Lung Adenocarcinoma: PARADIGM pathway analysis of mRNASeq expression and copy number data
(primary solid tumor cohort)
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 46 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
FOXM1 transcription factor network 170
Glypican 2 network 119
Angiopoietin receptor Tie2-mediated signaling 92
Aurora B signaling 90
HIF-1-alpha transcription factor network 85
Signaling events mediated by the Hedgehog family 67
PLK1 signaling events 57
Endothelins 54
Aurora C signaling 49
Signaling mediated by p38-alpha and p38-beta 44
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
FOXM1 transcription factor network 170 8670 51 -0.041 0.83 1000 -1000 -0.082 -1000
Glypican 2 network 119 479 4 0.083 0.14 1000 -1000 0.016 -1000
Angiopoietin receptor Tie2-mediated signaling 92 8110 88 -0.5 0.1 1000 -1000 -0.048 -1000
Aurora B signaling 90 6063 67 -0.15 0.29 1000 -1000 -0.032 -1000
HIF-1-alpha transcription factor network 85 6492 76 -0.045 0.43 1000 -1000 -0.031 -1000
Signaling events mediated by the Hedgehog family 67 3519 52 -0.23 0.11 1000 -1000 -0.032 -1000
PLK1 signaling events 57 4901 85 -0.054 0.2 1000 -1000 -0.021 -1000
Endothelins 54 5251 96 -0.3 0.2 1000 -1000 -0.045 -1000
Aurora C signaling 49 346 7 0 0.17 1000 -1000 -0.004 -1000
Signaling mediated by p38-alpha and p38-beta 44 1944 44 -0.096 0.022 1000 -1000 -0.02 -1000
Signaling events regulated by Ret tyrosine kinase 42 3479 82 -0.084 0.065 1000 -1000 -0.042 -1000
FOXA2 and FOXA3 transcription factor networks 41 1899 46 -0.23 0.15 1000 -1000 -0.078 -1000
Osteopontin-mediated events 40 1543 38 -0.004 0.25 1000 -1000 -0.02 -1000
Visual signal transduction: Cones 39 1506 38 -0.084 0.12 1000 -1000 -0.017 -1000
Fc-epsilon receptor I signaling in mast cells 39 3812 97 -0.11 0.022 1000 -1000 -0.046 -1000
IL4-mediated signaling events 36 3322 91 -0.64 0.35 1000 -1000 -0.12 -1000
BMP receptor signaling 36 2976 81 -0.19 0.24 1000 -1000 -0.024 -1000
amb2 Integrin signaling 36 2993 82 -0.31 0.08 1000 -1000 -0.023 -1000
RXR and RAR heterodimerization with other nuclear receptor 36 1904 52 -0.14 0.045 1000 -1000 -0.021 -1000
Ephrin B reverse signaling 34 1646 48 -0.078 0.08 1000 -1000 -0.022 -1000
Visual signal transduction: Rods 33 1726 52 -0.084 0.1 1000 -1000 -0.033 -1000
p75(NTR)-mediated signaling 28 3554 125 -0.14 0.14 1000 -1000 -0.051 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 27 1903 68 -0.15 0.066 1000 -1000 -0.056 -1000
IL23-mediated signaling events 27 1678 60 -0.18 0.027 1000 -1000 -0.078 -1000
Syndecan-1-mediated signaling events 25 867 34 0 0.22 1000 -1000 -0.023 -1000
LPA4-mediated signaling events 24 299 12 -0.075 0 1000 -1000 -0.016 -1000
HIF-2-alpha transcription factor network 24 1032 43 -0.14 0.15 1000 -1000 -0.036 -1000
Integrins in angiogenesis 24 2087 84 -0.09 0.25 1000 -1000 -0.036 -1000
TCGA08_retinoblastoma 24 199 8 -0.021 0.099 1000 -1000 -0.002 -1000
Thromboxane A2 receptor signaling 23 2500 105 -0.1 0.074 1000 -1000 -0.035 -1000
Arf6 signaling events 23 1485 62 -0.11 0.074 1000 -1000 -0.023 -1000
Glucocorticoid receptor regulatory network 23 2720 114 -0.29 0.17 1000 -1000 -0.042 -1000
Canonical Wnt signaling pathway 23 1180 51 -0.21 0.095 1000 -1000 -0.03 -1000
Neurotrophic factor-mediated Trk receptor signaling 23 2790 120 -0.16 0.14 1000 -1000 -0.04 -1000
Presenilin action in Notch and Wnt signaling 22 1359 61 -0.21 0.095 1000 -1000 -0.036 -1000
Reelin signaling pathway 21 1200 56 -0.04 0.047 1000 -1000 -0.026 -1000
Wnt signaling 21 150 7 -0.027 0.04 1000 -1000 -0.007 -1000
IL6-mediated signaling events 21 1586 75 -0.15 0.05 1000 -1000 -0.038 -1000
EGFR-dependent Endothelin signaling events 21 442 21 -0.022 0.074 1000 -1000 -0.032 -1000
Aurora A signaling 20 1251 60 -0.028 0.2 1000 -1000 -0.021 -1000
TCGA08_p53 20 144 7 -0.02 0.02 1000 -1000 -0.009 -1000
Noncanonical Wnt signaling pathway 19 495 26 -0.048 0.04 1000 -1000 -0.023 -1000
Glypican 1 network 19 929 48 -0.051 0.038 1000 -1000 -0.024 -1000
FoxO family signaling 18 1198 64 0 0.21 1000 -1000 -0.04 -1000
Effects of Botulinum toxin 18 489 26 0 0.041 1000 -1000 -0.009 -1000
Nongenotropic Androgen signaling 18 968 52 -0.069 0.05 1000 -1000 -0.023 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 17 589 33 -0.08 0.097 1000 -1000 -0.031 -1000
ErbB2/ErbB3 signaling events 16 1071 65 -0.05 0.031 1000 -1000 -0.033 -1000
Syndecan-4-mediated signaling events 16 1072 67 -0.042 0.14 1000 -1000 -0.03 -1000
ErbB4 signaling events 15 1096 69 -0.11 0.14 1000 -1000 -0.025 -1000
Syndecan-2-mediated signaling events 15 1042 69 -0.044 0.06 1000 -1000 -0.031 -1000
PDGFR-alpha signaling pathway 15 678 44 -0.19 0.038 1000 -1000 -0.028 -1000
IL1-mediated signaling events 15 971 62 -0.077 0.042 1000 -1000 -0.043 -1000
Calcium signaling in the CD4+ TCR pathway 15 485 31 -0.035 0.037 1000 -1000 -0.028 -1000
PLK2 and PLK4 events 14 42 3 -0.006 0.04 1000 -1000 -0.017 -1000
FAS signaling pathway (CD95) 14 664 47 -0.23 0.035 1000 -1000 -0.033 -1000
EPHB forward signaling 14 1197 85 -0.034 0.091 1000 -1000 -0.044 -1000
LPA receptor mediated events 14 1511 102 -0.055 0.072 1000 -1000 -0.043 -1000
Regulation of Androgen receptor activity 14 1011 70 -0.14 0.12 1000 -1000 -0.03 -1000
Nephrin/Neph1 signaling in the kidney podocyte 13 447 34 -0.034 0.058 1000 -1000 -0.026 -1000
IL12-mediated signaling events 13 1132 87 -0.13 0.061 1000 -1000 -0.058 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 13 716 54 -0.033 0.11 1000 -1000 -0.03 -1000
Signaling events mediated by PTP1B 13 997 76 -0.052 0.074 1000 -1000 -0.027 -1000
Plasma membrane estrogen receptor signaling 13 1171 86 -0.061 0.058 1000 -1000 -0.033 -1000
Class IB PI3K non-lipid kinase events 13 39 3 -0.008 0.008 1000 -1000 -0.019 -1000
S1P4 pathway 13 344 25 -0.028 0.028 1000 -1000 -0.016 -1000
Nectin adhesion pathway 12 771 63 -0.037 0.051 1000 -1000 -0.033 -1000
Ceramide signaling pathway 12 959 76 -0.021 0.074 1000 -1000 -0.034 -1000
S1P5 pathway 12 207 17 -0.02 0.021 1000 -1000 -0.006 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 12 945 78 -0.048 0.023 1000 -1000 -0.046 -1000
Coregulation of Androgen receptor activity 11 856 76 -0.063 0.096 1000 -1000 -0.025 -1000
BARD1 signaling events 11 627 57 -0.047 0.12 1000 -1000 -0.039 -1000
S1P1 pathway 11 404 36 -0.081 0.021 1000 -1000 -0.026 -1000
TCR signaling in naïve CD8+ T cells 11 1059 93 -0.028 0.033 1000 -1000 -0.035 -1000
BCR signaling pathway 11 1172 99 -0.045 0.081 1000 -1000 -0.043 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 10 887 85 -0.069 0.037 1000 -1000 -0.026 -1000
Signaling events mediated by HDAC Class III 10 403 40 -0.06 0.068 1000 -1000 -0.033 -1000
Stabilization and expansion of the E-cadherin adherens junction 10 804 74 -0.099 0.074 1000 -1000 -0.04 -1000
Caspase cascade in apoptosis 9 692 74 -0.029 0.084 1000 -1000 -0.033 -1000
Syndecan-3-mediated signaling events 9 335 35 -0.12 0.046 1000 -1000 -0.019 -1000
Regulation of p38-alpha and p38-beta 9 496 54 -0.04 0.057 1000 -1000 -0.042 -1000
Signaling events mediated by VEGFR1 and VEGFR2 9 1232 125 -0.19 0.042 1000 -1000 -0.044 -1000
IL2 signaling events mediated by STAT5 8 186 22 -0.027 0.1 1000 -1000 -0.026 -1000
Ephrin A reverse signaling 7 52 7 -0.014 0.03 1000 -1000 -0.009 -1000
IL27-mediated signaling events 7 390 51 -0.045 0.039 1000 -1000 -0.046 -1000
Class I PI3K signaling events 7 551 73 -0.042 0.05 1000 -1000 -0.031 -1000
Signaling events mediated by PRL 7 266 34 -0.025 0.089 1000 -1000 -0.03 -1000
Regulation of nuclear SMAD2/3 signaling 6 826 136 -0.18 0.072 1000 -1000 -0.025 -1000
JNK signaling in the CD4+ TCR pathway 6 103 17 -0.006 0.047 1000 -1000 -0.024 -1000
Cellular roles of Anthrax toxin 6 235 39 -0.034 0.029 1000 -1000 -0.014 -1000
Hedgehog signaling events mediated by Gli proteins 6 396 65 -0.14 0.049 1000 -1000 -0.031 -1000
mTOR signaling pathway 6 320 53 -0.056 0.025 1000 -1000 -0.029 -1000
IFN-gamma pathway 6 427 68 -0.029 0.062 1000 -1000 -0.038 -1000
Arf6 trafficking events 6 450 71 -0.039 0.039 1000 -1000 -0.029 -1000
Insulin Pathway 6 474 74 -0.11 0.051 1000 -1000 -0.038 -1000
VEGFR1 specific signals 6 372 56 -0.19 0.05 1000 -1000 -0.03 -1000
PDGFR-beta signaling pathway 6 669 97 -0.039 0.053 1000 -1000 -0.041 -1000
Sphingosine 1-phosphate (S1P) pathway 5 161 28 -0.02 0.033 1000 -1000 -0.018 -1000
EPO signaling pathway 5 311 55 -0.026 0.046 1000 -1000 -0.025 -1000
ceramide signaling pathway 5 275 49 -0.01 0.027 1000 -1000 -0.027 -1000
Retinoic acid receptors-mediated signaling 5 336 58 -0.096 0.041 1000 -1000 -0.029 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 5 261 45 -0.026 0.05 1000 -1000 -0.039 -1000
Regulation of Telomerase 5 581 102 -0.021 0.094 1000 -1000 -0.034 -1000
Ras signaling in the CD4+ TCR pathway 5 99 17 -0.004 0.031 1000 -1000 -0.018 -1000
Arf6 downstream pathway 4 200 43 -0.051 0.054 1000 -1000 -0.021 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 4 405 83 -0.061 0.041 1000 -1000 -0.022 -1000
Signaling events mediated by HDAC Class I 4 452 104 -0.035 0.048 1000 -1000 -0.029 -1000
IL2 signaling events mediated by PI3K 4 244 58 -0.015 0.07 1000 -1000 -0.043 -1000
E-cadherin signaling in the nascent adherens junction 4 378 76 -0.033 0.055 1000 -1000 -0.038 -1000
p38 MAPK signaling pathway 4 199 44 -0.009 0.062 1000 -1000 -0.012 -1000
Signaling events mediated by HDAC Class II 3 256 75 -0.02 0.058 1000 -1000 -0.022 -1000
Circadian rhythm pathway 3 72 22 -0.004 0.05 1000 -1000 -0.027 -1000
Class I PI3K signaling events mediated by Akt 3 239 68 -0.029 0.047 1000 -1000 -0.025 -1000
Signaling mediated by p38-gamma and p38-delta 3 59 15 -0.019 0.022 1000 -1000 -0.024 -1000
TCGA08_rtk_signaling 3 91 26 -0.011 0.049 1000 -1000 -0.011 -1000
IGF1 pathway 3 180 57 -0.033 0.048 1000 -1000 -0.03 -1000
S1P3 pathway 3 138 42 -0.025 0.035 1000 -1000 -0.024 -1000
E-cadherin signaling in keratinocytes 3 164 43 -0.016 0.04 1000 -1000 -0.016 -1000
Canonical NF-kappaB pathway 2 89 39 -0.017 0.043 1000 -1000 -0.025 -1000
Paxillin-independent events mediated by a4b1 and a4b7 2 78 37 -0.026 0.051 1000 -1000 -0.018 -1000
a4b1 and a4b7 Integrin signaling 1 7 5 0.02 0.031 1000 -1000 0.019 -1000
Insulin-mediated glucose transport 1 56 32 -0.017 0.038 1000 -1000 -0.023 -1000
TRAIL signaling pathway 1 82 48 -0.018 0.045 1000 -1000 -0.025 -1000
Paxillin-dependent events mediated by a4b1 1 52 36 -0.036 0.039 1000 -1000 -0.027 -1000
Rapid glucocorticoid signaling 1 27 20 -0.008 0.027 1000 -1000 -0.01 -1000
E-cadherin signaling events 1 6 5 0.019 0.039 1000 -1000 0.017 -1000
Arf1 pathway 1 94 54 -0.008 0.035 1000 -1000 -0.015 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 22 23 0 0.036 1000 -1000 -0.021 -1000
Atypical NF-kappaB pathway 0 26 31 -0.018 0.03 1000 -1000 -0.022 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 19 27 -0.02 0.045 1000 -1000 -0.027 -1000
Alternative NF-kappaB pathway 0 0 13 0 0.056 1000 -1000 0 -1000
Total 2439 144586 7203 -9.7 11 131000 -131000 -3.8 -131000
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.66 0.5 1 205 -10000 0 205
PLK1 0.39 0.33 0.69 179 -0.68 2 181
BIRC5 0.42 0.33 0.7 185 -0.71 1 186
HSPA1B 0.67 0.5 1.1 202 -10000 0 202
MAP2K1 0.2 0.15 0.33 187 -10000 0 187
BRCA2 0.66 0.5 1 200 -10000 0 200
FOXM1 0.83 0.66 1.3 209 -0.83 1 210
XRCC1 0.66 0.5 1.1 201 -10000 0 201
FOXM1B/p19 0.22 0.37 0.84 79 -0.79 2 81
Cyclin D1/CDK4 0.55 0.44 0.92 188 -10000 0 188
CDC2 0.74 0.57 1.2 212 -0.74 1 213
TGFA 0.58 0.46 0.95 201 -0.71 1 202
SKP2 0.72 0.55 1.1 211 -0.73 1 212
CCNE1 0.16 0.16 0.38 125 -10000 0 125
CKS1B 0.72 0.55 1.1 207 -10000 0 207
RB1 0.39 0.37 0.74 170 -0.67 2 172
FOXM1C/SP1 0.58 0.43 0.93 194 -0.77 2 196
AURKB 0.36 0.38 0.7 169 -0.7 14 183
CENPF 0.75 0.56 1.2 210 -10000 0 210
CDK4 0.09 0.069 0.18 97 -10000 0 97
MYC 0.43 0.44 0.87 160 -0.67 1 161
CHEK2 0.2 0.16 0.34 187 -10000 0 187
ONECUT1 0.63 0.49 1 199 -0.72 1 200
CDKN2A -0.041 0.15 0.25 35 -0.23 107 142
LAMA4 0.65 0.51 1 204 -1.1 4 208
FOXM1B/HNF6 0.64 0.5 1 191 -0.79 1 192
FOS 0.6 0.54 1.1 185 -0.93 2 187
SP1 0.022 0.006 -10000 0 -10000 0 0
CDC25B 0.66 0.5 1 201 -10000 0 201
response to radiation 0.14 0.11 0.23 189 -10000 0 189
CENPB 0.66 0.5 1 204 -10000 0 204
CENPA 0.75 0.57 1.2 209 -10000 0 209
NEK2 0.78 0.58 1.2 217 -10000 0 217
HIST1H2BA 0.66 0.5 1 205 -10000 0 205
CCNA2 0.14 0.16 0.4 96 -10000 0 96
EP300 0.021 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.72 0.55 1.1 203 -10000 0 203
CCNB2 0.74 0.57 1.2 209 -10000 0 209
CCNB1 0.77 0.6 1.2 209 -10000 0 209
ETV5 0.65 0.52 1.1 198 -1.1 2 200
ESR1 0.64 0.52 1 198 -1.1 3 201
CCND1 0.62 0.49 1 203 -10000 0 203
GSK3A 0.15 0.12 0.27 156 -10000 0 156
Cyclin A-E1/CDK1-2 0.28 0.22 0.45 191 -10000 0 191
CDK2 0.063 0.041 0.15 6 -10000 0 6
G2/M transition of mitotic cell cycle 0.18 0.15 0.3 200 -10000 0 200
FOXM1B/Cbp/p300 0.16 0.28 0.71 45 -0.75 2 47
GAS1 0.63 0.52 1 196 -1.1 4 200
MMP2 0.66 0.5 1 205 -10000 0 205
RB1/FOXM1C 0.53 0.45 0.92 183 -0.74 1 184
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.12 0.14 0.33 114 -9999 0 114
GPC2 0.083 0.12 0.33 71 -9999 0 71
GPC2/Midkine 0.14 0.14 0.29 147 -9999 0 147
neuron projection morphogenesis 0.14 0.14 0.29 147 -9999 0 147
Angiopoietin receptor Tie2-mediated signaling

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.4 0.46 -10000 0 -0.93 146 146
NCK1/PAK1/Dok-R -0.19 0.2 -10000 0 -0.42 150 150
NCK1/Dok-R -0.43 0.56 -10000 0 -1 146 146
PIK3CA 0.022 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.054 0.092 0.23 73 -10000 0 73
RELA 0.021 0.004 -10000 0 -10000 0 0
SHC1 0.013 0.014 -10000 0 -10000 0 0
Rac/GDP 0.014 0.005 -10000 0 -10000 0 0
F2 0.1 0.15 0.32 106 -10000 0 106
TNIP2 0.021 0.004 -10000 0 -10000 0 0
NF kappa B/RelA -0.39 0.52 -10000 0 -0.97 146 146
FN1 0.018 0.038 -10000 0 -0.34 4 4
PLD2 -0.45 0.57 -10000 0 -1.1 145 145
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GRB14 0.033 0.083 0.33 19 -0.34 5 24
ELK1 -0.42 0.5 -10000 0 -0.97 146 146
GRB7 0.019 0.027 -10000 0 -0.34 2 2
PAK1 0.021 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.41 0.55 -10000 0 -1 146 146
CDKN1A -0.29 0.31 -10000 0 -0.64 146 146
ITGA5 0.022 0.017 0.33 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.44 0.56 -10000 0 -1 146 146
CRK 0.02 0.007 -10000 0 -10000 0 0
mol:NO -0.29 0.33 -10000 0 -0.67 146 146
PLG -0.45 0.57 -10000 0 -1.1 146 146
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.37 0.43 -10000 0 -0.86 146 146
GRB2 0.021 0.005 -10000 0 -10000 0 0
PIK3R1 0.011 0.017 -10000 0 -10000 0 0
ANGPT2 -0.27 0.3 0.35 1 -0.65 110 111
BMX -0.49 0.59 -10000 0 -1.1 145 145
ANGPT1 -0.27 0.45 -10000 0 -1.1 73 73
tube development -0.33 0.35 -10000 0 -0.73 146 146
ANGPT4 -0.16 0.17 -10000 0 -0.34 171 171
response to hypoxia -0.028 0.031 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.46 0.6 -10000 0 -1.1 146 146
alpha5/beta1 Integrin 0.031 0.013 0.24 1 -10000 0 1
FGF2 -0.02 0.11 -10000 0 -0.34 40 40
STAT5A (dimer) -0.38 0.41 -10000 0 -0.84 147 147
mol:L-citrulline -0.29 0.33 -10000 0 -0.67 146 146
AGTR1 -0.08 0.16 -10000 0 -0.34 100 100
MAPK14 -0.5 0.61 -10000 0 -1.2 147 147
Tie2/SHP2 -0.39 0.51 -10000 0 -1 135 135
TEK -0.44 0.56 -10000 0 -1.1 134 134
RPS6KB1 -0.38 0.44 -10000 0 -0.88 147 147
Angiotensin II/AT1 -0.053 0.11 -10000 0 -0.23 100 100
Tie2/Ang1/GRB2 -0.46 0.6 -10000 0 -1.1 146 146
MAPK3 -0.42 0.51 -10000 0 -0.99 145 145
MAPK1 -0.41 0.51 -10000 0 -0.99 144 144
Tie2/Ang1/GRB7 -0.46 0.6 -10000 0 -1.1 146 146
NFKB1 0.022 0.003 -10000 0 -10000 0 0
MAPK8 -0.46 0.57 -10000 0 -1.1 146 146
PI3K -0.46 0.55 -10000 0 -1.1 147 147
FES -0.5 0.61 -10000 0 -1.2 147 147
Crk/Dok-R -0.43 0.56 -10000 0 -1 147 147
Tie2/Ang1/ABIN2 -0.46 0.6 -10000 0 -1.1 146 146
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.35 0.41 -10000 0 -0.82 146 146
STAT5A 0.02 0.019 -10000 0 -0.34 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.37 0.44 -10000 0 -0.87 147 147
Tie2/Ang2 -0.46 0.51 -10000 0 -1 147 147
Tie2/Ang1 -0.49 0.64 -10000 0 -1.2 146 146
FOXO1 -0.36 0.41 -10000 0 -0.83 146 146
ELF1 -0.025 0.065 -10000 0 -10000 0 0
ELF2 -0.45 0.57 -10000 0 -1.1 146 146
mol:Choline -0.43 0.54 -10000 0 -1 145 145
cell migration -0.11 0.11 -10000 0 -0.23 150 150
FYN -0.38 0.41 -10000 0 -0.84 146 146
DOK2 -0.005 0.088 -10000 0 -0.34 23 23
negative regulation of cell cycle -0.26 0.28 -10000 0 -0.58 146 146
ETS1 -0.042 0.1 -10000 0 -0.25 64 64
PXN -0.3 0.36 -10000 0 -0.71 147 147
ITGB1 0.021 0.004 -10000 0 -10000 0 0
NOS3 -0.33 0.38 -10000 0 -0.77 145 145
RAC1 0.019 0.007 -10000 0 -10000 0 0
TNF -0.055 0.12 -10000 0 -0.27 77 77
MAPKKK cascade -0.43 0.54 -10000 0 -1 145 145
RASA1 0.021 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.45 0.59 -10000 0 -1.1 146 146
NCK1 0.021 0.003 -10000 0 -10000 0 0
vasculogenesis -0.26 0.3 -10000 0 -0.6 146 146
mol:Phosphatidic acid -0.43 0.54 -10000 0 -1 145 145
mol:Angiotensin II 0 0.003 -10000 0 -10000 0 0
mol:NADP -0.29 0.33 -10000 0 -0.67 146 146
Rac1/GTP -0.35 0.41 -10000 0 -0.81 146 146
MMP2 -0.45 0.57 -10000 0 -1.1 146 146
Aurora B signaling

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
Condensin I complex 0.11 0.12 0.24 155 -0.18 6 161
STMN1 0.072 0.089 0.16 173 -10000 0 173
Aurora B/RasGAP/Survivin 0.22 0.18 0.37 196 -10000 0 196
Chromosomal passenger complex/Cul3 protein complex 0.091 0.11 0.2 154 -0.21 5 159
BIRC5 0.2 0.16 0.34 203 -10000 0 203
DES -0.15 0.28 -10000 0 -0.56 72 72
Aurora C/Aurora B/INCENP 0.12 0.098 0.22 167 -0.15 2 169
Aurora B/TACC1 0.093 0.1 0.21 141 -0.15 9 150
Aurora B/PP2A 0.12 0.11 0.24 161 -10000 0 161
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.036 0.037 0.14 14 -10000 0 14
mitotic metaphase/anaphase transition -0.005 0.006 -10000 0 -10000 0 0
NDC80 0.15 0.16 0.28 193 -10000 0 193
Cul3 protein complex 0.031 0.047 0.23 3 -0.2 10 13
KIF2C 0.17 0.13 0.26 216 -0.32 1 217
PEBP1 0.023 0.005 -10000 0 -10000 0 0
KIF20A 0.19 0.15 0.33 198 -10000 0 198
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.13 0.11 0.24 167 -10000 0 167
SEPT1 0.021 0.019 -10000 0 -0.34 1 1
SMC2 0.021 0.004 -10000 0 -10000 0 0
SMC4 0.021 0.004 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.11 0.19 0.29 95 -0.42 26 121
PSMA3 0.021 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.006 0.006 -10000 0 -10000 0 0
H3F3B 0.077 0.073 0.15 174 -10000 0 174
AURKB 0.17 0.16 0.34 174 -10000 0 174
AURKC 0.02 0.032 0.33 1 -0.34 2 3
CDCA8 0.14 0.15 0.34 131 -10000 0 131
cytokinesis 0.15 0.16 0.3 163 -0.32 3 166
Aurora B/Septin1 0.19 0.19 0.37 165 -0.26 7 172
AURKA 0.063 0.13 0.32 69 -10000 0 69
INCENP 0.029 0.01 -10000 0 -10000 0 0
KLHL13 0.014 0.066 0.33 3 -0.34 10 13
BUB1 0.098 0.15 0.33 102 -10000 0 102
hSgo1/Aurora B/Survivin 0.29 0.24 0.48 203 -10000 0 203
EVI5 0.027 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.18 0.16 0.35 137 -0.32 1 138
SGOL1 0.17 0.16 0.33 171 -10000 0 171
CENPA 0.17 0.16 0.31 187 -0.21 9 196
NCAPG 0.16 0.15 0.33 155 -10000 0 155
Aurora B/HC8 Proteasome 0.13 0.11 0.24 167 -10000 0 167
NCAPD2 0.02 0.006 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.13 0.11 0.24 169 -10000 0 169
RHOA 0.021 0.004 -10000 0 -10000 0 0
NCAPH 0.16 0.15 0.33 159 -10000 0 159
NPM1 0.075 0.14 0.23 16 -0.33 18 34
RASA1 0.021 0.005 -10000 0 -10000 0 0
KLHL9 0.018 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.002 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.13 0.11 0.24 167 -10000 0 167
PPP1CC 0.021 0.004 -10000 0 -10000 0 0
Centraspindlin 0.19 0.18 0.36 163 -0.26 2 165
RhoA/GDP 0.016 0.003 -10000 0 -10000 0 0
NSUN2 0.093 0.13 0.28 42 -0.3 14 56
MYLK 0.072 0.074 0.14 170 -0.14 5 175
KIF23 0.1 0.14 0.34 87 -10000 0 87
VIM 0.069 0.088 0.16 167 -10000 0 167
RACGAP1 0.032 0.034 0.33 4 -10000 0 4
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.077 0.13 0.2 69 -0.31 20 89
Chromosomal passenger complex 0.17 0.16 0.3 190 -0.22 4 194
Chromosomal passenger complex/EVI5 0.29 0.23 0.49 186 -10000 0 186
TACC1 0.01 0.057 -10000 0 -0.34 9 9
PPP2R5D 0.021 0.005 -10000 0 -10000 0 0
CUL3 0.022 0.003 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.28 0.24 0.54 106 -0.77 3 109
HDAC7 0.032 0.016 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.32 0.32 0.66 117 -0.85 3 120
SMAD4 0.019 0.01 -10000 0 -10000 0 0
ID2 0.29 0.24 0.54 108 -0.77 3 111
AP1 -0.001 0.079 -10000 0 -0.24 30 30
ABCG2 0.26 0.25 0.54 102 -0.73 4 106
HIF1A 0.1 0.093 0.24 69 -0.21 2 71
TFF3 0.31 0.28 0.59 128 -0.81 3 131
GATA2 -0.02 0.11 -10000 0 -0.35 31 31
AKT1 0.1 0.1 0.28 46 -0.25 3 49
response to hypoxia 0.081 0.1 0.2 97 -0.23 7 104
MCL1 0.23 0.24 0.53 88 -0.67 3 91
NDRG1 0.24 0.24 0.54 88 -0.72 3 91
SERPINE1 0.27 0.24 0.54 102 -0.77 3 105
FECH 0.25 0.25 0.54 98 -0.77 3 101
FURIN 0.28 0.25 0.56 106 -0.77 3 109
NCOA2 0.018 0.028 -10000 0 -0.34 2 2
EP300 0.12 0.14 0.3 85 -0.32 9 94
HMOX1 0.28 0.24 0.54 107 -0.72 3 110
BHLHE40 0.28 0.24 0.54 112 -0.77 3 115
BHLHE41 0.25 0.25 0.55 94 -0.69 5 99
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.13 0.14 0.37 53 -10000 0 53
ENG 0.11 0.1 0.29 30 -0.27 2 32
JUN 0.01 0.037 -10000 0 -0.35 2 2
RORA 0.27 0.25 0.54 104 -0.81 3 107
ABCB1 0.011 0.18 0.38 16 -0.73 13 29
TFRC 0.27 0.24 0.54 101 -0.78 3 104
CXCR4 0.29 0.24 0.53 111 -0.77 3 114
TF 0.32 0.29 0.62 125 -0.7 4 129
CITED2 0.27 0.25 0.54 102 -0.77 3 105
HIF1A/ARNT 0.43 0.41 0.85 138 -0.84 3 141
LDHA 0.053 0.11 0.43 10 -10000 0 10
ETS1 0.27 0.24 0.54 101 -0.67 3 104
PGK1 0.28 0.24 0.54 105 -0.77 3 108
NOS2 0.27 0.26 0.54 110 -0.86 3 113
ITGB2 0.28 0.24 0.54 107 -0.86 3 110
ALDOA 0.29 0.24 0.54 107 -0.77 3 110
Cbp/p300/CITED2 0.28 0.29 0.61 98 -1 3 101
FOS -0.013 0.095 -10000 0 -0.35 25 25
HK2 0.28 0.24 0.54 110 -0.75 4 114
SP1 0.015 0.038 -10000 0 -0.17 11 11
GCK 0.16 0.26 0.52 40 -1.1 9 49
HK1 0.28 0.24 0.54 108 -0.77 3 111
NPM1 0.27 0.24 0.54 103 -0.77 3 106
EGLN1 0.27 0.24 0.54 103 -0.72 3 106
CREB1 0.024 0.01 -10000 0 -10000 0 0
PGM1 0.28 0.24 0.54 103 -0.77 3 106
SMAD3 0.021 0.009 -10000 0 -10000 0 0
EDN1 -0.045 0.4 0.51 2 -0.98 49 51
IGFBP1 0.29 0.27 0.59 111 -0.77 3 114
VEGFA 0.26 0.24 0.52 106 -0.7 3 109
HIF1A/JAB1 0.08 0.068 0.22 26 -0.18 1 27
CP 0.38 0.3 0.62 174 -0.76 3 177
CXCL12 0.27 0.25 0.54 107 -0.86 3 110
COPS5 0.02 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4 0.027 0.015 -10000 0 -10000 0 0
BNIP3 0.28 0.24 0.54 104 -0.77 3 107
EGLN3 0.32 0.29 0.63 124 -0.67 3 127
CA9 0.41 0.3 0.63 193 -0.77 3 196
TERT 0.29 0.29 0.61 120 -0.68 3 123
ENO1 0.28 0.24 0.54 106 -0.77 3 109
PFKL 0.28 0.24 0.54 106 -0.77 3 109
NCOA1 0.022 0.002 -10000 0 -10000 0 0
ADM 0.28 0.25 0.55 103 -0.82 3 106
ARNT 0.091 0.089 0.26 43 -10000 0 43
HNF4A 0.066 0.14 0.33 63 -0.28 13 76
ADFP 0.26 0.25 0.5 129 -0.77 3 132
SLC2A1 0.34 0.28 0.6 150 -0.67 3 153
LEP 0.3 0.26 0.57 114 -0.77 3 117
HIF1A/ARNT/Cbp/p300 0.32 0.33 0.69 118 -0.88 3 121
EPO 0.22 0.23 0.55 64 -0.8 2 66
CREBBP 0.12 0.14 0.29 87 -0.28 8 95
HIF1A/ARNT/Cbp/p300/HDAC7 0.35 0.34 0.7 130 -0.82 3 133
PFKFB3 0.27 0.24 0.54 102 -0.77 3 105
NT5E 0.28 0.26 0.57 104 -0.77 3 107
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.09 0.18 0.32 6 -0.52 29 35
IHH -0.16 0.21 0.34 4 -0.38 164 168
SHH Np/Cholesterol/GAS1 -0.038 0.06 0.12 1 -0.19 46 47
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.038 0.06 0.19 46 -0.11 1 47
SMO/beta Arrestin2 -0.15 0.18 0.32 1 -0.42 40 41
SMO -0.15 0.19 0.34 1 -0.34 137 138
AKT1 -0.08 0.15 -10000 0 -0.5 23 23
ARRB2 0.02 0.006 -10000 0 -10000 0 0
BOC 0.021 0.004 -10000 0 -10000 0 0
ADRBK1 0.021 0.004 -10000 0 -10000 0 0
heart looping -0.15 0.18 0.34 1 -0.34 138 139
STIL -0.083 0.14 0.26 9 -0.32 44 53
DHH N/PTCH2 0.014 0.067 -10000 0 -0.24 23 23
DHH N/PTCH1 -0.11 0.15 -10000 0 -0.36 41 41
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
DHH -0.001 0.087 -10000 0 -0.34 22 22
PTHLH -0.12 0.22 0.39 6 -0.57 28 34
determination of left/right symmetry -0.15 0.18 0.34 1 -0.34 138 139
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
skeletal system development -0.12 0.22 0.39 6 -0.57 28 34
IHH N/Hhip -0.23 0.18 0.21 3 -0.32 264 267
DHH N/Hhip -0.13 0.15 -10000 0 -0.25 194 194
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.15 0.18 0.34 1 -0.34 138 139
pancreas development -0.17 0.18 -10000 0 -0.34 192 192
HHAT 0.018 0.028 -10000 0 -0.34 2 2
PI3K 0.03 0.009 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.011 0.06 -10000 0 -0.34 10 10
somite specification -0.15 0.18 0.34 1 -0.34 138 139
SHH Np/Cholesterol/PTCH1 -0.1 0.13 0.18 2 -0.33 50 52
SHH Np/Cholesterol/PTCH2 -0.035 0.055 0.12 1 -0.18 41 42
SHH Np/Cholesterol/Megalin -0.07 0.091 0.12 1 -0.2 103 104
SHH -0.041 0.072 0.16 1 -0.24 41 42
catabolic process -0.11 0.16 0.23 3 -0.4 29 32
SMO/Vitamin D3 -0.12 0.17 0.37 2 -0.4 45 47
SHH Np/Cholesterol/Hhip -0.11 0.1 0.12 1 -0.2 179 180
LRP2 -0.072 0.16 0.33 1 -0.34 93 94
receptor-mediated endocytosis -0.17 0.18 0.3 2 -0.41 91 93
SHH Np/Cholesterol/BOC -0.034 0.053 0.12 1 -0.18 39 40
SHH Np/Cholesterol/CDO -0.036 0.059 0.12 1 -0.19 42 43
mesenchymal cell differentiation 0.11 0.1 0.2 179 -0.11 1 180
mol:Vitamin D3 -0.093 0.15 0.36 5 -0.34 45 50
IHH N/PTCH2 -0.1 0.13 0.21 4 -0.22 193 197
CDON 0.013 0.05 -10000 0 -0.34 7 7
IHH N/PTCH1 -0.098 0.17 0.27 3 -0.4 29 32
Megalin/LRPAP1 -0.037 0.12 0.24 1 -0.24 90 91
PTCH2 0.021 0.019 -10000 0 -0.34 1 1
SHH Np/Cholesterol -0.03 0.054 -10000 0 -0.18 41 41
PTCH1 -0.11 0.16 0.23 3 -0.4 29 32
HHIP -0.17 0.18 -10000 0 -0.34 192 192
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.054 0.065 0.12 9 -0.12 171 180
BUB1B 0.078 0.077 0.15 166 -0.12 2 168
PLK1 0.033 0.042 0.095 84 -0.08 1 85
PLK1S1 0.016 0.038 0.12 2 -0.17 9 11
KIF2A 0.026 0.047 0.16 18 -10000 0 18
regulation of mitotic centrosome separation 0.033 0.041 0.096 78 -0.08 1 79
GOLGA2 0.021 0.004 -10000 0 -10000 0 0
Hec1/SPC24 0.19 0.18 0.35 179 -10000 0 179
WEE1 0.032 0.064 0.18 2 -0.26 9 11
cytokinesis 0.097 0.099 0.21 105 -0.2 2 107
PP2A-alpha B56 0.087 0.092 -10000 0 -0.48 3 3
AURKA 0.041 0.061 0.14 81 -0.19 4 85
PICH/PLK1 0.088 0.12 0.23 137 -10000 0 137
CENPE 0.038 0.057 0.14 64 -10000 0 64
RhoA/GTP 0.016 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.027 0.047 0.16 18 -10000 0 18
PPP2CA 0.021 0.005 -10000 0 -10000 0 0
FZR1 0.02 0.006 -10000 0 -10000 0 0
TPX2 0.079 0.069 0.14 201 -0.16 3 204
PAK1 0.02 0.006 -10000 0 -10000 0 0
SPC24 0.12 0.14 0.33 108 -10000 0 108
FBXW11 0.021 0.005 -10000 0 -10000 0 0
CLSPN 0.067 0.075 0.15 138 -0.18 4 142
GORASP1 0.021 0.004 -10000 0 -10000 0 0
metaphase 0 0.002 0.016 6 -0.011 1 7
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.015 0.02 0.054 37 -0.04 1 38
G2 phase of mitotic cell cycle 0.001 0.003 0.015 9 -10000 0 9
STAG2 0.022 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.004 0.094 -10000 0 -0.51 11 11
spindle elongation 0.033 0.041 0.096 78 -0.08 1 79
ODF2 0.022 0.007 -10000 0 -10000 0 0
BUB1 0.079 0.11 -10000 0 -0.52 3 3
TPT1 0.01 0.046 0.11 2 -0.16 19 21
CDC25C 0.11 0.097 0.17 227 -0.24 11 238
CDC25B 0.023 0.012 -10000 0 -10000 0 0
SGOL1 0.054 0.065 0.12 171 -0.12 9 180
RHOA 0.021 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.084 0.093 0.22 105 -10000 0 105
CDC14B -0.009 0.004 -10000 0 -10000 0 0
CDC20 0.2 0.15 0.33 209 -10000 0 209
PLK1/PBIP1 0.011 0.044 0.15 31 -10000 0 31
mitosis -0.004 0.007 0.02 6 -0.016 59 65
FBXO5 0.016 0.042 0.12 8 -0.11 2 10
CDC2 0.004 0.006 0.012 108 -0.01 6 114
NDC80 0.17 0.16 0.33 166 -10000 0 166
metaphase plate congression 0.023 0.046 -10000 0 -0.22 8 8
ERCC6L 0.09 0.11 0.22 128 -10000 0 128
NLP/gamma Tubulin 0.018 0.024 0.075 20 -0.093 2 22
microtubule cytoskeleton organization 0.01 0.046 0.11 2 -0.16 19 21
G2/M transition DNA damage checkpoint -0.001 0.002 0.014 1 -10000 0 1
PPP1R12A 0.022 0.006 -10000 0 -10000 0 0
interphase -0.001 0.002 0.014 1 -10000 0 1
PLK1/PRC1-2 0.18 0.16 0.31 194 -10000 0 194
GRASP65/GM130/RAB1/GTP/PLK1 0.054 0.033 -10000 0 -10000 0 0
RAB1A 0.022 0.001 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.027 0.037 0.085 81 -0.066 1 82
mitotic prometaphase 0.001 0.003 0.018 8 -10000 0 8
proteasomal ubiquitin-dependent protein catabolic process 0.048 0.059 0.18 1 -0.39 1 2
microtubule-based process 0.15 0.12 0.26 198 -10000 0 198
Golgi organization 0.033 0.041 0.096 78 -0.08 1 79
Cohesin/SA2 0.04 0.033 0.12 9 -10000 0 9
PPP1CB/MYPT1 0.032 0.007 -10000 0 -10000 0 0
KIF20A 0.2 0.15 0.33 198 -10000 0 198
APC/C/CDC20 0.16 0.12 0.26 210 -10000 0 210
PPP2R1A 0.021 0.004 -10000 0 -10000 0 0
chromosome segregation 0.011 0.044 0.14 31 -10000 0 31
PRC1 0.076 0.12 0.33 62 -10000 0 62
ECT2 0.036 0.063 0.18 40 -10000 0 40
C13orf34 0.027 0.035 0.081 75 -0.067 1 76
NUDC 0.023 0.046 -10000 0 -0.22 8 8
regulation of attachment of spindle microtubules to kinetochore 0.077 0.077 0.15 168 -0.11 2 170
spindle assembly 0.025 0.033 0.095 32 -0.071 1 33
spindle stabilization 0.016 0.037 0.12 2 -0.17 9 11
APC/C/HCDH1 0.016 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 0.15 0.12 0.26 198 -10000 0 198
CCNB1 0.12 0.15 0.33 114 -10000 0 114
PPP1CB 0.022 0.005 -10000 0 -10000 0 0
BTRC 0.022 0.003 -10000 0 -10000 0 0
ROCK2 0.028 0.036 0.17 2 -0.18 1 3
TUBG1 0.02 0.028 0.12 4 -0.21 2 6
G2/M transition of mitotic cell cycle 0.034 0.061 0.13 75 -10000 0 75
MLF1IP 0.006 0.046 0.16 28 -10000 0 28
INCENP 0.021 0.003 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.08 0.11 0.23 1 -0.28 49 50
PTK2B 0.018 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.13 0.28 -10000 0 -0.88 35 35
EDN1 -0.071 0.13 -10000 0 -0.35 48 48
EDN3 -0.072 0.16 0.33 1 -0.34 90 91
EDN2 0.1 0.14 0.33 93 -0.34 1 94
HRAS/GDP -0.16 0.19 -10000 0 -0.44 79 79
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.071 0.13 -10000 0 -0.36 44 44
ADCY4 -0.069 0.1 -10000 0 -0.28 39 39
ADCY5 -0.08 0.13 0.22 7 -0.3 55 62
ADCY6 -0.063 0.1 0.23 4 -0.28 30 34
ADCY7 -0.064 0.099 0.3 1 -0.28 30 31
ADCY1 -0.06 0.1 0.22 3 -0.28 31 34
ADCY2 -0.06 0.12 0.27 6 -0.3 35 41
ADCY3 -0.063 0.1 0.29 3 -0.27 32 35
ADCY8 -0.098 0.12 0.38 2 -0.26 83 85
ADCY9 -0.066 0.11 0.32 2 -0.28 37 39
arachidonic acid secretion -0.13 0.2 -10000 0 -0.49 65 65
ETB receptor/Endothelin-1/Gq/GTP -0.14 0.16 -10000 0 -0.3 139 139
GNAO1 0.02 0.032 0.33 1 -0.34 2 3
HRAS 0.021 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.05 0.12 0.31 1 -0.29 33 34
ETA receptor/Endothelin-1/Gs/GTP -0.051 0.12 0.29 1 -0.27 37 38
mol:GTP -0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.046 0.16 0.29 23 -0.33 30 53
EDNRB -0.16 0.18 -10000 0 -0.34 182 182
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.086 0.13 0.23 1 -0.38 32 33
CYSLTR1 -0.087 0.12 0.23 1 -0.37 32 33
SLC9A1 -0.048 0.08 0.16 1 -0.22 33 34
mol:GDP -0.16 0.2 -10000 0 -0.45 86 86
SLC9A3 -0.3 0.35 -10000 0 -0.77 86 86
RAF1 -0.16 0.2 -10000 0 -0.49 73 73
JUN -0.11 0.22 -10000 0 -0.66 34 34
JAK2 -0.076 0.11 0.23 1 -0.28 46 47
mol:IP3 -0.12 0.17 -10000 0 -0.4 70 70
ETA receptor/Endothelin-1 -0.08 0.15 0.36 1 -0.31 58 59
PLCB1 0.018 0.02 0.33 1 -10000 0 1
PLCB2 0.009 0.051 -10000 0 -0.34 7 7
ETA receptor/Endothelin-3 -0.078 0.12 0.19 1 -0.25 97 98
FOS -0.16 0.25 -10000 0 -0.69 50 50
Gai/GDP -0.051 0.2 -10000 0 -0.79 21 21
CRK 0.019 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.16 0.19 -10000 0 -0.43 87 87
BCAR1 0.02 0.02 -10000 0 -0.34 1 1
PRKCB1 -0.13 0.17 -10000 0 -0.39 71 71
GNAQ 0.014 0.025 -10000 0 -0.34 1 1
GNAZ -0.007 0.097 -10000 0 -0.34 28 28
GNAL 0.017 0.042 0.33 1 -0.34 4 5
Gs family/GDP -0.15 0.18 -10000 0 -0.44 72 72
ETA receptor/Endothelin-1/Gq/GTP -0.069 0.13 -10000 0 -0.37 37 37
MAPK14 -0.13 0.15 0.2 1 -0.34 88 89
TRPC6 -0.14 0.3 -10000 0 -0.95 35 35
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.021 0.005 -10000 0 -10000 0 0
GNAI1 0.02 0.02 -10000 0 -0.34 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.14 0.16 -10000 0 -0.35 94 94
ETB receptor/Endothelin-2 -0.077 0.15 0.24 30 -0.21 179 209
ETB receptor/Endothelin-3 -0.16 0.16 0.24 1 -0.28 207 208
ETB receptor/Endothelin-1 -0.15 0.16 0.21 6 -0.3 175 181
MAPK3 -0.17 0.25 -10000 0 -0.66 58 58
MAPK1 -0.18 0.25 -10000 0 -0.66 60 60
Rac1/GDP -0.14 0.19 -10000 0 -0.43 76 76
cAMP biosynthetic process -0.08 0.14 0.29 5 -0.34 47 52
MAPK8 -0.12 0.25 -10000 0 -0.71 43 43
SRC 0.021 0.004 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.13 0.14 -10000 0 -0.28 124 124
p130Cas/CRK/Src/PYK2 -0.17 0.23 0.31 1 -0.59 62 63
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.14 0.19 -10000 0 -0.44 71 71
COL1A2 -0.16 0.18 0.31 6 -0.37 108 114
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.043 0.12 0.22 92 -0.18 12 104
mol:DAG -0.12 0.17 -10000 0 -0.4 70 70
MAP2K2 -0.17 0.22 -10000 0 -0.55 65 65
MAP2K1 -0.17 0.22 -10000 0 -0.54 69 69
EDNRA -0.038 0.079 0.21 2 -0.21 20 22
positive regulation of muscle contraction -0.056 0.11 0.2 16 -0.27 35 51
Gq family/GDP -0.12 0.18 -10000 0 -0.43 61 61
HRAS/GTP -0.15 0.2 -10000 0 -0.46 74 74
PRKCH -0.13 0.16 -10000 0 -0.4 66 66
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.13 0.17 -10000 0 -0.4 67 67
PRKCB -0.13 0.17 -10000 0 -0.42 68 68
PRKCE -0.13 0.17 -10000 0 -0.4 71 71
PRKCD -0.13 0.16 -10000 0 -0.4 65 65
PRKCG -0.12 0.16 -10000 0 -0.4 62 62
regulation of vascular smooth muscle contraction -0.19 0.3 -10000 0 -0.82 50 50
PRKCQ -0.14 0.18 -10000 0 -0.42 77 77
PLA2G4A -0.14 0.22 -10000 0 -0.54 65 65
GNA14 0.006 0.062 -10000 0 -0.34 10 10
GNA15 0.015 0.016 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA11 0.015 0.016 -10000 0 -10000 0 0
Rac1/GTP -0.05 0.12 0.31 1 -0.26 43 44
MMP1 0.2 0.17 0.31 221 -0.68 2 223
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.022 0.003 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.12 0.095 0.22 167 -0.15 2 169
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.016 0.014 -10000 0 -10000 0 0
AURKB 0.17 0.16 0.33 174 -10000 0 174
AURKC 0.02 0.032 0.33 1 -0.34 2 3
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.078 0.26 0.31 4 -0.65 50 54
MKNK1 0.022 0.003 -10000 0 -10000 0 0
MAPK14 -0.018 0.12 -10000 0 -0.29 50 50
ATF2/c-Jun -0.032 0.1 -10000 0 -0.26 48 48
MAPK11 -0.016 0.12 -10000 0 -0.31 45 45
MITF -0.041 0.14 -10000 0 -0.36 53 53
MAPKAPK5 -0.037 0.13 -10000 0 -0.35 50 50
KRT8 -0.035 0.13 0.28 2 -0.34 51 53
MAPKAPK3 0.021 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.02 0.007 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.031 0.17 -10000 0 -0.41 52 52
CEBPB -0.035 0.13 -10000 0 -0.36 46 46
SLC9A1 -0.037 0.13 -10000 0 -0.35 50 50
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.037 0.13 0.23 2 -0.34 53 55
p38alpha-beta/MNK1 -0.01 0.14 -10000 0 -0.34 49 49
JUN -0.03 0.1 -10000 0 -0.26 48 48
PPARGC1A -0.096 0.18 -10000 0 -0.33 112 112
USF1 -0.028 0.12 0.3 2 -0.35 42 44
RAB5/GDP/GDI1 -0.025 0.1 -10000 0 -0.26 51 51
NOS2 -0.076 0.25 0.33 4 -0.62 51 55
DDIT3 -0.034 0.13 0.24 1 -0.34 49 50
RAB5A 0.021 0.004 -10000 0 -10000 0 0
HSPB1 -0.035 0.11 0.26 8 -0.3 44 52
p38alpha-beta/HBP1 -0.011 0.14 -10000 0 -0.34 48 48
CREB1 -0.042 0.14 0.24 1 -0.37 52 53
RAB5/GDP 0.016 0.003 -10000 0 -10000 0 0
EIF4E -0.054 0.11 -10000 0 -0.32 42 42
RPS6KA4 -0.038 0.13 0.19 1 -0.35 52 53
PLA2G4A -0.023 0.13 0.19 47 -0.32 39 86
GDI1 -0.036 0.13 -10000 0 -0.34 50 50
TP53 -0.059 0.15 0.26 1 -0.43 46 47
RPS6KA5 -0.035 0.13 0.3 2 -0.34 49 51
ESR1 -0.04 0.15 0.28 1 -0.38 51 52
HBP1 0.021 0.005 -10000 0 -10000 0 0
MEF2C -0.036 0.13 -10000 0 -0.35 49 49
MEF2A -0.037 0.13 -10000 0 -0.35 50 50
EIF4EBP1 -0.045 0.15 0.25 1 -0.39 53 54
KRT19 -0.037 0.13 -10000 0 -0.35 50 50
ELK4 -0.032 0.12 -10000 0 -0.34 46 46
ATF6 -0.029 0.12 0.32 1 -0.34 43 44
ATF1 -0.042 0.14 0.24 2 -0.37 53 55
p38alpha-beta/MAPKAPK2 -0.011 0.14 -10000 0 -0.34 47 47
p38alpha-beta/MAPKAPK3 -0.012 0.14 -10000 0 -0.34 50 50
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.007 0.054 -10000 0 -0.33 7 7
Crk/p130 Cas/Paxillin -0.062 0.091 -10000 0 -0.23 65 65
JUN -0.036 0.093 0.24 2 -0.29 7 9
HRAS 0.021 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.008 0.12 0.24 30 -0.18 72 102
RAP1A 0.021 0.005 -10000 0 -10000 0 0
FRS2 0.02 0.006 -10000 0 -10000 0 0
RAP1A/GDP 0.016 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.006 0.12 0.24 32 -0.18 81 113
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.02 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.017 0.094 0.22 5 -0.18 82 87
RHOA 0.021 0.004 -10000 0 -10000 0 0
RAP1A/GTP 0.003 0.11 0.34 2 -0.18 68 70
GRB7 0.019 0.027 -10000 0 -0.34 2 2
RET51/GFRalpha1/GDNF 0.003 0.12 0.24 31 -0.18 83 114
MAPKKK cascade -0.051 0.093 0.18 7 -0.21 64 71
BCAR1 0.02 0.02 -10000 0 -0.34 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.016 0.096 0.22 6 -0.18 83 89
lamellipodium assembly -0.042 0.091 0.13 1 -0.22 57 58
RET51/GFRalpha1/GDNF/SHC 0.007 0.11 0.24 29 -0.18 69 98
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.013 0.087 0.22 4 -0.18 68 72
RET9/GFRalpha1/GDNF/Shank3 -0.017 0.097 0.22 6 -0.18 83 89
MAPK3 -0.025 0.1 0.21 13 -0.31 1 14
DOK1 0.022 0.003 -10000 0 -10000 0 0
DOK6 -0.006 0.092 -10000 0 -0.34 25 25
PXN 0.021 0.004 -10000 0 -10000 0 0
neurite development -0.031 0.098 0.26 6 -0.24 11 17
DOK5 0.065 0.11 0.33 51 -10000 0 51
GFRA1 -0.084 0.16 0.33 1 -0.34 105 106
MAPK8 -0.042 0.09 0.16 5 -0.2 70 75
HRAS/GTP -0.008 0.12 0.35 2 -0.22 70 72
tube development -0.014 0.095 0.2 12 -0.18 79 91
MAPK1 -0.024 0.098 0.22 11 -0.31 1 12
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.034 0.086 0.15 2 -0.2 72 74
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
SRC 0.021 0.004 -10000 0 -10000 0 0
PDLIM7 0.021 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.004 0.13 0.24 28 -0.19 90 118
SHC1 0.018 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.007 0.12 0.24 31 -0.18 79 110
RET51/GFRalpha1/GDNF/Dok5 0.021 0.13 0.25 52 -0.18 73 125
PRKCA 0.019 0.027 -10000 0 -0.34 2 2
HRAS/GDP 0.016 0.003 -10000 0 -10000 0 0
CREB1 -0.025 0.098 0.2 2 -0.23 53 55
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.029 0.085 0.17 3 -0.2 63 66
RET51/GFRalpha1/GDNF/Grb7 0.005 0.12 0.24 31 -0.18 83 114
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.061 0.11 0.33 48 -0.34 3 51
DOK4 0.021 0.005 -10000 0 -10000 0 0
JNK cascade -0.035 0.093 0.23 2 -0.28 7 9
RET9/GFRalpha1/GDNF/FRS2 -0.015 0.093 0.22 6 -0.18 77 83
SHANK3 0.017 0.033 -10000 0 -0.34 3 3
RASA1 0.021 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.027 0.081 0.17 3 -0.2 61 64
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.023 0.098 0.18 9 -0.2 69 78
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.028 0.1 0.18 6 -0.2 72 78
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.014 0.092 0.19 9 -0.2 54 63
PI3K -0.052 0.14 0.27 2 -0.3 68 70
SOS1 0.022 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.009 0.097 0.22 6 -0.18 79 85
GRB10 0.02 0.007 -10000 0 -10000 0 0
activation of MAPKK activity -0.017 0.094 0.16 9 -0.19 66 75
RET51/GFRalpha1/GDNF/FRS2 0.006 0.12 0.24 31 -0.18 80 111
GAB1 0.021 0.019 -10000 0 -0.34 1 1
IRS1 0.021 0.019 -10000 0 -0.34 1 1
IRS2 0.02 0.02 -10000 0 -0.34 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.018 0.097 0.19 9 -0.21 58 67
RET51/GFRalpha1/GDNF/PKC alpha 0.005 0.12 0.24 31 -0.18 80 111
GRB2 0.021 0.005 -10000 0 -10000 0 0
PRKACA 0.02 0.006 -10000 0 -10000 0 0
GDNF 0.023 0.045 0.33 7 -10000 0 7
RAC1 0.019 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.005 0.12 0.24 32 -0.18 83 115
Rac1/GTP -0.036 0.12 0.22 1 -0.25 55 56
RET9/GFRalpha1/GDNF -0.026 0.097 0.21 6 -0.2 82 88
GFRalpha1/GDNF -0.034 0.12 0.24 6 -0.24 82 88
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 -0.036 0.29 0.55 23 -0.63 21 44
PCK1 0.053 0.24 0.58 32 -10000 0 32
HNF4A -0.12 0.47 0.69 38 -0.79 79 117
KCNJ11 0.002 0.3 0.59 26 -0.76 13 39
AKT1 0.031 0.19 0.41 31 -0.53 2 33
response to starvation -0.027 0.075 0.15 3 -0.21 27 30
DLK1 0.024 0.3 0.59 34 -0.64 8 42
NKX2-1 -0.061 0.34 0.52 5 -1.1 27 32
ACADM -0.039 0.29 0.52 26 -0.61 25 51
TAT 0.042 0.23 0.58 28 -10000 0 28
CEBPB 0.027 0.02 -10000 0 -10000 0 0
CEBPA 0.014 0.084 0.22 3 -0.33 17 20
TTR 0.061 0.28 0.67 34 -0.71 7 41
PKLR -0.013 0.3 0.58 28 -0.63 19 47
APOA1 -0.23 0.62 0.79 24 -1.1 102 126
CPT1C -0.037 0.3 0.54 26 -0.61 25 51
ALAS1 0.024 0.19 0.47 17 -0.48 2 19
TFRC 0.069 0.3 0.64 42 -0.79 9 51
FOXF1 -0.006 0.12 0.24 17 -0.34 37 54
NF1 0.023 0.004 -10000 0 -10000 0 0
HNF1A (dimer) 0.1 0.15 0.4 66 -0.34 1 67
CPT1A -0.034 0.3 0.53 27 -0.61 24 51
HMGCS1 -0.013 0.3 0.58 28 -0.6 23 51
NR3C1 0.044 0.045 0.2 7 -10000 0 7
CPT1B -0.038 0.29 0.54 25 -0.63 22 47
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.041 0.04 -10000 0 -10000 0 0
GCK -0.032 0.31 0.55 27 -0.64 27 54
CREB1 0.037 0.038 0.19 6 -10000 0 6
IGFBP1 0.023 0.21 0.49 33 -0.43 2 35
PDX1 0.086 0.27 0.66 43 -0.51 2 45
UCP2 -0.035 0.3 0.56 24 -0.63 20 44
ALDOB 0.022 0.31 0.65 31 -0.71 8 39
AFP 0.083 0.11 0.34 32 -10000 0 32
BDH1 -0.038 0.3 0.53 28 -0.61 24 52
HADH 0.007 0.29 0.58 25 -0.64 7 32
F2 -0.038 0.43 0.82 32 -0.84 22 54
HNF1A 0.1 0.15 0.4 66 -0.34 1 67
G6PC 0.076 0.13 0.47 19 -10000 0 19
SLC2A2 0.07 0.29 0.68 40 -0.74 2 42
INS -0.033 0.035 -10000 0 -10000 0 0
FOXA1 0.072 0.1 0.31 40 -0.34 1 41
FOXA3 0.15 0.19 0.42 94 -0.3 3 97
FOXA2 0.042 0.39 0.82 38 -0.66 19 57
ABCC8 -0.025 0.36 0.62 29 -0.77 39 68
ALB 0.094 0.13 0.37 35 -10000 0 35
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.079 0.078 0.2 61 -10000 0 61
NF kappa B1 p50/RelA/I kappa B alpha 0.088 0.097 0.29 27 -0.28 1 28
alphaV/beta3 Integrin/Osteopontin/Src 0.19 0.096 0.25 255 -10000 0 255
AP1 0.078 0.11 0.33 13 -10000 0 13
ILK 0.071 0.071 0.24 19 -10000 0 19
bone resorption 0.048 0.073 0.23 15 -10000 0 15
PTK2B 0.018 0.008 -10000 0 -10000 0 0
PYK2/p130Cas 0.14 0.12 0.29 57 -10000 0 57
ITGAV 0.027 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.03 0.021 -10000 0 -0.24 2 2
alphaV/beta3 Integrin/Osteopontin 0.19 0.12 0.26 249 -0.2 3 252
MAP3K1 0.07 0.07 0.21 27 -0.19 3 30
JUN 0.02 0.027 -10000 0 -0.34 2 2
MAPK3 0.065 0.084 0.22 63 -10000 0 63
MAPK1 0.063 0.082 0.22 59 -10000 0 59
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.003 -10000 0 -10000 0 0
MAPK8 0.048 0.062 0.21 19 -10000 0 19
ITGB3 0.038 0.082 0.34 19 -0.34 4 23
NFKBIA 0.06 0.087 0.23 59 -10000 0 59
FOS -0.004 0.092 -10000 0 -0.34 25 25
CD44 0.019 0.027 -10000 0 -0.34 2 2
CHUK 0.022 0.003 -10000 0 -10000 0 0
PLAU 0.091 0.14 0.35 61 -10000 0 61
NF kappa B1 p50/RelA 0.091 0.1 0.27 65 -10000 0 65
BCAR1 0.02 0.02 -10000 0 -0.34 1 1
RELA 0.021 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.048 0.061 0.26 19 -0.24 4 23
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.069 0.071 0.21 28 -0.19 4 32
VAV3 0.045 0.065 0.21 20 -0.3 2 22
MAP3K14 0.079 0.079 0.2 70 -0.19 3 73
ROCK2 0.022 0.002 -10000 0 -10000 0 0
SPP1 0.25 0.14 0.34 258 -10000 0 258
RAC1 0.019 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.039 0.062 0.19 17 -0.28 2 19
MMP2 0.032 0.076 0.3 5 -10000 0 5
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.034 0.043 0.2 10 -0.17 7 17
RGS9BP -0.029 0.12 -10000 0 -0.34 49 49
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.037 0.072 0.33 20 -10000 0 20
mol:Na + 0.1 0.11 0.24 130 -10000 0 130
mol:ADP -0.007 0.044 0.16 22 -10000 0 22
GNAT2 0.021 0.017 0.33 1 -10000 0 1
RGS9-1/Gbeta5/R9AP -0.059 0.13 -10000 0 -0.23 128 128
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.025 0.017 0.21 2 -10000 0 2
GRK7 0.021 0.017 0.33 1 -10000 0 1
CNGB3 0.062 0.11 0.33 50 -10000 0 50
Cone Metarhodopsin II/X-Arrestin 0.015 0.011 0.22 1 -10000 0 1
mol:Ca2+ 0.055 0.092 0.21 72 -10000 0 72
Cone PDE6 -0.041 0.12 -10000 0 -0.2 126 126
Cone Metarhodopsin II 0.035 0.043 0.2 21 -10000 0 21
Na + (4 Units) 0.11 0.11 0.24 133 -10000 0 133
GNAT2/GDP -0.045 0.12 -10000 0 -0.2 127 127
GNB5 0.021 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.014 0.028 0.17 7 -10000 0 7
Cone Transducin 0.037 0.046 0.22 10 -0.18 7 17
SLC24A2 0.044 0.086 0.33 29 -10000 0 29
GNB3/GNGT2 0.03 0.053 0.24 10 -0.24 7 17
GNB3 0.028 0.055 0.33 10 -0.34 1 11
GNAT2/GTP 0.016 0.011 0.22 1 -10000 0 1
CNGA3 0.12 0.14 0.33 112 -10000 0 112
ARR3 0.02 0.017 0.33 1 -10000 0 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.1 0.11 0.24 130 -10000 0 130
mol:Pi -0.059 0.13 -10000 0 -0.22 128 128
Cone CNG Channel 0.092 0.091 0.35 14 -10000 0 14
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.044 0.086 0.33 29 -10000 0 29
RGS9 -0.084 0.16 -10000 0 -0.34 103 103
PDE6C 0.019 0.003 -10000 0 -10000 0 0
GNGT2 0.015 0.046 -10000 0 -0.34 6 6
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.019 0.017 0.33 1 -10000 0 1
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.021 0.017 0.33 1 -10000 0 1
LAT2 -0.074 0.13 -10000 0 -0.31 62 62
AP1 -0.081 0.2 -10000 0 -0.47 56 56
mol:PIP3 -0.075 0.18 0.3 17 -0.36 71 88
IKBKB -0.027 0.12 0.26 26 -0.23 43 69
AKT1 -0.037 0.15 0.31 39 -0.27 30 69
IKBKG -0.037 0.12 0.23 20 -0.22 48 68
MS4A2 -0.062 0.15 -10000 0 -0.33 78 78
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.02 0.007 -10000 0 -10000 0 0
MAP3K1 -0.064 0.15 0.23 9 -0.36 49 58
mol:Ca2+ -0.055 0.15 0.26 20 -0.28 69 89
LYN 0.011 0.02 -10000 0 -10000 0 0
CBLB -0.075 0.13 -10000 0 -0.31 64 64
SHC1 0.018 0.008 -10000 0 -10000 0 0
RasGAP/p62DOK 0.02 0.061 -10000 0 -0.18 28 28
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.02 0.027 -10000 0 -0.34 2 2
PLD2 -0.044 0.16 0.3 40 -0.25 73 113
PTPN13 -0.087 0.17 -10000 0 -0.58 15 15
PTPN11 0.01 0.025 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.045 0.13 0.31 9 -0.29 25 34
SYK 0.011 0.033 -10000 0 -0.34 2 2
GRB2 0.021 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.086 0.16 -10000 0 -0.36 74 74
LAT -0.075 0.13 -10000 0 -0.31 65 65
PAK2 -0.07 0.17 0.25 8 -0.4 51 59
NFATC2 -0.034 0.091 -10000 0 -0.49 10 10
HRAS -0.073 0.18 0.25 7 -0.42 51 58
GAB2 0.017 0.038 -10000 0 -0.34 4 4
PLA2G1B -0.049 0.16 -10000 0 -0.92 11 11
Fc epsilon R1 -0.057 0.15 0.22 1 -0.26 109 110
Antigen/IgE/Fc epsilon R1 -0.049 0.13 0.21 1 -0.24 109 110
mol:GDP -0.089 0.18 -10000 0 -0.46 52 52
JUN 0.019 0.027 -10000 0 -0.34 2 2
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.02 0.007 -10000 0 -10000 0 0
FOS -0.005 0.092 -10000 0 -0.34 25 25
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.071 0.14 -10000 0 -0.32 65 65
CHUK -0.042 0.12 0.22 19 -0.22 52 71
KLRG1 -0.066 0.12 0.14 1 -0.28 57 58
VAV1 -0.071 0.13 -10000 0 -0.32 58 58
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.073 0.13 -10000 0 -0.31 62 62
negative regulation of mast cell degranulation -0.056 0.12 -10000 0 -0.32 40 40
BTK -0.098 0.2 -10000 0 -0.49 56 56
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.082 0.16 -10000 0 -0.32 83 83
GAB2/PI3K/SHP2 -0.082 0.087 -10000 0 -0.23 72 72
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.066 0.13 -10000 0 -0.28 75 75
RAF1 -0.013 0.18 -10000 0 -0.97 11 11
Fc epsilon R1/FcgammaRIIB/SHIP -0.035 0.14 -10000 0 -0.24 105 105
FCER1G 0.01 0.05 -10000 0 -0.34 6 6
FCER1A -0.067 0.15 0.33 1 -0.35 79 80
Antigen/IgE/Fc epsilon R1/Fyn -0.043 0.13 0.21 1 -0.22 108 109
MAPK3 -0.015 0.16 -10000 0 -0.89 11 11
MAPK1 -0.019 0.16 -10000 0 -0.9 11 11
NFKB1 0.022 0.003 -10000 0 -10000 0 0
MAPK8 -0.075 0.23 -10000 0 -0.66 38 38
DUSP1 -0.008 0.097 -10000 0 -0.34 28 28
NF-kappa-B/RelA -0.031 0.066 0.14 8 -0.15 37 45
actin cytoskeleton reorganization -0.071 0.17 -10000 0 -0.62 9 9
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.063 0.16 -10000 0 -0.38 48 48
FER -0.074 0.13 -10000 0 -0.31 63 63
RELA 0.021 0.004 -10000 0 -10000 0 0
ITK -0.025 0.067 -10000 0 -0.27 17 17
SOS1 0.022 0.003 -10000 0 -10000 0 0
PLCG1 -0.087 0.19 0.26 3 -0.44 56 59
cytokine secretion -0.028 0.041 -10000 0 -0.14 4 4
SPHK1 -0.073 0.12 -10000 0 -0.3 62 62
PTK2 -0.074 0.18 -10000 0 -0.65 9 9
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.087 0.17 0.22 1 -0.36 75 76
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.074 0.18 0.28 19 -0.35 72 91
MAP2K2 -0.02 0.16 -10000 0 -0.91 11 11
MAP2K1 -0.019 0.17 -10000 0 -0.91 11 11
MAP2K7 0.02 0.006 -10000 0 -10000 0 0
KLRG1/SHP2 -0.05 0.11 0.17 1 -0.29 40 41
MAP2K4 -0.11 0.34 -10000 0 -0.91 53 53
Fc epsilon R1/FcgammaRIIB -0.043 0.14 0.22 1 -0.24 109 110
mol:Choline -0.043 0.16 0.3 40 -0.24 73 113
SHC/Grb2/SOS1 -0.044 0.14 -10000 0 -0.3 54 54
FYN 0.02 0.007 -10000 0 -10000 0 0
DOK1 0.022 0.003 -10000 0 -10000 0 0
PXN -0.072 0.16 0.35 1 -0.6 9 10
HCLS1 -0.074 0.13 -10000 0 -0.32 60 60
PRKCB -0.056 0.15 0.26 19 -0.29 60 79
FCGR2B 0.019 0.008 -10000 0 -10000 0 0
IGHE -0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.057 0.12 -10000 0 -0.33 40 40
LCP2 0.019 0.027 -10000 0 -0.34 2 2
PLA2G4A -0.067 0.13 0.19 1 -0.31 58 59
RASA1 0.021 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.043 0.16 0.3 40 -0.24 73 113
IKK complex -0.019 0.11 0.24 27 -0.18 31 58
WIPF1 0.022 0.003 -10000 0 -10000 0 0
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.31 0.56 0.77 2 -1.2 65 67
STAT6 (cleaved dimer) -0.33 0.55 -10000 0 -1.3 69 69
IGHG1 -0.091 0.23 0.41 12 -0.62 12 24
IGHG3 -0.31 0.53 0.61 1 -1.2 73 74
AKT1 -0.15 0.32 0.54 1 -0.9 27 28
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.12 0.3 0.54 1 -0.92 26 27
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.15 0.32 0.48 3 -0.9 25 28
THY1 -0.32 0.56 0.67 2 -1.2 66 68
MYB 0.021 0.024 0.33 2 -10000 0 2
HMGA1 0.051 0.092 0.33 34 -10000 0 34
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.17 0.36 0.53 5 -0.76 52 57
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.15 0.33 0.48 3 -0.92 25 28
SP1 0.027 0.026 -10000 0 -10000 0 0
INPP5D 0.02 0.027 -10000 0 -0.34 2 2
SOCS5 0.012 0.037 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.32 0.55 0.61 1 -1.2 68 69
SOCS1 -0.2 0.35 0.57 1 -0.75 65 66
SOCS3 -0.15 0.3 0.52 1 -0.79 26 27
FCER2 -0.25 0.49 0.68 5 -1.1 53 58
PARP14 0.023 0.009 -10000 0 -10000 0 0
CCL17 -0.37 0.62 0.72 3 -1.4 77 80
GRB2 0.021 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.11 0.27 0.5 3 -0.73 25 28
T cell proliferation -0.33 0.56 0.63 1 -1.3 66 67
IL4R/JAK1 -0.32 0.55 -10000 0 -1.2 65 65
EGR2 -0.34 0.59 0.77 1 -1.3 65 66
JAK2 -0.008 0.059 0.18 1 -10000 0 1
JAK3 0.02 0.017 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
JAK1 0.002 0.034 -10000 0 -10000 0 0
COL1A2 -0.068 0.22 -10000 0 -1.3 3 3
CCL26 -0.3 0.56 0.71 4 -1.2 63 67
IL4R -0.33 0.6 0.76 3 -1.3 65 68
PTPN6 0.016 0.03 -10000 0 -10000 0 0
IL13RA2 -0.35 0.6 0.68 2 -1.3 74 76
IL13RA1 -0.008 0.064 -10000 0 -10000 0 0
IRF4 -0.062 0.26 0.54 2 -0.95 19 21
ARG1 -0.1 0.25 0.51 3 -0.67 30 33
CBL -0.17 0.33 0.52 2 -0.72 49 51
GTF3A 0.061 0.059 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.003 0.085 0.23 7 -10000 0 7
IRF4/BCL6 -0.064 0.23 -10000 0 -0.88 19 19
CD40LG 0.01 0.082 -10000 0 -0.34 17 17
MAPK14 -0.16 0.33 0.52 2 -0.78 37 39
mitosis -0.14 0.3 0.48 2 -0.84 27 29
STAT6 -0.37 0.68 0.87 2 -1.5 66 68
SPI1 0.003 0.084 -10000 0 -0.34 20 20
RPS6KB1 -0.14 0.29 0.52 1 -0.82 25 26
STAT6 (dimer) -0.37 0.68 0.87 2 -1.5 66 68
STAT6 (dimer)/PARP14 -0.35 0.6 0.67 1 -1.3 70 71
mast cell activation 0.005 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.18 0.36 0.47 3 -0.9 42 45
FRAP1 -0.15 0.32 0.54 1 -0.9 27 28
LTA -0.31 0.56 0.77 2 -1.2 64 66
FES 0.02 0.019 -10000 0 -0.34 1 1
T-helper 1 cell differentiation 0.35 0.64 1.4 69 -0.87 2 71
CCL11 -0.33 0.55 -10000 0 -1.2 69 69
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.15 0.33 0.47 3 -0.99 25 28
IL2RG 0.016 0.04 -10000 0 -0.32 4 4
IL10 -0.31 0.56 0.76 4 -1.3 65 69
IRS1 0.021 0.019 -10000 0 -0.34 1 1
IRS2 0.02 0.02 -10000 0 -0.34 1 1
IL4 -0.072 0.26 0.48 3 -1 15 18
IL5 -0.32 0.55 0.68 1 -1.2 65 66
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.26 0.49 0.64 6 -1 68 74
COL1A1 -0.025 0.29 0.55 12 -0.82 14 26
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.33 0.56 -10000 0 -1.3 64 64
IL2R gamma/JAK3 0.028 0.032 -10000 0 -0.2 4 4
TFF3 -0.32 0.59 0.74 2 -1.3 70 72
ALOX15 -0.64 0.72 0.68 1 -1.3 169 170
MYBL1 0.024 0.037 0.33 5 -10000 0 5
T-helper 2 cell differentiation -0.26 0.47 0.64 2 -1 67 69
SHC1 0.018 0.008 -10000 0 -10000 0 0
CEBPB 0.022 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.14 0.31 0.48 2 -0.82 26 28
mol:PI-3-4-5-P3 -0.15 0.32 0.55 1 -0.9 27 28
PI3K -0.16 0.34 0.55 1 -0.99 27 28
DOK2 -0.005 0.088 -10000 0 -0.34 23 23
ETS1 0.013 0.036 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.1 0.25 0.45 4 -0.69 21 25
ITGB3 -0.32 0.56 0.69 2 -1.3 63 65
PIGR -0.45 0.7 0.79 3 -1.4 108 111
IGHE 0.01 0.076 0.21 17 -0.19 6 23
MAPKKK cascade -0.098 0.25 0.45 4 -0.68 21 25
BCL6 0.019 0.012 -10000 0 -10000 0 0
OPRM1 -0.32 0.55 0.68 1 -1.2 65 66
RETNLB -0.32 0.56 0.68 1 -1.2 65 66
SELP -0.41 0.67 0.77 2 -1.4 90 92
AICDA -0.34 0.56 0.72 1 -1.2 72 73
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.023 0.11 0.4 2 -0.19 58 60
SMAD6-7/SMURF1 0.008 0.079 -10000 0 -0.21 40 40
NOG 0.009 0.095 0.33 8 -0.34 19 27
SMAD9 -0.12 0.22 -10000 0 -0.47 93 93
SMAD4 0.019 0.007 -10000 0 -10000 0 0
SMAD5 -0.048 0.1 -10000 0 -0.33 26 26
BMP7/USAG1 -0.13 0.15 0.24 7 -0.25 196 203
SMAD5/SKI -0.037 0.12 0.24 2 -0.33 28 30
SMAD1 -0.001 0.058 -10000 0 -0.29 6 6
BMP2 -0.025 0.12 -10000 0 -0.34 45 45
SMAD1/SMAD1/SMAD4 -0.011 0.076 -10000 0 -0.35 4 4
BMPR1A 0.021 0.003 -10000 0 -10000 0 0
BMPR1B -0.01 0.11 0.33 2 -0.34 33 35
BMPR1A-1B/BAMBI 0.024 0.084 0.23 12 -0.21 34 46
AHSG 0.041 0.079 0.33 24 -10000 0 24
CER1 0.02 0.029 0.33 3 -10000 0 3
BMP2-4/CER1 0.003 0.087 0.23 2 -0.21 48 50
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.035 0.11 -10000 0 -0.33 25 25
BMP2-4 (homodimer) -0.009 0.096 -10000 0 -0.24 49 49
RGMB 0.021 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.003 0.11 0.23 3 -0.21 74 77
RGMA 0.024 0.046 0.33 5 -0.34 2 7
SMURF1 0.021 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.032 0.092 -10000 0 -0.32 16 16
BMP2-4/USAG1 -0.12 0.14 -10000 0 -0.23 203 203
SMAD6/SMURF1/SMAD5 -0.034 0.12 0.24 2 -0.33 26 28
SOSTDC1 -0.19 0.17 -10000 0 -0.34 202 202
BMP7/BMPR2/BMPR1A-1B 0.015 0.1 0.23 11 -0.2 56 67
SKI 0.021 0.004 -10000 0 -10000 0 0
BMP6 (homodimer) -0.032 0.13 0.33 2 -0.34 54 56
HFE2 0.024 0.037 0.33 5 -10000 0 5
ZFYVE16 0.021 0.005 -10000 0 -10000 0 0
MAP3K7 0.02 0.007 -10000 0 -10000 0 0
BMP2-4/CHRD 0.01 0.086 0.23 5 -0.2 45 50
SMAD5/SMAD5/SMAD4 -0.034 0.12 0.24 2 -0.34 24 26
MAPK1 0.021 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.016 0.09 -10000 0 -0.28 15 15
BMP7 (homodimer) 0 0.12 0.33 13 -0.34 31 44
NUP214 0.021 0.004 -10000 0 -10000 0 0
BMP6/FETUA 0.006 0.11 0.24 24 -0.24 49 73
SMAD1/SKI 0.01 0.062 -10000 0 -0.31 3 3
SMAD6 -0.026 0.12 -10000 0 -0.34 46 46
CTDSP2 0.02 0.006 -10000 0 -10000 0 0
BMP2-4/FETUA 0.018 0.097 0.23 21 -0.2 45 66
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.24 0.14 0.33 246 -10000 0 246
BMPR2 (homodimer) 0.022 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.039 0.023 -10000 0 -0.2 2 2
BMPR1A-1B (homodimer) 0.007 0.081 0.24 2 -0.24 33 35
CHRDL1 -0.1 0.17 -10000 0 -0.34 120 120
ENDOFIN/SMAD1 0.009 0.061 0.23 1 -0.34 2 3
SMAD6-7/SMURF1/SMAD1 -0.002 0.087 -10000 0 -0.42 3 3
SMAD6/SMURF1 0.02 0.005 -10000 0 -10000 0 0
BAMBI 0.028 0.064 0.33 11 -0.34 3 14
SMURF2 0.021 0.004 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.068 0.14 -10000 0 -0.24 134 134
BMP2-4/GREM1 0.11 0.14 0.23 196 -0.17 48 244
SMAD7 0.018 0.02 -10000 0 -0.34 1 1
SMAD8A/SMAD8A/SMAD4 -0.1 0.21 -10000 0 -0.44 94 94
SMAD1/SMAD6 0.007 0.064 -10000 0 -0.3 4 4
TAK1/SMAD6 0.027 0.012 -10000 0 -10000 0 0
BMP7 0 0.12 0.33 13 -0.34 31 44
BMP6 -0.032 0.13 0.33 2 -0.34 54 56
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.033 0.11 -10000 0 -0.33 25 25
PPM1A 0.021 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 0.008 0.063 -10000 0 -0.31 3 3
SMAD7/SMURF1 0.026 0.019 -10000 0 -0.24 1 1
CTDSPL 0.021 0.004 -10000 0 -10000 0 0
PPP1CA 0.021 0.004 -10000 0 -10000 0 0
XIAP 0.022 0.003 -10000 0 -10000 0 0
CTDSP1 0.022 0.002 -10000 0 -10000 0 0
PPP1R15A 0.019 0.027 -10000 0 -0.34 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.034 0.11 -10000 0 -0.33 23 23
CHRD 0.027 0.05 0.33 8 -0.34 1 9
BMPR2 0.022 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.037 0.094 -10000 0 -0.33 15 15
BMP4 0.014 0.056 0.33 1 -0.34 8 9
FST 0.029 0.093 0.33 20 -0.34 9 29
BMP2-4/NOG -0.001 0.11 0.23 6 -0.23 55 61
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.022 0.096 -10000 0 -0.19 49 49
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.007 0.079 -10000 0 -0.29 15 15
alphaM/beta2 Integrin/GPIbA 0.004 0.083 0.23 1 -0.28 19 20
alphaM/beta2 Integrin/proMMP-9 0.04 0.1 0.23 55 -0.26 13 68
PLAUR 0.021 0.005 -10000 0 -10000 0 0
HMGB1 0.006 0.03 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.007 0.081 -10000 0 -0.3 15 15
AGER -0.31 0.11 -10000 0 -0.35 312 312
RAP1A 0.021 0.005 -10000 0 -10000 0 0
SELPLG 0.011 0.06 -10000 0 -0.34 10 10
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.2 0.12 -10000 0 -0.24 306 306
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.072 0.12 0.33 58 -10000 0 58
CYR61 0.005 0.075 -10000 0 -0.34 16 16
TLN1 0.02 0.02 -10000 0 -0.34 1 1
Rap1/GTP -0.048 0.14 -10000 0 -0.37 36 36
RHOA 0.021 0.004 -10000 0 -10000 0 0
P-selectin oligomer -0.045 0.14 -10000 0 -0.34 64 64
MYH2 -0.1 0.16 0.22 2 -0.39 59 61
MST1R 0.021 0.026 0.33 1 -0.34 1 2
leukocyte activation during inflammatory response 0.013 0.088 0.2 17 -0.22 25 42
APOB 0.028 0.1 0.33 21 -0.34 12 33
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.021 0.005 -10000 0 -10000 0 0
JAM3 0.019 0.027 -10000 0 -0.34 2 2
GP1BA 0.016 0.046 0.33 1 -0.34 5 6
alphaM/beta2 Integrin/CTGF 0 0.088 -10000 0 -0.27 24 24
alphaM/beta2 Integrin -0.067 0.15 0.19 3 -0.38 42 45
JAM3 homodimer 0.019 0.027 -10000 0 -0.34 2 2
ICAM2 0.018 0.033 -10000 0 -0.34 3 3
ICAM1 0.015 0.043 -10000 0 -0.34 5 5
phagocytosis triggered by activation of immune response cell surface activating receptor -0.065 0.15 0.21 2 -0.38 42 44
cell adhesion 0.004 0.083 0.23 1 -0.28 19 20
NFKB1 -0.23 0.17 -10000 0 -0.49 86 86
THY1 0.03 0.052 0.33 10 -10000 0 10
RhoA/GDP 0.016 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.029 0.063 0.21 23 -0.2 12 35
alphaM/beta2 Integrin/LRP/tPA 0.037 0.1 0.23 27 -0.3 14 41
IL6 -0.25 0.25 -10000 0 -0.66 82 82
ITGB2 -0.001 0.059 -10000 0 -0.33 8 8
elevation of cytosolic calcium ion concentration 0.046 0.11 0.22 57 -0.3 12 69
alphaM/beta2 Integrin/JAM2/JAM3 0 0.1 -10000 0 -0.25 37 37
JAM2 -0.01 0.1 -10000 0 -0.34 30 30
alphaM/beta2 Integrin/ICAM1 0.024 0.091 0.23 8 -0.27 17 25
alphaM/beta2 Integrin/uPA/Plg 0.049 0.11 0.23 62 -0.26 15 77
RhoA/GTP -0.078 0.16 0.23 2 -0.37 52 54
positive regulation of phagocytosis -0.051 0.14 -10000 0 -0.37 35 35
Ron/MSP 0.037 0.043 0.24 12 -0.24 2 14
alphaM/beta2 Integrin/uPAR/uPA 0.049 0.11 0.23 59 -0.3 12 71
alphaM/beta2 Integrin/uPAR 0.009 0.078 -10000 0 -0.32 12 12
PLAU 0.08 0.12 0.33 67 -10000 0 67
PLAT 0.053 0.1 0.33 40 -0.34 1 41
actin filament polymerization -0.1 0.15 0.22 2 -0.37 58 60
MST1 0.03 0.057 0.33 11 -0.34 1 12
alphaM/beta2 Integrin/lipoprotein(a) 0.017 0.091 0.22 17 -0.22 25 42
TNF -0.22 0.18 -10000 0 -0.5 83 83
RAP1B 0.02 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.043 0.12 0.23 63 -0.29 15 78
fibrinolysis 0.047 0.11 0.23 62 -0.26 15 77
HCK 0.009 0.065 -10000 0 -0.34 12 12
dendritic cell antigen processing and presentation -0.065 0.15 0.21 2 -0.38 42 44
VTN -0.032 0.14 0.33 5 -0.34 57 62
alphaM/beta2 Integrin/CYR61 -0.002 0.094 -10000 0 -0.28 27 27
LPA 0.02 0.024 0.33 2 -10000 0 2
LRP1 0.017 0.038 -10000 0 -0.34 4 4
cell migration 0.018 0.076 -10000 0 -0.24 12 12
FN1 0.018 0.038 -10000 0 -0.34 4 4
alphaM/beta2 Integrin/Thy1 0.012 0.084 0.23 9 -0.28 15 24
MPO 0.017 0.046 0.33 1 -0.34 5 6
KNG1 0.042 0.082 0.33 26 -10000 0 26
RAP1/GDP 0.027 0.009 -10000 0 -10000 0 0
ROCK1 -0.075 0.15 0.24 4 -0.39 41 45
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.025 0.047 0.33 8 -10000 0 8
CTGF 0.006 0.07 -10000 0 -0.34 14 14
alphaM/beta2 Integrin/Hck 0.003 0.092 -10000 0 -0.32 18 18
ITGAM -0.008 0.076 -10000 0 -0.35 14 14
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.024 0.12 -10000 0 -0.24 67 67
HP -0.04 0.16 0.33 14 -0.34 72 86
leukocyte adhesion -0.2 0.13 -10000 0 -0.35 98 98
SELP -0.045 0.14 -10000 0 -0.34 64 64
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.01 0.11 0.52 10 -10000 0 10
VDR 0.021 0.025 0.33 1 -0.34 1 2
FAM120B 0.02 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.087 0.12 -10000 0 -0.33 21 21
RXRs/LXRs/DNA/Oxysterols -0.088 0.13 -10000 0 -0.46 21 21
MED1 0.021 0.004 -10000 0 -10000 0 0
mol:9cRA -0.001 0.011 -10000 0 -0.093 2 2
RARs/THRs/DNA/Src-1 -0.009 0.068 -10000 0 -0.19 41 41
RXRs/NUR77 -0.096 0.14 -10000 0 -0.22 184 184
RXRs/PPAR -0.11 0.13 -10000 0 -0.23 174 174
NCOR2 0.021 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.016 0.017 0.22 1 -0.23 1 2
RARs/VDR/DNA/Vit D3 0.045 0.028 0.22 1 -0.18 3 4
RARA 0.021 0.004 -10000 0 -10000 0 0
NCOA1 0.022 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.025 0.33 1 -0.34 1 2
RARs/RARs/DNA/9cRA 0.032 0.024 -10000 0 -0.18 2 2
RARG 0.021 0.003 -10000 0 -10000 0 0
RPS6KB1 0.032 0.12 0.61 13 -10000 0 13
RARs/THRs/DNA/SMRT -0.01 0.068 -10000 0 -0.2 33 33
THRA 0.021 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.016 0.017 0.22 1 -0.23 1 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.066 0.11 -10000 0 -0.18 157 157
NR1H4 0.04 0.077 0.33 23 -10000 0 23
RXRs/LXRs/DNA -0.056 0.12 -10000 0 -0.28 9 9
NR1H2 0.019 0.016 -10000 0 -10000 0 0
NR1H3 0.019 0.018 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.057 0.11 -10000 0 -0.18 153 153
NR4A1 -0.051 0.14 -10000 0 -0.34 71 71
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.069 0.098 -10000 0 -0.18 146 146
RXRG -0.14 0.18 -10000 0 -0.34 158 158
RXR alpha/CCPG 0.027 0.017 -10000 0 -10000 0 0
RXRA 0.019 0.017 -10000 0 -10000 0 0
RXRB 0.019 0.016 -10000 0 -10000 0 0
THRB -0.012 0.1 -10000 0 -0.34 33 33
PPARG -0.025 0.12 -10000 0 -0.34 45 45
PPARD 0.021 0.005 -10000 0 -10000 0 0
TNF -0.099 0.19 -10000 0 -0.9 15 15
mol:Oxysterols -0.001 0.01 -10000 0 -10000 0 0
cholesterol transport -0.084 0.13 -10000 0 -0.45 21 21
PPARA 0.02 0.006 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.019 0.027 -10000 0 -0.34 2 2
RXRs/NUR77/BCL2 -0.12 0.13 -10000 0 -0.24 181 181
SREBF1 -0.079 0.12 -10000 0 -0.5 12 12
RXRs/RXRs/DNA/9cRA -0.066 0.11 -10000 0 -0.18 157 157
ABCA1 -0.082 0.12 -10000 0 -0.5 13 13
RARs/THRs 0.036 0.074 -10000 0 -0.19 32 32
RXRs/FXR -0.055 0.13 0.23 13 -0.19 149 162
BCL2 0.02 0.018 0.33 1 -10000 0 1
Ephrin B reverse signaling

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
EFNB2 0.018 0.033 -10000 0 -0.34 3 3
EPHB2 0.06 0.1 0.33 44 -10000 0 44
EFNB1 -0.013 0.028 0.2 4 -0.24 1 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.068 0.084 0.23 58 -0.21 4 62
Ephrin B2/EPHB1-2 0.074 0.087 0.23 70 -0.18 4 74
neuron projection morphogenesis 0.047 0.065 0.17 58 -0.22 3 61
Ephrin B1/EPHB1-2/Tiam1 0.077 0.092 0.24 68 -0.22 4 72
DNM1 0.024 0.029 0.34 3 -10000 0 3
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.057 0.16 -10000 0 -0.51 37 37
YES1 -0.066 0.23 -10000 0 -0.73 37 37
Ephrin B1/EPHB1-2/NCK2 0.08 0.087 0.24 70 -0.18 2 72
PI3K -0.025 0.17 -10000 0 -0.5 38 38
mol:GDP 0.075 0.089 0.24 68 -0.21 4 72
ITGA2B -0.013 0.11 0.33 1 -0.34 34 35
endothelial cell proliferation 0.024 0.022 -10000 0 -0.2 3 3
FYN -0.07 0.23 -10000 0 -0.73 37 37
MAP3K7 -0.056 0.16 -10000 0 -0.54 37 37
FGR -0.073 0.23 -10000 0 -0.73 37 37
TIAM1 0.017 0.038 -10000 0 -0.34 4 4
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
RGS3 0.021 0.005 -10000 0 -10000 0 0
cell adhesion -0.058 0.16 0.24 1 -0.5 36 37
LYN -0.064 0.23 -10000 0 -0.72 37 37
Ephrin B1/EPHB1-2/Src Family Kinases -0.062 0.21 -10000 0 -0.66 37 37
Ephrin B1/EPHB1-2 -0.055 0.18 -10000 0 -0.58 36 36
SRC -0.063 0.22 -10000 0 -0.72 37 37
ITGB3 0.034 0.08 0.33 19 -0.34 4 23
EPHB1 0.053 0.097 0.33 37 -0.34 1 38
EPHB4 0.021 0.005 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.024 0.023 -10000 0 -0.2 3 3
alphaIIb/beta3 Integrin 0.014 0.1 0.24 20 -0.24 37 57
BLK -0.065 0.23 -10000 0 -0.72 37 37
HCK -0.068 0.23 -10000 0 -0.74 37 37
regulation of stress fiber formation -0.078 0.085 0.18 2 -0.23 70 72
MAPK8 -0.057 0.15 0.25 1 -0.48 38 39
Ephrin B1/EPHB1-2/RGS3 0.077 0.084 0.24 66 -0.18 2 68
endothelial cell migration -0.04 0.14 0.2 11 -0.43 33 44
NCK2 0.022 0.002 -10000 0 -10000 0 0
PTPN13 -0.024 0.14 -10000 0 -0.45 35 35
regulation of focal adhesion formation -0.078 0.085 0.18 2 -0.23 70 72
chemotaxis -0.074 0.082 0.18 2 -0.23 66 68
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.059 0.075 0.2 58 -0.2 4 62
angiogenesis -0.055 0.18 -10000 0 -0.57 37 37
LCK -0.062 0.22 -10000 0 -0.72 37 37
Visual signal transduction: Rods

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
mol:K + 0.021 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.018 0.029 0.22 7 -10000 0 7
Metarhodopsin II/Arrestin 0.026 0.005 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.029 0.034 0.24 6 -0.17 2 8
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.025 0.044 0.33 7 -10000 0 7
GRK1 0.037 0.072 0.33 20 -10000 0 20
CNG Channel 0.046 0.086 0.27 11 -0.18 20 31
mol:Na + 0.084 0.085 0.28 25 -0.18 2 27
mol:ADP 0.037 0.072 0.33 20 -10000 0 20
RGS9-1/Gbeta5/R9AP -0.059 0.13 -10000 0 -0.23 128 128
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.1 0.1 0.33 25 -0.18 2 27
CNGB1 0.072 0.12 0.33 59 -0.34 1 60
RDH5 0.027 0.04 0.33 6 -10000 0 6
SAG 0.019 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.018 0.094 0.29 25 -10000 0 25
Na + (4 Units) 0.025 0.084 0.13 122 -0.17 2 124
RGS9 -0.084 0.16 -10000 0 -0.34 103 103
GNB1/GNGT1 0.064 0.08 0.24 61 -10000 0 61
GNAT1/GDP -0.043 0.12 0.21 3 -0.19 128 131
GUCY2D 0.02 0.04 0.33 3 -0.34 2 5
GNGT1 0.08 0.12 0.33 69 -10000 0 69
GUCY2F 0.019 0.002 -10000 0 -10000 0 0
GNB5 0.021 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.03 0.05 0.14 7 -0.18 26 33
mol:11-cis-retinal 0.026 0.04 0.33 6 -10000 0 6
mol:cGMP 0.062 0.078 0.22 59 -0.18 3 62
GNB1 0.021 0.004 -10000 0 -10000 0 0
Rhodopsin 0.033 0.028 0.24 6 -10000 0 6
SLC24A1 0.021 0.004 -10000 0 -10000 0 0
CNGA1 0.065 0.11 0.33 50 -10000 0 50
Metarhodopsin II 0.034 0.042 0.2 20 -10000 0 20
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.074 0.081 0.24 61 -0.18 4 65
RGS9BP -0.029 0.12 -10000 0 -0.34 49 49
Metarhodopsin II/Transducin 0.026 0.045 0.16 7 -0.17 3 10
GCAP Family/Ca ++ 0.067 0.073 0.22 61 -0.16 2 63
PDE6A/B 0.011 0.071 0.24 1 -0.24 26 27
mol:Pi -0.059 0.13 -10000 0 -0.22 128 128
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.068 0.074 0.22 63 -10000 0 63
PDE6B 0.019 0.027 -10000 0 -0.34 2 2
PDE6A -0.005 0.095 0.33 1 -0.34 26 27
PDE6G 0.021 0.036 0.33 2 -0.34 2 4
RHO 0.02 0.003 -10000 0 -10000 0 0
PDE6 -0.047 0.14 -10000 0 -0.22 124 124
GUCA1A 0.075 0.12 0.33 62 -10000 0 62
GC2/GCAP Family 0.078 0.075 0.23 60 -0.16 2 62
GUCA1C 0.018 0.003 -10000 0 -10000 0 0
GUCA1B 0.021 0.036 0.33 2 -0.34 2 4
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.029 0.022 -10000 0 -0.24 2 2
Necdin/E2F1 0.029 0.037 0.24 4 -0.23 4 8
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.047 0.075 0.23 18 -0.18 21 39
NGF (dimer)/p75(NTR)/BEX1 -0.017 0.13 0.23 23 -0.21 97 120
NT-4/5 (dimer)/p75(NTR) 0.017 0.071 0.24 6 -0.24 22 28
IKBKB 0.019 0.008 -10000 0 -10000 0 0
AKT1 -0.02 0.058 0.2 13 -10000 0 13
IKBKG 0.021 0.005 -10000 0 -10000 0 0
BDNF -0.14 0.18 -10000 0 -0.34 160 160
MGDIs/NGR/p75(NTR)/LINGO1 0.062 0.077 0.23 49 -0.19 7 56
FURIN 0.03 0.052 0.33 10 -10000 0 10
proBDNF (dimer)/p75(NTR)/Sortilin -0.069 0.13 0.23 4 -0.21 159 163
LINGO1 0.064 0.11 0.33 49 -10000 0 49
Sortilin/TRAF6/NRIF -0.03 0.02 -10000 0 -0.18 1 1
proBDNF (dimer) -0.14 0.18 -10000 0 -0.34 160 160
NTRK1 0.009 0.065 0.33 1 -0.34 11 12
RTN4R 0.02 0.02 -10000 0 -0.34 1 1
neuron apoptosis -0.096 0.14 0.36 3 -0.38 32 35
IRAK1 0.021 0.005 -10000 0 -10000 0 0
SHC1 -0.016 0.047 0.11 18 -0.2 12 30
ARHGDIA 0.021 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.016 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.046 0.032 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.047 0.07 0.23 18 -0.19 19 37
MAGEH1 0.021 0.004 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.042 0.076 0.23 17 -0.2 21 38
Mammalian IAPs/DIABLO 0.052 0.031 0.23 4 -0.19 2 6
proNGF (dimer) 0.023 0.09 0.33 15 -0.34 11 26
MAGED1 0.022 0.017 0.33 1 -10000 0 1
APP 0.021 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.004 0.077 -10000 0 -0.34 17 17
ZNF274 0.021 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.019 0.05 0.21 2 -0.17 17 19
NGF 0.023 0.09 0.33 15 -0.34 11 26
cell cycle arrest 0.001 0.073 0.23 13 -10000 0 13
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.006 0.061 0.18 7 -0.28 2 9
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.029 0.065 0.23 6 -0.2 22 28
NCSTN 0.019 0.008 -10000 0 -10000 0 0
mol:GTP 0.038 0.07 0.23 19 -0.2 17 36
PSENEN 0.02 0.006 -10000 0 -10000 0 0
mol:ceramide -0.017 0.056 0.2 10 -0.19 14 24
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.003 0.054 0.16 9 -0.29 3 12
p75(NTR)/beta APP 0.029 0.045 0.24 6 -0.23 6 12
BEX1 -0.06 0.17 0.33 11 -0.34 89 100
mol:GDP -0.016 0.049 0.21 1 -0.2 17 18
NGF (dimer) 0.072 0.099 0.24 71 -0.18 15 86
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.07 0.075 0.24 48 -0.19 6 54
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
RAC1/GTP 0.029 0.057 0.2 14 -0.17 16 30
MYD88 0.021 0.004 -10000 0 -10000 0 0
CHUK 0.022 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.039 0.07 0.23 19 -0.2 17 36
RHOB 0.022 0.002 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.031 0.022 0.24 3 -10000 0 3
NT3 (dimer) 0.002 0.083 0.33 1 -0.34 19 20
TP53 -0.084 0.098 0.29 6 -0.31 4 10
PRDM4 -0.02 0.058 0.2 10 -0.19 16 26
BDNF (dimer) 0.004 0.17 0.27 79 -0.17 126 205
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
SORT1 0.019 0.027 -10000 0 -0.34 2 2
activation of caspase activity 0.042 0.071 0.21 18 -0.18 21 39
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.047 0.07 0.23 18 -0.19 19 37
RHOC 0.021 0.005 -10000 0 -10000 0 0
XIAP 0.022 0.003 -10000 0 -10000 0 0
MAPK10 -0.074 0.13 0.31 9 -0.34 32 41
DIABLO 0.021 0.004 -10000 0 -10000 0 0
SMPD2 -0.017 0.057 0.2 10 -0.19 14 24
APH1B 0.02 0.019 -10000 0 -0.34 1 1
APH1A 0.018 0.009 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.037 0.072 0.23 18 -0.2 19 37
PSEN1 0.021 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.008 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.015 0.078 0.27 6 -0.24 24 30
MAPK8 -0.058 0.12 0.31 9 -0.31 18 27
MAPK9 -0.057 0.11 0.32 8 -0.3 18 26
APAF1 0.021 0.004 -10000 0 -10000 0 0
NTF3 0.002 0.083 0.33 1 -0.34 19 20
NTF4 0.004 0.077 -10000 0 -0.34 17 17
NDN 0.016 0.043 -10000 0 -0.34 5 5
RAC1/GDP 0.014 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.047 0.061 -10000 0 -0.17 16 16
p75 CTF/Sortilin/TRAF6/NRIF 0.05 0.025 -10000 0 -0.19 2 2
RhoA-B-C/GTP 0.038 0.069 0.22 19 -0.2 17 36
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.051 0.12 0.23 3 -0.18 152 155
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.057 0.12 0.23 4 -0.19 156 160
PRKACB 0.022 0.017 0.33 1 -10000 0 1
proBDNF (dimer)/p75 ECD -0.091 0.13 -10000 0 -0.24 159 159
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.022 0.043 0.33 4 -0.34 2 6
BIRC2 0.021 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis 0.006 0.075 0.23 9 -0.2 13 22
BAD -0.069 0.12 0.3 11 -0.32 22 33
RIPK2 0.019 0.007 -10000 0 -10000 0 0
NGFR 0.02 0.062 0.33 6 -0.34 6 12
CYCS -0.022 0.058 0.21 10 -10000 0 10
ADAM17 0.022 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.042 0.067 0.23 15 -0.19 17 32
BCL2L11 -0.069 0.12 0.31 10 -0.32 22 32
BDNF (dimer)/p75(NTR) -0.09 0.14 0.24 4 -0.24 160 164
PI3K 0.047 0.068 0.23 17 -0.19 16 33
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.045 0.071 0.23 18 -0.18 19 37
NDNL2 0.021 0.005 -10000 0 -10000 0 0
YWHAE 0.02 0.007 -10000 0 -10000 0 0
PRKCI 0.021 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.028 0.077 0.24 19 -0.24 17 36
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.047 0.07 0.23 18 -0.19 18 36
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCZ 0.019 0.027 -10000 0 -0.34 2 2
PLG 0.025 0.047 0.33 8 -10000 0 8
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.096 0.1 0.14 2 -0.2 155 157
SQSTM1 0.021 0.005 -10000 0 -10000 0 0
NGFRAP1 0.019 0.033 -10000 0 -0.34 3 3
CASP3 -0.066 0.12 0.3 10 -0.3 23 33
E2F1 0.024 0.033 0.33 4 -10000 0 4
CASP9 0.021 0.004 -10000 0 -10000 0 0
IKK complex 0.027 0.074 0.23 3 -0.27 9 12
NGF (dimer)/TRKA 0.02 0.073 0.24 13 -0.23 19 32
MMP7 0.065 0.13 0.33 57 -0.34 6 63
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.053 0.07 0.23 17 -0.18 18 35
MMP3 0.14 0.15 0.33 138 -10000 0 138
APAF-1/Caspase 9 -0.042 0.038 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.073 0.12 0.34 54 -0.22 2 56
NFATC2 0.009 0.14 -10000 0 -0.51 11 11
NFATC3 -0.006 0.086 -10000 0 -0.26 27 27
CD40LG -0.088 0.3 0.41 1 -0.77 46 47
ITCH -0.024 0.077 -10000 0 -0.2 54 54
CBLB -0.029 0.081 -10000 0 -0.2 63 63
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.026 0.26 0.41 18 -0.72 25 43
JUNB 0.018 0.027 -10000 0 -0.34 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.028 0.1 -10000 0 -0.24 65 65
T cell anergy -0.057 0.14 0.3 2 -0.34 60 62
TLE4 -0.007 0.1 -10000 0 -0.47 10 10
Jun/NFAT1-c-4/p21SNFT -0.032 0.3 0.51 1 -0.77 43 44
AP-1/NFAT1-c-4 -0.045 0.36 0.6 3 -0.85 45 48
IKZF1 -0.003 0.088 -10000 0 -0.43 6 6
T-helper 2 cell differentiation -0.026 0.19 0.36 1 -0.67 17 18
AP-1/NFAT1 0.017 0.13 0.34 2 -0.33 17 19
CALM1 -0.01 0.069 -10000 0 -0.18 1 1
EGR2 -0.09 0.33 -10000 0 -1 28 28
EGR3 -0.13 0.4 -10000 0 -1.2 44 44
NFAT1/FOXP3 0.06 0.15 0.39 16 -0.34 10 26
EGR1 -0.004 0.089 -10000 0 -0.34 23 23
JUN 0.014 0.037 -10000 0 -0.34 2 2
EGR4 0.046 0.088 0.33 30 -10000 0 30
mol:Ca2+ -0.025 0.056 -10000 0 -0.14 67 67
GBP3 -0.014 0.13 -10000 0 -0.53 15 15
FOSL1 0.037 0.081 0.33 21 -0.34 3 24
NFAT1-c-4/MAF/IRF4 -0.029 0.28 -10000 0 -0.74 42 42
DGKA -0.004 0.093 0.5 1 -0.37 10 11
CREM 0.021 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.069 0.3 -10000 0 -0.81 44 44
CTLA4 0.016 0.094 0.34 4 -0.3 7 11
NFAT1-c-4 (dimer)/EGR1 -0.059 0.31 0.46 1 -0.82 44 45
NFAT1-c-4 (dimer)/EGR4 -0.033 0.3 0.46 2 -0.78 44 46
FOS -0.009 0.096 -10000 0 -0.34 25 25
IFNG -0.025 0.22 0.36 2 -0.77 16 18
T cell activation -0.034 0.16 -10000 0 -0.58 13 13
MAF 0.02 0.02 -10000 0 -0.34 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.066 0.24 0.66 43 -10000 0 43
TNF -0.084 0.28 0.47 1 -0.76 44 45
FASLG -0.15 0.44 -10000 0 -1.2 47 47
TBX21 0.016 0.083 0.33 1 -0.33 16 17
BATF3 0.021 0.018 0.33 1 -10000 0 1
PRKCQ -0.02 0.11 -10000 0 -0.34 40 40
PTPN1 -0.005 0.092 0.34 1 -0.38 8 9
NFAT1-c-4/ICER1 -0.045 0.29 -10000 0 -0.76 44 44
GATA3 0.022 0.017 0.33 1 -10000 0 1
T-helper 1 cell differentiation -0.023 0.21 0.36 2 -0.73 17 19
IL2RA -0.013 0.27 0.46 22 -0.7 27 49
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.005 0.089 -10000 0 -0.38 8 8
E2F1 0.026 0.034 0.33 4 -10000 0 4
PPARG -0.025 0.12 -10000 0 -0.34 45 45
SLC3A2 -0.003 0.087 -10000 0 -0.37 8 8
IRF4 0.029 0.061 0.33 11 -0.34 2 13
PTGS2 -0.089 0.3 0.45 2 -0.79 44 46
CSF2 -0.089 0.3 0.45 5 -0.78 46 51
JunB/Fra1/NFAT1-c-4 -0.029 0.29 0.5 2 -0.74 44 46
IL4 -0.028 0.2 -10000 0 -0.7 17 17
IL5 -0.084 0.28 0.41 1 -0.75 46 47
IL2 -0.034 0.16 -10000 0 -0.59 13 13
IL3 -0.026 0.14 -10000 0 -0.76 8 8
RNF128 -0.081 0.17 -10000 0 -0.44 65 65
NFATC1 -0.066 0.24 -10000 0 -0.66 43 43
CDK4 0.046 0.16 0.54 21 -10000 0 21
PTPRK -0.002 0.086 -10000 0 -0.39 7 7
IL8 -0.075 0.3 0.44 9 -0.75 46 55
POU2F1 0.02 0.007 -10000 0 -10000 0 0
IL23-mediated signaling events

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
CCL2 -0.09 0.44 0.72 4 -1.1 34 38
IL23A -0.075 0.46 0.78 5 -1.1 36 41
NF kappa B1 p50/RelA/I kappa B alpha -0.08 0.43 0.64 3 -1.1 37 40
positive regulation of T cell mediated cytotoxicity -0.1 0.5 0.77 4 -1.2 43 47
ITGA3 -0.088 0.44 0.74 4 -1.1 33 37
IL17F -0.059 0.3 0.49 9 -0.67 41 50
IL12B 0.021 0.063 0.26 5 -0.35 1 6
STAT1 (dimer) -0.1 0.47 0.66 3 -1.1 43 46
CD4 -0.089 0.44 0.73 4 -1.2 31 35
IL23 -0.067 0.44 0.73 4 -1.1 36 40
IL23R 0.006 0.19 0.5 2 -0.93 9 11
IL1B -0.097 0.49 0.77 4 -1.2 37 41
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.072 0.43 0.73 5 -1.1 31 36
TYK2 0.017 0.045 0.19 1 -10000 0 1
STAT4 0.022 0.002 -10000 0 -10000 0 0
STAT3 0.022 0.003 -10000 0 -10000 0 0
IL18RAP 0.006 0.075 -10000 0 -0.34 16 16
IL12RB1 0.009 0.075 0.18 2 -0.36 9 11
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.02 0.068 0.2 2 -0.26 8 10
IL23R/JAK2 0.019 0.19 0.47 2 -0.91 8 10
positive regulation of chronic inflammatory response -0.1 0.5 0.77 4 -1.2 43 47
natural killer cell activation -0.001 0.01 -10000 0 -0.045 3 3
JAK2 0.02 0.053 0.19 3 -10000 0 3
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.014 0.021 -10000 0 -10000 0 0
RELA 0.014 0.021 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.06 0.42 0.72 4 -1 36 40
ALOX12B -0.075 0.44 0.66 8 -1.1 34 42
CXCL1 -0.1 0.46 0.79 3 -1.1 39 42
T cell proliferation -0.1 0.5 0.77 4 -1.2 43 47
NFKBIA 0.012 0.02 -10000 0 -10000 0 0
IL17A -0.013 0.26 0.47 18 -0.55 29 47
PI3K -0.097 0.45 0.63 3 -1.1 43 46
IFNG 0.01 0.048 0.14 25 -0.1 8 33
STAT3 (dimer) -0.089 0.44 0.62 2 -1 43 45
IL18R1 0.008 0.07 -10000 0 -0.33 14 14
IL23/IL23R/JAK2/TYK2/SOCS3 -0.053 0.34 0.5 13 -0.86 31 44
IL18/IL18R 0.027 0.09 0.19 1 -0.24 28 29
macrophage activation -0.002 0.025 0.051 27 -0.044 24 51
TNF -0.091 0.48 0.75 5 -1.2 35 40
STAT3/STAT4 -0.095 0.46 0.67 2 -1.1 43 45
STAT4 (dimer) -0.1 0.47 0.71 2 -1.1 43 45
IL18 0.013 0.055 -10000 0 -0.34 8 8
IL19 -0.071 0.43 0.69 6 -1.1 31 37
STAT5A (dimer) -0.1 0.47 0.71 2 -1.1 43 45
STAT1 0.022 0.002 -10000 0 -10000 0 0
SOCS3 0.019 0.027 -10000 0 -0.34 2 2
CXCL9 -0.086 0.45 0.68 8 -1.1 38 46
MPO -0.092 0.44 0.72 4 -1.1 36 40
positive regulation of humoral immune response -0.1 0.5 0.77 4 -1.2 43 47
IL23/IL23R/JAK2/TYK2 -0.11 0.53 0.77 4 -1.3 43 47
IL6 -0.18 0.57 0.72 3 -1.1 79 82
STAT5A 0.02 0.019 -10000 0 -0.34 1 1
IL2 0.014 0.029 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.001 0.01 -10000 0 -0.045 3 3
CD3E -0.09 0.44 0.71 3 -1.1 35 38
keratinocyte proliferation -0.1 0.5 0.77 4 -1.2 43 47
NOS2 -0.13 0.49 0.72 4 -1.1 52 56
Syndecan-1-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 0.021 0.004 -10000 0 -10000 0 0
CCL5 0.017 0.038 -10000 0 -0.34 4 4
SDCBP 0.02 0.007 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.078 0.081 0.24 26 -0.35 1 27
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.068 0.089 0.22 22 -0.33 3 25
Syndecan-1/Syntenin 0.067 0.09 0.23 22 -0.34 3 25
MAPK3 0.054 0.087 0.21 26 -0.3 3 29
HGF/MET 0.017 0.077 0.24 8 -0.25 23 31
TGFB1/TGF beta receptor Type II 0.021 0.004 -10000 0 -10000 0 0
BSG 0.02 0.006 -10000 0 -10000 0 0
keratinocyte migration 0.067 0.089 0.22 22 -0.33 3 25
Syndecan-1/RANTES 0.072 0.094 0.23 25 -0.3 5 30
Syndecan-1/CD147 0.081 0.092 0.26 11 -0.31 3 14
Syndecan-1/Syntenin/PIP2 0.062 0.085 0.21 21 -0.32 3 24
LAMA5 0.017 0.033 -10000 0 -0.34 3 3
positive regulation of cell-cell adhesion 0.06 0.083 0.2 21 -0.32 3 24
MMP7 0.065 0.13 0.33 57 -0.34 6 63
HGF 0.009 0.076 0.33 3 -0.34 14 17
Syndecan-1/CASK 0.056 0.085 0.19 27 -0.33 3 30
Syndecan-1/HGF/MET 0.07 0.11 0.28 11 -0.36 5 16
regulation of cell adhesion 0.045 0.081 0.19 27 -0.3 3 30
HPSE 0.023 0.023 0.33 2 -10000 0 2
positive regulation of cell migration 0.078 0.081 0.24 26 -0.35 1 27
SDC1 0.077 0.079 0.23 28 -0.35 1 29
Syndecan-1/Collagen 0.078 0.081 0.24 26 -0.35 1 27
PPIB 0.022 0.017 0.33 1 -10000 0 1
MET 0.014 0.073 0.33 5 -0.34 11 16
PRKACA 0.02 0.006 -10000 0 -10000 0 0
MMP9 0.072 0.12 0.33 58 -10000 0 58
MAPK1 0.054 0.085 0.2 26 -0.3 3 29
homophilic cell adhesion 0.073 0.092 0.24 28 -0.35 1 29
MMP1 0.22 0.15 0.33 230 -0.34 2 232
LPA4-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
ADCY4 -0.023 0.043 -10000 0 -0.21 17 17
ADCY5 -0.038 0.068 0.09 6 -0.2 47 53
ADCY6 -0.015 0.014 -10000 0 -0.2 2 2
ADCY7 -0.015 0.014 -10000 0 -0.2 2 2
ADCY1 -0.013 0.023 0.14 3 -0.2 3 6
ADCY2 -0.02 0.047 0.09 7 -0.2 21 28
ADCY3 -0.015 0.014 -10000 0 -0.2 2 2
ADCY8 -0.075 0.09 0.09 1 -0.2 119 120
PRKCE -0.01 0.017 -10000 0 -0.23 2 2
ADCY9 -0.019 0.031 -10000 0 -0.2 10 10
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.007 0.11 0.21 36 -0.2 21 57
HIF-2-alpha transcription factor network

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
MMP14 0.019 0.073 0.43 1 -0.55 4 5
oxygen homeostasis 0.01 0.014 -10000 0 -10000 0 0
TCEB2 0.021 0.003 -10000 0 -10000 0 0
TCEB1 0.02 0.018 0.33 1 -10000 0 1
VHL/Elongin B/Elongin C/HIF2A 0.074 0.1 0.29 7 -0.28 4 11
EPO 0.1 0.16 0.4 41 -0.39 1 42
FIH (dimer) 0.027 0.022 -10000 0 -10000 0 0
APEX1 0.03 0.027 -10000 0 -10000 0 0
SERPINE1 0.11 0.17 0.44 37 -0.41 1 38
FLT1 -0.008 0.13 -10000 0 -0.58 14 14
ADORA2A 0.11 0.16 0.38 45 -0.4 1 46
germ cell development 0.12 0.18 0.42 45 -0.42 3 48
SLC11A2 0.12 0.16 0.39 51 -0.41 1 52
BHLHE40 0.12 0.16 0.4 52 -0.41 1 53
HIF1AN 0.027 0.022 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.086 0.12 0.34 26 -0.29 2 28
ETS1 0.021 0.017 -10000 0 -10000 0 0
CITED2 -0.011 0.15 -10000 0 -0.53 21 21
KDR -0.002 0.14 -10000 0 -0.7 12 12
PGK1 0.12 0.16 0.42 41 -0.41 1 42
SIRT1 0.021 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.14 0.2 0.54 35 -0.45 1 36
EPAS1 0.057 0.1 0.25 36 -0.24 7 43
SP1 0.023 0.01 -10000 0 -10000 0 0
ABCG2 0.11 0.19 0.4 52 -0.46 6 58
EFNA1 0.096 0.15 0.39 38 -0.41 1 39
FXN 0.11 0.15 0.38 43 -0.38 1 44
POU5F1 0.12 0.18 0.43 45 -0.43 3 48
neuron apoptosis -0.14 0.2 0.44 1 -0.53 35 36
EP300 0.021 0.004 -10000 0 -10000 0 0
EGLN3 0.1 0.14 0.35 87 -0.33 1 88
EGLN2 0.027 0.023 -10000 0 -10000 0 0
EGLN1 0.025 0.022 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.038 0.019 0.23 1 -10000 0 1
VHL 0.021 0.004 -10000 0 -10000 0 0
ARNT 0.025 0.027 -10000 0 -10000 0 0
SLC2A1 0.15 0.19 0.42 89 -0.4 1 90
TWIST1 0.12 0.18 0.43 62 -10000 0 62
ELK1 0.022 0.008 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.094 0.13 0.35 24 -0.31 1 25
VEGFA 0.11 0.16 0.4 48 -0.41 1 49
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.026 0.036 -10000 0 -0.24 6 6
alphaV beta3 Integrin 0.022 0.094 0.23 17 -0.21 41 58
PTK2 -0.039 0.13 0.34 10 -0.36 19 29
IGF1R 0.02 0.019 -10000 0 -0.34 1 1
PI4KB 0.018 0.008 -10000 0 -10000 0 0
MFGE8 0.021 0.004 -10000 0 -10000 0 0
SRC 0.021 0.004 -10000 0 -10000 0 0
CDKN1B -0.055 0.16 0.18 4 -0.42 53 57
VEGFA 0.021 0.004 -10000 0 -10000 0 0
ILK -0.057 0.16 0.18 4 -0.41 56 60
ROCK1 0.021 0.005 -10000 0 -10000 0 0
AKT1 -0.062 0.14 -10000 0 -0.38 53 53
PTK2B -0.012 0.06 0.18 20 -0.31 1 21
alphaV/beta3 Integrin/JAM-A -0.002 0.12 0.23 20 -0.2 71 91
CBL 0.021 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.056 0.063 0.23 35 -0.2 4 39
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.049 0.038 0.23 1 -0.22 5 6
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.02 0.082 -10000 0 -0.32 10 10
alphaV/beta3 Integrin/Syndecan-1 0.05 0.051 0.23 19 -0.2 4 23
PI4KA 0.021 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.02 0.093 -10000 0 -0.21 37 37
PI4 Kinase 0.026 0.013 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.18 0.11 0.24 249 -0.19 4 253
RPS6KB1 -0.047 0.075 0.31 2 -0.36 7 9
TLN1 0.02 0.02 -10000 0 -0.34 1 1
MAPK3 -0.056 0.14 0.28 1 -0.44 37 38
GPR124 0.017 0.028 -10000 0 -0.34 2 2
MAPK1 -0.054 0.15 0.28 2 -0.44 38 40
PXN 0.021 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.028 0.13 0.23 15 -0.2 111 126
cell adhesion 0.041 0.058 0.22 19 -0.21 5 24
ANGPTL3 0.037 0.07 0.33 19 -10000 0 19
VEGFR2 homodimer/VEGFA homodimer/Src 0.037 0.032 -10000 0 -0.2 5 5
IGF-1R heterotetramer 0.02 0.019 -10000 0 -0.34 1 1
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
TGFBR2 0.016 0.043 -10000 0 -0.34 5 5
ITGB3 0.034 0.08 0.33 19 -0.34 4 23
IGF1 0.018 0.042 0.33 1 -0.34 4 5
RAC1 0.019 0.007 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.042 0.055 0.23 17 -0.23 5 22
apoptosis 0.022 0.002 -10000 0 -10000 0 0
CD47 0.02 0.019 -10000 0 -0.34 1 1
alphaV/beta3 Integrin/CD47 0.048 0.053 0.23 19 -0.2 5 24
VCL 0.022 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.033 0.081 0.24 17 -0.22 23 40
CSF1 0.02 0.02 -10000 0 -0.34 1 1
PIK3C2A -0.057 0.16 0.18 4 -0.41 56 60
PI4 Kinase/Pyk2 -0.053 0.075 -10000 0 -0.3 11 11
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.054 0.061 0.23 19 -0.2 9 28
FAK1/Vinculin -0.03 0.12 0.32 10 -0.31 16 26
alphaV beta3/Integrin/ppsTEM5 0.042 0.056 0.23 17 -0.23 5 22
RHOA 0.021 0.004 -10000 0 -10000 0 0
VTN -0.032 0.14 0.33 5 -0.34 57 62
BCAR1 0.02 0.02 -10000 0 -0.34 1 1
FGF2 -0.019 0.11 -10000 0 -0.34 40 40
F11R -0.035 0.063 -10000 0 -0.24 31 31
alphaV/beta3 Integrin/Lactadherin 0.049 0.051 0.23 19 -0.2 4 23
alphaV/beta3 Integrin/TGFBR2 0.045 0.06 0.23 19 -0.2 9 28
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.048 0.027 -10000 0 -0.19 2 2
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.045 0.05 0.22 18 -0.21 4 22
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.018 0.038 -10000 0 -0.34 4 4
alphaV/beta3 Integrin/Pyk2 0.033 0.06 0.21 16 -0.2 8 24
SDC1 0.022 0.002 -10000 0 -10000 0 0
VAV3 -0.019 0.047 0.18 1 -0.33 1 2
PTPN11 0.021 0.004 -10000 0 -10000 0 0
IRS1 0.021 0.019 -10000 0 -0.34 1 1
FAK1/Paxillin -0.031 0.12 0.3 9 -0.32 15 24
cell migration -0.032 0.11 0.26 12 -0.29 14 26
ITGAV 0.022 0.002 -10000 0 -10000 0 0
PI3K 0.014 0.11 0.28 2 -0.2 55 57
SPP1 0.25 0.14 0.33 258 -10000 0 258
KDR 0.015 0.046 -10000 0 -0.34 6 6
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.022 0.002 -10000 0 -10000 0 0
COL4A3 -0.09 0.17 -10000 0 -0.34 110 110
angiogenesis -0.049 0.17 0.28 2 -0.45 36 38
Rac1/GTP -0.019 0.044 -10000 0 -0.29 1 1
EDIL3 0 0.087 0.33 1 -0.34 21 22
cell proliferation 0.044 0.059 0.23 19 -0.2 9 28
TCGA08_retinoblastoma

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
CDKN2B 0.011 0.04 -10000 0 -0.32 4 4
CDKN2C 0 0.034 0.34 1 -10000 0 1
CDKN2A 0.099 0.14 0.33 92 -10000 0 92
CCND2 -0.019 0.041 0.15 4 -0.14 7 11
RB1 0.019 0.048 0.22 4 -0.16 3 7
CDK4 -0.021 0.045 0.17 4 -0.17 2 6
CDK6 -0.021 0.044 0.17 3 -0.14 8 11
G1/S progression 0.01 0.093 0.18 62 -0.25 5 67
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.017 0.033 -10000 0 -0.34 3 3
GNB1/GNG2 -0.046 0.066 -10000 0 -0.19 57 57
AKT1 -0.034 0.095 -10000 0 -0.26 18 18
EGF 0.074 0.12 0.33 63 -0.34 3 66
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.033 0.064 0.18 1 -0.24 14 15
mol:Ca2+ -0.054 0.13 -10000 0 -0.3 66 66
LYN -0.022 0.042 -10000 0 -0.21 3 3
RhoA/GTP -0.03 0.05 -10000 0 -0.13 49 49
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.064 0.14 -10000 0 -0.34 60 60
GNG2 0.02 0.02 -10000 0 -0.34 1 1
ARRB2 0.02 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.043 0.17 -10000 0 -0.62 25 25
G beta5/gamma2 -0.058 0.086 -10000 0 -0.24 56 56
PRKCH -0.064 0.15 -10000 0 -0.35 62 62
DNM1 0.024 0.029 0.33 3 -10000 0 3
TXA2/TP beta/beta Arrestin3 0.007 0.052 -10000 0 -0.53 3 3
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.013 0.05 -10000 0 -0.34 7 7
G12 family/GTP -0.052 0.12 -10000 0 -0.29 61 61
ADRBK1 0.021 0.004 -10000 0 -10000 0 0
ADRBK2 0.021 0.004 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.027 0.008 -10000 0 -10000 0 0
mol:GDP 0.038 0.11 0.34 19 -10000 0 19
mol:NADP 0.023 0.052 0.33 6 -0.34 3 9
RAB11A 0.021 0.004 -10000 0 -10000 0 0
PRKG1 -0.01 0.1 -10000 0 -0.34 31 31
mol:IP3 -0.07 0.16 -10000 0 -0.38 66 66
cell morphogenesis 0.027 0.008 -10000 0 -10000 0 0
PLCB2 -0.097 0.22 -10000 0 -0.51 67 67
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.004 0.068 0.22 3 -0.2 2 5
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.026 0.052 0.18 1 -0.23 7 8
RHOA 0.021 0.004 -10000 0 -10000 0 0
PTGIR 0.015 0.043 -10000 0 -0.34 5 5
PRKCB1 -0.067 0.16 -10000 0 -0.37 63 63
GNAQ 0.02 0.02 -10000 0 -0.34 1 1
mol:L-citrulline 0.023 0.052 0.33 6 -0.34 3 9
TXA2/TXA2-R family -0.096 0.21 -10000 0 -0.51 61 61
LCK -0.023 0.049 0.18 1 -0.22 4 5
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.011 0.051 -10000 0 -0.27 3 3
TXA2-R family/G12 family/GDP/G beta/gamma 0.005 0.075 -10000 0 -0.43 9 9
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.01 0.05 -10000 0 -0.27 3 3
MAPK14 -0.04 0.099 0.26 4 -0.23 53 57
TGM2/GTP -0.079 0.17 -10000 0 -0.41 67 67
MAPK11 -0.046 0.093 -10000 0 -0.23 55 55
ARHGEF1 -0.038 0.069 -10000 0 -0.18 51 51
GNAI2 0.021 0.004 -10000 0 -10000 0 0
JNK cascade -0.069 0.16 -10000 0 -0.38 60 60
RAB11/GDP 0.021 0.006 -10000 0 -10000 0 0
ICAM1 -0.05 0.12 -10000 0 -0.29 56 56
cAMP biosynthetic process -0.067 0.15 -10000 0 -0.34 68 68
Gq family/GTP/EBP50 -0.003 0.048 -10000 0 -0.2 16 16
actin cytoskeleton reorganization 0.027 0.008 -10000 0 -10000 0 0
SRC -0.023 0.045 0.18 1 -0.21 3 4
GNB5 0.021 0.004 -10000 0 -10000 0 0
GNB1 0.021 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.011 0.077 0.2 7 -0.24 10 17
VCAM1 -0.051 0.12 0.23 1 -0.29 56 57
TP beta/Gq family/GDP/G beta5/gamma2 -0.043 0.17 -10000 0 -0.62 25 25
platelet activation -0.054 0.13 0.29 3 -0.3 59 62
PGI2/IP 0.012 0.029 -10000 0 -0.23 5 5
PRKACA 0.002 0.041 -10000 0 -0.22 10 10
Gq family/GDP/G beta5/gamma2 -0.023 0.13 -10000 0 -0.57 15 15
TXA2/TP beta/beta Arrestin2 -0.006 0.062 -10000 0 -0.36 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.015 0.038 -10000 0 -0.22 10 10
mol:DAG -0.076 0.18 -10000 0 -0.42 64 64
EGFR 0.017 0.037 0.33 1 -0.34 3 4
TXA2/TP alpha -0.092 0.2 -10000 0 -0.47 69 69
Gq family/GTP -0.018 0.076 0.22 1 -0.24 32 33
YES1 -0.021 0.047 0.18 1 -0.2 3 4
GNAI2/GTP -0.027 0.037 -10000 0 -0.2 7 7
PGD2/DP 0.01 0.035 -10000 0 -0.23 7 7
SLC9A3R1 0.022 0.017 0.33 1 -10000 0 1
FYN -0.022 0.045 0.18 1 -0.2 3 4
mol:NO 0.023 0.052 0.33 6 -0.34 3 9
GNA15 0.02 0.006 -10000 0 -10000 0 0
PGK/cGMP 0.01 0.072 0.21 6 -0.2 31 37
RhoA/GDP 0.021 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.018 0.056 -10000 0 -0.24 6 6
NOS3 0.023 0.052 0.33 6 -0.34 3 9
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.063 0.15 0.27 2 -0.35 60 62
PRKCB -0.064 0.15 -10000 0 -0.36 59 59
PRKCE -0.063 0.15 0.29 1 -0.36 57 58
PRKCD -0.069 0.15 -10000 0 -0.38 61 61
PRKCG -0.068 0.16 -10000 0 -0.38 61 61
muscle contraction -0.091 0.2 -10000 0 -0.48 61 61
PRKCZ -0.064 0.14 -10000 0 -0.34 60 60
ARR3 0.02 0.017 0.33 1 -10000 0 1
TXA2/TP beta 0.007 0.052 -10000 0 -0.21 7 7
PRKCQ -0.075 0.15 -10000 0 -0.37 64 64
MAPKKK cascade -0.086 0.19 -10000 0 -0.45 66 66
SELE -0.062 0.14 -10000 0 -0.36 56 56
TP beta/GNAI2/GDP/G beta/gamma 0.02 0.053 -10000 0 -0.25 4 4
ROCK1 0.021 0.005 -10000 0 -10000 0 0
GNA14 0.011 0.06 -10000 0 -0.34 10 10
chemotaxis -0.1 0.23 -10000 0 -0.59 56 56
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.014 0.005 -10000 0 -10000 0 0
Arf6 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
CENTA1/KIF3B 0.022 0.017 -10000 0 -0.18 1 1
ARNO/beta Arrestin1-2 -0.056 0.18 -10000 0 -0.82 14 14
EGFR 0.017 0.037 0.33 1 -0.34 3 4
EPHA2 0.016 0.043 -10000 0 -0.34 5 5
USP6 0.02 0.006 -10000 0 -10000 0 0
IQSEC1 0.02 0.019 -10000 0 -0.34 1 1
EGFR/EGFR/EGF/EGF 0.055 0.086 0.24 52 -0.22 6 58
ARRB2 0.016 0.036 0.14 25 -10000 0 25
mol:GTP 0.003 0.042 0.14 7 -0.15 8 15
ARRB1 0.018 0.033 -10000 0 -0.34 3 3
FBXO8 0.021 0.004 -10000 0 -10000 0 0
TSHR 0.053 0.095 0.33 37 -10000 0 37
EGF 0.074 0.12 0.33 63 -0.34 3 66
somatostatin receptor activity 0 0 0.001 12 -0.001 40 52
ARAP2 0.008 0.068 -10000 0 -0.34 13 13
mol:GDP -0.062 0.15 0.18 6 -0.3 63 69
mol:PI-3-4-5-P3 0 0 0.001 11 -0.001 24 35
ITGA2B -0.013 0.11 0.33 1 -0.34 34 35
ARF6 0.021 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.04 0.036 -10000 0 -0.19 5 5
ADAP1 0.018 0.02 -10000 0 -0.34 1 1
KIF13B 0.018 0.008 -10000 0 -10000 0 0
HGF/MET 0.016 0.077 0.24 8 -0.25 23 31
PXN 0.021 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.046 0.12 0.25 10 -0.28 40 50
EGFR/EGFR/EGF/EGF/ARFGEP100 0.058 0.077 0.23 47 -0.18 7 54
ADRB2 -0.11 0.17 -10000 0 -0.34 127 127
receptor agonist activity 0 0 0.001 3 0 39 42
actin filament binding 0 0 0.001 9 -0.001 47 56
SRC 0.021 0.004 -10000 0 -10000 0 0
ITGB3 0.034 0.08 0.33 19 -0.34 4 23
GNAQ 0.02 0.02 -10000 0 -0.34 1 1
EFA6/PI-4-5-P2 0 0.001 0.001 15 -0.001 31 46
ARF6/GDP -0.042 0.15 0.45 1 -0.41 37 38
ARF6/GDP/GULP/ACAP1 -0.044 0.14 -10000 0 -0.35 38 38
alphaIIb/beta3 Integrin/paxillin/GIT1 0.036 0.09 0.23 19 -0.19 37 56
ACAP1 0.019 0.02 -10000 0 -0.34 1 1
ACAP2 0.021 0.005 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.03 0.069 0.25 28 -10000 0 28
EFNA1 0.017 0.021 -10000 0 -0.34 1 1
HGF 0.009 0.076 0.33 3 -0.34 14 17
CYTH3 -0.007 0.018 0.22 2 -10000 0 2
CYTH2 -0.025 0.2 -10000 0 -0.99 14 14
NCK1 0.021 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 10 0 33 43
endosomal lumen acidification 0 0 0 29 0 23 52
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.021 0.019 -10000 0 -0.34 1 1
GNAQ/ARNO -0.011 0.19 -10000 0 -0.92 14 14
mol:Phosphatidic acid 0 0 0 3 -10000 0 3
PIP3-E 0 0 0 6 0 6 12
MET 0.014 0.073 0.33 5 -0.34 11 16
GNA14 0.011 0.06 -10000 0 -0.34 10 10
GNA15 0.02 0.006 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 11 -0.001 32 43
GNA11 0.02 0.006 -10000 0 -10000 0 0
LHCGR 0.042 0.083 0.33 27 -10000 0 27
AGTR1 -0.081 0.16 -10000 0 -0.34 100 100
desensitization of G-protein coupled receptor protein signaling pathway 0.03 0.069 0.25 28 -10000 0 28
IPCEF1/ARNO 0.016 0.19 -10000 0 -0.84 14 14
alphaIIb/beta3 Integrin 0.014 0.1 0.24 20 -0.24 37 57
Glucocorticoid receptor regulatory network

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
PCK2 0.025 0.084 0.28 1 -0.33 1 2
SMARCC2 0.021 0.01 -10000 0 -0.14 1 1
SMARCC1 0.021 0.007 -10000 0 -10000 0 0
TBX21 -0.045 0.17 0.36 3 -0.49 29 32
SUMO2 0.019 0.014 -10000 0 -10000 0 0
STAT1 (dimer) 0.023 0.002 -10000 0 -10000 0 0
FKBP4 0.02 0.006 -10000 0 -10000 0 0
FKBP5 0.021 0.005 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.041 0.11 0.26 24 -10000 0 24
PRL -0.014 0.11 0.43 3 -10000 0 3
cortisol/GR alpha (dimer)/TIF2 0.062 0.21 0.49 40 -0.35 9 49
RELA -0.032 0.1 0.18 1 -0.2 75 76
FGG 0.012 0.29 0.49 56 -0.4 64 120
GR beta/TIF2 0.033 0.11 0.27 28 -0.21 2 30
IFNG -0.034 0.25 0.44 14 -0.58 32 46
apoptosis 0.004 0.14 0.45 9 -0.49 10 19
CREB1 0.042 0.048 0.2 1 -10000 0 1
histone acetylation -0.068 0.12 -10000 0 -0.31 34 34
BGLAP -0.015 0.1 -10000 0 -0.39 3 3
GR/PKAc 0.049 0.11 0.28 24 -10000 0 24
NF kappa B1 p50/RelA -0.056 0.18 0.29 1 -0.32 91 92
SMARCD1 0.021 0.007 -10000 0 -10000 0 0
MDM2 0.032 0.085 0.21 42 -10000 0 42
GATA3 0.023 0.017 0.33 1 -10000 0 1
AKT1 0.02 0.005 -10000 0 -10000 0 0
CSF2 -0.12 0.26 -10000 0 -0.88 30 30
GSK3B 0.019 0.014 -10000 0 -10000 0 0
NR1I3 0.021 0.14 0.45 8 -0.47 5 13
CSN2 0.045 0.17 0.35 48 -0.3 12 60
BRG1/BAF155/BAF170/BAF60A 0.049 0.03 -10000 0 -0.24 2 2
NFATC1 0.018 0.028 -10000 0 -0.34 2 2
POU2F1 0.023 0.018 -10000 0 -10000 0 0
CDKN1A -0.006 0.079 -10000 0 -1 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.006 -10000 0 -10000 0 0
SFN 0.026 0.047 0.33 7 -0.34 1 8
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.054 0.1 0.27 19 -10000 0 19
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.025 0.21 0.44 7 -0.69 25 32
JUN -0.002 0.18 0.34 27 -0.39 26 53
IL4 -0.03 0.12 -10000 0 -0.36 20 20
CDK5R1 0.026 0.048 0.33 8 -10000 0 8
PRKACA 0.02 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.042 0.067 0.17 3 -0.23 18 21
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.046 0.1 0.27 19 -10000 0 19
cortisol/GR alpha (monomer) 0.083 0.27 0.58 48 -0.39 12 60
NCOA2 0.017 0.028 -10000 0 -0.34 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.011 0.12 0.23 10 -0.31 21 31
AP-1/NFAT1-c-4 0.005 0.26 0.42 28 -0.46 47 75
AFP -0.004 0.17 0.43 10 -0.47 4 14
SUV420H1 0.021 0.004 -10000 0 -10000 0 0
IRF1 0.047 0.14 0.4 15 -10000 0 15
TP53 0.021 0.051 -10000 0 -0.92 1 1
PPP5C 0.021 0.005 -10000 0 -10000 0 0
KRT17 -0.043 0.29 0.46 16 -0.73 29 45
KRT14 0.036 0.18 0.41 12 -0.44 2 14
TBP 0.021 0.007 -10000 0 -10000 0 0
CREBBP -0.016 0.07 -10000 0 -0.27 1 1
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC2 0.024 0.022 -10000 0 -10000 0 0
AP-1 0.005 0.26 0.43 28 -0.46 47 75
MAPK14 0.019 0.014 -10000 0 -10000 0 0
MAPK10 -0.018 0.11 -10000 0 -0.34 38 38
MAPK11 0.016 0.03 -10000 0 -0.34 2 2
KRT5 -0.18 0.44 0.42 15 -0.92 85 100
interleukin-1 receptor activity 0.004 0.019 -10000 0 -10000 0 0
NCOA1 0.022 0.002 -10000 0 -10000 0 0
STAT1 0.023 0.002 -10000 0 -10000 0 0
CGA 0.004 0.13 0.33 10 -0.38 6 16
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.001 0.18 0.46 24 -0.31 13 37
MAPK3 0.019 0.014 -10000 0 -10000 0 0
MAPK1 0.019 0.013 -10000 0 -10000 0 0
ICAM1 -0.1 0.22 -10000 0 -0.57 41 41
NFKB1 -0.032 0.1 -10000 0 -0.21 55 55
MAPK8 -0.012 0.16 0.31 12 -0.35 32 44
MAPK9 0.019 0.013 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.003 0.15 0.45 9 -0.52 10 19
BAX -0.013 0.066 -10000 0 -10000 0 0
POMC -0.12 0.28 -10000 0 -0.89 27 27
EP300 -0.017 0.071 -10000 0 -0.27 1 1
cortisol/GR alpha (dimer)/p53 0.067 0.22 0.51 38 -0.36 5 43
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.071 0.21 20 -10000 0 20
SGK1 -0.027 0.11 -10000 0 -0.77 2 2
IL13 -0.041 0.19 -10000 0 -0.58 14 14
IL6 -0.2 0.37 -10000 0 -0.8 85 85
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.04 0.17 -10000 0 -0.62 6 6
IL2 -0.047 0.22 0.38 6 -0.51 38 44
CDK5 0.019 0.011 -10000 0 -10000 0 0
PRKACB 0.022 0.017 0.33 1 -10000 0 1
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
IL8 -0.081 0.2 0.31 6 -0.51 33 39
CDK5R1/CDK5 0.033 0.036 0.24 8 -10000 0 8
NF kappa B1 p50/RelA/PKAc -0.02 0.15 0.27 1 -0.28 53 54
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.067 0.21 0.48 39 -0.33 7 46
SMARCA4 0.02 0.02 -10000 0 -0.34 1 1
chromatin remodeling 0.037 0.13 0.34 26 -0.34 1 27
NF kappa B1 p50/RelA/Cbp -0.062 0.16 0.37 1 -0.35 47 48
JUN (dimer) -0.003 0.18 0.34 27 -0.39 25 52
YWHAH 0.021 0.004 -10000 0 -10000 0 0
VIPR1 -0.29 0.35 -10000 0 -0.69 150 150
NR3C1 0.052 0.17 0.38 44 -0.24 5 49
NR4A1 -0.064 0.17 -10000 0 -0.37 79 79
TIF2/SUV420H1 0.027 0.023 -10000 0 -0.24 2 2
MAPKKK cascade 0.004 0.14 0.45 9 -0.49 10 19
cortisol/GR alpha (dimer)/Src-1 0.081 0.23 0.5 47 -0.34 10 57
PBX1 0.014 0.06 -10000 0 -0.34 9 9
POU1F1 0.023 0.027 0.43 1 -10000 0 1
SELE -0.15 0.32 -10000 0 -0.8 60 60
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.036 0.13 0.34 26 -0.34 1 27
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.067 0.21 0.48 39 -0.33 7 46
mol:cortisol 0.046 0.15 0.34 49 -0.21 12 61
MMP1 0.17 0.2 0.38 64 -0.74 6 70
Canonical Wnt signaling pathway

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.024 0.017 0.19 1 -10000 0 1
AES 0.022 0.014 0.16 1 -10000 0 1
FBXW11 0.021 0.005 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.029 0.011 -10000 0 -10000 0 0
SMAD4 0.019 0.007 -10000 0 -10000 0 0
DKK2 -0.035 0.13 -10000 0 -0.34 55 55
TLE1 0.023 0.014 0.17 1 -10000 0 1
MACF1 0.019 0.033 -10000 0 -0.34 3 3
CTNNB1 0.083 0.1 0.29 20 -0.33 3 23
WIF1 -0.21 0.17 -10000 0 -0.34 229 229
beta catenin/RanBP3 0.052 0.1 0.46 13 -0.36 1 14
KREMEN2 0.095 0.13 0.33 84 -10000 0 84
DKK1 0.046 0.16 0.33 59 -0.34 27 86
beta catenin/beta TrCP1 0.084 0.099 0.31 13 -0.34 2 15
FZD1 0.021 0.005 -10000 0 -10000 0 0
AXIN2 -0.035 0.25 0.56 11 -1.2 14 25
AXIN1 0.022 0.004 -10000 0 -10000 0 0
RAN 0.023 0.024 0.33 2 -10000 0 2
Axin1/APC/GSK3/beta catenin 0.028 0.091 -10000 0 -0.65 5 5
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.01 0.18 0.28 1 -0.59 21 22
Axin1/APC/GSK3 0.052 0.075 0.23 17 -0.37 2 19
Axin1/APC/GSK3/beta catenin/Macf1 0.035 0.082 0.27 7 -0.36 4 11
HNF1A 0.075 0.12 0.33 61 -0.34 1 62
CTBP1 0.023 0.016 0.18 1 -10000 0 1
MYC 0.08 0.25 0.57 59 -1.3 2 61
RANBP3 0.02 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.038 0.11 0.23 57 -0.18 50 107
NKD1 -0.019 0.12 0.33 4 -0.34 42 46
TCF4 0.019 0.031 0.17 1 -0.34 2 3
TCF3 0.022 0.016 0.18 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.052 0.031 0.23 4 -10000 0 4
Ran/GTP 0.017 0.016 0.22 2 -10000 0 2
CtBP/CBP/TCF/TLE1/AES 0.006 0.12 0.42 12 -0.46 6 18
LEF1 0.026 0.028 0.28 3 -10000 0 3
DVL1 0.035 0.056 -10000 0 -0.34 3 3
CSNK2A1 0.021 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.016 0.18 -10000 0 -0.61 18 18
DKK1/LRP6/Kremen 2 0.088 0.13 0.26 105 -0.18 26 131
LRP6 0.021 0.006 -10000 0 -10000 0 0
CSNK1A1 0.024 0.015 -10000 0 -10000 0 0
NLK 0.019 0.01 -10000 0 -10000 0 0
CCND1 0.005 0.18 0.58 16 -1.3 3 19
WNT1 0.027 0.04 0.33 6 -10000 0 6
GSK3A 0.022 0.005 -10000 0 -10000 0 0
GSK3B 0.022 0.003 -10000 0 -10000 0 0
FRAT1 0.021 0.004 -10000 0 -10000 0 0
PPP2R5D 0.048 0.078 0.24 34 -0.22 5 39
APC -0.003 0.062 0.18 34 -10000 0 34
WNT1/LRP6/FZD1 0.093 0.09 0.22 23 -0.19 2 25
CREBBP 0.024 0.016 0.18 1 -10000 0 1
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.021 0.004 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.026 0.074 -10000 0 -0.25 20 20
NT3 (dimer)/TRKC -0.028 0.12 0.24 1 -0.26 71 72
NT3 (dimer)/TRKB -0.041 0.13 0.29 6 -0.22 114 120
SHC/Grb2/SOS1/GAB1/PI3K 0.008 0.026 -10000 0 -0.19 1 1
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
BDNF -0.14 0.18 -10000 0 -0.34 160 160
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
DYNLT1 0.02 0.006 -10000 0 -10000 0 0
NTRK1 0.009 0.065 0.33 1 -0.34 11 12
NTRK2 -0.085 0.17 0.33 3 -0.34 107 110
NTRK3 -0.045 0.14 -10000 0 -0.34 65 65
NT-4/5 (dimer)/TRKB -0.041 0.13 0.27 5 -0.22 117 122
neuron apoptosis 0.14 0.17 0.4 79 -10000 0 79
SHC 2-3/Grb2 -0.16 0.19 -10000 0 -0.44 79 79
SHC1 0.018 0.008 -10000 0 -10000 0 0
SHC2 -0.11 0.15 -10000 0 -0.43 48 48
SHC3 -0.16 0.22 -10000 0 -0.53 79 79
STAT3 (dimer) 0.02 0.03 -10000 0 -0.3 3 3
NT3 (dimer)/TRKA 0.022 0.074 0.25 6 -0.22 23 29
RIN/GDP -0.018 0.077 0.34 2 -0.23 9 11
GIPC1 0.02 0.006 -10000 0 -10000 0 0
KRAS 0.02 0.006 -10000 0 -10000 0 0
DNAJA3 -0.017 0.058 0.17 3 -0.26 7 10
RIN/GTP 0.013 0.012 0.22 1 -10000 0 1
CCND1 -0.02 0.054 -10000 0 -0.6 3 3
MAGED1 0.022 0.017 0.33 1 -10000 0 1
PTPN11 0.021 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.004 0.077 -10000 0 -0.34 17 17
SHC/GRB2/SOS1 0.035 0.018 -10000 0 -10000 0 0
GRB2 0.021 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.018 0.081 0.23 10 -0.21 31 41
TRKA/NEDD4-2 0.017 0.049 0.24 1 -0.24 11 12
ELMO1 0.018 0.027 -10000 0 -0.34 2 2
RhoG/GTP/ELMO1/DOCK1 0.025 0.019 -10000 0 -0.2 2 2
NGF 0.023 0.09 0.33 15 -0.34 11 26
HRAS 0.021 0.004 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
GAB2 0.017 0.038 -10000 0 -0.34 4 4
RIT2 0.018 0.018 0.33 1 -10000 0 1
RIT1 0.018 0.008 -10000 0 -10000 0 0
FRS2 0.02 0.006 -10000 0 -10000 0 0
DNM1 0.024 0.029 0.33 3 -10000 0 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.02 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.01 0.069 0.18 2 -0.26 10 12
mol:GDP -0.033 0.1 0.4 2 -0.32 14 16
NGF (dimer) 0.023 0.09 0.33 15 -0.34 11 26
RhoG/GDP 0.013 0.019 -10000 0 -0.23 2 2
RIT1/GDP -0.025 0.063 -10000 0 -0.24 6 6
TIAM1 0.017 0.038 -10000 0 -0.34 4 4
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.13 0.15 0.23 1 -0.24 215 216
KIDINS220/CRKL/C3G 0.03 0.008 -10000 0 -10000 0 0
SHC/RasGAP 0.026 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.039 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.044 0.027 -10000 0 -0.19 1 1
RIT1/GTP 0.014 0.006 -10000 0 -10000 0 0
NT3 (dimer) 0.002 0.083 0.33 1 -0.34 19 20
RAP1/GDP -0.023 0.062 -10000 0 -0.2 10 10
KIDINS220/CRKL 0.021 0.004 -10000 0 -10000 0 0
BDNF (dimer) -0.14 0.18 -10000 0 -0.34 160 160
ubiquitin-dependent protein catabolic process 0.025 0.066 0.23 11 -0.2 19 30
Schwann cell development -0.036 0.026 -10000 0 -10000 0 0
EHD4 0.021 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.048 0.024 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.005 0.047 -10000 0 -0.19 4 4
RAP1B 0.02 0.006 -10000 0 -10000 0 0
RAP1A 0.021 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.14 0.15 -10000 0 -0.34 92 92
ABL1 0.021 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.031 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.068 0.098 -10000 0 -0.42 13 13
STAT3 0.02 0.03 -10000 0 -0.3 3 3
axon guidance -0.16 0.12 -10000 0 -0.24 201 201
MAPK3 -0.017 0.081 0.18 29 -0.2 25 54
MAPK1 -0.015 0.08 0.18 30 -0.2 23 53
CDC42/GDP -0.019 0.079 0.34 2 -0.23 8 10
NTF3 0.002 0.083 0.33 1 -0.34 19 20
NTF4 0.004 0.077 -10000 0 -0.34 17 17
NGF (dimer)/TRKA/FAIM 0.031 0.067 0.23 13 -0.2 18 31
PI3K 0.03 0.009 -10000 0 -10000 0 0
FRS3 0.021 0.005 -10000 0 -10000 0 0
FAIM 0.021 0.003 -10000 0 -10000 0 0
GAB1 0.021 0.019 -10000 0 -0.34 1 1
RASGRF1 -0.063 0.092 0.15 1 -0.3 21 22
SOS1 0.022 0.003 -10000 0 -10000 0 0
MCF2L -0.056 0.086 0.21 1 -0.23 66 67
RGS19 0.02 0.006 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.003 0.086 0.27 1 -0.35 6 7
Rac1/GDP -0.022 0.071 -10000 0 -0.24 9 9
NGF (dimer)/TRKA/GRIT 0.019 0.063 0.21 13 -0.19 19 32
neuron projection morphogenesis 0.005 0.1 -10000 0 -0.89 2 2
NGF (dimer)/TRKA/NEDD4-2 0.025 0.066 0.23 11 -0.2 19 30
MAP2K1 0.013 0.09 0.19 66 -0.18 1 67
NGFR 0.02 0.062 0.33 6 -0.34 6 12
NGF (dimer)/TRKA/GIPC/GAIP -0.004 0.064 0.18 3 -0.28 5 8
RAS family/GTP/PI3K 0.004 0.03 -10000 0 -0.17 4 4
FRS2 family/SHP2/GRB2/SOS1 0.054 0.027 -10000 0 -10000 0 0
NRAS 0.021 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.031 0.008 -10000 0 -10000 0 0
PRKCI 0.021 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCZ 0.019 0.027 -10000 0 -0.34 2 2
MAPKKK cascade -0.069 0.19 -10000 0 -0.57 42 42
RASA1 0.021 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.019 0.049 0.24 1 -0.24 11 12
SQSTM1 0.021 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.12 0.14 0.23 2 -0.22 215 217
NGF (dimer)/TRKA/p62/Atypical PKCs 0.039 0.068 0.23 10 -0.19 17 27
MATK 0.005 0.072 -10000 0 -0.34 15 15
NEDD4L 0.019 0.007 -10000 0 -10000 0 0
RAS family/GDP -0.031 0.046 -10000 0 -0.18 12 12
NGF (dimer)/TRKA -0.001 0.065 0.19 4 -0.22 19 23
Rac1/GTP -0.065 0.074 -10000 0 -0.21 45 45
FRS2 family/SHP2/CRK family 0.05 0.031 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) 0.003 0.1 -10000 0 -0.41 18 18
HDAC1 0.021 0.005 -10000 0 -10000 0 0
AES 0.02 0.006 -10000 0 -10000 0 0
FBXW11 0.021 0.005 -10000 0 -10000 0 0
DTX1 0.023 0.024 0.33 2 -10000 0 2
LRP6/FZD1 0.028 0.011 -10000 0 -10000 0 0
TLE1 0.021 0.005 -10000 0 -10000 0 0
AP1 -0.028 0.092 -10000 0 -0.24 48 48
NCSTN 0.019 0.008 -10000 0 -10000 0 0
ADAM10 0.021 0.004 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.022 0.099 -10000 0 -0.58 7 7
NICD/RBPSUH 0.013 0.11 -10000 0 -0.42 17 17
WIF1 -0.21 0.17 -10000 0 -0.34 229 229
NOTCH1 -0.005 0.093 -10000 0 -0.44 15 15
PSENEN 0.02 0.006 -10000 0 -10000 0 0
KREMEN2 0.095 0.13 0.33 84 -10000 0 84
DKK1 0.046 0.16 0.33 59 -0.34 27 86
beta catenin/beta TrCP1 0.017 0.072 0.3 1 -0.32 1 2
APH1B 0.02 0.019 -10000 0 -0.34 1 1
APH1A 0.018 0.009 -10000 0 -10000 0 0
AXIN1 0.001 0.073 -10000 0 -0.42 5 5
CtBP/CBP/TCF1/TLE1/AES 0.019 0.055 0.27 1 -0.19 1 2
PSEN1 0.021 0.005 -10000 0 -10000 0 0
FOS -0.005 0.092 -10000 0 -0.34 25 25
JUN 0.019 0.027 -10000 0 -0.34 2 2
MAP3K7 0.019 0.007 -10000 0 -10000 0 0
CTNNB1 0.013 0.072 0.27 2 -0.32 1 3
MAPK3 0.022 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.038 0.11 0.23 57 -0.18 50 107
HNF1A 0.073 0.12 0.33 60 -0.34 1 61
CTBP1 0.021 0.005 -10000 0 -10000 0 0
MYC 0.008 0.091 -10000 0 -1.2 2 2
NKD1 -0.018 0.12 0.33 4 -0.34 42 46
FZD1 0.021 0.005 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.015 0.11 -10000 0 -0.41 18 18
apoptosis -0.028 0.092 -10000 0 -0.24 48 48
Delta 1/NOTCHprecursor 0.01 0.11 -10000 0 -0.41 18 18
DLL1 0.014 0.047 -10000 0 -0.34 6 6
PPARD 0.013 0.064 -10000 0 -0.8 2 2
Gamma Secretase 0.046 0.032 -10000 0 -10000 0 0
APC -0.011 0.098 -10000 0 -0.42 12 12
DVL1 -0.031 0.062 -10000 0 -0.26 20 20
CSNK2A1 0.021 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.088 0.13 0.26 105 -0.18 26 131
LRP6 0.02 0.006 -10000 0 -10000 0 0
CSNK1A1 0.021 0.005 -10000 0 -10000 0 0
NLK 0.006 0.005 -10000 0 -10000 0 0
CCND1 0.004 0.13 -10000 0 -1 5 5
WNT1 0.026 0.04 0.33 6 -10000 0 6
Axin1/APC/beta catenin 0.007 0.11 0.3 6 -0.43 7 13
DKK2 -0.035 0.13 -10000 0 -0.34 55 55
NOTCH1 precursor/DVL1 -0.032 0.11 -10000 0 -0.43 19 19
GSK3B 0.021 0.003 -10000 0 -10000 0 0
FRAT1 0.021 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.007 0.11 -10000 0 -0.42 17 17
PPP2R5D 0.012 0.076 0.2 12 -0.33 5 17
MAPK1 0.021 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.094 0.11 0.23 2 -0.19 208 210
RBPJ 0.021 0.005 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.035 0.032 0.24 8 -10000 0 8
VLDLR 0.014 0.047 -10000 0 -0.34 6 6
CRKL 0.021 0.004 -10000 0 -10000 0 0
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
FYN 0.02 0.007 -10000 0 -10000 0 0
ITGA3 0.018 0.033 -10000 0 -0.34 3 3
RELN/VLDLR/Fyn 0.009 0.085 0.23 5 -0.21 41 46
MAPK8IP1/MKK7/MAP3K11/JNK1 0.047 0.032 -10000 0 -0.18 1 1
AKT1 -0.034 0.074 0.21 2 -0.21 42 44
MAP2K7 0.02 0.006 -10000 0 -10000 0 0
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
DAB1 0.024 0.033 0.33 4 -10000 0 4
RELN/LRP8/DAB1 0.021 0.081 0.23 13 -0.18 38 51
LRPAP1/LRP8 0.034 0.026 0.24 5 -10000 0 5
RELN/LRP8/DAB1/Fyn 0.025 0.08 0.23 12 -0.17 38 50
DAB1/alpha3/beta1 Integrin 0.016 0.078 0.27 1 -0.18 38 39
long-term memory 0.013 0.11 0.34 4 -0.19 58 62
DAB1/LIS1 0.024 0.086 0.36 1 -0.18 40 41
DAB1/CRLK/C3G 0.016 0.079 0.27 1 -0.18 39 40
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
DAB1/NCK2 0.029 0.086 0.36 1 -0.18 40 41
ARHGEF2 0.018 0.008 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.009 0.15 0.33 30 -0.34 38 68
CDK5R1 0.028 0.046 0.33 8 -10000 0 8
RELN -0.014 0.12 0.33 5 -0.34 38 43
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.016 0.084 0.23 10 -0.2 38 48
GRIN2A/RELN/LRP8/DAB1/Fyn 0.022 0.12 0.24 30 -0.19 62 92
MAPK8 0.021 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.014 0.081 0.24 8 -0.19 40 48
ITGB1 0.021 0.004 -10000 0 -10000 0 0
MAP1B -0.027 0.075 0.17 19 -0.2 37 56
RELN/LRP8 0.018 0.084 0.23 9 -0.2 38 47
GRIN2B/RELN/LRP8/DAB1/Fyn 0.033 0.09 0.26 14 -0.18 36 50
PI3K 0.03 0.009 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.028 0.026 -10000 0 -0.24 3 3
RAP1A -0.033 0.076 0.25 4 -0.31 2 6
PAFAH1B1 0.02 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.022 0.003 -10000 0 -10000 0 0
CRLK/C3G 0.03 0.008 -10000 0 -10000 0 0
GRIN2B 0.025 0.047 0.33 8 -10000 0 8
NCK2 0.022 0.002 -10000 0 -10000 0 0
neuron differentiation -0.008 0.079 0.24 2 -0.32 8 10
neuron adhesion -0.034 0.086 0.3 8 -0.3 2 10
LRP8 0.027 0.04 0.33 6 -10000 0 6
GSK3B -0.036 0.07 0.19 2 -0.21 39 41
RELN/VLDLR/DAB1/Fyn 0.019 0.081 0.23 8 -0.18 40 48
MAP3K11 0.02 0.019 -10000 0 -0.34 1 1
RELN/VLDLR/DAB1/P13K -0.021 0.082 0.19 2 -0.22 42 44
CDK5 0.021 0.005 -10000 0 -10000 0 0
MAPT -0.003 0.13 0.77 7 -0.3 15 22
neuron migration -0.04 0.098 0.31 3 -0.27 35 38
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.008 0.079 0.24 2 -0.32 8 10
RELN/VLDLR 0.023 0.088 0.22 11 -0.2 41 52
Wnt 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
Noncanonical Wnts/FZD -0.027 0.099 0.18 2 -0.24 51 53
FZD6 0.018 0.02 -10000 0 -0.34 1 1
WNT6 0.04 0.073 0.33 21 -10000 0 21
WNT4 0.007 0.088 0.33 5 -0.34 18 23
FZD3 0.019 0.019 0.33 1 -10000 0 1
WNT5A 0.017 0.038 -10000 0 -0.34 4 4
WNT11 -0.025 0.12 0.33 1 -0.34 46 47
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.01 0.28 0.56 17 -0.68 6 23
CRP 0.028 0.3 0.57 27 -0.57 18 45
cell cycle arrest -0.001 0.31 0.55 22 -0.64 20 42
TIMP1 0.015 0.27 0.55 17 -0.64 10 27
IL6ST 0.009 0.06 -10000 0 -0.33 8 8
Rac1/GDP -0.002 0.14 0.32 13 -0.32 21 34
AP1 0.05 0.14 0.38 7 -0.45 7 14
GAB2 0.019 0.039 -10000 0 -0.33 4 4
TNFSF11 0.033 0.3 0.58 25 -0.71 6 31
HSP90B1 0.014 0.17 0.45 1 -0.67 14 15
GAB1 0.022 0.02 -10000 0 -0.34 1 1
MAPK14 -0.023 0.1 0.28 3 -0.45 6 9
AKT1 0.011 0.095 0.26 5 -0.57 5 10
FOXO1 0.009 0.093 0.32 2 -0.54 5 7
MAP2K6 -0.016 0.11 0.29 9 -0.29 21 30
mol:GTP 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.001 0.18 0.36 19 -0.38 21 40
MITF -0.004 0.13 0.28 16 -0.29 24 40
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.02 0.006 -10000 0 -10000 0 0
A2M -0.13 0.39 -10000 0 -1.2 44 44
CEBPB 0.025 0.01 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.017 0.097 0.28 4 -0.38 7 11
STAT3 -0.006 0.32 0.56 20 -0.68 20 40
STAT1 0.023 0.037 -10000 0 -10000 0 0
CEBPD 0.017 0.3 0.59 19 -0.85 6 25
PIK3CA 0.021 0.005 -10000 0 -10000 0 0
PI3K 0.03 0.01 -10000 0 -10000 0 0
JUN 0.02 0.027 -10000 0 -0.34 2 2
PIAS3/MITF 0.002 0.13 0.28 13 -0.29 23 36
MAPK11 -0.021 0.099 0.26 3 -0.45 6 9
STAT3 (dimer)/FOXO1 -0.02 0.26 0.51 18 -0.65 12 30
GRB2/SOS1/GAB family 0.009 0.12 0.27 3 -0.29 12 15
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.017 0.11 0.24 4 -0.28 30 34
GRB2 0.022 0.006 -10000 0 -10000 0 0
JAK2 0.019 0.007 -10000 0 -10000 0 0
LBP 0.047 0.28 0.54 36 -0.61 9 45
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
JAK1 0.012 0.026 -10000 0 -10000 0 0
MYC 0.03 0.3 0.61 19 -0.82 5 24
FGG -0.15 0.51 0.58 23 -0.89 105 128
macrophage differentiation -0.001 0.31 0.55 22 -0.64 20 42
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.001 0.097 0.26 1 -0.21 32 33
JUNB 0 0.27 0.54 14 -0.72 7 21
FOS -0.004 0.092 -10000 0 -0.34 25 25
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.003 0.13 0.3 18 -0.3 26 44
STAT1/PIAS1 0.014 0.16 0.34 20 -0.31 18 38
GRB2/SOS1/GAB family/SHP2/PI3K 0.013 0.093 -10000 0 -0.47 8 8
STAT3 (dimer) -0.005 0.31 0.56 21 -0.67 20 41
PRKCD 0.018 0.23 0.41 38 -0.44 20 58
IL6R 0.004 0.051 -10000 0 -0.33 6 6
SOCS3 -0.017 0.12 0.34 1 -1.1 2 3
gp130 (dimer)/JAK1/JAK1/LMO4 0.032 0.069 0.24 2 -0.2 6 8
Rac1/GTP -0.003 0.15 0.32 17 -0.34 22 39
HCK 0.009 0.064 -10000 0 -0.33 12 12
MAPKKK cascade 0.031 0.12 0.34 1 -0.5 9 10
bone resorption 0.036 0.3 0.57 26 -0.67 6 32
IRF1 0.003 0.28 0.56 14 -0.73 6 20
mol:GDP 0.001 0.13 0.29 18 -0.3 21 39
SOS1 0.024 0.007 -10000 0 -10000 0 0
VAV1 0.001 0.13 0.28 20 -0.3 21 41
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.018 0.11 0.38 1 -0.42 12 13
PTPN11 0.007 0.12 -10000 0 -0.71 8 8
IL6/IL6RA -0.017 0.1 0.17 1 -0.24 52 53
gp130 (dimer)/TYK2/TYK2/LMO4 0.03 0.057 0.2 1 -0.18 8 9
gp130 (dimer)/JAK2/JAK2/LMO4 0.029 0.055 0.2 1 -0.19 6 7
IL6 -0.047 0.14 -10000 0 -0.34 65 65
PIAS3 0.021 0.004 -10000 0 -10000 0 0
PTPRE -0.002 0.047 -10000 0 -0.28 3 3
PIAS1 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.016 0.015 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.019 0.1 0.24 3 -0.26 37 40
LMO4 0.017 0.033 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.024 0.28 0.51 17 -0.64 20 37
MCL1 0.039 0.12 0.4 4 -0.53 4 8
EGFR-dependent Endothelin signaling events

Figure S39.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S39.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.017 0.037 0.33 1 -0.34 3 4
EGF/EGFR 0.029 0.087 0.18 42 -0.16 41 83
EGF/EGFR dimer/SHC/GRB2/SOS1 0.062 0.073 0.23 38 -0.18 4 42
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.021 0.019 -10000 0 -0.34 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.074 0.12 0.33 63 -0.34 3 66
EGF/EGFR dimer/SHC 0.051 0.073 0.23 40 -0.19 5 45
mol:GDP 0.057 0.067 0.22 38 -0.18 4 42
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.022 0.12 -10000 0 -0.34 42 42
GRB2/SOS1 0.031 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.036 0.047 0.23 1 -0.17 3 4
SHC1 0.018 0.008 -10000 0 -10000 0 0
HRAS/GDP 0.051 0.059 0.3 1 -0.18 3 4
FRAP1 -0.013 0.033 0.17 4 -0.17 4 8
EGF/EGFR dimer 0.055 0.086 0.24 52 -0.22 6 58
SOS1 0.022 0.003 -10000 0 -10000 0 0
GRB2 0.021 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.002 0.088 -10000 0 -0.24 43 43
Aurora A 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
Aurora A/GADD45A -0.005 0.058 -10000 0 -10000 0 0
BIRC5 0.2 0.15 0.33 199 -10000 0 199
NFKBIA 0.002 0.076 0.27 20 -10000 0 20
CPEB1 -0.025 0.12 0.33 2 -0.34 47 49
AKT1 -0.013 0.046 0.27 2 -10000 0 2
NDEL1 0.02 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 -0.005 0.052 -10000 0 -10000 0 0
NDEL1/TACC3 0 0.056 -10000 0 -10000 0 0
GADD45A 0.021 0.004 -10000 0 -10000 0 0
GSK3B -0.017 0.032 -10000 0 -10000 0 0
PAK1/Aurora A -0.006 0.057 -10000 0 -10000 0 0
MDM2 0.02 0.006 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.088 0.097 0.17 200 -10000 0 200
TP53 -0.003 0.058 0.22 1 -0.24 8 9
DLG7 -0.008 0.041 -10000 0 -10000 0 0
AURKAIP1 0.021 0.004 -10000 0 -10000 0 0
ARHGEF7 0.021 0.005 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.001 0.059 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.052 -10000 0 -10000 0 0
AURKA -0.002 0.056 -10000 0 -10000 0 0
AURKB 0.1 0.09 0.19 159 -10000 0 159
CDC25B -0.002 0.042 -10000 0 -0.23 2 2
G2/M transition checkpoint -0.013 0.041 -10000 0 -10000 0 0
mRNA polyadenylation -0.028 0.081 0.36 1 -0.2 35 36
Aurora A/CPEB -0.028 0.081 0.36 1 -0.2 35 36
Aurora A/TACC1/TRAP/chTOG 0.003 0.068 -10000 0 -0.23 4 4
BRCA1 0.021 0.003 -10000 0 -10000 0 0
centrosome duplication -0.006 0.057 -10000 0 -10000 0 0
regulation of centrosome cycle 0 0.055 -10000 0 -10000 0 0
spindle assembly 0.003 0.067 -10000 0 -0.23 4 4
TDRD7 0.021 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.12 0.1 0.25 80 -10000 0 80
CENPA 0.11 0.094 0.21 157 -10000 0 157
Aurora A/PP2A -0.006 0.057 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.006 0.051 0.19 2 -10000 0 2
negative regulation of DNA binding -0.003 0.058 0.22 1 -0.24 8 9
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.03 0.009 -10000 0 -10000 0 0
RASA1 0.021 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A -0.013 0.041 -10000 0 -10000 0 0
mitotic prometaphase -0.014 0.032 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.002 0.056 -10000 0 -10000 0 0
TACC1 0.01 0.057 -10000 0 -0.34 9 9
TACC3 0.021 0.004 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.004 0.059 -10000 0 -10000 0 0
Aurora A/RasGAP -0.004 0.056 -10000 0 -10000 0 0
OAZ1 0.02 0.006 -10000 0 -10000 0 0
RAN 0.023 0.024 0.33 2 -10000 0 2
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.017 0.031 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.039 0.015 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.088 0.097 0.17 200 -10000 0 200
PPP2R5D 0.021 0.005 -10000 0 -10000 0 0
Aurora A/TPX2 0.055 0.086 0.19 72 -10000 0 72
PAK1 0.021 0.005 -10000 0 -10000 0 0
CKAP5 0.022 0.003 -10000 0 -10000 0 0
TCGA08_p53

Figure S41.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S41.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A 0.038 0.074 0.16 94 -10000 0 94
TP53 0.01 0.037 -10000 0 -0.12 11 11
Senescence 0.01 0.037 -10000 0 -0.12 10 10
Apoptosis 0.01 0.037 -10000 0 -0.12 10 10
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.02 0.08 0.26 17 -0.19 2 19
MDM4 0.02 0.007 -10000 0 -10000 0 0
Noncanonical Wnt 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
NFATC2 0.011 0.057 -10000 0 -0.34 9 9
GNB1/GNG2 -0.009 0.11 0.23 1 -0.31 18 19
mol:DAG -0.039 0.088 0.19 2 -0.29 16 18
PLCG1 -0.04 0.09 0.2 2 -0.3 16 18
YES1 -0.036 0.09 0.21 4 -0.23 47 51
FZD3 0.019 0.019 0.33 1 -10000 0 1
FZD6 0.018 0.02 -10000 0 -0.34 1 1
G protein -0.008 0.11 0.25 3 -0.3 16 19
MAP3K7 -0.045 0.095 0.19 2 -0.28 28 30
mol:Ca2+ -0.038 0.086 0.19 2 -0.28 16 18
mol:IP3 -0.039 0.088 0.19 2 -0.29 16 18
NLK -0.001 0.088 -10000 0 -0.82 4 4
GNB1 0.021 0.004 -10000 0 -10000 0 0
CAMK2A -0.048 0.1 0.2 1 -0.29 32 33
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.027 0.099 0.18 2 -0.24 51 53
CSNK1A1 0.021 0.005 -10000 0 -10000 0 0
GNAS -0.037 0.087 0.16 2 -0.23 46 48
GO:0007205 -0.036 0.086 0.19 2 -0.28 17 19
WNT6 0.04 0.073 0.33 21 -10000 0 21
WNT4 0.007 0.088 0.33 5 -0.34 18 23
NFAT1/CK1 alpha -0.017 0.1 0.3 3 -0.31 16 19
GNG2 0.02 0.02 -10000 0 -0.34 1 1
WNT5A 0.017 0.038 -10000 0 -0.34 4 4
WNT11 -0.025 0.12 0.33 1 -0.34 46 47
CDC42 -0.033 0.091 0.22 4 -0.3 17 21
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.012 0.077 -10000 0 -0.2 38 38
fibroblast growth factor receptor signaling pathway 0.011 0.077 -10000 0 -0.2 38 38
LAMA1 0.028 0.071 0.33 13 -0.34 4 17
PRNP 0.02 0.02 -10000 0 -0.34 1 1
GPC1/SLIT2 -0.024 0.11 -10000 0 -0.24 72 72
SMAD2 -0.022 0.027 0.17 2 -0.19 5 7
GPC1/PrPc/Cu2+ 0.026 0.021 -10000 0 -0.19 3 3
GPC1/Laminin alpha1 0.032 0.052 0.24 12 -0.23 6 18
TDGF1 0.021 0.079 0.33 11 -0.34 9 20
CRIPTO/GPC1 0.029 0.06 0.24 11 -0.24 11 22
APP/GPC1 0.028 0.022 -10000 0 -0.24 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.021 0.036 0.1 9 -0.2 9 18
FLT1 0.021 0.005 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.037 0.038 0.23 1 -0.2 7 8
SERPINC1 0.023 0.034 0.33 4 -10000 0 4
FYN -0.02 0.037 0.1 10 -0.2 9 19
FGR -0.036 0.064 0.1 9 -0.22 34 43
positive regulation of MAPKKK cascade -0.023 0.097 0.26 2 -0.32 21 23
SLIT2 -0.051 0.14 -10000 0 -0.34 71 71
GPC1/NRG -0.013 0.094 -10000 0 -0.24 52 52
NRG1 -0.032 0.12 -10000 0 -0.34 50 50
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.038 0.023 -10000 0 -0.2 2 2
LYN -0.019 0.036 0.1 11 -0.2 8 19
mol:Spermine -0.01 0.017 -10000 0 -0.23 2 2
cell growth 0.011 0.077 -10000 0 -0.2 38 38
BMP signaling pathway -0.019 0.027 0.34 2 -10000 0 2
SRC -0.021 0.038 0.1 11 -0.2 10 21
TGFBR1 0.022 0.017 0.33 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.011 0.12 0.33 8 -0.34 39 47
GPC1 0.019 0.027 -10000 0 -0.34 2 2
TGFBR1 (dimer) 0.022 0.017 0.33 1 -10000 0 1
VEGFA 0.021 0.004 -10000 0 -10000 0 0
BLK 0.001 0.069 0.16 44 -0.2 9 53
HCK -0.027 0.049 0.1 10 -0.2 21 31
FGF2 -0.019 0.11 -10000 0 -0.34 40 40
FGFR1 0.018 0.02 -10000 0 -0.34 1 1
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 0.016 0.043 -10000 0 -0.34 5 5
cell death 0.028 0.022 -10000 0 -0.24 2 2
ATIII/GPC1 0.029 0.032 0.24 4 -0.24 2 6
PLA2G2A/GPC1 0.005 0.092 0.24 8 -0.24 40 48
LCK -0.022 0.042 0.11 12 -0.2 12 24
neuron differentiation -0.013 0.094 -10000 0 -0.24 52 52
PrPc/Cu2+ 0.015 0.014 -10000 0 -0.23 1 1
APP 0.021 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.016 0.042 -10000 0 -0.34 5 5
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.016 0.069 0.35 1 -10000 0 1
PLK1 0.22 0.27 0.56 108 -10000 0 108
CDKN1B 0.14 0.18 0.37 95 -0.34 5 100
FOXO3 0.2 0.24 0.52 107 -10000 0 107
KAT2B 0.058 0.046 0.16 26 -10000 0 26
FOXO1/SIRT1 0.009 0.042 -10000 0 -0.24 1 1
CAT 0.16 0.25 0.56 45 -0.71 5 50
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.058 0.046 0.18 7 -10000 0 7
FOXO1 0.019 0.06 0.24 11 -0.25 1 12
MAPK10 0.016 0.067 0.2 30 -0.16 12 42
mol:GTP 0 0.001 -10000 0 -10000 0 0
FOXO4 0.034 0.074 0.27 2 -10000 0 2
response to oxidative stress 0.039 0.045 0.13 34 -10000 0 34
FOXO3A/SIRT1 0.17 0.21 0.44 101 -0.43 2 103
XPO1 0.022 0.002 -10000 0 -10000 0 0
EP300 0.024 0.008 -10000 0 -10000 0 0
BCL2L11 0.068 0.064 -10000 0 -10000 0 0
FOXO1/SKP2 0.023 0.044 0.2 2 -10000 0 2
mol:GDP 0.039 0.045 0.13 34 -10000 0 34
RAN 0.023 0.024 0.33 2 -10000 0 2
GADD45A 0.12 0.19 0.44 18 -0.62 7 25
YWHAQ 0.022 0.002 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.001 0.12 -10000 0 -0.46 14 14
MST1 0.066 0.073 0.22 36 -0.27 1 37
CSNK1D 0.021 0.004 -10000 0 -10000 0 0
CSNK1E 0.021 0.005 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.004 0.091 -10000 0 -0.41 8 8
YWHAB 0.021 0.005 -10000 0 -10000 0 0
MAPK8 0.028 0.062 0.2 35 -10000 0 35
MAPK9 0.027 0.062 0.2 34 -10000 0 34
YWHAG 0.021 0.005 -10000 0 -10000 0 0
YWHAE 0.02 0.007 -10000 0 -10000 0 0
YWHAZ 0.019 0.008 -10000 0 -10000 0 0
SIRT1 0.001 0.025 -10000 0 -10000 0 0
SOD2 0.13 0.19 0.44 40 -0.44 2 42
RBL2 0.14 0.22 0.52 30 -0.66 5 35
RAL/GDP 0.049 0.033 0.17 1 -10000 0 1
CHUK 0.059 0.046 0.16 26 -10000 0 26
Ran/GTP 0.017 0.016 0.22 2 -10000 0 2
CSNK1G2 0.02 0.006 -10000 0 -10000 0 0
RAL/GTP 0.048 0.031 0.19 1 -10000 0 1
CSNK1G1 0.021 0.004 -10000 0 -10000 0 0
FASLG 0.05 0.16 -10000 0 -1.1 5 5
SKP2 0.019 0.019 0.33 1 -10000 0 1
USP7 0.022 0.003 -10000 0 -10000 0 0
IKBKB 0.049 0.044 -10000 0 -10000 0 0
CCNB1 0.2 0.27 0.57 99 -10000 0 99
FOXO1-3a-4/beta catenin 0.13 0.16 0.39 55 -10000 0 55
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.044 0.2 4 -10000 0 4
CSNK1A1 0.021 0.005 -10000 0 -10000 0 0
SGK1 0.055 0.05 0.18 10 -0.27 1 11
CSNK1G3 0.021 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.015 0.21 2 -10000 0 2
ZFAND5 0.028 0.068 -10000 0 -10000 0 0
SFN 0.026 0.047 0.33 7 -0.34 1 8
CDK2 0.011 0.022 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.05 0.11 0.28 12 -0.42 5 17
CREBBP 0.01 0.022 -10000 0 -10000 0 0
FBXO32 0.21 0.27 0.62 69 -0.53 1 70
BCL6 0.14 0.23 0.52 29 -0.8 6 35
RALB 0.022 0.003 -10000 0 -10000 0 0
RALA 0.02 0.006 -10000 0 -10000 0 0
YWHAH 0.021 0.004 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.031 0.077 0.17 78 -10000 0 78
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.015 0.076 0.24 8 -0.24 24 32
STXBP1 0.018 0.033 -10000 0 -0.34 3 3
ACh/CHRNA1 0.028 0.074 0.25 26 -0.2 7 33
RAB3GAP2/RIMS1/UNC13B 0.024 0.065 0.23 6 -0.2 21 27
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.003 0.1 0.33 9 -0.34 24 33
mol:ACh 0.003 0.032 0.089 16 -0.11 7 23
RAB3GAP2 0.02 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.023 0.068 -10000 0 -0.16 21 21
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.027 0.074 0.25 26 -0.2 7 33
UNC13B 0.021 0.005 -10000 0 -10000 0 0
CHRNA1 0.037 0.093 0.33 25 -0.34 6 31
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.029 0.07 0.26 24 -0.18 4 28
SNAP25 0.004 0.033 0.12 13 -0.23 4 17
VAMP2 0.002 0.001 -10000 0 -10000 0 0
SYT1 0.037 0.09 0.33 24 -0.34 5 29
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.041 0.056 0.14 77 -0.2 3 80
STX1A/SNAP25 fragment 1/VAMP2 0.023 0.068 -10000 0 -0.16 21 21
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.008 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.014 0.071 0.21 1 -0.18 38 39
regulation of S phase of mitotic cell cycle -0.014 0.07 0.16 1 -0.21 37 38
GNAO1 0.02 0.032 0.33 1 -0.34 2 3
HRAS 0.018 0.012 -10000 0 -10000 0 0
SHBG/T-DHT 0.014 0.011 0.2 1 -10000 0 1
PELP1 0.017 0.012 -10000 0 -10000 0 0
AKT1 -0.009 0.002 -10000 0 -10000 0 0
MAP2K1 -0.041 0.066 0.17 10 -0.19 35 45
T-DHT/AR -0.013 0.079 0.22 1 -0.23 39 40
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.006 27 27
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.021 0.005 -10000 0 -10000 0 0
GNAI1 0.02 0.02 -10000 0 -0.34 1 1
mol:GDP -0.045 0.099 0.2 1 -0.31 42 43
cell proliferation -0.065 0.14 0.27 2 -0.44 31 33
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
FOS -0.069 0.2 0.24 4 -0.71 29 33
mol:Ca2+ -0.008 0.02 -10000 0 -0.058 37 37
MAPK3 -0.055 0.1 0.26 3 -0.33 29 32
MAPK1 -0.033 0.094 0.2 1 -0.33 21 22
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 26 26
cAMP biosynthetic process 0.001 0.02 0.23 1 -10000 0 1
GNG2 0.02 0.02 -10000 0 -0.34 1 1
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 26 26
HRAS/GTP 0.008 0.069 -10000 0 -0.17 37 37
actin cytoskeleton reorganization 0.027 0.015 -10000 0 -10000 0 0
SRC 0.018 0.012 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 26 26
PI3K 0.027 0.008 -10000 0 -10000 0 0
apoptosis 0.05 0.14 0.45 30 -0.26 1 31
T-DHT/AR/PELP1 0 0.072 0.2 1 -0.2 39 40
HRAS/GDP -0.046 0.094 0.19 1 -0.3 41 42
CREB1 -0.054 0.15 0.27 1 -0.49 30 31
RAC1-CDC42/GTP 0.034 0.018 -10000 0 -10000 0 0
AR -0.02 0.11 0.33 1 -0.34 39 40
GNB1 0.021 0.004 -10000 0 -10000 0 0
RAF1 -0.036 0.065 0.18 11 -0.18 33 44
RAC1-CDC42/GDP -0.014 0.1 0.2 1 -0.3 35 36
T-DHT/AR/PELP1/Src 0.01 0.071 0.2 1 -0.18 38 39
MAP2K2 -0.041 0.066 0.17 9 -0.26 10 19
T-DHT/AR/PELP1/Src/PI3K -0.014 0.071 0.16 1 -0.21 37 38
GNAZ -0.008 0.097 -10000 0 -0.34 28 28
SHBG 0.02 0.018 0.33 1 -10000 0 1
Gi family/GNB1/GNG2/GDP -0.022 0.097 -10000 0 -0.34 21 21
mol:T-DHT 0 0.001 -10000 0 -0.003 7 7
RAC1 0.019 0.007 -10000 0 -10000 0 0
GNRH1 -0.009 0.017 -10000 0 -0.23 2 2
Gi family/GTP -0.027 0.072 -10000 0 -0.21 38 38
CDC42 0.021 0.004 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.08 0.16 -10000 0 -0.34 99 99
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.021 0.003 -10000 0 -10000 0 0
TCEB1 0.02 0.018 0.33 1 -10000 0 1
HIF1A/p53 0.029 0.056 0.21 2 -0.25 7 9
HIF1A 0.013 0.048 -10000 0 -0.26 7 7
COPS5 0.019 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.053 0.028 -10000 0 -10000 0 0
FIH (dimer) 0.021 0.003 -10000 0 -10000 0 0
CDKN2A 0.097 0.14 0.33 92 -10000 0 92
ARNT/IPAS -0.038 0.11 -10000 0 -0.24 83 83
HIF1AN 0.022 0.003 -10000 0 -10000 0 0
GNB2L1 0.021 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.022 0.047 0.21 2 -0.24 4 6
CUL2 0.021 0.004 -10000 0 -10000 0 0
OS9 0.02 0.006 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.038 0.019 0.23 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.029 0.053 -10000 0 -0.25 7 7
PHD1-3/OS9 0.083 0.084 0.23 74 -10000 0 74
HIF1A/RACK1/Elongin B/Elongin C 0.041 0.055 0.24 2 -0.24 6 8
VHL 0.021 0.004 -10000 0 -10000 0 0
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.025 0.054 0.24 1 -0.25 7 8
EGLN3 0.094 0.14 0.33 87 -0.34 1 88
EGLN2 0.021 0.005 -10000 0 -10000 0 0
EGLN1 0.02 0.006 -10000 0 -10000 0 0
TP53 0.02 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.011 0.1 -10000 0 -0.5 12 12
ARNT 0.018 0.009 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.021 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF 0.069 0.1 0.22 88 -0.22 6 94
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.014 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.004 0.086 0.22 1 -0.23 5 6
NFATC4 -0.039 0.069 0.22 9 -0.18 4 13
ERBB2IP 0.02 0.01 -10000 0 -10000 0 0
HSP90 (dimer) 0.021 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.047 0.065 -10000 0 -0.2 41 41
JUN -0.005 0.065 0.26 3 -10000 0 3
HRAS 0.021 0.006 -10000 0 -10000 0 0
DOCK7 -0.049 0.065 -10000 0 -0.2 38 38
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.001 0.071 -10000 0 -0.19 39 39
AKT1 -0.009 0.007 -10000 0 -10000 0 0
BAD -0.014 0.005 -10000 0 -10000 0 0
MAPK10 -0.029 0.071 0.17 12 -0.19 14 26
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.05 0.07 -10000 0 -0.21 39 39
RAF1 -0.011 0.098 0.26 12 -0.25 5 17
ErbB2/ErbB3/neuregulin 2 -0.015 0.069 0.2 1 -0.19 39 40
STAT3 0.006 0.12 -10000 0 -0.85 7 7
cell migration -0.021 0.079 0.21 15 -0.2 10 25
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.031 0.18 0.38 5 -0.54 23 28
FOS -0.028 0.16 0.33 6 -0.42 37 43
NRAS 0.02 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.047 0.065 -10000 0 -0.2 41 41
MAPK3 -0.017 0.15 0.37 4 -0.49 13 17
MAPK1 -0.025 0.16 0.35 6 -0.52 17 23
JAK2 -0.047 0.065 -10000 0 -0.2 38 38
NF2 -0.034 0.15 -10000 0 -0.61 21 21
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.019 0.069 0.2 3 -0.21 37 40
NRG1 -0.033 0.12 -10000 0 -0.34 50 50
GRB2/SOS1 0.031 0.008 -10000 0 -10000 0 0
MAPK8 -0.045 0.085 -10000 0 -0.24 35 35
MAPK9 -0.02 0.062 0.17 14 -10000 0 14
ERBB2 -0.02 0.018 0.27 1 -10000 0 1
ERBB3 0.014 0.03 -10000 0 -0.34 2 2
SHC1 0.018 0.008 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
apoptosis 0.012 0.008 -10000 0 -10000 0 0
STAT3 (dimer) 0.006 0.12 -10000 0 -0.83 7 7
RNF41 -0.019 0.01 -10000 0 -10000 0 0
FRAP1 -0.007 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.043 0.043 -10000 0 -0.16 33 33
ErbB2/ErbB2/HSP90 (dimer) -0.021 0.016 0.2 1 -10000 0 1
CHRNA1 -0.005 0.14 0.31 15 -0.46 13 28
myelination -0.029 0.088 0.26 16 -10000 0 16
PPP3CB -0.048 0.06 -10000 0 -0.19 38 38
KRAS 0.02 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.002 0.078 -10000 0 -0.19 27 27
NRG2 -0.023 0.12 -10000 0 -0.34 43 43
mol:GDP -0.019 0.069 0.2 3 -0.21 37 40
SOS1 0.022 0.003 -10000 0 -10000 0 0
MAP2K2 -0.013 0.099 0.27 12 -0.27 5 17
SRC 0.021 0.004 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.049 0.066 -10000 0 -0.2 38 38
MAP2K1 -0.035 0.18 0.39 2 -0.52 22 24
heart morphogenesis -0.047 0.065 -10000 0 -0.2 41 41
RAS family/GDP 0.006 0.087 0.23 1 -0.22 5 6
GRB2 0.021 0.005 -10000 0 -10000 0 0
PRKACA -0.032 0.16 -10000 0 -0.65 21 21
CHRNE 0.002 0.021 0.16 3 -10000 0 3
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.009 0.007 -10000 0 -10000 0 0
nervous system development -0.047 0.065 -10000 0 -0.2 41 41
CDC42 0.021 0.004 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 0.013 0.11 -10000 0 -0.59 8 8
Syndecan-4/Syndesmos 0.03 0.16 0.32 3 -0.72 10 13
positive regulation of JNK cascade 0.029 0.15 0.31 3 -0.68 10 13
Syndecan-4/ADAM12 0.097 0.2 0.34 58 -0.73 10 68
CCL5 0.017 0.038 -10000 0 -0.34 4 4
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
DNM2 0.02 0.006 -10000 0 -10000 0 0
ITGA5 0.022 0.017 0.33 1 -10000 0 1
SDCBP 0.02 0.007 -10000 0 -10000 0 0
PLG 0.014 0.051 0.32 8 -10000 0 8
ADAM12 0.14 0.15 0.33 134 -10000 0 134
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.021 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.036 0.019 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.033 0.16 0.32 5 -0.72 10 15
Syndecan-4/CXCL12/CXCR4 0.03 0.16 0.33 2 -0.78 9 11
Syndecan-4/Laminin alpha3 -0.001 0.16 0.33 1 -0.68 12 13
MDK 0.12 0.14 0.33 114 -10000 0 114
Syndecan-4/FZD7 0.03 0.16 0.32 3 -0.73 10 13
Syndecan-4/Midkine 0.089 0.19 0.35 39 -0.73 10 49
FZD7 0.021 0.019 -10000 0 -0.34 1 1
Syndecan-4/FGFR1/FGF 0.016 0.16 0.31 1 -0.66 13 14
THBS1 0.021 0.005 -10000 0 -10000 0 0
integrin-mediated signaling pathway 0.039 0.16 0.32 9 -0.71 10 19
positive regulation of MAPKKK cascade 0.029 0.15 0.31 3 -0.68 10 13
Syndecan-4/TACI 0.037 0.17 0.33 15 -0.78 9 24
CXCR4 0.022 0.002 -10000 0 -10000 0 0
cell adhesion 0.006 0.04 0.19 8 -0.21 5 13
Syndecan-4/Dynamin 0.029 0.15 0.32 2 -0.78 9 11
Syndecan-4/TSP1 0.027 0.16 0.32 3 -0.73 10 13
Syndecan-4/GIPC 0.03 0.16 0.34 2 -0.78 9 11
Syndecan-4/RANTES 0.028 0.16 0.32 2 -0.74 10 12
ITGB1 0.021 0.004 -10000 0 -10000 0 0
LAMA1 0.028 0.071 0.33 13 -0.34 4 17
LAMA3 -0.042 0.14 -10000 0 -0.34 61 61
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA 0.002 0.14 0.74 11 -0.33 1 12
Syndecan-4/alpha-Actinin 0.028 0.16 0.34 2 -0.74 10 12
TFPI 0.01 0.065 -10000 0 -0.34 12 12
F2 0.062 0.11 0.33 47 -10000 0 47
alpha5/beta1 Integrin 0.031 0.013 0.24 1 -10000 0 1
positive regulation of cell adhesion -0.005 0.15 0.32 1 -0.62 13 14
ACTN1 0.021 0.005 -10000 0 -10000 0 0
TNC 0.035 0.091 0.33 23 -0.34 6 29
Syndecan-4/CXCL12 0.022 0.16 0.32 3 -0.76 10 13
FGF6 0.017 0.005 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
CXCL12 -0.001 0.087 -10000 0 -0.34 22 22
TNFRSF13B 0.035 0.089 0.33 23 -0.34 5 28
FGF2 -0.019 0.11 -10000 0 -0.34 40 40
FGFR1 0.018 0.02 -10000 0 -0.34 1 1
Syndecan-4/PI-4-5-P2 0.014 0.15 0.3 2 -0.73 10 12
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.013 0.042 -10000 0 -0.33 4 4
cell migration -0.022 0.013 -10000 0 -10000 0 0
PRKCD 0.017 0.019 -10000 0 -10000 0 0
vasculogenesis 0.028 0.15 0.32 3 -0.7 10 13
SDC4 0.022 0.15 0.33 2 -0.84 8 10
Syndecan-4/Tenascin C 0.039 0.17 0.32 9 -0.75 10 19
Syndecan-4/PI-4-5-P2/PKC alpha -0.029 0.015 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.026 0.16 0.32 3 -0.74 10 13
MMP9 0.072 0.12 0.33 58 -10000 0 58
Rac1/GTP 0.006 0.04 0.19 8 -0.22 5 13
cytoskeleton organization 0.031 0.15 0.32 3 -0.68 10 13
GIPC1 0.02 0.006 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.025 0.16 0.32 3 -0.75 10 13
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.044 0.1 -10000 0 -0.31 15 15
epithelial cell differentiation -0.025 0.09 -10000 0 -0.34 2 2
ITCH 0.031 0.018 -10000 0 -10000 0 0
WWP1 -0.017 0.074 -10000 0 -10000 0 0
FYN 0.02 0.007 -10000 0 -10000 0 0
EGFR 0.017 0.037 0.33 1 -0.34 3 4
PRL 0.026 0.047 0.33 8 -10000 0 8
neuron projection morphogenesis -0.026 0.098 0.33 4 -10000 0 4
PTPRZ1 0.029 0.16 0.33 47 -0.34 32 79
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.018 0.084 -10000 0 -0.24 17 17
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.039 0.083 -10000 0 -0.27 22 22
ADAM17 0.033 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.034 0.068 -10000 0 -0.33 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.088 0.12 -10000 0 -0.3 47 47
NCOR1 0.02 0.006 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.036 0.085 -10000 0 -0.26 20 20
GRIN2B -0.046 0.081 0.27 3 -0.35 1 4
ErbB4/ErbB2/betacellulin -0.012 0.067 -10000 0 -0.26 6 6
STAT1 0.022 0.002 -10000 0 -10000 0 0
HBEGF -0.029 0.12 -10000 0 -0.34 49 49
PRLR 0.027 0.095 0.33 21 -0.34 9 30
E4ICDs/ETO2 -0.031 0.091 -10000 0 -0.3 10 10
axon guidance -0.025 0.072 -10000 0 -0.33 2 2
NEDD4 0.03 0.026 -10000 0 -0.32 1 1
Prolactin receptor/Prolactin receptor/Prolactin 0.033 0.074 0.25 25 -0.24 9 34
CBFA2T3 -0.005 0.092 -10000 0 -0.34 25 25
ErbB4/ErbB2/HBEGF -0.03 0.084 -10000 0 -0.26 13 13
MAPK3 -0.034 0.084 -10000 0 -10000 0 0
STAT1 (dimer) -0.022 0.077 -10000 0 -0.29 1 1
MAPK1 -0.032 0.084 0.22 3 -10000 0 3
JAK2 0.019 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.05 0.075 -10000 0 -0.26 21 21
NRG1 -0.037 0.081 -10000 0 -0.23 49 49
NRG3 -0.11 0.18 0.33 1 -0.34 134 135
NRG2 -0.023 0.12 -10000 0 -0.34 43 43
NRG4 0.036 0.092 0.33 24 -0.34 6 30
heart development -0.025 0.072 -10000 0 -0.33 2 2
neural crest cell migration -0.05 0.075 -10000 0 -0.26 21 21
ERBB2 -0.001 0.031 0.3 2 -10000 0 2
WWOX/E4ICDs -0.021 0.076 -10000 0 -0.27 1 1
SHC1 0.018 0.008 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.001 0.091 0.3 1 -0.28 4 5
apoptosis 0.14 0.2 0.38 119 -10000 0 119
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.042 0.1 -10000 0 -0.3 21 21
ErbB4/ErbB2/epiregulin 0.003 0.12 0.32 4 -0.26 13 17
ErbB4/ErbB4/betacellulin/betacellulin -0.024 0.084 -10000 0 -0.31 7 7
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.008 0.11 0.3 3 -0.28 13 16
MDM2 -0.018 0.083 0.24 15 -0.29 1 16
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.03 0.077 -10000 0 -0.24 22 22
STAT5A -0.028 0.074 -10000 0 -0.34 1 1
ErbB4/EGFR/neuregulin 1 beta -0.03 0.083 -10000 0 -0.26 18 18
DLG4 0.02 0.006 -10000 0 -10000 0 0
GRB2/SHC 0.026 0.013 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.019 0.069 -10000 0 -0.27 1 1
STAT5A (dimer) -0.02 0.1 -10000 0 -0.36 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.018 0.082 -10000 0 -0.32 2 2
LRIG1 0.019 0.027 -10000 0 -0.34 2 2
EREG 0.019 0.19 0.33 58 -0.34 52 110
BTC 0.013 0.053 -10000 0 -0.34 8 8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.027 0.069 -10000 0 -0.33 2 2
ERBB4 -0.034 0.068 -10000 0 -0.33 1 1
STAT5B 0.021 0.003 -10000 0 -10000 0 0
YAP1 -0.008 0.071 -10000 0 -0.47 7 7
GRB2 0.021 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.002 0.08 -10000 0 -0.25 4 4
glial cell differentiation 0.019 0.069 0.27 1 -10000 0 1
WWOX 0.021 0.005 -10000 0 -10000 0 0
cell proliferation -0.055 0.11 0.34 3 -0.4 10 13
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.012 0.033 -10000 0 -0.22 6 6
EPHB2 0.06 0.1 0.33 44 -10000 0 44
Syndecan-2/TACI 0.025 0.062 0.23 23 -0.19 7 30
LAMA1 0.028 0.071 0.33 13 -0.34 4 17
Syndecan-2/alpha2 ITGB1 0.007 0.083 0.23 8 -0.18 46 54
HRAS 0.021 0.004 -10000 0 -10000 0 0
Syndecan-2/CASK -0.007 0.017 -10000 0 -0.19 3 3
ITGA5 0.022 0.017 0.33 1 -10000 0 1
BAX -0.014 0.014 -10000 0 -10000 0 0
EPB41 0.021 0.003 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.013 0.018 -10000 0 -0.18 3 3
LAMA3 -0.042 0.14 -10000 0 -0.34 61 61
EZR 0.02 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.044 0.14 -10000 0 -0.34 63 63
Syndecan-2/MMP2 0.014 0.021 -10000 0 -0.2 3 3
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.034 0.041 0.24 10 -0.24 2 12
dendrite morphogenesis 0.041 0.077 0.24 44 -0.2 3 47
Syndecan-2/GM-CSF 0.009 0.054 0.25 5 -0.2 17 22
determination of left/right symmetry -0.009 0.021 -10000 0 -0.23 3 3
Syndecan-2/PKC delta 0.014 0.021 -10000 0 -0.2 3 3
GNB2L1 0.021 0.004 -10000 0 -10000 0 0
MAPK3 -0.003 0.072 0.18 35 -0.18 16 51
MAPK1 -0.001 0.071 0.18 35 -0.18 13 48
Syndecan-2/RACK1 0.023 0.021 -10000 0 -0.17 3 3
NF1 0.021 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.009 0.021 -10000 0 -0.23 3 3
ITGA2 0.027 0.059 0.33 10 -0.34 2 12
MAPK8 -0.012 0.017 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.043 0.065 0.25 19 -0.2 5 24
Syndecan-2/Kininogen 0.029 0.06 0.23 26 -0.19 3 29
ITGB1 0.021 0.004 -10000 0 -10000 0 0
SRC 0.002 0.063 0.17 40 -0.17 2 42
Syndecan-2/CASK/Protein 4.1 0.013 0.019 -10000 0 -0.18 3 3
extracellular matrix organization 0.014 0.021 -10000 0 -0.2 3 3
actin cytoskeleton reorganization 0.012 0.033 -10000 0 -0.22 6 6
Syndecan-2/Caveolin-2/Ras -0.005 0.074 -10000 0 -0.18 51 51
Syndecan-2/Laminin alpha3 -0.017 0.076 -10000 0 -0.2 53 53
Syndecan-2/RasGAP 0.031 0.025 -10000 0 -0.16 3 3
alpha5/beta1 Integrin 0.031 0.013 0.24 1 -10000 0 1
PRKCD 0.021 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.042 0.077 0.24 44 -0.2 3 47
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.019 0.025 0.16 4 -10000 0 4
RHOA 0.021 0.004 -10000 0 -10000 0 0
SDCBP 0.02 0.007 -10000 0 -10000 0 0
TNFRSF13B 0.035 0.089 0.33 23 -0.34 5 28
RASA1 0.021 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.034 0.041 0.24 10 -0.24 2 12
Syndecan-2/Synbindin 0.015 0.017 -10000 0 -0.2 2 2
TGFB1 0.021 0.004 -10000 0 -10000 0 0
CASP3 0.003 0.064 0.18 38 -0.18 3 41
FN1 0.018 0.038 -10000 0 -0.34 4 4
Syndecan-2/IL8 0.024 0.054 0.24 17 -0.2 4 21
SDC2 -0.009 0.021 -10000 0 -0.23 3 3
KNG1 0.042 0.082 0.33 26 -10000 0 26
Syndecan-2/Neurofibromin 0.014 0.02 -10000 0 -0.19 3 3
TRAPPC4 0.021 0.005 -10000 0 -10000 0 0
CSF2 0.004 0.093 0.33 5 -0.34 21 26
Syndecan-2/TGFB1 0.014 0.021 -10000 0 -0.2 3 3
Syndecan-2/Syntenin/PI-4-5-P2 0.013 0.019 -10000 0 -0.18 3 3
Syndecan-2/Ezrin 0.023 0.023 -10000 0 -0.18 3 3
PRKACA 0.005 0.064 0.18 40 -0.18 2 42
angiogenesis 0.024 0.054 0.24 17 -0.2 4 21
MMP2 0.021 0.005 -10000 0 -10000 0 0
IL8 0.034 0.072 0.33 17 -0.34 2 19
calcineurin-NFAT signaling pathway 0.025 0.062 0.23 23 -0.19 7 30
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.013 0.038 -10000 0 -0.33 3 3
PDGF/PDGFRA/CRKL 0.024 0.03 -10000 0 -0.22 3 3
positive regulation of JUN kinase activity 0.037 0.029 -10000 0 -10000 0 0
CRKL 0.021 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.036 0.11 -10000 0 -0.24 78 78
AP1 -0.072 0.2 0.27 2 -0.73 27 29
mol:IP3 -0.022 0.026 -10000 0 -0.24 2 2
PLCG1 -0.022 0.026 -10000 0 -0.24 2 2
PDGF/PDGFRA/alphaV Integrin 0.024 0.03 -10000 0 -0.22 3 3
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
CRK 0.02 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.022 0.026 -10000 0 -0.24 2 2
CAV3 -0.059 0.15 -10000 0 -0.34 77 77
CAV1 -0.19 0.18 -10000 0 -0.34 204 204
SHC/Grb2/SOS1 0.038 0.03 -10000 0 -10000 0 0
PDGF/PDGFRA/Shf 0.025 0.034 0.24 2 -0.22 3 5
FOS -0.074 0.19 0.3 1 -0.72 27 28
JUN -0.026 0.026 -10000 0 -0.24 2 2
oligodendrocyte development 0.024 0.03 -10000 0 -0.22 3 3
GRB2 0.021 0.005 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
mol:DAG -0.022 0.026 -10000 0 -0.24 2 2
PDGF/PDGFRA 0.013 0.038 -10000 0 -0.33 3 3
actin cytoskeleton reorganization 0.022 0.03 -10000 0 -0.22 3 3
SRF -0.014 0.013 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
PI3K 0.033 0.03 -10000 0 -0.18 3 3
PDGF/PDGFRA/Crk/C3G 0.031 0.031 -10000 0 -0.18 3 3
JAK1 -0.019 0.019 -10000 0 -0.22 2 2
ELK1/SRF -0.024 0.038 0.21 2 -0.2 2 4
SHB 0.02 0.006 -10000 0 -10000 0 0
SHF 0.023 0.024 0.33 2 -10000 0 2
CSNK2A1 0.023 0.017 -10000 0 -10000 0 0
GO:0007205 -0.017 0.027 -10000 0 -0.27 2 2
SOS1 0.022 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.037 0.029 -10000 0 -10000 0 0
PDGF/PDGFRA/SHB 0.022 0.03 -10000 0 -0.22 3 3
PDGF/PDGFRA/Caveolin-1 -0.13 0.14 -10000 0 -0.25 198 198
ITGAV 0.022 0.002 -10000 0 -10000 0 0
ELK1 -0.023 0.03 -10000 0 -0.24 2 2
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.021 0.03 -10000 0 -0.22 3 3
JAK-STAT cascade -0.019 0.019 -10000 0 -0.22 2 2
cell proliferation 0.024 0.034 0.24 2 -0.21 3 5
IL1-mediated signaling events

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
UBC13/UEV1A 0.029 0.015 0.24 1 -10000 0 1
PRKCZ 0.019 0.027 -10000 0 -0.34 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.02 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0 0.058 -10000 0 -0.27 10 10
IRAK/TOLLIP -0.021 0.016 0.19 1 -10000 0 1
IKBKB 0.019 0.008 -10000 0 -10000 0 0
IKBKG 0.021 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.036 0.14 0.24 16 -0.24 100 116
IL1A -0.077 0.16 0.33 2 -0.34 99 101
IL1B -0.029 0.052 0.16 1 -0.24 20 21
IRAK/TRAF6/p62/Atypical PKCs 0.042 0.039 -10000 0 -0.18 2 2
IL1R2 0.032 0.071 0.33 15 -0.34 3 18
IL1R1 0.02 0.027 -10000 0 -0.34 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.007 0.053 -10000 0 -0.28 4 4
TOLLIP 0.021 0.004 -10000 0 -10000 0 0
TICAM2 0.02 0.02 -10000 0 -0.34 1 1
MAP3K3 0.021 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.013 0.005 -10000 0 -10000 0 0
IKK complex/ELKS -0.008 0.065 -10000 0 -0.33 1 1
JUN -0.02 0.043 0.15 17 -0.17 1 18
MAP3K7 0.02 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.035 0.06 -10000 0 -0.18 19 19
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.015 0.11 0.23 1 -0.19 99 100
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.008 0.11 0.23 1 -0.18 98 99
IL1 beta fragment/IL1R1/IL1RAP 0.016 0.055 -10000 0 -0.19 21 21
NFKB1 0.022 0.003 -10000 0 -10000 0 0
MAPK8 -0.015 0.048 0.16 19 -10000 0 19
IRAK1 -0.018 0.016 0.15 2 -10000 0 2
IL1RN/IL1R1 0.026 0.044 0.24 1 -0.24 9 10
IRAK4 0.021 0.004 -10000 0 -10000 0 0
PRKCI 0.021 0.005 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
PI3K 0.03 0.009 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.003 0.059 -10000 0 -0.28 8 8
CHUK 0.022 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.016 0.055 -10000 0 -0.19 21 21
IL1 beta/IL1R2 0.017 0.071 0.22 13 -0.22 21 34
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.003 0.026 0.16 1 -10000 0 1
NF kappa B1 p50/RelA 0.024 0.055 -10000 0 -0.18 16 16
IRAK3 0.012 0.057 -10000 0 -0.34 9 9
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.034 0.061 -10000 0 -0.18 20 20
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.046 0.1 -10000 0 -0.21 93 93
IL1 alpha/IL1R1/IL1RAP -0.026 0.11 0.23 2 -0.2 99 101
RELA 0.021 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.021 0.005 -10000 0 -10000 0 0
MYD88 0.021 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.033 0.031 0.19 1 -10000 0 1
IL1RAP 0.021 0.005 -10000 0 -10000 0 0
UBE2N 0.021 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.046 0.034 -10000 0 -10000 0 0
CASP1 0.019 0.027 -10000 0 -0.34 2 2
IL1RN/IL1R2 0.034 0.065 0.24 16 -0.26 9 25
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.027 0.056 -10000 0 -0.19 21 21
TMEM189-UBE2V1 0.02 0.017 0.33 1 -10000 0 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.037 0.096 -10000 0 -0.33 15 15
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
IL1RN 0.016 0.053 0.33 1 -0.34 7 8
TRAF6/TAK1/TAB1/TAB2 0.034 0.02 0.18 1 -10000 0 1
MAP2K6 -0.008 0.056 0.18 26 -10000 0 26
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.009 0.03 0.11 1 -0.23 2 3
NFATC2 -0.013 0.041 0.11 1 -0.22 9 10
NFATC3 -0.009 0.026 0.11 1 -10000 0 1
CD40LG -0.032 0.14 0.28 18 -0.38 23 41
PTGS2 -0.035 0.15 0.29 21 -0.36 33 54
JUNB 0.018 0.027 -10000 0 -0.34 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.021 -10000 0 -10000 0 0
CaM/Ca2+ 0.011 0.021 -10000 0 -10000 0 0
CALM1 0.014 0.021 -10000 0 -10000 0 0
JUN 0.012 0.034 -10000 0 -0.34 2 2
mol:Ca2+ -0.001 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.012 -10000 0 -10000 0 0
FOSL1 0.037 0.081 0.33 21 -0.34 3 24
CREM 0.021 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.023 0.096 0.27 15 -0.25 8 23
FOS -0.01 0.094 -10000 0 -0.34 25 25
IFNG -0.014 0.15 0.34 30 -0.35 16 46
AP-1/NFAT1-c-4 0.022 0.17 0.46 15 -0.38 16 31
FASLG -0.026 0.13 0.28 18 -0.33 18 36
NFAT1-c-4/ICER1 0.01 0.064 0.26 1 -0.21 7 8
IL2RA -0.012 0.16 0.35 33 -0.34 16 49
FKBP12/FK506 0.015 0.004 -10000 0 -10000 0 0
CSF2 -0.034 0.15 0.32 19 -0.38 28 47
JunB/Fra1/NFAT1-c-4 0.027 0.089 0.25 20 -0.24 7 27
IL4 -0.028 0.13 0.28 18 -0.34 16 34
IL2 -0.001 0.11 -10000 0 -0.82 6 6
IL3 -0.013 0.13 -10000 0 -0.64 15 15
FKBP1A 0.021 0.005 -10000 0 -10000 0 0
BATF3 0.021 0.018 0.33 1 -10000 0 1
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.02 0.007 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.021 0.005 -10000 0 -9999 0 0
PLK4 0.04 0.073 0.33 21 -9999 0 21
regulation of centriole replication -0.006 0.043 0.16 21 -9999 0 21
FAS signaling pathway (CD95)

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
SPTAN1 -0.015 0.033 -10000 0 -0.19 11 11
RFC1 -0.01 0.045 0.22 7 -0.19 10 17
PRKDC -0.001 0.059 0.22 19 -0.19 6 25
RIPK1 0.023 0.007 -10000 0 -10000 0 0
CASP7 -0.015 0.1 -10000 0 -0.69 7 7
FASLG/FAS/FADD/FAF1 0.003 0.057 0.16 19 -0.27 3 22
MAP2K4 -0.061 0.14 0.23 3 -0.32 64 67
mol:ceramide -0.019 0.078 -10000 0 -0.26 13 13
GSN -0.015 0.033 -10000 0 -0.19 11 11
FASLG/FAS/FADD/FAF1/Caspase 8 -0.004 0.061 0.21 1 -0.33 2 3
FAS 0.007 0.04 -10000 0 -0.35 3 3
BID -0.023 0.016 -10000 0 -0.2 2 2
MAP3K1 -0.03 0.1 0.24 2 -0.47 9 11
MAP3K7 0.011 0.018 -10000 0 -10000 0 0
RB1 -0.014 0.031 -10000 0 -0.19 10 10
CFLAR 0.024 0.005 -10000 0 -10000 0 0
HGF/MET 0.009 0.1 0.23 8 -0.23 45 53
ARHGDIB -0.011 0.039 0.22 4 -0.18 10 14
FADD 0.009 0.023 -10000 0 -10000 0 0
actin filament polymerization 0.015 0.033 0.19 11 -10000 0 11
NFKB1 -0.022 0.11 -10000 0 -0.61 5 5
MAPK8 -0.1 0.2 0.24 1 -0.47 76 77
DFFA -0.014 0.037 0.21 2 -0.19 11 13
DNA fragmentation during apoptosis -0.012 0.041 0.21 4 -0.19 11 15
FAS/FADD/MET 0.018 0.06 0.23 5 -0.21 12 17
CFLAR/RIP1 0.035 0.011 -10000 0 -10000 0 0
FAIM3 0.022 0.024 0.33 2 -10000 0 2
FAF1 0.009 0.025 -10000 0 -10000 0 0
PARP1 -0.014 0.036 0.22 1 -0.19 12 13
DFFB -0.012 0.041 0.21 4 -0.19 11 15
CHUK -0.028 0.098 -10000 0 -0.64 4 4
FASLG 0.007 0.035 -10000 0 -0.34 2 2
FAS/FADD 0.014 0.04 -10000 0 -0.26 3 3
HGF 0.009 0.076 0.33 3 -0.34 14 17
LMNA -0.009 0.052 0.18 16 -0.23 1 17
CASP6 -0.014 0.037 0.21 2 -0.19 11 13
CASP10 0.009 0.03 -10000 0 -0.35 1 1
CASP3 -0.006 0.019 -10000 0 -0.27 1 1
PTPN13 -0.014 0.11 -10000 0 -0.34 35 35
CASP8 -0.022 0.018 -10000 0 -0.23 2 2
IL6 -0.23 0.46 -10000 0 -1.1 78 78
MET 0.014 0.073 0.33 5 -0.34 11 16
ICAD/CAD -0.015 0.047 0.3 4 -0.24 1 5
FASLG/FAS/FADD/FAF1/Caspase 10 -0.019 0.078 -10000 0 -0.26 13 13
activation of caspase activity by cytochrome c -0.023 0.016 -10000 0 -0.2 2 2
PAK2 -0.01 0.044 0.21 7 -0.18 10 17
BCL2 0.021 0.018 0.33 1 -10000 0 1
EPHB forward signaling

Figure S57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S57.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.048 0.066 0.22 42 -0.18 3 45
cell-cell adhesion 0.02 0.033 0.16 6 -10000 0 6
Ephrin B/EPHB2/RasGAP 0.068 0.069 0.23 39 -0.18 5 44
ITSN1 0.021 0.004 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.031 0.029 0.21 7 -0.2 1 8
Ephrin B1/EPHB1 0.046 0.059 0.21 36 -0.2 2 38
HRAS/GDP 0.013 0.071 -10000 0 -0.24 9 9
Ephrin B/EPHB1/GRB7 0.062 0.065 0.23 27 -0.18 7 34
Endophilin/SYNJ1 -0.008 0.049 0.18 13 -10000 0 13
KRAS 0.02 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.064 0.064 0.23 30 -0.18 5 35
endothelial cell migration 0.037 0.027 -10000 0 -0.18 3 3
GRB2 0.021 0.005 -10000 0 -10000 0 0
GRB7 0.019 0.027 -10000 0 -0.34 2 2
PAK1 -0.012 0.056 0.24 5 -0.3 1 6
HRAS 0.021 0.004 -10000 0 -10000 0 0
RRAS -0.012 0.049 0.18 10 -0.2 5 15
DNM1 0.024 0.029 0.33 3 -10000 0 3
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.012 0.05 0.2 11 -0.17 5 16
lamellipodium assembly -0.02 0.033 -10000 0 -0.16 6 6
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.013 0.052 0.19 4 -0.19 6 10
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
EPHB2 0.06 0.1 0.33 44 -10000 0 44
EPHB3 0.027 0.043 0.33 7 -10000 0 7
EPHB1 0.053 0.097 0.33 37 -0.34 1 38
EPHB4 0.021 0.005 -10000 0 -10000 0 0
mol:GDP -0.006 0.053 0.22 7 -0.28 4 11
Ephrin B/EPHB2 0.06 0.065 0.22 42 -0.17 5 47
Ephrin B/EPHB3 0.043 0.04 0.22 6 -0.17 5 11
JNK cascade -0.001 0.064 0.26 10 -0.18 2 12
Ephrin B/EPHB1 0.055 0.06 0.22 30 -0.17 6 36
RAP1/GDP -0.011 0.081 0.24 13 -0.26 7 20
EFNB2 0.018 0.033 -10000 0 -0.34 3 3
EFNB3 0.02 0.026 0.33 1 -0.34 1 2
EFNB1 0.021 0.019 -10000 0 -0.34 1 1
Ephrin B2/EPHB1-2 0.074 0.087 0.23 70 -0.18 4 74
RAP1B 0.02 0.006 -10000 0 -10000 0 0
RAP1A 0.021 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.043 0.066 0.21 5 -0.22 5 10
Rap1/GTP -0.019 0.044 0.099 5 -0.17 5 10
axon guidance 0.048 0.066 0.22 42 -0.18 3 45
MAPK3 -0.003 0.05 0.25 5 -10000 0 5
MAPK1 -0.003 0.045 0.22 3 -10000 0 3
Rac1/GDP -0.017 0.07 0.22 6 -0.25 9 15
actin cytoskeleton reorganization -0.027 0.044 0.093 4 -0.19 4 8
CDC42/GDP -0.011 0.082 0.24 14 -0.25 8 22
PI3K 0.041 0.028 -10000 0 -0.18 3 3
EFNA5 0.019 0.037 0.33 1 -0.34 3 4
Ephrin B2/EPHB4 0.024 0.023 -10000 0 -0.2 3 3
Ephrin B/EPHB2/Intersectin/N-WASP 0.01 0.06 0.18 3 -0.19 13 16
CDC42 0.021 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.023 0.039 -10000 0 -0.17 4 4
PTK2 0.058 0.19 0.53 48 -10000 0 48
MAP4K4 -0.001 0.065 0.26 10 -0.18 2 12
SRC 0.021 0.004 -10000 0 -10000 0 0
KALRN 0.018 0.033 -10000 0 -0.34 3 3
Intersectin/N-WASP 0.03 0.009 -10000 0 -10000 0 0
neuron projection morphogenesis 0.003 0.087 0.27 17 -0.32 1 18
MAP2K1 0.002 0.048 0.2 6 -0.18 5 11
WASL 0.021 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.091 0.086 0.25 72 -0.19 2 74
cell migration 0.012 0.085 0.29 11 -0.26 3 14
NRAS 0.021 0.005 -10000 0 -10000 0 0
SYNJ1 -0.009 0.049 0.18 13 -10000 0 13
PXN 0.021 0.004 -10000 0 -10000 0 0
TF 0.006 0.071 0.21 15 -10000 0 15
HRAS/GTP 0.043 0.051 0.18 6 -0.17 6 12
Ephrin B1/EPHB1-2 0.077 0.085 0.23 72 -0.18 2 74
cell adhesion mediated by integrin 0.015 0.037 0.18 5 -0.2 6 11
RAC1 0.019 0.007 -10000 0 -10000 0 0
mol:GTP 0.051 0.058 0.22 8 -0.17 6 14
RAC1-CDC42/GTP -0.023 0.036 -10000 0 -0.17 5 5
RASA1 0.021 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.017 0.07 0.22 6 -0.26 7 13
ruffle organization 0.008 0.096 0.36 12 -10000 0 12
NCK1 0.021 0.003 -10000 0 -10000 0 0
receptor internalization -0.014 0.046 0.17 12 -10000 0 12
Ephrin B/EPHB2/KALRN 0.068 0.074 0.23 41 -0.2 7 48
ROCK1 -0.012 0.033 0.18 8 -0.18 1 9
RAS family/GDP -0.034 0.037 -10000 0 -0.21 4 4
Rac1/GTP -0.017 0.042 0.12 5 -0.17 6 11
Ephrin B/EPHB1/Src/Paxillin 0.006 0.058 0.15 1 -0.19 16 17
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.037 0.02 -10000 0 -0.18 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.012 0.11 0.25 1 -0.35 17 18
AP1 0.003 0.076 -10000 0 -0.17 52 52
mol:PIP3 -0.036 0.042 -10000 0 -0.17 25 25
AKT1 -0.012 0.068 0.23 3 -0.31 5 8
PTK2B -0.044 0.13 0.25 1 -0.36 27 28
RHOA -0.007 0.075 0.18 4 -0.37 10 14
PIK3CB 0.021 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.03 0.085 0.24 5 -0.33 12 17
MAGI3 0.017 0.038 -10000 0 -0.34 4 4
RELA 0.021 0.004 -10000 0 -10000 0 0
apoptosis -0.012 0.059 -10000 0 -0.2 30 30
HRAS/GDP 0.016 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.049 0.12 0.25 4 -0.39 20 24
NF kappa B1 p50/RelA -0.054 0.087 -10000 0 -0.26 36 36
endothelial cell migration -0.011 0.005 -10000 0 -10000 0 0
ADCY4 -0.015 0.056 0.24 1 -0.26 4 5
ADCY5 -0.026 0.077 0.22 2 -0.26 19 21
ADCY6 -0.009 0.05 0.24 1 -0.25 4 5
ADCY7 -0.01 0.044 -10000 0 -0.2 4 4
ADCY1 -0.008 0.049 0.24 1 -0.22 6 7
ADCY2 -0.013 0.055 0.24 1 -0.24 7 8
ADCY3 -0.008 0.046 0.24 1 -0.2 4 5
ADCY8 -0.055 0.081 -10000 0 -0.24 11 11
ADCY9 -0.013 0.056 0.24 1 -0.25 8 9
GSK3B -0.045 0.12 0.19 5 -0.36 25 30
arachidonic acid secretion -0.016 0.05 -10000 0 -0.28 6 6
GNG2 0.019 0.02 -10000 0 -0.34 1 1
TRIP6 0.01 0.018 -10000 0 -0.3 1 1
GNAO1 -0.012 0.018 0.17 1 -0.2 2 3
HRAS 0.021 0.004 -10000 0 -10000 0 0
NFKBIA -0.03 0.12 0.26 4 -0.31 35 39
GAB1 0.021 0.019 -10000 0 -0.34 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.008 0.19 -10000 0 -0.84 17 17
JUN 0.019 0.027 -10000 0 -0.34 2 2
LPA/LPA2/NHERF2 0.025 0.025 -10000 0 -0.2 4 4
TIAM1 -0.023 0.22 -10000 0 -0.98 17 17
PIK3R1 0.02 0.007 -10000 0 -10000 0 0
mol:IP3 -0.024 0.074 0.22 6 -0.22 26 32
PLCB3 -0.014 0.035 0.18 8 -0.18 4 12
FOS -0.005 0.092 -10000 0 -0.34 25 25
positive regulation of mitosis -0.016 0.05 -10000 0 -0.28 6 6
LPA/LPA1-2-3 0.024 0.065 0.22 4 -0.18 30 34
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.02 0.02 -10000 0 -0.34 1 1
stress fiber formation -0.027 0.099 0.23 1 -0.37 14 15
GNAZ -0.026 0.05 -10000 0 -0.2 28 28
EGFR/PI3K-beta/Gab1 -0.035 0.046 -10000 0 -0.18 23 23
positive regulation of dendritic cell cytokine production 0.022 0.065 0.21 4 -0.18 30 34
LPA/LPA2/MAGI-3 0.025 0.025 -10000 0 -0.2 4 4
ARHGEF1 0.004 0.069 0.18 43 -0.17 1 44
GNAI2 -0.012 0.005 -10000 0 -10000 0 0
GNAI3 -0.011 0.005 -10000 0 -10000 0 0
GNAI1 -0.011 0.011 -10000 0 -0.2 1 1
LPA/LPA3 -0.002 0.073 0.22 4 -0.23 30 34
LPA/LPA2 0.016 0.005 -10000 0 -10000 0 0
LPA/LPA1 0.017 0.005 -10000 0 -10000 0 0
HB-EGF/EGFR -0.016 0.085 0.13 48 -0.21 36 84
HBEGF -0.017 0.1 0.16 54 -0.23 45 99
mol:DAG -0.024 0.074 0.22 6 -0.22 26 32
cAMP biosynthetic process -0.021 0.066 0.3 2 -0.24 7 9
NFKB1 0.022 0.003 -10000 0 -10000 0 0
SRC 0.021 0.004 -10000 0 -10000 0 0
GNB1 0.02 0.007 -10000 0 -10000 0 0
LYN -0.033 0.11 0.28 3 -0.3 34 37
GNAQ -0.012 0.061 -10000 0 -0.21 28 28
LPAR2 0.021 0.005 -10000 0 -10000 0 0
LPAR3 -0.006 0.11 0.33 4 -0.34 30 34
LPAR1 0.022 0.006 -10000 0 -10000 0 0
IL8 -0.016 0.12 0.3 16 -0.37 13 29
PTK2 -0.025 0.05 0.17 6 -0.17 21 27
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
CASP3 -0.012 0.06 -10000 0 -0.2 30 30
EGFR 0.017 0.037 0.33 1 -0.34 3 4
PLCG1 -0.016 0.074 0.14 5 -0.24 28 33
PLD2 -0.024 0.057 0.19 10 -0.17 25 35
G12/G13 0.036 0.017 -10000 0 -10000 0 0
PI3K-beta -0.027 0.049 -10000 0 -0.33 6 6
cell migration -0.009 0.063 -10000 0 -0.25 16 16
SLC9A3R2 0.017 0.038 -10000 0 -0.34 4 4
PXN -0.027 0.1 0.23 1 -0.38 14 15
HRAS/GTP -0.017 0.05 -10000 0 -0.28 6 6
RAC1 0.019 0.007 -10000 0 -10000 0 0
MMP9 0.072 0.12 0.33 58 -10000 0 58
PRKCE 0.019 0.028 -10000 0 -0.34 2 2
PRKCD -0.037 0.085 0.27 3 -0.34 12 15
Gi(beta/gamma) -0.01 0.045 -10000 0 -0.24 2 2
mol:LPA 0.001 0.001 -10000 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.011 0.089 -10000 0 -0.36 9 9
MAPKKK cascade -0.016 0.05 -10000 0 -0.28 6 6
contractile ring contraction involved in cytokinesis -0.005 0.075 0.18 4 -0.37 10 14
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.017 0.07 -10000 0 -0.22 35 35
GNA15 -0.01 0.057 -10000 0 -0.2 27 27
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
MAPT -0.051 0.12 0.25 4 -0.39 21 25
GNA11 -0.01 0.057 -10000 0 -0.2 27 27
Rac1/GTP -0.009 0.2 -10000 0 -0.89 17 17
MMP2 -0.011 0.005 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 -0.017 0.005 -10000 0 -10000 0 0
SMARCC1 0.002 0.013 -10000 0 -10000 0 0
REL 0.021 0.007 -10000 0 -10000 0 0
HDAC7 -0.037 0.076 0.28 2 -0.29 12 14
JUN 0.019 0.027 -10000 0 -0.34 2 2
EP300 0.021 0.004 -10000 0 -10000 0 0
KAT2B 0.021 0.004 -10000 0 -10000 0 0
KAT5 0.021 0.004 -10000 0 -10000 0 0
MAPK14 -0.013 0.036 0.17 10 -0.26 1 11
FOXO1 0.021 0.005 -10000 0 -10000 0 0
T-DHT/AR -0.035 0.079 -10000 0 -0.3 12 12
MAP2K6 0.023 0.056 0.33 9 -0.35 1 10
BRM/BAF57 0.027 0.023 -10000 0 -0.24 2 2
MAP2K4 0.016 0.016 -10000 0 -10000 0 0
SMARCA2 0.018 0.028 -10000 0 -0.34 2 2
PDE9A -0.03 0.15 -10000 0 -0.88 8 8
NCOA2 0.018 0.028 -10000 0 -0.34 2 2
CEBPA 0.003 0.077 -10000 0 -0.34 17 17
EHMT2 0.021 0.005 -10000 0 -10000 0 0
cell proliferation -0.029 0.14 0.38 11 -0.37 19 30
NR0B1 0.082 0.12 0.33 71 -10000 0 71
EGR1 -0.002 0.089 -10000 0 -0.34 23 23
RXRs/9cRA -0.064 0.11 -10000 0 -0.18 157 157
AR/RACK1/Src -0.013 0.084 0.32 7 -0.33 1 8
AR/GR -0.025 0.082 0.23 2 -0.23 34 36
GNB2L1 0.021 0.005 -10000 0 -10000 0 0
PKN1 0.02 0.006 -10000 0 -10000 0 0
RCHY1 0.021 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 0.016 1 -10000 0 1
MAPK8 -0.016 0.014 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.019 0.067 0.23 1 -0.29 2 3
SRC -0.024 0.03 0.19 2 -0.23 1 3
NR3C1 0.021 0.004 -10000 0 -10000 0 0
KLK3 0.009 0.098 -10000 0 -0.42 1 1
APPBP2 0.016 0.017 -10000 0 -10000 0 0
TRIM24 0.021 0.005 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.022 0.063 0.2 4 -0.35 1 5
TMPRSS2 -0.089 0.28 -10000 0 -0.91 35 35
RXRG -0.14 0.18 -10000 0 -0.34 158 158
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.021 0.004 -10000 0 -10000 0 0
RXRB 0.021 0.005 -10000 0 -10000 0 0
CARM1 0.021 0.006 -10000 0 -10000 0 0
NR2C2 0.021 0.004 -10000 0 -10000 0 0
KLK2 -0.006 0.081 0.29 14 -10000 0 14
AR -0.026 0.075 0.19 2 -0.25 32 34
SENP1 0.021 0.004 -10000 0 -10000 0 0
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
MDM2 0.019 0.01 -10000 0 -10000 0 0
SRY 0 0.003 -10000 0 -0.028 5 5
GATA2 -0.01 0.1 -10000 0 -0.34 31 31
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 0.12 0.15 0.33 118 -10000 0 118
T-DHT/AR/RACK1/Src -0.018 0.078 0.36 5 -0.34 1 6
positive regulation of transcription -0.01 0.1 -10000 0 -0.34 31 31
DNAJA1 0.016 0.017 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.013 0.18 2 -10000 0 2
NCOA1 0.024 0.015 -10000 0 -10000 0 0
SPDEF 0.11 0.15 0.33 109 -0.34 3 112
T-DHT/AR/TIF2 -0.008 0.071 0.22 7 -0.29 6 13
T-DHT/AR/Hsp90 -0.021 0.061 0.21 3 -0.35 1 4
GSK3B 0.018 0.013 -10000 0 -10000 0 0
NR2C1 0.021 0.007 -10000 0 -10000 0 0
mol:T-DHT -0.022 0.029 0.21 1 -0.24 1 2
SIRT1 0.021 0.004 -10000 0 -10000 0 0
ZMIZ2 0.019 0.01 -10000 0 -10000 0 0
POU2F1 0.009 0.04 -10000 0 -0.14 5 5
T-DHT/AR/DAX-1 0.018 0.11 0.27 22 -0.35 1 23
CREBBP 0.021 0.004 -10000 0 -10000 0 0
SMARCE1 0.021 0.005 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.034 0.054 0.25 4 -0.24 15 19
KIRREL 0.017 0.04 -10000 0 -0.34 4 4
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.034 0.054 0.24 15 -0.25 4 19
PLCG1 0.021 0.005 -10000 0 -10000 0 0
ARRB2 0.02 0.006 -10000 0 -10000 0 0
WASL 0.021 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.05 0.053 0.22 15 -0.19 4 19
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.013 0.037 0.16 2 -0.19 5 7
FYN 0.017 0.087 0.21 49 -0.18 4 53
mol:Ca2+ 0.048 0.051 0.21 15 -0.19 4 19
mol:DAG 0.049 0.052 0.22 15 -0.19 4 19
NPHS2 -0.004 0.024 -10000 0 -10000 0 0
mol:IP3 0.049 0.052 0.22 15 -0.19 4 19
regulation of endocytosis 0.035 0.046 0.2 14 -0.17 4 18
Nephrin/NEPH1/podocin/Cholesterol 0.04 0.048 0.21 15 -0.18 4 19
establishment of cell polarity 0.034 0.054 0.24 15 -0.25 4 19
Nephrin/NEPH1/podocin/NCK1-2 0.058 0.054 0.22 15 -0.18 4 19
Nephrin/NEPH1/beta Arrestin2 0.037 0.047 0.21 14 -0.18 4 18
NPHS1 0.037 0.076 0.34 19 -10000 0 19
Nephrin/NEPH1/podocin 0.037 0.046 0.21 15 -0.18 4 19
TJP1 0.021 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
NCK2 0.022 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.05 0.053 0.22 15 -0.19 4 19
CD2AP 0.021 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.05 0.052 0.22 14 -0.18 4 18
GRB2 0.021 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.007 0.098 0.27 29 -0.18 21 50
cytoskeleton organization -0.004 0.052 0.22 10 -0.21 4 14
Nephrin/NEPH1 0.029 0.042 0.19 15 -0.17 4 19
Nephrin/NEPH1/ZO-1 0.04 0.049 0.22 14 -0.2 4 18
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.013 0.097 -10000 0 -0.32 20 20
TBX21 -0.1 0.32 -10000 0 -1.1 24 24
B2M 0.021 0.007 -10000 0 -10000 0 0
TYK2 0.01 0.028 -10000 0 -10000 0 0
IL12RB1 0.001 0.064 -10000 0 -0.36 9 9
GADD45B -0.096 0.28 -10000 0 -1 20 20
IL12RB2 0.038 0.098 0.33 32 -0.36 1 33
GADD45G -0.088 0.27 -10000 0 -0.93 23 23
natural killer cell activation -0.004 0.012 -10000 0 -10000 0 0
RELB 0.021 0.005 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
IL18 0.006 0.056 -10000 0 -0.34 8 8
IL2RA 0.045 0.088 0.33 29 -0.34 1 30
IFNG 0.043 0.089 0.33 28 -0.34 2 30
STAT3 (dimer) -0.076 0.23 -10000 0 -0.7 27 27
HLA-DRB5 -0.015 0.1 -10000 0 -0.34 31 31
FASLG -0.075 0.27 -10000 0 -0.95 19 19
NF kappa B2 p52/RelB -0.073 0.27 -10000 0 -0.87 23 23
CD4 0.01 0.048 -10000 0 -0.34 6 6
SOCS1 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:6955 -0.002 0.008 -10000 0 -10000 0 0
CD3D 0.014 0.033 -10000 0 -0.36 2 2
CD3E 0.014 0.032 -10000 0 -0.34 2 2
CD3G 0.011 0.046 -10000 0 -0.34 5 5
IL12Rbeta2/JAK2 0.035 0.073 0.24 28 -0.28 1 29
CCL3 -0.087 0.27 -10000 0 -1 17 17
CCL4 -0.087 0.27 -10000 0 -1 18 18
HLA-A 0.021 0.007 -10000 0 -10000 0 0
IL18/IL18R 0.014 0.092 -10000 0 -0.26 28 28
NOS2 -0.13 0.37 -10000 0 -1.1 37 37
IL12/IL12R/TYK2/JAK2/SPHK2 -0.015 0.1 -10000 0 -0.32 23 23
IL1R1 -0.088 0.27 -10000 0 -1 17 17
IL4 0.004 0.027 -10000 0 -10000 0 0
JAK2 0.01 0.027 -10000 0 -10000 0 0
EntrezGene:6957 -0.001 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.014 0.12 -10000 0 -1 4 4
RAB7A -0.079 0.23 -10000 0 -0.82 16 16
lysosomal transport -0.074 0.22 -10000 0 -0.77 16 16
FOS -0.12 0.34 -10000 0 -0.96 43 43
STAT4 (dimer) -0.075 0.26 -10000 0 -0.82 23 23
STAT5A (dimer) -0.063 0.28 -10000 0 -0.84 24 24
GZMA -0.085 0.26 -10000 0 -0.97 18 18
GZMB -0.094 0.29 -10000 0 -1.1 18 18
HLX 0.016 0.038 -10000 0 -0.34 4 4
LCK -0.088 0.29 -10000 0 -0.95 23 23
TCR/CD3/MHC II/CD4 -0.028 0.11 -10000 0 -0.3 33 33
IL2/IL2R 0.061 0.064 0.23 29 -0.28 3 32
MAPK14 -0.095 0.28 -10000 0 -0.88 27 27
CCR5 -0.082 0.26 -10000 0 -0.88 22 22
IL1B -0.008 0.088 0.34 1 -0.35 19 20
STAT6 -0.01 0.074 -10000 0 -0.3 1 1
STAT4 0.022 0.002 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT1 0.022 0.002 -10000 0 -10000 0 0
NFKB1 0.022 0.003 -10000 0 -10000 0 0
NFKB2 0.022 0.003 -10000 0 -10000 0 0
IL12B 0.012 0.043 0.31 3 -0.35 1 4
CD8A 0.02 0.039 0.33 1 -0.35 3 4
CD8B 0.02 0.048 0.33 3 -0.34 4 7
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.012 0.096 0.31 20 -10000 0 20
IL2RB 0.019 0.027 -10000 0 -0.34 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.067 0.24 -10000 0 -0.74 23 23
IL2RG 0.018 0.038 -10000 0 -0.34 4 4
IL12 0.019 0.049 0.24 2 -0.27 3 5
STAT5A 0.02 0.019 -10000 0 -0.34 1 1
CD247 0.015 0.025 -10000 0 -0.34 1 1
IL2 0.02 0.003 -10000 0 -10000 0 0
SPHK2 0.02 0.02 -10000 0 -0.34 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.007 0.051 0.34 1 -0.36 4 5
IL12/IL12R/TYK2/JAK2 -0.089 0.32 -10000 0 -1 23 23
MAP2K3 -0.1 0.29 -10000 0 -0.93 26 26
RIPK2 0.019 0.007 -10000 0 -10000 0 0
MAP2K6 -0.09 0.28 -10000 0 -0.91 25 25
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.004 0.066 -10000 0 -0.34 12 12
IL18RAP -0.001 0.077 -10000 0 -0.34 16 16
IL12Rbeta1/TYK2 0.011 0.055 -10000 0 -0.26 8 8
EOMES -0.006 0.14 -10000 0 -0.59 15 15
STAT1 (dimer) -0.056 0.23 -10000 0 -0.74 22 22
T cell proliferation -0.062 0.19 0.36 1 -0.58 26 27
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.001 0.072 -10000 0 -0.34 14 14
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.066 0.22 -10000 0 -0.6 35 35
ATF2 -0.088 0.26 -10000 0 -0.8 27 27
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.021 0.005 -10000 0 -10000 0 0
VLDLR 0.014 0.047 -10000 0 -0.34 6 6
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
NUDC 0.021 0.004 -10000 0 -10000 0 0
RELN/LRP8 0.018 0.084 0.23 9 -0.2 38 47
CaM/Ca2+ 0.015 0.004 -10000 0 -10000 0 0
KATNA1 0.02 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.028 0.069 0.17 16 -0.19 36 52
IQGAP1/CaM 0.03 0.009 -10000 0 -10000 0 0
DAB1 0.024 0.033 0.33 4 -10000 0 4
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
PLA2G7 0.023 0.038 0.33 4 -0.34 1 5
CALM1 0.021 0.005 -10000 0 -10000 0 0
DYNLT1 0.02 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.034 0.026 0.24 5 -10000 0 5
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.021 0.004 -10000 0 -10000 0 0
CDK5R1 0.028 0.046 0.33 8 -10000 0 8
LIS1/Poliovirus Protein 3A -0.013 0.005 -10000 0 -10000 0 0
CDK5R2 0.11 0.14 0.33 100 -10000 0 100
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.013 0.089 0.25 8 -0.21 40 48
YWHAE 0.02 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.005 0.095 0.29 15 -0.22 2 17
MAP1B 0.004 0.01 -10000 0 -10000 0 0
RAC1 0.004 0.002 -10000 0 -10000 0 0
p35/CDK5 -0.03 0.072 0.18 21 -10000 0 21
RELN -0.014 0.12 0.33 5 -0.34 38 43
PAFAH/LIS1 -0.016 0.029 0.22 4 -0.2 1 5
LIS1/CLIP170 -0.018 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.02 0.065 0.16 2 -10000 0 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.021 0.091 0.26 2 -0.23 36 38
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0 0.08 0.22 15 -0.23 1 16
LIS1/IQGAP1 -0.019 0.008 -10000 0 -10000 0 0
RHOA 0.005 0.002 -10000 0 -10000 0 0
PAFAH1B1 -0.016 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.032 0.059 0.33 13 -10000 0 13
PAFAH1B2 0.021 0.005 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.01 0.03 -10000 0 -0.19 1 1
NDEL1/Katanin 60/Dynein heavy chain 0.001 0.096 0.28 14 -0.23 2 16
LRP8 0.027 0.04 0.33 6 -10000 0 6
NDEL1/Katanin 60 0.003 0.096 0.29 16 -0.22 3 19
P39/CDK5 0.022 0.12 0.2 98 -10000 0 98
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.018 0.008 -10000 0 -10000 0 0
CDK5 -0.033 0.062 0.17 12 -0.18 35 47
PPP2R5D 0.021 0.005 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.015 0.006 -10000 0 -10000 0 0
CSNK2A1 0.021 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.013 0.082 0.26 7 -0.18 40 47
RELN/VLDLR 0.023 0.088 0.22 11 -0.2 41 52
CDC42 0.005 0.002 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.021 0.005 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.003 0.13 -10000 0 -0.35 28 28
PTP1B/AKT1 0.013 0.077 0.21 3 -0.31 9 12
FYN 0.02 0.007 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.006 0.083 0.24 4 -0.35 8 12
EGFR 0.018 0.041 0.3 2 -0.34 3 5
EGF/EGFR 0.036 0.1 0.22 38 -0.32 7 45
CSF1 0.02 0.02 -10000 0 -0.34 1 1
AKT1 0.019 0.01 -10000 0 -10000 0 0
INSR 0.02 0.008 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.032 0.098 0.24 29 -0.34 7 36
Insulin Receptor/Insulin 0.022 0.076 -10000 0 -0.36 5 5
HCK 0.009 0.065 -10000 0 -0.34 12 12
CRK 0.02 0.007 -10000 0 -10000 0 0
TYK2 0.002 0.079 0.28 4 -0.38 6 10
EGF 0.074 0.12 0.33 63 -0.34 3 66
YES1 0.02 0.006 -10000 0 -10000 0 0
CAV1 -0.052 0.11 0.23 6 -0.32 20 26
TXN 0.022 0.018 0.33 1 -10000 0 1
PTP1B/IRS1/GRB2 0.022 0.079 0.25 2 -0.32 7 9
cell migration -0.006 0.083 0.35 8 -0.24 4 12
STAT3 0.022 0.003 -10000 0 -10000 0 0
PRLR 0.027 0.095 0.33 21 -0.34 9 30
ITGA2B -0.013 0.11 0.33 1 -0.34 34 35
CSF1R 0.015 0.046 -10000 0 -0.34 6 6
Prolactin Receptor/Prolactin 0.033 0.074 0.25 25 -0.24 9 34
FGR -0.008 0.098 -10000 0 -0.34 29 29
PTP1B/p130 Cas 0.013 0.081 0.23 4 -0.34 8 12
Crk/p130 Cas 0.02 0.081 0.24 3 -0.34 7 10
DOK1 0.002 0.088 0.24 4 -0.34 11 15
JAK2 -0.005 0.13 0.23 4 -0.36 28 32
Jak2/Leptin Receptor/Leptin 0.028 0.1 0.22 15 -0.33 8 23
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
PTPN1 0.005 0.083 0.24 4 -0.35 8 12
LYN 0.02 0.007 -10000 0 -10000 0 0
CDH2 0.045 0.1 0.33 33 -0.34 4 37
SRC 0.01 0.086 -10000 0 -0.43 10 10
ITGB3 0.031 0.082 0.33 19 -0.34 4 23
CAT1/PTP1B -0.029 0.14 0.3 4 -0.37 32 36
CAPN1 0.021 0.006 -10000 0 -10000 0 0
CSK 0.021 0.004 -10000 0 -10000 0 0
PI3K 0.026 0.072 -10000 0 -0.32 4 4
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.094 0.21 10 -0.29 9 19
negative regulation of transcription -0.004 0.13 0.23 4 -0.35 28 32
FCGR2A 0.017 0.028 -10000 0 -0.34 2 2
FER 0.021 0.007 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.014 0.1 0.24 20 -0.24 37 57
BLK 0.05 0.098 0.33 37 -0.34 1 38
Insulin Receptor/Insulin/Shc 0.033 0.018 -10000 0 -10000 0 0
RHOA 0.021 0.005 -10000 0 -10000 0 0
LEPR 0.003 0.078 -10000 0 -0.33 18 18
BCAR1 0.02 0.02 -10000 0 -0.34 1 1
p210 bcr-abl/Grb2 0.021 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.046 0.16 0.2 3 -0.36 48 51
PRL 0.025 0.047 0.33 8 -10000 0 8
SOCS3 -0.001 0.14 -10000 0 -1.1 6 6
SPRY2 0.019 0.021 -10000 0 -0.34 1 1
Insulin Receptor/Insulin/IRS1 0.038 0.018 -10000 0 -0.19 1 1
CSF1/CSF1R 0.02 0.086 0.23 2 -0.35 9 11
Ras protein signal transduction 0.007 0.12 0.55 14 -10000 0 14
IRS1 0.021 0.019 -10000 0 -0.34 1 1
INS 0.012 0.016 -10000 0 -10000 0 0
LEP 0.052 0.096 0.33 37 -10000 0 37
STAT5B 0.007 0.093 0.23 6 -0.32 13 19
STAT5A 0.007 0.094 0.23 6 -0.32 14 20
GRB2 0.021 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.015 0.081 0.23 4 -0.33 8 12
CSN2 0.022 0.067 0.49 1 -10000 0 1
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
LAT 0.017 0.062 -10000 0 -0.39 5 5
YBX1 0.024 0.004 -10000 0 -10000 0 0
LCK 0.022 0.025 0.33 1 -0.34 1 2
SHC1 0.018 0.008 -10000 0 -10000 0 0
NOX4 0.033 0.059 0.33 13 -10000 0 13
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.042 0.046 0.22 8 -0.17 8 16
ER alpha/Gai/GDP/Gbeta gamma -0.034 0.13 -10000 0 -0.46 19 19
AKT1 -0.061 0.23 -10000 0 -0.66 43 43
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.058 0.24 -10000 0 -0.68 43 43
mol:Ca2+ -0.025 0.075 -10000 0 -0.33 17 17
IGF1R 0.02 0.019 -10000 0 -0.34 1 1
E2/ER alpha (dimer)/Striatin 0.027 0.046 0.21 10 -0.2 7 17
SHC1 0.018 0.008 -10000 0 -10000 0 0
apoptosis 0.058 0.22 0.63 43 -10000 0 43
RhoA/GTP -0.025 0.027 -10000 0 -0.16 7 7
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.018 0.12 0.24 2 -0.38 20 22
regulation of stress fiber formation 0.017 0.056 0.25 1 -0.18 9 10
E2/ERA-ERB (dimer) 0.026 0.047 0.21 10 -0.2 8 18
KRAS 0.02 0.006 -10000 0 -10000 0 0
G13/GTP 0.026 0.042 0.2 10 -0.17 7 17
pseudopodium formation -0.017 0.056 0.18 9 -0.25 1 10
E2/ER alpha (dimer)/PELP1 0.024 0.045 0.21 8 -0.19 8 16
GRB2 0.021 0.005 -10000 0 -10000 0 0
GNG2 0.02 0.02 -10000 0 -0.34 1 1
GNAO1 0.02 0.032 0.33 1 -0.34 2 3
HRAS 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.039 0.16 0.24 3 -0.4 44 47
E2/ER beta (dimer) 0.016 0.003 -10000 0 -10000 0 0
mol:GDP -0.005 0.073 0.18 11 -0.28 9 20
mol:NADP -0.039 0.16 0.24 3 -0.4 44 47
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
mol:IP3 -0.026 0.077 -10000 0 -0.34 17 17
IGF-1R heterotetramer 0.02 0.019 -10000 0 -0.34 1 1
PLCB1 -0.01 0.074 -10000 0 -0.37 13 13
PLCB2 -0.013 0.076 -10000 0 -0.36 14 14
IGF1 0.018 0.042 0.33 1 -0.34 4 5
mol:L-citrulline -0.039 0.16 0.24 3 -0.4 44 47
RHOA 0.021 0.004 -10000 0 -10000 0 0
Gai/GDP -0.022 0.15 -10000 0 -0.61 19 19
JNK cascade 0.015 0.003 -10000 0 -10000 0 0
BCAR1 0.02 0.02 -10000 0 -0.34 1 1
ESR2 0.021 0.005 -10000 0 -10000 0 0
GNAQ 0.02 0.02 -10000 0 -0.34 1 1
ESR1 0.021 0.075 0.33 10 -0.34 8 18
Gq family/GDP/Gbeta gamma -0.054 0.22 -10000 0 -0.73 31 31
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.012 0.068 -10000 0 -0.6 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.016 0.12 0.22 2 -0.37 19 21
GNAZ -0.007 0.097 -10000 0 -0.34 28 28
E2/ER alpha (dimer) 0.015 0.051 0.22 10 -0.23 8 18
STRN 0.022 0.003 -10000 0 -10000 0 0
GNAL 0.017 0.042 0.33 1 -0.34 4 5
PELP1 0.02 0.006 -10000 0 -10000 0 0
MAPK11 -0.013 0.019 0.22 1 -0.2 2 3
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.021 0.005 -10000 0 -10000 0 0
GNAI1 0.02 0.02 -10000 0 -0.34 1 1
HBEGF -0.041 0.15 0.37 7 -0.44 24 31
cAMP biosynthetic process 0.019 0.043 0.14 11 -0.19 10 21
SRC -0.034 0.12 -10000 0 -0.43 19 19
PI3K 0.03 0.009 -10000 0 -10000 0 0
GNB1 0.021 0.004 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.018 0.07 0.2 1 -0.26 7 8
SOS1 0.022 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.026 0.091 -10000 0 -0.31 20 20
Gs family/GTP 0.025 0.047 0.17 11 -0.19 10 21
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.016 -10000 0 -10000 0 0
vasodilation -0.037 0.15 0.24 3 -0.38 44 47
mol:DAG -0.026 0.077 -10000 0 -0.34 17 17
Gs family/GDP/Gbeta gamma -0.001 0.067 -10000 0 -0.28 9 9
MSN -0.018 0.058 0.18 9 -0.27 1 10
Gq family/GTP -0.003 0.083 -10000 0 -0.38 15 15
mol:PI-3-4-5-P3 -0.055 0.23 -10000 0 -0.65 43 43
NRAS 0.021 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.037 0.15 0.38 44 -0.24 3 47
GRB2/SOS1 0.031 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.006 0.075 0.19 9 -0.27 9 18
NOS3 -0.042 0.17 0.24 3 -0.42 44 47
GNA11 0.02 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.032 0.16 0.32 3 -0.46 37 40
E2/ER alpha (dimer)/PELP1/Src -0.019 0.13 0.26 6 -0.39 20 26
ruffle organization -0.017 0.056 0.18 9 -0.25 1 10
ROCK2 -0.012 0.061 0.27 3 -10000 0 3
GNA14 0.011 0.06 -10000 0 -0.34 10 10
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
MMP9 -0.026 0.12 0.35 2 -0.42 18 20
MMP2 -0.032 0.13 0.27 7 -0.41 20 27
Class IB PI3K non-lipid kinase events

Figure S65.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S65.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.008 0.067 0.34 13 -10000 0 13
PI3K Class IB/PDE3B 0.008 0.067 -10000 0 -0.34 13 13
PDE3B 0.008 0.068 -10000 0 -0.34 13 13
S1P4 pathway

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.02 0.032 0.33 1 -0.34 2 3
CDC42/GTP -0.016 0.082 -10000 0 -0.26 12 12
PLCG1 -0.028 0.069 -10000 0 -0.23 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.021 0.005 -10000 0 -10000 0 0
G12/G13 0.028 0.011 -10000 0 -10000 0 0
cell migration -0.016 0.081 -10000 0 -0.26 12 12
S1PR5 -0.001 0.088 0.33 1 -0.34 22 23
S1PR4 0.003 0.077 -10000 0 -0.34 17 17
MAPK3 -0.028 0.07 -10000 0 -0.21 26 26
MAPK1 -0.025 0.062 -10000 0 -0.21 15 15
S1P/S1P5/Gi -0.02 0.082 -10000 0 -0.2 51 51
GNAI1 0.02 0.02 -10000 0 -0.34 1 1
CDC42/GDP 0.016 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.012 0.055 0.21 1 -0.2 21 22
RHOA -0.006 0.074 0.18 37 -0.18 14 51
S1P/S1P4/Gi -0.017 0.077 -10000 0 -0.2 48 48
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.007 0.097 -10000 0 -0.34 28 28
S1P/S1P4/G12/G13 0.024 0.047 -10000 0 -0.18 15 15
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.021 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.039 0.056 0.24 19 -0.24 4 23
PTK2 -0.018 0.1 -10000 0 -0.37 16 16
positive regulation of JNK cascade -0.016 0.11 -10000 0 -0.3 24 24
CDC42/GDP -0.014 0.15 -10000 0 -0.4 24 24
Rac1/GDP -0.017 0.14 -10000 0 -0.4 23 23
RAP1B 0.02 0.006 -10000 0 -10000 0 0
RAP1A 0.021 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.015 0.13 -10000 0 -0.36 23 23
nectin-3/I-afadin 0.015 0.06 -10000 0 -0.23 19 19
RAPGEF1 -0.031 0.14 0.28 1 -0.37 39 40
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.037 0.14 -10000 0 -0.41 39 39
PDGFB-D/PDGFRB 0.021 0.005 -10000 0 -10000 0 0
TLN1 -0.023 0.057 -10000 0 -0.38 7 7
Rap1/GTP -0.022 0.1 -10000 0 -0.28 37 37
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.034 0.017 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.015 0.06 -10000 0 -0.23 19 19
PVR 0.021 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.021 0.005 -10000 0 -10000 0 0
mol:GDP -0.031 0.17 -10000 0 -0.47 27 27
MLLT4 0.02 0.007 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
PI3K 0.042 0.053 -10000 0 -0.18 12 12
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.033 0.035 0.24 9 -10000 0 9
positive regulation of lamellipodium assembly -0.018 0.11 -10000 0 -0.32 24 24
PVRL1 0.029 0.049 0.33 9 -10000 0 9
PVRL3 0.003 0.083 0.33 1 -0.34 19 20
PVRL2 0.021 0.005 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
CDH1 0.019 0.027 -10000 0 -0.34 2 2
CLDN1 0.025 0.051 0.33 7 -0.34 2 9
JAM-A/CLDN1 0.036 0.064 0.23 7 -0.21 15 22
SRC -0.037 0.16 -10000 0 -0.44 41 41
ITGB3 0.034 0.08 0.33 19 -0.34 4 23
nectin-1(dimer)/I-afadin/I-afadin 0.033 0.035 0.24 9 -10000 0 9
FARP2 -0.026 0.17 -10000 0 -0.49 22 22
RAC1 0.019 0.007 -10000 0 -10000 0 0
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.026 0.053 -10000 0 -0.2 17 17
nectin-1/I-afadin 0.033 0.035 0.24 9 -10000 0 9
nectin-2/I-afadin 0.028 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.026 0.01 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.03 0.059 0.23 7 -0.2 16 23
CDC42/GTP/IQGAP1/filamentous actin 0.028 0.007 -10000 0 -10000 0 0
F11R 0.018 0.02 -10000 0 -0.34 1 1
positive regulation of filopodium formation -0.016 0.11 -10000 0 -0.3 24 24
alphaV/beta3 Integrin/Talin -0.023 0.084 0.2 17 -0.35 9 26
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.028 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.028 0.011 -10000 0 -10000 0 0
PIP5K1C -0.018 0.061 -10000 0 -0.25 17 17
VAV2 -0.032 0.18 -10000 0 -0.52 23 23
RAP1/GDP -0.013 0.13 -10000 0 -0.35 25 25
ITGAV 0.022 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.026 0.055 -10000 0 -0.2 18 18
nectin-3(dimer)/I-afadin/I-afadin 0.015 0.06 -10000 0 -0.23 19 19
Rac1/GTP -0.02 0.14 -10000 0 -0.39 24 24
PTPRM -0.01 0.073 -10000 0 -0.26 21 21
E-cadherin/beta catenin/alpha catenin 0.051 0.042 -10000 0 -0.18 1 1
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.021 0.036 -10000 0 -0.24 9 9
MAP4K4 -0.005 0.053 -10000 0 -0.27 4 4
BAG4 0.019 0.008 -10000 0 -10000 0 0
PKC zeta/ceramide 0.004 0.063 -10000 0 -0.18 35 35
NFKBIA 0.018 0.008 -10000 0 -10000 0 0
BIRC3 0.022 0.043 0.33 4 -0.34 2 6
BAX -0.008 0.076 -10000 0 -0.34 15 15
RIPK1 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.008 0.12 0.71 10 -10000 0 10
BAD -0.011 0.06 0.2 2 -0.18 36 38
SMPD1 0.006 0.059 0.21 8 -0.19 3 11
RB1 -0.012 0.058 -10000 0 -0.18 36 36
FADD/Caspase 8 0.002 0.061 0.23 2 -0.31 2 4
MAP2K4 -0.014 0.057 0.18 3 -0.17 33 36
NSMAF 0.02 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.013 0.064 0.22 7 -0.17 34 41
EGF 0.074 0.12 0.33 63 -0.34 3 66
mol:ceramide -0.007 0.062 0.13 4 -0.18 36 40
MADD 0.022 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.018 0.032 -10000 0 -0.24 7 7
ASAH1 0.018 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.012 0.058 -10000 0 -0.17 36 36
cell proliferation 0.004 0.067 0.21 5 -0.23 2 7
BID -0.002 0.11 -10000 0 -0.59 10 10
MAP3K1 -0.01 0.061 0.19 4 -0.18 35 39
EIF2A -0.012 0.072 0.21 15 -0.18 26 41
TRADD 0.021 0.004 -10000 0 -10000 0 0
CRADD 0.022 0.017 0.33 1 -10000 0 1
MAPK3 -0.013 0.062 0.21 7 -0.17 16 23
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.016 0.064 0.21 7 -0.18 16 23
Cathepsin D/ceramide 0.005 0.064 -10000 0 -0.18 36 36
FADD -0.004 0.05 -10000 0 -0.27 4 4
KSR1 -0.008 0.068 0.24 7 -0.18 36 43
MAPK8 -0.009 0.064 -10000 0 -0.27 3 3
PRKRA -0.01 0.065 0.23 5 -0.18 36 41
PDGFA 0.011 0.053 -10000 0 -0.34 8 8
TRAF2 0.021 0.004 -10000 0 -10000 0 0
IGF1 0.018 0.042 0.33 1 -0.34 4 5
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.007 0.062 0.13 4 -0.18 36 40
CTSD 0.021 0.004 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.031 0.007 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.005 0.071 0.23 5 -0.24 2 7
PRKCD 0.021 0.004 -10000 0 -10000 0 0
PRKCZ 0.019 0.027 -10000 0 -0.34 2 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.018 0.032 -10000 0 -0.24 7 7
RelA/NF kappa B1 0.031 0.007 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.021 0.004 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.002 0.049 0.16 2 -0.28 3 5
TNFR1A/BAG4/TNF-alpha 0.027 0.049 0.23 1 -0.2 13 14
mol:Sphingosine-1-phosphate -0.021 0.036 -10000 0 -0.24 9 9
MAP2K1 -0.016 0.063 0.19 10 -0.18 23 33
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
CYCS 0.006 0.053 0.18 3 -0.18 8 11
TNFRSF1A 0.02 0.006 -10000 0 -10000 0 0
NFKB1 0.022 0.003 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.013 -10000 0 -10000 0 0
EIF2AK2 -0.012 0.063 0.2 8 -0.17 33 41
TNF-alpha/TNFR1A/FAN 0.027 0.05 0.23 1 -0.2 13 14
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.052 -10000 0 -0.32 4 4
MAP2K2 -0.017 0.061 0.21 7 -0.18 23 30
SMPD3 0.006 0.059 0.18 4 -0.26 6 10
TNF 0.007 0.072 0.33 1 -0.34 14 15
PKC zeta/PAR4 0.029 0.022 -10000 0 -0.24 2 2
mol:PHOSPHOCHOLINE -0.018 0.065 0.19 6 -0.18 14 20
NF kappa B1/RelA/I kappa B alpha 0.049 0.031 -10000 0 -0.18 1 1
AIFM1 -0.001 0.061 0.17 4 -0.18 11 15
BCL2 0.02 0.018 0.33 1 -10000 0 1
S1P5 pathway

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.016 0.084 0.27 14 -10000 0 14
GNAI2 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.012 0.055 0.21 1 -0.2 21 22
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.02 0.032 0.33 1 -0.34 2 3
RhoA/GTP -0.017 0.086 -10000 0 -0.27 14 14
negative regulation of cAMP metabolic process -0.019 0.082 -10000 0 -0.2 51 51
GNAZ -0.007 0.097 -10000 0 -0.34 28 28
GNAI3 0.021 0.005 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
S1PR5 -0.001 0.088 0.33 1 -0.34 22 23
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.02 0.082 -10000 0 -0.2 51 51
RhoA/GDP 0.016 0.003 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.02 -10000 0 -0.34 1 1
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.016 0.095 0.42 2 -0.38 14 16
CRKL -0.02 0.089 0.48 1 -0.4 15 16
HRAS -0.008 0.083 -10000 0 -0.38 10 10
mol:PIP3 0.003 0.11 0.37 2 -0.4 16 18
SPRED1 0.021 0.005 -10000 0 -10000 0 0
SPRED2 0.022 0.001 -10000 0 -10000 0 0
GAB1 -0.015 0.096 0.32 1 -0.41 17 18
FOXO3 -0.005 0.11 0.33 1 -0.4 19 20
AKT1 -0.001 0.12 -10000 0 -0.42 19 19
BAD -0.003 0.11 -10000 0 -0.4 19 19
megakaryocyte differentiation -0.029 0.1 -10000 0 -0.4 20 20
GSK3B -0.003 0.11 0.25 1 -0.4 19 20
RAF1 -0.008 0.079 0.22 4 -0.31 10 14
SHC1 0.018 0.008 -10000 0 -10000 0 0
STAT3 -0.017 0.098 0.32 1 -0.41 18 19
STAT1 -0.045 0.21 0.44 1 -0.94 17 18
HRAS/SPRED1 0.005 0.079 -10000 0 -0.31 10 10
cell proliferation -0.017 0.094 -10000 0 -0.4 17 17
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
TEC 0.021 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.003 0.11 0.24 1 -0.43 18 19
HRAS/SPRED2 0.005 0.079 -10000 0 -0.31 10 10
LYN/TEC/p62DOK 0.017 0.1 0.31 1 -0.4 15 16
MAPK3 -0.002 0.07 0.25 3 -0.24 6 9
STAP1 -0.019 0.098 0.32 1 -0.4 18 19
GRAP2 0.012 0.057 -10000 0 -0.34 9 9
JAK2 -0.04 0.19 0.42 1 -0.81 17 18
STAT1 (dimer) -0.043 0.21 0.44 1 -0.92 17 18
mol:Gleevec 0 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.017 0.099 -10000 0 -0.4 13 13
actin filament polymerization -0.015 0.088 0.32 1 -0.38 15 16
LYN 0.02 0.007 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.034 0.14 0.35 1 -0.55 19 20
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.006 0.088 0.41 2 -0.37 11 13
PI3K 0.015 0.11 -10000 0 -0.43 15 15
PTEN 0.021 0.004 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.029 0.24 -10000 0 -1.1 17 17
MAPK8 -0.017 0.096 -10000 0 -0.41 17 17
STAT3 (dimer) -0.016 0.097 0.32 1 -0.4 18 19
positive regulation of transcription 0 0.062 0.2 6 -0.2 4 10
mol:GDP -0.003 0.085 -10000 0 -0.4 10 10
PIK3C2B -0.016 0.1 0.44 2 -0.41 16 18
CBL/CRKL -0.004 0.093 0.42 2 -0.39 13 15
FER -0.017 0.096 0.32 1 -0.41 17 18
SH2B3 -0.017 0.097 0.32 1 -0.42 17 18
PDPK1 0.002 0.11 0.33 5 -0.38 15 20
SNAI2 -0.015 0.095 0.32 1 -0.41 16 17
positive regulation of cell proliferation -0.036 0.17 0.4 1 -0.69 18 19
KITLG 0.013 0.044 -10000 0 -0.36 4 4
cell motility -0.036 0.17 0.4 1 -0.69 18 19
PTPN6 0.019 0.012 -10000 0 -10000 0 0
EPOR -0.026 0.17 -10000 0 -0.62 20 20
STAT5A (dimer) -0.027 0.14 0.38 1 -0.56 19 20
SOCS1 0.021 0.004 -10000 0 -10000 0 0
cell migration 0.023 0.098 0.41 18 -10000 0 18
SOS1 0.022 0.003 -10000 0 -10000 0 0
EPO 0.019 0.026 0.32 2 -10000 0 2
VAV1 0.017 0.033 -10000 0 -0.34 3 3
GRB10 -0.016 0.094 0.33 1 -0.42 15 16
PTPN11 0.019 0.011 -10000 0 -10000 0 0
SCF/KIT -0.012 0.1 0.35 1 -0.43 18 19
GO:0007205 0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.006 0.069 0.2 5 -0.25 8 13
CBL 0.021 0.005 -10000 0 -10000 0 0
KIT -0.038 0.26 0.47 1 -1 21 22
MAP2K2 -0.005 0.067 0.2 5 -0.25 9 14
SHC/Grb2/SOS1 0.013 0.094 -10000 0 -0.41 11 11
STAT5A -0.026 0.15 0.38 1 -0.58 19 20
GRB2 0.021 0.005 -10000 0 -10000 0 0
response to radiation -0.014 0.094 0.28 2 -0.4 16 18
SHC/GRAP2 0.023 0.034 -10000 0 -0.24 5 5
PTPRO -0.028 0.1 -10000 0 -0.42 19 19
SH2B2 -0.015 0.09 0.32 1 -0.39 15 16
DOK1 0.022 0.003 -10000 0 -10000 0 0
MATK -0.023 0.1 -10000 0 -0.42 18 18
CREBBP 0.02 0.035 0.29 1 -10000 0 1
BCL2 -0.048 0.2 0.47 1 -0.7 19 20
Coregulation of Androgen receptor activity

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
NRIP1 0.021 0.006 -10000 0 -10000 0 0
SVIL 0.022 0.004 -10000 0 -10000 0 0
ZNF318 0.02 0.01 -10000 0 -10000 0 0
JMJD2C 0.006 0.027 0.13 16 -10000 0 16
T-DHT/AR/Ubc9 0.007 0.087 0.18 4 -0.21 40 44
CARM1 0.02 0.006 -10000 0 -10000 0 0
PRDX1 0.021 0.005 -10000 0 -10000 0 0
PELP1 0.019 0.008 -10000 0 -10000 0 0
CTNNB1 0.022 0.004 -10000 0 -10000 0 0
AKT1 0.02 0.008 -10000 0 -10000 0 0
PTK2B 0.018 0.008 -10000 0 -10000 0 0
MED1 0.02 0.007 -10000 0 -10000 0 0
MAK 0.011 0.062 0.33 1 -0.34 10 11
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.018 0.033 -10000 0 -0.34 3 3
GSN 0.022 0.005 -10000 0 -10000 0 0
NCOA2 0.017 0.028 -10000 0 -0.34 2 2
NCOA6 0.021 0.006 -10000 0 -10000 0 0
DNA-PK 0.037 0.019 -10000 0 -10000 0 0
NCOA4 0.022 0.003 -10000 0 -10000 0 0
PIAS3 0.021 0.005 -10000 0 -10000 0 0
cell proliferation -0.008 0.11 0.26 1 -0.61 10 11
XRCC5 0.021 0.006 -10000 0 -10000 0 0
UBE3A 0.021 0.006 -10000 0 -10000 0 0
T-DHT/AR/SNURF 0.002 0.092 0.18 4 -0.21 47 51
FHL2 0.047 0.11 0.32 41 -10000 0 41
RANBP9 0.021 0.005 -10000 0 -10000 0 0
JMJD1A -0.01 0.038 -10000 0 -0.13 32 32
CDK6 0.02 0.02 -10000 0 -0.34 1 1
TGFB1I1 0.02 0.027 -10000 0 -0.34 2 2
T-DHT/AR/CyclinD1 0.008 0.085 0.18 4 -0.21 37 41
XRCC6 0.021 0.007 -10000 0 -10000 0 0
T-DHT/AR 0.02 0.11 0.26 7 -0.22 44 51
CTDSP1 0.022 0.002 -10000 0 -10000 0 0
CTDSP2 0.02 0.009 -10000 0 -10000 0 0
BRCA1 0.022 0.004 -10000 0 -10000 0 0
TCF4 0.016 0.028 -10000 0 -0.34 2 2
CDKN2A 0.096 0.14 0.33 92 -10000 0 92
SRF 0.041 0.048 0.17 1 -10000 0 1
NKX3-1 -0.028 0.12 -10000 0 -0.42 22 22
KLK3 -0.011 0.061 -10000 0 -10000 0 0
TMF1 0.021 0.004 -10000 0 -10000 0 0
HNRNPA1 0.021 0.007 -10000 0 -10000 0 0
AOF2 0 0.002 -10000 0 -10000 0 0
APPL1 -0.017 0.006 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 0.008 0.086 0.18 3 -0.21 39 42
AR -0.017 0.12 0.33 1 -0.35 39 40
UBA3 0.021 0.004 -10000 0 -10000 0 0
PATZ1 0.02 0.008 -10000 0 -10000 0 0
PAWR 0.021 0.004 -10000 0 -10000 0 0
PRKDC 0.019 0.009 -10000 0 -10000 0 0
PA2G4 0.02 0.008 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.008 0.078 0.17 3 -0.19 39 42
RPS6KA3 0.021 0.005 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.009 0.087 0.18 4 -0.21 39 43
LATS2 0.02 0.008 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.009 0.078 0.17 3 -0.19 39 42
Cyclin D3/CDK11 p58 0.015 0.005 -10000 0 -10000 0 0
VAV3 0.02 0.032 0.33 1 -0.34 2 3
KLK2 0.007 0.079 0.31 13 -0.35 3 16
CASP8 0.021 0.006 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.018 0.08 0.2 2 -0.19 34 36
TMPRSS2 -0.063 0.23 -10000 0 -0.77 32 32
CCND1 0.018 0.033 -10000 0 -0.34 3 3
PIAS1 0.022 0.005 -10000 0 -10000 0 0
mol:T-DHT 0.002 0.019 0.056 5 -0.057 16 21
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.021 0.008 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.008 0.085 0.18 3 -0.21 38 41
CMTM2 -0.045 0.14 -10000 0 -0.34 64 64
SNURF 0.012 0.053 -10000 0 -0.34 8 8
ZMIZ1 0.02 0.028 -10000 0 -10000 0 0
CCND3 0.021 0.005 -10000 0 -10000 0 0
TGIF1 0.019 0.009 -10000 0 -10000 0 0
FKBP4 0.021 0.006 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.03 0.023 0.24 2 -0.24 1 3
ATM 0.021 0.005 -10000 0 -10000 0 0
UBE2D3 0.022 0.003 -10000 0 -10000 0 0
PRKDC 0.02 0.007 -10000 0 -10000 0 0
ATR 0.021 0.003 -10000 0 -10000 0 0
UBE2L3 0.021 0.004 -10000 0 -10000 0 0
FANCD2 0.011 0.011 0.15 2 -10000 0 2
protein ubiquitination 0.1 0.079 0.21 98 -10000 0 98
XRCC5 0.022 0.003 -10000 0 -10000 0 0
XRCC6 0.021 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.036 0.018 -10000 0 -10000 0 0
MRE11A 0.021 0.005 -10000 0 -10000 0 0
DNA-PK 0.038 0.016 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.001 0.094 -10000 0 -0.54 8 8
FANCF 0.021 0.004 -10000 0 -10000 0 0
BRCA1 0.021 0.003 -10000 0 -10000 0 0
CCNE1 0.12 0.14 0.33 110 -10000 0 110
CDK2/Cyclin E1 0.091 0.097 0.24 105 -10000 0 105
FANCG 0.021 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.032 0.022 0.24 2 -0.24 1 3
FANCE 0.021 0.005 -10000 0 -10000 0 0
FANCC 0.021 0.005 -10000 0 -10000 0 0
NBN 0.019 0.007 -10000 0 -10000 0 0
FANCA 0.029 0.049 0.33 9 -10000 0 9
DNA repair 0.004 0.071 0.21 5 -0.36 5 10
BRCA1/BARD1/ubiquitin 0.032 0.022 0.24 2 -0.24 1 3
BARD1/DNA-PK 0.048 0.025 0.23 1 -0.17 1 2
FANCL 0.022 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.03 0.023 0.24 1 -0.24 2 3
BRCA1/BARD1/CTIP/M/R/N Complex 0.012 0.042 -10000 0 -0.22 5 5
BRCA1/BACH1/BARD1/TopBP1 0.043 0.022 0.23 2 -0.2 1 3
BRCA1/BARD1/P53 0.049 0.025 0.23 1 -0.19 1 2
BARD1/CSTF1/BRCA1 0.041 0.023 0.23 2 -0.2 1 3
BRCA1/BACH1 0.021 0.003 -10000 0 -10000 0 0
BARD1 0.022 0.03 0.33 2 -0.34 1 3
PCNA 0.021 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.042 0.019 0.23 1 -0.2 1 2
BRCA1/BARD1/UbcH7 0.041 0.02 0.23 1 -0.2 1 2
BRCA1/BARD1/RAD51/PCNA 0.082 0.076 0.24 63 -0.15 1 64
BARD1/DNA-PK/P53 0.05 0.031 -10000 0 -0.16 1 1
BRCA1/BARD1/Ubiquitin 0.032 0.022 0.24 2 -0.24 1 3
BRCA1/BARD1/CTIP 0.028 0.019 0.22 1 -0.17 1 2
FA complex 0.008 0.045 -10000 0 -0.28 4 4
BARD1/EWS 0.031 0.022 0.24 2 -0.24 1 3
RBBP8 -0.016 0.006 -10000 0 -10000 0 0
TP53 0.02 0.006 -10000 0 -10000 0 0
TOPBP1 0.021 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.047 0.024 0.19 1 -0.22 1 2
BRCA1/BARD1 0.11 0.085 0.23 98 -10000 0 98
CSTF1 0.02 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.017 0.02 0.22 2 -0.23 1 3
CDK2 0.021 0.004 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.08 0.12 0.33 68 -10000 0 68
RAD50 0.021 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.032 0.022 0.24 2 -0.24 1 3
EWSR1 0.021 0.004 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.022 0.039 -10000 0 -0.24 6 6
PDGFRB 0.015 0.016 -10000 0 -10000 0 0
SPHK1 -0.001 0.064 -10000 0 -0.62 3 3
mol:S1P -0.007 0.06 -10000 0 -0.53 3 3
S1P1/S1P/Gi -0.035 0.13 0.21 6 -0.38 34 40
GNAO1 0.016 0.035 0.33 1 -0.34 2 3
PDGFB-D/PDGFRB/PLCgamma1 -0.03 0.13 0.25 4 -0.36 32 36
PLCG1 -0.042 0.12 0.2 8 -0.37 32 40
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.015 0.016 -10000 0 -10000 0 0
GNAI2 0.017 0.015 -10000 0 -10000 0 0
GNAI3 0.018 0.014 -10000 0 -10000 0 0
GNAI1 0.016 0.024 -10000 0 -0.34 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.018 0.026 -10000 0 -0.2 6 6
S1P1/S1P -0.021 0.061 0.21 1 -0.33 5 6
negative regulation of cAMP metabolic process -0.034 0.13 0.2 6 -0.37 34 40
MAPK3 -0.056 0.17 0.26 8 -0.55 32 40
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.003 -10000 0 -10000 0 0
KDR 0.012 0.048 -10000 0 -0.34 6 6
PLCB2 -0.015 0.072 0.27 4 -0.31 6 10
RAC1 0.019 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.025 0.048 -10000 0 -0.29 5 5
receptor internalization -0.021 0.056 -10000 0 -0.31 5 5
PTGS2 -0.081 0.28 0.33 4 -0.91 32 36
Rac1/GTP -0.024 0.048 -10000 0 -0.29 5 5
RHOA 0.021 0.004 -10000 0 -10000 0 0
VEGFA 0.017 0.014 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.034 0.13 0.2 6 -0.37 34 40
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.011 0.098 -10000 0 -0.34 28 28
MAPK1 -0.055 0.17 0.24 6 -0.55 31 37
S1P1/S1P/PDGFB-D/PDGFRB -0.023 0.069 0.24 3 -0.3 5 8
ABCC1 0.017 0.014 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.038 0.1 0.26 23 -0.34 9 32
FYN 0.005 0.12 0.27 7 -0.38 15 22
LAT/GRAP2/SLP76 0.017 0.11 0.28 4 -0.37 14 18
IKBKB 0.019 0.008 -10000 0 -10000 0 0
AKT1 -0.001 0.097 0.28 6 -0.33 14 20
B2M 0.019 0.012 -10000 0 -10000 0 0
IKBKG 0 0.034 0.11 9 -0.1 4 13
MAP3K8 0.02 0.019 -10000 0 -0.34 1 1
mol:Ca2+ -0.017 0.015 0.084 2 -0.06 10 12
integrin-mediated signaling pathway 0.024 0.02 -10000 0 -0.2 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.004 0.12 0.26 4 -0.42 17 21
TRPV6 0 0.26 1.1 14 -10000 0 14
CD28 0.02 0.008 -10000 0 -10000 0 0
SHC1 0.023 0.12 0.26 33 -0.42 10 43
receptor internalization -0.005 0.12 0.2 1 -0.43 17 18
PRF1 -0.028 0.22 -10000 0 -0.89 19 19
KRAS 0.02 0.006 -10000 0 -10000 0 0
GRB2 0.021 0.005 -10000 0 -10000 0 0
COT/AKT1 0.01 0.084 0.27 5 -0.28 12 17
LAT 0.002 0.12 0.28 8 -0.39 16 24
EntrezGene:6955 -0.001 0.005 -10000 0 -10000 0 0
CD3D 0.018 0.03 -10000 0 -0.35 2 2
CD3E 0.018 0.03 -10000 0 -0.35 2 2
CD3G 0.014 0.044 -10000 0 -0.34 5 5
RASGRP2 -0.009 0.042 -10000 0 -0.15 25 25
RASGRP1 -0.01 0.1 0.27 4 -0.36 13 17
HLA-A 0.02 0.012 -10000 0 -10000 0 0
RASSF5 0.018 0.028 -10000 0 -0.34 2 2
RAP1A/GTP/RAPL 0.024 0.02 -10000 0 -0.2 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.053 0.15 17 -0.13 6 23
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.013 0.033 -10000 0 -0.15 7 7
PRKCA -0.007 0.053 0.16 4 -0.2 7 11
GRAP2 0.012 0.057 -10000 0 -0.34 9 9
mol:IP3 0.017 0.088 0.18 30 -0.29 13 43
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.008 0.08 -10000 0 -0.38 10 10
ORAI1 -0.021 0.21 0.4 1 -0.97 14 15
CSK 0.002 0.11 0.27 3 -0.39 15 18
B7 family/CD28 0.021 0.12 -10000 0 -0.42 14 14
CHUK 0.022 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.002 0.12 -10000 0 -0.42 17 17
PTPN6 -0.004 0.1 0.22 4 -0.39 13 17
VAV1 -0.003 0.11 0.23 2 -0.4 16 18
Monovalent TCR/CD3 0.003 0.046 -10000 0 -0.3 6 6
CBL 0.021 0.005 -10000 0 -10000 0 0
LCK 0.006 0.11 0.28 4 -0.4 12 16
PAG1 0.008 0.11 0.24 9 -0.38 15 24
RAP1A 0.021 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.002 0.11 -10000 0 -0.42 15 15
CD80 0.013 0.051 -10000 0 -0.34 7 7
CD86 0.014 0.047 -10000 0 -0.34 6 6
PDK1/CARD11/BCL10/MALT1 0.004 0.048 0.19 1 -0.19 7 8
HRAS 0.021 0.004 -10000 0 -10000 0 0
GO:0035030 -0.013 0.095 0.19 5 -0.32 19 24
CD8A 0.018 0.039 0.33 1 -0.35 3 4
CD8B 0.019 0.05 0.33 3 -0.35 4 7
PTPRC 0.015 0.043 -10000 0 -0.34 5 5
PDK1/PKC theta -0.01 0.12 0.32 7 -0.36 19 26
CSK/PAG1 0.006 0.11 0.24 13 -0.38 14 27
SOS1 0.022 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.028 0.017 -10000 0 -10000 0 0
GRAP2/SLP76 0.02 0.12 -10000 0 -0.41 15 15
STIM1 -0.001 0.078 1.2 1 -10000 0 1
RAS family/GTP 0.012 0.062 0.18 9 -0.17 10 19
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.006 0.12 -10000 0 -0.46 17 17
mol:DAG -0.019 0.064 0.1 1 -0.24 17 18
RAP1A/GDP 0.009 0.024 0.08 9 -0.063 4 13
PLCG1 0.021 0.005 -10000 0 -10000 0 0
CD247 0.018 0.022 -10000 0 -0.34 1 1
cytotoxic T cell degranulation -0.025 0.21 -10000 0 -0.82 20 20
RAP1A/GTP -0.005 0.016 -10000 0 -0.06 24 24
mol:PI-3-4-5-P3 -0.001 0.11 0.24 5 -0.37 15 20
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.022 0.11 0.23 11 -0.36 13 24
NRAS 0.021 0.005 -10000 0 -10000 0 0
ZAP70 0.016 0.047 -10000 0 -0.34 6 6
GRB2/SOS1 0.031 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.008 0.1 0.28 3 -0.36 14 17
MALT1 0.019 0.007 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.029 0.054 0.31 3 -0.33 5 8
CARD11 0.033 0.063 0.33 15 -10000 0 15
PRKCB -0.011 0.059 0.15 2 -0.23 11 13
PRKCE -0.009 0.057 0.16 4 -0.24 6 10
PRKCQ -0.012 0.12 0.27 3 -0.39 21 24
LCP2 0.019 0.027 -10000 0 -0.34 2 2
BCL10 0.021 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0.001 0.087 0.25 8 -0.29 12 20
IKK complex 0.008 0.054 0.21 11 -0.11 3 14
RAS family/GDP -0.004 0.008 -10000 0 -10000 0 0
MAP3K14 -0.003 0.064 0.22 6 -0.21 10 16
PDPK1 0 0.096 0.28 8 -0.32 13 21
TCR/CD3/MHC I/CD8/Fyn -0.011 0.12 -10000 0 -0.5 13 13
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.032 0.12 0.27 15 -0.44 7 22
IKBKB 0.025 0.094 0.26 6 -0.28 11 17
AKT1 0.033 0.081 0.24 24 -0.23 1 25
IKBKG 0.031 0.069 0.25 4 -0.26 5 9
CALM1 0.019 0.089 0.26 5 -0.43 6 11
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
MAP3K1 0.039 0.13 0.28 18 -0.44 7 25
MAP3K7 0.02 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.019 0.096 0.22 1 -0.48 6 7
DOK1 0.022 0.003 -10000 0 -10000 0 0
AP-1 0.018 0.079 0.22 9 -0.25 7 16
LYN 0.019 0.007 -10000 0 -10000 0 0
BLNK 0.02 0.019 -10000 0 -0.34 1 1
SHC1 0.018 0.008 -10000 0 -10000 0 0
BCR complex 0.07 0.098 0.26 67 -0.33 2 69
CD22 0.011 0.07 0.24 9 -0.47 2 11
CAMK2G 0.014 0.085 0.26 4 -0.41 6 10
CSNK2A1 0.021 0.005 -10000 0 -10000 0 0
INPP5D 0.02 0.027 -10000 0 -0.34 2 2
SHC/GRB2/SOS1 -0.006 0.049 0.16 5 -10000 0 5
GO:0007205 0.019 0.098 0.22 1 -0.5 6 7
SYK 0.019 0.027 -10000 0 -0.34 2 2
ELK1 0.014 0.093 0.25 1 -0.47 6 7
NFATC1 0.034 0.098 0.25 18 -0.36 6 24
B-cell antigen/BCR complex 0.07 0.098 0.26 67 -0.33 2 69
PAG1/CSK 0.028 0.012 -10000 0 -10000 0 0
NFKBIB 0.023 0.042 0.14 5 -0.13 6 11
HRAS 0.023 0.084 0.25 9 -0.4 4 13
NFKBIA 0.023 0.041 0.14 5 -0.12 6 11
NF-kappa-B/RelA/I kappa B beta 0.025 0.038 0.14 6 -10000 0 6
RasGAP/Csk 0.079 0.083 0.24 62 -0.16 2 64
mol:GDP 0.019 0.097 0.22 1 -0.45 7 8
PTEN 0.021 0.004 -10000 0 -10000 0 0
CD79B 0.025 0.045 0.33 6 -0.34 1 7
NF-kappa-B/RelA/I kappa B alpha 0.025 0.037 0.14 6 -10000 0 6
GRB2 0.021 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.048 0.12 0.31 10 -0.46 7 17
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
mol:IP3 0.02 0.096 0.23 1 -0.55 5 6
CSK 0.021 0.004 -10000 0 -10000 0 0
FOS 0.003 0.098 0.26 5 -0.39 9 14
CHUK 0.027 0.075 0.25 4 -0.25 9 13
IBTK 0.02 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.033 0.082 -10000 0 -0.36 5 5
PTPN6 0.006 0.068 0.22 9 -0.42 3 12
RELA 0.021 0.004 -10000 0 -10000 0 0
BCL2A1 0.016 0.029 0.12 1 -10000 0 1
VAV2 0.047 0.093 0.26 14 -0.41 4 18
ubiquitin-dependent protein catabolic process 0.024 0.041 0.14 6 -0.12 7 13
BTK -0.045 0.25 -10000 0 -0.96 25 25
CD19 0.046 0.09 0.26 19 -0.4 2 21
MAP4K1 0.016 0.038 -10000 0 -0.34 4 4
CD72 0.021 0.017 0.33 1 -10000 0 1
PAG1 0.019 0.007 -10000 0 -10000 0 0
MAPK14 0.041 0.12 0.28 25 -0.4 6 31
SH3BP5 0.019 0.027 -10000 0 -0.34 2 2
PIK3AP1 0.02 0.094 0.24 1 -0.55 5 6
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.013 0.14 -10000 0 -0.58 11 11
RAF1 0.017 0.08 0.25 7 -0.38 4 11
RasGAP/p62DOK/SHIP 0.075 0.077 0.36 5 -0.17 2 7
CD79A 0.077 0.12 0.33 66 -0.34 2 68
re-entry into mitotic cell cycle 0.017 0.079 0.22 9 -0.24 8 17
RASA1 0.021 0.005 -10000 0 -10000 0 0
MAPK3 0.011 0.076 0.23 8 -0.33 4 12
MAPK1 0.013 0.07 0.24 6 -0.33 3 9
CD72/SHP1 0.024 0.092 0.25 19 -0.36 4 23
NFKB1 0.022 0.003 -10000 0 -10000 0 0
MAPK8 0.035 0.12 0.28 14 -0.4 6 20
actin cytoskeleton organization 0.059 0.1 0.28 28 -0.43 2 30
NF-kappa-B/RelA 0.05 0.073 0.25 6 -0.21 3 9
Calcineurin 0.033 0.082 0.32 1 -0.42 4 5
PI3K 0.002 0.067 0.19 5 -0.28 5 10
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.02 0.089 0.26 1 -0.52 5 6
SOS1 0.022 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.037 0.12 -10000 0 -0.58 9 9
DAPP1 0.023 0.13 -10000 0 -0.64 9 9
cytokine secretion 0.034 0.095 0.25 18 -0.33 6 24
mol:DAG 0.02 0.096 0.23 1 -0.55 5 6
PLCG2 0.018 0.033 -10000 0 -0.34 3 3
MAP2K1 0.013 0.077 0.25 6 -0.35 4 10
B-cell antigen/BCR complex/FcgammaRIIB 0.071 0.088 0.24 64 -0.18 2 66
mol:PI-3-4-5-P3 0.015 0.071 0.22 10 -0.26 2 12
ETS1 0.013 0.079 0.24 7 -0.38 4 11
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.081 0.086 0.4 5 -0.26 2 7
B-cell antigen/BCR complex/LYN 0.03 0.067 0.29 5 -0.4 3 8
MALT1 0.019 0.007 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.059 0.1 0.28 27 -0.46 2 29
B-cell antigen/BCR complex/LYN/SYK 0.056 0.1 0.37 9 -0.32 4 13
CARD11 0.034 0.1 0.29 9 -0.44 6 15
FCGR2B 0.019 0.008 -10000 0 -10000 0 0
PPP3CA 0.022 0.003 -10000 0 -10000 0 0
BCL10 0.021 0.004 -10000 0 -10000 0 0
IKK complex 0.023 0.049 0.14 22 -0.12 2 24
PTPRC 0.015 0.043 -10000 0 -0.34 5 5
PDPK1 0.02 0.073 0.22 23 -0.21 1 24
PPP3CB 0.022 0.003 -10000 0 -10000 0 0
PPP3CC 0.018 0.008 -10000 0 -10000 0 0
POU2F2 0.019 0.028 0.12 5 -10000 0 5
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.025 0.052 0.24 5 -0.24 10 15
CRKL -0.001 0.092 0.29 4 -0.4 8 12
mol:PIP3 0.01 0.009 -10000 0 -10000 0 0
AKT1 0.005 0.042 -10000 0 -10000 0 0
PTK2B 0.018 0.008 -10000 0 -10000 0 0
RAPGEF1 -0.005 0.086 0.27 4 -0.37 8 12
RANBP10 0.021 0.004 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.03 0.065 0.23 8 -0.2 20 28
MAP3K5 -0.004 0.095 0.27 5 -0.38 9 14
HGF/MET/CIN85/CBL/ENDOPHILINS 0.037 0.068 0.23 7 -0.2 21 28
AP1 -0.024 0.064 -10000 0 -0.21 23 23
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
apoptosis -0.069 0.25 -10000 0 -0.71 45 45
STAT3 (dimer) -0.012 0.078 0.23 1 -0.33 8 9
GAB1/CRKL/SHP2/PI3K 0.021 0.091 0.29 1 -0.38 8 9
INPP5D 0.02 0.027 -10000 0 -0.34 2 2
CBL/CRK 0.008 0.09 0.35 2 -0.36 8 10
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.021 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.004 -10000 0 -10000 0 0
ELK1 0.007 0.097 0.31 24 -10000 0 24
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.003 0.048 0.14 1 -0.25 6 7
PAK1 0.008 0.059 0.39 2 -10000 0 2
HGF/MET/RANBP10 0.029 0.069 0.23 8 -0.21 21 29
HRAS -0.008 0.12 0.29 1 -0.49 16 17
DOCK1 -0.006 0.089 0.27 5 -0.39 8 13
GAB1 0 0.087 0.23 3 -0.39 8 11
CRK -0.003 0.092 0.37 2 -0.4 8 10
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.01 0.12 -10000 0 -0.42 26 26
JUN 0.019 0.027 -10000 0 -0.34 2 2
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.002 0.053 0.15 4 -0.19 21 25
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
cell morphogenesis -0.013 0.099 0.34 8 -0.36 6 14
GRB2/SHC 0.019 0.055 0.21 1 -0.21 10 11
FOS -0.005 0.092 -10000 0 -0.34 25 25
GLMN 0.002 0.001 -10000 0 -10000 0 0
cell motility 0.007 0.096 0.31 24 -10000 0 24
HGF/MET/MUC20 0.016 0.066 0.21 8 -0.2 23 31
cell migration 0.019 0.054 0.21 1 -0.2 10 11
GRB2 0.021 0.005 -10000 0 -10000 0 0
CBL 0.021 0.005 -10000 0 -10000 0 0
MET/RANBP10 0.024 0.052 0.24 5 -0.24 10 15
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.009 0.067 0.18 1 -0.31 6 7
MET/MUC20 0.01 0.05 0.22 5 -0.23 11 16
RAP1B 0.001 0.09 0.27 7 -0.35 8 15
RAP1A -0.009 0.082 0.25 5 -0.35 8 13
HGF/MET/RANBP9 0.029 0.069 0.23 8 -0.21 21 29
RAF1 -0.007 0.11 0.27 1 -0.46 16 17
STAT3 -0.012 0.079 0.23 1 -0.33 8 9
cell proliferation 0.001 0.11 0.29 14 -0.33 15 29
RPS6KB1 0.005 0.029 -10000 0 -0.2 2 2
MAPK3 -0.003 0.083 0.51 2 -10000 0 2
MAPK1 0.015 0.14 0.64 11 -10000 0 11
RANBP9 0.021 0.004 -10000 0 -10000 0 0
MAPK8 -0.001 0.09 0.26 4 -0.35 8 12
SRC -0.022 0.058 0.16 1 -0.3 5 6
PI3K 0.02 0.06 0.21 1 -0.2 15 16
MET/Glomulin 0.01 0.051 0.24 5 -0.2 11 16
SOS1 0.022 0.003 -10000 0 -10000 0 0
MAP2K1 -0.01 0.11 0.26 1 -0.44 16 17
MET 0.014 0.073 0.33 5 -0.34 11 16
MAP4K1 -0.001 0.1 0.28 5 -0.41 9 14
PTK2 0.019 0.008 -10000 0 -10000 0 0
MAP2K2 -0.01 0.11 0.26 1 -0.43 16 17
BAD 0.001 0.044 0.4 1 -10000 0 1
MAP2K4 -0.007 0.087 0.25 5 -0.35 9 14
SHP2/GRB2/SOS1/GAB1 0.011 0.086 -10000 0 -0.34 12 12
INPPL1 0.021 0.004 -10000 0 -10000 0 0
PXN 0.021 0.004 -10000 0 -10000 0 0
SH3KBP1 0.021 0.005 -10000 0 -10000 0 0
HGS -0.011 0.046 0.14 4 -0.18 19 23
PLCgamma1/PKC 0.015 0.004 -10000 0 -10000 0 0
HGF 0.009 0.076 0.33 3 -0.34 14 17
RASA1 0.021 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
PTPRJ 0.022 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.02 0.061 0.21 1 -0.19 21 22
PDPK1 0.006 0.03 -10000 0 -10000 0 0
HGF/MET/SHIP 0.027 0.075 0.23 7 -0.22 23 30
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.021 0.004 -10000 0 -10000 0 0
HDAC4 0.021 0.004 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.003 0.052 -10000 0 -0.17 27 27
CDKN1A -0.012 0.005 -10000 0 -10000 0 0
KAT2B 0.021 0.004 -10000 0 -10000 0 0
BAX 0.021 0.005 -10000 0 -10000 0 0
FOXO3 -0.002 0.002 -10000 0 -10000 0 0
FOXO1 0.021 0.005 -10000 0 -10000 0 0
FOXO4 0.006 0.002 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.021 0.004 -10000 0 -10000 0 0
TAT 0.044 0.081 0.33 26 -10000 0 26
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.018 0.014 0.16 2 -10000 0 2
PPARGC1A -0.06 0.15 0.33 1 -0.34 81 82
FHL2 0.068 0.11 0.33 53 -10000 0 53
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.031 0.014 0.25 1 -10000 0 1
HIST2H4A -0.003 0.052 0.17 27 -10000 0 27
SIRT1/FOXO3a 0.014 0.026 0.24 1 -0.2 1 2
SIRT1 0.021 0.018 0.35 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.036 0.021 0.24 1 -10000 0 1
SIRT1/Histone H1b 0.025 0.042 0.32 1 -0.22 3 4
apoptosis -0.04 0.016 -10000 0 -0.24 1 1
SIRT1/PGC1A -0.022 0.096 0.22 2 -0.2 79 81
p53/SIRT1 0.029 0.03 0.56 1 -10000 0 1
SIRT1/FOXO4 0.017 0.033 0.24 1 -0.22 3 4
FOXO1/FHL2/SIRT1 0.063 0.064 0.22 51 -10000 0 51
HIST1H1E 0.015 0.031 0.24 1 -10000 0 1
SIRT1/p300 0.031 0.014 0.25 1 -10000 0 1
muscle cell differentiation -0.025 0.021 -10000 0 -0.21 4 4
TP53 0.02 0.019 0.35 1 -10000 0 1
KU70/SIRT1/BAX 0.041 0.016 0.24 1 -10000 0 1
CREBBP 0.021 0.004 -10000 0 -10000 0 0
MEF2D 0.018 0.008 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.044 0.054 0.24 25 -10000 0 25
ACSS2 -0.017 0.02 0.27 1 -0.24 1 2
SIRT1/PCAF/MYOD 0.026 0.021 0.22 4 -10000 0 4
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.006 0.031 -10000 0 -0.18 7 7
epithelial cell differentiation 0.041 0.022 -10000 0 -0.18 2 2
CYFIP2 0.016 0.043 -10000 0 -0.34 5 5
ENAH -0.018 0.061 0.4 2 -0.24 1 3
EGFR 0.017 0.037 0.33 1 -0.34 3 4
EPHA2 0.016 0.043 -10000 0 -0.34 5 5
MYO6 -0.018 0.046 0.43 2 -0.17 2 4
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.039 0.026 -10000 0 -0.2 3 3
AQP5 -0.061 0.17 0.44 3 -0.38 67 70
CTNND1 0.021 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.018 0.047 0.43 2 -10000 0 2
regulation of calcium-dependent cell-cell adhesion -0.098 0.079 0.16 3 -0.17 172 175
EGF 0.074 0.12 0.33 63 -0.34 3 66
NCKAP1 0.022 0.002 -10000 0 -10000 0 0
AQP3 -0.025 0.081 0.24 1 -0.31 22 23
cortical microtubule organization 0.041 0.022 -10000 0 -0.18 2 2
GO:0000145 -0.017 0.045 0.42 2 -0.16 2 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.046 0.023 -10000 0 -0.18 2 2
MLLT4 0.02 0.007 -10000 0 -10000 0 0
ARF6/GDP -0.034 0.026 -10000 0 -0.17 5 5
ARF6 0.021 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.04 0.036 -10000 0 -0.19 5 5
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.01 0.045 0.42 2 -10000 0 2
PVRL2 0.021 0.005 -10000 0 -10000 0 0
ZYX -0.019 0.047 0.43 2 -0.17 2 4
ARF6/GTP 0.043 0.037 -10000 0 -0.18 4 4
CDH1 0.019 0.027 -10000 0 -0.34 2 2
EGFR/EGFR/EGF/EGF 0.042 0.054 0.25 1 -0.17 6 7
RhoA/GDP 0.042 0.023 -10000 0 -0.17 2 2
actin cytoskeleton organization -0.02 0.044 0.41 2 -0.18 2 4
IGF-1R heterotetramer 0.02 0.019 -10000 0 -0.34 1 1
GIT1 0.021 0.004 -10000 0 -10000 0 0
IGF1R 0.02 0.019 -10000 0 -0.34 1 1
IGF1 0.018 0.042 0.33 1 -0.34 4 5
DIAPH1 0.013 0.13 -10000 0 -0.53 14 14
Wnt receptor signaling pathway -0.041 0.022 0.18 2 -10000 0 2
RHOA 0.021 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.035 0.029 -10000 0 -0.19 6 6
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
VCL -0.02 0.044 0.42 2 -0.18 2 4
EFNA1 0.017 0.021 -10000 0 -0.34 1 1
LPP -0.022 0.045 0.21 10 -10000 0 10
Ephrin A1/EPHA2 0.027 0.038 -10000 0 -0.19 7 7
SEC6/SEC8 -0.026 0.02 -10000 0 -0.17 1 1
MGAT3 -0.099 0.08 0.16 3 -0.18 172 175
HGF/MET 0.022 0.057 -10000 0 -0.18 22 22
HGF 0.009 0.076 0.33 3 -0.34 14 17
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.006 0.031 -10000 0 -0.18 7 7
actin cable formation 0.01 0.092 0.34 11 -0.25 3 14
KIAA1543 -0.021 0.033 0.17 8 -0.16 2 10
KIFC3 -0.024 0.026 -10000 0 -0.17 3 3
NCK1 0.021 0.003 -10000 0 -10000 0 0
EXOC3 0.017 0.009 -10000 0 -10000 0 0
ACTN1 -0.019 0.046 0.43 2 -0.17 1 3
NCK1/GIT1 0.031 0.007 -10000 0 -10000 0 0
mol:GDP 0.041 0.022 -10000 0 -0.18 2 2
EXOC4 0.021 0.005 -10000 0 -10000 0 0
STX4 -0.022 0.034 0.34 1 -0.17 2 3
PIP5K1C -0.018 0.047 0.43 2 -10000 0 2
LIMA1 0.022 0.003 -10000 0 -10000 0 0
ABI1 0.021 0.004 -10000 0 -10000 0 0
ROCK1 -0.005 0.084 0.34 7 -0.27 1 8
adherens junction assembly -0.027 0.1 0.34 7 -0.46 8 15
IGF-1R heterotetramer/IGF1 0.032 0.034 -10000 0 -0.17 7 7
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.028 0.011 -10000 0 -10000 0 0
MET 0.014 0.073 0.33 5 -0.34 11 16
PLEKHA7 -0.021 0.035 0.34 1 -10000 0 1
mol:GTP 0.039 0.036 -10000 0 -0.19 5 5
establishment of epithelial cell apical/basal polarity 0.019 0.098 0.32 12 -10000 0 12
cortical actin cytoskeleton stabilization 0.006 0.031 -10000 0 -0.18 7 7
regulation of cell-cell adhesion -0.02 0.044 0.41 2 -0.18 2 4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.006 0.031 -10000 0 -0.18 7 7
Caspase cascade in apoptosis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 -0.012 0.085 -10000 0 -0.35 12 12
ACTA1 -0.02 0.083 -10000 0 -0.31 16 16
NUMA1 -0.009 0.078 -10000 0 -0.36 9 9
SPTAN1 -0.025 0.084 -10000 0 -0.31 18 18
LIMK1 -0.019 0.091 0.21 10 -0.32 16 26
BIRC3 0.022 0.043 0.33 4 -0.34 2 6
BIRC2 0.021 0.005 -10000 0 -10000 0 0
BAX 0.021 0.005 -10000 0 -10000 0 0
CASP10 -0.029 0.047 -10000 0 -0.24 16 16
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.022 0.003 -10000 0 -10000 0 0
PTK2 -0.01 0.078 -10000 0 -0.39 8 8
DIABLO 0.021 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.025 0.083 -10000 0 -0.31 18 18
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.022 0.017 0.33 1 -10000 0 1
GSN -0.025 0.083 -10000 0 -0.31 18 18
MADD 0.022 0.003 -10000 0 -10000 0 0
TFAP2A 0.084 0.15 0.38 1 -0.48 16 17
BID -0.011 0.035 -10000 0 -0.16 16 16
MAP3K1 -0.015 0.091 -10000 0 -0.41 15 15
TRADD 0.021 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.008 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.023 0.088 0.26 2 -0.31 18 20
CASP9 0.021 0.004 -10000 0 -10000 0 0
DNA repair -0.001 0.037 0.17 2 -0.16 1 3
neuron apoptosis -0.01 0.12 -10000 0 -0.61 14 14
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.016 0.087 -10000 0 -0.4 9 9
APAF1 0.021 0.004 -10000 0 -10000 0 0
CASP6 -0.006 0.11 -10000 0 -0.83 5 5
TRAF2 0.021 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.026 0.088 0.36 3 -0.32 16 19
CASP7 -0.003 0.059 0.24 2 -0.23 5 7
KRT18 0.012 0.039 -10000 0 -0.49 1 1
apoptosis -0.022 0.087 -10000 0 -0.43 9 9
DFFA -0.024 0.085 0.2 2 -0.31 18 20
DFFB -0.023 0.085 0.19 4 -0.32 17 21
PARP1 0.001 0.038 0.16 1 -0.17 2 3
actin filament polymerization 0 0.11 0.28 14 -0.3 15 29
TNF 0.007 0.072 0.33 1 -0.34 14 15
CYCS 0.002 0.045 0.16 8 -0.19 4 12
SATB1 -0.012 0.11 -10000 0 -0.81 5 5
SLK -0.025 0.083 -10000 0 -0.31 18 18
p15 BID/BAX 0.007 0.048 0.18 2 -0.25 3 5
CASP2 -0.001 0.058 0.19 10 -0.25 3 13
JNK cascade 0.015 0.091 0.41 15 -10000 0 15
CASP3 -0.022 0.088 -10000 0 -0.32 18 18
LMNB2 -0.014 0.13 0.21 2 -0.44 21 23
RIPK1 0.021 0.004 -10000 0 -10000 0 0
CASP4 0.021 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.052 0.031 0.23 4 -0.19 2 6
negative regulation of DNA binding 0.084 0.15 0.38 1 -0.48 16 17
stress fiber formation -0.026 0.082 -10000 0 -0.31 18 18
GZMB -0.029 0.056 -10000 0 -0.27 16 16
CASP1 0.006 0.02 -10000 0 -0.25 2 2
LMNB1 0 0.12 -10000 0 -0.48 11 11
APP -0.01 0.13 -10000 0 -0.62 14 14
TNFRSF1A 0.02 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.009 0.001 -10000 0 -10000 0 0
VIM -0.017 0.088 -10000 0 -0.41 10 10
LMNA 0.005 0.068 -10000 0 -0.33 5 5
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.002 0.055 -10000 0 -0.29 4 4
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.023 0.085 -10000 0 -0.31 18 18
APAF-1/Caspase 9 0.001 0.1 -10000 0 -0.65 8 8
nuclear fragmentation during apoptosis -0.008 0.077 -10000 0 -0.36 9 9
CFL2 -0.001 0.11 0.3 15 -0.29 14 29
GAS2 -0.027 0.09 0.26 2 -0.32 18 20
positive regulation of apoptosis -0.003 0.11 0.22 1 -0.46 11 12
PRF1 0.008 0.068 -10000 0 -0.34 13 13
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.021 0.005 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.031 0.072 -10000 0 -0.23 1 1
Syndecan-3/Neurocan 0.024 0.041 0.31 2 -0.23 2 4
POMC 0.013 0.078 0.33 5 -0.34 13 18
EGFR 0.017 0.037 0.33 1 -0.34 3 4
Syndecan-3/EGFR 0.018 0.033 0.3 1 -0.25 2 3
AGRP -0.12 0.17 -10000 0 -0.34 135 135
NCSTN 0.019 0.008 -10000 0 -10000 0 0
PSENEN 0.02 0.006 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.02 0.019 -10000 0 -0.34 1 1
APH1A 0.018 0.009 -10000 0 -10000 0 0
NCAN 0.027 0.047 0.33 8 -10000 0 8
long-term memory 0.038 0.034 -10000 0 -0.22 1 1
Syndecan-3/IL8 0.029 0.054 0.26 6 -0.25 2 8
PSEN1 0.021 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.03 0.009 -10000 0 -10000 0 0
FYN 0.02 0.007 -10000 0 -10000 0 0
limb bud formation 0.005 0.003 -10000 0 -10000 0 0
MC4R 0.041 0.082 0.33 26 -10000 0 26
SRC 0.021 0.004 -10000 0 -10000 0 0
PTN -0.02 0.12 0.33 4 -0.34 44 48
FGFR/FGF/Syndecan-3 0.005 0.003 -10000 0 -10000 0 0
neuron projection morphogenesis -0.015 0.061 0.3 1 -10000 0 1
Syndecan-3/AgRP -0.036 0.083 -10000 0 -0.29 3 3
Syndecan-3/AgRP/MC4R -0.02 0.1 0.26 3 -0.31 2 5
Fyn/Cortactin 0.028 0.011 -10000 0 -10000 0 0
SDC3 0.005 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.029 0.053 0.26 6 -0.24 2 8
IL8 0.034 0.072 0.33 17 -0.34 2 19
Syndecan-3/Fyn/Cortactin 0.039 0.035 -10000 0 -0.23 1 1
Syndecan-3/CASK 0.003 0.019 -10000 0 -0.24 2 2
alpha-MSH/MC4R 0.034 0.074 0.24 26 -0.21 13 39
Gamma Secretase 0.046 0.032 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.027 0.008 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.028 0.053 0.33 9 -0.34 1 10
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.02 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.016 0.032 0.15 5 -0.17 1 6
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.02 0.006 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.021 0.005 -10000 0 -10000 0 0
FYN 0.02 0.007 -10000 0 -10000 0 0
MAP3K12 0.021 0.003 -10000 0 -10000 0 0
FGR -0.008 0.098 -10000 0 -0.34 29 29
p38 alpha/TAB1 -0.04 0.086 -10000 0 -0.28 30 30
PRKG1 -0.01 0.1 -10000 0 -0.34 31 31
DUSP8 0.014 0.05 -10000 0 -0.34 7 7
PGK/cGMP/p38 alpha -0.018 0.12 -10000 0 -0.32 31 31
apoptosis -0.039 0.083 -10000 0 -0.27 30 30
RAL/GTP 0.027 0.009 -10000 0 -10000 0 0
LYN 0.02 0.007 -10000 0 -10000 0 0
DUSP1 -0.008 0.097 -10000 0 -0.34 28 28
PAK1 0.021 0.005 -10000 0 -10000 0 0
SRC 0.021 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.044 0.024 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.02 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.025 0.011 -10000 0 -10000 0 0
MAPK11 -0.008 0.12 0.28 5 -0.32 20 25
BLK 0.05 0.098 0.33 37 -0.34 1 38
HCK 0.009 0.065 -10000 0 -0.34 12 12
MAP2K3 0.02 0.006 -10000 0 -10000 0 0
DUSP16 0.02 0.006 -10000 0 -10000 0 0
DUSP10 0.019 0.02 -10000 0 -0.34 1 1
TRAF6/MEKK3 0.026 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.007 0.12 0.24 8 -0.34 21 29
positive regulation of innate immune response -0.01 0.14 0.32 5 -0.37 24 29
LCK 0.022 0.025 0.33 1 -0.34 1 2
p38alpha-beta/MKP7 -0.002 0.14 0.34 4 -0.37 21 25
p38alpha-beta/MKP5 -0.002 0.13 0.34 4 -0.37 20 24
PGK/cGMP -0.006 0.07 -10000 0 -0.23 31 31
PAK2 0.021 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.009 0.14 0.34 4 -0.37 25 29
CDC42 0.021 0.004 -10000 0 -10000 0 0
RALB 0.022 0.003 -10000 0 -10000 0 0
RALA 0.02 0.006 -10000 0 -10000 0 0
PAK3 0.057 0.11 0.33 45 -0.34 4 49
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.039 0.056 0.24 19 -0.24 4 23
AKT1 -0.021 0.1 0.37 5 -0.42 8 13
PTK2B -0.029 0.09 0.33 2 -0.45 7 9
VEGFR2 homodimer/Frs2 -0.008 0.086 -10000 0 -0.24 35 35
CAV1 -0.19 0.18 -10000 0 -0.34 204 204
CALM1 0.021 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.005 0.083 -10000 0 -0.23 32 32
endothelial cell proliferation -0.022 0.12 0.42 6 -0.37 13 19
mol:Ca2+ -0.036 0.075 -10000 0 -0.42 6 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.012 0.087 -10000 0 -0.46 6 6
RP11-342D11.1 -0.033 0.075 0.16 6 -0.44 6 12
CDH5 -0.016 0.11 -10000 0 -0.34 36 36
VEGFA homodimer 0.042 0.025 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
SHC2 0.014 0.047 -10000 0 -0.34 6 6
HRAS/GDP 0.008 0.071 -10000 0 -0.38 6 6
SH2D2A 0.02 0.018 0.33 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.021 0.13 -10000 0 -0.42 25 25
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.004 0.086 -10000 0 -0.48 6 6
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.024 0.082 -10000 0 -0.41 6 6
GRB10 -0.035 0.076 -10000 0 -0.45 6 6
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GRB2 0.021 0.005 -10000 0 -10000 0 0
PAK1 0.021 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.007 0.12 -10000 0 -0.42 16 16
HRAS 0.021 0.004 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.01 0.076 -10000 0 -0.32 11 11
HIF1A 0.021 0.005 -10000 0 -10000 0 0
FRS2 0.02 0.006 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.011 0.085 -10000 0 -0.46 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.012 0.057 -10000 0 -0.34 9 9
Nck/Pak 0.03 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.002 0.088 -10000 0 -0.48 6 6
mol:GDP 0.014 0.076 -10000 0 -0.4 6 6
mol:NADP -0.026 0.13 0.36 5 -0.39 26 31
eNOS/Hsp90 -0.017 0.13 0.42 3 -0.38 25 28
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
mol:IP3 -0.037 0.076 -10000 0 -0.42 6 6
HIF1A/ARNT 0.025 0.014 -10000 0 -10000 0 0
SHB 0.02 0.006 -10000 0 -10000 0 0
VEGFA 0.021 0.005 -10000 0 -10000 0 0
VEGFC 0.02 0.032 0.33 1 -0.34 2 3
FAK1/Vinculin -0.007 0.12 0.3 8 -0.46 11 19
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.023 0.1 -10000 0 -0.46 7 7
PTPN6 0.02 0.006 -10000 0 -10000 0 0
EPAS1 -0.018 0.12 -10000 0 -0.35 39 39
mol:L-citrulline -0.026 0.13 0.36 5 -0.39 26 31
ITGAV 0.022 0.002 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.015 0.08 -10000 0 -0.38 6 6
VEGFR2 homodimer/VEGFA homodimer 0.005 0.088 -10000 0 -0.48 6 6
VEGFR2/3 heterodimer -0.012 0.099 -10000 0 -0.42 12 12
VEGFB 0.021 0.003 -10000 0 -10000 0 0
MAPK11 -0.027 0.088 0.3 3 -0.45 6 9
VEGFR2 homodimer -0.043 0.094 -10000 0 -0.29 36 36
FLT1 0.021 0.005 -10000 0 -10000 0 0
NEDD4 0.02 0.019 -10000 0 -0.34 1 1
MAPK3 -0.027 0.089 0.33 5 -0.42 6 11
MAPK1 -0.025 0.087 0.31 6 -0.42 5 11
VEGFA145/NRP2 0.03 0.021 -10000 0 -0.23 2 2
VEGFR1/2 heterodimer -0.009 0.09 -10000 0 -0.52 6 6
KDR -0.044 0.095 -10000 0 -0.29 36 36
VEGFA165/NRP1/VEGFR2 homodimer 0.006 0.084 -10000 0 -0.47 6 6
SRC 0.021 0.004 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.023 0.099 0.34 8 -0.42 6 14
PI3K -0.038 0.077 -10000 0 -0.44 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.005 0.087 -10000 0 -0.48 6 6
FES -0.038 0.078 -10000 0 -0.46 6 6
GAB1 -0.023 0.095 -10000 0 -0.41 11 11
VEGFR2 homodimer/VEGFA homodimer/Src 0.004 0.086 -10000 0 -0.23 34 34
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
SOS1 0.022 0.003 -10000 0 -10000 0 0
ARNT 0.018 0.009 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.097 0.13 -10000 0 -0.45 27 27
VEGFR2 homodimer/VEGFA homodimer/Yes 0.004 0.086 -10000 0 -0.48 6 6
PI3K/GAB1 -0.011 0.095 -10000 0 -0.42 8 8
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.026 0.085 -10000 0 -0.4 6 6
PRKACA 0.02 0.006 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.002 0.097 -10000 0 -0.45 9 9
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
CDC42 -0.036 0.078 -10000 0 -0.46 6 6
actin cytoskeleton reorganization 0.004 0.085 -10000 0 -0.48 6 6
PTK2 -0.023 0.11 0.35 3 -0.49 12 15
EDG1 -0.033 0.075 0.16 6 -0.44 6 12
mol:DAG -0.037 0.076 -10000 0 -0.42 6 6
CaM/Ca2+ -0.032 0.075 -10000 0 -0.4 6 6
MAP2K3 -0.031 0.075 0.34 1 -0.36 6 7
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.016 0.098 -10000 0 -0.46 6 6
PLCG1 -0.037 0.076 -10000 0 -0.43 6 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.014 0.085 -10000 0 -0.43 6 6
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
YES1 0.02 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.004 0.088 -10000 0 -0.48 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.005 0.084 -10000 0 -0.45 6 6
cell migration -0.018 0.12 0.29 5 -0.47 11 16
mol:PI-3-4-5-P3 -0.036 0.073 -10000 0 -0.42 6 6
FYN 0.02 0.007 -10000 0 -10000 0 0
VEGFB/NRP1 -0.035 0.073 -10000 0 -0.43 6 6
mol:NO -0.026 0.13 0.36 5 -0.39 26 31
PXN 0.021 0.004 -10000 0 -10000 0 0
HRAS/GTP -0.041 0.058 -10000 0 -0.38 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.041 0.07 -10000 0 -0.46 6 6
VHL 0.021 0.004 -10000 0 -10000 0 0
ITGB3 0.034 0.08 0.33 19 -0.34 4 23
NOS3 -0.031 0.15 0.4 4 -0.44 26 30
VEGFR2 homodimer/VEGFA homodimer/Sck 0 0.094 -10000 0 -0.46 8 8
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.033 0.077 -10000 0 -0.44 5 5
PRKCB -0.037 0.08 -10000 0 -0.43 6 6
VCL 0.022 0.003 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.033 0.076 -10000 0 -0.44 6 6
VEGFR1/2 heterodimer/VEGFA homodimer 0.004 0.087 -10000 0 -0.48 6 6
VEGFA165/NRP2 0.03 0.021 -10000 0 -0.23 2 2
MAPKKK cascade -0.024 0.086 0.31 1 -0.42 5 6
NRP2 0.02 0.027 -10000 0 -0.34 2 2
VEGFC homodimer 0.02 0.032 0.33 1 -0.34 2 3
NCK1 0.021 0.003 -10000 0 -10000 0 0
ROCK1 0.021 0.005 -10000 0 -10000 0 0
FAK1/Paxillin -0.008 0.12 0.27 7 -0.48 11 18
MAP3K13 -0.034 0.073 -10000 0 -0.4 6 6
PDPK1 -0.035 0.072 0.24 2 -0.38 6 8
IL2 signaling events mediated by STAT5

Figure S83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.017 0.038 -10000 0 -0.34 4 4
ELF1 0.035 0.043 -10000 0 -10000 0 0
CCNA2 0.1 0.14 0.33 95 -10000 0 95
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
JAK3 0.02 0.006 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
JAK1 0.021 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.015 0.076 -10000 0 -0.44 3 3
SHC1 0.019 0.008 -10000 0 -10000 0 0
SP1 0.017 0.046 -10000 0 -0.3 7 7
IL2RA 0.012 0.087 0.3 29 -10000 0 29
IL2RB 0.019 0.027 -10000 0 -0.34 2 2
SOS1 0.022 0.003 -10000 0 -10000 0 0
IL2RG 0.018 0.038 -10000 0 -0.34 4 4
G1/S transition of mitotic cell cycle 0.031 0.12 0.3 17 -0.44 9 26
PTPN11 0.021 0.004 -10000 0 -10000 0 0
CCND2 -0.027 0.082 -10000 0 -0.6 7 7
LCK 0.022 0.025 0.33 1 -0.34 1 2
GRB2 0.021 0.005 -10000 0 -10000 0 0
IL2 0.02 0.003 -10000 0 -10000 0 0
CDK6 0.02 0.02 -10000 0 -0.34 1 1
CCND3 0.017 0.081 0.3 3 -0.39 3 6
Ephrin A reverse signaling

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
MAPKKK cascade 0.029 0.034 0.21 8 -0.18 3 11
EFNA5 0.019 0.037 0.33 1 -0.34 3 4
FYN -0.014 0.029 0.18 5 -0.18 2 7
neuron projection morphogenesis 0.029 0.034 0.21 8 -0.18 3 11
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.03 0.035 0.21 8 -0.18 3 11
EPHA5 0.027 0.046 0.33 8 -10000 0 8
IL27-mediated signaling events

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
TGFB1 0.024 0.016 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.015 0.11 0.44 8 -10000 0 8
IL27/IL27R/JAK1 0.039 0.093 -10000 0 -0.88 1 1
TBX21 -0.019 0.12 0.88 1 -0.61 3 4
IL12B 0.024 0.035 0.32 3 -0.34 1 4
IL12A -0.009 0.026 0.16 1 -0.23 4 5
IL6ST 0.012 0.056 -10000 0 -0.34 8 8
IL27RA/JAK1 0.01 0.066 0.37 1 -1.1 1 2
IL27 0.012 0.053 -10000 0 -0.34 7 7
TYK2 0.022 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.016 0.13 0.48 1 -10000 0 1
T-helper 2 cell differentiation 0.015 0.11 0.44 8 -10000 0 8
T cell proliferation during immune response 0.015 0.11 0.44 8 -10000 0 8
MAPKKK cascade -0.015 0.11 -10000 0 -0.44 8 8
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT2 0.021 0.004 -10000 0 -10000 0 0
STAT1 0.021 0.01 -10000 0 -10000 0 0
IL12RB1 0.012 0.057 -10000 0 -0.34 9 9
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.005 0.12 0.39 9 -0.55 3 12
IL27/IL27R/JAK2/TYK2 -0.015 0.11 -10000 0 -0.45 8 8
positive regulation of T cell mediated cytotoxicity -0.015 0.11 -10000 0 -0.44 8 8
STAT1 (dimer) 0.035 0.13 -10000 0 -0.82 2 2
JAK2 0.022 0.014 -10000 0 -10000 0 0
JAK1 0.02 0.011 -10000 0 -10000 0 0
STAT2 (dimer) -0.006 0.12 0.44 1 -0.44 8 9
T cell proliferation -0.039 0.13 0.34 3 -0.45 13 16
IL12/IL12R/TYK2/JAK2 -0.035 0.25 -10000 0 -0.81 30 30
IL17A -0.019 0.12 0.48 1 -10000 0 1
mast cell activation 0.015 0.11 0.44 8 -10000 0 8
IFNG 0.005 0.043 0.11 30 -0.098 16 46
T cell differentiation -0.001 0.005 0.013 8 -0.021 7 15
STAT3 (dimer) -0.007 0.12 0.44 1 -0.45 8 9
STAT5A (dimer) -0.008 0.12 0.44 1 -0.46 8 9
STAT4 (dimer) -0.008 0.12 0.44 1 -0.44 9 10
STAT4 0.022 0.002 -10000 0 -10000 0 0
T cell activation -0.003 0.007 0.11 1 -10000 0 1
IL27R/JAK2/TYK2 0.035 0.077 -10000 0 -0.86 1 1
GATA3 -0.006 0.062 0.59 3 -10000 0 3
IL18 -0.012 0.034 -10000 0 -0.23 8 8
positive regulation of mast cell cytokine production -0.007 0.12 0.44 1 -0.44 8 9
IL27/EBI3 0.027 0.043 -10000 0 -0.24 7 7
IL27RA 0.001 0.064 -10000 0 -1.1 1 1
IL6 -0.045 0.14 -10000 0 -0.34 66 66
STAT5A 0.02 0.019 -10000 0 -0.34 1 1
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 -0.01 0.032 0.36 2 -10000 0 2
IL1B -0.019 0.051 0.16 1 -0.23 19 20
EBI3 0.021 0.015 -10000 0 -10000 0 0
TNF -0.016 0.045 0.16 1 -0.23 14 15
Class I PI3K signaling events

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
ARF5/GTP -0.011 0.064 0.24 3 -10000 0 3
DAPP1 -0.022 0.11 0.22 3 -0.3 29 32
Src family/SYK family/BLNK-LAT/BTK-ITK -0.042 0.17 0.24 1 -0.46 34 35
mol:DAG -0.017 0.073 0.2 8 -0.21 14 22
HRAS 0.021 0.008 -10000 0 -10000 0 0
RAP1A 0.021 0.008 -10000 0 -10000 0 0
ARF5/GDP -0.003 0.094 0.22 1 -0.33 16 17
PLCG2 0.018 0.033 -10000 0 -0.34 3 3
PLCG1 0.021 0.005 -10000 0 -10000 0 0
ARF5 0.021 0.005 -10000 0 -10000 0 0
mol:GTP -0.019 0.048 0.15 22 -10000 0 22
ARF1/GTP -0.005 0.05 0.26 2 -10000 0 2
RHOA 0.021 0.004 -10000 0 -10000 0 0
YES1 0.02 0.006 -10000 0 -10000 0 0
RAP1A/GTP -0.019 0.046 0.16 20 -10000 0 20
ADAP1 -0.018 0.052 0.28 3 -0.29 1 4
ARAP3 -0.019 0.047 0.15 22 -10000 0 22
INPPL1 0.021 0.004 -10000 0 -10000 0 0
PREX1 0.016 0.038 -10000 0 -0.34 4 4
ARHGEF6 0.011 0.06 -10000 0 -0.34 10 10
ARHGEF7 0.021 0.005 -10000 0 -10000 0 0
ARF1 0.02 0.006 -10000 0 -10000 0 0
NRAS 0.021 0.008 -10000 0 -10000 0 0
FYN 0.02 0.007 -10000 0 -10000 0 0
ARF6 0.021 0.005 -10000 0 -10000 0 0
FGR -0.008 0.098 -10000 0 -0.34 29 29
mol:Ca2+ -0.012 0.041 0.17 3 -0.13 5 8
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.017 0.038 -10000 0 -0.34 4 4
ZAP70 0.016 0.046 -10000 0 -0.34 6 6
mol:IP3 -0.019 0.055 0.16 8 -0.17 8 16
LYN 0.02 0.007 -10000 0 -10000 0 0
ARF1/GDP -0.001 0.089 0.22 1 -0.31 16 17
RhoA/GDP -0.012 0.066 0.26 3 -0.27 3 6
PDK1/Src/Hsp90 0.04 0.014 -10000 0 -10000 0 0
BLNK 0.021 0.019 -10000 0 -0.34 1 1
actin cytoskeleton reorganization -0.009 0.09 0.3 6 -0.32 10 16
SRC 0.021 0.004 -10000 0 -10000 0 0
PLEKHA2 -0.018 0.008 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PTEN 0.02 0.015 -10000 0 -10000 0 0
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.024 0.046 0.28 1 -10000 0 1
RhoA/GTP -0.021 0.049 0.22 4 -10000 0 4
Src family/SYK family/BLNK-LAT -0.02 0.1 -10000 0 -0.3 27 27
BLK 0.05 0.098 0.33 37 -0.34 1 38
PDPK1 0.021 0.003 -10000 0 -10000 0 0
CYTH1 -0.021 0.049 0.28 3 -10000 0 3
HCK 0.009 0.065 -10000 0 -0.34 12 12
CYTH3 -0.018 0.05 0.24 4 -10000 0 4
CYTH2 -0.021 0.049 0.28 3 -10000 0 3
KRAS 0.02 0.008 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.004 0.047 -10000 0 -0.34 4 4
SGK1 -0.018 0.1 -10000 0 -0.34 30 30
INPP5D 0.02 0.027 -10000 0 -0.34 2 2
mol:GDP -0.013 0.095 0.2 2 -0.31 21 23
SOS1 0.022 0.003 -10000 0 -10000 0 0
SYK 0.019 0.027 -10000 0 -0.34 2 2
ARF6/GDP -0.015 0.059 0.27 2 -0.27 2 4
mol:PI-3-4-5-P3 -0.02 0.042 0.19 3 -10000 0 3
ARAP3/RAP1A/GTP -0.019 0.047 0.16 20 -10000 0 20
VAV1 0.017 0.033 -10000 0 -0.34 3 3
mol:PI-3-4-P2 -0.018 0.012 -10000 0 -0.24 1 1
RAS family/GTP/PI3K Class I -0.023 0.037 0.19 2 -10000 0 2
PLEKHA1 -0.021 0.011 -10000 0 -0.2 1 1
Rac1/GDP -0.005 0.09 -10000 0 -0.31 19 19
LAT 0.022 0.017 0.33 1 -10000 0 1
Rac1/GTP -0.002 0.089 -10000 0 -0.36 15 15
ITK -0.026 0.048 0.27 1 -10000 0 1
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.028 0.093 0.24 6 -0.28 17 23
LCK 0.022 0.025 0.33 1 -0.34 1 2
BTK -0.03 0.059 0.27 2 -0.3 2 4
Signaling events mediated by PRL

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
CCNE1 0.12 0.14 0.33 110 -10000 0 110
mol:Halofuginone 0.001 0 -10000 0 -10000 0 0
ITGA1 0.019 0.02 -10000 0 -0.34 1 1
CDKN1A 0.002 0.03 -10000 0 -0.32 2 2
PRL-3/alpha Tubulin 0.027 0.012 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.066 0.17 35 -0.24 4 39
AGT 0.055 0.11 0.33 44 -0.34 4 48
CCNA2 -0.007 0.059 0.35 4 -10000 0 4
TUBA1B 0.021 0.003 -10000 0 -10000 0 0
EGR1 -0.021 0.055 -10000 0 -0.23 23 23
CDK2/Cyclin E1 0.089 0.099 0.37 5 -0.3 2 7
MAPK3 -0.015 0.017 0.28 1 -10000 0 1
PRL-2 /Rab GGTase beta 0.031 0.007 -10000 0 -10000 0 0
MAPK1 -0.015 0.007 -10000 0 -10000 0 0
PTP4A1 -0.024 0.038 -10000 0 -10000 0 0
PTP4A3 0.019 0.008 -10000 0 -10000 0 0
PTP4A2 0.022 0.003 -10000 0 -10000 0 0
ITGB1 -0.015 0.017 0.28 1 -10000 0 1
SRC 0.021 0.004 -10000 0 -10000 0 0
RAC1 0 0.042 -10000 0 -0.41 3 3
Rab GGTase beta/Rab GGTase alpha 0.03 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.023 0.048 -10000 0 -10000 0 0
RABGGTA 0.021 0.005 -10000 0 -10000 0 0
BCAR1 -0.019 0.017 -10000 0 -0.21 2 2
RHOC -0.002 0.052 -10000 0 -0.37 6 6
RHOA -0.002 0.049 -10000 0 -0.34 6 6
cell motility 0.002 0.067 0.26 2 -0.35 5 7
PRL-1/alpha Tubulin -0.025 0.046 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.025 0.019 -10000 0 -0.24 1 1
ROCK1 -0.001 0.055 0.27 1 -0.39 3 4
RABGGTB 0.021 0.004 -10000 0 -10000 0 0
CDK2 0.021 0.004 -10000 0 -10000 0 0
mitosis -0.024 0.038 -10000 0 -10000 0 0
ATF5 0.022 0.017 0.33 1 -10000 0 1
Regulation of nuclear SMAD2/3 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
EP300 0.016 0.018 -10000 0 -10000 0 0
HSPA8 0.02 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.022 0.067 0.24 8 -0.22 8 16
AKT1 0.014 0.027 -10000 0 -10000 0 0
GSC 0.043 0.13 0.47 9 -0.42 5 14
NKX2-5 0.04 0.079 0.33 24 -10000 0 24
muscle cell differentiation -0.009 0.075 0.28 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.046 0.063 -10000 0 -10000 0 0
SMAD4 0.016 0.031 -10000 0 -10000 0 0
CBFB 0.021 0.004 -10000 0 -10000 0 0
SAP18 0.02 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.026 0.063 0.22 5 -0.2 17 22
SMAD3/SMAD4/VDR 0.039 0.053 -10000 0 -0.24 1 1
MYC 0.018 0.03 -10000 0 -0.34 2 2
CDKN2B -0.18 0.39 -10000 0 -1.2 38 38
AP1 0.003 0.061 -10000 0 -0.24 7 7
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.023 0.095 -10000 0 -0.33 19 19
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.024 0.098 -10000 0 -0.34 22 22
SP3 0.022 0.003 -10000 0 -10000 0 0
CREB1 0.022 0.003 -10000 0 -10000 0 0
FOXH1 0.044 0.081 0.33 25 -10000 0 25
SMAD3/SMAD4/GR 0.028 0.043 -10000 0 -10000 0 0
GATA3 0.022 0.021 0.33 1 -10000 0 1
SKI/SIN3/HDAC complex/NCoR1 -0.017 0.074 -10000 0 -0.34 10 10
MEF2C/TIF2 0.008 0.068 0.24 5 -0.24 1 6
endothelial cell migration -0.013 0.083 0.71 3 -10000 0 3
MAX 0.02 0.01 -10000 0 -10000 0 0
RBBP7 0.021 0.005 -10000 0 -10000 0 0
RBBP4 0.022 0.003 -10000 0 -10000 0 0
RUNX2 0.027 0.043 0.33 7 -10000 0 7
RUNX3 0.019 0.027 -10000 0 -0.34 2 2
RUNX1 0.021 0.004 -10000 0 -10000 0 0
CTBP1 0.021 0.004 -10000 0 -10000 0 0
NR3C1 0.02 0.011 -10000 0 -10000 0 0
VDR 0.021 0.025 0.33 1 -0.34 1 2
CDKN1A -0.003 0.061 -10000 0 -0.85 1 1
KAT2B 0.017 0.014 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.056 0.074 0.25 23 -10000 0 23
DCP1A 0.021 0.004 -10000 0 -10000 0 0
SKI 0.021 0.004 -10000 0 -10000 0 0
SERPINE1 0.013 0.084 -10000 0 -0.72 3 3
SMAD3/SMAD4/ATF2 0.03 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.02 0.058 -10000 0 -0.22 11 11
SAP30 0.021 0.004 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.035 0.031 -10000 0 -10000 0 0
JUN -0.022 0.055 0.22 1 -0.24 6 7
SMAD3/SMAD4/IRF7 0.03 0.042 -10000 0 -10000 0 0
TFE3 0.022 0.008 -10000 0 -10000 0 0
COL1A2 0.02 0.083 0.31 13 -0.58 3 16
mesenchymal cell differentiation -0.033 0.048 -10000 0 -0.24 5 5
DLX1 0.036 0.068 0.33 18 -10000 0 18
TCF3 0.02 0.006 -10000 0 -10000 0 0
FOS -0.009 0.093 -10000 0 -0.34 24 24
SMAD3/SMAD4/Max 0.029 0.043 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.035 0.025 -10000 0 -10000 0 0
ZBTB17 0.022 0.009 -10000 0 -10000 0 0
LAMC1 -0.013 0.031 0.18 3 -10000 0 3
TGIF2/HDAC complex/SMAD3/SMAD4 0.029 0.041 -10000 0 -10000 0 0
IRF7 0.022 0.017 0.33 1 -10000 0 1
ESR1 0.017 0.077 0.33 10 -0.34 8 18
HNF4A 0.066 0.14 0.33 63 -0.34 9 72
MEF2C 0.021 0.083 0.26 14 -10000 0 14
SMAD2-3/SMAD4 0.034 0.051 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.035 0.028 -10000 0 -10000 0 0
IGHV3OR16-13 0.003 0.019 -10000 0 -0.32 1 1
TGIF2/HDAC complex 0.021 0.005 -10000 0 -10000 0 0
CREBBP 0.017 0.016 -10000 0 -10000 0 0
SKIL 0.021 0.005 -10000 0 -10000 0 0
HDAC1 0.022 0.003 -10000 0 -10000 0 0
HDAC2 0.02 0.007 -10000 0 -10000 0 0
SNIP1 0.021 0.007 -10000 0 -10000 0 0
GCN5L2 -0.001 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.033 0.043 -10000 0 -10000 0 0
MSG1/HSC70 0.021 0.065 0.24 6 -0.24 17 23
SMAD2 0.019 0.026 -10000 0 -10000 0 0
SMAD3 0.007 0.034 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0 0.047 -10000 0 -0.24 1 1
SMAD2/SMAD2/SMAD4 -0.015 0.076 0.19 2 -0.29 14 16
NCOR1 0.02 0.006 -10000 0 -10000 0 0
NCOA2 0.017 0.028 -10000 0 -0.34 2 2
NCOA1 0.022 0.002 -10000 0 -10000 0 0
MYOD/E2A 0.027 0.009 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.052 0.067 -10000 0 -10000 0 0
IFNB1 -0.014 0.031 0.3 1 -10000 0 1
SMAD3/SMAD4/MEF2C 0.049 0.071 0.27 1 -10000 0 1
CITED1 0.009 0.088 0.33 6 -0.34 17 23
SMAD2-3/SMAD4/ARC105 0.043 0.052 -10000 0 -10000 0 0
RBL1 0.021 0.004 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.044 0.15 -10000 0 -0.51 27 27
RUNX1-3/PEBPB2 0.039 0.022 -10000 0 -0.19 2 2
SMAD7 -0.004 0.081 -10000 0 -0.45 4 4
MYC/MIZ-1 0.027 0.025 0.2 1 -0.24 1 2
SMAD3/SMAD4 -0.01 0.068 -10000 0 -0.3 3 3
IL10 -0.016 0.046 0.3 2 -0.32 3 5
PIASy/HDAC complex 0.018 0.014 -10000 0 -10000 0 0
PIAS3 0.017 0.014 -10000 0 -10000 0 0
CDK2 0.017 0.016 -10000 0 -10000 0 0
IL5 -0.017 0.033 -10000 0 -10000 0 0
CDK4 0.016 0.016 -10000 0 -10000 0 0
PIAS4 0.018 0.014 -10000 0 -10000 0 0
ATF3 0.009 0.062 -10000 0 -0.34 11 11
SMAD3/SMAD4/SP1 0.034 0.052 -10000 0 -10000 0 0
FOXG1 0.045 0.089 0.33 31 -10000 0 31
FOXO3 -0.02 0.022 -10000 0 -0.15 1 1
FOXO1 -0.021 0.023 -10000 0 -0.14 1 1
FOXO4 -0.022 0.022 -10000 0 -10000 0 0
heart looping 0.021 0.082 0.26 14 -10000 0 14
CEBPB 0.015 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.038 0.056 0.24 12 -10000 0 12
MYOD1 0.02 0.024 0.33 2 -10000 0 2
SMAD3/SMAD4/HNF4 0.053 0.093 0.24 46 -0.21 9 55
SMAD3/SMAD4/GATA3 0.03 0.046 -10000 0 -10000 0 0
SnoN/SIN3/HDAC complex/NCoR1 0.021 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.043 0.05 -10000 0 -0.22 1 1
SMAD3/SMAD4/SP1-3 0.043 0.055 -10000 0 -10000 0 0
MED15 0.021 0.004 -10000 0 -10000 0 0
SP1 0.019 0.023 -10000 0 -0.14 1 1
SIN3B 0.021 0.005 -10000 0 -10000 0 0
SIN3A 0.021 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.072 0.089 0.37 11 -10000 0 11
ITGB5 -0.015 0.043 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP -0.01 0.064 -10000 0 -0.33 6 6
SMAD3/SMAD4/AR 0.005 0.087 -10000 0 -0.22 37 37
AR -0.017 0.11 0.33 1 -0.34 39 40
negative regulation of cell growth -0.006 0.066 -10000 0 -0.25 11 11
SMAD3/SMAD4/MYOD 0.028 0.043 0.26 1 -10000 0 1
E2F5 0.019 0.007 -10000 0 -10000 0 0
E2F4 0.021 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.069 0.073 0.28 8 -10000 0 8
SMAD2-3/SMAD4/FOXO1-3a-4 -0.02 0.096 -10000 0 -0.38 21 21
TFDP1 0.021 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.02 0.068 -10000 0 -0.24 7 7
SMAD3/SMAD4/RUNX2 0.033 0.048 0.24 5 -10000 0 5
TGIF2 0.021 0.005 -10000 0 -10000 0 0
TGIF1 0.02 0.006 -10000 0 -10000 0 0
ATF2 0.022 0.003 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.042 0.05 0.23 1 -0.22 10 11
MAP4K1 0.016 0.038 -10000 0 -0.34 4 4
MAP3K8 0.02 0.019 -10000 0 -0.34 1 1
PRKCB 0.015 0.046 -10000 0 -0.34 6 6
DBNL 0.02 0.006 -10000 0 -10000 0 0
CRKL 0.021 0.004 -10000 0 -10000 0 0
MAP3K1 -0.006 0.055 -10000 0 -0.28 7 7
JUN -0.006 0.11 -10000 0 -0.55 13 13
MAP3K7 -0.004 0.05 -10000 0 -0.23 9 9
GRAP2 0.012 0.057 -10000 0 -0.34 9 9
CRK 0.02 0.007 -10000 0 -10000 0 0
MAP2K4 -0.005 0.075 0.2 1 -0.42 6 7
LAT 0.022 0.017 0.33 1 -10000 0 1
LCP2 0.019 0.027 -10000 0 -0.34 2 2
MAPK8 -0.002 0.12 -10000 0 -0.56 14 14
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.005 0.066 -10000 0 -0.27 12 12
LAT/GRAP2/SLP76/HPK1/HIP-55 0.047 0.047 0.23 1 -0.23 6 7
Cellular roles of Anthrax toxin

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
ANTXR1 0.021 0.019 -10000 0 -0.34 1 1
ANTXR2 0.022 0.003 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.002 -10000 0 -0.048 1 1
monocyte activation -0.017 0.11 -10000 0 -0.37 30 30
MAP2K2 -0.034 0.16 -10000 0 -0.57 28 28
MAP2K1 -0.008 0.003 -10000 0 -10000 0 0
MAP2K7 -0.008 0.002 -10000 0 -10000 0 0
MAP2K6 -0.006 0.019 0.08 10 -0.16 1 11
CYAA -0.012 0.008 -10000 0 -0.16 1 1
MAP2K4 -0.008 0.003 -10000 0 -10000 0 0
IL1B -0.015 0.038 0.16 3 -0.16 16 19
Channel 0.027 0.012 -10000 0 -0.18 1 1
NLRP1 -0.008 0.009 -10000 0 -0.16 1 1
CALM1 0.021 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.059 -10000 0 -0.39 8 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.002 0.048 1 -10000 0 1
MAPK3 -0.008 0.003 -10000 0 -10000 0 0
MAPK1 -0.008 0.002 -10000 0 -10000 0 0
PGR -0.031 0.055 -10000 0 -0.16 52 52
PA/Cellular Receptors 0.029 0.013 -10000 0 -0.2 1 1
apoptosis -0.003 0.002 -10000 0 -0.048 1 1
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.027 0.011 -10000 0 -0.17 1 1
macrophage activation -0.013 0.003 -10000 0 -10000 0 0
TNF 0.007 0.072 0.33 1 -0.34 14 15
VCAM1 -0.016 0.11 -10000 0 -0.38 28 28
platelet activation -0.002 0.059 -10000 0 -0.39 8 8
MAPKKK cascade 0.006 0.019 0.088 1 -0.092 3 4
IL18 -0.011 0.031 0.14 2 -0.2 7 9
negative regulation of macrophage activation -0.003 0.002 -10000 0 -0.048 1 1
LEF -0.003 0.002 -10000 0 -0.048 1 1
CASP1 -0.004 0.013 -10000 0 -0.15 2 2
mol:cAMP -0.002 0.06 -10000 0 -0.39 8 8
necrosis -0.003 0.002 -10000 0 -0.048 1 1
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.027 0.011 -10000 0 -0.16 1 1
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.022 0.003 -10000 0 -10000 0 0
HDAC2 0.02 0.007 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.026 0.23 1 -0.2 2 3
forebrain development -0.035 0.14 -10000 0 -0.51 14 14
GNAO1 0.013 0.035 0.33 1 -0.34 2 3
SMO/beta Arrestin2 0.021 0.032 0.23 3 -0.21 1 4
SMO 0.016 0.038 0.33 3 -0.34 1 4
ARRB2 0.013 0.016 -10000 0 -10000 0 0
GLI3/SPOP 0.002 0.082 -10000 0 -0.34 9 9
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.021 0.003 -10000 0 -10000 0 0
GNAI2 0.015 0.016 -10000 0 -10000 0 0
SIN3/HDAC complex 0.049 0.022 -10000 0 -10000 0 0
GNAI1 0.014 0.024 -10000 0 -0.34 1 1
XPO1 0.013 0.02 -10000 0 -10000 0 0
GLI1/Su(fu) -0.033 0.13 -10000 0 -0.52 13 13
SAP30 0.021 0.004 -10000 0 -10000 0 0
mol:GDP 0.016 0.038 0.33 3 -0.34 1 4
MIM/GLI2A 0.001 0.049 -10000 0 -0.23 2 2
IFT88 0.02 0.006 -10000 0 -10000 0 0
GNAI3 0.014 0.016 -10000 0 -10000 0 0
GLI2 -0.011 0.084 0.19 1 -0.38 11 12
GLI3 -0.01 0.083 -10000 0 -0.35 10 10
CSNK1D 0.021 0.004 -10000 0 -10000 0 0
CSNK1E 0.021 0.005 -10000 0 -10000 0 0
SAP18 0.021 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.02 0.006 -10000 0 -10000 0 0
GNG2 0.02 0.02 -10000 0 -0.34 1 1
Gi family/GTP -0.014 0.07 -10000 0 -0.21 32 32
SIN3B 0.021 0.006 -10000 0 -10000 0 0
SIN3A 0.022 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) -0.011 0.089 -10000 0 -0.35 13 13
GLI2/Su(fu) -0.009 0.09 -10000 0 -0.38 13 13
FOXA2 -0.14 0.34 -10000 0 -0.86 63 63
neural tube patterning -0.035 0.14 -10000 0 -0.51 14 14
SPOP 0.021 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.012 0.041 -10000 0 -10000 0 0
GNB1 0.021 0.004 -10000 0 -10000 0 0
CSNK1G2 0.02 0.006 -10000 0 -10000 0 0
CSNK1G3 0.021 0.005 -10000 0 -10000 0 0
MTSS1 0.001 0.049 -10000 0 -0.23 2 2
embryonic limb morphogenesis -0.035 0.14 -10000 0 -0.51 14 14
SUFU 0.007 0.015 -10000 0 -10000 0 0
LGALS3 0.021 0.005 -10000 0 -10000 0 0
catabolic process -0.006 0.12 -10000 0 -0.49 14 14
GLI3A/CBP 0.006 0.064 -10000 0 -0.34 10 10
KIF3A 0.021 0.005 -10000 0 -10000 0 0
GLI1 -0.035 0.14 -10000 0 -0.53 14 14
RAB23 0.021 0.005 -10000 0 -10000 0 0
CSNK1A1 0.021 0.005 -10000 0 -10000 0 0
IFT172 0.022 0.002 -10000 0 -10000 0 0
RBBP7 0.021 0.005 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.011 0.041 -10000 0 -10000 0 0
GNAZ -0.013 0.097 -10000 0 -0.34 28 28
RBBP4 0.022 0.003 -10000 0 -10000 0 0
CSNK1G1 0.021 0.004 -10000 0 -10000 0 0
PIAS1 0.021 0.003 -10000 0 -10000 0 0
PRKACA 0.02 0.006 -10000 0 -10000 0 0
GLI2/SPOP -0.002 0.088 -10000 0 -0.39 11 11
STK36 0.013 0.02 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.013 0.066 -10000 0 -0.23 16 16
PTCH1 -0.039 0.15 -10000 0 -0.81 7 7
MIM/GLI1 -0.05 0.18 -10000 0 -0.46 49 49
CREBBP 0.006 0.064 -10000 0 -0.34 10 10
Su(fu)/SIN3/HDAC complex -0.002 0.067 -10000 0 -0.36 6 6
mTOR 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.022 0.003 -10000 0 -10000 0 0
mol:PIP3 -0.014 0.026 -10000 0 -0.2 5 5
FRAP1 -0.006 0.086 -10000 0 -0.44 12 12
AKT1 -0.011 0.037 -10000 0 -0.24 4 4
INSR 0.02 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.025 0.008 -10000 0 -10000 0 0
mol:GTP -0.012 0.047 0.24 2 -0.22 2 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.016 0.026 -10000 0 -0.19 3 3
TSC2 0.021 0.004 -10000 0 -10000 0 0
RHEB/GDP -0.023 0.026 -10000 0 -0.19 2 2
TSC1 0.021 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.014 0.029 -10000 0 -0.22 5 5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.013 0.037 -10000 0 -0.21 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.022 0.003 -10000 0 -10000 0 0
RPS6KB1 0.007 0.059 0.24 3 -0.33 3 6
MAP3K5 -0.012 0.056 0.18 4 -0.18 31 35
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
apoptosis -0.012 0.056 0.18 4 -0.18 31 35
mol:LY294002 0 0 -10000 0 -0.001 2 2
EIF4B 0.005 0.061 0.28 3 -0.29 3 6
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.022 0.05 0.23 2 -0.26 2 4
eIF4E/eIF4G1/eIF4A1 0.003 0.055 -10000 0 -0.28 12 12
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.025 0.032 -10000 0 -0.21 5 5
mTOR/RHEB/GTP/Raptor/GBL -0.005 0.035 0.14 8 -0.15 3 11
FKBP1A 0.021 0.005 -10000 0 -10000 0 0
RHEB/GTP -0.016 0.041 0.2 1 -0.19 2 3
mol:Amino Acids 0 0 -10000 0 -0.001 2 2
FKBP12/Rapamycin 0.015 0.004 -10000 0 -10000 0 0
PDPK1 -0.017 0.032 0.15 6 -0.21 4 10
EIF4E 0.022 0.003 -10000 0 -10000 0 0
ASK1/PP5C -0.031 0.18 -10000 0 -0.52 39 39
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.004 0.042 0.18 1 -0.23 10 11
TSC1/TSC2 -0.013 0.051 0.26 2 -0.23 2 4
tumor necrosis factor receptor activity 0 0 0.001 2 -10000 0 2
RPS6 0.02 0.007 -10000 0 -10000 0 0
PPP5C 0.021 0.005 -10000 0 -10000 0 0
EIF4G1 0.021 0.004 -10000 0 -10000 0 0
IRS1 0.001 0.029 -10000 0 -0.24 5 5
INS 0.018 0.003 -10000 0 -10000 0 0
PTEN 0.021 0.005 -10000 0 -10000 0 0
PDK2 -0.017 0.032 0.15 6 -0.21 4 10
EIF4EBP1 -0.056 0.29 -10000 0 -1 28 28
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
PPP2R5D -0.003 0.087 0.29 1 -0.4 12 13
peptide biosynthetic process -0.017 0.016 0.17 2 -10000 0 2
RHEB 0.021 0.005 -10000 0 -10000 0 0
EIF4A1 0.02 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 6 -0.003 1 7
EEF2 -0.017 0.016 0.17 2 -10000 0 2
eIF4E/4E-BP1 -0.045 0.27 -10000 0 -0.96 28 28
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.049 0.06 0.22 27 -0.17 2 29
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.021 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.007 0.059 0.27 2 -10000 0 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.039 0.024 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.018 0.038 -10000 0 -10000 0 0
CaM/Ca2+ 0.046 0.055 -10000 0 -0.17 2 2
RAP1A 0.021 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.007 0.049 0.16 1 -0.17 2 3
AKT1 -0.008 0.059 0.3 4 -10000 0 4
MAP2K1 -0.011 0.051 0.19 7 -10000 0 7
MAP3K11 -0.008 0.052 0.22 5 -0.17 3 8
IFNGR1 0.021 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.001 0.12 0.23 4 -0.32 31 35
Rap1/GTP -0.029 0.025 -10000 0 -10000 0 0
CRKL/C3G 0.03 0.008 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.058 0.063 0.23 27 -0.18 2 29
CEBPB -0.002 0.096 0.37 1 -0.41 8 9
STAT3 0.021 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.056 0.082 -10000 0 -0.69 2 2
STAT1 -0.007 0.052 0.22 5 -0.17 2 7
CALM1 0.021 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.041 0.091 0.33 28 -0.34 2 30
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.007 0.058 0.27 3 -10000 0 3
CEBPB/PTGES2/Cbp/p300 0.008 0.062 -10000 0 -0.29 6 6
mol:Ca2+ 0.046 0.057 0.21 27 -0.17 2 29
MAPK3 0.004 0.067 -10000 0 -0.44 2 2
STAT1 (dimer) -0.021 0.051 -10000 0 -10000 0 0
MAPK1 -0.014 0.13 -10000 0 -0.66 11 11
JAK2 0.02 0.011 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
JAK1 0.022 0.009 -10000 0 -10000 0 0
CAMK2D 0.022 0.003 -10000 0 -10000 0 0
DAPK1 -0.005 0.094 0.29 2 -0.51 7 9
SMAD7 -0.002 0.039 0.2 4 -0.17 1 5
CBL/CRKL/C3G -0.009 0.058 0.27 3 -10000 0 3
PI3K 0.041 0.051 -10000 0 -0.17 2 2
IFNG 0.041 0.091 0.33 28 -0.34 2 30
apoptosis -0.004 0.09 -10000 0 -0.42 11 11
CAMK2G 0.022 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.021 0.003 -10000 0 -10000 0 0
CAMK2A -0.012 0.11 0.33 1 -0.34 33 34
CAMK2B 0.062 0.11 0.33 48 -10000 0 48
FRAP1 -0.01 0.054 0.28 4 -10000 0 4
PRKCD -0.01 0.061 0.28 5 -10000 0 5
RAP1B 0.02 0.006 -10000 0 -10000 0 0
negative regulation of cell growth -0.018 0.038 -10000 0 -10000 0 0
PTPN2 0.021 0.005 -10000 0 -10000 0 0
EP300 0.021 0.004 -10000 0 -10000 0 0
IRF1 -0.011 0.047 0.22 2 -10000 0 2
STAT1 (dimer)/PIASy -0.007 0.056 0.27 3 -10000 0 3
SOCS1 0.013 0.078 -10000 0 -1 2 2
mol:GDP -0.01 0.055 0.25 3 -10000 0 3
CASP1 -0.003 0.04 0.2 4 -0.17 1 5
PTGES2 0.021 0.004 -10000 0 -10000 0 0
IRF9 -0.003 0.032 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.029 0.041 -10000 0 -0.17 2 2
RAP1/GDP -0.026 0.035 -10000 0 -10000 0 0
CBL -0.006 0.052 0.22 5 -0.17 2 7
MAP3K1 -0.007 0.051 0.22 5 -0.17 2 7
PIAS1 0.021 0.003 -10000 0 -10000 0 0
PIAS4 0.02 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.018 0.038 -10000 0 -10000 0 0
PTPN11 -0.004 0.05 0.15 25 -0.17 2 27
CREBBP 0.021 0.004 -10000 0 -10000 0 0
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 0.018 0.037 0.33 1 -0.34 3 4
CLTC 0.015 0.067 0.23 2 -0.44 5 7
calcium ion-dependent exocytosis 0.011 0.031 0.19 3 -0.16 1 4
Dynamin 2/GTP -0.001 0.048 0.13 38 -10000 0 38
EXOC4 0.021 0.005 -10000 0 -10000 0 0
CD59 0.012 0.043 -10000 0 -0.31 4 4
CPE -0.005 0.045 0.2 14 -10000 0 14
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
membrane fusion 0.01 0.027 -10000 0 -10000 0 0
CTNND1 -0.001 0.056 0.2 20 -10000 0 20
DNM2 0.02 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.006 0.051 0.18 6 -0.26 4 10
TSHR 0.006 0.057 0.17 37 -10000 0 37
INS 0.001 0.072 -10000 0 -0.48 7 7
BIN1 0.022 0.001 -10000 0 -10000 0 0
mol:Choline 0.01 0.027 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.069 0.19 42 -10000 0 42
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.021 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.047 0.13 38 -10000 0 38
JUP 0.011 0.038 -10000 0 -0.3 3 3
ASAP2/amphiphysin II 0.039 0.011 -10000 0 -10000 0 0
ARF6/GTP 0.015 0.004 -10000 0 -10000 0 0
CDH1 0.012 0.045 -10000 0 -0.31 4 4
clathrin-independent pinocytosis 0.015 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.021 0.004 -10000 0 -10000 0 0
positive regulation of endocytosis 0.015 0.004 -10000 0 -10000 0 0
EXOC2 0.021 0.005 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.006 0.021 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.021 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.031 0.051 0.3 4 -10000 0 4
positive regulation of phagocytosis -0.013 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.027 0.008 -10000 0 -10000 0 0
ACAP1 0.014 0.027 -10000 0 -0.15 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.011 0.068 -10000 0 -0.31 4 4
clathrin heavy chain/ACAP1 0.014 0.06 0.23 6 -0.33 5 11
JIP4/KLC1 0.038 0.013 -10000 0 -10000 0 0
EXOC1 0.021 0.004 -10000 0 -10000 0 0
exocyst 0.006 0.021 -10000 0 -10000 0 0
RALA/GTP 0.015 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.027 0.008 -10000 0 -10000 0 0
receptor recycling 0.015 0.004 -10000 0 -10000 0 0
CTNNA1 -0.001 0.056 0.2 20 -10000 0 20
NME1 0.011 0.069 0.19 42 -10000 0 42
clathrin coat assembly 0.015 0.068 0.24 3 -0.43 5 8
IL2RA 0.015 0.048 -10000 0 -0.33 4 4
VAMP3 -0.013 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.016 0.053 0.22 1 -0.31 5 6
EXOC6 0.021 0.003 -10000 0 -10000 0 0
PLD1 0.004 0.006 -10000 0 -10000 0 0
PLD2 0.005 0.005 -10000 0 -10000 0 0
EXOC5 0.021 0.005 -10000 0 -10000 0 0
PIP5K1C 0.006 0.05 0.18 5 -0.26 4 9
SDC1 0.012 0.044 -10000 0 -0.31 4 4
ARF6/GDP 0.03 0.038 0.14 39 -10000 0 39
EXOC7 0.021 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.033 0.053 -10000 0 -0.3 4 4
mol:Phosphatidic acid 0.01 0.027 -10000 0 -10000 0 0
endocytosis -0.038 0.011 -10000 0 -10000 0 0
SCAMP2 0.021 0.003 -10000 0 -10000 0 0
ADRB2 -0.039 0.097 0.22 1 -0.49 5 6
EXOC3 0.017 0.009 -10000 0 -10000 0 0
ASAP2 0.022 0.002 -10000 0 -10000 0 0
Dynamin 2/GDP 0.035 0.051 0.17 38 -10000 0 38
KLC1 0.021 0.005 -10000 0 -10000 0 0
AVPR2 -0.016 0.098 0.28 7 -0.44 5 12
RALA 0.02 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.023 0.056 0.33 2 -0.29 4 6
Insulin 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
CBL/APS/CAP 0.026 0.048 -10000 0 -0.17 14 14
TC10/GTP 0.023 0.043 -10000 0 -0.17 13 13
Insulin Receptor/Insulin/IRS1/Shp2 0.05 0.023 -10000 0 -0.16 1 1
HRAS 0.021 0.004 -10000 0 -10000 0 0
APS homodimer 0.02 0.02 -10000 0 -0.34 1 1
GRB14 0.033 0.083 0.33 19 -0.34 5 24
FOXO3 -0.056 0.21 -10000 0 -0.63 40 40
AKT1 -0.022 0.054 0.31 3 -10000 0 3
INSR 0.022 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.041 0.031 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.02 0.007 -10000 0 -10000 0 0
SORBS1 0.003 0.079 -10000 0 -0.34 18 18
CRK 0.02 0.007 -10000 0 -10000 0 0
PTPN1 -0.014 0.021 -10000 0 -10000 0 0
CAV1 -0.11 0.081 -10000 0 -0.18 178 178
CBL/APS/CAP/Crk-II/C3G 0.04 0.055 -10000 0 -0.18 15 15
Insulin Receptor/Insulin/IRS1/NCK2 0.05 0.022 -10000 0 -0.16 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.038 0.021 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.006 0.08 -10000 0 -0.32 17 17
RPS6KB1 -0.026 0.047 0.29 2 -10000 0 2
PARD6A 0.02 0.02 -10000 0 -0.34 1 1
CBL 0.021 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.011 0.045 -10000 0 -0.57 2 2
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.03 0.041 -10000 0 -10000 0 0
HRAS/GTP -0.029 0.02 -10000 0 -10000 0 0
Insulin Receptor 0.022 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.048 0.031 -10000 0 -10000 0 0
PRKCI -0.002 0.083 -10000 0 -0.34 3 3
Insulin Receptor/Insulin/GRB14/PDK1 -0.026 0.033 -10000 0 -0.18 3 3
SHC1 0.018 0.008 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.029 0.045 -10000 0 -0.49 2 2
PI3K 0.046 0.025 -10000 0 -10000 0 0
NCK2 0.022 0.002 -10000 0 -10000 0 0
RHOQ 0.022 0.003 -10000 0 -10000 0 0
mol:H2O2 -0.002 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.016 0.003 -10000 0 -10000 0 0
AKT2 -0.023 0.054 0.31 3 -10000 0 3
PRKCZ -0.007 0.094 -10000 0 -0.35 10 10
SH2B2 0.02 0.02 -10000 0 -0.34 1 1
SHC/SHIP -0.02 0.024 -10000 0 -0.18 2 2
F2RL2 0.039 0.089 0.33 25 -0.34 4 29
TRIP10 0.02 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.032 0.019 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.048 0.031 -10000 0 -10000 0 0
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
RASA1 0.021 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.035 0.052 -10000 0 -0.19 15 15
TC10/GDP 0.016 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.04 0.026 -10000 0 -10000 0 0
INPP5D -0.02 0.022 0.15 2 -0.18 2 4
SOS1 0.022 0.003 -10000 0 -10000 0 0
SGK1 -0.054 0.2 -10000 0 -0.66 34 34
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
IRS1 0.021 0.019 -10000 0 -0.34 1 1
p62DOK/RasGAP 0.029 0.046 -10000 0 -0.49 2 2
INS -0.015 0.015 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.02 0.022 0.15 2 -0.18 2 4
GRB2 0.021 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.02 0.053 0.23 4 -10000 0 4
PTPRA 0.022 0.007 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.027 0.009 -10000 0 -10000 0 0
PDPK1 0.021 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.007 0.026 -10000 0 -0.19 1 1
Insulin Receptor/Insulin/IRS1 0.038 0.018 -10000 0 -0.15 1 1
Insulin Receptor/Insulin/IRS3 0.03 0.013 -10000 0 -10000 0 0
Par3/Par6 0.051 0.05 0.22 21 -0.17 4 25
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.018 0.006 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.012 0.004 -10000 0 -10000 0 0
mol:DAG -0.014 0.037 0.24 4 -10000 0 4
VEGFR1 homodimer/NRP1/VEGFR 121 0.016 0.006 -10000 0 -10000 0 0
CaM/Ca2+ -0.018 0.031 0.22 1 -10000 0 1
HIF1A 0.023 0.005 -10000 0 -10000 0 0
GAB1 0.021 0.019 -10000 0 -0.34 1 1
AKT1 -0.015 0.044 0.38 2 -10000 0 2
PLCG1 -0.014 0.037 0.24 4 -10000 0 4
NOS3 -0.012 0.086 0.4 4 -0.37 7 11
CBL 0.021 0.005 -10000 0 -10000 0 0
mol:NO -0.008 0.094 0.44 6 -0.36 7 13
FLT1 -0.015 0.005 -10000 0 -10000 0 0
PGF 0.032 0.059 0.33 13 -10000 0 13
VEGFR1 homodimer/NRP2/VEGFR121 0.028 0.019 -10000 0 -10000 0 0
CALM1 0.021 0.005 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
eNOS/Hsp90 -0.017 0.088 0.37 3 -0.4 6 9
endothelial cell proliferation -0.007 0.054 0.37 4 -10000 0 4
mol:Ca2+ -0.014 0.037 0.24 4 -10000 0 4
MAPK3 -0.02 0.043 0.3 4 -10000 0 4
MAPK1 -0.02 0.04 0.34 3 -10000 0 3
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
PLGF homodimer 0.032 0.059 0.33 13 -10000 0 13
PRKACA 0.02 0.006 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.19 0.18 -10000 0 -0.34 204 204
VEGFA homodimer 0.021 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.018 0.007 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.023 0.048 0.37 4 -10000 0 4
PI3K 0.043 0.038 -10000 0 -10000 0 0
PRKCA -0.02 0.029 0.27 2 -10000 0 2
PRKCB -0.02 0.036 0.23 4 -10000 0 4
VEGFR1 homodimer/PLGF homodimer 0.026 0.04 0.22 13 -10000 0 13
VEGFA 0.021 0.004 -10000 0 -10000 0 0
VEGFB 0.021 0.003 -10000 0 -10000 0 0
mol:IP3 -0.014 0.037 0.24 4 -10000 0 4
RASA1 -0.017 0.029 -10000 0 -10000 0 0
NRP2 0.02 0.027 -10000 0 -0.34 2 2
VEGFR1 homodimer -0.015 0.005 -10000 0 -10000 0 0
VEGFB homodimer 0.021 0.003 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.092 0.11 0.44 2 -0.38 20 22
PTPN11 0.021 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.042 0.037 -10000 0 -10000 0 0
mol:L-citrulline -0.008 0.094 0.44 6 -0.36 7 13
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.037 0.019 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.029 0.012 -10000 0 -10000 0 0
CD2AP 0.021 0.005 -10000 0 -10000 0 0
PI3K/GAB1 0.05 0.042 -10000 0 -10000 0 0
PDPK1 -0.014 0.058 0.36 5 -10000 0 5
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.012 -10000 0 -10000 0 0
mol:NADP -0.008 0.094 0.44 6 -0.36 7 13
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.036 0.018 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.017 0.018 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.003 0.076 0.2 1 -0.29 14 15
PDGFB-D/PDGFRB/SLAP 0.023 0.034 -10000 0 -0.24 5 5
PDGFB-D/PDGFRB/APS/CBL 0.038 0.02 -10000 0 -0.21 1 1
AKT1 -0.014 0.082 0.35 9 -10000 0 9
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.003 0.095 0.33 3 -0.33 15 18
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
FGR -0.037 0.16 0.33 2 -0.49 33 35
mol:Ca2+ -0.006 0.1 0.36 3 -0.38 16 19
MYC 0.032 0.13 0.39 10 -0.76 2 12
SHC1 0.018 0.008 -10000 0 -10000 0 0
HRAS/GDP -0.015 0.038 0.16 16 -10000 0 16
LRP1/PDGFRB/PDGFB 0.035 0.037 -10000 0 -0.2 7 7
GRB10 0.02 0.007 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GO:0007205 -0.006 0.1 0.36 3 -0.38 16 19
PTEN 0.021 0.004 -10000 0 -10000 0 0
GRB2 0.021 0.005 -10000 0 -10000 0 0
GRB7 0.019 0.027 -10000 0 -0.34 2 2
PDGFB-D/PDGFRB/SHP2 0.03 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.028 0.012 -10000 0 -10000 0 0
cell cycle arrest 0.023 0.034 -10000 0 -0.24 5 5
HRAS 0.021 0.004 -10000 0 -10000 0 0
HIF1A -0.018 0.076 0.33 9 -10000 0 9
GAB1 -0.005 0.1 0.37 3 -0.35 13 16
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.004 0.091 0.34 5 -0.31 9 14
PDGFB-D/PDGFRB 0.039 0.017 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.031 0.008 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.005 0.06 0.2 1 -0.28 3 4
positive regulation of MAPKKK cascade 0.03 0.009 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
mol:IP3 -0.006 0.1 0.36 3 -0.38 16 19
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.019 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.029 0.022 -10000 0 -0.24 2 2
SHB 0.02 0.006 -10000 0 -10000 0 0
BLK -0.039 0.17 -10000 0 -0.39 53 53
PTPN2 0.02 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.031 0.009 -10000 0 -10000 0 0
BCAR1 0.02 0.02 -10000 0 -0.34 1 1
VAV2 -0.007 0.11 0.34 4 -0.39 14 18
CBL 0.021 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.031 0.009 -10000 0 -10000 0 0
LCK 0.006 0.059 0.33 2 -0.47 2 4
PDGFRB 0.02 0.009 -10000 0 -10000 0 0
ACP1 0.022 0.002 -10000 0 -10000 0 0
HCK -0.014 0.12 0.33 1 -0.53 15 16
ABL1 -0.009 0.1 0.29 5 -0.34 16 21
PDGFB-D/PDGFRB/CBL -0.011 0.11 0.29 1 -0.39 18 19
PTPN1 0.019 0.01 -10000 0 -10000 0 0
SNX15 0.021 0.004 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT1 0.022 0.002 -10000 0 -10000 0 0
cell proliferation 0.033 0.12 0.37 12 -0.67 2 14
SLA 0.012 0.047 -10000 0 -0.34 6 6
actin cytoskeleton reorganization -0.016 0.06 0.32 4 -10000 0 4
SRC -0.001 0.087 0.31 1 -0.64 5 6
PI3K -0.035 0.021 -10000 0 -0.18 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.026 -10000 0 -0.2 2 2
SH2B2 0.02 0.02 -10000 0 -0.34 1 1
PLCgamma1/SPHK1 0.003 0.097 0.34 3 -0.34 15 18
LYN 0.002 0.061 0.31 1 -0.45 3 4
LRP1 0.017 0.038 -10000 0 -0.34 4 4
SOS1 0.022 0.003 -10000 0 -10000 0 0
STAT5B 0.021 0.003 -10000 0 -10000 0 0
STAT5A 0.02 0.019 -10000 0 -0.34 1 1
NCK1-2/p130 Cas 0.053 0.032 -10000 0 -0.18 1 1
SPHK1 0.023 0.03 0.33 3 -10000 0 3
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG -0.006 0.1 0.36 3 -0.38 16 19
PLCG1 -0.007 0.11 0.36 3 -0.39 16 19
NHERF/PDGFRB 0.038 0.031 0.23 1 -0.2 4 5
YES1 -0.014 0.12 0.34 1 -0.58 14 15
cell migration 0.037 0.031 0.23 1 -0.2 4 5
SHC/Grb2/SOS1 0.046 0.033 -10000 0 -10000 0 0
SLC9A3R2 0.017 0.038 -10000 0 -0.34 4 4
SLC9A3R1 0.022 0.017 0.33 1 -10000 0 1
NHERF1-2/PDGFRB/PTEN 0.048 0.034 0.23 1 -0.19 4 5
FYN -0.03 0.13 0.31 1 -0.4 32 33
DOK1 -0.013 0.042 0.16 18 -10000 0 18
HRAS/GTP 0.016 0.003 -10000 0 -10000 0 0
PDGFB 0.017 0.038 -10000 0 -0.34 4 4
RAC1 0.008 0.12 0.37 7 -0.44 8 15
PRKCD -0.012 0.042 0.16 18 -10000 0 18
FER -0.013 0.041 0.17 17 -10000 0 17
MAPKKK cascade 0.011 0.092 0.38 10 -10000 0 10
RASA1 -0.013 0.04 0.17 16 -10000 0 16
NCK1 0.021 0.003 -10000 0 -10000 0 0
NCK2 0.022 0.002 -10000 0 -10000 0 0
p62DOK/Csk -0.017 0.04 0.16 17 -10000 0 17
PDGFB-D/PDGFRB/SHB 0.029 0.011 -10000 0 -10000 0 0
chemotaxis -0.009 0.098 0.28 5 -0.33 15 20
STAT1-3-5/STAT1-3-5 0.043 0.028 -10000 0 -0.19 1 1
Bovine Papilomavirus E5/PDGFRB 0.015 0.006 -10000 0 -10000 0 0
PTPRJ 0.022 0.003 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.02 0.02 -10000 0 -0.34 1 1
SPHK1 0.024 0.029 0.33 3 -10000 0 3
GNAI2 0.021 0.004 -10000 0 -10000 0 0
mol:S1P 0.006 0.016 -10000 0 -0.22 1 1
GNAO1 0.02 0.032 0.33 1 -0.34 2 3
mol:Sphinganine-1-P -0.016 0.02 0.16 3 -0.24 1 4
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.033 0.037 -10000 0 -0.21 2 2
GNAI3 0.021 0.005 -10000 0 -10000 0 0
G12/G13 0.028 0.011 -10000 0 -10000 0 0
S1PR3 0.022 0.017 0.33 1 -10000 0 1
S1PR2 0.02 0.006 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.001 0.03 -10000 0 -0.24 2 2
S1PR5 -0.001 0.088 0.33 1 -0.34 22 23
S1PR4 0.003 0.077 -10000 0 -0.34 17 17
GNAI1 0.02 0.02 -10000 0 -0.34 1 1
S1P/S1P5/G12 0.014 0.059 0.22 1 -0.18 20 21
S1P/S1P3/Gq 0.001 0.075 -10000 0 -0.3 17 17
S1P/S1P4/Gi -0.02 0.093 -10000 0 -0.27 26 26
GNAQ 0.02 0.02 -10000 0 -0.34 1 1
GNAZ -0.007 0.097 -10000 0 -0.34 28 28
GNA14 0.011 0.06 -10000 0 -0.34 10 10
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.006 -10000 0 -10000 0 0
ABCC1 0.021 0.003 -10000 0 -10000 0 0
EPO signaling 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
BCL2L1 0.018 0.065 0.34 2 -10000 0 2
CRKL -0.01 0.051 0.26 5 -10000 0 5
mol:DAG 0.008 0.035 0.24 1 -0.23 1 2
HRAS 0.002 0.079 0.26 11 -10000 0 11
MAPK8 0.001 0.063 0.17 41 -10000 0 41
RAP1A -0.009 0.052 0.26 5 -10000 0 5
GAB1 -0.01 0.052 0.22 8 -10000 0 8
MAPK14 0 0.061 0.17 39 -10000 0 39
EPO 0.009 0.032 0.33 2 -10000 0 2
PLCG1 0.008 0.036 0.24 1 -0.24 1 2
EPOR/TRPC2/IP3 Receptors 0.022 0.009 -10000 0 -10000 0 0
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.038 0.028 0.22 1 -0.21 2 3
GAB1/SHC/GRB2/SOS1 -0.017 0.048 0.24 3 -10000 0 3
EPO/EPOR (dimer) 0.031 0.021 0.24 2 -10000 0 2
IRS2 -0.01 0.052 0.26 5 -10000 0 5
STAT1 0.009 0.039 0.32 1 -0.24 1 2
STAT5B 0.009 0.037 0.28 1 -0.24 1 2
cell proliferation -0.001 0.068 0.17 43 -10000 0 43
GAB1/SHIP/PIK3R1/SHP2/SHC -0.026 0.038 -10000 0 -0.29 1 1
TEC -0.009 0.052 0.26 5 -10000 0 5
SOCS3 0.019 0.027 -10000 0 -0.34 2 2
STAT1 (dimer) 0.009 0.039 0.32 1 -0.23 1 2
JAK2 0.021 0.01 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.046 0.04 0.36 1 -0.16 2 3
EPO/EPOR 0.031 0.021 0.24 2 -10000 0 2
LYN 0.02 0.007 -10000 0 -10000 0 0
TEC/VAV2 -0.013 0.051 0.26 4 -10000 0 4
elevation of cytosolic calcium ion concentration 0.022 0.009 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.038 0.025 0.22 2 -10000 0 2
mol:IP3 0.008 0.035 0.24 1 -0.23 1 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.014 0.058 0.26 4 -0.3 1 5
SH2B3 0.021 0.028 -10000 0 -0.34 2 2
NFKB1 0.001 0.063 0.17 42 -10000 0 42
EPO/EPOR (dimer)/JAK2/SOCS3 0.003 0.045 0.19 1 -0.23 9 10
PTPN6 -0.008 0.046 0.29 1 -0.17 1 2
TEC/VAV2/GRB2 -0.016 0.051 0.26 4 -10000 0 4
EPOR 0.022 0.009 -10000 0 -10000 0 0
INPP5D 0.02 0.027 -10000 0 -0.34 2 2
mol:GDP -0.017 0.048 0.24 3 -10000 0 3
SOS1 0.022 0.003 -10000 0 -10000 0 0
PLCG2 0.018 0.033 -10000 0 -0.34 3 3
CRKL/CBL/C3G -0.016 0.052 0.26 4 -10000 0 4
VAV2 -0.009 0.052 0.22 9 -10000 0 9
CBL -0.009 0.052 0.26 5 -10000 0 5
SHC/Grb2/SOS1 0.023 0.026 0.19 1 -10000 0 1
STAT5A 0.008 0.042 0.28 1 -0.31 2 3
GRB2 0.021 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.02 0.044 0.38 1 -0.35 1 2
LYN/PLCgamma2 0.026 0.027 -10000 0 -0.24 3 3
PTPN11 0.021 0.004 -10000 0 -10000 0 0
BTK -0.017 0.063 0.22 8 -0.3 1 9
BCL2 0.007 0.08 0.39 2 -10000 0 2
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.009 0.078 -10000 0 -0.39 7 7
BAG4 0.019 0.008 -10000 0 -10000 0 0
BAD -0.002 0.039 0.3 2 -0.14 4 6
NFKBIA 0.018 0.008 -10000 0 -10000 0 0
BIRC3 0.022 0.043 0.33 4 -0.34 2 6
BAX -0.002 0.034 0.16 2 -0.13 3 5
EnzymeConsortium:3.1.4.12 0 0.023 0.081 3 -0.085 7 10
IKBKB 0.004 0.094 0.28 8 -0.36 7 15
MAP2K2 -0.006 0.039 0.16 8 -10000 0 8
MAP2K1 -0.007 0.043 0.16 11 -0.16 1 12
SMPD1 -0.001 0.027 0.11 2 -0.12 4 6
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.001 0.081 0.24 2 -0.38 7 9
MAP2K4 -0.003 0.039 0.19 6 -0.15 1 7
protein ubiquitination -0.001 0.087 0.25 3 -0.37 7 10
EnzymeConsortium:2.7.1.37 -0.009 0.046 0.17 8 -0.17 1 9
response to UV 0 0.001 0.004 2 -0.002 1 3
RAF1 -0.004 0.041 0.17 8 -0.15 1 9
CRADD 0.022 0.017 0.33 1 -10000 0 1
mol:ceramide 0.001 0.036 0.12 5 -0.13 6 11
I-kappa-B-alpha/RELA/p50/ubiquitin 0.024 0.012 -10000 0 -10000 0 0
MADD 0.021 0.003 -10000 0 -10000 0 0
MAP3K1 0 0.041 0.2 6 -0.15 2 8
TRADD 0.021 0.004 -10000 0 -10000 0 0
RELA/p50 0.021 0.004 -10000 0 -10000 0 0
MAPK3 -0.005 0.042 0.16 8 -10000 0 8
MAPK1 -0.007 0.046 0.16 8 -0.24 1 9
p50/RELA/I-kappa-B-alpha 0.027 0.013 -10000 0 -10000 0 0
FADD -0.004 0.08 -10000 0 -0.38 7 7
KSR1 0 0.043 0.18 8 -0.14 3 11
MAPK8 -0.007 0.042 0.18 9 -10000 0 9
TRAF2 0.021 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.002 2 -10000 0 2
CHUK -0.01 0.078 -10000 0 -0.37 7 7
TNF R/SODD 0.026 0.013 -10000 0 -10000 0 0
TNF 0.007 0.072 0.33 1 -0.34 14 15
CYCS 0.007 0.045 0.16 7 -0.14 1 8
IKBKG -0.004 0.081 0.25 2 -0.36 6 8
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.005 0.08 -10000 0 -0.4 7 7
RELA 0.021 0.004 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
AIFM1 0.002 0.041 0.19 3 -0.13 2 5
TNF/TNF R/SODD 0.027 0.049 0.23 1 -0.2 13 14
TNFRSF1A 0.02 0.006 -10000 0 -10000 0 0
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.011 0.078 -10000 0 -0.56 6 6
NSMAF 0.005 0.091 0.24 4 -0.38 7 11
response to hydrogen peroxide 0 0.001 0.004 2 -0.002 1 3
BCL2 0.02 0.018 0.33 1 -10000 0 1
Retinoic acid receptors-mediated signaling

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
HDAC1 0.022 0.003 -10000 0 -10000 0 0
HDAC3 0.021 0.004 -10000 0 -10000 0 0
VDR 0.021 0.025 0.33 1 -0.34 1 2
Cbp/p300/PCAF 0.041 0.012 -10000 0 -10000 0 0
EP300 0.021 0.004 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.01 0.044 -10000 0 -0.34 2 2
KAT2B 0.021 0.004 -10000 0 -10000 0 0
MAPK14 0.021 0.005 -10000 0 -10000 0 0
AKT1 0.005 0.046 0.26 1 -0.23 2 3
RAR alpha/9cRA/Cyclin H 0.03 0.052 -10000 0 -0.24 3 3
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.007 0.052 0.2 1 -0.2 15 16
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.019 0.037 -10000 0 -0.21 3 3
NCOR2 0.021 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.016 0.017 0.22 1 -0.23 1 2
RXRs/RARs/NRIP1/9cRA -0.019 0.099 0.42 1 -0.46 9 10
NCOA2 0.017 0.028 -10000 0 -0.34 2 2
NCOA3 0.021 0.005 -10000 0 -10000 0 0
NCOA1 0.022 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.025 0.33 1 -0.34 1 2
RARG 0.022 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.027 0.009 -10000 0 -10000 0 0
MAPK3 0.022 0.003 -10000 0 -10000 0 0
MAPK1 0.021 0.005 -10000 0 -10000 0 0
MAPK8 0.022 0.003 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.015 0.087 -10000 0 -0.38 10 10
RARA 0.012 0.029 0.17 1 -0.2 2 3
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.005 0.049 0.2 1 -0.2 15 16
PRKCA 0.02 0.027 -10000 0 -0.34 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.024 0.11 0.31 2 -0.5 9 11
RXRG -0.096 0.13 0.25 1 -0.26 136 137
RXRA 0.006 0.024 0.18 1 -0.19 2 3
RXRB 0.018 0.046 0.31 3 -0.25 2 5
VDR/Vit D3/DNA 0.016 0.017 0.22 1 -0.23 1 2
RBP1 0.024 0.038 0.33 4 -0.34 1 5
CRBP1/9-cic-RA 0.017 0.026 0.22 4 -0.23 1 5
RARB 0.019 0.027 -10000 0 -0.34 2 2
PRKCG 0.038 0.07 0.33 19 -10000 0 19
MNAT1 0.021 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.022 0.089 -10000 0 -0.41 10 10
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.013 0.086 0.41 1 -0.39 8 9
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.075 0.33 2 -0.31 8 10
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.024 0.11 0.31 2 -0.5 9 11
positive regulation of DNA binding 0.021 0.045 -10000 0 -0.23 3 3
NRIP1 -0.022 0.11 -10000 0 -0.52 7 7
RXRs/RARs -0.027 0.11 -10000 0 -0.5 10 10
RXRs/RXRs/DNA/9cRA -0.026 0.081 -10000 0 -0.38 10 10
PRKACA 0.02 0.006 -10000 0 -10000 0 0
CDK7 0.021 0.005 -10000 0 -10000 0 0
TFIIH 0.04 0.014 -10000 0 -10000 0 0
RAR alpha/9cRA 0.04 0.043 -10000 0 -0.22 1 1
CCNH 0.021 0.005 -10000 0 -10000 0 0
CREBBP 0.021 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.034 0.02 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.019 0.008 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.021 0.05 -10000 0 -0.27 2 2
NEF -0.002 0.022 -10000 0 -0.18 5 5
NFKBIA 0.019 0.01 -10000 0 -10000 0 0
BIRC3 0.007 0.071 0.3 4 -10000 0 4
CYCS -0.003 0.053 0.16 20 -0.3 2 22
RIPK1 0.021 0.004 -10000 0 -10000 0 0
CD247 0.018 0.024 -10000 0 -0.22 3 3
MAP2K7 -0.026 0.19 -10000 0 -0.64 27 27
protein ubiquitination -0.001 0.074 0.31 3 -0.31 4 7
CRADD 0.022 0.017 0.33 1 -10000 0 1
DAXX 0.021 0.005 -10000 0 -10000 0 0
FAS 0.018 0.033 -10000 0 -0.34 3 3
BID 0.007 0.051 0.16 20 -0.28 3 23
NF-kappa-B/RelA/I kappa B alpha 0.04 0.027 0.22 4 -10000 0 4
TRADD 0.021 0.004 -10000 0 -10000 0 0
MAP3K5 0.02 0.007 -10000 0 -10000 0 0
CFLAR 0.022 0.003 -10000 0 -10000 0 0
FADD 0.021 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.04 0.027 0.23 4 -10000 0 4
MAPK8 -0.026 0.18 0.35 2 -0.61 26 28
APAF1 0.021 0.004 -10000 0 -10000 0 0
TRAF1 0.021 0.004 -10000 0 -10000 0 0
TRAF2 0.021 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.009 0.035 -10000 0 -0.29 3 3
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.001 0.073 -10000 0 -0.31 9 9
CHUK -0.002 0.077 0.31 3 -0.34 4 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.05 0.032 -10000 0 -0.18 1 1
TCRz/NEF 0.014 0.024 -10000 0 -0.24 3 3
TNF 0.007 0.072 0.33 1 -0.34 14 15
FASLG -0.014 0.034 -10000 0 -0.36 3 3
NFKB1 0.022 0.013 -10000 0 -0.13 2 2
TNFR1A/BAG4/TNF-alpha 0.027 0.049 0.23 1 -0.2 13 14
CASP6 0.027 0.073 -10000 0 -0.48 3 3
CASP7 0.027 0.1 0.31 14 -0.3 2 16
RELA 0.021 0.013 -10000 0 -0.13 2 2
CASP2 0.021 0.005 -10000 0 -10000 0 0
CASP3 0.025 0.095 0.32 11 -10000 0 11
TNFRSF1A 0.02 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.013 -10000 0 -10000 0 0
CASP8 0.022 0.003 -10000 0 -10000 0 0
CASP9 0.021 0.004 -10000 0 -10000 0 0
MAP3K14 0 0.073 0.19 1 -0.37 4 5
APAF-1/Caspase 9 -0.011 0.055 0.17 4 -0.28 1 5
BCL2 -0.023 0.16 0.31 3 -0.55 26 29
Regulation of Telomerase

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
Telomerase catalytic core complex 0.09 0.15 0.4 26 -0.42 2 28
RAD9A 0.021 0.004 -10000 0 -10000 0 0
AP1 0.017 0.072 -10000 0 -0.23 26 26
IFNAR2 0.028 0.014 -10000 0 -10000 0 0
AKT1 0.02 0.037 -10000 0 -0.35 1 1
ER alpha/Oestrogen 0.019 0.051 0.23 10 -0.22 8 18
NFX1/SIN3/HDAC complex 0.008 0.054 -10000 0 -0.31 5 5
EGF 0.076 0.12 0.33 63 -0.32 3 66
SMG5 0.018 0.008 -10000 0 -10000 0 0
SMG6 0.02 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.039 0.024 -10000 0 -10000 0 0
TERT/c-Abl 0.084 0.14 0.38 15 -0.39 2 17
SAP18 0.021 0.007 -10000 0 -10000 0 0
MRN complex 0.036 0.018 -10000 0 -10000 0 0
WT1 0.016 0.092 0.35 7 -0.33 17 24
WRN 0.018 0.008 -10000 0 -10000 0 0
SP1 0.03 0.018 -10000 0 -10000 0 0
SP3 0.024 0.008 -10000 0 -10000 0 0
TERF2IP 0.021 0.005 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.059 0.11 -10000 0 -0.39 2 2
Mad/Max 0.038 0.016 -10000 0 -10000 0 0
TERT 0.091 0.16 0.41 23 -0.43 2 25
CCND1 0.084 0.17 0.49 8 -0.89 3 11
MAX 0.024 0.008 -10000 0 -10000 0 0
RBBP7 0.022 0.006 -10000 0 -10000 0 0
RBBP4 0.023 0.004 -10000 0 -10000 0 0
TERF2 -0.019 0.014 -10000 0 -10000 0 0
PTGES3 0.021 0.004 -10000 0 -10000 0 0
SIN3A 0.022 0.005 -10000 0 -10000 0 0
Telomerase/911 0.051 0.061 0.22 2 -0.31 1 3
CDKN1B 0.002 0.041 0.22 2 -0.2 2 4
RAD1 0.018 0.008 -10000 0 -10000 0 0
XRCC5 0.022 0.003 -10000 0 -10000 0 0
XRCC6 0.021 0.004 -10000 0 -10000 0 0
SAP30 0.022 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.029 0.011 -10000 0 -10000 0 0
UBE3A 0.023 0.008 -10000 0 -10000 0 0
JUN 0.022 0.028 -10000 0 -0.33 2 2
E6 0.003 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.021 0.013 -10000 0 -10000 0 0
FOS -0.002 0.091 -10000 0 -0.33 25 25
IFN-gamma/IRF1 0.052 0.064 0.25 28 -0.24 2 30
PARP2 0.021 0.005 -10000 0 -10000 0 0
BLM 0.055 0.096 0.33 38 -10000 0 38
Telomerase 0.029 0.079 0.22 9 -0.36 4 13
IRF1 0.025 0.009 -10000 0 -10000 0 0
ESR1 0.022 0.075 0.33 10 -0.33 8 18
KU/TER 0.031 0.007 -10000 0 -10000 0 0
ATM/TRF2 0.029 0.014 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.008 0.052 -10000 0 -0.28 4 4
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.008 0.052 -10000 0 -0.29 4 4
HDAC1 0.023 0.003 -10000 0 -10000 0 0
HDAC2 0.027 0.017 -10000 0 -10000 0 0
ATM 0.009 0.008 -10000 0 -10000 0 0
SMAD3 -0.021 0.009 -10000 0 -10000 0 0
ABL1 0.021 0.004 -10000 0 -10000 0 0
MXD1 0.025 0.007 -10000 0 -10000 0 0
MRE11A 0.021 0.005 -10000 0 -10000 0 0
HUS1 0.02 0.006 -10000 0 -10000 0 0
RPS6KB1 0.021 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.088 0.14 0.39 10 -0.44 1 11
NR2F2 0.006 0.026 -10000 0 -10000 0 0
MAPK3 -0.007 0.02 -10000 0 -10000 0 0
MAPK1 -0.008 0.019 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.01 0.02 -10000 0 -10000 0 0
NFKB1 0.022 0.003 -10000 0 -10000 0 0
HNRNPC 0.021 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.008 -10000 0 -10000 0 0
NBN 0.019 0.007 -10000 0 -10000 0 0
EGFR 0.019 0.037 0.34 1 -0.32 3 4
mol:Oestrogen 0.002 0.003 -10000 0 -10000 0 0
EGF/EGFR 0.06 0.086 0.25 52 -0.2 6 58
MYC 0.019 0.029 -10000 0 -0.33 2 2
IL2 0.029 0.018 -10000 0 -10000 0 0
KU 0.031 0.007 -10000 0 -10000 0 0
RAD50 0.021 0.005 -10000 0 -10000 0 0
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
TGFB1 0.01 0.02 -10000 0 -10000 0 0
TRF2/BLM 0.049 0.06 0.23 35 -10000 0 35
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.094 0.14 0.39 13 -0.4 2 15
SP1/HDAC2 0.045 0.034 -10000 0 -10000 0 0
PINX1 0.018 0.008 -10000 0 -10000 0 0
Telomerase/EST1A 0.054 0.1 -10000 0 -0.38 2 2
Smad3/Myc -0.02 0.017 -10000 0 -0.18 2 2
911 complex 0.033 0.02 -10000 0 -10000 0 0
IFNG 0.047 0.089 0.34 28 -0.34 2 30
Telomerase/PinX1 0.046 0.1 -10000 0 -0.38 2 2
Telomerase/AKT1/mTOR/p70S6K 0.046 0.088 0.31 5 -0.41 3 8
SIN3B 0.022 0.007 -10000 0 -10000 0 0
YWHAE 0.02 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.05 0.099 -10000 0 -0.38 1 1
response to DNA damage stimulus 0.002 0.018 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.048 0.028 -10000 0 -10000 0 0
TRF2/WRN 0.025 0.013 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.057 0.11 -10000 0 -0.39 2 2
E2F1 0.032 0.04 0.32 6 -10000 0 6
ZNFX1 0.022 0.006 -10000 0 -10000 0 0
PIF1 0.055 0.097 0.33 39 -10000 0 39
NCL 0.022 0.003 -10000 0 -10000 0 0
DKC1 0.021 0.005 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.007 0.11 -9999 0 -0.34 24 24
MAP3K8 0.017 0.022 -9999 0 -0.34 1 1
FOS 0.006 0.081 -9999 0 -0.4 5 5
PRKCA 0.015 0.03 -9999 0 -0.34 2 2
PTPN7 0.015 0.016 -9999 0 -10000 0 0
HRAS 0.018 0.011 -9999 0 -10000 0 0
PRKCB 0.012 0.048 -9999 0 -0.34 6 6
NRAS 0.018 0.011 -9999 0 -10000 0 0
RAS family/GTP 0.031 0.023 -9999 0 -10000 0 0
MAPK3 0.012 0.04 -9999 0 -10000 0 0
MAP2K1 -0.004 0.081 -9999 0 -0.4 9 9
ELK1 0.017 0.017 -9999 0 -10000 0 0
BRAF -0.002 0.058 -9999 0 -0.35 8 8
mol:GTP 0 0.001 -9999 0 -0.004 27 27
MAPK1 0.003 0.076 -9999 0 -0.41 8 8
RAF1 -0.003 0.059 -9999 0 -0.34 9 9
KRAS 0.018 0.011 -9999 0 -10000 0 0
Arf6 downstream 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
PLAUR 0.01 0.018 -10000 0 -10000 0 0
regulation of axonogenesis 0.003 0.019 0.25 2 -10000 0 2
myoblast fusion -0.01 0.028 0.32 1 -10000 0 1
mol:GTP 0.015 0.022 -10000 0 -0.16 5 5
regulation of calcium-dependent cell-cell adhesion -0.051 0.063 0.21 3 -0.22 34 37
ARF1/GTP 0.025 0.021 -10000 0 -0.12 3 3
mol:GM1 0.004 0.015 -10000 0 -0.12 4 4
mol:Choline -0.011 0.011 -10000 0 -10000 0 0
lamellipodium assembly 0.001 0.045 -10000 0 -0.38 4 4
MAPK3 0.011 0.014 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.052 0.064 0.22 34 -0.21 3 37
ARF1 0.02 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.01 0.028 -10000 0 -0.32 1 1
ARF1/GDP 0.011 0.034 -10000 0 -0.23 3 3
ARF6 0.026 0.01 -10000 0 -10000 0 0
RAB11A 0.021 0.004 -10000 0 -10000 0 0
TIAM1 0.016 0.038 -10000 0 -0.33 4 4
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.012 0.013 -10000 0 -10000 0 0
actin filament bundle formation -0.015 0.037 0.24 4 -10000 0 4
KALRN 0.002 0.023 -10000 0 -0.21 3 3
RAB11FIP3/RAB11A 0.031 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.038 -10000 0 -0.24 4 4
NME1 0.054 0.098 0.33 39 -10000 0 39
Rac1/GDP 0.013 0.037 -10000 0 -0.24 4 4
substrate adhesion-dependent cell spreading 0.015 0.022 -10000 0 -0.16 5 5
cortical actin cytoskeleton organization 0.001 0.045 -10000 0 -0.38 4 4
RAC1 0.019 0.007 -10000 0 -10000 0 0
liver development 0.015 0.022 -10000 0 -0.16 5 5
ARF6/GTP 0.015 0.022 -10000 0 -0.16 5 5
RhoA/GTP 0.025 0.022 -10000 0 -10000 0 0
mol:GDP 0.002 0.026 -10000 0 -0.24 3 3
ARF6/GTP/RAB11FIP3/RAB11A 0.037 0.023 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
PLD1 0.009 0.017 -10000 0 -0.12 3 3
RAB11FIP3 0.021 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.001 0.045 -10000 0 -0.38 4 4
ruffle organization -0.003 0.019 -10000 0 -0.25 2 2
regulation of epithelial cell migration 0.015 0.022 -10000 0 -0.16 5 5
PLD2 0.009 0.014 -10000 0 -0.12 3 3
PIP5K1A -0.003 0.019 -10000 0 -0.25 2 2
mol:Phosphatidic acid -0.011 0.011 -10000 0 -10000 0 0
Rac1/GTP 0.001 0.045 -10000 0 -0.38 4 4
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.021 0.005 -10000 0 -10000 0 0
NFATC1 -0.018 0.1 0.4 1 -0.39 13 14
NFATC2 -0.014 0.062 0.18 2 -0.27 9 11
NFATC3 0.006 0.018 -10000 0 -0.3 1 1
YWHAE 0.02 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.018 0.086 0.18 1 -0.31 16 17
Exportin 1/Ran/NUP214 0.041 0.018 0.23 2 -10000 0 2
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0 0.08 -10000 0 -0.3 12 12
BCL2/BAX 0.028 0.016 0.24 1 -10000 0 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.016 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.016 -10000 0 -10000 0 0
BAX 0.021 0.005 -10000 0 -10000 0 0
MAPK14 0.013 0.016 -10000 0 -10000 0 0
BAD 0.021 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D -0.005 0.079 -10000 0 -0.32 12 12
Calcineurin A alpha-beta B1/BCL2 0.02 0.018 0.33 1 -10000 0 1
FKBP8 0.02 0.02 -10000 0 -0.34 1 1
activation-induced cell death of T cells 0.005 0.078 0.31 12 -10000 0 12
KPNB1 0.021 0.004 -10000 0 -10000 0 0
KPNA2 0.025 0.033 0.33 4 -10000 0 4
XPO1 0.022 0.002 -10000 0 -10000 0 0
SFN 0.026 0.047 0.33 7 -0.34 1 8
MAP3K8 0.012 0.025 -10000 0 -0.34 1 1
NFAT4/CK1 alpha 0.007 0.026 -10000 0 -0.16 1 1
MEF2D/NFAT1/Cbp/p300 -0.019 0.11 -10000 0 -0.24 53 53
CABIN1 -0.018 0.083 0.18 1 -0.3 15 16
CALM1 0.012 0.018 -10000 0 -10000 0 0
RAN 0.023 0.024 0.33 2 -10000 0 2
MAP3K1 0.021 0.005 -10000 0 -10000 0 0
CAMK4 0.02 0.032 0.33 1 -0.34 2 3
mol:Ca2+ -0.002 0.005 -10000 0 -10000 0 0
MAPK3 0.022 0.003 -10000 0 -10000 0 0
YWHAH 0.021 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.027 0.022 -10000 0 -0.24 2 2
YWHAB 0.021 0.005 -10000 0 -10000 0 0
MAPK8 0.013 0.018 -10000 0 -10000 0 0
MAPK9 0.021 0.005 -10000 0 -10000 0 0
YWHAG 0.021 0.005 -10000 0 -10000 0 0
FKBP1A 0.021 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.019 0.11 0.33 2 -0.39 15 17
PRKCH 0.021 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.017 0.029 -10000 0 -10000 0 0
CASP3 0.013 0.017 -10000 0 -10000 0 0
PIM1 0.021 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.011 -10000 0 -10000 0 0
apoptosis 0.011 0.019 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.036 -10000 0 -0.26 1 1
PRKCB 0.015 0.046 -10000 0 -0.34 6 6
PRKCE 0.019 0.027 -10000 0 -0.34 2 2
JNK2/NFAT4 0.016 0.037 -10000 0 -0.27 1 1
BAD/BCL-XL 0.03 0.009 -10000 0 -10000 0 0
PRKCD 0.021 0.004 -10000 0 -10000 0 0
NUP214 0.021 0.004 -10000 0 -10000 0 0
PRKCZ 0.011 0.032 -10000 0 -0.34 2 2
PRKCA 0.019 0.027 -10000 0 -0.34 2 2
PRKCG 0.037 0.07 0.33 19 -10000 0 19
PRKCQ -0.02 0.11 -10000 0 -0.34 40 40
FKBP38/BCL2 0.027 0.022 0.24 1 -0.24 1 2
EP300 0.011 0.021 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.021 0.005 -10000 0 -10000 0 0
NFATc/JNK1 -0.012 0.1 0.38 1 -0.38 12 13
CaM/Ca2+/FKBP38 0.016 0.025 -10000 0 -0.21 1 1
FKBP12/FK506 0.015 0.004 -10000 0 -10000 0 0
CSNK1A1 -0.016 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.017 0.029 0.21 1 -0.2 2 3
NFATc/ERK1 -0.008 0.1 0.38 1 -0.38 12 13
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.003 0.088 -10000 0 -0.29 15 15
NR4A1 -0.061 0.16 0.24 4 -0.37 62 66
GSK3B 0.013 0.017 -10000 0 -10000 0 0
positive T cell selection 0.006 0.018 -10000 0 -0.29 1 1
NFAT1/CK1 alpha -0.012 0.045 0.15 1 -0.22 6 7
RCH1/ KPNB1 0.033 0.023 0.24 4 -10000 0 4
YWHAQ 0.022 0.002 -10000 0 -10000 0 0
PRKACA 0.012 0.017 -10000 0 -10000 0 0
AKAP5 0.019 0.027 -10000 0 -0.34 2 2
MEF2D 0.009 0.02 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.008 -10000 0 -10000 0 0
NFATc/p38 alpha -0.015 0.099 -10000 0 -0.37 13 13
CREBBP 0.011 0.021 -10000 0 -10000 0 0
BCL2 0.02 0.018 0.33 1 -10000 0 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.027 0.071 -10000 0 -0.26 14 14
Ran/GTP/Exportin 1/HDAC1 -0.019 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.005 0.071 -10000 0 -0.3 12 12
SUMO1 0.022 0.003 -10000 0 -10000 0 0
ZFPM1 0.022 0.017 0.33 1 -10000 0 1
NPC/RanGAP1/SUMO1/Ubc9 0.006 0.002 -10000 0 -10000 0 0
FKBP3 0.021 0.005 -10000 0 -10000 0 0
Histones 0.033 0.059 -10000 0 -0.3 2 2
YY1/LSF 0.014 0.044 -10000 0 -0.24 4 4
SMG5 0.018 0.008 -10000 0 -10000 0 0
RAN 0.023 0.024 0.33 2 -10000 0 2
I kappa B alpha/HDAC3 0.001 0.04 -10000 0 -0.2 10 10
I kappa B alpha/HDAC1 0.012 0.044 -10000 0 -0.33 1 1
SAP18 0.02 0.006 -10000 0 -10000 0 0
RELA 0.006 0.053 -10000 0 -0.22 11 11
HDAC1/Smad7 0.036 0.022 -10000 0 -0.2 1 1
RANGAP1 0.021 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.014 0.054 -10000 0 -0.32 2 2
NuRD/MBD3 Complex 0 0.066 -10000 0 -0.3 8 8
NF kappa B1 p50/RelA 0.011 0.075 -10000 0 -0.31 10 10
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.01 0.1 -10000 0 -0.34 31 31
GATA1 -0.015 0.11 -10000 0 -0.34 35 35
Mad/Max 0.031 0.007 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.022 0.095 -10000 0 -0.33 16 16
RBBP7 0.021 0.005 -10000 0 -10000 0 0
NPC 0.013 0.001 -10000 0 -10000 0 0
RBBP4 0.022 0.003 -10000 0 -10000 0 0
MAX 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.021 0.005 -10000 0 -10000 0 0
NFKBIA 0.005 0.026 -10000 0 -10000 0 0
KAT2B 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.013 0.056 -10000 0 -0.37 3 3
SIN3 complex 0.048 0.021 -10000 0 -10000 0 0
SMURF1 0.021 0.005 -10000 0 -10000 0 0
CHD3 0.02 0.007 -10000 0 -10000 0 0
SAP30 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.02 0.006 -10000 0 -10000 0 0
YY1/HDAC3 0.004 0.05 -10000 0 -0.26 8 8
YY1/HDAC2 0.014 0.041 -10000 0 -0.24 4 4
YY1/HDAC1 0.014 0.044 -10000 0 -0.24 4 4
NuRD/MBD2 Complex (MeCP1) -0.004 0.069 -10000 0 -0.34 7 7
PPARG -0.026 0.12 -10000 0 -0.3 43 43
HDAC8/hEST1B 0.035 0.019 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.02 0.006 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.014 0.053 -10000 0 -0.32 2 2
MBD3L2 0.017 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.035 0.021 -10000 0 -0.2 1 1
CREBBP 0.021 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex -0.005 0.086 -10000 0 -0.31 18 18
HDAC1 0.022 0.003 -10000 0 -10000 0 0
HDAC3 0.005 0.032 -10000 0 -0.35 1 1
HDAC2 0.02 0.007 -10000 0 -10000 0 0
YY1 0.007 0.003 -10000 0 -10000 0 0
HDAC8 0.022 0.003 -10000 0 -10000 0 0
SMAD7 0.018 0.02 -10000 0 -0.34 1 1
NCOR2 0.021 0.004 -10000 0 -10000 0 0
MXD1 0.022 0.002 -10000 0 -10000 0 0
STAT3 0.011 0.003 -10000 0 -10000 0 0
NFKB1 0.022 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.022 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.025 0.045 -10000 0 -0.22 4 4
YY1/SAP30/HDAC1 0.025 0.045 -10000 0 -0.22 4 4
EP300 0.021 0.004 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.011 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.005 0.026 -10000 0 -10000 0 0
histone deacetylation -0.004 0.068 -10000 0 -0.34 7 7
STAT3 (dimer non-phopshorylated)/HDAC3 0.004 0.041 -10000 0 -0.22 6 6
nuclear export -0.035 0.018 -10000 0 -10000 0 0
PRKACA 0.02 0.006 -10000 0 -10000 0 0
GATAD2B 0.018 0.008 -10000 0 -10000 0 0
GATAD2A 0.021 0.005 -10000 0 -10000 0 0
GATA2/HDAC3 0 0.074 -10000 0 -0.28 7 7
GATA1/HDAC1 0.004 0.081 -10000 0 -0.24 35 35
GATA1/HDAC3 -0.004 0.078 -10000 0 -0.32 7 7
CHD4 0.02 0.006 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.019 0.053 0.24 1 -0.24 13 14
SIN3/HDAC complex/Mad/Max -0.011 0.062 -10000 0 -0.3 7 7
NuRD Complex -0.008 0.08 -10000 0 -0.3 14 14
positive regulation of chromatin silencing 0.031 0.058 -10000 0 -0.3 2 2
SIN3B 0.021 0.005 -10000 0 -10000 0 0
MTA2 0.022 0.003 -10000 0 -10000 0 0
SIN3A 0.021 0.003 -10000 0 -10000 0 0
XPO1 0.022 0.002 -10000 0 -10000 0 0
SUMO1/HDAC1 0.029 0.027 -10000 0 -0.18 2 2
HDAC complex 0.048 0.02 -10000 0 -10000 0 0
GATA1/Fog1 0.004 0.079 -10000 0 -0.23 35 35
FKBP25/HDAC1/HDAC2 0.038 0.016 -10000 0 -10000 0 0
TNF 0.007 0.072 0.33 1 -0.34 14 15
negative regulation of cell growth -0.01 0.061 -10000 0 -0.3 7 7
NuRD/MBD2/PRMT5 Complex -0.004 0.069 -10000 0 -0.34 7 7
Ran/GTP/Exportin 1 0.029 0.028 0.2 1 -0.18 2 3
NF kappa B/RelA/I kappa B alpha -0.005 0.062 -10000 0 -0.29 12 12
SIN3/HDAC complex/NCoR1 -0.015 0.073 -10000 0 -0.34 10 10
TFCP2 0.021 0.003 -10000 0 -10000 0 0
NR2C1 0.021 0.003 -10000 0 -10000 0 0
MBD3 0.018 0.027 -10000 0 -0.34 2 2
MBD2 0.019 0.007 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0 0.065 -10000 0 -0.51 1 1
UGCG -0.002 0.11 -10000 0 -0.62 10 10
AKT1/mTOR/p70S6K/Hsp90/TERT 0.05 0.086 0.26 8 -0.4 3 11
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.001 0.11 -10000 0 -0.62 10 10
mol:DAG 0.002 0.088 -10000 0 -0.78 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.023 0.082 0.28 1 -0.41 5 6
FRAP1 0.017 0.091 0.31 1 -0.46 5 6
FOXO3 0.011 0.087 -10000 0 -0.46 5 5
AKT1 0.014 0.093 -10000 0 -0.5 5 5
GAB2 0.017 0.038 -10000 0 -0.34 4 4
SMPD1 0.004 0.089 -10000 0 -0.6 7 7
SGMS1 0.01 0.064 -10000 0 -0.56 4 4
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 -0.013 0.005 -10000 0 -10000 0 0
CALM1 0.021 0.005 -10000 0 -10000 0 0
cell proliferation 0.024 0.088 0.22 3 -0.36 10 13
EIF3A 0.022 0.003 -10000 0 -10000 0 0
PI3K 0.031 0.011 -10000 0 -10000 0 0
RPS6KB1 0.015 0.056 -10000 0 -0.95 1 1
mol:sphingomyelin 0.002 0.088 -10000 0 -0.78 4 4
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 0.021 0.006 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
JAK1 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.003 -10000 0 -10000 0 0
MYC 0.038 0.12 0.37 2 -0.78 3 5
MYB 0.006 0.096 -10000 0 -1 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.014 0.076 -10000 0 -0.4 4 4
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.035 0.055 -10000 0 -0.87 1 1
mol:PI-3-4-5-P3 0.014 0.075 -10000 0 -0.4 4 4
Rac1/GDP -0.015 0.008 -10000 0 -10000 0 0
T cell proliferation 0.01 0.072 -10000 0 -0.36 3 3
SHC1 0.018 0.009 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.008 0.088 2 -0.066 2 4
PRKCZ 0.01 0.071 -10000 0 -0.37 2 2
NF kappa B1 p50/RelA 0.033 0.089 0.3 1 -0.42 5 6
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.001 0.056 -10000 0 -0.38 4 4
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
IL2RA 0.045 0.088 0.33 29 -0.34 1 30
IL2RB 0.019 0.027 -10000 0 -0.34 2 2
TERT 0.07 0.12 0.33 61 -10000 0 61
E2F1 0.014 0.065 0.24 2 -0.39 7 9
SOS1 0.022 0.004 -10000 0 -10000 0 0
RPS6 0.02 0.007 -10000 0 -10000 0 0
mol:cAMP -0.001 0.004 0.032 2 -0.047 2 4
PTPN11 0.021 0.005 -10000 0 -10000 0 0
IL2RG 0.018 0.038 -10000 0 -0.33 4 4
actin cytoskeleton organization 0.01 0.072 -10000 0 -0.36 3 3
GRB2 0.021 0.006 -10000 0 -10000 0 0
IL2 0.02 0.005 -10000 0 -10000 0 0
PIK3CA 0.021 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.033 0.018 -10000 0 -10000 0 0
LCK 0.022 0.026 0.33 1 -0.34 1 2
BCL2 0.016 0.081 0.46 1 -0.42 2 3
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.005 0.068 -10000 0 -0.31 15 15
KLHL20 0 0.053 0.17 2 -0.21 8 10
CYFIP2 0.016 0.043 -10000 0 -0.34 5 5
Rac1/GDP -0.011 0.063 0.38 2 -0.26 6 8
ENAH -0.005 0.068 -10000 0 -0.31 15 15
AP1M1 0.021 0.005 -10000 0 -10000 0 0
RAP1B 0.02 0.006 -10000 0 -10000 0 0
RAP1A 0.021 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.027 0.027 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.015 0.026 -10000 0 -0.14 9 9
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.045 0.03 -10000 0 -0.19 3 3
RAPGEF1 -0.01 0.06 0.21 1 -0.29 10 11
CTNND1 0.021 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.005 0.073 -10000 0 -0.32 16 16
CRK -0.012 0.06 -10000 0 -0.31 12 12
E-cadherin/gamma catenin/alpha catenin 0.039 0.023 -10000 0 -0.2 2 2
alphaE/beta7 Integrin 0.028 0.018 -10000 0 -0.24 1 1
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
NCKAP1 0.022 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.034 0.017 -10000 0 -10000 0 0
DLG1 -0.003 0.064 -10000 0 -0.31 13 13
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.027 0.017 -10000 0 -0.14 2 2
MLLT4 0.02 0.007 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.053 0.059 0.22 35 -0.18 3 38
PI3K -0.033 0.021 -10000 0 -0.17 2 2
ARF6 0.021 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.029 0.022 -10000 0 -0.24 2 2
TIAM1 0.017 0.038 -10000 0 -0.34 4 4
E-cadherin(dimer)/Ca2+ 0.046 0.023 -10000 0 -0.18 2 2
AKT1 -0.017 0.027 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
CDH1 0.019 0.027 -10000 0 -0.34 2 2
RhoA/GDP -0.011 0.067 0.38 2 -0.26 5 7
actin cytoskeleton organization 0.004 0.047 0.17 8 -0.16 8 16
CDC42/GDP -0.012 0.066 0.38 2 -0.26 6 8
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.008 0.018 -10000 0 -0.18 3 3
ITGB7 0.02 0.019 -10000 0 -0.34 1 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.05 0.025 -10000 0 -0.19 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin 0.034 0.019 -10000 0 -0.17 2 2
mol:GDP -0.011 0.072 0.4 2 -0.29 6 8
CDC42/GTP/IQGAP1 0.028 0.007 -10000 0 -10000 0 0
JUP 0.021 0.004 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP -0.013 0.06 -10000 0 -0.26 4 4
RAC1/GTP/IQGAP1 0.026 0.01 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.03 0.009 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.005 0.042 0.16 9 -0.16 3 12
NME1 0.055 0.097 0.33 39 -10000 0 39
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.002 0.061 -10000 0 -0.32 11 11
regulation of cell-cell adhesion -0.027 0.019 -10000 0 -0.15 2 2
WASF2 -0.003 0.024 0.078 1 -10000 0 1
Rap1/GTP -0.025 0.03 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.05 0.035 -10000 0 -0.18 3 3
CCND1 0.004 0.042 0.15 7 -0.18 4 11
VAV2 -0.007 0.12 -10000 0 -0.6 11 11
RAP1/GDP -0.021 0.046 -10000 0 -0.23 3 3
adherens junction assembly -0.003 0.064 -10000 0 -0.31 13 13
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.021 0.004 -10000 0 -10000 0 0
PIP5K1C 0.02 0.006 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.035 0.032 -10000 0 -0.18 3 3
E-cadherin/beta catenin 0.004 0.023 -10000 0 -0.28 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.006 0.071 -10000 0 -0.31 16 16
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.005 0.065 -10000 0 -0.33 10 10
E-cadherin/beta catenin/alpha catenin 0.039 0.022 -10000 0 -0.2 2 2
ITGAE 0.02 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.005 0.075 -10000 0 -0.32 16 16
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.014 0.01 -10000 0 -10000 0 0
TRAF2/ASK1 0.026 0.01 -10000 0 -10000 0 0
ATM 0.021 0.005 -10000 0 -10000 0 0
MAP2K3 -0.009 0.096 0.29 2 -0.32 17 19
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.004 0.083 0.28 2 -0.34 9 11
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.019 0.037 0.33 1 -0.34 3 4
TXN 0.005 0.013 0.17 2 -10000 0 2
CALM1 0.021 0.005 -10000 0 -10000 0 0
GADD45A 0.021 0.004 -10000 0 -10000 0 0
GADD45B 0.018 0.027 -10000 0 -0.34 2 2
MAP3K1 0.021 0.005 -10000 0 -10000 0 0
MAP3K6 0.021 0.003 -10000 0 -10000 0 0
MAP3K7 0.02 0.007 -10000 0 -10000 0 0
MAP3K4 0.02 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.029 0.01 -10000 0 -10000 0 0
TAK1/TAB family 0.002 0.02 0.14 2 -0.13 1 3
RAC1/OSM/MEKK3 0.035 0.016 -10000 0 -10000 0 0
TRAF2 0.021 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0.078 -10000 0 -0.29 12 12
TRAF6 0.004 0.001 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.062 0.11 0.33 48 -10000 0 48
CCM2 0.02 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.05 0.064 0.21 46 -10000 0 46
MAPK11 0.018 0.027 -10000 0 -0.34 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.054 0.062 0.22 41 -10000 0 41
OSM/MEKK3 0.028 0.011 -10000 0 -10000 0 0
TAOK1 0.007 0.002 -10000 0 -10000 0 0
TAOK2 0.007 0.002 -10000 0 -10000 0 0
TAOK3 0.007 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.021 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.02 0.007 -10000 0 -10000 0 0
MAP3K10 0.018 0.033 -10000 0 -0.34 3 3
MAP3K3 0.021 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.015 0.02 0.16 1 -10000 0 1
GADD45/MTK1/MTK1 0.041 0.037 0.22 1 -0.21 4 5
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.048 0.023 -10000 0 -0.19 1 1
HDAC3 0.021 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.019 0.006 -10000 0 -10000 0 0
GATA1/HDAC4 0.005 0.079 -10000 0 -0.24 34 34
GATA1/HDAC5 0.004 0.08 -10000 0 -0.24 34 34
GATA2/HDAC5 0.008 0.075 -10000 0 -0.24 30 30
HDAC5/BCL6/BCoR 0.04 0.014 -10000 0 -10000 0 0
HDAC9 0.021 0.05 0.33 5 -0.34 3 8
Glucocorticoid receptor/Hsp90/HDAC6 0.04 0.014 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.03 0.008 -10000 0 -10000 0 0
HDAC5/YWHAB 0.03 0.009 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.006 0.002 -10000 0 -10000 0 0
GATA2 -0.01 0.1 -10000 0 -0.34 31 31
HDAC4/RFXANK 0.03 0.009 -10000 0 -10000 0 0
BCOR 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.019 0.02 -10000 0 -0.34 1 1
HDAC5 0.021 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.029 0.017 -10000 0 -0.24 1 1
Histones 0.01 0.052 -10000 0 -0.26 4 4
ADRBK1 0.021 0.004 -10000 0 -10000 0 0
HDAC4 0.021 0.004 -10000 0 -10000 0 0
XPO1 0.022 0.002 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.031 0.008 -10000 0 -10000 0 0
HDAC4/Ubc9 0.031 0.007 -10000 0 -10000 0 0
HDAC7 0.021 0.004 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.029 0.011 -10000 0 -10000 0 0
TUBA1B 0.021 0.003 -10000 0 -10000 0 0
HDAC6 0.021 0.004 -10000 0 -10000 0 0
HDAC5/RFXANK 0.03 0.009 -10000 0 -10000 0 0
CAMK4 0.02 0.032 0.33 1 -0.34 2 3
Tubulin/HDAC6 0.044 0.027 0.23 6 -10000 0 6
SUMO1 0.022 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.021 0.005 -10000 0 -10000 0 0
GATA1 -0.015 0.11 -10000 0 -0.34 35 35
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.02 0.007 -10000 0 -10000 0 0
NR3C1 0.021 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.029 0.025 -10000 0 -0.18 2 2
SRF 0.021 0.005 -10000 0 -10000 0 0
HDAC4/YWHAB 0.03 0.009 -10000 0 -10000 0 0
Tubulin 0.034 0.028 0.24 6 -10000 0 6
HDAC4/14-3-3 E 0.029 0.011 -10000 0 -10000 0 0
GNB1 0.021 0.004 -10000 0 -10000 0 0
RANGAP1 0.021 0.004 -10000 0 -10000 0 0
BCL6/BCoR 0.03 0.009 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.041 0.013 -10000 0 -10000 0 0
HDAC4/SRF 0.039 0.025 0.23 1 -0.2 2 3
HDAC4/ER alpha 0.028 0.053 0.24 9 -0.24 8 17
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.01 0.051 -10000 0 -0.26 4 4
cell motility 0.043 0.027 0.23 6 -10000 0 6
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.03 0.008 -10000 0 -10000 0 0
BCL6 0.021 0.005 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.021 0.004 -10000 0 -10000 0 0
Hsp90/HDAC6 0.03 0.009 -10000 0 -10000 0 0
ESR1 0.021 0.075 0.33 10 -0.34 8 18
HDAC6/HDAC11 0.031 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.029 0.028 0.2 1 -0.18 2 3
NPC 0.013 0.001 -10000 0 -10000 0 0
MEF2C 0.021 0.005 -10000 0 -10000 0 0
RAN 0.023 0.024 0.33 2 -10000 0 2
HDAC4/MEF2C 0.058 0.024 -10000 0 -10000 0 0
GNG2 0.02 0.02 -10000 0 -0.34 1 1
NCOR2 0.021 0.004 -10000 0 -10000 0 0
TUBB2A 0.026 0.04 0.33 6 -10000 0 6
HDAC11 0.021 0.004 -10000 0 -10000 0 0
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
RANBP2 0.022 0.002 -10000 0 -10000 0 0
ANKRA2 0.021 0.004 -10000 0 -10000 0 0
RFXANK 0.021 0.005 -10000 0 -10000 0 0
nuclear import -0.02 0.009 -10000 0 -10000 0 0
Circadian rhythm 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
chromatin modification 0.049 0.061 0.41 4 -10000 0 4
CLOCK 0.022 0.005 -10000 0 -10000 0 0
TIMELESS/CRY2 0.027 0.034 -10000 0 -10000 0 0
DEC1/BMAL1 0.029 0.009 -10000 0 -10000 0 0
ATR 0.021 0.003 -10000 0 -10000 0 0
NR1D1 0.008 0.026 -10000 0 -10000 0 0
ARNTL 0.022 0.005 -10000 0 -10000 0 0
TIMELESS 0.01 0.041 0.38 2 -10000 0 2
NPAS2 0.024 0.024 0.33 2 -10000 0 2
CRY2 0.022 0.003 -10000 0 -10000 0 0
mol:CO -0.004 0.013 -10000 0 -0.1 6 6
CHEK1 0.042 0.078 0.33 24 -10000 0 24
mol:HEME 0.004 0.013 0.1 6 -10000 0 6
PER1 0.009 0.062 -10000 0 -0.34 11 11
BMAL/CLOCK/NPAS2 0.046 0.024 0.23 2 -10000 0 2
BMAL1/CLOCK 0.01 0.047 -10000 0 -0.38 1 1
S phase of mitotic cell cycle 0.049 0.061 0.41 4 -10000 0 4
TIMELESS/CHEK1/ATR 0.05 0.062 0.42 4 -10000 0 4
mol:NADPH 0.004 0.013 0.1 6 -10000 0 6
PER1/TIMELESS 0.02 0.046 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.019 0.004 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.016 0.006 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.024 0.014 -10000 0 -10000 0 0
CDKN1B 0.005 0.046 -10000 0 -0.29 6 6
CDKN1A 0.007 0.052 -10000 0 -0.29 7 7
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.02 0.007 -10000 0 -10000 0 0
FOXO3 0.006 0.034 -10000 0 -0.29 3 3
AKT1 -0.001 0.042 -10000 0 -0.3 7 7
BAD 0.021 0.003 -10000 0 -10000 0 0
AKT3 0.006 0.014 -10000 0 -0.25 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.004 0.048 -10000 0 -0.29 7 7
AKT1/ASK1 0.024 0.06 -10000 0 -0.27 7 7
BAD/YWHAZ 0.035 0.018 -10000 0 -10000 0 0
RICTOR 0.018 0.009 -10000 0 -10000 0 0
RAF1 0.021 0.004 -10000 0 -10000 0 0
JNK cascade -0.022 0.056 0.26 7 -10000 0 7
TSC1 0.006 0.038 -10000 0 -0.29 4 4
YWHAZ 0.019 0.008 -10000 0 -10000 0 0
AKT1/RAF1 0.029 0.065 0.23 2 -0.28 7 9
EP300 0.021 0.004 -10000 0 -10000 0 0
mol:GDP 0.009 0.048 -10000 0 -0.29 7 7
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.003 0.046 -10000 0 -0.29 7 7
YWHAQ 0.022 0.002 -10000 0 -10000 0 0
TBC1D4 -0.006 0.002 -10000 0 -10000 0 0
MAP3K5 0.02 0.007 -10000 0 -10000 0 0
MAPKAP1 0.021 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.018 0.07 0.28 5 -0.25 6 11
YWHAH 0.021 0.004 -10000 0 -10000 0 0
AKT1S1 0.006 0.043 -10000 0 -0.3 5 5
CASP9 0.007 0.044 -10000 0 -0.3 5 5
YWHAB 0.021 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.028 0.069 0.28 6 -0.28 7 13
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.04 0.014 -10000 0 -10000 0 0
YWHAE 0.02 0.007 -10000 0 -10000 0 0
SRC 0.021 0.004 -10000 0 -10000 0 0
AKT2/p21CIP1 0.008 0.055 0.23 3 -0.26 5 8
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.007 0.042 0.18 1 -0.32 4 5
CHUK 0.004 0.047 -10000 0 -0.29 7 7
BAD/BCL-XL 0.025 0.059 -10000 0 -0.28 7 7
mTORC2 0.022 0.012 -10000 0 -10000 0 0
AKT2 0.007 0.002 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.018 0.089 0.3 6 -0.37 6 12
PDPK1 0.021 0.003 -10000 0 -10000 0 0
MDM2 0.015 0.061 -10000 0 -0.29 6 6
MAPKKK cascade -0.029 0.064 0.28 7 -0.22 2 9
MDM2/Cbp/p300 0.047 0.077 0.32 4 -0.28 6 10
TSC1/TSC2 0 0.05 0.27 3 -0.28 7 10
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.074 0.3 4 -0.27 6 10
glucose import -0.011 0.022 0.2 2 -0.17 3 5
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.008 0.04 -10000 0 -0.22 5 5
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.012 0.016 -10000 0 -0.17 3 3
GSK3A 0.007 0.048 -10000 0 -0.29 6 6
FOXO1 0.005 0.04 -10000 0 -0.29 5 5
GSK3B 0.005 0.044 -10000 0 -0.29 6 6
SFN 0.026 0.047 0.33 7 -0.34 1 8
G1/S transition of mitotic cell cycle 0.005 0.057 0.22 4 -0.28 7 11
p27Kip1/14-3-3 family 0.012 0.043 -10000 0 -10000 0 0
PRKACA 0.02 0.006 -10000 0 -10000 0 0
KPNA1 0.021 0.003 -10000 0 -10000 0 0
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
YWHAG 0.021 0.005 -10000 0 -10000 0 0
RHEB 0.021 0.005 -10000 0 -10000 0 0
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.019 0.008 -10000 0 -10000 0 0
SNTA1 0.022 0.017 0.33 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.016 0.034 0.41 2 -10000 0 2
MAPK12 -0.008 0.02 0.18 2 -0.17 1 3
CCND1 0 0.049 -10000 0 -0.38 5 5
p38 gamma/SNTA1 -0.011 0.046 0.18 11 -0.29 1 12
MAP2K3 0.02 0.006 -10000 0 -10000 0 0
PKN1 0.02 0.006 -10000 0 -10000 0 0
G2/M transition checkpoint -0.004 0.035 0.19 9 -0.17 1 10
MAP2K6 -0.004 0.023 0.22 2 -0.19 1 3
MAPT -0.007 0.07 0.22 9 -0.25 14 23
MAPK13 -0.016 0.006 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.002 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA 0.018 0.033 -10000 0 -0.34 3 3
HRAS 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.017 0.037 0.33 1 -0.34 3 4
AKT 0.032 0.068 0.24 10 -0.22 3 13
FOXO3 0.02 0.007 -10000 0 -10000 0 0
AKT1 0.021 0.005 -10000 0 -10000 0 0
FOXO1 0.021 0.005 -10000 0 -10000 0 0
AKT3 0.018 0.027 -10000 0 -0.34 2 2
FOXO4 0.022 0.002 -10000 0 -10000 0 0
MET 0.014 0.073 0.33 5 -0.34 11 16
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
PIK3CB 0.021 0.004 -10000 0 -10000 0 0
NRAS 0.021 0.005 -10000 0 -10000 0 0
PIK3CG 0.014 0.05 -10000 0 -0.34 7 7
PIK3R3 0.021 0.019 -10000 0 -0.34 1 1
PIK3R2 0.021 0.005 -10000 0 -10000 0 0
NF1 0.021 0.004 -10000 0 -10000 0 0
RAS 0.019 0.041 0.19 4 -10000 0 4
ERBB2 0.021 0.004 -10000 0 -10000 0 0
proliferation/survival/translation -0.011 0.072 0.27 11 -10000 0 11
PI3K 0.024 0.063 0.22 18 -0.28 1 19
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
KRAS 0.02 0.006 -10000 0 -10000 0 0
FOXO 0.049 0.052 0.23 11 -10000 0 11
AKT2 0.021 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.004 -10000 0 -10000 0 0
IGF1 pathway

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
NCK2 0.022 0.002 -10000 0 -10000 0 0
PTK2 0.019 0.008 -10000 0 -10000 0 0
CRKL -0.02 0.027 0.15 1 -0.21 5 6
GRB2/SOS1/SHC 0.035 0.018 -10000 0 -10000 0 0
HRAS 0.021 0.004 -10000 0 -10000 0 0
IRS1/Crk -0.019 0.025 0.11 1 -0.21 5 6
IGF-1R heterotetramer/IGF1/PTP1B 0.036 0.031 0.21 1 -0.2 4 5
AKT1 -0.025 0.036 0.16 1 -0.25 1 2
BAD -0.028 0.035 0.15 1 -0.24 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.019 0.026 0.15 1 -0.21 5 6
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.019 0.032 0.19 2 -0.21 5 7
RAF1 -0.018 0.071 0.26 1 -0.39 10 11
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.042 0.038 0.2 1 -0.21 4 5
YWHAZ 0.019 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.023 0.032 0.2 1 -0.22 5 6
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.024 0.038 0.16 1 -0.25 1 2
GNB2L1 0.021 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.006 0.069 0.25 3 -0.32 4 7
PXN 0.021 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.031 0.008 -10000 0 -10000 0 0
HRAS/GTP -0.025 0.018 0.092 1 -0.18 1 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.048 0.034 0.22 1 -0.17 1 2
IGF-1R heterotetramer 0.019 0.025 -10000 0 -0.35 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck 0.033 0.037 0.2 1 -0.21 5 6
Crk/p130 Cas/Paxillin 0.037 0.039 -10000 0 -0.19 6 6
IGF1R 0.019 0.025 -10000 0 -0.35 1 1
IGF1 0.018 0.045 0.34 1 -0.36 4 5
IRS2/Crk -0.022 0.028 0.14 1 -0.2 6 7
PI3K 0.04 0.039 0.2 1 -0.2 5 6
apoptosis 0.024 0.042 0.22 1 -0.27 1 2
HRAS/GDP 0.016 0.003 -10000 0 -10000 0 0
PRKCD -0.004 0.04 -10000 0 -0.25 5 5
RAF1/14-3-3 E -0.011 0.076 0.27 3 -0.34 10 13
BAD/14-3-3 -0.025 0.044 0.28 1 -0.23 1 2
PRKCZ -0.026 0.04 -10000 0 -0.25 1 1
Crk/p130 Cas/Paxillin/FAK1 -0.033 0.032 -10000 0 -0.23 1 1
PTPN1 0.02 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0 0.042 -10000 0 -0.27 4 4
BCAR1 0.02 0.02 -10000 0 -0.34 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.039 0.033 0.22 1 -0.18 2 3
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.022 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.018 0.034 -10000 0 -0.21 5 5
GRB10 0.02 0.007 -10000 0 -10000 0 0
PTPN11 -0.019 0.027 0.15 1 -0.21 5 6
IRS1 -0.015 0.032 0.12 6 -0.22 5 11
IRS2 -0.02 0.028 0.15 1 -0.2 6 7
IGF-1R heterotetramer/IGF1 0.027 0.039 0.23 1 -0.27 5 6
GRB2 0.021 0.005 -10000 0 -10000 0 0
PDPK1 -0.022 0.039 0.16 8 -0.26 1 9
YWHAE 0.02 0.007 -10000 0 -10000 0 0
PRKD1 -0.008 0.047 -10000 0 -0.32 3 3
SHC1 0.018 0.008 -10000 0 -10000 0 0
S1P3 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
PDGFRB 0.021 0.005 -10000 0 -10000 0 0
mol:S1P 0 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.008 0.062 -10000 0 -0.2 32 32
GNAO1 0.02 0.032 0.33 1 -0.34 2 3
S1P/S1P3/G12/G13 0.035 0.017 -10000 0 -10000 0 0
AKT1 0.005 0.064 -10000 0 -0.41 7 7
AKT3 -0.008 0.11 -10000 0 -0.99 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.021 0.005 -10000 0 -10000 0 0
GNAI2 0.021 0.007 -10000 0 -10000 0 0
GNAI3 0.021 0.006 -10000 0 -10000 0 0
GNAI1 0.019 0.02 -10000 0 -0.34 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.022 0.018 0.33 1 -10000 0 1
S1PR2 0.02 0.006 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.068 -10000 0 -0.3 5 5
MAPK3 -0.014 0.062 -10000 0 -0.6 1 1
MAPK1 -0.012 0.058 -10000 0 -0.58 1 1
JAK2 -0.025 0.082 0.2 1 -0.35 9 10
CXCR4 -0.015 0.064 -10000 0 -0.44 2 2
FLT1 0.02 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
SRC -0.014 0.065 0.27 1 -0.44 2 3
S1P/S1P3/Gi -0.007 0.069 -10000 0 -0.3 5 5
RAC1 0.019 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.002 0.073 -10000 0 -0.33 4 4
VEGFA 0.021 0.007 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.008 0.069 -10000 0 -0.29 6 6
VEGFR1 homodimer/VEGFA homodimer 0.03 0.013 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.005 0.043 -10000 0 -0.23 10 10
GNAQ 0.02 0.02 -10000 0 -0.34 1 1
GNAZ -0.007 0.097 -10000 0 -0.34 28 28
G12/G13 0.028 0.011 -10000 0 -10000 0 0
GNA14 0.011 0.06 -10000 0 -0.34 10 10
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.07 -10000 0 -0.31 5 5
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.004 0.042 0.3 2 -0.25 3 5
adherens junction organization -0.005 0.046 -10000 0 -0.24 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.013 0.049 0.19 5 -0.21 2 7
FMN1 -0.011 0.049 -10000 0 -0.23 9 9
mol:IP3 -0.012 0.026 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.003 0.048 -10000 0 -0.23 10 10
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
AKT1 -0.013 0.034 0.23 1 -0.2 2 3
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0.085 -10000 0 -0.41 9 9
CTNND1 0.021 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.007 0.037 -10000 0 -0.22 7 7
VASP -0.004 0.036 -10000 0 -0.23 5 5
ZYX -0.008 0.042 -10000 0 -0.22 9 9
JUB 0 0.045 -10000 0 -0.22 10 10
EGFR(dimer) 0.009 0.055 0.2 2 -0.23 10 12
E-cadherin/beta catenin-gamma catenin 0.04 0.022 -10000 0 -0.19 2 2
mol:PI-3-4-5-P3 0.023 0.045 0.25 1 -0.21 2 3
PIK3CA 0.02 0.009 -10000 0 -10000 0 0
PI3K 0.023 0.046 0.25 1 -0.21 2 3
FYN -0.016 0.058 0.38 1 -0.24 5 6
mol:Ca2+ -0.012 0.025 -10000 0 -10000 0 0
JUP 0.022 0.004 -10000 0 -10000 0 0
PIK3R1 0.02 0.008 -10000 0 -10000 0 0
mol:DAG -0.012 0.026 -10000 0 -10000 0 0
CDH1 0.019 0.027 -10000 0 -0.34 2 2
RhoA/GDP -0.004 0.062 0.19 5 -0.2 1 6
establishment of polarity of embryonic epithelium -0.004 0.035 -10000 0 -0.23 5 5
SRC 0.021 0.004 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.017 0.037 0.33 1 -0.34 3 4
CASR -0.008 0.043 0.3 2 -10000 0 2
RhoA/GTP 0.011 0.034 -10000 0 -0.19 1 1
AKT2 -0.012 0.034 0.23 1 -0.2 2 3
actin cable formation -0.013 0.042 -10000 0 -0.24 5 5
apoptosis -0.006 0.046 0.21 3 -0.27 5 8
CTNNA1 0.021 0.005 -10000 0 -10000 0 0
mol:GDP -0.013 0.04 0.18 4 -0.2 1 5
PIP5K1A -0.007 0.037 -10000 0 -0.23 7 7
PLCG1 -0.013 0.026 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.055 -10000 0 -0.22 9 9
homophilic cell adhesion -0.001 0.002 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.021 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.016 0.063 0.2 3 -0.31 4 7
ERC1 0.02 0.006 -10000 0 -10000 0 0
RIP2/NOD2 0.027 0.012 -10000 0 -10000 0 0
NFKBIA -0.017 0.019 0.19 2 -10000 0 2
BIRC2 0.021 0.005 -10000 0 -10000 0 0
IKBKB 0.019 0.008 -10000 0 -10000 0 0
RIPK2 0.019 0.007 -10000 0 -10000 0 0
IKBKG -0.002 0.063 -10000 0 -0.38 8 8
IKK complex/A20 0.024 0.081 -10000 0 -0.38 6 6
NEMO/A20/RIP2 0.019 0.007 -10000 0 -10000 0 0
XPO1 0.022 0.002 -10000 0 -10000 0 0
NEMO/ATM 0.022 0.077 -10000 0 -0.37 8 8
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.023 0.024 0.33 2 -10000 0 2
Exportin 1/RanGTP 0.029 0.015 0.21 2 -10000 0 2
IKK complex/ELKS 0.021 0.07 -10000 0 -0.36 7 7
BCL10/MALT1/TRAF6 0.037 0.017 -10000 0 -10000 0 0
NOD2 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.003 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
MALT1 0.019 0.007 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.031 0.008 -10000 0 -10000 0 0
ATM 0.021 0.005 -10000 0 -10000 0 0
TNF/TNFR1A 0.019 0.053 0.24 1 -0.24 13 14
TRAF6 0.021 0.003 -10000 0 -10000 0 0
PRKCA 0.019 0.027 -10000 0 -0.34 2 2
CHUK 0.022 0.003 -10000 0 -10000 0 0
UBE2D3 0.022 0.003 -10000 0 -10000 0 0
TNF 0.007 0.072 0.33 1 -0.34 14 15
NF kappa B1 p50/RelA 0.043 0.013 -10000 0 -10000 0 0
BCL10 0.021 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.017 0.019 0.19 2 -10000 0 2
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.02 0.006 -10000 0 -10000 0 0
IKK complex 0.025 0.076 -10000 0 -0.38 7 7
CYLD 0.021 0.005 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.029 0.076 -10000 0 -0.37 7 7
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.008 0.02 -10000 0 -0.24 2 2
CRKL 0.021 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
ITGA4 0.02 0.027 -10000 0 -0.34 2 2
alpha4/beta7 Integrin/MAdCAM1 0.048 0.032 0.23 2 -0.18 3 5
EPO 0.021 0.024 0.33 2 -10000 0 2
alpha4/beta7 Integrin 0.029 0.025 -10000 0 -0.24 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.02 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.031 0.016 -10000 0 -0.24 1 1
EPO/EPOR (dimer) 0.029 0.019 0.24 2 -10000 0 2
lamellipodium assembly 0 0.06 -10000 0 -0.46 4 4
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
PI3K 0.03 0.009 -10000 0 -10000 0 0
ARF6 0.021 0.005 -10000 0 -10000 0 0
JAK2 0.009 0.024 0.19 1 -0.3 1 2
PXN 0.021 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
MADCAM1 0.022 0.029 0.33 3 -10000 0 3
cell adhesion 0.046 0.031 0.22 2 -0.18 3 5
CRKL/CBL 0.03 0.009 -10000 0 -10000 0 0
ITGB1 0.021 0.004 -10000 0 -10000 0 0
SRC -0.018 0.036 0.17 10 -0.19 2 12
ITGB7 0.02 0.019 -10000 0 -0.34 1 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.039 0.028 0.23 1 -0.2 3 4
p130Cas/Crk/Dock1 -0.026 0.038 0.17 9 -10000 0 9
VCAM1 0.02 0.032 0.33 1 -0.34 2 3
RHOA 0.021 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.051 0.021 -10000 0 -0.19 1 1
BCAR1 -0.022 0.037 0.17 10 -0.18 3 13
EPOR 0.021 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.021 0.005 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.001 0.062 -10000 0 -0.47 4 4
a4b1 and a4b7 Integrin signaling

Figure S121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.021 0.004 -9999 0 -10000 0 0
ITGB7 0.02 0.019 -9999 0 -0.34 1 1
ITGA4 0.02 0.027 -9999 0 -0.34 2 2
alpha4/beta7 Integrin 0.029 0.025 -9999 0 -0.24 3 3
alpha4/beta1 Integrin 0.031 0.016 -9999 0 -0.24 1 1
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.005 0.11 -10000 0 -0.38 13 13
CaM/Ca2+ 0.015 0.004 -10000 0 -10000 0 0
AKT1 0.021 0.005 -10000 0 -10000 0 0
AKT2 0.021 0.005 -10000 0 -10000 0 0
STXBP4 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.012 0.11 0.21 1 -0.41 14 15
YWHAZ 0.019 0.008 -10000 0 -10000 0 0
CALM1 0.021 0.005 -10000 0 -10000 0 0
YWHAQ 0.022 0.002 -10000 0 -10000 0 0
TBC1D4 -0.017 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.021 0.004 -10000 0 -10000 0 0
YWHAB 0.021 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.038 0.016 -10000 0 -10000 0 0
YWHAG 0.021 0.005 -10000 0 -10000 0 0
ASIP 0.02 0.017 0.33 1 -10000 0 1
PRKCI 0.021 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.015 0.004 -10000 0 -10000 0 0
RHOQ 0.022 0.003 -10000 0 -10000 0 0
GYS1 -0.006 0.002 -10000 0 -10000 0 0
PRKCZ 0.019 0.027 -10000 0 -0.34 2 2
TRIP10 0.02 0.006 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.027 0.009 -10000 0 -10000 0 0
AS160/14-3-3 0.004 0.052 -10000 0 -0.28 3 3
VAMP2 0.02 0.007 -10000 0 -10000 0 0
SLC2A4 -0.014 0.12 -10000 0 -0.46 14 14
STX4 0.021 0.003 -10000 0 -10000 0 0
GSK3B 0.01 0.004 -10000 0 -10000 0 0
SFN 0.026 0.047 0.33 7 -0.34 1 8
LNPEP 0.021 0.005 -10000 0 -10000 0 0
YWHAE 0.02 0.007 -10000 0 -10000 0 0
TRAIL 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
TNFSF10 0.018 0.033 -10000 0 -0.34 3 3
positive regulation of NF-kappaB transcription factor activity 0.023 0.027 -10000 0 -0.23 3 3
MAP2K4 0.005 0.025 -10000 0 -0.24 1 1
IKBKB 0.019 0.008 -10000 0 -10000 0 0
TNFRSF10B 0.018 0.008 -10000 0 -10000 0 0
TNFRSF10A 0.018 0.008 -10000 0 -10000 0 0
SMPD1 0.004 0.016 0.14 1 -0.15 3 4
IKBKG 0.021 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.017 0.021 -10000 0 -0.34 1 1
TRAIL/TRAILR2 0.023 0.027 -10000 0 -0.23 3 3
TRAIL/TRAILR3 0.021 0.037 -10000 0 -0.24 6 6
TRAIL/TRAILR1 0.023 0.027 -10000 0 -0.23 3 3
TRAIL/TRAILR4 0.023 0.027 -10000 0 -0.23 3 3
TRAIL/TRAILR1/DAP3/GTP 0.028 0.025 -10000 0 -0.18 2 2
IKK complex -0.002 0.051 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.014 0.006 -10000 0 -10000 0 0
MAPK3 -0.018 0.026 0.28 1 -0.24 3 4
MAP3K1 0.013 0.021 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.017 0.021 -10000 0 -0.34 1 1
TRADD 0.021 0.004 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.008 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.04 -10000 0 -0.19 2 2
CFLAR 0.022 0.003 -10000 0 -10000 0 0
MAPK1 -0.017 0.023 0.28 1 -0.24 2 3
TRAIL/TRAILR1/FADD/TRADD/RIP 0.045 0.037 -10000 0 -0.18 2 2
mol:ceramide 0.004 0.016 0.14 1 -0.15 3 4
FADD 0.021 0.005 -10000 0 -10000 0 0
MAPK8 -0.008 0.043 -10000 0 -0.25 2 2
TRAF2 0.021 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.014 0.038 -10000 0 -0.34 4 4
CHUK 0.022 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.032 0.028 -10000 0 -0.2 3 3
DAP3 0.018 0.008 -10000 0 -10000 0 0
CASP10 -0.003 0.045 0.26 2 -0.23 2 4
JNK cascade 0.023 0.027 -10000 0 -0.23 3 3
TRAIL (trimer) 0.018 0.033 -10000 0 -0.34 3 3
TNFRSF10C 0.014 0.038 -10000 0 -0.34 4 4
TRAIL/TRAILR1/DAP3/GTP/FADD 0.034 0.031 -10000 0 -0.18 2 2
TRAIL/TRAILR2/FADD 0.032 0.028 -10000 0 -0.2 3 3
cell death 0.004 0.016 0.14 1 -0.14 3 4
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.001 0.04 -10000 0 -0.19 2 2
TRAILR2 (trimer) 0.018 0.008 -10000 0 -10000 0 0
CASP8 0.01 0.045 -10000 0 -0.6 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.045 0.037 -10000 0 -0.18 2 2
Paxillin-dependent events mediated by a4b1

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
CRKL 0.021 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.011 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
ITGA4 0.02 0.027 -10000 0 -0.34 2 2
RAC1 0.019 0.007 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.029 0.025 -10000 0 -0.24 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.02 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.039 0.019 -10000 0 -0.2 1 1
alpha4/beta7 Integrin/Paxillin 0.027 0.023 -10000 0 -0.19 3 3
lamellipodium assembly -0.01 0.085 -10000 0 -0.4 11 11
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
PI3K 0.03 0.009 -10000 0 -10000 0 0
ARF6 0.021 0.005 -10000 0 -10000 0 0
TLN1 0.02 0.02 -10000 0 -0.34 1 1
PXN -0.017 0.005 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.035 0.022 -10000 0 -0.17 1 1
cell adhesion 0.035 0.023 -10000 0 -0.17 2 2
CRKL/CBL 0.03 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.028 0.016 -10000 0 -0.19 1 1
ITGB1 0.021 0.004 -10000 0 -10000 0 0
ITGB7 0.02 0.019 -10000 0 -0.34 1 1
ARF6/GDP 0.023 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.037 0.028 0.22 1 -0.18 3 4
p130Cas/Crk/Dock1 0.037 0.021 -10000 0 -0.2 1 1
VCAM1 0.02 0.032 0.33 1 -0.34 2 3
alpha4/beta1 Integrin/Paxillin/Talin 0.037 0.024 -10000 0 -0.17 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.037 0.021 -10000 0 -0.18 1 1
BCAR1 0.02 0.02 -10000 0 -0.34 1 1
mol:GDP -0.036 0.02 0.18 1 -10000 0 1
CBL 0.021 0.005 -10000 0 -10000 0 0
PRKACA 0.02 0.006 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.037 0.024 -10000 0 -0.17 2 2
Rac1/GTP -0.011 0.093 -10000 0 -0.44 11 11
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.032 0.027 0.2 1 -0.17 4 5
MAPK9 0.004 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.013 0.16 2 -10000 0 2
GNB1/GNG2 0.027 0.015 -10000 0 -0.2 1 1
GNB1 0.021 0.004 -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 0.004 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.012 0.022 0.19 1 -0.17 4 5
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.002 0.005 0.049 4 -10000 0 4
GNAL 0.017 0.042 0.33 1 -0.34 4 5
GNG2 0.02 0.02 -10000 0 -0.34 1 1
CRH 0.019 0.024 0.33 2 -10000 0 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.001 -10000 0 -10000 0 0
MAPK11 0.002 0.019 -10000 0 -0.25 2 2
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.039 0.023 -9999 0 -0.2 2 2
E-cadherin/beta catenin 0.029 0.022 -9999 0 -0.24 2 2
CTNNB1 0.021 0.004 -9999 0 -10000 0 0
JUP 0.021 0.004 -9999 0 -10000 0 0
CDH1 0.019 0.027 -9999 0 -0.34 2 2
Arf1 pathway

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
coatomer protein complex 0.008 0.044 0.15 25 -0.2 1 26
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.016 0.039 0.12 21 -0.15 2 23
AP2 0.03 0.008 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.022 0.017 -10000 0 -10000 0 0
CLTB 0.021 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.008 0.005 -10000 0 -10000 0 0
CD4 0.014 0.047 -10000 0 -0.34 6 6
CLTA 0.02 0.006 -10000 0 -10000 0 0
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ARFGAP1 -0.008 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.009 -10000 0 -10000 0 0
ARF1/GTP 0.022 0.016 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.005 0.015 -10000 0 -10000 0 0
mol:Choline -0.002 0.009 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.01 -10000 0 -10000 0 0
DDEF1 -0.001 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.001 0.017 -10000 0 -0.1 5 5
AP2M1 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.008 0.011 -10000 0 -10000 0 0
Rac/GTP 0.015 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.025 0.013 -10000 0 -10000 0 0
ARFIP2 0.009 0.021 -10000 0 -10000 0 0
COPA 0.019 0.008 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex -0.001 0.036 -10000 0 -0.18 7 7
ARF1/GTP/ARHGAP10 0.012 0.008 -10000 0 -10000 0 0
GGA3 0.021 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.012 0.022 -10000 0 -0.29 1 1
AP2A1 0.021 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.001 0.029 -10000 0 -0.21 2 2
ARF1/GDP/Membrin 0.017 0.026 -10000 0 -0.32 1 1
Arfaptin 2/Rac/GDP 0.019 0.019 -10000 0 -10000 0 0
CYTH2 0.025 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.013 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.014 0.005 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.003 0.041 -10000 0 -0.2 9 9
PLD2 -0.002 0.009 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.008 0.003 -10000 0 -10000 0 0
PIP5K1A -0.002 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.008 0.022 -10000 0 -0.13 2 2
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.009 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.008 0.003 -10000 0 -10000 0 0
GOSR2 0.006 0.006 -10000 0 -10000 0 0
USO1 0.003 0.03 -10000 0 -0.32 3 3
GBF1 0.004 0.03 -10000 0 -0.32 3 3
ARF1/GTP/Arfaptin 2 0.024 0.017 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.035 0.034 -10000 0 -0.2 6 6
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.019 0.007 -10000 0 -10000 0 0
SMAD2 0 0.045 0.22 1 -0.22 4 5
SMAD3 0.009 0.038 -10000 0 -10000 0 0
SMAD3/SMAD4 0.022 0.039 -10000 0 -0.48 1 1
SMAD4/Ubc9/PIASy 0.036 0.018 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.028 0.051 -10000 0 -0.22 2 2
PPM1A 0.021 0.005 -10000 0 -10000 0 0
CALM1 0.021 0.005 -10000 0 -10000 0 0
SMAD2/SMAD4 0.006 0.043 -10000 0 -0.21 6 6
MAP3K1 0.021 0.005 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.027 0.022 -10000 0 -0.23 2 2
MAPK3 0.022 0.003 -10000 0 -10000 0 0
MAPK1 0.021 0.005 -10000 0 -10000 0 0
NUP214 0.021 0.004 -10000 0 -10000 0 0
CTDSP1 0.022 0.002 -10000 0 -10000 0 0
CTDSP2 0.02 0.006 -10000 0 -10000 0 0
CTDSPL 0.021 0.004 -10000 0 -10000 0 0
KPNB1 0.021 0.004 -10000 0 -10000 0 0
TGFBRAP1 0.02 0.027 -10000 0 -0.34 2 2
UBE2I 0.021 0.004 -10000 0 -10000 0 0
NUP153 0.021 0.004 -10000 0 -10000 0 0
KPNA2 0.025 0.033 0.33 4 -10000 0 4
PIAS4 0.02 0.006 -10000 0 -10000 0 0
Atypical 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
BCL3/RelA 0.029 0.017 -10000 0 -0.24 1 1
FBXW11 0.021 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.018 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.018 0.043 -10000 0 -10000 0 0
NFKBIA 0.001 0.01 -10000 0 -0.17 1 1
MAPK14 0.021 0.005 -10000 0 -10000 0 0
NF kappa B1 p105/p50 -0.017 0.009 -10000 0 -10000 0 0
ARRB2 0.007 0.003 -10000 0 -10000 0 0
REL 0.022 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.018 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.018 0.008 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
NF kappa B1 p50 dimer -0.014 0.016 0.24 1 -10000 0 1
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
NFKB1 -0.015 0.007 -10000 0 -10000 0 0
RELA 0.021 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.007 0.035 -10000 0 -0.19 3 3
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.016 0.043 -10000 0 -0.21 1 1
SRC 0.021 0.004 -10000 0 -10000 0 0
PI3K 0.03 0.009 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.007 0.036 -10000 0 -0.19 3 3
IKBKB 0.019 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
SYK 0.019 0.027 -10000 0 -0.34 2 2
I kappa B alpha/PIK3R1 0.028 0.056 0.26 8 -0.18 2 10
cell death 0.015 0.041 -10000 0 -0.2 1 1
NF kappa B1 p105/c-Rel -0.018 0.008 -10000 0 -10000 0 0
LCK 0.022 0.025 0.33 1 -0.34 1 2
BCL3 0.02 0.02 -10000 0 -0.34 1 1
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 0.022 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.02 0.009 -10000 0 -10000 0 0
MDM2/SUMO1 0.028 0.029 0.18 2 -0.18 2 4
HDAC4 0.021 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.02 0.009 -10000 0 -10000 0 0
SUMO1 0.022 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.005 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.005 0.013 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.023 0.024 0.33 2 -10000 0 2
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.022 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.029 0.025 -10000 0 -0.18 2 2
SUMO1/HDAC1 0.029 0.027 -10000 0 -0.18 2 2
RANGAP1 0.021 0.004 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.045 0.026 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.006 0.002 -10000 0 -10000 0 0
Ran/GTP 0.019 0.027 0.2 1 -0.18 2 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.02 0.006 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.015 0.032 0.21 4 -0.18 2 6
NPC 0.013 0.001 -10000 0 -10000 0 0
PIAS2 0.019 0.007 -10000 0 -10000 0 0
PIAS1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.031 0.007 -9999 0 -9999 0 0
FBXW11 0.021 0.005 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -9999 0 -9999 0 0
CHUK 0.022 0.003 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.056 0.023 -9999 0 -9999 0 0
NFKB1 0.022 0.003 -9999 0 -9999 0 0
MAP3K14 0.021 0.004 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.031 0.008 -9999 0 -9999 0 0
RELB 0.021 0.005 -9999 0 -9999 0 0
NFKB2 0.022 0.003 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.028 0.008 -9999 0 -9999 0 0
regulation of B cell activation 0.027 0.007 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 352 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.J2.8194 TCGA.J2.8192 TCGA.99.8033 TCGA.99.8032
109_MAP3K5 -0.025 0.0078 0.0078 0.0078
47_PPARGC1A 0 0.022 0.022 0.022
105_BMP4 0.022 0.022 0.022 0.022
105_BMP6 0.022 0.022 0.022 0.022
105_BMP7 0.022 0.022 -0.34 0.022
105_BMP2 0.022 0.022 0.022 0.022
131_RELN/VLDLR 0.057 0.057 0.057 0.057
30_TGFB1/TGF beta receptor Type II 0.022 0.022 0.022 -0.025
84_STAT5B -0.038 0.11 0.039 0.02
84_STAT5A -0.038 0.11 0.039 0.02
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LUAD-TP/2844133/LUAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/LUAD-TP/2865477/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

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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