5
CSNK1A1 0.053 0.047 0.23 20 -10000 0 20
NLK 0.028 0.027 -10000 0 -0.43 1 1
CCND1 -0.15 0.6 0.57 75 -1.4 87 162
WNT1 0.034 0.021 -10000 0 -0.42 1 1
GSK3A 0.035 0.004 -10000 0 -10000 0 0
GSK3B 0.035 0.005 -10000 0 -10000 0 0
FRAT1 0.028 0.054 -10000 0 -0.42 7 7
PPP2R5D 0.029 0.065 0.23 3 -0.28 15 18
APC -0.013 0.058 0.36 2 -0.22 6 8
WNT1/LRP6/FZD1 0.022 0.049 -10000 0 -0.24 7 7
CREBBP 0.048 0.044 0.22 17 -10000 0 17
Coregulation of Androgen receptor activity

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
NRIP1 -0.01 0.14 -9999 0 -0.42 51 51
SVIL 0.022 0.078 -9999 0 -0.42 15 15
ZNF318 0.032 0.006 -9999 0 -10000 0 0
JMJD2C 0.039 0.01 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.038 0.12 -9999 0 -0.25 107 107
CARM1 0.034 0.021 -9999 0 -0.42 1 1
PRDX1 0.032 0.036 -9999 0 -0.42 3 3
PELP1 0.032 0.011 -9999 0 -10000 0 0
CTNNB1 0.025 0.067 -9999 0 -0.42 11 11
AKT1 0.031 0.036 -9999 0 -0.42 3 3
PTK2B 0.028 0.015 -9999 0 -10000 0 0
MED1 -0.001 0 -9999 0 -10000 0 0
MAK 0.024 0.046 -9999 0 -0.42 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.036 0.006 -9999 0 -10000 0 0
GSN 0.022 0.08 -9999 0 -0.42 16 16
NCOA2 0.025 0.047 -9999 0 -0.42 5 5
NCOA6 0.036 0.008 -9999 0 -10000 0 0
DNA-PK 0.054 0.035 -9999 0 -0.25 2 2
NCOA4 0.03 0.05 -9999 0 -0.42 6 6
PIAS3 0.036 0.006 -9999 0 -10000 0 0
cell proliferation -0.014 0.096 -9999 0 -0.57 12 12
XRCC5 0.035 0.004 -9999 0 -10000 0 0
UBE3A 0.036 0.029 -9999 0 -0.42 2 2
T-DHT/AR/SNURF -0.052 0.12 -9999 0 -0.25 113 113
FHL2 -0.12 0.32 -9999 0 -0.9 68 68
RANBP9 0.036 0.007 -9999 0 -10000 0 0
JMJD1A 0.009 0.072 -9999 0 -0.15 85 85
CDK6 0.025 0.054 -9999 0 -0.42 7 7
TGFB1I1 0.017 0.085 -9999 0 -0.42 18 18
T-DHT/AR/CyclinD1 -0.074 0.17 -9999 0 -0.33 133 133
XRCC6 0.033 0.009 -9999 0 -10000 0 0
T-DHT/AR -0.065 0.14 -9999 0 -0.22 212 212
CTDSP1 0.034 0.029 -9999 0 -0.42 2 2
CTDSP2 0.032 0.029 -9999 0 -0.42 2 2
BRCA1 0.022 0.07 -9999 0 -0.42 12 12
TCF4 0.015 0.089 -9999 0 -0.42 20 20
CDKN2A 0.014 0.075 -9999 0 -0.42 14 14
SRF 0.016 0.061 -9999 0 -0.14 63 63
NKX3-1 -0.048 0.1 -9999 0 -0.24 92 92
KLK3 0.021 0.053 -9999 0 -10000 0 0
TMF1 0.035 0.007 -9999 0 -10000 0 0
HNRNPA1 -0.001 0 -9999 0 -10000 0 0
AOF2 0.036 0.008 -9999 0 -10000 0 0
APPL1 -0.001 0.024 -9999 0 -0.3 3 3
T-DHT/AR/Caspase 8 -0.04 0.13 -9999 0 -0.25 112 112
AR -0.078 0.18 -9999 0 -0.43 100 100
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 -0.001 0 -9999 0 -10000 0 0
PAWR 0.024 0.072 -9999 0 -0.42 13 13
PRKDC 0.028 0.031 -9999 0 -0.42 2 2
PA2G4 0.034 0.005 -9999 0 -10000 0 0
UBE2I 0.032 0.011 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.032 0.12 -9999 0 -0.23 106 106
RPS6KA3 0.033 0.041 -9999 0 -0.42 4 4
T-DHT/AR/ARA70 -0.042 0.13 -9999 0 -0.26 116 116
LATS2 0.024 0.061 -9999 0 -0.42 9 9
T-DHT/AR/PRX1 -0.036 0.12 -9999 0 -0.23 111 111
Cyclin D3/CDK11 p58 0.025 0.005 -9999 0 -10000 0 0
VAV3 -0.039 0.17 -9999 0 -0.42 81 81
KLK2 -0.014 0.088 -9999 0 -0.38 16 16
CASP8 0.035 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.022 0.12 -9999 0 -0.23 97 97
TMPRSS2 -0.15 0.35 -9999 0 -0.86 94 94
CCND1 -0.042 0.16 -9999 0 -0.42 79 79
PIAS1 0.036 0.007 -9999 0 -10000 0 0
mol:T-DHT -0.013 0.03 -9999 0 -0.065 119 119
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.034 0.036 -9999 0 -0.42 3 3
T-DHT/AR/CDK6 -0.042 0.13 -9999 0 -0.26 114 114
CMTM2 0.028 0.024 -9999 0 -0.42 1 1
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 -0.013 0.03 -9999 0 -0.065 119 119
CCND3 0.035 0.007 -9999 0 -10000 0 0
TGIF1 -0.001 0 -9999 0 -10000 0 0
FKBP4 0.03 0.046 -9999 0 -0.42 5 5
Signaling events mediated by PTP1B

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
PDGFRB 0.028 0.057 -10000 0 -0.42 8 8
Jak2/Leptin Receptor -0.035 0.14 -10000 0 -0.35 49 49
PTP1B/AKT1 -0.043 0.14 0.26 3 -0.31 65 68
FYN 0.027 0.05 -10000 0 -0.42 6 6
p210 bcr-abl/PTP1B -0.06 0.14 0.28 3 -0.32 72 75
EGFR -0.023 0.13 -10000 0 -0.43 47 47
EGF/EGFR -0.089 0.18 0.29 2 -0.32 153 155
CSF1 0.034 0.021 -10000 0 -0.42 1 1
AKT1 0.032 0.036 -10000 0 -0.43 3 3
INSR 0.033 0.029 -10000 0 -0.42 2 2
PTP1B/N-cadherin -0.054 0.15 0.29 2 -0.35 64 66
Insulin Receptor/Insulin -0.008 0.13 0.31 2 -0.34 36 38
HCK 0.017 0.087 -10000 0 -0.42 19 19
CRK 0.031 0.023 -10000 0 -0.42 1 1
TYK2 -0.058 0.13 0.26 6 -0.33 60 66
EGF -0.074 0.19 -10000 0 -0.43 110 110
YES1 0.029 0.05 -10000 0 -0.42 6 6
CAV1 -0.069 0.15 0.27 3 -0.34 74 77
TXN 0.033 0.007 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.054 0.16 0.3 2 -0.33 80 82
cell migration 0.06 0.14 0.32 72 -0.28 3 75
STAT3 0.028 0.031 -10000 0 -0.42 2 2
PRLR 0.001 0.12 -10000 0 -0.41 42 42
ITGA2B 0.033 0.009 -10000 0 -10000 0 0
CSF1R 0.035 0.006 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.027 0.098 -10000 0 -0.3 41 41
FGR 0.034 0.007 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.043 0.14 0.25 2 -0.33 60 62
Crk/p130 Cas -0.036 0.14 0.3 1 -0.33 53 54
DOK1 -0.053 0.14 0.26 3 -0.36 55 58
JAK2 -0.043 0.14 -10000 0 -0.36 51 51
Jak2/Leptin Receptor/Leptin -0.042 0.14 0.25 1 -0.39 35 36
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
PTPN1 -0.06 0.14 0.28 3 -0.32 72 75
LYN 0.03 0.013 -10000 0 -10000 0 0
CDH2 0.011 0.093 -10000 0 -0.42 22 22
SRC -0.004 0.12 -10000 0 -0.62 15 15
ITGB3 0.028 0.046 -10000 0 -0.42 5 5
CAT1/PTP1B -0.082 0.2 0.31 3 -0.44 80 83
CAPN1 0.024 0.065 -10000 0 -0.43 10 10
CSK 0.033 0.022 -10000 0 -0.42 1 1
PI3K -0.003 0.14 0.28 2 -0.34 39 41
mol:H2O2 -0.001 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.033 0.13 -10000 0 -0.38 32 32
negative regulation of transcription -0.042 0.13 -10000 0 -0.36 51 51
FCGR2A 0.017 0.07 -10000 0 -0.42 12 12
FER 0.031 0.022 -10000 0 -0.43 1 1
alphaIIb/beta3 Integrin 0.043 0.035 -10000 0 -0.31 4 4
BLK 0.021 0.038 -10000 0 -0.42 3 3
Insulin Receptor/Insulin/Shc 0.052 0.04 -10000 0 -0.26 3 3
RHOA 0.025 0.062 -10000 0 -0.43 9 9
LEPR 0.026 0.057 -10000 0 -0.42 8 8
BCAR1 0.029 0.014 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.033 0.01 -10000 0 -10000 0 0
mol:NADPH -0.002 0.004 -10000 0 -10000 0 0
TRPV6 -0.067 0.21 0.24 2 -0.48 76 78
PRL 0.035 0.026 -10000 0 -0.26 3 3
SOCS3 0.009 0.18 -10000 0 -1.3 9 9
SPRY2 0.005 0.1 -10000 0 -0.43 28 28
Insulin Receptor/Insulin/IRS1 0.031 0.11 -10000 0 -0.27 55 55
CSF1/CSF1R -0.034 0.14 0.3 2 -0.32 59 61
Ras protein signal transduction 0.054 0.17 0.62 39 -10000 0 39
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
INS 0.034 0.022 -10000 0 -0.43 1 1
LEP -0.002 0.12 -10000 0 -0.42 36 36
STAT5B -0.05 0.13 0.23 3 -0.32 62 65
STAT5A -0.052 0.13 0.23 3 -0.33 63 66
GRB2 0.033 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.049 0.15 0.26 3 -0.34 68 71
CSN2 0.021 0.1 0.4 1 -1.4 2 3
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
LAT -0.009 0.12 -10000 0 -0.54 19 19
YBX1 0.037 0.043 -10000 0 -0.38 5 5
LCK -0.018 0.14 -10000 0 -0.42 54 54
SHC1 0.027 0.025 -10000 0 -0.42 1 1
NOX4 -0.022 0.14 -10000 0 -0.43 57 57
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.024 0.025 -10000 0 -0.3 3 3
alphaV beta3 Integrin 0.029 0.1 -10000 0 -0.26 52 52
PTK2 0.009 0.12 0.36 4 -0.41 19 23
IGF1R -0.043 0.17 -10000 0 -0.42 84 84
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.016 0.085 -10000 0 -0.42 18 18
SRC 0.032 0.03 -10000 0 -0.42 2 2
CDKN1B -0.009 0.12 -10000 0 -0.46 29 29
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.015 0.06 -10000 0 -0.5 4 4
ROCK1 0.035 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.072 0.21 3 -0.41 8 11
PTK2B 0.005 0.06 0.21 9 -0.24 21 30
alphaV/beta3 Integrin/JAM-A 0.058 0.1 -10000 0 -0.23 43 43
CBL 0.031 0.012 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.049 0.076 -10000 0 -0.27 25 25
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.04 0.2 -10000 0 -0.32 153 153
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.007 0.068 -10000 0 -0.23 27 27
alphaV/beta3 Integrin/Syndecan-1 0.029 0.11 -10000 0 -0.27 56 56
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.08 0.21 -10000 0 -0.33 188 188
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
alphaV/beta3 Integrin/Osteopontin -0.021 0.15 -10000 0 -0.27 126 126
RPS6KB1 -0.12 0.17 0.52 1 -0.44 78 79
TLN1 0.034 0.021 -10000 0 -0.42 1 1
MAPK3 -0.048 0.2 -10000 0 -0.55 56 56
GPR124 0.017 0.073 -10000 0 -0.42 13 13
MAPK1 -0.05 0.2 -10000 0 -0.55 59 59
PXN 0.036 0.004 -10000 0 -10000 0 0
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
alphaV/beta3 Integrin/Tumstatin 0.052 0.074 -10000 0 -0.28 22 22
cell adhesion 0.023 0.1 -10000 0 -0.27 49 49
ANGPTL3 0.03 0.046 -10000 0 -0.42 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.043 0.029 -10000 0 -0.25 4 4
IGF-1R heterotetramer -0.043 0.17 -10000 0 -0.42 84 84
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
TGFBR2 0.032 0.036 -10000 0 -0.42 3 3
ITGB3 0.028 0.046 -10000 0 -0.42 5 5
IGF1 -0.041 0.17 -10000 0 -0.42 81 81
RAC1 0.035 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.034 0.087 -10000 0 -0.3 27 27
apoptosis 0.021 0.08 -10000 0 -0.42 16 16
CD47 0.018 0.085 -10000 0 -0.42 18 18
alphaV/beta3 Integrin/CD47 0.041 0.089 -10000 0 -0.26 38 38
VCL 0.035 0.021 -10000 0 -0.42 1 1
alphaV/beta3 Integrin/Del1 -0.01 0.15 -10000 0 -0.28 104 104
CSF1 0.034 0.021 -10000 0 -0.42 1 1
PIK3C2A 0.01 0.085 -10000 0 -0.55 9 9
PI4 Kinase/Pyk2 0.003 0.076 -10000 0 -0.21 51 51
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.05 0.068 -10000 0 -0.25 21 21
FAK1/Vinculin 0.027 0.11 0.31 6 -0.33 19 25
alphaV beta3/Integrin/ppsTEM5 0.034 0.087 -10000 0 -0.3 27 27
RHOA 0.026 0.061 -10000 0 -0.42 9 9
VTN 0.034 0.007 -10000 0 -10000 0 0
BCAR1 0.029 0.014 -10000 0 -10000 0 0
FGF2 -0.001 0.11 -10000 0 -0.42 34 34
F11R -0.005 0.072 -10000 0 -0.3 28 28
alphaV/beta3 Integrin/Lactadherin 0.043 0.093 -10000 0 -0.31 28 28
alphaV/beta3 Integrin/TGFBR2 0.051 0.072 -10000 0 -0.27 22 22
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.058 0.067 -10000 0 -0.24 16 16
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.05 0.064 -10000 0 -0.24 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.009 0.13 -10000 0 -0.42 48 48
alphaV/beta3 Integrin/Pyk2 0.034 0.066 0.2 3 -0.24 21 24
SDC1 -0.002 0.12 -10000 0 -0.42 41 41
VAV3 -0.051 0.088 0.18 2 -0.24 88 90
PTPN11 0.036 0.003 -10000 0 -10000 0 0
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
FAK1/Paxillin 0.027 0.12 0.33 5 -0.33 19 24
cell migration 0.02 0.11 0.25 13 -0.3 19 32
ITGAV 0.021 0.08 -10000 0 -0.42 16 16
PI3K 0.057 0.11 -10000 0 -0.22 53 53
SPP1 -0.074 0.19 -10000 0 -0.42 116 116
KDR 0.033 0.035 -10000 0 -0.42 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.021 0.08 -10000 0 -0.42 16 16
COL4A3 0.032 0.036 -10000 0 -0.42 3 3
angiogenesis -0.038 0.21 0.27 1 -0.54 58 59
Rac1/GTP -0.013 0.097 -10000 0 -0.22 87 87
EDIL3 -0.056 0.18 -10000 0 -0.42 97 97
cell proliferation 0.051 0.072 -10000 0 -0.27 22 22
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.005 0.1 -10000 0 -0.3 50 50
EPHB2 0.032 0.03 -10000 0 -0.42 2 2
Syndecan-2/TACI 0.011 0.063 -10000 0 -0.25 27 27
LAMA1 0.034 0.009 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.02 0.13 -10000 0 -0.24 84 84
HRAS 0.032 0.036 -10000 0 -0.42 3 3
Syndecan-2/CASK -0.005 0.057 -10000 0 -0.24 27 27
ITGA5 0.033 0.035 -10000 0 -0.42 3 3
BAX -0.007 0.051 -10000 0 -10000 0 0
EPB41 0.034 0.021 -10000 0 -0.42 1 1
positive regulation of cell-cell adhesion 0.008 0.065 -10000 0 -0.23 33 33
LAMA3 -0.019 0.14 -10000 0 -0.42 57 57
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.014 0.091 -10000 0 -0.42 21 21
Syndecan-2/MMP2 0 0.088 -10000 0 -0.29 38 38
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.016 0.1 -10000 0 -0.3 46 46
dendrite morphogenesis 0.012 0.064 -10000 0 -0.24 28 28
Syndecan-2/GM-CSF 0.011 0.065 -10000 0 -0.25 29 29
determination of left/right symmetry -0.005 0.068 -10000 0 -0.29 27 27
Syndecan-2/PKC delta 0.012 0.066 -10000 0 -0.25 29 29
GNB2L1 0.033 0.035 -10000 0 -0.42 3 3
MAPK3 0.032 0.09 0.2 82 -0.22 27 109
MAPK1 0.037 0.094 0.2 94 -0.22 28 122
Syndecan-2/RACK1 0.025 0.066 -10000 0 -0.22 30 30
NF1 0.032 0.03 -10000 0 -0.42 2 2
FGFR/FGF/Syndecan-2 -0.005 0.068 -10000 0 -0.29 27 27
ITGA2 -0.009 0.13 -10000 0 -0.42 47 47
MAPK8 -0.005 0.058 -10000 0 -0.24 28 28
Syndecan-2/alpha2/beta1 Integrin 0.044 0.11 -10000 0 -0.24 48 48
Syndecan-2/Kininogen 0.013 0.064 -10000 0 -0.25 27 27
ITGB1 0.033 0.029 -10000 0 -0.42 2 2
SRC 0.037 0.093 0.19 97 -0.22 28 125
Syndecan-2/CASK/Protein 4.1 0.012 0.058 -10000 0 -0.22 28 28
extracellular matrix organization 0.013 0.064 -10000 0 -0.25 27 27
actin cytoskeleton reorganization -0.005 0.1 -10000 0 -0.3 50 50
Syndecan-2/Caveolin-2/Ras 0.017 0.089 -10000 0 -0.27 39 39
Syndecan-2/Laminin alpha3 -0.012 0.1 -10000 0 -0.26 67 67
Syndecan-2/RasGAP 0.033 0.075 -10000 0 -0.21 35 35
alpha5/beta1 Integrin 0.047 0.037 -10000 0 -0.3 5 5
PRKCD 0.032 0.03 -10000 0 -0.42 2 2
Syndecan-2 dimer 0.012 0.065 -10000 0 -0.25 28 28
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.018 0.066 -10000 0 -0.21 33 33
RHOA 0.026 0.061 -10000 0 -0.42 9 9
SDCBP 0.022 0.061 -10000 0 -0.42 9 9
TNFRSF13B 0.032 0.012 -10000 0 -10000 0 0
RASA1 0.028 0.054 -10000 0 -0.42 7 7
alpha2/beta1 Integrin 0.016 0.1 -10000 0 -0.3 46 46
Syndecan-2/Synbindin 0.011 0.063 -10000 0 -0.24 27 27
TGFB1 0.035 0.021 -10000 0 -0.42 1 1
CASP3 0.036 0.094 0.2 92 -0.22 28 120
FN1 -0.009 0.13 -10000 0 -0.42 48 48
Syndecan-2/IL8 -0.007 0.094 -10000 0 -0.27 52 52
SDC2 -0.005 0.068 -10000 0 -0.29 27 27
KNG1 0.034 0.008 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.011 0.066 -10000 0 -0.25 29 29
TRAPPC4 0.031 0.012 -10000 0 -10000 0 0
CSF2 0.03 0.036 -10000 0 -0.42 3 3
Syndecan-2/TGFB1 0.013 0.064 -10000 0 -0.25 27 27
Syndecan-2/Syntenin/PI-4-5-P2 0.008 0.065 -10000 0 -0.23 33 33
Syndecan-2/Ezrin 0.009 0.062 -10000 0 -0.22 32 32
PRKACA 0.037 0.096 0.2 96 -0.22 29 125
angiogenesis -0.007 0.093 -10000 0 -0.27 52 52
MMP2 0.006 0.098 -10000 0 -0.42 25 25
IL8 -0.005 0.12 -10000 0 -0.42 37 37
calcineurin-NFAT signaling pathway 0.011 0.063 -10000 0 -0.24 27 27
Cellular roles of Anthrax toxin

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
ANTXR1 0.005 0.11 -10000 0 -0.42 33 33
ANTXR2 0.022 0.075 -10000 0 -0.42 14 14
negative regulation of myeloid dendritic cell antigen processing and presentation -0.006 0.017 -10000 0 -0.062 41 41
monocyte activation -0.015 0.12 -10000 0 -0.37 53 53
MAP2K2 0.003 0.1 -10000 0 -0.62 13 13
MAP2K1 -0.009 0.015 -10000 0 -0.087 5 5
MAP2K7 -0.009 0.018 -10000 0 -0.11 6 6
MAP2K6 -0.013 0.042 0.13 4 -0.22 16 20
CYAA -0.025 0.065 -10000 0 -0.24 41 41
MAP2K4 -0.008 0.018 -10000 0 -0.11 6 6
IL1B -0.027 0.069 0.14 1 -0.21 53 54
Channel 0.02 0.084 -10000 0 -0.25 41 41
NLRP1 -0.006 0.016 -10000 0 -0.057 41 41
CALM1 0.035 0.007 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.074 -10000 0 -0.43 13 13
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.006 0.017 0.062 41 -10000 0 41
MAPK3 -0.007 0.023 0.14 5 -0.11 6 11
MAPK1 -0.009 0.018 -10000 0 -0.066 37 37
PGR -0.074 0.1 -10000 0 -0.22 169 169
PA/Cellular Receptors 0.02 0.092 -10000 0 -0.28 41 41
apoptosis -0.006 0.017 -10000 0 -0.062 41 41
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.02 0.08 -10000 0 -0.24 41 41
macrophage activation 0.002 0.053 0.17 39 -0.21 2 41
TNF 0.026 0.061 -10000 0 -0.42 9 9
VCAM1 -0.016 0.12 -10000 0 -0.37 53 53
platelet activation -0.001 0.074 -10000 0 -0.43 13 13
MAPKKK cascade 0.002 0.032 0.13 5 -0.12 5 10
IL18 -0.02 0.063 -10000 0 -0.24 33 33
negative regulation of macrophage activation -0.006 0.017 -10000 0 -0.062 41 41
LEF -0.006 0.017 -10000 0 -0.062 41 41
CASP1 -0.008 0.031 -10000 0 -0.083 63 63
mol:cAMP -0.001 0.075 -10000 0 -0.44 13 13
necrosis -0.006 0.017 -10000 0 -0.062 41 41
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.02 0.079 -10000 0 -0.24 41 41
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.005 0.11 -10000 0 -0.48 10 10
ACTA1 -0.016 0.12 0.22 13 -0.29 53 66
NUMA1 -0.014 0.12 0.21 1 -0.4 18 19
SPTAN1 -0.021 0.12 0.24 7 -0.31 49 56
LIMK1 -0.033 0.13 0.23 3 -0.33 52 55
BIRC3 -0.009 0.12 -10000 0 -0.42 41 41
BIRC2 0.031 0.012 -10000 0 -10000 0 0
BAX 0.035 0.007 -10000 0 -10000 0 0
CASP10 -0.049 0.092 -10000 0 -0.27 75 75
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.01 0.12 0.26 1 -0.48 12 13
DIABLO 0.036 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.021 0.12 0.24 7 -0.31 47 54
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.029 0.054 -10000 0 -0.42 7 7
GSN -0.028 0.13 0.26 5 -0.32 54 59
MADD 0.035 0.005 -10000 0 -10000 0 0
TFAP2A 0.001 0.15 -10000 0 -0.57 30 30
BID -0.022 0.07 -10000 0 -0.17 82 82
MAP3K1 -0.033 0.14 -10000 0 -0.41 51 51
TRADD 0.029 0.014 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.047 0.037 -10000 0 -0.3 5 5
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.03 0.13 0.32 5 -0.33 54 59
CASP9 0.033 0.021 -10000 0 -0.42 1 1
DNA repair -0.022 0.069 0.28 9 -0.18 18 27
neuron apoptosis -0.029 0.19 -10000 0 -0.67 40 40
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.018 0.12 0.21 1 -0.3 48 49
APAF1 0.032 0.041 -10000 0 -0.42 4 4
CASP6 -0.013 0.15 -10000 0 -0.77 14 14
TRAF2 0.033 0.029 -10000 0 -0.42 2 2
ICAD/CAD -0.024 0.12 0.23 4 -0.31 45 49
CASP7 0.031 0.1 0.26 40 -0.34 12 52
KRT18 -0.067 0.22 -10000 0 -0.57 74 74
apoptosis -0.016 0.12 0.28 3 -0.38 22 25
DFFA -0.023 0.12 0.23 4 -0.32 46 50
DFFB -0.023 0.12 0.23 3 -0.31 48 51
PARP1 0.022 0.07 0.18 18 -0.28 9 27
actin filament polymerization 0.033 0.13 0.32 49 -0.3 7 56
TNF 0.026 0.061 -10000 0 -0.42 9 9
CYCS -0.009 0.056 0.15 1 -0.2 10 11
SATB1 -0.026 0.15 -10000 0 -0.69 16 16
SLK -0.023 0.12 0.25 4 -0.31 49 53
p15 BID/BAX -0.002 0.077 -10000 0 -0.26 14 14
CASP2 -0.016 0.1 0.22 5 -0.34 24 29
JNK cascade 0.033 0.14 0.4 51 -10000 0 51
CASP3 -0.021 0.13 0.22 7 -0.32 51 58
LMNB2 -0.008 0.12 0.24 1 -0.44 19 20
RIPK1 0.034 0.007 -10000 0 -10000 0 0
CASP4 0.023 0.061 -10000 0 -0.42 9 9
Mammalian IAPs/DIABLO 0.032 0.082 -10000 0 -0.23 40 40
negative regulation of DNA binding 0.001 0.15 -10000 0 -0.56 30 30
stress fiber formation -0.023 0.12 0.24 4 -0.3 49 53
GZMB -0.033 0.12 -10000 0 -0.31 75 75
CASP1 -0.009 0.1 -10000 0 -0.36 33 33
LMNB1 -0.06 0.15 0.24 1 -0.39 46 47
APP -0.03 0.2 -10000 0 -0.68 40 40
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0.001 -10000 0 -10000 0 0
VIM -0.012 0.13 0.29 2 -0.4 22 24
LMNA -0.008 0.097 0.24 1 -0.32 18 19
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.017 0.11 -10000 0 -0.34 33 33
LRDD 0.034 0.007 -10000 0 -10000 0 0
SREBF1 -0.036 0.13 0.25 2 -0.32 50 52
APAF-1/Caspase 9 0.017 0.11 -10000 0 -0.64 12 12
nuclear fragmentation during apoptosis -0.013 0.12 0.21 1 -0.39 18 19
CFL2 -0.034 0.13 0.3 7 -0.33 49 56
GAS2 -0.031 0.13 0.25 4 -0.33 51 55
positive regulation of apoptosis -0.027 0.12 0.26 1 -0.38 24 25
PRF1 0.026 0.058 -10000 0 -0.42 8 8
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.018 0.11 -10000 0 -0.31 41 41
alphaM/beta2 Integrin/GPIbA 0.033 0.084 -10000 0 -0.29 22 22
alphaM/beta2 Integrin/proMMP-9 0.007 0.12 -10000 0 -0.29 62 62
PLAUR 0.009 0.11 -10000 0 -0.42 29 29
HMGB1 0.025 0.03 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.036 0.087 -10000 0 -0.3 23 23
AGER 0.024 0.038 -10000 0 -0.42 1 1
RAP1A 0.03 0.05 -10000 0 -0.42 6 6
SELPLG 0.023 0.072 -10000 0 -0.42 13 13
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.041 0.12 -10000 0 -0.24 63 63
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.014 0.14 -10000 0 -0.42 52 52
CYR61 -0.003 0.12 -10000 0 -0.42 39 39
TLN1 0.034 0.021 -10000 0 -0.42 1 1
Rap1/GTP 0.01 0.13 -10000 0 -0.36 33 33
RHOA 0.026 0.061 -10000 0 -0.42 9 9
P-selectin oligomer -0.04 0.16 -10000 0 -0.42 73 73
MYH2 -0.018 0.14 0.23 1 -0.44 31 32
MST1R -0.005 0.13 -10000 0 -0.42 43 43
leukocyte activation during inflammatory response 0.04 0.078 -10000 0 -0.25 22 22
APOB 0.036 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.006 0.098 -10000 0 -0.42 25 25
JAM3 0.015 0.085 -10000 0 -0.42 18 18
GP1BA 0.03 0.014 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CTGF 0.017 0.12 -10000 0 -0.32 44 44
alphaM/beta2 Integrin -0.008 0.13 -10000 0 -0.38 37 37
JAM3 homodimer 0.015 0.085 -10000 0 -0.42 18 18
ICAM2 0.026 0.046 -10000 0 -0.42 5 5
ICAM1 0.016 0.089 -10000 0 -0.42 20 20
phagocytosis triggered by activation of immune response cell surface activating receptor -0.008 0.13 -10000 0 -0.38 37 37
cell adhesion 0.033 0.083 -10000 0 -0.29 22 22
NFKB1 -0.001 0.15 0.38 1 -0.37 53 54
THY1 0.017 0.08 -10000 0 -0.42 16 16
RhoA/GDP 0.019 0.043 -10000 0 -0.3 9 9
Lipoprotein(a) 0.044 0.014 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.017 0.11 -10000 0 -0.26 59 59
IL6 -0.05 0.23 0.36 2 -0.6 65 67
ITGB2 0.005 0.098 -10000 0 -0.44 21 21
elevation of cytosolic calcium ion concentration 0.014 0.15 -10000 0 -0.36 60 60
alphaM/beta2 Integrin/JAM2/JAM3 0.024 0.12 -10000 0 -0.31 49 49
JAM2 0.011 0.099 -10000 0 -0.42 25 25
alphaM/beta2 Integrin/ICAM1 0.038 0.13 -10000 0 -0.28 64 64
alphaM/beta2 Integrin/uPA/Plg 0.025 0.12 -10000 0 -0.29 57 57
RhoA/GTP -0.029 0.14 -10000 0 -0.45 35 35
positive regulation of phagocytosis 0.001 0.14 -10000 0 -0.42 35 35
Ron/MSP 0.02 0.099 -10000 0 -0.3 43 43
alphaM/beta2 Integrin/uPAR/uPA 0.016 0.15 -10000 0 -0.36 60 60
alphaM/beta2 Integrin/uPAR 0.023 0.11 -10000 0 -0.33 39 39
PLAU -0.012 0.14 -10000 0 -0.42 50 50
PLAT -0.02 0.13 -10000 0 -0.42 49 49
actin filament polymerization -0.015 0.14 0.24 3 -0.42 31 34
MST1 0.034 0.008 -10000 0 -10000 0 0
alphaM/beta2 Integrin/lipoprotein(a) 0.046 0.082 -10000 0 -0.26 22 22
TNF -0.016 0.16 0.35 2 -0.41 52 54
RAP1B 0.032 0.03 -10000 0 -0.42 2 2
alphaM/beta2 Integrin/uPA 0.012 0.13 -10000 0 -0.32 55 55
fibrinolysis 0.023 0.12 -10000 0 -0.28 57 57
HCK 0.017 0.087 -10000 0 -0.42 19 19
dendritic cell antigen processing and presentation -0.008 0.13 -10000 0 -0.38 37 37
VTN 0.034 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 0.018 0.12 -10000 0 -0.3 48 48
LPA 0.033 0.01 -10000 0 -10000 0 0
LRP1 0.035 0.021 -10000 0 -0.42 1 1
cell migration -0.012 0.13 -10000 0 -0.28 75 75
FN1 -0.009 0.13 -10000 0 -0.42 48 48
alphaM/beta2 Integrin/Thy1 0.024 0.1 -10000 0 -0.29 36 36
MPO 0.031 0.012 -10000 0 -10000 0 0
KNG1 0.034 0.008 -10000 0 -10000 0 0
RAP1/GDP 0.041 0.037 -10000 0 -0.25 7 7
ROCK1 -0.019 0.14 0.21 2 -0.43 34 36
ELA2 0.034 0.007 -10000 0 -10000 0 0
PLG 0.031 0.03 -10000 0 -0.42 2 2
CTGF 0.003 0.11 -10000 0 -0.42 32 32
alphaM/beta2 Integrin/Hck 0.029 0.11 -10000 0 -0.37 27 27
ITGAM 0.021 0.053 -10000 0 -0.43 5 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.001 0.14 -10000 0 -0.28 78 78
HP 0.027 0.037 -10000 0 -0.42 3 3
leukocyte adhesion 0 0.15 -10000 0 -0.38 43 43
SELP -0.04 0.16 -10000 0 -0.42 73 73
TCGA08_retinoblastoma

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
CDKN2B 0.021 0.065 -10000 0 -0.39 11 11
CDKN2C 0.023 0.064 -10000 0 -0.39 11 11
CDKN2A 0.018 0.071 -10000 0 -0.39 14 14
CCND2 0.003 0.046 0.18 27 -0.13 2 29
RB1 -0.011 0.061 0.24 2 -0.21 38 40
CDK4 0.007 0.055 0.21 30 -10000 0 30
CDK6 0.005 0.057 0.21 28 -0.17 6 34
G1/S progression 0.018 0.075 0.21 56 -0.26 3 59
BMP receptor signaling

Figure S48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.046 0.1 -9999 0 -0.24 46 46
SMAD6-7/SMURF1 0.067 0.024 -9999 0 -0.26 1 1
NOG 0.029 0.037 -9999 0 -0.42 3 3
SMAD9 -0.029 0.16 -9999 0 -0.45 54 54
SMAD4 0.028 0.054 -9999 0 -0.42 7 7
SMAD5 -0.028 0.12 -9999 0 -0.34 40 40
BMP7/USAG1 -0.063 0.16 -9999 0 -0.31 139 139
SMAD5/SKI -0.016 0.13 -9999 0 -0.39 29 29
SMAD1 0.011 0.07 -9999 0 -0.32 6 6
BMP2 0.021 0.07 -9999 0 -0.42 12 12
SMAD1/SMAD1/SMAD4 0.033 0.077 -9999 0 -0.28 6 6
BMPR1A 0.031 0.045 -9999 0 -0.42 5 5
BMPR1B -0.004 0.11 -9999 0 -0.42 30 30
BMPR1A-1B/BAMBI -0.021 0.14 -9999 0 -0.26 120 120
AHSG 0.034 0.008 -9999 0 -10000 0 0
CER1 0.034 0.009 -9999 0 -10000 0 0
BMP2-4/CER1 0.014 0.12 -9999 0 -0.26 71 71
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.017 0.13 -9999 0 -0.36 32 32
BMP2-4 (homodimer) -0.007 0.13 -9999 0 -0.31 74 74
RGMB 0.026 0.061 -9999 0 -0.42 9 9
BMP6/BMPR2/BMPR1A-1B 0.05 0.09 -9999 0 -0.24 41 41
RGMA 0.019 0.073 -9999 0 -0.42 13 13
SMURF1 0.035 0.005 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.031 0.12 -9999 0 -0.38 31 31
BMP2-4/USAG1 -0.079 0.17 -9999 0 -0.29 192 192
SMAD6/SMURF1/SMAD5 -0.015 0.13 -9999 0 -0.39 28 28
SOSTDC1 -0.11 0.2 -9999 0 -0.42 154 154
BMP7/BMPR2/BMPR1A-1B 0.04 0.094 -9999 0 -0.24 45 45
SKI 0.036 0.002 -9999 0 -10000 0 0
BMP6 (homodimer) 0.027 0.05 -9999 0 -0.42 6 6
HFE2 0.026 0.064 -9999 0 -0.42 10 10
ZFYVE16 0.033 0.029 -9999 0 -0.42 2 2
MAP3K7 0.033 0.01 -9999 0 -10000 0 0
BMP2-4/CHRD 0.012 0.12 -9999 0 -0.28 71 71
SMAD5/SMAD5/SMAD4 -0.019 0.13 -9999 0 -0.39 30 30
MAPK1 0.033 0.022 -9999 0 -0.42 1 1
TAK1/TAB family 0.012 0.14 -9999 0 -0.37 24 24
BMP7 (homodimer) 0.015 0.072 -9999 0 -0.42 13 13
NUP214 0.034 0.021 -9999 0 -0.42 1 1
BMP6/FETUA 0.043 0.041 -9999 0 -0.3 6 6
SMAD1/SKI 0.027 0.08 -9999 0 -0.31 8 8
SMAD6 0.034 0.007 -9999 0 -10000 0 0
CTDSP2 0.034 0.029 -9999 0 -0.42 2 2
BMP2-4/FETUA 0.015 0.12 -9999 0 -0.26 70 70
MAP3K7IP1 0.033 0.009 -9999 0 -10000 0 0
GREM1 -0.003 0.12 -9999 0 -0.42 40 40
BMPR2 (homodimer) 0.034 0.029 -9999 0 -0.42 2 2
GADD34/PP1CA 0.059 0.041 -9999 0 -0.26 5 5
BMPR1A-1B (homodimer) 0.019 0.087 -9999 0 -0.3 34 34
CHRDL1 0.03 0.036 -9999 0 -0.42 3 3
ENDOFIN/SMAD1 0.025 0.08 -9999 0 -0.31 8 8
SMAD6-7/SMURF1/SMAD1 0.055 0.085 -9999 0 -0.31 5 5
SMAD6/SMURF1 0.035 0.005 -9999 0 -10000 0 0
BAMBI -0.055 0.17 -9999 0 -0.42 93 93
SMURF2 0.028 0.042 -9999 0 -0.42 4 4
BMP2-4/CHRDL1 0.012 0.12 -9999 0 -0.27 75 75
BMP2-4/GREM1 -0.01 0.15 -9999 0 -0.29 102 102
SMAD7 0.034 0.021 -9999 0 -0.42 1 1
SMAD8A/SMAD8A/SMAD4 -0.022 0.17 -9999 0 -0.43 59 59
SMAD1/SMAD6 0.026 0.08 -9999 0 -0.31 8 8
TAK1/SMAD6 0.048 0.016 -9999 0 -10000 0 0
BMP7 0.015 0.073 -9999 0 -0.42 13 13
BMP6 0.027 0.05 -9999 0 -0.42 6 6
MAP3K7IP2 0.031 0.03 -9999 0 -0.42 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.02 0.12 -9999 0 -0.34 36 36
PPM1A 0.034 0.021 -9999 0 -0.42 1 1
SMAD1/SMURF2 0.022 0.076 -9999 0 -0.31 7 7
SMAD7/SMURF1 0.05 0.02 -9999 0 -0.3 1 1
CTDSPL 0.028 0.054 -9999 0 -0.42 7 7
PPP1CA 0.031 0.03 -9999 0 -0.42 2 2
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.034 0.029 -9999 0 -0.42 2 2
PPP1R15A 0.034 0.021 -9999 0 -0.42 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.033 0.13 -9999 0 -0.4 35 35
CHRD 0.029 0.046 -9999 0 -0.42 5 5
BMPR2 0.034 0.029 -9999 0 -0.42 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.031 0.12 -9999 0 -0.39 30 30
BMP4 -0.029 0.15 -9999 0 -0.42 65 65
FST 0.024 0.058 -9999 0 -0.42 8 8
BMP2-4/NOG 0.01 0.12 -9999 0 -0.26 73 73
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.051 0.097 -9999 0 -0.23 45 45
Nectin adhesion 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
PDGFRB 0.028 0.057 -10000 0 -0.42 8 8
alphaV beta3 Integrin 0.035 0.073 -10000 0 -0.32 20 20
PTK2 -0.024 0.14 -10000 0 -0.43 36 36
positive regulation of JNK cascade -0.001 0.12 -10000 0 -0.32 42 42
CDC42/GDP 0.009 0.17 -10000 0 -0.42 46 46
Rac1/GDP 0.01 0.16 -10000 0 -0.41 47 47
RAP1B 0.032 0.03 -10000 0 -0.42 2 2
RAP1A 0.03 0.05 -10000 0 -0.42 6 6
CTNNB1 0.024 0.067 -10000 0 -0.42 11 11
CDC42/GTP 0.002 0.15 -10000 0 -0.39 42 42
nectin-3/I-afadin 0.022 0.097 -10000 0 -0.33 34 34
RAPGEF1 -0.015 0.16 -10000 0 -0.44 48 48
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.02 0.18 -10000 0 -0.47 60 60
PDGFB-D/PDGFRB 0.028 0.057 -10000 0 -0.42 8 8
TLN1 -0.014 0.071 0.19 4 -0.33 14 18
Rap1/GTP -0.006 0.12 -10000 0 -0.33 44 44
IQGAP1 0.034 0.008 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.047 0.063 -10000 0 -0.23 21 21
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.022 0.097 -10000 0 -0.33 34 34
PVR 0.032 0.036 -10000 0 -0.42 3 3
Necl-5(dimer) 0.032 0.036 -10000 0 -0.42 3 3
mol:GDP -0.012 0.19 -10000 0 -0.51 48 48
MLLT4 0.02 0.075 -10000 0 -0.42 14 14
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PI3K 0.052 0.12 -10000 0 -0.27 49 49
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.033 0.062 -10000 0 -0.3 15 15
positive regulation of lamellipodium assembly 0.005 0.13 -10000 0 -0.32 48 48
PVRL1 0.03 0.024 -10000 0 -0.42 1 1
PVRL3 0.011 0.099 -10000 0 -0.42 25 25
PVRL2 0.026 0.064 -10000 0 -0.42 10 10
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
CDH1 -0.012 0.13 -10000 0 -0.42 45 45
CLDN1 -0.048 0.17 -10000 0 -0.42 86 86
JAM-A/CLDN1 0.001 0.14 -10000 0 -0.27 87 87
SRC -0.033 0.19 -10000 0 -0.51 62 62
ITGB3 0.028 0.046 -10000 0 -0.42 5 5
nectin-1(dimer)/I-afadin/I-afadin 0.033 0.062 -10000 0 -0.3 15 15
FARP2 -0.014 0.2 -10000 0 -0.53 43 43
RAC1 0.035 0.006 -10000 0 -10000 0 0
CTNNA1 0.035 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.038 0.095 -10000 0 -0.28 36 36
nectin-1/I-afadin 0.033 0.062 -10000 0 -0.3 15 15
nectin-2/I-afadin 0.032 0.074 -10000 0 -0.3 23 23
RAC1/GTP/IQGAP1/filamentous actin 0.045 0.012 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.035 0.092 -10000 0 -0.28 35 35
CDC42/GTP/IQGAP1/filamentous actin 0.045 0.013 -10000 0 -10000 0 0
F11R 0.026 0.038 -10000 0 -0.42 3 3
positive regulation of filopodium formation -0.001 0.12 -10000 0 -0.32 42 42
alphaV/beta3 Integrin/Talin 0.008 0.11 0.27 1 -0.31 30 31
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.074 -10000 0 -0.3 23 23
nectin-2(dimer)/I-afadin/I-afadin 0.032 0.074 -10000 0 -0.3 23 23
PIP5K1C -0.01 0.074 -10000 0 -0.23 37 37
VAV2 -0.007 0.19 -10000 0 -0.52 44 44
RAP1/GDP 0.01 0.15 -10000 0 -0.39 46 46
ITGAV 0.021 0.08 -10000 0 -0.42 16 16
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.035 0.099 -10000 0 -0.28 41 41
nectin-3(dimer)/I-afadin/I-afadin 0.022 0.097 -10000 0 -0.33 34 34
Rac1/GTP 0.008 0.15 -10000 0 -0.39 48 48
PTPRM -0.005 0.085 -10000 0 -0.26 38 38
E-cadherin/beta catenin/alpha catenin 0.025 0.12 -10000 0 -0.22 76 76
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.034 0.007 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.03 0.046 -10000 0 -0.42 5 5
GNAT1/GTP 0.023 0.025 -10000 0 -0.3 3 3
Metarhodopsin II/Arrestin 0.008 0.095 -10000 0 -0.25 58 58
PDE6G/GNAT1/GTP 0.041 0.027 -10000 0 -0.25 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.032 0.036 -10000 0 -0.42 3 3
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.018 0.12 -10000 0 -0.22 125 125
mol:Na + 0.023 0.098 -10000 0 -0.24 50 50
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.007 0.12 -10000 0 -0.27 72 72
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.034 0.11 -10000 0 -0.24 50 50
CNGB1 0.03 0.014 -10000 0 -10000 0 0
RDH5 0.033 0.01 -10000 0 -10000 0 0
SAG -0.025 0.14 -10000 0 -0.42 59 59
mol:Ca2+ -0.034 0.088 0.33 7 -0.39 9 16
Na + (4 Units) 0.014 0.093 -10000 0 -0.23 49 49
RGS9 0.017 0.067 -10000 0 -0.42 11 11
GNB1/GNGT1 0.034 0.064 -10000 0 -0.3 17 17
GNAT1/GDP 0.019 0.11 -10000 0 -0.23 75 75
GUCY2D 0.032 0.011 -10000 0 -10000 0 0
GNGT1 0.016 0.07 -10000 0 -0.42 12 12
GUCY2F 0.027 0.064 -10000 0 -0.42 10 10
GNB5 0.024 0.067 -10000 0 -0.42 11 11
mol:GMP (4 units) -0.022 0.1 -10000 0 -0.22 107 107
mol:11-cis-retinal 0.033 0.01 -10000 0 -10000 0 0
mol:cGMP 0.047 0.084 -10000 0 -0.26 29 29
GNB1 0.031 0.045 -10000 0 -0.42 5 5
Rhodopsin 0.05 0.011 -10000 0 -10000 0 0
SLC24A1 0.03 0.046 -10000 0 -0.42 5 5
CNGA1 0.003 0.11 -10000 0 -0.42 29 29
Metarhodopsin II 0.023 0.003 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.063 0.077 -10000 0 -0.25 23 23
RGS9BP -0.022 0.15 -10000 0 -0.42 60 60
Metarhodopsin II/Transducin 0.014 0.048 -10000 0 -0.22 21 21
GCAP Family/Ca ++ 0.05 0.068 -10000 0 -0.25 23 23
PDE6A/B -0.028 0.15 -10000 0 -0.3 113 113
mol:Pi 0.007 0.12 -10000 0 -0.27 72 72
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.048 0.059 -10000 0 -0.23 20 20
PDE6B -0.066 0.19 -10000 0 -0.42 112 112
PDE6A 0.033 0.029 -10000 0 -0.42 2 2
PDE6G 0.033 0.01 -10000 0 -10000 0 0
RHO 0.035 0.005 -10000 0 -10000 0 0
PDE6 -0.016 0.15 -10000 0 -0.24 142 142
GUCA1A 0.022 0.075 -10000 0 -0.42 14 14
GC2/GCAP Family 0.065 0.089 -10000 0 -0.28 29 29
GUCA1C 0.026 0.064 -10000 0 -0.42 10 10
GUCA1B 0.034 0.022 -10000 0 -0.42 1 1
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.036 0.029 -10000 0 -0.41 1 1
HSPA8 0.018 0.073 -10000 0 -0.42 13 13
SMAD3/SMAD4/ER alpha -0.033 0.17 0.24 3 -0.3 133 136
AKT1 0.029 0.043 -10000 0 -0.42 3 3
GSC -0.19 0.48 -10000 0 -1.3 75 75
NKX2-5 0.028 0.022 -10000 0 -10000 0 0
muscle cell differentiation 0.011 0.17 0.39 53 -10000 0 53
SMAD2-3/SMAD4/SP1 0.024 0.18 -10000 0 -0.36 57 57
SMAD4 -0.004 0.096 -10000 0 -0.25 41 41
CBFB 0.029 0.014 -10000 0 -10000 0 0
SAP18 0.033 0.01 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.061 0.046 -10000 0 -0.22 3 3
SMAD3/SMAD4/VDR 0.059 0.12 -10000 0 -0.26 30 30
MYC -0.002 0.1 -10000 0 -0.42 29 29
CDKN2B -0.1 0.32 -10000 0 -1.2 29 29
AP1 -0.031 0.18 -10000 0 -0.44 65 65
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.007 0.099 -10000 0 -0.34 21 21
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.007 0.091 -10000 0 -0.28 38 38
SP3 0.028 0.03 -10000 0 -0.11 1 1
CREB1 0.034 0.021 -10000 0 -0.42 1 1
FOXH1 0.013 0.059 -10000 0 -0.2 7 7
SMAD3/SMAD4/GR 0.026 0.12 -10000 0 -0.28 42 42
GATA3 -0.043 0.17 -10000 0 -0.42 90 90
SKI/SIN3/HDAC complex/NCoR1 0.014 0.072 -10000 0 -0.3 14 14
MEF2C/TIF2 -0.014 0.13 0.33 1 -0.35 40 41
endothelial cell migration 0.003 0.24 1.3 15 -10000 0 15
MAX 0.034 0.011 -10000 0 -10000 0 0
RBBP7 0.033 0.029 -10000 0 -0.42 2 2
RBBP4 0.034 0.021 -10000 0 -0.42 1 1
RUNX2 0.031 0.041 -10000 0 -0.42 4 4
RUNX3 -0.01 0.13 -10000 0 -0.42 46 46
RUNX1 0.008 0.11 -10000 0 -0.42 29 29
CTBP1 0.034 0.008 -10000 0 -10000 0 0
NR3C1 0.021 0.078 -10000 0 -0.42 15 15
VDR 0.02 0.082 -10000 0 -0.42 17 17
CDKN1A -0.039 0.23 -10000 0 -1.2 16 16
KAT2B 0.001 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.016 0.14 -10000 0 -0.28 80 80
DCP1A 0.033 0.022 -10000 0 -0.42 1 1
SKI 0.036 0.002 -10000 0 -10000 0 0
SERPINE1 -0.003 0.24 -10000 0 -1.3 15 15
SMAD3/SMAD4/ATF2 0.034 0.11 -10000 0 -0.26 31 31
SMAD3/SMAD4/ATF3 0.015 0.12 -10000 0 -0.3 42 42
SAP30 0.03 0.046 -10000 0 -0.42 5 5
Cbp/p300/PIAS3 0.066 0.049 0.22 3 -10000 0 3
JUN -0.043 0.18 -10000 0 -0.44 63 63
SMAD3/SMAD4/IRF7 0.033 0.12 -10000 0 -0.28 37 37
TFE3 0.033 0.034 -10000 0 -0.16 4 4
COL1A2 -0.072 0.32 -10000 0 -0.86 68 68
mesenchymal cell differentiation -0.03 0.11 0.28 32 -10000 0 32
DLX1 0.032 0.011 -10000 0 -10000 0 0
TCF3 0.031 0.036 -10000 0 -0.42 3 3
FOS -0.039 0.16 -10000 0 -0.45 66 66
SMAD3/SMAD4/Max 0.032 0.11 -10000 0 -0.26 30 30
Cbp/p300/SNIP1 0.059 0.043 -10000 0 -0.26 3 3
ZBTB17 0.034 0.012 -10000 0 -10000 0 0
LAMC1 -0.006 0.1 -10000 0 -0.4 24 24
TGIF2/HDAC complex/SMAD3/SMAD4 0.027 0.11 -10000 0 -0.27 36 36
IRF7 0.029 0.056 -10000 0 -0.42 7 7
ESR1 -0.082 0.19 -10000 0 -0.41 130 130
HNF4A 0.032 0.03 -10000 0 -0.42 2 2
MEF2C -0.029 0.14 0.34 3 -0.35 53 56
SMAD2-3/SMAD4 0.018 0.13 -10000 0 -0.27 45 45
Cbp/p300/Src-1 0.061 0.047 -10000 0 -0.23 4 4
IGHV3OR16-13 -0.003 0.063 -10000 0 -0.46 7 7
TGIF2/HDAC complex 0.027 0.054 -10000 0 -0.42 7 7
CREBBP 0.033 0.019 -10000 0 -10000 0 0
SKIL 0.028 0.05 -10000 0 -0.42 6 6
HDAC1 0.034 0.021 -10000 0 -0.42 1 1
HDAC2 0.031 0.023 -10000 0 -0.42 1 1
SNIP1 0.031 0.036 -10000 0 -0.42 3 3
GCN5L2 0.031 0.028 -10000 0 -0.42 1 1
SMAD3/SMAD4/TFE3 0.04 0.12 -10000 0 -0.31 35 35
MSG1/HSC70 0.031 0.062 -10000 0 -0.3 15 15
SMAD2 0.012 0.058 -10000 0 -0.15 10 10
SMAD3 0.01 0.09 -10000 0 -0.32 20 20
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.001 0.078 -10000 0 -0.25 26 26
SMAD2/SMAD2/SMAD4 -0.001 0.062 0.26 4 -0.22 16 20
NCOR1 0.032 0.011 -10000 0 -10000 0 0
NCOA2 0.024 0.047 -10000 0 -0.42 5 5
NCOA1 0.031 0.045 -10000 0 -0.42 5 5
MYOD/E2A 0.03 0.08 -10000 0 -0.3 27 27
SMAD2-3/SMAD4/SP1/MIZ-1 0.037 0.18 -10000 0 -0.35 53 53
IFNB1 -0.004 0.095 0.36 1 -0.32 23 24
SMAD3/SMAD4/MEF2C -0.003 0.16 -10000 0 -0.4 47 47
CITED1 0.028 0.031 -10000 0 -0.42 2 2
SMAD2-3/SMAD4/ARC105 0.022 0.12 -10000 0 -0.24 43 43
RBL1 0.032 0.022 -10000 0 -0.42 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.003 0.12 -10000 0 -0.42 30 30
RUNX1-3/PEBPB2 0.012 0.12 -10000 0 -0.26 71 71
SMAD7 -0.04 0.2 -10000 0 -0.56 43 43
MYC/MIZ-1 0.015 0.083 0.19 6 -0.3 29 35
SMAD3/SMAD4 0.041 0.13 0.32 37 -0.41 15 52
IL10 -0.034 0.12 -10000 0 -0.31 52 52
PIASy/HDAC complex 0.023 0.043 -10000 0 -0.42 3 3
PIAS3 0.036 0.011 -10000 0 -10000 0 0
CDK2 0.035 0.033 -10000 0 -0.42 2 2
IL5 -0.034 0.13 -10000 0 -0.33 47 47
CDK4 0.037 0.017 -10000 0 -10000 0 0
PIAS4 0.023 0.043 -10000 0 -0.42 3 3
ATF3 0.011 0.084 -10000 0 -0.42 18 18
SMAD3/SMAD4/SP1 0.015 0.16 -10000 0 -0.34 64 64
FOXG1 -0.001 0.003 -10000 0 -10000 0 0
FOXO3 0.005 0.032 -10000 0 -0.25 4 4
FOXO1 0.005 0.032 -10000 0 -0.3 3 3
FOXO4 0.005 0.032 -10000 0 -0.3 3 3
heart looping -0.028 0.14 0.34 3 -0.35 53 56
CEBPB 0.024 0.053 -10000 0 -0.42 6 6
SMAD3/SMAD4/DLX1 0.033 0.1 -10000 0 -0.26 30 30
MYOD1 0.013 0.097 -10000 0 -0.42 24 24
SMAD3/SMAD4/HNF4 0.032 0.11 -10000 0 -0.26 31 31
SMAD3/SMAD4/GATA3 -0.01 0.17 -10000 0 -0.3 103 103
SnoN/SIN3/HDAC complex/NCoR1 0.028 0.05 -10000 0 -0.42 6 6
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.016 0.15 -10000 0 -0.28 76 76
SMAD3/SMAD4/SP1-3 0.03 0.18 -10000 0 -0.36 63 63
MED15 0 0 -10000 0 -10000 0 0
SP1 0.01 0.075 -10000 0 -0.19 37 37
SIN3B 0.035 0.005 -10000 0 -10000 0 0
SIN3A 0.034 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.033 0.15 -10000 0 -0.27 86 86
ITGB5 -0.044 0.18 -10000 0 -0.49 59 59
TGIF/SIN3/HDAC complex/CtBP 0.018 0.06 -10000 0 -0.29 9 9
SMAD3/SMAD4/AR -0.023 0.17 -10000 0 -0.31 114 114
AR -0.054 0.18 -10000 0 -0.42 99 99
negative regulation of cell growth 0.011 0.099 -10000 0 -0.34 20 20
SMAD3/SMAD4/MYOD 0.018 0.12 -10000 0 -0.26 54 54
E2F5 0.011 0.087 -10000 0 -0.42 19 19
E2F4 0.029 0.014 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.047 0.13 -10000 0 -0.25 47 47
SMAD2-3/SMAD4/FOXO1-3a-4 -0.003 0.099 -10000 0 -0.31 38 38
TFDP1 0.031 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.008 0.2 -10000 0 -0.44 65 65
SMAD3/SMAD4/RUNX2 0.031 0.11 -10000 0 -0.28 32 32
TGIF2 0.027 0.054 -10000 0 -0.42 7 7
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0.036 0.003 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.025 0.16 0.25 4 -0.42 46 50
IKBKB 0.017 0.09 0.27 5 -0.27 8 13
AKT1 0.022 0.11 0.25 36 -0.23 19 55
IKBKG 0.026 0.079 0.24 5 -0.27 8 13
CALM1 -0.012 0.13 0.25 5 -0.42 27 32
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
MAP3K1 -0.021 0.18 0.29 5 -0.48 44 49
MAP3K7 0.033 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.012 0.14 0.26 5 -0.38 38 43
DOK1 0.027 0.061 -10000 0 -0.42 9 9
AP-1 -0.02 0.1 0.21 3 -0.25 44 47
LYN 0.03 0.013 -10000 0 -10000 0 0
BLNK 0.012 0.1 -10000 0 -0.42 26 26
SHC1 0.027 0.025 -10000 0 -0.42 1 1
BCR complex 0.024 0.076 -10000 0 -0.3 24 24
CD22 -0.021 0.12 0.26 1 -0.47 28 29
CAMK2G -0.01 0.12 0.24 7 -0.4 25 32
CSNK2A1 0.034 0.008 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.003 0.079 -10000 0 -0.25 35 35
GO:0007205 -0.012 0.14 0.26 5 -0.39 38 43
SYK 0.005 0.11 -10000 0 -0.42 33 33
ELK1 -0.014 0.13 0.25 5 -0.42 28 33
NFATC1 0.019 0.14 0.26 21 -0.37 30 51
B-cell antigen/BCR complex 0.024 0.076 -10000 0 -0.3 24 24
PAG1/CSK 0.034 0.05 -10000 0 -0.3 9 9
NFKBIB 0.027 0.05 0.14 10 -0.12 21 31
HRAS 0.002 0.12 0.25 14 -0.36 26 40
NFKBIA 0.027 0.049 0.14 10 -0.12 21 31
NF-kappa-B/RelA/I kappa B beta 0.032 0.044 0.14 11 -0.093 6 17
RasGAP/Csk 0.037 0.1 -10000 0 -0.26 37 37
mol:GDP -0.011 0.13 0.26 5 -0.4 33 38
PTEN 0.027 0.061 -10000 0 -0.42 9 9
CD79B 0.006 0.096 -10000 0 -0.42 24 24
NF-kappa-B/RelA/I kappa B alpha 0.032 0.044 0.14 11 -0.092 4 15
GRB2 0.033 0.01 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.011 0.18 0.33 3 -0.5 41 44
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
mol:IP3 -0.014 0.14 0.27 4 -0.39 39 43
CSK 0.033 0.022 -10000 0 -0.42 1 1
FOS -0.038 0.14 0.24 4 -0.39 43 47
CHUK 0.015 0.1 0.24 5 -0.32 21 26
IBTK 0.032 0.03 -10000 0 -0.42 2 2
CARD11/BCL10/MALT1/TAK1 0.008 0.13 0.27 1 -0.4 25 26
PTPN6 -0.012 0.12 0.25 1 -0.47 25 26
RELA 0.035 0.006 -10000 0 -10000 0 0
BCL2A1 0.023 0.034 0.13 4 -0.1 1 5
VAV2 -0.002 0.14 0.26 3 -0.5 26 29
ubiquitin-dependent protein catabolic process 0.03 0.049 0.15 10 -0.12 21 31
BTK -0.012 0.19 -10000 0 -1.1 15 15
CD19 -0.02 0.12 0.26 1 -0.47 27 28
MAP4K1 0.034 0.007 -10000 0 -10000 0 0
CD72 0.008 0.1 -10000 0 -0.42 27 27
PAG1 0.02 0.061 -10000 0 -0.42 9 9
MAPK14 -0.016 0.16 0.27 5 -0.42 41 46
SH3BP5 0.021 0.078 -10000 0 -0.42 15 15
PIK3AP1 -0.021 0.15 0.28 4 -0.45 36 40
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.02 0.16 -10000 0 -0.46 43 43
RAF1 0.002 0.11 0.25 10 -0.36 20 30
RasGAP/p62DOK/SHIP 0.025 0.1 -10000 0 -0.27 41 41
CD79A 0.031 0.023 -10000 0 -0.42 1 1
re-entry into mitotic cell cycle -0.02 0.1 0.21 2 -0.25 45 47
RASA1 0.028 0.054 -10000 0 -0.42 7 7
MAPK3 0.012 0.11 0.28 10 -0.31 16 26
MAPK1 0.001 0.1 0.27 7 -0.32 17 24
CD72/SHP1 0.016 0.16 0.29 17 -0.46 32 49
NFKB1 0.035 0.005 -10000 0 -10000 0 0
MAPK8 -0.017 0.16 0.28 7 -0.42 41 48
actin cytoskeleton organization 0.017 0.14 0.28 19 -0.44 28 47
NF-kappa-B/RelA 0.064 0.087 0.27 9 -0.22 8 17
Calcineurin 0.003 0.13 0.25 1 -0.38 27 28
PI3K -0.027 0.11 -10000 0 -0.39 29 29
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.012 0.15 0.27 6 -0.43 38 44
SOS1 0.034 0.021 -10000 0 -0.42 1 1
Bam32/HPK1 -0.067 0.31 -10000 0 -0.73 81 81
DAPP1 -0.1 0.34 -10000 0 -0.83 80 80
cytokine secretion 0.02 0.13 0.25 24 -0.35 30 54
mol:DAG -0.014 0.14 0.27 4 -0.39 39 43
PLCG2 0.02 0.055 -10000 0 -0.42 7 7
MAP2K1 0.001 0.11 0.25 8 -0.35 18 26
B-cell antigen/BCR complex/FcgammaRIIB 0.019 0.094 -10000 0 -0.29 35 35
mol:PI-3-4-5-P3 -0.002 0.11 0.25 20 -0.31 22 42
ETS1 -0.011 0.11 0.23 7 -0.38 24 31
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.033 0.12 -10000 0 -0.26 56 56
B-cell antigen/BCR complex/LYN -0.014 0.13 0.27 1 -0.45 32 33
MALT1 0.03 0.041 -10000 0 -0.42 4 4
TRAF6 0.034 0.021 -10000 0 -0.42 1 1
RAC1 0.007 0.14 0.29 11 -0.47 28 39
B-cell antigen/BCR complex/LYN/SYK -0.004 0.14 -10000 0 -0.49 26 26
CARD11 -0.014 0.14 0.26 7 -0.44 28 35
FCGR2B 0.001 0.11 -10000 0 -0.42 30 30
PPP3CA 0.027 0.061 -10000 0 -0.42 9 9
BCL10 0.034 0.007 -10000 0 -10000 0 0
IKK complex 0.024 0.05 0.16 21 -0.12 5 26
PTPRC 0.006 0.095 -10000 0 -0.42 23 23
PDPK1 0.003 0.085 0.21 28 -0.22 15 43
PPP3CB 0.035 0.021 -10000 0 -0.42 1 1
PPP3CC 0.024 0.043 -10000 0 -0.42 4 4
POU2F2 0.025 0.032 0.13 5 -0.1 1 6
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.031 0.023 -10000 0 -0.42 1 1
MKNK1 0.035 0.006 -10000 0 -10000 0 0
mol:PIP3 -0.024 0.1 0.26 5 -0.27 64 69
FRAP1 -0.008 0.12 -10000 0 -0.46 22 22
AKT1 -0.024 0.096 0.17 24 -0.25 58 82
INSR 0.033 0.029 -10000 0 -0.42 2 2
Insulin Receptor/Insulin 0.044 0.025 -10000 0 -0.25 3 3
mol:GTP 0.011 0.096 0.33 1 -0.22 53 54
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.006 0.051 -10000 0 -0.2 17 17
TSC2 0.031 0.023 -10000 0 -0.42 1 1
RHEB/GDP 0.005 0.08 -10000 0 -0.19 52 52
TSC1 0.035 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.009 0.11 -10000 0 -0.31 63 63
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.011 0.068 -10000 0 -0.24 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0 0.093 0.24 4 -0.34 18 22
MAP3K5 -0.013 0.084 0.19 8 -0.25 48 56
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
apoptosis -0.013 0.084 0.19 8 -0.25 48 56
mol:LY294002 0 0 0.001 1 -0.001 56 57
EIF4B -0.002 0.085 0.23 4 -0.3 18 22
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.012 0.083 0.22 4 -0.28 17 21
eIF4E/eIF4G1/eIF4A1 0.001 0.075 -10000 0 -0.32 14 14
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.003 0.12 -10000 0 -0.27 75 75
mTOR/RHEB/GTP/Raptor/GBL 0.01 0.06 0.22 3 -0.22 9 12
FKBP1A 0.034 0.008 -10000 0 -10000 0 0
RHEB/GTP 0.019 0.09 0.31 1 -0.27 12 13
mol:Amino Acids 0 0 0.001 1 -0.001 56 57
FKBP12/Rapamycin 0.025 0.006 -10000 0 -10000 0 0
PDPK1 -0.032 0.093 0.17 21 -0.26 59 80
EIF4E 0.035 0.005 -10000 0 -10000 0 0
ASK1/PP5C -0.032 0.21 -10000 0 -0.58 57 57
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.052 -10000 0 -0.39 1 1
TSC1/TSC2 0.013 0.1 0.36 1 -0.23 53 54
tumor necrosis factor receptor activity 0 0 0.001 56 -0.001 1 57
RPS6 0.034 0.022 -10000 0 -0.42 1 1
PPP5C 0.031 0.041 -10000 0 -0.42 4 4
EIF4G1 0.031 0.041 -10000 0 -0.42 4 4
IRS1 -0.031 0.11 -10000 0 -0.32 63 63
INS 0.034 0.021 -10000 0 -0.42 1 1
PTEN 0.026 0.06 -10000 0 -0.42 9 9
PDK2 -0.032 0.1 0.18 26 -0.26 65 91
EIF4EBP1 -0.067 0.31 -10000 0 -1.1 38 38
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PPP2R5D -0.006 0.11 -10000 0 -0.41 22 22
peptide biosynthetic process 0.017 0.03 0.19 5 -0.23 5 10
RHEB 0.035 0.007 -10000 0 -10000 0 0
EIF4A1 0.032 0.012 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 14 -0.003 7 21
EEF2 0.017 0.03 0.19 5 -0.23 5 10
eIF4E/4E-BP1 -0.047 0.3 -10000 0 -1.1 38 38
Reelin 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
CDK5R1/CDK5 0.048 0.016 -10000 0 -10000 0 0
VLDLR -0.006 0.12 -10000 0 -0.42 41 41
CRKL 0.03 0.041 -10000 0 -0.42 4 4
LRPAP1 0.034 0.007 -10000 0 -10000 0 0
FYN 0.027 0.05 -10000 0 -0.42 6 6
ITGA3 0.023 0.07 -10000 0 -0.42 12 12
RELN/VLDLR/Fyn 0.028 0.1 -10000 0 -0.27 49 49
MAPK8IP1/MKK7/MAP3K11/JNK1 0.068 0.071 -10000 0 -0.22 16 16
AKT1 -0.017 0.088 -10000 0 -0.23 58 58
MAP2K7 0.034 0.021 -10000 0 -0.42 1 1
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
DAB1 0.035 0.006 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.039 0.08 -10000 0 -0.23 39 39
LRPAP1/LRP8 0.023 0.088 -10000 0 -0.3 34 34
RELN/LRP8/DAB1/Fyn 0.045 0.087 -10000 0 -0.22 45 45
DAB1/alpha3/beta1 Integrin 0.017 0.11 -10000 0 -0.22 76 76
long-term memory 0.049 0.1 -10000 0 -0.22 53 53
DAB1/LIS1 0.033 0.12 -10000 0 -0.22 76 76
DAB1/CRLK/C3G 0.021 0.11 -10000 0 -0.39 3 3
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
DAB1/NCK2 0.04 0.12 -10000 0 -0.22 77 77
ARHGEF2 0.021 0.058 -10000 0 -0.42 8 8
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.032 0.011 -10000 0 -10000 0 0
CDK5R1 0.033 0.01 -10000 0 -10000 0 0
RELN 0.03 0.046 -10000 0 -0.42 5 5
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
RELN/LRP8/Fyn 0.032 0.093 -10000 0 -0.26 45 45
GRIN2A/RELN/LRP8/DAB1/Fyn 0.055 0.092 -10000 0 -0.22 39 39
MAPK8 0.033 0.035 -10000 0 -0.42 3 3
RELN/VLDLR/DAB1 0.032 0.087 -10000 0 -0.24 45 45
ITGB1 0.033 0.029 -10000 0 -0.42 2 2
MAP1B -0.027 0.11 0.32 5 -0.24 94 99
RELN/LRP8 0.038 0.088 -10000 0 -0.26 39 39
GRIN2B/RELN/LRP8/DAB1/Fyn 0.046 0.11 -10000 0 -0.23 61 61
PI3K 0.035 0.067 -10000 0 -0.3 18 18
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.04 0.057 -10000 0 -0.32 11 11
RAP1A -0.042 0.096 0.34 7 -0.44 3 10
PAFAH1B1 0.032 0.023 -10000 0 -0.42 1 1
MAPK8IP1 0.033 0.029 -10000 0 -0.42 2 2
CRLK/C3G 0.047 0.034 -10000 0 -0.3 4 4
GRIN2B 0.017 0.085 -10000 0 -0.42 18 18
NCK2 0.035 0.004 -10000 0 -10000 0 0
neuron differentiation 0.018 0.081 -10000 0 -0.34 6 6
neuron adhesion -0.042 0.1 0.35 7 -0.4 5 12
LRP8 0 0.11 -10000 0 -0.42 34 34
GSK3B -0.016 0.092 0.19 5 -0.41 10 15
RELN/VLDLR/DAB1/Fyn 0.04 0.095 -10000 0 -0.23 49 49
MAP3K11 0.033 0.029 -10000 0 -0.42 2 2
RELN/VLDLR/DAB1/P13K -0.007 0.095 -10000 0 -0.24 60 60
CDK5 0.035 0.007 -10000 0 -10000 0 0
MAPT -0.071 0.17 0.79 4 -0.39 96 100
neuron migration -0.024 0.11 0.3 10 -0.36 13 23
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.017 0.081 -10000 0 -0.34 6 6
RELN/VLDLR 0.026 0.12 -10000 0 -0.24 78 78
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.026 0.004 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0.031 0.03 -10000 0 -0.42 2 2
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.01 0.11 -10000 0 -0.37 29 29
IRAK/TOLLIP 0.04 0.017 0.18 5 -10000 0 5
IKBKB 0.029 0.014 -10000 0 -10000 0 0
IKBKG 0.036 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.024 0.091 -10000 0 -0.3 36 36
IL1A 0.031 0.041 -10000 0 -0.42 4 4
IL1B -0.024 0.11 -10000 0 -0.34 54 54
IRAK/TRAF6/p62/Atypical PKCs 0.059 0.049 -10000 0 -0.21 12 12
IL1R2 0.003 0.11 -10000 0 -0.42 32 32
IL1R1 -0.005 0.13 -10000 0 -0.42 43 43
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.023 0.12 -10000 0 -0.41 30 30
TOLLIP 0.034 0.007 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.012 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.06 0.034 -10000 0 -0.26 2 2
IKK complex/ELKS 0.026 0.077 0.27 1 -0.31 9 10
JUN -0.028 0.072 0.23 7 -0.45 2 9
MAP3K7 0.033 0.01 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.005 0.15 -10000 0 -0.28 96 96
IL1 alpha/IL1R1/IL1RAP/MYD88 0.051 0.098 -10000 0 -0.23 51 51
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.062 0.1 -10000 0 -0.22 53 53
IL1 beta fragment/IL1R1/IL1RAP -0.013 0.14 -10000 0 -0.29 87 87
NFKB1 0.035 0.005 -10000 0 -10000 0 0
MAPK8 -0.013 0.063 0.24 10 -0.38 1 11
IRAK1 0.018 0.003 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.004 0.13 -10000 0 -0.32 73 73
IRAK4 0.033 0.035 -10000 0 -0.42 3 3
PRKCI 0.024 0.067 -10000 0 -0.42 11 11
TRAF6 0.034 0.021 -10000 0 -0.42 1 1
PI3K 0.035 0.067 -10000 0 -0.3 18 18
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.019 0.13 -10000 0 -0.39 39 39
CHUK 0.025 0.067 -10000 0 -0.42 11 11
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.013 0.14 -10000 0 -0.29 87 87
IL1 beta/IL1R2 -0.021 0.13 -10000 0 -0.3 86 86
IRAK/TRAF6/TAK1/TAB1/TAB2 0.075 0.044 -10000 0 -0.21 3 3
NF kappa B1 p50/RelA -0.005 0.14 -10000 0 -0.27 95 95
IRAK3 0.026 0.046 -10000 0 -0.42 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0 0.14 -10000 0 -0.27 88 88
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.008 0.085 -10000 0 -0.23 53 53
IL1 alpha/IL1R1/IL1RAP 0.036 0.095 -10000 0 -0.26 47 47
RELA 0.035 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0.033 0.009 -10000 0 -10000 0 0
SQSTM1 0.034 0.021 -10000 0 -0.42 1 1
MYD88 0.031 0.041 -10000 0 -0.42 4 4
IRAK/TRAF6/MEKK3 0.053 0.029 -10000 0 -0.22 1 1
IL1RAP 0.033 0.022 -10000 0 -0.42 1 1
UBE2N 0.035 0.005 -10000 0 -10000 0 0
IRAK/TRAF6 -0.016 0.11 -10000 0 -0.25 86 86
CASP1 0.001 0.11 -10000 0 -0.42 31 31
IL1RN/IL1R2 0.002 0.13 -10000 0 -0.32 63 63
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.002 0.14 -10000 0 -0.28 88 88
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.003 0.11 -10000 0 -0.33 45 45
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
IL1RN 0 0.12 -10000 0 -0.42 37 37
TRAF6/TAK1/TAB1/TAB2 0.07 0.042 -10000 0 -0.22 3 3
MAP2K6 -0.01 0.062 0.25 8 -0.39 1 9
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.004 0.11 -10000 0 -0.31 50 50
VEGFR1 homodimer/NRP1 -0.015 0.1 -10000 0 -0.3 50 50
mol:DAG -0.009 0.1 -10000 0 -0.29 42 42
VEGFR1 homodimer/NRP1/VEGFR 121 -0.014 0.095 -10000 0 -0.28 50 50
CaM/Ca2+ 0.009 0.1 -10000 0 -0.54 8 8
HIF1A -0.005 0.14 -10000 0 -0.42 51 51
GAB1 0.027 0.061 -10000 0 -0.42 9 9
AKT1 -0.016 0.1 -10000 0 -0.43 15 15
PLCG1 -0.009 0.1 -10000 0 -0.29 42 42
NOS3 0.002 0.11 0.38 2 -0.46 16 18
CBL 0.031 0.012 -10000 0 -10000 0 0
mol:NO 0.005 0.11 0.34 4 -0.44 16 20
FLT1 -0.013 0.12 -10000 0 -0.37 45 45
PGF 0.031 0.041 -10000 0 -0.42 4 4
VEGFR1 homodimer/NRP2/VEGFR121 0.004 0.1 -10000 0 -0.28 50 50
CALM1 0.035 0.007 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
eNOS/Hsp90 -0.001 0.1 0.27 1 -0.43 16 17
endothelial cell proliferation 0.001 0.11 0.3 9 -0.45 13 22
mol:Ca2+ -0.009 0.1 -10000 0 -0.29 42 42
MAPK3 -0.024 0.079 0.35 1 -0.48 9 10
MAPK1 -0.028 0.083 0.2 6 -0.49 8 14
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
PLGF homodimer 0.031 0.041 -10000 0 -0.42 4 4
PRKACA 0.035 0.004 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.028 0.05 -10000 0 -0.42 6 6
VEGFA homodimer 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.015 0.1 -10000 0 -0.3 50 50
platelet activating factor biosynthetic process -0.003 0.1 0.33 6 -0.45 9 15
PI3K 0.027 0.13 -10000 0 -0.27 62 62
PRKCA -0.027 0.089 0.2 11 -0.53 8 19
PRKCB -0.027 0.091 0.18 13 -0.53 8 21
VEGFR1 homodimer/PLGF homodimer 0.003 0.12 -10000 0 -0.31 53 53
VEGFA 0 0 -10000 0 -10000 0 0
VEGFB 0.034 0.021 -10000 0 -0.42 1 1
mol:IP3 -0.009 0.1 -10000 0 -0.29 42 42
RASA1 -0.012 0.11 -10000 0 -0.29 54 54
NRP2 0.034 0.021 -10000 0 -0.42 1 1
VEGFR1 homodimer -0.013 0.12 -10000 0 -0.36 45 45
VEGFB homodimer 0.034 0.021 -10000 0 -0.42 1 1
NCK1 0.034 0.021 -10000 0 -0.42 1 1
eNOS/Caveolin-1 0.017 0.12 0.36 3 -0.45 17 20
PTPN11 0.036 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.025 0.12 -10000 0 -0.27 64 64
mol:L-citrulline 0.005 0.11 0.34 4 -0.44 16 20
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.018 0.1 -10000 0 -0.27 46 46
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.004 0.1 -10000 0 -0.28 51 51
CD2AP 0.034 0.007 -10000 0 -10000 0 0
PI3K/GAB1 0.033 0.13 -10000 0 -0.26 68 68
PDPK1 -0.006 0.1 0.34 1 -0.46 11 12
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.005 0.1 -10000 0 -0.28 50 50
mol:NADP 0.005 0.11 0.34 4 -0.44 16 20
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.016 0.1 -10000 0 -0.27 46 46
VEGFR1 homodimer/NRP2 0.004 0.11 -10000 0 -0.31 50 50
Aurora B signaling

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
Condensin I complex -0.008 0.034 -10000 0 -0.097 61 61
STMN1 0.005 0.051 -10000 0 -0.34 10 10
Aurora B/RasGAP/Survivin 0.027 0.1 -10000 0 -0.28 44 44
Chromosomal passenger complex/Cul3 protein complex -0.046 0.12 -10000 0 -0.33 48 48
BIRC5 -0.004 0.13 -10000 0 -0.44 38 38
DES -0.064 0.26 -10000 0 -0.68 73 73
Aurora C/Aurora B/INCENP 0.052 0.051 -10000 0 -0.24 11 11
Aurora B/TACC1 0.023 0.063 -10000 0 -0.25 22 22
Aurora B/PP2A 0.044 0.034 -10000 0 -0.32 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.008 0.025 -10000 0 -0.19 7 7
mitotic metaphase/anaphase transition 0.001 0.005 0.015 44 -0.01 3 47
NDC80 0.004 0.025 -10000 0 -0.31 3 3
Cul3 protein complex 0.015 0.12 -10000 0 -0.26 76 76
KIF2C -0.057 0.22 -10000 0 -0.67 49 49
PEBP1 -0.001 0.004 0.012 1 -0.014 38 39
KIF20A 0.004 0.12 -10000 0 -0.42 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.038 0.053 -10000 0 -0.31 10 10
SEPT1 0.031 0.023 -10000 0 -0.42 1 1
SMC2 0 0 -10000 0 -10000 0 0
SMC4 0 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.045 0.18 -10000 0 -0.51 61 61
PSMA3 0.035 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.004 0.01 54 -0.008 9 63
H3F3B 0.013 0.028 -10000 0 -0.29 4 4
AURKB 0.029 0.04 -10000 0 -0.45 3 3
AURKC 0.034 0.021 -10000 0 -0.42 1 1
CDCA8 0.015 0.09 -10000 0 -0.45 18 18
cytokinesis -0.046 0.23 -10000 0 -0.65 49 49
Aurora B/Septin1 -0.029 0.22 -10000 0 -0.65 41 41
AURKA 0 0.004 0.01 54 -0.008 9 63
INCENP 0.024 0.057 -10000 0 -0.44 7 7
KLHL13 -0.035 0.16 -10000 0 -0.42 73 73
BUB1 -0.011 0.14 -10000 0 -0.42 51 51
hSgo1/Aurora B/Survivin 0.024 0.12 -10000 0 -0.34 39 39
EVI5 0.031 0.041 -10000 0 -0.42 4 4
RhoA/GTP -0.023 0.22 -10000 0 -0.59 50 50
SGOL1 0.02 0.08 -10000 0 -0.42 16 16
CENPA -0.04 0.15 -10000 0 -0.38 60 60
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.044 0.033 -10000 0 -0.32 3 3
NCAPD2 0 0 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.043 0.043 -10000 0 -0.31 6 6
RHOA 0.026 0.061 -10000 0 -0.42 9 9
NCAPH 0 0 -10000 0 -10000 0 0
NPM1 -0.02 0.12 -10000 0 -0.33 51 51
RASA1 0.028 0.054 -10000 0 -0.42 7 7
KLHL9 0.031 0.03 -10000 0 -0.42 2 2
mitotic prometaphase -0.001 0.004 0.012 1 -0.014 38 39
proteasomal ubiquitin-dependent protein catabolic process 0.044 0.033 -10000 0 -0.31 3 3
PPP1CC 0.033 0.035 -10000 0 -0.42 3 3
Centraspindlin -0.032 0.24 -10000 0 -0.62 52 52
RhoA/GDP 0.019 0.043 -10000 0 -0.3 9 9
NSUN2 -0.018 0.11 -10000 0 -0.36 26 26
MYLK 0.006 0.057 -10000 0 -0.31 16 16
KIF23 0.006 0.11 -10000 0 -0.43 30 30
VIM -0.006 0.072 -10000 0 -0.31 27 27
RACGAP1 0.019 0.085 -10000 0 -0.44 17 17
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.021 0.12 -10000 0 -0.44 20 20
Chromosomal passenger complex -0.051 0.19 -10000 0 -0.47 60 60
Chromosomal passenger complex/EVI5 0.037 0.14 -10000 0 -0.34 48 48
TACC1 0.012 0.087 -10000 0 -0.42 19 19
PPP2R5D 0.035 0.006 -10000 0 -10000 0 0
CUL3 0.032 0.041 -10000 0 -0.42 4 4
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Arf6 downstream pathway

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.029 0.23 -10000 0 -0.98 28 28
regulation of axonogenesis 0 0.058 0.3 12 -10000 0 12
myoblast fusion -0.006 0.11 0.4 31 -10000 0 31
mol:GTP 0.01 0.066 -10000 0 -0.23 34 34
regulation of calcium-dependent cell-cell adhesion -0.047 0.081 0.24 33 -10000 0 33
ARF1/GTP 0.024 0.056 -10000 0 -0.19 25 25
mol:GM1 0 0.047 -10000 0 -0.18 30 30
mol:Choline -0.002 0.057 -10000 0 -0.27 16 16
lamellipodium assembly -0.006 0.12 -10000 0 -0.45 34 34
MAPK3 0.008 0.085 -10000 0 -0.33 29 29
ARF6/GTP/NME1/Tiam1 0.048 0.082 -10000 0 -0.24 33 33
ARF1 0.027 0.025 -10000 0 -0.42 1 1
ARF6/GDP 0.006 0.11 -10000 0 -0.4 31 31
ARF1/GDP 0.008 0.1 -10000 0 -0.36 29 29
ARF6 0.03 0.056 -10000 0 -0.29 6 6
RAB11A 0.034 0.021 -10000 0 -0.42 1 1
TIAM1 0.025 0.06 -10000 0 -0.42 8 8
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.009 0.085 -10000 0 -0.34 28 28
actin filament bundle formation -0.016 0.11 0.35 39 -10000 0 39
KALRN 0.001 0.082 -10000 0 -0.31 31 31
RAB11FIP3/RAB11A 0.046 0.042 -10000 0 -0.3 7 7
RhoA/GDP 0.016 0.11 -10000 0 -0.35 39 39
NME1 0.03 0.02 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.11 -10000 0 -0.37 33 33
substrate adhesion-dependent cell spreading 0.01 0.066 -10000 0 -0.23 34 34
cortical actin cytoskeleton organization -0.006 0.13 -10000 0 -0.46 34 34
RAC1 0.035 0.006 -10000 0 -10000 0 0
liver development 0.01 0.066 -10000 0 -0.23 34 34
ARF6/GTP 0.01 0.066 -10000 0 -0.23 34 34
RhoA/GTP 0.025 0.071 -10000 0 -0.21 38 38
mol:GDP -0.008 0.1 -10000 0 -0.39 32 32
ARF6/GTP/RAB11FIP3/RAB11A 0.047 0.067 -10000 0 -0.18 31 31
RHOA 0.026 0.061 -10000 0 -0.42 9 9
PLD1 0.006 0.068 -10000 0 -0.23 32 32
RAB11FIP3 0.03 0.05 -10000 0 -0.42 6 6
tube morphogenesis -0.006 0.12 -10000 0 -0.45 34 34
ruffle organization 0 0.058 -10000 0 -0.3 12 12
regulation of epithelial cell migration 0.01 0.066 -10000 0 -0.23 34 34
PLD2 0.01 0.054 -10000 0 -0.2 25 25
PIP5K1A 0 0.058 -10000 0 -0.3 12 12
mol:Phosphatidic acid -0.002 0.057 -10000 0 -0.27 16 16
Rac1/GTP -0.006 0.13 -10000 0 -0.46 34 34
PDGFR-alpha signaling 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
PDGFRA -0.004 0.11 -10000 0 -0.44 29 29
PDGF/PDGFRA/CRKL 0.019 0.088 -10000 0 -0.3 32 32
positive regulation of JUN kinase activity 0.047 0.072 -10000 0 -0.23 22 22
CRKL 0.03 0.041 -10000 0 -0.42 4 4
PDGF/PDGFRA/Caveolin-3 0.021 0.086 -10000 0 -0.3 30 30
AP1 -0.14 0.3 -10000 0 -0.81 76 76
mol:IP3 -0.013 0.079 -10000 0 -0.33 26 26
PLCG1 -0.014 0.079 -10000 0 -0.33 26 26
PDGF/PDGFRA/alphaV Integrin 0.013 0.11 -10000 0 -0.32 43 43
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
CRK 0.031 0.023 -10000 0 -0.42 1 1
mol:Ca2+ -0.013 0.078 -10000 0 -0.33 26 26
CAV3 0.034 0.021 -10000 0 -0.42 1 1
CAV1 0.028 0.05 -10000 0 -0.42 6 6
SHC/Grb2/SOS1 0.049 0.074 -10000 0 -0.23 22 22
PDGF/PDGFRA/Shf 0.021 0.086 -10000 0 -0.3 30 30
FOS -0.14 0.29 0.31 2 -0.8 76 78
JUN -0.051 0.081 -10000 0 -0.34 34 34
oligodendrocyte development 0.012 0.1 -10000 0 -0.32 43 43
GRB2 0.033 0.01 -10000 0 -10000 0 0
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
mol:DAG -0.013 0.079 -10000 0 -0.33 26 26
PDGF/PDGFRA -0.004 0.11 -10000 0 -0.44 29 29
actin cytoskeleton reorganization 0.019 0.089 -10000 0 -0.3 33 33
SRF 0.017 0.012 -10000 0 -10000 0 0
SHC1 0.027 0.025 -10000 0 -0.42 1 1
PI3K 0.034 0.1 -10000 0 -0.28 41 41
PDGF/PDGFRA/Crk/C3G 0.044 0.078 -10000 0 -0.26 30 30
JAK1 -0.01 0.079 -10000 0 -0.31 30 30
ELK1/SRF -0.026 0.071 0.15 24 -0.26 29 53
SHB 0.03 0.046 -10000 0 -0.42 5 5
SHF 0.033 0.022 -10000 0 -0.42 1 1
CSNK2A1 0.039 0.022 -10000 0 -10000 0 0
GO:0007205 -0.023 0.083 -10000 0 -0.36 27 27
SOS1 0.034 0.021 -10000 0 -0.42 1 1
Ras protein signal transduction 0.047 0.072 -10000 0 -0.23 22 22
PDGF/PDGFRA/SHB 0.019 0.09 -10000 0 -0.3 33 33
PDGF/PDGFRA/Caveolin-1 0.017 0.095 -10000 0 -0.32 33 33
ITGAV 0.021 0.08 -10000 0 -0.42 16 16
ELK1 -0.035 0.077 0.17 1 -0.32 29 30
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PDGF/PDGFRA/Crk 0.019 0.085 -10000 0 -0.3 30 30
JAK-STAT cascade -0.01 0.079 -10000 0 -0.31 30 30
cell proliferation 0.021 0.085 -10000 0 -0.3 30 30
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.03 0.24 -10000 0 -0.75 24 24
PCK1 0.018 0.17 -10000 0 -0.99 5 5
HNF4A -0.006 0.26 0.56 7 -0.76 23 30
KCNJ11 -0.052 0.34 -10000 0 -0.98 45 45
AKT1 -0.002 0.17 -10000 0 -0.42 24 24
response to starvation 0.004 0.002 -10000 0 -10000 0 0
DLK1 -0.02 0.27 0.63 1 -0.79 23 24
NKX2-1 0.039 0.13 0.35 5 -0.34 8 13
ACADM -0.03 0.26 -10000 0 -0.77 28 28
TAT -0.004 0.16 -10000 0 -0.65 4 4
CEBPB 0.03 0.051 -10000 0 -0.42 6 6
CEBPA 0.029 0.07 -10000 0 -0.42 12 12
TTR -0.026 0.28 0.57 1 -0.72 40 41
PKLR 0.015 0.25 0.56 1 -0.72 22 23
APOA1 -0.024 0.28 -10000 0 -0.88 22 22
CPT1C -0.028 0.27 0.56 1 -0.82 29 30
ALAS1 0.011 0.18 -10000 0 -1.1 4 4
TFRC -0.04 0.35 -10000 0 -1.2 37 37
FOXF1 0.026 0.032 -10000 0 -0.42 2 2
NF1 0.036 0.035 -10000 0 -0.36 3 3
HNF1A (dimer) 0.008 0.02 -10000 0 -0.21 4 4
CPT1A -0.022 0.27 0.56 3 -0.85 26 29
HMGCS1 -0.021 0.24 -10000 0 -0.72 25 25
NR3C1 0.032 0.079 -10000 0 -0.4 16 16
CPT1B -0.022 0.24 -10000 0 -0.74 23 23
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.035 0.021 -10000 0 -0.42 1 1
GCK -0.024 0.25 -10000 0 -0.75 25 25
CREB1 0.041 0.028 -10000 0 -0.28 3 3
IGFBP1 0.01 0.14 -10000 0 -1.3 1 1
PDX1 0.007 0.15 -10000 0 -0.37 24 24
UCP2 -0.049 0.31 0.56 2 -0.85 46 48
ALDOB -0.022 0.27 -10000 0 -0.78 24 24
AFP -0.024 0.12 -10000 0 -0.82 3 3
BDH1 -0.033 0.26 -10000 0 -0.76 32 32
HADH -0.022 0.26 -10000 0 -0.61 54 54
F2 -0.007 0.29 -10000 0 -0.86 23 23
HNF1A 0.008 0.02 -10000 0 -0.21 4 4
G6PC 0.04 0.091 -10000 0 -1.3 1 1
SLC2A2 0.004 0.2 -10000 0 -0.95 6 6
INS 0.024 0.024 0.2 1 -0.43 1 2
FOXA1 -0.037 0.18 -10000 0 -0.4 97 97
FOXA3 0.043 0.076 -10000 0 -0.26 8 8
FOXA2 -0.009 0.32 -10000 0 -0.71 52 52
ABCC8 -0.2 0.48 -10000 0 -0.9 150 150
ALB -0.03 0.15 -10000 0 -0.95 7 7
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.001 0.047 0.2 23 -0.12 4 27
BUB1B -0.018 0.097 0.12 2 -0.3 42 44
PLK1 0.004 0.034 0.093 12 -0.087 21 33
PLK1S1 0.002 0.019 0.052 15 -0.047 20 35
KIF2A 0.003 0.03 0.082 12 -0.079 20 32
regulation of mitotic centrosome separation 0.004 0.034 0.093 12 -0.088 20 32
GOLGA2 0.035 0.005 -10000 0 -10000 0 0
Hec1/SPC24 -0.008 0.019 -10000 0 -0.07 27 27
WEE1 -0.004 0.093 -10000 0 -0.36 24 24
cytokinesis -0.023 0.14 0.16 1 -0.44 40 41
PP2A-alpha B56 -0.034 0.28 -10000 0 -0.71 70 70
AURKA 0.003 0.02 0.059 15 -0.049 13 28
PICH/PLK1 -0.018 0.095 -10000 0 -0.33 35 35
CENPE -0.013 0.069 0.2 3 -0.25 32 35
RhoA/GTP 0.019 0.043 -10000 0 -0.3 9 9
positive regulation of microtubule depolymerization 0.003 0.03 0.081 12 -0.079 20 32
PPP2CA 0.03 0.046 -10000 0 -0.42 5 5
FZR1 0.035 0.006 -10000 0 -10000 0 0
TPX2 -0.008 0.08 0.12 2 -0.27 40 42
PAK1 0.014 0.086 -10000 0 -0.43 18 18
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.034 0.021 -10000 0 -0.42 1 1
CLSPN 0.004 0.058 -10000 0 -0.28 18 18
GORASP1 0.034 0.022 -10000 0 -0.42 1 1
metaphase 0.002 0.006 0.019 48 -10000 0 48
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.019 0.052 15 -0.047 20 35
G2 phase of mitotic cell cycle -0.001 0.002 0.011 2 -10000 0 2
STAG2 0.036 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.008 0.11 -10000 0 -0.52 19 19
spindle elongation 0.004 0.034 0.093 12 -0.088 20 32
ODF2 0.036 0.005 -10000 0 -10000 0 0
BUB1 -0.073 0.29 -10000 0 -0.76 72 72
TPT1 -0.008 0.063 -10000 0 -0.19 49 49
CDC25C -0.014 0.11 -10000 0 -0.36 42 42
CDC25B 0.027 0.045 -10000 0 -0.44 4 4
SGOL1 0.001 0.047 0.12 4 -0.2 23 27
RHOA 0.026 0.061 -10000 0 -0.42 9 9
CCNB1/CDK1 0.028 0.13 -10000 0 -0.37 41 41
CDC14B 0.005 0.024 -10000 0 -0.3 3 3
CDC20 0.016 0.087 -10000 0 -0.42 19 19
PLK1/PBIP1 -0.005 0.057 0.095 3 -0.21 28 31
mitosis 0 0.003 0.013 11 -10000 0 11
FBXO5 -0.002 0.05 0.12 10 -0.2 11 21
CDC2 0.013 0.097 -10000 0 -0.44 22 22
NDC80 0 0 -10000 0 -10000 0 0
metaphase plate congression 0.004 0.054 -10000 0 -0.25 20 20
ERCC6L -0.013 0.11 -10000 0 -0.35 41 41
NLP/gamma Tubulin 0.007 0.028 0.075 14 -0.082 8 22
microtubule cytoskeleton organization -0.008 0.063 -10000 0 -0.19 49 49
G2/M transition DNA damage checkpoint 0 0.003 0.011 18 -10000 0 18
PPP1R12A 0.035 0.021 -10000 0 -0.42 1 1
interphase 0 0.003 0.011 18 -10000 0 18
PLK1/PRC1-2 0.013 0.11 -10000 0 -0.33 43 43
GRASP65/GM130/RAB1/GTP/PLK1 0.049 0.048 -10000 0 -0.19 2 2
RAB1A 0.034 0.021 -10000 0 -0.42 1 1
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.003 0.025 0.07 16 -0.069 12 28
mitotic prometaphase -0.001 0.004 0.018 20 -10000 0 20
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.055 -10000 0 -0.35 4 4
microtubule-based process 0.007 0.077 0.12 3 -0.25 35 38
Golgi organization 0.004 0.034 0.093 12 -0.088 20 32
Cohesin/SA2 0.021 0.035 0.11 3 -0.11 1 4
PPP1CB/MYPT1 0.051 0.018 -10000 0 -0.3 1 1
KIF20A 0.003 0.12 -10000 0 -0.42 35 35
APC/C/CDC20 0.013 0.064 0.12 3 -0.25 20 23
PPP2R1A 0.035 0.007 -10000 0 -10000 0 0
chromosome segregation -0.005 0.056 0.094 3 -0.21 28 31
PRC1 0.008 0.1 -10000 0 -0.42 28 28
ECT2 0.004 0.071 0.22 27 -0.22 17 44
C13orf34 0.003 0.028 0.075 16 -0.075 17 33
NUDC 0.004 0.054 -10000 0 -0.25 20 20
regulation of attachment of spindle microtubules to kinetochore -0.018 0.096 0.12 2 -0.3 42 44
spindle assembly 0.01 0.036 0.091 20 -0.083 11 31
spindle stabilization 0.002 0.019 0.052 15 -0.047 20 35
APC/C/HCDH1 0.03 0.023 -10000 0 -0.25 3 3
MKLP2/PLK1 0.007 0.078 0.12 3 -0.25 35 38
CCNB1 0.011 0.1 -10000 0 -0.44 25 25
PPP1CB 0.036 0.005 -10000 0 -10000 0 0
BTRC 0.034 0.022 -10000 0 -0.42 1 1
ROCK2 0.007 0.062 0.21 1 -0.3 12 13
TUBG1 0.009 0.038 0.099 1 -0.17 14 15
G2/M transition of mitotic cell cycle -0.021 0.11 -10000 0 -0.36 41 41
MLF1IP -0.009 0.07 -10000 0 -0.3 27 27
INCENP 0.027 0.055 -10000 0 -0.43 7 7
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.046 0.056 -10000 0 -0.23 17 17
RGS9BP -0.022 0.15 -10000 0 -0.42 60 60
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.023 0.062 -10000 0 -0.26 20 20
mol:ADP 0.007 0.019 -10000 0 -0.3 2 2
GNAT2 0.018 0.087 -10000 0 -0.42 19 19
RGS9-1/Gbeta5/R9AP 0.007 0.12 -10000 0 -0.27 72 72
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.025 0.077 -10000 0 -0.27 31 31
GRK7 0.033 0.029 -10000 0 -0.42 2 2
CNGB3 0.022 0.051 -10000 0 -0.42 6 6
Cone Metarhodopsin II/X-Arrestin 0.027 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.039 0.089 0.19 92 -0.24 21 113
Cone PDE6 0.021 0.13 -10000 0 -0.24 83 83
Cone Metarhodopsin II 0.022 0.016 -10000 0 -0.22 2 2
Na + (4 Units) 0.037 0.065 -10000 0 -0.24 21 21
GNAT2/GDP 0.011 0.12 -10000 0 -0.23 85 85
GNB5 0.024 0.067 -10000 0 -0.42 11 11
mol:GMP (4 units) 0.004 0.079 0.19 16 -0.25 35 51
Cone Transducin 0.05 0.06 -10000 0 -0.24 17 17
SLC24A2 0.031 0.036 -10000 0 -0.42 3 3
GNB3/GNGT2 0.047 0.022 -10000 0 -0.3 1 1
GNB3 0.034 0.009 -10000 0 -10000 0 0
GNAT2/GTP 0.014 0.061 -10000 0 -0.3 19 19
CNGA3 0.017 0.08 -10000 0 -0.42 16 16
ARR3 0.036 0.002 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.023 0.062 -10000 0 -0.26 20 20
mol:Pi 0.007 0.12 -10000 0 -0.27 72 72
Cone CNG Channel 0.032 0.1 -10000 0 -0.26 45 45
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.031 0.036 -10000 0 -0.42 3 3
RGS9 0.017 0.067 -10000 0 -0.42 11 11
PDE6C 0.029 0.05 -10000 0 -0.42 6 6
GNGT2 0.033 0.029 -10000 0 -0.42 2 2
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.021 0.075 -10000 0 -0.42 14 14
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.04 0.11 -10000 0 -0.45 19 19
HDAC1 0.04 0.028 -10000 0 -0.42 1 1
AES 0.037 0.008 -10000 0 -10000 0 0
FBXW11 0.034 0.021 -10000 0 -0.42 1 1
DTX1 0.032 0.035 -10000 0 -0.42 3 3
LRP6/FZD1 0.041 0.053 -10000 0 -0.3 11 11
TLE1 0.006 0.11 -10000 0 -0.42 33 33
AP1 -0.026 0.11 -10000 0 -0.26 87 87
NCSTN 0.028 0.025 -10000 0 -0.42 1 1
ADAM10 0.033 0.03 -10000 0 -0.42 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.037 0.15 -10000 0 -0.65 9 9
NICD/RBPSUH 0.005 0.098 -10000 0 -0.45 19 19
WIF1 0.029 0.014 -10000 0 -10000 0 0
NOTCH1 0.013 0.1 -10000 0 -0.48 19 19
PSENEN 0.035 0.006 -10000 0 -10000 0 0
KREMEN2 -0.091 0.19 -10000 0 -0.42 129 129
DKK1 -0.028 0.15 -10000 0 -0.42 61 61
beta catenin/beta TrCP1 0.013 0.099 0.26 2 -0.34 16 18
APH1B 0.024 0.07 -10000 0 -0.42 12 12
APH1A 0.031 0.036 -10000 0 -0.42 3 3
AXIN1 0.015 0.051 -10000 0 -0.47 1 1
CtBP/CBP/TCF1/TLE1/AES 0.026 0.088 0.29 3 -0.24 26 29
PSEN1 0.032 0.036 -10000 0 -0.42 3 3
FOS -0.031 0.15 -10000 0 -0.42 66 66
JUN -0.001 0.12 -10000 0 -0.42 39 39
MAP3K7 0.035 0.013 -10000 0 -10000 0 0
CTNNB1 -0.003 0.096 0.26 2 -0.35 17 19
MAPK3 0.032 0.023 -10000 0 -0.42 1 1
DKK2/LRP6/Kremen 2 -0.045 0.15 -10000 0 -0.26 153 153
HNF1A 0.002 0.006 -10000 0 -10000 0 0
CTBP1 0.036 0.01 -10000 0 -10000 0 0
MYC -0.083 0.34 -10000 0 -1.3 35 35
NKD1 0.027 0.038 -10000 0 -0.42 3 3
FZD1 0.028 0.054 -10000 0 -0.42 7 7
NOTCH1 precursor/Deltex homolog 1 0.041 0.11 -10000 0 -0.46 19 19
apoptosis -0.026 0.11 -10000 0 -0.25 87 87
Delta 1/NOTCHprecursor 0.039 0.11 -10000 0 -0.45 19 19
DLL1 0.033 0.01 -10000 0 -10000 0 0
PPARD 0.006 0.1 -10000 0 -0.84 6 6
Gamma Secretase 0.067 0.069 -10000 0 -0.22 14 14
APC -0.001 0.1 -10000 0 -0.49 14 14
DVL1 0.024 0.028 -10000 0 -0.24 3 3
CSNK2A1 0.034 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0.036 0.012 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.062 0.16 -10000 0 -0.28 169 169
LRP6 0.029 0.046 -10000 0 -0.42 5 5
CSNK1A1 0.034 0.006 -10000 0 -10000 0 0
NLK 0.029 0.024 -10000 0 -0.24 1 1
CCND1 -0.2 0.5 -10000 0 -1.3 84 84
WNT1 0.034 0.021 -10000 0 -0.42 1 1
Axin1/APC/beta catenin 0.022 0.099 0.34 2 -0.48 7 9
DKK2 0.006 0.11 -10000 0 -0.42 31 31
NOTCH1 precursor/DVL1 0.037 0.1 -10000 0 -0.54 9 9
GSK3B 0.036 0.005 -10000 0 -10000 0 0
FRAT1 0.03 0.054 -10000 0 -0.42 7 7
NOTCH/Deltex homolog 1 0.041 0.11 -10000 0 -0.46 19 19
PPP2R5D 0.011 0.068 0.24 3 -0.31 18 21
MAPK1 0.033 0.022 -10000 0 -0.42 1 1
WNT1/LRP6/FZD1 0.07 0.056 -10000 0 -0.23 12 12
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.026 0.02 -10000 0 -10000 0 0
Glypican 1 network

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.019 0.1 -10000 0 -0.27 53 53
fibroblast growth factor receptor signaling pathway 0.019 0.1 -10000 0 -0.27 53 53
LAMA1 0.034 0.009 -10000 0 -10000 0 0
PRNP 0.027 0.054 -10000 0 -0.42 7 7
GPC1/SLIT2 0.013 0.11 -10000 0 -0.31 51 51
SMAD2 0.004 0.064 0.19 5 -0.24 29 34
GPC1/PrPc/Cu2+ 0.029 0.068 -10000 0 -0.26 25 25
GPC1/Laminin alpha1 0.035 0.068 -10000 0 -0.3 19 19
TDGF1 0.034 0.008 -10000 0 -10000 0 0
CRIPTO/GPC1 0.036 0.068 -10000 0 -0.3 19 19
APP/GPC1 0.016 0.1 -10000 0 -0.31 46 46
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.005 0.06 -10000 0 -0.26 25 25
FLT1 0.026 0.054 -10000 0 -0.42 7 7
GPC1/TGFB/TGFBR1/TGFBR2 0.049 0.081 -10000 0 -0.26 30 30
SERPINC1 0.027 0.025 -10000 0 -0.42 1 1
FYN 0.006 0.056 -10000 0 -0.26 22 22
FGR 0.008 0.053 -10000 0 -0.26 19 19
positive regulation of MAPKKK cascade -0.023 0.12 0.28 1 -0.36 41 42
SLIT2 0.003 0.11 -10000 0 -0.42 34 34
GPC1/NRG 0.028 0.068 -10000 0 -0.3 19 19
NRG1 0.028 0.015 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.028 0.069 -10000 0 -0.26 25 25
LYN 0.009 0.045 -10000 0 -0.26 14 14
mol:Spermine -0.003 0.058 -10000 0 -0.3 19 19
cell growth 0.019 0.1 -10000 0 -0.27 53 53
BMP signaling pathway -0.017 0.087 0.42 19 -10000 0 19
SRC 0.007 0.056 -10000 0 -0.27 19 19
TGFBR1 0.027 0.061 -10000 0 -0.42 9 9
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.013 0.08 -10000 0 -0.42 16 16
GPC1 0.017 0.087 -10000 0 -0.42 19 19
TGFBR1 (dimer) 0.027 0.061 -10000 0 -0.42 9 9
VEGFA 0 0 -10000 0 -10000 0 0
BLK 0.006 0.045 -10000 0 -0.25 14 14
HCK 0 0.068 -10000 0 -0.26 33 33
FGF2 -0.001 0.11 -10000 0 -0.42 34 34
FGFR1 0.021 0.061 -10000 0 -0.42 9 9
VEGFR1 homodimer 0.026 0.054 -10000 0 -0.42 7 7
TGFBR2 0.032 0.036 -10000 0 -0.42 3 3
cell death 0.016 0.1 -10000 0 -0.3 46 46
ATIII/GPC1 0.029 0.065 -10000 0 -0.3 17 17
PLA2G2A/GPC1 0.022 0.089 -10000 0 -0.3 34 34
LCK -0.019 0.095 -10000 0 -0.26 67 67
neuron differentiation 0.028 0.068 -10000 0 -0.3 19 19
PrPc/Cu2+ 0.02 0.038 -10000 0 -0.3 7 7
APP 0.008 0.1 -10000 0 -0.42 28 28
TGFBR2 (dimer) 0.032 0.036 -10000 0 -0.42 3 3
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.045 0.084 -10000 0 -0.22 37 37
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.03 0.041 -10000 0 -0.42 4 4
STAT1 (dimer)/Cbp/p300 0.034 0.098 0.31 1 -0.32 16 17
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.052 0.05 -10000 0 -0.26 4 4
antigen processing and presentation of peptide antigen via MHC class I -0.017 0.093 -10000 0 -0.25 48 48
CaM/Ca2+ 0.048 0.084 -10000 0 -0.21 37 37
RAP1A 0.03 0.05 -10000 0 -0.42 6 6
STAT1 (dimer)/SHP2 0.017 0.093 0.28 3 -0.24 45 48
AKT1 -0.012 0.092 0.28 9 -0.29 11 20
MAP2K1 -0.025 0.078 0.26 2 -0.27 15 17
MAP3K11 0.005 0.077 0.26 5 -0.21 38 43
IFNGR1 0.03 0.021 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.005 0.13 -10000 0 -0.41 23 23
Rap1/GTP 0.002 0.066 -10000 0 -0.26 11 11
CRKL/C3G 0.047 0.034 -10000 0 -0.3 4 4
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.059 0.091 -10000 0 -0.22 37 37
CEBPB -0.016 0.16 0.39 1 -0.52 30 31
STAT3 0.028 0.031 -10000 0 -0.42 2 2
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.054 0.13 -10000 0 -0.84 6 6
STAT1 -0.002 0.088 0.29 3 -0.24 45 48
CALM1 0.035 0.007 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.006 0.12 -10000 0 -0.42 37 37
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
STAT1 (dimer)/PIAS1 0.017 0.091 0.29 3 -0.27 21 24
CEBPB/PTGES2/Cbp/p300 0.004 0.11 -10000 0 -0.33 31 31
mol:Ca2+ 0.042 0.082 -10000 0 -0.21 37 37
MAPK3 -0.015 0.14 -10000 0 -0.67 11 11
STAT1 (dimer) -0.011 0.13 -10000 0 -0.34 48 48
MAPK1 -0.044 0.21 0.4 1 -0.71 35 36
JAK2 0.028 0.036 -10000 0 -0.43 2 2
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
JAK1 0.028 0.04 -10000 0 -0.41 3 3
CAMK2D 0.022 0.072 -10000 0 -0.42 13 13
DAPK1 -0.007 0.13 0.34 1 -0.5 20 21
SMAD7 -0.001 0.058 0.16 6 -0.17 15 21
CBL/CRKL/C3G 0.034 0.082 0.3 2 -0.25 8 10
PI3K 0.035 0.095 -10000 0 -0.22 46 46
IFNG -0.006 0.12 -10000 0 -0.42 37 37
apoptosis -0.058 0.18 0.31 1 -0.42 83 84
CAMK2G 0.035 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.031 -10000 0 -0.42 2 2
CAMK2A 0.034 0.021 -10000 0 -0.42 1 1
CAMK2B -0.013 0.13 -10000 0 -0.42 48 48
FRAP1 -0.019 0.083 0.28 6 -0.32 6 12
PRKCD -0.012 0.091 0.29 9 -0.3 10 19
RAP1B 0.032 0.03 -10000 0 -0.42 2 2
negative regulation of cell growth -0.017 0.093 -10000 0 -0.25 48 48
PTPN2 0.034 0.008 -10000 0 -10000 0 0
EP300 0.033 0.022 -10000 0 -0.42 1 1
IRF1 -0.005 0.1 0.32 7 -0.41 16 23
STAT1 (dimer)/PIASy 0.013 0.092 0.29 3 -0.25 31 34
SOCS1 0.018 0.12 -10000 0 -1.1 6 6
mol:GDP 0.03 0.078 0.28 2 -0.24 8 10
CASP1 -0.013 0.083 0.16 7 -0.24 44 51
PTGES2 0.035 0.005 -10000 0 -10000 0 0
IRF9 0 0.049 0.12 1 -0.15 16 17
mol:PI-3-4-5-P3 0.021 0.086 -10000 0 -0.22 46 46
RAP1/GDP 0.025 0.078 -10000 0 -0.28 10 10
CBL 0.004 0.072 0.29 2 -0.21 34 36
MAP3K1 -0.006 0.087 0.25 4 -0.22 56 60
PIAS1 0.035 0.006 -10000 0 -10000 0 0
PIAS4 0.032 0.036 -10000 0 -0.42 3 3
antigen processing and presentation of peptide antigen via MHC class II -0.017 0.093 -10000 0 -0.25 48 48
PTPN11 0.009 0.079 0.28 5 -0.22 37 42
CREBBP 0.033 0.011 -10000 0 -10000 0 0
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.019 0.073 -10000 0 -0.29 26 26
PDGFRB 0.028 0.058 -10000 0 -0.43 8 8
SPHK1 -0.034 0.2 -10000 0 -0.76 35 35
mol:S1P -0.02 0.18 -10000 0 -0.65 35 35
S1P1/S1P/Gi -0.019 0.16 0.23 1 -0.5 33 34
GNAO1 0.03 0.015 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 0.001 0.15 0.3 3 -0.47 26 29
PLCG1 -0.015 0.15 0.28 3 -0.47 30 33
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.028 0.058 -10000 0 -0.43 8 8
GNAI2 0.028 0.058 -10000 0 -0.42 8 8
GNAI3 0.036 0.008 -10000 0 -10000 0 0
GNAI1 0.018 0.086 -10000 0 -0.42 18 18
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.002 0.12 -10000 0 -0.52 25 25
S1P1/S1P -0.011 0.17 -10000 0 -0.48 47 47
negative regulation of cAMP metabolic process -0.018 0.16 0.22 1 -0.48 33 34
MAPK3 -0.013 0.16 0.32 11 -0.54 27 38
calcium-dependent phospholipase C activity 0 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.043 -10000 0 -0.3 9 9
KDR 0.028 0.059 -10000 0 -0.21 23 23
PLCB2 -0.01 0.15 0.24 2 -0.43 46 48
RAC1 0.035 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.018 0.14 -10000 0 -0.4 48 48
receptor internalization -0.01 0.16 -10000 0 -0.44 47 47
PTGS2 -0.011 0.17 -10000 0 -0.72 16 16
Rac1/GTP -0.015 0.14 -10000 0 -0.4 46 46
RHOA 0.026 0.061 -10000 0 -0.42 9 9
VEGFA -0.004 0.034 -10000 0 -0.15 26 26
negative regulation of T cell proliferation -0.018 0.16 0.22 1 -0.48 33 34
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.024 0.068 -10000 0 -0.42 11 11
MAPK1 -0.02 0.15 -10000 0 -0.54 28 28
S1P1/S1P/PDGFB-D/PDGFRB 0.008 0.18 0.31 2 -0.47 43 45
ABCC1 0.029 0.042 -10000 0 -0.42 4 4
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.027 0.025 -10000 0 -0.42 1 1
Caspase 8 (4 units) 0.03 0.13 -10000 0 -0.4 22 22
NEF -0.012 0.049 -10000 0 -0.17 45 45
NFKBIA 0.021 0.05 -10000 0 -0.35 3 3
BIRC3 -0.014 0.14 -10000 0 -0.46 41 41
CYCS -0.004 0.12 -10000 0 -0.43 20 20
RIPK1 0.034 0.007 -10000 0 -10000 0 0
CD247 -0.012 0.049 -10000 0 -0.17 45 45
MAP2K7 0.005 0.18 -10000 0 -0.76 16 16
protein ubiquitination -0.015 0.12 0.22 2 -0.36 25 27
CRADD 0.029 0.054 -10000 0 -0.42 7 7
DAXX 0.035 0.005 -10000 0 -10000 0 0
FAS 0.008 0.1 -10000 0 -0.42 28 28
BID -0.006 0.12 -10000 0 -0.34 41 41
NF-kappa-B/RelA/I kappa B alpha 0.041 0.099 -10000 0 -0.26 40 40
TRADD 0.029 0.014 -10000 0 -10000 0 0
MAP3K5 0.013 0.093 -10000 0 -0.42 22 22
CFLAR 0.031 0.045 -10000 0 -0.42 5 5
FADD 0.029 0.014 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.04 0.1 -10000 0 -0.26 40 40
MAPK8 0.003 0.16 0.42 1 -0.68 16 17
APAF1 0.032 0.041 -10000 0 -0.42 4 4
TRAF1 0.034 0.021 -10000 0 -0.42 1 1
TRAF2 0.033 0.029 -10000 0 -0.42 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.003 0.13 -10000 0 -0.35 38 38
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.014 0.14 -10000 0 -0.39 35 35
CHUK -0.018 0.13 -10000 0 -0.39 26 26
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.055 0.094 -10000 0 -0.24 35 35
TCRz/NEF -0.018 0.085 -10000 0 -0.29 45 45
TNF 0.026 0.061 -10000 0 -0.42 9 9
FASLG -0.02 0.13 -10000 0 -0.52 34 34
NFKB1 0.022 0.041 -10000 0 -0.14 3 3
TNFR1A/BAG4/TNF-alpha 0.048 0.049 -10000 0 -0.25 7 7
CASP6 0.024 0.15 -10000 0 -0.54 22 22
CASP7 -0.042 0.2 0.29 1 -0.46 70 71
RELA 0.022 0.042 -10000 0 -0.1 40 40
CASP2 0.034 0.007 -10000 0 -10000 0 0
CASP3 -0.04 0.19 -10000 0 -0.46 67 67
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
TNFR1A/BAG4 0.039 0.028 -10000 0 -0.3 1 1
CASP8 0.035 0.004 -10000 0 -10000 0 0
CASP9 0.034 0.022 -10000 0 -0.42 1 1
MAP3K14 -0.013 0.13 0.24 2 -0.38 32 34
APAF-1/Caspase 9 -0.013 0.14 -10000 0 -0.35 51 51
BCL2 -0.031 0.16 0.58 1 -0.56 20 21
Calcium signaling in the CD4+ TCR 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
NFATC1 0.008 0.054 -10000 0 -0.26 15 15
NFATC2 0.013 0.035 -10000 0 -0.27 3 3
NFATC3 0.015 0.026 -10000 0 -10000 0 0
CD40LG -0.019 0.18 0.38 3 -0.44 54 57
PTGS2 -0.02 0.17 0.38 3 -0.44 49 52
JUNB 0.032 0.041 -10000 0 -0.42 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.025 -10000 0 -0.11 1 1
CaM/Ca2+ 0.021 0.025 -10000 0 -0.11 1 1
CALM1 0.032 0.019 -10000 0 -10000 0 0
JUN -0.003 0.12 -10000 0 -0.42 39 39
mol:Ca2+ -0.001 0.009 -10000 0 -0.084 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0.022 0.01 -10000 0 -10000 0 0
FOSL1 0.035 0.007 -10000 0 -10000 0 0
CREM 0.034 0.008 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.016 0.12 -10000 0 -0.32 29 29
FOS -0.033 0.15 -10000 0 -0.42 66 66
IFNG -0.035 0.2 0.38 3 -0.5 60 63
AP-1/NFAT1-c-4 0.001 0.22 -10000 0 -0.5 53 53
FASLG -0.031 0.2 0.38 3 -0.51 52 55
NFAT1-c-4/ICER1 0.027 0.081 0.28 2 -0.23 18 20
IL2RA -0.029 0.2 0.38 3 -0.48 60 63
FKBP12/FK506 0.025 0.006 -10000 0 -10000 0 0
CSF2 -0.02 0.18 0.38 3 -0.44 54 57
JunB/Fra1/NFAT1-c-4 0.045 0.093 0.26 1 -0.28 9 10
IL4 -0.019 0.18 0.38 3 -0.43 56 59
IL2 0.008 0.14 -10000 0 -0.98 10 10
IL3 0.019 0.12 -10000 0 -0.69 12 12
FKBP1A 0.034 0.008 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.033 0.017 -10000 0 -10000 0 0
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate 0.015 0.15 0.32 2 -0.45 24 26
PDGFB-D/PDGFRB/SLAP 0.031 0.055 -10000 0 -0.31 11 11
PDGFB-D/PDGFRB/APS/CBL 0.037 0.04 -10000 0 -0.25 8 8
AKT1 -0.01 0.14 0.34 22 -0.39 12 34
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.006 0.14 0.3 2 -0.49 20 22
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
FGR 0.003 0.11 0.3 3 -0.41 24 27
mol:Ca2+ 0.008 0.13 0.26 4 -0.49 20 24
MYC 0.012 0.24 0.37 13 -0.72 40 53
SHC1 0.027 0.025 -10000 0 -0.42 1 1
HRAS/GDP 0.034 0.066 0.19 2 -0.22 17 19
LRP1/PDGFRB/PDGFB 0.058 0.06 -10000 0 -0.29 12 12
GRB10 0.022 0.075 -10000 0 -0.42 14 14
PTPN11 0.036 0.003 -10000 0 -10000 0 0
GO:0007205 0.007 0.13 0.28 3 -0.5 20 23
PTEN 0.026 0.061 -10000 0 -0.42 9 9
GRB2 0.033 0.01 -10000 0 -10000 0 0
GRB7 0.023 0.058 -10000 0 -0.42 8 8
PDGFB-D/PDGFRB/SHP2 0.046 0.046 -10000 0 -0.31 8 8
PDGFB-D/PDGFRB/GRB10 0.036 0.073 -10000 0 -0.3 22 22
cell cycle arrest 0.031 0.055 -10000 0 -0.3 11 11
HRAS 0.032 0.036 -10000 0 -0.42 3 3
HIF1A -0.025 0.13 0.33 19 -0.34 19 38
GAB1 -0.002 0.14 0.29 3 -0.47 27 30
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.003 0.14 0.3 5 -0.45 23 28
PDGFB-D/PDGFRB 0.051 0.055 -10000 0 -0.27 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.044 0.053 -10000 0 -0.31 11 11
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.009 0.14 0.3 1 -0.43 26 27
positive regulation of MAPKKK cascade 0.046 0.046 -10000 0 -0.3 8 8
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
mol:IP3 0.007 0.13 0.28 3 -0.5 20 23
E5 -0.001 0.002 -10000 0 -10000 0 0
CSK 0.033 0.022 -10000 0 -0.42 1 1
PDGFB-D/PDGFRB/GRB7 0.036 0.063 -10000 0 -0.3 16 16
SHB 0.03 0.046 -10000 0 -0.42 5 5
BLK -0.066 0.19 0.28 1 -0.42 97 98
PTPN2 0.034 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.044 0.046 -10000 0 -0.3 8 8
BCAR1 0.029 0.014 -10000 0 -10000 0 0
VAV2 -0.005 0.16 0.3 4 -0.48 31 35
CBL 0.031 0.012 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.041 0.058 -10000 0 -0.3 13 13
LCK -0.053 0.21 0.27 1 -0.54 69 70
PDGFRB 0.027 0.059 -10000 0 -0.43 8 8
ACP1 0.033 0.035 -10000 0 -0.42 3 3
HCK -0.006 0.14 0.32 2 -0.52 29 31
ABL1 -0.005 0.14 0.24 11 -0.42 30 41
PDGFB-D/PDGFRB/CBL -0.009 0.16 0.27 1 -0.53 29 30
PTPN1 0.029 0.031 -10000 0 -0.42 2 2
SNX15 0.034 0.007 -10000 0 -10000 0 0
STAT3 0.028 0.031 -10000 0 -0.42 2 2
STAT1 0.02 0.075 -10000 0 -0.42 14 14
cell proliferation 0.018 0.22 0.34 19 -0.64 40 59
SLA 0.021 0.047 -10000 0 -0.42 5 5
actin cytoskeleton reorganization 0.037 0.071 0.43 2 -0.22 10 12
SRC 0.01 0.095 0.3 3 -0.47 10 13
PI3K -0.04 0.095 -10000 0 -0.24 81 81
PDGFB-D/PDGFRB/GRB7/SHC 0.042 0.062 -10000 0 -0.26 15 15
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.005 0.14 0.3 2 -0.51 20 22
LYN 0.013 0.077 0.29 3 -0.36 8 11
LRP1 0.035 0.021 -10000 0 -0.42 1 1
SOS1 0.034 0.021 -10000 0 -0.42 1 1
STAT5B 0.03 0.024 -10000 0 -0.42 1 1
STAT5A 0.028 0.037 -10000 0 -0.42 3 3
NCK1-2/p130 Cas 0.066 0.068 -10000 0 -0.22 9 9
SPHK1 0.005 0.11 -10000 0 -0.42 30 30
EDG1 0.011 0.099 -10000 0 -0.42 25 25
mol:DAG 0.007 0.13 0.28 3 -0.5 20 23
PLCG1 0.007 0.14 0.3 2 -0.52 20 22
NHERF/PDGFRB 0.001 0.13 -10000 0 -0.28 80 80
YES1 -0.006 0.14 0.28 2 -0.51 27 29
cell migration 0.001 0.13 -10000 0 -0.28 80 80
SHC/Grb2/SOS1 0.058 0.067 -10000 0 -0.23 9 9
SLC9A3R2 -0.005 0.12 -10000 0 -0.42 40 40
SLC9A3R1 -0.009 0.13 -10000 0 -0.42 46 46
NHERF1-2/PDGFRB/PTEN 0.011 0.14 -10000 0 -0.27 84 84
FYN -0.013 0.16 0.28 2 -0.53 32 34
DOK1 0.021 0.072 0.19 45 -0.24 15 60
HRAS/GTP 0.023 0.025 -10000 0 -0.3 3 3
PDGFB 0.029 0.046 -10000 0 -0.42 5 5
RAC1 -0.02 0.2 0.31 3 -0.54 45 48
PRKCD 0.023 0.07 0.19 41 -0.26 10 51
FER 0.024 0.069 0.19 45 -0.24 10 55
MAPKKK cascade 0.044 0.11 0.33 25 -0.22 8 33
RASA1 0.021 0.073 0.19 41 -0.24 15 56
NCK1 0.034 0.021 -10000 0 -0.42 1 1
NCK2 0.035 0.004 -10000 0 -10000 0 0
p62DOK/Csk 0.042 0.065 0.34 1 -0.22 16 17
PDGFB-D/PDGFRB/SHB 0.041 0.058 -10000 0 -0.31 13 13
chemotaxis -0.004 0.13 0.23 12 -0.41 30 42
STAT1-3-5/STAT1-3-5 0.048 0.074 -10000 0 -0.22 25 25
Bovine Papilomavirus E5/PDGFRB 0.019 0.042 -10000 0 -0.31 8 8
PTPRJ 0.03 0.046 -10000 0 -0.42 5 5
TRAIL 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
TNFSF10 -0.008 0.13 -10000 0 -0.42 45 45
positive regulation of NF-kappaB transcription factor activity 0.01 0.097 -10000 0 -0.29 45 45
MAP2K4 -0.009 0.1 -10000 0 -0.35 27 27
IKBKB 0.029 0.014 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.016 -10000 0 -10000 0 0
TNFRSF10A 0.023 0.047 -10000 0 -0.42 5 5
SMPD1 -0.007 0.073 -10000 0 -0.22 44 44
IKBKG 0.036 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.015 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.009 0.1 -10000 0 -0.3 45 45
TRAIL/TRAILR3 0.007 0.097 -10000 0 -0.29 46 46
TRAIL/TRAILR1 0.007 0.1 -10000 0 -0.31 47 47
TRAIL/TRAILR4 0.01 0.097 -10000 0 -0.29 45 45
TRAIL/TRAILR1/DAP3/GTP 0.019 0.081 -10000 0 -0.24 36 36
IKK complex 0.014 0.092 -10000 0 -0.4 15 15
RIPK1 0.034 0.007 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.02 0.018 -10000 0 -0.3 1 1
MAPK3 -0.011 0.085 -10000 0 -0.3 40 40
MAP3K1 -0.007 0.11 -10000 0 -0.38 28 28
TRAILR4 (trimer) 0.027 0.015 -10000 0 -10000 0 0
TRADD 0.029 0.014 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.023 0.047 -10000 0 -0.42 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.004 0.087 -10000 0 -0.3 35 35
CFLAR 0.031 0.045 -10000 0 -0.42 5 5
MAPK1 -0.009 0.083 -10000 0 -0.3 38 38
TRAIL/TRAILR1/FADD/TRADD/RIP 0.034 0.09 -10000 0 -0.23 34 34
mol:ceramide -0.007 0.073 -10000 0 -0.22 44 44
FADD 0.029 0.014 -10000 0 -10000 0 0
MAPK8 -0.024 0.11 -10000 0 -0.36 32 32
TRAF2 0.033 0.029 -10000 0 -0.42 2 2
TRAILR3 (trimer) 0.024 0.026 -10000 0 -0.42 1 1
CHUK 0.025 0.067 -10000 0 -0.42 11 11
TRAIL/TRAILR1/FADD 0.021 0.087 -10000 0 -0.26 35 35
DAP3 0.027 0.025 -10000 0 -0.42 1 1
CASP10 0.014 0.084 0.33 4 -0.29 18 22
JNK cascade 0.01 0.097 -10000 0 -0.29 45 45
TRAIL (trimer) -0.008 0.13 -10000 0 -0.42 45 45
TNFRSF10C 0.024 0.026 -10000 0 -0.42 1 1
TRAIL/TRAILR1/DAP3/GTP/FADD 0.025 0.077 -10000 0 -0.23 28 28
TRAIL/TRAILR2/FADD 0.023 0.083 -10000 0 -0.26 34 34
cell death -0.007 0.073 -10000 0 -0.21 44 44
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.002 0.085 -10000 0 -0.29 34 34
TRAILR2 (trimer) 0.027 0.015 -10000 0 -10000 0 0
CASP8 0.024 0.043 -10000 0 -0.66 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.035 0.087 -10000 0 -0.22 33 33
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.019 0.059 0.19 12 -0.2 20 32
DAPP1 -0.039 0.16 0.24 1 -0.39 61 62
Src family/SYK family/BLNK-LAT/BTK-ITK -0.06 0.22 -10000 0 -0.55 65 65
mol:DAG -0.016 0.091 0.21 7 -0.23 43 50
HRAS 0.031 0.038 -10000 0 -0.42 3 3
RAP1A 0.029 0.051 -10000 0 -0.42 6 6
ARF5/GDP -0.004 0.11 -10000 0 -0.32 30 30
PLCG2 0.02 0.055 -10000 0 -0.42 7 7
PLCG1 0.033 0.009 -10000 0 -10000 0 0
ARF5 0.034 0.021 -10000 0 -0.42 1 1
mol:GTP -0.018 0.06 0.21 11 -0.21 20 31
ARF1/GTP -0.009 0.053 0.22 8 -0.2 16 24
RHOA 0.026 0.061 -10000 0 -0.42 9 9
YES1 0.029 0.05 -10000 0 -0.42 6 6
RAP1A/GTP -0.018 0.061 0.18 27 -0.21 20 47
ADAP1 -0.018 0.056 0.19 11 -0.2 20 31
ARAP3 -0.018 0.06 0.21 11 -0.21 20 31
INPPL1 0.03 0.036 -10000 0 -0.42 3 3
PREX1 -0.036 0.16 -10000 0 -0.42 74 74
ARHGEF6 0.015 0.093 -10000 0 -0.42 22 22
ARHGEF7 0.032 0.011 -10000 0 -10000 0 0
ARF1 0.027 0.025 -10000 0 -0.42 1 1
NRAS 0.028 0.05 -10000 0 -0.41 6 6
FYN 0.027 0.05 -10000 0 -0.42 6 6
ARF6 0.033 0.029 -10000 0 -0.42 2 2
FGR 0.034 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.05 0.14 9 -0.13 18 27
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.028 0.057 -10000 0 -0.42 8 8
ZAP70 0.033 0.022 -10000 0 -0.42 1 1
mol:IP3 -0.016 0.067 0.17 9 -0.18 30 39
LYN 0.03 0.013 -10000 0 -10000 0 0
ARF1/GDP -0.003 0.1 -10000 0 -0.32 24 24
RhoA/GDP 0.011 0.091 0.24 4 -0.26 23 27
PDK1/Src/Hsp90 0.041 0.025 -10000 0 -0.25 2 2
BLNK 0.012 0.1 -10000 0 -0.42 26 26
actin cytoskeleton reorganization -0.021 0.11 0.23 5 -0.34 25 30
SRC 0.032 0.03 -10000 0 -0.42 2 2
PLEKHA2 -0.009 0.022 -10000 0 -0.25 4 4
RAC1 0.035 0.006 -10000 0 -10000 0 0
PTEN 0.026 0.059 -10000 0 -0.4 9 9
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.02 0.059 0.2 13 -0.2 20 33
RhoA/GTP -0.023 0.068 0.2 11 -0.25 23 34
Src family/SYK family/BLNK-LAT -0.027 0.16 -10000 0 -0.44 49 49
BLK 0.021 0.038 -10000 0 -0.42 3 3
PDPK1 0.031 0.023 -10000 0 -0.42 1 1
CYTH1 -0.018 0.056 0.19 11 -0.2 20 31
HCK 0.017 0.087 -10000 0 -0.42 19 19
CYTH3 -0.018 0.056 0.19 11 -0.2 20 31
CYTH2 -0.018 0.056 0.19 11 -0.2 20 31
KRAS 0.026 0.059 -10000 0 -0.42 8 8
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.005 0.038 0.23 2 -0.2 2 4
SGK1 0.008 0.041 0.24 2 -0.21 2 4
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.02 0.11 -10000 0 -0.33 30 30
SOS1 0.034 0.021 -10000 0 -0.42 1 1
SYK 0.005 0.11 -10000 0 -0.42 33 33
ARF6/GDP -0.004 0.074 0.23 4 -0.26 12 16
mol:PI-3-4-5-P3 -0.018 0.061 0.23 10 -0.21 20 30
ARAP3/RAP1A/GTP -0.018 0.061 0.18 27 -0.21 20 47
VAV1 0.018 0.082 -10000 0 -0.42 17 17
mol:PI-3-4-P2 0.006 0.024 -10000 0 -0.3 3 3
RAS family/GTP/PI3K Class I 0.045 0.065 0.22 13 -0.21 20 33
PLEKHA1 -0.012 0.029 -10000 0 -0.25 7 7
Rac1/GDP -0.004 0.11 -10000 0 -0.33 27 27
LAT 0.029 0.031 -10000 0 -0.42 2 2
Rac1/GTP -0.018 0.12 -10000 0 -0.4 25 25
ITK -0.032 0.072 0.2 9 -0.22 48 57
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.027 0.12 0.25 6 -0.31 47 53
LCK -0.018 0.14 -10000 0 -0.42 54 54
BTK -0.026 0.068 0.2 10 -0.23 30 40
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.012 0.1 -10000 0 -0.23 75 75
TC10/GTP 0.03 0.066 -10000 0 -0.21 31 31
Insulin Receptor/Insulin/IRS1/Shp2 0.053 0.11 -10000 0 -0.25 55 55
HRAS 0.032 0.036 -10000 0 -0.42 3 3
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 -0.063 0.18 -10000 0 -0.42 98 98
FOXO3 -0.015 0.022 -10000 0 -10000 0 0
AKT1 -0.047 0.13 0.32 6 -0.37 17 23
INSR 0.037 0.031 -10000 0 -0.42 2 2
Insulin Receptor/Insulin 0.079 0.06 -10000 0 -0.3 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.022 0.075 -10000 0 -0.42 14 14
SORBS1 0.008 0.1 -10000 0 -0.42 28 28
CRK 0.031 0.023 -10000 0 -0.42 1 1
PTPN1 0.004 0.037 -10000 0 -0.3 5 5
CAV1 -0.007 0.083 0.18 5 -0.23 58 63
CBL/APS/CAP/Crk-II/C3G 0.052 0.074 -10000 0 -0.22 29 29
Insulin Receptor/Insulin/IRS1/NCK2 0.054 0.11 -10000 0 -0.25 54 54
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.028 0.1 -10000 0 -0.22 67 67
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.019 0.08 -10000 0 -0.42 6 6
RPS6KB1 -0.041 0.11 0.3 6 -0.35 15 21
PARD6A 0.023 0.054 -10000 0 -0.42 7 7
CBL 0.031 0.012 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.007 0.11 -10000 0 -0.67 12 12
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.007 0.12 -10000 0 -0.34 18 18
HRAS/GTP -0.001 0.063 -10000 0 -0.2 40 40
Insulin Receptor 0.037 0.031 -10000 0 -0.42 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.048 0.1 -10000 0 -0.23 42 42
PRKCI 0.003 0.11 -10000 0 -0.45 26 26
Insulin Receptor/Insulin/GRB14/PDK1 -0.037 0.12 -10000 0 -0.23 136 136
SHC1 0.027 0.025 -10000 0 -0.42 1 1
negative regulation of MAPKKK cascade 0.045 0.11 -10000 0 -0.6 12 12
PI3K 0.04 0.11 -10000 0 -0.23 67 67
NCK2 0.035 0.004 -10000 0 -10000 0 0
RHOQ 0.033 0.035 -10000 0 -0.42 3 3
mol:H2O2 0 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.023 0.025 -10000 0 -0.3 3 3
AKT2 -0.047 0.13 0.32 6 -0.38 15 21
PRKCZ -0.007 0.081 -10000 0 -0.41 16 16
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.001 0.069 0.17 3 -0.21 44 47
F2RL2 -0.018 0.14 -10000 0 -0.42 56 56
TRIP10 0.032 0.041 -10000 0 -0.42 4 4
Insulin Receptor/Insulin/Shc 0.053 0.041 -10000 0 -0.22 3 3
TC10/GTP/CIP4/Exocyst 0.043 0.036 -10000 0 -0.25 7 7
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.074 0.06 -10000 0 -0.22 4 4
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
RASA1 0.028 0.054 -10000 0 -0.42 7 7
NCK1 0.034 0.021 -10000 0 -0.42 1 1
CBL/APS/CAP/Crk-II 0.039 0.071 -10000 0 -0.23 29 29
TC10/GDP 0.024 0.025 -10000 0 -0.3 3 3
Insulin Receptor/Insulin/SHC/GRB10 0.062 0.066 -10000 0 -0.23 13 13
INPP5D -0.03 0.07 -10000 0 -0.22 55 55
SOS1 0.034 0.021 -10000 0 -0.42 1 1
SGK1 -0.008 0.01 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.036 0.003 -10000 0 -10000 0 0
IRS1 -0.014 0.14 -10000 0 -0.42 54 54
p62DOK/RasGAP 0.045 0.11 -10000 0 -0.61 12 12
INS 0.037 0.024 -10000 0 -0.42 1 1
mol:PI-3-4-P2 -0.03 0.069 -10000 0 -0.22 55 55
GRB2 0.033 0.01 -10000 0 -10000 0 0
EIF4EBP1 -0.05 0.1 0.26 2 -0.35 16 18
PTPRA 0.037 0.013 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
TC10/GTP/CIP4 0.043 0.036 -10000 0 -0.25 7 7
PDPK1 0.031 0.023 -10000 0 -0.42 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.006 0.077 -10000 0 -0.22 38 38
Insulin Receptor/Insulin/IRS1 0.034 0.1 -10000 0 -0.24 55 55
Insulin Receptor/Insulin/IRS3 0.054 0.034 -10000 0 -0.3 3 3
Par3/Par6 0.025 0.1 -10000 0 -0.22 66 66
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.007 0.052 -10000 0 -0.3 14 14
MAP4K4 -0.025 0.11 0.22 1 -0.33 34 35
BAG4 0.027 0.025 -10000 0 -0.42 1 1
PKC zeta/ceramide -0.008 0.047 0.12 2 -0.22 13 15
NFKBIA 0.033 0.03 -10000 0 -0.42 2 2
BIRC3 -0.009 0.12 -10000 0 -0.42 41 41
BAX 0.011 0.034 -10000 0 -0.37 2 2
RIPK1 0.034 0.007 -10000 0 -10000 0 0
AKT1 0.001 0.084 0.66 7 -0.39 3 10
BAD -0.011 0.049 0.19 2 -0.24 11 13
SMPD1 0.006 0.064 0.18 3 -0.23 17 20
RB1 -0.015 0.056 -10000 0 -0.24 20 20
FADD/Caspase 8 0.01 0.12 0.27 4 -0.34 20 24
MAP2K4 -0.022 0.063 0.18 1 -0.22 34 35
NSMAF 0.025 0.047 -10000 0 -0.42 5 5
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.009 0.053 0.19 8 -0.24 10 18
EGF -0.069 0.19 -10000 0 -0.42 110 110
mol:ceramide -0.008 0.051 0.13 7 -0.24 13 20
MADD 0.035 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.005 0.075 -10000 0 -0.31 28 28
ASAH1 0.008 0.089 -10000 0 -0.42 20 20
negative regulation of cell cycle -0.015 0.056 0.16 1 -0.23 20 21
cell proliferation -0.013 0.092 0.22 2 -0.22 31 33
BID -0.014 0.14 -10000 0 -0.66 14 14
MAP3K1 -0.021 0.065 -10000 0 -0.22 36 36
EIF2A -0.015 0.063 0.2 4 -0.22 23 27
TRADD 0.029 0.014 -10000 0 -10000 0 0
CRADD 0.029 0.054 -10000 0 -0.42 7 7
MAPK3 -0.006 0.053 0.19 7 -0.23 10 17
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.011 0.06 0.19 7 -0.25 9 16
Cathepsin D/ceramide 0.006 0.06 -10000 0 -0.22 17 17
FADD 0.006 0.12 0.22 54 -0.33 22 76
KSR1 -0.009 0.05 0.19 3 -0.24 11 14
MAPK8 -0.012 0.058 -10000 0 -0.22 20 20
PRKRA -0.009 0.05 0.19 3 -0.23 12 15
PDGFA 0.022 0.078 -10000 0 -0.42 15 15
TRAF2 0.033 0.029 -10000 0 -0.42 2 2
IGF1 -0.041 0.17 -10000 0 -0.42 81 81
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.008 0.051 0.13 9 -0.24 13 22
CTSD 0.029 0.046 -10000 0 -0.42 5 5
regulation of nitric oxide biosynthetic process 0.051 0.012 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.013 0.098 0.24 2 -0.24 31 33
PRKCD 0.032 0.03 -10000 0 -0.42 2 2
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.005 0.075 -10000 0 -0.31 28 28
RelA/NF kappa B1 0.051 0.012 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.024 0.072 -10000 0 -0.42 13 13
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.015 0.11 -10000 0 -0.36 28 28
TNFR1A/BAG4/TNF-alpha 0.048 0.049 -10000 0 -0.25 7 7
mol:Sphingosine-1-phosphate 0.007 0.052 -10000 0 -0.3 14 14
MAP2K1 -0.01 0.052 0.18 11 -0.23 9 20
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
CYCS 0.031 0.069 0.21 13 -0.19 2 15
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
NFKB1 0.035 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.039 0.028 -10000 0 -0.3 1 1
EIF2AK2 -0.017 0.06 0.18 4 -0.22 26 30
TNF-alpha/TNFR1A/FAN 0.05 0.052 -10000 0 -0.26 9 9
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.008 0.09 -10000 0 -0.34 18 18
MAP2K2 -0.011 0.053 0.18 8 -0.23 10 18
SMPD3 -0.027 0.12 0.19 1 -0.3 75 76
TNF 0.026 0.061 -10000 0 -0.42 9 9
PKC zeta/PAR4 0.018 0.051 -10000 0 -0.3 13 13
mol:PHOSPHOCHOLINE 0.037 0.093 0.2 103 -0.21 3 106
NF kappa B1/RelA/I kappa B alpha 0.068 0.056 -10000 0 -0.22 15 15
AIFM1 0.027 0.066 0.16 63 -0.19 3 66
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
Regulation of Telomerase

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
Telomerase catalytic core complex -0.072 0.23 -10000 0 -0.63 42 42
RAD9A 0.033 0.01 -10000 0 -10000 0 0
AP1 -0.026 0.15 -10000 0 -0.34 89 89
IFNAR2 0.027 0.03 -10000 0 -0.43 1 1
AKT1 -0.034 0.11 -10000 0 -0.24 65 65
ER alpha/Oestrogen -0.062 0.14 -10000 0 -0.3 130 130
NFX1/SIN3/HDAC complex 0.012 0.072 -10000 0 -0.33 14 14
EGF -0.07 0.19 -10000 0 -0.42 110 110
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.038 0.036 -10000 0 -0.3 1 1
TERT/c-Abl -0.06 0.22 -10000 0 -0.59 42 42
SAP18 0.033 0.01 -10000 0 -10000 0 0
MRN complex 0.047 0.044 -10000 0 -0.26 4 4
WT1 -0.024 0.14 -10000 0 -0.42 52 52
WRN 0.027 0.025 -10000 0 -0.42 1 1
SP1 0.026 0.033 -10000 0 -0.43 1 1
SP3 0.035 0.007 -10000 0 -10000 0 0
TERF2IP 0.029 0.014 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.045 0.21 -10000 0 -0.54 44 44
Mad/Max 0.047 0.019 -10000 0 -10000 0 0
TERT -0.075 0.24 -10000 0 -0.67 39 39
CCND1 -0.15 0.44 -10000 0 -1.1 86 86
MAX 0.033 0.009 -10000 0 -10000 0 0
RBBP7 0.033 0.029 -10000 0 -0.42 2 2
RBBP4 0.034 0.021 -10000 0 -0.42 1 1
TERF2 0.027 0.031 -10000 0 -0.37 2 2
PTGES3 0.034 0.021 -10000 0 -0.42 1 1
SIN3A 0.034 0.007 -10000 0 -10000 0 0
Telomerase/911 0.021 0.069 -10000 0 -0.4 7 7
CDKN1B -0.028 0.14 -10000 0 -0.37 65 65
RAD1 0.033 0.029 -10000 0 -0.42 2 2
XRCC5 0.035 0.004 -10000 0 -10000 0 0
XRCC6 0.033 0.009 -10000 0 -10000 0 0
SAP30 0.03 0.046 -10000 0 -0.42 5 5
TRF2/PARP2 0.043 0.031 -10000 0 -0.29 2 2
UBE3A 0.033 0.029 -10000 0 -0.42 2 2
JUN -0.002 0.12 -10000 0 -0.42 39 39
E6 -0.001 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.02 0.027 -10000 0 -0.3 2 2
FOS -0.032 0.15 -10000 0 -0.42 66 66
IFN-gamma/IRF1 0.001 0.12 -10000 0 -0.3 69 69
PARP2 0.036 0.002 -10000 0 -10000 0 0
BLM 0.011 0.097 -10000 0 -0.42 24 24
Telomerase 0.012 0.044 0.18 1 -10000 0 1
IRF1 0.015 0.085 -10000 0 -0.27 35 35
ESR1 -0.088 0.2 -10000 0 -0.42 130 130
KU/TER 0.049 0.015 -10000 0 -10000 0 0
ATM/TRF2 0.035 0.035 -10000 0 -0.19 2 2
ubiquitin-dependent protein catabolic process 0.023 0.06 -10000 0 -0.26 12 12
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.025 0.055 -10000 0 -0.27 8 8
HDAC1 0.034 0.021 -10000 0 -0.42 1 1
HDAC2 0.024 0.032 -10000 0 -0.42 1 1
ATM 0.02 0.025 0.19 2 -10000 0 2
SMAD3 0.01 0.044 -10000 0 -0.3 10 10
ABL1 0.035 0.005 -10000 0 -10000 0 0
MXD1 0.034 0.008 -10000 0 -10000 0 0
MRE11A 0.031 0.012 -10000 0 -10000 0 0
HUS1 0.035 0.006 -10000 0 -10000 0 0
RPS6KB1 0.031 0.012 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.056 0.23 -10000 0 -0.58 52 52
NR2F2 -0.011 0.14 -10000 0 -0.42 49 49
MAPK3 0.007 0.032 -10000 0 -0.3 4 4
MAPK1 0.008 0.032 -10000 0 -0.3 4 4
TGFB1/TGF beta receptor Type II 0.035 0.021 -10000 0 -0.42 1 1
NFKB1 0.035 0.005 -10000 0 -10000 0 0
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.02 0.025 0.19 2 -10000 0 2
NBN 0.027 0.025 -10000 0 -0.42 1 1
EGFR -0.013 0.13 -10000 0 -0.42 47 47
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.063 0.16 -10000 0 -0.31 151 151
MYC -0.002 0.1 -10000 0 -0.42 29 29
IL2 0.024 0.043 -10000 0 -0.42 3 3
KU 0.049 0.015 -10000 0 -10000 0 0
RAD50 0.03 0.046 -10000 0 -0.42 5 5
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.035 0.021 -10000 0 -0.42 1 1
TRF2/BLM 0.026 0.073 -10000 0 -0.28 25 25
FRAP1 0.034 0.007 -10000 0 -10000 0 0
KU/TERT -0.047 0.23 -10000 0 -0.59 42 42
SP1/HDAC2 0.038 0.043 -10000 0 -0.3 2 2
PINX1 0.028 0.015 -10000 0 -10000 0 0
Telomerase/EST1A -0.059 0.2 -10000 0 -0.51 50 50
Smad3/Myc 0.006 0.074 -10000 0 -0.26 35 35
911 complex 0.062 0.032 -10000 0 -0.26 2 2
IFNG -0.013 0.12 -10000 0 -0.33 59 59
Telomerase/PinX1 -0.056 0.2 -10000 0 -0.53 46 46
Telomerase/AKT1/mTOR/p70S6K -0.007 0.1 -10000 0 -0.41 17 17
SIN3B 0.035 0.005 -10000 0 -10000 0 0
YWHAE 0.032 0.011 -10000 0 -10000 0 0
Telomerase/EST1B -0.059 0.2 -10000 0 -0.51 50 50
response to DNA damage stimulus -0.001 0.034 0.13 1 -0.1 36 37
MRN complex/TRF2/Rap1 0.058 0.06 -10000 0 -0.27 4 4
TRF2/WRN 0.033 0.036 -10000 0 -0.28 3 3
Telomerase/hnRNP C1/C2 -0.059 0.2 -10000 0 -0.51 50 50
E2F1 0.02 0.057 -10000 0 -0.42 7 7
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.035 0.005 -10000 0 -10000 0 0
DKC1 0.036 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.01 0.02 -10000 0 -0.26 3 3
RAS family/GTP 0.029 0.11 0.24 1 -0.3 17 18
NFATC4 -0.031 0.067 0.23 1 -0.29 10 11
ERBB2IP 0.034 0.022 -10000 0 -0.42 1 1
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.004 0.087 -10000 0 -0.26 36 36
JUN 0.007 0.073 0.2 2 -10000 0 2
HRAS 0.031 0.036 -10000 0 -0.42 3 3
DOCK7 -0.037 0.074 0.26 1 -0.27 28 29
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.019 0.088 -10000 0 -0.27 34 34
AKT1 0.002 0.025 -10000 0 -0.3 3 3
BAD -0.011 0.022 -10000 0 -0.25 4 4
MAPK10 -0.025 0.061 0.2 6 -0.2 17 23
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.004 0.094 -10000 0 -0.28 36 36
RAF1 0.01 0.11 0.27 11 -0.32 17 28
ErbB2/ErbB3/neuregulin 2 0.011 0.092 -10000 0 -0.28 44 44
STAT3 0.006 0.17 -10000 0 -0.88 18 18
cell migration -0.019 0.064 0.22 8 -0.21 11 19
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation -0.046 0.25 -10000 0 -0.62 62 62
FOS -0.047 0.21 0.31 1 -0.44 105 106
NRAS 0.029 0.05 -10000 0 -0.42 6 6
mol:Ca2+ -0.004 0.087 -10000 0 -0.26 36 36
MAPK3 -0.02 0.2 0.34 2 -0.51 49 51
MAPK1 -0.033 0.21 0.34 2 -0.55 50 52
JAK2 -0.035 0.076 0.26 1 -0.26 29 30
NF2 0.01 0.047 -10000 0 -0.68 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.001 0.071 0.18 3 -0.26 26 29
NRG1 0.028 0.015 -10000 0 -10000 0 0
GRB2/SOS1 0.047 0.022 -10000 0 -0.3 1 1
MAPK8 -0.021 0.097 0.22 1 -0.28 30 31
MAPK9 -0.024 0.059 0.2 6 -0.21 11 17
ERBB2 -0.031 0.055 0.6 1 -0.32 13 14
ERBB3 0.006 0.11 -10000 0 -0.42 32 32
SHC1 0.027 0.025 -10000 0 -0.42 1 1
RAC1 0.035 0.006 -10000 0 -10000 0 0
apoptosis 0.006 0.031 0.32 3 -0.21 3 6
STAT3 (dimer) 0.006 0.17 -10000 0 -0.86 18 18
RNF41 -0.014 0.019 -10000 0 -0.24 3 3
FRAP1 -0.01 0.016 -10000 0 -0.26 2 2
RAC1-CDC42/GTP -0.022 0.058 -10000 0 -0.2 29 29
ErbB2/ErbB2/HSP90 (dimer) -0.025 0.04 -10000 0 -0.26 13 13
CHRNA1 -0.007 0.17 0.32 2 -0.41 49 51
myelination -0.025 0.082 0.28 10 -0.32 7 17
PPP3CB -0.035 0.072 0.24 1 -0.25 30 31
KRAS 0.027 0.058 -10000 0 -0.42 8 8
RAC1-CDC42/GDP 0.038 0.095 0.25 1 -0.24 25 26
NRG2 0.025 0.058 -10000 0 -0.42 8 8
mol:GDP 0.001 0.07 0.18 3 -0.26 26 29
SOS1 0.034 0.021 -10000 0 -0.42 1 1
MAP2K2 -0.003 0.11 0.25 9 -0.32 23 32
SRC 0.032 0.03 -10000 0 -0.42 2 2
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.036 0.076 0.26 1 -0.26 29 30
MAP2K1 -0.03 0.2 -10000 0 -0.57 37 37
heart morphogenesis -0.004 0.087 -10000 0 -0.26 36 36
RAS family/GDP 0.039 0.11 0.26 1 -0.29 16 17
GRB2 0.033 0.01 -10000 0 -10000 0 0
PRKACA 0.014 0.054 -10000 0 -0.67 3 3
CHRNE 0.008 0.018 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity -0.002 0.025 0.3 3 -10000 0 3
nervous system development -0.004 0.087 -10000 0 -0.26 36 36
CDC42 0.034 0.007 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.036 0.14 -10000 0 -0.43 36 36
BAG4 0.027 0.025 -10000 0 -0.42 1 1
BAD -0.007 0.05 0.19 2 -0.17 14 16
NFKBIA 0.033 0.03 -10000 0 -0.42 2 2
BIRC3 -0.01 0.12 -10000 0 -0.42 41 41
BAX -0.004 0.055 0.2 8 -0.17 11 19
EnzymeConsortium:3.1.4.12 -0.006 0.034 0.075 4 -0.097 29 33
IKBKB -0.017 0.14 0.3 2 -0.41 28 30
MAP2K2 -0.008 0.055 0.19 11 -0.22 4 15
MAP2K1 -0.007 0.052 0.19 10 -0.2 3 13
SMPD1 -0.006 0.041 -10000 0 -0.15 16 16
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.003 0.15 0.32 4 -0.43 25 29
MAP2K4 -0.016 0.057 0.18 1 -0.18 25 26
protein ubiquitination -0.032 0.14 -10000 0 -0.42 31 31
EnzymeConsortium:2.7.1.37 -0.011 0.057 0.2 9 -0.2 6 15
response to UV 0 0.001 0.002 12 -0.002 5 17
RAF1 -0.007 0.053 0.2 8 -0.19 6 14
CRADD 0.029 0.054 -10000 0 -0.42 7 7
mol:ceramide -0.006 0.05 0.11 2 -0.15 28 30
I-kappa-B-alpha/RELA/p50/ubiquitin 0.044 0.023 -10000 0 -0.25 2 2
MADD 0.035 0.005 -10000 0 -10000 0 0
MAP3K1 -0.017 0.061 -10000 0 -0.18 36 36
TRADD 0.029 0.014 -10000 0 -10000 0 0
RELA/p50 0.035 0.006 -10000 0 -10000 0 0
MAPK3 -0.004 0.055 0.2 8 -0.19 4 12
MAPK1 -0.008 0.062 0.2 8 -0.2 10 18
p50/RELA/I-kappa-B-alpha 0.048 0.026 -10000 0 -0.3 2 2
FADD -0.002 0.15 0.3 3 -0.43 26 29
KSR1 -0.007 0.05 0.19 3 -0.17 11 14
MAPK8 -0.02 0.059 0.21 3 -0.18 25 28
TRAF2 0.034 0.029 -10000 0 -0.42 2 2
response to radiation 0 0 0.002 3 -10000 0 3
CHUK -0.043 0.14 -10000 0 -0.42 36 36
TNF R/SODD 0.039 0.028 -10000 0 -0.3 1 1
TNF 0.026 0.061 -10000 0 -0.42 9 9
CYCS 0.014 0.069 0.17 25 -0.17 7 32
IKBKG -0.04 0.14 -10000 0 -0.43 31 31
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.031 0.15 -10000 0 -0.45 35 35
RELA 0.035 0.006 -10000 0 -10000 0 0
RIPK1 0.035 0.007 -10000 0 -10000 0 0
AIFM1 0.012 0.067 0.15 27 -0.16 12 39
TNF/TNF R/SODD 0.048 0.049 -10000 0 -0.25 7 7
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
response to heat 0 0 0.002 3 -10000 0 3
CASP8 0.011 0.12 -10000 0 -0.63 16 16
NSMAF -0.011 0.14 0.27 1 -0.42 28 29
response to hydrogen peroxide 0 0.001 0.002 12 -0.002 5 17
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.039 0.038 -10000 0 -0.25 7 7
cell-cell adhesion 0.035 0.059 0.22 39 -10000 0 39
Ephrin B/EPHB2/RasGAP 0.069 0.079 -10000 0 -0.24 21 21
ITSN1 0.034 0.029 -10000 0 -0.42 2 2
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
SHC1 0.027 0.025 -10000 0 -0.42 1 1
Ephrin B1/EPHB3 0.035 0.058 -10000 0 -0.25 19 19
Ephrin B1/EPHB1 0.041 0.036 -10000 0 -0.25 7 7
HRAS/GDP 0.001 0.11 -10000 0 -0.28 37 37
Ephrin B/EPHB1/GRB7 0.064 0.082 -10000 0 -0.22 28 28
Endophilin/SYNJ1 -0.012 0.051 0.18 14 -0.21 18 32
KRAS 0.027 0.057 -10000 0 -0.42 8 8
Ephrin B/EPHB1/Src 0.069 0.076 -10000 0 -0.24 20 20
endothelial cell migration 0.034 0.092 -10000 0 -0.23 47 47
GRB2 0.033 0.01 -10000 0 -10000 0 0
GRB7 0.023 0.058 -10000 0 -0.42 8 8
PAK1 -0.019 0.066 0.21 9 -0.22 26 35
HRAS 0.032 0.036 -10000 0 -0.42 3 3
RRAS -0.014 0.055 0.18 13 -0.22 20 33
DNM1 0.032 0.041 -10000 0 -0.42 4 4
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.012 0.056 0.18 16 -0.22 17 33
lamellipodium assembly -0.035 0.059 -10000 0 -0.22 39 39
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.016 0.068 -10000 0 -0.45 5 5
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
EPHB2 0.032 0.03 -10000 0 -0.42 2 2
EPHB3 0.018 0.085 -10000 0 -0.42 18 18
EPHB1 0.026 0.05 -10000 0 -0.42 6 6
EPHB4 0.017 0.087 -10000 0 -0.42 19 19
mol:GDP -0.016 0.085 -10000 0 -0.33 22 22
Ephrin B/EPHB2 0.058 0.062 -10000 0 -0.22 17 17
Ephrin B/EPHB3 0.048 0.08 -10000 0 -0.23 31 31
JNK cascade -0.014 0.057 0.26 9 -0.23 16 25
Ephrin B/EPHB1 0.056 0.066 -10000 0 -0.22 20 20
RAP1/GDP -0.004 0.11 -10000 0 -0.28 37 37
EFNB2 0.019 0.075 -10000 0 -0.42 14 14
EFNB3 0.031 0.012 -10000 0 -10000 0 0
EFNB1 0.034 0.021 -10000 0 -0.42 1 1
Ephrin B2/EPHB1-2 0.044 0.065 -10000 0 -0.24 21 21
RAP1B 0.032 0.03 -10000 0 -0.42 2 2
RAP1A 0.03 0.05 -10000 0 -0.42 6 6
CDC42/GTP 0.036 0.09 -10000 0 -0.27 20 20
Rap1/GTP 0.015 0.068 -10000 0 -0.26 19 19
axon guidance 0.039 0.037 -10000 0 -0.25 7 7
MAPK3 0.025 0.072 0.27 1 -0.41 5 6
MAPK1 0.016 0.065 0.22 3 -0.41 5 8
Rac1/GDP -0.015 0.1 -10000 0 -0.28 37 37
actin cytoskeleton reorganization -0.022 0.074 -10000 0 -0.24 26 26
CDC42/GDP -0.014 0.1 -10000 0 -0.29 35 35
PI3K 0.039 0.095 -10000 0 -0.24 47 47
EFNA5 0.029 0.046 -10000 0 -0.42 5 5
Ephrin B2/EPHB4 0.023 0.077 -10000 0 -0.27 31 31
Ephrin B/EPHB2/Intersectin/N-WASP 0.012 0.073 -10000 0 -0.24 27 27
CDC42 0.034 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.008 0.065 -10000 0 -0.22 24 24
PTK2 0.11 0.23 0.55 111 -10000 0 111
MAP4K4 -0.014 0.058 0.26 9 -0.23 16 25
SRC 0.032 0.03 -10000 0 -0.42 2 2
KALRN 0.033 0.022 -10000 0 -0.42 1 1
Intersectin/N-WASP 0.044 0.048 -10000 0 -0.3 9 9
neuron projection morphogenesis -0.015 0.082 0.26 2 -0.3 16 18
MAP2K1 0.01 0.062 0.21 1 -0.43 5 6
WASL 0.029 0.054 -10000 0 -0.42 7 7
Ephrin B1/EPHB1-2/NCK1 0.077 0.05 -10000 0 -0.23 10 10
cell migration 0.03 0.093 0.26 6 -0.39 8 14
NRAS 0.029 0.05 -10000 0 -0.42 6 6
SYNJ1 -0.012 0.052 0.18 14 -0.21 18 32
PXN 0.036 0.004 -10000 0 -10000 0 0
TF -0.017 0.048 0.17 14 -0.21 14 28
HRAS/GTP 0.041 0.074 -10000 0 -0.22 27 27
Ephrin B1/EPHB1-2 0.057 0.042 -10000 0 -0.23 9 9
cell adhesion mediated by integrin 0.01 0.058 0.23 15 -0.21 12 27
RAC1 0.035 0.006 -10000 0 -10000 0 0
mol:GTP 0.047 0.074 -10000 0 -0.23 26 26
RAC1-CDC42/GTP -0.033 0.061 -10000 0 -0.22 36 36
RASA1 0.028 0.054 -10000 0 -0.42 7 7
RAC1-CDC42/GDP -0.001 0.11 -10000 0 -0.28 35 35
ruffle organization -0.03 0.073 -10000 0 -0.4 5 5
NCK1 0.034 0.021 -10000 0 -0.42 1 1
receptor internalization -0.019 0.05 0.17 13 -0.2 22 35
Ephrin B/EPHB2/KALRN 0.073 0.072 -10000 0 -0.23 17 17
ROCK1 0.017 0.06 0.19 22 -0.23 19 41
RAS family/GDP -0.046 0.067 -10000 0 -0.25 27 27
Rac1/GTP 0.001 0.074 -10000 0 -0.23 39 39
Ephrin B/EPHB1/Src/Paxillin 0.014 0.072 -10000 0 -0.27 21 21
Ras signaling in the CD4+ TCR pathway

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.016 0.15 -9999 0 -0.34 48 48
MAP3K8 0.002 0.11 -9999 0 -0.42 32 32
FOS 0.019 0.099 -9999 0 -0.44 7 7
PRKCA 0.025 0.022 -9999 0 -10000 0 0
PTPN7 0.02 0.032 -9999 0 -0.44 1 1
HRAS 0.031 0.036 -9999 0 -0.42 3 3
PRKCB -0.002 0.006 -9999 0 -0.016 73 73
NRAS 0.029 0.05 -9999 0 -0.42 6 6
RAS family/GTP 0.05 0.055 -9999 0 -0.23 15 15
MAPK3 0.027 0.07 -9999 0 -0.45 6 6
MAP2K1 0.008 0.066 -9999 0 -0.25 9 9
ELK1 0.024 0.038 -9999 0 -0.42 2 2
BRAF 0.005 0.05 -9999 0 -0.35 8 8
mol:GTP -0.001 0.002 -9999 0 -0.005 73 73
MAPK1 0.012 0.1 -9999 0 -0.4 19 19
RAF1 0.01 0.023 -9999 0 -0.24 1 1
KRAS 0.027 0.057 -9999 0 -0.42 8 8
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.026 0.1 0.9 1 -0.78 1 2
VDR 0.02 0.082 -10000 0 -0.42 17 17
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.004 0.1 -10000 0 -0.28 45 45
RXRs/LXRs/DNA/Oxysterols 0.013 0.16 -10000 0 -0.42 48 48
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA -0.001 0.019 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.003 0.092 -10000 0 -0.24 49 49
RXRs/NUR77 0.054 0.08 -10000 0 -0.25 12 12
RXRs/PPAR 0.009 0.072 -10000 0 -0.28 16 16
NCOR2 0.035 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.058 -10000 0 -0.3 17 17
RARs/VDR/DNA/Vit D3 0.051 0.085 -10000 0 -0.23 37 37
RARA 0.027 0.054 -10000 0 -0.42 7 7
NCOA1 0.031 0.045 -10000 0 -0.42 5 5
VDR/VDR/DNA 0.02 0.082 -10000 0 -0.42 17 17
RARs/RARs/DNA/9cRA 0.039 0.065 -10000 0 -0.22 25 25
RARG 0.035 0.004 -10000 0 -10000 0 0
RPS6KB1 0.053 0.15 0.54 41 -10000 0 41
RARs/THRs/DNA/SMRT 0.005 0.09 -10000 0 -0.24 48 48
THRA 0.02 0.075 -10000 0 -0.42 14 14
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.015 0.058 -10000 0 -0.3 17 17
RXRs/PPAR/9cRA/PGJ2/DNA 0.039 0.083 -10000 0 -0.24 15 15
NR1H4 0.035 0.021 -10000 0 -0.42 1 1
RXRs/LXRs/DNA 0.058 0.11 -10000 0 -0.32 5 5
NR1H2 0.029 0.031 -10000 0 -10000 0 0
NR1H3 0.026 0.052 -10000 0 -0.43 4 4
RXRs/VDR/DNA/Vit D3 0.043 0.084 -10000 0 -0.24 20 20
NR4A1 0.034 0.021 -10000 0 -0.42 1 1
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.025 0.065 -10000 0 -0.22 16 16
RXRG 0.016 0.063 -10000 0 -0.43 8 8
RXR alpha/CCPG 0.021 0.029 -10000 0 -0.31 2 2
RXRA 0.027 0.042 -10000 0 -0.44 2 2
RXRB 0.027 0.043 -10000 0 -0.42 2 2
THRB 0.024 0.07 -10000 0 -0.42 12 12
PPARG 0.012 0.091 -10000 0 -0.42 21 21
PPARD 0.035 0.006 -10000 0 -10000 0 0
TNF -0.001 0.19 -10000 0 -0.8 17 17
mol:Oxysterols -0.001 0.016 -10000 0 -10000 0 0
cholesterol transport 0.014 0.16 -10000 0 -0.42 48 48
PPARA 0.032 0.023 -10000 0 -0.42 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.014 0.089 -10000 0 -0.42 20 20
RXRs/NUR77/BCL2 -0.02 0.097 -10000 0 -0.22 83 83
SREBF1 -0.046 0.29 -10000 0 -0.94 45 45
RXRs/RXRs/DNA/9cRA 0.039 0.083 -10000 0 -0.24 15 15
ABCA1 -0.006 0.21 -10000 0 -0.92 17 17
RARs/THRs 0.061 0.1 -10000 0 -0.24 47 47
RXRs/FXR 0.055 0.082 -10000 0 -0.25 13 13
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
Atypical NF-kappaB 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
BCL3/RelA 0.045 0.045 -10000 0 -0.3 8 8
FBXW11 0.034 0.021 -10000 0 -0.42 1 1
NF kappa B1 p50/c-Rel 0.026 0.039 -10000 0 -0.25 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.004 0.098 0.2 1 -0.31 22 23
NFKBIA -0.014 0.1 -10000 0 -0.24 73 73
MAPK14 0.035 0.005 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.03 0.021 -10000 0 -0.26 1 1
ARRB2 0.017 0.006 -10000 0 -10000 0 0
REL 0.024 0.07 -10000 0 -0.42 12 12
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.026 0.037 -10000 0 -0.25 7 7
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.03 0.017 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
NF kappa B1 p50 dimer 0.023 0.021 0.26 3 -10000 0 3
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
NFKB1 0.013 0.007 -10000 0 -10000 0 0
RELA 0.035 0.006 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.004 0.099 -10000 0 -0.23 67 67
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.004 0.1 -10000 0 -0.3 27 27
SRC 0.032 0.03 -10000 0 -0.42 2 2
PI3K 0.035 0.067 -10000 0 -0.3 18 18
NF kappa B1 p50/RelA -0.003 0.098 -10000 0 -0.23 66 66
IKBKB 0.029 0.014 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.034 0.021 -10000 0 -0.42 1 1
SYK 0.005 0.11 -10000 0 -0.42 33 33
I kappa B alpha/PIK3R1 -0.007 0.11 -10000 0 -0.24 82 82
cell death 0.004 0.097 -10000 0 -0.28 28 28
NF kappa B1 p105/c-Rel 0.026 0.039 -10000 0 -0.25 8 8
LCK -0.018 0.14 -10000 0 -0.42 54 54
BCL3 0.028 0.057 -10000 0 -0.42 8 8
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.047 0.04 -10000 0 -0.3 6 6
Necdin/E2F1 0.013 0.11 -10000 0 -0.31 52 52
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.03 0.11 -10000 0 -0.23 71 71
NGF (dimer)/p75(NTR)/BEX1 0.037 0.035 -10000 0 -0.25 6 6
NT-4/5 (dimer)/p75(NTR) 0.022 0.026 -10000 0 -0.3 3 3
IKBKB 0.029 0.014 -10000 0 -10000 0 0
AKT1 0.018 0.068 0.19 39 -0.22 22 61
IKBKG 0.036 0 -10000 0 -10000 0 0
BDNF 0.03 0.024 -10000 0 -0.42 1 1
MGDIs/NGR/p75(NTR)/LINGO1 0.033 0.051 -10000 0 -0.25 14 14
FURIN 0.026 0.057 -10000 0 -0.42 8 8
proBDNF (dimer)/p75(NTR)/Sortilin 0.058 0.047 -10000 0 -0.25 9 9
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.026 0.055 -10000 0 -0.22 18 18
proBDNF (dimer) 0.03 0.023 -10000 0 -0.42 1 1
NTRK1 0.025 0.032 -10000 0 -0.42 2 2
RTN4R 0.023 0.067 -10000 0 -0.42 11 11
neuron apoptosis -0.009 0.1 0.28 1 -0.46 9 10
IRAK1 0.036 0.004 -10000 0 -10000 0 0
SHC1 0.012 0.022 -10000 0 -0.25 3 3
ARHGDIA 0.032 0.022 -10000 0 -0.42 1 1
RhoA/GTP 0.019 0.043 -10000 0 -0.3 9 9
Gamma Secretase 0.068 0.069 -10000 0 -0.22 14 14
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.04 0.083 -10000 0 -0.24 38 38
MAGEH1 0.006 0.11 -10000 0 -0.42 33 33
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.03 0.097 -10000 0 -0.24 54 54
Mammalian IAPs/DIABLO 0.032 0.082 -10000 0 -0.23 40 40
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.015 0.095 -10000 0 -0.42 23 23
APP 0.008 0.1 -10000 0 -0.42 28 28
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.034 0.029 -10000 0 -0.42 2 2
RhoA/GDP/RHOGDI 0.037 0.044 0.18 3 -0.22 12 15
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.011 0.048 0.2 16 -0.22 9 25
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.021 0.031 -10000 0 -0.21 6 6
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.042 0.029 -10000 0 -0.25 4 4
NCSTN 0.028 0.025 -10000 0 -0.42 1 1
mol:GTP 0.025 0.067 -10000 0 -0.25 27 27
PSENEN 0.035 0.006 -10000 0 -10000 0 0
mol:ceramide 0.015 0.043 0.19 11 -0.23 10 21
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.013 0.037 -10000 0 -10000 0 0
p75(NTR)/beta APP 0.027 0.082 -10000 0 -0.3 29 29
BEX1 0.026 0.037 -10000 0 -0.42 3 3
mol:GDP -0.006 0.019 -10000 0 -0.25 3 3
NGF (dimer) 0.007 0.11 -10000 0 -0.24 76 76
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.048 0.055 -10000 0 -0.23 15 15
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
RAC1/GTP 0.037 0.023 -10000 0 -0.21 3 3
MYD88 0.031 0.041 -10000 0 -0.42 4 4
CHUK 0.025 0.067 -10000 0 -0.42 11 11
NGF (dimer)/p75(NTR)/PKA 0.026 0.068 -10000 0 -0.25 27 27
RHOB -0.011 0.14 -10000 0 -0.42 51 51
RHOA 0.026 0.061 -10000 0 -0.42 9 9
MAGE-G1/E2F1 0.043 0.044 -10000 0 -0.3 7 7
NT3 (dimer) 0.024 0.054 -10000 0 -0.42 7 7
TP53 -0.019 0.065 0.35 1 -0.4 1 2
PRDM4 0.019 0.045 0.19 16 -0.23 9 25
BDNF (dimer) -0.02 0.16 -10000 0 -0.3 114 114
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
SORT1 0.029 0.05 -10000 0 -0.42 6 6
activation of caspase activity 0.024 0.11 -10000 0 -0.23 71 71
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.057 0.044 -10000 0 -0.23 9 9
RHOC 0.032 0.036 -10000 0 -0.42 3 3
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.017 0.078 0.22 1 -0.28 15 16
DIABLO 0.036 0.004 -10000 0 -10000 0 0
SMPD2 0.015 0.043 0.19 11 -0.23 10 21
APH1B 0.024 0.07 -10000 0 -0.42 12 12
APH1A 0.031 0.036 -10000 0 -0.42 3 3
proNGF (dimer)/p75(NTR)/Sortilin 0.039 0.041 -10000 0 -0.25 9 9
PSEN1 0.032 0.036 -10000 0 -0.42 3 3
APAF-1/Pro-Caspase 9 0.047 0.037 -10000 0 -0.3 5 5
NT3 (dimer)/p75(NTR) 0.038 0.051 -10000 0 -0.3 10 10
MAPK8 -0.01 0.065 -10000 0 -0.27 7 7
MAPK9 -0.016 0.078 -10000 0 -0.32 11 11
APAF1 0.032 0.041 -10000 0 -0.42 4 4
NTF3 0.024 0.054 -10000 0 -0.42 7 7
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.012 0.14 -10000 0 -0.42 52 52
RAC1/GDP 0.026 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.02 0.11 -10000 0 -0.21 84 84
p75 CTF/Sortilin/TRAF6/NRIF 0.081 0.047 -10000 0 -0.24 8 8
RhoA-B-C/GTP 0.025 0.067 -10000 0 -0.25 27 27
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.086 0.058 -10000 0 -0.22 12 12
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.074 0.052 -10000 0 -0.23 10 10
PRKACB 0.009 0.097 -10000 0 -0.42 24 24
proBDNF (dimer)/p75 ECD 0.048 0.02 -10000 0 -0.3 1 1
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.009 0.12 -10000 0 -0.42 41 41
BIRC2 0.031 0.012 -10000 0 -10000 0 0
neuron projection morphogenesis -0.037 0.078 -10000 0 -0.26 38 38
BAD -0.019 0.079 0.21 1 -0.29 10 11
RIPK2 0.028 0.015 -10000 0 -10000 0 0
NGFR 0.03 0.036 -10000 0 -0.42 3 3
CYCS 0.005 0.064 0.19 12 -0.22 32 44
ADAM17 0.035 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.047 0.04 -10000 0 -0.23 4 4
BCL2L11 -0.019 0.079 0.21 1 -0.29 10 11
BDNF (dimer)/p75(NTR) 0.043 0.034 -10000 0 -0.3 4 4
PI3K 0.046 0.061 -10000 0 -0.23 20 20
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.055 0.044 -10000 0 -0.23 9 9
NDNL2 0.034 0.008 -10000 0 -10000 0 0
YWHAE 0.032 0.011 -10000 0 -10000 0 0
PRKCI 0.024 0.067 -10000 0 -0.42 11 11
NGF (dimer)/p75(NTR) 0.022 0.026 -10000 0 -0.3 3 3
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.044 0.074 -10000 0 -0.23 32 32
TRAF6 0.034 0.021 -10000 0 -0.42 1 1
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.031 0.03 -10000 0 -0.42 2 2
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.018 0.046 -10000 0 -0.24 14 14
SQSTM1 0.034 0.021 -10000 0 -0.42 1 1
NGFRAP1 -0.026 0.16 -10000 0 -0.42 68 68
CASP3 -0.018 0.077 0.2 1 -0.27 11 12
E2F1 0.028 0.054 -10000 0 -0.42 7 7
CASP9 0.034 0.022 -10000 0 -0.42 1 1
IKK complex 0.041 0.064 -10000 0 -0.32 1 1
NGF (dimer)/TRKA 0.019 0.023 -10000 0 -0.3 2 2
MMP7 -0.033 0.16 -10000 0 -0.42 69 69
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.07 0.05 -10000 0 -0.22 11 11
MMP3 -0.047 0.17 -10000 0 -0.42 83 83
APAF-1/Caspase 9 -0.044 0.063 -10000 0 -0.2 67 67
Syndecan-3-mediated signaling events

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
CTTN 0.027 0.032 -9999 0 -0.42 2 2
Syndecan-3/Src/Cortactin 0.006 0.14 -9999 0 -0.5 25 25
Syndecan-3/Neurocan -0.018 0.12 -9999 0 -0.49 28 28
POMC 0.031 0.036 -9999 0 -0.42 3 3
EGFR -0.013 0.13 -9999 0 -0.42 47 47
Syndecan-3/EGFR -0.011 0.15 -9999 0 -0.54 29 29
AGRP 0.028 0.024 -9999 0 -0.42 1 1
NCSTN 0.028 0.025 -9999 0 -0.42 1 1
PSENEN 0.035 0.006 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.024 0.07 -9999 0 -0.42 12 12
APH1A 0.031 0.036 -9999 0 -0.42 3 3
NCAN 0 0 -9999 0 -10000 0 0
long-term memory 0.017 0.12 -9999 0 -0.46 26 26
Syndecan-3/IL8 -0.007 0.14 -9999 0 -0.53 29 29
PSEN1 0.032 0.036 -9999 0 -0.42 3 3
Src/Cortactin 0.038 0.038 -9999 0 -0.3 4 4
FYN 0.027 0.05 -9999 0 -0.42 6 6
limb bud formation -0.015 0.12 -9999 0 -0.53 26 26
MC4R 0.033 0.022 -9999 0 -0.42 1 1
SRC 0.032 0.03 -9999 0 -0.42 2 2
PTN -0.028 0.15 -9999 0 -0.42 63 63
FGFR/FGF/Syndecan-3 -0.016 0.12 -9999 0 -0.53 26 26
neuron projection morphogenesis -0.031 0.12 -9999 0 -0.49 24 24
Syndecan-3/AgRP 0.008 0.13 -9999 0 -0.5 27 27
Syndecan-3/AgRP/MC4R 0.023 0.13 -9999 0 -0.5 25 25
Fyn/Cortactin 0.035 0.043 -9999 0 -0.3 6 6
SDC3 -0.016 0.12 -9999 0 -0.54 26 26
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.007 0.14 -9999 0 -0.52 29 29
IL8 -0.005 0.12 -9999 0 -0.42 37 37
Syndecan-3/Fyn/Cortactin 0.018 0.13 -9999 0 -0.49 24 24
Syndecan-3/CASK -0.018 0.12 -9999 0 -0.49 28 28
alpha-MSH/MC4R 0.047 0.034 -9999 0 -0.3 4 4
Gamma Secretase 0.068 0.069 -9999 0 -0.22 14 14
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.034 0.021 -10000 0 -0.42 1 1
HDAC2 0.032 0.023 -10000 0 -0.42 1 1
GNB1/GNG2 0.034 0.099 -10000 0 -0.26 51 51
forebrain development -0.003 0.14 -10000 0 -0.56 17 17
GNAO1 0.03 0.014 -10000 0 -10000 0 0
SMO/beta Arrestin2 0.015 0.1 -10000 0 -0.3 46 46
SMO -0.008 0.13 -10000 0 -0.42 46 46
ARRB2 0.032 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.003 0.15 0.24 2 -0.41 31 33
mol:GTP 0 0 -10000 0 -10000 0 0
GSK3B 0.035 0.004 -10000 0 -10000 0 0
GNAI2 0.027 0.057 -10000 0 -0.42 8 8
SIN3/HDAC complex 0.076 0.044 -10000 0 -0.23 5 5
GNAI1 0.018 0.085 -10000 0 -0.42 18 18
XPO1 0.036 0.005 -10000 0 -10000 0 0
GLI1/Su(fu) -0.018 0.17 -10000 0 -0.55 26 26
SAP30 0.03 0.046 -10000 0 -0.42 5 5
mol:GDP -0.008 0.13 -10000 0 -0.42 46 46
MIM/GLI2A 0.001 0.11 -10000 0 -0.42 31 31
IFT88 0.02 0.075 -10000 0 -0.42 14 14
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GLI2 0.013 0.081 -10000 0 -0.33 16 16
GLI3 -0.011 0.15 0.24 3 -0.43 30 33
CSNK1D 0.033 0.009 -10000 0 -10000 0 0
CSNK1E 0.033 0.009 -10000 0 -10000 0 0
SAP18 0.033 0.01 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.02 0.075 -10000 0 -0.42 14 14
GNG2 0.034 0.021 -10000 0 -0.42 1 1
Gi family/GTP -0.016 0.11 -10000 0 -0.29 54 54
SIN3B 0.035 0.005 -10000 0 -10000 0 0
SIN3A 0.034 0.007 -10000 0 -10000 0 0
GLI3/Su(fu) -0.008 0.14 -10000 0 -0.41 39 39
GLI2/Su(fu) 0.004 0.11 -10000 0 -0.39 19 19
FOXA2 -0.024 0.2 -10000 0 -0.68 40 40
neural tube patterning -0.003 0.14 -10000 0 -0.56 17 17
SPOP 0.033 0.022 -10000 0 -0.42 1 1
Su(fu)/PIAS1 0.009 0.09 -10000 0 -0.33 16 16
GNB1 0.031 0.045 -10000 0 -0.42 5 5
CSNK1G2 0.033 0.029 -10000 0 -0.42 2 2
CSNK1G3 0.035 0.007 -10000 0 -10000 0 0
MTSS1 0.001 0.11 -10000 0 -0.42 31 31
embryonic limb morphogenesis -0.003 0.14 -10000 0 -0.56 17 17
SUFU -0.001 0.084 -10000 0 -0.35 16 16
LGALS3 -0.01 0.14 -10000 0 -0.42 49 49
catabolic process 0.013 0.15 -10000 0 -0.48 22 22
GLI3A/CBP 0.034 0.042 -10000 0 -0.33 6 6
KIF3A 0.027 0.061 -10000 0 -0.42 9 9
GLI1 -0.004 0.14 -10000 0 -0.57 17 17
RAB23 0.031 0.041 -10000 0 -0.42 4 4
CSNK1A1 0.035 0.005 -10000 0 -10000 0 0
IFT172 0.033 0.035 -10000 0 -0.42 3 3
RBBP7 0.033 0.029 -10000 0 -0.42 2 2
Su(fu)/Galectin3 -0.014 0.12 -10000 0 -0.29 61 61
GNAZ 0.024 0.067 -10000 0 -0.42 11 11
RBBP4 0.034 0.021 -10000 0 -0.42 1 1
CSNK1G1 0.035 0.007 -10000 0 -10000 0 0
PIAS1 0.035 0.006 -10000 0 -10000 0 0
PRKACA 0.035 0.004 -10000 0 -10000 0 0
GLI2/SPOP 0.027 0.083 -10000 0 -0.33 14 14
STK36 0.021 0.083 -10000 0 -0.42 17 17
Gi family/GNB1/GNG2/GDP -0.02 0.12 -10000 0 -0.38 35 35
PTCH1 -0.002 0.13 -10000 0 -0.5 17 17
MIM/GLI1 0.001 0.13 -10000 0 -0.5 18 18
CREBBP 0.034 0.042 -10000 0 -0.33 6 6
Su(fu)/SIN3/HDAC complex 0.009 0.097 -10000 0 -0.39 19 19
EPO signaling 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
BCL2L1 -0.004 0.14 -10000 0 -0.48 1 1
CRKL -0.001 0.075 0.26 4 -0.24 10 14
mol:DAG 0.019 0.08 0.25 2 -10000 0 2
HRAS 0.024 0.1 0.28 20 -10000 0 20
MAPK8 0.035 0.072 0.2 56 -0.25 2 58
RAP1A 0 0.077 0.26 4 -0.24 12 16
GAB1 -0.001 0.076 0.24 3 -0.24 11 14
MAPK14 0.035 0.069 0.2 54 -10000 0 54
EPO 0.023 0.027 -10000 0 -10000 0 0
PLCG1 0.018 0.08 0.25 2 -10000 0 2
EPOR/TRPC2/IP3 Receptors 0.026 0.028 -10000 0 -10000 0 0
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.046 0.052 -10000 0 -0.27 4 4
GAB1/SHC/GRB2/SOS1 0.027 0.074 0.29 1 -0.21 1 2
EPO/EPOR (dimer) 0.036 0.039 -10000 0 -10000 0 0
IRS2 -0.01 0.087 0.27 3 -0.25 29 32
STAT1 -0.003 0.13 0.26 2 -0.33 35 37
STAT5B 0.02 0.083 0.26 1 -0.26 2 3
cell proliferation 0.013 0.078 0.19 74 -0.24 2 76
GAB1/SHIP/PIK3R1/SHP2/SHC 0.007 0.074 -10000 0 -0.21 22 22
TEC 0 0.075 0.27 3 -0.23 11 14
SOCS3 0.028 0.046 -10000 0 -0.42 5 5
STAT1 (dimer) -0.003 0.13 0.26 2 -0.32 35 37
JAK2 0.027 0.036 -10000 0 -0.44 2 2
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
EPO/EPOR (dimer)/JAK2 0.036 0.088 -10000 0 -0.17 34 34
EPO/EPOR 0.036 0.039 -10000 0 -10000 0 0
LYN 0.02 0.026 -10000 0 -10000 0 0
TEC/VAV2 0.014 0.08 0.29 2 -0.22 11 13
elevation of cytosolic calcium ion concentration 0.026 0.028 -10000 0 -10000 0 0
SHC1 0.027 0.025 -10000 0 -0.42 1 1
EPO/EPOR (dimer)/LYN 0.043 0.053 -10000 0 -10000 0 0
mol:IP3 0.019 0.08 0.25 2 -10000 0 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.006 0.095 0.29 1 -0.23 44 45
SH2B3 -0.003 0.009 -10000 0 -10000 0 0
NFKB1 0.036 0.07 0.2 56 -10000 0 56
EPO/EPOR (dimer)/JAK2/SOCS3 0.022 0.034 -10000 0 -0.21 6 6
PTPN6 -0.002 0.067 -10000 0 -0.25 7 7
TEC/VAV2/GRB2 0.026 0.083 0.3 2 -0.21 8 10
EPOR 0.026 0.028 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.026 0.075 0.29 1 -0.21 2 3
SOS1 0.034 0.021 -10000 0 -0.42 1 1
PLCG2 0.02 0.055 -10000 0 -0.42 7 7
CRKL/CBL/C3G 0.02 0.084 0.3 1 -0.26 6 7
VAV2 0.002 0.073 0.26 4 -0.25 6 10
CBL 0 0.07 0.24 3 -0.25 6 9
SHC/Grb2/SOS1 0.015 0.062 -10000 0 -0.2 4 4
STAT5A 0.019 0.084 0.26 1 -0.26 3 4
GRB2 0.033 0.01 -10000 0 -10000 0 0
STAT5 (dimer) 0.017 0.13 0.28 1 -0.31 47 48
LYN/PLCgamma2 0.029 0.046 -10000 0 -0.3 7 7
PTPN11 0.036 0.003 -10000 0 -10000 0 0
BTK -0.004 0.082 0.26 4 -0.25 19 23
BCL2 -0.11 0.33 -10000 0 -0.74 105 105
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.035 0.006 -10000 0 -10000 0 0
VLDLR -0.006 0.12 -10000 0 -0.42 41 41
LRPAP1 0.034 0.007 -10000 0 -10000 0 0
NUDC 0.035 0.007 -10000 0 -10000 0 0
RELN/LRP8 0.038 0.088 -10000 0 -0.26 39 39
CaM/Ca2+ 0.026 0.005 -10000 0 -10000 0 0
KATNA1 0.033 0.01 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.001 0.072 0.19 9 -0.23 39 48
IQGAP1/CaM 0.049 0.015 -10000 0 -10000 0 0
DAB1 0.035 0.006 -10000 0 -10000 0 0
IQGAP1 0.034 0.008 -10000 0 -10000 0 0
PLA2G7 -0.036 0.16 -10000 0 -0.42 74 74
CALM1 0.035 0.007 -10000 0 -10000 0 0
DYNLT1 0.033 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.023 0.088 -10000 0 -0.3 34 34
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 0.033 0.01 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.01 0.012 -10000 0 -0.25 1 1
CDK5R2 0.035 0.005 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.033 0.096 -10000 0 -0.26 45 45
YWHAE 0.032 0.011 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.015 0.069 0.33 1 -0.25 5 6
MAP1B -0.007 0.06 -10000 0 -0.26 26 26
RAC1 0.015 0.007 -10000 0 -10000 0 0
p35/CDK5 0.007 0.066 0.19 7 -0.21 38 45
RELN 0.03 0.046 -10000 0 -0.42 5 5
PAFAH/LIS1 -0.011 0.1 -10000 0 -0.25 73 73
LIS1/CLIP170 0.01 0.012 -10000 0 -0.25 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.017 0.068 -10000 0 -0.23 2 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.006 0.1 -10000 0 -0.26 57 57
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.003 0.062 0.26 2 -0.26 5 7
LIS1/IQGAP1 0.033 0.014 -10000 0 -10000 0 0
RHOA 0.008 0.056 -10000 0 -0.4 9 9
PAFAH1B1 0.014 0.015 -10000 0 -0.3 1 1
PAFAH1B3 0.029 0.054 -10000 0 -0.42 7 7
PAFAH1B2 0.031 0.012 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.016 0.058 -10000 0 -0.18 25 25
NDEL1/Katanin 60/Dynein heavy chain 0.022 0.078 0.33 1 -0.25 5 6
LRP8 0 0.11 -10000 0 -0.42 34 34
NDEL1/Katanin 60 0.008 0.072 0.33 1 -0.25 5 6
P39/CDK5 0.008 0.067 0.2 2 -0.21 39 41
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0.019 -10000 0 -0.26 1 1
CDK5 -0.028 0.061 0.18 8 -0.22 38 46
PPP2R5D 0.035 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.009 0.011 -10000 0 -0.21 1 1
CSNK2A1 0.034 0.008 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.036 0.091 -10000 0 -0.23 45 45
RELN/VLDLR 0.026 0.12 -10000 0 -0.24 78 78
CDC42 0.015 0.007 -10000 0 -10000 0 0
Aurora A 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
Aurora A/GADD45A 0.032 0.055 -10000 0 -0.24 15 15
BIRC5 -0.002 0.12 -10000 0 -0.42 38 38
NFKBIA 0.013 0.052 0.25 15 -0.25 2 17
CPEB1 0.03 0.041 -10000 0 -0.42 4 4
AKT1 0.009 0.044 0.25 7 -0.25 3 10
NDEL1 0.032 0.011 -10000 0 -10000 0 0
Aurora A/BRCA1 0.028 0.047 -10000 0 -0.23 12 12
NDEL1/TACC3 0.041 0.049 -10000 0 -0.19 6 6
GADD45A 0.019 0.08 -10000 0 -0.42 16 16
GSK3B 0.038 0.016 -10000 0 -10000 0 0
PAK1/Aurora A 0.027 0.06 -10000 0 -0.24 18 18
MDM2 0.034 0.009 -10000 0 -10000 0 0
JUB 0.002 0.12 -10000 0 -0.42 36 36
TPX2 -0.008 0.084 -10000 0 -0.3 38 38
TP53 -0.005 0.093 -10000 0 -0.23 67 67
DLG7 -0.011 0.059 0.25 5 -0.19 40 45
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 0.032 0.011 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.044 0.052 -10000 0 -0.21 6 6
G2/M transition of mitotic cell cycle 0.027 0.047 -10000 0 -0.23 12 12
AURKA 0.023 0.035 -10000 0 -10000 0 0
AURKB 0 0.062 -10000 0 -0.18 43 43
CDC25B 0.014 0.048 -10000 0 -0.29 5 5
G2/M transition checkpoint 0.018 0.07 -10000 0 -0.22 36 36
mRNA polyadenylation 0.033 0.033 -10000 0 -0.2 4 4
Aurora A/CPEB 0.033 0.033 -10000 0 -0.2 4 4
Aurora A/TACC1/TRAP/chTOG 0.05 0.076 -10000 0 -0.23 22 22
BRCA1 0.021 0.07 -10000 0 -0.42 12 12
centrosome duplication 0.027 0.06 -10000 0 -0.24 18 18
regulation of centrosome cycle 0.04 0.048 -10000 0 -0.19 6 6
spindle assembly 0.048 0.075 -10000 0 -0.23 22 22
TDRD7 0.026 0.064 -10000 0 -0.42 10 10
Aurora A/RasGAP/Survivin 0.033 0.081 -10000 0 -0.2 31 31
CENPA -0.005 0.084 -10000 0 -0.28 43 43
Aurora A/PP2A 0.041 0.029 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0 0.048 0.17 5 -0.32 2 7
negative regulation of DNA binding -0.006 0.097 -10000 0 -0.23 69 69
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.045 0.024 -10000 0 -0.3 1 1
RASA1 0.028 0.054 -10000 0 -0.42 7 7
Ajuba/Aurora A 0.018 0.07 -10000 0 -0.22 36 36
mitotic prometaphase 0.004 0.024 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.035 -10000 0 -10000 0 0
TACC1 0.012 0.087 -10000 0 -0.42 19 19
TACC3 0.017 0.087 -10000 0 -0.42 19 19
Aurora A/Antizyme1 0.036 0.025 -10000 0 -10000 0 0
Aurora A/RasGAP 0.037 0.044 -10000 0 -0.25 7 7
OAZ1 0.035 0.006 -10000 0 -10000 0 0
RAN 0.035 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.038 0.016 -10000 0 -10000 0 0
GIT1 0.033 0.022 -10000 0 -0.42 1 1
GIT1/beta-PIX/PAK1 0.043 0.068 -10000 0 -0.27 18 18
Importin alpha/Importin beta/TPX2 -0.008 0.084 -10000 0 -0.3 38 38
PPP2R5D 0.035 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 0.007 0.052 -10000 0 -0.2 8 8
PAK1 0.014 0.085 -10000 0 -0.42 18 18
CKAP5 0.035 0.006 -10000 0 -10000 0 0
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 -0.003 0.27 -10000 0 -1 31 31
oxygen homeostasis 0.005 0.009 -10000 0 -10000 0 0
TCEB2 0.032 0.011 -10000 0 -10000 0 0
TCEB1 0.028 0.025 -10000 0 -0.42 1 1
VHL/Elongin B/Elongin C/HIF2A 0.053 0.11 0.28 1 -0.33 11 12
EPO 0.073 0.17 -10000 0 -0.52 14 14
FIH (dimer) 0.037 0.019 -10000 0 -10000 0 0
APEX1 0.035 0.027 -10000 0 -10000 0 0
SERPINE1 0.058 0.2 -10000 0 -0.55 25 25
FLT1 -0.038 0.28 -10000 0 -0.8 44 44
ADORA2A 0.045 0.18 0.35 1 -0.52 24 25
germ cell development 0.066 0.18 -10000 0 -0.52 19 19
SLC11A2 0.067 0.18 -10000 0 -0.53 21 21
BHLHE40 0.055 0.18 0.33 1 -0.49 25 26
HIF1AN 0.037 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.075 0.15 0.33 1 -0.38 19 20
ETS1 0.037 0.032 -10000 0 -0.42 1 1
CITED2 0.017 0.18 -10000 0 -0.78 19 19
KDR -0.013 0.23 -10000 0 -0.79 27 27
PGK1 0.068 0.18 -10000 0 -0.54 19 19
SIRT1 0.036 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.11 0.22 -10000 0 -0.59 21 21
EPAS1 0.027 0.12 -10000 0 -0.33 24 24
SP1 0.034 0.037 -10000 0 -0.42 1 1
ABCG2 0.062 0.19 -10000 0 -0.57 21 21
EFNA1 0.033 0.18 -10000 0 -0.51 31 31
FXN 0.053 0.17 0.34 5 -0.52 19 24
POU5F1 0.066 0.18 -10000 0 -0.54 19 19
neuron apoptosis -0.11 0.22 0.57 21 -10000 0 21
EP300 0.033 0.022 -10000 0 -0.42 1 1
EGLN3 -0.013 0.14 -10000 0 -0.42 52 52
EGLN2 0.033 0.045 -10000 0 -0.42 4 4
EGLN1 0.023 0.057 -10000 0 -0.42 7 7
VHL/Elongin B/Elongin C 0.053 0.035 -10000 0 -0.26 1 1
VHL 0.035 0.007 -10000 0 -10000 0 0
ARNT 0.035 0.027 -10000 0 -10000 0 0
SLC2A1 0.048 0.18 0.34 4 -0.51 23 27
TWIST1 0.041 0.2 0.35 1 -0.56 34 35
ELK1 0.038 0.032 -10000 0 -0.42 2 2
HIF2A/ARNT/Cbp/p300 0.071 0.15 0.34 1 -0.38 19 20
VEGFA 0.055 0.18 0.33 1 -0.49 25 26
CREBBP 0.032 0.011 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.041 0.018 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.034 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.017 0.078 -10000 0 -0.42 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.029 0.024 -10000 0 -0.42 1 1
RAC1-CDC42/GTP/PAK family 0.002 0.064 -10000 0 -0.21 38 38
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.029 0.05 -10000 0 -0.42 6 6
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.031 0.012 -10000 0 -10000 0 0
FYN 0.027 0.05 -10000 0 -0.42 6 6
MAP3K12 0.035 0.004 -10000 0 -10000 0 0
FGR 0.034 0.007 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.004 0.14 0.2 5 -0.33 53 58
PRKG1 0.035 0.005 -10000 0 -10000 0 0
DUSP8 0.02 0.08 -10000 0 -0.42 16 16
PGK/cGMP/p38 alpha -0.008 0.14 0.19 1 -0.32 57 58
apoptosis -0.005 0.13 0.19 5 -0.32 53 58
RAL/GTP 0.044 0.028 -10000 0 -0.25 4 4
LYN 0.03 0.013 -10000 0 -10000 0 0
DUSP1 0.001 0.12 -10000 0 -0.42 35 35
PAK1 0.014 0.085 -10000 0 -0.42 18 18
SRC 0.032 0.03 -10000 0 -0.42 2 2
RAC1/OSM/MEKK3/MKK3 0.072 0.04 -10000 0 -0.24 1 1
TRAF6 0.034 0.021 -10000 0 -0.42 1 1
RAC1 0.035 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.035 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.045 0.013 -10000 0 -10000 0 0
MAPK11 -0.013 0.14 0.22 4 -0.39 39 43
BLK 0.021 0.038 -10000 0 -0.42 3 3
HCK 0.017 0.087 -10000 0 -0.42 19 19
MAP2K3 0.032 0.023 -10000 0 -0.42 1 1
DUSP16 0.029 0.046 -10000 0 -0.42 5 5
DUSP10 0.012 0.082 -10000 0 -0.42 17 17
TRAF6/MEKK3 0.039 0.02 -10000 0 -0.23 1 1
MAP3K7IP1 0.033 0.009 -10000 0 -10000 0 0
MAPK14 -0.017 0.14 0.2 6 -0.34 59 65
positive regulation of innate immune response -0.018 0.17 0.24 6 -0.41 50 56
LCK -0.018 0.14 -10000 0 -0.42 54 54
p38alpha-beta/MKP7 -0.006 0.17 0.25 5 -0.4 50 55
p38alpha-beta/MKP5 -0.012 0.16 0.25 5 -0.4 49 54
PGK/cGMP 0.026 0.004 -10000 0 -10000 0 0
PAK2 0.036 0 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.018 0.17 0.25 5 -0.4 55 60
CDC42 0.034 0.007 -10000 0 -10000 0 0
RALB 0.032 0.041 -10000 0 -0.42 4 4
RALA 0.035 0.006 -10000 0 -10000 0 0
PAK3 0.016 0.082 -10000 0 -0.42 17 17
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.03 0.041 -10000 0 -0.42 4 4
RAS family/GTP/Tiam1 0.012 0.067 -10000 0 -0.27 19 19
NT3 (dimer)/TRKC 0.039 0.044 -10000 0 -0.3 7 7
NT3 (dimer)/TRKB 0.046 0.07 -10000 0 -0.26 21 21
SHC/Grb2/SOS1/GAB1/PI3K 0.016 0.05 -10000 0 -0.21 18 18
RAPGEF1 0.036 0.004 -10000 0 -10000 0 0
BDNF 0.03 0.024 -10000 0 -0.42 1 1
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
DYNLT1 0.033 0.01 -10000 0 -10000 0 0
NTRK1 0.025 0.032 -10000 0 -0.42 2 2
NTRK2 0.019 0.078 -10000 0 -0.42 15 15
NTRK3 0.031 0.012 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB 0.033 0.055 -10000 0 -0.25 17 17
neuron apoptosis 0.003 0.14 0.31 54 -0.25 2 56
SHC 2-3/Grb2 -0.004 0.15 -10000 0 -0.34 54 54
SHC1 0.027 0.025 -10000 0 -0.42 1 1
SHC2 -0.037 0.18 0.24 2 -0.44 77 79
SHC3 0.019 0.11 0.24 3 -0.4 21 24
STAT3 (dimer) -0.017 0.13 -10000 0 -0.34 70 70
NT3 (dimer)/TRKA 0.042 0.053 -10000 0 -0.26 10 10
RIN/GDP 0.068 0.084 0.24 26 -0.26 7 33
GIPC1 0.033 0.035 -10000 0 -0.42 3 3
KRAS 0.027 0.057 -10000 0 -0.42 8 8
DNAJA3 0.007 0.056 0.21 18 -0.26 5 23
RIN/GTP 0.024 0.021 -10000 0 -0.3 2 2
CCND1 -0.079 0.24 -10000 0 -0.69 68 68
MAGED1 0.015 0.095 -10000 0 -0.42 23 23
PTPN11 0.036 0.003 -10000 0 -10000 0 0
RICS 0.023 0.061 -10000 0 -0.42 9 9
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.051 0.036 -10000 0 -0.26 1 1
GRB2 0.033 0.01 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.032 0.033 -10000 0 -0.25 4 4
TRKA/NEDD4-2 0.021 0.078 -10000 0 -0.3 26 26
ELMO1 0.035 0.006 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.041 0.039 -10000 0 -0.25 8 8
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.032 0.036 -10000 0 -0.42 3 3
DOCK1 0.027 0.057 -10000 0 -0.42 8 8
GAB2 0.031 0.013 -10000 0 -10000 0 0
RIT2 0.033 0.029 -10000 0 -0.42 2 2
RIT1 0.026 0.032 -10000 0 -0.42 2 2
FRS2 0.033 0.022 -10000 0 -0.42 1 1
DNM1 0.032 0.041 -10000 0 -0.42 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.023 -10000 0 -0.42 1 1
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.043 0.067 0.23 20 -0.25 5 25
mol:GDP 0.071 0.11 0.29 26 -0.39 6 32
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.026 0.005 -10000 0 -10000 0 0
RIT1/GDP 0.04 0.07 0.25 6 -0.24 6 12
TIAM1 0.028 0.057 -10000 0 -0.42 8 8
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
BDNF (dimer)/TRKB 0.052 0.064 -10000 0 -0.26 19 19
KIDINS220/CRKL/C3G 0.047 0.034 -10000 0 -0.3 4 4
SHC/RasGAP 0.035 0.046 -10000 0 -0.3 7 7
FRS2 family/SHP2 0.066 0.025 -10000 0 -0.26 1 1
SHC/GRB2/SOS1/GAB1 0.06 0.054 -10000 0 -0.24 6 6
RIT1/GTP 0.02 0.023 -10000 0 -0.3 2 2
NT3 (dimer) 0.024 0.054 -10000 0 -0.42 7 7
RAP1/GDP 0.048 0.067 0.18 17 -0.23 6 23
KIDINS220/CRKL 0.03 0.041 -10000 0 -0.42 4 4
BDNF (dimer) 0.03 0.023 -10000 0 -0.42 1 1
ubiquitin-dependent protein catabolic process 0.02 0.067 -10000 0 -0.25 26 26
Schwann cell development -0.007 0.013 -10000 0 -10000 0 0
EHD4 0.031 0.041 -10000 0 -0.42 4 4
FRS2 family/GRB2/SOS1 0.076 0.041 -10000 0 -0.44 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.025 0.06 -10000 0 -0.32 2 2
RAP1B 0.032 0.03 -10000 0 -0.42 2 2
RAP1A 0.03 0.05 -10000 0 -0.42 6 6
CDC42/GTP 0.043 0.068 -10000 0 -0.22 25 25
ABL1 0.035 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.047 0.022 -10000 0 -0.3 1 1
Rap1/GTP 0.022 0.091 -10000 0 -0.4 10 10
STAT3 -0.017 0.13 -10000 0 -0.34 70 70
axon guidance 0.026 0.06 -10000 0 -0.21 25 25
MAPK3 0.051 0.078 0.19 104 -0.23 5 109
MAPK1 0.052 0.078 0.19 107 -0.23 5 112
CDC42/GDP 0.069 0.085 0.24 29 -0.26 6 35
NTF3 0.024 0.054 -10000 0 -0.42 7 7
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.035 0.03 -10000 0 -0.25 3 3
PI3K 0.035 0.067 -10000 0 -0.3 18 18
FRS3 0.035 0.007 -10000 0 -10000 0 0
FAIM 0.034 0.021 -10000 0 -0.42 1 1
GAB1 0.027 0.061 -10000 0 -0.42 9 9
RASGRF1 0.007 0.06 0.22 18 -0.24 8 26
SOS1 0.034 0.021 -10000 0 -0.42 1 1
MCF2L 0.013 0.035 -10000 0 -0.25 8 8
RGS19 0.03 0.031 -10000 0 -0.42 2 2
CDC42 0.034 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.067 0.1 0.32 3 -0.37 8 11
Rac1/GDP 0.068 0.085 0.24 27 -0.26 6 33
NGF (dimer)/TRKA/GRIT 0.026 0.047 -10000 0 -0.25 11 11
neuron projection morphogenesis -0.001 0.19 0.44 2 -0.84 16 18
NGF (dimer)/TRKA/NEDD4-2 0.02 0.067 -10000 0 -0.25 26 26
MAP2K1 0.036 0.1 0.2 131 -0.22 6 137
NGFR 0.03 0.036 -10000 0 -0.42 3 3
NGF (dimer)/TRKA/GIPC/GAIP 0.017 0.044 -10000 0 -0.3 7 7
RAS family/GTP/PI3K 0.012 0.066 -10000 0 -0.24 28 28
FRS2 family/SHP2/GRB2/SOS1 0.088 0.046 -10000 0 -0.42 1 1
NRAS 0.029 0.05 -10000 0 -0.42 6 6
GRB2/SOS1 0.047 0.022 -10000 0 -0.3 1 1
PRKCI 0.024 0.067 -10000 0 -0.42 11 11
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.004 0.061 -10000 0 -0.42 6 6
RASA1 0.028 0.054 -10000 0 -0.42 7 7
TRKA/c-Abl 0.039 0.031 -10000 0 -0.3 2 2
SQSTM1 0.034 0.021 -10000 0 -0.42 1 1
BDNF (dimer)/TRKB/GIPC 0.067 0.064 -10000 0 -0.23 18 18
NGF (dimer)/TRKA/p62/Atypical PKCs 0.039 0.048 -10000 0 -0.22 11 11
MATK 0.031 0.03 -10000 0 -0.42 2 2
NEDD4L 0.006 0.11 -10000 0 -0.42 31 31
RAS family/GDP -0.012 0.036 -10000 0 -0.18 10 10
NGF (dimer)/TRKA 0.01 0.057 0.22 16 -0.27 5 21
Rac1/GTP -0.001 0.052 -10000 0 -0.22 14 14
FRS2 family/SHP2/CRK family 0.081 0.055 -10000 0 -0.22 6 6
Regulation of Androgen receptor activity

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 0.015 -10000 0 -0.3 1 1
SMARCC1 0.002 0.12 -10000 0 -1.1 5 5
REL 0.023 0.07 -10000 0 -0.42 12 12
HDAC7 -0.037 0.1 0.21 2 -0.32 35 37
JUN -0.001 0.12 -10000 0 -0.42 39 39
EP300 0.033 0.022 -10000 0 -0.42 1 1
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.001 0.058 -10000 0 -0.31 15 15
FOXO1 0 0 -10000 0 -10000 0 0
T-DHT/AR -0.009 0.13 0.27 1 -0.33 35 36
MAP2K6 0.011 0.08 -10000 0 -0.43 15 15
BRM/BAF57 0.047 0.024 -10000 0 -0.3 1 1
MAP2K4 0.022 0.031 -10000 0 -0.42 1 1
SMARCA2 0.033 0.022 -10000 0 -0.42 1 1
PDE9A -0.001 0.11 -10000 0 -0.98 4 4
NCOA2 0.025 0.047 -10000 0 -0.42 5 5
CEBPA 0.024 0.07 -10000 0 -0.42 12 12
EHMT2 0.036 0.005 -10000 0 -10000 0 0
cell proliferation 0.028 0.12 0.29 24 -0.35 12 36
NR0B1 0.03 0.036 -10000 0 -0.42 3 3
EGR1 -0.037 0.16 -10000 0 -0.42 75 75
RXRs/9cRA 0.047 0.052 -10000 0 -0.23 12 12
AR/RACK1/Src 0.004 0.098 0.28 5 -0.28 17 22
AR/GR -0.028 0.12 0.23 2 -0.24 91 93
GNB2L1 0.034 0.035 -10000 0 -0.42 3 3
PKN1 0.033 0.035 -10000 0 -0.42 3 3
RCHY1 0.022 0.075 -10000 0 -0.42 14 14
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.033 -10000 0 -0.31 3 3
T-DHT/AR/TIF2/CARM1 0.009 0.091 0.36 1 -0.29 13 14
SRC -0.009 0.073 0.19 37 -0.25 17 54
NR3C1 0.021 0.078 -10000 0 -0.42 15 15
KLK3 -0.016 0.093 -10000 0 -10000 0 0
APPBP2 0.024 0.024 -10000 0 -10000 0 0
TRIM24 0.035 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.032 0.07 0.14 1 -0.28 23 24
TMPRSS2 -0.14 0.38 -10000 0 -0.95 88 88
RXRG 0.021 0.058 -10000 0 -0.42 8 8
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.034 0.029 -10000 0 -0.42 2 2
RXRB 0.034 0.029 -10000 0 -0.42 2 2
CARM1 0.035 0.021 -10000 0 -0.42 1 1
NR2C2 0.034 0.008 -10000 0 -10000 0 0
KLK2 0.011 0.073 0.31 3 -0.29 2 5
AR -0.033 0.11 0.19 1 -0.24 92 93
SENP1 0.035 0.005 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 0.033 0.008 -10000 0 -10000 0 0
SRY 0.023 0.07 -10000 0 -0.42 12 12
GATA2 0.029 0.046 -10000 0 -0.42 5 5
MYST2 0.032 0.03 -10000 0 -0.42 2 2
HOXB13 0.023 0.018 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src 0 0.1 0.29 5 -0.28 19 24
positive regulation of transcription 0.029 0.046 -10000 0 -0.42 5 5
DNAJA1 0.023 0.042 -10000 0 -0.42 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.052 -10000 0 -0.29 14 14
NCOA1 0.035 0.054 -10000 0 -0.33 9 9
SPDEF -0.045 0.18 -10000 0 -0.42 90 90
T-DHT/AR/TIF2 0.015 0.078 0.24 8 -0.3 6 14
T-DHT/AR/Hsp90 -0.032 0.07 0.14 1 -0.28 23 24
GSK3B 0.035 0.006 -10000 0 -10000 0 0
NR2C1 0.029 0.054 -10000 0 -0.42 7 7
mol:T-DHT -0.009 0.072 0.21 29 -0.26 14 43
SIRT1 0.035 0.005 -10000 0 -10000 0 0
ZMIZ2 -0.001 0 -10000 0 -10000 0 0
POU2F1 0.016 0.054 -10000 0 -0.18 2 2
T-DHT/AR/DAX-1 -0.008 0.097 0.27 3 -0.29 22 25
CREBBP 0.032 0.011 -10000 0 -10000 0 0
SMARCE1 0.034 0.01 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.014 0.037 -10000 0 -0.25 12 12
ADCY5 -0.012 0.038 -10000 0 -0.25 12 12
ADCY6 -0.011 0.024 -10000 0 -0.25 5 5
ADCY7 -0.01 0.024 -10000 0 -0.25 5 5
ADCY1 -0.011 0.022 -10000 0 -0.25 4 4
ADCY2 -0.028 0.069 -10000 0 -0.25 43 43
ADCY3 -0.014 0.036 -10000 0 -0.25 11 11
ADCY8 -0.008 0.019 -10000 0 -0.25 3 3
PRKCE 0.006 0.03 -10000 0 -0.3 5 5
ADCY9 -0.016 0.046 -10000 0 -0.27 16 16
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.022 0.083 0.2 41 -0.26 6 47
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.034 0.021 -9999 0 -0.42 1 1
SPHK1 0.005 0.11 -9999 0 -0.42 30 30
GNAI2 0.027 0.057 -9999 0 -0.42 8 8
mol:S1P 0.001 0.066 -9999 0 -0.27 26 26
GNAO1 0.03 0.014 -9999 0 -10000 0 0
mol:Sphinganine-1-P -0.004 0.075 -9999 0 -0.3 30 30
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.04 0.07 -9999 0 -0.21 24 24
GNAI3 0.035 0.006 -9999 0 -10000 0 0
G12/G13 0.043 0.036 -9999 0 -0.3 4 4
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.011 0.099 -9999 0 -0.42 25 25
S1P1/S1P 0.022 0.09 -9999 0 -0.25 40 40
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 0.017 0.085 -9999 0 -0.42 18 18
S1P/S1P5/G12 0.029 0.067 -9999 0 -0.22 26 26
S1P/S1P3/Gq -0.003 0.095 -9999 0 -0.25 53 53
S1P/S1P4/Gi 0.002 0.095 -9999 0 -0.32 24 24
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.023 0.067 -9999 0 -0.42 11 11
GNA14 -0.01 0.13 -9999 0 -0.42 44 44
GNA15 0.029 0.046 -9999 0 -0.42 5 5
GNA12 0.035 0.006 -9999 0 -10000 0 0
GNA13 0.028 0.042 -9999 0 -0.42 4 4
GNA11 0.032 0.036 -9999 0 -0.42 3 3
ABCC1 0.029 0.042 -9999 0 -0.42 4 4
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.014 0.096 -10000 0 -1 4 4
MKNK1 0.035 0.006 -10000 0 -10000 0 0
MAPK14 0.031 0.048 -10000 0 -0.3 4 4
ATF2/c-Jun -0.022 0.16 -10000 0 -0.55 40 40
MAPK11 0.03 0.047 -10000 0 -0.3 4 4
MITF 0.021 0.051 -10000 0 -0.34 7 7
MAPKAPK5 0.023 0.043 -10000 0 -0.33 4 4
KRT8 0.01 0.075 -10000 0 -0.29 25 25
MAPKAPK3 0.034 0.008 -10000 0 -10000 0 0
MAPKAPK2 0.025 0.042 -10000 0 -0.42 4 4
p38alpha-beta/CK2 0.041 0.064 -10000 0 -0.43 4 4
CEBPB 0.018 0.053 -10000 0 -0.32 9 9
SLC9A1 0.023 0.042 -10000 0 -0.33 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.016 0.072 0.23 1 -0.31 10 11
p38alpha-beta/MNK1 0.056 0.06 -10000 0 -0.36 3 3
JUN -0.025 0.16 -10000 0 -0.55 40 40
PPARGC1A 0.016 0.068 -10000 0 -0.34 13 13
USF1 0.013 0.057 -10000 0 -0.29 13 13
RAB5/GDP/GDI1 0.024 0.053 -10000 0 -0.23 5 5
NOS2 0.016 0.042 -10000 0 -0.34 4 4
DDIT3 0.023 0.045 -10000 0 -0.32 5 5
RAB5A 0.035 0.006 -10000 0 -10000 0 0
HSPB1 -0.012 0.085 0.28 2 -0.26 48 50
p38alpha-beta/HBP1 0.053 0.067 -10000 0 -0.31 7 7
CREB1 0.015 0.062 -10000 0 -0.3 10 10
RAB5/GDP 0.026 0.004 -10000 0 -10000 0 0
EIF4E 0.016 0.044 0.24 2 -0.32 3 5
RPS6KA4 0.022 0.048 -10000 0 -0.36 5 5
PLA2G4A 0.001 0.066 -10000 0 -0.28 21 21
GDI1 0.023 0.045 -10000 0 -0.32 5 5
TP53 -0.001 0.062 -10000 0 -0.33 9 9
RPS6KA5 0.009 0.075 -10000 0 -0.28 27 27
ESR1 -0.054 0.14 -10000 0 -0.28 130 130
HBP1 0.032 0.036 -10000 0 -0.42 3 3
MEF2C 0.01 0.081 -10000 0 -0.33 23 23
MEF2A 0.022 0.044 -10000 0 -0.32 5 5
EIF4EBP1 0.009 0.067 -10000 0 -0.31 12 12
KRT19 -0.003 0.092 -10000 0 -0.29 42 42
ELK4 0.018 0.041 -10000 0 -0.31 4 4
ATF6 0.018 0.043 -10000 0 -0.32 5 5
ATF1 0.015 0.063 -10000 0 -0.3 10 10
p38alpha-beta/MAPKAPK2 0.042 0.069 -10000 0 -0.35 6 6
p38alpha-beta/MAPKAPK3 0.054 0.062 -10000 0 -0.35 4 4
Glypican 2 network

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
MDK 0.017 0.085 -9999 0 -0.42 18 18
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine 0.013 0.06 -9999 0 -0.3 18 18
neuron projection morphogenesis 0.013 0.06 -9999 0 -0.3 18 18
IL2 signaling events mediated by STAT5

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
GAB2 0.031 0.013 -10000 0 -10000 0 0
ELF1 0.013 0.099 -10000 0 -0.35 34 34
CCNA2 0.009 0.1 -10000 0 -0.42 28 28
PIK3CA 0.034 0.022 -10000 0 -0.42 1 1
JAK3 0.036 0.005 -10000 0 -10000 0 0
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
JAK1 0.032 0.036 -10000 0 -0.42 3 3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.021 0.14 0.25 2 -0.39 27 29
SHC1 0.028 0.025 -10000 0 -0.42 1 1
SP1 0.032 0.069 -10000 0 -0.36 14 14
IL2RA -0.025 0.17 -10000 0 -0.6 37 37
IL2RB 0.012 0.095 -10000 0 -0.42 23 23
SOS1 0.035 0.021 -10000 0 -0.42 1 1
IL2RG 0.031 0.041 -10000 0 -0.42 4 4
G1/S transition of mitotic cell cycle -0.019 0.19 -10000 0 -0.7 23 23
PTPN11 0.036 0.003 -10000 0 -10000 0 0
CCND2 0.005 0.11 -10000 0 -0.68 13 13
LCK -0.017 0.14 -10000 0 -0.42 54 54
GRB2 0.033 0.011 -10000 0 -10000 0 0
IL2 0.032 0.036 -10000 0 -0.42 3 3
CDK6 0.025 0.054 -10000 0 -0.42 7 7
CCND3 0.024 0.13 0.35 3 -0.44 8 11
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.014 0.057 -10000 0 -0.19 29 29
TRAF2/ASK1 0.029 0.065 -10000 0 -0.25 24 24
ATM 0.031 0.013 -10000 0 -10000 0 0
MAP2K3 -0.05 0.16 0.28 2 -0.39 67 69
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.04 0.14 0.29 1 -0.34 55 56
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.026 0.064 -10000 0 -0.42 10 10
TXN 0.009 0.002 -10000 0 -10000 0 0
CALM1 0.035 0.007 -10000 0 -10000 0 0
GADD45A 0.019 0.08 -10000 0 -0.42 16 16
GADD45B 0.024 0.067 -10000 0 -0.42 11 11
MAP3K1 0.01 0.099 -10000 0 -0.42 25 25
MAP3K6 0.034 0.022 -10000 0 -0.42 1 1
MAP3K7 0.033 0.01 -10000 0 -10000 0 0
MAP3K4 0.033 0.01 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.074 -10000 0 -0.3 23 23
TAK1/TAB family 0.014 0.037 -10000 0 -0.24 7 7
RAC1/OSM/MEKK3 0.058 0.026 -10000 0 -10000 0 0
TRAF2 0.033 0.029 -10000 0 -0.42 2 2
RAC1/OSM/MEKK3/MKK3 -0.017 0.13 -10000 0 -0.32 47 47
TRAF6 0.015 0.024 -10000 0 -0.29 3 3
RAC1 0.035 0.006 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.014 0.13 -10000 0 -0.42 48 48
CCM2 0.035 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.014 0.087 -10000 0 -0.25 48 48
MAPK11 0.033 0.01 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.017 0.1 -10000 0 -0.23 68 68
OSM/MEKK3 0.045 0.019 -10000 0 -10000 0 0
TAOK1 0.013 0.031 -10000 0 -0.29 5 5
TAOK2 0.015 0.008 -10000 0 -10000 0 0
TAOK3 0.015 0.015 -10000 0 -0.29 1 1
MAP3K7IP1 0.033 0.009 -10000 0 -10000 0 0
MAPK14 0.035 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0.031 0.03 -10000 0 -0.42 2 2
MAP3K5 0.013 0.093 -10000 0 -0.42 22 22
MAP3K10 0.022 0.075 -10000 0 -0.42 14 14
MAP3K3 0.031 0.012 -10000 0 -10000 0 0
TRX/ASK1 0.017 0.059 -10000 0 -0.21 29 29
GADD45/MTK1/MTK1 0.054 0.081 -10000 0 -0.23 33 33
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.045 0.037 -10000 0 -0.3 5 5
CRKL 0.007 0.1 0.27 3 -0.46 14 17
mol:PIP3 0.01 0.066 0.39 9 -0.84 1 10
AKT1 0.02 0.084 0.41 1 -0.74 1 2
PTK2B 0.028 0.015 -10000 0 -10000 0 0
RAPGEF1 0.004 0.095 0.3 1 -0.43 14 15
RANBP10 0.029 0.014 -10000 0 -10000 0 0
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
HGF/MET/SHIP2 0.054 0.059 -10000 0 -0.26 15 15
MAP3K5 0.001 0.11 0.26 2 -0.43 15 17
HGF/MET/CIN85/CBL/ENDOPHILINS 0.064 0.073 -10000 0 -0.25 20 20
AP1 -0.024 0.13 -10000 0 -0.3 89 89
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.027 0.025 -10000 0 -0.42 1 1
apoptosis -0.14 0.34 -10000 0 -0.77 111 111
STAT3 (dimer) 0.009 0.067 -10000 0 -0.31 6 6
GAB1/CRKL/SHP2/PI3K 0.042 0.12 0.32 1 -0.41 16 17
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.024 0.095 -10000 0 -0.43 13 13
PTPN11 0.036 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.033 0.009 -10000 0 -10000 0 0
PTEN 0.026 0.061 -10000 0 -0.42 9 9
ELK1 -0.002 0.071 0.27 16 -10000 0 16
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.014 0.046 -10000 0 -0.2 7 7
PAK1 0.026 0.1 0.4 9 -0.71 1 10
HGF/MET/RANBP10 0.049 0.057 -10000 0 -0.25 13 13
HRAS 0.013 0.1 -10000 0 -0.48 14 14
DOCK1 0.003 0.097 0.3 2 -0.43 14 16
GAB1 0.008 0.1 -10000 0 -0.47 14 14
CRK 0.006 0.095 -10000 0 -0.44 14 14
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.1 -10000 0 -0.46 16 16
JUN -0.001 0.12 -10000 0 -0.42 39 39
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.006 0.045 -10000 0 -0.21 18 18
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
cell morphogenesis 0.007 0.1 0.34 4 -0.34 9 13
GRB2/SHC 0.032 0.054 -10000 0 -0.21 9 9
FOS -0.031 0.15 -10000 0 -0.42 66 66
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility -0.002 0.071 0.27 16 -10000 0 16
HGF/MET/MUC20 0.038 0.048 -10000 0 -0.25 13 13
cell migration 0.031 0.053 -10000 0 -0.21 9 9
GRB2 0.033 0.01 -10000 0 -10000 0 0
CBL 0.031 0.012 -10000 0 -10000 0 0
MET/RANBP10 0.038 0.039 -10000 0 -0.29 5 5
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.014 0.055 -10000 0 -0.23 16 16
MET/MUC20 0.021 0.033 -10000 0 -0.3 5 5
RAP1B 0.008 0.097 0.28 6 -0.41 13 19
RAP1A 0.001 0.095 0.28 1 -0.42 16 17
HGF/MET/RANBP9 0.058 0.055 -10000 0 -0.26 13 13
RAF1 0.017 0.1 -10000 0 -0.46 14 14
STAT3 0.009 0.068 -10000 0 -0.31 6 6
cell proliferation 0.043 0.1 0.28 20 -0.32 9 29
RPS6KB1 0.008 0.048 -10000 0 -0.28 11 11
MAPK3 -0.017 0.082 0.68 5 -10000 0 5
MAPK1 0.007 0.15 0.62 28 -10000 0 28
RANBP9 0.035 0.007 -10000 0 -10000 0 0
MAPK8 0.011 0.1 0.27 1 -0.38 17 18
SRC 0.008 0.062 -10000 0 -0.26 5 5
PI3K 0.031 0.077 -10000 0 -0.23 26 26
MET/Glomulin 0.019 0.04 -10000 0 -0.25 6 6
SOS1 0.034 0.021 -10000 0 -0.42 1 1
MAP2K1 0.015 0.097 -10000 0 -0.44 13 13
MET 0.028 0.046 -10000 0 -0.42 5 5
MAP4K1 0.008 0.1 0.28 1 -0.45 14 15
PTK2 0.027 0.015 -10000 0 -10000 0 0
MAP2K2 0.014 0.099 -10000 0 -0.43 15 15
BAD 0.016 0.079 0.37 1 -0.71 1 2
MAP2K4 -0.001 0.099 0.25 1 -0.4 15 16
SHP2/GRB2/SOS1/GAB1 0.044 0.095 -10000 0 -0.37 16 16
INPPL1 0.03 0.036 -10000 0 -0.42 3 3
PXN 0.036 0.004 -10000 0 -10000 0 0
SH3KBP1 0.027 0.061 -10000 0 -0.42 9 9
HGS -0.001 0.041 -10000 0 -0.19 20 20
PLCgamma1/PKC 0.025 0.007 -10000 0 -10000 0 0
HGF 0.028 0.057 -10000 0 -0.42 8 8
RASA1 0.028 0.054 -10000 0 -0.42 7 7
NCK1 0.034 0.021 -10000 0 -0.42 1 1
PTPRJ 0.03 0.046 -10000 0 -0.42 5 5
NCK/PLCgamma1 0.046 0.055 -10000 0 -0.19 15 15
PDPK1 0.025 0.087 0.35 2 -0.78 1 3
HGF/MET/SHIP 0.038 0.048 -10000 0 -0.25 13 13
FoxO family 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
G6PC 0.041 0.096 -10000 0 -1.3 1 1
PLK1 0.01 0.2 -10000 0 -0.79 12 12
CDKN1B 0.044 0.16 -10000 0 -0.46 29 29
FOXO3 -0.007 0.22 -10000 0 -0.76 19 19
KAT2B 0.001 0.019 -10000 0 -0.043 65 65
FOXO1/SIRT1 0.045 0.053 -10000 0 -0.32 2 2
CAT -0.009 0.23 -10000 0 -0.99 13 13
CTNNB1 0.024 0.067 -10000 0 -0.42 11 11
AKT1 0.027 0.05 -10000 0 -0.41 3 3
FOXO1 0.027 0.053 0.24 1 -0.3 3 4
MAPK10 0.007 0.06 0.2 8 -0.21 25 33
mol:GTP 0 0.002 -10000 0 -10000 0 0
FOXO4 0.016 0.098 0.28 1 -0.31 21 22
response to oxidative stress 0.004 0.02 -10000 0 -0.054 23 23
FOXO3A/SIRT1 0.019 0.2 -10000 0 -0.64 19 19
XPO1 0.035 0.005 -10000 0 -10000 0 0
EP300 0.035 0.023 -10000 0 -0.42 1 1
BCL2L11 0.028 0.086 -10000 0 -1.2 2 2
FOXO1/SKP2 0.042 0.049 -10000 0 -0.3 2 2
mol:GDP 0.004 0.02 -10000 0 -0.054 23 23
RAN 0.036 0.005 -10000 0 -10000 0 0
GADD45A 0.013 0.22 -10000 0 -0.77 28 28
YWHAQ 0.033 0.029 -10000 0 -0.42 2 2
FOXO1/14-3-3 family 0.039 0.12 -10000 0 -0.42 13 13
MST1 0.027 0.036 -10000 0 -10000 0 0
CSNK1D 0.033 0.009 -10000 0 -10000 0 0
CSNK1E 0.033 0.009 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.008 0.13 -10000 0 -0.4 27 27
YWHAB 0.034 0.009 -10000 0 -10000 0 0
MAPK8 0.017 0.043 0.19 9 -0.21 7 16
MAPK9 0.008 0.059 0.2 7 -0.22 23 30
YWHAG 0.035 0.005 -10000 0 -10000 0 0
YWHAE 0.032 0.011 -10000 0 -10000 0 0
YWHAZ 0.026 0.016 -10000 0 -10000 0 0
SIRT1 0.036 0.02 -10000 0 -10000 0 0
SOD2 0.031 0.16 -10000 0 -0.62 12 12
RBL2 -0.078 0.31 -10000 0 -0.71 83 83
RAL/GDP 0.045 0.037 -10000 0 -0.24 4 4
CHUK 0.018 0.074 -10000 0 -0.42 11 11
Ran/GTP 0.026 0.01 -10000 0 -10000 0 0
CSNK1G2 0.033 0.029 -10000 0 -0.42 2 2
RAL/GTP 0.046 0.038 -10000 0 -0.22 4 4
CSNK1G1 0.035 0.007 -10000 0 -10000 0 0
FASLG -0.092 0.4 -10000 0 -1.4 45 45
SKP2 0.034 0.009 -10000 0 -10000 0 0
USP7 0.032 0.011 -10000 0 -10000 0 0
IKBKB 0.023 0.035 -10000 0 -10000 0 0
CCNB1 -0.052 0.33 -10000 0 -1.1 37 37
FOXO1-3a-4/beta catenin 0.038 0.16 0.42 1 -0.41 29 30
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.049 -10000 0 -0.3 2 2
CSNK1A1 0.035 0.005 -10000 0 -10000 0 0
SGK1 0.001 0.019 -10000 0 -0.043 65 65
CSNK1G3 0.035 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.048 0.013 -10000 0 -10000 0 0
ZFAND5 0.017 0.084 0.26 1 -0.26 20 21
SFN 0.011 0.099 -10000 0 -0.42 25 25
CDK2 0.036 0.03 -10000 0 -0.42 2 2
FOXO3A/14-3-3 0.015 0.12 -10000 0 -0.38 24 24
CREBBP 0.035 0.013 -10000 0 -10000 0 0
FBXO32 0.019 0.31 -10000 0 -1.2 21 21
BCL6 -0.008 0.27 -10000 0 -1.1 21 21
RALB 0.032 0.041 -10000 0 -0.42 4 4
RALA 0.035 0.007 -10000 0 -10000 0 0
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.034 0.021 -10000 0 -0.42 1 1
HDAC3 0.035 0.005 -10000 0 -10000 0 0
VDR 0.02 0.082 -10000 0 -0.42 17 17
Cbp/p300/PCAF 0.04 0.023 -10000 0 -0.24 1 1
EP300 0.033 0.022 -10000 0 -0.42 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.015 0.056 0.19 1 -0.31 4 5
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.035 0.005 -10000 0 -10000 0 0
AKT1 0.027 0.092 0.21 54 -0.23 17 71
RAR alpha/9cRA/Cyclin H 0.044 0.1 0.26 1 -0.35 7 8
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.019 0.064 -10000 0 -0.22 16 16
CDC2 0.01 0.094 -10000 0 -0.42 22 22
response to UV -0.002 0.008 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.03 0.062 -10000 0 -0.27 10 10
NCOR2 0.035 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.058 -10000 0 -0.3 17 17
RXRs/RARs/NRIP1/9cRA -0.003 0.19 -10000 0 -0.53 52 52
NCOA2 0.024 0.047 -10000 0 -0.42 5 5
NCOA3 0.03 0.036 -10000 0 -0.42 3 3
NCOA1 0.031 0.045 -10000 0 -0.42 5 5
VDR/VDR/DNA 0.02 0.082 -10000 0 -0.42 17 17
RARG 0.031 0.017 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.046 0.01 -10000 0 -10000 0 0
MAPK3 0.026 0.029 -10000 0 -0.42 1 1
MAPK1 0.033 0.022 -10000 0 -0.42 1 1
MAPK8 0.027 0.041 -10000 0 -0.42 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.027 0.13 -10000 0 -0.42 11 11
RARA 0.009 0.047 -10000 0 -0.23 12 12
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.015 0.053 -10000 0 -0.33 3 3
PRKCA 0.024 0.032 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.008 0.2 -10000 0 -0.57 51 51
RXRG 0.01 0.047 -10000 0 -0.29 7 7
RXRA 0.016 0.09 -10000 0 -0.34 7 7
RXRB 0.017 0.037 -10000 0 -0.28 2 2
VDR/Vit D3/DNA 0.015 0.058 -10000 0 -0.3 17 17
RBP1 -0.028 0.15 -10000 0 -0.42 67 67
CRBP1/9-cic-RA -0.019 0.11 -10000 0 -0.3 67 67
RARB 0.011 0.09 -10000 0 -0.42 20 20
PRKCG 0.028 0.031 -10000 0 -10000 0 0
MNAT1 0.035 0.007 -10000 0 -10000 0 0
RAR alpha/RXRs 0.004 0.14 0.42 1 -0.43 15 16
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.029 0.11 0.27 1 -0.37 11 12
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.074 0.23 1 -0.33 6 7
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.009 0.2 -10000 0 -0.58 51 51
positive regulation of DNA binding 0.033 0.094 -10000 0 -0.33 7 7
NRIP1 -0.071 0.38 -10000 0 -1.2 51 51
RXRs/RARs 0.011 0.16 -10000 0 -0.44 38 38
RXRs/RXRs/DNA/9cRA -0.008 0.11 -10000 0 -0.38 10 10
PRKACA 0.035 0.004 -10000 0 -10000 0 0
CDK7 0.034 0.008 -10000 0 -10000 0 0
TFIIH 0.067 0.024 -10000 0 -0.24 1 1
RAR alpha/9cRA 0.065 0.067 -10000 0 -0.22 3 3
CCNH 0.034 0.021 -10000 0 -0.42 1 1
CREBBP 0.032 0.011 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.064 0.028 -10000 0 -0.2 1 1
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.028 0.057 -9999 0 -0.42 8 8
mol:S1P 0.001 0.002 -9999 0 -0.026 2 2
S1P1/S1P/Gi -0.017 0.11 -9999 0 -0.3 43 43
GNAO1 0.03 0.015 -9999 0 -10000 0 0
S1P/S1P3/G12/G13 0.039 0.03 -9999 0 -0.23 4 4
AKT1 0.005 0.12 -9999 0 -0.47 27 27
AKT3 -0.002 0.11 -9999 0 -0.78 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.028 0.057 -9999 0 -0.42 8 8
GNAI2 0.028 0.058 -9999 0 -0.42 8 8
GNAI3 0.036 0.008 -9999 0 -10000 0 0
GNAI1 0.018 0.085 -9999 0 -0.42 18 18
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.001 0.002 -9999 0 -0.03 2 2
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.011 0.099 -9999 0 -0.42 25 25
mol:Ca2+ 0.006 0.08 -9999 0 -0.3 20 20
MAPK3 -0.001 0.073 -9999 0 -0.33 12 12
MAPK1 0 0.074 -9999 0 -0.3 18 18
JAK2 -0.013 0.1 -9999 0 -0.34 26 26
CXCR4 -0.015 0.1 -9999 0 -0.35 26 26
FLT1 0.028 0.055 -9999 0 -0.42 7 7
RhoA/GDP 0.019 0.043 -9999 0 -0.3 9 9
Rac1/GDP 0.026 0.004 -9999 0 -10000 0 0
SRC -0.004 0.079 -9999 0 -0.33 15 15
S1P/S1P3/Gi 0.006 0.081 -9999 0 -0.31 20 20
RAC1 0.035 0.006 -9999 0 -10000 0 0
RhoA/GTP 0.005 0.094 -9999 0 -0.3 19 19
VEGFA 0.002 0.003 -9999 0 -0.04 2 2
S1P/S1P2/Gi 0.004 0.079 -9999 0 -0.29 22 22
VEGFR1 homodimer/VEGFA homodimer 0.025 0.04 -9999 0 -0.3 7 7
RHOA 0.026 0.061 -9999 0 -0.42 9 9
S1P/S1P3/Gq -0.007 0.079 -9999 0 -0.22 56 56
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.024 0.067 -9999 0 -0.42 11 11
G12/G13 0.043 0.036 -9999 0 -0.3 4 4
GNA14 -0.01 0.13 -9999 0 -0.42 44 44
GNA15 0.029 0.046 -9999 0 -0.42 5 5
GNA12 0.035 0.006 -9999 0 -10000 0 0
GNA13 0.028 0.042 -9999 0 -0.42 4 4
GNA11 0.032 0.036 -9999 0 -0.42 3 3
Rac1/GTP 0.008 0.09 -9999 0 -0.31 16 16
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 -10000 0 0
CDC42/GTP 0.002 0.087 -10000 0 -0.27 20 20
PLCG1 -0.008 0.073 -10000 0 -0.29 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.057 -10000 0 -0.42 8 8
GNAI3 0.035 0.006 -10000 0 -10000 0 0
G12/G13 0.043 0.036 -10000 0 -0.3 4 4
cell migration 0.002 0.085 -10000 0 -0.27 20 20
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.006 0.07 -10000 0 -0.28 18 18
MAPK1 -0.005 0.071 -10000 0 -0.23 38 38
S1P/S1P5/Gi 0 0.077 -10000 0 -0.24 40 40
GNAI1 0.017 0.085 -10000 0 -0.42 18 18
CDC42/GDP 0.025 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.024 0.004 -10000 0 -10000 0 0
RHOA 0.031 0.069 0.19 59 -0.24 12 71
S1P/S1P4/Gi 0 0.077 -10000 0 -0.24 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.023 0.067 -10000 0 -0.42 11 11
S1P/S1P4/G12/G13 0.037 0.029 -10000 0 -0.23 4 4
GNA12 0.035 0.006 -10000 0 -10000 0 0
GNA13 0.028 0.042 -10000 0 -0.42 4 4
CDC42 0.034 0.007 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.001 0.09 0.25 30 -10000 0 30
GNAI2 0.027 0.057 -10000 0 -0.42 8 8
S1P/S1P5/G12 0.024 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.03 0.014 -10000 0 -10000 0 0
RhoA/GTP -0.001 0.092 -10000 0 -0.26 30 30
negative regulation of cAMP metabolic process 0 0.077 -10000 0 -0.24 40 40
GNAZ 0.023 0.067 -10000 0 -0.42 11 11
GNAI3 0.035 0.006 -10000 0 -10000 0 0
GNA12 0.035 0.006 -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 0.077 -10000 0 -0.24 40 40
RhoA/GDP 0.019 0.043 -10000 0 -0.3 9 9
RHOA 0.026 0.061 -10000 0 -0.42 9 9
GNAI1 0.017 0.085 -10000 0 -0.42 18 18
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.035 0.006 -10000 0 -10000 0 0
NFATC1 0.019 0.092 0.3 2 -0.38 9 11
NFATC2 0.018 0.049 0.16 1 -0.19 7 8
NFATC3 0.013 0.007 -10000 0 -10000 0 0
YWHAE 0.032 0.011 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.019 0.091 0.21 4 -0.35 11 15
Exportin 1/Ran/NUP214 0.069 0.022 -10000 0 -0.26 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.042 0.086 -10000 0 -0.44 4 4
BCL2/BAX -0.018 0.14 -10000 0 -0.3 95 95
CaM/Ca2+/Calcineurin A alpha-beta B1 0.027 0.006 -10000 0 -10000 0 0
CaM/Ca2+ 0.027 0.006 -10000 0 -10000 0 0
BAX 0.035 0.007 -10000 0 -10000 0 0
MAPK14 0.036 0.005 -10000 0 -10000 0 0
BAD 0.034 0.021 -10000 0 -0.42 1 1
CABIN1/MEF2D 0.029 0.083 -10000 0 -0.37 7 7
Calcineurin A alpha-beta B1/BCL2 -0.057 0.18 -10000 0 -0.42 99 99
FKBP8 0.035 0.005 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.029 0.082 0.36 7 -10000 0 7
KPNB1 0.031 0.041 -10000 0 -0.42 4 4
KPNA2 0.023 0.061 -10000 0 -0.42 9 9
XPO1 0.035 0.005 -10000 0 -10000 0 0
SFN 0.011 0.099 -10000 0 -0.42 25 25
MAP3K8 0.003 0.11 -10000 0 -0.42 32 32
NFAT4/CK1 alpha 0.016 0.056 -10000 0 -0.21 23 23
MEF2D/NFAT1/Cbp/p300 0.055 0.064 -10000 0 -0.22 3 3
CABIN1 0.02 0.09 0.21 4 -0.37 10 14
CALM1 0.035 0.007 -10000 0 -10000 0 0
RAN 0.035 0.005 -10000 0 -10000 0 0
MAP3K1 0.01 0.099 -10000 0 -0.42 25 25
CAMK4 0.032 0.03 -10000 0 -0.42 2 2
mol:Ca2+ 0.001 0.001 -10000 0 -10000 0 0
MAPK3 0.032 0.023 -10000 0 -0.42 1 1
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
Calcineurin A alpha-beta B1/AKAP79/PKA 0.023 0.092 -10000 0 -0.3 37 37
YWHAB 0.034 0.009 -10000 0 -10000 0 0
MAPK8 0.033 0.035 -10000 0 -0.42 3 3
MAPK9 0.018 0.087 -10000 0 -0.42 19 19
YWHAG 0.035 0.005 -10000 0 -10000 0 0
FKBP1A 0.034 0.008 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.031 0.092 0.28 2 -0.35 9 11
PRKCH 0.03 0.046 -10000 0 -0.42 5 5
CABIN1/Cbp/p300 0.045 0.025 -10000 0 -0.28 1 1
CASP3 0.035 0.008 -10000 0 -10000 0 0
PIM1 0.035 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.024 0.005 -10000 0 -10000 0 0
apoptosis 0.002 0.048 -10000 0 -0.29 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.029 0.058 -10000 0 -0.22 2 2
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.031 0.045 -10000 0 -0.42 5 5
JNK2/NFAT4 -0.002 0.08 -10000 0 -0.16 101 101
BAD/BCL-XL 0.049 0.02 -10000 0 -0.3 1 1
PRKCD 0.032 0.03 -10000 0 -0.42 2 2
NUP214 0.034 0.021 -10000 0 -0.42 1 1
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.031 0.012 -10000 0 -10000 0 0
PRKCG 0.036 0 -10000 0 -10000 0 0
PRKCQ 0.025 0.054 -10000 0 -0.42 7 7
FKBP38/BCL2 -0.019 0.14 -10000 0 -0.3 97 97
EP300 0.033 0.022 -10000 0 -0.42 1 1
PRKCB1 0.003 0.11 -10000 0 -0.42 29 29
CSNK2A1 0.034 0.008 -10000 0 -10000 0 0
NFATc/JNK1 0.036 0.096 0.31 2 -0.36 9 11
CaM/Ca2+/FKBP38 0.047 0.011 -10000 0 -10000 0 0
FKBP12/FK506 0.025 0.006 -10000 0 -10000 0 0
CSNK1A1 0.018 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.045 0.023 -10000 0 -0.25 2 2
NFATc/ERK1 0.033 0.092 0.31 2 -0.35 8 10
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.05 0.096 -10000 0 -0.38 7 7
NR4A1 0.064 0.078 0.23 14 -0.43 1 15
GSK3B 0.036 0.005 -10000 0 -10000 0 0
positive T cell selection 0.013 0.007 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.021 0.036 -10000 0 -0.18 2 2
RCH1/ KPNB1 0.037 0.056 -10000 0 -0.3 12 12
YWHAQ 0.033 0.029 -10000 0 -0.42 2 2
PRKACA 0.036 0.005 -10000 0 -10000 0 0
AKAP5 -0.001 0.12 -10000 0 -0.42 38 38
MEF2D 0.028 0.015 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.026 0.016 -10000 0 -10000 0 0
NFATc/p38 alpha 0.037 0.094 0.33 1 -0.36 9 10
CREBBP 0.033 0.011 -10000 0 -10000 0 0
BCL2 -0.057 0.18 -10000 0 -0.42 99 99
Effects of Botulinum toxin

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
STX1A 0.009 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.046 0.027 -10000 0 -0.3 2 2
STXBP1 0.035 0.005 -10000 0 -10000 0 0
ACh/CHRNA1 0.015 0.046 -10000 0 -0.14 25 25
RAB3GAP2/RIMS1/UNC13B 0.051 0.039 -10000 0 -0.25 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.031 0.012 -10000 0 -10000 0 0
mol:ACh -0.005 0.03 0.087 4 -0.11 18 22
RAB3GAP2 0.028 0.025 -10000 0 -0.42 1 1
STX1A/SNAP25/VAMP2 0.033 0.057 -10000 0 -0.18 3 3
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.015 0.046 -10000 0 -0.14 25 25
UNC13B 0.032 0.03 -10000 0 -0.42 2 2
CHRNA1 0.029 0.053 -10000 0 -0.42 7 7
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.043 0.11 -10000 0 -0.27 97 97
SNAP25 -0.001 0.043 -10000 0 -0.26 14 14
VAMP2 0.005 0.011 -10000 0 -0.23 1 1
SYT1 -0.063 0.18 -10000 0 -0.42 97 97
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.032 0.007 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.033 0.057 -10000 0 -0.18 3 3
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.035 0.073 -10000 0 -0.32 20 20
AKT1 0.011 0.12 0.32 1 -0.43 15 16
PTK2B 0 0.091 0.36 1 -0.51 8 9
VEGFR2 homodimer/Frs2 0.029 0.075 -10000 0 -0.39 11 11
CAV1 0.028 0.05 -10000 0 -0.42 6 6
CALM1 0.035 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.026 0.08 -10000 0 -0.38 11 11
endothelial cell proliferation 0.036 0.12 0.31 15 -0.45 8 23
mol:Ca2+ 0.005 0.096 -10000 0 -0.48 9 9
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.044 0.084 -10000 0 -0.48 7 7
RP11-342D11.1 -0.011 0.096 -10000 0 -0.47 10 10
CDH5 0.027 0.037 -10000 0 -0.42 3 3
VEGFA homodimer 0.037 0.086 -10000 0 -0.24 43 43
SHC1 0.027 0.025 -10000 0 -0.42 1 1
SHC2 -0.026 0.16 -10000 0 -0.42 67 67
HRAS/GDP 0.019 0.09 -10000 0 -0.42 8 8
SH2D2A -0.001 0.1 -10000 0 -0.42 29 29
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.037 0.11 -10000 0 -0.45 13 13
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.005 0.097 -10000 0 -0.28 37 37
VEGFR1 homodimer 0.026 0.054 -10000 0 -0.42 7 7
SHC/GRB2/SOS1 0.041 0.11 -10000 0 -0.46 8 8
GRB10 -0.003 0.12 -10000 0 -0.51 20 20
PTPN11 0.036 0.003 -10000 0 -10000 0 0
GRB2 0.033 0.01 -10000 0 -10000 0 0
PAK1 0.014 0.085 -10000 0 -0.42 18 18
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.042 0.1 -10000 0 -0.46 10 10
HRAS 0.032 0.036 -10000 0 -0.42 3 3
VEGF/Rho/ROCK1/Integrin Complex 0.004 0.1 -10000 0 -0.37 23 23
HIF1A -0.007 0.13 -10000 0 -0.42 45 45
FRS2 0.033 0.022 -10000 0 -0.42 1 1
oxygen and reactive oxygen species metabolic process 0.042 0.082 -10000 0 -0.47 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.035 0.006 -10000 0 -10000 0 0
Nck/Pak 0.031 0.068 -10000 0 -0.3 19 19
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.022 0.092 -10000 0 -0.38 15 15
mol:GDP 0.029 0.097 -10000 0 -0.44 8 8
mol:NADP 0.021 0.1 -10000 0 -0.42 11 11
eNOS/Hsp90 0.019 0.096 -10000 0 -0.4 11 11
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
mol:IP3 0.005 0.097 -10000 0 -0.49 9 9
HIF1A/ARNT 0.02 0.099 -10000 0 -0.3 43 43
SHB 0.03 0.046 -10000 0 -0.42 5 5
VEGFA -0.002 0.016 -10000 0 -10000 0 0
VEGFC 0.022 0.072 -10000 0 -0.42 13 13
FAK1/Vinculin 0.015 0.12 0.36 1 -0.5 11 12
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.026 0.061 -10000 0 -0.42 9 9
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.033 0.1 -10000 0 -0.5 9 9
PTPN6 0.032 0.03 -10000 0 -0.42 2 2
EPAS1 0.029 0.071 -10000 0 -0.39 12 12
mol:L-citrulline 0.021 0.1 -10000 0 -0.42 11 11
ITGAV 0.021 0.08 -10000 0 -0.42 16 16
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.041 0.08 -10000 0 -0.47 6 6
VEGFR2 homodimer/VEGFA homodimer 0.022 0.11 -10000 0 -0.33 35 35
VEGFR2/3 heterodimer 0.03 0.076 -10000 0 -0.42 10 10
VEGFB 0.034 0.021 -10000 0 -0.42 1 1
MAPK11 -0.015 0.11 0.26 1 -0.44 16 17
VEGFR2 homodimer 0.012 0.081 -10000 0 -0.46 11 11
FLT1 0.026 0.054 -10000 0 -0.42 7 7
NEDD4 0.02 0.074 -10000 0 -0.42 12 12
MAPK3 0.005 0.095 0.26 10 -0.41 9 19
MAPK1 0 0.095 0.25 6 -0.43 9 15
VEGFA145/NRP2 0.023 0.024 -10000 0 -0.32 1 1
VEGFR1/2 heterodimer 0.024 0.085 -10000 0 -0.37 16 16
KDR 0.012 0.081 -10000 0 -0.46 11 11
VEGFA165/NRP1/VEGFR2 homodimer 0.023 0.11 -10000 0 -0.47 11 11
SRC 0.032 0.03 -10000 0 -0.42 2 2
platelet activating factor biosynthetic process 0.005 0.099 0.28 4 -0.43 9 13
PI3K 0.006 0.12 -10000 0 -0.5 14 14
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.027 0.082 -10000 0 -0.5 7 7
FES 0 0.11 -10000 0 -0.54 9 9
GAB1 0.016 0.12 -10000 0 -0.42 22 22
VEGFR2 homodimer/VEGFA homodimer/Src 0.026 0.079 -10000 0 -0.42 9 9
CTNNB1 0.024 0.067 -10000 0 -0.42 11 11
SOS1 0.034 0.021 -10000 0 -0.42 1 1
ARNT 0.035 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.032 0.11 -10000 0 -0.42 12 12
VEGFR2 homodimer/VEGFA homodimer/Yes 0.023 0.087 -10000 0 -0.45 9 9
PI3K/GAB1 0.02 0.13 0.28 1 -0.44 18 19
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.042 0.096 -10000 0 -0.43 7 7
PRKACA 0.035 0.004 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.041 0.095 -10000 0 -0.4 14 14
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 0.003 0.1 -10000 0 -0.51 9 9
actin cytoskeleton reorganization 0.005 0.096 -10000 0 -0.28 37 37
PTK2 -0.005 0.1 -10000 0 -0.55 11 11
EDG1 -0.008 0.14 -10000 0 -0.53 27 27
mol:DAG 0.005 0.097 -10000 0 -0.49 9 9
CaM/Ca2+ 0.02 0.095 -10000 0 -0.47 8 8
MAP2K3 -0.012 0.099 -10000 0 -0.47 11 11
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.015 0.13 -10000 0 -0.52 20 20
PLCG1 0.005 0.098 -10000 0 -0.5 9 9
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.04 0.086 -10000 0 -0.42 8 8
IQGAP1 0.034 0.008 -10000 0 -10000 0 0
YES1 0.029 0.05 -10000 0 -0.42 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.028 0.082 -10000 0 -0.47 8 8
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.027 0.081 -10000 0 -0.5 7 7
cell migration 0.018 0.1 0.31 2 -0.49 9 11
mol:PI-3-4-5-P3 0.007 0.12 -10000 0 -0.46 14 14
FYN 0.027 0.05 -10000 0 -0.42 6 6
VEGFB/NRP1 0.009 0.1 -10000 0 -0.5 9 9
mol:NO 0.021 0.1 -10000 0 -0.42 11 11
PXN 0.036 0.004 -10000 0 -10000 0 0
HRAS/GTP 0.003 0.082 -10000 0 -0.42 8 8
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.004 0.13 -10000 0 -0.51 20 20
VHL 0.035 0.007 -10000 0 -10000 0 0
ITGB3 0.028 0.046 -10000 0 -0.42 5 5
NOS3 0.02 0.11 -10000 0 -0.48 11 11
VEGFR2 homodimer/VEGFA homodimer/Sck -0.006 0.12 -10000 0 -0.26 70 70
RAC1 0.035 0.006 -10000 0 -10000 0 0
PRKCA -0.005 0.083 -10000 0 -0.46 7 7
PRKCB -0.008 0.088 -10000 0 -0.46 9 9
VCL 0.035 0.021 -10000 0 -0.42 1 1
VEGFA165/NRP1 -0.007 0.096 -10000 0 -0.3 34 34
VEGFR1/2 heterodimer/VEGFA homodimer 0.021 0.089 -10000 0 -0.35 16 16
VEGFA165/NRP2 0.023 0.024 -10000 0 -0.32 1 1
MAPKKK cascade 0.033 0.13 0.37 5 -0.45 15 20
NRP2 0.034 0.021 -10000 0 -0.42 1 1
VEGFC homodimer 0.022 0.072 -10000 0 -0.42 13 13
NCK1 0.034 0.021 -10000 0 -0.42 1 1
ROCK1 0.035 0.005 -10000 0 -10000 0 0
FAK1/Paxillin 0.016 0.12 0.36 1 -0.49 12 13
MAP3K13 0 0.11 -10000 0 -0.49 11 11
PDPK1 -0.002 0.099 0.25 2 -0.4 15 17
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.024 0.16 -10000 0 -0.8 13 13
NCK1/PAK1/Dok-R -0.028 0.075 -10000 0 -0.39 13 13
NCK1/Dok-R 0.032 0.14 -10000 0 -0.86 9 9
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
mol:beta2-estradiol -0.007 0.015 0.31 1 -10000 0 1
RELA 0.035 0.006 -10000 0 -10000 0 0
SHC1 0.028 0.025 -10000 0 -0.42 1 1
Rac/GDP 0.026 0.004 -10000 0 -10000 0 0
F2 0.012 0.025 -10000 0 -10000 0 0
TNIP2 0.032 0.03 -10000 0 -0.42 2 2
NF kappa B/RelA 0.063 0.14 -10000 0 -0.79 9 9
FN1 -0.009 0.13 -10000 0 -0.42 48 48
PLD2 0.02 0.13 -10000 0 -0.85 9 9
PTPN11 0.036 0.003 -10000 0 -10000 0 0
GRB14 -0.063 0.18 -10000 0 -0.42 98 98
ELK1 0.025 0.13 -10000 0 -0.78 10 10
GRB7 0.023 0.058 -10000 0 -0.42 8 8
PAK1 0.014 0.085 -10000 0 -0.42 18 18
Tie2/Ang1/alpha5/beta1 Integrin 0.042 0.16 -10000 0 -0.88 9 9
CDKN1A 0.002 0.19 -10000 0 -0.73 25 25
ITGA5 0.033 0.035 -10000 0 -0.42 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.028 0.15 -10000 0 -0.86 9 9
CRK 0.031 0.023 -10000 0 -0.42 1 1
mol:NO 0.027 0.13 -10000 0 -0.59 12 12
PLG 0.02 0.13 -10000 0 -0.85 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.018 0.15 -10000 0 -0.82 10 10
GRB2 0.033 0.01 -10000 0 -10000 0 0
PIK3R1 0.018 0.083 -10000 0 -0.42 17 17
ANGPT2 -0.055 0.21 -10000 0 -0.69 28 28
BMX 0.009 0.15 -10000 0 -0.94 10 10
ANGPT1 0.015 0.035 -10000 0 -10000 0 0
tube development -0.001 0.16 -10000 0 -0.68 17 17
ANGPT4 0.033 0.03 -10000 0 -0.42 2 2
response to hypoxia 0 0.01 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.008 0.16 -10000 0 -0.88 9 9
alpha5/beta1 Integrin 0.047 0.037 -10000 0 -0.3 5 5
FGF2 -0.002 0.11 -10000 0 -0.42 34 34
STAT5A (dimer) -0.001 0.2 -10000 0 -0.77 22 22
mol:L-citrulline 0.027 0.13 -10000 0 -0.59 12 12
AGTR1 -0.045 0.16 -10000 0 -0.42 79 79
MAPK14 0.02 0.18 -10000 0 -1.1 11 11
Tie2/SHP2 0.012 0.17 -10000 0 -0.88 11 11
TEK 0.007 0.17 -10000 0 -0.96 11 11
RPS6KB1 0.037 0.16 -10000 0 -0.82 11 11
Angiotensin II/AT1 -0.029 0.12 -10000 0 -0.3 79 79
Tie2/Ang1/GRB2 0.035 0.14 -10000 0 -0.85 9 9
MAPK3 0.026 0.13 -10000 0 -0.78 9 9
MAPK1 0.016 0.12 -10000 0 -0.8 9 9
Tie2/Ang1/GRB7 0.031 0.14 -10000 0 -0.86 9 9
NFKB1 0.035 0.005 -10000 0 -10000 0 0
MAPK8 0.021 0.13 -10000 0 -0.85 9 9
PI3K 0.021 0.18 -10000 0 -0.95 12 12
FES 0.016 0.19 -10000 0 -1 13 13
Crk/Dok-R 0.031 0.15 -10000 0 -0.86 9 9
Tie2/Ang1/ABIN2 0.036 0.14 -10000 0 -0.86 9 9
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.027 0.15 -10000 0 -0.71 13 13
STAT5A 0.028 0.037 -10000 0 -0.42 3 3
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.056 0.17 -10000 0 -0.8 10 10
Tie2/Ang2 -0.01 0.21 -10000 0 -1 14 14
Tie2/Ang1 0.027 0.14 -10000 0 -0.9 9 9
FOXO1 0.027 0.15 -10000 0 -0.73 13 13
ELF1 0.034 0.053 -10000 0 -0.3 10 10
ELF2 0.027 0.13 -10000 0 -0.85 9 9
mol:Choline 0.02 0.12 -10000 0 -0.82 9 9
cell migration -0.013 0.051 -10000 0 -0.22 15 15
FYN -0.006 0.18 -10000 0 -0.78 17 17
DOK2 0.01 0.084 -10000 0 -0.42 18 18
negative regulation of cell cycle 0.006 0.17 -10000 0 -0.65 25 25
ETS1 0.034 0.028 -10000 0 -0.43 1 1
PXN 0.056 0.15 0.39 1 -0.64 11 12
ITGB1 0.033 0.029 -10000 0 -0.42 2 2
NOS3 0.025 0.14 -10000 0 -0.67 12 12
RAC1 0.035 0.006 -10000 0 -10000 0 0
TNF 0.033 0.065 -10000 0 -0.42 10 10
MAPKKK cascade 0.02 0.12 -10000 0 -0.82 9 9
RASA1 0.028 0.054 -10000 0 -0.42 7 7
Tie2/Ang1/Shc 0.029 0.14 -10000 0 -0.89 8 8
NCK1 0.034 0.021 -10000 0 -0.42 1 1
vasculogenesis 0.029 0.12 -10000 0 -0.53 12 12
mol:Phosphatidic acid 0.02 0.12 -10000 0 -0.82 9 9
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP 0.027 0.13 -10000 0 -0.59 12 12
Rac1/GTP 0.035 0.16 -10000 0 -0.75 12 12
MMP2 0.012 0.14 -10000 0 -0.97 8 8
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.039 0.048 0.31 6 -10000 0 6
KIRREL 0.026 0.053 -10000 0 -0.43 6 6
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.039 0.048 -10000 0 -0.31 6 6
PLCG1 0.033 0.009 -10000 0 -10000 0 0
ARRB2 0.032 0.011 -10000 0 -10000 0 0
WASL 0.029 0.054 -10000 0 -0.42 7 7
Nephrin/NEPH1/podocin/CD2AP 0.064 0.057 -10000 0 -0.24 6 6
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.022 0.044 -10000 0 -0.21 12 12
FYN 0.058 0.1 0.28 69 -0.21 11 80
mol:Ca2+ 0.058 0.056 -10000 0 -0.24 6 6
mol:DAG 0.059 0.057 -10000 0 -0.24 6 6
NPHS2 0.03 0.029 -10000 0 -0.43 1 1
mol:IP3 0.059 0.057 -10000 0 -0.24 6 6
regulation of endocytosis 0.046 0.054 -10000 0 -0.2 11 11
Nephrin/NEPH1/podocin/Cholesterol 0.049 0.048 -10000 0 -0.23 6 6
establishment of cell polarity 0.039 0.048 -10000 0 -0.31 6 6
Nephrin/NEPH1/podocin/NCK1-2 0.076 0.064 -10000 0 -0.22 7 7
Nephrin/NEPH1/beta Arrestin2 0.051 0.057 -10000 0 -0.2 11 11
NPHS1 0.041 0.03 -10000 0 -0.39 1 1
Nephrin/NEPH1/podocin 0.048 0.055 0.2 12 -0.21 11 23
TJP1 0.031 0.036 -10000 0 -0.42 3 3
NCK1 0.034 0.021 -10000 0 -0.42 1 1
NCK2 0.035 0.004 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.06 0.057 -10000 0 -0.24 6 6
CD2AP 0.034 0.007 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.06 0.057 -10000 0 -0.24 6 6
GRB2 0.033 0.01 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.057 0.1 0.29 69 -0.23 11 80
cytoskeleton organization 0.023 0.067 0.23 30 -0.25 6 36
Nephrin/NEPH1 0.033 0.036 -10000 0 -0.21 6 6
Nephrin/NEPH1/ZO-1 0.05 0.054 -10000 0 -0.25 9 9
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.044 0.035 -10000 0 -0.3 4 4
ATM 0.031 0.013 -10000 0 -10000 0 0
UBE2D3 0.035 0.005 -10000 0 -10000 0 0
PRKDC 0.029 0.031 -10000 0 -0.42 2 2
ATR 0.035 0.006 -10000 0 -10000 0 0
UBE2L3 0.034 0.008 -10000 0 -10000 0 0
FANCD2 0.023 0.011 -10000 0 -10000 0 0
protein ubiquitination 0.059 0.072 -10000 0 -0.23 20 20
XRCC5 0.035 0.004 -10000 0 -10000 0 0
XRCC6 0.033 0.009 -10000 0 -10000 0 0
M/R/N Complex 0.047 0.044 -10000 0 -0.26 4 4
MRE11A 0.031 0.012 -10000 0 -10000 0 0
DNA-PK 0.056 0.036 -10000 0 -0.25 2 2
FA complex/FANCD2/Ubiquitin 0.001 0.096 -10000 0 -0.42 12 12
FANCF 0.031 0.041 -10000 0 -0.42 4 4
BRCA1 0.021 0.07 -10000 0 -0.42 12 12
CCNE1 0.027 0.046 -10000 0 -0.42 5 5
CDK2/Cyclin E1 0.044 0.045 -10000 0 -0.34 6 6
FANCG 0.035 0.006 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.037 0.061 -10000 0 -0.3 15 15
FANCE 0.032 0.036 -10000 0 -0.42 3 3
FANCC 0.034 0.021 -10000 0 -0.42 1 1
NBN 0.027 0.025 -10000 0 -0.42 1 1
FANCA 0.015 0.067 -10000 0 -0.42 11 11
DNA repair -0.014 0.11 0.28 3 -0.35 17 20
BRCA1/BARD1/ubiquitin 0.037 0.061 -10000 0 -0.3 15 15
BARD1/DNA-PK 0.069 0.049 -10000 0 -0.23 5 5
FANCL 0.035 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.044 0.035 0.3 4 -10000 0 4
BRCA1/BARD1/CTIP/M/R/N Complex 0.016 0.082 -10000 0 -0.28 11 11
BRCA1/BACH1/BARD1/TopBP1 0.054 0.059 -10000 0 -0.26 15 15
BRCA1/BARD1/P53 0.049 0.091 -10000 0 -0.25 35 35
BARD1/CSTF1/BRCA1 0.049 0.06 -10000 0 -0.26 14 14
BRCA1/BACH1 0.021 0.07 -10000 0 -0.42 12 12
BARD1 0.033 0.035 -10000 0 -0.42 3 3
PCNA 0.03 0.041 -10000 0 -0.42 4 4
BRCA1/BARD1/UbcH5C 0.054 0.06 -10000 0 -0.26 15 15
BRCA1/BARD1/UbcH7 0.051 0.059 -10000 0 -0.26 14 14
BRCA1/BARD1/RAD51/PCNA 0.037 0.11 -10000 0 -0.24 58 58
BARD1/DNA-PK/P53 0.057 0.085 -10000 0 -0.22 29 29
BRCA1/BARD1/Ubiquitin 0.037 0.061 -10000 0 -0.3 15 15
BRCA1/BARD1/CTIP 0.032 0.063 -10000 0 -0.23 23 23
FA complex 0.019 0.057 -10000 0 -0.23 14 14
BARD1/EWS 0.047 0.031 -10000 0 -0.3 3 3
RBBP8 0.008 0.044 -10000 0 -0.3 10 10
TP53 0.008 0.1 -10000 0 -0.42 26 26
TOPBP1 0.035 0.006 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.047 0.089 0.25 35 -10000 0 35
BRCA1/BARD1 0.066 0.076 -10000 0 -0.23 20 20
CSTF1 0.031 0.023 -10000 0 -0.42 1 1
BARD1/EWS-Fli1 0.024 0.025 -10000 0 -0.3 3 3
CDK2 0.033 0.029 -10000 0 -0.42 2 2
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.005 0.13 -10000 0 -0.42 43 43
RAD50 0.03 0.046 -10000 0 -0.42 5 5
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.037 0.061 -10000 0 -0.3 15 15
EWSR1 0.033 0.009 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.013 0.06 -10000 0 -0.34 13 13
CRKL 0.03 0.041 -10000 0 -0.42 4 4
Rac1/GDP 0.026 0.004 -10000 0 -10000 0 0
DOCK1 0.027 0.057 -10000 0 -0.42 8 8
ITGA4 0.021 0.078 -10000 0 -0.42 15 15
alpha4/beta7 Integrin/MAdCAM1 0.068 0.074 -10000 0 -0.25 22 22
EPO 0.03 0.014 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.041 0.06 -10000 0 -0.3 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.023 -10000 0 -0.42 1 1
alpha4/beta1 Integrin 0.039 0.068 -10000 0 -0.33 15 15
EPO/EPOR (dimer) 0.047 0.014 -10000 0 -10000 0 0
lamellipodium assembly 0.012 0.084 -10000 0 -0.38 10 10
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PI3K 0.035 0.067 -10000 0 -0.3 18 18
ARF6 0.033 0.029 -10000 0 -0.42 2 2
JAK2 0.024 0.048 -10000 0 -0.26 13 13
PXN 0.036 0.004 -10000 0 -10000 0 0
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
MADCAM1 0.034 0.008 -10000 0 -10000 0 0
cell adhesion 0.065 0.073 -10000 0 -0.25 22 22
CRKL/CBL 0.042 0.036 -10000 0 -0.3 4 4
ITGB1 0.033 0.029 -10000 0 -0.42 2 2
SRC 0.001 0.083 0.19 14 -0.27 37 51
ITGB7 0.035 0.004 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.04 0.099 -10000 0 -0.3 36 36
p130Cas/Crk/Dock1 0.02 0.087 -10000 0 -0.25 25 25
VCAM1 0.009 0.1 -10000 0 -0.42 27 27
RHOA 0.026 0.061 -10000 0 -0.42 9 9
alpha4/beta1 Integrin/Paxillin/GIT1 0.073 0.066 -10000 0 -0.26 16 16
BCAR1 -0.024 0.072 0.18 14 -0.25 33 47
EPOR 0.035 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.031 0.012 -10000 0 -10000 0 0
GIT1 0.033 0.022 -10000 0 -0.42 1 1
Rac1/GTP 0.012 0.086 -10000 0 -0.4 10 10
Paxillin-dependent events mediated by a4b1

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
CRKL 0.03 0.041 -10000 0 -0.42 4 4
Rac1/GDP 0.035 0.013 -10000 0 -10000 0 0
DOCK1 0.027 0.057 -10000 0 -0.42 8 8
ITGA4 0.021 0.078 -10000 0 -0.42 15 15
RAC1 0.035 0.006 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.041 0.06 -10000 0 -0.3 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.031 0.023 -10000 0 -0.42 1 1
alpha4/beta1 Integrin 0.058 0.064 -10000 0 -0.28 15 15
alpha4/beta7 Integrin/Paxillin 0.048 0.051 -10000 0 -0.23 15 15
lamellipodium assembly -0.013 0.13 -10000 0 -0.43 32 32
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PI3K 0.035 0.067 -10000 0 -0.3 18 18
ARF6 0.033 0.029 -10000 0 -0.42 2 2
TLN1 0.034 0.021 -10000 0 -0.42 1 1
PXN 0.016 0.003 -10000 0 -10000 0 0
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
ARF6/GTP 0.059 0.062 -10000 0 -0.23 18 18
cell adhesion 0.062 0.061 -10000 0 -0.25 16 16
CRKL/CBL 0.042 0.036 -10000 0 -0.3 4 4
alpha4/beta1 Integrin/Paxillin 0.046 0.057 -10000 0 -0.26 15 15
ITGB1 0.033 0.029 -10000 0 -0.42 2 2
ITGB7 0.035 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.033 0.031 -10000 0 -0.42 2 2
alpha4/beta1 Integrin/Paxillin/VCAM1 0.049 0.092 -10000 0 -0.26 36 36
p130Cas/Crk/Dock1 0.049 0.052 -10000 0 -0.25 9 9
VCAM1 0.009 0.1 -10000 0 -0.42 27 27
alpha4/beta1 Integrin/Paxillin/Talin 0.064 0.063 -10000 0 -0.25 16 16
alpha4/beta1 Integrin/Paxillin/GIT1 0.063 0.062 -10000 0 -0.25 16 16
BCAR1 0.029 0.014 -10000 0 -10000 0 0
mol:GDP -0.061 0.061 0.24 16 -10000 0 16
CBL 0.031 0.012 -10000 0 -10000 0 0
PRKACA 0.035 0.004 -10000 0 -10000 0 0
GIT1 0.033 0.022 -10000 0 -0.42 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.064 0.063 -10000 0 -0.25 16 16
Rac1/GTP -0.017 0.14 -10000 0 -0.48 32 32
TCGA08_rtk_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
PDGFRA 0.009 0.11 -10000 0 -0.42 29 29
HRAS 0.032 0.036 -10000 0 -0.42 3 3
EGFR -0.013 0.13 -10000 0 -0.42 47 47
AKT 0.025 0.085 0.26 3 -0.28 11 14
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0.032 0.036 -10000 0 -0.42 3 3
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 0.024 0.032 -10000 0 -0.42 2 2
FOXO4 0 0 -10000 0 -10000 0 0
MET 0.028 0.046 -10000 0 -0.42 5 5
PIK3CA 0.033 0.022 -10000 0 -0.42 1 1
PIK3CB 0.031 0.045 -10000 0 -0.42 5 5
NRAS 0.029 0.05 -10000 0 -0.42 6 6
PIK3CG 0.022 0.072 -10000 0 -0.42 13 13
PIK3R3 0.025 0.067 -10000 0 -0.42 11 11
PIK3R2 0.036 0.004 -10000 0 -10000 0 0
NF1 0.032 0.03 -10000 0 -0.42 2 2
RAS -0.003 0.077 0.17 3 -0.29 21 24
ERBB2 0.017 0.078 -10000 0 -0.42 15 15
proliferation/survival/translation -0.026 0.057 0.24 8 -0.18 3 11
PI3K 0.003 0.084 0.24 4 -0.23 37 41
PIK3R1 0.018 0.082 -10000 0 -0.42 17 17
KRAS 0.027 0.057 -10000 0 -0.42 8 8
FOXO 0.042 0.039 0.19 7 -10000 0 7
AKT2 0.035 0.005 -10000 0 -10000 0 0
PTEN 0.026 0.061 -10000 0 -0.42 9 9
Signaling events mediated by PRL

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
CCNE1 0.027 0.046 -10000 0 -0.42 5 5
mol:Halofuginone 0.004 0.009 -10000 0 -0.19 1 1
ITGA1 0.023 0.072 -10000 0 -0.42 13 13
CDKN1A -0.004 0.12 -10000 0 -0.44 27 27
PRL-3/alpha Tubulin 0.02 0.018 -10000 0 -0.3 1 1
mol:Ca2+ -0.037 0.082 0.34 1 -0.31 39 40
AGT -0.024 0.14 -10000 0 -0.42 54 54
CCNA2 -0.036 0.096 -10000 0 -0.52 3 3
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 -0.028 0.11 -10000 0 -0.29 76 76
CDK2/Cyclin E1 0.021 0.12 -10000 0 -0.39 31 31
MAPK3 0.011 0.016 -10000 0 -0.3 1 1
PRL-2 /Rab GGTase beta 0.046 0.043 -10000 0 -0.3 7 7
MAPK1 0.012 0.016 -10000 0 -0.3 1 1
PTP4A1 -0.026 0.083 -10000 0 -0.48 3 3
PTP4A3 0.027 0.025 -10000 0 -0.42 1 1
PTP4A2 0.028 0.054 -10000 0 -0.42 7 7
ITGB1 0.011 0.021 -10000 0 -0.3 2 2
SRC 0.032 0.03 -10000 0 -0.42 2 2
RAC1 0.013 0.059 -10000 0 -0.44 5 5
Rab GGTase beta/Rab GGTase alpha 0.05 0.013 -10000 0 -10000 0 0
PRL-1/ATF-5 0.001 0.096 0.37 1 -0.46 3 4
RABGGTA 0.035 0.007 -10000 0 -10000 0 0
BCAR1 -0.017 0.02 0.34 1 -10000 0 1
RHOC 0.01 0.071 -10000 0 -0.41 10 10
RHOA 0.002 0.091 -10000 0 -0.39 21 21
cell motility 0.015 0.085 0.35 1 -0.35 12 13
PRL-1/alpha Tubulin -0.026 0.078 -10000 0 -0.45 3 3
PRL-3/alpha1 Integrin 0.032 0.058 -10000 0 -0.32 11 11
ROCK1 0.019 0.081 0.35 1 -0.36 11 12
RABGGTB 0.035 0.007 -10000 0 -10000 0 0
CDK2 0.033 0.029 -10000 0 -0.42 2 2
mitosis -0.026 0.082 -10000 0 -0.48 3 3
ATF5 0.033 0.022 -10000 0 -0.42 1 1
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.074 0.047 -10000 0 -0.23 6 6
HDAC3 0.035 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.012 0.009 -10000 0 -0.19 1 1
GATA1/HDAC4 0.051 0.018 -10000 0 -0.3 1 1
GATA1/HDAC5 0.049 0.021 -10000 0 -0.3 1 1
GATA2/HDAC5 0.044 0.041 -10000 0 -0.3 6 6
HDAC5/BCL6/BCoR 0.048 0.074 -10000 0 -0.26 26 26
HDAC9 0.033 0.022 -10000 0 -0.42 1 1
Glucocorticoid receptor/Hsp90/HDAC6 0.038 0.052 -10000 0 -0.25 15 15
HDAC4/ANKRA2 0.04 0.059 -10000 0 -0.3 14 14
HDAC5/YWHAB 0.046 0.024 -10000 0 -0.3 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.016 0.011 -10000 0 -0.17 1 1
GATA2 0.029 0.046 -10000 0 -0.42 5 5
HDAC4/RFXANK 0.05 0.02 -10000 0 -0.3 1 1
BCOR 0.028 0.06 -10000 0 -0.42 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.031 0.03 -10000 0 -0.42 2 2
HDAC5 0.033 0.022 -10000 0 -0.42 1 1
GNB1/GNG2 0.047 0.039 -10000 0 -0.3 6 6
Histones 0.008 0.068 -10000 0 -0.22 31 31
ADRBK1 0.033 0.009 -10000 0 -10000 0 0
HDAC4 0.034 0.021 -10000 0 -0.42 1 1
XPO1 0.035 0.005 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.059 -10000 0 -0.3 14 14
HDAC4/Ubc9 0.045 0.024 -10000 0 -0.3 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.045 0.024 -10000 0 -0.3 1 1
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0.036 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.048 0.022 -10000 0 -0.3 1 1
CAMK4 0.032 0.03 -10000 0 -0.42 2 2
Tubulin/HDAC6 0.036 0.055 -10000 0 -0.25 17 17
SUMO1 0.035 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.034 0.009 -10000 0 -10000 0 0
GATA1 0.036 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.032 0.011 -10000 0 -10000 0 0
NR3C1 0.021 0.078 -10000 0 -0.42 15 15
SUMO1/HDAC4 0.052 0.043 -10000 0 -0.21 2 2
SRF 0.035 0.007 -10000 0 -10000 0 0
HDAC4/YWHAB 0.048 0.022 -10000 0 -0.3 1 1
Tubulin 0.014 0.058 -10000 0 -0.3 17 17
HDAC4/14-3-3 E 0.046 0.023 -10000 0 -0.29 1 1
GNB1 0.031 0.045 -10000 0 -0.42 5 5
RANGAP1 0.032 0.022 -10000 0 -0.42 1 1
BCL6/BCoR 0.032 0.08 -10000 0 -0.3 27 27
HDAC4/HDAC3/SMRT (N-CoR2) 0.068 0.022 -10000 0 -0.26 1 1
HDAC4/SRF 0.064 0.033 -10000 0 -0.26 3 3
HDAC4/ER alpha -0.045 0.15 -10000 0 -0.3 131 131
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.008 0.068 -10000 0 -0.22 31 31
cell motility 0.036 0.054 -10000 0 -0.25 17 17
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.032 0.011 -10000 0 -10000 0 0
HDAC7/HDAC3 0.026 0.004 -10000 0 -10000 0 0
BCL6 0.018 0.085 -10000 0 -0.42 18 18
HDAC4/CaMK II delta B 0.034 0.021 -10000 0 -0.42 1 1
Hsp90/HDAC6 0.027 0 -10000 0 -10000 0 0
ESR1 -0.088 0.2 -10000 0 -0.42 130 130
HDAC6/HDAC11 0.034 0.077 -10000 0 -0.3 25 25
Ran/GTP/Exportin 1 0.053 0.042 -10000 0 -0.24 1 1
NPC 0.021 0.002 -10000 0 -10000 0 0
MEF2C 0.016 0.089 -10000 0 -0.42 20 20
RAN 0.035 0.005 -10000 0 -10000 0 0
HDAC4/MEF2C 0.076 0.072 -10000 0 -0.22 19 19
GNG2 0.034 0.021 -10000 0 -0.42 1 1
NCOR2 0.035 0.004 -10000 0 -10000 0 0
TUBB2A 0.018 0.082 -10000 0 -0.42 17 17
HDAC11 0.012 0.099 -10000 0 -0.42 25 25
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 0.036 0.004 -10000 0 -10000 0 0
ANKRA2 0.022 0.072 -10000 0 -0.42 13 13
RFXANK 0.035 0.005 -10000 0 -10000 0 0
nuclear import -0.036 0.028 0.26 2 -10000 0 2
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.033 0.029 -9999 0 -0.42 2 2
ITGB7 0.035 0.004 -9999 0 -10000 0 0
ITGA4 0.021 0.078 -9999 0 -0.42 15 15
alpha4/beta7 Integrin 0.041 0.06 -9999 0 -0.3 15 15
alpha4/beta1 Integrin 0.039 0.068 -9999 0 -0.33 15 15
Signaling events mediated by HDAC Class III

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
EP300 0.033 0.022 -10000 0 -0.42 1 1
HDAC4 0.034 0.021 -10000 0 -0.42 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.005 0.016 -10000 0 -0.13 4 4
CDKN1A -0.017 0.095 0.4 1 -0.57 13 14
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.035 0.007 -10000 0 -10000 0 0
FOXO3 -0.007 0.016 0.34 1 -10000 0 1
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.011 0.02 -10000 0 -0.42 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.033 0.009 -10000 0 -10000 0 0
TAT 0.027 0.016 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.006 0.065 -10000 0 -0.3 24 24
PPARGC1A 0.023 0.064 -10000 0 -0.42 10 10
FHL2 -0.026 0.15 -10000 0 -0.42 64 64
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.048 0.019 -10000 0 -10000 0 0
HIST2H4A -0.005 0.016 0.13 4 -10000 0 4
SIRT1/FOXO3a 0.028 0.038 0.24 4 -0.2 3 7
SIRT1 0.034 0.019 0.21 4 -10000 0 4
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.053 0.036 -10000 0 -0.26 1 1
SIRT1/Histone H1b 0.021 0.077 -10000 0 -0.22 31 31
apoptosis -0.063 0.024 -10000 0 -10000 0 0
SIRT1/PGC1A 0.038 0.044 -10000 0 -0.25 10 10
p53/SIRT1 0.025 0.079 0.4 4 -0.31 22 26
SIRT1/FOXO4 0.032 0.044 -10000 0 -0.31 1 1
FOXO1/FHL2/SIRT1 0.009 0.09 -10000 0 -0.23 62 62
HIST1H1E 0 0.065 -10000 0 -0.26 30 30
SIRT1/p300 0.047 0.022 -10000 0 -0.23 1 1
muscle cell differentiation -0.008 0.06 0.25 24 -0.19 1 25
TP53 0.009 0.095 0.21 4 -0.42 22 26
KU70/SIRT1/BAX 0.064 0.024 -10000 0 -10000 0 0
CREBBP 0.032 0.011 -10000 0 -10000 0 0
MEF2D 0.028 0.015 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.04 0.024 -10000 0 -10000 0 0
ACSS2 -0.006 0.025 0.19 4 -10000 0 4
SIRT1/PCAF/MYOD 0.008 0.061 0.19 1 -0.25 24 25
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.025 0.061 0.42 9 -10000 0 9
PI3K Class IB/PDE3B 0.025 0.061 -10000 0 -0.42 9 9
PDE3B 0.025 0.061 -10000 0 -0.42 9 9
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.027 0.1 0.21 2 -0.24 41 43
CaM/Ca2+ 0.026 0.005 -10000 0 -10000 0 0
AKT1 0.032 0.036 -10000 0 -0.42 3 3
AKT2 0.035 0.005 -10000 0 -10000 0 0
STXBP4 0.03 0.036 -10000 0 -0.42 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.007 0.1 0.19 4 -0.23 56 60
YWHAZ 0.026 0.016 -10000 0 -10000 0 0
CALM1 0.035 0.007 -10000 0 -10000 0 0
YWHAQ 0.033 0.029 -10000 0 -0.42 2 2
TBC1D4 0.008 0.044 -10000 0 -0.3 10 10
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
YWHAB 0.034 0.009 -10000 0 -10000 0 0
SNARE/Synip 0.037 0.032 -10000 0 -0.25 4 4
YWHAG 0.035 0.005 -10000 0 -10000 0 0
ASIP 0 0 -10000 0 -10000 0 0
PRKCI 0.024 0.067 -10000 0 -0.42 11 11
AS160/CaM/Ca2+ 0.026 0.005 -10000 0 -10000 0 0
RHOQ 0.033 0.035 -10000 0 -0.42 3 3
GYS1 0.017 0.04 0.25 11 -0.24 3 14
PRKCZ 0 0 -10000 0 -10000 0 0
TRIP10 0.032 0.041 -10000 0 -0.42 4 4
TC10/GTP/CIP4/Exocyst 0.043 0.036 -10000 0 -0.25 7 7
AS160/14-3-3 0.017 0.074 -10000 0 -0.26 13 13
VAMP2 0.031 0.023 -10000 0 -0.42 1 1
SLC2A4 0.005 0.11 0.2 3 -0.25 56 59
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.025 0.025 -10000 0 -0.28 3 3
SFN 0.011 0.099 -10000 0 -0.42 25 25
LNPEP 0.032 0.03 -10000 0 -0.42 2 2
YWHAE 0.032 0.011 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A 0.034 0.007 -9999 0 -10000 0 0
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.032 0.011 -9999 0 -10000 0 0
TCEB1 0.028 0.025 -9999 0 -0.42 1 1
HIF1A/p53 0.006 0.097 -9999 0 -0.27 24 24
HIF1A -0.001 0.081 -9999 0 -0.26 21 21
COPS5 0.026 0.042 -9999 0 -0.42 4 4
VHL/Elongin B/Elongin C/RBX1/CUL2 0.071 0.052 -9999 0 -0.22 1 1
FIH (dimer) 0.035 0.005 -9999 0 -10000 0 0
CDKN2A 0.015 0.075 -9999 0 -0.42 14 14
ARNT/IPAS 0.05 0.013 -9999 0 -10000 0 0
HIF1AN 0.035 0.005 -9999 0 -10000 0 0
GNB2L1 0.033 0.035 -9999 0 -0.42 3 3
HIF1A/ARNT 0.018 0.087 -9999 0 -0.27 16 16
CUL2 0.035 0.007 -9999 0 -10000 0 0
OS9 0.033 0.029 -9999 0 -0.42 2 2
RACK1/Elongin B/Elongin C 0.053 0.037 -9999 0 -0.26 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.004 0.076 -9999 0 -0.27 16 16
PHD1-3/OS9 0.032 0.1 -9999 0 -0.24 49 49
HIF1A/RACK1/Elongin B/Elongin C 0.035 0.083 -9999 0 -0.3 4 4
VHL 0.035 0.007 -9999 0 -10000 0 0
HSP90AA1 0 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.013 0.08 -9999 0 -0.27 13 13
EGLN3 -0.016 0.14 -9999 0 -0.42 52 52
EGLN2 0.031 0.041 -9999 0 -0.42 4 4
EGLN1 0.021 0.055 -9999 0 -0.42 7 7
TP53 0.008 0.1 -9999 0 -0.42 26 26
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.037 0.06 -9999 0 -0.46 3 3
ARNT 0.035 0.006 -9999 0 -10000 0 0
ARD1A 0.036 0.003 -9999 0 -10000 0 0
RBX1 0.033 0.009 -9999 0 -10000 0 0
HIF1A/p19ARF 0.003 0.093 -9999 0 -0.29 20 20
JNK signaling in the CD4+ TCR pathway

Figure S119.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S119.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.067 0.058 -10000 0 -0.26 9 9
MAP4K1 0.034 0.007 -10000 0 -10000 0 0
MAP3K8 0.003 0.11 -10000 0 -0.42 32 32
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.033 0.029 -10000 0 -0.42 2 2
CRKL 0.03 0.041 -10000 0 -0.42 4 4
MAP3K1 0.005 0.069 -10000 0 -0.32 4 4
JUN -0.01 0.098 -10000 0 -0.54 9 9
MAP3K7 0.014 0.061 0.21 4 -0.31 5 9
GRAP2 0.032 0.023 -10000 0 -0.42 1 1
CRK 0.031 0.023 -10000 0 -0.42 1 1
MAP2K4 -0.004 0.084 0.21 1 -0.34 15 16
LAT 0.029 0.031 -10000 0 -0.42 2 2
LCP2 0.023 0.07 -10000 0 -0.42 12 12
MAPK8 0.009 0.081 -10000 0 -0.59 8 8
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.02 0.067 -10000 0 -0.32 6 6
LAT/GRAP2/SLP76/HPK1/HIP-55 0.078 0.062 -10000 0 -0.25 9 9
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.016 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.041 0.03 -10000 0 -0.24 1 1
CDKN1B 0.01 0.082 0.26 2 -0.37 11 13
CDKN1A 0.011 0.073 -10000 0 -0.33 15 15
FRAP1 0.034 0.007 -10000 0 -10000 0 0
PRKDC 0.029 0.031 -10000 0 -0.42 2 2
FOXO3 0.011 0.061 -10000 0 -0.31 15 15
AKT1 0.012 0.064 -10000 0 -0.33 15 15
BAD 0.034 0.021 -10000 0 -0.42 1 1
AKT3 0.011 0.024 -10000 0 -0.29 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.011 0.061 -10000 0 -0.31 15 15
AKT1/ASK1 0.037 0.087 0.28 1 -0.31 15 16
BAD/YWHAZ 0.051 0.036 -10000 0 -0.26 1 1
RICTOR 0.035 0.006 -10000 0 -10000 0 0
RAF1 0.035 0.006 -10000 0 -10000 0 0
JNK cascade -0.035 0.084 0.3 15 -10000 0 15
TSC1 0.014 0.065 -10000 0 -0.32 14 14
YWHAZ 0.026 0.016 -10000 0 -10000 0 0
AKT1/RAF1 0.054 0.083 0.29 3 -0.31 15 18
EP300 0.033 0.022 -10000 0 -0.42 1 1
mol:GDP 0.012 0.064 -10000 0 -0.32 15 15
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.008 0.065 0.26 1 -0.38 9 10
YWHAQ 0.033 0.029 -10000 0 -0.42 2 2
TBC1D4 0.004 0.034 0.24 2 -0.24 8 10
MAP3K5 0.013 0.093 -10000 0 -0.42 22 22
MAPKAP1 0.035 0.021 -10000 0 -0.42 1 1
negative regulation of cell cycle -0.035 0.074 0.24 7 -0.2 3 10
YWHAH 0.031 0.036 -10000 0 -0.42 3 3
AKT1S1 0.017 0.077 0.27 1 -0.33 15 16
CASP9 0.016 0.055 -10000 0 -0.35 5 5
YWHAB 0.034 0.009 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.045 0.098 0.29 6 -0.4 8 14
GBL 0.031 0.023 -10000 0 -0.42 1 1
PDK1/Src/Hsp90 0.041 0.025 -10000 0 -0.25 2 2
YWHAE 0.032 0.011 -10000 0 -10000 0 0
SRC 0.032 0.03 -10000 0 -0.42 2 2
AKT2/p21CIP1 0.014 0.068 0.25 1 -0.36 7 8
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.036 0.075 -10000 0 -0.36 12 12
CHUK 0.01 0.073 -10000 0 -0.33 15 15
BAD/BCL-XL 0.055 0.081 0.28 2 -0.39 6 8
mTORC2 0.075 0.04 -10000 0 -0.24 2 2
AKT2 0.016 0.015 -10000 0 -0.29 1 1
FOXO1-3a-4/14-3-3 family 0.046 0.095 0.24 15 -0.33 8 23
PDPK1 0.031 0.023 -10000 0 -0.42 1 1
MDM2 0.016 0.071 0.27 1 -0.32 15 16
MAPKKK cascade -0.053 0.082 0.31 15 -0.28 3 18
MDM2/Cbp/p300 0.054 0.081 0.3 4 -0.39 6 10
TSC1/TSC2 0.017 0.084 0.3 19 -0.39 8 27
proteasomal ubiquitin-dependent protein catabolic process 0.051 0.078 0.28 4 -0.37 6 10
glucose import -0.001 0.031 0.21 2 -0.22 8 10
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.032 0.083 -10000 0 -0.49 6 6
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.001 0.031 0.21 2 -0.22 8 10
GSK3A 0.014 0.067 -10000 0 -0.36 9 9
FOXO1 0.011 0.061 -10000 0 -0.31 15 15
GSK3B 0.014 0.067 -10000 0 -0.32 15 15
SFN 0.011 0.099 -10000 0 -0.42 25 25
G1/S transition of mitotic cell cycle 0.02 0.074 0.31 1 -0.4 6 7
p27Kip1/14-3-3 family 0.022 0.054 -10000 0 -0.34 2 2
PRKACA 0.035 0.004 -10000 0 -10000 0 0
KPNA1 0.035 0.004 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG 0.035 0.005 -10000 0 -10000 0 0
RHEB 0.035 0.007 -10000 0 -10000 0 0
CREBBP 0.032 0.011 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.028 0.054 -10000 0 -0.42 7 7
SMAD2 0 0.059 0.21 2 -0.22 12 14
SMAD3 0.019 0.059 0.28 1 -0.25 5 6
SMAD3/SMAD4 0.03 0.089 -10000 0 -0.4 14 14
SMAD4/Ubc9/PIASy 0.054 0.052 -10000 0 -0.26 10 10
SMAD2/SMAD2/SMAD4 0.05 0.08 -10000 0 -0.25 5 5
PPM1A 0.034 0.021 -10000 0 -0.42 1 1
CALM1 0.035 0.007 -10000 0 -10000 0 0
SMAD2/SMAD4 0.013 0.067 0.19 2 -0.21 21 23
MAP3K1 0.01 0.099 -10000 0 -0.42 25 25
TRAP-1/SMAD4 0.046 0.043 -10000 0 -0.3 7 7
MAPK3 0.032 0.023 -10000 0 -0.42 1 1
MAPK1 0.033 0.022 -10000 0 -0.42 1 1
NUP214 0.034 0.021 -10000 0 -0.42 1 1
CTDSP1 0.034 0.029 -10000 0 -0.42 2 2
CTDSP2 0.034 0.029 -10000 0 -0.42 2 2
CTDSPL 0.028 0.054 -10000 0 -0.42 7 7
KPNB1 0.031 0.041 -10000 0 -0.42 4 4
TGFBRAP1 0.036 0.004 -10000 0 -10000 0 0
UBE2I 0.032 0.011 -10000 0 -10000 0 0
NUP153 0.034 0.007 -10000 0 -10000 0 0
KPNA2 0.023 0.061 -10000 0 -0.42 9 9
PIAS4 0.032 0.036 -10000 0 -0.42 3 3
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.041 0.037 -10000 0 -0.25 7 7
EFNA5 0.029 0.046 -10000 0 -0.42 5 5
FYN 0.011 0.041 0.19 2 -0.23 13 15
neuron projection morphogenesis 0.041 0.037 -10000 0 -0.25 7 7
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.041 0.037 -10000 0 -0.25 7 7
EPHA5 0.034 0.029 -10000 0 -0.42 2 2
Arf6 trafficking events

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
SLC2A4 0.029 0.024 -10000 0 -0.42 1 1
CLTC 0.025 0.062 0.26 2 -0.42 6 8
calcium ion-dependent exocytosis 0.017 0.038 -10000 0 -0.22 5 5
Dynamin 2/GTP 0.031 0.02 -10000 0 -0.23 2 2
EXOC4 0.034 0.021 -10000 0 -0.42 1 1
CD59 0.016 0.049 -10000 0 -0.36 5 5
CPE -0.008 0.079 -10000 0 -0.26 43 43
CTNNB1 0.024 0.067 -10000 0 -0.42 11 11
membrane fusion 0.013 0.033 -10000 0 -0.23 4 4
CTNND1 -0.002 0.054 0.2 30 -0.22 3 33
DNM2 0.035 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.046 0.18 3 -0.26 5 8
TSHR 0.013 0.034 -10000 0 -0.25 8 8
INS 0.008 0.094 -10000 0 -0.47 18 18
BIN1 0.033 0.029 -10000 0 -0.42 2 2
mol:Choline 0.013 0.033 -10000 0 -0.23 4 4
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.018 -10000 0 -0.25 2 2
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.033 0.029 -10000 0 -0.42 2 2
mol:Ca2+ 0.03 0.02 -10000 0 -0.23 2 2
JUP 0.02 0.053 -10000 0 -0.37 5 5
ASAP2/amphiphysin II 0.042 0.026 -10000 0 -0.23 4 4
ARF6/GTP 0.024 0.021 -10000 0 -0.3 2 2
CDH1 -0.002 0.069 -10000 0 -0.38 6 6
clathrin-independent pinocytosis 0.024 0.021 -10000 0 -0.3 2 2
MAPK8IP3 0.023 0.064 -10000 0 -0.42 10 10
positive regulation of endocytosis 0.024 0.021 -10000 0 -0.3 2 2
EXOC2 0.029 0.05 -10000 0 -0.42 6 6
substrate adhesion-dependent cell spreading 0.017 0.075 -10000 0 -0.33 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.032 0.022 -10000 0 -0.42 1 1
regulation of calcium-dependent cell-cell adhesion -0.029 0.085 0.4 5 -10000 0 5
positive regulation of phagocytosis 0.015 0.021 -10000 0 -0.25 3 3
ARF6/GTP/JIP3 0.035 0.048 -10000 0 -0.25 12 12
ACAP1 0.013 0.032 -10000 0 -0.19 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.017 0.045 -10000 0 -0.35 5 5
clathrin heavy chain/ACAP1 0.022 0.064 0.28 3 -0.32 8 11
JIP4/KLC1 0.04 0.025 -10000 0 -0.23 3 3
EXOC1 0.035 0.005 -10000 0 -10000 0 0
exocyst 0.017 0.075 -10000 0 -0.33 4 4
RALA/GTP 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.042 0.027 -10000 0 -0.25 3 3
receptor recycling 0.024 0.021 -10000 0 -0.3 2 2
CTNNA1 -0.001 0.053 0.2 30 -0.22 2 32
NME1 0.015 0.018 -10000 0 -0.25 2 2
clathrin coat assembly 0.027 0.067 0.26 3 -0.39 7 10
IL2RA 0.009 0.067 -10000 0 -0.31 9 9
VAMP3 0.015 0.021 -10000 0 -0.25 3 3
GLUT4/clathrin heavy chain/ACAP1 0.029 0.061 -10000 0 -0.31 7 7
EXOC6 0.01 0.1 -10000 0 -0.42 28 28
PLD1 0.01 0.044 -10000 0 -0.29 9 9
PLD2 0.014 0.024 -10000 0 -0.24 3 3
EXOC5 0.034 0.021 -10000 0 -0.42 1 1
PIP5K1C 0.015 0.042 0.19 2 -0.27 5 7
SDC1 0.003 0.068 -10000 0 -0.43 5 5
ARF6/GDP 0.029 0.02 -10000 0 -0.25 2 2
EXOC7 0.033 0.01 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.031 0.088 -10000 0 -0.41 5 5
mol:Phosphatidic acid 0.013 0.033 -10000 0 -0.23 4 4
endocytosis -0.04 0.026 0.23 4 -10000 0 4
SCAMP2 0.033 0.029 -10000 0 -0.42 2 2
ADRB2 0.01 0.087 0.25 3 -0.42 9 12
EXOC3 0.036 0.002 -10000 0 -10000 0 0
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.038 0.028 0.18 9 -0.23 2 11
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 0.021 0.069 0.25 3 -0.38 8 11
RALA 0.035 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.024 0.085 -10000 0 -0.39 5 5
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.04 0.057 -9999 0 -0.3 13 13
FBXW11 0.034 0.021 -9999 0 -0.42 1 1
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.034 0.021 -9999 0 -0.42 1 1
CHUK 0.025 0.067 -9999 0 -0.42 11 11
NF kappa B2 p100/RelB 0.082 0.073 -9999 0 -0.24 19 19
NFKB1 0.035 0.005 -9999 0 -10000 0 0
MAP3K14 0.032 0.03 -9999 0 -0.42 2 2
NF kappa B1 p50/RelB 0.046 0.04 -9999 0 -0.3 6 6
RELB 0.029 0.05 -9999 0 -0.42 6 6
NFKB2 0.034 0.021 -9999 0 -0.42 1 1
NF kappa B2 p52/RelB 0.042 0.036 -9999 0 -0.25 7 7
regulation of B cell activation 0.041 0.036 -9999 0 -0.25 7 7
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.035 0.023 -10000 0 -0.42 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.046 0.1 0.26 11 -0.27 7 18
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 0.02 0.011 -10000 0 -10000 0 0
NFKBIA 0.011 0.036 0.21 4 -0.37 3 7
BIRC2 0.031 0.012 -10000 0 -10000 0 0
IKBKB 0.029 0.014 -10000 0 -10000 0 0
RIPK2 0.028 0.015 -10000 0 -10000 0 0
IKBKG 0.01 0.098 -10000 0 -0.34 19 19
IKK complex/A20 0.033 0.12 -10000 0 -0.33 17 17
NEMO/A20/RIP2 0.028 0.015 -10000 0 -10000 0 0
XPO1 0.035 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.022 0.11 -10000 0 -0.31 23 23
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.035 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.047 0.009 -10000 0 -10000 0 0
IKK complex/ELKS 0.011 0.1 -10000 0 -0.31 19 19
BCL10/MALT1/TRAF6 0.063 0.041 -10000 0 -0.31 4 4
NOD2 0 0 -10000 0 -10000 0 0
NFKB1 0.037 0.011 -10000 0 -10000 0 0
RELA 0.036 0.011 -10000 0 -0.098 2 2
MALT1 0.031 0.041 -10000 0 -0.42 4 4
cIAP1/UbcH5C 0.046 0.019 -10000 0 -10000 0 0
ATM 0.031 0.013 -10000 0 -10000 0 0
TNF/TNFR1A 0.043 0.048 -10000 0 -0.3 9 9
TRAF6 0.034 0.021 -10000 0 -0.42 1 1
PRKCA 0.031 0.012 -10000 0 -10000 0 0
CHUK 0.025 0.067 -10000 0 -0.42 11 11
UBE2D3 0.035 0.005 -10000 0 -10000 0 0
TNF 0.026 0.061 -10000 0 -0.42 9 9
NF kappa B1 p50/RelA 0.074 0.034 -10000 0 -0.21 4 4
BCL10 0.034 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.036 0.21 4 -0.37 3 7
beta TrCP1/SCF ubiquitin ligase complex 0.035 0.023 -10000 0 -0.42 1 1
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
IKK complex 0.023 0.12 -10000 0 -0.33 19 19
CYLD 0.029 0.024 -10000 0 -0.42 1 1
IKK complex/PKC alpha 0.028 0.11 -10000 0 -0.32 15 15
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.035 0.087 -10000 0 -1.2 1 1
CLOCK 0.037 0.021 -10000 0 -0.42 1 1
TIMELESS/CRY2 0.042 0.061 -10000 0 -1.2 1 1
DEC1/BMAL1 0.043 0.061 -10000 0 -0.32 13 13
ATR 0.035 0.006 -10000 0 -10000 0 0
NR1D1 0.022 0.024 -10000 0 -10000 0 0
ARNTL 0.029 0.061 -10000 0 -0.42 9 9
TIMELESS 0.022 0.059 -10000 0 -1.3 1 1
NPAS2 0.027 0.064 -10000 0 -0.42 10 10
CRY2 0.035 0.005 -10000 0 -10000 0 0
mol:CO -0.01 0.006 0.14 1 -10000 0 1
CHEK1 0 0.11 -10000 0 -0.42 31 31
mol:HEME 0.01 0.006 -10000 0 -0.14 1 1
PER1 0.031 0.012 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.066 0.069 -10000 0 -0.25 20 20
BMAL1/CLOCK 0.026 0.076 -10000 0 -0.49 3 3
S phase of mitotic cell cycle 0.035 0.087 -10000 0 -1.2 1 1
TIMELESS/CHEK1/ATR 0.035 0.089 -10000 0 -1.3 1 1
mol:NADPH 0.01 0.006 -10000 0 -0.14 1 1
PER1/TIMELESS 0.038 0.06 -10000 0 -1.2 1 1
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.031 0.045 -10000 0 -0.42 5 5
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.028 0.054 -9999 0 -0.42 7 7
Aurora C/Aurora B/INCENP 0.052 0.049 -9999 0 -0.23 11 11
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.012 0.03 -9999 0 -0.4 2 2
AURKB 0.029 0.037 -9999 0 -0.42 3 3
AURKC 0.034 0.021 -9999 0 -0.42 1 1
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 0.072 0.069 -10000 0 -0.27 11 11
Ran/GTP/Exportin 1/HDAC1 -0.012 0.009 -10000 0 -0.19 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.043 0.074 0.24 1 -0.3 11 12
SUMO1 0.035 0.004 -10000 0 -10000 0 0
ZFPM1 0.022 0.055 -10000 0 -0.42 7 7
NPC/RanGAP1/SUMO1/Ubc9 0.016 0.011 -10000 0 -0.17 1 1
FKBP3 0.032 0.035 -10000 0 -0.42 3 3
Histones 0.07 0.061 -10000 0 -0.31 2 2
YY1/LSF 0.03 0.059 -10000 0 -0.23 13 13
SMG5 0 0 -10000 0 -10000 0 0
RAN 0.035 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.027 0.039 -10000 0 -0.24 9 9
I kappa B alpha/HDAC1 0.04 0.054 -10000 0 -0.29 6 6
SAP18 0.033 0.01 -10000 0 -10000 0 0
RELA 0.021 0.051 0.28 1 -0.22 8 9
HDAC1/Smad7 0.067 0.027 -10000 0 -0.25 2 2
RANGAP1 0.032 0.022 -10000 0 -0.42 1 1
HDAC3/TR2 0.039 0.056 -10000 0 -0.24 10 10
NuRD/MBD3 Complex 0.032 0.066 -10000 0 -0.34 7 7
NF kappa B1 p50/RelA 0.037 0.072 0.25 1 -0.25 11 12
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.029 0.046 -10000 0 -0.42 5 5
GATA1 0.036 0 -10000 0 -10000 0 0
Mad/Max 0.051 0.012 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.017 0.092 -10000 0 -0.4 11 11
RBBP7 0.033 0.029 -10000 0 -0.42 2 2
NPC 0.021 0.002 -10000 0 -10000 0 0
RBBP4 0.034 0.021 -10000 0 -0.42 1 1
MAX 0.034 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.034 0.021 -10000 0 -0.42 1 1
NFKBIA 0.022 0.042 -10000 0 -0.24 10 10
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.021 0.057 -10000 0 -0.33 5 5
SIN3 complex 0.076 0.044 -10000 0 -0.23 5 5
SMURF1 0.035 0.005 -10000 0 -10000 0 0
CHD3 0.031 0.023 -10000 0 -0.42 1 1
SAP30 0.03 0.046 -10000 0 -0.42 5 5
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.032 0.011 -10000 0 -10000 0 0
YY1/HDAC3 0.029 0.049 -10000 0 -0.28 4 4
YY1/HDAC2 0.034 0.045 -10000 0 -0.22 4 4
YY1/HDAC1 0.036 0.046 -10000 0 -0.25 3 3
NuRD/MBD2 Complex (MeCP1) 0.032 0.066 -10000 0 -0.34 6 6
PPARG 0.011 0.092 0.3 1 -0.36 23 24
HDAC8/hEST1B 0.047 0.02 -10000 0 -0.25 2 2
UBE2I 0.032 0.011 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.034 0.021 -10000 0 -0.42 1 1
TNFRSF1A 0.033 0.022 -10000 0 -0.42 1 1
HDAC3/SMRT (N-CoR2) 0.042 0.048 -10000 0 -0.28 3 3
MBD3L2 0.028 0.057 -10000 0 -0.42 8 8
ubiquitin-dependent protein catabolic process 0.066 0.027 -10000 0 -0.25 2 2
CREBBP 0.032 0.011 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.035 0.079 -10000 0 -0.38 6 6
HDAC1 0.034 0.021 -10000 0 -0.42 1 1
HDAC3 0.025 0.029 -10000 0 -0.33 1 1
HDAC2 0.032 0.023 -10000 0 -0.42 1 1
YY1 0.016 0.014 -10000 0 -0.24 1 1
HDAC8 0.034 0.029 -10000 0 -0.42 2 2
SMAD7 0.034 0.021 -10000 0 -0.42 1 1
NCOR2 0.035 0.004 -10000 0 -10000 0 0
MXD1 0.035 0.005 -10000 0 -10000 0 0
STAT3 0.019 0.027 -10000 0 -0.36 2 2
NFKB1 0.035 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.036 0.004 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.048 0.061 -10000 0 -0.22 13 13
YY1/SAP30/HDAC1 0.049 0.058 -10000 0 -0.25 8 8
EP300 0.033 0.022 -10000 0 -0.42 1 1
STAT3 (dimer non-phopshorylated) 0.019 0.027 -10000 0 -0.36 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.042 -10000 0 -0.24 10 10
histone deacetylation 0.032 0.065 -10000 0 -0.33 6 6
STAT3 (dimer non-phopshorylated)/HDAC3 0.023 0.056 -10000 0 -0.38 4 4
nuclear export -0.046 0.02 0.25 2 -10000 0 2
PRKACA 0.035 0.004 -10000 0 -10000 0 0
GATAD2B 0.027 0.025 -10000 0 -0.42 1 1
GATAD2A 0.035 0.006 -10000 0 -10000 0 0
GATA2/HDAC3 0.04 0.049 -10000 0 -0.25 6 6
GATA1/HDAC1 0.051 0.018 -10000 0 -0.3 1 1
GATA1/HDAC3 0.043 0.048 -10000 0 -0.29 3 3
CHD4 0.033 0.022 -10000 0 -0.42 1 1
TNF-alpha/TNFR1A 0.043 0.048 -10000 0 -0.3 9 9
SIN3/HDAC complex/Mad/Max 0.025 0.06 -10000 0 -0.3 7 7
NuRD Complex 0.036 0.076 -10000 0 -0.36 6 6
positive regulation of chromatin silencing 0.067 0.06 -10000 0 -0.3 2 2
SIN3B 0.035 0.005 -10000 0 -10000 0 0
MTA2 0.033 0.029 -10000 0 -0.42 2 2
SIN3A 0.035 0.007 -10000 0 -10000 0 0
XPO1 0.035 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.052 0.044 -10000 0 -0.26 2 2
HDAC complex 0.08 0.042 -10000 0 -0.24 5 5
GATA1/Fog1 0.037 0.046 -10000 0 -0.3 7 7
FKBP25/HDAC1/HDAC2 0.061 0.04 -10000 0 -0.26 5 5
TNF 0.026 0.061 -10000 0 -0.42 9 9
negative regulation of cell growth 0.025 0.059 -10000 0 -0.3 7 7
NuRD/MBD2/PRMT5 Complex 0.032 0.066 -10000 0 -0.34 6 6
Ran/GTP/Exportin 1 0.053 0.042 -10000 0 -0.24 1 1
NF kappa B/RelA/I kappa B alpha 0.022 0.065 -10000 0 -0.27 17 17
SIN3/HDAC complex/NCoR1 0.016 0.06 -10000 0 -0.28 10 10
TFCP2 0.027 0.064 -10000 0 -0.42 10 10
NR2C1 0.029 0.054 -10000 0 -0.42 7 7
MBD3 0.034 0.007 -10000 0 -10000 0 0
MBD2 0.034 0.007 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.015 0.039 0.16 5 -0.18 1 6
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.021 0.042 0.16 8 -0.17 5 13
AP2 0.046 0.034 -10000 0 -0.3 4 4
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.042 0.035 -10000 0 -0.24 7 7
CLTB 0.033 0.029 -10000 0 -0.42 2 2
coatomer protein complex/ARF1/GTP/ER cargo protein 0.017 0.022 -10000 0 -0.22 3 3
CD4 0.034 0.009 -10000 0 -10000 0 0
CLTA 0.035 0.006 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
ARFGAP1 0.008 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.033 0.17 5 -0.16 1 6
ARF1/GTP 0.016 0.017 -10000 0 -0.17 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.021 0.045 0.17 37 -0.19 1 38
mol:Choline 0.019 0.033 0.18 5 -0.17 1 6
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.027 0.026 -10000 0 -0.43 1 1
DDEF1 0.013 0.029 0.16 3 -0.17 1 4
ARF1/GDP 0.001 0.02 -10000 0 -0.11 5 5
AP2M1 0.031 0.041 -10000 0 -0.42 4 4
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.011 0.013 -10000 0 -0.23 1 1
Rac/GTP 0.027 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.032 0.027 -10000 0 -0.21 1 1
ARFIP2 0.02 0.053 -10000 0 -0.39 7 7
COPA 0.029 0.014 -10000 0 -10000 0 0
RAC1 0.035 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.015 0.028 -10000 0 -0.18 3 3
ARF1/GTP/ARHGAP10 0.018 0.016 -10000 0 -0.25 1 1
GGA3 0.032 0.022 -10000 0 -0.42 1 1
ARF1/GTP/Membrin 0.016 0.046 -10000 0 -0.24 13 13
AP2A1 0.035 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.01 0.03 -10000 0 -0.22 4 4
ARF1/GDP/Membrin 0.016 0.052 -10000 0 -0.27 14 14
Arfaptin 2/Rac/GDP 0.039 0.037 -10000 0 -0.25 7 7
CYTH2 -0.001 0.003 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.033 0.026 -10000 0 -0.26 1 1
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.026 0.004 -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 0.023 0.04 -10000 0 -0.4 2 2
PLD2 0.019 0.033 0.18 5 -0.17 1 6
ARF-GAP1/v-SNARE 0.008 0.003 -10000 0 -10000 0 0
PIP5K1A 0.019 0.033 0.17 5 -0.16 1 6
ARF1/GTP/Membrin/GBF1/p115 0.013 0.025 -10000 0 -0.22 1 1
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.019 0.033 0.18 5 -0.16 1 6
KDEL Receptor/Ligand/ARF-GAP1 0.008 0.003 -10000 0 -10000 0 0
GOSR2 0.018 0.038 -10000 0 -0.32 5 5
USO1 0.009 0.017 0.091 5 -0.077 1 6
GBF1 0.019 0.036 -10000 0 -0.32 4 4
ARF1/GTP/Arfaptin 2 0.034 0.032 -10000 0 -0.25 3 3
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.06 0.038 -10000 0 -0.26 4 4
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.055 0.04 -10000 0 -0.24 7 7
MAPK9 -0.002 0.057 -10000 0 -0.29 19 19
adrenocorticotropin secretion 0.005 0.024 -10000 0 -0.3 3 3
GNB1/GNG2 0.044 0.033 -10000 0 -0.25 6 6
GNB1 0.031 0.045 -10000 0 -0.42 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 0.009 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.02 0.02 -10000 0 -0.22 3 3
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 0.002 0.005 0.062 3 -10000 0 3
GNAL 0.031 0.036 -10000 0 -0.42 3 3
GNG2 0.034 0.021 -10000 0 -0.42 1 1
CRH 0.026 0.037 -10000 0 -0.42 3 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.008 0.023 -10000 0 -0.29 3 3
MAPK11 0.009 0.003 -10000 0 -10000 0 0
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 0.034 0.021 -10000 0 -0.42 1 1
Ran/GTP/Exportin 1/HDAC4 0.006 0.014 -10000 0 -0.18 1 1
MDM2/SUMO1 0.05 0.042 -10000 0 -10000 0 0
HDAC4 0.034 0.021 -10000 0 -0.42 1 1
Ran/GTP/Exportin 1/HDAC1 0.006 0.015 -10000 0 -0.21 1 1
SUMO1 0.035 0.004 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.013 0.02 -10000 0 -0.25 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.006 0.024 -10000 0 -0.26 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.035 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.036 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.052 0.043 -10000 0 -0.21 2 2
SUMO1/HDAC1 0.052 0.044 -10000 0 -0.26 2 2
RANGAP1 0.032 0.022 -10000 0 -0.42 1 1
MDM2/SUMO1/SUMO1 0.08 0.036 -10000 0 -0.24 2 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.016 0.011 -10000 0 -0.17 1 1
Ran/GTP 0.036 0.039 -10000 0 -0.2 2 2
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.034 0.009 -10000 0 -10000 0 0
UBE2I 0.032 0.011 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.035 0.04 0.21 5 -0.24 1 6
NPC 0.021 0.002 -10000 0 -10000 0 0
PIAS2 0.033 0.03 -10000 0 -0.42 2 2
PIAS1 0.035 0.006 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 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 = /xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/BRCA/1768720/1.GetReducedSegments.Finished/BRCA.RS.tsv

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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