Thyroid Adenocarcinoma: PARADIGM pathway analysis of mRNASeq expression data
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/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 59 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
Ephrin A reverse signaling 103
IL4-mediated signaling events 99
IL23-mediated signaling events 89
TCR signaling in naïve CD8+ T cells 68
Syndecan-1-mediated signaling events 67
Syndecan-4-mediated signaling events 64
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 62
IL12-mediated signaling events 61
PDGFR-alpha signaling pathway 60
Glucocorticoid receptor regulatory network 59
Results
Summary Table

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
Ephrin A reverse signaling 103 725 7 -0.22 0 1000 -1000 -0.051 -1000
IL4-mediated signaling events 99 9078 91 -0.88 0.78 1000 -1000 -0.14 -1000
IL23-mediated signaling events 89 5340 60 -0.76 0.016 1000 -1000 -0.16 -1000
TCR signaling in naïve CD8+ T cells 68 6385 93 -0.36 0.11 1000 -1000 -0.11 -1000
Syndecan-1-mediated signaling events 67 2308 34 -0.35 0.016 1000 -1000 -0.1 -1000
Syndecan-4-mediated signaling events 64 4294 67 -0.39 0.024 1000 -1000 -0.087 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 62 4234 68 -0.7 0.19 1000 -1000 -0.12 -1000
IL12-mediated signaling events 61 5323 87 -0.43 0.11 1000 -1000 -0.14 -1000
PDGFR-alpha signaling pathway 60 2677 44 -0.26 0.031 1000 -1000 -0.083 -1000
Glucocorticoid receptor regulatory network 59 6807 114 -0.77 0.47 1000 -1000 -0.089 -1000
Glypican 2 network 57 229 4 -0.12 -0.056 1000 -1000 -0.049 -1000
FOXA2 and FOXA3 transcription factor networks 52 2415 46 -0.62 0.025 1000 -1000 -0.041 -1000
amb2 Integrin signaling 52 4334 82 -0.36 0.016 1000 -1000 -0.11 -1000
Wnt signaling 52 366 7 -0.21 0.016 1000 -1000 -0.032 -1000
Signaling events regulated by Ret tyrosine kinase 51 4190 82 -0.33 0.016 1000 -1000 -0.11 -1000
Calcium signaling in the CD4+ TCR pathway 49 1531 31 -0.51 0.016 1000 -1000 -0.14 -1000
Endothelins 47 4567 96 -0.4 0.016 1000 -1000 -0.1 -1000
Class IB PI3K non-lipid kinase events 39 117 3 -0.055 -1000 1000 -1000 -0.014 -1000
a4b1 and a4b7 Integrin signaling 38 193 5 -0.11 -0.04 1000 -1000 -0.05 -1000
HIF-1-alpha transcription factor network 37 2883 76 -0.3 0.084 1000 -1000 -0.12 -1000
p75(NTR)-mediated signaling 37 4710 125 -0.31 0.016 1000 -1000 -0.14 -1000
BCR signaling pathway 37 3713 99 -0.34 0.016 1000 -1000 -0.12 -1000
Glypican 1 network 36 1764 48 -0.32 0.029 1000 -1000 -0.07 -1000
Noncanonical Wnt signaling pathway 35 930 26 -0.21 0.016 1000 -1000 -0.11 -1000
IL27-mediated signaling events 35 1791 51 -0.23 0.087 1000 -1000 -0.11 -1000
IL6-mediated signaling events 35 2661 75 -0.28 0.072 1000 -1000 -0.11 -1000
TCGA08_retinoblastoma 34 278 8 -0.11 0.043 1000 -1000 -0.025 -1000
LPA4-mediated signaling events 32 393 12 -0.2 0.024 1000 -1000 -0.035 -1000
Fc-epsilon receptor I signaling in mast cells 32 3199 97 -0.29 0.043 1000 -1000 -0.12 -1000
Osteopontin-mediated events 31 1180 38 -0.25 0.016 1000 -1000 -0.14 -1000
Syndecan-2-mediated signaling events 31 2202 69 -0.27 0.041 1000 -1000 -0.09 -1000
Signaling mediated by p38-alpha and p38-beta 31 1364 44 -0.24 0.016 1000 -1000 -0.064 -1000
Effects of Botulinum toxin 31 806 26 -0.37 0.022 1000 -1000 -0.09 -1000
JNK signaling in the CD4+ TCR pathway 27 460 17 -0.15 0.016 1000 -1000 -0.087 -1000
Thromboxane A2 receptor signaling 27 2894 105 -0.15 0.032 1000 -1000 -0.096 -1000
Ras signaling in the CD4+ TCR pathway 27 469 17 -0.15 0.016 1000 -1000 -0.064 -1000
Plasma membrane estrogen receptor signaling 26 2248 86 -0.14 0.067 1000 -1000 -0.11 -1000
FOXM1 transcription factor network 26 1347 51 -0.16 0.1 1000 -1000 -0.16 -1000
Caspase cascade in apoptosis 25 1853 74 -0.15 0.059 1000 -1000 -0.084 -1000
BMP receptor signaling 25 2076 81 -0.32 0.052 1000 -1000 -0.12 -1000
Nephrin/Neph1 signaling in the kidney podocyte 24 839 34 -0.089 0.016 1000 -1000 -0.077 -1000
Reelin signaling pathway 24 1354 56 -0.26 0.016 1000 -1000 -0.12 -1000
IL1-mediated signaling events 24 1530 62 -0.26 0.082 1000 -1000 -0.13 -1000
IL2 signaling events mediated by STAT5 24 547 22 -0.17 0.023 1000 -1000 -0.048 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 24 1872 78 -0.16 0.075 1000 -1000 -0.1 -1000
Visual signal transduction: Cones 23 909 38 -0.083 0.014 1000 -1000 -0.07 -1000
Arf6 signaling events 23 1457 62 -0.23 0.017 1000 -1000 -0.083 -1000
Nongenotropic Androgen signaling 23 1232 52 -0.13 0.034 1000 -1000 -0.087 -1000
Aurora B signaling 23 1600 67 -0.2 0.016 1000 -1000 -0.099 -1000
Coregulation of Androgen receptor activity 22 1723 76 -0.34 0.049 1000 -1000 -0.075 -1000
Neurotrophic factor-mediated Trk receptor signaling 22 2714 120 -0.26 0.15 1000 -1000 -0.1 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 21 1805 85 -0.14 0.016 1000 -1000 -0.097 -1000
IL2 signaling events mediated by PI3K 21 1272 58 -0.16 0.037 1000 -1000 -0.098 -1000
Visual signal transduction: Rods 21 1126 52 -0.16 0.016 1000 -1000 -0.095 -1000
Integrins in angiogenesis 20 1686 84 -0.27 0.017 1000 -1000 -0.14 -1000
Angiopoietin receptor Tie2-mediated signaling 20 1808 88 -0.27 0.02 1000 -1000 -0.15 -1000
Signaling events mediated by PTP1B 19 1481 76 -0.24 0.025 1000 -1000 -0.097 -1000
Arf6 downstream pathway 19 842 43 -0.19 0.077 1000 -1000 -0.059 -1000
LPA receptor mediated events 19 1950 102 -0.18 0.038 1000 -1000 -0.11 -1000
S1P1 pathway 18 671 36 -0.17 0.016 1000 -1000 -0.074 -1000
FAS signaling pathway (CD95) 18 861 47 -0.28 0.033 1000 -1000 -0.07 -1000
Signaling events mediated by the Hedgehog family 17 905 52 -0.11 0.06 1000 -1000 -0.12 -1000
Syndecan-3-mediated signaling events 17 603 35 -0.2 0.016 1000 -1000 -0.087 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 17 800 45 -0.21 0.016 1000 -1000 -0.12 -1000
Circadian rhythm pathway 16 367 22 -0.11 0.016 1000 -1000 -0.097 -1000
Aurora C signaling 16 113 7 -0.083 0 1000 -1000 -0.06 -1000
EGFR-dependent Endothelin signaling events 16 347 21 -0.11 0.016 1000 -1000 -0.1 -1000
ErbB2/ErbB3 signaling events 15 990 65 -0.15 0.031 1000 -1000 -0.094 -1000
ErbB4 signaling events 15 1046 69 -0.28 0.091 1000 -1000 -0.1 -1000
Cellular roles of Anthrax toxin 15 593 39 -0.15 0.023 1000 -1000 -0.049 -1000
RXR and RAR heterodimerization with other nuclear receptor 15 831 52 -0.15 0.036 1000 -1000 -0.088 -1000
Regulation of nuclear SMAD2/3 signaling 14 2029 136 -0.19 0.14 1000 -1000 -0.11 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 14 779 54 -0.26 0.032 1000 -1000 -0.12 -1000
Paxillin-independent events mediated by a4b1 and a4b7 14 552 37 -0.14 0.016 1000 -1000 -0.12 -1000
Regulation of p38-alpha and p38-beta 14 780 54 -0.24 0.016 1000 -1000 -0.084 -1000
Presenilin action in Notch and Wnt signaling 12 741 61 -0.14 0.054 1000 -1000 -0.094 -1000
S1P5 pathway 12 210 17 -0.069 0.046 1000 -1000 -0.068 -1000
TCGA08_p53 12 90 7 -0.08 0.049 1000 -1000 -0.022 -1000
EPHB forward signaling 12 1052 85 -0.15 0.063 1000 -1000 -0.13 -1000
IGF1 pathway 12 696 57 -0.14 0.016 1000 -1000 -0.13 -1000
VEGFR1 specific signals 12 699 56 -0.079 0.027 1000 -1000 -0.1 -1000
Regulation of Androgen receptor activity 12 881 70 -0.22 0.041 1000 -1000 -0.086 -1000
Signaling events mediated by VEGFR1 and VEGFR2 11 1385 125 -0.13 0.077 1000 -1000 -0.15 -1000
Class I PI3K signaling events 11 853 73 -0.24 0.022 1000 -1000 -0.097 -1000
Sphingosine 1-phosphate (S1P) pathway 10 299 28 -0.084 0.023 1000 -1000 -0.075 -1000
Hedgehog signaling events mediated by Gli proteins 10 665 65 -0.39 0.076 1000 -1000 -0.079 -1000
Ceramide signaling pathway 10 773 76 -0.15 0.03 1000 -1000 -0.085 -1000
Ephrin B reverse signaling 10 516 48 -0.13 0.07 1000 -1000 -0.1 -1000
Canonical Wnt signaling pathway 10 521 51 -0.14 0.067 1000 -1000 -0.079 -1000
TCGA08_rtk_signaling 10 279 26 -0.19 0.041 1000 -1000 -0.028 -1000
S1P3 pathway 10 429 42 -0.084 0.033 1000 -1000 -0.074 -1000
PDGFR-beta signaling pathway 10 1017 97 -0.14 0.06 1000 -1000 -0.12 -1000
BARD1 signaling events 9 549 57 -0.046 0.048 1000 -1000 -0.098 -1000
Insulin-mediated glucose transport 9 317 32 -0.25 0.045 1000 -1000 -0.087 -1000
Nectin adhesion pathway 9 572 63 -0.089 0.05 1000 -1000 -0.098 -1000
Regulation of Telomerase 9 946 102 -0.15 0.066 1000 -1000 -0.11 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 9 312 33 -0.13 0.036 1000 -1000 -0.08 -1000
S1P4 pathway 9 241 25 -0.069 0.029 1000 -1000 -0.067 -1000
Canonical NF-kappaB pathway 8 347 39 -0.15 0.075 1000 -1000 -0.12 -1000
Signaling events mediated by HDAC Class III 8 333 40 -0.18 0.029 1000 -1000 -0.059 -1000
ceramide signaling pathway 8 429 49 -0.15 0.026 1000 -1000 -0.065 -1000
Paxillin-dependent events mediated by a4b1 8 299 36 -0.11 0.03 1000 -1000 -0.095 -1000
Rapid glucocorticoid signaling 8 175 20 -0.052 0.016 1000 -1000 -0.062 -1000
PLK1 signaling events 7 630 85 -0.068 0.025 1000 -1000 -0.067 -1000
TRAIL signaling pathway 7 341 48 -0.042 0.051 1000 -1000 -0.1 -1000
Signaling events mediated by PRL 7 238 34 -0.1 0.029 1000 -1000 -0.082 -1000
Aurora A signaling 6 360 60 -0.09 0.047 1000 -1000 -0.082 -1000
HIF-2-alpha transcription factor network 6 295 43 -0.13 0.13 1000 -1000 -0.1 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 6 517 83 -0.25 0.067 1000 -1000 -0.098 -1000
Retinoic acid receptors-mediated signaling 6 351 58 -0.075 0.049 1000 -1000 -0.1 -1000
Stabilization and expansion of the E-cadherin adherens junction 6 447 74 -0.14 0.1 1000 -1000 -0.12 -1000
IFN-gamma pathway 5 365 68 -0.15 0.042 1000 -1000 -0.13 -1000
Signaling mediated by p38-gamma and p38-delta 5 75 15 -0.012 0.033 1000 -1000 -0.047 -1000
p38 MAPK signaling pathway 5 261 44 -0.057 0.027 1000 -1000 -0.089 -1000
Class I PI3K signaling events mediated by Akt 4 281 68 -0.25 0.062 1000 -1000 -0.09 -1000
FoxO family signaling 4 264 64 -0.25 0.17 1000 -1000 -0.08 -1000
Atypical NF-kappaB pathway 4 135 31 -0.093 0.031 1000 -1000 -0.094 -1000
E-cadherin signaling in the nascent adherens junction 4 313 76 -0.095 0.082 1000 -1000 -0.11 -1000
Signaling events mediated by HDAC Class II 3 298 75 -0.13 0.038 1000 -1000 -0.093 -1000
PLK2 and PLK4 events 3 10 3 0.009 0.023 1000 -1000 -0.025 -1000
Signaling events mediated by HDAC Class I 3 340 104 -0.15 0.071 1000 -1000 -0.098 -1000
Insulin Pathway 3 271 74 -0.16 0.056 1000 -1000 -0.13 -1000
EPO signaling pathway 2 147 55 -0.044 0.087 1000 -1000 -0.12 -1000
mTOR signaling pathway 2 115 53 -0.008 0.041 1000 -1000 -0.083 -1000
E-cadherin signaling in keratinocytes 2 111 43 -0.02 0.06 1000 -1000 -0.095 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 45 23 -0.036 0.061 1000 -1000 -0.1 -1000
Arf6 trafficking events 1 124 71 -0.081 0.057 1000 -1000 -0.099 -1000
E-cadherin signaling events 1 6 5 -0.003 0.016 1000 -1000 -0.069 -1000
Alternative NF-kappaB pathway 1 17 13 -0.007 0.016 1000 -1000 -0.09 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 1 27 -0.001 0.038 1000 -1000 -0.075 -1000
Arf1 pathway 0 27 54 -0.017 0.038 1000 -1000 -0.064 -1000
Total 2877 166359 7203 -26 -990 131000 -131000 -12 -131000
Ephrin A reverse signaling

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
MAPKKK cascade -0.2 0.26 -9999 0 -0.49 158 158
EFNA5 -0.085 0.26 -9999 0 -0.74 51 51
FYN -0.17 0.26 -9999 0 -0.57 76 76
neuron projection morphogenesis -0.2 0.26 -9999 0 -0.49 158 158
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.21 0.27 -9999 0 -0.5 158 158
EPHA5 -0.22 0.33 -9999 0 -0.68 124 124
IL4-mediated signaling events

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
BCL2L1 -0.67 0.59 -10000 0 -1.3 139 139
STAT6 (cleaved dimer) -0.8 0.62 -10000 0 -1.3 202 202
IGHG1 -0.2 0.18 -10000 0 -0.42 6 6
IGHG3 -0.66 0.56 -10000 0 -1.2 180 180
AKT1 -0.43 0.44 -10000 0 -0.9 137 137
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.45 0.55 -10000 0 -1 132 132
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.43 0.46 -10000 0 -0.9 136 136
THY1 -0.68 0.6 -10000 0 -1.3 152 152
MYB -0.06 0.23 -10000 0 -0.74 38 38
HMGA1 -0.03 0.19 -10000 0 -0.81 21 21
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.62 0.64 -10000 0 -1.1 179 179
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.44 0.47 -10000 0 -0.9 138 138
SP1 0.022 0.01 -10000 0 -10000 0 0
INPP5D -0.011 0.13 -10000 0 -0.66 15 15
SOCS5 0.03 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.78 0.62 -10000 0 -1.3 194 194
SOCS1 -0.45 0.37 -10000 0 -0.82 144 144
SOCS3 -0.48 0.46 -10000 0 -1 129 129
FCER2 -0.68 0.58 -10000 0 -1.2 165 165
PARP14 0.001 0.1 -10000 0 -0.81 6 6
CCL17 -0.88 0.73 -10000 0 -1.5 191 191
GRB2 0.016 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.36 0.4 -10000 0 -0.82 117 117
T cell proliferation -0.72 0.64 -10000 0 -1.3 166 166
IL4R/JAK1 -0.68 0.59 -10000 0 -1.3 139 139
EGR2 -0.75 0.65 -10000 0 -1.4 162 162
JAK2 -0.003 0.028 -10000 0 -10000 0 0
JAK3 -0.12 0.31 -10000 0 -0.79 67 67
PIK3R1 0.016 0 -10000 0 -10000 0 0
JAK1 0.005 0.014 -10000 0 -10000 0 0
COL1A2 -0.27 0.35 -10000 0 -0.93 57 57
CCL26 -0.76 0.66 -10000 0 -1.4 154 154
IL4R -0.72 0.65 -10000 0 -1.4 143 143
PTPN6 0.027 0.034 -10000 0 -0.59 1 1
IL13RA2 -0.76 0.64 -10000 0 -1.4 161 161
IL13RA1 -0.003 0.028 -10000 0 -10000 0 0
IRF4 -0.5 0.64 -10000 0 -1.2 137 137
ARG1 -0.18 0.24 -10000 0 -0.86 25 25
CBL -0.55 0.55 -10000 0 -1.1 159 159
GTF3A 0.017 0.015 -10000 0 -10000 0 0
PIK3CA 0.011 0.06 -10000 0 -0.81 2 2
IL13RA1/JAK2 -0.013 0.044 -10000 0 -10000 0 0
IRF4/BCL6 -0.46 0.57 -10000 0 -1.2 128 128
CD40LG -0.16 0.32 -10000 0 -0.72 93 93
MAPK14 -0.56 0.57 -10000 0 -1.1 156 156
mitosis -0.4 0.4 -10000 0 -0.83 137 137
STAT6 -0.83 0.81 -10000 0 -1.5 177 177
SPI1 -0.04 0.2 -10000 0 -0.72 30 30
RPS6KB1 -0.38 0.38 -10000 0 -0.82 120 120
STAT6 (dimer) -0.84 0.82 -10000 0 -1.5 177 177
STAT6 (dimer)/PARP14 -0.76 0.68 -10000 0 -1.4 177 177
mast cell activation 0.015 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.51 0.58 -10000 0 -1.1 146 146
FRAP1 -0.43 0.44 -10000 0 -0.9 137 137
LTA -0.8 0.68 -10000 0 -1.4 176 176
FES 0.016 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.78 0.72 1.4 178 -10000 0 178
CCL11 -0.66 0.57 -10000 0 -1.3 137 137
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.5 0.56 -10000 0 -1.1 144 144
IL2RG -0.16 0.31 -10000 0 -0.7 97 97
IL10 -0.74 0.66 -10000 0 -1.4 162 162
IRS1 0.001 0.11 -10000 0 -0.71 8 8
IRS2 -0.01 0.14 -10000 0 -0.81 12 12
IL4 -0.14 0.12 -10000 0 -0.26 22 22
IL5 -0.68 0.59 -10000 0 -1.2 180 180
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.5 0.42 -10000 0 -0.9 160 160
COL1A1 -0.46 0.59 -10000 0 -1.3 103 103
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.69 0.62 -10000 0 -1.4 137 137
IL2R gamma/JAK3 -0.22 0.37 -10000 0 -0.68 128 128
TFF3 -0.87 0.69 -10000 0 -1.5 190 190
ALOX15 -0.68 0.6 -10000 0 -1.3 152 152
MYBL1 0.008 0.071 -10000 0 -0.61 5 5
T-helper 2 cell differentiation -0.62 0.54 -10000 0 -1.1 176 176
SHC1 0.014 0.032 -10000 0 -0.61 1 1
CEBPB 0.019 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.42 0.46 -10000 0 -0.91 128 128
mol:PI-3-4-5-P3 -0.43 0.44 -10000 0 -0.9 137 137
PI3K -0.48 0.5 -10000 0 -1 137 137
DOK2 -0.072 0.24 -10000 0 -0.74 44 44
ETS1 0.025 0.067 -10000 0 -0.71 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.34 0.38 -10000 0 -0.81 110 110
ITGB3 -0.7 0.63 -10000 0 -1.3 154 154
PIGR -0.78 0.67 -10000 0 -1.4 164 164
IGHE 0.038 0.068 -10000 0 -0.69 1 1
MAPKKK cascade -0.33 0.36 -10000 0 -0.78 110 110
BCL6 0.015 0.043 -10000 0 -0.81 1 1
OPRM1 -0.68 0.59 -10000 0 -1.2 180 180
RETNLB -0.68 0.59 -10000 0 -1.2 180 180
SELP -0.7 0.63 -10000 0 -1.4 138 138
AICDA -0.68 0.58 -10000 0 -1.3 151 151
IL23-mediated signaling events

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
CCL2 -0.56 0.62 -10000 0 -1.3 126 126
IL23A -0.59 0.64 -10000 0 -1.3 136 136
NF kappa B1 p50/RelA/I kappa B alpha -0.61 0.58 -10000 0 -1.3 146 146
positive regulation of T cell mediated cytotoxicity -0.65 0.74 -10000 0 -1.5 143 143
ITGA3 -0.55 0.6 -10000 0 -1.3 121 121
IL17F -0.33 0.38 -10000 0 -0.76 127 127
IL12B -0.085 0.24 -10000 0 -0.7 46 46
STAT1 (dimer) -0.62 0.7 -10000 0 -1.4 142 142
CD4 -0.53 0.59 -10000 0 -1.3 122 122
IL23 -0.59 0.62 -10000 0 -1.3 134 134
IL23R -0.066 0.13 -10000 0 -0.6 8 8
IL1B -0.61 0.67 -10000 0 -1.4 133 133
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.58 0.62 -10000 0 -1.3 147 147
TYK2 0.01 0.019 -10000 0 -10000 0 0
STAT4 -0.13 0.3 -10000 0 -0.74 72 72
STAT3 0.016 0 -10000 0 -10000 0 0
IL18RAP -0.067 0.23 -10000 0 -0.73 41 41
IL12RB1 -0.11 0.27 -10000 0 -0.72 63 63
PIK3CA 0.011 0.06 -10000 0 -0.81 2 2
IL12Rbeta1/TYK2 -0.086 0.21 -10000 0 -0.55 63 63
IL23R/JAK2 -0.073 0.15 -10000 0 -0.6 6 6
positive regulation of chronic inflammatory response -0.65 0.74 -10000 0 -1.5 143 143
natural killer cell activation 0.007 0.011 0.052 10 -10000 0 10
JAK2 0.013 0.027 -10000 0 -10000 0 0
PIK3R1 0.016 0 -10000 0 -10000 0 0
NFKB1 0.013 0.004 -10000 0 -10000 0 0
RELA 0.013 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.55 0.57 -10000 0 -1.2 135 135
ALOX12B -0.59 0.63 -10000 0 -1.3 145 145
CXCL1 -0.65 0.66 -10000 0 -1.3 160 160
T cell proliferation -0.65 0.74 -10000 0 -1.5 143 143
NFKBIA 0.013 0.004 -10000 0 -10000 0 0
IL17A -0.24 0.3 -10000 0 -0.58 112 112
PI3K -0.62 0.59 -10000 0 -1.3 146 146
IFNG -0.047 0.055 -10000 0 -0.13 48 48
STAT3 (dimer) -0.58 0.54 -10000 0 -1.2 141 141
IL18R1 -0.15 0.31 -10000 0 -0.73 84 84
IL23/IL23R/JAK2/TYK2/SOCS3 -0.32 0.39 -10000 0 -0.89 73 73
IL18/IL18R -0.22 0.36 -10000 0 -0.7 115 115
macrophage activation -0.026 0.018 -10000 0 -0.045 119 119
TNF -0.63 0.68 -10000 0 -1.4 143 143
STAT3/STAT4 -0.66 0.6 -10000 0 -1.3 155 155
STAT4 (dimer) -0.66 0.71 -10000 0 -1.4 149 149
IL18 -0.12 0.3 -10000 0 -0.76 66 66
IL19 -0.55 0.59 -10000 0 -1.2 128 128
STAT5A (dimer) -0.62 0.69 -10000 0 -1.4 138 138
STAT1 -0.008 0.13 -10000 0 -0.73 12 12
SOCS3 -0.041 0.2 -10000 0 -0.7 30 30
CXCL9 -0.64 0.65 -10000 0 -1.3 149 149
MPO -0.57 0.62 -10000 0 -1.3 144 144
positive regulation of humoral immune response -0.65 0.74 -10000 0 -1.5 143 143
IL23/IL23R/JAK2/TYK2 -0.76 0.96 -10000 0 -1.8 143 143
IL6 -0.64 0.67 -10000 0 -1.4 148 148
STAT5A 0.016 0 -10000 0 -10000 0 0
IL2 -0.012 0.1 -10000 0 -0.61 10 10
positive regulation of tyrosine phosphorylation of STAT protein 0.007 0.011 0.052 10 -10000 0 10
CD3E -0.58 0.64 -10000 0 -1.3 131 131
keratinocyte proliferation -0.65 0.74 -10000 0 -1.5 143 143
NOS2 -0.58 0.62 -10000 0 -1.3 146 146
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.21 0.29 -10000 0 -0.66 98 98
FYN -0.24 0.44 -10000 0 -0.87 112 112
LAT/GRAP2/SLP76 -0.23 0.34 -10000 0 -0.72 113 113
IKBKB 0.016 0 -10000 0 -10000 0 0
AKT1 -0.13 0.27 -10000 0 -0.51 115 115
B2M 0 0.1 -10000 0 -0.78 6 6
IKBKG -0.059 0.072 -10000 0 -0.18 35 35
MAP3K8 0.012 0.053 -10000 0 -0.71 2 2
mol:Ca2+ -0.043 0.057 -10000 0 -0.13 110 110
integrin-mediated signaling pathway -0.007 0.062 -10000 0 -0.54 5 5
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.23 0.41 -10000 0 -0.8 118 118
TRPV6 -0.2 0.33 -10000 0 -0.72 110 110
CD28 -0.12 0.28 -10000 0 -0.7 70 70
SHC1 -0.24 0.43 -10000 0 -0.83 117 117
receptor internalization -0.27 0.46 -10000 0 -0.91 117 117
PRF1 -0.22 0.43 -10000 0 -0.94 84 84
KRAS 0.016 0 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
COT/AKT1 -0.092 0.22 -10000 0 -0.4 99 99
LAT -0.24 0.44 -10000 0 -0.86 115 115
EntrezGene:6955 -0.001 0.004 -10000 0 -10000 0 0
CD3D -0.21 0.34 -10000 0 -0.72 116 116
CD3E -0.16 0.31 -10000 0 -0.7 90 90
CD3G -0.18 0.33 -10000 0 -0.71 104 104
RASGRP2 -0.011 0.041 -10000 0 -0.12 25 25
RASGRP1 -0.15 0.3 -10000 0 -0.55 116 116
HLA-A 0.007 0.057 -10000 0 -0.62 3 3
RASSF5 0.005 0.095 -10000 0 -0.81 5 5
RAP1A/GTP/RAPL -0.007 0.062 -10000 0 -0.54 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.015 0.087 -10000 0 -0.14 69 69
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.11 0.13 -10000 0 -0.32 79 79
PRKCA -0.1 0.16 -10000 0 -0.33 97 97
GRAP2 -0.097 0.26 -10000 0 -0.69 61 61
mol:IP3 -0.13 0.28 0.27 55 -0.51 106 161
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.26 0.49 -10000 0 -0.9 114 114
ORAI1 0.11 0.16 0.36 110 -10000 0 110
CSK -0.25 0.44 -10000 0 -0.87 114 114
B7 family/CD28 -0.36 0.44 -10000 0 -0.92 127 127
CHUK 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.31 0.53 -10000 0 -1 119 119
PTPN6 -0.25 0.44 -10000 0 -0.88 114 114
VAV1 -0.27 0.47 -10000 0 -0.9 122 122
Monovalent TCR/CD3 -0.26 0.47 -10000 0 -0.81 131 131
CBL 0.016 0 -10000 0 -10000 0 0
LCK -0.27 0.48 -10000 0 -0.93 115 115
PAG1 -0.25 0.44 -10000 0 -0.86 118 118
RAP1A 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.3 0.52 -10000 0 -1 117 117
CD80 -0.15 0.31 -10000 0 -0.71 84 84
CD86 -0.069 0.24 -10000 0 -0.74 42 42
PDK1/CARD11/BCL10/MALT1 -0.14 0.16 -10000 0 -0.37 105 105
HRAS 0.013 0.045 -10000 0 -0.61 2 2
GO:0035030 -0.23 0.37 -10000 0 -0.71 124 124
CD8A -0.074 0.23 -10000 0 -0.66 49 49
CD8B -0.18 0.33 -10000 0 -0.72 98 98
PTPRC -0.099 0.26 -10000 0 -0.69 60 60
PDK1/PKC theta -0.17 0.34 -10000 0 -0.65 110 110
CSK/PAG1 -0.24 0.43 -10000 0 -0.84 114 114
SOS1 0.016 0 -10000 0 -10000 0 0
peptide-MHC class I -0.013 0.085 -10000 0 -0.55 9 9
GRAP2/SLP76 -0.28 0.41 -10000 0 -0.85 115 115
STIM1 0.059 0.084 -10000 0 -10000 0 0
RAS family/GTP -0.023 0.12 -10000 0 -0.2 27 27
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.3 0.52 -10000 0 -1 117 117
mol:DAG -0.14 0.22 -10000 0 -0.46 107 107
RAP1A/GDP -0.004 0.038 -10000 0 -10000 0 0
PLCG1 0.016 0 -10000 0 -10000 0 0
CD247 -0.11 0.27 -10000 0 -0.69 67 67
cytotoxic T cell degranulation -0.21 0.41 -10000 0 -0.85 91 91
RAP1A/GTP -0.006 0.012 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.17 0.33 -10000 0 -0.62 117 117
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.19 0.36 0.29 52 -0.7 106 158
NRAS 0.016 0 -10000 0 -10000 0 0
ZAP70 -0.11 0.27 -10000 0 -0.68 69 69
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.23 0.33 -10000 0 -0.7 112 112
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.014 0.043 -10000 0 -0.81 1 1
CD8 heterodimer -0.2 0.32 -10000 0 -0.67 111 111
CARD11 -0.18 0.33 -10000 0 -0.73 99 99
PRKCB -0.12 0.18 -10000 0 -0.39 105 105
PRKCE -0.095 0.15 -10000 0 -0.31 94 94
PRKCQ -0.21 0.39 -10000 0 -0.75 117 117
LCP2 -0.004 0.11 -10000 0 -0.63 12 12
BCL10 0.016 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.11 0.23 -10000 0 -0.43 112 112
IKK complex -0.004 0.086 -10000 0 -0.14 4 4
RAS family/GDP -0.01 0.013 -10000 0 -10000 0 0
MAP3K14 -0.059 0.17 -10000 0 -0.31 71 71
PDPK1 -0.12 0.26 -10000 0 -0.49 109 109
TCR/CD3/MHC I/CD8/Fyn -0.31 0.53 -10000 0 -1 115 115
Syndecan-1-mediated signaling events

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
TGFB1 -0.002 0.12 -9999 0 -0.81 8 8
CCL5 -0.13 0.28 -9999 0 -0.67 79 79
SDCBP 0.016 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.28 0.37 -9999 0 -0.81 95 95
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.26 0.36 -9999 0 -0.77 95 95
Syndecan-1/Syntenin -0.26 0.36 -9999 0 -0.77 95 95
MAPK3 -0.22 0.32 -9999 0 -0.75 76 76
HGF/MET -0.14 0.26 -9999 0 -0.6 89 89
TGFB1/TGF beta receptor Type II -0.002 0.12 -9999 0 -0.81 8 8
BSG 0.013 0.045 -9999 0 -0.61 2 2
keratinocyte migration -0.25 0.34 -9999 0 -0.75 95 95
Syndecan-1/RANTES -0.33 0.4 -9999 0 -0.77 132 132
Syndecan-1/CD147 -0.26 0.33 -9999 0 -0.77 88 88
Syndecan-1/Syntenin/PIP2 -0.27 0.33 -9999 0 -0.74 95 95
LAMA5 0.016 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.26 0.31 -9999 0 -0.71 95 95
MMP7 -0.31 0.37 -9999 0 -0.72 165 165
HGF -0.077 0.25 -9999 0 -0.72 48 48
Syndecan-1/CASK -0.27 0.36 -9999 0 -0.78 95 95
Syndecan-1/HGF/MET -0.35 0.41 -9999 0 -0.88 114 114
regulation of cell adhesion -0.2 0.31 -9999 0 -0.72 75 75
HPSE -0.097 0.28 -9999 0 -0.79 53 53
positive regulation of cell migration -0.28 0.37 -9999 0 -0.81 95 95
SDC1 -0.28 0.38 -9999 0 -0.83 95 95
Syndecan-1/Collagen -0.28 0.37 -9999 0 -0.81 95 95
PPIB 0.014 0.032 -9999 0 -0.61 1 1
MET -0.085 0.27 -9999 0 -0.81 46 46
PRKACA 0.016 0 -9999 0 -10000 0 0
MMP9 -0.18 0.33 -9999 0 -0.73 100 100
MAPK1 -0.22 0.32 -9999 0 -0.75 76 76
homophilic cell adhesion -0.27 0.36 -9999 0 -0.79 95 95
MMP1 -0.18 0.32 -9999 0 -0.71 103 103
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.22 0.35 -9999 0 -0.74 111 111
Syndecan-4/Syndesmos -0.27 0.43 -9999 0 -0.96 93 93
positive regulation of JNK cascade -0.3 0.36 -9999 0 -0.8 114 114
Syndecan-4/ADAM12 -0.34 0.44 -9999 0 -0.91 118 118
CCL5 -0.13 0.28 -9999 0 -0.67 79 79
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.016 0 -9999 0 -10000 0 0
ITGA5 0.014 0.043 -9999 0 -0.81 1 1
SDCBP 0.016 0 -9999 0 -10000 0 0
PLG 0.006 0.017 -9999 0 -10000 0 0
ADAM12 -0.13 0.28 -9999 0 -0.65 82 82
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.057 0.067 -9999 0 -0.16 87 87
Syndecan-4/Laminin alpha1 -0.33 0.48 -9999 0 -0.99 115 115
Syndecan-4/CXCL12/CXCR4 -0.33 0.41 -9999 0 -0.9 112 112
Syndecan-4/Laminin alpha3 -0.32 0.45 -9999 0 -0.92 116 116
MDK -0.082 0.26 -9999 0 -0.79 46 46
Syndecan-4/FZD7 -0.28 0.45 -9999 0 -0.98 96 96
Syndecan-4/Midkine -0.31 0.49 -9999 0 -1 100 100
FZD7 -0.005 0.13 -9999 0 -0.79 10 10
Syndecan-4/FGFR1/FGF -0.28 0.38 -9999 0 -0.86 98 98
THBS1 -0.098 0.26 -9999 0 -0.69 61 61
integrin-mediated signaling pathway -0.34 0.46 -9999 0 -0.92 127 127
positive regulation of MAPKKK cascade -0.3 0.36 -9999 0 -0.8 114 114
Syndecan-4/TACI -0.39 0.44 -9999 0 -0.91 128 128
CXCR4 -0.038 0.18 -9999 0 -0.65 31 31
cell adhesion -0.14 0.21 -9999 0 -0.43 112 112
Syndecan-4/Dynamin -0.27 0.43 -9999 0 -0.96 93 93
Syndecan-4/TSP1 -0.32 0.45 -9999 0 -0.92 116 116
Syndecan-4/GIPC -0.27 0.43 -9999 0 -0.96 93 93
Syndecan-4/RANTES -0.34 0.46 -9999 0 -0.94 116 116
ITGB1 0.016 0 -9999 0 -10000 0 0
LAMA1 -0.11 0.3 -9999 0 -0.81 59 59
LAMA3 -0.088 0.25 -9999 0 -0.7 55 55
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.024 0.15 -9999 0 -0.5 22 22
Syndecan-4/alpha-Actinin -0.27 0.44 -9999 0 -0.96 95 95
TFPI -0.002 0.11 -9999 0 -0.67 10 10
F2 -0.001 0.009 -9999 0 -10000 0 0
alpha5/beta1 Integrin -0.002 0.032 -9999 0 -0.62 1 1
positive regulation of cell adhesion -0.35 0.47 -9999 0 -0.91 135 135
ACTN1 0.008 0.08 -9999 0 -0.76 4 4
TNC -0.21 0.36 -9999 0 -0.76 110 110
Syndecan-4/CXCL12 -0.3 0.44 -9999 0 -0.95 103 103
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CXCL12 -0.048 0.21 -9999 0 -0.76 31 31
TNFRSF13B -0.22 0.33 -9999 0 -0.68 124 124
FGF2 -0.008 0.14 -9999 0 -0.81 11 11
FGFR1 0.003 0.1 -9999 0 -0.81 6 6
Syndecan-4/PI-4-5-P2 -0.28 0.43 -9999 0 -0.93 99 99
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.26 0.37 -9999 0 -0.75 135 135
cell migration -0.014 0.019 -9999 0 -10000 0 0
PRKCD 0.021 0.018 -9999 0 -10000 0 0
vasculogenesis -0.3 0.41 -9999 0 -0.85 116 116
SDC4 -0.31 0.49 -9999 0 -1 99 99
Syndecan-4/Tenascin C -0.37 0.51 -9999 0 -1 127 127
Syndecan-4/PI-4-5-P2/PKC alpha -0.045 0.052 -9999 0 -0.12 87 87
Syndecan-4/Syntenin -0.27 0.43 -9999 0 -0.96 93 93
MMP9 -0.18 0.33 -9999 0 -0.72 100 100
Rac1/GTP -0.14 0.21 -9999 0 -0.44 112 112
cytoskeleton organization -0.25 0.4 -9999 0 -0.89 93 93
GIPC1 0.016 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.28 0.44 -9999 0 -0.94 98 98
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.19 0.33 -10000 0 -0.8 80 80
NFATC2 -0.18 0.35 -10000 0 -0.79 72 72
NFATC3 -0.035 0.099 -10000 0 -10000 0 0
CD40LG -0.57 0.59 -10000 0 -1.2 159 159
ITCH 0.06 0.034 -10000 0 -10000 0 0
CBLB 0.056 0.064 -10000 0 -0.52 4 4
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.66 0.64 -10000 0 -1.3 181 181
JUNB 0.002 0.1 -10000 0 -0.73 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.033 -10000 0 -10000 0 0
T cell anergy 0.031 0.073 -10000 0 -10000 0 0
TLE4 -0.12 0.29 -10000 0 -0.82 36 36
Jun/NFAT1-c-4/p21SNFT -0.44 0.51 -10000 0 -1.1 106 106
AP-1/NFAT1-c-4 -0.7 0.73 -10000 0 -1.5 145 145
IKZF1 -0.18 0.37 -10000 0 -0.79 80 80
T-helper 2 cell differentiation -0.26 0.35 -10000 0 -0.78 93 93
AP-1/NFAT1 -0.26 0.32 -10000 0 -0.73 88 88
CALM1 0.033 0.022 -10000 0 -10000 0 0
EGR2 -0.3 0.55 -10000 0 -1.3 62 62
EGR3 -0.31 0.57 -10000 0 -1.3 67 67
NFAT1/FOXP3 -0.33 0.4 -10000 0 -0.81 128 128
EGR1 -0.053 0.21 -10000 0 -0.7 35 35
JUN -0.038 0.16 -10000 0 -0.67 22 22
EGR4 -0.05 0.18 -10000 0 -0.62 35 35
mol:Ca2+ 0.018 0.024 -10000 0 -10000 0 0
GBP3 -0.2 0.41 -10000 0 -1 63 63
FOSL1 -0.096 0.26 -10000 0 -0.69 60 60
NFAT1-c-4/MAF/IRF4 -0.44 0.49 -10000 0 -1.1 111 111
DGKA -0.12 0.28 -10000 0 -0.79 34 34
CREM 0.016 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.35 0.45 -10000 0 -1.1 78 78
CTLA4 -0.41 0.52 -10000 0 -0.93 168 168
NFAT1-c-4 (dimer)/EGR1 -0.38 0.5 -10000 0 -1.2 88 88
NFAT1-c-4 (dimer)/EGR4 -0.38 0.47 -10000 0 -1.1 91 91
FOS -0.13 0.28 -10000 0 -0.73 65 65
IFNG -0.38 0.47 -10000 0 -1.1 96 96
T cell activation -0.21 0.31 -10000 0 -0.88 39 39
MAF 0.014 0.032 -10000 0 -0.61 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.19 0.33 0.77 66 -10000 0 66
TNF -0.4 0.53 -10000 0 -1.1 124 124
FASLG -0.44 0.68 -10000 0 -1.5 87 87
TBX21 -0.1 0.27 -10000 0 -0.72 57 57
BATF3 -0.067 0.23 -10000 0 -0.71 43 43
PRKCQ 0.006 0.063 -10000 0 -0.81 2 2
PTPN1 -0.11 0.26 -10000 0 -0.71 39 39
NFAT1-c-4/ICER1 -0.34 0.44 -10000 0 -1.1 78 78
GATA3 -0.065 0.24 -10000 0 -0.79 38 38
T-helper 1 cell differentiation -0.37 0.45 -10000 0 -1 97 97
IL2RA -0.54 0.55 -10000 0 -1.1 149 149
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.11 0.26 -10000 0 -0.76 32 32
E2F1 0.005 0.12 -10000 0 -0.78 9 9
PPARG -0.007 0.12 -10000 0 -0.64 13 13
SLC3A2 -0.11 0.26 -10000 0 -0.69 42 42
IRF4 -0.23 0.34 -10000 0 -0.7 130 130
PTGS2 -0.56 0.6 -10000 0 -1.2 141 141
CSF2 -0.57 0.59 -10000 0 -1.2 147 147
JunB/Fra1/NFAT1-c-4 -0.38 0.48 -10000 0 -1.1 84 84
IL4 -0.28 0.37 -10000 0 -0.83 93 93
IL5 -0.51 0.54 -10000 0 -1.1 145 145
IL2 -0.21 0.32 -10000 0 -0.91 37 37
IL3 -0.087 0.11 -10000 0 -0.82 4 4
RNF128 0.057 0.072 -10000 0 -0.86 2 2
NFATC1 -0.19 0.33 -10000 0 -0.77 66 66
CDK4 0.14 0.22 0.67 17 -10000 0 17
PTPRK -0.11 0.26 -10000 0 -0.7 41 41
IL8 -0.58 0.61 -10000 0 -1.2 153 153
POU2F1 0.008 0.075 -10000 0 -0.71 4 4
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.12 0.25 -10000 0 -0.59 52 52
TBX21 -0.33 0.62 -10000 0 -1.3 95 95
B2M 0 0.1 -10000 0 -0.78 6 6
TYK2 0.018 0.023 -10000 0 -10000 0 0
IL12RB1 -0.1 0.28 -10000 0 -0.71 63 63
GADD45B -0.26 0.5 -10000 0 -0.97 97 97
IL12RB2 -0.087 0.26 -10000 0 -0.7 56 56
GADD45G -0.25 0.49 -10000 0 -1 81 81
natural killer cell activation 0 0.029 -10000 0 -10000 0 0
RELB 0.011 0.06 -10000 0 -0.81 2 2
RELA 0.016 0 -10000 0 -10000 0 0
IL18 -0.12 0.3 -10000 0 -0.76 66 66
IL2RA -0.14 0.3 -10000 0 -0.73 78 78
IFNG -0.16 0.3 -10000 0 -0.66 95 95
STAT3 (dimer) -0.24 0.45 -10000 0 -0.88 105 105
HLA-DRB5 -0.17 0.32 -10000 0 -0.72 95 95
FASLG -0.37 0.65 -10000 0 -1.3 111 111
NF kappa B2 p52/RelB -0.37 0.5 -10000 0 -1.1 102 102
CD4 -0.013 0.14 -10000 0 -0.68 15 15
SOCS1 -0.024 0.16 -10000 0 -0.66 22 22
EntrezGene:6955 -0.006 0.014 -10000 0 -10000 0 0
CD3D -0.21 0.34 -10000 0 -0.72 116 116
CD3E -0.16 0.31 -10000 0 -0.7 90 90
CD3G -0.19 0.33 -10000 0 -0.72 104 104
IL12Rbeta2/JAK2 -0.053 0.21 -10000 0 -0.53 56 56
CCL3 -0.34 0.63 -10000 0 -1.3 104 104
CCL4 -0.33 0.62 -10000 0 -1.3 91 91
HLA-A 0.008 0.056 -10000 0 -0.61 3 3
IL18/IL18R -0.19 0.38 -10000 0 -0.71 114 114
NOS2 -0.34 0.61 -10000 0 -1.2 109 109
IL12/IL12R/TYK2/JAK2/SPHK2 -0.1 0.24 -10000 0 -0.59 43 43
IL1R1 -0.29 0.56 -10000 0 -1.2 88 88
IL4 0 0.029 -10000 0 -10000 0 0
JAK2 0.018 0.023 -10000 0 -10000 0 0
EntrezGene:6957 -0.005 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.4 0.65 -10000 0 -1.2 128 128
RAB7A -0.18 0.4 -10000 0 -0.8 72 72
lysosomal transport -0.17 0.38 -10000 0 -0.75 72 72
FOS -0.38 0.58 -10000 0 -1 140 140
STAT4 (dimer) -0.3 0.53 -10000 0 -1 106 106
STAT5A (dimer) -0.43 0.52 -10000 0 -1.1 122 122
GZMA -0.34 0.64 -10000 0 -1.3 99 99
GZMB -0.34 0.64 -10000 0 -1.3 98 98
HLX -0.001 0.1 -10000 0 -0.63 10 10
LCK -0.37 0.68 -10000 0 -1.3 111 111
TCR/CD3/MHC II/CD4 -0.34 0.53 -10000 0 -0.89 139 139
IL2/IL2R -0.25 0.39 -10000 0 -0.81 105 105
MAPK14 -0.25 0.49 -10000 0 -0.96 96 96
CCR5 -0.31 0.57 -10000 0 -1.2 89 89
IL1B -0.12 0.3 -10000 0 -0.74 70 70
STAT6 -0.043 0.15 -10000 0 -10000 0 0
STAT4 -0.13 0.3 -10000 0 -0.74 72 72
STAT3 0.016 0 -10000 0 -10000 0 0
STAT1 -0.008 0.13 -10000 0 -0.73 12 12
NFKB1 0.016 0 -10000 0 -10000 0 0
NFKB2 0.011 0.06 -10000 0 -0.81 2 2
IL12B -0.071 0.23 -10000 0 -0.68 46 46
CD8A -0.074 0.23 -10000 0 -0.67 49 49
CD8B -0.18 0.33 -10000 0 -0.72 98 98
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.11 0.25 0.58 53 -10000 0 53
IL2RB -0.089 0.26 -10000 0 -0.71 55 55
proteasomal ubiquitin-dependent protein catabolic process -0.26 0.47 -10000 0 -0.9 105 105
IL2RG -0.17 0.32 -10000 0 -0.7 97 97
IL12 -0.099 0.26 -10000 0 -0.6 74 74
STAT5A 0.016 0 -10000 0 -10000 0 0
CD247 -0.11 0.27 -10000 0 -0.69 67 67
IL2 -0.012 0.099 -10000 0 -0.61 10 10
SPHK2 0.016 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.064 0.24 -10000 0 -0.72 42 42
IL12/IL12R/TYK2/JAK2 -0.4 0.79 -10000 0 -1.5 103 103
MAP2K3 -0.26 0.5 -10000 0 -0.95 102 102
RIPK2 0.016 0 -10000 0 -10000 0 0
MAP2K6 -0.26 0.5 -10000 0 -0.95 105 105
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.098 0.27 -10000 0 -0.73 57 57
IL18RAP -0.065 0.24 -10000 0 -0.74 41 41
IL12Rbeta1/TYK2 -0.068 0.22 -10000 0 -0.54 63 63
EOMES -0.22 0.46 -10000 0 -1.5 36 36
STAT1 (dimer) -0.3 0.46 -10000 0 -0.9 118 118
T cell proliferation -0.2 0.38 -10000 0 -0.7 105 105
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.15 0.32 -10000 0 -0.73 84 84
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.33 0.35 -10000 0 -0.8 116 116
ATF2 -0.23 0.45 -10000 0 -0.87 95 95
PDGFR-alpha signaling pathway

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
PDGFRA -0.2 0.34 -9999 0 -0.74 105 105
PDGF/PDGFRA/CRKL -0.15 0.25 -9999 0 -0.55 105 105
positive regulation of JUN kinase activity -0.11 0.19 -9999 0 -0.46 67 67
CRKL 0.016 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.16 0.25 -9999 0 -0.56 105 105
AP1 -0.26 0.41 -9999 0 -1.1 57 57
mol:IP3 -0.14 0.27 -9999 0 -0.56 105 105
PLCG1 -0.14 0.27 -9999 0 -0.56 105 105
PDGF/PDGFRA/alphaV Integrin -0.16 0.26 -9999 0 -0.56 107 107
RAPGEF1 0.016 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ -0.14 0.27 -9999 0 -0.56 105 105
CAV3 0 0 -9999 0 -10000 0 0
CAV1 -0.025 0.17 -9999 0 -0.73 21 21
SHC/Grb2/SOS1 -0.11 0.19 -9999 0 -0.47 67 67
PDGF/PDGFRA/Shf -0.17 0.3 -9999 0 -0.61 107 107
FOS -0.22 0.42 -9999 0 -1.1 57 57
JUN -0.046 0.13 -9999 0 -0.56 22 22
oligodendrocyte development -0.16 0.26 -9999 0 -0.56 107 107
GRB2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
mol:DAG -0.14 0.27 -9999 0 -0.56 105 105
PDGF/PDGFRA -0.2 0.34 -9999 0 -0.74 105 105
actin cytoskeleton reorganization -0.15 0.25 -9999 0 -0.54 105 105
SRF 0.031 0.042 -9999 0 -0.43 3 3
SHC1 0.014 0.032 -9999 0 -0.61 1 1
PI3K -0.13 0.21 -9999 0 -0.52 69 69
PDGF/PDGFRA/Crk/C3G -0.13 0.21 -9999 0 -0.52 67 67
JAK1 -0.13 0.26 -9999 0 -0.54 105 105
ELK1/SRF -0.11 0.19 -9999 0 -0.47 68 68
SHB 0.016 0 -9999 0 -10000 0 0
SHF -0.016 0.16 -9999 0 -0.8 15 15
CSNK2A1 0.02 0.025 -9999 0 -10000 0 0
GO:0007205 -0.14 0.27 -9999 0 -0.56 105 105
SOS1 0.016 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.11 0.19 -9999 0 -0.46 67 67
PDGF/PDGFRA/SHB -0.15 0.25 -9999 0 -0.55 105 105
PDGF/PDGFRA/Caveolin-1 -0.18 0.28 -9999 0 -0.57 120 120
ITGAV 0.007 0.085 -9999 0 -0.81 4 4
ELK1 -0.11 0.24 -9999 0 -0.56 72 72
PIK3CA 0.011 0.06 -9999 0 -0.81 2 2
PDGF/PDGFRA/Crk -0.15 0.25 -9999 0 -0.55 105 105
JAK-STAT cascade -0.13 0.26 -9999 0 -0.54 105 105
cell proliferation -0.17 0.3 -9999 0 -0.6 107 107
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.073 0.12 0.39 2 -10000 0 2
SMARCC2 0.017 0.012 -10000 0 -10000 0 0
SMARCC1 0.017 0.012 -10000 0 -10000 0 0
TBX21 -0.25 0.34 -10000 0 -0.78 87 87
SUMO2 0.018 0.014 -10000 0 -10000 0 0
STAT1 (dimer) -0.002 0.14 -10000 0 -0.77 12 12
FKBP4 0.013 0.045 -10000 0 -0.61 2 2
FKBP5 -0.018 0.15 -10000 0 -0.66 19 19
GR alpha/HSP90/FKBP51/HSP90 0.14 0.16 0.37 43 -0.42 1 44
PRL -0.14 0.14 -10000 0 -0.34 87 87
cortisol/GR alpha (dimer)/TIF2 0.32 0.33 0.6 176 -0.5 8 184
RELA -0.048 0.11 -10000 0 -10000 0 0
FGG 0.32 0.2 0.48 189 -10000 0 189
GR beta/TIF2 0.12 0.24 0.38 62 -0.52 35 97
IFNG -0.58 0.45 -10000 0 -1 143 143
apoptosis 0.083 0.21 0.53 41 -0.5 1 42
CREB1 0.012 0.039 -10000 0 -10000 0 0
histone acetylation -0.084 0.17 0.37 6 -0.43 34 40
BGLAP -0.15 0.19 -10000 0 -0.64 15 15
GR/PKAc 0.16 0.13 0.35 43 -10000 0 43
NF kappa B1 p50/RelA -0.095 0.19 -10000 0 -0.52 20 20
SMARCD1 0.017 0.012 -10000 0 -10000 0 0
MDM2 0.16 0.11 0.29 127 -10000 0 127
GATA3 -0.064 0.24 -10000 0 -0.79 38 38
AKT1 0.001 0.01 -10000 0 -10000 0 0
CSF2 -0.37 0.55 -10000 0 -1.4 76 76
GSK3B 0.018 0.014 -10000 0 -10000 0 0
NR1I3 0.1 0.23 0.55 30 -0.78 9 39
CSN2 0.26 0.16 0.39 178 -10000 0 178
BRG1/BAF155/BAF170/BAF60A -0.002 0.037 -10000 0 -0.4 1 1
NFATC1 0.004 0.096 -10000 0 -0.74 6 6
POU2F1 0.008 0.075 -10000 0 -0.71 4 4
CDKN1A -0.005 0.25 -10000 0 -1.6 9 9
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.002 0.013 -10000 0 -10000 0 0
SFN -0.25 0.37 -10000 0 -0.74 133 133
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.036 0.26 0.37 14 -0.66 12 26
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.075 0.28 0.51 34 -0.91 16 50
JUN -0.32 0.25 -10000 0 -0.63 109 109
IL4 -0.18 0.19 -10000 0 -0.36 165 165
CDK5R1 0.001 0.095 -10000 0 -0.61 9 9
PRKACA 0.016 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.35 0.33 0.27 1 -0.7 136 137
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.15 0.15 0.37 34 -10000 0 34
cortisol/GR alpha (monomer) 0.47 0.35 0.74 205 -10000 0 205
NCOA2 -0.061 0.24 -10000 0 -0.81 35 35
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.28 -10000 0 -0.78 65 65
AP-1/NFAT1-c-4 -0.6 0.42 -10000 0 -0.94 180 180
AFP -0.21 0.18 -10000 0 -0.46 80 80
SUV420H1 0.016 0 -10000 0 -10000 0 0
IRF1 0.23 0.19 0.5 69 -10000 0 69
TP53 0.033 0.074 -10000 0 -0.46 7 7
PPP5C 0.016 0 -10000 0 -10000 0 0
KRT17 -0.77 0.63 -10000 0 -1.3 197 197
KRT14 -0.5 0.57 -10000 0 -1.1 146 146
TBP 0.026 0.019 -10000 0 -10000 0 0
CREBBP 0.093 0.11 0.35 13 -10000 0 13
HDAC1 0.016 0 -10000 0 -10000 0 0
HDAC2 0.026 0.041 -10000 0 -10000 0 0
AP-1 -0.6 0.42 -10000 0 -0.95 180 180
MAPK14 0.017 0.012 -10000 0 -10000 0 0
MAPK10 0.015 0.045 -10000 0 -0.82 1 1
MAPK11 0.016 0.036 -10000 0 -0.62 1 1
KRT5 -0.72 0.57 -10000 0 -1.2 199 199
interleukin-1 receptor activity 0.017 0.038 -10000 0 -10000 0 0
NCOA1 0.021 0.007 -10000 0 -10000 0 0
STAT1 -0.002 0.14 -10000 0 -0.77 12 12
CGA -0.18 0.2 -10000 0 -0.59 35 35
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.28 0.25 0.57 131 -10000 0 131
MAPK3 0.017 0.013 -10000 0 -10000 0 0
MAPK1 0.017 0.012 -10000 0 -10000 0 0
ICAM1 -0.43 0.56 -10000 0 -1.1 114 114
NFKB1 -0.048 0.11 -10000 0 -10000 0 0
MAPK8 -0.27 0.23 -10000 0 -0.54 116 116
MAPK9 0.017 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.08 0.21 0.54 41 -0.52 1 42
BAX 0.024 0.07 -10000 0 -10000 0 0
POMC -0.41 0.53 -10000 0 -1.3 71 71
EP300 0.094 0.12 0.34 20 -0.82 1 21
cortisol/GR alpha (dimer)/p53 0.4 0.28 0.63 195 -10000 0 195
proteasomal ubiquitin-dependent protein catabolic process 0.11 0.083 0.24 52 -10000 0 52
SGK1 0.16 0.24 -10000 0 -1.5 5 5
IL13 -0.41 0.34 -10000 0 -0.87 97 97
IL6 -0.5 0.59 -10000 0 -1.1 146 146
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.35 0.27 -10000 0 -0.56 185 185
IL2 -0.46 0.32 -10000 0 -0.84 122 122
CDK5 0.016 0.008 -10000 0 -10000 0 0
PRKACB -0.001 0.1 -10000 0 -0.61 10 10
HSP90AA1 0.016 0 -10000 0 -10000 0 0
IL8 -0.51 0.62 -10000 0 -1.4 109 109
CDK5R1/CDK5 -0.002 0.071 -10000 0 -0.44 9 9
NF kappa B1 p50/RelA/PKAc -0.053 0.16 -10000 0 -0.59 9 9
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.37 0.25 0.59 182 -10000 0 182
SMARCA4 0.017 0.012 -10000 0 -10000 0 0
chromatin remodeling 0.26 0.16 0.43 145 -0.39 1 146
NF kappa B1 p50/RelA/Cbp 0.009 0.2 0.47 6 -0.59 2 8
JUN (dimer) -0.32 0.25 -10000 0 -0.62 109 109
YWHAH 0.016 0 -10000 0 -10000 0 0
VIPR1 -0.28 0.38 -10000 0 -0.9 87 87
NR3C1 0.29 0.23 0.54 131 -10000 0 131
NR4A1 -0.14 0.29 -10000 0 -0.65 85 85
TIF2/SUV420H1 -0.057 0.18 -10000 0 -0.62 35 35
MAPKKK cascade 0.083 0.21 0.53 41 -0.5 1 42
cortisol/GR alpha (dimer)/Src-1 0.4 0.27 0.62 197 -10000 0 197
PBX1 0.014 0.043 -10000 0 -0.81 1 1
POU1F1 -0.001 0.071 -10000 0 -0.61 5 5
SELE -0.45 0.52 -10000 0 -1.1 117 117
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.26 0.17 0.43 143 -0.4 1 144
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.37 0.25 0.59 182 -10000 0 182
mol:cortisol 0.28 0.24 0.44 216 -10000 0 216
MMP1 -0.36 0.51 -10000 0 -1.1 94 94
Glypican 2 network

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
MDK -0.082 0.26 -9999 0 -0.79 46 46
GPC2 -0.056 0.22 -9999 0 -0.72 37 37
GPC2/Midkine -0.12 0.27 -9999 0 -0.64 73 73
neuron projection morphogenesis -0.12 0.26 -9999 0 -0.63 73 73
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.33 0.42 -9999 0 -0.96 79 79
PCK1 -0.24 0.3 -9999 0 -0.81 47 47
HNF4A -0.39 0.48 -9999 0 -1 108 108
KCNJ11 -0.35 0.46 -9999 0 -1.1 68 68
AKT1 -0.047 0.14 -9999 0 -0.46 1 1
response to starvation -0.011 0.028 -9999 0 -10000 0 0
DLK1 -0.34 0.43 -9999 0 -0.88 107 107
NKX2-1 -0.074 0.22 -9999 0 -1.5 1 1
ACADM -0.33 0.42 -9999 0 -0.98 76 76
TAT -0.21 0.28 -9999 0 -0.88 28 28
CEBPB 0.016 0 -9999 0 -10000 0 0
CEBPA -0.021 0.15 -9999 0 -0.65 21 21
TTR -0.24 0.28 -9999 0 -0.62 99 99
PKLR -0.34 0.42 -9999 0 -0.98 80 80
APOA1 -0.46 0.58 -9999 0 -1.3 88 88
CPT1C -0.38 0.48 -9999 0 -1 92 92
ALAS1 -0.11 0.18 -9999 0 -10000 0 0
TFRC -0.26 0.34 -9999 0 -0.89 47 47
FOXF1 -0.027 0.14 -9999 0 -0.73 14 14
NF1 0.025 0.001 -9999 0 -10000 0 0
HNF1A (dimer) 0.014 0.042 -9999 0 -0.81 1 1
CPT1A -0.33 0.42 -9999 0 -0.96 79 79
HMGCS1 -0.33 0.42 -9999 0 -0.98 75 75
NR3C1 0.019 0.028 -9999 0 -10000 0 0
CPT1B -0.34 0.45 -9999 0 -1 81 81
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.016 0 -9999 0 -10000 0 0
GCK -0.43 0.52 -9999 0 -1.1 98 98
CREB1 0.012 0.029 -9999 0 -10000 0 0
IGFBP1 -0.14 0.22 -9999 0 -0.79 12 12
PDX1 -0.13 0.18 -9999 0 -0.39 37 37
UCP2 -0.36 0.49 -9999 0 -1.1 76 76
ALDOB -0.35 0.44 -9999 0 -1 73 73
AFP -0.15 0.23 -9999 0 -0.44 116 116
BDH1 -0.33 0.42 -9999 0 -0.98 76 76
HADH -0.33 0.43 -9999 0 -1 63 63
F2 -0.37 0.46 -9999 0 -0.95 113 113
HNF1A 0.014 0.043 -9999 0 -0.81 1 1
G6PC -0.048 0.14 -9999 0 -0.38 11 11
SLC2A2 -0.17 0.22 -9999 0 -0.48 61 61
INS -0.008 0.031 -9999 0 -10000 0 0
FOXA1 -0.16 0.3 -9999 0 -0.72 79 79
FOXA3 -0.16 0.33 -9999 0 -0.74 90 90
FOXA2 -0.39 0.49 -9999 0 -1 105 105
ABCC8 -0.62 0.6 -9999 0 -1.2 163 163
ALB -0.21 0.38 -9999 0 -1 49 49
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.15 0.34 -9999 0 -0.88 58 58
alphaM/beta2 Integrin/GPIbA -0.16 0.33 -9999 0 -0.82 67 67
alphaM/beta2 Integrin/proMMP-9 -0.24 0.43 -9999 0 -0.93 85 85
PLAUR -0.15 0.32 -9999 0 -0.76 83 83
HMGB1 0.005 0.02 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.13 0.31 -9999 0 -0.87 51 51
AGER -0.12 0.28 -9999 0 -0.72 64 64
RAP1A 0.016 0 -9999 0 -10000 0 0
SELPLG -0.03 0.18 -9999 0 -0.74 23 23
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.25 0.37 -9999 0 -0.89 76 76
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.18 0.33 -9999 0 -0.73 100 100
CYR61 -0.044 0.19 -9999 0 -0.65 34 34
TLN1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP -0.24 0.33 -9999 0 -0.77 82 82
RHOA 0.016 0 -9999 0 -10000 0 0
P-selectin oligomer -0.041 0.2 -9999 0 -0.75 28 28
MYH2 -0.26 0.34 -9999 0 -0.7 111 111
MST1R -0.098 0.28 -9999 0 -0.81 52 52
leukocyte activation during inflammatory response -0.15 0.3 -9999 0 -0.85 51 51
APOB -0.039 0.17 -9999 0 -0.62 30 30
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.029 0.18 -9999 0 -0.72 23 23
JAM3 0.012 0.053 -9999 0 -0.71 2 2
GP1BA -0.045 0.2 -9999 0 -0.66 34 34
alphaM/beta2 Integrin/CTGF -0.18 0.34 -9999 0 -0.82 68 68
alphaM/beta2 Integrin -0.28 0.43 -9999 0 -0.78 118 118
JAM3 homodimer 0.012 0.053 -9999 0 -0.71 2 2
ICAM2 0.01 0.062 -9999 0 -0.68 3 3
ICAM1 -0.1 0.29 -9999 0 -0.81 53 53
phagocytosis triggered by activation of immune response cell surface activating receptor -0.27 0.41 -9999 0 -0.75 118 118
cell adhesion -0.16 0.33 -9999 0 -0.81 67 67
NFKB1 -0.28 0.46 -9999 0 -1 82 82
THY1 -0.001 0.11 -9999 0 -0.68 9 9
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.053 0.14 -9999 0 -0.41 49 49
alphaM/beta2 Integrin/LRP/tPA -0.14 0.31 -9999 0 -0.82 57 57
IL6 -0.36 0.51 -9999 0 -1.1 111 111
ITGB2 -0.09 0.26 -9999 0 -0.77 46 46
elevation of cytosolic calcium ion concentration -0.31 0.5 -9999 0 -0.99 105 105
alphaM/beta2 Integrin/JAM2/JAM3 -0.12 0.3 -9999 0 -0.87 48 48
JAM2 0.002 0.1 -9999 0 -0.76 7 7
alphaM/beta2 Integrin/ICAM1 -0.24 0.46 -9999 0 -1 77 77
alphaM/beta2 Integrin/uPA/Plg -0.24 0.4 -9999 0 -0.83 91 91
RhoA/GTP -0.28 0.38 -9999 0 -0.77 111 111
positive regulation of phagocytosis -0.23 0.34 -9999 0 -0.83 77 77
Ron/MSP -0.1 0.24 -9999 0 -0.65 59 59
alphaM/beta2 Integrin/uPAR/uPA -0.32 0.52 -9999 0 -1 105 105
alphaM/beta2 Integrin/uPAR -0.23 0.44 -9999 0 -0.88 92 92
PLAU -0.2 0.34 -9999 0 -0.73 108 108
PLAT -0.025 0.17 -9999 0 -0.72 21 21
actin filament polymerization -0.24 0.32 -9999 0 -0.65 111 111
MST1 -0.007 0.13 -9999 0 -0.78 11 11
alphaM/beta2 Integrin/lipoprotein(a) -0.16 0.31 -9999 0 -0.87 51 51
TNF -0.31 0.49 -9999 0 -1 98 98
RAP1B 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.25 0.42 -9999 0 -0.87 94 94
fibrinolysis -0.23 0.39 -9999 0 -0.82 91 91
HCK -0.067 0.24 -9999 0 -0.75 41 41
dendritic cell antigen processing and presentation -0.27 0.41 -9999 0 -0.75 118 118
VTN -0.085 0.25 -9999 0 -0.69 54 54
alphaM/beta2 Integrin/CYR61 -0.16 0.34 -9999 0 -0.86 59 59
LPA -0.031 0.14 -9999 0 -0.61 22 22
LRP1 0.009 0.073 -9999 0 -0.81 3 3
cell migration -0.25 0.43 -9999 0 -0.9 89 89
FN1 -0.27 0.38 -9999 0 -0.78 135 135
alphaM/beta2 Integrin/Thy1 -0.14 0.32 -9999 0 -0.86 54 54
MPO -0.066 0.23 -9999 0 -0.72 41 41
KNG1 -0.019 0.12 -9999 0 -0.61 16 16
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.25 0.34 -9999 0 -0.72 104 104
ELA2 0 0 -9999 0 -10000 0 0
PLG 0 0 -9999 0 -10000 0 0
CTGF -0.072 0.23 -9999 0 -0.68 48 48
alphaM/beta2 Integrin/Hck -0.17 0.42 -9999 0 -1 59 59
ITGAM -0.086 0.26 -9999 0 -0.79 43 43
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.17 0.4 -9999 0 -0.99 59 59
HP -0.18 0.32 -9999 0 -0.71 103 103
leukocyte adhesion -0.22 0.34 -9999 0 -0.88 64 64
SELP -0.041 0.2 -9999 0 -0.76 28 28
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.17 0.24 -9999 0 -0.57 67 67
FZD6 0.016 0 -9999 0 -10000 0 0
WNT6 -0.067 0.24 -9999 0 -0.74 41 41
WNT4 -0.21 0.33 -9999 0 -0.68 124 124
FZD3 0.016 0 -9999 0 -10000 0 0
WNT5A -0.043 0.21 -9999 0 -0.8 27 27
WNT11 -0.18 0.32 -9999 0 -0.69 107 107
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.066 0.059 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.15 0.15 -9999 0 -0.49 28 28
JUN -0.14 0.2 -9999 0 -0.54 43 43
HRAS 0.013 0.045 -9999 0 -0.61 2 2
RET51/GFRalpha1/GDNF/GRB10 -0.29 0.27 -9999 0 -0.59 128 128
RAP1A 0.016 0 -9999 0 -10000 0 0
FRS2 0.016 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.28 0.27 -9999 0 -0.59 128 128
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.14 0.2 -9999 0 -0.43 122 122
RHOA 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.25 0.24 -9999 0 -0.52 128 128
GRB7 -0.054 0.23 -9999 0 -0.81 32 32
RET51/GFRalpha1/GDNF -0.28 0.27 -9999 0 -0.59 128 128
MAPKKK cascade -0.21 0.21 -9999 0 -0.6 41 41
BCAR1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.14 0.22 -9999 0 -0.44 125 125
lamellipodium assembly -0.14 0.14 -9999 0 -0.44 30 30
RET51/GFRalpha1/GDNF/SHC -0.28 0.27 -9999 0 -0.59 128 128
PIK3CA 0.011 0.06 -9999 0 -0.81 2 2
RET9/GFRalpha1/GDNF/SHC -0.14 0.2 -9999 0 -0.42 122 122
RET9/GFRalpha1/GDNF/Shank3 -0.14 0.2 -9999 0 -0.42 121 121
MAPK3 -0.22 0.25 -9999 0 -0.66 41 41
DOK1 0.016 0 -9999 0 -10000 0 0
DOK6 -0.07 0.24 -9999 0 -0.7 45 45
PXN 0.016 0 -9999 0 -10000 0 0
neurite development -0.23 0.21 -9999 0 -0.59 60 60
DOK5 -0.064 0.22 -9999 0 -0.67 44 44
GFRA1 -0.22 0.34 -9999 0 -0.71 121 121
MAPK8 -0.14 0.18 -9999 0 -0.56 25 25
HRAS/GTP -0.24 0.24 -9999 0 -0.53 128 128
tube development -0.12 0.19 -9999 0 -0.47 60 60
MAPK1 -0.22 0.25 -9999 0 -0.66 41 41
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.059 0.14 -9999 0 -0.33 60 60
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.012 0.053 -9999 0 -0.71 2 2
PDLIM7 0.012 0.053 -9999 0 -0.71 2 2
RET51/GFRalpha1/GDNF/Dok6 -0.31 0.29 -9999 0 -0.62 140 140
SHC1 0.014 0.032 -9999 0 -0.61 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.28 0.27 -9999 0 -0.59 128 128
RET51/GFRalpha1/GDNF/Dok5 -0.33 0.29 -9999 0 -0.63 142 142
PRKCA -0.022 0.15 -9999 0 -0.64 22 22
HRAS/GDP -0.002 0.033 -9999 0 -0.45 2 2
CREB1 -0.13 0.16 -9999 0 -0.43 62 62
PIK3R1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.06 0.14 -9999 0 -0.33 60 60
RET51/GFRalpha1/GDNF/Grb7 -0.33 0.28 -9999 0 -0.6 153 153
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.26 0.35 -9999 0 -0.69 146 146
DOK4 0.016 0 -9999 0 -10000 0 0
JNK cascade -0.14 0.2 -9999 0 -0.53 43 43
RET9/GFRalpha1/GDNF/FRS2 -0.14 0.2 -9999 0 -0.42 121 121
SHANK3 0.016 0 -9999 0 -10000 0 0
RASA1 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.06 0.14 -9999 0 -0.34 60 60
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.16 0.19 -9999 0 -0.49 41 41
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.16 0.19 -9999 0 -0.49 41 41
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.16 0.22 -9999 0 -0.4 128 128
PI3K -0.19 0.26 -9999 0 -0.59 69 69
SOS1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.12 0.19 -9999 0 -0.47 60 60
GRB10 0.014 0.043 -9999 0 -0.81 1 1
activation of MAPKK activity -0.13 0.16 -9999 0 -0.52 21 21
RET51/GFRalpha1/GDNF/FRS2 -0.28 0.27 -9999 0 -0.59 128 128
GAB1 0.016 0 -9999 0 -10000 0 0
IRS1 0.001 0.11 -9999 0 -0.71 8 8
IRS2 -0.01 0.14 -9999 0 -0.81 12 12
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.16 0.22 -9999 0 -0.4 128 128
RET51/GFRalpha1/GDNF/PKC alpha -0.3 0.28 -9999 0 -0.61 134 134
GRB2 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GDNF 0 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.29 0.28 -9999 0 -0.6 130 130
Rac1/GTP -0.17 0.17 -9999 0 -0.54 30 30
RET9/GFRalpha1/GDNF -0.15 0.22 -9999 0 -0.47 121 121
GFRalpha1/GDNF -0.17 0.26 -9999 0 -0.54 121 121
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.013 0.078 -9999 0 -0.53 6 6
NFATC2 -0.065 0.18 -9999 0 -0.56 40 40
NFATC3 -0.004 0.042 -9999 0 -10000 0 0
CD40LG -0.41 0.46 -9999 0 -0.95 133 133
PTGS2 -0.42 0.45 -9999 0 -0.9 145 145
JUNB 0.002 0.1 -9999 0 -0.73 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.013 0.018 -9999 0 -10000 0 0
CaM/Ca2+ -0.013 0.018 -9999 0 -10000 0 0
CALM1 0.008 0.012 -9999 0 -10000 0 0
JUN -0.032 0.16 -9999 0 -0.68 22 22
mol:Ca2+ -0.015 0.017 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.001 0.003 -9999 0 -10000 0 0
FOSL1 -0.096 0.26 -9999 0 -0.69 60 60
CREM 0.016 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.23 0.27 -9999 0 -0.76 63 63
FOS -0.12 0.28 -9999 0 -0.73 65 65
IFNG -0.42 0.44 -9999 0 -0.9 143 143
AP-1/NFAT1-c-4 -0.51 0.5 -9999 0 -1 155 155
FASLG -0.41 0.46 -9999 0 -0.93 140 140
NFAT1-c-4/ICER1 -0.11 0.17 -9999 0 -0.58 30 30
IL2RA -0.4 0.46 -9999 0 -0.92 135 135
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.42 0.46 -9999 0 -0.9 150 150
JunB/Fra1/NFAT1-c-4 -0.16 0.23 -9999 0 -0.67 51 51
IL4 -0.36 0.39 -9999 0 -0.8 137 137
IL2 -0.022 0.08 -9999 0 -10000 0 0
IL3 -0.04 0.091 -9999 0 -1.2 2 2
FKBP1A 0.016 0 -9999 0 -10000 0 0
BATF3 -0.067 0.23 -9999 0 -0.71 43 43
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.008 0.075 -9999 0 -0.71 4 4
Endothelins

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
AKT1 -0.12 0.3 -10000 0 -0.85 32 32
PTK2B 0.009 0.074 -10000 0 -0.81 3 3
mol:Ca2+ -0.053 0.24 -10000 0 -0.74 20 20
EDN1 -0.097 0.25 -10000 0 -0.76 33 33
EDN3 -0.4 0.36 -10000 0 -0.71 216 216
EDN2 -0.089 0.25 -10000 0 -0.69 56 56
HRAS/GDP -0.091 0.24 -10000 0 -0.62 40 40
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.089 0.23 -10000 0 -0.56 48 48
ADCY4 -0.13 0.29 -10000 0 -0.73 49 49
ADCY5 -0.2 0.34 -10000 0 -0.74 77 77
ADCY6 -0.13 0.28 -10000 0 -0.73 48 48
ADCY7 -0.13 0.3 -10000 0 -0.76 49 49
ADCY1 -0.15 0.32 -10000 0 -0.74 63 63
ADCY2 -0.2 0.33 -10000 0 -0.74 77 77
ADCY3 -0.13 0.28 -10000 0 -0.73 48 48
ADCY8 -0.31 0.35 -10000 0 -0.75 107 107
ADCY9 -0.13 0.29 -10000 0 -0.74 48 48
arachidonic acid secretion -0.093 0.26 -10000 0 -0.58 56 56
ETB receptor/Endothelin-1/Gq/GTP -0.096 0.22 -10000 0 -0.55 51 51
GNAO1 -0.069 0.25 -10000 0 -0.79 40 40
HRAS 0.011 0.045 -10000 0 -0.61 2 2
ETA receptor/Endothelin-1/G12/GTP -0.1 0.3 0.36 44 -0.78 34 78
ETA receptor/Endothelin-1/Gs/GTP -0.14 0.32 0.34 40 -0.78 49 89
mol:GTP 0.001 0.005 -10000 0 -10000 0 0
COL3A1 -0.18 0.4 -10000 0 -0.87 74 74
EDNRB -0.059 0.22 -10000 0 -0.75 34 34
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.28 0.46 -10000 0 -0.92 106 106
CYSLTR1 -0.13 0.33 -10000 0 -0.9 37 37
SLC9A1 -0.062 0.14 -10000 0 -0.38 22 22
mol:GDP -0.11 0.26 -10000 0 -0.63 48 48
SLC9A3 -0.092 0.27 -10000 0 -0.73 37 37
RAF1 -0.11 0.26 -10000 0 -0.62 48 48
JUN -0.065 0.27 -10000 0 -0.83 23 23
JAK2 -0.12 0.3 -10000 0 -0.86 31 31
mol:IP3 -0.1 0.25 -10000 0 -0.58 54 54
ETA receptor/Endothelin-1 -0.14 0.36 0.42 45 -0.86 42 87
PLCB1 -0.013 0.14 -10000 0 -0.73 14 14
PLCB2 -0.037 0.19 -10000 0 -0.73 26 26
ETA receptor/Endothelin-3 -0.34 0.29 -10000 0 -0.57 207 207
FOS -0.14 0.35 -10000 0 -0.9 51 51
Gai/GDP -0.065 0.26 -10000 0 -0.83 36 36
CRK 0.016 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.17 0.34 -10000 0 -0.79 60 60
BCAR1 0.016 0.001 -10000 0 -10000 0 0
PRKCB1 -0.099 0.24 -10000 0 -0.56 54 54
GNAQ 0.015 0.008 -10000 0 -10000 0 0
GNAZ 0.002 0.1 -10000 0 -0.76 7 7
GNAL -0.052 0.22 -10000 0 -0.72 35 35
Gs family/GDP -0.16 0.24 -10000 0 -0.64 60 60
ETA receptor/Endothelin-1/Gq/GTP -0.093 0.24 -10000 0 -0.55 54 54
MAPK14 -0.077 0.22 -10000 0 -0.54 44 44
TRPC6 -0.057 0.25 -10000 0 -0.81 18 18
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 -0.012 0.13 -10000 0 -0.61 17 17
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.092 0.23 -10000 0 -0.53 56 56
ETB receptor/Endothelin-2 -0.13 0.25 -10000 0 -0.58 82 82
ETB receptor/Endothelin-3 -0.35 0.31 -10000 0 -0.57 231 231
ETB receptor/Endothelin-1 -0.13 0.26 -10000 0 -0.65 59 59
MAPK3 -0.13 0.32 -10000 0 -0.76 58 58
MAPK1 -0.13 0.32 -10000 0 -0.74 61 61
Rac1/GDP -0.089 0.24 -10000 0 -0.62 38 38
cAMP biosynthetic process -0.2 0.29 -10000 0 -0.71 64 64
MAPK8 -0.071 0.26 -10000 0 -0.66 36 36
SRC 0.012 0.053 -10000 0 -0.71 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.056 0.18 -10000 0 -0.5 32 32
p130Cas/CRK/Src/PYK2 -0.082 0.26 -10000 0 -0.65 40 40
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.089 0.24 -10000 0 -0.61 41 41
COL1A2 -0.19 0.4 -10000 0 -0.86 75 75
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.11 0.22 -10000 0 -0.57 61 61
mol:DAG -0.1 0.25 -10000 0 -0.58 54 54
MAP2K2 -0.11 0.28 -10000 0 -0.62 61 61
MAP2K1 -0.11 0.28 -10000 0 -0.67 47 47
EDNRA -0.055 0.18 -10000 0 -0.84 9 9
positive regulation of muscle contraction -0.092 0.27 -10000 0 -0.77 31 31
Gq family/GDP -0.16 0.27 -10000 0 -0.73 55 55
HRAS/GTP -0.11 0.25 -10000 0 -0.61 49 49
PRKCH -0.091 0.24 -10000 0 -0.62 40 40
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA -0.11 0.26 -10000 0 -0.61 56 56
PRKCB -0.15 0.29 -10000 0 -0.66 65 65
PRKCE -0.091 0.24 -10000 0 -0.62 40 40
PRKCD -0.089 0.24 -10000 0 -0.62 39 39
PRKCG -0.11 0.24 -10000 0 -0.62 44 44
regulation of vascular smooth muscle contraction -0.16 0.4 -10000 0 -1.1 49 49
PRKCQ -0.091 0.24 -10000 0 -0.61 41 41
PLA2G4A -0.1 0.28 -10000 0 -0.64 56 56
GNA14 -0.077 0.23 -10000 0 -0.64 54 54
GNA15 -0.085 0.26 -10000 0 -0.76 49 49
GNA12 0.016 0 -10000 0 -10000 0 0
GNA11 -0.009 0.14 -10000 0 -0.81 11 11
Rac1/GTP -0.1 0.3 0.36 43 -0.81 31 74
MMP1 -0.16 0.44 -10000 0 -0.85 93 93
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.055 0.21 0.67 39 -10000 0 39
PI3K Class IB/PDE3B -0.055 0.21 -10000 0 -0.67 39 39
PDE3B -0.055 0.21 -10000 0 -0.67 39 39
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.016 0 -9999 0 -10000 0 0
ITGB7 -0.085 0.26 -9999 0 -0.73 51 51
ITGA4 -0.04 0.18 -9999 0 -0.64 32 32
alpha4/beta7 Integrin -0.11 0.23 -9999 0 -0.55 78 78
alpha4/beta1 Integrin -0.04 0.13 -9999 0 -0.47 32 32
HIF-1-alpha transcription factor network

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
PKM2 -0.13 0.56 -9999 0 -1.2 52 52
HDAC7 0.019 0.006 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.2 0.34 -9999 0 -0.87 47 47
SMAD4 0.018 0.004 -9999 0 -10000 0 0
ID2 -0.13 0.55 -9999 0 -1.2 50 50
AP1 -0.12 0.25 -9999 0 -0.62 73 73
ABCG2 -0.16 0.58 -9999 0 -1.2 55 55
HIF1A 0.009 0.096 -9999 0 -0.77 1 1
TFF3 -0.3 0.62 -9999 0 -1.2 81 81
GATA2 0.008 0.082 -9999 0 -0.69 5 5
AKT1 0.001 0.11 -9999 0 -10000 0 0
response to hypoxia -0.022 0.12 -9999 0 -10000 0 0
MCL1 -0.13 0.55 -9999 0 -1.2 50 50
NDRG1 -0.13 0.55 -9999 0 -1.2 50 50
SERPINE1 -0.17 0.58 -9999 0 -1.2 61 61
FECH -0.13 0.55 -9999 0 -1.2 51 51
FURIN -0.13 0.55 -9999 0 -1.2 50 50
NCOA2 -0.059 0.24 -9999 0 -0.81 35 35
EP300 0.007 0.19 -9999 0 -0.35 14 14
HMOX1 -0.15 0.58 -9999 0 -1.2 54 54
BHLHE40 -0.15 0.59 -9999 0 -1.3 56 56
BHLHE41 -0.14 0.57 -9999 0 -1.2 53 53
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.008 0.055 -9999 0 -10000 0 0
ENG 0.084 0.13 -9999 0 -0.64 1 1
JUN -0.023 0.16 -9999 0 -0.66 22 22
RORA -0.14 0.56 -9999 0 -1.2 50 50
ABCB1 -0.077 0.23 -9999 0 -1.4 10 10
TFRC -0.13 0.55 -9999 0 -1.2 51 51
CXCR4 -0.16 0.58 -9999 0 -1.2 53 53
TF -0.17 0.59 -9999 0 -1.2 60 60
CITED2 -0.14 0.56 -9999 0 -1.2 51 51
HIF1A/ARNT -0.29 0.57 -9999 0 -1.3 67 67
LDHA -0.026 0.044 -9999 0 -10000 0 0
ETS1 -0.13 0.56 -9999 0 -1.2 50 50
PGK1 -0.13 0.55 -9999 0 -1.2 50 50
NOS2 -0.18 0.59 -9999 0 -1.3 55 55
ITGB2 -0.17 0.61 -9999 0 -1.3 59 59
ALDOA -0.13 0.56 -9999 0 -1.2 51 51
Cbp/p300/CITED2 -0.18 0.57 -9999 0 -1.2 53 53
FOS -0.11 0.28 -9999 0 -0.72 65 65
HK2 -0.14 0.57 -9999 0 -1.2 52 52
SP1 0.027 0.008 -9999 0 -10000 0 0
GCK -0.13 0.51 -9999 0 -1.1 55 55
HK1 -0.13 0.55 -9999 0 -1.2 50 50
NPM1 -0.13 0.55 -9999 0 -1.2 50 50
EGLN1 -0.13 0.55 -9999 0 -1.2 51 51
CREB1 0.026 0 -9999 0 -10000 0 0
PGM1 -0.13 0.55 -9999 0 -1.2 50 50
SMAD3 0.018 0.004 -9999 0 -10000 0 0
EDN1 -0.067 0.34 -9999 0 -0.97 25 25
IGFBP1 -0.16 0.57 -9999 0 -1.2 53 53
VEGFA -0.042 0.41 -9999 0 -0.85 22 22
HIF1A/JAB1 -0.01 0.038 -9999 0 -0.58 1 1
CP -0.28 0.64 -9999 0 -1.3 81 81
CXCL12 -0.16 0.59 -9999 0 -1.3 56 56
COPS5 0.017 0.002 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.005 -9999 0 -10000 0 0
BNIP3 -0.13 0.56 -9999 0 -1.2 50 50
EGLN3 -0.2 0.62 -9999 0 -1.3 66 66
CA9 -0.17 0.58 -9999 0 -1.3 54 54
TERT -0.14 0.55 -9999 0 -1.1 59 59
ENO1 -0.13 0.55 -9999 0 -1.2 50 50
PFKL -0.13 0.55 -9999 0 -1.2 50 50
NCOA1 0.016 0.001 -9999 0 -10000 0 0
ADM -0.16 0.59 -9999 0 -1.3 56 56
ARNT 0.008 0.086 -9999 0 -10000 0 0
HNF4A -0.015 0.041 -9999 0 -10000 0 0
ADFP -0.14 0.55 -9999 0 -1.1 59 59
SLC2A1 -0.041 0.41 -9999 0 -0.84 22 22
LEP -0.17 0.57 -9999 0 -1.2 60 60
HIF1A/ARNT/Cbp/p300 -0.19 0.38 -9999 0 -0.89 51 51
EPO -0.044 0.37 -9999 0 -1 14 14
CREBBP 0.008 0.19 -9999 0 -0.36 12 12
HIF1A/ARNT/Cbp/p300/HDAC7 -0.2 0.34 -9999 0 -0.9 40 40
PFKFB3 -0.14 0.57 -9999 0 -1.2 51 51
NT5E -0.17 0.6 -9999 0 -1.3 57 57
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.002 0.032 -9999 0 -0.62 1 1
Necdin/E2F1 -0.028 0.13 -9999 0 -0.6 18 18
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.12 0.2 -9999 0 -0.47 74 74
NGF (dimer)/p75(NTR)/BEX1 -0.28 0.32 -9999 0 -0.67 130 130
NT-4/5 (dimer)/p75(NTR) -0.24 0.33 -9999 0 -0.64 143 143
IKBKB 0.016 0 -9999 0 -10000 0 0
AKT1 -0.086 0.22 -9999 0 -0.47 76 76
IKBKG 0.016 0 -9999 0 -10000 0 0
BDNF -0.084 0.25 -9999 0 -0.71 52 52
MGDIs/NGR/p75(NTR)/LINGO1 -0.15 0.24 -9999 0 -0.58 73 73
FURIN 0.016 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.19 0.27 -9999 0 -0.59 94 94
LINGO1 -0.008 0.12 -9999 0 -0.64 14 14
Sortilin/TRAF6/NRIF -0.001 0.02 -9999 0 -10000 0 0
proBDNF (dimer) -0.084 0.25 -9999 0 -0.71 52 52
NTRK1 -0.054 0.19 -9999 0 -0.62 40 40
RTN4R 0.007 0.085 -9999 0 -0.81 4 4
neuron apoptosis -0.1 0.25 -9999 0 -0.78 16 16
IRAK1 0.016 0 -9999 0 -10000 0 0
SHC1 -0.12 0.25 -9999 0 -0.49 113 113
ARHGDIA 0.016 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.13 0.21 -9999 0 -0.51 74 74
MAGEH1 0.016 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.14 0.22 -9999 0 -0.52 80 80
Mammalian IAPs/DIABLO -0.092 0.18 -9999 0 -0.48 48 48
proNGF (dimer) -0.014 0.14 -9999 0 -0.68 16 16
MAGED1 0.016 0 -9999 0 -10000 0 0
APP 0.016 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.12 0.29 -9999 0 -0.74 67 67
ZNF274 0.016 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.12 0.2 -9999 0 -0.48 74 74
NGF -0.014 0.14 -9999 0 -0.69 16 16
cell cycle arrest -0.085 0.23 -9999 0 -0.46 74 74
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.048 0.16 -9999 0 -0.51 7 7
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.21 0.29 -9999 0 -0.62 106 106
NCSTN 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.15 0.24 -9999 0 -0.58 74 74
PSENEN 0.016 0 -9999 0 -10000 0 0
mol:ceramide -0.098 0.23 -9999 0 -0.5 74 74
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.023 0.13 -9999 0 -0.5 4 4
p75(NTR)/beta APP -0.15 0.25 -9999 0 -0.56 101 101
BEX1 -0.21 0.34 -9999 0 -0.71 117 117
mol:GDP -0.13 0.25 -9999 0 -0.5 112 112
NGF (dimer) -0.2 0.24 -9999 0 -0.53 98 98
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.13 0.22 -9999 0 -0.53 73 73
PIK3R1 0.016 0 -9999 0 -10000 0 0
RAC1/GTP -0.13 0.2 -9999 0 -0.49 74 74
MYD88 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.16 0.25 -9999 0 -0.58 74 74
RHOB 0.008 0.071 -9999 0 -0.61 5 5
RHOA 0.016 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.014 0.092 -9999 0 -0.6 9 9
NT3 (dimer) -0.12 0.28 -9999 0 -0.7 70 70
TP53 -0.11 0.24 -9999 0 -0.72 16 16
PRDM4 -0.099 0.23 -9999 0 -0.5 74 74
BDNF (dimer) -0.3 0.3 -9999 0 -0.62 140 140
PIK3CA 0.011 0.06 -9999 0 -0.81 2 2
SORT1 0.016 0 -9999 0 -10000 0 0
activation of caspase activity -0.12 0.2 -9999 0 -0.46 74 74
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.13 0.22 -9999 0 -0.51 75 75
RHOC 0.016 0 -9999 0 -10000 0 0
XIAP 0.016 0 -9999 0 -10000 0 0
MAPK10 -0.072 0.22 -9999 0 -0.65 13 13
DIABLO 0.016 0 -9999 0 -10000 0 0
SMPD2 -0.099 0.23 -9999 0 -0.5 74 74
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.15 0.23 -9999 0 -0.56 74 74
PSEN1 0.016 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.24 0.31 -9999 0 -0.59 156 156
MAPK8 -0.074 0.22 -9999 0 -0.7 11 11
MAPK9 -0.071 0.22 -9999 0 -0.66 12 12
APAF1 0.016 0 -9999 0 -10000 0 0
NTF3 -0.12 0.28 -9999 0 -0.7 70 70
NTF4 -0.12 0.29 -9999 0 -0.74 67 67
NDN -0.003 0.12 -9999 0 -0.79 9 9
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.12 0.19 -9999 0 -0.75 10 10
p75 CTF/Sortilin/TRAF6/NRIF -0.005 0.06 -9999 0 -0.64 3 3
RhoA-B-C/GTP -0.15 0.24 -9999 0 -0.57 74 74
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.16 0.23 -9999 0 -0.77 16 16
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.17 0.24 -9999 0 -0.54 95 95
PRKACB -0.001 0.1 -9999 0 -0.61 10 10
proBDNF (dimer)/p75 ECD -0.078 0.19 -9999 0 -0.54 55 55
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.15 0.31 -9999 0 -0.73 84 84
BIRC2 0.016 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.077 0.24 -9999 0 -0.54 41 41
BAD -0.062 0.22 -9999 0 -0.65 11 11
RIPK2 0.016 0 -9999 0 -10000 0 0
NGFR -0.19 0.34 -9999 0 -0.75 101 101
CYCS -0.091 0.23 -9999 0 -0.73 11 11
ADAM17 0.009 0.073 -9999 0 -0.81 3 3
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.13 0.22 -9999 0 -0.51 75 75
BCL2L11 -0.062 0.22 -9999 0 -0.65 11 11
BDNF (dimer)/p75(NTR) -0.22 0.31 -9999 0 -0.6 138 138
PI3K -0.13 0.22 -9999 0 -0.51 76 76
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.13 0.21 -9999 0 -0.51 74 74
NDNL2 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
PRKCI 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.17 0.27 -9999 0 -0.58 112 112
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.13 0.21 -9999 0 -0.51 74 74
TRAF6 0.014 0.043 -9999 0 -0.81 1 1
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCZ 0.014 0.032 -9999 0 -0.61 1 1
PLG 0 0 -9999 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.14 0.26 -9999 0 -0.56 79 79
SQSTM1 0.016 0 -9999 0 -10000 0 0
NGFRAP1 0.016 0 -9999 0 -10000 0 0
CASP3 -0.053 0.2 -9999 0 -0.58 11 11
E2F1 -0.003 0.12 -9999 0 -0.79 9 9
CASP9 0.016 0 -9999 0 -10000 0 0
IKK complex -0.075 0.12 -9999 0 -0.62 4 4
NGF (dimer)/TRKA -0.068 0.17 -9999 0 -0.47 55 55
MMP7 -0.31 0.37 -9999 0 -0.72 165 165
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.12 0.2 -9999 0 -0.74 7 7
MMP3 -0.094 0.25 -9999 0 -0.68 55 55
APAF-1/Caspase 9 -0.15 0.2 -9999 0 -0.64 35 35
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.14 0.18 -10000 0 -0.43 60 60
IKBKB -0.066 0.1 -10000 0 -0.42 1 1
AKT1 -0.12 0.13 -10000 0 -0.29 18 18
IKBKG -0.067 0.11 -10000 0 -0.45 1 1
CALM1 -0.089 0.13 0.3 1 -0.49 5 6
PIK3CA 0.012 0.06 -10000 0 -0.81 2 2
MAP3K1 -0.22 0.26 -10000 0 -0.59 88 88
MAP3K7 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ -0.1 0.14 0.3 1 -0.38 42 43
DOK1 0.016 0 -10000 0 -10000 0 0
AP-1 -0.08 0.11 -10000 0 -0.29 14 14
LYN 0.016 0 -10000 0 -10000 0 0
BLNK 0.003 0.1 -10000 0 -0.81 6 6
SHC1 0.014 0.032 -10000 0 -0.61 1 1
BCR complex -0.3 0.32 -10000 0 -0.6 192 192
CD22 -0.29 0.29 -10000 0 -0.74 83 83
CAMK2G -0.075 0.13 -10000 0 -0.47 4 4
CSNK2A1 0.016 0 -10000 0 -10000 0 0
INPP5D -0.011 0.13 -10000 0 -0.66 15 15
SHC/GRB2/SOS1 -0.19 0.2 -10000 0 -0.56 43 43
GO:0007205 -0.1 0.14 0.3 1 -0.38 42 43
SYK 0.016 0 -10000 0 -10000 0 0
ELK1 -0.091 0.14 0.3 1 -0.5 5 6
NFATC1 -0.18 0.22 -10000 0 -0.5 78 78
B-cell antigen/BCR complex -0.3 0.32 -10000 0 -0.6 192 192
PAG1/CSK -0.015 0.094 -10000 0 -0.58 10 10
NFKBIB -0.013 0.037 -10000 0 -10000 0 0
HRAS -0.097 0.15 -10000 0 -0.5 7 7
NFKBIA -0.012 0.036 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta -0.001 0.03 -10000 0 -10000 0 0
RasGAP/Csk -0.28 0.29 -10000 0 -0.77 64 64
mol:GDP -0.096 0.13 0.31 1 -0.36 42 43
PTEN 0.014 0.043 -10000 0 -0.81 1 1
CD79B -0.054 0.2 -10000 0 -0.62 42 42
NF-kappa-B/RelA/I kappa B alpha 0 0.029 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.23 0.24 -10000 0 -0.54 86 86
PIK3R1 0.016 0 -10000 0 -10000 0 0
mol:IP3 -0.11 0.14 0.3 1 -0.38 42 43
CSK 0.014 0.032 -10000 0 -0.61 1 1
FOS -0.14 0.18 -10000 0 -0.48 56 56
CHUK -0.067 0.11 -10000 0 -0.37 2 2
IBTK 0.016 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.16 0.2 -10000 0 -0.53 64 64
PTPN6 -0.27 0.27 -10000 0 -0.7 79 79
RELA 0.016 0 -10000 0 -10000 0 0
BCL2A1 -0.018 0.06 -10000 0 -0.13 68 68
VAV2 -0.31 0.3 -10000 0 -0.74 89 89
ubiquitin-dependent protein catabolic process -0.006 0.036 -10000 0 -10000 0 0
BTK -0.11 0.34 0.38 8 -1.2 31 39
CD19 -0.34 0.33 -10000 0 -0.67 156 156
MAP4K1 -0.1 0.27 -10000 0 -0.72 61 61
CD72 -0.018 0.14 -10000 0 -0.63 20 20
PAG1 -0.003 0.12 -10000 0 -0.79 9 9
MAPK14 -0.17 0.22 -10000 0 -0.54 57 57
SH3BP5 0.013 0.045 -10000 0 -0.61 2 2
PIK3AP1 -0.093 0.14 -10000 0 -0.57 8 8
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.16 0.24 -10000 0 -0.51 94 94
RAF1 -0.083 0.14 -10000 0 -0.5 5 5
RasGAP/p62DOK/SHIP -0.27 0.29 -10000 0 -0.76 69 69
CD79A -0.34 0.36 -10000 0 -0.69 192 192
re-entry into mitotic cell cycle -0.08 0.11 -10000 0 -0.28 14 14
RASA1 0.016 0 -10000 0 -10000 0 0
MAPK3 -0.053 0.13 -10000 0 -0.44 5 5
MAPK1 -0.053 0.13 -10000 0 -0.44 5 5
CD72/SHP1 -0.24 0.29 -10000 0 -0.72 77 77
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 -0.18 0.23 -10000 0 -0.54 60 60
actin cytoskeleton organization -0.24 0.27 -10000 0 -0.62 83 83
NF-kappa-B/RelA 0.006 0.057 -10000 0 -10000 0 0
Calcineurin -0.077 0.095 -10000 0 -0.43 2 2
PI3K -0.28 0.22 -10000 0 -0.57 105 105
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.11 0.14 -10000 0 -0.4 27 27
SOS1 0.016 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.28 0.38 -10000 0 -0.91 86 86
DAPP1 -0.3 0.4 -10000 0 -0.99 76 76
cytokine secretion -0.16 0.21 -10000 0 -0.46 78 78
mol:DAG -0.11 0.14 0.3 1 -0.38 42 43
PLCG2 0.007 0.077 -10000 0 -0.65 5 5
MAP2K1 -0.068 0.14 -10000 0 -0.48 6 6
B-cell antigen/BCR complex/FcgammaRIIB -0.33 0.33 -10000 0 -0.69 139 139
mol:PI-3-4-5-P3 -0.2 0.15 -10000 0 -0.39 89 89
ETS1 -0.063 0.12 -10000 0 -0.5 5 5
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.22 0.24 -10000 0 -0.64 43 43
B-cell antigen/BCR complex/LYN -0.23 0.26 -10000 0 -0.66 68 68
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.014 0.042 -10000 0 -0.81 1 1
RAC1 -0.26 0.29 -10000 0 -0.68 83 83
B-cell antigen/BCR complex/LYN/SYK -0.3 0.28 -10000 0 -0.73 82 82
CARD11 -0.19 0.25 -10000 0 -0.58 93 93
FCGR2B -0.099 0.27 -10000 0 -0.71 60 60
PPP3CA 0.016 0 -10000 0 -10000 0 0
BCL10 0.016 0 -10000 0 -10000 0 0
IKK complex -0.021 0.046 -10000 0 -0.14 1 1
PTPRC -0.095 0.26 -10000 0 -0.69 60 60
PDPK1 -0.12 0.12 -10000 0 -0.3 19 19
PPP3CB 0.016 0 -10000 0 -10000 0 0
PPP3CC 0.016 0 -10000 0 -10000 0 0
POU2F2 -0.006 0.045 -10000 0 -0.11 35 35
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.029 0.13 -10000 0 -0.57 19 19
fibroblast growth factor receptor signaling pathway -0.029 0.13 -10000 0 -0.56 19 19
LAMA1 -0.11 0.3 -10000 0 -0.81 59 59
PRNP 0.016 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.12 0.24 -10000 0 -0.58 76 76
SMAD2 0.029 0.088 -10000 0 -0.52 8 8
GPC1/PrPc/Cu2+ -0.006 0.051 -10000 0 -0.44 5 5
GPC1/Laminin alpha1 -0.1 0.23 -10000 0 -0.61 63 63
TDGF1 -0.18 0.32 -10000 0 -0.7 104 104
CRIPTO/GPC1 -0.15 0.24 -10000 0 -0.53 107 107
APP/GPC1 -0.007 0.059 -10000 0 -0.51 5 5
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.1 0.22 -10000 0 -0.55 47 47
FLT1 -0.008 0.14 -10000 0 -0.79 11 11
GPC1/TGFB/TGFBR1/TGFBR2 -0.015 0.09 -10000 0 -0.57 8 8
SERPINC1 0.007 0.07 -10000 0 -0.66 4 4
FYN -0.1 0.22 -10000 0 -0.55 49 49
FGR -0.12 0.24 -10000 0 -0.56 61 61
positive regulation of MAPKKK cascade -0.18 0.28 -10000 0 -0.65 71 71
SLIT2 -0.13 0.31 -10000 0 -0.77 72 72
GPC1/NRG -0.086 0.21 -10000 0 -0.59 55 55
NRG1 -0.092 0.27 -10000 0 -0.77 52 52
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.024 0.11 -10000 0 -0.57 13 13
LYN -0.1 0.22 -10000 0 -0.55 47 47
mol:Spermine 0.008 0.062 -10000 0 -0.52 5 5
cell growth -0.029 0.13 -10000 0 -0.56 19 19
BMP signaling pathway -0.007 0.081 0.69 5 -10000 0 5
SRC -0.1 0.23 -10000 0 -0.55 48 48
TGFBR1 0.005 0.09 -10000 0 -0.77 5 5
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.32 0.37 -10000 0 -0.71 175 175
GPC1 0.007 0.081 -10000 0 -0.69 5 5
TGFBR1 (dimer) 0.005 0.09 -10000 0 -0.77 5 5
VEGFA 0.01 0.068 -10000 0 -0.74 3 3
BLK -0.26 0.31 -10000 0 -0.64 115 115
HCK -0.15 0.28 -10000 0 -0.61 73 73
FGF2 -0.008 0.14 -10000 0 -0.81 11 11
FGFR1 0.003 0.1 -10000 0 -0.81 6 6
VEGFR1 homodimer -0.008 0.14 -10000 0 -0.79 11 11
TGFBR2 0.011 0.06 -10000 0 -0.81 2 2
cell death -0.007 0.059 -10000 0 -0.51 5 5
ATIII/GPC1 -0.012 0.077 -10000 0 -0.5 9 9
PLA2G2A/GPC1 -0.25 0.28 -10000 0 -0.54 177 177
LCK -0.17 0.28 -10000 0 -0.62 73 73
neuron differentiation -0.086 0.21 -10000 0 -0.59 55 55
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.016 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.011 0.06 -10000 0 -0.81 2 2
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.07 0.25 -9999 0 -0.8 40 40
GNB1/GNG2 -0.17 0.2 -9999 0 -0.55 54 54
mol:DAG -0.12 0.2 -9999 0 -0.56 32 32
PLCG1 -0.12 0.21 -9999 0 -0.58 32 32
YES1 -0.15 0.23 -9999 0 -0.58 53 53
FZD3 0.016 0 -9999 0 -10000 0 0
FZD6 0.016 0 -9999 0 -10000 0 0
G protein -0.16 0.19 -9999 0 -0.6 36 36
MAP3K7 -0.11 0.19 -9999 0 -0.54 24 24
mol:Ca2+ -0.12 0.2 -9999 0 -0.54 32 32
mol:IP3 -0.12 0.2 -9999 0 -0.56 32 32
NLK -0.005 0.009 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.13 0.21 -9999 0 -0.56 37 37
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.17 0.24 -9999 0 -0.57 67 67
CSNK1A1 0.016 0 -9999 0 -10000 0 0
GNAS -0.16 0.24 -9999 0 -0.6 59 59
GO:0007205 -0.12 0.2 -9999 0 -0.54 32 32
WNT6 -0.067 0.24 -9999 0 -0.74 41 41
WNT4 -0.21 0.33 -9999 0 -0.68 124 124
NFAT1/CK1 alpha -0.19 0.22 -9999 0 -0.63 45 45
GNG2 0.011 0.055 -9999 0 -0.61 3 3
WNT5A -0.043 0.21 -9999 0 -0.8 27 27
WNT11 -0.18 0.32 -9999 0 -0.69 107 107
CDC42 -0.14 0.22 -9999 0 -0.54 53 53
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 -0.002 0.12 -10000 0 -0.81 8 8
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.087 0.19 0.53 25 -10000 0 25
IL27/IL27R/JAK1 -0.17 0.25 -10000 0 -0.76 26 26
TBX21 -0.16 0.31 -10000 0 -0.69 67 67
IL12B -0.074 0.22 -10000 0 -0.67 46 46
IL12A -0.049 0.17 -10000 0 -0.53 42 42
IL6ST -0.092 0.28 -10000 0 -0.82 48 48
IL27RA/JAK1 0.007 0.11 -10000 0 -1.1 3 3
IL27 -0.012 0.11 -10000 0 -0.62 11 11
TYK2 0.013 0.01 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.093 0.16 -10000 0 -0.32 99 99
T-helper 2 cell differentiation 0.087 0.19 0.53 25 -10000 0 25
T cell proliferation during immune response 0.087 0.19 0.53 25 -10000 0 25
MAPKKK cascade -0.087 0.19 -10000 0 -0.53 25 25
STAT3 0.016 0 -10000 0 -10000 0 0
STAT2 0.016 0 -10000 0 -10000 0 0
STAT1 -0.008 0.13 -10000 0 -0.73 12 12
IL12RB1 -0.1 0.26 -10000 0 -0.68 63 63
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.17 0.31 -10000 0 -0.69 66 66
IL27/IL27R/JAK2/TYK2 -0.089 0.19 -10000 0 -0.54 25 25
positive regulation of T cell mediated cytotoxicity -0.087 0.19 -10000 0 -0.53 25 25
STAT1 (dimer) -0.22 0.33 0.53 6 -0.86 53 59
JAK2 0.017 0.013 -10000 0 -10000 0 0
JAK1 0.016 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.076 0.18 -10000 0 -0.59 14 14
T cell proliferation -0.21 0.26 -10000 0 -0.6 81 81
IL12/IL12R/TYK2/JAK2 -0.11 0.25 -10000 0 -0.78 27 27
IL17A -0.093 0.16 -10000 0 -0.32 99 99
mast cell activation 0.087 0.19 0.53 25 -10000 0 25
IFNG -0.027 0.052 0.091 3 -0.11 60 63
T cell differentiation -0.007 0.009 0.02 3 -0.025 43 46
STAT3 (dimer) -0.076 0.18 -10000 0 -0.6 13 13
STAT5A (dimer) -0.076 0.18 -10000 0 -0.6 13 13
STAT4 (dimer) -0.15 0.28 -10000 0 -0.65 68 68
STAT4 -0.13 0.3 -10000 0 -0.74 72 72
T cell activation -0.012 0.013 0.1 4 -10000 0 4
IL27R/JAK2/TYK2 -0.066 0.19 -10000 0 -0.83 7 7
GATA3 -0.11 0.44 -10000 0 -1.5 34 34
IL18 -0.09 0.23 -10000 0 -0.59 66 66
positive regulation of mast cell cytokine production -0.075 0.18 -10000 0 -0.58 13 13
IL27/EBI3 -0.12 0.25 -10000 0 -0.57 84 84
IL27RA -0.002 0.12 -10000 0 -1.2 3 3
IL6 -0.23 0.34 -10000 0 -0.7 128 128
STAT5A 0.016 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 0.001 0.074 0.5 2 -10000 0 2
IL1B -0.091 0.22 -10000 0 -0.55 70 70
EBI3 -0.14 0.31 -10000 0 -0.76 74 74
TNF -0.11 0.24 -10000 0 -0.54 85 85
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 -0.11 0.29 -10000 0 -0.76 21 21
CRP -0.11 0.3 -10000 0 -0.75 25 25
cell cycle arrest -0.14 0.33 -10000 0 -0.73 59 59
TIMP1 -0.21 0.42 -10000 0 -0.96 75 75
IL6ST -0.09 0.27 -10000 0 -0.81 48 48
Rac1/GDP -0.14 0.3 -10000 0 -0.69 62 62
AP1 -0.067 0.22 -10000 0 -0.64 29 29
GAB2 0.005 0.095 -10000 0 -0.81 5 5
TNFSF11 -0.28 0.5 -10000 0 -1 102 102
HSP90B1 0.02 0.069 -10000 0 -0.55 1 1
GAB1 0.017 0.001 -10000 0 -10000 0 0
MAPK14 -0.092 0.29 -10000 0 -0.74 43 43
AKT1 0.064 0.048 -10000 0 -10000 0 0
FOXO1 0.072 0.046 -10000 0 -10000 0 0
MAP2K6 -0.1 0.28 -10000 0 -0.67 51 51
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.13 0.31 -10000 0 -0.7 57 57
MITF -0.091 0.26 -10000 0 -0.63 44 44
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.016 0 -10000 0 -10000 0 0
A2M 0.027 0.082 -10000 0 -1.6 1 1
CEBPB 0.026 0.004 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.037 0.15 -10000 0 -1 5 5
STAT3 -0.15 0.35 -10000 0 -0.78 59 59
STAT1 -0.032 0.16 -10000 0 -1.2 7 7
CEBPD -0.13 0.33 -10000 0 -0.91 26 26
PIK3CA 0.014 0.06 -10000 0 -0.81 2 2
PI3K -0.003 0.045 -10000 0 -0.62 2 2
JUN -0.025 0.16 -10000 0 -0.66 22 22
PIAS3/MITF -0.079 0.24 -10000 0 -0.64 35 35
MAPK11 -0.092 0.29 -10000 0 -0.74 44 44
STAT3 (dimer)/FOXO1 -0.038 0.27 0.55 1 -0.64 19 20
GRB2/SOS1/GAB family -0.15 0.24 -10000 0 -0.73 40 40
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.17 0.31 -10000 0 -0.64 80 80
GRB2 0.017 0.001 -10000 0 -10000 0 0
JAK2 0.016 0 -10000 0 -10000 0 0
LBP -0.11 0.28 -10000 0 -0.63 43 43
PIK3R1 0.018 0 -10000 0 -10000 0 0
JAK1 0.015 0.008 -10000 0 -10000 0 0
MYC -0.13 0.34 -10000 0 -0.92 31 31
FGG -0.12 0.29 -10000 0 -0.62 59 59
macrophage differentiation -0.14 0.33 -10000 0 -0.73 59 59
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.22 0.3 -10000 0 -0.68 79 79
JUNB -0.11 0.3 -10000 0 -0.8 26 26
FOS -0.11 0.28 -10000 0 -0.72 65 65
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.11 0.28 0.35 3 -0.58 64 67
STAT1/PIAS1 -0.091 0.25 0.41 1 -0.57 51 52
GRB2/SOS1/GAB family/SHP2/PI3K 0.034 0.055 -10000 0 -10000 0 0
STAT3 (dimer) -0.15 0.35 -10000 0 -0.77 59 59
PRKCD -0.12 0.32 -10000 0 -0.75 48 48
IL6R -0.04 0.2 -10000 0 -0.75 28 28
SOCS3 -0.099 0.34 -10000 0 -0.96 36 36
gp130 (dimer)/JAK1/JAK1/LMO4 -0.045 0.19 -10000 0 -0.54 47 47
Rac1/GTP -0.19 0.28 0.31 1 -0.69 66 67
HCK -0.067 0.24 -10000 0 -0.75 41 41
MAPKKK cascade 0 0.14 -10000 0 -1 5 5
bone resorption -0.25 0.46 -10000 0 -0.92 104 104
IRF1 -0.11 0.3 -10000 0 -0.74 30 30
mol:GDP -0.16 0.32 -10000 0 -0.69 71 71
SOS1 0.014 0.005 -10000 0 -10000 0 0
VAV1 -0.16 0.33 -10000 0 -0.7 71 71
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.1 0.29 -10000 0 -0.7 51 51
PTPN11 -0.008 0.022 -10000 0 -10000 0 0
IL6/IL6RA -0.2 0.31 -10000 0 -0.58 143 143
gp130 (dimer)/TYK2/TYK2/LMO4 -0.052 0.18 -10000 0 -0.53 47 47
gp130 (dimer)/JAK2/JAK2/LMO4 -0.052 0.18 -10000 0 -0.53 47 47
IL6 -0.23 0.35 -10000 0 -0.71 128 128
PIAS3 0.016 0 -10000 0 -10000 0 0
PTPRE -0.15 0.32 -10000 0 -0.8 74 74
PIAS1 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0.002 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.09 0.25 0.31 3 -0.55 55 58
LMO4 0.014 0.014 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.19 0.29 0.45 2 -0.73 58 60
MCL1 0.071 0.044 -10000 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B -0.016 0.14 -10000 0 -0.65 17 17
CDKN2C 0.016 0.084 -10000 0 -0.67 5 5
CDKN2A -0.11 0.27 -10000 0 -0.67 69 69
CCND2 0.035 0.089 0.26 36 -0.18 5 41
RB1 -0.039 0.092 -10000 0 -0.27 36 36
CDK4 0.043 0.096 0.29 36 -10000 0 36
CDK6 0.04 0.097 0.29 36 -0.19 2 38
G1/S progression 0.022 0.1 0.27 36 -10000 0 36
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.022 0.046 -9999 0 -0.49 3 3
ADCY5 -0.073 0.2 -9999 0 -0.46 77 77
ADCY6 0.024 0.036 -9999 0 -0.46 2 2
ADCY7 0.017 0.068 -9999 0 -0.47 7 7
ADCY1 -0.011 0.12 -9999 0 -0.4 33 33
ADCY2 -0.064 0.2 -9999 0 -0.47 69 69
ADCY3 0.024 0.036 -9999 0 -0.46 2 2
ADCY8 -0.2 0.25 -9999 0 -0.48 167 167
PRKCE 0.012 0.041 -9999 0 -0.54 2 2
ADCY9 0.022 0.046 -9999 0 -0.49 3 3
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.097 0.15 -9999 0 -0.45 28 28
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.01 0.062 -9999 0 -0.68 3 3
LAT2 -0.12 0.26 -9999 0 -0.69 44 44
AP1 -0.2 0.27 -9999 0 -0.68 74 74
mol:PIP3 -0.15 0.31 -9999 0 -0.7 64 64
IKBKB -0.068 0.17 -9999 0 -0.36 46 46
AKT1 -0.12 0.27 -9999 0 -0.72 36 36
IKBKG -0.068 0.17 -9999 0 -0.36 46 46
MS4A2 -0.12 0.28 -9999 0 -0.72 66 66
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.06 -9999 0 -0.82 2 2
MAP3K1 -0.094 0.25 -9999 0 -0.64 46 46
mol:Ca2+ -0.1 0.22 -9999 0 -0.48 62 62
LYN 0.013 0.008 -9999 0 -10000 0 0
CBLB -0.096 0.21 -9999 0 -0.6 35 35
SHC1 0.014 0.032 -9999 0 -0.61 1 1
RasGAP/p62DOK -0.034 0.12 -9999 0 -0.49 15 15
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.011 0.13 -9999 0 -0.66 15 15
PLD2 -0.17 0.3 -9999 0 -0.8 44 44
PTPN13 -0.078 0.2 -9999 0 -0.56 31 31
PTPN11 0.011 0.01 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.049 0.18 -9999 0 -0.43 33 33
SYK 0.013 0.008 -9999 0 -10000 0 0
GRB2 0.015 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.21 0.28 -9999 0 -0.73 65 65
LAT -0.11 0.23 -9999 0 -0.64 41 41
PAK2 -0.12 0.28 -9999 0 -0.73 50 50
NFATC2 -0.14 0.25 -9999 0 -0.82 39 39
HRAS -0.14 0.32 -9999 0 -0.77 62 62
GAB2 0.005 0.095 -9999 0 -0.81 5 5
PLA2G1B 0.043 0.028 -9999 0 -10000 0 0
Fc epsilon R1 -0.25 0.34 -9999 0 -0.69 114 114
Antigen/IgE/Fc epsilon R1 -0.23 0.31 -9999 0 -0.64 114 114
mol:GDP -0.16 0.35 -9999 0 -0.83 63 63
JUN -0.024 0.16 -9999 0 -0.66 22 22
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.015 0.002 -9999 0 -10000 0 0
FOS -0.11 0.28 -9999 0 -0.72 65 65
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.14 0.2 -9999 0 -0.52 57 57
CHUK -0.068 0.17 -9999 0 -0.35 49 49
KLRG1 -0.1 0.21 -9999 0 -0.58 37 37
VAV1 -0.16 0.3 -9999 0 -0.7 67 67
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.093 0.21 -9999 0 -0.6 33 33
negative regulation of mast cell degranulation -0.098 0.21 -9999 0 -0.57 41 41
BTK -0.19 0.33 -9999 0 -0.94 50 50
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.19 0.35 -9999 0 -0.9 57 57
GAB2/PI3K/SHP2 -0.18 0.26 -9999 0 -0.75 46 46
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.11 0.22 -9999 0 -0.66 32 32
RAF1 0.03 0.031 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.28 0.39 -9999 0 -0.79 108 108
FCER1G -0.052 0.21 -9999 0 -0.73 31 31
FCER1A -0.21 0.35 -9999 0 -0.76 109 109
Antigen/IgE/Fc epsilon R1/Fyn -0.22 0.3 -9999 0 -0.64 95 95
MAPK3 0.042 0.028 -9999 0 -10000 0 0
MAPK1 0.042 0.028 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 -0.012 0.099 -9999 0 -0.68 4 4
DUSP1 -0.045 0.2 -9999 0 -0.7 32 32
NF-kappa-B/RelA -0.06 0.075 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.088 0.2 -9999 0 -0.56 35 35
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.17 0.27 -9999 0 -0.73 59 59
FER -0.095 0.21 -9999 0 -0.6 35 35
RELA 0.016 0 -9999 0 -10000 0 0
ITK -0.12 0.21 -9999 0 -0.54 60 60
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG1 -0.16 0.35 -9999 0 -0.83 62 62
cytokine secretion -0.044 0.054 -9999 0 -10000 0 0
SPHK1 -0.1 0.23 -9999 0 -0.63 38 38
PTK2 -0.092 0.21 -9999 0 -0.59 35 35
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.22 0.3 -9999 0 -0.77 65 65
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.14 0.29 -9999 0 -0.68 60 60
MAP2K2 0.038 0.027 -9999 0 -10000 0 0
MAP2K1 0.037 0.033 -9999 0 -10000 0 0
MAP2K7 0.016 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.12 0.18 -9999 0 -0.55 37 37
MAP2K4 0.019 0.014 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.29 0.39 -9999 0 -0.76 125 125
mol:Choline -0.17 0.29 -9999 0 -0.78 44 44
SHC/Grb2/SOS1 -0.11 0.17 -9999 0 -0.58 28 28
FYN 0.011 0.06 -9999 0 -0.81 2 2
DOK1 0.016 0 -9999 0 -10000 0 0
PXN -0.076 0.19 -9999 0 -0.57 29 29
HCLS1 -0.11 0.23 -9999 0 -0.6 43 43
PRKCB -0.12 0.23 -9999 0 -0.48 75 75
FCGR2B -0.099 0.27 -9999 0 -0.71 60 60
IGHE -0.004 0.009 -9999 0 -10000 0 0
KLRG1/SHIP -0.1 0.22 -9999 0 -0.59 41 41
LCP2 -0.005 0.11 -9999 0 -0.63 12 12
PLA2G4A -0.13 0.27 -9999 0 -0.68 52 52
RASA1 0.016 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.17 0.29 -9999 0 -0.78 44 44
IKK complex -0.032 0.13 -9999 0 -0.29 6 6
WIPF1 0.014 0.032 -9999 0 -0.61 1 1
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.084 0.26 -9999 0 -0.67 41 41
NF kappa B1 p50/RelA/I kappa B alpha -0.13 0.22 -9999 0 -0.68 41 41
alphaV/beta3 Integrin/Osteopontin/Src -0.13 0.24 -9999 0 -0.58 82 82
AP1 -0.2 0.3 -9999 0 -0.92 37 37
ILK -0.086 0.26 -9999 0 -0.65 40 40
bone resorption -0.12 0.23 -9999 0 -0.89 19 19
PTK2B 0.009 0.073 -9999 0 -0.81 3 3
PYK2/p130Cas -0.11 0.22 -9999 0 -0.86 14 14
ITGAV 0.008 0.084 -9999 0 -0.81 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.036 0.14 -9999 0 -0.62 22 22
alphaV/beta3 Integrin/Osteopontin -0.14 0.26 -9999 0 -0.63 69 69
MAP3K1 -0.09 0.27 -9999 0 -0.59 68 68
JUN -0.024 0.16 -9999 0 -0.67 22 22
MAPK3 -0.097 0.28 -9999 0 -0.73 41 41
MAPK1 -0.097 0.28 -9999 0 -0.73 42 42
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 -0.079 0.27 -9999 0 -0.66 42 42
ITGB3 -0.032 0.2 -9999 0 -0.82 22 22
NFKBIA -0.095 0.29 -9999 0 -0.76 43 43
FOS -0.11 0.28 -9999 0 -0.72 65 65
CD44 -0.004 0.13 -9999 0 -0.81 9 9
CHUK 0.016 0 -9999 0 -10000 0 0
PLAU -0.25 0.51 -9999 0 -1.2 70 70
NF kappa B1 p50/RelA -0.14 0.23 -9999 0 -0.71 41 41
BCAR1 0.016 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.043 0.17 -9999 0 -0.67 24 24
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.088 0.26 -9999 0 -0.58 68 68
VAV3 -0.11 0.3 -9999 0 -0.7 52 52
MAP3K14 -0.099 0.28 -9999 0 -0.71 42 42
ROCK2 -0.013 0.15 -9999 0 -0.81 13 13
SPP1 -0.14 0.32 -9999 0 -0.75 80 80
RAC1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.14 0.24 -9999 0 -0.78 29 29
MMP2 -0.12 0.29 -9999 0 -0.78 35 35
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.19 0.26 -9999 0 -0.52 137 137
EPHB2 0.003 0.1 -9999 0 -0.81 6 6
Syndecan-2/TACI -0.15 0.21 -9999 0 -0.44 128 128
LAMA1 -0.11 0.3 -9999 0 -0.81 59 59
Syndecan-2/alpha2 ITGB1 -0.12 0.22 -9999 0 -0.54 61 61
HRAS 0.013 0.045 -9999 0 -0.61 2 2
Syndecan-2/CASK -0.007 0.062 -9999 0 -0.54 5 5
ITGA5 0.014 0.043 -9999 0 -0.81 1 1
BAX 0.041 0.079 -9999 0 -10000 0 0
EPB41 0.016 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.006 0.055 -9999 0 -0.48 5 5
LAMA3 -0.088 0.25 -9999 0 -0.7 55 55
EZR 0.014 0.043 -9999 0 -0.81 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.004 0.13 -9999 0 -0.81 9 9
Syndecan-2/MMP2 -0.035 0.14 -9999 0 -0.51 26 26
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.087 0.2 -9999 0 -0.56 59 59
dendrite morphogenesis -0.015 0.089 -9999 0 -0.53 11 11
Syndecan-2/GM-CSF -0.12 0.22 -9999 0 -0.51 89 89
determination of left/right symmetry 0.018 0.073 -9999 0 -0.62 5 5
Syndecan-2/PKC delta -0.007 0.061 -9999 0 -0.53 5 5
GNB2L1 0.016 0 -9999 0 -10000 0 0
MAPK3 -0.077 0.22 -9999 0 -0.5 69 69
MAPK1 -0.077 0.22 -9999 0 -0.5 69 69
Syndecan-2/RACK1 -0.008 0.056 -9999 0 -0.45 5 5
NF1 0.016 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.018 0.073 -9999 0 -0.62 5 5
ITGA2 -0.1 0.28 -9999 0 -0.74 59 59
MAPK8 0.032 0.087 -9999 0 -0.52 9 9
Syndecan-2/alpha2/beta1 Integrin -0.14 0.24 -9999 0 -0.52 89 89
Syndecan-2/Kininogen -0.023 0.095 -9999 0 -0.41 21 21
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.038 0.066 -9999 0 -0.42 6 6
Syndecan-2/CASK/Protein 4.1 -0.006 0.056 -9999 0 -0.49 5 5
extracellular matrix organization -0.018 0.1 -9999 0 -0.57 12 12
actin cytoskeleton reorganization -0.19 0.25 -9999 0 -0.51 137 137
Syndecan-2/Caveolin-2/Ras -0.02 0.1 -9999 0 -0.52 13 13
Syndecan-2/Laminin alpha3 -0.071 0.17 -9999 0 -0.46 59 59
Syndecan-2/RasGAP -0.007 0.053 -9999 0 -0.43 5 5
alpha5/beta1 Integrin -0.002 0.032 -9999 0 -0.62 1 1
PRKCD 0.016 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.015 0.09 -9999 0 -0.53 11 11
GO:0007205 0.005 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.009 0.056 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
SDCBP 0.016 0 -9999 0 -10000 0 0
TNFRSF13B -0.22 0.33 -9999 0 -0.68 124 124
RASA1 0.016 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.087 0.2 -9999 0 -0.56 59 59
Syndecan-2/Synbindin -0.007 0.061 -9999 0 -0.53 5 5
TGFB1 -0.002 0.12 -9999 0 -0.81 8 8
CASP3 0.036 0.059 -9999 0 -0.48 5 5
FN1 -0.27 0.38 -9999 0 -0.78 135 135
Syndecan-2/IL8 -0.14 0.23 -9999 0 -0.49 113 113
SDC2 0.018 0.074 -9999 0 -0.62 5 5
KNG1 -0.019 0.12 -9999 0 -0.61 16 16
Syndecan-2/Neurofibromin -0.007 0.061 -9999 0 -0.53 5 5
TRAPPC4 0.016 0 -9999 0 -10000 0 0
CSF2 -0.16 0.33 -9999 0 -0.77 87 87
Syndecan-2/TGFB1 -0.018 0.1 -9999 0 -0.57 12 12
Syndecan-2/Syntenin/PI-4-5-P2 -0.006 0.056 -9999 0 -0.49 5 5
Syndecan-2/Ezrin -0.008 0.06 -9999 0 -0.48 6 6
PRKACA 0.036 0.059 -9999 0 -0.48 5 5
angiogenesis -0.14 0.23 -9999 0 -0.48 113 113
MMP2 -0.029 0.18 -9999 0 -0.72 23 23
IL8 -0.2 0.35 -9999 0 -0.75 109 109
calcineurin-NFAT signaling pathway -0.15 0.21 -9999 0 -0.44 128 128
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.24 0.52 -9999 0 -1.3 67 67
MKNK1 0.016 0 -9999 0 -10000 0 0
MAPK14 -0.061 0.16 -9999 0 -0.41 23 23
ATF2/c-Jun -0.068 0.23 -9999 0 -0.77 24 24
MAPK11 -0.063 0.16 -9999 0 -0.49 14 14
MITF -0.063 0.2 -9999 0 -0.54 25 25
MAPKAPK5 -0.061 0.19 -9999 0 -0.52 24 24
KRT8 -0.061 0.19 -9999 0 -0.5 28 28
MAPKAPK3 0.016 0 -9999 0 -10000 0 0
MAPKAPK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.095 0.25 -9999 0 -0.5 89 89
CEBPB -0.061 0.19 -9999 0 -0.5 28 28
SLC9A1 -0.062 0.2 -9999 0 -0.53 25 25
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.071 0.21 -9999 0 -0.56 31 31
p38alpha-beta/MNK1 -0.062 0.2 -9999 0 -0.6 19 19
JUN -0.067 0.23 -9999 0 -0.76 24 24
PPARGC1A -0.17 0.28 -9999 0 -0.57 90 90
USF1 -0.061 0.19 -9999 0 -0.52 24 24
RAB5/GDP/GDI1 -0.071 0.12 -9999 0 -0.44 14 14
NOS2 -0.15 0.42 -9999 0 -1.2 40 40
DDIT3 -0.075 0.21 -9999 0 -0.56 29 29
RAB5A 0.016 0 -9999 0 -10000 0 0
HSPB1 -0.041 0.16 -9999 0 -0.48 14 14
p38alpha-beta/HBP1 -0.062 0.2 -9999 0 -0.58 22 22
CREB1 -0.061 0.2 -9999 0 -0.4 85 85
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.046 0.18 -9999 0 -0.58 14 14
RPS6KA4 -0.061 0.19 -9999 0 -0.52 24 24
PLA2G4A -0.085 0.24 -9999 0 -0.67 38 38
GDI1 -0.061 0.19 -9999 0 -0.52 24 24
TP53 -0.083 0.24 -9999 0 -0.63 28 28
RPS6KA5 -0.066 0.2 -9999 0 -0.54 29 29
ESR1 -0.15 0.31 -9999 0 -0.68 65 65
HBP1 0.016 0 -9999 0 -10000 0 0
MEF2C -0.061 0.19 -9999 0 -0.52 24 24
MEF2A -0.062 0.2 -9999 0 -0.52 24 24
EIF4EBP1 -0.062 0.2 -9999 0 -0.41 85 85
KRT19 -0.18 0.36 -9999 0 -0.74 85 85
ELK4 -0.061 0.19 -9999 0 -0.5 28 28
ATF6 -0.063 0.2 -9999 0 -0.52 28 28
ATF1 -0.061 0.2 -9999 0 -0.4 85 85
p38alpha-beta/MAPKAPK2 -0.062 0.2 -9999 0 -0.58 22 22
p38alpha-beta/MAPKAPK3 -0.062 0.2 -9999 0 -0.58 22 22
Effects of Botulinum toxin

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
STX1A 0.014 0.024 -9999 0 -0.45 1 1
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.009 0.067 -9999 0 -0.49 7 7
STXBP1 0.016 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.11 0.21 -9999 0 -0.51 75 75
RAB3GAP2/RIMS1/UNC13B -0.008 0.057 -9999 0 -0.53 2 2
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0.001 0.093 -9999 0 -0.67 7 7
mol:ACh -0.022 0.066 -9999 0 -0.15 78 78
RAB3GAP2 0.016 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.042 0.085 -9999 0 -0.45 4 4
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.11 0.21 -9999 0 -0.5 75 75
UNC13B 0.016 0 -9999 0 -10000 0 0
CHRNA1 -0.13 0.29 -9999 0 -0.71 75 75
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.27 0.27 -9999 0 -0.52 197 197
SNAP25 -0.074 0.16 -9999 0 -0.37 83 83
VAMP2 0.009 0 -9999 0 -10000 0 0
SYT1 -0.37 0.37 -9999 0 -0.72 197 197
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.022 0.021 -9999 0 -0.38 1 1
STX1A/SNAP25 fragment 1/VAMP2 -0.042 0.085 -9999 0 -0.45 4 4
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.15 0.3 -9999 0 -0.69 72 72
MAP4K1 -0.1 0.27 -9999 0 -0.72 61 61
MAP3K8 0.012 0.053 -9999 0 -0.71 2 2
PRKCB -0.1 0.26 -9999 0 -0.66 66 66
DBNL 0.016 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
MAP3K1 -0.035 0.19 -9999 0 -0.63 23 23
JUN -0.051 0.2 -9999 0 -0.64 28 28
MAP3K7 -0.034 0.19 -9999 0 -0.63 22 22
GRAP2 -0.097 0.26 -9999 0 -0.69 61 61
CRK 0.016 0 -9999 0 -10000 0 0
MAP2K4 -0.022 0.19 -9999 0 -0.6 23 23
LAT -0.012 0.14 -9999 0 -0.73 14 14
LCP2 -0.004 0.11 -9999 0 -0.63 12 12
MAPK8 -0.041 0.19 -9999 0 -0.73 20 20
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.048 0.2 -9999 0 -0.67 22 22
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.14 0.28 -9999 0 -0.88 34 34
Thromboxane A2 receptor signaling

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
TGM2 -0.043 0.19 -10000 0 -0.67 30 30
GNB1/GNG2 -0.069 0.084 -10000 0 -0.22 41 41
AKT1 -0.021 0.13 -10000 0 -0.25 1 1
EGF -0.11 0.26 -10000 0 -0.65 70 70
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.035 0.11 -10000 0 -0.54 8 8
mol:Ca2+ -0.063 0.19 -10000 0 -0.34 64 64
LYN -0.02 0.064 -10000 0 -0.52 1 1
RhoA/GTP -0.044 0.054 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.066 0.2 -10000 0 -0.37 53 53
GNG2 0.011 0.055 -10000 0 -0.61 3 3
ARRB2 0.014 0.032 -10000 0 -0.61 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 -0.042 0.19 -10000 0 -0.5 47 47
G beta5/gamma2 -0.091 0.11 -10000 0 -0.29 44 44
PRKCH -0.075 0.21 -10000 0 -0.41 46 46
DNM1 -0.038 0.18 -10000 0 -0.66 30 30
TXA2/TP beta/beta Arrestin3 -0.019 0.057 -10000 0 -0.26 11 11
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.031 0.18 -10000 0 -0.7 25 25
G12 family/GTP -0.11 0.14 -10000 0 -0.32 69 69
ADRBK1 0.016 0 -10000 0 -10000 0 0
ADRBK2 0.016 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.028 0.13 0.34 19 -10000 0 19
mol:NADP 0.014 0.042 -10000 0 -0.81 1 1
RAB11A 0.016 0 -10000 0 -10000 0 0
PRKG1 -0.088 0.26 -10000 0 -0.74 52 52
mol:IP3 -0.087 0.23 -10000 0 -0.43 64 64
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.13 0.3 -10000 0 -0.57 91 91
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.12 0.16 -10000 0 -0.48 24 24
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.055 0.13 -10000 0 -0.53 12 12
RHOA 0.016 0 -10000 0 -10000 0 0
PTGIR -0.001 0.11 -10000 0 -0.76 8 8
PRKCB1 -0.087 0.22 -10000 0 -0.4 97 97
GNAQ 0.016 0 -10000 0 -10000 0 0
mol:L-citrulline 0.014 0.042 -10000 0 -0.81 1 1
TXA2/TXA2-R family -0.13 0.3 -10000 0 -0.55 101 101
LCK -0.065 0.14 -10000 0 -0.47 21 21
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.027 0.085 -10000 0 -0.71 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.032 0.032 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.027 0.085 -10000 0 -0.58 2 2
MAPK14 -0.029 0.14 -10000 0 -0.26 3 3
TGM2/GTP -0.1 0.25 -10000 0 -0.5 63 63
MAPK11 -0.03 0.15 -10000 0 -0.34 1 1
ARHGEF1 -0.024 0.11 -10000 0 -10000 0 0
GNAI2 0.016 0 -10000 0 -10000 0 0
JNK cascade -0.084 0.23 -10000 0 -0.4 100 100
RAB11/GDP 0.016 0.002 -10000 0 -10000 0 0
ICAM1 -0.072 0.2 -10000 0 -0.4 72 72
cAMP biosynthetic process -0.082 0.21 -10000 0 -0.4 66 66
Gq family/GTP/EBP50 -0.037 0.14 -10000 0 -0.36 49 49
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.022 0.067 -10000 0 -0.52 1 1
GNB5 0.014 0.043 -10000 0 -0.81 1 1
GNB1 0.016 0 -10000 0 -10000 0 0
EGF/EGFR -0.035 0.14 -10000 0 -0.39 20 20
VCAM1 -0.065 0.19 -10000 0 -0.37 49 49
TP beta/Gq family/GDP/G beta5/gamma2 -0.042 0.19 -10000 0 -0.5 47 47
platelet activation -0.043 0.19 -10000 0 -0.34 33 33
PGI2/IP -0.012 0.085 -10000 0 -0.59 8 8
PRKACA -0.012 0.093 -10000 0 -0.38 17 17
Gq family/GDP/G beta5/gamma2 -0.038 0.18 -10000 0 -0.46 48 48
TXA2/TP beta/beta Arrestin2 -0.028 0.1 -10000 0 -0.63 8 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.002 0.11 -10000 0 -0.46 6 6
mol:DAG -0.1 0.25 -10000 0 -0.46 91 91
EGFR -0.02 0.17 -10000 0 -0.79 17 17
TXA2/TP alpha -0.12 0.28 -10000 0 -0.55 67 67
Gq family/GTP -0.057 0.12 -10000 0 -0.31 49 49
YES1 -0.02 0.064 -10000 0 -0.52 1 1
GNAI2/GTP -0.024 0.075 -10000 0 -0.62 1 1
PGD2/DP -0.035 0.13 -10000 0 -0.53 25 25
SLC9A3R1 0.001 0.095 -10000 0 -0.61 9 9
FYN -0.022 0.069 -10000 0 -0.52 1 1
mol:NO 0.014 0.042 -10000 0 -0.81 1 1
GNA15 -0.084 0.26 -10000 0 -0.76 49 49
PGK/cGMP -0.068 0.17 -10000 0 -0.49 52 52
RhoA/GDP 0.016 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.051 0.13 -10000 0 -0.58 12 12
NOS3 0.014 0.043 -10000 0 -0.81 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA -0.086 0.22 -10000 0 -0.43 74 74
PRKCB -0.11 0.24 -10000 0 -0.47 79 79
PRKCE -0.075 0.21 -10000 0 -0.4 63 63
PRKCD -0.08 0.22 -10000 0 -0.41 68 68
PRKCG -0.092 0.23 -10000 0 -0.43 71 71
muscle contraction -0.11 0.28 -10000 0 -0.51 101 101
PRKCZ -0.066 0.2 -10000 0 -0.38 51 51
ARR3 0.004 0.032 -10000 0 -0.61 1 1
TXA2/TP beta -0.027 0.085 -10000 0 -0.72 1 1
PRKCQ -0.073 0.21 -10000 0 -0.41 45 45
MAPKKK cascade -0.11 0.26 -10000 0 -0.48 100 100
SELE -0.082 0.21 -10000 0 -0.41 66 66
TP beta/GNAI2/GDP/G beta/gamma -0.027 0.082 -10000 0 -0.69 1 1
ROCK1 0.016 0 -10000 0 -10000 0 0
GNA14 -0.076 0.23 -10000 0 -0.63 54 54
chemotaxis -0.15 0.33 -10000 0 -0.63 102 102
GNA12 0.016 0 -10000 0 -10000 0 0
GNA13 0.016 0 -10000 0 -10000 0 0
GNA11 -0.008 0.14 -10000 0 -0.81 11 11
Rac1/GTP 0 0 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.1 0.26 -9999 0 -0.63 43 43
MAP3K8 0.01 0.053 -9999 0 -0.71 2 2
FOS -0.096 0.24 -9999 0 -0.65 41 41
PRKCA -0.024 0.15 -9999 0 -0.64 22 22
PTPN7 -0.15 0.31 -9999 0 -0.69 90 90
HRAS 0.012 0.045 -9999 0 -0.61 2 2
PRKCB -0.1 0.26 -9999 0 -0.66 66 66
NRAS 0.016 0.001 -9999 0 -10000 0 0
RAS family/GTP -0.002 0.024 -9999 0 -10000 0 0
MAPK3 -0.078 0.21 -9999 0 -0.62 38 38
MAP2K1 -0.03 0.17 -9999 0 -0.6 21 21
ELK1 0.014 0.007 -9999 0 -10000 0 0
BRAF -0.068 0.16 -9999 0 -0.61 21 21
mol:GTP -0.001 0.002 -9999 0 -0.006 63 63
MAPK1 -0.078 0.21 -9999 0 -0.61 39 39
RAF1 -0.067 0.16 -9999 0 -0.61 21 21
KRAS 0.016 0.001 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.084 0.17 -10000 0 -0.49 37 37
ER alpha/Gai/GDP/Gbeta gamma -0.064 0.25 -10000 0 -0.62 47 47
AKT1 -0.073 0.29 -10000 0 -0.9 38 38
PIK3CA 0.011 0.06 -10000 0 -0.81 2 2
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.075 0.29 -10000 0 -0.91 38 38
mol:Ca2+ -0.086 0.22 -10000 0 -0.56 49 49
IGF1R 0.011 0.06 -10000 0 -0.81 2 2
E2/ER alpha (dimer)/Striatin -0.12 0.23 -10000 0 -0.5 94 94
SHC1 0.014 0.032 -10000 0 -0.61 1 1
apoptosis 0.067 0.27 0.84 38 -10000 0 38
RhoA/GTP -0.067 0.14 -10000 0 -0.68 1 1
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.099 0.2 -10000 0 -0.65 36 36
regulation of stress fiber formation 0.007 0.15 0.54 5 -10000 0 5
E2/ERA-ERB (dimer) -0.099 0.2 -10000 0 -0.47 80 80
KRAS 0.016 0 -10000 0 -10000 0 0
G13/GTP -0.085 0.17 -10000 0 -0.42 77 77
pseudopodium formation -0.007 0.15 -10000 0 -0.54 5 5
E2/ER alpha (dimer)/PELP1 -0.092 0.19 -10000 0 -0.46 77 77
GRB2 0.016 0 -10000 0 -10000 0 0
GNG2 0.011 0.055 -10000 0 -0.61 3 3
GNAO1 -0.069 0.25 -10000 0 -0.79 40 40
HRAS 0.013 0.045 -10000 0 -0.61 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.042 0.23 -10000 0 -0.67 37 37
E2/ER beta (dimer) -0.008 0.065 -10000 0 -0.51 6 6
mol:GDP -0.082 0.18 -10000 0 -0.57 37 37
mol:NADP -0.042 0.23 -10000 0 -0.67 37 37
PIK3R1 0.016 0 -10000 0 -10000 0 0
mol:IP3 -0.092 0.24 -10000 0 -0.6 49 49
IGF-1R heterotetramer 0.011 0.06 -10000 0 -0.81 2 2
PLCB1 -0.078 0.2 -10000 0 -0.53 45 45
PLCB2 -0.09 0.23 -10000 0 -0.6 47 47
IGF1 -0.14 0.29 -10000 0 -0.68 86 86
mol:L-citrulline -0.042 0.23 -10000 0 -0.67 37 37
RHOA 0.016 0 -10000 0 -10000 0 0
Gai/GDP -0.091 0.26 -10000 0 -0.87 36 36
JNK cascade -0.008 0.065 -10000 0 -0.51 6 6
BCAR1 0.016 0 -10000 0 -10000 0 0
ESR2 0.005 0.087 -10000 0 -0.68 6 6
GNAQ 0.016 0 -10000 0 -10000 0 0
ESR1 -0.13 0.29 -10000 0 -0.7 77 77
Gq family/GDP/Gbeta gamma -0.063 0.23 -10000 0 -0.62 48 48
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.008 0.12 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.1 0.2 -10000 0 -0.65 36 36
GNAZ 0.002 0.1 -10000 0 -0.76 7 7
E2/ER alpha (dimer) -0.11 0.22 -10000 0 -0.54 77 77
STRN -0.034 0.2 -10000 0 -0.81 23 23
GNAL -0.052 0.22 -10000 0 -0.72 35 35
PELP1 0.016 0 -10000 0 -10000 0 0
MAPK11 0.016 0.061 -10000 0 -0.42 7 7
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 -0.012 0.13 -10000 0 -0.61 17 17
HBEGF -0.1 0.25 -10000 0 -0.7 37 37
cAMP biosynthetic process -0.11 0.2 -10000 0 -0.5 55 55
SRC -0.051 0.24 -10000 0 -0.74 26 26
PI3K -0.003 0.045 -10000 0 -0.62 2 2
GNB1 0.016 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.073 0.16 -10000 0 -0.5 36 36
SOS1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.13 0.19 -10000 0 -0.64 26 26
Gs family/GTP -0.12 0.2 -10000 0 -0.52 55 55
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.002 0.024 -10000 0 -10000 0 0
vasodilation -0.038 0.22 -10000 0 -0.63 37 37
mol:DAG -0.092 0.24 -10000 0 -0.6 49 49
Gs family/GDP/Gbeta gamma -0.092 0.17 -10000 0 -0.5 39 39
MSN -0.01 0.16 -10000 0 -0.6 5 5
Gq family/GTP -0.1 0.17 -10000 0 -0.56 35 35
mol:PI-3-4-5-P3 -0.07 0.28 -10000 0 -0.86 38 38
NRAS 0.016 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.038 0.22 0.63 37 -10000 0 37
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.076 0.17 -10000 0 -0.53 37 37
NOS3 -0.047 0.24 -10000 0 -0.72 37 37
GNA11 -0.008 0.14 -10000 0 -0.81 11 11
MAPKKK cascade -0.059 0.26 -10000 0 -0.7 42 42
E2/ER alpha (dimer)/PELP1/Src -0.11 0.22 -10000 0 -0.69 37 37
ruffle organization -0.007 0.15 -10000 0 -0.54 5 5
ROCK2 -0.024 0.17 -10000 0 -0.69 5 5
GNA14 -0.076 0.23 -10000 0 -0.63 54 54
GNA15 -0.084 0.26 -10000 0 -0.76 49 49
GNA13 0.016 0 -10000 0 -10000 0 0
MMP9 -0.14 0.3 -10000 0 -0.77 45 45
MMP2 -0.06 0.24 -10000 0 -0.86 19 19
FOXM1 transcription factor network

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
NFATC3 0.1 0.48 -10000 0 -1.1 29 29
PLK1 0.052 0.15 -10000 0 -0.59 14 14
BIRC5 -0.029 0.39 -10000 0 -1.1 34 34
HSPA1B 0.096 0.48 -10000 0 -1.1 29 29
MAP2K1 0.049 0.057 -10000 0 -0.61 1 1
BRCA2 0.086 0.51 -10000 0 -1.2 34 34
FOXM1 0.054 0.63 -10000 0 -1.6 34 34
XRCC1 0.1 0.48 -10000 0 -1.1 32 32
FOXM1B/p19 -0.16 0.39 0.48 7 -1.1 39 46
Cyclin D1/CDK4 0.081 0.46 -10000 0 -1.1 30 30
CDC2 0.092 0.51 -10000 0 -1.2 34 34
TGFA 0.066 0.5 -10000 0 -1.1 40 40
SKP2 0.097 0.48 -10000 0 -1.1 30 30
CCNE1 0.021 0.013 -10000 0 -10000 0 0
CKS1B 0.1 0.48 -10000 0 -1.1 32 32
RB1 -0.066 0.16 -10000 0 -0.84 7 7
FOXM1C/SP1 0.062 0.55 -10000 0 -1.4 33 33
AURKB -0.051 0.43 -10000 0 -1.6 24 24
CENPF 0.08 0.53 -10000 0 -1.3 33 33
CDK4 0.028 0.02 -10000 0 -10000 0 0
MYC 0.091 0.46 -10000 0 -1 33 33
CHEK2 0.049 0.065 -10000 0 -0.86 1 1
ONECUT1 0.083 0.48 -10000 0 -1.1 35 35
CDKN2A -0.12 0.27 -10000 0 -0.68 69 69
LAMA4 0.093 0.49 -10000 0 -1.2 31 31
FOXM1B/HNF6 0.054 0.57 -10000 0 -1.4 35 35
FOS -0.007 0.6 -10000 0 -1.1 63 63
SP1 0.017 0.006 -10000 0 -10000 0 0
CDC25B 0.094 0.49 -10000 0 -1.1 30 30
response to radiation 0.029 0.044 -10000 0 -10000 0 0
CENPB 0.1 0.48 -10000 0 -1.1 30 30
CENPA 0.066 0.55 -10000 0 -1.3 40 40
NEK2 0.069 0.55 -10000 0 -1.3 38 38
HIST1H2BA 0.089 0.48 -10000 0 -1.1 36 36
CCNA2 -0.004 0.13 -10000 0 -0.68 14 14
EP300 0.014 0.043 -10000 0 -0.81 1 1
CCNB1/CDK1 0.075 0.55 -10000 0 -1.4 32 32
CCNB2 0.095 0.5 -10000 0 -1.1 34 34
CCNB1 0.095 0.51 -10000 0 -1.2 32 32
ETV5 0.079 0.53 -10000 0 -1.2 35 35
ESR1 -0.006 0.6 -10000 0 -1.2 62 62
CCND1 0.091 0.47 -10000 0 -1.1 32 32
GSK3A 0.047 0.038 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.042 0.11 -10000 0 -0.51 6 6
CDK2 0.021 0.013 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.033 0.051 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.16 0.37 -10000 0 -1.2 38 38
GAS1 0.065 0.52 -10000 0 -1.2 34 34
MMP2 0.07 0.54 -10000 0 -1.2 39 39
RB1/FOXM1C 0.087 0.48 -10000 0 -1.1 31 31
CREBBP 0.016 0 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.019 0.19 -10000 0 -0.44 50 50
ACTA1 -0.044 0.23 -10000 0 -0.57 46 46
NUMA1 -0.019 0.19 -10000 0 -0.44 50 50
SPTAN1 -0.03 0.23 -10000 0 -0.58 40 40
LIMK1 -0.03 0.23 -10000 0 -0.56 45 45
BIRC3 -0.15 0.31 -10000 0 -0.73 84 84
BIRC2 0.016 0 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
CASP10 -0.086 0.26 -10000 0 -0.67 52 52
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.016 0 -10000 0 -10000 0 0
PTK2 -0.019 0.19 -10000 0 -0.44 50 50
DIABLO 0.016 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.028 0.23 -10000 0 -0.57 40 40
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
GSN -0.035 0.24 -10000 0 -0.59 42 42
MADD 0.016 0 -10000 0 -10000 0 0
TFAP2A -0.089 0.25 -10000 0 -0.68 49 49
BID -0.041 0.14 -10000 0 -0.32 65 65
MAP3K1 0.003 0.086 -10000 0 -0.25 10 10
TRADD 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.03 0.23 -10000 0 -0.58 42 42
CASP9 0.016 0 -10000 0 -10000 0 0
DNA repair -0.028 0.087 -10000 0 -0.23 38 38
neuron apoptosis 0.021 0.029 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.022 0.22 -10000 0 -0.56 40 40
APAF1 0.016 0 -10000 0 -10000 0 0
CASP6 -0.007 0.13 -10000 0 -0.4 17 17
TRAF2 0.016 0 -10000 0 -10000 0 0
ICAD/CAD -0.019 0.22 -10000 0 -0.58 35 35
CASP7 0.059 0.13 0.32 70 -10000 0 70
KRT18 0.009 0.048 -10000 0 -0.64 1 1
apoptosis -0.004 0.2 -10000 0 -0.5 37 37
DFFA -0.03 0.23 -10000 0 -0.58 42 42
DFFB -0.03 0.23 -10000 0 -0.58 42 42
PARP1 0.028 0.087 0.23 38 -10000 0 38
actin filament polymerization 0.016 0.21 0.55 35 -10000 0 35
TNF -0.15 0.31 -10000 0 -0.71 85 85
CYCS -0.027 0.097 -10000 0 -0.25 34 34
SATB1 0.003 0.12 -10000 0 -0.48 4 4
SLK -0.032 0.23 -10000 0 -0.58 42 42
p15 BID/BAX -0.029 0.13 -10000 0 -0.36 25 25
CASP2 -0.025 0.14 -10000 0 -0.45 16 16
JNK cascade -0.003 0.085 0.25 10 -10000 0 10
CASP3 -0.041 0.24 0.3 1 -0.6 45 46
LMNB2 -0.006 0.11 -10000 0 -0.42 7 7
RIPK1 0.016 0 -10000 0 -10000 0 0
CASP4 -0.003 0.11 -10000 0 -0.63 11 11
Mammalian IAPs/DIABLO -0.092 0.18 -10000 0 -0.48 48 48
negative regulation of DNA binding -0.088 0.24 -10000 0 -0.67 49 49
stress fiber formation -0.031 0.23 -10000 0 -0.57 42 42
GZMB -0.11 0.29 -10000 0 -0.66 76 76
CASP1 0.005 0.094 -10000 0 -0.41 15 15
LMNB1 -0.008 0.11 -10000 0 -0.42 10 10
APP 0.021 0.029 -10000 0 -10000 0 0
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.015 0 -10000 0 -10000 0 0
VIM -0.007 0.2 0.3 1 -0.5 35 36
LMNA -0.006 0.11 -10000 0 -0.42 7 7
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.038 0.15 -10000 0 -0.47 17 17
LRDD 0.016 0 -10000 0 -10000 0 0
SREBF1 -0.032 0.23 -10000 0 -0.56 46 46
APAF-1/Caspase 9 0.014 0.061 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.019 0.18 -10000 0 -0.43 50 50
CFL2 -0.018 0.22 -10000 0 -0.57 35 35
GAS2 -0.036 0.24 -10000 0 -0.58 46 46
positive regulation of apoptosis -0.004 0.11 -10000 0 -0.41 8 8
PRF1 -0.036 0.18 -10000 0 -0.68 28 28
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.18 0.26 -9999 0 -0.57 97 97
SMAD6-7/SMURF1 -0.001 0.027 -9999 0 -0.53 1 1
NOG -0.16 0.33 -9999 0 -0.77 84 84
SMAD9 -0.072 0.15 -9999 0 -0.55 28 28
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD5 -0.025 0.14 -9999 0 -0.56 5 5
BMP7/USAG1 -0.2 0.25 -9999 0 -0.51 146 146
SMAD5/SKI -0.015 0.13 -9999 0 -0.56 4 4
SMAD1 0.044 0.034 -9999 0 -10000 0 0
BMP2 -0.015 0.14 -9999 0 -0.64 18 18
SMAD1/SMAD1/SMAD4 -0.001 0.019 -9999 0 -10000 0 0
BMPR1A 0.016 0 -9999 0 -10000 0 0
BMPR1B -0.14 0.29 -9999 0 -0.69 83 83
BMPR1A-1B/BAMBI -0.14 0.23 -9999 0 -0.63 45 45
AHSG -0.028 0.14 -9999 0 -0.61 22 22
CER1 0 0 -9999 0 -10000 0 0
BMP2-4/CER1 -0.065 0.16 -9999 0 -0.45 55 55
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.042 0.13 -9999 0 -0.56 8 8
BMP2-4 (homodimer) -0.075 0.19 -9999 0 -0.52 55 55
RGMB 0.016 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.087 0.16 -9999 0 -0.48 33 33
RGMA -0.016 0.16 -9999 0 -0.75 16 16
SMURF1 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.038 0.14 -9999 0 -0.5 11 11
BMP2-4/USAG1 -0.23 0.26 -9999 0 -0.61 80 80
SMAD6/SMURF1/SMAD5 -0.015 0.13 -9999 0 -0.56 4 4
SOSTDC1 -0.26 0.35 -9999 0 -0.69 146 146
BMP7/BMPR2/BMPR1A-1B -0.084 0.16 -9999 0 -0.48 32 32
SKI 0.016 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.01 0.062 -9999 0 -0.68 3 3
HFE2 -0.003 0.071 -9999 0 -0.61 5 5
ZFYVE16 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.085 0.19 -9999 0 -0.57 33 33
SMAD5/SMAD5/SMAD4 -0.015 0.13 -9999 0 -0.56 4 4
MAPK1 0.016 0 -9999 0 -10000 0 0
TAK1/TAB family -0.055 0.098 -9999 0 -0.56 4 4
BMP7 (homodimer) 0.016 0 -9999 0 -10000 0 0
NUP214 0.016 0 -9999 0 -10000 0 0
BMP6/FETUA -0.03 0.11 -9999 0 -0.45 25 25
SMAD1/SKI 0.052 0.032 -9999 0 -10000 0 0
SMAD6 0.014 0.043 -9999 0 -0.81 1 1
CTDSP2 0.016 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.085 0.18 -9999 0 -0.6 23 23
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.26 0.36 -9999 0 -0.7 144 144
BMPR2 (homodimer) 0.016 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.009 0.056 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.11 0.22 -9999 0 -0.51 83 83
CHRDL1 -0.32 0.37 -9999 0 -0.71 174 174
ENDOFIN/SMAD1 0.052 0.032 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.002 0.023 -9999 0 -10000 0 0
SMAD6/SMURF1 0.016 0 -9999 0 -10000 0 0
BAMBI -0.057 0.22 -9999 0 -0.69 39 39
SMURF2 0.016 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.27 0.29 -9999 0 -0.63 108 108
BMP2-4/GREM1 -0.23 0.26 -9999 0 -0.6 86 86
SMAD7 0.016 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.036 0.15 -9999 0 -0.51 27 27
SMAD1/SMAD6 0.052 0.032 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 0.016 0 -9999 0 -10000 0 0
BMP6 0.01 0.062 -9999 0 -0.68 3 3
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.021 0.12 -9999 0 -0.48 8 8
PPM1A 0.016 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.052 0.032 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.016 0 -9999 0 -10000 0 0
PPP1CA 0.016 0 -9999 0 -10000 0 0
XIAP 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
PPP1R15A 0.001 0.095 -9999 0 -0.61 9 9
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.12 0.24 -9999 0 -0.69 39 39
CHRD -0.018 0.16 -9999 0 -0.78 16 16
BMPR2 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.043 0.15 -9999 0 -0.54 12 12
BMP4 -0.057 0.22 -9999 0 -0.71 38 38
FST -0.18 0.33 -9999 0 -0.71 101 101
BMP2-4/NOG -0.17 0.26 -9999 0 -0.59 86 86
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.077 0.15 -9999 0 -0.45 32 32
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.088 0.21 0.56 60 -10000 0 60
KIRREL -0.054 0.22 -10000 0 -0.82 30 30
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.089 0.21 -10000 0 -0.56 60 60
PLCG1 0.016 0 -10000 0 -10000 0 0
ARRB2 0.014 0.032 -10000 0 -0.61 1 1
WASL 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.066 0.16 -10000 0 -0.52 31 31
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.014 0.12 -10000 0 -0.38 31 31
FYN -0.046 0.16 -10000 0 -0.48 33 33
mol:Ca2+ -0.065 0.16 -10000 0 -0.51 31 31
mol:DAG -0.066 0.16 -10000 0 -0.51 31 31
NPHS2 -0.008 0.025 -10000 0 -10000 0 0
mol:IP3 -0.066 0.16 -10000 0 -0.51 31 31
regulation of endocytosis -0.059 0.14 -10000 0 -0.45 33 33
Nephrin/NEPH1/podocin/Cholesterol -0.068 0.16 -10000 0 -0.43 60 60
establishment of cell polarity -0.088 0.21 -10000 0 -0.56 60 60
Nephrin/NEPH1/podocin/NCK1-2 -0.059 0.14 -10000 0 -0.47 31 31
Nephrin/NEPH1/beta Arrestin2 -0.06 0.14 -10000 0 -0.46 33 33
NPHS1 -0.055 0.18 -10000 0 -0.62 33 33
Nephrin/NEPH1/podocin -0.064 0.15 -10000 0 -0.49 33 33
TJP1 0.016 0 -10000 0 -10000 0 0
NCK1 0.016 0 -10000 0 -10000 0 0
NCK2 0.016 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.066 0.16 -10000 0 -0.52 31 31
CD2AP 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.066 0.16 -10000 0 -0.52 31 31
GRB2 0.016 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.05 0.17 -10000 0 -0.49 33 33
cytoskeleton organization -0.018 0.16 -10000 0 -0.48 31 31
Nephrin/NEPH1 -0.065 0.16 -10000 0 -0.41 60 60
Nephrin/NEPH1/ZO-1 -0.071 0.17 -10000 0 -0.55 31 31
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.01 0.067 -9999 0 -0.44 9 9
VLDLR -0.015 0.14 -9999 0 -0.67 17 17
CRKL 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.014 0.043 -9999 0 -0.81 1 1
FYN 0.011 0.06 -9999 0 -0.81 2 2
ITGA3 -0.006 0.13 -9999 0 -0.81 10 10
RELN/VLDLR/Fyn -0.19 0.24 -9999 0 -0.58 64 64
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.007 0.055 -9999 0 -0.45 5 5
AKT1 -0.073 0.15 -9999 0 -0.65 4 4
MAP2K7 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
DAB1 -0.006 0.094 -9999 0 -0.61 9 9
RELN/LRP8/DAB1 -0.19 0.23 -9999 0 -0.54 72 72
LRPAP1/LRP8 -0.028 0.12 -9999 0 -0.53 20 20
RELN/LRP8/DAB1/Fyn -0.18 0.22 -9999 0 -0.52 73 73
DAB1/alpha3/beta1 Integrin -0.18 0.21 -9999 0 -0.72 21 21
long-term memory -0.22 0.25 -9999 0 -0.74 38 38
DAB1/LIS1 -0.17 0.2 -9999 0 -0.73 15 15
DAB1/CRLK/C3G -0.16 0.2 -9999 0 -0.7 15 15
PIK3CA 0.011 0.06 -9999 0 -0.81 2 2
DAB1/NCK2 -0.17 0.21 -9999 0 -0.73 15 15
ARHGEF2 0.014 0.043 -9999 0 -0.81 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.1 0.27 -9999 0 -0.7 64 64
CDK5R1 0.001 0.095 -9999 0 -0.61 9 9
RELN -0.26 0.35 -9999 0 -0.69 149 149
PIK3R1 0.016 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.2 0.24 -9999 0 -0.57 68 68
GRIN2A/RELN/LRP8/DAB1/Fyn -0.23 0.26 -9999 0 -0.76 38 38
MAPK8 0.007 0.085 -9999 0 -0.81 4 4
RELN/VLDLR/DAB1 -0.18 0.22 -9999 0 -0.54 69 69
ITGB1 0.016 0 -9999 0 -10000 0 0
MAP1B -0.15 0.23 -9999 0 -0.51 73 73
RELN/LRP8 -0.19 0.24 -9999 0 -0.56 68 68
GRIN2B/RELN/LRP8/DAB1/Fyn -0.18 0.22 -9999 0 -0.52 73 73
PI3K -0.003 0.045 -9999 0 -0.62 2 2
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.016 0.099 -9999 0 -0.62 10 10
RAP1A -0.11 0.21 -9999 0 -0.65 15 15
PAFAH1B1 0.016 0 -9999 0 -10000 0 0
MAPK8IP1 0.013 0.045 -9999 0 -0.61 2 2
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0 0 -9999 0 -10000 0 0
NCK2 0.016 0 -9999 0 -10000 0 0
neuron differentiation -0.038 0.12 -9999 0 -0.44 9 9
neuron adhesion -0.1 0.22 -9999 0 -0.67 15 15
LRP8 -0.02 0.16 -9999 0 -0.71 19 19
GSK3B -0.06 0.14 -9999 0 -0.61 4 4
RELN/VLDLR/DAB1/Fyn -0.17 0.21 -9999 0 -0.51 69 69
MAP3K11 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.09 0.16 -9999 0 -0.36 70 70
CDK5 0.016 0 -9999 0 -10000 0 0
MAPT -0.037 0.19 -9999 0 -0.57 40 40
neuron migration -0.08 0.2 -9999 0 -0.62 10 10
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.039 0.12 -9999 0 -0.44 9 9
RELN/VLDLR -0.19 0.22 -9999 0 -0.53 72 72
IL1-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
UBC13/UEV1A -0.001 0.023 -9999 0 -0.44 1 1
PRKCZ 0.014 0.032 -9999 0 -0.61 1 1
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.1 0.19 -9999 0 -0.76 21 21
IRAK/TOLLIP -0.001 0.016 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
IKBKG 0.016 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.24 0.32 -9999 0 -0.61 149 149
IL1A -0.092 0.26 -9999 0 -0.72 55 55
IL1B -0.088 0.24 -9999 0 -0.56 75 75
IRAK/TRAF6/p62/Atypical PKCs -0.002 0.028 -9999 0 -10000 0 0
IL1R2 -0.21 0.35 -9999 0 -0.75 112 112
IL1R1 0.011 0.06 -9999 0 -0.81 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.083 0.16 -9999 0 -0.63 21 21
TOLLIP 0.016 0 -9999 0 -10000 0 0
TICAM2 0.009 0.073 -9999 0 -0.81 3 3
MAP3K3 0.016 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.082 0.026 -9999 0 -10000 0 0
JUN 0.022 0.12 -9999 0 -0.63 2 2
MAP3K7 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.15 0.25 -9999 0 -0.85 24 24
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.14 0.24 -9999 0 -0.55 85 85
PIK3R1 0.016 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.13 0.23 -9999 0 -0.51 85 85
IL1 beta fragment/IL1R1/IL1RAP -0.17 0.28 -9999 0 -0.6 93 93
NFKB1 0.016 0 -9999 0 -10000 0 0
MAPK8 0.033 0.088 -9999 0 -0.81 1 1
IRAK1 0.027 0.021 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.1 0.22 -9999 0 -0.56 70 70
IRAK4 0.016 0 -9999 0 -10000 0 0
PRKCI 0.016 0 -9999 0 -10000 0 0
TRAF6 0.014 0.043 -9999 0 -0.81 1 1
PI3K -0.003 0.045 -9999 0 -0.62 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.07 0.22 -9999 0 -0.79 21 21
CHUK 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.17 0.28 -9999 0 -0.6 93 93
IL1 beta/IL1R2 -0.23 0.3 -9999 0 -0.64 106 106
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.002 0.026 -9999 0 -0.43 1 1
NF kappa B1 p50/RelA -0.13 0.22 -9999 0 -0.75 24 24
IRAK3 0.01 0.068 -9999 0 -0.74 3 3
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.15 0.25 -9999 0 -0.85 24 24
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.066 0.21 -9999 0 -0.87 12 12
IL1 alpha/IL1R1/IL1RAP -0.16 0.27 -9999 0 -0.6 85 85
RELA 0.016 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.016 0 -9999 0 -10000 0 0
MYD88 0.016 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.002 0.028 -9999 0 -0.46 1 1
IL1RAP -0.13 0.31 -9999 0 -0.81 65 65
UBE2N 0.016 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.12 0.2 -9999 0 -0.71 21 21
CASP1 -0.001 0.11 -9999 0 -0.7 9 9
IL1RN/IL1R2 -0.26 0.34 -9999 0 -0.64 154 154
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.16 0.26 -9999 0 -0.88 24 24
TMEM189-UBE2V1 0.003 0.032 -9999 0 -0.61 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.073 0.14 -9999 0 -0.67 12 12
PIK3CA 0.011 0.06 -9999 0 -0.81 2 2
IL1RN -0.12 0.3 -9999 0 -0.75 68 68
TRAF6/TAK1/TAB1/TAB2 -0.002 0.027 -9999 0 -0.45 1 1
MAP2K6 0.028 0.072 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.006 0.095 -9999 0 -0.81 5 5
ELF1 -0.05 0.15 -9999 0 -0.4 48 48
CCNA2 -0.009 0.13 -9999 0 -0.67 14 14
PIK3CA 0.012 0.06 -9999 0 -0.81 2 2
JAK3 -0.13 0.31 -9999 0 -0.8 67 67
PIK3R1 0.017 0.001 -9999 0 -10000 0 0
JAK1 0.017 0.001 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.11 0.34 -9999 0 -0.83 48 48
SHC1 0.015 0.032 -9999 0 -0.61 1 1
SP1 0.02 0.05 -9999 0 -0.38 6 6
IL2RA -0.14 0.37 -9999 0 -0.81 80 80
IL2RB -0.088 0.26 -9999 0 -0.7 55 55
SOS1 0.017 0.001 -9999 0 -10000 0 0
IL2RG -0.17 0.32 -9999 0 -0.7 97 97
G1/S transition of mitotic cell cycle 0.012 0.15 -9999 0 -0.67 14 14
PTPN11 0.017 0.001 -9999 0 -10000 0 0
CCND2 0.023 0.13 -9999 0 -1 6 6
LCK -0.092 0.26 -9999 0 -0.68 59 59
GRB2 0.017 0.001 -9999 0 -10000 0 0
IL2 -0.011 0.099 -9999 0 -0.61 10 10
CDK6 0.003 0.097 -9999 0 -0.7 7 7
CCND3 -0.07 0.27 -9999 0 -0.8 28 28
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.083 0.22 -10000 0 -0.61 31 31
CRKL -0.033 0.16 -10000 0 -0.44 29 29
HRAS -0.08 0.22 -10000 0 -0.58 31 31
mol:PIP3 -0.05 0.16 -10000 0 -0.43 31 31
SPRED1 0.016 0 -10000 0 -10000 0 0
SPRED2 0.016 0 -10000 0 -10000 0 0
GAB1 -0.046 0.17 -10000 0 -0.47 30 30
FOXO3 -0.024 0.15 -10000 0 -0.55 5 5
AKT1 -0.037 0.16 -10000 0 -0.44 30 30
BAD -0.024 0.15 -10000 0 -0.55 5 5
megakaryocyte differentiation -0.1 0.24 -10000 0 -0.53 70 70
GSK3B -0.024 0.15 -10000 0 -0.55 5 5
RAF1 -0.051 0.18 -10000 0 -0.48 21 21
SHC1 0.014 0.032 -10000 0 -0.61 1 1
STAT3 -0.046 0.17 -10000 0 -0.47 30 30
STAT1 -0.11 0.36 -10000 0 -0.99 40 40
HRAS/SPRED1 -0.1 0.14 -10000 0 -0.44 31 31
cell proliferation -0.049 0.18 -10000 0 -0.48 33 33
PIK3CA 0.011 0.06 -10000 0 -0.82 2 2
TEC 0.016 0 -10000 0 -10000 0 0
RPS6KB1 -0.046 0.17 -10000 0 -0.45 36 36
HRAS/SPRED2 -0.1 0.14 -10000 0 -0.45 28 28
LYN/TEC/p62DOK -0.074 0.13 -10000 0 -0.63 4 4
MAPK3 -0.019 0.14 -10000 0 -0.34 10 10
STAP1 -0.16 0.26 -10000 0 -0.54 85 85
GRAP2 -0.097 0.26 -10000 0 -0.69 61 61
JAK2 -0.15 0.27 -10000 0 -0.84 36 36
STAT1 (dimer) -0.1 0.35 -10000 0 -0.96 40 40
mol:Gleevec 0 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.15 0.22 -10000 0 -0.63 40 40
actin filament polymerization -0.045 0.17 -10000 0 -0.46 31 31
LYN 0.016 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.16 0.29 -10000 0 -0.7 57 57
PIK3R1 0.016 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.066 0.12 -10000 0 -0.62 3 3
PI3K -0.078 0.14 -10000 0 -0.46 30 30
PTEN 0.014 0.042 -10000 0 -0.81 1 1
SCF/KIT/EPO/EPOR -0.12 0.42 -10000 0 -1.4 30 30
MAPK8 -0.05 0.18 -10000 0 -0.5 33 33
STAT3 (dimer) -0.044 0.17 -10000 0 -0.46 30 30
positive regulation of transcription -0.011 0.12 -10000 0 -10000 0 0
mol:GDP -0.15 0.21 -10000 0 -0.58 52 52
PIK3C2B -0.045 0.17 -10000 0 -0.47 30 30
CBL/CRKL -0.022 0.16 -10000 0 -0.59 4 4
FER -0.048 0.18 -10000 0 -0.5 30 30
SH2B3 -0.046 0.17 -10000 0 -0.47 30 30
PDPK1 -0.039 0.15 -10000 0 -0.4 30 30
SNAI2 -0.054 0.18 -10000 0 -0.48 35 35
positive regulation of cell proliferation -0.073 0.27 -10000 0 -0.71 41 41
KITLG -0.007 0.14 -10000 0 -0.81 11 11
cell motility -0.073 0.27 -10000 0 -0.71 41 41
PTPN6 0.008 0.035 -10000 0 -0.62 1 1
EPOR -0.003 0.15 -10000 0 -0.91 3 3
STAT5A (dimer) -0.059 0.23 -10000 0 -0.62 36 36
SOCS1 -0.024 0.16 -10000 0 -0.66 22 22
cell migration 0.075 0.2 0.5 47 -10000 0 47
SOS1 0.016 0 -10000 0 -10000 0 0
EPO 0.005 0.033 -10000 0 -0.6 1 1
VAV1 -0.1 0.28 -10000 0 -0.73 61 61
GRB10 -0.047 0.17 -10000 0 -0.47 31 31
PTPN11 0.008 0.012 -10000 0 -10000 0 0
SCF/KIT -0.075 0.17 -10000 0 -0.46 42 42
GO:0007205 0.001 0.01 -10000 0 -10000 0 0
MAP2K1 -0.028 0.15 -10000 0 -0.39 10 10
CBL 0.016 0 -10000 0 -10000 0 0
KIT -0.14 0.42 -10000 0 -1.5 28 28
MAP2K2 -0.027 0.15 -10000 0 -0.37 15 15
SHC/Grb2/SOS1 -0.075 0.14 -10000 0 -0.57 6 6
STAT5A -0.061 0.24 -10000 0 -0.64 36 36
GRB2 0.016 0 -10000 0 -10000 0 0
response to radiation -0.053 0.18 -10000 0 -0.47 35 35
SHC/GRAP2 -0.083 0.19 -10000 0 -0.51 62 62
PTPRO -0.1 0.24 -10000 0 -0.55 70 70
SH2B2 -0.046 0.17 -10000 0 -0.48 31 31
DOK1 0.016 0 -10000 0 -10000 0 0
MATK -0.078 0.21 -10000 0 -0.52 47 47
CREBBP 0.036 0.022 -10000 0 -10000 0 0
BCL2 -0.014 0.2 -10000 0 -1.5 4 4
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.054 0.15 -9999 0 -0.48 34 34
RGS9BP -0.039 0.2 -9999 0 -0.75 27 27
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.071 0.24 -9999 0 -0.75 43 43
mol:Na + -0.061 0.16 -9999 0 -0.47 49 49
mol:ADP -0.046 0.19 -9999 0 -0.57 44 44
GNAT2 0.003 0.078 -9999 0 -0.61 6 6
RGS9-1/Gbeta5/R9AP -0.083 0.19 -9999 0 -0.57 37 37
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.006 0.048 -9999 0 -0.39 6 6
GRK7 0.006 0.033 -9999 0 -0.61 1 1
CNGB3 0 0 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin -0.001 0.023 -9999 0 -0.45 1 1
mol:Ca2+ -0.065 0.18 -9999 0 -0.43 68 68
Cone PDE6 -0.072 0.17 -9999 0 -0.5 37 37
Cone Metarhodopsin II -0.053 0.15 -9999 0 -0.46 44 44
Na + (4 Units) -0.077 0.17 -9999 0 -0.43 68 68
GNAT2/GDP -0.076 0.17 -9999 0 -0.51 38 38
GNB5 0.014 0.043 -9999 0 -0.81 1 1
mol:GMP (4 units) 0.003 0.045 -9999 0 -0.35 6 6
Cone Transducin -0.057 0.16 -9999 0 -0.5 34 34
SLC24A2 -0.032 0.15 -9999 0 -0.61 23 23
GNB3/GNGT2 -0.065 0.19 -9999 0 -0.6 41 41
GNB3 -0.057 0.23 -9999 0 -0.8 34 34
GNAT2/GTP -0.007 0.056 -9999 0 -0.45 6 6
CNGA3 -0.079 0.25 -9999 0 -0.72 49 49
ARR3 0.004 0.032 -9999 0 -0.61 1 1
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.062 0.16 -9999 0 -0.48 49 49
mol:Pi -0.083 0.19 -9999 0 -0.57 37 37
Cone CNG Channel -0.056 0.14 -9999 0 -0.4 53 53
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.032 0.15 -9999 0 -0.61 23 23
RGS9 -0.061 0.22 -9999 0 -0.7 41 41
PDE6C 0 0 -9999 0 -10000 0 0
GNGT2 0.001 0.1 -9999 0 -0.69 8 8
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0 0 -9999 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B 0 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.035 0.1 -9999 0 -0.51 9 9
EGFR -0.02 0.17 -9999 0 -0.79 17 17
EPHA2 0.007 0.085 -9999 0 -0.81 4 4
USP6 -0.007 0.12 -9999 0 -0.61 14 14
IQSEC1 0.016 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.11 0.22 -9999 0 -0.52 83 83
ARRB2 -0.007 0.082 -9999 0 -0.44 3 3
mol:GTP 0.017 0.028 -9999 0 -10000 0 0
ARRB1 0.009 0.073 -9999 0 -0.81 3 3
FBXO8 0.016 0 -9999 0 -10000 0 0
TSHR 0.011 0.06 -9999 0 -0.81 2 2
EGF -0.11 0.26 -9999 0 -0.65 70 70
somatostatin receptor activity 0 0 -9999 0 -0.001 35 35
ARAP2 0.014 0.043 -9999 0 -0.81 1 1
mol:GDP -0.073 0.14 -9999 0 -0.33 58 58
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 16 16
ITGA2B -0.032 0.18 -9999 0 -0.74 24 24
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.005 0.049 -9999 0 -0.48 4 4
ADAP1 0.016 0 -9999 0 -10000 0 0
KIF13B 0.016 0 -9999 0 -10000 0 0
HGF/MET -0.14 0.26 -9999 0 -0.6 89 89
PXN 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.061 0.14 -9999 0 -0.32 42 42
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.097 0.19 -9999 0 -0.58 30 30
ADRB2 -0.026 0.17 -9999 0 -0.68 23 23
receptor agonist activity 0 0 -9999 0 0 33 33
actin filament binding 0 0 -9999 0 -0.001 40 40
SRC 0.012 0.053 -9999 0 -0.71 2 2
ITGB3 -0.032 0.19 -9999 0 -0.81 22 22
GNAQ 0.016 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 27 27
ARF6/GDP 0.003 0.12 -9999 0 -0.44 14 14
ARF6/GDP/GULP/ACAP1 -0.16 0.21 -9999 0 -0.57 55 55
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.055 0.17 -9999 0 -0.56 35 35
ACAP1 -0.063 0.22 -9999 0 -0.68 43 43
ACAP2 0.016 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.033 0.11 -9999 0 -0.4 31 31
EFNA1 0.016 0 -9999 0 -10000 0 0
HGF -0.077 0.25 -9999 0 -0.72 48 48
CYTH3 0.014 0.024 -9999 0 -0.45 1 1
CYTH2 0.011 0.002 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 -0.001 35 35
endosomal lumen acidification 0 0 -9999 0 -0.001 39 39
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.091 0.27 -9999 0 -0.74 54 54
GNAQ/ARNO 0.014 0.011 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 5 5
MET -0.085 0.27 -9999 0 -0.81 46 46
GNA14 -0.077 0.23 -9999 0 -0.63 54 54
GNA15 -0.084 0.26 -9999 0 -0.76 49 49
GIT1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 29 29
GNA11 -0.008 0.14 -9999 0 -0.81 11 11
LHCGR -0.043 0.18 -9999 0 -0.63 31 31
AGTR1 -0.23 0.35 -9999 0 -0.72 126 126
desensitization of G-protein coupled receptor protein signaling pathway -0.033 0.11 -9999 0 -0.4 31 31
IPCEF1/ARNO -0.075 0.15 -9999 0 -0.46 30 30
alphaIIb/beta3 Integrin -0.069 0.21 -9999 0 -0.67 39 39
Nongenotropic Androgen 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
PTK2 0.015 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.087 0.17 -10000 0 -0.49 35 35
regulation of S phase of mitotic cell cycle -0.023 0.13 -10000 0 -0.35 37 37
GNAO1 -0.069 0.25 -10000 0 -0.79 40 40
HRAS 0.012 0.045 -10000 0 -0.61 2 2
SHBG/T-DHT -0.018 0.092 -10000 0 -0.47 15 15
PELP1 0.016 0.001 -10000 0 -10000 0 0
AKT1 0.015 0 -10000 0 -10000 0 0
MAP2K1 -0.033 0.17 -10000 0 -0.52 13 13
T-DHT/AR -0.11 0.22 -10000 0 -0.53 79 79
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.006 62 62
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 -0.012 0.13 -10000 0 -0.61 17 17
mol:GDP -0.089 0.19 -10000 0 -0.61 36 36
cell proliferation -0.041 0.2 -10000 0 -0.61 15 15
PIK3CA 0.011 0.06 -10000 0 -0.81 2 2
FOS -0.08 0.3 -10000 0 -0.8 46 46
mol:Ca2+ -0.018 0.031 -10000 0 -0.1 25 25
MAPK3 -0.035 0.18 -10000 0 -0.58 14 14
MAPK1 -0.012 0.099 -10000 0 -0.3 9 9
PIK3R1 0.016 0 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.004 65 65
cAMP biosynthetic process 0 0.092 -10000 0 -0.42 15 15
GNG2 0.011 0.055 -10000 0 -0.61 3 3
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 65 65
HRAS/GTP -0.081 0.16 -10000 0 -0.47 36 36
actin cytoskeleton reorganization -0.002 0.031 -10000 0 -0.43 2 2
SRC 0.012 0.053 -10000 0 -0.71 2 2
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 65 65
PI3K -0.003 0.039 -10000 0 -0.54 2 2
apoptosis 0.034 0.18 0.42 46 -10000 0 46
T-DHT/AR/PELP1 -0.094 0.19 -10000 0 -0.45 79 79
HRAS/GDP -0.084 0.18 -10000 0 -0.58 37 37
CREB1 -0.039 0.19 -10000 0 -0.45 46 46
RAC1-CDC42/GTP -0.002 0.032 -10000 0 -0.44 2 2
AR -0.13 0.3 -10000 0 -0.7 79 79
GNB1 0.016 0 -10000 0 -10000 0 0
RAF1 -0.041 0.17 -10000 0 -0.53 12 12
RAC1-CDC42/GDP -0.078 0.17 -10000 0 -0.55 35 35
T-DHT/AR/PELP1/Src -0.087 0.17 -10000 0 -0.51 36 36
MAP2K2 -0.032 0.17 -10000 0 -0.52 12 12
T-DHT/AR/PELP1/Src/PI3K -0.023 0.13 -10000 0 -0.4 13 13
GNAZ 0.002 0.1 -10000 0 -0.76 7 7
SHBG -0.013 0.14 -10000 0 -0.7 15 15
Gi family/GNB1/GNG2/GDP -0.016 0.16 -10000 0 -0.47 36 36
mol:T-DHT 0 0.001 -10000 0 -0.003 46 46
RAC1 0.016 0 -10000 0 -10000 0 0
GNRH1 0.001 0.09 -10000 0 -0.57 9 9
Gi family/GTP -0.07 0.13 -10000 0 -0.49 20 20
CDC42 0.016 0 -10000 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.03 0.22 -9999 0 -0.72 30 30
STMN1 -0.035 0.19 -9999 0 -0.54 45 45
Aurora B/RasGAP/Survivin -0.079 0.25 -9999 0 -0.72 45 45
Chromosomal passenger complex/Cul3 protein complex -0.042 0.17 -9999 0 -0.53 24 24
BIRC5 -0.056 0.22 -9999 0 -0.74 36 36
DES -0.2 0.37 -9999 0 -0.84 75 75
Aurora C/Aurora B/INCENP -0.07 0.18 -9999 0 -0.53 33 33
Aurora B/TACC1 -0.043 0.16 -9999 0 -0.46 44 44
Aurora B/PP2A -0.05 0.18 -9999 0 -0.54 44 44
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.001 0.06 -9999 0 -0.2 24 24
mitotic metaphase/anaphase transition 0.001 0.005 -9999 0 -10000 0 0
NDC80 -0.055 0.23 -9999 0 -0.61 51 51
Cul3 protein complex -0.069 0.16 -9999 0 -0.53 27 27
KIF2C -0.031 0.084 -9999 0 -0.28 30 30
PEBP1 0.014 0.006 -9999 0 -10000 0 0
KIF20A -0.069 0.24 -9999 0 -0.73 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.05 0.18 -9999 0 -0.54 44 44
SEPT1 -0.042 0.18 -9999 0 -0.61 35 35
SMC2 0.016 0 -9999 0 -10000 0 0
SMC4 0.016 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.036 0.24 -9999 0 -0.94 24 24
PSMA3 0.016 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.004 -9999 0 -10000 0 0
H3F3B -0.021 0.13 -9999 0 -0.36 44 44
AURKB -0.067 0.24 -9999 0 -0.73 44 44
AURKC -0.041 0.19 -9999 0 -0.64 33 33
CDCA8 0.008 0.066 -9999 0 -0.63 4 4
cytokinesis -0.12 0.29 -9999 0 -0.9 39 39
Aurora B/Septin1 -0.11 0.3 -9999 0 -0.89 40 40
AURKA 0.007 0.071 -9999 0 -0.61 5 5
INCENP 0.008 0.07 -9999 0 -0.77 3 3
KLHL13 -0.096 0.26 -9999 0 -0.7 59 59
BUB1 -0.054 0.22 -9999 0 -0.75 35 35
hSgo1/Aurora B/Survivin -0.1 0.28 -9999 0 -0.73 55 55
EVI5 0.015 0.005 -9999 0 -10000 0 0
RhoA/GTP -0.092 0.25 -9999 0 -0.83 33 33
SGOL1 -0.032 0.18 -9999 0 -0.71 25 25
CENPA -0.052 0.24 -9999 0 -0.63 43 43
NCAPG -0.048 0.21 -9999 0 -0.72 33 33
Aurora B/HC8 Proteasome -0.05 0.18 -9999 0 -0.54 44 44
NCAPD2 0.016 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.05 0.18 -9999 0 -0.54 44 44
RHOA 0.016 0 -9999 0 -10000 0 0
NCAPH -0.04 0.2 -9999 0 -0.74 28 28
NPM1 -0.054 0.19 -9999 0 -0.76 24 24
RASA1 0.016 0 -9999 0 -10000 0 0
KLHL9 0.016 0 -9999 0 -10000 0 0
mitotic prometaphase -0.002 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.05 0.18 -9999 0 -0.54 44 44
PPP1CC 0.016 0 -9999 0 -10000 0 0
Centraspindlin -0.1 0.28 -9999 0 -0.93 34 34
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.054 0.19 -9999 0 -0.76 24 24
MYLK -0.026 0.14 -9999 0 -0.46 29 29
KIF23 -0.028 0.18 -9999 0 -0.73 22 22
VIM -0.034 0.18 -9999 0 -0.54 44 44
RACGAP1 0.014 0.006 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.054 0.19 -9999 0 -0.76 24 24
Chromosomal passenger complex -0.058 0.26 -9999 0 -0.67 46 46
Chromosomal passenger complex/EVI5 -0.063 0.25 -9999 0 -0.68 44 44
TACC1 0.016 0 -9999 0 -10000 0 0
PPP2R5D 0.016 0 -9999 0 -10000 0 0
CUL3 0.016 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Coregulation of Androgen receptor activity

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 -0.005 0.095 -9999 0 -0.72 6 6
SVIL 0.005 0.047 -9999 0 -0.83 1 1
ZNF318 0.044 0.06 -9999 0 -10000 0 0
JMJD2C -0.035 0.065 -9999 0 -0.11 145 145
T-DHT/AR/Ubc9 -0.12 0.2 -9999 0 -0.53 67 67
CARM1 0.014 0.004 -9999 0 -10000 0 0
PRDX1 0.016 0.032 -9999 0 -0.6 1 1
PELP1 0.021 0.009 -9999 0 -10000 0 0
CTNNB1 0.008 0.015 -9999 0 -10000 0 0
AKT1 0.024 0.015 -9999 0 -10000 0 0
PTK2B 0.003 0.075 -9999 0 -0.82 3 3
MED1 0.025 0.016 -9999 0 -10000 0 0
MAK 0.017 0.14 -9999 0 -0.6 15 15
response to oxidative stress 0.002 0.004 -9999 0 -10000 0 0
HIP1 -0.006 0.1 -9999 0 -0.82 6 6
GSN -0.002 0.087 -9999 0 -0.82 4 4
NCOA2 -0.062 0.24 -9999 0 -0.81 35 35
NCOA6 0.005 0.046 -9999 0 -0.81 1 1
DNA-PK 0.042 0.073 -9999 0 -0.54 1 1
NCOA4 0.014 0.004 -9999 0 -10000 0 0
PIAS3 0.008 0.015 -9999 0 -10000 0 0
cell proliferation -0.011 0.12 -9999 0 -0.78 5 5
XRCC5 0.023 0.013 -9999 0 -10000 0 0
UBE3A -0.001 0.032 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.15 0.23 -9999 0 -0.55 82 82
FHL2 -0.078 0.27 -9999 0 -1 21 21
RANBP9 0.007 0.019 -9999 0 -10000 0 0
JMJD1A -0.007 0.055 -9999 0 -0.12 69 69
CDK6 0.004 0.097 -9999 0 -0.7 7 7
TGFB1I1 0.005 0.047 -9999 0 -0.84 1 1
T-DHT/AR/CyclinD1 -0.14 0.21 -9999 0 -0.52 83 83
XRCC6 0.023 0.013 -9999 0 -10000 0 0
T-DHT/AR -0.14 0.25 -9999 0 -0.58 69 69
CTDSP1 0.011 0.008 -9999 0 -10000 0 0
CTDSP2 0.032 0.041 -9999 0 -10000 0 0
BRCA1 0.004 0.05 -9999 0 -0.63 2 2
TCF4 0.024 0.079 -9999 0 -0.8 3 3
CDKN2A -0.099 0.27 -9999 0 -0.66 69 69
SRF 0.023 0.068 -9999 0 -0.64 3 3
NKX3-1 -0.091 0.16 -9999 0 -0.73 10 10
KLK3 -0.24 0.5 -9999 0 -1.6 40 40
TMF1 0.011 0.007 -9999 0 -10000 0 0
HNRNPA1 0.027 0.02 -9999 0 -10000 0 0
AOF2 -0.014 0.025 -9999 0 -0.075 38 38
APPL1 0.049 0.033 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.12 0.21 -9999 0 -0.5 76 76
AR -0.16 0.3 -9999 0 -0.74 79 79
UBA3 0.011 0.008 -9999 0 -10000 0 0
PATZ1 0.027 0.02 -9999 0 -10000 0 0
PAWR 0.009 0.043 -9999 0 -0.81 1 1
PRKDC 0.021 0.045 -9999 0 -0.81 1 1
PA2G4 0.03 0.025 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.11 0.2 -9999 0 -0.49 67 67
RPS6KA3 0.007 0.021 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.13 0.2 -9999 0 -0.51 78 78
LATS2 0.027 0.02 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.099 0.2 -9999 0 -0.47 76 76
Cyclin D3/CDK11 p58 -0.002 0.032 -9999 0 -0.63 1 1
VAV3 -0.067 0.22 -9999 0 -0.71 40 40
KLK2 -0.34 0.46 -9999 0 -0.84 145 145
CASP8 0.019 0.007 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.16 0.25 -9999 0 -0.58 88 88
TMPRSS2 -0.2 0.4 -9999 0 -1 62 62
CCND1 0.001 0.092 -9999 0 -0.79 5 5
PIAS1 -0.001 0.032 -9999 0 -10000 0 0
mol:T-DHT -0.026 0.043 -9999 0 -0.086 95 95
CDC2L1 0.001 0.002 -9999 0 -10000 0 0
PIAS4 -0.012 0.052 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.13 0.21 -9999 0 -0.52 82 82
CMTM2 -0.027 0.18 -9999 0 -0.76 22 22
SNURF -0.017 0.16 -9999 0 -0.81 15 15
ZMIZ1 -0.004 0.036 -9999 0 -10000 0 0
CCND3 0.015 0.043 -9999 0 -0.81 1 1
TGIF1 0.027 0.02 -9999 0 -10000 0 0
FKBP4 0.004 0.051 -9999 0 -0.65 2 2
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.016 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.11 0.17 -10000 0 -0.57 30 30
NT3 (dimer)/TRKC -0.21 0.3 -10000 0 -0.58 136 136
NT3 (dimer)/TRKB -0.22 0.28 -10000 0 -0.62 96 96
SHC/Grb2/SOS1/GAB1/PI3K 0.046 0.029 -10000 0 -10000 0 0
RAPGEF1 0.016 0 -10000 0 -10000 0 0
BDNF -0.084 0.25 -10000 0 -0.71 52 52
PIK3CA 0.011 0.06 -10000 0 -0.81 2 2
DYNLT1 0.011 0.055 -10000 0 -0.61 3 3
NTRK1 -0.054 0.19 -10000 0 -0.62 40 40
NTRK2 -0.004 0.13 -10000 0 -0.81 9 9
NTRK3 -0.14 0.31 -10000 0 -0.73 81 81
NT-4/5 (dimer)/TRKB -0.22 0.3 -10000 0 -0.63 111 111
neuron apoptosis 0.15 0.21 0.61 48 -10000 0 48
SHC 2-3/Grb2 -0.16 0.24 -10000 0 -0.72 43 43
SHC1 0.014 0.032 -10000 0 -0.61 1 1
SHC2 -0.11 0.17 -10000 0 -0.71 16 16
SHC3 -0.19 0.29 -10000 0 -0.77 60 60
STAT3 (dimer) 0.021 0.043 -10000 0 -0.38 4 4
NT3 (dimer)/TRKA -0.25 0.28 -10000 0 -0.59 113 113
RIN/GDP -0.029 0.11 -10000 0 -0.3 10 10
GIPC1 0.016 0 -10000 0 -10000 0 0
KRAS 0.016 0 -10000 0 -10000 0 0
DNAJA3 -0.12 0.17 -10000 0 -0.44 73 73
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.027 0.11 -10000 0 -0.93 5 5
MAGED1 0.016 0 -10000 0 -10000 0 0
PTPN11 0.016 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.12 0.29 -10000 0 -0.74 67 67
SHC/GRB2/SOS1 -0.001 0.019 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.093 0.2 -10000 0 -0.63 27 27
TRKA/NEDD4-2 -0.047 0.14 -10000 0 -0.44 40 40
ELMO1 -0.072 0.22 -10000 0 -0.61 53 53
RhoG/GTP/ELMO1/DOCK1 -0.056 0.14 -10000 0 -0.39 55 55
NGF -0.014 0.14 -10000 0 -0.69 16 16
HRAS 0.013 0.045 -10000 0 -0.61 2 2
DOCK1 0.011 0.06 -10000 0 -0.81 2 2
GAB2 0.005 0.095 -10000 0 -0.81 5 5
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0.016 0 -10000 0 -10000 0 0
FRS2 0.016 0 -10000 0 -10000 0 0
DNM1 -0.038 0.18 -10000 0 -0.66 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.16 0.22 -10000 0 -0.53 77 77
mol:GDP -0.046 0.16 -10000 0 -0.44 17 17
NGF (dimer) -0.014 0.14 -10000 0 -0.68 16 16
RhoG/GDP -0.064 0.16 -10000 0 -0.46 53 53
RIT1/GDP -0.022 0.11 -10000 0 -0.32 2 2
TIAM1 -0.095 0.28 -10000 0 -0.79 52 52
PIK3R1 0.016 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.074 0.19 -10000 0 -0.6 31 31
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.001 0.023 -10000 0 -0.44 1 1
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 -0.001 0.017 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.12 0.28 -10000 0 -0.7 70 70
RAP1/GDP -0.047 0.07 -10000 0 -10000 0 0
KIDINS220/CRKL 0.016 0 -10000 0 -10000 0 0
BDNF (dimer) -0.084 0.25 -10000 0 -0.71 52 52
ubiquitin-dependent protein catabolic process -0.057 0.14 -10000 0 -0.39 55 55
Schwann cell development -0.044 0.041 -10000 0 -10000 0 0
EHD4 0.016 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.049 0.035 -10000 0 -10000 0 0
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.18 0.26 -10000 0 -0.76 43 43
ABL1 0.016 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.022 0.056 -10000 0 -10000 0 0
STAT3 0.021 0.043 -10000 0 -0.38 4 4
axon guidance -0.18 0.24 -10000 0 -0.71 43 43
MAPK3 -0.05 0.19 -10000 0 -0.57 27 27
MAPK1 -0.05 0.19 -10000 0 -0.57 27 27
CDC42/GDP -0.022 0.11 -10000 0 -0.32 2 2
NTF3 -0.12 0.28 -10000 0 -0.7 70 70
NTF4 -0.12 0.29 -10000 0 -0.74 67 67
NGF (dimer)/TRKA/FAIM -0.057 0.14 -10000 0 -0.39 55 55
PI3K -0.003 0.045 -10000 0 -0.62 2 2
FRS3 0.016 0 -10000 0 -10000 0 0
FAIM 0.016 0 -10000 0 -10000 0 0
GAB1 0.016 0 -10000 0 -10000 0 0
RASGRF1 -0.26 0.31 -10000 0 -0.66 123 123
SOS1 0.016 0 -10000 0 -10000 0 0
MCF2L -0.16 0.27 -10000 0 -0.6 76 76
RGS19 0.016 0 -10000 0 -10000 0 0
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP -0.012 0.1 -10000 0 -10000 0 0
Rac1/GDP -0.022 0.11 -10000 0 -0.32 2 2
NGF (dimer)/TRKA/GRIT -0.059 0.14 -10000 0 -0.4 55 55
neuron projection morphogenesis -0.079 0.18 -10000 0 -0.61 9 9
NGF (dimer)/TRKA/NEDD4-2 -0.057 0.14 -10000 0 -0.39 55 55
MAP2K1 0.05 0.025 -10000 0 -10000 0 0
NGFR -0.19 0.34 -10000 0 -0.75 101 101
NGF (dimer)/TRKA/GIPC/GAIP -0.008 0.12 -10000 0 -0.52 3 3
RAS family/GTP/PI3K 0.038 0.036 -10000 0 -0.42 2 2
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.016 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.014 0.032 -10000 0 -0.61 1 1
MAPKKK cascade -0.054 0.11 -10000 0 -0.71 7 7
RASA1 0.016 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.047 0.14 -10000 0 -0.44 40 40
SQSTM1 0.016 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.069 0.17 -10000 0 -0.54 31 31
NGF (dimer)/TRKA/p62/Atypical PKCs -0.047 0.12 -10000 0 -0.47 8 8
MATK -0.043 0.2 -10000 0 -0.7 31 31
NEDD4L 0.016 0 -10000 0 -10000 0 0
RAS family/GDP -0.044 0.066 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.13 0.18 -10000 0 -0.46 78 78
Rac1/GTP -0.17 0.18 -10000 0 -0.45 96 96
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.075 0.2 -10000 0 -0.62 46 46
CRKL -0.022 0.14 -10000 0 -0.5 7 7
mol:PIP3 -0.024 0.041 0.76 1 -10000 0 1
AKT1 0.001 0.045 0.49 1 -0.51 2 3
PTK2B 0.009 0.073 -10000 0 -0.81 3 3
RAPGEF1 -0.011 0.14 -10000 0 -0.47 7 7
RANBP10 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.011 0.06 -10000 0 -0.81 2 2
HGF/MET/SHIP2 -0.12 0.23 -10000 0 -0.56 70 70
MAP3K5 -0.046 0.2 -10000 0 -0.59 26 26
HGF/MET/CIN85/CBL/ENDOPHILINS -0.11 0.21 -10000 0 -0.51 70 70
AP1 -0.12 0.24 -10000 0 -0.57 73 73
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.014 0.032 -10000 0 -0.61 1 1
apoptosis -0.093 0.25 -10000 0 -0.77 40 40
STAT3 (dimer) -0.027 0.17 -10000 0 -0.67 8 8
GAB1/CRKL/SHP2/PI3K -0.053 0.11 -10000 0 -0.52 4 4
INPP5D -0.011 0.13 -10000 0 -0.66 15 15
CBL/CRK -0.012 0.14 -10000 0 -0.47 7 7
PTPN11 0.016 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.016 0 -10000 0 -10000 0 0
PTEN 0.014 0.043 -10000 0 -0.81 1 1
ELK1 -0.033 0.09 -10000 0 -0.28 46 46
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.041 0.08 -10000 0 -0.36 5 5
PAK1 0.011 0.042 0.45 1 -0.47 2 3
HGF/MET/RANBP10 -0.12 0.23 -10000 0 -0.56 70 70
HRAS -0.088 0.28 -10000 0 -0.77 46 46
DOCK1 -0.013 0.14 -10000 0 -0.48 9 9
GAB1 -0.034 0.15 -10000 0 -0.37 47 47
CRK -0.022 0.14 -10000 0 -0.5 7 7
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.13 0.27 -10000 0 -0.68 70 70
JUN -0.024 0.16 -10000 0 -0.66 22 22
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.069 0.14 -10000 0 -0.34 70 70
PIK3R1 0.016 0 -10000 0 -10000 0 0
cell morphogenesis 0.007 0.17 -10000 0 -0.66 6 6
GRB2/SHC -0.058 0.12 -10000 0 -0.48 5 5
FOS -0.11 0.28 -10000 0 -0.72 65 65
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.033 0.09 -10000 0 -0.27 46 46
HGF/MET/MUC20 -0.12 0.23 -10000 0 -0.53 89 89
cell migration -0.057 0.11 -10000 0 -0.47 5 5
GRB2 0.016 0 -10000 0 -10000 0 0
CBL 0.016 0 -10000 0 -10000 0 0
MET/RANBP10 -0.075 0.2 -10000 0 -0.62 46 46
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.037 0.17 -10000 0 -0.68 8 8
MET/MUC20 -0.077 0.21 -10000 0 -0.63 46 46
RAP1B 0 0.13 -10000 0 -0.46 4 4
RAP1A 0 0.13 -10000 0 -0.46 4 4
HGF/MET/RANBP9 -0.12 0.23 -10000 0 -0.56 70 70
RAF1 -0.072 0.26 -10000 0 -0.71 46 46
STAT3 -0.027 0.17 -10000 0 -0.68 8 8
cell proliferation -0.038 0.22 -10000 0 -0.75 8 8
RPS6KB1 -0.023 0.046 -10000 0 -10000 0 0
MAPK3 -0.036 0.082 -10000 0 -0.26 44 44
MAPK1 -0.036 0.082 -10000 0 -0.26 45 45
RANBP9 0.016 0 -10000 0 -10000 0 0
MAPK8 -0.013 0.17 -10000 0 -0.6 9 9
SRC -0.026 0.17 -10000 0 -0.69 8 8
PI3K -0.06 0.12 -10000 0 -0.5 7 7
MET/Glomulin -0.056 0.19 -10000 0 -0.57 46 46
SOS1 0.016 0 -10000 0 -10000 0 0
MAP2K1 -0.056 0.24 -10000 0 -0.64 46 46
MET -0.085 0.27 -10000 0 -0.81 46 46
MAP4K1 -0.045 0.18 -10000 0 -0.56 22 22
PTK2 0.016 0 -10000 0 -10000 0 0
MAP2K2 -0.055 0.24 -10000 0 -0.64 46 46
BAD 0.011 0.042 0.45 1 -0.47 2 3
MAP2K4 -0.031 0.18 -10000 0 -0.52 26 26
SHP2/GRB2/SOS1/GAB1 -0.078 0.17 -10000 0 -0.5 46 46
INPPL1 0.016 0 -10000 0 -10000 0 0
PXN 0.016 0 -10000 0 -10000 0 0
SH3KBP1 0.016 0 -10000 0 -10000 0 0
HGS -0.039 0.14 -10000 0 -0.35 46 46
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.077 0.25 -10000 0 -0.72 48 48
RASA1 0.016 0 -10000 0 -10000 0 0
NCK1 0.016 0 -10000 0 -10000 0 0
PTPRJ 0.016 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.059 0.12 -10000 0 -0.49 5 5
PDPK1 -0.012 0.049 0.56 1 -0.55 2 3
HGF/MET/SHIP -0.14 0.24 -10000 0 -0.58 74 74
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.1 0.31 -10000 0 -0.9 36 36
UGCG -0.069 0.21 -10000 0 -0.86 22 22
AKT1/mTOR/p70S6K/Hsp90/TERT -0.031 0.2 -10000 0 -0.48 39 39
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.045 0.21 -10000 0 -0.84 22 22
mol:DAG -0.004 0.007 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.12 0.21 -10000 0 -0.63 40 40
FRAP1 -0.076 0.3 -10000 0 -0.75 44 44
FOXO3 -0.066 0.29 -10000 0 -0.76 38 38
AKT1 -0.087 0.32 -10000 0 -0.78 47 47
GAB2 0.005 0.095 -10000 0 -0.81 5 5
SMPD1 -0.021 0.035 -10000 0 -10000 0 0
SGMS1 -0.021 0.035 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.042 -10000 0 -0.54 2 2
CALM1 0.016 0 -10000 0 -10000 0 0
cell proliferation -0.04 0.2 -10000 0 -0.49 37 37
EIF3A 0.016 0 -10000 0 -10000 0 0
PI3K 0.02 0.048 -10000 0 -0.62 2 2
RPS6KB1 0.002 0.072 -10000 0 -10000 0 0
mol:sphingomyelin -0.004 0.007 -10000 0 -10000 0 0
natural killer cell activation 0.001 0.002 -10000 0 -10000 0 0
JAK3 -0.13 0.31 -10000 0 -0.8 67 67
PIK3R1 0.019 0.005 -10000 0 -10000 0 0
JAK1 0.019 0.004 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
MYC -0.068 0.3 -10000 0 -0.82 36 36
MYB -0.076 0.37 -10000 0 -1.4 26 26
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.11 0.36 -10000 0 -0.77 62 62
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.009 0.054 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.1 0.33 -10000 0 -0.72 62 62
Rac1/GDP 0.029 0.04 -10000 0 -0.48 2 2
T cell proliferation -0.084 0.3 -10000 0 -0.71 50 50
SHC1 0.015 0.033 -10000 0 -0.62 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.019 -10000 0 -0.058 33 33
PRKCZ -0.092 0.32 -10000 0 -0.76 50 50
NF kappa B1 p50/RelA -0.12 0.2 -10000 0 -0.66 34 34
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.13 0.35 -10000 0 -0.78 65 65
HSP90AA1 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL2RA -0.14 0.3 -10000 0 -0.73 78 78
IL2RB -0.086 0.26 -10000 0 -0.7 55 55
TERT 0 0 -10000 0 -10000 0 0
E2F1 -0.02 0.17 -10000 0 -0.55 29 29
SOS1 0.016 0.004 -10000 0 -10000 0 0
RPS6 0.016 0 -10000 0 -10000 0 0
mol:cAMP -0.001 0.009 0.026 38 -10000 0 38
PTPN11 0.016 0.004 -10000 0 -10000 0 0
IL2RG -0.16 0.32 -10000 0 -0.7 97 97
actin cytoskeleton organization -0.084 0.3 -10000 0 -0.71 50 50
GRB2 0.016 0.004 -10000 0 -10000 0 0
IL2 -0.008 0.099 -10000 0 -0.61 10 10
PIK3CA 0.014 0.06 -10000 0 -0.81 2 2
Rac1/GTP 0.037 0.04 -10000 0 -0.46 2 2
LCK -0.09 0.26 -10000 0 -0.68 59 59
BCL2 -0.046 0.25 -10000 0 -0.69 30 30
Visual signal transduction: Rods

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
mol:K + 0.016 0 -9999 0 -10000 0 0
GNAT1/GTP -0.007 0.056 -9999 0 -0.45 6 6
Metarhodopsin II/Arrestin -0.003 0.034 -9999 0 -0.39 3 3
PDE6G/GNAT1/GTP -0.075 0.18 -9999 0 -0.47 61 61
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.005 0.077 -9999 0 -0.61 6 6
GRK1 -0.071 0.24 -9999 0 -0.75 43 43
CNG Channel -0.14 0.24 -9999 0 -0.8 28 28
mol:Na + -0.1 0.2 -9999 0 -0.7 18 18
mol:ADP -0.071 0.24 -9999 0 -0.75 43 43
RGS9-1/Gbeta5/R9AP -0.083 0.19 -9999 0 -0.57 37 37
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.11 0.2 -9999 0 -0.76 16 16
CNGB1 -0.064 0.23 -9999 0 -0.71 41 41
RDH5 -0.16 0.34 -9999 0 -0.8 82 82
SAG 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.062 0.21 -9999 0 -0.7 16 16
Na + (4 Units) -0.097 0.18 -9999 0 -0.67 16 16
RGS9 -0.061 0.22 -9999 0 -0.7 41 41
GNB1/GNGT1 0 0 -9999 0 -10000 0 0
GNAT1/GDP -0.076 0.17 -9999 0 -0.51 37 37
GUCY2D -0.05 0.22 -9999 0 -0.74 33 33
GNGT1 0 0 -9999 0 -10000 0 0
GUCY2F 0 0 -9999 0 -10000 0 0
GNB5 0.014 0.043 -9999 0 -0.81 1 1
mol:GMP (4 units) -0.065 0.2 -9999 0 -0.53 41 41
mol:11-cis-retinal -0.16 0.33 -9999 0 -0.79 82 82
mol:cGMP -0.052 0.15 -9999 0 -0.51 28 28
GNB1 0.016 0 -9999 0 -10000 0 0
Rhodopsin -0.14 0.26 -9999 0 -0.61 84 84
SLC24A1 0.016 0 -9999 0 -10000 0 0
CNGA1 -0.034 0.18 -9999 0 -0.68 27 27
Metarhodopsin II -0.055 0.15 -9999 0 -0.45 46 46
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.055 0.16 -9999 0 -0.54 28 28
RGS9BP -0.039 0.2 -9999 0 -0.75 27 27
Metarhodopsin II/Transducin 0.01 0.032 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.017 0.085 -9999 0 -0.42 15 15
PDE6A/B -0.039 0.14 -9999 0 -0.51 29 29
mol:Pi -0.083 0.19 -9999 0 -0.57 37 37
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.005 0.043 -9999 0 -0.34 6 6
PDE6B 0.016 0 -9999 0 -10000 0 0
PDE6A -0.041 0.19 -9999 0 -0.69 29 29
PDE6G -0.092 0.26 -9999 0 -0.7 57 57
RHO 0.004 0.055 -9999 0 -0.61 3 3
PDE6 -0.14 0.23 -9999 0 -0.73 28 28
GUCA1A -0.006 0.094 -9999 0 -0.61 9 9
GC2/GCAP Family -0.017 0.085 -9999 0 -0.42 15 15
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.002 0.1 -9999 0 -0.76 7 7
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.031 0.14 -9999 0 -0.61 19 19
alphaV beta3 Integrin -0.051 0.19 -9999 0 -0.64 30 30
PTK2 -0.017 0.24 -9999 0 -0.7 26 26
IGF1R 0.011 0.06 -9999 0 -0.81 2 2
PI4KB 0.016 0 -9999 0 -10000 0 0
MFGE8 -0.043 0.21 -9999 0 -0.81 27 27
SRC 0.012 0.053 -9999 0 -0.71 2 2
CDKN1B -0.072 0.17 -9999 0 -0.6 27 27
VEGFA 0.01 0.068 -9999 0 -0.74 3 3
ILK -0.072 0.17 -9999 0 -0.6 27 27
ROCK1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.065 0.16 -9999 0 -0.6 21 21
PTK2B -0.01 0.19 -9999 0 -0.54 38 38
alphaV/beta3 Integrin/JAM-A -0.095 0.21 -9999 0 -0.57 49 49
CBL 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.04 0.15 -9999 0 -0.59 24 24
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.096 0.18 -9999 0 -0.51 33 33
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.011 0.14 -9999 0 -0.55 11 11
alphaV/beta3 Integrin/Syndecan-1 -0.041 0.16 -9999 0 -0.59 26 26
PI4KA 0.016 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.25 0.33 -9999 0 -0.9 56 56
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.06 -9999 0 -0.81 2 2
alphaV/beta3 Integrin/Osteopontin -0.14 0.26 -9999 0 -0.61 68 68
RPS6KB1 -0.19 0.32 -9999 0 -0.83 51 51
TLN1 0.016 0 -9999 0 -10000 0 0
MAPK3 -0.14 0.27 -9999 0 -0.98 30 30
GPR124 0.005 0.09 -9999 0 -0.77 5 5
MAPK1 -0.14 0.27 -9999 0 -0.98 30 30
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.061 0.2 -9999 0 -0.66 35 35
cell adhesion -0.067 0.21 -9999 0 -0.73 24 24
ANGPTL3 0.002 0.064 -9999 0 -0.61 4 4
VEGFR2 homodimer/VEGFA homodimer/Src -0.029 0.13 -9999 0 -0.58 16 16
IGF-1R heterotetramer 0.011 0.06 -9999 0 -0.81 2 2
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.011 0.06 -9999 0 -0.81 2 2
ITGB3 -0.032 0.19 -9999 0 -0.81 22 22
IGF1 -0.14 0.29 -9999 0 -0.68 86 86
RAC1 0.016 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.043 0.15 -9999 0 -0.56 28 28
apoptosis 0.007 0.084 -9999 0 -0.81 4 4
CD47 0.014 0.043 -9999 0 -0.81 1 1
alphaV/beta3 Integrin/CD47 -0.038 0.15 -9999 0 -0.59 24 24
VCL 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.079 0.22 -9999 0 -0.65 42 42
CSF1 -0.01 0.14 -9999 0 -0.81 12 12
PIK3C2A -0.074 0.18 -9999 0 -0.63 27 27
PI4 Kinase/Pyk2 -0.097 0.21 -9999 0 -0.79 20 20
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.057 0.17 -9999 0 -0.55 37 37
FAK1/Vinculin 0.002 0.18 -9999 0 -0.54 20 20
alphaV beta3/Integrin/ppsTEM5 -0.043 0.15 -9999 0 -0.57 28 28
RHOA 0.016 0 -9999 0 -10000 0 0
VTN -0.085 0.25 -9999 0 -0.69 54 54
BCAR1 0.016 0 -9999 0 -10000 0 0
FGF2 -0.008 0.14 -9999 0 -0.81 11 11
F11R 0.011 0.11 -9999 0 -0.62 11 11
alphaV/beta3 Integrin/Lactadherin -0.073 0.22 -9999 0 -0.66 42 42
alphaV/beta3 Integrin/TGFBR2 -0.039 0.15 -9999 0 -0.59 25 25
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.02 0.11 -9999 0 -0.55 14 14
HSP90AA1 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.034 0.13 -9999 0 -0.53 24 24
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.27 0.38 -9999 0 -0.78 135 135
alphaV/beta3 Integrin/Pyk2 -0.056 0.17 -9999 0 -0.58 26 26
SDC1 0.008 0.08 -9999 0 -0.76 4 4
VAV3 -0.012 0.18 -9999 0 -0.56 21 21
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.001 0.11 -9999 0 -0.71 8 8
FAK1/Paxillin 0.002 0.18 -9999 0 -0.54 21 21
cell migration 0.017 0.17 -9999 0 -0.5 16 16
ITGAV 0.007 0.085 -9999 0 -0.81 4 4
PI3K -0.086 0.19 -9999 0 -0.81 14 14
SPP1 -0.14 0.31 -9999 0 -0.74 80 80
KDR -0.02 0.16 -9999 0 -0.78 17 17
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.007 0.085 -9999 0 -0.81 4 4
COL4A3 -0.023 0.18 -9999 0 -0.81 18 18
angiogenesis -0.1 0.29 -9999 0 -0.92 32 32
Rac1/GTP -0.051 0.14 -9999 0 -0.78 6 6
EDIL3 -0.053 0.22 -9999 0 -0.77 33 33
cell proliferation -0.039 0.15 -9999 0 -0.59 25 25
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.012 0.28 -10000 0 -0.98 22 22
NCK1/PAK1/Dok-R -0.065 0.13 -10000 0 -0.44 27 27
NCK1/Dok-R -0.14 0.32 -10000 0 -1.2 24 24
PIK3CA 0.011 0.06 -10000 0 -0.81 2 2
mol:beta2-estradiol 0.003 0.058 0.23 16 -10000 0 16
RELA 0.016 0 -10000 0 -10000 0 0
SHC1 0.014 0.032 -10000 0 -0.61 1 1
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0 0.059 0.24 16 -10000 0 16
TNIP2 0.016 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.088 0.27 -10000 0 -1.1 22 22
FN1 -0.27 0.38 -10000 0 -0.78 135 135
PLD2 -0.037 0.34 -10000 0 -1.3 22 22
PTPN11 0.016 0 -10000 0 -10000 0 0
GRB14 -0.002 0.11 -10000 0 -0.72 9 9
ELK1 -0.012 0.3 -10000 0 -1.1 22 22
GRB7 -0.054 0.23 -10000 0 -0.81 32 32
PAK1 0.016 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.22 0.33 -10000 0 -1.2 27 27
CDKN1A -0.02 0.25 -10000 0 -0.76 28 28
ITGA5 0.014 0.043 -10000 0 -0.81 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.14 0.32 -10000 0 -1.2 24 24
CRK 0.016 0 -10000 0 -10000 0 0
mol:NO 0.012 0.22 -10000 0 -0.7 22 22
PLG -0.047 0.34 -10000 0 -1.3 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.065 0.24 -10000 0 -0.94 22 22
GRB2 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.015 0.005 -10000 0 -10000 0 0
ANGPT2 -0.093 0.26 -10000 0 -0.85 26 26
BMX -0.065 0.36 -10000 0 -1.3 22 22
ANGPT1 -0.082 0.35 -10000 0 -1.3 24 24
tube development -0.025 0.24 -10000 0 -0.74 27 27
ANGPT4 -0.054 0.21 -10000 0 -0.7 37 37
response to hypoxia -0.002 0.02 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.052 0.36 -10000 0 -1.4 23 23
alpha5/beta1 Integrin -0.002 0.032 -10000 0 -0.62 1 1
FGF2 -0.009 0.14 -10000 0 -0.81 11 11
STAT5A (dimer) -0.031 0.28 -10000 0 -0.9 27 27
mol:L-citrulline 0.012 0.22 -10000 0 -0.7 22 22
AGTR1 -0.23 0.35 -10000 0 -0.72 126 126
MAPK14 -0.04 0.33 -10000 0 -1.3 22 22
Tie2/SHP2 -0.047 0.22 -10000 0 -1.4 10 10
TEK -0.011 0.26 -10000 0 -1.5 10 10
RPS6KB1 -0.007 0.26 -10000 0 -0.93 22 22
Angiotensin II/AT1 -0.17 0.27 -10000 0 -0.54 126 126
Tie2/Ang1/GRB2 -0.044 0.36 -10000 0 -1.4 22 22
MAPK3 -0.019 0.31 -10000 0 -1.2 22 22
MAPK1 -0.019 0.31 -10000 0 -1.2 22 22
Tie2/Ang1/GRB7 -0.084 0.38 -10000 0 -1.4 23 23
NFKB1 0.016 0 -10000 0 -10000 0 0
MAPK8 -0.04 0.35 -10000 0 -1.3 22 22
PI3K -0.029 0.32 -10000 0 -1.2 22 22
FES -0.04 0.33 -10000 0 -1.3 22 22
Crk/Dok-R -0.14 0.32 -10000 0 -1.2 24 24
Tie2/Ang1/ABIN2 -0.044 0.36 -10000 0 -1.4 22 22
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.005 0.25 -10000 0 -0.86 22 22
STAT5A 0.016 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.007 0.26 -10000 0 -0.93 22 22
Tie2/Ang2 -0.058 0.32 -10000 0 -1.1 26 26
Tie2/Ang1 -0.055 0.39 -10000 0 -1.5 22 22
FOXO1 -0.002 0.26 -10000 0 -0.86 22 22
ELF1 0.02 0.062 -10000 0 -0.8 2 2
ELF2 -0.042 0.34 -10000 0 -1.3 22 22
mol:Choline -0.031 0.32 -10000 0 -1.2 22 22
cell migration -0.067 0.082 -10000 0 -0.24 29 29
FYN -0.035 0.27 -10000 0 -0.86 27 27
DOK2 -0.072 0.24 -10000 0 -0.74 44 44
negative regulation of cell cycle -0.013 0.22 -10000 0 -0.66 29 29
ETS1 0.007 0.09 -10000 0 -0.79 3 3
PXN 0.012 0.22 -10000 0 -0.75 22 22
ITGB1 0.016 0 -10000 0 -10000 0 0
NOS3 0.006 0.24 -10000 0 -0.81 22 22
RAC1 0.016 0 -10000 0 -10000 0 0
TNF -0.15 0.32 -10000 0 -0.72 85 85
MAPKKK cascade -0.031 0.32 -10000 0 -1.2 22 22
RASA1 0.016 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.047 0.36 -10000 0 -1.4 22 22
NCK1 0.016 0 -10000 0 -10000 0 0
vasculogenesis 0.017 0.2 -10000 0 -0.62 22 22
mol:Phosphatidic acid -0.031 0.32 -10000 0 -1.2 22 22
mol:Angiotensin II 0.001 0.005 -10000 0 -10000 0 0
mol:NADP 0.012 0.22 -10000 0 -0.7 22 22
Rac1/GTP -0.081 0.21 -10000 0 -0.86 22 22
MMP2 -0.06 0.36 -10000 0 -1.4 22 22
Signaling events mediated by PTP1B

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
PDGFRB -0.014 0.15 -10000 0 -0.8 14 14
Jak2/Leptin Receptor -0.039 0.11 -10000 0 -0.44 9 9
PTP1B/AKT1 0.013 0.088 -10000 0 -0.38 7 7
FYN 0.011 0.06 -10000 0 -0.81 2 2
p210 bcr-abl/PTP1B 0.005 0.098 -10000 0 -0.36 16 16
EGFR -0.022 0.17 -10000 0 -0.8 17 17
EGF/EGFR -0.091 0.18 -10000 0 -0.53 42 42
CSF1 -0.01 0.14 -10000 0 -0.81 12 12
AKT1 0.016 0.001 -10000 0 -10000 0 0
INSR 0.016 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.095 0.22 -10000 0 -0.47 87 87
Insulin Receptor/Insulin -0.016 0.054 -10000 0 -10000 0 0
HCK -0.067 0.24 -10000 0 -0.75 41 41
CRK 0.016 0 -10000 0 -10000 0 0
TYK2 0.015 0.094 -10000 0 -0.39 9 9
EGF -0.11 0.26 -10000 0 -0.65 70 70
YES1 0.016 0 -10000 0 -10000 0 0
CAV1 -0.005 0.13 -10000 0 -0.45 18 18
TXN 0.012 0.033 -10000 0 -0.61 1 1
PTP1B/IRS1/GRB2 -0.031 0.085 -10000 0 -0.41 8 8
cell migration -0.005 0.098 0.36 16 -10000 0 16
STAT3 0.016 0.001 -10000 0 -10000 0 0
PRLR -0.12 0.28 -10000 0 -0.7 71 71
ITGA2B -0.033 0.18 -10000 0 -0.74 24 24
CSF1R -0.018 0.16 -10000 0 -0.78 16 16
Prolactin Receptor/Prolactin -0.096 0.21 -10000 0 -0.53 71 71
FGR -0.019 0.16 -10000 0 -0.76 17 17
PTP1B/p130 Cas 0.013 0.093 -10000 0 -0.41 7 7
Crk/p130 Cas -0.023 0.07 -10000 0 -0.4 5 5
DOK1 0.015 0.1 -10000 0 -0.38 10 10
JAK2 -0.015 0.1 -10000 0 -0.38 9 9
Jak2/Leptin Receptor/Leptin -0.088 0.17 -10000 0 -0.59 25 25
PIK3R1 0.016 0 -10000 0 -10000 0 0
PTPN1 0.005 0.099 -10000 0 -0.36 16 16
LYN 0.016 0 -10000 0 -10000 0 0
CDH2 -0.17 0.34 -10000 0 -0.78 89 89
SRC 0.021 0.047 -10000 0 -0.47 1 1
ITGB3 -0.033 0.19 -10000 0 -0.82 22 22
CAT1/PTP1B -0.11 0.22 -10000 0 -0.6 36 36
CAPN1 0.015 0.004 -10000 0 -10000 0 0
CSK 0.014 0.032 -10000 0 -0.61 1 1
PI3K -0.014 0.058 -10000 0 -0.63 1 1
mol:H2O2 -0.001 0.004 0.011 10 -0.01 20 30
STAT3 (dimer) -0.083 0.17 -10000 0 -0.61 24 24
negative regulation of transcription -0.013 0.1 -10000 0 -0.37 9 9
FCGR2A -0.029 0.18 -10000 0 -0.76 22 22
FER 0.009 0.061 -10000 0 -0.82 2 2
alphaIIb/beta3 Integrin -0.069 0.21 -10000 0 -0.68 39 39
BLK -0.24 0.34 -10000 0 -0.69 135 135
Insulin Receptor/Insulin/Shc -0.001 0.019 -10000 0 -0.38 1 1
RHOA 0.015 0.004 -10000 0 -10000 0 0
LEPR -0.01 0.12 -10000 0 -0.64 13 13
BCAR1 0.016 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.016 0 -10000 0 -10000 0 0
mol:NADPH 0 0.003 0.007 1 -0.01 13 14
TRPV6 -0.16 0.26 -10000 0 -0.62 58 58
PRL 0 0.004 0.014 22 -10000 0 22
SOCS3 -0.06 0.3 -10000 0 -1.5 14 14
SPRY2 0.005 0.076 -10000 0 -0.65 5 5
Insulin Receptor/Insulin/IRS1 -0.01 0.068 -10000 0 -0.46 8 8
CSF1/CSF1R -0.054 0.16 -10000 0 -0.55 27 27
Ras protein signal transduction 0.017 0.03 -10000 0 -10000 0 0
IRS1 0.001 0.11 -10000 0 -0.71 8 8
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.054 0.18 -10000 0 -0.61 38 38
STAT5B 0.002 0.09 -10000 0 -0.35 10 10
STAT5A 0.002 0.09 -10000 0 -0.35 10 10
GRB2 0.016 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.004 0.13 -10000 0 -0.46 20 20
CSN2 -0.029 0.072 -10000 0 -0.17 70 70
PIK3CA 0.011 0.06 -10000 0 -0.81 2 2
LAT -0.018 0.18 -10000 0 -0.66 21 21
YBX1 0.025 0.002 -10000 0 -10000 0 0
LCK -0.093 0.26 -10000 0 -0.68 59 59
SHC1 0.014 0.032 -10000 0 -0.61 1 1
NOX4 -0.046 0.21 -10000 0 -0.77 29 29
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 -0.19 0.49 -10000 0 -1.3 60 60
regulation of axonogenesis -0.004 0.068 -10000 0 -10000 0 0
myoblast fusion 0.074 0.15 0.38 60 -10000 0 60
mol:GTP -0.045 0.087 -10000 0 -0.28 1 1
regulation of calcium-dependent cell-cell adhesion 0.077 0.23 0.62 46 -10000 0 46
ARF1/GTP -0.031 0.06 -10000 0 -10000 0 0
mol:GM1 -0.023 0.071 -10000 0 -10000 0 0
mol:Choline 0.007 0.062 -10000 0 -10000 0 0
lamellipodium assembly -0.068 0.16 -10000 0 -0.46 37 37
MAPK3 -0.038 0.14 -10000 0 -0.34 60 60
ARF6/GTP/NME1/Tiam1 -0.077 0.23 -10000 0 -0.63 46 46
ARF1 0.016 0 -10000 0 -10000 0 0
ARF6/GDP -0.074 0.15 -10000 0 -0.38 60 60
ARF1/GDP -0.034 0.15 -10000 0 -0.39 37 37
ARF6 -0.01 0.049 -10000 0 -10000 0 0
RAB11A 0.016 0 -10000 0 -10000 0 0
TIAM1 -0.097 0.28 -10000 0 -0.8 52 52
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.038 0.14 -10000 0 -0.34 60 60
actin filament bundle formation 0.066 0.13 0.39 37 -10000 0 37
KALRN -0.05 0.12 -10000 0 -0.33 37 37
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.067 0.13 -10000 0 -0.39 37 37
NME1 0.013 0.009 -10000 0 -10000 0 0
Rac1/GDP -0.067 0.13 -10000 0 -0.39 37 37
substrate adhesion-dependent cell spreading -0.045 0.087 -10000 0 -0.28 1 1
cortical actin cytoskeleton organization -0.069 0.16 -10000 0 -0.47 37 37
RAC1 0.016 0 -10000 0 -10000 0 0
liver development -0.045 0.087 -10000 0 -0.28 1 1
ARF6/GTP -0.045 0.087 -10000 0 -0.28 1 1
RhoA/GTP -0.031 0.059 -10000 0 -10000 0 0
mol:GDP -0.066 0.15 -10000 0 -0.38 60 60
ARF6/GTP/RAB11FIP3/RAB11A -0.023 0.046 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
PLD1 -0.009 0.071 -10000 0 -10000 0 0
RAB11FIP3 0.016 0 -10000 0 -10000 0 0
tube morphogenesis -0.068 0.16 -10000 0 -0.46 37 37
ruffle organization 0.004 0.068 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.045 0.087 -10000 0 -0.28 1 1
PLD2 -0.009 0.071 -10000 0 -10000 0 0
PIP5K1A 0.002 0.067 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.062 -10000 0 -10000 0 0
Rac1/GTP -0.069 0.16 -10000 0 -0.47 37 37
LPA receptor mediated events

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
GNB1/GNG2 -0.028 0.098 -9999 0 -0.55 7 7
NF kappa B1 p50/RelA/I kappa B alpha -0.049 0.098 -9999 0 -0.5 3 3
AP1 -0.15 0.23 -9999 0 -0.67 40 40
mol:PIP3 -0.078 0.15 -9999 0 -0.59 8 8
AKT1 -0.014 0.054 -9999 0 -0.44 1 1
PTK2B 0.002 0.1 -9999 0 -0.6 5 5
RHOA 0.038 0.051 -9999 0 -0.38 1 1
PIK3CB 0.016 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.027 0.14 -9999 0 -0.47 10 10
MAGI3 0.014 0.042 -9999 0 -0.81 1 1
RELA 0.016 0 -9999 0 -10000 0 0
apoptosis -0.062 0.14 -9999 0 -0.43 32 32
HRAS/GDP -0.002 0.033 -9999 0 -0.45 2 2
positive regulation of microtubule depolymerization -0.012 0.14 -9999 0 -0.48 17 17
NF kappa B1 p50/RelA -0.069 0.14 -9999 0 -0.55 7 7
endothelial cell migration -0.023 0.21 -9999 0 -0.72 28 28
ADCY4 -0.01 0.15 -9999 0 -0.5 18 18
ADCY5 -0.044 0.16 -9999 0 -0.49 25 25
ADCY6 -0.008 0.15 -9999 0 -0.49 17 17
ADCY7 -0.011 0.16 -9999 0 -0.51 19 19
ADCY1 -0.02 0.16 -9999 0 -0.5 21 21
ADCY2 -0.045 0.18 -9999 0 -0.54 29 29
ADCY3 -0.008 0.15 -9999 0 -0.48 18 18
ADCY8 -0.096 0.2 -9999 0 -0.58 34 34
ADCY9 -0.009 0.15 -9999 0 -0.49 18 18
GSK3B 0.012 0.098 -9999 0 -0.74 3 3
arachidonic acid secretion -0.006 0.15 -9999 0 -0.49 16 16
GNG2 0.011 0.055 -9999 0 -0.61 3 3
TRIP6 0.026 0.038 -9999 0 -0.52 1 1
GNAO1 -0.053 0.2 -9999 0 -0.53 48 48
HRAS 0.013 0.045 -9999 0 -0.61 2 2
NFKBIA -0.013 0.14 -9999 0 -0.53 6 6
GAB1 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.12 0.32 -9999 0 -0.98 47 47
JUN -0.024 0.16 -9999 0 -0.66 22 22
LPA/LPA2/NHERF2 -0.008 0.043 -9999 0 -0.43 3 3
TIAM1 -0.15 0.39 -9999 0 -1.2 47 47
PIK3R1 0.016 0.001 -9999 0 -10000 0 0
mol:IP3 -0.028 0.14 -9999 0 -0.48 10 10
PLCB3 0.029 0.044 -9999 0 -0.41 2 2
FOS -0.11 0.28 -9999 0 -0.72 65 65
positive regulation of mitosis -0.006 0.15 -9999 0 -0.49 16 16
LPA/LPA1-2-3 -0.085 0.17 -9999 0 -0.52 33 33
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0.001 -9999 0 -10000 0 0
BCAR1 0.016 0 -9999 0 -10000 0 0
stress fiber formation -0.004 0.12 -9999 0 -0.45 9 9
GNAZ -0.005 0.14 -9999 0 -0.51 18 18
EGFR/PI3K-beta/Gab1 -0.081 0.15 -9999 0 -0.62 8 8
positive regulation of dendritic cell cytokine production -0.084 0.17 -9999 0 -0.52 33 33
LPA/LPA2/MAGI-3 -0.007 0.046 -9999 0 -0.58 2 2
ARHGEF1 0.025 0.097 -9999 0 -0.49 6 6
GNAI2 0.005 0.11 -9999 0 -0.48 11 11
GNAI3 0.005 0.11 -9999 0 -0.53 8 8
GNAI1 -0.013 0.14 -9999 0 -0.61 8 8
LPA/LPA3 -0.084 0.18 -9999 0 -0.5 60 60
LPA/LPA2 -0.008 0.042 -9999 0 -0.63 1 1
LPA/LPA1 -0.035 0.12 -9999 0 -0.46 23 23
HB-EGF/EGFR -0.16 0.27 -9999 0 -0.49 139 139
HBEGF -0.17 0.28 -9999 0 -0.54 130 130
mol:DAG -0.028 0.14 -9999 0 -0.48 10 10
cAMP biosynthetic process -0.04 0.18 -9999 0 -0.51 32 32
NFKB1 0.016 0 -9999 0 -10000 0 0
SRC 0.012 0.053 -9999 0 -0.71 2 2
GNB1 0.016 0.001 -9999 0 -10000 0 0
LYN -0.013 0.14 -9999 0 -0.53 6 6
GNAQ -0.031 0.12 -9999 0 -0.38 24 24
LPAR2 0.014 0.043 -9999 0 -0.81 1 1
LPAR3 -0.094 0.25 -9999 0 -0.66 60 60
LPAR1 -0.01 0.13 -9999 0 -0.73 11 11
IL8 -0.18 0.27 -9999 0 -0.55 102 102
PTK2 -0.038 0.18 -9999 0 -0.48 33 33
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.064 0.14 -9999 0 -0.43 32 32
EGFR -0.021 0.17 -9999 0 -0.79 17 17
PLCG1 -0.052 0.15 -9999 0 -0.41 34 34
PLD2 -0.038 0.18 -9999 0 -0.48 33 33
G12/G13 -0.026 0.092 -9999 0 -0.53 6 6
PI3K-beta -0.017 0.063 -9999 0 -0.5 2 2
cell migration -0.052 0.097 -9999 0 -0.3 13 13
SLC9A3R2 0.013 0.045 -9999 0 -0.61 2 2
PXN -0.004 0.12 -9999 0 -0.46 9 9
HRAS/GTP -0.06 0.13 -9999 0 -0.5 16 16
RAC1 0.016 0 -9999 0 -10000 0 0
MMP9 -0.18 0.33 -9999 0 -0.73 100 100
PRKCE 0.01 0.053 -9999 0 -0.71 2 2
PRKCD -0.017 0.13 -9999 0 -0.57 3 3
Gi(beta/gamma) -0.018 0.14 -9999 0 -0.51 12 12
mol:LPA -0.007 0.048 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.057 0.14 -9999 0 -0.57 7 7
MAPKKK cascade -0.006 0.15 -9999 0 -0.49 16 16
contractile ring contraction involved in cytokinesis 0.038 0.051 -9999 0 -0.38 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.073 0.16 -9999 0 -0.43 34 34
GNA15 -0.082 0.2 -9999 0 -0.47 62 62
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
MAPT -0.013 0.15 -9999 0 -0.5 17 17
GNA11 -0.044 0.14 -9999 0 -0.4 35 35
Rac1/GTP -0.13 0.35 -9999 0 -1 47 47
MMP2 -0.024 0.21 -9999 0 -0.72 28 28
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.031 0.14 -9999 0 -0.61 19 19
PDGFRB -0.017 0.15 -9999 0 -0.8 14 14
SPHK1 -0.033 0.13 -9999 0 -1.1 6 6
mol:S1P -0.034 0.12 -9999 0 -0.96 6 6
S1P1/S1P/Gi -0.07 0.26 -9999 0 -0.69 37 37
GNAO1 -0.071 0.25 -9999 0 -0.8 40 40
PDGFB-D/PDGFRB/PLCgamma1 -0.059 0.24 -9999 0 -0.63 38 38
PLCG1 -0.057 0.24 -9999 0 -0.65 36 36
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.017 0.15 -9999 0 -0.8 14 14
GNAI2 0.013 0.008 -9999 0 -10000 0 0
GNAI3 0.013 0.008 -9999 0 -10000 0 0
GNAI1 -0.015 0.13 -9999 0 -0.62 17 17
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.007 0.12 -9999 0 -0.53 19 19
S1P1/S1P -0.054 0.14 -9999 0 -0.55 21 21
negative regulation of cAMP metabolic process -0.066 0.25 -9999 0 -0.67 37 37
MAPK3 -0.091 0.31 -9999 0 -0.66 71 71
calcium-dependent phospholipase C activity -0.002 0.004 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR -0.022 0.16 -9999 0 -0.78 17 17
PLCB2 -0.026 0.17 -9999 0 -0.52 28 28
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.044 0.11 -9999 0 -0.51 14 14
receptor internalization -0.05 0.12 -9999 0 -0.5 21 21
PTGS2 -0.17 0.46 -9999 0 -1.1 69 69
Rac1/GTP -0.044 0.11 -9999 0 -0.51 14 14
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFA 0.008 0.068 -9999 0 -0.74 3 3
negative regulation of T cell proliferation -0.066 0.25 -9999 0 -0.67 37 37
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.001 0.11 -9999 0 -0.77 7 7
MAPK1 -0.091 0.31 -9999 0 -0.66 71 71
S1P1/S1P/PDGFB-D/PDGFRB -0.021 0.19 -9999 0 -0.76 15 15
ABCC1 0.015 0.003 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.021 0.06 0.31 5 -10000 0 5
RFC1 0.021 0.06 0.31 5 -10000 0 5
PRKDC 0.02 0.066 0.31 5 -0.52 1 6
RIPK1 0.016 0.006 -10000 0 -10000 0 0
CASP7 -0.005 0.065 0.28 1 -10000 0 1
FASLG/FAS/FADD/FAF1 -0.051 0.14 0.26 2 -0.39 40 42
MAP2K4 -0.055 0.17 -10000 0 -0.47 27 27
mol:ceramide -0.071 0.18 -10000 0 -0.49 43 43
GSN 0.015 0.076 0.3 4 -0.52 3 7
FASLG/FAS/FADD/FAF1/Caspase 8 -0.078 0.15 -10000 0 -0.47 40 40
FAS 0.001 0.095 -10000 0 -0.82 5 5
BID -0.004 0.13 0.33 7 -0.54 17 24
MAP3K1 -0.011 0.11 -10000 0 -0.46 1 1
MAP3K7 0.011 0.008 -10000 0 -10000 0 0
RB1 0.021 0.06 0.31 5 -10000 0 5
CFLAR 0.016 0.006 -10000 0 -10000 0 0
HGF/MET -0.12 0.23 -10000 0 -0.57 71 71
ARHGDIB 0.021 0.06 0.31 5 -10000 0 5
FADD 0.011 0.008 -10000 0 -10000 0 0
actin filament polymerization -0.015 0.075 0.52 3 -0.3 4 7
NFKB1 -0.071 0.089 -10000 0 -10000 0 0
MAPK8 -0.086 0.22 -10000 0 -0.47 62 62
DFFA 0.021 0.06 0.31 5 -10000 0 5
DNA fragmentation during apoptosis 0.021 0.06 0.31 5 -10000 0 5
FAS/FADD/MET -0.072 0.19 -10000 0 -0.57 48 48
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.052 0.2 -10000 0 -0.65 39 39
FAF1 0.012 0.008 -10000 0 -10000 0 0
PARP1 0.021 0.06 0.31 5 -10000 0 5
DFFB 0.021 0.06 0.31 5 -10000 0 5
CHUK -0.059 0.077 -10000 0 -10000 0 0
FASLG -0.16 0.31 -10000 0 -0.71 88 88
FAS/FADD -0.008 0.072 -10000 0 -0.63 5 5
HGF -0.077 0.25 -10000 0 -0.72 48 48
LMNA 0.02 0.056 0.29 4 -10000 0 4
CASP6 0.021 0.06 0.31 5 -10000 0 5
CASP10 0.007 0.061 -10000 0 -0.82 2 2
CASP3 0.025 0.07 0.38 5 -10000 0 5
PTPN13 0.011 0.06 -10000 0 -0.81 2 2
CASP8 0.033 0.1 0.32 39 -10000 0 39
IL6 -0.28 0.52 -10000 0 -1.3 69 69
MET -0.085 0.27 -10000 0 -0.81 46 46
ICAD/CAD 0.021 0.058 0.35 1 -10000 0 1
FASLG/FAS/FADD/FAF1/Caspase 10 -0.072 0.19 -10000 0 -0.5 43 43
activation of caspase activity by cytochrome c -0.004 0.13 0.33 7 -0.54 17 24
PAK2 0.021 0.059 0.31 5 -10000 0 5
BCL2 -0.006 0.12 -10000 0 -0.68 12 12
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.064 0.3 -10000 0 -0.79 39 39
IHH -0.031 0.14 -10000 0 -0.58 22 22
SHH Np/Cholesterol/GAS1 -0.06 0.14 -10000 0 -0.56 8 8
LRPAP1 0.014 0.043 -10000 0 -0.81 1 1
dorsoventral neural tube patterning 0.06 0.14 0.56 8 -10000 0 8
SMO/beta Arrestin2 0.005 0.15 -10000 0 -0.84 4 4
SMO -0.002 0.16 -10000 0 -0.9 4 4
AKT1 0.025 0.09 -10000 0 -1 1 1
ARRB2 0.014 0.032 -10000 0 -0.61 1 1
BOC -0.018 0.16 -10000 0 -0.78 16 16
ADRBK1 0.016 0 -10000 0 -10000 0 0
heart looping -0.001 0.15 -10000 0 -0.87 4 4
STIL -0.01 0.16 -10000 0 -0.75 6 6
DHH N/PTCH2 -0.059 0.18 -10000 0 -0.6 37 37
DHH N/PTCH1 -0.061 0.19 -10000 0 -0.63 24 24
PIK3CA 0.011 0.06 -10000 0 -0.81 2 2
DHH -0.027 0.18 -10000 0 -0.79 20 20
PTHLH -0.088 0.38 -10000 0 -1.1 39 39
determination of left/right symmetry -0.001 0.15 -10000 0 -0.87 4 4
PIK3R1 0.016 0 -10000 0 -10000 0 0
skeletal system development -0.086 0.37 -10000 0 -1.1 39 39
IHH N/Hhip -0.05 0.17 -10000 0 -0.52 36 36
DHH N/Hhip -0.071 0.18 -10000 0 -0.52 52 52
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.001 0.15 -10000 0 -0.87 4 4
pancreas development -0.043 0.18 -10000 0 -0.61 34 34
HHAT 0.014 0.043 -10000 0 -0.81 1 1
PI3K -0.003 0.045 -10000 0 -0.62 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.06 0.21 -10000 0 -0.64 44 44
somite specification -0.001 0.15 -10000 0 -0.87 4 4
SHH Np/Cholesterol/PTCH1 -0.021 0.16 -10000 0 -0.67 8 8
SHH Np/Cholesterol/PTCH2 -0.04 0.13 -10000 0 -0.52 16 16
SHH Np/Cholesterol/Megalin -0.094 0.19 -10000 0 -0.53 44 44
SHH -0.006 0.1 -10000 0 -0.45 20 20
catabolic process -0.021 0.17 -10000 0 -0.65 9 9
SMO/Vitamin D3 -0.01 0.16 -10000 0 -0.77 6 6
SHH Np/Cholesterol/Hhip -0.048 0.13 -10000 0 -0.64 6 6
LRP2 -0.11 0.29 -10000 0 -0.75 64 64
receptor-mediated endocytosis -0.1 0.17 -10000 0 -0.71 15 15
SHH Np/Cholesterol/BOC -0.038 0.13 -10000 0 -0.54 16 16
SHH Np/Cholesterol/CDO -0.064 0.14 -10000 0 -0.66 5 5
mesenchymal cell differentiation 0.048 0.13 0.64 6 -10000 0 6
mol:Vitamin D3 -0.018 0.16 -10000 0 -0.67 8 8
IHH N/PTCH2 -0.032 0.16 -10000 0 -0.65 20 20
CDON -0.069 0.22 -10000 0 -0.61 51 51
IHH N/PTCH1 -0.022 0.17 -10000 0 -0.66 9 9
Megalin/LRPAP1 -0.096 0.22 -10000 0 -0.56 65 65
PTCH2 -0.021 0.16 -10000 0 -0.76 18 18
SHH Np/Cholesterol -0.019 0.079 -10000 0 -0.35 20 20
PTCH1 -0.021 0.17 -10000 0 -0.66 9 9
HHIP -0.044 0.18 -10000 0 -0.61 34 34
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.016 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.04 0.12 -9999 0 -0.62 2 2
Syndecan-3/Neurocan -0.053 0.14 -9999 0 -0.46 31 31
POMC -0.11 0.28 -9999 0 -0.72 65 65
EGFR -0.02 0.17 -9999 0 -0.79 17 17
Syndecan-3/EGFR -0.021 0.097 -9999 0 -0.47 16 16
AGRP -0.014 0.12 -9999 0 -0.61 14 14
NCSTN 0.016 0 -9999 0 -10000 0 0
PSENEN 0.016 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
NCAN -0.082 0.25 -9999 0 -0.73 49 49
long-term memory -0.004 0.046 -9999 0 -0.5 3 3
Syndecan-3/IL8 -0.12 0.19 -9999 0 -0.46 75 75
PSEN1 0.016 0 -9999 0 -10000 0 0
Src/Cortactin -0.003 0.039 -9999 0 -0.53 2 2
FYN 0.011 0.06 -9999 0 -0.81 2 2
limb bud formation -0.002 0.039 -9999 0 -0.75 1 1
MC4R -0.009 0.099 -9999 0 -0.61 10 10
SRC 0.012 0.053 -9999 0 -0.71 2 2
PTN -0.061 0.23 -9999 0 -0.75 38 38
FGFR/FGF/Syndecan-3 -0.002 0.039 -9999 0 -0.76 1 1
neuron projection morphogenesis -0.082 0.16 -9999 0 -0.66 9 9
Syndecan-3/AgRP -0.013 0.068 -9999 0 -0.73 1 1
Syndecan-3/AgRP/MC4R -0.02 0.078 -9999 0 -0.71 1 1
Fyn/Cortactin -0.003 0.045 -9999 0 -0.62 2 2
SDC3 -0.002 0.04 -9999 0 -0.77 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.12 0.19 -9999 0 -0.45 75 75
IL8 -0.2 0.35 -9999 0 -0.75 109 109
Syndecan-3/Fyn/Cortactin -0.004 0.047 -9999 0 -0.52 3 3
Syndecan-3/CASK -0.002 0.038 -9999 0 -0.73 1 1
alpha-MSH/MC4R -0.1 0.22 -9999 0 -0.55 73 73
Gamma Secretase 0 0 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.005 0.095 -9999 0 -0.81 5 5
Caspase 8 (4 units) -0.061 0.13 -9999 0 -0.64 10 10
NEF -0.026 0.068 -9999 0 -10000 0 0
NFKBIA -0.005 0.049 -9999 0 -10000 0 0
BIRC3 -0.11 0.32 -9999 0 -0.7 84 84
CYCS -0.044 0.2 -9999 0 -0.68 18 18
RIPK1 0.016 0 -9999 0 -10000 0 0
CD247 -0.14 0.32 -9999 0 -0.8 67 67
MAP2K7 -0.018 0.14 -9999 0 -0.6 10 10
protein ubiquitination 0.011 0.12 -9999 0 -0.48 4 4
CRADD 0.016 0 -9999 0 -10000 0 0
DAXX 0.016 0 -9999 0 -10000 0 0
FAS 0.005 0.095 -9999 0 -0.81 5 5
BID -0.051 0.2 -9999 0 -0.58 26 26
NF-kappa-B/RelA/I kappa B alpha -0.066 0.12 -9999 0 -10000 0 0
TRADD 0.016 0 -9999 0 -10000 0 0
MAP3K5 -0.013 0.15 -9999 0 -0.81 13 13
CFLAR 0.016 0 -9999 0 -10000 0 0
FADD 0.016 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.066 0.12 -9999 0 -10000 0 0
MAPK8 -0.011 0.14 -9999 0 -0.56 10 10
APAF1 0.016 0 -9999 0 -10000 0 0
TRAF1 0.005 0.083 -9999 0 -0.64 6 6
TRAF2 0.016 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.081 0.15 -9999 0 -0.72 10 10
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.012 0.15 -9999 0 -0.65 4 4
CHUK 0.01 0.13 -9999 0 -0.54 4 4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.021 0.11 -9999 0 -0.54 15 15
TCRz/NEF -0.16 0.29 -9999 0 -0.62 93 93
TNF -0.15 0.31 -9999 0 -0.71 85 85
FASLG -0.21 0.42 -9999 0 -0.87 99 99
NFKB1 -0.005 0.049 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.11 0.2 -9999 0 -0.53 47 47
CASP6 -0.039 0.09 -9999 0 -0.61 4 4
CASP7 -0.061 0.26 -9999 0 -0.63 49 49
RELA -0.005 0.049 -9999 0 -10000 0 0
CASP2 0.016 0 -9999 0 -10000 0 0
CASP3 -0.061 0.26 -9999 0 -0.63 49 49
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.008 0.071 -9999 0 -0.62 5 5
CASP8 0.016 0 -9999 0 -10000 0 0
CASP9 0.016 0 -9999 0 -10000 0 0
MAP3K14 -0.002 0.14 -9999 0 -0.62 4 4
APAF-1/Caspase 9 -0.13 0.2 -9999 0 -0.51 65 65
BCL2 -0.011 0.14 -9999 0 -0.52 9 9
Circadian rhythm 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
chromatin modification -0.034 0.088 -10000 0 -10000 0 0
CLOCK -0.028 0.19 -10000 0 -0.81 20 20
TIMELESS/CRY2 0.005 0.12 -10000 0 -10000 0 0
DEC1/BMAL1 -0.08 0.21 -10000 0 -0.62 48 48
ATR 0.016 0 -10000 0 -10000 0 0
NR1D1 -0.098 0.43 -10000 0 -1.5 32 32
ARNTL -0.088 0.27 -10000 0 -0.8 48 48
TIMELESS -0.002 0.13 -10000 0 -10000 0 0
NPAS2 -0.002 0.12 -10000 0 -0.74 9 9
CRY2 0.016 0 -10000 0 -10000 0 0
mol:CO -0.005 0.044 0.13 35 -10000 0 35
CHEK1 0.016 0 -10000 0 -10000 0 0
mol:HEME 0.005 0.044 -10000 0 -0.13 35 35
PER1 0.013 0.045 -10000 0 -0.61 2 2
BMAL/CLOCK/NPAS2 -0.07 0.26 -10000 0 -0.6 64 64
BMAL1/CLOCK -0.11 0.35 -10000 0 -0.98 39 39
S phase of mitotic cell cycle -0.034 0.088 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.034 0.089 -10000 0 -10000 0 0
mol:NADPH 0.005 0.044 -10000 0 -0.13 35 35
PER1/TIMELESS 0.003 0.12 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0 0 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.01 0.068 -9999 0 -0.74 3 3
Aurora C/Aurora B/INCENP -0.083 0.17 -9999 0 -0.52 33 33
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.022 0.046 -9999 0 -10000 0 0
AURKB -0.07 0.24 -9999 0 -0.72 44 44
AURKC -0.041 0.19 -9999 0 -0.64 33 33
EGFR-dependent Endothelin signaling events

Figure S67.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S67.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.013 0.045 -9999 0 -0.61 2 2
EGFR -0.02 0.17 -9999 0 -0.79 17 17
EGF/EGFR -0.11 0.2 -9999 0 -0.54 46 46
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.081 0.16 -9999 0 -0.84 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.001 0.11 -9999 0 -0.7 9 9
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.11 0.26 -9999 0 -0.65 70 70
EGF/EGFR dimer/SHC -0.098 0.2 -9999 0 -0.59 30 30
mol:GDP -0.08 0.16 -9999 0 -0.82 4 4
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.037 0.19 -9999 0 -0.68 29 29
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.074 0.15 -9999 0 -0.75 6 6
SHC1 0.014 0.032 -9999 0 -0.61 1 1
HRAS/GDP -0.075 0.16 -9999 0 -0.76 6 6
FRAP1 -0.038 0.18 -9999 0 -0.8 4 4
EGF/EGFR dimer -0.11 0.22 -9999 0 -0.52 83 83
SOS1 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.05 0.16 -9999 0 -0.53 36 36
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.024 0.007 -9999 0 -10000 0 0
RAS family/GTP -0.088 0.15 -9999 0 -0.7 8 8
NFATC4 -0.053 0.17 -9999 0 -0.56 12 12
ERBB2IP 0.011 0.01 -9999 0 -10000 0 0
HSP90 (dimer) 0.016 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.11 0.18 -9999 0 -0.67 7 7
JUN 0.002 0.12 -9999 0 -0.39 14 14
HRAS 0.012 0.045 -9999 0 -0.61 2 2
DOCK7 -0.074 0.19 -9999 0 -0.62 7 7
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.14 0.23 -9999 0 -0.49 101 101
AKT1 0.013 0.004 -9999 0 -10000 0 0
BAD 0.025 0.004 -9999 0 -10000 0 0
MAPK10 -0.052 0.083 -9999 0 -0.28 6 6
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.096 0.22 -9999 0 -0.75 7 7
RAF1 -0.039 0.18 -9999 0 -0.7 6 6
ErbB2/ErbB3/neuregulin 2 -0.15 0.24 -9999 0 -0.53 94 94
STAT3 -0.001 0.058 -9999 0 -1.1 1 1
cell migration -0.001 0.11 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.003 -9999 0 -10000 0 0
cell proliferation -0.1 0.28 -9999 0 -0.67 42 42
FOS -0.079 0.24 -9999 0 -0.48 67 67
NRAS 0.016 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.11 0.18 -9999 0 -0.67 7 7
MAPK3 -0.078 0.24 -9999 0 -0.64 24 24
MAPK1 -0.078 0.24 -9999 0 -0.64 24 24
JAK2 -0.074 0.19 -9999 0 -0.62 7 7
NF2 -0.004 0.006 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.082 0.2 -9999 0 -0.39 101 101
NRG1 -0.095 0.27 -9999 0 -0.77 52 52
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.06 0.17 -9999 0 -0.46 8 8
MAPK9 -0.051 0.082 -9999 0 -0.28 5 5
ERBB2 0 0 -9999 0 -10000 0 0
ERBB3 -0.13 0.31 -9999 0 -0.81 65 65
SHC1 0.013 0.032 -9999 0 -0.61 1 1
RAC1 0.016 0 -9999 0 -10000 0 0
apoptosis 0.007 0.013 -9999 0 -10000 0 0
STAT3 (dimer) -0.001 0.056 -9999 0 -1.1 1 1
RNF41 0.031 0.011 -9999 0 -10000 0 0
FRAP1 0.012 0.004 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.073 0.12 -9999 0 -0.41 7 7
ErbB2/ErbB2/HSP90 (dimer) 0 0 -9999 0 -10000 0 0
CHRNA1 -0.089 0.26 -9999 0 -0.66 44 44
myelination -0.041 0.17 -9999 0 -0.5 12 12
PPP3CB -0.068 0.18 -9999 0 -0.57 7 7
KRAS 0.016 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.09 0.16 -9999 0 -0.78 7 7
NRG2 -0.097 0.27 -9999 0 -0.71 59 59
mol:GDP -0.08 0.2 -9999 0 -0.38 101 101
SOS1 0.016 0.001 -9999 0 -10000 0 0
MAP2K2 -0.031 0.17 -9999 0 -0.57 8 8
SRC 0.012 0.053 -9999 0 -0.71 2 2
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.075 0.19 -9999 0 -0.62 7 7
MAP2K1 -0.087 0.23 -9999 0 -0.59 31 31
heart morphogenesis -0.11 0.18 -9999 0 -0.67 7 7
RAS family/GDP -0.087 0.15 -9999 0 -0.72 8 8
GRB2 0.016 0.001 -9999 0 -10000 0 0
PRKACA -0.007 0.011 -9999 0 -10000 0 0
CHRNE 0.01 0.05 -9999 0 -0.22 14 14
HSP90AA1 0.016 0 -9999 0 -10000 0 0
activation of caspase activity -0.013 0.004 -9999 0 -10000 0 0
nervous system development -0.11 0.18 -9999 0 -0.67 7 7
CDC42 0.016 0 -9999 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.01 0.13 -10000 0 -0.55 6 6
epithelial cell differentiation -0.081 0.14 -10000 0 -0.55 9 9
ITCH 0.021 0.014 -10000 0 -10000 0 0
WWP1 0.029 0.057 -10000 0 -10000 0 0
FYN 0.011 0.06 -10000 0 -0.81 2 2
EGFR -0.02 0.17 -10000 0 -0.79 17 17
PRL 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.004 0.18 -10000 0 -0.77 4 4
PTPRZ1 -0.1 0.27 -10000 0 -0.72 60 60
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.073 0.17 -10000 0 -0.73 7 7
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.036 0.19 -10000 0 -0.51 45 45
ADAM17 0.014 0.074 -10000 0 -0.8 3 3
ErbB4/ErbB4 0.025 0.071 -10000 0 -0.51 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.027 0.17 -10000 0 -0.52 32 32
NCOR1 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.071 0.16 -10000 0 -0.6 11 11
GRIN2B -0.024 0.18 -10000 0 -0.57 11 11
ErbB4/ErbB2/betacellulin -0.032 0.13 -10000 0 -0.71 9 9
STAT1 -0.008 0.13 -10000 0 -0.73 12 12
HBEGF -0.044 0.19 -10000 0 -0.63 35 35
PRLR -0.12 0.28 -10000 0 -0.7 71 71
E4ICDs/ETO2 0.014 0.095 -10000 0 -0.49 6 6
axon guidance 0.033 0.092 -10000 0 -0.41 1 1
NEDD4 0.019 0.044 -10000 0 -0.78 1 1
Prolactin receptor/Prolactin receptor/Prolactin -0.099 0.21 -10000 0 -0.53 71 71
CBFA2T3 -0.005 0.12 -10000 0 -0.7 11 11
ErbB4/ErbB2/HBEGF -0.039 0.11 -10000 0 -0.76 3 3
MAPK3 -0.007 0.18 -10000 0 -0.81 4 4
STAT1 (dimer) 0.012 0.11 -10000 0 -0.52 10 10
MAPK1 -0.007 0.18 -10000 0 -0.81 4 4
JAK2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.068 0.16 -10000 0 -0.59 10 10
NRG1 -0.057 0.22 -10000 0 -0.6 54 54
NRG3 -0.068 0.24 -10000 0 -0.74 42 42
NRG2 -0.097 0.27 -10000 0 -0.71 59 59
NRG4 -0.003 0.11 -10000 0 -0.65 10 10
heart development 0.033 0.092 -10000 0 -0.41 1 1
neural crest cell migration -0.067 0.16 -10000 0 -0.58 10 10
ERBB2 0.028 0.056 -10000 0 -0.6 3 3
WWOX/E4ICDs 0.026 0.062 -10000 0 -0.44 1 1
SHC1 0.014 0.032 -10000 0 -0.61 1 1
ErbB4/EGFR/neuregulin 4 -0.041 0.13 -10000 0 -0.52 20 20
apoptosis 0.091 0.18 0.59 31 -10000 0 31
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.045 0.18 -10000 0 -0.5 37 37
ErbB4/ErbB2/epiregulin -0.16 0.2 -10000 0 -0.54 27 27
ErbB4/ErbB4/betacellulin/betacellulin 0.003 0.14 -10000 0 -0.6 17 17
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.099 0.17 -10000 0 -0.71 7 7
MDM2 0.033 0.061 -10000 0 -0.44 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.066 0.16 -10000 0 -0.49 43 43
STAT5A 0.041 0.085 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.088 0.18 -10000 0 -0.61 15 15
DLG4 -0.013 0.15 -10000 0 -0.81 13 13
GRB2/SHC -0.001 0.023 -10000 0 -0.44 1 1
E4ICDs/TAB2/NCoR1 -0.013 0.04 -10000 0 -0.41 1 1
STAT5A (dimer) -0.086 0.15 -10000 0 -0.6 9 9
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.038 0.082 -10000 0 -10000 0 0
LRIG1 0.01 0.062 -10000 0 -0.68 3 3
EREG -0.28 0.36 -10000 0 -0.72 154 154
BTC -0.021 0.17 -10000 0 -0.81 17 17
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.034 0.092 -10000 0 -0.41 1 1
ERBB4 0.025 0.071 -10000 0 -0.51 1 1
STAT5B 0.016 0 -10000 0 -10000 0 0
YAP1 -0.004 0.014 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.02 0.078 -10000 0 -0.55 3 3
glial cell differentiation 0.013 0.04 0.41 1 -10000 0 1
WWOX 0.014 0.032 -10000 0 -0.61 1 1
cell proliferation -0.023 0.2 -10000 0 -0.94 6 6
Cellular roles of Anthrax toxin

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
ANTXR1 -0.002 0.11 -10000 0 -0.72 9 9
ANTXR2 0.005 0.083 -10000 0 -0.64 6 6
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.017 -10000 0 -0.093 13 13
monocyte activation -0.081 0.19 -10000 0 -0.47 63 63
MAP2K2 -0.001 0.007 -10000 0 -10000 0 0
MAP2K1 -0.003 0.022 -10000 0 -0.33 1 1
MAP2K7 -0.003 0.014 -10000 0 -10000 0 0
MAP2K6 -0.015 0.07 -10000 0 -0.39 12 12
CYAA 0.005 0.086 -10000 0 -0.44 13 13
MAP2K4 -0.003 0.014 -10000 0 -10000 0 0
IL1B -0.06 0.17 -10000 0 -0.41 70 70
Channel -0.016 0.088 -10000 0 -0.47 13 13
NLRP1 -0.006 0.045 -10000 0 -0.48 3 3
CALM1 0.016 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.004 0.02 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.017 0.093 13 -10000 0 13
MAPK3 -0.003 0.014 -10000 0 -10000 0 0
MAPK1 -0.003 0.014 -10000 0 -10000 0 0
PGR -0.077 0.17 -10000 0 -0.45 64 64
PA/Cellular Receptors -0.017 0.095 -10000 0 -0.51 13 13
apoptosis -0.003 0.017 -10000 0 -0.093 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.015 0.081 -10000 0 -0.43 13 13
macrophage activation 0.023 0.016 -10000 0 -10000 0 0
TNF -0.15 0.31 -10000 0 -0.71 85 85
VCAM1 -0.097 0.19 -10000 0 -0.47 63 63
platelet activation -0.004 0.02 -10000 0 -10000 0 0
MAPKKK cascade -0.016 0.026 0.16 2 -10000 0 2
IL18 -0.06 0.18 -10000 0 -0.42 69 69
negative regulation of macrophage activation -0.003 0.017 -10000 0 -0.093 13 13
LEF -0.003 0.017 -10000 0 -0.093 13 13
CASP1 -0.005 0.025 -10000 0 -0.22 3 3
mol:cAMP -0.004 0.02 -10000 0 -10000 0 0
necrosis -0.003 0.017 -10000 0 -0.093 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.015 0.084 -10000 0 -0.44 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.01 0.22 -9999 0 -1.5 8 8
VDR 0.008 0.08 -9999 0 -0.76 4 4
FAM120B 0.016 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.036 0.18 -9999 0 -0.53 22 22
RXRs/LXRs/DNA/Oxysterols -0.042 0.21 -9999 0 -0.6 23 23
MED1 0.016 0 -9999 0 -10000 0 0
mol:9cRA -0.002 0.021 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.036 0.065 -9999 0 -10000 0 0
RXRs/NUR77 -0.12 0.25 -9999 0 -0.56 73 73
RXRs/PPAR -0.023 0.16 -9999 0 -0.42 21 21
NCOR2 0.016 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.006 0.06 -9999 0 -0.59 4 4
RARs/VDR/DNA/Vit D3 -0.006 0.052 -9999 0 -0.46 4 4
RARA 0.016 0 -9999 0 -10000 0 0
NCOA1 0.016 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.008 0.08 -9999 0 -0.76 4 4
RARs/RARs/DNA/9cRA -0.002 0.029 -9999 0 -0.46 1 1
RARG 0.016 0 -9999 0 -10000 0 0
RPS6KB1 0.022 0.08 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.036 0.065 -9999 0 -10000 0 0
THRA 0.016 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.006 0.06 -9999 0 -0.59 4 4
RXRs/PPAR/9cRA/PGJ2/DNA -0.062 0.21 -9999 0 -0.51 64 64
NR1H4 -0.012 0.099 -9999 0 -0.61 10 10
RXRs/LXRs/DNA -0.039 0.21 -9999 0 -0.59 22 22
NR1H2 0.018 0.013 -9999 0 -10000 0 0
NR1H3 0.018 0.015 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.087 0.19 -9999 0 -0.49 64 64
NR4A1 -0.1 0.25 -9999 0 -0.64 67 67
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.028 0.13 -9999 0 -0.36 24 24
RXRG -0.12 0.31 -9999 0 -0.81 65 65
RXR alpha/CCPG 0 0 -9999 0 -10000 0 0
RXRA 0.018 0.013 -9999 0 -10000 0 0
RXRB 0.017 0.015 -9999 0 -10000 0 0
THRB -0.008 0.14 -9999 0 -0.81 11 11
PPARG -0.007 0.12 -9999 0 -0.64 13 13
PPARD 0.016 0 -9999 0 -10000 0 0
TNF -0.15 0.44 -9999 0 -1.1 52 52
mol:Oxysterols -0.001 0.019 -9999 0 -10000 0 0
cholesterol transport -0.041 0.21 -9999 0 -0.6 23 23
PPARA 0.016 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.012 0.053 -9999 0 -0.71 2 2
RXRs/NUR77/BCL2 -0.099 0.18 -9999 0 -0.4 75 75
SREBF1 -0.029 0.21 -9999 0 -0.65 16 16
RXRs/RXRs/DNA/9cRA -0.061 0.21 -9999 0 -0.51 64 64
ABCA1 -0.028 0.21 -9999 0 -0.66 15 15
RARs/THRs -0.015 0.08 -9999 0 -10000 0 0
RXRs/FXR -0.064 0.22 -9999 0 -0.52 64 64
BCL2 -0.006 0.12 -9999 0 -0.68 12 12
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.016 0.045 -10000 0 -0.81 1 1
HSPA8 0.009 0.068 -10000 0 -0.74 3 3
SMAD3/SMAD4/ER alpha -0.082 0.22 -10000 0 -0.55 49 49
AKT1 0.018 0.011 -10000 0 -10000 0 0
GSC -0.14 0.47 -10000 0 -1.6 34 34
NKX2-5 0.003 0.001 -10000 0 -10000 0 0
muscle cell differentiation 0.017 0.065 0.43 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.027 0.11 -10000 0 -0.56 2 2
SMAD4 0.001 0.062 -10000 0 -0.36 1 1
CBFB 0.016 0 -10000 0 -10000 0 0
SAP18 0.015 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.12 0.23 -10000 0 -0.54 78 78
SMAD3/SMAD4/VDR 0.007 0.072 -10000 0 -10000 0 0
MYC -0.024 0.17 -10000 0 -0.74 19 19
CDKN2B 0.015 0.19 -10000 0 -1.6 4 4
AP1 -0.049 0.25 -10000 0 -0.77 27 27
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.059 0.059 -10000 0 -0.65 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.025 0.086 -10000 0 -0.41 1 1
SP3 0.019 0.008 -10000 0 -10000 0 0
CREB1 0.016 0 -10000 0 -10000 0 0
FOXH1 -0.043 0.2 -10000 0 -0.74 26 26
SMAD3/SMAD4/GR -0.004 0.061 -10000 0 -0.44 1 1
GATA3 -0.083 0.25 -10000 0 -0.8 38 38
SKI/SIN3/HDAC complex/NCoR1 0.053 0.032 -10000 0 -10000 0 0
MEF2C/TIF2 -0.07 0.17 -10000 0 -0.64 12 12
endothelial cell migration 0.053 0.25 1.5 7 -10000 0 7
MAX 0.018 0.012 -10000 0 -10000 0 0
RBBP7 0.015 0.005 -10000 0 -10000 0 0
RBBP4 0.01 0.06 -10000 0 -0.81 2 2
RUNX2 -0.17 0.35 -10000 0 -0.81 87 87
RUNX3 -0.092 0.26 -10000 0 -0.69 58 58
RUNX1 -0.096 0.28 -10000 0 -0.81 51 51
CTBP1 0.016 0 -10000 0 -10000 0 0
NR3C1 0.018 0.012 -10000 0 -10000 0 0
VDR 0.008 0.08 -10000 0 -0.76 4 4
CDKN1A 0.021 0.24 -10000 0 -1.4 9 9
KAT2B 0.014 0.043 -10000 0 -0.81 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.046 0.15 -10000 0 -0.55 20 20
DCP1A 0.016 0 -10000 0 -10000 0 0
SKI 0.015 0.005 -10000 0 -10000 0 0
SERPINE1 -0.055 0.25 -10000 0 -1.5 7 7
SMAD3/SMAD4/ATF2 -0.021 0.1 -10000 0 -0.55 10 10
SMAD3/SMAD4/ATF3 -0.13 0.23 -10000 0 -0.57 64 64
SAP30 0.013 0.043 -10000 0 -0.81 1 1
Cbp/p300/PIAS3 0.015 0.049 -10000 0 -0.53 1 1
JUN -0.044 0.25 -10000 0 -0.76 27 27
SMAD3/SMAD4/IRF7 -0.01 0.069 -10000 0 -0.58 1 1
TFE3 0.022 0.01 -10000 0 -10000 0 0
COL1A2 -0.073 0.29 -10000 0 -0.62 66 66
mesenchymal cell differentiation 0.14 0.24 0.57 85 -10000 0 85
DLX1 -0.065 0.24 -10000 0 -0.77 39 39
TCF3 0.016 0 -10000 0 -10000 0 0
FOS -0.11 0.29 -10000 0 -0.73 65 65
SMAD3/SMAD4/Max -0.004 0.061 -10000 0 -0.44 1 1
Cbp/p300/SNIP1 0.003 0.032 -10000 0 -0.53 1 1
ZBTB17 0.015 0.01 -10000 0 -10000 0 0
LAMC1 0.04 0.065 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.008 0.059 -10000 0 -0.44 1 1
IRF7 0.015 0.018 -10000 0 -10000 0 0
ESR1 -0.13 0.3 -10000 0 -0.7 77 77
HNF4A 0 0 -10000 0 -10000 0 0
MEF2C 0.008 0.13 -10000 0 -0.61 3 3
SMAD2-3/SMAD4 -0.014 0.062 -10000 0 -0.47 1 1
Cbp/p300/Src-1 0.01 0.04 -10000 0 -0.53 1 1
IGHV3OR16-13 -0.026 0.047 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.016 0 -10000 0 -10000 0 0
CREBBP 0.017 0.01 -10000 0 -10000 0 0
SKIL 0.01 0.068 -10000 0 -0.74 3 3
HDAC1 0.015 0.005 -10000 0 -10000 0 0
HDAC2 0.015 0.005 -10000 0 -10000 0 0
SNIP1 0.014 0.006 -10000 0 -10000 0 0
GCN5L2 0.001 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.002 0.061 -10000 0 -0.43 1 1
MSG1/HSC70 -0.16 0.26 -10000 0 -0.58 102 102
SMAD2 0.013 0.032 -10000 0 -10000 0 0
SMAD3 0.006 0.057 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.028 0.081 -10000 0 -0.62 1 1
SMAD2/SMAD2/SMAD4 0.017 0.037 -10000 0 -0.34 1 1
NCOR1 0.015 0.005 -10000 0 -10000 0 0
NCOA2 -0.061 0.24 -10000 0 -0.81 35 35
NCOA1 0.016 0 -10000 0 -10000 0 0
MYOD/E2A 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.04 0.1 -10000 0 -0.58 1 1
IFNB1 0.02 0.11 -10000 0 -0.58 8 8
SMAD3/SMAD4/MEF2C 0.01 0.14 -10000 0 -0.56 3 3
CITED1 -0.19 0.35 -10000 0 -0.77 100 100
SMAD2-3/SMAD4/ARC105 -0.006 0.054 -10000 0 -10000 0 0
RBL1 -0.01 0.14 -10000 0 -0.81 12 12
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.056 0.084 -10000 0 -0.52 4 4
RUNX1-3/PEBPB2 -0.14 0.25 -10000 0 -0.62 63 63
SMAD7 0.013 0.17 -10000 0 -0.75 3 3
MYC/MIZ-1 -0.023 0.13 -10000 0 -0.56 19 19
SMAD3/SMAD4 0.01 0.13 0.32 14 -0.47 6 20
IL10 -0.11 0.32 -10000 0 -0.71 66 66
PIASy/HDAC complex 0.016 0.009 -10000 0 -10000 0 0
PIAS3 0.015 0.007 -10000 0 -10000 0 0
CDK2 0.017 0.01 -10000 0 -10000 0 0
IL5 -0.051 0.2 -10000 0 -0.54 36 36
CDK4 0.017 0.011 -10000 0 -10000 0 0
PIAS4 0.016 0.009 -10000 0 -10000 0 0
ATF3 -0.17 0.32 -10000 0 -0.71 98 98
SMAD3/SMAD4/SP1 -0.025 0.089 -10000 0 -0.56 2 2
FOXG1 -0.091 0.24 -10000 0 -0.66 56 56
FOXO3 0.033 0.015 -10000 0 -10000 0 0
FOXO1 0.033 0.015 -10000 0 -10000 0 0
FOXO4 0.033 0.015 -10000 0 -10000 0 0
heart looping 0.008 0.13 -10000 0 -0.6 3 3
CEBPB 0.017 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.064 0.18 -10000 0 -0.57 36 36
MYOD1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.013 0.061 -10000 0 -0.4 2 2
SMAD3/SMAD4/GATA3 -0.091 0.2 -10000 0 -0.6 36 36
SnoN/SIN3/HDAC complex/NCoR1 0.01 0.068 -10000 0 -0.74 3 3
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.12 0.24 -10000 0 -0.64 42 42
SMAD3/SMAD4/SP1-3 -0.009 0.081 -10000 0 -0.5 1 1
MED15 0.016 0 -10000 0 -10000 0 0
SP1 0.007 0.047 -10000 0 -10000 0 0
SIN3B 0.015 0.005 -10000 0 -10000 0 0
SIN3A 0.015 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.036 0.13 -10000 0 -0.5 19 19
ITGB5 0.041 0.1 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.055 0.029 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.11 0.21 -10000 0 -0.55 51 51
AR -0.13 0.29 -10000 0 -0.7 79 79
negative regulation of cell growth -0.005 0.12 -10000 0 -0.49 4 4
SMAD3/SMAD4/MYOD -0.013 0.061 -10000 0 -0.4 2 2
E2F5 0.014 0.043 -10000 0 -0.81 1 1
E2F4 0.016 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.032 0.12 -10000 0 -0.53 6 6
SMAD2-3/SMAD4/FOXO1-3a-4 0.051 0.068 -10000 0 -0.48 1 1
TFDP1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.045 0.26 -10000 0 -0.78 27 27
SMAD3/SMAD4/RUNX2 -0.14 0.24 -10000 0 -0.57 85 85
TGIF2 0.016 0 -10000 0 -10000 0 0
TGIF1 0.016 0 -10000 0 -10000 0 0
ATF2 -0.004 0.13 -10000 0 -0.81 9 9
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.016 0 -9999 0 -10000 0 0
VLDLR -0.015 0.14 -9999 0 -0.67 17 17
LRPAP1 0.014 0.043 -9999 0 -0.81 1 1
NUDC 0.016 0 -9999 0 -10000 0 0
RELN/LRP8 -0.19 0.24 -9999 0 -0.56 68 68
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.016 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.15 0.23 -9999 0 -0.51 68 68
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.006 0.094 -9999 0 -0.61 9 9
IQGAP1 0.016 0 -9999 0 -10000 0 0
PLA2G7 -0.052 0.22 -9999 0 -0.72 35 35
CALM1 0.016 0 -9999 0 -10000 0 0
DYNLT1 0.011 0.055 -9999 0 -0.61 3 3
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.028 0.12 -9999 0 -0.53 20 20
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.016 0 -9999 0 -10000 0 0
CDK5R1 0.001 0.095 -9999 0 -0.61 9 9
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.01 0.099 -9999 0 -0.61 10 10
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.2 0.24 -9999 0 -0.58 69 69
YWHAE 0.016 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.092 0.2 -9999 0 -0.61 8 8
MAP1B -0.001 0.016 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.12 0.22 -9999 0 -0.66 12 12
RELN -0.26 0.35 -9999 0 -0.69 149 149
PAFAH/LIS1 -0.042 0.14 -9999 0 -0.53 19 19
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.099 0.12 -9999 0 -0.52 4 4
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.079 0.16 -9999 0 -0.65 6 6
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.11 0.21 -9999 0 -0.66 8 8
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.03 0 -9999 0 -10000 0 0
PAFAH1B3 0.014 0.032 -9999 0 -0.61 1 1
PAFAH1B2 -0.002 0.12 -9999 0 -0.81 8 8
MAP1B/LIS1/Dynein heavy chain 0.032 0.011 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.12 0.15 -9999 0 -0.59 7 7
LRP8 -0.02 0.16 -9999 0 -0.71 19 19
NDEL1/Katanin 60 -0.092 0.2 -9999 0 -0.61 8 8
P39/CDK5 -0.13 0.22 -9999 0 -0.68 12 12
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.13 0.22 -9999 0 -0.47 68 68
PPP2R5D 0.016 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.16 0.2 -9999 0 -0.49 69 69
RELN/VLDLR -0.19 0.22 -9999 0 -0.53 72 72
CDC42 0 0 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.044 0.18 -9999 0 -0.48 35 35
CRKL 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.011 0.06 -9999 0 -0.81 2 2
ITGA4 -0.04 0.18 -9999 0 -0.64 32 32
alpha4/beta7 Integrin/MAdCAM1 -0.14 0.21 -9999 0 -0.57 48 48
EPO 0.006 0.033 -9999 0 -0.61 1 1
alpha4/beta7 Integrin -0.11 0.23 -9999 0 -0.55 78 78
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.04 0.13 -9999 0 -0.47 32 32
EPO/EPOR (dimer) -0.009 0.064 -9999 0 -0.47 7 7
lamellipodium assembly 0.003 0.037 -9999 0 -0.46 2 2
PIK3CA 0.011 0.06 -9999 0 -0.81 2 2
PI3K -0.003 0.045 -9999 0 -0.62 2 2
ARF6 0.016 0 -9999 0 -10000 0 0
JAK2 -0.024 0.075 -9999 0 -0.61 1 1
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
MADCAM1 -0.082 0.22 -9999 0 -0.61 57 57
cell adhesion -0.13 0.21 -9999 0 -0.56 48 48
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC -0.032 0.2 -9999 0 -0.58 34 34
ITGB7 -0.085 0.26 -9999 0 -0.73 51 51
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.075 0.2 -9999 0 -0.65 33 33
p130Cas/Crk/Dock1 -0.059 0.15 -9999 0 -0.57 18 18
VCAM1 -0.054 0.21 -9999 0 -0.68 38 38
RHOA 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.029 0.098 -9999 0 -0.48 5 5
BCAR1 -0.018 0.18 -9999 0 -0.63 18 18
EPOR 0.005 0.083 -9999 0 -0.64 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.016 0 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP 0.003 0.038 -9999 0 -0.47 2 2
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.006 0.12 -9999 0 -0.68 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.038 0.12 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
FYN 0.011 0.06 -9999 0 -0.81 2 2
MAP3K12 0.014 0.032 -9999 0 -0.61 1 1
FGR -0.019 0.16 -9999 0 -0.76 17 17
p38 alpha/TAB1 -0.061 0.11 -9999 0 -0.42 22 22
PRKG1 -0.088 0.26 -9999 0 -0.74 52 52
DUSP8 -0.022 0.17 -9999 0 -0.75 19 19
PGK/cGMP/p38 alpha -0.1 0.16 -9999 0 -0.44 58 58
apoptosis -0.059 0.11 -9999 0 -0.41 21 21
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.016 0 -9999 0 -10000 0 0
DUSP1 -0.045 0.2 -9999 0 -0.7 32 32
PAK1 0.016 0 -9999 0 -10000 0 0
SRC 0.012 0.053 -9999 0 -0.71 2 2
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0.014 0.043 -9999 0 -0.81 1 1
RAC1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.058 0.18 -9999 0 -0.54 27 27
BLK -0.24 0.34 -9999 0 -0.69 135 135
HCK -0.067 0.24 -9999 0 -0.75 41 41
MAP2K3 0.016 0 -9999 0 -10000 0 0
DUSP16 0.016 0 -9999 0 -10000 0 0
DUSP10 -0.002 0.11 -9999 0 -0.67 10 10
TRAF6/MEKK3 -0.001 0.026 -9999 0 -0.5 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.03 0.14 -9999 0 -0.46 21 21
positive regulation of innate immune response -0.055 0.19 -9999 0 -0.59 25 25
LCK -0.093 0.26 -9999 0 -0.68 59 59
p38alpha-beta/MKP7 -0.044 0.18 -9999 0 -0.63 16 16
p38alpha-beta/MKP5 -0.052 0.19 -9999 0 -0.63 19 19
PGK/cGMP -0.078 0.2 -9999 0 -0.57 52 52
PAK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.072 0.2 -9999 0 -0.64 23 23
CDC42 0.016 0 -9999 0 -10000 0 0
RALB 0.016 0 -9999 0 -10000 0 0
RALA 0.016 0 -9999 0 -10000 0 0
PAK3 -0.2 0.34 -9999 0 -0.72 112 112
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.021 0.11 -10000 0 -0.74 7 7
HDAC1 0.003 0.011 -10000 0 -10000 0 0
AES 0.015 0.002 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
DTX1 -0.008 0.14 -10000 0 -0.81 11 11
LRP6/FZD1 -0.011 0.084 -10000 0 -0.62 7 7
TLE1 0.015 0.002 -10000 0 -10000 0 0
AP1 -0.061 0.19 -10000 0 -0.42 64 64
NCSTN 0.016 0 -10000 0 -10000 0 0
ADAM10 0 0.11 -10000 0 -0.81 7 7
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.047 0.065 -10000 0 -10000 0 0
NICD/RBPSUH -0.014 0.1 -10000 0 -0.76 7 7
WIF1 -0.056 0.18 -10000 0 -0.61 38 38
NOTCH1 -0.014 0.1 -10000 0 -0.76 7 7
PSENEN 0.016 0 -10000 0 -10000 0 0
KREMEN2 -0.047 0.22 -10000 0 -0.78 30 30
DKK1 -0.14 0.31 -10000 0 -0.72 83 83
beta catenin/beta TrCP1 0.047 0.057 -10000 0 -10000 0 0
APH1B 0.016 0 -10000 0 -10000 0 0
APH1A 0.016 0 -10000 0 -10000 0 0
AXIN1 -0.001 0.037 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.009 0.041 -10000 0 -10000 0 0
PSEN1 0.016 0 -10000 0 -10000 0 0
FOS -0.11 0.28 -10000 0 -0.72 65 65
JUN -0.024 0.16 -10000 0 -0.66 22 22
MAP3K7 0.014 0.004 -10000 0 -10000 0 0
CTNNB1 0.04 0.062 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.11 0.23 -10000 0 -0.58 61 61
HNF1A 0.013 0.043 -10000 0 -0.81 1 1
CTBP1 0.015 0.002 -10000 0 -10000 0 0
MYC -0.027 0.28 -10000 0 -1.6 12 12
NKD1 -0.05 0.21 -10000 0 -0.73 33 33
FZD1 0.001 0.11 -10000 0 -0.81 7 7
NOTCH1 precursor/Deltex homolog 1 -0.026 0.12 -10000 0 -0.71 7 7
apoptosis -0.06 0.19 -10000 0 -0.42 64 64
Delta 1/NOTCHprecursor -0.021 0.11 -10000 0 -0.71 7 7
DLL1 0.002 0.1 -10000 0 -0.76 7 7
PPARD 0.028 0.022 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.001 0.037 -10000 0 -10000 0 0
DVL1 -0.006 0.016 -10000 0 -10000 0 0
CSNK2A1 0.016 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.14 0.23 -10000 0 -0.57 66 66
LRP6 0.016 0 -10000 0 -10000 0 0
CSNK1A1 0.016 0.004 -10000 0 -10000 0 0
NLK 0.018 0.01 -10000 0 -10000 0 0
CCND1 0.011 0.16 -10000 0 -1.6 4 4
WNT1 -0.011 0.12 -10000 0 -0.62 14 14
Axin1/APC/beta catenin 0.054 0.05 -10000 0 -10000 0 0
DKK2 -0.094 0.27 -10000 0 -0.77 53 53
NOTCH1 precursor/DVL1 -0.012 0.088 -10000 0 -0.65 7 7
GSK3B 0.016 0.001 -10000 0 -10000 0 0
FRAT1 0.015 0.002 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.026 0.12 -10000 0 -0.74 7 7
PPP2R5D 0.026 0.098 0.34 33 -10000 0 33
MAPK1 0.016 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.054 0.14 -10000 0 -0.59 9 9
RBPJ 0.014 0.032 -10000 0 -0.61 1 1
CREBBP 0.02 0.005 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.046 0.11 0.48 9 -10000 0 9
GNAI2 0.016 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.019 0.096 -10000 0 -0.49 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.069 0.25 -10000 0 -0.79 40 40
RhoA/GTP -0.047 0.11 -10000 0 -0.5 9 9
negative regulation of cAMP metabolic process -0.015 0.14 -10000 0 -0.36 49 49
GNAZ 0.002 0.1 -10000 0 -0.76 7 7
GNAI3 0.016 0 -10000 0 -10000 0 0
GNA12 0.016 0 -10000 0 -10000 0 0
S1PR5 -0.014 0.15 -10000 0 -0.74 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.016 0.14 -10000 0 -0.36 49 49
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
GNAI1 -0.012 0.13 -10000 0 -0.61 17 17
TCGA08_p53

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
CDKN2A -0.08 0.2 -10000 0 -0.51 69 69
TP53 -0.027 0.059 -10000 0 -10000 0 0
Senescence -0.027 0.059 -10000 0 -10000 0 0
Apoptosis -0.027 0.059 -10000 0 -10000 0 0
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.049 0.1 0.34 21 -10000 0 21
MDM4 0.016 0 -10000 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.073 0.19 -10000 0 -0.51 54 54
cell-cell adhesion 0.058 0.13 0.65 4 -10000 0 4
Ephrin B/EPHB2/RasGAP -0.039 0.12 -10000 0 -10000 0 0
ITSN1 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.011 0.06 -10000 0 -0.81 2 2
SHC1 0.014 0.032 -10000 0 -0.61 1 1
Ephrin B1/EPHB3 -0.11 0.22 -10000 0 -0.54 78 78
Ephrin B1/EPHB1 -0.046 0.14 -10000 0 -0.43 41 41
HRAS/GDP -0.045 0.11 -10000 0 -0.53 4 4
Ephrin B/EPHB1/GRB7 -0.11 0.22 -10000 0 -0.79 20 20
Endophilin/SYNJ1 0.007 0.13 -10000 0 -0.42 24 24
KRAS 0.016 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.071 0.16 -10000 0 -0.73 4 4
endothelial cell migration -0.002 0.033 -10000 0 -0.45 2 2
GRB2 0.016 0 -10000 0 -10000 0 0
GRB7 -0.054 0.23 -10000 0 -0.81 32 32
PAK1 0.016 0.14 -10000 0 -0.72 2 2
HRAS 0.013 0.045 -10000 0 -0.61 2 2
RRAS 0.002 0.14 -10000 0 -0.44 28 28
DNM1 -0.038 0.18 -10000 0 -0.66 30 30
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.024 0.16 -10000 0 -0.68 3 3
lamellipodium assembly -0.058 0.13 -10000 0 -0.65 4 4
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.003 0.11 -10000 0 -0.46 3 3
PIK3R1 0.016 0 -10000 0 -10000 0 0
EPHB2 0.003 0.1 -10000 0 -0.81 6 6
EPHB3 -0.15 0.33 -10000 0 -0.8 78 78
EPHB1 -0.058 0.22 -10000 0 -0.67 41 41
EPHB4 0.016 0 -10000 0 -10000 0 0
mol:GDP -0.016 0.13 -10000 0 -0.5 3 3
Ephrin B/EPHB2 -0.04 0.12 -10000 0 -0.46 23 23
Ephrin B/EPHB3 -0.12 0.23 -10000 0 -0.52 87 87
JNK cascade 0.003 0.14 -10000 0 -0.88 2 2
Ephrin B/EPHB1 -0.07 0.16 -10000 0 -0.48 30 30
RAP1/GDP -0.009 0.12 -10000 0 -0.46 1 1
EFNB2 0.016 0 -10000 0 -10000 0 0
EFNB3 -0.046 0.21 -10000 0 -0.72 32 32
EFNB1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.049 0.14 -10000 0 -0.55 16 16
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.061 0.14 -10000 0 -0.7 4 4
Rap1/GTP -0.058 0.13 -10000 0 -0.67 4 4
axon guidance -0.073 0.18 -10000 0 -0.51 54 54
MAPK3 0.023 0.1 -10000 0 -10000 0 0
MAPK1 0.023 0.1 -10000 0 -10000 0 0
Rac1/GDP 0.035 0.13 -10000 0 -0.49 1 1
actin cytoskeleton reorganization -0.038 0.088 -10000 0 -0.51 3 3
CDC42/GDP 0.035 0.13 -10000 0 -0.49 1 1
PI3K -0.002 0.033 -10000 0 -0.46 2 2
EFNA5 -0.085 0.26 -10000 0 -0.74 51 51
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.018 0.095 -10000 0 -10000 0 0
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP -0.057 0.12 -10000 0 -0.64 4 4
PTK2 0.011 0.032 -10000 0 -10000 0 0
MAP4K4 0.002 0.14 -10000 0 -0.9 2 2
SRC 0.012 0.053 -10000 0 -0.71 2 2
KALRN 0.011 0.055 -10000 0 -0.61 3 3
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.034 0.14 -10000 0 -0.58 2 2
MAP2K1 0.013 0.1 -10000 0 -0.43 3 3
WASL 0.016 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.048 0.14 -10000 0 -0.54 16 16
cell migration 0.026 0.11 -10000 0 -0.46 2 2
NRAS 0.016 0 -10000 0 -10000 0 0
SYNJ1 0.007 0.13 -10000 0 -0.43 24 24
PXN 0.016 0 -10000 0 -10000 0 0
TF -0.028 0.17 -10000 0 -0.57 4 4
HRAS/GTP -0.065 0.14 -10000 0 -0.68 5 5
Ephrin B1/EPHB1-2 -0.049 0.14 -10000 0 -0.55 16 16
cell adhesion mediated by integrin 0.063 0.14 0.49 28 -10000 0 28
RAC1 0.016 0 -10000 0 -10000 0 0
mol:GTP -0.069 0.15 -10000 0 -0.74 5 5
RAC1-CDC42/GTP -0.13 0.22 -10000 0 -0.65 42 42
RASA1 0.016 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.009 0.12 -10000 0 -0.46 1 1
ruffle organization 0.009 0.16 -10000 0 -0.67 4 4
NCK1 0.016 0 -10000 0 -10000 0 0
receptor internalization -0.01 0.16 -10000 0 -0.66 6 6
Ephrin B/EPHB2/KALRN -0.041 0.13 -10000 0 -0.48 23 23
ROCK1 -0.073 0.21 -10000 0 -0.49 74 74
RAS family/GDP -0.033 0.084 -10000 0 -0.52 2 2
Rac1/GTP -0.062 0.14 -10000 0 -0.71 4 4
Ephrin B/EPHB1/Src/Paxillin -0.005 0.12 -10000 0 -0.53 3 3
IGF1 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
NCK2 0.016 0 -10000 0 -10000 0 0
PTK2 0.016 0 -10000 0 -10000 0 0
CRKL -0.05 0.16 -10000 0 -0.46 29 29
GRB2/SOS1/SHC -0.001 0.019 -10000 0 -10000 0 0
HRAS 0.013 0.045 -10000 0 -0.61 2 2
IRS1/Crk -0.051 0.16 -10000 0 -0.46 29 29
IGF-1R heterotetramer/IGF1/PTP1B -0.09 0.17 -10000 0 -0.52 29 29
AKT1 -0.018 0.15 -10000 0 -0.71 3 3
BAD -0.007 0.14 -10000 0 -0.65 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.05 0.16 -10000 0 -0.46 29 29
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.077 0.15 -10000 0 -0.46 29 29
RAF1 0.001 0.13 -10000 0 -0.62 3 3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.071 0.14 -10000 0 -0.77 2 2
YWHAZ 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.086 0.16 -10000 0 -0.49 33 33
PIK3CA 0.011 0.06 -10000 0 -0.81 2 2
RPS6KB1 -0.018 0.15 -10000 0 -0.71 3 3
GNB2L1 0.016 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.001 0.12 -10000 0 -0.51 3 3
PXN 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.016 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.062 0.12 -10000 0 -0.62 3 3
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.068 0.13 -10000 0 -0.66 2 2
IGF-1R heterotetramer -0.006 0.071 -10000 0 -0.87 2 2
IGF-1R heterotetramer/IGF1/IRS/Nck -0.077 0.15 -10000 0 -0.46 29 29
Crk/p130 Cas/Paxillin -0.066 0.13 -10000 0 -0.73 2 2
IGF1R -0.006 0.071 -10000 0 -0.87 2 2
IGF1 -0.14 0.29 -10000 0 -0.67 86 86
IRS2/Crk -0.053 0.18 -10000 0 -0.57 14 14
PI3K -0.073 0.14 -10000 0 -0.6 4 4
apoptosis -0.004 0.12 0.53 3 -10000 0 3
HRAS/GDP -0.002 0.033 -10000 0 -0.45 2 2
PRKCD -0.023 0.16 -10000 0 -0.51 28 28
RAF1/14-3-3 E 0.011 0.12 -10000 0 -0.51 3 3
BAD/14-3-3 0.004 0.13 -10000 0 -0.58 3 3
PRKCZ -0.019 0.15 -10000 0 -0.71 3 3
Crk/p130 Cas/Paxillin/FAK1 -0.049 0.097 -10000 0 -0.58 3 3
PTPN1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.035 0.17 -10000 0 -0.55 28 28
BCAR1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.078 0.15 -10000 0 -0.46 30 30
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.076 0.14 -10000 0 -0.45 29 29
GRB10 0.014 0.043 -10000 0 -0.81 1 1
PTPN11 -0.05 0.16 -10000 0 -0.46 29 29
IRS1 -0.066 0.17 -10000 0 -0.48 33 33
IRS2 -0.066 0.18 -10000 0 -0.49 39 39
IGF-1R heterotetramer/IGF1 -0.12 0.22 -10000 0 -0.5 87 87
GRB2 0.016 0 -10000 0 -10000 0 0
PDPK1 -0.03 0.15 -10000 0 -0.76 3 3
YWHAE 0.016 0 -10000 0 -10000 0 0
PRKD1 -0.023 0.16 -10000 0 -0.51 28 28
SHC1 0.014 0.032 -10000 0 -0.61 1 1
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.027 0.15 -9999 0 -0.88 11 11
VEGFR1 homodimer/NRP1 -0.027 0.15 -9999 0 -0.85 12 12
mol:DAG -0.025 0.2 -9999 0 -0.76 16 16
VEGFR1 homodimer/NRP1/VEGFR 121 -0.028 0.15 -9999 0 -0.84 12 12
CaM/Ca2+ -0.016 0.19 -9999 0 -0.84 11 11
HIF1A 0.012 0.078 -9999 0 -0.42 11 11
GAB1 0.016 0 -9999 0 -10000 0 0
AKT1 0.008 0.19 -9999 0 -0.79 13 13
PLCG1 -0.026 0.2 -9999 0 -0.77 16 16
NOS3 0.017 0.18 -9999 0 -0.79 11 11
CBL 0.016 0 -9999 0 -10000 0 0
mol:NO 0.018 0.17 -9999 0 -0.74 11 11
FLT1 0.009 0.18 -9999 0 -0.95 12 12
PGF -0.073 0.22 -9999 0 -0.63 52 52
VEGFR1 homodimer/NRP2/VEGFR121 -0.067 0.2 -9999 0 -0.93 10 10
CALM1 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.06 -9999 0 -0.81 2 2
eNOS/Hsp90 0.026 0.17 -9999 0 -0.73 10 10
endothelial cell proliferation -0.057 0.24 -9999 0 -0.77 24 24
mol:Ca2+ -0.025 0.2 -9999 0 -0.75 16 16
MAPK3 -0.021 0.2 -9999 0 -0.68 21 21
MAPK1 -0.021 0.2 -9999 0 -0.68 21 21
PIK3R1 0.016 0 -9999 0 -10000 0 0
PLGF homodimer -0.073 0.22 -9999 0 -0.63 52 52
PRKACA 0.016 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.025 0.17 -9999 0 -0.73 21 21
VEGFA homodimer 0.01 0.068 -9999 0 -0.74 3 3
VEGFR1 homodimer/VEGFA homodimer -0.03 0.16 -9999 0 -0.89 12 12
platelet activating factor biosynthetic process -0.01 0.2 -9999 0 -0.65 21 21
PI3K -0.067 0.18 -9999 0 -0.9 11 11
PRKCA -0.033 0.21 -9999 0 -0.73 21 21
PRKCB -0.079 0.24 -9999 0 -0.8 24 24
VEGFR1 homodimer/PLGF homodimer -0.078 0.2 -9999 0 -0.82 17 17
VEGFA 0.01 0.068 -9999 0 -0.74 3 3
VEGFB 0.016 0 -9999 0 -10000 0 0
mol:IP3 -0.025 0.2 -9999 0 -0.76 16 16
RASA1 0.027 0.15 -9999 0 -0.85 10 10
NRP2 -0.054 0.23 -9999 0 -0.78 33 33
VEGFR1 homodimer 0.009 0.18 -9999 0 -0.94 12 12
VEGFB homodimer 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.005 0.19 -9999 0 -0.72 14 14
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.066 0.18 -9999 0 -0.88 11 11
mol:L-citrulline 0.018 0.17 -9999 0 -0.74 11 11
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.027 0.14 -9999 0 -0.86 10 10
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.028 0.15 -9999 0 -0.9 10 10
CD2AP 0.016 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.062 0.17 -9999 0 -0.84 11 11
PDPK1 -0.008 0.19 -9999 0 -0.82 13 13
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.028 0.15 -9999 0 -0.86 11 11
mol:NADP 0.018 0.17 -9999 0 -0.74 11 11
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.026 0.14 -9999 0 -0.84 10 10
VEGFR1 homodimer/NRP2 -0.07 0.2 -9999 0 -0.63 39 39
Regulation of Androgen receptor activity

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
HDAC1 0.028 0.004 -10000 0 -10000 0 0
SMARCC1 0.009 0.014 -10000 0 -10000 0 0
REL -0.026 0.19 -10000 0 -0.78 22 22
HDAC7 0.016 0.13 -10000 0 -0.58 2 2
JUN -0.028 0.16 -10000 0 -0.67 22 22
EP300 0.013 0.042 -10000 0 -0.81 1 1
KAT2B 0.012 0.043 -10000 0 -0.81 1 1
KAT5 0.016 0.001 -10000 0 -10000 0 0
MAPK14 0.007 0.096 -10000 0 -0.51 12 12
FOXO1 0.015 0.001 -10000 0 -10000 0 0
T-DHT/AR 0.005 0.14 -10000 0 -0.57 6 6
MAP2K6 -0.009 0.12 -10000 0 -0.68 12 12
BRM/BAF57 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.013 0.008 -10000 0 -10000 0 0
SMARCA2 0.011 0.008 -10000 0 -10000 0 0
PDE9A -0.024 0.17 -10000 0 -1.1 7 7
NCOA2 -0.066 0.24 -10000 0 -0.82 35 35
CEBPA -0.02 0.15 -10000 0 -0.65 21 21
EHMT2 0.011 0.008 -10000 0 -10000 0 0
cell proliferation -0.002 0.16 -10000 0 -0.6 3 3
NR0B1 0 0 -10000 0 -10000 0 0
EGR1 -0.055 0.21 -10000 0 -0.71 35 35
RXRs/9cRA -0.085 0.19 -10000 0 -0.5 64 64
AR/RACK1/Src -0.029 0.14 -10000 0 -0.55 7 7
AR/GR -0.02 0.13 -10000 0 -0.5 7 7
GNB2L1 0.012 0.007 -10000 0 -10000 0 0
PKN1 0.014 0.004 -10000 0 -10000 0 0
RCHY1 0.016 0 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.003 0.005 -10000 0 -10000 0 0
MAPK8 0.017 0.069 -10000 0 -0.63 4 4
T-DHT/AR/TIF2/CARM1 -0.051 0.2 -10000 0 -0.63 20 20
SRC 0.013 0.1 -10000 0 -0.49 4 4
NR3C1 0.016 0 -10000 0 -10000 0 0
KLK3 -0.22 0.41 -10000 0 -1.2 46 46
APPBP2 0.015 0.007 -10000 0 -10000 0 0
TRIM24 0.011 0.008 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.001 0.12 -10000 0 -0.54 7 7
TMPRSS2 -0.15 0.4 -10000 0 -1.2 42 42
RXRG -0.13 0.31 -10000 0 -0.81 65 65
mol:9cRA -0.002 0.003 -10000 0 -10000 0 0
RXRA 0.015 0.002 -10000 0 -10000 0 0
RXRB 0.015 0.002 -10000 0 -10000 0 0
CARM1 0.011 0.008 -10000 0 -10000 0 0
NR2C2 0.006 0.085 -10000 0 -0.81 4 4
KLK2 -0.22 0.36 -10000 0 -0.77 87 87
AR -0.037 0.14 -10000 0 -0.46 15 15
SENP1 0.015 0.002 -10000 0 -10000 0 0
HSP90AA1 0.016 0 -10000 0 -10000 0 0
MDM2 0.023 0.013 -10000 0 -10000 0 0
SRY 0.007 0.013 0.025 122 -10000 0 122
GATA2 0.007 0.081 -10000 0 -0.69 5 5
MYST2 0.017 0.002 -10000 0 -10000 0 0
HOXB13 -0.008 0.014 -10000 0 -0.027 122 122
T-DHT/AR/RACK1/Src -0.008 0.12 -10000 0 -0.55 6 6
positive regulation of transcription 0.007 0.081 -10000 0 -0.69 5 5
DNAJA1 0.015 0.007 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.041 0.004 -10000 0 -10000 0 0
NCOA1 0.015 0.01 -10000 0 -10000 0 0
SPDEF -0.059 0.22 -10000 0 -0.72 36 36
T-DHT/AR/TIF2 -0.002 0.14 -10000 0 -0.76 5 5
T-DHT/AR/Hsp90 -0.001 0.12 -10000 0 -0.55 6 6
GSK3B 0.012 0.007 -10000 0 -10000 0 0
NR2C1 0.017 0.003 -10000 0 -10000 0 0
mol:T-DHT 0.01 0.1 -10000 0 -0.5 8 8
SIRT1 0.013 0.042 -10000 0 -0.81 1 1
ZMIZ2 0.023 0.014 -10000 0 -10000 0 0
POU2F1 0.025 0.077 -10000 0 -0.7 4 4
T-DHT/AR/DAX-1 -0.041 0.099 -10000 0 -0.52 10 10
CREBBP 0.014 0.004 -10000 0 -10000 0 0
SMARCE1 0.011 0.008 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.042 0.16 -9999 0 -0.66 24 24
AKT1 0.076 0.18 -9999 0 -0.74 15 15
PTK2B 0.001 0.24 -9999 0 -0.89 19 19
VEGFR2 homodimer/Frs2 -0.041 0.19 -9999 0 -0.98 14 14
CAV1 -0.025 0.17 -9999 0 -0.73 21 21
CALM1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.041 0.19 -9999 0 -0.94 14 14
endothelial cell proliferation 0.05 0.18 -9999 0 -0.65 15 15
mol:Ca2+ 0.034 0.18 -9999 0 -0.85 14 14
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.039 0.18 -9999 0 -0.9 14 14
RP11-342D11.1 0.023 0.18 -9999 0 -0.86 14 14
CDH5 0.014 0.043 -9999 0 -0.81 1 1
VEGFA homodimer -0.007 0.067 -9999 0 -0.6 4 4
SHC1 0.014 0.032 -9999 0 -0.61 1 1
SHC2 0.005 0.09 -9999 0 -0.77 5 5
HRAS/GDP -0.033 0.15 -9999 0 -0.72 15 15
SH2D2A -0.13 0.29 -9999 0 -0.7 80 80
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.031 0.14 -9999 0 -0.68 14 14
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.12 0.25 -9999 0 -0.98 18 18
VEGFR1 homodimer -0.008 0.14 -9999 0 -0.79 11 11
SHC/GRB2/SOS1 -0.037 0.16 -9999 0 -0.84 14 14
GRB10 0.033 0.19 -9999 0 -0.88 14 14
PTPN11 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
PAK1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.038 0.18 -9999 0 -0.89 14 14
HRAS 0.013 0.045 -9999 0 -0.61 2 2
VEGF/Rho/ROCK1/Integrin Complex 0.026 0.13 -9999 0 -0.67 6 6
HIF1A 0.014 0.043 -9999 0 -0.81 1 1
FRS2 0.016 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.038 0.17 -9999 0 -0.88 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.005 0.13 -9999 0 -0.79 10 10
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.044 0.19 -9999 0 -0.94 14 14
mol:GDP -0.035 0.16 -9999 0 -0.8 14 14
mol:NADP 0.073 0.14 -9999 0 -0.56 14 14
eNOS/Hsp90 0.077 0.13 -9999 0 -0.55 10 10
PIK3R1 0.016 0 -9999 0 -10000 0 0
mol:IP3 0.033 0.19 -9999 0 -0.87 14 14
HIF1A/ARNT -0.002 0.032 -9999 0 -0.62 1 1
SHB 0.016 0 -9999 0 -10000 0 0
VEGFA 0.013 0.068 -9999 0 -0.74 3 3
VEGFC 0.014 0.043 -9999 0 -0.81 1 1
FAK1/Vinculin 0.034 0.21 -9999 0 -0.85 16 16
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.068 0.22 -9999 0 -0.97 16 16
PTPN6 0.014 0.032 -9999 0 -0.61 1 1
EPAS1 0.005 0.12 -9999 0 -1 3 3
mol:L-citrulline 0.073 0.14 -9999 0 -0.56 14 14
ITGAV 0.007 0.085 -9999 0 -0.81 4 4
PIK3CA 0.011 0.06 -9999 0 -0.81 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.039 0.18 -9999 0 -0.9 14 14
VEGFR2 homodimer/VEGFA homodimer -0.042 0.19 -9999 0 -0.95 14 14
VEGFR2/3 heterodimer -0.053 0.23 -9999 0 -0.99 19 19
VEGFB 0.016 0 -9999 0 -10000 0 0
MAPK11 0.033 0.19 -9999 0 -0.87 15 15
VEGFR2 homodimer 0 0.22 -9999 0 -0.96 18 18
FLT1 -0.008 0.14 -9999 0 -0.79 11 11
NEDD4 0.017 0.042 -9999 0 -0.81 1 1
MAPK3 0.015 0.18 -9999 0 -0.77 14 14
MAPK1 0.015 0.18 -9999 0 -0.77 14 14
VEGFA145/NRP2 -0.056 0.17 -9999 0 -0.59 36 36
VEGFR1/2 heterodimer -0.054 0.25 -9999 0 -1.2 16 16
KDR 0 0.22 -9999 0 -0.96 18 18
VEGFA165/NRP1/VEGFR2 homodimer -0.072 0.2 -9999 0 -0.9 14 14
SRC 0.012 0.053 -9999 0 -0.71 2 2
platelet activating factor biosynthetic process 0.017 0.18 -9999 0 -0.8 14 14
PI3K -0.046 0.2 -9999 0 -0.99 15 15
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.041 0.19 -9999 0 -0.94 14 14
FES 0.033 0.19 -9999 0 -0.89 14 14
GAB1 -0.046 0.21 -9999 0 -1 14 14
VEGFR2 homodimer/VEGFA homodimer/Src -0.043 0.19 -9999 0 -0.94 15 15
CTNNB1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.058 0.15 -9999 0 -0.56 11 11
VEGFR2 homodimer/VEGFA homodimer/Yes -0.041 0.19 -9999 0 -0.94 14 14
PI3K/GAB1 0.077 0.18 -9999 0 -0.75 15 15
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.037 0.17 -9999 0 -0.86 14 14
PRKACA 0.016 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.051 0.22 -9999 0 -1 16 16
HSP90AA1 0.016 0 -9999 0 -10000 0 0
CDC42 0.033 0.19 -9999 0 -0.89 14 14
actin cytoskeleton reorganization -0.12 0.24 -9999 0 -0.96 18 18
PTK2 0.024 0.23 -9999 0 -0.93 17 17
EDG1 0.023 0.18 -9999 0 -0.86 14 14
mol:DAG 0.033 0.19 -9999 0 -0.87 14 14
CaM/Ca2+ -0.035 0.16 -9999 0 -0.79 14 14
MAP2K3 0.025 0.21 -9999 0 -0.88 15 15
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.041 0.19 -9999 0 -0.93 14 14
PLCG1 0.033 0.19 -9999 0 -0.89 14 14
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.041 0.18 -9999 0 -0.89 15 15
IQGAP1 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.041 0.19 -9999 0 -0.94 14 14
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.042 0.19 -9999 0 -0.94 14 14
cell migration 0.069 0.18 -9999 0 -0.68 16 16
mol:PI-3-4-5-P3 -0.04 0.18 -9999 0 -0.86 15 15
FYN 0.011 0.06 -9999 0 -0.81 2 2
VEGFB/NRP1 -0.036 0.16 -9999 0 -0.8 14 14
mol:NO 0.073 0.14 -9999 0 -0.56 14 14
PXN 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.034 0.15 -9999 0 -0.72 15 15
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.041 0.19 -9999 0 -0.93 14 14
VHL 0.011 0.06 -9999 0 -0.81 2 2
ITGB3 -0.032 0.19 -9999 0 -0.81 22 22
NOS3 0.072 0.15 -9999 0 -0.66 14 14
VEGFR2 homodimer/VEGFA homodimer/Sck -0.047 0.2 -9999 0 -0.97 14 14
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.024 0.19 -9999 0 -0.78 15 15
PRKCB -0.021 0.22 -9999 0 -0.84 15 15
VCL 0.016 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.039 0.17 -9999 0 -0.86 14 14
VEGFR1/2 heterodimer/VEGFA homodimer -0.054 0.24 -9999 0 -1.2 15 15
VEGFA165/NRP2 -0.056 0.17 -9999 0 -0.59 36 36
MAPKKK cascade -0.034 0.15 -9999 0 -0.74 14 14
NRP2 -0.054 0.23 -9999 0 -0.78 33 33
VEGFC homodimer 0.014 0.042 -9999 0 -0.81 1 1
NCK1 0.016 0 -9999 0 -10000 0 0
ROCK1 0.016 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.034 0.21 -9999 0 -0.85 16 16
MAP3K13 0.014 0.22 -9999 0 -0.95 15 15
PDPK1 0.066 0.18 -9999 0 -0.74 15 15
Class I PI3K signaling events

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
ARF5/GTP -0.002 0.032 0.31 1 -10000 0 1
DAPP1 -0.12 0.28 -10000 0 -0.73 44 44
Src family/SYK family/BLNK-LAT/BTK-ITK -0.14 0.31 -10000 0 -0.73 62 62
mol:DAG -0.033 0.14 -10000 0 -0.32 26 26
HRAS 0.014 0.045 -10000 0 -0.6 2 2
RAP1A 0.017 0.002 -10000 0 -10000 0 0
ARF5/GDP -0.005 0.13 -10000 0 -0.48 17 17
PLCG2 0.007 0.077 -10000 0 -0.65 5 5
PLCG1 0.016 0 -10000 0 -10000 0 0
ARF5 0.016 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.031 -10000 0 -10000 0 0
ARF1/GTP -0.002 0.03 0.3 1 -10000 0 1
RHOA 0.016 0 -10000 0 -10000 0 0
YES1 0.016 0 -10000 0 -10000 0 0
RAP1A/GTP -0.002 0.03 -10000 0 -10000 0 0
ADAP1 -0.001 0.029 -10000 0 -10000 0 0
ARAP3 -0.002 0.031 0.28 1 -10000 0 1
INPPL1 0.016 0 -10000 0 -10000 0 0
PREX1 0.016 0 -10000 0 -10000 0 0
ARHGEF6 -0.001 0.11 -10000 0 -0.68 9 9
ARHGEF7 0.016 0 -10000 0 -10000 0 0
ARF1 0.016 0 -10000 0 -10000 0 0
NRAS 0.017 0.002 -10000 0 -10000 0 0
FYN 0.011 0.06 -10000 0 -0.81 2 2
ARF6 0.016 0 -10000 0 -10000 0 0
FGR -0.019 0.16 -10000 0 -0.76 17 17
mol:Ca2+ -0.004 0.075 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.095 0.28 -10000 0 -0.79 52 52
ZAP70 -0.11 0.27 -10000 0 -0.68 69 69
mol:IP3 -0.011 0.1 -10000 0 -10000 0 0
LYN 0.016 0 -10000 0 -10000 0 0
ARF1/GDP -0.005 0.13 -10000 0 -0.48 17 17
RhoA/GDP -0.016 0.055 0.3 1 -0.57 1 2
PDK1/Src/Hsp90 -0.005 0.051 -10000 0 -0.53 3 3
BLNK 0.003 0.1 -10000 0 -0.81 6 6
actin cytoskeleton reorganization 0.031 0.11 -10000 0 -0.57 2 2
SRC 0.012 0.053 -10000 0 -0.71 2 2
PLEKHA2 0.022 0.089 -10000 0 -0.53 4 4
RAC1 0.016 0 -10000 0 -10000 0 0
PTEN -0.002 0.041 -10000 0 -0.79 1 1
HSP90AA1 0.016 0 -10000 0 -10000 0 0
ARF6/GTP -0.001 0.03 0.31 1 -10000 0 1
RhoA/GTP -0.002 0.029 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.12 0.27 -10000 0 -0.73 42 42
BLK -0.24 0.34 -10000 0 -0.69 135 135
PDPK1 0.011 0.06 -10000 0 -0.81 2 2
CYTH1 -0.001 0.029 -10000 0 -10000 0 0
HCK -0.067 0.24 -10000 0 -0.75 41 41
CYTH3 -0.002 0.032 -10000 0 -10000 0 0
CYTH2 -0.001 0.029 -10000 0 -10000 0 0
KRAS 0.017 0.002 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.013 0.072 -10000 0 -0.52 6 6
SGK1 -0.014 0.079 0.25 1 -0.58 6 7
INPP5D -0.011 0.13 -10000 0 -0.66 15 15
mol:GDP -0.015 0.14 -10000 0 -0.52 17 17
SOS1 0.016 0 -10000 0 -10000 0 0
SYK 0.016 0 -10000 0 -10000 0 0
ARF6/GDP -0.016 0.055 0.31 1 -0.57 1 2
mol:PI-3-4-5-P3 -0.001 0.034 0.37 1 -10000 0 1
ARAP3/RAP1A/GTP -0.002 0.031 -10000 0 -10000 0 0
VAV1 -0.1 0.28 -10000 0 -0.73 61 61
mol:PI-3-4-P2 0.009 0.1 -10000 0 -0.49 15 15
RAS family/GTP/PI3K Class I -0.002 0.028 -10000 0 -10000 0 0
PLEKHA1 0.022 0.089 -10000 0 -0.41 15 15
Rac1/GDP -0.005 0.13 -10000 0 -0.48 17 17
LAT -0.012 0.14 -10000 0 -0.73 14 14
Rac1/GTP -0.036 0.18 -10000 0 -0.63 18 18
ITK -0.09 0.16 -10000 0 -0.81 1 1
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.058 0.2 -10000 0 -0.46 38 38
LCK -0.093 0.26 -10000 0 -0.68 59 59
BTK -0.057 0.14 -10000 0 -0.81 1 1
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.016 0 -9999 0 -10000 0 0
SPHK1 0.001 0.11 -9999 0 -0.78 7 7
GNAI2 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.023 0.05 -9999 0 -0.36 6 6
GNAO1 -0.069 0.25 -9999 0 -0.79 40 40
mol:Sphinganine-1-P 0.018 0.084 -9999 0 -0.59 7 7
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.015 0.078 -9999 0 -0.46 10 10
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.01 0.062 -9999 0 -0.68 3 3
S1PR2 -0.005 0.13 -9999 0 -0.79 10 10
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.005 0.04 -9999 0 -0.31 6 6
S1PR5 -0.014 0.15 -9999 0 -0.74 15 15
S1PR4 -0.007 0.12 -9999 0 -0.61 14 14
GNAI1 -0.012 0.13 -9999 0 -0.61 17 17
S1P/S1P5/G12 -0.021 0.089 -9999 0 -0.47 10 10
S1P/S1P3/Gq -0.027 0.15 -9999 0 -0.44 22 22
S1P/S1P4/Gi -0.002 0.14 -9999 0 -0.51 11 11
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ 0.002 0.1 -9999 0 -0.76 7 7
GNA14 -0.076 0.23 -9999 0 -0.63 54 54
GNA15 -0.084 0.26 -9999 0 -0.76 49 49
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 -0.008 0.14 -9999 0 -0.81 11 11
ABCC1 0.016 0 -9999 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.016 0.001 -9999 0 -10000 0 0
HDAC2 0.017 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.006 0.05 -9999 0 -0.53 1 1
forebrain development -0.11 0.21 -9999 0 -0.61 31 31
GNAO1 -0.074 0.25 -9999 0 -0.79 40 40
SMO/beta Arrestin2 0.011 0.054 -9999 0 -0.49 4 4
SMO 0.005 0.063 -9999 0 -0.68 3 3
ARRB2 0.009 0.033 -9999 0 -0.61 1 1
GLI3/SPOP 0.059 0.045 -9999 0 -10000 0 0
mol:GTP -0.002 0.004 -9999 0 -10000 0 0
GSK3B 0.016 0 -9999 0 -10000 0 0
GNAI2 0.011 0.008 -9999 0 -10000 0 0
SIN3/HDAC complex -0.001 0.025 -9999 0 -0.48 1 1
GNAI1 -0.017 0.13 -9999 0 -0.61 17 17
XPO1 0.012 0.01 -9999 0 -10000 0 0
GLI1/Su(fu) -0.12 0.14 -9999 0 -0.51 19 19
SAP30 0.014 0.043 -9999 0 -0.81 1 1
mol:GDP 0.005 0.063 -9999 0 -0.68 3 3
MIM/GLI2A -0.004 0.12 -9999 0 -0.71 10 10
IFT88 0.016 0 -9999 0 -10000 0 0
GNAI3 0.011 0.008 -9999 0 -10000 0 0
GLI2 0.038 0.068 -9999 0 -10000 0 0
GLI3 0.053 0.047 -9999 0 -10000 0 0
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
SAP18 0.016 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.016 0 -9999 0 -10000 0 0
GNG2 0.011 0.055 -9999 0 -0.61 3 3
Gi family/GTP -0.019 0.14 -9999 0 -0.38 40 40
SIN3B 0.017 0.001 -9999 0 -10000 0 0
SIN3A 0.016 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.044 0.05 -9999 0 -10000 0 0
GLI2/Su(fu) 0.031 0.066 -9999 0 -10000 0 0
FOXA2 -0.39 0.53 -9999 0 -1.2 93 93
neural tube patterning -0.11 0.21 -9999 0 -0.61 31 31
SPOP 0.016 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.002 0.018 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CSNK1G2 0.016 0 -9999 0 -10000 0 0
CSNK1G3 0.016 0 -9999 0 -10000 0 0
MTSS1 -0.004 0.12 -9999 0 -0.71 10 10
embryonic limb morphogenesis -0.11 0.21 -9999 0 -0.61 31 31
SUFU 0.021 0.031 -9999 0 -10000 0 0
LGALS3 -0.14 0.32 -9999 0 -0.81 71 71
catabolic process 0.076 0.065 -9999 0 -10000 0 0
GLI3A/CBP -0.059 0.14 -9999 0 -10000 0 0
KIF3A 0.016 0 -9999 0 -10000 0 0
GLI1 -0.12 0.22 -9999 0 -0.63 31 31
RAB23 0.009 0.073 -9999 0 -0.81 3 3
CSNK1A1 0.016 0 -9999 0 -10000 0 0
IFT172 0.016 0 -9999 0 -10000 0 0
RBBP7 0.017 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.092 0.19 -9999 0 -0.49 70 70
GNAZ -0.003 0.1 -9999 0 -0.76 7 7
RBBP4 0.012 0.06 -9999 0 -0.81 2 2
CSNK1G1 0.016 0 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GLI2/SPOP 0.043 0.063 -9999 0 -10000 0 0
STK36 0.012 0.01 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.007 0.11 -9999 0 -0.45 9 9
PTCH1 -0.1 0.22 -9999 0 -0.69 22 22
MIM/GLI1 -0.21 0.32 -9999 0 -0.6 111 111
CREBBP -0.059 0.14 -9999 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.066 0.027 -9999 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.03 0 -10000 0 -10000 0 0
MAP4K4 -0.045 0.18 -10000 0 -0.68 17 17
BAG4 0.005 0.095 -10000 0 -0.81 5 5
PKC zeta/ceramide -0.019 0.038 -10000 0 -0.34 1 1
NFKBIA 0.016 0 -10000 0 -10000 0 0
BIRC3 -0.15 0.31 -10000 0 -0.73 84 84
BAX -0.005 0.017 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
AKT1 0.029 0.008 -10000 0 -10000 0 0
BAD -0.017 0.035 -10000 0 -10000 0 0
SMPD1 -0.025 0.11 -10000 0 -0.27 42 42
RB1 -0.017 0.035 -10000 0 -10000 0 0
FADD/Caspase 8 -0.027 0.17 -10000 0 -0.65 16 16
MAP2K4 -0.008 0.04 -10000 0 -0.46 1 1
NSMAF 0.016 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.007 0.033 -10000 0 -10000 0 0
EGF -0.11 0.26 -10000 0 -0.65 70 70
mol:ceramide -0.031 0.037 -10000 0 -10000 0 0
MADD 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.028 0.033 -10000 0 -0.62 1 1
ASAH1 0.014 0.043 -10000 0 -0.81 1 1
negative regulation of cell cycle -0.018 0.034 -10000 0 -10000 0 0
cell proliferation -0.072 0.13 -10000 0 -0.39 29 29
BID -0.064 0.21 -10000 0 -0.66 31 31
MAP3K1 -0.018 0.042 -10000 0 -0.5 1 1
EIF2A 0.004 0.031 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
MAPK3 0.008 0.032 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.008 0.032 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.018 0.034 -10000 0 -10000 0 0
FADD -0.045 0.18 -10000 0 -0.68 17 17
KSR1 -0.017 0.035 -10000 0 -10000 0 0
MAPK8 -0.004 0.05 -10000 0 -0.33 5 5
PRKRA -0.017 0.035 -10000 0 -10000 0 0
PDGFA 0.016 0 -10000 0 -10000 0 0
TRAF2 0.016 0 -10000 0 -10000 0 0
IGF1 -0.14 0.29 -10000 0 -0.68 86 86
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.03 0.036 -10000 0 -10000 0 0
CTSD 0.016 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.077 0.14 -10000 0 -0.42 29 29
PRKCD 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.014 0.032 -10000 0 -0.61 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.028 0.033 -10000 0 -0.62 1 1
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.014 0.043 -10000 0 -0.81 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.059 0.19 -10000 0 -0.72 17 17
TNFR1A/BAG4/TNF-alpha -0.11 0.2 -10000 0 -0.53 47 47
mol:Sphingosine-1-phosphate 0.03 0 -10000 0 -10000 0 0
MAP2K1 0.003 0.035 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
CYCS -0.008 0.042 0.18 3 -0.21 7 10
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
NFKB1 0.016 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.008 0.071 -10000 0 -0.62 5 5
EIF2AK2 -0.007 0.033 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.1 0.19 -10000 0 -0.53 42 42
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.042 0.077 -10000 0 -0.32 16 16
MAP2K2 0.004 0.031 -10000 0 -10000 0 0
SMPD3 -0.035 0.13 -10000 0 -0.32 47 47
TNF -0.15 0.31 -10000 0 -0.71 85 85
PKC zeta/PAR4 -0.003 0.039 -10000 0 -0.53 2 2
mol:PHOSPHOCHOLINE 0.011 0.089 0.21 43 -10000 0 43
NF kappa B1/RelA/I kappa B alpha -0.002 0.027 -10000 0 -0.45 1 1
AIFM1 -0.006 0.037 0.18 3 -0.21 4 7
BCL2 -0.006 0.12 -10000 0 -0.68 12 12
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.016 0 -10000 0 -10000 0 0
EPHB2 0.002 0.1 -10000 0 -0.82 6 6
EFNB1 -0.013 0.14 -10000 0 -0.49 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.12 0.23 -10000 0 -0.76 27 27
Ephrin B2/EPHB1-2 -0.049 0.14 -10000 0 -0.55 16 16
neuron projection morphogenesis -0.12 0.22 -10000 0 -0.72 27 27
Ephrin B1/EPHB1-2/Tiam1 -0.13 0.25 -10000 0 -0.78 31 31
DNM1 -0.039 0.19 -10000 0 -0.66 30 30
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 0.019 0.059 -10000 0 -0.76 2 2
YES1 -0.004 0.073 -10000 0 -1 2 2
Ephrin B1/EPHB1-2/NCK2 -0.071 0.16 -10000 0 -0.72 10 10
PI3K -0.001 0.078 -10000 0 -0.82 3 3
mol:GDP -0.13 0.24 -10000 0 -0.76 32 32
ITGA2B -0.032 0.18 -10000 0 -0.74 24 24
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.005 0.075 -10000 0 -1 2 2
MAP3K7 -0.005 0.06 -10000 0 -0.82 2 2
FGR -0.011 0.081 -10000 0 -1 2 2
TIAM1 -0.095 0.28 -10000 0 -0.79 52 52
PIK3R1 0.016 0 -10000 0 -10000 0 0
RGS3 0.016 0 -10000 0 -10000 0 0
cell adhesion -0.017 0.19 -10000 0 -0.62 22 22
LYN -0.004 0.073 -10000 0 -1 2 2
Ephrin B1/EPHB1-2/Src Family Kinases -0.007 0.069 -10000 0 -0.95 2 2
Ephrin B1/EPHB1-2 -0.012 0.065 -10000 0 -0.88 2 2
SRC -0.005 0.074 -10000 0 -1 2 2
ITGB3 -0.032 0.19 -10000 0 -0.81 22 22
EPHB1 -0.059 0.22 -10000 0 -0.67 41 41
EPHB4 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.069 0.21 -10000 0 -0.67 39 39
BLK -0.045 0.095 -10000 0 -1 2 2
HCK -0.019 0.088 -10000 0 -1 2 2
regulation of stress fiber formation 0.07 0.16 0.7 10 -10000 0 10
MAPK8 0.023 0.083 -10000 0 -0.64 5 5
Ephrin B1/EPHB1-2/RGS3 -0.071 0.16 -10000 0 -0.72 10 10
endothelial cell migration 0 0.053 -10000 0 -0.71 2 2
NCK2 0.016 0 -10000 0 -10000 0 0
PTPN13 0.01 0.07 -10000 0 -0.93 2 2
regulation of focal adhesion formation 0.07 0.16 0.7 10 -10000 0 10
chemotaxis 0.07 0.16 0.7 10 -10000 0 10
PIK3CA 0.011 0.06 -10000 0 -0.81 2 2
Rac1/GTP -0.12 0.22 -10000 0 -0.76 27 27
angiogenesis -0.012 0.064 -10000 0 -0.87 2 2
LCK -0.021 0.086 -10000 0 -1 2 2
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.006 0.021 -10000 0 -10000 0 0
AES 0.005 0.018 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.011 0.083 -10000 0 -0.62 7 7
SMAD4 0.016 0 -10000 0 -10000 0 0
DKK2 -0.094 0.27 -10000 0 -0.77 53 53
TLE1 0.005 0.017 -10000 0 -10000 0 0
MACF1 0.016 0 -10000 0 -10000 0 0
CTNNB1 0.029 0.09 -10000 0 -0.51 1 1
WIF1 -0.056 0.18 -10000 0 -0.61 38 38
beta catenin/RanBP3 0.002 0.1 0.36 14 -0.43 1 15
KREMEN2 -0.047 0.22 -10000 0 -0.78 30 30
DKK1 -0.14 0.31 -10000 0 -0.72 83 83
beta catenin/beta TrCP1 0.037 0.084 -10000 0 -0.46 1 1
FZD1 0.001 0.11 -10000 0 -0.81 7 7
AXIN2 -0.003 0.18 -10000 0 -1.6 4 4
AXIN1 0.016 0.001 -10000 0 -10000 0 0
RAN 0.016 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.005 0.021 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.057 0.084 -10000 0 -0.74 1 1
Axin1/APC/GSK3 0.011 0.051 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.05 0.087 -10000 0 -10000 0 0
HNF1A 0.003 0.046 -10000 0 -0.82 1 1
CTBP1 0.005 0.018 -10000 0 -10000 0 0
MYC -0.038 0.29 -10000 0 -1.6 12 12
RANBP3 0.016 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.11 0.23 -10000 0 -0.58 61 61
NKD1 -0.05 0.21 -10000 0 -0.73 33 33
TCF4 -0.001 0.073 -10000 0 -0.79 3 3
TCF3 0.005 0.018 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.021 0.09 -10000 0 -0.49 8 8
Ran/GTP 0 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.015 0.12 0.45 16 -0.63 1 17
LEF1 -0.043 0.18 -10000 0 -0.72 25 25
DVL1 0.014 0.037 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.067 0.1 -10000 0 -0.72 1 1
DKK1/LRP6/Kremen 2 -0.14 0.23 -10000 0 -0.57 66 66
LRP6 0.016 0.001 -10000 0 -10000 0 0
CSNK1A1 0.006 0.021 -10000 0 -10000 0 0
NLK 0.016 0.005 -10000 0 -10000 0 0
CCND1 -0.002 0.17 -10000 0 -1.6 4 4
WNT1 -0.01 0.12 -10000 0 -0.62 14 14
GSK3A 0.016 0.001 -10000 0 -10000 0 0
GSK3B 0.016 0.001 -10000 0 -10000 0 0
FRAT1 0.016 0.001 -10000 0 -10000 0 0
PPP2R5D 0.045 0.092 0.34 33 -10000 0 33
APC 0.025 0.094 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.032 0.079 0.23 1 -0.34 2 3
CREBBP 0.005 0.018 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.19 0.34 -9999 0 -0.74 105 105
HRAS 0.013 0.045 -9999 0 -0.61 2 2
EGFR -0.02 0.17 -9999 0 -0.79 17 17
AKT 0.03 0.06 -9999 0 -0.46 4 4
FOXO3 0.016 0 -9999 0 -10000 0 0
AKT1 0.016 0 -9999 0 -10000 0 0
FOXO1 0.016 0 -9999 0 -10000 0 0
AKT3 0.016 0 -9999 0 -10000 0 0
FOXO4 0.016 0 -9999 0 -10000 0 0
MET -0.085 0.27 -9999 0 -0.81 46 46
PIK3CA 0.011 0.06 -9999 0 -0.81 2 2
PIK3CB 0.016 0 -9999 0 -10000 0 0
NRAS 0.016 0 -9999 0 -10000 0 0
PIK3CG -0.049 0.21 -9999 0 -0.73 33 33
PIK3R3 0.011 0.06 -9999 0 -0.81 2 2
PIK3R2 0.016 0 -9999 0 -10000 0 0
NF1 0.016 0 -9999 0 -10000 0 0
RAS -0.048 0.14 -9999 0 -0.44 28 28
ERBB2 0.016 0 -9999 0 -10000 0 0
proliferation/survival/translation -0.027 0.043 -9999 0 -10000 0 0
PI3K -0.03 0.13 -9999 0 -0.36 34 34
PIK3R1 0.016 0 -9999 0 -10000 0 0
KRAS 0.016 0 -9999 0 -10000 0 0
FOXO 0.041 0.036 -9999 0 -10000 0 0
AKT2 0.008 0.071 -9999 0 -0.61 5 5
PTEN 0.014 0.043 -9999 0 -0.81 1 1
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.014 0.15 -9999 0 -0.8 14 14
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0 0.12 -9999 0 -0.44 13 13
GNAO1 -0.066 0.25 -9999 0 -0.78 40 40
S1P/S1P3/G12/G13 -0.003 0.035 -9999 0 -0.49 1 1
AKT1 -0.031 0.1 -9999 0 -0.53 13 13
AKT3 0.033 0.096 -9999 0 -0.53 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.014 0.15 -9999 0 -0.8 14 14
GNAI2 0.018 0 -9999 0 -10000 0 0
GNAI3 0.018 0 -9999 0 -10000 0 0
GNAI1 -0.01 0.13 -9999 0 -0.61 17 17
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.013 0.062 -9999 0 -0.68 3 3
S1PR2 -0.005 0.13 -9999 0 -0.79 10 10
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.01 0.13 -9999 0 -0.49 8 8
MAPK3 0.02 0.12 -9999 0 -0.46 8 8
MAPK1 0.02 0.12 -9999 0 -0.46 8 8
JAK2 0.008 0.14 -9999 0 -0.49 12 12
CXCR4 -0.01 0.17 -9999 0 -0.58 16 16
FLT1 -0.004 0.14 -9999 0 -0.79 11 11
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.017 0.13 -9999 0 -0.46 9 9
S1P/S1P3/Gi 0.009 0.13 -9999 0 -0.49 8 8
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.037 0.098 -9999 0 -0.44 8 8
VEGFA 0.014 0.068 -9999 0 -0.74 3 3
S1P/S1P2/Gi -0.004 0.15 -9999 0 -0.52 13 13
VEGFR1 homodimer/VEGFA homodimer 0.012 0.12 -9999 0 -0.63 13 13
RHOA 0.016 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.044 0.16 -9999 0 -0.4 55 55
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ 0.004 0.1 -9999 0 -0.75 7 7
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.076 0.23 -9999 0 -0.63 54 54
GNA15 -0.084 0.26 -9999 0 -0.76 49 49
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 -0.008 0.14 -9999 0 -0.81 11 11
Rac1/GTP -0.037 0.098 -9999 0 -0.44 8 8
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.033 0.13 -9999 0 -0.55 19 19
PDGFB-D/PDGFRB/SLAP -0.044 0.15 -9999 0 -0.53 32 32
PDGFB-D/PDGFRB/APS/CBL -0.02 0.099 -9999 0 -0.53 13 13
AKT1 -0.013 0.08 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.004 0.14 -9999 0 -0.58 19 19
PIK3CA 0.011 0.06 -9999 0 -0.81 2 2
FGR -0.038 0.17 -9999 0 -0.62 25 25
mol:Ca2+ -0.005 0.14 -9999 0 -0.68 13 13
MYC -0.012 0.2 -9999 0 -0.79 16 16
SHC1 0.014 0.032 -9999 0 -0.61 1 1
HRAS/GDP -0.014 0.083 -9999 0 -0.45 1 1
LRP1/PDGFRB/PDGFB -0.023 0.11 -9999 0 -0.53 16 16
GRB10 0.014 0.043 -9999 0 -0.81 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 -0.006 0.14 -9999 0 -0.7 13 13
PTEN 0.014 0.043 -9999 0 -0.81 1 1
GRB2 0.016 0 -9999 0 -10000 0 0
GRB7 -0.054 0.23 -9999 0 -0.81 32 32
PDGFB-D/PDGFRB/SHP2 -0.022 0.11 -9999 0 -0.6 14 14
PDGFB-D/PDGFRB/GRB10 -0.024 0.12 -9999 0 -0.61 15 15
cell cycle arrest -0.044 0.15 -9999 0 -0.52 32 32
HRAS 0.013 0.045 -9999 0 -0.61 2 2
HIF1A 0.06 0.093 -9999 0 -0.57 1 1
GAB1 -0.022 0.15 -9999 0 -0.63 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.013 0.14 -9999 0 -0.58 16 16
PDGFB-D/PDGFRB -0.004 0.1 -9999 0 -0.54 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.022 0.11 -9999 0 -0.6 14 14
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.04 0.13 -9999 0 -0.56 17 17
positive regulation of MAPKKK cascade -0.022 0.11 -9999 0 -0.6 14 14
PIK3R1 0.016 0 -9999 0 -10000 0 0
mol:IP3 -0.006 0.14 -9999 0 -0.71 13 13
E5 0 0.002 -9999 0 -10000 0 0
CSK 0.014 0.032 -9999 0 -0.61 1 1
PDGFB-D/PDGFRB/GRB7 -0.075 0.2 -9999 0 -0.62 46 46
SHB 0.016 0 -9999 0 -10000 0 0
BLK -0.14 0.25 -9999 0 -0.64 64 64
PTPN2 0.015 0.004 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.022 0.11 -9999 0 -0.6 14 14
BCAR1 0.016 0 -9999 0 -10000 0 0
VAV2 -0.023 0.16 -9999 0 -0.63 17 17
CBL 0.016 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.022 0.11 -9999 0 -0.6 14 14
LCK -0.07 0.2 -9999 0 -0.65 33 33
PDGFRB -0.014 0.16 -9999 0 -0.8 14 14
ACP1 0.016 0 -9999 0 -10000 0 0
HCK -0.064 0.21 -9999 0 -0.63 40 40
ABL1 -0.023 0.15 -9999 0 -0.6 16 16
PDGFB-D/PDGFRB/CBL -0.028 0.16 -9999 0 -0.69 16 16
PTPN1 0.015 0.004 -9999 0 -10000 0 0
SNX15 0.016 0 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
STAT1 -0.008 0.13 -9999 0 -0.73 12 12
cell proliferation -0.007 0.18 -9999 0 -0.67 17 17
SLA -0.015 0.14 -9999 0 -0.63 18 18
actin cytoskeleton reorganization 0.011 0.085 -9999 0 -10000 0 0
SRC -0.014 0.1 -9999 0 -0.52 14 14
PI3K -0.023 0.084 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.065 0.17 -9999 0 -0.53 45 45
SH2B2 0.014 0.032 -9999 0 -0.61 1 1
PLCgamma1/SPHK1 -0.005 0.15 -9999 0 -0.66 15 15
LYN -0.011 0.098 -9999 0 -0.52 13 13
LRP1 0.009 0.073 -9999 0 -0.81 3 3
SOS1 0.016 0 -9999 0 -10000 0 0
STAT5B 0.016 0 -9999 0 -10000 0 0
STAT5A 0.016 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.012 0.079 -9999 0 -10000 0 0
SPHK1 0.001 0.11 -9999 0 -0.78 7 7
EDG1 0 0.003 -9999 0 -10000 0 0
mol:DAG -0.006 0.14 -9999 0 -0.71 13 13
PLCG1 -0.007 0.15 -9999 0 -0.73 13 13
NHERF/PDGFRB -0.03 0.11 -9999 0 -0.53 13 13
YES1 -0.012 0.098 -9999 0 -0.52 13 13
cell migration -0.03 0.11 -9999 0 -0.53 13 13
SHC/Grb2/SOS1 -0.013 0.08 -9999 0 -10000 0 0
SLC9A3R2 0.013 0.045 -9999 0 -0.61 2 2
SLC9A3R1 0.001 0.095 -9999 0 -0.61 9 9
NHERF1-2/PDGFRB/PTEN -0.028 0.1 -9999 0 -0.48 14 14
FYN -0.015 0.11 -9999 0 -0.55 15 15
DOK1 0.023 0.097 -9999 0 -0.48 13 13
HRAS/GTP -0.002 0.033 -9999 0 -0.45 2 2
PDGFB 0.016 0 -9999 0 -10000 0 0
RAC1 -0.012 0.17 -9999 0 -0.58 21 21
PRKCD 0.023 0.098 -9999 0 -0.48 13 13
FER 0.021 0.1 -9999 0 -0.48 15 15
MAPKKK cascade -0.015 0.078 -9999 0 -10000 0 0
RASA1 0.023 0.098 -9999 0 -0.48 13 13
NCK1 0.016 0 -9999 0 -10000 0 0
NCK2 0.016 0 -9999 0 -10000 0 0
p62DOK/Csk 0.003 0.09 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB -0.022 0.11 -9999 0 -0.6 14 14
chemotaxis -0.022 0.14 -9999 0 -0.58 16 16
STAT1-3-5/STAT1-3-5 -0.025 0.094 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB -0.023 0.12 -9999 0 -0.62 14 14
PTPRJ 0.016 0 -9999 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 -0.044 0.16 -10000 0 -0.62 27 27
ATM 0.014 0.043 -10000 0 -0.81 1 1
UBE2D3 0.016 0 -10000 0 -10000 0 0
PRKDC 0.014 0.043 -10000 0 -0.81 1 1
ATR 0.016 0 -10000 0 -10000 0 0
UBE2L3 0.016 0 -10000 0 -10000 0 0
FANCD2 0.03 0.041 -10000 0 -0.43 3 3
protein ubiquitination -0.034 0.12 -10000 0 -10000 0 0
XRCC5 0.016 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.016 0 -10000 0 -10000 0 0
DNA-PK -0.001 0.027 -10000 0 -0.53 1 1
FA complex/FANCD2/Ubiquitin -0.011 0.059 -10000 0 -0.81 1 1
FANCF 0.016 0 -10000 0 -10000 0 0
BRCA1 0.013 0.045 -10000 0 -0.61 2 2
CCNE1 0.016 0 -10000 0 -10000 0 0
CDK2/Cyclin E1 0 0 -10000 0 -10000 0 0
FANCG 0.016 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.046 0.16 -10000 0 -0.61 29 29
FANCE 0.014 0.043 -10000 0 -0.81 1 1
FANCC 0.016 0 -10000 0 -10000 0 0
NBN 0.016 0 -10000 0 -10000 0 0
FANCA -0.016 0.16 -10000 0 -0.8 15 15
DNA repair 0.048 0.15 -10000 0 -0.6 9 9
BRCA1/BARD1/ubiquitin -0.046 0.16 -10000 0 -0.61 29 29
BARD1/DNA-PK -0.036 0.13 -10000 0 -0.48 28 28
FANCL 0.016 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.044 0.16 0.62 27 -10000 0 27
BRCA1/BARD1/CTIP/M/R/N Complex 0.024 0.099 -10000 0 -0.57 1 1
BRCA1/BACH1/BARD1/TopBP1 -0.04 0.14 -10000 0 -0.53 27 27
BRCA1/BARD1/P53 -0.036 0.13 -10000 0 -0.48 27 27
BARD1/CSTF1/BRCA1 -0.04 0.14 -10000 0 -0.53 27 27
BRCA1/BACH1 0.013 0.045 -10000 0 -0.61 2 2
BARD1 -0.043 0.21 -10000 0 -0.81 27 27
PCNA 0.016 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.04 0.14 -10000 0 -0.53 27 27
BRCA1/BARD1/UbcH7 -0.04 0.14 -10000 0 -0.53 27 27
BRCA1/BARD1/RAD51/PCNA -0.045 0.15 -10000 0 -0.51 31 31
BARD1/DNA-PK/P53 -0.033 0.12 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.046 0.16 -10000 0 -0.61 29 29
BRCA1/BARD1/CTIP -0.039 0.13 -10000 0 -0.48 29 29
FA complex 0.037 0.084 -10000 0 -0.95 1 1
BARD1/EWS -0.044 0.16 -10000 0 -0.62 27 27
RBBP8 0.027 0.047 -10000 0 -0.62 2 2
TP53 0.016 0 -10000 0 -10000 0 0
TOPBP1 0.016 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.036 0.12 0.48 27 -10000 0 27
BRCA1/BARD1 -0.035 0.12 -10000 0 -10000 0 0
CSTF1 0.016 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.045 0.16 -10000 0 -0.63 27 27
CDK2 0.016 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.001 0.11 -10000 0 -0.76 8 8
RAD50 0.016 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.046 0.16 -10000 0 -0.61 29 29
EWSR1 0.016 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.031 0.085 -10000 0 -0.42 6 6
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.016 0 -10000 0 -10000 0 0
AKT2 0.008 0.071 -10000 0 -0.61 5 5
STXBP4 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.045 0.13 0.3 44 -10000 0 44
YWHAZ 0.016 0 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.022 0.059 -10000 0 -0.44 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
YWHAB 0.016 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
ASIP -0.13 0.29 -10000 0 -0.72 72 72
PRKCI 0.016 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.016 0 -10000 0 -10000 0 0
GYS1 0.039 0.027 -10000 0 -10000 0 0
PRKCZ 0.014 0.032 -10000 0 -0.61 1 1
TRIP10 0.016 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 -0.029 0.13 -10000 0 -0.38 6 6
VAMP2 0.016 0 -10000 0 -10000 0 0
SLC2A4 0.045 0.14 0.33 28 -10000 0 28
STX4 0.016 0 -10000 0 -10000 0 0
GSK3B 0.03 0.032 -10000 0 -10000 0 0
SFN -0.25 0.37 -10000 0 -0.74 133 133
LNPEP -0.019 0.17 -10000 0 -0.81 16 16
YWHAE 0.016 0 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.014 0.15 -9999 0 -0.8 14 14
alphaV beta3 Integrin -0.042 0.16 -9999 0 -0.66 24 24
PTK2 -0.04 0.15 -9999 0 -0.74 13 13
positive regulation of JNK cascade -0.016 0.068 -9999 0 -0.36 13 13
CDC42/GDP 0.048 0.11 -9999 0 -0.5 13 13
Rac1/GDP 0.05 0.11 -9999 0 -0.5 13 13
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.016 0 -9999 0 -10000 0 0
CDC42/GTP -0.02 0.085 -9999 0 -0.46 13 13
nectin-3/I-afadin -0.029 0.13 -9999 0 -0.56 20 20
RAPGEF1 0.041 0.13 -9999 0 -0.58 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.03 0.15 -9999 0 -0.69 13 13
PDGFB-D/PDGFRB -0.014 0.15 -9999 0 -0.8 14 14
TLN1 0.027 0.089 -9999 0 -0.76 3 3
Rap1/GTP -0.016 0.073 -9999 0 -0.44 7 7
IQGAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.029 0.13 -9999 0 -0.56 20 20
PVR 0.016 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.016 0 -9999 0 -10000 0 0
mol:GDP 0.043 0.14 -9999 0 -0.64 13 13
MLLT4 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.06 -9999 0 -0.81 2 2
PI3K -0.039 0.14 -9999 0 -0.91 3 3
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.009 0.063 -9999 0 -0.44 8 8
positive regulation of lamellipodium assembly -0.017 0.072 -9999 0 -0.38 13 13
PVRL1 0.003 0.09 -9999 0 -0.61 8 8
PVRL3 -0.024 0.17 -9999 0 -0.74 20 20
PVRL2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
CDH1 0.011 0.06 -9999 0 -0.81 2 2
CLDN1 -0.089 0.28 -9999 0 -0.81 48 48
JAM-A/CLDN1 -0.083 0.19 -9999 0 -0.51 58 58
SRC -0.036 0.15 -9999 0 -0.8 13 13
ITGB3 -0.032 0.19 -9999 0 -0.81 22 22
nectin-1(dimer)/I-afadin/I-afadin -0.009 0.063 -9999 0 -0.44 8 8
FARP2 0.036 0.13 -9999 0 -0.63 13 13
RAC1 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.025 0.11 -9999 0 -0.53 13 13
nectin-1/I-afadin -0.009 0.063 -9999 0 -0.44 8 8
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.033 0.12 -9999 0 -0.53 13 13
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.016 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.016 0.068 -9999 0 -0.36 13 13
alphaV/beta3 Integrin/Talin -0.041 0.16 -9999 0 -0.86 8 8
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C 0.018 0.094 -9999 0 -0.82 3 3
VAV2 0.034 0.14 -9999 0 -0.64 13 13
RAP1/GDP -0.019 0.086 -9999 0 -0.46 13 13
ITGAV 0.007 0.085 -9999 0 -0.81 4 4
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.025 0.11 -9999 0 -0.53 13 13
nectin-3(dimer)/I-afadin/I-afadin -0.029 0.13 -9999 0 -0.56 20 20
Rac1/GTP -0.02 0.089 -9999 0 -0.48 13 13
PTPRM -0.019 0.097 -9999 0 -0.41 14 14
E-cadherin/beta catenin/alpha catenin -0.008 0.049 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.005 0.099 -9999 0 -0.47 5 5
RAD9A 0.014 0.032 -9999 0 -0.61 1 1
AP1 -0.12 0.25 -9999 0 -0.61 73 73
IFNAR2 0.017 0.002 -9999 0 -10000 0 0
AKT1 -0.034 0.11 -9999 0 -10000 0 0
ER alpha/Oestrogen -0.11 0.22 -9999 0 -0.54 77 77
NFX1/SIN3/HDAC complex 0.059 0.025 -9999 0 -10000 0 0
EGF -0.11 0.26 -9999 0 -0.65 70 70
SMG5 0.016 0 -9999 0 -10000 0 0
SMG6 0.016 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0 -9999 0 -10000 0 0
TERT/c-Abl -0.023 0.075 -9999 0 -0.43 5 5
SAP18 0.016 0.002 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.054 0.19 -9999 0 -0.61 40 40
WRN 0.014 0.043 -9999 0 -0.81 1 1
SP1 0.017 0.002 -9999 0 -10000 0 0
SP3 0.016 0.002 -9999 0 -10000 0 0
TERF2IP 0.016 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.022 0.058 -9999 0 -0.42 1 1
Mad/Max 0 0 -9999 0 -10000 0 0
TERT -0.005 0.1 -9999 0 -0.48 5 5
CCND1 -0.003 0.15 -9999 0 -1.1 5 5
MAX 0.016 0.002 -9999 0 -10000 0 0
RBBP7 0.016 0.002 -9999 0 -10000 0 0
RBBP4 0.012 0.06 -9999 0 -0.81 2 2
TERF2 0 0.005 -9999 0 -10000 0 0
PTGES3 0.016 0 -9999 0 -10000 0 0
SIN3A 0.016 0.002 -9999 0 -10000 0 0
Telomerase/911 0.046 0.026 -9999 0 -10000 0 0
CDKN1B -0.071 0.21 -9999 0 -0.56 36 36
RAD1 0.016 0 -9999 0 -10000 0 0
XRCC5 0.016 0 -9999 0 -10000 0 0
XRCC6 0.016 0 -9999 0 -10000 0 0
SAP30 0.014 0.043 -9999 0 -0.81 1 1
TRF2/PARP2 0 0.005 -9999 0 -10000 0 0
UBE3A 0.016 0.002 -9999 0 -10000 0 0
JUN -0.023 0.16 -9999 0 -0.66 22 22
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0 -9999 0 -10000 0 0
FOS -0.11 0.28 -9999 0 -0.72 65 65
IFN-gamma/IRF1 -0.13 0.23 -9999 0 -0.51 95 95
PARP2 0.016 0 -9999 0 -10000 0 0
BLM 0.008 0.08 -9999 0 -0.76 4 4
Telomerase 0.009 0.11 -9999 0 -0.5 11 11
IRF1 0.004 0.1 -9999 0 -0.6 11 11
ESR1 -0.13 0.29 -9999 0 -0.7 77 77
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.028 -9999 0 -0.55 1 1
ubiquitin-dependent protein catabolic process 0.065 0.025 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.066 0.026 -9999 0 -10000 0 0
HDAC1 0.016 0.002 -9999 0 -10000 0 0
HDAC2 0.017 0.002 -9999 0 -10000 0 0
ATM -0.001 0.029 -9999 0 -0.56 1 1
SMAD3 0.016 0.093 -9999 0 -0.62 8 8
ABL1 0.016 0 -9999 0 -10000 0 0
MXD1 0.016 0.002 -9999 0 -10000 0 0
MRE11A 0.016 0 -9999 0 -10000 0 0
HUS1 0.016 0 -9999 0 -10000 0 0
RPS6KB1 0.016 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.034 0.081 -9999 0 -0.46 1 1
NR2F2 0.015 0.002 -9999 0 -10000 0 0
MAPK3 0.008 0.074 -9999 0 -0.44 10 10
MAPK1 0.008 0.074 -9999 0 -0.44 10 10
TGFB1/TGF beta receptor Type II -0.002 0.12 -9999 0 -0.81 8 8
NFKB1 0.016 0 -9999 0 -10000 0 0
HNRNPC 0.016 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.029 -9999 0 -0.56 1 1
NBN 0.016 0 -9999 0 -10000 0 0
EGFR -0.02 0.17 -9999 0 -0.79 17 17
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.11 0.22 -9999 0 -0.52 83 83
MYC -0.021 0.17 -9999 0 -0.74 19 19
IL2 -0.01 0.099 -9999 0 -0.61 10 10
KU 0 0 -9999 0 -10000 0 0
RAD50 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
TGFB1 -0.002 0.12 -9999 0 -0.81 8 8
TRF2/BLM -0.005 0.056 -9999 0 -0.58 3 3
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.02 0.072 -9999 0 -0.44 4 4
SP1/HDAC2 0 0 -9999 0 -10000 0 0
PINX1 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.022 0.058 -9999 0 -0.42 1 1
Smad3/Myc -0.034 0.13 -9999 0 -0.56 19 19
911 complex -0.001 0.019 -9999 0 -10000 0 0
IFNG -0.15 0.29 -9999 0 -0.65 95 95
Telomerase/PinX1 -0.022 0.058 -9999 0 -0.42 1 1
Telomerase/AKT1/mTOR/p70S6K 0.019 0.059 -9999 0 -10000 0 0
SIN3B 0.016 0.002 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.022 0.058 -9999 0 -10000 0 0
response to DNA damage stimulus 0.004 0.008 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0.005 -9999 0 -10000 0 0
TRF2/WRN -0.001 0.03 -9999 0 -0.58 1 1
Telomerase/hnRNP C1/C2 -0.022 0.058 -9999 0 -0.42 1 1
E2F1 -0.002 0.12 -9999 0 -0.79 9 9
ZNFX1 0.016 0.002 -9999 0 -10000 0 0
PIF1 -0.036 0.19 -9999 0 -0.69 28 28
NCL 0.016 0 -9999 0 -10000 0 0
DKC1 0.016 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.059 0.22 -9999 0 -0.67 41 41
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.014 0.032 -9999 0 -0.61 1 1
TCEB1 0.016 0 -9999 0 -10000 0 0
HIF1A/p53 0.018 0.052 -9999 0 -10000 0 0
HIF1A 0.008 0.054 -9999 0 -0.31 1 1
COPS5 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.045 -9999 0 -0.61 2 2
FIH (dimer) 0.016 0 -9999 0 -10000 0 0
CDKN2A -0.11 0.27 -9999 0 -0.67 69 69
ARNT/IPAS -0.054 0.16 -9999 0 -0.5 41 41
HIF1AN 0.016 0 -9999 0 -10000 0 0
GNB2L1 0.016 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.018 0.052 -9999 0 -10000 0 0
CUL2 0.016 0 -9999 0 -10000 0 0
OS9 0.016 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.001 0.019 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.018 0.052 -9999 0 -10000 0 0
PHD1-3/OS9 -0.082 0.17 -9999 0 -0.48 49 49
HIF1A/RACK1/Elongin B/Elongin C -0.013 0.032 -9999 0 -10000 0 0
VHL 0.011 0.06 -9999 0 -0.81 2 2
HSP90AA1 0.016 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.018 0.052 -9999 0 -10000 0 0
EGLN3 -0.13 0.3 -9999 0 -0.75 72 72
EGLN2 0.016 0 -9999 0 -10000 0 0
EGLN1 0.016 0 -9999 0 -10000 0 0
TP53 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.036 0.064 -9999 0 -0.8 2 2
ARNT 0.016 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.016 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.048 0.15 -9999 0 -0.43 32 32
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.069 0.25 -9999 0 -0.79 40 40
CDC42/GTP -0.043 0.1 -9999 0 -0.46 9 9
PLCG1 0.001 0.13 -9999 0 -0.47 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.016 0 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.042 0.1 -9999 0 -0.45 9 9
S1PR5 -0.014 0.15 -9999 0 -0.74 15 15
S1PR4 -0.007 0.12 -9999 0 -0.61 14 14
MAPK3 0.001 0.13 -9999 0 -0.47 9 9
MAPK1 0.001 0.13 -9999 0 -0.47 9 9
S1P/S1P5/Gi -0.016 0.14 -9999 0 -0.36 49 49
GNAI1 -0.012 0.13 -9999 0 -0.61 17 17
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.019 0.096 -9999 0 -0.49 15 15
RHOA 0.029 0.065 -9999 0 -10000 0 0
S1P/S1P4/Gi -0.011 0.13 -9999 0 -0.36 39 39
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.002 0.1 -9999 0 -0.76 7 7
S1P/S1P4/G12/G13 -0.012 0.063 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.02 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.075 0.078 -9999 0 -10000 0 0
ERC1 0.016 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.094 0.21 -9999 0 -0.56 63 63
NFKBIA 0.062 0 -9999 0 -10000 0 0
BIRC2 0.016 0 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
RIPK2 0.016 0 -9999 0 -10000 0 0
IKBKG -0.034 0.08 -9999 0 -10000 0 0
IKK complex/A20 -0.098 0.17 -9999 0 -0.62 19 19
NEMO/A20/RIP2 0.016 0 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
NEMO/ATM 0.023 0.099 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.025 0.06 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.001 0.027 -9999 0 -0.53 1 1
NOD2 -0.11 0.29 -9999 0 -0.75 63 63
NFKB1 0.02 0 -9999 0 -10000 0 0
RELA 0.02 0 -9999 0 -10000 0 0
MALT1 0.016 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.014 0.043 -9999 0 -0.81 1 1
TNF/TNFR1A -0.12 0.22 -9999 0 -0.53 85 85
TRAF6 0.014 0.043 -9999 0 -0.81 1 1
PRKCA -0.022 0.15 -9999 0 -0.64 22 22
CHUK 0.016 0 -9999 0 -10000 0 0
UBE2D3 0.016 0 -9999 0 -10000 0 0
TNF -0.15 0.31 -9999 0 -0.71 85 85
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.016 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.062 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
IKK complex -0.028 0.067 -9999 0 -10000 0 0
CYLD 0.016 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.041 0.097 -9999 0 -0.51 7 7
Signaling events mediated by HDAC Class III

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
EP300 0.014 0.043 -10000 0 -0.81 1 1
HDAC4 0.014 0.032 -10000 0 -0.61 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.021 0.073 0.58 5 -10000 0 5
CDKN1A -0.023 0.15 -10000 0 -0.97 9 9
KAT2B 0.014 0.043 -10000 0 -0.81 1 1
BAX 0.016 0 -10000 0 -10000 0 0
FOXO3 0.002 0.03 0.57 1 -10000 0 1
FOXO1 0.016 0 -10000 0 -10000 0 0
FOXO4 0.029 0.02 -10000 0 -0.36 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
TAT -0.003 0.089 -10000 0 -0.61 8 8
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.013 0.033 -10000 0 -0.63 1 1
PPARGC1A -0.18 0.33 -10000 0 -0.71 101 101
FHL2 -0.041 0.2 -10000 0 -0.7 30 30
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.002 0.04 -10000 0 -0.62 1 1
HIST2H4A 0.021 0.073 -10000 0 -0.59 5 5
SIRT1/FOXO3a 0.003 0.04 0.34 1 -0.55 1 2
SIRT1 0.003 0.053 -10000 0 -0.81 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.001 0.041 -10000 0 -0.53 1 1
SIRT1/Histone H1b -0.025 0.085 -10000 0 -0.53 2 2
apoptosis -0.002 0.036 0.53 1 -10000 0 1
SIRT1/PGC1A -0.12 0.21 -10000 0 -0.46 101 101
p53/SIRT1 0.009 0.074 0.44 9 -0.62 1 10
SIRT1/FOXO4 0.002 0.041 -10000 0 -0.52 1 1
FOXO1/FHL2/SIRT1 -0.03 0.12 -10000 0 -0.49 14 14
HIST1H1E -0.007 0.1 -10000 0 -0.38 17 17
SIRT1/p300 0.001 0.052 -10000 0 -0.62 2 2
muscle cell differentiation -0.001 0.046 0.54 2 -10000 0 2
TP53 0.005 0.033 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.002 0.037 -10000 0 -0.53 1 1
CREBBP 0.016 0 -10000 0 -10000 0 0
MEF2D 0.016 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.007 0.076 -10000 0 -0.46 9 9
ACSS2 0.026 0.045 -10000 0 -0.53 2 2
SIRT1/PCAF/MYOD 0.001 0.046 -10000 0 -0.54 2 2
ceramide signaling 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
MAP4K4 -0.037 0.17 -10000 0 -0.54 17 17
BAG4 0.005 0.095 -10000 0 -0.81 5 5
BAD 0.007 0.057 -10000 0 -10000 0 0
NFKBIA 0.016 0 -10000 0 -10000 0 0
BIRC3 -0.15 0.31 -10000 0 -0.73 84 84
BAX 0.007 0.057 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 -0.006 0.042 -10000 0 -0.12 17 17
IKBKB -0.025 0.16 -10000 0 -0.5 16 16
MAP2K2 0.022 0.059 -10000 0 -10000 0 0
MAP2K1 0.021 0.061 -10000 0 -10000 0 0
SMPD1 0.001 0.042 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.025 0.16 -10000 0 -0.52 16 16
MAP2K4 0.015 0.061 -10000 0 -0.44 1 1
protein ubiquitination -0.023 0.16 -10000 0 -0.51 16 16
EnzymeConsortium:2.7.1.37 0.026 0.065 -10000 0 -10000 0 0
response to UV 0 0.001 -10000 0 -10000 0 0
RAF1 0.015 0.06 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
mol:ceramide -0.003 0.059 -10000 0 -0.16 16 16
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.016 0 -10000 0 -10000 0 0
MAP3K1 0.006 0.063 -10000 0 -0.48 1 1
TRADD 0.016 0 -10000 0 -10000 0 0
RELA/p50 0.016 0 -10000 0 -10000 0 0
MAPK3 0.025 0.06 -10000 0 -10000 0 0
MAPK1 0.025 0.06 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD -0.037 0.17 -10000 0 -0.54 17 17
KSR1 0.007 0.059 -10000 0 -10000 0 0
MAPK8 0.02 0.073 -10000 0 -0.4 5 5
TRAF2 0.016 0.001 -10000 0 -10000 0 0
response to radiation 0 0.001 -10000 0 -10000 0 0
CHUK -0.025 0.16 -10000 0 -0.5 16 16
TNF R/SODD -0.008 0.071 -10000 0 -0.62 5 5
TNF -0.15 0.31 -10000 0 -0.71 85 85
CYCS 0.01 0.059 0.16 1 -0.25 1 2
IKBKG -0.025 0.16 -10000 0 -0.5 16 16
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.049 0.17 -10000 0 -0.57 17 17
RELA 0.016 0 -10000 0 -10000 0 0
RIPK1 0.016 0.001 -10000 0 -10000 0 0
AIFM1 0.011 0.058 0.16 1 -10000 0 1
TNF/TNF R/SODD -0.11 0.2 -10000 0 -0.53 47 47
TNFRSF1A 0.016 0.001 -10000 0 -10000 0 0
response to heat 0 0.001 -10000 0 -10000 0 0
CASP8 0.012 0.043 -10000 0 -10000 0 0
NSMAF -0.036 0.16 -10000 0 -0.53 17 17
response to hydrogen peroxide 0 0.001 -10000 0 -10000 0 0
BCL2 -0.006 0.12 -10000 0 -0.68 12 12
Paxillin-dependent events mediated by a4b1

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
CRKL 0.016 0 -10000 0 -10000 0 0
Rac1/GDP 0.005 0.017 -10000 0 -10000 0 0
DOCK1 0.011 0.06 -10000 0 -0.81 2 2
ITGA4 -0.04 0.18 -10000 0 -0.64 32 32
RAC1 0.016 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.11 0.23 -10000 0 -0.55 78 78
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.033 0.11 -10000 0 -0.53 5 5
alpha4/beta7 Integrin/Paxillin -0.086 0.18 -10000 0 -0.53 35 35
lamellipodium assembly 0.002 0.054 -10000 0 -0.62 2 2
PIK3CA 0.011 0.06 -10000 0 -0.81 2 2
PI3K -0.003 0.045 -10000 0 -0.62 2 2
ARF6 0.016 0 -10000 0 -10000 0 0
TLN1 0.016 0 -10000 0 -10000 0 0
PXN 0.03 0 -10000 0 -10000 0 0
PIK3R1 0.016 0 -10000 0 -10000 0 0
ARF6/GTP -0.024 0.08 -10000 0 -10000 0 0
cell adhesion -0.027 0.089 -10000 0 -0.44 5 5
CRKL/CBL 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.029 0.098 -10000 0 -0.48 5 5
ITGB1 0.016 0 -10000 0 -10000 0 0
ITGB7 -0.085 0.26 -10000 0 -0.73 51 51
ARF6/GDP 0.005 0.017 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.063 0.17 -10000 0 -0.64 18 18
p130Cas/Crk/Dock1 -0.003 0.039 -10000 0 -0.53 2 2
VCAM1 -0.054 0.21 -10000 0 -0.68 38 38
alpha4/beta1 Integrin/Paxillin/Talin -0.027 0.09 -10000 0 -0.45 5 5
alpha4/beta1 Integrin/Paxillin/GIT1 -0.027 0.09 -10000 0 -0.45 5 5
BCAR1 0.016 0 -10000 0 -10000 0 0
mol:GDP 0.027 0.089 0.44 5 -10000 0 5
CBL 0.016 0 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
GIT1 0.016 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.027 0.09 -10000 0 -0.45 5 5
Rac1/GTP 0.001 0.062 -10000 0 -0.72 2 2
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.039 0.12 -10000 0 -0.47 19 19
MAPK9 0.011 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.016 0.1 -10000 0 -0.45 20 20
GNB1/GNG2 -0.003 0.033 -10000 0 -0.38 3 3
GNB1 0.016 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.011 0 -10000 0 -10000 0 0
Gs family/GTP -0.041 0.13 -10000 0 -0.44 35 35
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 0.01 0.03 0.1 35 -10000 0 35
GNAL -0.052 0.22 -10000 0 -0.72 35 35
GNG2 0.011 0.055 -10000 0 -0.61 3 3
CRH -0.024 0.14 -10000 0 -0.61 20 20
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.048 -10000 0 -0.46 4 4
MAPK11 0.01 0.014 -10000 0 -0.26 1 1
PLK1 signaling events

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.001 0.063 0.23 25 -10000 0 25
BUB1B 0.015 0.07 -10000 0 -0.32 13 13
PLK1 0.018 0.027 -10000 0 -0.16 5 5
PLK1S1 0.017 0.015 -10000 0 -10000 0 0
KIF2A 0.025 0.045 -10000 0 -0.5 2 2
regulation of mitotic centrosome separation 0.018 0.027 -10000 0 -0.15 5 5
GOLGA2 0.016 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.05 0.15 -10000 0 -0.47 40 40
WEE1 0.022 0.04 -10000 0 -10000 0 0
cytokinesis -0.025 0.19 -10000 0 -0.55 35 35
PP2A-alpha B56 -0.051 0.19 -10000 0 -0.79 23 23
AURKA 0.017 0.024 -10000 0 -0.16 4 4
PICH/PLK1 -0.016 0.068 -10000 0 -0.43 6 6
CENPE 0.002 0.12 -10000 0 -0.44 23 23
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.025 0.045 -10000 0 -0.5 2 2
PPP2CA 0.016 0 -10000 0 -10000 0 0
FZR1 0.016 0 -10000 0 -10000 0 0
TPX2 0.006 0.056 -10000 0 -0.22 18 18
PAK1 0.015 0.001 -10000 0 -10000 0 0
SPC24 -0.044 0.21 -10000 0 -0.76 29 29
FBXW11 0.016 0 -10000 0 -10000 0 0
CLSPN 0 0.077 -10000 0 -0.26 26 26
GORASP1 0.016 0 -10000 0 -10000 0 0
metaphase 0 0.003 -10000 0 -0.018 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.01 0.015 -10000 0 -0.091 3 3
G2 phase of mitotic cell cycle 0 0.001 -10000 0 -10000 0 0
STAG2 0.016 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.002 0.009 -10000 0 -10000 0 0
spindle elongation 0.018 0.027 -10000 0 -0.15 5 5
ODF2 0.015 0.002 -10000 0 -10000 0 0
BUB1 -0.059 0.22 -10000 0 -0.88 23 23
TPT1 0.017 0.015 -10000 0 -0.13 1 1
CDC25C -0.008 0.1 -10000 0 -0.35 26 26
CDC25B 0.006 0.083 -10000 0 -0.64 6 6
SGOL1 -0.001 0.063 -10000 0 -0.23 25 25
RHOA 0.016 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.009 0.049 -10000 0 -0.49 1 1
CDC14B 0.01 0.058 -10000 0 -0.64 3 3
CDC20 0.004 0.089 -10000 0 -0.64 7 7
PLK1/PBIP1 -0.008 0.056 -10000 0 -0.47 5 5
mitosis 0 0.004 0.028 5 -0.029 1 6
FBXO5 0.025 0.022 -10000 0 -0.18 1 1
CDC2 0.001 0.003 -10000 0 -0.015 4 4
NDC80 -0.014 0.14 -10000 0 -0.7 16 16
metaphase plate congression 0.017 0.017 -10000 0 -10000 0 0
ERCC6L -0.014 0.067 -10000 0 -0.45 6 6
NLP/gamma Tubulin 0.015 0.016 -10000 0 -0.16 1 1
microtubule cytoskeleton organization 0.017 0.014 -10000 0 -0.13 1 1
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -10000 0 0
PPP1R12A 0.014 0.043 -10000 0 -0.82 1 1
interphase 0 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.049 0.14 -10000 0 -0.47 34 34
GRASP65/GM130/RAB1/GTP/PLK1 -0.001 0.011 -10000 0 -10000 0 0
RAB1A 0.016 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.023 0.034 -10000 0 -0.54 1 1
mitotic prometaphase 0 0.002 -10000 0 -0.015 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.035 -10000 0 -0.47 1 1
microtubule-based process -0.025 0.15 -10000 0 -0.44 43 43
Golgi organization 0.018 0.027 -10000 0 -0.15 5 5
Cohesin/SA2 -0.003 0.017 -10000 0 -10000 0 0
PPP1CB/MYPT1 -0.002 0.032 -10000 0 -0.63 1 1
KIF20A -0.068 0.24 -10000 0 -0.73 43 43
APC/C/CDC20 0.019 0.063 -10000 0 -0.41 7 7
PPP2R1A 0.016 0 -10000 0 -10000 0 0
chromosome segregation -0.008 0.055 -10000 0 -0.46 5 5
PRC1 0.012 0.053 -10000 0 -0.71 2 2
ECT2 0.025 0.046 -10000 0 -0.5 2 2
C13orf34 0.023 0.035 -10000 0 -0.55 1 1
NUDC 0.017 0.017 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.015 0.069 -10000 0 -0.31 13 13
spindle assembly 0.019 0.022 -10000 0 -0.21 1 1
spindle stabilization 0.017 0.014 -10000 0 -10000 0 0
APC/C/HCDH1 0.018 0.051 -10000 0 -0.55 3 3
MKLP2/PLK1 -0.025 0.15 -10000 0 -0.44 43 43
CCNB1 0.016 0.002 -10000 0 -10000 0 0
PPP1CB 0.016 0.001 -10000 0 -10000 0 0
BTRC 0.016 0 -10000 0 -10000 0 0
ROCK2 0.01 0.1 -10000 0 -0.52 13 13
TUBG1 0.017 0.015 -10000 0 -0.13 1 1
G2/M transition of mitotic cell cycle -0.01 0.048 -10000 0 -0.48 1 1
MLF1IP 0.007 0.072 -10000 0 -0.61 5 5
INCENP 0.009 0.069 -10000 0 -0.75 3 3
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.002 0.11 -10000 0 -0.67 10 10
positive regulation of NF-kappaB transcription factor activity -0.023 0.11 -10000 0 -0.54 16 16
MAP2K4 0.048 0.056 -10000 0 -0.45 1 1
IKBKB 0.016 0 -10000 0 -10000 0 0
TNFRSF10B 0.016 0 -10000 0 -10000 0 0
TNFRSF10A -0.021 0.17 -10000 0 -0.81 17 17
SMPD1 -0.006 0.035 -10000 0 -0.29 3 3
IKBKG 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.003 0.1 -10000 0 -0.81 6 6
TRAIL/TRAILR2 -0.013 0.08 -10000 0 -0.49 10 10
TRAIL/TRAILR3 -0.042 0.16 -10000 0 -0.59 27 27
TRAIL/TRAILR1 -0.041 0.15 -10000 0 -0.59 26 26
TRAIL/TRAILR4 -0.023 0.11 -10000 0 -0.54 16 16
TRAIL/TRAILR1/DAP3/GTP -0.032 0.12 -10000 0 -0.47 26 26
IKK complex -0.008 0.031 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0.016 0.085 -10000 0 -0.49 10 10
MAP3K1 -0.011 0.046 -10000 0 -0.49 1 1
TRAILR4 (trimer) 0.003 0.1 -10000 0 -0.81 6 6
TRADD 0.016 0 -10000 0 -10000 0 0
TRAILR1 (trimer) -0.021 0.17 -10000 0 -0.81 17 17
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.025 0.089 -10000 0 -0.66 1 1
CFLAR 0.016 0 -10000 0 -10000 0 0
MAPK1 0.016 0.085 -10000 0 -0.49 10 10
TRAIL/TRAILR1/FADD/TRADD/RIP -0.029 0.11 -10000 0 -0.47 19 19
mol:ceramide -0.006 0.035 -10000 0 -0.28 3 3
FADD 0.016 0 -10000 0 -10000 0 0
MAPK8 0.051 0.077 -10000 0 -0.52 3 3
TRAF2 0.016 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.023 0.18 -10000 0 -0.81 18 18
CHUK 0.016 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.035 0.13 -10000 0 -0.56 19 19
DAP3 0.016 0 -10000 0 -10000 0 0
CASP10 -0.018 0.089 0.32 2 -0.53 5 7
JNK cascade -0.023 0.11 -10000 0 -0.54 16 16
TRAIL (trimer) -0.002 0.11 -10000 0 -0.67 10 10
TNFRSF10C -0.023 0.18 -10000 0 -0.81 18 18
TRAIL/TRAILR1/DAP3/GTP/FADD -0.03 0.11 -10000 0 -0.48 19 19
TRAIL/TRAILR2/FADD -0.011 0.068 -10000 0 -0.53 3 3
cell death -0.006 0.035 -10000 0 -0.28 3 3
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.042 0.043 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.016 0 -10000 0 -10000 0 0
CASP8 0.001 0.023 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.009 0.056 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.016 0 -10000 0 -10000 0 0
mol:Halofuginone 0.007 0.001 -10000 0 -10000 0 0
ITGA1 -0.003 0.12 -10000 0 -0.77 9 9
CDKN1A 0.015 0.089 -10000 0 -0.43 9 9
PRL-3/alpha Tubulin -0.003 0.039 -10000 0 -0.53 2 2
mol:Ca2+ -0.09 0.21 0.28 1 -0.57 60 61
AGT -0.1 0.28 -10000 0 -0.74 60 60
CCNA2 0.003 0.15 -10000 0 -0.9 2 2
TUBA1B 0.016 0 -10000 0 -10000 0 0
EGR1 -0.019 0.16 -10000 0 -0.52 35 35
CDK2/Cyclin E1 -0.019 0.063 -10000 0 -10000 0 0
MAPK3 0.027 0.041 -10000 0 -0.53 2 2
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.027 0.041 -10000 0 -0.53 2 2
PTP4A1 0.007 0.13 -10000 0 -0.8 1 1
PTP4A3 0.012 0.053 -10000 0 -0.71 2 2
PTP4A2 0.016 0 -10000 0 -10000 0 0
ITGB1 0.027 0.041 -10000 0 -0.53 2 2
SRC 0.012 0.053 -10000 0 -0.71 2 2
RAC1 0.025 0.061 -10000 0 -0.43 1 1
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.008 0.16 -10000 0 -0.72 5 5
RABGGTA 0.016 0 -10000 0 -10000 0 0
BCAR1 0.002 0.028 0.38 2 -10000 0 2
RHOC 0.025 0.061 -10000 0 -0.43 1 1
RHOA 0.025 0.061 -10000 0 -0.43 1 1
cell motility 0.029 0.065 -10000 0 -0.43 1 1
PRL-1/alpha Tubulin 0.014 0.12 -10000 0 -0.75 1 1
PRL-3/alpha1 Integrin -0.017 0.097 -10000 0 -0.57 11 11
ROCK1 0.029 0.065 -10000 0 -0.43 1 1
RABGGTB 0.016 0 -10000 0 -10000 0 0
CDK2 0.016 0 -10000 0 -10000 0 0
mitosis 0.007 0.13 -10000 0 -0.79 1 1
ATF5 -0.024 0.15 -10000 0 -0.61 24 24
Aurora A signaling

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
Aurora A/GADD45A -0.013 0.099 -9999 0 -0.53 10 10
BIRC5 -0.054 0.22 -9999 0 -0.72 36 36
NFKBIA 0.04 0.031 -9999 0 -10000 0 0
CPEB1 -0.09 0.28 -9999 0 -0.8 49 49
AKT1 0.04 0.031 -9999 0 -10000 0 0
NDEL1 0.016 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.002 0.037 -9999 0 -10000 0 0
NDEL1/TACC3 -0.002 0.049 -9999 0 -0.47 2 2
GADD45A -0.013 0.15 -9999 0 -0.76 14 14
GSK3B 0.016 0.011 -9999 0 -10000 0 0
PAK1/Aurora A 0.006 0.032 -9999 0 -10000 0 0
MDM2 0.016 0 -9999 0 -10000 0 0
JUB 0.003 0.1 -9999 0 -0.81 6 6
TPX2 -0.004 0.13 -9999 0 -0.5 24 24
TP53 0.007 0.027 -9999 0 -10000 0 0
DLG7 0.005 0.032 -9999 0 -10000 0 0
AURKAIP1 0.013 0.045 -9999 0 -0.61 2 2
ARHGEF7 0.016 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0 0.054 -9999 0 -0.5 2 2
G2/M transition of mitotic cell cycle 0.002 0.037 -9999 0 -10000 0 0
AURKA 0.032 0.038 -9999 0 -10000 0 0
AURKB -0.036 0.1 -9999 0 -0.37 27 27
CDC25B 0 0.053 -9999 0 -0.4 2 2
G2/M transition checkpoint -0.004 0.074 -9999 0 -0.55 6 6
mRNA polyadenylation -0.059 0.17 -9999 0 -0.49 47 47
Aurora A/CPEB -0.06 0.17 -9999 0 -0.5 47 47
Aurora A/TACC1/TRAP/chTOG 0.004 0.026 -9999 0 -10000 0 0
BRCA1 0.013 0.045 -9999 0 -0.61 2 2
centrosome duplication 0.006 0.032 -9999 0 -10000 0 0
regulation of centrosome cycle -0.004 0.046 -9999 0 -0.46 2 2
spindle assembly 0 0.018 -9999 0 -10000 0 0
TDRD7 0.016 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.037 0.11 -9999 0 -0.44 15 15
CENPA -0.032 0.094 -9999 0 -0.37 21 21
Aurora A/PP2A 0.006 0.032 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.047 0.027 -9999 0 -10000 0 0
negative regulation of DNA binding 0.039 0.021 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.016 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.004 0.075 -9999 0 -0.55 6 6
mitotic prometaphase 0.009 0.028 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.038 -9999 0 -10000 0 0
TACC1 0.016 0 -9999 0 -10000 0 0
TACC3 0.008 0.071 -9999 0 -0.61 5 5
Aurora A/Antizyme1 0.003 0.038 -9999 0 -10000 0 0
Aurora A/RasGAP 0.006 0.032 -9999 0 -10000 0 0
OAZ1 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.016 0.011 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.004 0.13 -9999 0 -0.5 24 24
PPP2R5D 0.016 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.018 0.11 -9999 0 -0.48 11 11
PAK1 0.016 0 -9999 0 -10000 0 0
CKAP5 0.016 0 -9999 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0 0.093 -10000 0 -1.5 1 1
oxygen homeostasis 0.014 0.019 -10000 0 -10000 0 0
TCEB2 0.014 0.032 -10000 0 -0.61 1 1
TCEB1 0.016 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.039 0.095 -10000 0 -0.51 4 4
EPO 0.13 0.24 -10000 0 -0.71 4 4
FIH (dimer) 0.031 0.019 -10000 0 -10000 0 0
APEX1 0.028 0.017 -10000 0 -10000 0 0
SERPINE1 0.088 0.32 -10000 0 -0.84 14 14
FLT1 -0.036 0.25 -10000 0 -1.3 13 13
ADORA2A 0.12 0.27 -10000 0 -0.8 8 8
germ cell development 0.12 0.27 -10000 0 -0.8 8 8
SLC11A2 0.13 0.27 -10000 0 -0.8 7 7
BHLHE40 0.1 0.33 -10000 0 -0.86 19 19
HIF1AN 0.031 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.038 0.11 -10000 0 -0.52 7 7
ETS1 0.027 0.072 -10000 0 -0.74 3 3
CITED2 -0.012 0.12 -10000 0 -1.2 3 3
KDR -0.049 0.28 -10000 0 -1.4 16 16
PGK1 0.13 0.27 -10000 0 -0.8 7 7
SIRT1 0.014 0.043 -10000 0 -0.81 1 1
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.13 0.3 -10000 0 -0.94 9 9
EPAS1 0.06 0.18 -10000 0 -0.46 8 8
SP1 0.026 0.003 -10000 0 -10000 0 0
ABCG2 0.1 0.33 -10000 0 -0.93 16 16
EFNA1 0.13 0.27 -10000 0 -0.8 7 7
FXN 0.13 0.26 -10000 0 -0.77 7 7
POU5F1 0.12 0.28 -10000 0 -0.85 8 8
neuron apoptosis -0.13 0.29 0.89 9 -10000 0 9
EP300 0.014 0.043 -10000 0 -0.81 1 1
EGLN3 -0.11 0.3 -10000 0 -0.74 72 72
EGLN2 0.03 0.018 -10000 0 -10000 0 0
EGLN1 0.031 0.019 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.004 0.052 -10000 0 -0.7 2 2
VHL 0.011 0.06 -10000 0 -0.81 2 2
ARNT 0.028 0.017 -10000 0 -10000 0 0
SLC2A1 0.13 0.26 -10000 0 -0.78 8 8
TWIST1 0.087 0.33 -10000 0 -0.87 17 17
ELK1 0.025 0.009 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.036 0.11 -10000 0 -0.52 6 6
VEGFA 0.13 0.28 -10000 0 -0.87 7 7
CREBBP 0.016 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.016 0 -10000 0 -10000 0 0
NFATC1 0.061 0.061 -10000 0 -10000 0 0
NFATC2 0.021 0.075 -10000 0 -0.36 5 5
NFATC3 0.025 0.02 -10000 0 -10000 0 0
YWHAE 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.001 0.097 -10000 0 -0.43 6 6
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.061 0.13 -10000 0 -0.52 13 13
BCL2/BAX -0.016 0.089 -10000 0 -0.5 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.002 -10000 0 -10000 0 0
CaM/Ca2+ -0.001 0.002 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
MAPK14 0.014 0.006 -10000 0 -10000 0 0
BAD 0.016 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.009 0.092 -10000 0 -0.47 3 3
Calcineurin A alpha-beta B1/BCL2 -0.006 0.12 -10000 0 -0.68 12 12
FKBP8 0.016 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.009 0.09 0.46 3 -10000 0 3
KPNB1 0.016 0 -10000 0 -10000 0 0
KPNA2 0.016 0 -10000 0 -10000 0 0
XPO1 0.016 0.001 -10000 0 -10000 0 0
SFN -0.25 0.37 -10000 0 -0.74 133 133
MAP3K8 0.01 0.054 -10000 0 -0.72 2 2
NFAT4/CK1 alpha -0.002 0.026 -10000 0 -0.46 1 1
MEF2D/NFAT1/Cbp/p300 -0.054 0.11 -10000 0 -0.69 3 3
CABIN1 0.001 0.098 -10000 0 -0.44 6 6
CALM1 0.014 0.006 -10000 0 -10000 0 0
RAN 0.016 0.001 -10000 0 -10000 0 0
MAP3K1 0.014 0.043 -10000 0 -0.81 1 1
CAMK4 -0.059 0.22 -10000 0 -0.67 41 41
mol:Ca2+ -0.002 0.007 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.004 0.045 -10000 0 -0.5 3 3
YWHAB 0.016 0 -10000 0 -10000 0 0
MAPK8 0.005 0.085 -10000 0 -0.81 4 4
MAPK9 0.016 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
FKBP1A 0.016 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.006 0.041 -10000 0 -10000 0 0
PRKCH 0.014 0.043 -10000 0 -0.81 1 1
CABIN1/Cbp/p300 -0.001 0.033 -10000 0 -0.64 1 1
CASP3 0.014 0.006 -10000 0 -10000 0 0
PIM1 -0.001 0.1 -10000 0 -0.63 10 10
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.005 0.028 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.021 0.11 -10000 0 -10000 0 0
PRKCB -0.1 0.26 -10000 0 -0.66 66 66
PRKCE 0.012 0.053 -10000 0 -0.71 2 2
JNK2/NFAT4 0.002 0.016 -10000 0 -10000 0 0
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.016 0 -10000 0 -10000 0 0
NUP214 0.016 0.001 -10000 0 -10000 0 0
PRKCZ 0.012 0.033 -10000 0 -0.62 1 1
PRKCA -0.022 0.15 -10000 0 -0.64 22 22
PRKCG -0.017 0.12 -10000 0 -0.61 15 15
PRKCQ 0.011 0.06 -10000 0 -0.81 2 2
FKBP38/BCL2 -0.016 0.089 -10000 0 -0.5 12 12
EP300 0.013 0.043 -10000 0 -0.82 1 1
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
NFATc/JNK1 0.054 0.078 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.022 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.047 0.14 -10000 0 -0.43 41 41
NFATc/ERK1 0.067 0.058 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.061 0.13 -10000 0 -0.52 13 13
NR4A1 -0.03 0.24 -10000 0 -0.54 67 67
GSK3B 0.014 0.006 -10000 0 -10000 0 0
positive T cell selection 0.025 0.019 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.016 0.043 -10000 0 -10000 0 0
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
PRKACA 0.014 0.006 -10000 0 -10000 0 0
AKAP5 0.01 0.062 -10000 0 -0.68 3 3
MEF2D 0.015 0.004 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.016 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.059 0.063 -10000 0 -10000 0 0
CREBBP 0.015 0.004 -10000 0 -10000 0 0
BCL2 -0.006 0.12 -10000 0 -0.68 12 12
Retinoic acid receptors-mediated signaling

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
HDAC1 0.016 0 -10000 0 -10000 0 0
HDAC3 0.016 0 -10000 0 -10000 0 0
VDR 0.008 0.08 -10000 0 -0.76 4 4
Cbp/p300/PCAF -0.003 0.039 -10000 0 -0.53 2 2
EP300 0.014 0.043 -10000 0 -0.81 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.049 0.043 -10000 0 -0.42 1 1
KAT2B 0.014 0.043 -10000 0 -0.81 1 1
MAPK14 0.016 0 -10000 0 -10000 0 0
AKT1 0.041 0.065 0.25 17 -0.33 1 18
RAR alpha/9cRA/Cyclin H -0.018 0.058 -10000 0 -0.43 2 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.045 0.043 -10000 0 -0.35 2 2
CDC2 0.001 0.002 -10000 0 -10000 0 0
response to UV 0.001 0.003 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.02 0.083 -10000 0 -0.73 4 4
NCOR2 0.016 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.006 0.06 -10000 0 -0.59 4 4
RXRs/RARs/NRIP1/9cRA 0.027 0.12 -10000 0 -0.65 5 5
NCOA2 -0.061 0.24 -10000 0 -0.81 35 35
NCOA3 0.016 0 -10000 0 -10000 0 0
NCOA1 0.016 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.008 0.08 -10000 0 -0.76 4 4
RARG 0.017 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.017 0.002 -10000 0 -10000 0 0
MAPK1 0.016 0 -10000 0 -10000 0 0
MAPK8 0.008 0.085 -10000 0 -0.81 4 4
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.047 0.11 -10000 0 -0.59 8 8
RARA 0.012 0.074 -10000 0 -0.36 7 7
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.017 0.11 -10000 0 -0.5 6 6
PRKCA -0.018 0.15 -10000 0 -0.63 22 22
RXRs/RARs/NRIP1/9cRA/HDAC1 0.011 0.14 -10000 0 -0.66 6 6
RXRG -0.075 0.22 -10000 0 -0.51 66 66
RXRA 0.02 0.077 -10000 0 -0.39 5 5
RXRB 0.004 0.089 -10000 0 -0.44 3 3
VDR/Vit D3/DNA -0.006 0.06 -10000 0 -0.59 4 4
RBP1 -0.066 0.23 -10000 0 -0.7 43 43
CRBP1/9-cic-RA -0.061 0.17 -10000 0 -0.54 43 43
RARB 0.015 0.053 -10000 0 -0.71 2 2
PRKCG -0.013 0.12 -10000 0 -0.6 15 15
MNAT1 0.016 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.031 0.12 -10000 0 -0.59 4 4
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.036 0.099 -10000 0 -0.52 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.06 -10000 0 -0.35 3 3
RXRs/RARs/NRIP1/9cRA/HDAC3 0.011 0.14 -10000 0 -0.66 6 6
positive regulation of DNA binding -0.017 0.055 -10000 0 -0.4 2 2
NRIP1 0.006 0.17 -10000 0 -1.2 4 4
RXRs/RARs 0.004 0.13 -10000 0 -0.57 6 6
RXRs/RXRs/DNA/9cRA -0.047 0.11 -10000 0 -0.55 7 7
PRKACA 0.016 0 -10000 0 -10000 0 0
CDK7 0.016 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.009 0.034 -10000 0 -10000 0 0
CCNH 0.016 0 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.037 0.037 -10000 0 -0.32 4 4
epithelial cell differentiation -0.002 0.033 -10000 0 -0.45 2 2
CYFIP2 0.007 0.085 -10000 0 -0.81 4 4
ENAH 0.084 0.042 -10000 0 -10000 0 0
EGFR -0.02 0.17 -10000 0 -0.79 17 17
EPHA2 0.007 0.085 -10000 0 -0.81 4 4
MYO6 0.048 0.035 -10000 0 -10000 0 0
CTNNB1 0.016 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.006 0.054 -10000 0 -0.53 4 4
AQP5 -0.11 0.21 -10000 0 -0.58 60 60
CTNND1 0.016 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.047 0.034 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.094 0.21 -10000 0 -0.85 1 1
EGF -0.11 0.26 -10000 0 -0.65 70 70
NCKAP1 0.016 0 -10000 0 -10000 0 0
AQP3 -0.087 0.19 -10000 0 -0.58 48 48
cortical microtubule organization -0.002 0.033 -10000 0 -0.45 2 2
GO:0000145 0.046 0.032 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.002 0.033 -10000 0 -0.46 2 2
MLLT4 0.016 0 -10000 0 -10000 0 0
ARF6/GDP -0.005 0.043 -10000 0 -10000 0 0
ARF6 0.016 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.005 0.049 -10000 0 -0.48 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.058 0.048 -10000 0 -10000 0 0
PVRL2 0.016 0 -10000 0 -10000 0 0
ZYX 0.048 0.035 -10000 0 -10000 0 0
ARF6/GTP -0.005 0.045 -10000 0 -10000 0 0
CDH1 0.011 0.06 -10000 0 -0.81 2 2
EGFR/EGFR/EGF/EGF -0.075 0.15 -10000 0 -0.71 6 6
RhoA/GDP -0.002 0.03 -10000 0 -10000 0 0
actin cytoskeleton organization 0.056 0.033 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.011 0.06 -10000 0 -0.81 2 2
GIT1 0.016 0 -10000 0 -10000 0 0
IGF1R 0.011 0.06 -10000 0 -0.81 2 2
IGF1 -0.14 0.29 -10000 0 -0.68 86 86
DIAPH1 -0.008 0.072 -10000 0 -0.7 4 4
Wnt receptor signaling pathway 0.002 0.033 0.45 2 -10000 0 2
RHOA 0.016 0 -10000 0 -10000 0 0
RhoA/GTP -0.005 0.043 -10000 0 -10000 0 0
CTNNA1 0.016 0 -10000 0 -10000 0 0
VCL 0.056 0.034 -10000 0 -10000 0 0
EFNA1 0.016 0 -10000 0 -10000 0 0
LPP 0.048 0.072 -10000 0 -0.57 1 1
Ephrin A1/EPHA2 -0.006 0.051 -10000 0 -10000 0 0
SEC6/SEC8 -0.002 0.026 -10000 0 -10000 0 0
MGAT3 -0.096 0.22 -10000 0 -0.88 1 1
HGF/MET -0.096 0.18 -10000 0 -0.76 6 6
HGF -0.077 0.25 -10000 0 -0.72 48 48
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.037 0.037 -10000 0 -10000 0 0
actin cable formation 0.1 0.047 -10000 0 -10000 0 0
KIAA1543 0.05 0.064 -10000 0 -10000 0 0
KIFC3 0.048 0.035 -10000 0 -10000 0 0
NCK1 0.016 0 -10000 0 -10000 0 0
EXOC3 0.016 0 -10000 0 -10000 0 0
ACTN1 0.043 0.057 -10000 0 -10000 0 0
NCK1/GIT1 0 0 -10000 0 -10000 0 0
mol:GDP -0.002 0.033 -10000 0 -0.45 2 2
EXOC4 0.016 0 -10000 0 -10000 0 0
STX4 0.048 0.035 -10000 0 -0.43 2 2
PIP5K1C 0.048 0.035 -10000 0 -10000 0 0
LIMA1 0.011 0.06 -10000 0 -0.81 2 2
ABI1 0.016 0 -10000 0 -10000 0 0
ROCK1 -0.005 0.037 -10000 0 -10000 0 0
adherens junction assembly 0.072 0.059 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.075 0.14 -10000 0 -0.84 1 1
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -10000 0 -10000 0 0
MET -0.085 0.27 -10000 0 -0.81 46 46
PLEKHA7 0.042 0.062 -10000 0 -0.43 4 4
mol:GTP -0.005 0.049 -10000 0 -0.48 4 4
establishment of epithelial cell apical/basal polarity 0.081 0.031 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.037 0.037 -10000 0 -0.32 4 4
regulation of cell-cell adhesion 0.056 0.033 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.037 0.037 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.075 0.14 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.002 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.075 0.14 -9999 0 -0.79 3 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.009 0.017 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.039 0.069 -9999 0 -0.36 3 3
CaM/Ca2+ -0.068 0.12 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.071 0.15 -9999 0 -0.63 4 4
AKT1 -0.06 0.11 -9999 0 -10000 0 0
MAP2K1 -0.014 0.14 -9999 0 -10000 0 0
MAP3K11 -0.026 0.15 -9999 0 -10000 0 0
IFNGR1 0.011 0.013 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.059 0.14 -9999 0 -0.58 18 18
Rap1/GTP -0.048 0.087 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.08 0.14 -9999 0 -10000 0 0
CEBPB 0.014 0.16 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.1 0.21 -9999 0 -1.3 6 6
STAT1 -0.039 0.17 -9999 0 -0.64 4 4
CALM1 0.016 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.15 0.29 -9999 0 -0.66 95 95
PIK3CA 0.012 0.06 -9999 0 -0.81 2 2
STAT1 (dimer)/PIAS1 -0.071 0.14 -9999 0 -0.6 4 4
CEBPB/PTGES2/Cbp/p300 -0.039 0.068 -9999 0 -10000 0 0
mol:Ca2+ -0.075 0.13 -9999 0 -10000 0 0
MAPK3 0.004 0.13 -9999 0 -10000 0 0
STAT1 (dimer) -0.051 0.094 -9999 0 -0.53 3 3
MAPK1 0.004 0.13 -9999 0 -10000 0 0
JAK2 0.011 0.013 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
JAK1 0.011 0.013 -9999 0 -10000 0 0
CAMK2D 0.012 0.06 -9999 0 -0.81 2 2
DAPK1 0.008 0.19 -9999 0 -0.66 22 22
SMAD7 0.036 0.071 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.06 0.11 -9999 0 -10000 0 0
PI3K -0.067 0.12 -9999 0 -10000 0 0
IFNG -0.15 0.29 -9999 0 -0.66 95 95
apoptosis 0.004 0.14 -9999 0 -0.44 22 22
CAMK2G 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.045 0.19 -9999 0 -0.69 31 31
CAMK2B -0.005 0.13 -9999 0 -0.79 10 10
FRAP1 -0.003 0.13 -9999 0 -10000 0 0
PRKCD -0.007 0.14 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.039 0.069 -9999 0 -0.36 3 3
PTPN2 0.016 0 -9999 0 -10000 0 0
EP300 0.014 0.042 -9999 0 -0.81 1 1
IRF1 0 0.18 -9999 0 -0.63 13 13
STAT1 (dimer)/PIASy -0.069 0.14 -9999 0 -0.6 4 4
SOCS1 -0.034 0.22 -9999 0 -1.6 6 6
mol:GDP -0.058 0.1 -9999 0 -10000 0 0
CASP1 0.031 0.087 -9999 0 -0.33 9 9
PTGES2 0.016 0 -9999 0 -10000 0 0
IRF9 0.042 0.069 -9999 0 -0.36 2 2
mol:PI-3-4-5-P3 -0.065 0.12 -9999 0 -10000 0 0
RAP1/GDP -0.048 0.088 -9999 0 -10000 0 0
CBL -0.027 0.15 -9999 0 -10000 0 0
MAP3K1 -0.027 0.15 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PIAS4 0.016 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.039 0.069 -9999 0 -0.36 3 3
PTPN11 -0.038 0.16 -9999 0 -10000 0 0
CREBBP 0.016 0.001 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.034 0.058 -9999 0 -0.53 4 4
SNTA1 -0.012 0.13 -9999 0 -0.61 17 17
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.033 0.062 -9999 0 -0.53 4 4
MAPK12 0.021 0.091 -9999 0 -0.52 5 5
CCND1 0.016 0.061 -9999 0 -0.45 4 4
p38 gamma/SNTA1 0.012 0.11 -9999 0 -0.5 6 6
MAP2K3 0.016 0 -9999 0 -10000 0 0
PKN1 0.016 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.021 0.09 -9999 0 -0.51 5 5
MAP2K6 0.015 0.087 -9999 0 -0.41 14 14
MAPT 0.008 0.094 -9999 0 -0.44 8 8
MAPK13 0.023 0.067 -9999 0 -0.62 4 4
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.018 0.039 -9999 0 -0.35 4 4
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.017 0.088 -9999 0 -0.47 14 14
TRAF2/ASK1 -0.019 0.099 -9999 0 -0.54 13 13
ATM 0.014 0.043 -9999 0 -0.81 1 1
MAP2K3 0.027 0.088 -9999 0 -0.81 2 2
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.017 0.12 -9999 0 -0.48 14 14
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G -0.019 0.15 -9999 0 -0.64 20 20
TXN 0.01 0.014 -9999 0 -0.26 1 1
CALM1 0.016 0 -9999 0 -10000 0 0
GADD45A -0.013 0.15 -9999 0 -0.76 14 14
GADD45B -0.031 0.17 -9999 0 -0.66 26 26
MAP3K1 0.014 0.043 -9999 0 -0.81 1 1
MAP3K6 0.011 0.06 -9999 0 -0.81 2 2
MAP3K7 0.016 0 -9999 0 -10000 0 0
MAP3K4 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.025 0.12 -9999 0 -0.62 15 15
TAK1/TAB family 0 0.014 -9999 0 -0.22 1 1
RAC1/OSM/MEKK3 0 0 -9999 0 -10000 0 0
TRAF2 0.016 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.012 0.05 -9999 0 -0.55 2 2
TRAF6 0.01 0.024 -9999 0 -0.46 1 1
RAC1 0.016 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.005 0.13 -9999 0 -0.79 10 10
CCM2 0.016 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.014 0.085 -9999 0 -0.53 10 10
MAPK11 0.014 0.032 -9999 0 -0.61 1 1
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.029 0.12 -9999 0 -0.53 21 21
OSM/MEKK3 0 0 -9999 0 -10000 0 0
TAOK1 -0.027 0.15 -9999 0 -0.46 39 39
TAOK2 0.021 0.024 -9999 0 -0.44 1 1
TAOK3 0.021 0.024 -9999 0 -0.44 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.016 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 -0.013 0.15 -9999 0 -0.81 13 13
MAP3K10 0.016 0 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
TRX/ASK1 0 0.1 -9999 0 -0.54 13 13
GADD45/MTK1/MTK1 -0.057 0.15 -9999 0 -0.54 25 25
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.03 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -10000 0 -10000 0 0
CDKN1B 0.046 0.033 -10000 0 -0.5 1 1
CDKN1A 0.035 0.079 -10000 0 -0.44 10 10
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.014 0.043 -10000 0 -0.81 1 1
FOXO3 0.046 0.033 -10000 0 -0.5 1 1
AKT1 -0.003 0.03 -10000 0 -0.53 1 1
BAD 0.016 0 -10000 0 -10000 0 0
AKT3 0.02 0.034 -10000 0 -0.44 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.046 0.033 -10000 0 -0.5 1 1
AKT1/ASK1 -0.017 0.087 -10000 0 -0.45 13 13
BAD/YWHAZ 0 0 -10000 0 -10000 0 0
RICTOR 0.016 0 -10000 0 -10000 0 0
RAF1 0.016 0 -10000 0 -10000 0 0
JNK cascade 0.016 0.083 0.44 13 -10000 0 13
TSC1 0.046 0.033 -10000 0 -0.5 1 1
YWHAZ 0.016 0 -10000 0 -10000 0 0
AKT1/RAF1 0.045 0.032 -10000 0 -0.5 1 1
EP300 0.014 0.043 -10000 0 -0.81 1 1
mol:GDP -0.003 0.03 -10000 0 -0.52 1 1
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.045 0.037 -10000 0 -0.5 1 1
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.021 0.066 -10000 0 -0.39 8 8
MAP3K5 -0.013 0.15 -10000 0 -0.81 13 13
MAPKAP1 0.016 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.001 0.083 0.37 1 -10000 0 1
YWHAH 0.016 0 -10000 0 -10000 0 0
AKT1S1 0.046 0.033 -10000 0 -0.5 1 1
CASP9 0.046 0.033 -10000 0 -0.5 1 1
YWHAB 0.016 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.053 0.031 -10000 0 -0.46 1 1
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 -0.005 0.051 -10000 0 -0.53 3 3
YWHAE 0.016 0 -10000 0 -10000 0 0
SRC 0.012 0.053 -10000 0 -0.71 2 2
AKT2/p21CIP1 -0.014 0.072 -10000 0 -0.42 10 10
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.023 0.01 -10000 0 -10000 0 0
CHUK 0.046 0.033 -10000 0 -0.5 1 1
BAD/BCL-XL 0.062 0.031 -10000 0 -0.45 1 1
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0.016 0.046 -10000 0 -0.31 7 7
FOXO1-3a-4/14-3-3 family 0.013 0.095 -10000 0 -0.55 1 1
PDPK1 0.011 0.06 -10000 0 -0.81 2 2
MDM2 0.046 0.033 -10000 0 -0.5 1 1
MAPKKK cascade -0.044 0.032 0.49 1 -10000 0 1
MDM2/Cbp/p300 -0.003 0.031 -10000 0 -0.44 1 1
TSC1/TSC2 0.054 0.036 -10000 0 -0.48 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.03 -10000 0 -0.42 1 1
glucose import -0.028 0.16 -10000 0 -0.48 19 19
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.04 0.02 -10000 0 -0.29 1 1
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.028 0.16 -10000 0 -0.49 19 19
GSK3A 0.046 0.033 -10000 0 -0.5 1 1
FOXO1 0.046 0.033 -10000 0 -0.5 1 1
GSK3B 0.046 0.033 -10000 0 -0.5 1 1
SFN -0.25 0.37 -10000 0 -0.74 133 133
G1/S transition of mitotic cell cycle 0.055 0.032 -10000 0 -0.48 1 1
p27Kip1/14-3-3 family -0.02 0.12 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
KPNA1 0.016 0 -10000 0 -10000 0 0
HSP90AA1 0.016 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
RHEB 0.016 0 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.041 0.014 -9999 0 -10000 0 0
PLK1 0.08 0.19 -9999 0 -0.87 3 3
CDKN1B 0.17 0.086 -9999 0 -0.38 1 1
FOXO3 0.087 0.17 -9999 0 -0.59 6 6
KAT2B 0.023 0.047 -9999 0 -0.82 1 1
FOXO1/SIRT1 0.021 0.045 -9999 0 -0.46 1 1
CAT 0.087 0.19 -9999 0 -1.2 3 3
CTNNB1 0.016 0 -9999 0 -10000 0 0
AKT1 0.029 0.017 -9999 0 -10000 0 0
FOXO1 0.046 0.015 -9999 0 -10000 0 0
MAPK10 0.049 0.03 -9999 0 -0.46 1 1
mol:GTP 0.003 0.002 -9999 0 -10000 0 0
FOXO4 0.13 0.068 -9999 0 -0.45 2 2
response to oxidative stress 0.013 0.02 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.013 0.11 -9999 0 -0.52 2 2
XPO1 0.017 0.001 -9999 0 -10000 0 0
EP300 0.015 0.043 -9999 0 -0.81 1 1
BCL2L11 0.041 0.039 -9999 0 -10000 0 0
FOXO1/SKP2 0.047 0.029 -9999 0 -0.46 1 1
mol:GDP 0.013 0.02 -9999 0 -10000 0 0
RAN 0.018 0.003 -9999 0 -10000 0 0
GADD45A 0.12 0.21 -9999 0 -0.98 11 11
YWHAQ 0.016 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.032 0.094 -9999 0 -10000 0 0
MST1 0.002 0.14 -9999 0 -0.78 11 11
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family -0.028 0.16 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
MAPK8 0.046 0.056 -9999 0 -0.48 4 4
MAPK9 0.051 0.014 -9999 0 -10000 0 0
YWHAG 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
SIRT1 0.013 0.05 -9999 0 -0.81 1 1
SOD2 0.17 0.11 -9999 0 -0.54 1 1
RBL2 0.11 0.16 -9999 0 -1.2 2 2
RAL/GDP 0.033 0.022 -9999 0 -10000 0 0
CHUK 0.025 0.017 -9999 0 -10000 0 0
Ran/GTP 0.017 0.004 -9999 0 -10000 0 0
CSNK1G2 0.016 0 -9999 0 -10000 0 0
RAL/GTP 0.047 0.018 -9999 0 -10000 0 0
CSNK1G1 0.016 0 -9999 0 -10000 0 0
FASLG -0.18 0.5 -9999 0 -1.3 52 52
SKP2 0.014 0.043 -9999 0 -0.81 1 1
USP7 0.018 0.003 -9999 0 -10000 0 0
IKBKB 0.025 0.017 -9999 0 -10000 0 0
CCNB1 0.092 0.16 -9999 0 -0.65 1 1
FOXO1-3a-4/beta catenin -0.013 0.062 -9999 0 -0.41 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.047 0.029 -9999 0 -0.46 1 1
CSNK1A1 0.016 0 -9999 0 -10000 0 0
SGK1 0.001 0.13 -9999 0 -0.68 13 13
CSNK1G3 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.007 -9999 0 -10000 0 0
ZFAND5 0.13 0.06 -9999 0 -10000 0 0
SFN -0.25 0.37 -9999 0 -0.74 133 133
CDK2 0.016 0.001 -9999 0 -10000 0 0
FOXO3A/14-3-3 -0.006 0.14 -9999 0 -0.43 3 3
CREBBP 0.016 0.001 -9999 0 -10000 0 0
FBXO32 0.081 0.2 -9999 0 -1.2 3 3
BCL6 0.11 0.14 -9999 0 -1.3 1 1
RALB 0.018 0.001 -9999 0 -10000 0 0
RALA 0.018 0.001 -9999 0 -10000 0 0
YWHAH 0.016 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.005 0.05 -9999 0 -0.48 4 4
FBXW11 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.03 0.12 -9999 0 -0.53 19 19
NF kappa B1 p50/RelA/I kappa B alpha 0.031 0.076 -9999 0 -10000 0 0
NFKBIA 0.003 0.087 -9999 0 -0.33 1 1
MAPK14 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0 0 -9999 0 -10000 0 0
ARRB2 0.022 0.014 -9999 0 -10000 0 0
REL -0.031 0.19 -9999 0 -0.78 22 22
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.004 0.042 -9999 0 -0.53 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.06 -9999 0 -0.81 2 2
NF kappa B1 p50 dimer 0.026 0 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
NFKB1 0.03 0 -9999 0 -10000 0 0
RELA 0.016 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.012 0.085 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.02 0.051 -9999 0 -10000 0 0
SRC 0.012 0.053 -9999 0 -0.71 2 2
PI3K -0.003 0.045 -9999 0 -0.62 2 2
NF kappa B1 p50/RelA 0.012 0.085 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
SYK 0.016 0 -9999 0 -10000 0 0
I kappa B alpha/PIK3R1 0.012 0.081 -9999 0 -10000 0 0
cell death -0.019 0.049 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.03 0.12 -9999 0 -0.53 19 19
LCK -0.093 0.26 -9999 0 -0.68 59 59
BCL3 0.009 0.07 -9999 0 -0.66 4 4
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.003 0.041 -9999 0 -0.57 2 2
KLHL20 -0.022 0.057 -9999 0 -0.33 4 4
CYFIP2 0.007 0.085 -9999 0 -0.81 4 4
Rac1/GDP 0.082 0.04 -9999 0 -10000 0 0
ENAH -0.003 0.041 -9999 0 -0.57 2 2
AP1M1 0.016 0 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.016 0 -9999 0 -10000 0 0
CDC42/GTP -0.003 0.025 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.015 0.04 -9999 0 -0.23 6 6
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.061 0.15 -9999 0 -0.49 34 34
RAPGEF1 0.067 0.047 -9999 0 -0.47 2 2
CTNND1 0.016 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.003 0.043 -9999 0 -0.6 2 2
CRK 0.06 0.051 -9999 0 -0.52 2 2
E-cadherin/gamma catenin/alpha catenin -0.003 0.039 -9999 0 -0.53 2 2
alphaE/beta7 Integrin -0.076 0.19 -9999 0 -0.56 52 52
IQGAP1 0.016 0 -9999 0 -10000 0 0
NCKAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 -0.003 0.041 -9999 0 -0.57 2 2
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.023 -9999 0 -10000 0 0
MLLT4 0.016 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.065 0.16 -9999 0 -0.49 46 46
PI3K -0.004 0.029 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.003 0.045 -9999 0 -0.62 2 2
TIAM1 -0.095 0.28 -9999 0 -0.79 52 52
E-cadherin(dimer)/Ca2+ -0.002 0.033 -9999 0 -0.46 2 2
AKT1 -0.002 0.016 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
CDH1 0.012 0.06 -9999 0 -0.81 2 2
RhoA/GDP 0.082 0.04 -9999 0 -10000 0 0
actin cytoskeleton organization -0.016 0.042 -9999 0 -0.23 4 4
CDC42/GDP 0.082 0.04 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.031 0.027 -9999 0 -0.34 2 2
ITGB7 -0.085 0.26 -9999 0 -0.73 51 51
RAC1 0.016 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.003 0.035 -9999 0 -0.48 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin -0.002 0.034 -9999 0 -0.47 2 2
mol:GDP 0.08 0.046 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.016 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP -0.003 0.03 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.031 0.051 -9999 0 -0.27 5 5
NME1 0.016 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.003 0.041 -9999 0 -0.57 2 2
regulation of cell-cell adhesion -0.002 0.022 -9999 0 -10000 0 0
WASF2 -0.007 0.02 -9999 0 -10000 0 0
Rap1/GTP -0.003 0.029 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.056 0.14 -9999 0 -0.62 1 1
CCND1 -0.014 0.046 -9999 0 -0.35 5 5
VAV2 0.065 0.049 -9999 0 -0.5 2 2
RAP1/GDP -0.003 0.03 -9999 0 -10000 0 0
adherens junction assembly 0.052 0.044 -9999 0 -0.55 2 2
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
PIP5K1C 0.016 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.053 0.13 -9999 0 -0.59 1 1
E-cadherin/beta catenin -0.003 0.036 -9999 0 -0.5 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.044 0.056 -9999 0 -0.57 2 2
PIK3CA 0.012 0.06 -9999 0 -0.81 2 2
Rac1/GTP -0.034 0.091 -9999 0 -0.61 4 4
E-cadherin/beta catenin/alpha catenin -0.003 0.039 -9999 0 -0.53 2 2
ITGAE 0.013 0.045 -9999 0 -0.61 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.003 0.044 -9999 0 -0.61 2 2
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.003 0.029 -9999 0 -10000 0 0
HDAC3 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.001 0.014 -9999 0 -10000 0 0
GATA1/HDAC4 -0.001 0.023 -9999 0 -0.44 1 1
GATA1/HDAC5 0 0 -9999 0 -10000 0 0
GATA2/HDAC5 -0.007 0.059 -9999 0 -0.51 5 5
HDAC5/BCL6/BCoR -0.001 0.027 -9999 0 -0.53 1 1
HDAC9 -0.026 0.17 -9999 0 -0.71 22 22
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 -0.001 0.023 -9999 0 -0.44 1 1
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.029 0 -9999 0 -10000 0 0
GATA2 0.007 0.081 -9999 0 -0.69 5 5
HDAC4/RFXANK -0.002 0.032 -9999 0 -0.44 2 2
BCOR 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.016 0 -9999 0 -10000 0 0
HDAC5 0.016 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.003 0.039 -9999 0 -0.44 3 3
Histones 0.038 0.061 -9999 0 -0.47 1 1
ADRBK1 0.016 0 -9999 0 -10000 0 0
HDAC4 0.014 0.032 -9999 0 -0.61 1 1
XPO1 0.016 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 -0.001 0.023 -9999 0 -0.44 1 1
HDAC7 0.016 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.016 0 -9999 0 -10000 0 0
HDAC6 0.016 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.001 0.023 -9999 0 -0.44 1 1
CAMK4 -0.059 0.22 -9999 0 -0.67 41 41
Tubulin/HDAC6 -0.013 0.075 -9999 0 -0.53 4 4
SUMO1 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
GATA1 0.011 0.007 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
NR3C1 0.016 0 -9999 0 -10000 0 0
SUMO1/HDAC4 -0.001 0.015 -9999 0 -10000 0 0
SRF 0.011 0.055 -9999 0 -0.61 3 3
HDAC4/YWHAB -0.001 0.023 -9999 0 -0.44 1 1
Tubulin -0.016 0.089 -9999 0 -0.5 12 12
HDAC4/14-3-3 E -0.001 0.023 -9999 0 -0.44 1 1
GNB1 0.016 0 -9999 0 -10000 0 0
RANGAP1 0.016 0 -9999 0 -10000 0 0
BCL6/BCoR -0.002 0.032 -9999 0 -0.62 1 1
HDAC4/HDAC3/SMRT (N-CoR2) -0.001 0.019 -9999 0 -10000 0 0
HDAC4/SRF -0.049 0.14 -9999 0 -0.53 13 13
HDAC4/ER alpha -0.11 0.22 -9999 0 -0.52 78 78
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.038 0.061 -9999 0 -0.47 1 1
cell motility -0.013 0.075 -9999 0 -0.53 4 4
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.014 0.043 -9999 0 -0.81 1 1
HDAC4/CaMK II delta B 0.014 0.032 -9999 0 -0.61 1 1
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.13 0.29 -9999 0 -0.7 77 77
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.001 0.015 -9999 0 -10000 0 0
GNG2 0.011 0.055 -9999 0 -0.61 3 3
NCOR2 0.016 0 -9999 0 -10000 0 0
TUBB2A -0.006 0.12 -9999 0 -0.68 12 12
HDAC11 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
RANBP2 0.016 0 -9999 0 -10000 0 0
ANKRA2 0.016 0 -9999 0 -10000 0 0
RFXANK 0.014 0.032 -9999 0 -0.61 1 1
nuclear import 0.001 0.013 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.009 0.064 -9999 0 -0.61 4 4
PLK4 0.014 0.043 -9999 0 -0.81 1 1
regulation of centriole replication 0.023 0.058 -9999 0 -0.48 5 5
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.083 0.16 -9999 0 -0.49 42 42
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.065 0.13 -9999 0 -0.66 1 1
SUMO1 0.016 0 -9999 0 -10000 0 0
ZFPM1 0.008 0.071 -9999 0 -0.61 5 5
NPC/RanGAP1/SUMO1/Ubc9 0.029 0 -9999 0 -10000 0 0
FKBP3 0.016 0 -9999 0 -10000 0 0
Histones -0.033 0.066 -9999 0 -10000 0 0
YY1/LSF 0.034 0.054 -9999 0 -0.51 3 3
SMG5 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.062 0.12 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 -0.042 0.082 -9999 0 -10000 0 0
SAP18 0.016 0 -9999 0 -10000 0 0
RELA -0.015 0.13 -9999 0 -0.73 1 1
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.016 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.042 0.082 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.061 0.018 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.006 0.12 -9999 0 -0.68 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.007 0.081 -9999 0 -0.69 5 5
GATA1 0.011 0.007 -9999 0 -10000 0 0
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.071 0.027 -9999 0 -10000 0 0
RBBP7 0.016 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.011 0.06 -9999 0 -0.81 2 2
MAX 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.016 0 -9999 0 -10000 0 0
NFKBIA -0.021 0.11 -9999 0 -10000 0 0
KAT2B 0.014 0.043 -9999 0 -0.81 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.055 0.027 -9999 0 -10000 0 0
SIN3 complex -0.001 0.025 -9999 0 -0.48 1 1
SMURF1 0.016 0 -9999 0 -10000 0 0
CHD3 0.016 0 -9999 0 -10000 0 0
SAP30 0.014 0.043 -9999 0 -0.81 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.016 0 -9999 0 -10000 0 0
YY1/HDAC3 -0.035 0.075 -9999 0 -0.48 1 1
YY1/HDAC2 0.038 0.024 -9999 0 -10000 0 0
YY1/HDAC1 0.038 0.024 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.061 0.018 -9999 0 -10000 0 0
PPARG -0.08 0.16 -9999 0 -0.46 42 42
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.042 0.082 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex -0.001 0.015 -9999 0 -10000 0 0
HDAC1 0.016 0 -9999 0 -10000 0 0
HDAC3 -0.021 0.11 -9999 0 -10000 0 0
HDAC2 0.016 0 -9999 0 -10000 0 0
YY1 0.038 0.028 -9999 0 -0.35 2 2
HDAC8 0.016 0 -9999 0 -10000 0 0
SMAD7 0.016 0 -9999 0 -10000 0 0
NCOR2 0.016 0 -9999 0 -10000 0 0
MXD1 0.016 0 -9999 0 -10000 0 0
STAT3 0.032 0.024 -9999 0 -0.43 1 1
NFKB1 0.016 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.005 0.045 -9999 0 -0.47 3 3
YY1/SAP30/HDAC1 -0.003 0.03 -9999 0 -0.47 1 1
EP300 0.014 0.043 -9999 0 -0.81 1 1
STAT3 (dimer non-phopshorylated) 0.032 0.024 -9999 0 -0.43 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.021 0.11 -9999 0 -10000 0 0
histone deacetylation 0.061 0.018 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.037 0.075 -9999 0 -0.54 1 1
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GATAD2B 0.016 0 -9999 0 -10000 0 0
GATAD2A 0.016 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.047 0.091 -9999 0 -0.48 2 2
GATA1/HDAC1 0 0 -9999 0 -10000 0 0
GATA1/HDAC3 -0.043 0.083 -9999 0 -10000 0 0
CHD4 0.016 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.12 0.22 -9999 0 -0.53 85 85
SIN3/HDAC complex/Mad/Max 0.06 0.023 -9999 0 -10000 0 0
NuRD Complex -0.001 0.015 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.033 0.065 -9999 0 -10000 0 0
SIN3B 0.016 0 -9999 0 -10000 0 0
MTA2 0.016 0 -9999 0 -10000 0 0
SIN3A 0.016 0 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex -0.003 0.035 -9999 0 -0.48 2 2
GATA1/Fog1 -0.006 0.051 -9999 0 -0.44 5 5
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.15 0.31 -9999 0 -0.71 85 85
negative regulation of cell growth 0.06 0.022 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.061 0.018 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.07 0.14 -9999 0 -0.43 42 42
SIN3/HDAC complex/NCoR1 0.057 0.026 -9999 0 -10000 0 0
TFCP2 0.009 0.073 -9999 0 -0.81 3 3
NR2C1 0.016 0 -9999 0 -10000 0 0
MBD3 0.016 0 -9999 0 -10000 0 0
MBD2 0.016 0 -9999 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.014 0.067 -9999 0 -10000 0 0
TC10/GTP -0.006 0.044 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 -0.009 0.061 -9999 0 -0.5 4 4
HRAS 0.013 0.045 -9999 0 -0.61 2 2
APS homodimer 0.014 0.032 -9999 0 -0.61 1 1
GRB14 -0.002 0.11 -9999 0 -0.72 9 9
FOXO3 -0.014 0.08 -9999 0 -0.66 5 5
AKT1 0.047 0.093 -9999 0 -0.74 1 1
INSR 0.018 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.014 0.043 -9999 0 -0.81 1 1
SORBS1 0.003 0.093 -9999 0 -0.67 7 7
CRK 0.016 0 -9999 0 -10000 0 0
PTPN1 0.047 0 -9999 0 -10000 0 0
CAV1 0.002 0.12 -9999 0 -0.47 16 16
CBL/APS/CAP/Crk-II/C3G -0.007 0.049 -9999 0 -0.45 2 2
Insulin Receptor/Insulin/IRS1/NCK2 -0.009 0.061 -9999 0 -0.5 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.01 0.061 -9999 0 -0.44 6 6
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.005 0.032 -9999 0 -10000 0 0
RPS6KB1 0.056 0.086 -9999 0 -0.65 1 1
PARD6A 0.013 0.045 -9999 0 -0.61 2 2
CBL 0.016 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.007 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.015 0.069 -9999 0 -0.63 1 1
HRAS/GTP -0.019 0.071 -9999 0 -10000 0 0
Insulin Receptor 0.018 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.009 0.058 -9999 0 -0.46 4 4
PRKCI -0.004 0.017 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.019 0.085 -9999 0 -0.82 1 1
SHC1 0.014 0.032 -9999 0 -0.61 1 1
negative regulation of MAPKKK cascade 0 0.006 -9999 0 -10000 0 0
PI3K -0.01 0.062 -9999 0 -0.44 6 6
NCK2 0.016 0 -9999 0 -10000 0 0
RHOQ 0.016 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.002 0.033 -9999 0 -0.45 2 2
AKT2 0.043 0.098 -9999 0 -0.74 1 1
PRKCZ -0.004 0.02 -9999 0 -10000 0 0
SH2B2 0.014 0.032 -9999 0 -0.61 1 1
SHC/SHIP -0.021 0.084 -9999 0 -0.44 8 8
F2RL2 -0.16 0.32 -9999 0 -0.71 93 93
TRIP10 0.016 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.001 0.018 -9999 0 -0.35 1 1
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.001 0.016 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
RASA1 0.016 0 -9999 0 -10000 0 0
NCK1 0.016 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.008 0.053 -9999 0 -0.48 2 2
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.002 0.031 -9999 0 -0.5 1 1
INPP5D 0.011 0.099 -9999 0 -0.47 8 8
SOS1 0.016 0 -9999 0 -10000 0 0
SGK1 -0.019 0.12 -9999 0 -1 5 5
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.001 0.11 -9999 0 -0.71 8 8
p62DOK/RasGAP 0 0.006 -9999 0 -10000 0 0
INS 0.004 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.011 0.098 -9999 0 -0.46 8 8
GRB2 0.016 0 -9999 0 -10000 0 0
EIF4EBP1 0.053 0.091 -9999 0 -0.65 1 1
PTPRA 0.018 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.06 -9999 0 -0.81 2 2
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.011 0.06 -9999 0 -0.81 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.037 0.044 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.009 0.063 -9999 0 -0.43 8 8
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.095 0.17 -9999 0 -0.47 46 46
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.083 0.081 -9999 0 -10000 0 0
CRKL 0.054 0.048 -9999 0 -10000 0 0
mol:DAG 0.03 0.054 -9999 0 -10000 0 0
HRAS 0.081 0.051 -9999 0 -10000 0 0
MAPK8 0.033 0.074 -9999 0 -0.48 5 5
RAP1A 0.054 0.048 -9999 0 -10000 0 0
GAB1 0.054 0.048 -9999 0 -10000 0 0
MAPK14 0.039 0.05 -9999 0 -0.45 1 1
EPO 0.011 0.032 -9999 0 -0.6 1 1
PLCG1 0.03 0.055 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.009 0.082 -9999 0 -0.63 6 6
RAPGEF1 0.016 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.044 0.14 -9999 0 -0.47 31 31
GAB1/SHC/GRB2/SOS1 -0.005 0.033 -9999 0 -10000 0 0
EPO/EPOR (dimer) 0.002 0.064 -9999 0 -0.46 7 7
IRS2 0.039 0.096 -9999 0 -10000 0 0
STAT1 0.059 0.096 -9999 0 -0.67 1 1
STAT5B 0.067 0.053 -9999 0 -10000 0 0
cell proliferation 0.043 0.07 -9999 0 -0.45 4 4
GAB1/SHIP/PIK3R1/SHP2/SHC -0.015 0.064 -9999 0 -0.56 1 1
TEC 0.054 0.048 -9999 0 -10000 0 0
SOCS3 -0.041 0.2 -9999 0 -0.7 30 30
STAT1 (dimer) 0.059 0.094 -9999 0 -0.65 1 1
JAK2 0.018 0.005 -9999 0 -10000 0 0
PIK3R1 0.016 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.06 0.053 -9999 0 -10000 0 0
EPO/EPOR 0.002 0.064 -9999 0 -0.46 7 7
LYN 0.018 0.003 -9999 0 -10000 0 0
TEC/VAV2 0.064 0.046 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.009 0.082 -9999 0 -0.63 6 6
SHC1 0.014 0.032 -9999 0 -0.61 1 1
EPO/EPOR (dimer)/LYN 0.036 0.056 -9999 0 -0.5 1 1
mol:IP3 0.03 0.054 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.028 0.094 -9999 0 -0.57 2 2
SH2B3 0.018 0.005 -9999 0 -10000 0 0
NFKB1 0.039 0.05 -9999 0 -0.45 1 1
EPO/EPOR (dimer)/JAK2/SOCS3 -0.019 0.062 -9999 0 -10000 0 0
PTPN6 0.045 0.05 -9999 0 -10000 0 0
TEC/VAV2/GRB2 -0.004 0.032 -9999 0 -10000 0 0
EPOR 0.009 0.082 -9999 0 -0.63 6 6
INPP5D -0.011 0.13 -9999 0 -0.66 15 15
mol:GDP -0.005 0.034 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG2 0.007 0.077 -9999 0 -0.65 5 5
CRKL/CBL/C3G -0.004 0.032 -9999 0 -10000 0 0
VAV2 0.054 0.048 -9999 0 -10000 0 0
CBL 0.054 0.048 -9999 0 -10000 0 0
SHC/Grb2/SOS1 -0.006 0.036 -9999 0 -10000 0 0
STAT5A 0.067 0.053 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.087 0.065 -9999 0 -10000 0 0
LYN/PLCgamma2 -0.006 0.055 -9999 0 -0.48 5 5
PTPN11 0.016 0 -9999 0 -10000 0 0
BTK -0.01 0.16 -9999 0 -0.53 6 6
BCL2 0.07 0.14 -9999 0 -0.97 4 4
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.016 0 -10000 0 -10000 0 0
mol:PIP3 -0.007 0.053 0.34 1 -0.38 6 7
FRAP1 0.019 0.02 -10000 0 -10000 0 0
AKT1 -0.007 0.052 0.25 1 -0.52 2 3
INSR 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.006 0.04 -10000 0 -0.51 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.012 -10000 0 -10000 0 0
TSC2 0.014 0.032 -10000 0 -0.61 1 1
RHEB/GDP -0.005 0.036 -10000 0 -0.46 1 1
TSC1 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.014 0.049 -10000 0 -0.42 4 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.002 0.014 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.016 0 -10000 0 -10000 0 0
RPS6KB1 0.033 0.034 -10000 0 -0.36 1 1
MAP3K5 -0.002 0.085 -10000 0 -0.45 13 13
PIK3R1 0.016 0 -10000 0 -10000 0 0
apoptosis -0.002 0.084 -10000 0 -0.45 13 13
mol:LY294002 0 0 0.001 1 -0.001 8 9
EIF4B 0.041 0.031 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.003 0.021 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0.006 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.022 0.057 -10000 0 -0.4 6 6
mTOR/RHEB/GTP/Raptor/GBL 0.039 0.026 0.19 1 -0.26 1 2
FKBP1A 0.016 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.005 0.035 -10000 0 -0.45 1 1
mol:Amino Acids 0 0 0.001 1 -0.001 8 9
FKBP12/Rapamycin 0 0.001 -10000 0 -10000 0 0
PDPK1 -0.008 0.063 0.27 1 -0.56 3 4
EIF4E 0.016 0 -10000 0 -10000 0 0
ASK1/PP5C 0.004 0.12 -10000 0 -0.63 13 13
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.022 0.002 -10000 0 -10000 0 0
TSC1/TSC2 -0.007 0.044 -10000 0 -0.56 1 1
tumor necrosis factor receptor activity 0 0 0.001 8 -0.001 1 9
RPS6 0.016 0 -10000 0 -10000 0 0
PPP5C 0.016 0 -10000 0 -10000 0 0
EIF4G1 0.016 0 -10000 0 -10000 0 0
IRS1 0.004 0.052 -10000 0 -0.32 8 8
INS 0 0 -10000 0 -10000 0 0
PTEN 0.013 0.042 -10000 0 -0.81 1 1
PDK2 -0.006 0.047 0.27 1 -0.42 2 3
EIF4EBP1 0.013 0.024 -10000 0 -10000 0 0
PIK3CA 0.012 0.06 -10000 0 -0.81 2 2
PPP2R5D 0.027 0.018 -10000 0 -10000 0 0
peptide biosynthetic process 0.022 0 -10000 0 -10000 0 0
RHEB 0.016 0 -10000 0 -10000 0 0
EIF4A1 0.016 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.004 1 -0.003 2 3
EEF2 0.022 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.021 0.021 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.061 0.041 -10000 0 -0.42 2 2
adherens junction organization 0.045 0.052 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.018 0.076 -10000 0 -10000 0 0
FMN1 0.019 0.13 -10000 0 -0.43 27 27
mol:IP3 -0.003 0.031 -10000 0 -0.39 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.047 0.028 -10000 0 -10000 0 0
CTNNB1 0.015 0.001 -10000 0 -10000 0 0
AKT1 0.06 0.037 -10000 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.05 0.051 -10000 0 -0.49 3 3
CTNND1 0.017 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.054 0.04 -10000 0 -0.54 1 1
VASP 0.056 0.027 -10000 0 -10000 0 0
ZYX 0.056 0.027 -10000 0 -10000 0 0
JUB 0.048 0.065 -10000 0 -0.42 6 6
EGFR(dimer) 0.033 0.098 -10000 0 -0.42 15 15
E-cadherin/beta catenin-gamma catenin -0.002 0.038 -10000 0 -0.52 2 2
mol:PI-3-4-5-P3 -0.003 0.033 -10000 0 -0.41 2 2
PIK3CA 0.013 0.06 -10000 0 -0.81 2 2
PI3K -0.003 0.034 -10000 0 -0.42 2 2
FYN 0.055 0.062 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.03 -10000 0 -0.38 2 2
JUP 0.015 0.001 -10000 0 -10000 0 0
PIK3R1 0.017 0.001 -10000 0 -10000 0 0
mol:DAG -0.003 0.031 -10000 0 -0.39 2 2
CDH1 0.011 0.06 -10000 0 -0.81 2 2
RhoA/GDP -0.018 0.076 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.056 0.027 -10000 0 -10000 0 0
SRC 0.012 0.053 -10000 0 -0.71 2 2
RAC1 0.016 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
EGFR -0.02 0.17 -10000 0 -0.79 17 17
CASR 0.046 0.062 -10000 0 -10000 0 0
RhoA/GTP -0.003 0.027 -10000 0 -10000 0 0
AKT2 0.056 0.051 -10000 0 -10000 0 0
actin cable formation 0.028 0.13 -10000 0 -0.53 2 2
apoptosis 0.003 0.032 0.4 2 -10000 0 2
CTNNA1 0.017 0.001 -10000 0 -10000 0 0
mol:GDP 0.043 0.098 -10000 0 -10000 0 0
PIP5K1A 0.055 0.041 -10000 0 -0.55 1 1
PLCG1 -0.003 0.031 -10000 0 -0.4 2 2
Rac1/GTP -0.018 0.077 -10000 0 -0.38 15 15
homophilic cell adhesion 0.002 0.001 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD2 0.019 0.008 -9999 0 -10000 0 0
SMAD3 0.055 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.061 0 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0 0 -9999 0 -10000 0 0
PPM1A 0.016 0 -9999 0 -10000 0 0
CALM1 0.016 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.027 0.006 -9999 0 -10000 0 0
MAP3K1 0.014 0.043 -9999 0 -0.81 1 1
TRAP-1/SMAD4 -0.036 0.14 -9999 0 -0.62 22 22
MAPK3 0.016 0 -9999 0 -10000 0 0
MAPK1 0.016 0 -9999 0 -10000 0 0
NUP214 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
CTDSPL 0.016 0 -9999 0 -10000 0 0
KPNB1 0.016 0 -9999 0 -10000 0 0
TGFBRAP1 -0.032 0.19 -9999 0 -0.81 22 22
UBE2I 0.016 0 -9999 0 -10000 0 0
NUP153 0.016 0 -9999 0 -10000 0 0
KPNA2 0.016 0 -9999 0 -10000 0 0
PIAS4 0.016 0 -9999 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.081 0.24 -10000 0 -0.68 53 53
CLTC 0.042 0 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.035 0 -10000 0 -10000 0 0
Dynamin 2/GTP 0 0 -10000 0 -10000 0 0
EXOC4 0.016 0 -10000 0 -10000 0 0
CD59 0.037 0.015 -10000 0 -10000 0 0
CPE -0.007 0.13 -10000 0 -0.55 21 21
CTNNB1 0.016 0 -10000 0 -10000 0 0
membrane fusion 0 0 -10000 0 -10000 0 0
CTNND1 0.042 0 -10000 0 -10000 0 0
DNM2 0.016 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.043 0 -10000 0 -10000 0 0
TSHR 0.021 0.041 -10000 0 -0.55 2 2
INS 0.016 0 -10000 0 -10000 0 0
BIN1 0.016 0 -10000 0 -10000 0 0
mol:Choline 0 0 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.024 0 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
JUP 0.038 0 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.003 0.036 -10000 0 -0.49 2 2
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.037 0.022 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.016 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.016 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.056 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.016 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.001 0.012 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.024 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 0.025 0.028 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.031 0 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.048 0.007 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.016 0 -10000 0 -10000 0 0
exocyst 0.057 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.042 0 -10000 0 -10000 0 0
NME1 0.024 0 -10000 0 -10000 0 0
clathrin coat assembly 0.042 0 -10000 0 -10000 0 0
IL2RA -0.014 0.1 -10000 0 -10000 0 0
VAMP3 0.024 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.042 0.11 -10000 0 -0.39 17 17
EXOC6 0.016 0 -10000 0 -10000 0 0
PLD1 0 0 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.016 0 -10000 0 -10000 0 0
PIP5K1C 0.043 0 -10000 0 -10000 0 0
SDC1 0.035 0.028 -10000 0 -10000 0 0
ARF6/GDP 0.023 0 -10000 0 -10000 0 0
EXOC7 0.016 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.001 0.013 -10000 0 -10000 0 0
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
endocytosis 0.003 0.035 0.49 2 -10000 0 2
SCAMP2 0.016 0 -10000 0 -10000 0 0
ADRB2 0.027 0.092 -10000 0 -0.42 8 8
EXOC3 0.016 0 -10000 0 -10000 0 0
ASAP2 0.011 0.06 -10000 0 -0.81 2 2
Dynamin 2/GDP 0 0 -10000 0 -10000 0 0
KLC1 0.016 0 -10000 0 -10000 0 0
AVPR2 0.025 0.1 -10000 0 -0.42 17 17
RALA 0.016 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.001 0.011 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.003 0.039 -9999 0 -0.53 2 2
E-cadherin/beta catenin -0.003 0.045 -9999 0 -0.62 2 2
CTNNB1 0.016 0 -9999 0 -10000 0 0
JUP 0.016 0 -9999 0 -10000 0 0
CDH1 0.011 0.06 -9999 0 -0.81 2 2
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.003 0.045 -9999 0 -0.62 2 2
FBXW11 0.016 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.007 0.065 -9999 0 -0.91 1 1
NFKB1 0.016 0 -9999 0 -10000 0 0
MAP3K14 0.011 0.06 -9999 0 -0.81 2 2
NF kappa B1 p50/RelB -0.003 0.045 -9999 0 -0.62 2 2
RELB 0.011 0.06 -9999 0 -0.81 2 2
NFKB2 0.011 0.06 -9999 0 -0.81 2 2
NF kappa B2 p52/RelB -0.006 0.066 -9999 0 -0.71 3 3
regulation of B cell activation -0.006 0.065 -9999 0 -0.7 3 3
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.001 0.013 -9999 0 -10000 0 0
MDM2/SUMO1 0 0 -9999 0 -10000 0 0
HDAC4 0.014 0.032 -9999 0 -0.61 1 1
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
SUMO1 0.016 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.022 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.038 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0 -9999 0 -10000 0 0
SUMO1/HDAC4 -0.001 0.015 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
RANGAP1 0.016 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.029 0 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.016 0 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0.016 0 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex -0.001 0.016 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.026 0.012 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.003 -9999 0 -10000 0 0
CLTB 0.014 0.032 -9999 0 -0.61 1 1
coatomer protein complex/ARF1/GTP/ER cargo protein 0.033 0.011 -9999 0 -10000 0 0
CD4 -0.012 0.14 -9999 0 -0.68 15 15
CLTA 0.016 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
ARFGAP1 0.015 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 -0.001 0.022 -9999 0 -0.42 1 1
ARF1/GTP -0.001 0.012 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.036 0.006 -9999 0 -10000 0 0
mol:Choline -0.001 0.021 -9999 0 -0.42 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
DDEF1 -0.001 0.022 -9999 0 -0.42 1 1
ARF1/GDP 0 0.006 -9999 0 -10000 0 0
AP2M1 0.016 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0.001 -9999 0 -10000 0 0
Rac/GTP 0 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0.002 -9999 0 -10000 0 0
ARFIP2 0 0.004 -9999 0 -10000 0 0
COPA 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.033 0.012 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.001 -9999 0 -10000 0 0
GGA3 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0.007 -9999 0 -10000 0 0
AP2A1 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.035 0.009 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0.007 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.003 -9999 0 -10000 0 0
CYTH2 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0.002 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.038 0.045 -9999 0 -10000 0 0
PLD2 -0.001 0.022 -9999 0 -0.42 1 1
ARF-GAP1/v-SNARE 0.015 0 -9999 0 -10000 0 0
PIP5K1A -0.001 0.022 -9999 0 -0.42 1 1
ARF1/GTP/Membrin/GBF1/p115 -0.001 0.012 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.021 -9999 0 -0.42 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.015 0 -9999 0 -10000 0 0
GOSR2 0 0.008 -9999 0 -10000 0 0
USO1 0 0.008 -9999 0 -10000 0 0
GBF1 0 0.008 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0.003 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.017 0.084 -9999 0 -0.53 5 5
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 379 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.J8.A3YH TCGA.J8.A3YG TCGA.J8.A3YE TCGA.J8.A3YD
109_MAP3K5 0.072 0.072 0.072 0.072
47_PPARGC1A -0.81 0.016 -0.61 0.016
105_BMP4 -0.61 0.016 -0.81 0.016
105_BMP6 0.016 0.016 0.016 0.016
105_BMP7 0.016 0.016 0.016 0.016
105_BMP2 0.016 0.016 0.016 0.016
131_RELN/VLDLR 0 -0.32 -0.48 -0.32
30_TGFB1/TGF beta receptor Type II 0.016 0.015 0.016 0.015
84_STAT5B 0.058 0.041 -0.12 0.058
84_STAT5A 0.058 0.041 -0.12 0.058
Methods & Data
Input

  • Expression Data Normalization = Expression data was not used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/THCA-TP/2284143/0.mRNAseq_preprocessor.Finished/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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