Ovarian Serous Cystadenocarcinoma: PARADIGM pathway analysis of mRNA expression and copy number data
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 108 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
PLK2 and PLK4 events 186
FOXM1 transcription factor network 142
TCGA08_p53 100
Wnt signaling 96
Ephrin B reverse signaling 95
Endothelins 94
LPA receptor mediated events 92
HIF-1-alpha transcription factor network 91
Osteopontin-mediated events 90
Syndecan-1-mediated signaling events 88
Results

The following list describes the columns found in Table 2.

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

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway.

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
PLK2 and PLK4 events 186 559 3 -0.011 0.036 1000 -1000 -0.018 -1000
FOXM1 transcription factor network 142 7248 51 -0.51 0.038 1000 -1000 -0.01 -1000
TCGA08_p53 100 705 7 -0.062 0.038 1000 -1000 -0.01 -1000
Wnt signaling 96 676 7 -0.019 0.041 1000 -1000 0.001 -1000
Ephrin B reverse signaling 95 4577 48 -0.2 0.08 1000 -1000 -0.054 -1000
Endothelins 94 9030 96 -0.18 0.044 1000 -1000 -0.019 -1000
LPA receptor mediated events 92 9409 102 -0.047 0.041 1000 -1000 -0.045 -1000
HIF-1-alpha transcription factor network 91 6953 76 -0.048 0.093 1000 -1000 0 -1000
Osteopontin-mediated events 90 3453 38 -0.18 0.041 1000 -1000 -0.007 -1000
Syndecan-1-mediated signaling events 88 3009 34 -0.038 0.04 1000 -1000 0 -1000
amb2 Integrin signaling 82 6725 82 -0.082 0.081 1000 -1000 -0.014 -1000
TCGA08_retinoblastoma 82 657 8 -0.012 0.019 1000 -1000 -0.005 -1000
Nectin adhesion pathway 77 4855 63 -0.083 0.062 1000 -1000 -0.014 -1000
Thromboxane A2 receptor signaling 76 8012 105 -0.15 0.072 1000 -1000 -0.021 -1000
PDGFR-alpha signaling pathway 76 3380 44 -0.12 0.05 1000 -1000 -0.026 -1000
TRAIL signaling pathway 76 3649 48 -0.022 0.042 1000 -1000 -0.017 -1000
BARD1 signaling events 73 4207 57 -0.038 0.064 1000 -1000 -0.062 -1000
Syndecan-4-mediated signaling events 73 4896 67 -0.064 0.045 1000 -1000 -0.032 -1000
TCGA08_rtk_signaling 72 1888 26 -0.016 0.04 1000 -1000 -0.018 -1000
IL6-mediated signaling events 71 5336 75 -0.14 0.049 1000 -1000 -0.03 -1000
Signaling events mediated by the Hedgehog family 70 3677 52 -0.065 0.058 1000 -1000 -0.026 -1000
Paxillin-dependent events mediated by a4b1 70 2554 36 -0.065 0.068 1000 -1000 -0.054 -1000
Nongenotropic Androgen signaling 70 3671 52 -0.12 0.062 1000 -1000 -0.019 -1000
LPA4-mediated signaling events 69 837 12 -0.015 0.058 1000 -1000 -0.014 -1000
Integrins in angiogenesis 69 5846 84 -0.058 0.056 1000 -1000 -0.017 -1000
Signaling events mediated by PTP1B 67 5121 76 -0.059 0.069 1000 -1000 -0.013 -1000
IL1-mediated signaling events 66 4138 62 -0.044 0.071 1000 -1000 -0.017 -1000
E-cadherin signaling in keratinocytes 66 2860 43 -0.028 0.049 1000 -1000 -0.008 -1000
Ras signaling in the CD4+ TCR pathway 66 1122 17 -0.003 0.053 1000 -1000 0 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 65 5551 85 -0.16 0.05 1000 -1000 -0.044 -1000
IL4-mediated signaling events 65 5985 91 -0.22 0.059 1000 -1000 -0.038 -1000
IL23-mediated signaling events 65 3922 60 -0.17 0.055 1000 -1000 -0.026 -1000
Cellular roles of Anthrax toxin 64 2523 39 -0.081 0.04 1000 -1000 -0.015 -1000
IGF1 pathway 64 3652 57 -0.021 0.065 1000 -1000 -0.016 -1000
Canonical Wnt signaling pathway 62 3178 51 -0.18 0.097 1000 -1000 -0.017 -1000
Fc-epsilon receptor I signaling in mast cells 61 5960 97 -0.073 0.046 1000 -1000 -0.037 -1000
FoxO family signaling 61 3951 64 -0.19 0.046 1000 -1000 -0.026 -1000
IL2 signaling events mediated by STAT5 61 1354 22 -0.042 0.047 1000 -1000 -0.001 -1000
Noncanonical Wnt signaling pathway 60 1583 26 -0.029 0.041 1000 -1000 -0.027 -1000
BMP receptor signaling 60 4887 81 -0.02 0.07 1000 -1000 0 -1000
a4b1 and a4b7 Integrin signaling 59 297 5 0.032 0.039 1000 -1000 0.038 -1000
TCR signaling in naïve CD8+ T cells 58 5443 93 -0.076 0.081 1000 -1000 -0.021 -1000
EPO signaling pathway 56 3091 55 0 0.073 1000 -1000 -0.009 -1000
FAS signaling pathway (CD95) 56 2647 47 -0.06 0.052 1000 -1000 -0.028 -1000
EPHB forward signaling 56 4837 85 -0.056 0.16 1000 -1000 -0.037 -1000
Paxillin-independent events mediated by a4b1 and a4b7 55 2036 37 -0.019 0.07 1000 -1000 -0.011 -1000
HIF-2-alpha transcription factor network 55 2394 43 -0.061 0.069 1000 -1000 -0.085 -1000
E-cadherin signaling events 55 279 5 0.035 0.048 1000 -1000 0.038 -1000
E-cadherin signaling in the nascent adherens junction 54 4134 76 -0.054 0.072 1000 -1000 -0.03 -1000
IL12-mediated signaling events 53 4645 87 -0.18 0.061 1000 -1000 -0.034 -1000
Syndecan-2-mediated signaling events 53 3666 69 0 0.063 1000 -1000 -0.018 -1000
Retinoic acid receptors-mediated signaling 53 3089 58 -0.083 0.059 1000 -1000 -0.009 -1000
Plasma membrane estrogen receptor signaling 53 4588 86 -0.089 0.085 1000 -1000 -0.019 -1000
BCR signaling pathway 52 5242 99 -0.077 0.07 1000 -1000 -0.03 -1000
IFN-gamma pathway 51 3477 68 -0.05 0.061 1000 -1000 -0.031 -1000
IL2 signaling events mediated by PI3K 50 2934 58 -0.062 0.041 1000 -1000 -0.016 -1000
Circadian rhythm pathway 49 1087 22 -0.081 0.044 1000 -1000 -0.022 -1000
Class I PI3K signaling events 49 3609 73 -0.015 0.05 1000 -1000 -0.02 -1000
Caspase cascade in apoptosis 48 3614 74 -0.11 0.051 1000 -1000 -0.022 -1000
Presenilin action in Notch and Wnt signaling 48 2967 61 -0.16 0.075 1000 -1000 -0.035 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 48 2173 45 -0.057 0.075 1000 -1000 -0.017 -1000
Arf6 signaling events 46 2884 62 0 0.081 1000 -1000 0 -1000
Reelin signaling pathway 46 2608 56 -0.012 0.094 1000 -1000 -0.004 -1000
Stabilization and expansion of the E-cadherin adherens junction 46 3451 74 -0.076 0.067 1000 -1000 -0.057 -1000
Aurora B signaling 46 3085 67 -0.057 0.066 1000 -1000 -0.016 -1000
ErbB4 signaling events 45 3106 69 -0.07 0.057 1000 -1000 -0.022 -1000
Regulation of Telomerase 45 4624 102 -0.11 0.071 1000 -1000 -0.017 -1000
PLK1 signaling events 44 3813 85 -0.043 0.05 1000 -1000 -0.01 -1000
Canonical NF-kappaB pathway 43 1697 39 -0.035 0.063 1000 -1000 -0.015 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 43 1435 33 -0.006 0.085 1000 -1000 -0.01 -1000
Signaling events mediated by PRL 43 1470 34 -0.018 0.04 1000 -1000 -0.03 -1000
Regulation of Androgen receptor activity 43 3059 70 -0.086 0.07 1000 -1000 -0.023 -1000
p75(NTR)-mediated signaling 42 5299 125 -0.058 0.098 1000 -1000 -0.035 -1000
RXR and RAR heterodimerization with other nuclear receptor 40 2121 52 -0.038 0.094 1000 -1000 -0.011 -1000
Regulation of p38-alpha and p38-beta 40 2187 54 -0.028 0.09 1000 -1000 0 -1000
EGFR-dependent Endothelin signaling events 39 831 21 -0.016 0.081 1000 -1000 -0.006 -1000
ErbB2/ErbB3 signaling events 38 2472 65 -0.034 0.048 1000 -1000 -0.045 -1000
Arf6 downstream pathway 38 1659 43 -0.034 0.061 1000 -1000 -0.048 -1000
S1P3 pathway 38 1615 42 -0.02 0.053 1000 -1000 -0.006 -1000
Neurotrophic factor-mediated Trk receptor signaling 38 4626 120 -0.049 0.091 1000 -1000 -0.024 -1000
Insulin-mediated glucose transport 37 1185 32 -0.018 0.046 1000 -1000 -0.017 -1000
mTOR signaling pathway 37 1964 53 -0.049 0.056 1000 -1000 -0.034 -1000
p38 MAPK signaling pathway 36 1609 44 -0.044 0.072 1000 -1000 0 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 35 1929 54 -0.018 0.055 1000 -1000 -0.018 -1000
Signaling mediated by p38-gamma and p38-delta 35 537 15 -0.039 0.039 1000 -1000 -0.017 -1000
Syndecan-3-mediated signaling events 35 1242 35 -0.013 0.072 1000 -1000 -0.018 -1000
PDGFR-beta signaling pathway 35 3459 97 -0.036 0.085 1000 -1000 -0.036 -1000
Aurora A signaling 34 2063 60 -0.043 0.066 1000 -1000 -0.017 -1000
ceramide signaling pathway 34 1676 49 -0.03 0.059 1000 -1000 -0.007 -1000
Class IB PI3K non-lipid kinase events 34 102 3 -0.039 0.039 1000 -1000 -0.037 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 33 768 23 -0.016 0.066 1000 -1000 -0.002 -1000
Ephrin A reverse signaling 33 232 7 -0.013 0.04 1000 -1000 -0.013 -1000
FOXA2 and FOXA3 transcription factor networks 33 1563 46 -0.13 0.056 1000 -1000 -0.01 -1000
Class I PI3K signaling events mediated by Akt 33 2247 68 -0.034 0.078 1000 -1000 -0.017 -1000
JNK signaling in the CD4+ TCR pathway 32 554 17 -0.005 0.078 1000 -1000 0 -1000
Hedgehog signaling events mediated by Gli proteins 32 2142 65 0 0.074 1000 -1000 -0.006 -1000
Ceramide signaling pathway 32 2492 76 -0.019 0.081 1000 -1000 -0.017 -1000
S1P5 pathway 32 546 17 -0.007 0.041 1000 -1000 -0.017 -1000
Signaling events mediated by HDAC Class I 32 3358 104 -0.041 0.074 1000 -1000 -0.04 -1000
S1P4 pathway 32 802 25 -0.013 0.053 1000 -1000 -0.008 -1000
Regulation of nuclear SMAD2/3 signaling 31 4219 136 -0.091 0.1 1000 -1000 -0.055 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 31 2649 83 -0.014 0.072 1000 -1000 -0.02 -1000
Coregulation of Androgen receptor activity 29 2209 76 -0.011 0.052 1000 -1000 -0.009 -1000
Sphingosine 1-phosphate (S1P) pathway 29 838 28 -0.019 0.053 1000 -1000 -0.018 -1000
Glypican 1 network 29 1407 48 -0.04 0.068 1000 -1000 -0.038 -1000
Signaling events regulated by Ret tyrosine kinase 29 2380 82 -0.008 0.091 1000 -1000 -0.022 -1000
Atypical NF-kappaB pathway 29 912 31 -0.016 0.041 1000 -1000 -0.017 -1000
Signaling events mediated by VEGFR1 and VEGFR2 29 3733 125 -0.022 0.072 1000 -1000 -0.02 -1000
Nephrin/Neph1 signaling in the kidney podocyte 28 952 34 -0.049 0.085 1000 -1000 -0.047 -1000
VEGFR1 specific signals 27 1527 56 -0.03 0.045 1000 -1000 -0.017 -1000
Alternative NF-kappaB pathway 27 354 13 0 0.095 1000 -1000 0 -1000
Insulin Pathway 26 1946 74 -0.027 0.1 1000 -1000 -0.03 -1000
Signaling events mediated by HDAC Class II 25 1905 75 -0.037 0.094 1000 -1000 -0.026 -1000
Glucocorticoid receptor regulatory network 25 2946 114 -0.1 0.075 1000 -1000 -0.043 -1000
Calcium signaling in the CD4+ TCR pathway 25 802 31 -0.042 0.084 1000 -1000 -0.022 -1000
Angiopoietin receptor Tie2-mediated signaling 25 2275 88 -0.045 0.074 1000 -1000 -0.048 -1000
Signaling events mediated by HDAC Class III 23 945 40 -0.064 0.072 1000 -1000 -0.052 -1000
IL27-mediated signaling events 23 1208 51 -0.009 0.079 1000 -1000 -0.031 -1000
Sumoylation by RanBP2 regulates transcriptional repression 23 642 27 -0.031 0.083 1000 -1000 -0.024 -1000
Rapid glucocorticoid signaling 21 422 20 -0.01 0.048 1000 -1000 -0.009 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 21 1673 78 -0.018 0.066 1000 -1000 -0.018 -1000
Arf1 pathway 21 1156 54 -0.01 0.052 1000 -1000 -0.01 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 20 1389 68 -0.075 0.094 1000 -1000 -0.028 -1000
S1P1 pathway 19 696 36 -0.002 0.043 1000 -1000 -0.007 -1000
Effects of Botulinum toxin 19 499 26 -0.01 0.071 1000 -1000 -0.009 -1000
Arf6 trafficking events 19 1379 71 -0.046 0.05 1000 -1000 -0.037 -1000
Signaling mediated by p38-alpha and p38-beta 18 832 44 -0.021 0.056 1000 -1000 -0.006 -1000
Aurora C signaling 17 123 7 0 0.064 1000 -1000 0 -1000
Glypican 2 network 17 71 4 0.04 0.054 1000 -1000 0.038 -1000
Visual signal transduction: Cones 15 602 38 -0.01 0.087 1000 -1000 -0.01 -1000
Visual signal transduction: Rods 13 720 52 -0.018 0.098 1000 -1000 0 -1000
Total 6456 353768 7203 -7.1 8.4 131000 -131000 -2.6 -131000
PLK2 and PLK4 events

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
PLK2 0.026 0.02 -9999 0 0 215 215
PLK4 0.036 0.015 -9999 0 0 82 82
regulation of centriole replication -0.011 0.01 0 262 -9999 0 262
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.35 0.6 -10000 0 -1.1 163 163
PLK1 -0.046 0.3 -10000 0 -1.2 33 33
BIRC5 -0.049 0.32 -10000 0 -1.3 33 33
HSPA1B -0.35 0.6 -10000 0 -1.1 176 176
MAP2K1 0.002 0.07 -10000 0 -10000 0 0
BRCA2 -0.36 0.61 -10000 0 -1.2 167 167
FOXM1 -0.51 0.88 -10000 0 -1.6 175 175
XRCC1 -0.35 0.6 -10000 0 -1.1 167 167
FOXM1B/p19 -0.43 0.66 -10000 0 -1.3 179 179
Cyclin D1/CDK4 -0.36 0.55 -10000 0 -1 186 186
CDC2 -0.41 0.68 -10000 0 -1.3 181 181
TGFA -0.32 0.52 -10000 0 -0.97 173 173
SKP2 -0.34 0.61 -10000 0 -1.1 167 167
CCNE1 0.02 0.028 -10000 0 -0.008 251 251
CKS1B -0.35 0.6 -10000 0 -1.2 166 166
RB1 -0.31 0.48 -10000 0 -0.97 164 164
FOXM1C/SP1 -0.43 0.71 -10000 0 -1.3 179 179
AURKB -0.094 0.39 -10000 0 -1.2 56 56
CENPF -0.39 0.63 -10000 0 -1.2 182 182
CDK4 0.007 0.044 0.11 2 -0.038 194 196
MYC -0.34 0.48 -10000 0 -0.94 181 181
CHEK2 0.005 0.065 -10000 0 -10000 0 0
ONECUT1 -0.36 0.57 -10000 0 -1.1 174 174
CDKN2A 0.026 0.02 0.094 1 -0.034 8 9
LAMA4 -0.39 0.63 -10000 0 -1.2 185 185
FOXM1B/HNF6 -0.45 0.71 -10000 0 -1.4 173 173
FOS -0.42 0.65 -10000 0 -1.2 212 212
SP1 0.036 0.023 -10000 0 -0.033 48 48
CDC25B -0.35 0.6 -10000 0 -1.1 168 168
response to radiation -0.005 0.036 0.092 6 -10000 0 6
CENPB -0.34 0.6 -10000 0 -1.1 163 163
CENPA -0.35 0.6 -10000 0 -1.1 165 165
NEK2 -0.36 0.61 -10000 0 -1.2 171 171
HIST1H2BA -0.34 0.6 -10000 0 -1.1 165 165
CCNA2 0.023 0.029 -10000 0 -0.011 204 204
EP300 0.036 0.014 -10000 0 0 72 72
CCNB1/CDK1 -0.48 0.78 -10000 0 -1.5 178 178
CCNB2 -0.38 0.62 0.8 1 -1.2 178 179
CCNB1 -0.39 0.66 -10000 0 -1.3 170 170
ETV5 -0.36 0.64 0.73 1 -1.1 194 195
ESR1 -0.39 0.61 -10000 0 -1.1 189 189
CCND1 -0.36 0.55 -10000 0 -1 186 186
GSK3A 0.005 0.062 0.15 2 -10000 0 2
Cyclin A-E1/CDK1-2 -0.006 0.11 -10000 0 -0.17 122 122
CDK2 0.028 0.028 -10000 0 -0.019 129 129
G2/M transition of mitotic cell cycle -0.007 0.043 0.097 8 -10000 0 8
FOXM1B/Cbp/p300 -0.4 0.66 -10000 0 -1.3 175 175
GAS1 -0.36 0.6 -10000 0 -1.1 171 171
MMP2 -0.43 0.65 -10000 0 -1.2 217 217
RB1/FOXM1C -0.41 0.59 0.67 1 -1.1 187 188
CREBBP 0.038 0.012 -10000 0 0 49 49
TCGA08_p53

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
CDKN2A -0.007 0.005 0 176 -10000 0 176
TP53 -0.051 0.12 0.18 13 -0.24 141 154
Senescence -0.062 0.12 0.18 13 -0.24 144 157
Apoptosis -0.062 0.12 0.18 13 -0.24 144 157
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.005 0.038 0.3 8 -10000 0 8
MDM4 0.038 0.012 -10000 0 0 53 53
Wnt 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
Noncanonical Wnts/FZD -0.019 0.096 -9999 0 -0.2 94 94
FZD6 0.029 0.019 -9999 0 0 173 173
WNT6 0.041 0.006 -9999 0 0 12 12
WNT4 0.04 0.008 -9999 0 0 19 19
FZD3 0.029 0.019 -9999 0 0 166 166
WNT5A 0.035 0.015 -9999 0 0 90 90
WNT11 0.033 0.017 -9999 0 0 122 122
Ephrin B reverse signaling

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
EFNB2 0.031 0.018 -10000 0 0 141 141
EPHB2 0.042 0.013 0.067 3 0 38 41
EFNB1 -0.001 0.024 0.029 203 -10000 0 203
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.077 0.066 0.23 1 -0.12 18 19
Ephrin B2/EPHB1-2 0.041 0.069 -10000 0 -0.1 77 77
neuron projection morphogenesis 0.052 0.051 -10000 0 -0.11 20 20
Ephrin B1/EPHB1-2/Tiam1 0.071 0.061 0.21 2 -0.12 25 27
DNM1 0.041 0.011 -10000 0 0 36 36
cell-cell signaling 0.003 0.006 0.025 1 -10000 0 1
MAP2K4 -0.14 0.21 0.24 2 -0.46 162 164
YES1 -0.2 0.33 -10000 0 -0.69 167 167
Ephrin B1/EPHB1-2/NCK2 0.079 0.053 0.22 2 -0.11 16 18
PI3K -0.11 0.23 -10000 0 -0.44 165 165
mol:GDP 0.068 0.059 0.21 2 -0.12 25 27
ITGA2B 0.04 0.009 -10000 0 0 29 29
endothelial cell proliferation 0.024 0.061 -10000 0 -0.11 83 83
FYN -0.2 0.33 -10000 0 -0.7 166 166
MAP3K7 -0.14 0.23 0.22 4 -0.49 159 163
FGR -0.19 0.32 -10000 0 -0.68 170 170
TIAM1 0.037 0.014 -10000 0 0 70 70
PIK3R1 0.034 0.016 -10000 0 0 106 106
RGS3 0.04 0.008 -10000 0 0 21 21
cell adhesion -0.11 0.21 -10000 0 -0.42 164 164
LYN -0.19 0.33 -10000 0 -0.7 161 161
Ephrin B1/EPHB1-2/Src Family Kinases -0.18 0.3 -10000 0 -0.62 169 169
Ephrin B1/EPHB1-2 -0.14 0.24 -10000 0 -0.53 151 151
SRC -0.19 0.32 -10000 0 -0.68 166 166
ITGB3 0.033 0.017 -10000 0 0 120 120
EPHB1 0.04 0.014 -10000 0 0 57 57
EPHB4 0.04 0.009 -10000 0 0 27 27
RAC1 0.039 0.01 -10000 0 0 35 35
Ephrin B2/EPHB4 0.025 0.061 -10000 0 -0.11 83 83
alphaIIb/beta3 Integrin 0.039 0.05 -10000 0 -0.14 34 34
BLK -0.2 0.32 -10000 0 -0.69 163 163
HCK -0.19 0.32 -10000 0 -0.68 164 164
regulation of stress fiber formation -0.077 0.051 0.11 16 -0.22 2 18
MAPK8 -0.14 0.21 0.24 1 -0.44 164 165
Ephrin B1/EPHB1-2/RGS3 0.08 0.052 0.21 4 -0.11 16 20
endothelial cell migration -0.11 0.18 0.19 4 -0.4 144 148
NCK2 0.041 0.006 -10000 0 0 10 10
PTPN13 0.021 0.022 -10000 0 0 276 276
regulation of focal adhesion formation -0.077 0.051 0.11 16 -0.22 2 18
chemotaxis -0.077 0.051 0.11 17 -0.21 3 20
PIK3CA 0.03 0.019 -10000 0 0 150 150
Rac1/GTP 0.065 0.059 0.2 1 -0.12 19 20
angiogenesis -0.14 0.24 -10000 0 -0.52 156 156
LCK -0.19 0.32 -10000 0 -0.68 168 168
Endothelins

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
AKT1 -0.004 0.14 0.21 57 -0.23 118 175
PTK2B 0.033 0.017 -10000 0 0 116 116
mol:Ca2+ -0.034 0.2 0.4 1 -0.5 46 47
EDN1 -0.005 0.1 0.22 7 -0.18 121 128
EDN3 0.036 0.015 -10000 0 0 79 79
EDN2 0.037 0.014 -10000 0 0 67 67
HRAS/GDP -0.053 0.19 0.27 2 -0.35 116 118
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.032 0.14 0.2 2 -0.27 105 107
ADCY4 0.009 0.13 0.2 86 -0.23 74 160
ADCY5 0.008 0.13 0.2 78 -0.23 74 152
ADCY6 0.008 0.14 0.2 87 -0.23 80 167
ADCY7 0.005 0.13 0.2 80 -0.23 77 157
ADCY1 0.008 0.14 0.2 76 -0.23 74 150
ADCY2 0.01 0.13 0.2 78 -0.23 63 141
ADCY3 0.007 0.14 0.2 85 -0.23 77 162
ADCY8 -0.003 0.1 0.2 40 -0.22 51 91
ADCY9 0.008 0.14 0.2 85 -0.23 79 164
arachidonic acid secretion -0.1 0.26 0.3 2 -0.49 135 137
ETB receptor/Endothelin-1/Gq/GTP -0.003 0.11 -10000 0 -0.23 65 65
GNAO1 0.034 0.016 -10000 0 0 101 101
HRAS 0.039 0.009 -10000 0 0 29 29
ETA receptor/Endothelin-1/G12/GTP -0.007 0.13 0.35 6 -0.21 126 132
ETA receptor/Endothelin-1/Gs/GTP -0.005 0.12 0.32 7 -0.2 122 129
mol:GTP 0 0.006 -10000 0 -0.025 3 3
COL3A1 -0.057 0.16 0.23 17 -0.34 121 138
EDNRB 0.021 0.054 0.091 4 -0.089 93 97
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.003 0.14 0.22 29 -0.24 114 143
CYSLTR1 -0.015 0.15 0.23 21 -0.26 112 133
SLC9A1 -0.016 0.084 0.2 7 -0.17 89 96
mol:GDP -0.067 0.19 0.25 4 -0.36 118 122
SLC9A3 -0.024 0.19 -10000 0 -0.51 37 37
RAF1 -0.079 0.22 0.27 3 -0.41 133 136
JUN -0.075 0.3 -10000 0 -0.81 59 59
JAK2 -0.008 0.14 0.2 51 -0.24 114 165
mol:IP3 -0.026 0.15 0.21 2 -0.3 85 87
ETA receptor/Endothelin-1 -0.027 0.15 0.39 6 -0.27 133 139
PLCB1 0.034 0.016 -10000 0 0 104 104
PLCB2 0.037 0.015 -10000 0 -0.005 55 55
ETA receptor/Endothelin-3 0.014 0.084 0.19 7 -0.12 112 119
FOS -0.14 0.36 -10000 0 -0.85 106 106
Gai/GDP -0.029 0.23 -10000 0 -0.68 56 56
CRK 0.039 0.011 -10000 0 0 45 45
mol:Ca ++ -0.033 0.19 0.25 33 -0.34 114 147
BCAR1 0.036 0.014 -10000 0 0 74 74
PRKCB1 -0.029 0.14 0.23 8 -0.29 88 96
GNAQ 0.035 0.022 -10000 0 -0.039 30 30
GNAZ 0.039 0.011 -10000 0 0 38 38
GNAL 0.04 0.009 -10000 0 0 27 27
Gs family/GDP -0.053 0.18 0.26 2 -0.34 113 115
ETA receptor/Endothelin-1/Gq/GTP -0.019 0.14 0.22 5 -0.26 90 95
MAPK14 -0.021 0.11 0.25 2 -0.24 74 76
TRPC6 -0.037 0.21 -10000 0 -0.53 45 45
GNAI2 0.041 0.006 -10000 0 0 13 13
GNAI3 0.038 0.012 -10000 0 0 46 46
GNAI1 0.035 0.016 -10000 0 0 94 94
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.015 0.11 -10000 0 -0.24 74 74
ETB receptor/Endothelin-2 0.03 0.054 -10000 0 -0.071 89 89
ETB receptor/Endothelin-3 0.032 0.051 -10000 0 -0.067 80 80
ETB receptor/Endothelin-1 0.006 0.1 0.2 5 -0.18 99 104
MAPK3 -0.13 0.34 -10000 0 -0.77 112 112
MAPK1 -0.14 0.35 -10000 0 -0.76 117 117
Rac1/GDP -0.054 0.19 0.28 1 -0.35 114 115
cAMP biosynthetic process 0.044 0.13 0.23 78 -0.22 34 112
MAPK8 -0.054 0.24 -10000 0 -0.53 79 79
SRC 0.04 0.01 -10000 0 0 31 31
ETB receptor/Endothelin-1/Gi/GTP -0.01 0.11 -10000 0 -0.26 59 59
p130Cas/CRK/Src/PYK2 -0.063 0.2 0.31 4 -0.4 95 99
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.055 0.19 0.26 3 -0.35 116 119
COL1A2 -0.073 0.21 0.27 5 -0.48 103 108
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.011 0.088 0.19 8 -0.13 126 134
mol:DAG -0.027 0.15 0.21 2 -0.3 86 88
MAP2K2 -0.1 0.27 0.3 1 -0.56 120 121
MAP2K1 -0.11 0.27 0.3 1 -0.56 124 125
EDNRA -0.003 0.1 0.22 8 -0.17 131 139
positive regulation of muscle contraction -0.013 0.12 0.19 34 -0.21 102 136
Gq family/GDP -0.015 0.19 0.28 1 -0.32 112 113
HRAS/GTP -0.056 0.18 0.24 3 -0.34 121 124
PRKCH -0.034 0.15 0.26 2 -0.29 96 98
RAC1 0.039 0.01 -10000 0 0 35 35
PRKCA -0.033 0.15 0.24 4 -0.3 91 95
PRKCB -0.031 0.15 0.19 2 -0.29 99 101
PRKCE -0.031 0.14 0.29 4 -0.29 88 92
PRKCD -0.034 0.15 0.22 3 -0.3 89 92
PRKCG -0.037 0.15 0.2 1 -0.3 96 97
regulation of vascular smooth muscle contraction -0.18 0.44 -10000 0 -1 105 105
PRKCQ -0.033 0.15 0.28 10 -0.31 91 101
PLA2G4A -0.12 0.28 0.3 2 -0.54 135 137
GNA14 0.036 0.021 -10000 0 -0.039 31 31
GNA15 0.034 0.022 -10000 0 -0.036 28 28
GNA12 0.039 0.01 -10000 0 0 36 36
GNA11 0.034 0.022 -10000 0 -0.036 29 29
Rac1/GTP -0.006 0.13 0.35 6 -0.21 125 131
MMP1 0.022 0.13 0.32 24 -0.58 10 34
LPA receptor mediated 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
GNB1/GNG2 0.02 0.081 -10000 0 -0.13 113 113
NF kappa B1 p50/RelA/I kappa B alpha -0.009 0.11 0.21 3 -0.23 65 68
AP1 -0.027 0.068 -10000 0 -0.12 170 170
mol:PIP3 -0.037 0.057 -10000 0 -0.13 127 127
AKT1 -0.006 0.095 0.24 16 -0.24 17 33
PTK2B -0.047 0.11 0.12 3 -0.19 180 183
RHOA 0.001 0.06 0.16 2 -0.32 8 10
PIK3CB 0.034 0.016 -10000 0 0 99 99
mol:Ca2+ -0.01 0.048 0.19 8 -0.14 18 26
MAGI3 0.039 0.01 -10000 0 0 33 33
RELA 0.041 0.006 -10000 0 0 10 10
apoptosis 0.001 0.069 0.071 120 -0.14 95 215
HRAS/GDP 0.029 0.007 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.047 0.1 0.19 18 -0.2 117 135
NF kappa B1 p50/RelA -0.03 0.076 0.11 2 -0.16 113 115
endothelial cell migration -0.042 0.12 -10000 0 -0.3 101 101
ADCY4 -0.02 0.095 0.15 5 -0.2 99 104
ADCY5 -0.02 0.094 0.16 4 -0.19 104 108
ADCY6 -0.02 0.095 0.15 4 -0.2 104 108
ADCY7 -0.019 0.093 0.15 5 -0.19 100 105
ADCY1 -0.018 0.092 0.15 5 -0.19 99 104
ADCY2 -0.014 0.09 0.13 4 -0.19 90 94
ADCY3 -0.021 0.095 0.15 5 -0.19 107 112
ADCY8 -0.003 0.087 0.12 38 -0.18 83 121
ADCY9 -0.023 0.099 0.14 7 -0.2 108 115
GSK3B -0.046 0.11 0.2 17 -0.18 177 194
arachidonic acid secretion -0.031 0.097 0.14 2 -0.19 125 127
GNG2 0.039 0.01 -10000 0 0 34 34
TRIP6 0.012 0.051 -10000 0 -0.24 18 18
GNAO1 0.004 0.072 0.089 111 -0.14 96 207
HRAS 0.04 0.009 -10000 0 0 29 29
NFKBIA -0.031 0.092 0.17 9 -0.25 53 62
GAB1 0.038 0.012 -10000 0 0 49 49
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.013 0.26 -10000 0 -0.88 47 47
JUN 0.036 0.015 -10000 0 0 80 80
LPA/LPA2/NHERF2 0.015 0.037 -10000 0 -0.062 96 96
TIAM1 -0.039 0.3 -10000 0 -1 47 47
PIK3R1 0.034 0.016 -10000 0 0 106 106
mol:IP3 -0.005 0.044 0.19 8 -0.14 14 22
PLCB3 0.015 0.044 0.17 11 -0.062 93 104
FOS 0.026 0.02 -10000 0 0 205 205
positive regulation of mitosis -0.031 0.097 0.14 2 -0.19 125 127
LPA/LPA1-2-3 -0.018 0.05 -10000 0 -0.12 102 102
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.036 0.014 -10000 0 0 74 74
stress fiber formation -0.012 0.1 0.16 1 -0.24 51 52
GNAZ 0.007 0.074 0.09 119 -0.15 90 209
EGFR/PI3K-beta/Gab1 -0.026 0.066 -10000 0 -0.13 128 128
positive regulation of dendritic cell cytokine production -0.018 0.05 -10000 0 -0.12 102 102
LPA/LPA2/MAGI-3 0.015 0.037 -10000 0 -0.061 98 98
ARHGEF1 0.005 0.076 0.2 11 -0.14 90 101
GNAI2 0.005 0.077 0.09 122 -0.14 100 222
GNAI3 0.003 0.079 0.09 118 -0.15 99 217
GNAI1 0.002 0.079 0.09 116 -0.16 95 211
LPA/LPA3 -0.011 0.026 -10000 0 -0.065 102 102
LPA/LPA2 -0.011 0.026 -10000 0 -0.064 102 102
LPA/LPA1 -0.025 0.068 -10000 0 -0.17 102 102
HB-EGF/EGFR 0.023 0.052 -10000 0 -0.13 49 49
HBEGF -0.014 0.01 -10000 0 -10000 0 0
mol:DAG -0.005 0.044 0.19 8 -0.14 14 22
cAMP biosynthetic process -0.023 0.097 0.2 5 -0.2 96 101
NFKB1 0.035 0.015 -10000 0 0 85 85
SRC 0.039 0.01 -10000 0 0 31 31
GNB1 0.041 0.005 -10000 0 0 7 7
LYN -0.025 0.094 0.17 15 -0.23 59 74
GNAQ 0.008 0.032 0.043 119 -0.053 103 222
LPAR2 0 0.001 -10000 0 -10000 0 0
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.017 0.041 -10000 0 -0.1 102 102
IL8 -0.026 0.18 0.26 4 -0.37 91 95
PTK2 0.005 0.061 0.093 78 -0.12 76 154
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
CASP3 0.001 0.069 0.072 120 -0.14 95 215
EGFR 0.036 0.014 -10000 0 0 73 73
PLCG1 0.005 0.037 -10000 0 -0.095 31 31
PLD2 0.015 0.067 0.093 121 -0.12 94 215
G12/G13 0.021 0.079 -10000 0 -0.14 102 102
PI3K-beta -0.028 0.076 -10000 0 -0.21 46 46
cell migration -0.01 0.086 -10000 0 -0.25 46 46
SLC9A3R2 0.038 0.012 -10000 0 0 51 51
PXN -0.013 0.1 0.16 1 -0.25 51 52
HRAS/GTP -0.03 0.098 0.14 2 -0.19 122 124
RAC1 0.039 0.01 -10000 0 0 35 35
MMP9 0.029 0.019 -10000 0 0 170 170
PRKCE 0.039 0.011 -10000 0 0 38 38
PRKCD -0.016 0.055 0.18 12 -0.16 20 32
Gi(beta/gamma) -0.021 0.1 0.15 1 -0.19 121 122
mol:LPA -0.017 0.041 -10000 0 -0.1 102 102
TRIP6/p130 Cas/FAK1/Paxillin -0.007 0.1 0.19 1 -0.19 89 90
MAPKKK cascade -0.031 0.097 0.14 2 -0.19 125 127
contractile ring contraction involved in cytokinesis 0.001 0.062 0.16 2 -0.3 10 12
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.008 0.033 0.043 120 -0.052 110 230
GNA15 0.008 0.031 0.043 112 -0.054 96 208
GNA12 0.039 0.01 -10000 0 0 36 36
GNA13 0.04 0.009 -10000 0 0 28 28
MAPT -0.047 0.11 0.19 18 -0.2 118 136
GNA11 0.008 0.032 0.043 113 -0.054 99 212
Rac1/GTP -0.016 0.28 -10000 0 -0.93 47 47
MMP2 -0.042 0.12 -10000 0 -0.3 101 101
HIF-1-alpha transcription factor network

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
PKM2 0.029 0.33 0.54 45 -0.53 88 133
HDAC7 -0.001 0.004 -10000 0 -0.037 1 1
HIF1A/ARNT/Cbp/p300/Src-1 0.028 0.32 0.59 9 -0.59 54 63
SMAD4 0.039 0.012 -10000 0 0 49 49
ID2 0.03 0.33 0.55 46 -0.53 88 134
AP1 0.005 0.085 -10000 0 -0.15 117 117
ABCG2 0.022 0.33 0.54 44 -0.53 89 133
HIF1A 0.029 0.1 0.2 38 -0.14 77 115
TFF3 0.009 0.32 0.55 37 -0.53 87 124
GATA2 0.04 0.019 -10000 0 -0.058 12 12
AKT1 0.04 0.096 0.22 29 -0.11 73 102
response to hypoxia 0.005 0.068 0.15 39 -0.1 58 97
MCL1 0.033 0.34 0.54 49 -0.53 90 139
NDRG1 -0.019 0.29 0.53 22 -0.55 80 102
SERPINE1 -0.013 0.3 0.54 25 -0.53 86 111
FECH 0.026 0.33 0.55 44 -0.54 85 129
FURIN 0.032 0.33 0.55 48 -0.53 87 135
NCOA2 0.038 0.015 -10000 0 -0.052 1 1
EP300 0.042 0.11 0.29 36 -0.24 19 55
HMOX1 0.015 0.33 0.55 39 -0.55 86 125
BHLHE40 -0.027 0.3 0.5 37 -0.52 88 125
BHLHE41 -0.027 0.3 0.5 37 -0.52 88 125
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.093 0.16 0.36 13 -0.19 43 56
ENG 0.018 0.11 0.26 17 -0.2 27 44
JUN 0.035 0.019 -10000 0 -0.043 10 10
RORA 0.03 0.33 0.55 46 -0.53 89 135
ABCB1 0.018 0.098 -10000 0 -0.55 4 4
TFRC -0.009 0.31 0.54 31 -0.54 85 116
CXCR4 0.005 0.33 0.54 39 -0.54 92 131
TF 0.024 0.32 0.54 45 -0.53 85 130
CITED2 0.027 0.33 0.54 45 -0.53 88 133
HIF1A/ARNT 0.015 0.38 -10000 0 -0.66 63 63
LDHA -0.048 0.3 -10000 0 -0.91 53 53
ETS1 0.006 0.32 0.53 34 -0.55 90 124
PGK1 0.029 0.34 0.55 45 -0.55 90 135
NOS2 -0.027 0.3 0.5 37 -0.52 88 125
ITGB2 0.008 0.33 0.55 36 -0.55 92 128
ALDOA 0.036 0.34 0.54 50 -0.53 88 138
Cbp/p300/CITED2 0.009 0.33 0.57 22 -0.59 74 96
FOS 0.026 0.022 -10000 0 -0.048 5 5
HK2 0.03 0.34 0.55 45 -0.54 87 132
SP1 0.048 0.008 -10000 0 -10000 0 0
GCK 0.064 0.15 0.48 11 -0.36 1 12
HK1 0.031 0.34 0.55 44 -0.53 89 133
NPM1 0.035 0.34 0.54 50 -0.53 91 141
EGLN1 0.034 0.33 0.55 48 -0.53 83 131
CREB1 0.035 0.042 -10000 0 -0.11 41 41
PGM1 0.023 0.34 0.55 41 -0.54 90 131
SMAD3 0.04 0.009 -10000 0 0 25 25
EDN1 0.034 0.21 0.46 4 -1.1 12 16
IGFBP1 0.036 0.34 0.54 47 -0.53 86 133
VEGFA -0.01 0.26 0.47 31 -0.48 72 103
HIF1A/JAB1 0.033 0.098 0.19 10 -0.14 83 93
CP -0.016 0.31 0.53 31 -0.56 86 117
CXCL12 -0.023 0.31 0.53 25 -0.53 96 121
COPS5 0.036 0.016 -10000 0 -0.049 1 1
SMAD3/SMAD4 0.052 0.033 -10000 0 -0.14 11 11
BNIP3 0.012 0.33 0.54 39 -0.55 87 126
EGLN3 -0.021 0.32 0.55 25 -0.56 94 119
CA9 -0.019 0.3 0.55 24 -0.53 88 112
TERT 0.018 0.32 0.54 41 -0.53 84 125
ENO1 0.031 0.34 0.55 45 -0.54 88 133
PFKL 0.033 0.34 0.55 47 -0.53 88 135
NCOA1 0.04 0.01 -10000 0 -0.001 29 29
ADM -0.003 0.32 0.55 23 -0.54 89 112
ARNT 0.03 0.098 0.2 36 -0.12 78 114
HNF4A 0.042 0.011 -10000 0 -10000 0 0
ADFP -0.004 0.32 0.54 35 -0.54 93 128
SLC2A1 0.002 0.28 0.47 28 -0.51 74 102
LEP 0.035 0.33 0.55 45 -0.53 85 130
HIF1A/ARNT/Cbp/p300 0.01 0.32 0.58 6 -0.6 56 62
EPO 0.03 0.28 0.51 22 -0.54 50 72
CREBBP 0.048 0.11 0.28 42 -0.22 14 56
HIF1A/ARNT/Cbp/p300/HDAC7 0.003 0.31 0.55 3 -0.59 58 61
PFKFB3 0.025 0.33 0.54 46 -0.55 86 132
NT5E -0.041 0.3 0.54 16 -0.55 95 111
Osteopontin-mediated events

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
IKK alpha homodimer -0.012 0.13 0.21 9 -0.22 111 120
NF kappa B1 p50/RelA/I kappa B alpha -0.048 0.19 0.28 1 -0.36 117 118
alphaV/beta3 Integrin/Osteopontin/Src -0.008 0.11 -10000 0 -0.17 152 152
AP1 -0.046 0.18 0.27 2 -0.29 149 151
ILK -0.028 0.11 0.19 11 -0.24 71 82
bone resorption -0.04 0.1 0.19 2 -0.25 57 59
PTK2B 0.033 0.017 -10000 0 0 116 116
PYK2/p130Cas 0.004 0.12 -10000 0 -0.2 81 81
ITGAV 0.026 0.032 -10000 0 -0.048 63 63
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.029 0.067 -10000 0 -0.14 66 66
alphaV/beta3 Integrin/Osteopontin 0.004 0.13 -10000 0 -0.17 159 159
MAP3K1 -0.027 0.11 0.18 12 -0.24 69 81
JUN 0.036 0.015 -10000 0 0 80 80
MAPK3 -0.047 0.14 0.19 14 -0.28 111 125
MAPK1 -0.046 0.14 0.19 15 -0.28 110 125
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
NFKB1 0.035 0.015 -10000 0 0 85 85
MAPK8 -0.032 0.1 0.17 13 -0.22 86 99
ITGB3 0.023 0.034 -10000 0 -0.048 75 75
NFKBIA -0.064 0.17 0.19 12 -0.36 108 120
FOS 0.026 0.02 -10000 0 0 205 205
CD44 0.035 0.016 -10000 0 0 94 94
CHUK 0.038 0.012 -10000 0 0 52 52
PLAU -0.18 0.42 -10000 0 -1 107 107
NF kappa B1 p50/RelA -0.033 0.2 -10000 0 -0.37 121 121
BCAR1 0.036 0.014 -10000 0 0 74 74
RELA 0.041 0.006 -10000 0 0 10 10
alphaV beta3 Integrin 0.004 0.091 -10000 0 -0.14 138 138
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.03 0.1 0.18 12 -0.23 73 85
VAV3 -0.039 0.1 0.18 11 -0.23 88 99
MAP3K14 -0.026 0.12 0.19 12 -0.22 114 126
ROCK2 0.037 0.013 -10000 0 0 62 62
SPP1 0.024 0.031 -10000 0 -0.05 51 51
RAC1 0.039 0.01 -10000 0 0 35 35
Rac1/GTP -0.035 0.11 0.18 11 -0.22 88 99
MMP2 -0.088 0.14 0.25 2 -0.31 135 137
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.037 0.013 -10000 0 0 61 61
CCL5 0.03 0.019 -10000 0 0 162 162
SDCBP 0.036 0.014 -10000 0 0 77 77
FGFR/FGF2/Syndecan-1 -0.014 0.12 0.2 21 -0.33 40 61
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 -0.014 0.13 0.21 16 -0.29 58 74
Syndecan-1/Syntenin -0.016 0.14 0.22 20 -0.28 69 89
MAPK3 -0.024 0.13 0.2 19 -0.28 63 82
HGF/MET 0.013 0.075 -10000 0 -0.14 104 104
TGFB1/TGF beta receptor Type II 0.037 0.013 -10000 0 0 61 61
BSG 0.036 0.014 -10000 0 0 75 75
keratinocyte migration -0.014 0.13 0.21 16 -0.29 58 74
Syndecan-1/RANTES -0.019 0.14 0.23 20 -0.29 76 96
Syndecan-1/CD147 -0.004 0.15 0.25 14 -0.29 64 78
Syndecan-1/Syntenin/PIP2 -0.018 0.14 0.21 20 -0.27 69 89
LAMA5 0.035 0.015 -10000 0 0 90 90
positive regulation of cell-cell adhesion -0.018 0.13 0.21 20 -0.27 69 89
MMP7 0.016 0.02 -10000 0 0 336 336
HGF 0.04 0.009 -10000 0 0 29 29
Syndecan-1/CASK -0.038 0.12 0.15 5 -0.28 65 70
Syndecan-1/HGF/MET -0.02 0.14 0.25 14 -0.27 82 96
regulation of cell adhesion -0.032 0.12 0.2 14 -0.28 60 74
HPSE 0.035 0.015 -10000 0 0 89 89
positive regulation of cell migration -0.014 0.12 0.2 21 -0.33 40 61
SDC1 -0.019 0.12 0.17 7 -0.34 36 43
Syndecan-1/Collagen -0.014 0.12 0.2 21 -0.33 40 61
PPIB 0.04 0.009 -10000 0 0 24 24
MET 0.027 0.02 -10000 0 0 195 195
PRKACA 0.035 0.015 -10000 0 0 87 87
MMP9 0.029 0.019 -10000 0 0 170 170
MAPK1 -0.023 0.13 0.2 20 -0.28 64 84
homophilic cell adhesion -0.013 0.13 0.2 29 -0.32 44 73
MMP1 0.03 0.019 -10000 0 0 155 155
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.005 0.086 -10000 0 -0.13 129 129
alphaM/beta2 Integrin/GPIbA 0.053 0.069 -10000 0 -0.11 65 65
alphaM/beta2 Integrin/proMMP-9 0.03 0.082 -10000 0 -0.13 84 84
PLAUR 0.036 0.014 -10000 0 0 74 74
HMGB1 0.041 0.016 -10000 0 -0.054 10 10
alphaM/beta2 Integrin/Talin 0.047 0.076 -10000 0 -0.12 75 75
AGER 0.041 0.016 -10000 0 -0.054 10 10
RAP1A 0.039 0.01 -10000 0 0 35 35
SELPLG 0.04 0.009 -10000 0 0 27 27
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.081 0.083 -10000 0 -0.18 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.029 0.019 -10000 0 0 170 170
CYR61 0.03 0.019 -10000 0 0 156 156
TLN1 0.038 0.012 -10000 0 0 47 47
Rap1/GTP -0.061 0.17 -10000 0 -0.31 141 141
RHOA 0.041 0.007 -10000 0 0 14 14
P-selectin oligomer 0.039 0.011 -10000 0 0 39 39
MYH2 -0.081 0.17 0.2 2 -0.33 141 143
MST1R 0.039 0.011 -10000 0 0 41 41
leukocyte activation during inflammatory response 0.058 0.065 -10000 0 -0.1 51 51
APOB 0.041 0.007 -10000 0 0 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.021 0.021 -10000 0 0 269 269
JAM3 0.038 0.013 -10000 0 0 56 56
GP1BA 0.039 0.01 -10000 0 0 31 31
alphaM/beta2 Integrin/CTGF 0.034 0.081 -10000 0 -0.12 96 96
alphaM/beta2 Integrin -0.063 0.17 -10000 0 -0.34 124 124
JAM3 homodimer 0.038 0.013 -10000 0 0 56 56
ICAM2 0.039 0.011 -10000 0 0 40 40
ICAM1 0.026 0.02 -10000 0 0 206 206
phagocytosis triggered by activation of immune response cell surface activating receptor -0.063 0.17 -10000 0 -0.34 123 123
cell adhesion 0.052 0.068 -10000 0 -0.11 65 65
NFKB1 0.021 0.075 0.26 4 -0.22 24 28
THY1 0.025 0.02 -10000 0 0 217 217
RhoA/GDP 0.029 0.014 -10000 0 -0.13 4 4
Lipoprotein(a) 0.049 0.019 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.024 0.1 -10000 0 -0.13 134 134
IL6 -0.019 0.076 0.26 3 -0.43 10 13
ITGB2 0.034 0.022 -10000 0 -0.052 9 9
elevation of cytosolic calcium ion concentration 0.033 0.11 -10000 0 -0.16 104 104
alphaM/beta2 Integrin/JAM2/JAM3 0.066 0.074 -10000 0 -0.11 55 55
JAM2 0.037 0.013 -10000 0 0 59 59
alphaM/beta2 Integrin/ICAM1 0.052 0.1 -10000 0 -0.14 86 86
alphaM/beta2 Integrin/uPA/Plg 0.041 0.098 -10000 0 -0.14 99 99
RhoA/GTP -0.082 0.18 0.2 1 -0.35 141 142
positive regulation of phagocytosis -0.043 0.15 0.2 5 -0.29 107 112
Ron/MSP 0.054 0.029 -10000 0 -0.14 9 9
alphaM/beta2 Integrin/uPAR/uPA 0.035 0.11 -10000 0 -0.16 104 104
alphaM/beta2 Integrin/uPAR 0.045 0.081 -10000 0 -0.14 66 66
PLAU 0.026 0.02 -10000 0 0 212 212
PLAT 0.026 0.02 -10000 0 0 213 213
actin filament polymerization -0.077 0.16 0.2 2 -0.32 139 141
MST1 0.041 0.007 -10000 0 0 15 15
alphaM/beta2 Integrin/lipoprotein(a) 0.064 0.068 -10000 0 -0.1 51 51
TNF -0.011 0.072 0.26 4 -0.34 8 12
RAP1B 0.038 0.013 -10000 0 0 57 57
alphaM/beta2 Integrin/uPA 0.017 0.094 -10000 0 -0.15 103 103
fibrinolysis 0.038 0.097 -10000 0 -0.14 99 99
HCK 0.036 0.015 -10000 0 0 79 79
dendritic cell antigen processing and presentation -0.063 0.17 -10000 0 -0.34 123 123
VTN 0.04 0.008 -10000 0 0 21 21
alphaM/beta2 Integrin/CYR61 0.024 0.084 -10000 0 -0.12 110 110
LPA 0.037 0.013 -10000 0 0 58 58
LRP1 0.036 0.014 -10000 0 0 73 73
cell migration 0.017 0.095 0.19 12 -0.13 132 144
FN1 0.021 0.021 -10000 0 0 273 273
alphaM/beta2 Integrin/Thy1 0.008 0.092 -10000 0 -0.13 149 149
MPO 0.04 0.008 -10000 0 0 19 19
KNG1 0.034 0.017 -10000 0 0 108 108
RAP1/GDP 0.039 0.049 -10000 0 -0.12 41 41
ROCK1 -0.082 0.17 0.24 3 -0.33 143 146
ELA2 0.037 0.014 -10000 0 0 70 70
PLG 0.038 0.012 -10000 0 0 50 50
CTGF 0.033 0.017 -10000 0 0 113 113
alphaM/beta2 Integrin/Hck 0.049 0.073 -10000 0 -0.13 53 53
ITGAM 0.041 0.016 -10000 0 -0.054 10 10
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.072 0.076 -10000 0 -0.12 53 53
HP 0.01 0.018 -10000 0 0 419 419
leukocyte adhesion 0.019 0.11 -10000 0 -0.21 25 25
SELP 0.039 0.011 -10000 0 0 39 39
TCGA08_retinoblastoma

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
CDKN2B 0.029 0.026 -10000 0 -0.047 40 40
CDKN2C 0.029 0.029 -10000 0 -0.044 53 53
CDKN2A 0.021 0.029 -10000 0 -0.039 59 59
CCND2 0.009 0.046 0.11 78 -0.12 2 80
RB1 -0.012 0.066 0.24 6 -0.14 84 90
CDK4 0.01 0.056 0.13 79 -0.12 20 99
CDK6 0.006 0.063 0.13 79 -0.12 44 123
G1/S progression 0.019 0.074 0.14 105 -0.23 8 113
Nectin adhesion pathway

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
PDGFRB 0.037 0.013 -10000 0 0 64 64
alphaV beta3 Integrin 0.014 0.079 -10000 0 -0.15 92 92
PTK2 -0.045 0.13 -10000 0 -0.31 95 95
positive regulation of JNK cascade -0.032 0.14 -10000 0 -0.28 90 90
CDC42/GDP -0.038 0.2 -10000 0 -0.38 94 94
Rac1/GDP -0.04 0.19 -10000 0 -0.38 90 90
RAP1B 0.038 0.013 -10000 0 0 57 57
RAP1A 0.039 0.01 -10000 0 0 35 35
CTNNB1 0.039 0.01 -10000 0 0 32 32
CDC42/GTP -0.037 0.18 -10000 0 -0.35 89 89
nectin-3/I-afadin 0.01 0.074 -10000 0 -0.14 96 96
RAPGEF1 -0.058 0.18 -10000 0 -0.37 117 117
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.064 0.2 -10000 0 -0.41 118 118
PDGFB-D/PDGFRB 0.037 0.013 -10000 0 0 64 64
TLN1 -0.04 0.084 0.19 1 -0.25 60 61
Rap1/GTP -0.046 0.14 -10000 0 -0.29 118 118
IQGAP1 0.037 0.014 -10000 0 0 67 67
Rap1/GTP/I-afadin 0.042 0.065 -10000 0 -0.11 64 64
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.01 0.074 -10000 0 -0.14 96 96
PVR 0.04 0.009 -10000 0 0 24 24
Necl-5(dimer) 0.04 0.009 -10000 0 0 24 24
mol:GDP -0.066 0.22 -10000 0 -0.45 94 94
MLLT4 0.033 0.017 -10000 0 0 110 110
PIK3CA 0.03 0.019 -10000 0 0 150 150
PI3K 0.024 0.091 -10000 0 -0.13 89 89
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.041 0.046 -10000 0 -0.14 26 26
positive regulation of lamellipodium assembly -0.04 0.15 -10000 0 -0.3 93 93
PVRL1 0.04 0.008 -10000 0 0 23 23
PVRL3 0.029 0.019 -10000 0 0 169 169
PVRL2 0.039 0.011 -10000 0 0 43 43
PIK3R1 0.034 0.016 -10000 0 0 106 106
CDH1 0.035 0.016 -10000 0 0 96 96
CLDN1 0.023 0.021 -10000 0 0 253 253
JAM-A/CLDN1 0.013 0.089 -10000 0 -0.12 124 124
SRC -0.083 0.21 -10000 0 -0.44 124 124
ITGB3 0.033 0.017 -10000 0 0 120 120
nectin-1(dimer)/I-afadin/I-afadin 0.041 0.046 -10000 0 -0.14 26 26
FARP2 -0.059 0.22 -10000 0 -0.49 58 58
RAC1 0.039 0.01 -10000 0 0 35 35
CTNNA1 0.039 0.01 -10000 0 0 36 36
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.024 0.077 -10000 0 -0.12 96 96
nectin-1/I-afadin 0.041 0.046 -10000 0 -0.14 26 26
nectin-2/I-afadin 0.038 0.05 -10000 0 -0.14 31 31
RAC1/GTP/IQGAP1/filamentous actin 0.038 0.046 -10000 0 -0.11 40 40
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.024 0.076 -10000 0 -0.12 91 91
CDC42/GTP/IQGAP1/filamentous actin 0.04 0.046 -10000 0 -0.11 40 40
F11R 0.04 0.009 -10000 0 0 29 29
positive regulation of filopodium formation -0.032 0.14 -10000 0 -0.28 90 90
alphaV/beta3 Integrin/Talin -0.031 0.11 0.26 2 -0.22 96 98
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.05 -10000 0 -0.14 31 31
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.05 -10000 0 -0.14 31 31
PIP5K1C -0.031 0.086 -10000 0 -0.18 113 113
VAV2 -0.073 0.23 -10000 0 -0.49 80 80
RAP1/GDP -0.039 0.18 -10000 0 -0.35 103 103
ITGAV 0.033 0.017 -10000 0 0 115 115
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.021 0.077 -10000 0 -0.12 98 98
nectin-3(dimer)/I-afadin/I-afadin 0.01 0.074 -10000 0 -0.14 96 96
Rac1/GTP -0.047 0.19 -10000 0 -0.37 93 93
PTPRM -0.027 0.096 -10000 0 -0.18 116 116
E-cadherin/beta catenin/alpha catenin 0.062 0.09 -10000 0 -0.13 54 54
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.04 0.008 -10000 0 0 22 22
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.034 0.016 -10000 0 0 101 101
GNB1/GNG2 -0.064 0.086 -10000 0 -0.18 188 188
AKT1 -0.027 0.14 0.25 2 -0.24 55 57
EGF 0.038 0.012 -10000 0 0 52 52
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.005 0.06 0.2 12 -0.18 2 14
mol:Ca2+ -0.053 0.19 0.29 3 -0.3 188 191
LYN 0.002 0.057 0.2 12 -0.17 4 16
RhoA/GTP -0.02 0.088 0.14 6 -0.13 178 184
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.073 0.21 0.32 2 -0.34 189 191
GNG2 0.039 0.01 -10000 0 0 34 34
ARRB2 0.039 0.01 -10000 0 0 37 37
TP alpha/Gq family/GDP/G beta5/gamma2 -0.025 0.16 -10000 0 -0.52 47 47
G beta5/gamma2 -0.074 0.12 -10000 0 -0.24 186 186
PRKCH -0.073 0.22 0.33 1 -0.35 188 189
DNM1 0.039 0.01 -10000 0 0 36 36
TXA2/TP beta/beta Arrestin3 0.029 0.023 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR 0.041 0.006 -10000 0 0 12 12
G12 family/GTP -0.068 0.18 -10000 0 -0.3 186 186
ADRBK1 0.041 0.005 -10000 0 0 7 7
ADRBK2 0.036 0.015 -10000 0 0 80 80
RhoA/GTP/ROCK1 0.051 0.024 -10000 0 -0.11 9 9
mol:GDP 0.03 0.16 0.44 44 -0.22 2 46
mol:NADP 0.038 0.012 -10000 0 0 46 46
RAB11A 0.04 0.009 -10000 0 0 24 24
PRKG1 0.04 0.009 -10000 0 0 30 30
mol:IP3 -0.076 0.23 0.35 1 -0.37 188 189
cell morphogenesis 0.05 0.024 -10000 0 -0.11 9 9
PLCB2 -0.12 0.3 -10000 0 -0.5 188 188
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.002 0.054 0.22 8 -0.18 2 10
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.003 0.057 0.2 11 -0.18 3 14
RHOA 0.041 0.007 -10000 0 0 14 14
PTGIR 0.04 0.009 -10000 0 0 28 28
PRKCB1 -0.079 0.23 0.34 1 -0.38 187 188
GNAQ 0.038 0.012 -10000 0 0 50 50
mol:L-citrulline 0.038 0.012 -10000 0 0 46 46
TXA2/TXA2-R family -0.12 0.3 0.38 1 -0.51 190 191
LCK 0.004 0.059 0.21 11 -0.18 2 13
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.053 0.049 0.2 6 -0.15 7 13
TXA2-R family/G12 family/GDP/G beta/gamma 0.014 0.11 -10000 0 -0.41 32 32
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.049 0.05 0.2 6 -0.15 7 13
MAPK14 -0.041 0.15 0.24 6 -0.23 178 184
TGM2/GTP -0.087 0.25 0.4 1 -0.41 170 171
MAPK11 -0.048 0.14 0.25 3 -0.22 186 189
ARHGEF1 -0.031 0.12 0.2 11 -0.18 181 192
GNAI2 0.041 0.006 -10000 0 0 13 13
JNK cascade -0.079 0.24 0.33 2 -0.38 190 192
RAB11/GDP 0.04 0.009 -10000 0 0 24 24
ICAM1 -0.059 0.2 0.27 6 -0.32 180 186
cAMP biosynthetic process -0.072 0.21 0.33 1 -0.34 176 177
Gq family/GTP/EBP50 0.01 0.049 0.25 2 -0.14 43 45
actin cytoskeleton reorganization 0.05 0.024 -10000 0 -0.11 9 9
SRC 0.003 0.059 0.2 11 -0.18 2 13
GNB5 0.04 0.009 -10000 0 0 28 28
GNB1 0.041 0.005 -10000 0 0 7 7
EGF/EGFR 0.003 0.076 0.22 11 -0.21 12 23
VCAM1 -0.063 0.21 0.27 6 -0.33 188 194
TP beta/Gq family/GDP/G beta5/gamma2 -0.025 0.16 -10000 0 -0.52 47 47
platelet activation -0.058 0.19 0.32 2 -0.3 187 189
PGI2/IP 0.028 0.016 -10000 0 -0.13 5 5
PRKACA 0.019 0.022 -10000 0 -0.16 6 6
Gq family/GDP/G beta5/gamma2 -0.017 0.13 0.17 1 -0.44 40 41
TXA2/TP beta/beta Arrestin2 0.016 0.058 -10000 0 -0.29 13 13
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.003 0.023 0.11 5 -0.16 6 11
mol:DAG -0.091 0.26 0.36 1 -0.42 188 189
EGFR 0.036 0.014 -10000 0 0 73 73
TXA2/TP alpha -0.1 0.28 0.38 1 -0.46 176 177
Gq family/GTP -0.009 0.066 -10000 0 -0.18 63 63
YES1 0.002 0.057 0.2 11 -0.18 2 13
GNAI2/GTP 0.027 0.045 -10000 0 -0.13 12 12
PGD2/DP 0.03 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.038 0.012 -10000 0 0 47 47
FYN 0.002 0.058 0.2 11 -0.16 7 18
mol:NO 0.038 0.012 -10000 0 0 46 46
GNA15 0.037 0.014 -10000 0 0 69 69
PGK/cGMP 0.049 0.019 -10000 0 -10000 0 0
RhoA/GDP 0.041 0.007 -10000 0 0 14 14
TP alpha/TGM2/GDP/G beta/gamma 0.062 0.063 0.25 2 -0.18 7 9
NOS3 0.038 0.012 -10000 0 0 46 46
RAC1 0.039 0.01 -10000 0 0 35 35
PRKCA -0.073 0.22 0.33 4 -0.36 183 187
PRKCB -0.071 0.22 0.31 1 -0.35 189 190
PRKCE -0.072 0.22 0.32 5 -0.36 183 188
PRKCD -0.082 0.23 0.33 1 -0.38 188 189
PRKCG -0.081 0.24 0.34 1 -0.38 190 191
muscle contraction -0.11 0.28 0.38 1 -0.47 190 191
PRKCZ -0.071 0.21 0.3 2 -0.34 190 192
ARR3 0.042 0.002 -10000 0 0 1 1
TXA2/TP beta 0.045 0.051 0.24 1 -0.14 8 9
PRKCQ -0.073 0.22 0.36 3 -0.36 183 186
MAPKKK cascade -0.1 0.27 0.36 1 -0.44 186 187
SELE -0.052 0.18 0.28 3 -0.29 189 192
TP beta/GNAI2/GDP/G beta/gamma 0.072 0.059 0.25 2 -0.16 8 10
ROCK1 0.04 0.007 -10000 0 0 18 18
GNA14 0.039 0.01 -10000 0 0 33 33
chemotaxis -0.15 0.34 -10000 0 -0.6 189 189
GNA12 0.039 0.01 -10000 0 0 36 36
GNA13 0.04 0.009 -10000 0 0 28 28
GNA11 0.037 0.013 -10000 0 0 63 63
Rac1/GTP 0.028 0.01 -10000 0 -0.13 1 1
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.018 0.035 -10000 0 -0.055 77 77
PDGF/PDGFRA/CRKL 0.012 0.071 -10000 0 -0.14 81 81
positive regulation of JUN kinase activity 0.048 0.082 -10000 0 -0.12 94 94
CRKL 0.039 0.01 -10000 0 0 35 35
PDGF/PDGFRA/Caveolin-3 0.012 0.073 -10000 0 -0.14 86 86
AP1 -0.12 0.26 -10000 0 -0.66 98 98
mol:IP3 -0.016 0.046 0.065 40 -0.098 81 121
PLCG1 -0.016 0.046 0.065 40 -0.098 81 121
PDGF/PDGFRA/alphaV Integrin -0.008 0.091 -10000 0 -0.16 127 127
RAPGEF1 0.04 0.008 -10000 0 0 22 22
CRK 0.038 0.011 -10000 0 0 45 45
mol:Ca2+ -0.016 0.046 0.065 40 -0.098 81 121
CAV3 0.04 0.008 -10000 0 0 21 21
CAV1 0.036 0.015 -10000 0 0 80 80
SHC/Grb2/SOS1 0.05 0.084 -10000 0 -0.12 94 94
PDGF/PDGFRA/Shf 0.011 0.071 -10000 0 -0.14 83 83
FOS -0.12 0.26 0.32 1 -0.66 98 99
JUN -0.034 0.042 0.23 3 -0.2 10 13
oligodendrocyte development -0.008 0.091 -10000 0 -0.16 127 127
GRB2 0.041 0.007 -10000 0 0 14 14
PIK3R1 0.034 0.016 -10000 0 0 106 106
mol:DAG -0.016 0.046 0.065 40 -0.098 81 121
PDGF/PDGFRA 0.017 0.035 -10000 0 -0.055 77 77
actin cytoskeleton reorganization 0.013 0.072 -10000 0 -0.14 84 84
SRF -0.007 0.024 0.033 126 -10000 0 126
SHC1 0.04 0.009 -10000 0 0 29 29
PI3K 0.011 0.081 -10000 0 -0.14 93 93
PDGF/PDGFRA/Crk/C3G 0.034 0.072 -10000 0 -0.12 84 84
JAK1 -0.011 0.02 0.033 7 -10000 0 7
ELK1/SRF -0.028 0.061 0.15 12 -0.15 57 69
SHB 0.041 0.007 -10000 0 0 16 16
SHF 0.039 0.011 -10000 0 0 41 41
CSNK2A1 0.038 0.03 0.084 1 -0.028 57 58
GO:0007205 -0.025 0.072 0.087 22 -0.2 61 83
SOS1 0.038 0.013 -10000 0 0 57 57
Ras protein signal transduction 0.048 0.082 -10000 0 -0.12 94 94
PDGF/PDGFRA/SHB 0.013 0.072 -10000 0 -0.14 84 84
PDGF/PDGFRA/Caveolin-1 0.01 0.074 -10000 0 -0.15 76 76
ITGAV 0.033 0.017 -10000 0 0 115 115
ELK1 -0.028 0.077 0.19 11 -0.18 66 77
PIK3CA 0.03 0.019 -10000 0 0 150 150
PDGF/PDGFRA/Crk 0.011 0.071 -10000 0 -0.14 84 84
JAK-STAT cascade -0.011 0.02 0.033 7 -10000 0 7
cell proliferation 0.011 0.071 -10000 0 -0.14 83 83
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.021 0.021 -10000 0 0 271 271
positive regulation of NF-kappaB transcription factor activity 0.003 0.066 -10000 0 -0.13 92 92
MAP2K4 -0.014 0.095 0.18 1 -0.27 37 38
IKBKB 0.038 0.011 -10000 0 0 44 44
TNFRSF10B 0.033 0.017 -10000 0 0 123 123
TNFRSF10A 0.031 0.018 -10000 0 0 138 138
SMPD1 -0.007 0.044 -10000 0 -0.1 90 90
IKBKG 0.042 0.003 -10000 0 0 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.032 0.018 -10000 0 0 134 134
TRAIL/TRAILR2 0.003 0.067 -10000 0 -0.13 93 93
TRAIL/TRAILR3 0.002 0.067 -10000 0 -0.13 97 97
TRAIL/TRAILR1 0 0.068 -10000 0 -0.13 98 98
TRAIL/TRAILR4 0.003 0.067 -10000 0 -0.13 92 92
TRAIL/TRAILR1/DAP3/GTP 0.011 0.066 -10000 0 -0.1 97 97
IKK complex 0.021 0.089 -10000 0 -0.29 26 26
RIPK1 0.038 0.012 -10000 0 0 48 48
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.027 0.021 -10000 0 -0.13 9 9
MAPK3 -0.01 0.01 -10000 0 -10000 0 0
MAP3K1 -0.007 0.098 -10000 0 -0.29 35 35
TRAILR4 (trimer) 0.032 0.018 -10000 0 0 134 134
TRADD 0.036 0.014 -10000 0 0 76 76
TRAILR1 (trimer) 0.031 0.018 -10000 0 0 138 138
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.022 0.082 -10000 0 -0.25 32 32
CFLAR 0.04 0.008 -10000 0 0 21 21
MAPK1 -0.01 0.01 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP 0.027 0.082 -10000 0 -0.11 66 66
mol:ceramide -0.007 0.044 -10000 0 -0.1 90 90
FADD 0.04 0.008 -10000 0 0 21 21
MAPK8 -0.021 0.099 0.2 5 -0.27 44 49
TRAF2 0.04 0.009 -10000 0 0 25 25
TRAILR3 (trimer) 0.032 0.018 -10000 0 0 131 131
CHUK 0.038 0.012 -10000 0 0 52 52
TRAIL/TRAILR1/FADD 0.011 0.07 -10000 0 -0.12 95 95
DAP3 0.039 0.011 -10000 0 0 38 38
CASP10 -0.007 0.1 0.16 79 -0.2 77 156
JNK cascade 0.003 0.066 -10000 0 -0.13 92 92
TRAIL (trimer) 0.021 0.021 -10000 0 0 271 271
TNFRSF10C 0.032 0.018 -10000 0 0 131 131
TRAIL/TRAILR1/DAP3/GTP/FADD 0.022 0.073 -10000 0 -0.1 93 93
TRAIL/TRAILR2/FADD 0.014 0.069 -10000 0 -0.11 91 91
cell death -0.007 0.044 -10000 0 -0.1 90 90
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.021 0.082 -10000 0 -0.24 34 34
TRAILR2 (trimer) 0.032 0.017 -10000 0 0 123 123
CASP8 -0.001 0.11 -10000 0 -0.65 13 13
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.029 0.082 -10000 0 -0.11 60 60
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.038 0.053 -10000 0 -0.14 38 38
ATM 0.036 0.014 -10000 0 0 72 72
UBE2D3 0.038 0.012 -10000 0 0 50 50
PRKDC 0.038 0.011 -10000 0 0 44 44
ATR 0.035 0.016 -10000 0 0 92 92
UBE2L3 0.039 0.01 -10000 0 0 37 37
FANCD2 -0.004 0.089 -10000 0 -0.25 56 56
protein ubiquitination 0.014 0.1 -10000 0 -0.13 149 149
XRCC5 0.039 0.011 -10000 0 0 38 38
XRCC6 0.037 0.014 -10000 0 0 69 69
M/R/N Complex 0.049 0.07 -10000 0 -0.15 48 48
MRE11A 0.038 0.012 -10000 0 0 51 51
DNA-PK 0.053 0.066 -10000 0 -0.14 45 45
FA complex/FANCD2/Ubiquitin -0.007 0.12 -10000 0 -0.41 31 31
FANCF 0.04 0.009 -10000 0 0 28 28
BRCA1 0.034 0.016 -10000 0 0 99 99
CCNE1 0.028 0.02 -10000 0 0 188 188
CDK2/Cyclin E1 0.011 0.077 -10000 0 -0.14 102 102
FANCG 0.04 0.008 -10000 0 0 21 21
BRCA1/BACH1/BARD1 0.027 0.069 -10000 0 -0.14 73 73
FANCE 0.04 0.008 -10000 0 0 20 20
FANCC 0.04 0.009 -10000 0 0 27 27
NBN 0.035 0.016 -10000 0 0 96 96
FANCA 0.035 0.016 -10000 0 0 94 94
DNA repair -0.023 0.13 0.26 10 -0.38 36 46
BRCA1/BARD1/ubiquitin 0.027 0.069 -10000 0 -0.14 73 73
BARD1/DNA-PK 0.064 0.082 -10000 0 -0.14 58 58
FANCL 0.038 0.013 -10000 0 0 56 56
mRNA polyadenylation -0.038 0.053 0.14 38 -10000 0 38
BRCA1/BARD1/CTIP/M/R/N Complex -0.023 0.14 0.17 3 -0.29 78 81
BRCA1/BACH1/BARD1/TopBP1 0.038 0.077 -10000 0 -0.13 79 79
BRCA1/BARD1/P53 0.004 0.1 -10000 0 -0.13 186 186
BARD1/CSTF1/BRCA1 0.037 0.072 -10000 0 -0.12 74 74
BRCA1/BACH1 0.034 0.016 -10000 0 0 99 99
BARD1 0.037 0.013 -10000 0 0 65 65
PCNA 0.035 0.015 -10000 0 0 88 88
BRCA1/BARD1/UbcH5C 0.041 0.072 -10000 0 -0.12 74 74
BRCA1/BARD1/UbcH7 0.043 0.072 -10000 0 -0.12 72 72
BRCA1/BARD1/RAD51/PCNA 0.034 0.096 -10000 0 -0.13 118 118
BARD1/DNA-PK/P53 0.021 0.12 -10000 0 -0.13 160 160
BRCA1/BARD1/Ubiquitin 0.027 0.069 -10000 0 -0.14 73 73
BRCA1/BARD1/CTIP 0.015 0.087 0.18 11 -0.13 119 130
FA complex 0.011 0.087 -10000 0 -0.29 27 27
BARD1/EWS 0.042 0.05 -10000 0 -0.13 35 35
RBBP8 -0.015 0.009 -10000 0 -10000 0 0
TP53 0.027 0.02 -10000 0 0 200 200
TOPBP1 0.037 0.013 -10000 0 0 58 58
G1/S transition of mitotic cell cycle -0.002 0.1 0.13 186 -10000 0 186
BRCA1/BARD1 0.019 0.11 -10000 0 -0.13 149 149
CSTF1 0.037 0.014 -10000 0 0 69 69
BARD1/EWS-Fli1 0.019 0.038 -10000 0 -0.13 34 34
CDK2 0.038 0.013 -10000 0 0 56 56
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.035 0.016 -10000 0 0 93 93
RAD50 0.039 0.011 -10000 0 0 38 38
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.027 0.069 -10000 0 -0.14 73 73
EWSR1 0.038 0.012 -10000 0 0 51 51
Syndecan-4-mediated signaling events

Figure S18.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S18.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.059 0.22 -10000 0 -0.35 167 167
Syndecan-4/Syndesmos -0.04 0.2 -10000 0 -0.42 82 82
positive regulation of JNK cascade -0.06 0.19 -10000 0 -0.41 87 87
Syndecan-4/ADAM12 -0.057 0.19 -10000 0 -0.42 81 81
CCL5 0.03 0.019 -10000 0 0 162 162
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
DNM2 0.036 0.014 -10000 0 0 72 72
ITGA5 0.037 0.013 -10000 0 0 58 58
SDCBP 0.036 0.014 -10000 0 0 77 77
PLG 0.032 0.029 -10000 0 -0.043 54 54
ADAM12 0.03 0.019 -10000 0 0 159 159
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.039 0.01 -10000 0 0 31 31
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.023 0.023 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.043 0.19 -10000 0 -0.41 81 81
Syndecan-4/CXCL12/CXCR4 -0.064 0.2 -10000 0 -0.44 86 86
Syndecan-4/Laminin alpha3 -0.05 0.2 -10000 0 -0.43 82 82
MDK 0.04 0.009 -10000 0 0 25 25
Syndecan-4/FZD7 -0.045 0.2 -10000 0 -0.43 81 81
Syndecan-4/Midkine -0.042 0.2 -10000 0 -0.42 84 84
FZD7 0.037 0.014 -10000 0 0 66 66
Syndecan-4/FGFR1/FGF -0.029 0.19 -10000 0 -0.41 70 70
THBS1 0.027 0.02 -10000 0 0 198 198
integrin-mediated signaling pathway -0.059 0.19 -10000 0 -0.42 83 83
positive regulation of MAPKKK cascade -0.06 0.19 -10000 0 -0.41 87 87
Syndecan-4/TACI -0.041 0.2 -10000 0 -0.42 83 83
CXCR4 0.033 0.017 -10000 0 0 116 116
cell adhesion -0.033 0.099 0.21 5 -0.2 127 132
Syndecan-4/Dynamin -0.039 0.19 -10000 0 -0.42 75 75
Syndecan-4/TSP1 -0.062 0.2 -10000 0 -0.44 81 81
Syndecan-4/GIPC -0.04 0.19 -10000 0 -0.42 74 74
Syndecan-4/RANTES -0.054 0.2 -10000 0 -0.44 82 82
ITGB1 0.039 0.011 -10000 0 0 39 39
LAMA1 0.034 0.017 -10000 0 0 108 108
LAMA3 0.031 0.018 -10000 0 0 147 147
RAC1 0.039 0.01 -10000 0 0 35 35
PRKCA 0.005 0.13 0.81 11 -10000 0 11
Syndecan-4/alpha-Actinin -0.043 0.2 -10000 0 -0.42 83 83
TFPI 0.039 0.01 -10000 0 0 37 37
F2 0.037 0.026 0.084 9 -0.038 48 57
alpha5/beta1 Integrin 0.045 0.046 -10000 0 -0.14 28 28
positive regulation of cell adhesion -0.058 0.18 -10000 0 -0.41 80 80
ACTN1 0.039 0.011 -10000 0 0 39 39
TNC 0.027 0.02 -10000 0 0 192 192
Syndecan-4/CXCL12 -0.061 0.2 -10000 0 -0.44 85 85
FGF6 0.037 0.014 -10000 0 0 68 68
RHOA 0.041 0.007 -10000 0 0 14 14
CXCL12 0.029 0.019 -10000 0 0 175 175
TNFRSF13B 0.039 0.011 -10000 0 0 38 38
FGF2 0.038 0.012 -10000 0 0 46 46
FGFR1 0.033 0.017 -10000 0 0 121 121
Syndecan-4/PI-4-5-P2 -0.062 0.18 -10000 0 -0.42 84 84
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.017 0.025 -10000 0 -0.041 26 26
cell migration -0.011 0.013 -10000 0 -10000 0 0
PRKCD 0.034 0.027 -10000 0 -0.041 43 43
vasculogenesis -0.059 0.19 -10000 0 -0.42 83 83
SDC4 -0.054 0.19 -10000 0 -0.44 77 77
Syndecan-4/Tenascin C -0.061 0.2 -10000 0 -0.44 83 83
Syndecan-4/PI-4-5-P2/PKC alpha -0.019 0.018 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.043 0.2 -10000 0 -0.44 76 76
MMP9 0.027 0.024 -10000 0 -0.04 18 18
Rac1/GTP -0.033 0.1 0.21 5 -0.2 126 131
cytoskeleton organization -0.038 0.19 -10000 0 -0.4 82 82
GIPC1 0.035 0.015 -10000 0 0 89 89
Syndecan-4/TFPI -0.043 0.2 -10000 0 -0.42 84 84
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.03 0.019 -10000 0 0 162 162
HRAS 0.04 0.009 -10000 0 0 29 29
EGFR 0.036 0.014 -10000 0 0 73 73
AKT 0.016 0.093 0.22 6 -0.19 36 42
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0.039 0.011 -10000 0 0 38 38
FOXO1 0 0 -10000 0 -10000 0 0
AKT3 0.03 0.019 -10000 0 0 156 156
FOXO4 0 0 -10000 0 -10000 0 0
MET 0.027 0.02 -10000 0 0 195 195
PIK3CA 0.03 0.019 -10000 0 0 150 150
PIK3CB 0.034 0.016 -10000 0 0 99 99
NRAS 0.039 0.01 -10000 0 0 31 31
PIK3CG 0.033 0.017 -10000 0 0 120 120
PIK3R3 0.034 0.016 -10000 0 0 97 97
PIK3R2 0.037 0.013 -10000 0 0 64 64
NF1 0.034 0.016 -10000 0 0 98 98
RAS 0.004 0.078 0.15 33 -0.24 20 53
ERBB2 0.038 0.012 -10000 0 0 49 49
proliferation/survival/translation -0.016 0.087 0.22 31 -0.22 16 47
PI3K 0.002 0.09 0.17 23 -0.22 45 68
PIK3R1 0.034 0.016 -10000 0 0 106 106
KRAS 0.034 0.016 -10000 0 0 103 103
FOXO 0.037 0.054 0.16 24 -10000 0 24
AKT2 0.038 0.011 -10000 0 0 45 45
PTEN 0.039 0.011 -10000 0 0 39 39
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.087 0.34 -10000 0 -0.78 85 85
CRP -0.081 0.33 0.49 2 -0.75 82 84
cell cycle arrest -0.12 0.39 -10000 0 -0.84 99 99
TIMP1 -0.1 0.36 -10000 0 -0.76 110 110
IL6ST 0.024 0.036 -10000 0 -0.04 100 100
Rac1/GDP -0.012 0.17 0.29 5 -0.35 71 76
AP1 -0.03 0.21 -10000 0 -0.48 69 69
GAB2 0.032 0.021 -10000 0 -0.001 144 144
TNFSF11 -0.085 0.33 -10000 0 -0.76 81 81
HSP90B1 0.013 0.092 -10000 0 -1.1 2 2
GAB1 0.039 0.014 -10000 0 -0.001 51 51
MAPK14 -0.027 0.17 0.26 1 -0.52 40 41
AKT1 -0.012 0.16 0.28 4 -0.46 35 39
FOXO1 -0.012 0.15 0.27 4 -0.44 35 39
MAP2K6 -0.021 0.15 0.22 4 -0.38 57 61
mol:GTP 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.033 0.21 0.31 7 -0.41 90 97
MITF -0.018 0.15 0.23 6 -0.33 68 74
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.037 0.014 -10000 0 0 67 67
A2M -0.12 0.41 -10000 0 -1.2 67 67
CEBPB 0.037 0.014 -10000 0 0 73 73
GRB2/SOS1/GAB family/SHP2 -0.01 0.16 0.31 5 -0.41 54 59
STAT3 -0.14 0.42 -10000 0 -0.92 99 99
STAT1 -0.071 0.28 -10000 0 -0.83 64 64
CEBPD -0.084 0.34 0.52 2 -0.78 80 82
PIK3CA 0.031 0.02 -10000 0 -0.001 152 152
PI3K 0.024 0.062 -10000 0 -0.15 49 49
JUN 0.036 0.015 -10000 0 0 80 80
PIAS3/MITF -0.008 0.15 -10000 0 -0.34 61 61
MAPK11 -0.026 0.16 0.26 1 -0.55 36 37
STAT3 (dimer)/FOXO1 -0.098 0.35 0.45 3 -0.72 107 110
GRB2/SOS1/GAB family 0.03 0.13 0.29 9 -0.29 32 41
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.007 0.11 0.19 3 -0.26 55 58
GRB2 0.042 0.009 -10000 0 -0.005 16 16
JAK2 0.034 0.017 -10000 0 0 108 108
LBP -0.032 0.26 0.44 1 -0.57 75 76
PIK3R1 0.034 0.018 -10000 0 -0.001 109 109
JAK1 0.033 0.029 -10000 0 -0.045 54 54
MYC -0.065 0.42 0.5 9 -0.86 102 111
FGG -0.085 0.33 -10000 0 -0.76 81 81
macrophage differentiation -0.12 0.39 -10000 0 -0.84 99 99
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.047 0.1 -10000 0 -0.17 50 50
JUNB -0.1 0.39 0.5 4 -0.85 100 104
FOS 0.026 0.02 -10000 0 0 205 205
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.01 0.16 0.24 3 -0.34 70 73
STAT1/PIAS1 -0.021 0.18 0.3 1 -0.38 78 79
GRB2/SOS1/GAB family/SHP2/PI3K -0.012 0.16 -10000 0 -0.42 46 46
STAT3 (dimer) -0.13 0.41 -10000 0 -0.9 99 99
PRKCD -0.06 0.26 0.34 4 -0.53 102 106
IL6R 0.032 0.028 -10000 0 -0.044 46 46
SOCS3 -0.039 0.22 0.34 1 -0.97 24 25
gp130 (dimer)/JAK1/JAK1/LMO4 0.043 0.089 -10000 0 -0.12 83 83
Rac1/GTP -0.018 0.18 0.3 5 -0.38 77 82
HCK 0.036 0.015 -10000 0 0 79 79
MAPKKK cascade -0.026 0.22 -10000 0 -0.51 72 72
bone resorption -0.077 0.31 -10000 0 -0.71 81 81
IRF1 -0.14 0.42 -10000 0 -0.92 112 112
mol:GDP -0.021 0.15 0.24 6 -0.35 66 72
SOS1 0.039 0.015 -10000 0 -0.001 59 59
VAV1 -0.022 0.15 0.22 5 -0.35 67 72
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.016 0.18 -10000 0 -0.47 57 57
PTPN11 -0.001 0.17 -10000 0 -0.79 22 22
IL6/IL6RA 0.028 0.064 -10000 0 -0.14 42 42
gp130 (dimer)/TYK2/TYK2/LMO4 0.049 0.066 -10000 0 -0.099 58 58
gp130 (dimer)/JAK2/JAK2/LMO4 0.04 0.076 -10000 0 -0.11 80 80
IL6 0.023 0.037 -10000 0 -0.041 100 100
PIAS3 0.04 0.008 -10000 0 0 23 23
PTPRE 0.027 0.038 0.098 16 -0.046 47 63
PIAS1 0.04 0.009 -10000 0 0 28 28
RAC1 0.039 0.01 -10000 0 0 35 35
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.002 0.093 -10000 0 -0.24 44 44
LMO4 0.028 0.038 -10000 0 -0.04 115 115
STAT3 (dimer)/PIAS3 -0.1 0.4 -10000 0 -0.84 97 97
MCL1 -0.011 0.16 -10000 0 -0.59 22 22
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.065 0.18 -10000 0 -0.39 122 122
IHH 0.022 0.066 -10000 0 -0.099 125 125
SHH Np/Cholesterol/GAS1 0.028 0.025 -10000 0 -0.1 12 12
LRPAP1 0.036 0.015 -10000 0 0 79 79
dorsoventral neural tube patterning -0.028 0.025 0.1 12 -10000 0 12
SMO/beta Arrestin2 0.018 0.12 0.24 2 -0.2 101 103
SMO -0.003 0.11 -10000 0 -0.2 109 109
AKT1 -0.013 0.13 -10000 0 -0.4 35 35
ARRB2 0.039 0.01 -10000 0 0 37 37
BOC 0.035 0.015 -10000 0 0 86 86
ADRBK1 0.041 0.005 -10000 0 0 7 7
heart looping -0.002 0.11 0.19 3 -0.2 109 112
STIL 0 0.096 0.21 28 -0.17 102 130
DHH N/PTCH2 0.058 0.016 -10000 0 -10000 0 0
DHH N/PTCH1 0.004 0.11 -10000 0 -0.19 124 124
PIK3CA 0.03 0.019 -10000 0 0 150 150
DHH 0.041 0.007 -10000 0 0 14 14
PTHLH -0.033 0.17 -10000 0 -0.38 106 106
determination of left/right symmetry -0.002 0.11 0.19 3 -0.2 109 112
PIK3R1 0.034 0.016 -10000 0 0 106 106
skeletal system development -0.032 0.17 -10000 0 -0.38 106 106
IHH N/Hhip 0.035 0.054 -10000 0 -0.06 117 117
DHH N/Hhip 0.054 0.022 -10000 0 -0.14 1 1
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.002 0.11 0.19 3 -0.2 109 112
pancreas development 0.038 0.013 -10000 0 0 55 55
HHAT 0.04 0.008 -10000 0 0 20 20
PI3K 0.024 0.062 -10000 0 -0.15 47 47
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.037 0.013 -10000 0 0 65 65
somite specification -0.002 0.11 0.19 3 -0.2 109 112
SHH Np/Cholesterol/PTCH1 -0.006 0.085 -10000 0 -0.17 108 108
SHH Np/Cholesterol/PTCH2 0.032 0.015 -10000 0 -0.1 1 1
SHH Np/Cholesterol/Megalin 0.021 0.028 -10000 0 -0.1 16 16
SHH -0.018 0.007 -10000 0 -10000 0 0
catabolic process -0.036 0.095 -10000 0 -0.21 126 126
SMO/Vitamin D3 -0.007 0.1 0.2 17 -0.2 107 124
SHH Np/Cholesterol/Hhip 0.031 0.017 -10000 0 -0.1 2 2
LRP2 0.03 0.019 -10000 0 0 162 162
receptor-mediated endocytosis 0.001 0.1 0.19 20 -0.18 104 124
SHH Np/Cholesterol/BOC 0.026 0.028 -10000 0 -0.1 17 17
SHH Np/Cholesterol/CDO 0.023 0.034 -10000 0 -0.1 28 28
mesenchymal cell differentiation -0.03 0.017 0.1 2 -10000 0 2
mol:Vitamin D3 -0.013 0.088 0.2 23 -0.17 107 130
IHH N/PTCH2 0.039 0.054 -10000 0 -0.059 116 116
CDON 0.035 0.016 -10000 0 0 91 91
IHH N/PTCH1 -0.02 0.11 -10000 0 -0.21 126 126
Megalin/LRPAP1 0.027 0.055 -10000 0 -0.14 40 40
PTCH2 0.04 0.009 -10000 0 0 26 26
SHH Np/Cholesterol 0.034 0.046 0.2 40 -0.098 1 41
PTCH1 -0.036 0.096 -10000 0 -0.21 126 126
HHIP 0.038 0.013 -10000 0 0 55 55
Paxillin-dependent events mediated by a4b1

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
CRKL 0.039 0.01 -10000 0 0 35 35
Rac1/GDP 0.032 0.026 -10000 0 -0.024 70 70
DOCK1 0.037 0.013 -10000 0 0 63 63
ITGA4 0.035 0.015 -10000 0 0 90 90
RAC1 0.039 0.01 -10000 0 0 35 35
alpha4/beta7 Integrin 0.032 0.066 -10000 0 -0.14 65 65
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.038 0.011 -10000 0 0 45 45
alpha4/beta1 Integrin 0.046 0.063 -10000 0 -0.12 49 49
alpha4/beta7 Integrin/Paxillin 0.051 0.069 0.18 54 -0.12 50 104
lamellipodium assembly -0.028 0.15 -10000 0 -0.34 87 87
PIK3CA 0.03 0.019 -10000 0 0 150 150
PI3K 0.024 0.062 -10000 0 -0.15 47 47
ARF6 0.04 0.007 -10000 0 0 18 18
TLN1 0.038 0.012 -10000 0 0 47 47
PXN -0.017 0.008 -10000 0 -10000 0 0
PIK3R1 0.034 0.016 -10000 0 0 106 106
ARF6/GTP 0.062 0.072 -10000 0 -0.11 51 51
cell adhesion 0.06 0.077 0.2 45 -0.12 58 103
CRKL/CBL 0.055 0.02 -10000 0 -0.14 1 1
alpha4/beta1 Integrin/Paxillin 0.05 0.067 0.18 49 -0.11 48 97
ITGB1 0.039 0.011 -10000 0 0 39 39
ITGB7 0.039 0.011 -10000 0 0 39 39
ARF6/GDP 0.033 0.025 -10000 0 -0.024 69 69
alpha4/beta1 Integrin/Paxillin/VCAM1 0.024 0.094 0.2 27 -0.13 117 144
p130Cas/Crk/Dock1 0.056 0.053 -10000 0 -0.12 27 27
VCAM1 0.02 0.021 -10000 0 0 287 287
alpha4/beta1 Integrin/Paxillin/Talin 0.063 0.079 0.2 45 -0.12 58 103
alpha4/beta1 Integrin/Paxillin/GIT1 0.068 0.073 0.2 45 -0.11 48 93
BCAR1 0.036 0.014 -10000 0 0 74 74
mol:GDP -0.065 0.071 0.11 48 -0.2 45 93
CBL 0.04 0.008 -10000 0 0 23 23
PRKACA 0.035 0.015 -10000 0 0 87 87
GIT1 0.04 0.008 -10000 0 0 23 23
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.063 0.079 0.2 45 -0.12 58 103
Rac1/GTP -0.033 0.17 -10000 0 -0.38 87 87
Nongenotropic Androgen signaling

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
PTK2 -0.007 0.005 0 206 -10000 0 206
GNB1/GNG2 0.042 0.07 -10000 0 -0.11 86 86
regulation of S phase of mitotic cell cycle -0.011 0.076 -10000 0 -0.17 87 87
GNAO1 0.034 0.016 -10000 0 0 101 101
HRAS 0.039 0.009 -10000 0 0 29 29
SHBG/T-DHT 0.027 0.006 -10000 0 -10000 0 0
PELP1 0.039 0.009 -10000 0 0 29 29
AKT1 -0.009 0.004 0.002 47 -10000 0 47
MAP2K1 -0.034 0.078 0.17 23 -0.17 81 104
T-DHT/AR 0.006 0.054 -10000 0 -0.13 76 76
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.007 102 102
GNAI2 0.041 0.006 -10000 0 0 13 13
GNAI3 0.038 0.012 -10000 0 0 46 46
GNAI1 0.035 0.016 -10000 0 0 94 94
mol:GDP -0.042 0.087 -10000 0 -0.26 68 68
cell proliferation -0.072 0.17 0.24 5 -0.4 105 110
PIK3CA 0.03 0.019 -10000 0 0 150 150
FOS -0.12 0.29 -10000 0 -0.7 104 104
mol:Ca2+ -0.006 0.021 -10000 0 -0.049 77 77
MAPK3 -0.054 0.13 0.23 6 -0.3 95 101
MAPK1 -0.041 0.13 -10000 0 -0.35 52 52
PIK3R1 0.034 0.016 -10000 0 0 106 106
mol:IP3 0 0.002 0.002 6 -0.004 101 107
cAMP biosynthetic process -0.001 0.024 0.18 5 -10000 0 5
GNG2 0.039 0.01 -10000 0 0 34 34
potassium channel inhibitor activity 0 0.002 0.002 6 -0.004 101 107
HRAS/GTP 0.027 0.077 -10000 0 -0.092 137 137
actin cytoskeleton reorganization 0.029 0.052 -10000 0 -0.11 46 46
SRC 0.039 0.01 -10000 0 0 31 31
voltage-gated calcium channel activity 0 0.002 0.002 6 -0.004 101 107
PI3K 0.023 0.053 -10000 0 -0.12 47 47
apoptosis 0.062 0.18 0.39 110 -0.25 1 111
T-DHT/AR/PELP1 0.026 0.058 -10000 0 -0.11 76 76
HRAS/GDP -0.006 0.11 -10000 0 -0.25 68 68
CREB1 -0.077 0.18 0.25 1 -0.42 110 111
RAC1-CDC42/GTP 0.038 0.059 -10000 0 -0.11 46 46
AR 0.032 0.017 -10000 0 0 119 119
GNB1 0.041 0.005 -10000 0 0 7 7
RAF1 -0.021 0.075 0.18 25 -0.18 16 41
RAC1-CDC42/GDP 0.016 0.11 0.19 1 -0.24 67 68
T-DHT/AR/PELP1/Src 0.041 0.065 -10000 0 -0.11 73 73
MAP2K2 -0.03 0.073 0.17 19 -0.17 70 89
T-DHT/AR/PELP1/Src/PI3K -0.011 0.077 -10000 0 -0.17 87 87
GNAZ 0.039 0.011 -10000 0 0 38 38
SHBG 0.04 0.009 -10000 0 0 30 30
Gi family/GNB1/GNG2/GDP -0.005 0.097 -10000 0 -0.3 31 31
mol:T-DHT 0 0.001 -10000 0 -0.004 20 20
RAC1 0.039 0.01 -10000 0 0 35 35
GNRH1 -0.008 0.004 0 121 -10000 0 121
Gi family/GTP -0.02 0.076 -10000 0 -0.18 69 69
CDC42 0.04 0.008 -10000 0 0 22 22
LPA4-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
ADCY4 -0.014 0.006 -10000 0 -10000 0 0
ADCY5 -0.014 0.006 0 88 -10000 0 88
ADCY6 -0.015 0.005 0 58 -10000 0 58
ADCY7 -0.014 0.006 -10000 0 -10000 0 0
ADCY1 -0.015 0.005 0 54 -10000 0 54
ADCY2 -0.014 0.006 0 102 -10000 0 102
ADCY3 -0.015 0.005 0 55 -10000 0 55
ADCY8 -0.008 0.008 0 284 -10000 0 284
PRKCE -0.01 0.003 0 38 -10000 0 38
ADCY9 -0.014 0.006 0 77 -10000 0 77
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process 0.058 0.086 0.22 77 -0.19 4 81
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.028 0.013 -10000 0 -0.13 3 3
alphaV beta3 Integrin 0.028 0.079 -10000 0 -0.13 90 90
PTK2 -0.012 0.13 0.23 11 -0.27 75 86
IGF1R 0.033 0.017 -10000 0 0 116 116
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.031 0.018 -10000 0 0 139 139
SRC 0.039 0.01 -10000 0 0 31 31
CDKN1B 0.001 0.089 -10000 0 -0.32 34 34
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.014 0.061 -10000 0 -0.26 17 17
ROCK1 0.04 0.007 -10000 0 0 18 18
AKT1 0.006 0.055 0.21 5 -0.25 14 19
PTK2B -0.013 0.062 0.18 20 -0.18 11 31
alphaV/beta3 Integrin/JAM-A 0.04 0.081 0.2 8 -0.12 87 95
CBL 0.04 0.008 -10000 0 0 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.03 0.079 -10000 0 -0.13 90 90
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.056 0.084 -10000 0 -0.12 84 84
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.005 0.083 -10000 0 -0.17 91 91
alphaV/beta3 Integrin/Syndecan-1 0.029 0.079 -10000 0 -0.13 91 91
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.018 0.1 -10000 0 -0.14 168 168
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA 0.03 0.019 -10000 0 0 150 150
alphaV/beta3 Integrin/Osteopontin 0.005 0.099 -10000 0 -0.16 125 125
RPS6KB1 -0.033 0.1 0.26 11 -0.2 56 67
TLN1 0.038 0.012 -10000 0 0 47 47
MAPK3 -0.053 0.16 0.23 1 -0.33 122 123
GPR124 0.037 0.013 -10000 0 0 62 62
MAPK1 -0.05 0.16 0.23 1 -0.34 115 116
PXN 0.041 0.007 -10000 0 0 14 14
PIK3R1 0.034 0.016 -10000 0 0 106 106
alphaV/beta3 Integrin/Tumstatin 0.031 0.08 -10000 0 -0.13 91 91
cell adhesion -0.001 0.1 -10000 0 -0.16 132 132
ANGPTL3 0.04 0.009 -10000 0 0 24 24
VEGFR2 homodimer/VEGFA homodimer/Src 0.05 0.02 -10000 0 -0.11 2 2
IGF-1R heterotetramer 0.033 0.017 -10000 0 0 116 116
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
TGFBR2 0.039 0.011 -10000 0 0 38 38
ITGB3 0.033 0.017 -10000 0 0 120 120
IGF1 0.036 0.015 -10000 0 0 82 82
RAC1 0.039 0.01 -10000 0 0 35 35
regulation of cell-matrix adhesion 0.029 0.076 -10000 0 -0.13 82 82
apoptosis 0.033 0.017 -10000 0 0 115 115
CD47 0.037 0.013 -10000 0 0 60 60
alphaV/beta3 Integrin/CD47 0.023 0.087 -10000 0 -0.14 101 101
VCL 0.039 0.01 -10000 0 0 35 35
alphaV/beta3 Integrin/Del1 0.005 0.082 -10000 0 -0.13 111 111
CSF1 0.035 0.015 -10000 0 0 89 89
PIK3C2A -0.005 0.1 -10000 0 -0.33 46 46
PI4 Kinase/Pyk2 0.005 0.055 -10000 0 -0.11 81 81
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.028 0.074 -10000 0 -0.12 92 92
FAK1/Vinculin 0.006 0.12 0.24 11 -0.23 73 84
alphaV beta3/Integrin/ppsTEM5 0.029 0.076 -10000 0 -0.13 82 82
RHOA 0.041 0.007 -10000 0 0 14 14
VTN 0.04 0.008 -10000 0 0 21 21
BCAR1 0.036 0.014 -10000 0 0 74 74
FGF2 0.038 0.012 -10000 0 0 46 46
F11R -0.018 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.008 0.088 -10000 0 -0.14 121 121
alphaV/beta3 Integrin/TGFBR2 0.027 0.084 -10000 0 -0.14 93 93
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.046 0.09 -10000 0 -0.13 94 94
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.026 0.077 -10000 0 -0.12 98 98
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.021 0.021 -10000 0 0 273 273
alphaV/beta3 Integrin/Pyk2 0.017 0.067 0.21 2 -0.11 86 88
SDC1 0.04 0.009 -10000 0 0 29 29
VAV3 -0.03 0.074 0.19 20 -0.21 37 57
PTPN11 0.04 0.009 -10000 0 0 29 29
IRS1 0.04 0.008 -10000 0 0 22 22
FAK1/Paxillin 0.008 0.12 0.23 11 -0.23 72 83
cell migration -0.002 0.11 0.21 12 -0.22 72 84
ITGAV 0.033 0.017 -10000 0 0 115 115
PI3K 0.028 0.091 -10000 0 -0.15 72 72
SPP1 0.03 0.019 -10000 0 0 153 153
KDR 0.039 0.01 -10000 0 0 34 34
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.033 0.017 -10000 0 0 115 115
COL4A3 0.041 0.005 -10000 0 0 8 8
angiogenesis -0.058 0.17 0.25 2 -0.36 119 121
Rac1/GTP -0.032 0.076 0.19 19 -0.2 34 53
EDIL3 0.027 0.02 -10000 0 0 201 201
cell proliferation 0.026 0.084 -10000 0 -0.14 93 93
Signaling events mediated by PTP1B

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
PDGFRB 0.037 0.013 -10000 0 0 64 64
Jak2/Leptin Receptor -0.019 0.15 -10000 0 -0.39 55 55
PTP1B/AKT1 -0.036 0.12 -10000 0 -0.23 95 95
FYN 0.034 0.016 -10000 0 0 102 102
p210 bcr-abl/PTP1B -0.054 0.11 0.17 1 -0.25 98 99
EGFR 0.036 0.017 -10000 0 -0.003 82 82
EGF/EGFR -0.027 0.12 -10000 0 -0.23 95 95
CSF1 0.035 0.015 -10000 0 0 89 89
AKT1 0.039 0.011 -10000 0 0 38 38
INSR 0.038 0.013 -10000 0 0 53 53
PTP1B/N-cadherin -0.055 0.12 -10000 0 -0.24 125 125
Insulin Receptor/Insulin -0.009 0.12 -10000 0 -0.22 63 63
HCK 0.036 0.015 -10000 0 0 79 79
CRK 0.038 0.011 -10000 0 0 45 45
TYK2 -0.038 0.12 0.23 21 -0.25 81 102
EGF 0.036 0.017 -10000 0 -0.007 68 68
YES1 0.037 0.013 -10000 0 0 59 59
CAV1 -0.037 0.11 0.19 1 -0.24 82 83
TXN 0.037 0.012 -10000 0 0 48 48
PTP1B/IRS1/GRB2 -0.029 0.13 -10000 0 -0.24 98 98
cell migration 0.054 0.11 0.25 98 -0.17 1 99
STAT3 0.038 0.012 -10000 0 0 52 52
PRLR 0.038 0.017 -10000 0 -10000 0 0
ITGA2B 0.039 0.009 -10000 0 0 29 29
CSF1R 0.035 0.016 -10000 0 0 96 96
Prolactin Receptor/Prolactin 0.055 0.029 -10000 0 -10000 0 0
FGR 0.041 0.007 -10000 0 0 16 16
PTP1B/p130 Cas -0.038 0.12 -10000 0 -0.24 98 98
Crk/p130 Cas -0.031 0.13 -10000 0 -0.24 92 92
DOK1 -0.038 0.11 0.18 2 -0.24 73 75
JAK2 -0.032 0.14 -10000 0 -0.4 58 58
Jak2/Leptin Receptor/Leptin -0.025 0.14 0.26 1 -0.27 77 78
PIK3R1 0.034 0.016 -10000 0 0 106 106
PTPN1 -0.054 0.12 0.17 1 -0.25 98 99
LYN 0.036 0.015 -10000 0 0 83 83
CDH2 0.019 0.021 -10000 0 0 297 297
SRC 0.007 0.089 -10000 0 -0.48 13 13
ITGB3 0.032 0.017 -10000 0 0 120 120
CAT1/PTP1B -0.038 0.13 0.24 5 -0.29 72 77
CAPN1 0.039 0.009 -10000 0 0 25 25
CSK 0.04 0.008 -10000 0 0 22 22
PI3K -0.012 0.11 -10000 0 -0.22 53 53
mol:H2O2 0.002 0.005 0.03 1 -10000 0 1
STAT3 (dimer) -0.022 0.13 0.25 1 -0.26 74 75
negative regulation of transcription -0.031 0.14 -10000 0 -0.4 58 58
FCGR2A 0.032 0.018 -10000 0 0 126 126
FER 0.037 0.012 -10000 0 0 53 53
alphaIIb/beta3 Integrin 0.038 0.051 -10000 0 -0.14 34 34
BLK 0.033 0.017 -10000 0 0 115 115
Insulin Receptor/Insulin/Shc 0.068 0.037 -10000 0 -0.12 5 5
RHOA 0.04 0.007 -10000 0 0 14 14
LEPR 0.039 0.012 -10000 0 0 44 44
BCAR1 0.036 0.014 -10000 0 0 74 74
p210 bcr-abl/Grb2 0.041 0.007 -10000 0 0 14 14
mol:NADPH -0.001 0.002 -10000 0 -10000 0 0
TRPV6 -0.007 0.12 0.22 6 -0.3 40 46
PRL 0.042 0.012 -10000 0 -10000 0 0
SOCS3 -0.024 0.26 -10000 0 -1.1 27 27
SPRY2 0.024 0.021 -10000 0 0 243 243
Insulin Receptor/Insulin/IRS1 0.069 0.038 -10000 0 -0.12 8 8
CSF1/CSF1R -0.045 0.14 -10000 0 -0.26 107 107
Ras protein signal transduction 0.005 0.066 0.6 5 -10000 0 5
IRS1 0.04 0.008 -10000 0 0 22 22
INS 0.04 0.01 -10000 0 0 30 30
LEP 0.039 0.01 -10000 0 0 33 33
STAT5B -0.042 0.12 -10000 0 -0.27 81 81
STAT5A -0.044 0.13 -10000 0 -0.27 85 85
GRB2 0.041 0.007 -10000 0 0 14 14
PDGFB-D/PDGFRB -0.045 0.12 -10000 0 -0.24 101 101
CSN2 0.04 0.069 0.43 2 -10000 0 2
PIK3CA 0.03 0.019 -10000 0 0 150 150
LAT -0.059 0.19 -10000 0 -0.48 87 87
YBX1 0.048 0.02 -10000 0 -0.28 1 1
LCK 0.04 0.009 -10000 0 0 28 28
SHC1 0.04 0.009 -10000 0 0 29 29
NOX4 0.021 0.021 -10000 0 0 279 279
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.028 0.019 -10000 0 -0.13 8 8
PRKCZ 0.042 0 -10000 0 -10000 0 0
MAP3K7IP2 0.037 0.013 -10000 0 0 63 63
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.034 0.13 -10000 0 -0.29 94 94
IRAK/TOLLIP 0.04 0.027 0.19 4 -0.1 11 15
IKBKB 0.038 0.011 -10000 0 0 44 44
IKBKG 0.042 0.003 -10000 0 0 2 2
IL1 alpha/IL1R2 0.046 0.039 -10000 0 -0.14 16 16
IL1A 0.039 0.01 -10000 0 0 31 31
IL1B -0.012 0.01 -10000 0 -10000 0 0
IRAK/TRAF6/p62/Atypical PKCs 0.046 0.078 0.22 2 -0.12 63 65
IL1R2 0.036 0.015 -10000 0 0 82 82
IL1R1 0.031 0.018 -10000 0 0 142 142
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.044 0.14 -10000 0 -0.35 71 71
TOLLIP 0.04 0.009 -10000 0 0 28 28
TICAM2 0.038 0.013 -10000 0 0 57 57
MAP3K3 0.04 0.008 -10000 0 0 19 19
TAK1/TAB1/TAB2 0.06 0.056 -10000 0 -0.14 26 26
IKK complex/ELKS 0.013 0.088 0.25 3 -0.28 26 29
JUN -0.034 0.06 0.15 25 -0.2 17 42
MAP3K7 0.038 0.012 -10000 0 0 47 47
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0 0.12 0.22 2 -0.17 127 129
IL1 alpha/IL1R1/IL1RAP/MYD88 0.038 0.085 -10000 0 -0.12 92 92
PIK3R1 0.034 0.016 -10000 0 0 106 106
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.039 0.099 -10000 0 -0.13 101 101
IL1 beta fragment/IL1R1/IL1RAP -0.011 0.096 0.18 6 -0.15 143 149
NFKB1 0.035 0.015 -10000 0 0 85 85
MAPK8 -0.025 0.057 0.17 23 -0.2 16 39
IRAK1 0.016 0.014 -10000 0 -0.11 6 6
IL1RN/IL1R1 0.023 0.07 -10000 0 -0.14 79 79
IRAK4 0.037 0.014 -10000 0 0 70 70
PRKCI 0.027 0.02 -10000 0 0 193 193
TRAF6 0.04 0.009 -10000 0 0 24 24
PI3K 0.024 0.062 -10000 0 -0.15 47 47
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.035 0.15 0.17 2 -0.3 98 100
CHUK 0.038 0.012 -10000 0 0 52 52
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.011 0.096 0.18 6 -0.15 143 149
IL1 beta/IL1R2 -0.003 0.089 0.24 3 -0.15 130 133
IRAK/TRAF6/TAK1/TAB1/TAB2 0.07 0.07 0.22 1 -0.14 32 33
NF kappa B1 p50/RelA -0.014 0.11 -10000 0 -0.18 122 122
IRAK3 0.034 0.016 -10000 0 0 97 97
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.004 0.12 0.22 2 -0.17 134 136
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.014 0.098 -10000 0 -0.19 101 101
IL1 alpha/IL1R1/IL1RAP 0.016 0.077 -10000 0 -0.13 92 92
RELA 0.041 0.006 -10000 0 0 10 10
MAP3K7IP1 0.038 0.012 -10000 0 0 51 51
SQSTM1 0.038 0.012 -10000 0 0 48 48
MYD88 0.041 0.007 -10000 0 0 15 15
IRAK/TRAF6/MEKK3 0.06 0.038 0.2 4 -0.11 18 22
IL1RAP 0.027 0.02 -10000 0 0 192 192
UBE2N 0.04 0.008 -10000 0 0 19 19
IRAK/TRAF6 -0.021 0.095 -10000 0 -0.21 68 68
CASP1 0.028 0.02 -10000 0 0 187 187
IL1RN/IL1R2 0.042 0.049 -10000 0 -0.14 30 30
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.003 0.1 0.2 6 -0.15 137 143
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.02 0.13 0.21 1 -0.29 81 82
PIK3CA 0.03 0.019 -10000 0 0 150 150
IL1RN 0.039 0.01 -10000 0 0 37 37
TRAF6/TAK1/TAB1/TAB2 0.071 0.068 -10000 0 -0.14 31 31
MAP2K6 -0.021 0.06 0.19 23 -0.2 14 37
E-cadherin signaling in keratinocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation -0.007 0.11 0.15 55 -0.28 43 98
adherens junction organization -0.028 0.13 0.17 7 -0.32 62 69
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.011 0.11 0.21 15 -0.26 35 50
FMN1 -0.024 0.12 0.15 3 -0.28 67 70
mol:IP3 0.003 0.099 0.16 60 -0.22 48 108
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.016 0.13 0.16 2 -0.29 65 67
CTNNB1 0.041 0.011 0.068 3 0 32 35
AKT1 -0.017 0.091 0.17 6 -0.23 55 61
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.011 0.15 -10000 0 -0.38 50 50
CTNND1 0.042 0.009 -10000 0 -0.002 18 18
mol:PI-4-5-P2 -0.022 0.12 0.21 3 -0.28 63 66
VASP -0.022 0.12 0.16 2 -0.29 62 64
ZYX -0.017 0.11 0.15 5 -0.29 53 58
JUB -0.024 0.12 0.15 4 -0.29 63 67
EGFR(dimer) -0.006 0.13 0.19 1 -0.28 72 73
E-cadherin/beta catenin-gamma catenin 0.049 0.06 -10000 0 -0.11 47 47
mol:PI-3-4-5-P3 -0.005 0.1 0.24 1 -0.26 48 49
PIK3CA 0.03 0.02 -10000 0 -0.001 154 154
PI3K -0.005 0.11 0.24 1 -0.26 48 49
FYN -0.013 0.12 0.2 10 -0.27 66 76
mol:Ca2+ 0.003 0.098 0.16 60 -0.22 48 108
JUP 0.038 0.014 -10000 0 0 67 67
PIK3R1 0.035 0.018 -10000 0 0 107 107
mol:DAG 0.003 0.099 0.16 60 -0.22 48 108
CDH1 0.035 0.016 -10000 0 0 96 96
RhoA/GDP 0.013 0.12 0.22 15 -0.26 35 50
establishment of polarity of embryonic epithelium -0.021 0.12 0.21 4 -0.28 62 66
SRC 0.039 0.01 -10000 0 0 31 31
RAC1 0.039 0.01 -10000 0 0 35 35
RHOA 0.041 0.007 -10000 0 0 14 14
EGFR 0.036 0.014 -10000 0 0 73 73
CASR -0.005 0.093 0.15 58 -0.22 46 104
RhoA/GTP 0.015 0.1 0.2 5 -0.24 36 41
AKT2 -0.018 0.091 0.17 5 -0.23 55 60
actin cable formation -0.027 0.11 0.2 7 -0.29 60 67
apoptosis 0.002 0.11 0.26 47 -0.16 64 111
CTNNA1 0.04 0.012 -10000 0 -0.001 37 37
mol:GDP -0.005 0.1 0.16 58 -0.22 52 110
PIP5K1A -0.023 0.12 0.15 3 -0.28 65 68
PLCG1 0.003 0.1 0.16 60 -0.23 48 108
Rac1/GTP 0.003 0.13 -10000 0 -0.26 70 70
homophilic cell adhesion 0 0.004 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

Figure S29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S29.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.014 0.15 -10000 0 -0.36 29 29
MAP3K8 0.04 0.009 -10000 0 0 22 22
FOS 0.014 0.11 -10000 0 -0.32 20 20
PRKCA 0.026 0.029 -10000 0 -0.015 170 170
PTPN7 0.03 0.033 -10000 0 -0.031 115 115
HRAS 0.039 0.009 -10000 0 0 29 29
PRKCB 0 0.007 0.01 94 -0.013 102 196
NRAS 0.039 0.01 -10000 0 0 31 31
RAS family/GTP 0.053 0.05 -10000 0 -0.11 28 28
MAPK3 0.029 0.081 -10000 0 -0.44 9 9
MAP2K1 0.001 0.096 -10000 0 -0.28 43 43
ELK1 0.028 0.032 -10000 0 -0.038 103 103
BRAF 0 0.073 -10000 0 -0.29 28 28
mol:GTP 0 0.002 0.002 27 -0.004 102 129
MAPK1 0.013 0.11 -10000 0 -0.38 31 31
RAF1 -0.003 0.079 -10000 0 -0.29 36 36
KRAS 0.034 0.016 -10000 0 0 103 103
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.01 0.076 -10000 0 -0.14 103 103
CRKL -0.032 0.14 0.33 1 -0.42 42 43
mol:PIP3 0.009 0.081 0.31 1 -0.82 4 5
AKT1 0.003 0.085 0.38 4 -0.73 4 8
PTK2B 0.033 0.017 -10000 0 0 116 116
RAPGEF1 -0.035 0.13 0.31 1 -0.4 41 42
RANBP10 0.036 0.014 -10000 0 0 77 77
PIK3CA 0.03 0.019 -10000 0 0 150 150
HGF/MET/SHIP2 0.029 0.078 -10000 0 -0.12 101 101
MAP3K5 -0.024 0.14 0.28 2 -0.38 46 48
HGF/MET/CIN85/CBL/ENDOPHILINS 0.05 0.085 -10000 0 -0.11 104 104
AP1 -0.004 0.082 0.16 9 -0.14 103 112
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.04 0.009 -10000 0 0 29 29
apoptosis -0.16 0.35 -10000 0 -0.77 134 134
STAT3 (dimer) -0.011 0.11 0.19 4 -0.29 39 43
GAB1/CRKL/SHP2/PI3K -0.012 0.15 -10000 0 -0.38 44 44
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.01 0.15 0.29 3 -0.39 43 46
PTPN11 0.04 0.009 -10000 0 0 29 29
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.039 0.011 -10000 0 0 39 39
PTEN 0.039 0.011 -10000 0 0 39 39
ELK1 0.013 0.12 0.32 51 -10000 0 51
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.013 0.085 0.17 2 -0.22 49 51
PAK1 0.01 0.1 0.37 9 -0.69 4 13
HGF/MET/RANBP10 0.024 0.076 -10000 0 -0.11 103 103
HRAS -0.071 0.22 -10000 0 -0.48 118 118
DOCK1 -0.031 0.14 0.26 6 -0.4 42 48
GAB1 -0.029 0.15 0.25 1 -0.44 41 42
CRK -0.028 0.14 0.28 3 -0.41 42 45
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.057 0.19 -10000 0 -0.42 115 115
JUN 0.036 0.015 -10000 0 0 80 80
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.02 0.072 0.096 2 -0.16 103 105
PIK3R1 0.034 0.016 -10000 0 0 106 106
cell morphogenesis -0.011 0.15 0.27 30 -0.33 45 75
GRB2/SHC 0.019 0.096 0.19 3 -0.16 106 109
FOS 0.026 0.02 -10000 0 0 205 205
GLMN 0.005 0.007 0.069 6 -10000 0 6
cell motility 0.013 0.12 0.31 51 -10000 0 51
HGF/MET/MUC20 0.014 0.064 -10000 0 -0.11 104 104
cell migration 0.018 0.095 0.19 3 -0.16 106 109
GRB2 0.041 0.007 -10000 0 0 14 14
CBL 0.04 0.008 -10000 0 0 23 23
MET/RANBP10 0.01 0.073 -10000 0 -0.13 104 104
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.017 0.081 -10000 0 -0.18 79 79
MET/MUC20 -0.004 0.061 -10000 0 -0.13 106 106
RAP1B -0.034 0.13 0.27 2 -0.38 40 42
RAP1A -0.039 0.13 0.3 2 -0.39 42 44
HGF/MET/RANBP9 0.026 0.078 -10000 0 -0.12 101 101
RAF1 -0.072 0.21 -10000 0 -0.46 119 119
STAT3 -0.01 0.11 0.19 4 -0.21 83 87
cell proliferation -0.031 0.14 0.29 7 -0.28 97 104
RPS6KB1 -0.011 0.084 -10000 0 -0.28 37 37
MAPK3 -0.007 0.13 0.62 15 -10000 0 15
MAPK1 0.027 0.2 0.69 39 -10000 0 39
RANBP9 0.038 0.013 -10000 0 0 55 55
MAPK8 -0.021 0.15 -10000 0 -0.39 51 51
SRC -0.007 0.094 0.2 8 -0.18 83 91
PI3K -0.001 0.097 0.19 3 -0.18 96 99
MET/Glomulin 0.013 0.046 -10000 0 -0.13 39 39
SOS1 0.038 0.013 -10000 0 0 57 57
MAP2K1 -0.071 0.2 -10000 0 -0.43 118 118
MET 0.027 0.02 -10000 0 0 195 195
MAP4K1 -0.022 0.15 0.29 1 -0.42 42 43
PTK2 0.026 0.02 -10000 0 0 206 206
MAP2K2 -0.072 0.19 -10000 0 -0.43 119 119
BAD -0.001 0.082 0.34 4 -0.7 4 8
MAP2K4 -0.025 0.13 0.26 2 -0.36 44 46
SHP2/GRB2/SOS1/GAB1 -0.011 0.15 -10000 0 -0.36 52 52
INPPL1 0.04 0.009 -10000 0 0 29 29
PXN 0.041 0.007 -10000 0 0 14 14
SH3KBP1 0.041 0.007 -10000 0 0 16 16
HGS -0.026 0.071 0.084 2 -0.16 111 113
PLCgamma1/PKC 0.027 0.021 -10000 0 -0.13 9 9
HGF 0.04 0.009 -10000 0 0 29 29
RASA1 0.036 0.014 -10000 0 0 73 73
NCK1 0.036 0.014 -10000 0 0 77 77
PTPRJ 0.039 0.01 -10000 0 0 36 36
NCK/PLCgamma1 0.014 0.096 0.19 3 -0.16 102 105
PDPK1 0.003 0.079 0.4 1 -0.77 4 5
HGF/MET/SHIP 0.014 0.064 -10000 0 -0.11 104 104
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.064 0.5 0.87 1 -1 74 75
STAT6 (cleaved dimer) -0.11 0.46 -10000 0 -0.94 90 90
IGHG1 0.037 0.23 0.46 4 -0.67 8 12
IGHG3 -0.066 0.45 -10000 0 -0.93 80 80
AKT1 -0.053 0.37 0.5 1 -0.77 80 81
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.045 0.36 0.45 1 -0.81 75 76
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.049 0.4 -10000 0 -0.85 78 78
THY1 -0.22 0.66 0.77 1 -1.2 158 159
MYB 0.034 0.016 -10000 0 0 106 106
HMGA1 0.037 0.014 -10000 0 0 69 69
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.024 0.38 0.52 2 -0.68 88 90
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.054 0.4 -10000 0 -0.86 78 78
SP1 0.022 0.073 -10000 0 -0.13 103 103
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.001 0.05 -10000 0 -0.086 2 2
STAT6 (dimer)/ETS1 -0.086 0.47 -10000 0 -0.95 86 86
SOCS1 -0.03 0.35 0.52 1 -0.64 82 83
SOCS3 -0.035 0.37 -10000 0 -0.82 64 64
FCER2 -0.029 0.39 -10000 0 -0.75 70 70
PARP14 0.033 0.019 -10000 0 0 135 135
CCL17 -0.059 0.48 -10000 0 -0.99 74 74
GRB2 0.041 0.007 -10000 0 0 14 14
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.009 0.3 0.42 1 -0.62 66 67
T cell proliferation -0.084 0.5 -10000 0 -1 88 88
IL4R/JAK1 -0.077 0.49 -10000 0 -1 81 81
EGR2 -0.056 0.48 -10000 0 -1 72 72
JAK2 0.032 0.072 0.17 3 -0.097 1 4
JAK3 0.033 0.026 -10000 0 -0.038 45 45
PIK3R1 0.034 0.016 -10000 0 0 106 106
JAK1 0.041 0.041 0.11 4 -0.04 8 12
COL1A2 -0.15 0.56 -10000 0 -1.3 107 107
CCL26 -0.07 0.49 -10000 0 -1 76 76
IL4R -0.066 0.53 -10000 0 -1.1 78 78
PTPN6 0.006 0.043 -10000 0 -0.08 2 2
IL13RA2 -0.058 0.48 -10000 0 -0.99 73 73
IL13RA1 0.037 0.075 0.18 7 -0.097 1 8
IRF4 0.059 0.15 -10000 0 -1.3 1 1
ARG1 0.049 0.19 -10000 0 -0.86 3 3
CBL -0.025 0.35 0.56 2 -0.64 90 92
GTF3A 0.014 0.079 -10000 0 -0.13 119 119
PIK3CA 0.03 0.019 -10000 0 0 150 150
IL13RA1/JAK2 0.042 0.12 0.25 4 -0.18 27 31
IRF4/BCL6 0.043 0.14 -10000 0 -1.2 1 1
CD40LG 0.049 0.01 -10000 0 -0.12 1 1
MAPK14 -0.028 0.36 0.51 1 -0.7 82 83
mitosis -0.045 0.35 0.49 1 -0.72 80 81
STAT6 -0.063 0.55 0.78 2 -1.1 79 81
SPI1 0.045 0.01 -10000 0 -10000 0 0
RPS6KB1 -0.048 0.34 0.48 2 -0.69 82 84
STAT6 (dimer) -0.062 0.55 0.78 2 -1.1 79 81
STAT6 (dimer)/PARP14 -0.1 0.49 -10000 0 -1 79 79
mast cell activation -0.005 0.019 -10000 0 -0.044 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.074 0.39 -10000 0 -0.8 87 87
FRAP1 -0.053 0.37 0.5 1 -0.77 80 81
LTA -0.058 0.48 -10000 0 -0.98 74 74
FES 0.04 0.008 -10000 0 0 22 22
T-helper 1 cell differentiation 0.055 0.54 1.1 79 -0.78 2 81
CCL11 -0.09 0.5 -10000 0 -1 88 88
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.047 0.39 -10000 0 -0.82 77 77
IL2RG 0.027 0.026 0.094 1 -0.039 22 23
IL10 -0.055 0.48 -10000 0 -1 71 71
IRS1 0.04 0.008 -10000 0 0 22 22
IRS2 0.039 0.01 -10000 0 0 36 36
IL4 0.041 0.22 -10000 0 -0.93 12 12
IL5 -0.06 0.48 -10000 0 -1 72 72
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.044 0.47 0.69 2 -0.87 88 90
COL1A1 -0.21 0.65 -10000 0 -1.3 137 137
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.083 0.5 -10000 0 -1.1 77 77
IL2R gamma/JAK3 0.019 0.074 -10000 0 -0.13 92 92
TFF3 -0.065 0.5 -10000 0 -1 77 77
ALOX15 -0.059 0.48 -10000 0 -0.99 74 74
MYBL1 0.036 0.014 -10000 0 0 73 73
T-helper 2 cell differentiation -0.1 0.48 -10000 0 -0.91 97 97
SHC1 0.04 0.009 -10000 0 0 29 29
CEBPB 0.041 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.051 0.4 -10000 0 -0.83 81 81
mol:PI-3-4-5-P3 -0.052 0.37 0.5 1 -0.77 80 81
PI3K -0.063 0.4 0.5 1 -0.84 80 81
DOK2 0.032 0.018 -10000 0 0 130 130
ETS1 0.001 0.047 -10000 0 -0.098 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.006 0.29 0.41 2 -0.6 65 67
ITGB3 -0.093 0.54 -10000 0 -1.1 88 88
PIGR -0.056 0.49 -10000 0 -1 77 77
IGHE -0.004 0.088 0.18 39 -0.21 15 54
MAPKKK cascade -0.005 0.29 0.41 2 -0.59 65 67
BCL6 0.03 0.018 -10000 0 0 141 141
OPRM1 -0.059 0.48 -10000 0 -1 70 70
RETNLB -0.053 0.48 -10000 0 -0.99 73 73
SELP -0.054 0.48 -10000 0 -1 69 69
AICDA -0.049 0.46 -10000 0 -0.95 72 72
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.17 0.61 0.67 1 -1.2 120 121
IL23A -0.11 0.55 -10000 0 -1.2 81 81
NF kappa B1 p50/RelA/I kappa B alpha -0.11 0.54 -10000 0 -1.2 88 88
positive regulation of T cell mediated cytotoxicity -0.13 0.61 0.68 1 -1.3 88 89
ITGA3 -0.16 0.58 -10000 0 -1.1 119 119
IL17F -0.043 0.36 0.49 9 -0.7 87 96
IL12B 0.034 0.073 0.16 9 -0.079 7 16
STAT1 (dimer) -0.15 0.58 -10000 0 -1.3 87 87
CD4 -0.11 0.57 0.71 2 -1.2 97 99
IL23 -0.11 0.52 -10000 0 -1.2 81 81
IL23R 0.037 0.15 -10000 0 -1.2 3 3
IL1B -0.13 0.59 -10000 0 -1.3 93 93
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.096 0.51 -10000 0 -1.1 82 82
TYK2 0.025 0.055 0.13 1 -10000 0 1
STAT4 0.04 0.009 -10000 0 0 28 28
STAT3 0.038 0.012 -10000 0 0 52 52
IL18RAP 0.041 0.007 -10000 0 -10000 0 0
IL12RB1 0.024 0.057 0.13 1 -10000 0 1
PIK3CA 0.031 0.019 -10000 0 0 150 150
IL12Rbeta1/TYK2 0.038 0.069 -10000 0 -10000 0 0
IL23R/JAK2 0.047 0.17 -10000 0 -1.2 3 3
positive regulation of chronic inflammatory response -0.13 0.61 0.68 1 -1.3 88 89
natural killer cell activation -0.002 0.01 -10000 0 -10000 0 0
JAK2 0.031 0.069 0.16 9 -0.08 4 13
PIK3R1 0.034 0.017 -10000 0 0 106 106
NFKB1 0.037 0.016 -10000 0 0 85 85
RELA 0.043 0.008 -10000 0 0 10 10
positive regulation of dendritic cell antigen processing and presentation -0.096 0.5 -10000 0 -1.1 81 81
ALOX12B -0.098 0.51 -10000 0 -1.1 82 82
CXCL1 -0.13 0.57 -10000 0 -1.2 110 110
T cell proliferation -0.13 0.61 0.68 1 -1.3 88 89
NFKBIA 0.038 0.015 -10000 0 0 66 66
IL17A -0.031 0.29 0.45 5 -0.54 90 95
PI3K -0.15 0.53 -10000 0 -1.2 87 87
IFNG 0.006 0.04 0.1 4 -0.11 13 17
STAT3 (dimer) -0.13 0.5 -10000 0 -1.1 85 85
IL18R1 0.041 0.008 -10000 0 -10000 0 0
IL23/IL23R/JAK2/TYK2/SOCS3 -0.013 0.34 0.55 3 -0.66 74 77
IL18/IL18R 0.055 0.066 -10000 0 -0.11 61 61
macrophage activation -0.007 0.021 0.034 1 -0.045 77 78
TNF -0.11 0.54 -10000 0 -1.2 82 82
STAT3/STAT4 -0.12 0.55 -10000 0 -1.2 86 86
STAT4 (dimer) -0.13 0.58 -10000 0 -1.3 86 86
IL18 0.031 0.019 -10000 0 -10000 0 0
IL19 -0.097 0.52 -10000 0 -1.1 84 84
STAT5A (dimer) -0.13 0.58 -10000 0 -1.3 88 88
STAT1 0.034 0.017 -10000 0 0 108 108
SOCS3 0.037 0.014 -10000 0 0 67 67
CXCL9 -0.16 0.61 -10000 0 -1.2 122 122
MPO -0.097 0.52 -10000 0 -1.1 83 83
positive regulation of humoral immune response -0.13 0.61 0.68 1 -1.3 88 89
IL23/IL23R/JAK2/TYK2 -0.16 0.65 -10000 0 -1.4 88 88
IL6 -0.1 0.53 -10000 0 -1.2 86 86
STAT5A 0.038 0.012 -10000 0 0 50 50
IL2 0.039 0.018 -10000 0 -0.033 12 12
positive regulation of tyrosine phosphorylation of STAT protein -0.002 0.01 -10000 0 -10000 0 0
CD3E -0.11 0.55 0.69 1 -1.2 90 91
keratinocyte proliferation -0.13 0.61 0.68 1 -1.3 88 89
NOS2 -0.098 0.51 -10000 0 -1.1 90 90
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.033 0.017 -10000 0 0 118 118
ANTXR2 0.035 0.016 -10000 0 0 96 96
negative regulation of myeloid dendritic cell antigen processing and presentation -0.006 0.011 -10000 0 -0.033 74 74
monocyte activation -0.078 0.17 -10000 0 -0.35 153 153
MAP2K2 -0.042 0.18 -10000 0 -0.58 57 57
MAP2K1 -0.011 0.011 0.007 37 -0.037 69 106
MAP2K7 -0.01 0.011 0.007 36 -0.037 68 104
MAP2K6 -0.009 0.012 0.007 32 -0.039 59 91
CYAA -0.023 0.033 -10000 0 -0.1 73 73
MAP2K4 -0.01 0.012 0.007 32 -0.039 68 100
IL1B -0.012 0.042 0.13 7 -0.09 82 89
Channel 0.022 0.056 -10000 0 -0.11 74 74
NLRP1 -0.006 0.01 -10000 0 -0.031 73 73
CALM1 0.04 0.009 -10000 0 0 30 30
negative regulation of phagocytosis 0.003 0.077 -10000 0 -0.43 16 16
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.006 0.011 0.033 74 -10000 0 74
MAPK3 -0.011 0.011 0.007 36 -0.037 72 108
MAPK1 -0.01 0.011 0.007 35 -0.038 66 101
PGR -0.008 0.011 0.007 36 -0.037 52 88
PA/Cellular Receptors 0.022 0.062 -10000 0 -0.12 73 73
apoptosis -0.006 0.011 -10000 0 -0.033 74 74
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.021 0.056 -10000 0 -0.11 74 74
macrophage activation -0.013 0.021 0.17 3 -0.11 1 4
TNF 0.04 0.009 -10000 0 0 25 25
VCAM1 -0.081 0.17 -10000 0 -0.35 151 151
platelet activation 0.003 0.077 -10000 0 -0.43 16 16
MAPKKK cascade 0.007 0.028 0.084 7 -0.097 4 11
IL18 -0.009 0.042 0.14 4 -0.093 72 76
negative regulation of macrophage activation -0.006 0.011 -10000 0 -0.033 74 74
LEF -0.006 0.011 -10000 0 -0.033 74 74
CASP1 0 0.012 0.018 34 -0.03 48 82
mol:cAMP 0 0.077 -10000 0 -0.44 16 16
necrosis -0.006 0.011 -10000 0 -0.033 74 74
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.022 0.054 -10000 0 -0.1 74 74
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.041 0.006 -10000 0 0 10 10
PTK2 0.026 0.02 -10000 0 0 206 206
CRKL -0.021 0.052 0.12 14 -0.13 67 81
GRB2/SOS1/SHC 0.065 0.05 -10000 0 -0.12 25 25
HRAS 0.04 0.009 -10000 0 0 29 29
IRS1/Crk 0.012 0.056 -10000 0 -0.12 73 73
IGF-1R heterotetramer/IGF1/PTP1B 0.034 0.072 -10000 0 -0.12 72 72
AKT1 0 0.092 0.18 84 -0.18 15 99
BAD -0.007 0.085 0.16 80 -0.17 14 94
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.02 0.051 0.11 12 -0.13 63 75
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.012 0.069 0.21 6 -0.13 91 97
RAF1 0.014 0.12 0.28 13 -0.44 16 29
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.045 0.087 0.21 2 -0.13 85 87
YWHAZ 0.034 0.016 -10000 0 0 104 104
IGF-1R heterotetramer/IGF1/IRS1 0.019 0.067 0.18 2 -0.13 80 82
PIK3CA 0.03 0.019 -10000 0 0 150 150
RPS6KB1 0.001 0.095 0.18 89 -0.18 20 109
GNB2L1 0.041 0.005 -10000 0 0 7 7
positive regulation of MAPKKK cascade 0.011 0.11 0.26 18 -0.36 14 32
PXN 0.041 0.007 -10000 0 0 14 14
PIK3R1 0.034 0.016 -10000 0 0 106 106
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.048 0.046 -10000 0 -0.14 26 26
HRAS/GTP 0.014 0.067 -10000 0 -0.13 79 79
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.061 0.09 -10000 0 -0.12 81 81
IGF-1R heterotetramer 0.034 0.024 0.1 2 -0.051 15 17
IGF-1R heterotetramer/IGF1/IRS/Nck 0.038 0.074 0.2 2 -0.13 80 82
Crk/p130 Cas/Paxillin 0.043 0.08 0.25 8 -0.13 68 76
IGF1R 0.034 0.024 0.1 2 -0.051 15 17
IGF1 0.028 0.034 0.1 2 -0.053 65 67
IRS2/Crk 0.01 0.053 0.17 1 -0.13 56 57
PI3K 0.025 0.082 0.21 2 -0.12 91 93
apoptosis -0.002 0.09 0.17 15 -0.18 69 84
HRAS/GDP 0.029 0.007 -10000 0 -10000 0 0
PRKCD -0.009 0.092 0.21 6 -0.21 66 72
RAF1/14-3-3 E 0.032 0.12 0.29 13 -0.39 15 28
BAD/14-3-3 0.002 0.094 0.19 69 -0.17 15 84
PRKCZ 0.002 0.095 0.18 93 -0.18 15 108
Crk/p130 Cas/Paxillin/FAK1 0.009 0.079 0.19 17 -0.16 40 57
PTPN1 0.038 0.012 -10000 0 0 46 46
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.009 0.092 -10000 0 -0.21 70 70
BCAR1 0.036 0.014 -10000 0 0 74 74
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.055 0.077 -10000 0 -0.11 73 73
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.038 0.013 -10000 0 0 57 57
IRS1/NCK2 0.026 0.068 0.14 17 -0.12 80 97
GRB10 0.04 0.008 -10000 0 0 23 23
PTPN11 -0.02 0.052 0.11 15 -0.13 64 79
IRS1 0.005 0.062 0.13 19 -0.13 80 99
IRS2 -0.02 0.051 0.11 15 -0.13 64 79
IGF-1R heterotetramer/IGF1 0.021 0.074 0.16 1 -0.16 71 72
GRB2 0.041 0.007 -10000 0 0 14 14
PDPK1 0.009 0.099 0.19 88 -0.18 14 102
YWHAE 0.038 0.012 -10000 0 0 50 50
PRKD1 -0.011 0.095 0.2 8 -0.22 71 79
SHC1 0.04 0.009 -10000 0 0 29 29
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.054 0.062 0.15 115 -0.032 31 146
AES 0.052 0.056 0.14 117 -0.032 15 132
FBXW11 0.04 0.008 -10000 0 0 23 23
mol:GTP 0.001 0.003 0.033 1 -10000 0 1
LRP6/FZD1 0.041 0.049 -10000 0 -0.14 31 31
SMAD4 0.038 0.012 -10000 0 0 49 49
DKK2 0.038 0.012 -10000 0 0 49 49
TLE1 0.052 0.052 0.13 110 -0.033 12 122
MACF1 0.033 0.017 -10000 0 0 119 119
CTNNB1 0.034 0.12 0.29 30 -0.42 11 41
WIF1 0.04 0.01 -10000 0 -0.001 32 32
beta catenin/RanBP3 0.097 0.22 0.47 113 -0.41 8 121
KREMEN2 0.04 0.009 -10000 0 0 26 26
DKK1 0.039 0.011 -10000 0 0 41 41
beta catenin/beta TrCP1 0.053 0.12 0.3 29 -0.41 10 39
FZD1 0.041 0.007 -10000 0 0 17 17
AXIN2 -0.045 0.22 0.69 7 -0.89 21 28
AXIN1 0.042 0.004 -10000 0 0 4 4
RAN 0.042 0.007 0.076 1 0 11 12
Axin1/APC/GSK3/beta catenin 0.047 0.088 0.41 1 -0.55 7 8
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.03 0.17 0.33 8 -0.46 48 56
Axin1/APC/GSK3 0.03 0.07 0.2 16 -0.24 11 27
Axin1/APC/GSK3/beta catenin/Macf1 0.021 0.089 0.29 15 -0.29 7 22
HNF1A 0.019 0.05 0.09 132 -10000 0 132
CTBP1 0.052 0.053 0.14 109 -0.033 12 121
MYC 0.055 0.55 0.63 166 -1.1 71 237
RANBP3 0.04 0.012 0.076 1 0 41 42
DKK2/LRP6/Kremen 2 0.057 0.054 -10000 0 -0.12 28 28
NKD1 0.038 0.012 -10000 0 0 50 50
TCF4 0.054 0.059 0.14 114 -0.033 13 127
TCF3 0.051 0.055 0.14 115 -0.034 13 128
WNT1/LRP6/FZD1/Axin1 0.08 0.06 -10000 0 -0.11 30 30
Ran/GTP 0.031 0.013 0.1 1 -0.12 3 4
CtBP/CBP/TCF/TLE1/AES 0.054 0.3 0.61 90 -0.42 20 110
LEF1 0.036 0.05 0.14 72 -0.033 13 85
DVL1 0.032 0.078 0.24 13 -0.3 14 27
CSNK2A1 0.039 0.011 -10000 0 0 40 40
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.067 0.19 -10000 0 -0.45 72 72
DKK1/LRP6/Kremen 2 0.057 0.053 -10000 0 -0.12 27 27
LRP6 0.034 0.016 -10000 0 0 103 103
CSNK1A1 0.059 0.066 0.15 128 -0.032 32 160
NLK 0.032 0.024 -10000 0 -0.024 77 77
CCND1 -0.18 0.5 0.71 17 -1.2 95 112
WNT1 0.041 0.007 -10000 0 0 15 15
GSK3A 0.039 0.011 0.065 1 0 37 38
GSK3B 0.04 0.009 -10000 0 0 29 29
FRAT1 0.039 0.009 -10000 0 -0.002 26 26
PPP2R5D 0.034 0.064 0.24 2 -0.28 13 15
APC -0.005 0.083 0.21 61 -10000 0 61
WNT1/LRP6/FZD1 0.019 0.062 0.23 2 -0.31 4 6
CREBBP 0.054 0.054 0.14 115 -0.033 15 130
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.037 0.014 -10000 0 0 67 67
LAT2 -0.018 0.1 0.19 4 -0.21 85 89
AP1 -0.031 0.18 0.28 1 -0.42 67 68
mol:PIP3 -0.033 0.13 0.29 5 -0.33 54 59
IKBKB -0.013 0.087 0.2 19 -0.19 53 72
AKT1 0.012 0.12 0.25 52 -0.23 9 61
IKBKG -0.021 0.082 0.22 5 -0.19 56 61
MS4A2 0.046 0.012 0.07 34 -0.004 10 44
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.03 0.019 -10000 0 0 150 150
MAP3K1 -0.033 0.12 0.22 3 -0.31 65 68
mol:Ca2+ -0.023 0.11 0.27 5 -0.26 50 55
LYN 0.036 0.019 0.09 2 -0.003 92 94
CBLB -0.014 0.095 0.2 5 -0.22 72 77
SHC1 0.04 0.009 -10000 0 0 29 29
RasGAP/p62DOK 0.021 0.072 -10000 0 -0.11 107 107
positive regulation of cell migration -0.01 0.002 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.011 0.079 0.29 19 -0.16 5 24
PTPN13 -0.057 0.2 -10000 0 -0.64 39 39
PTPN11 0.039 0.02 0.1 2 -0.033 24 26
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.008 0.13 0.3 18 -0.32 31 49
SYK 0.037 0.017 0.09 2 -0.003 74 76
GRB2 0.041 0.007 -10000 0 0 14 14
LAT/PLCgamma1/GRB2/SLP76/GADs -0.024 0.13 -10000 0 -0.29 79 79
LAT -0.017 0.095 -10000 0 -0.21 80 80
PAK2 -0.03 0.14 0.23 3 -0.31 73 76
NFATC2 0.004 0.056 -10000 0 -0.41 9 9
HRAS -0.025 0.14 0.24 3 -0.33 70 73
GAB2 0.031 0.018 -10000 0 0 142 142
PLA2G1B 0.01 0.15 -10000 0 -0.89 14 14
Fc epsilon R1 0.035 0.071 -10000 0 -0.096 104 104
Antigen/IgE/Fc epsilon R1 0.037 0.063 -10000 0 -0.082 95 95
mol:GDP -0.023 0.16 0.28 2 -0.4 57 59
JUN 0.036 0.015 -10000 0 0 80 80
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.034 0.017 -10000 0 0 106 106
FOS 0.026 0.02 -10000 0 0 205 205
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.009 0.1 -10000 0 -0.22 84 84
CHUK -0.023 0.083 0.22 5 -0.2 62 67
KLRG1 -0.014 0.079 0.18 4 -0.2 51 55
VAV1 -0.014 0.095 0.18 3 -0.22 71 74
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.017 0.097 0.2 3 -0.21 80 83
negative regulation of mast cell degranulation -0.02 0.074 0.13 1 -0.21 40 41
BTK -0.03 0.18 0.26 1 -0.5 49 50
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.027 0.11 -10000 0 -0.22 101 101
GAB2/PI3K/SHP2 -0.04 0.056 -10000 0 -0.15 66 66
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.002 0.066 -10000 0 -0.15 84 84
RAF1 0.013 0.16 -10000 0 -0.98 14 14
Fc epsilon R1/FcgammaRIIB/SHIP 0.033 0.092 -10000 0 -0.12 120 120
FCER1G 0.027 0.02 0.066 1 0 195 196
FCER1A 0.039 0.015 0.1 1 -0.006 45 46
Antigen/IgE/Fc epsilon R1/Fyn 0.041 0.077 -10000 0 -0.098 89 89
MAPK3 0.011 0.15 -10000 0 -0.9 14 14
MAPK1 0.004 0.15 -10000 0 -0.9 14 14
NFKB1 0.035 0.015 -10000 0 0 85 85
MAPK8 -0.033 0.22 -10000 0 -0.55 63 63
DUSP1 0.027 0.02 -10000 0 0 202 202
NF-kappa-B/RelA 0.001 0.068 0.16 7 -0.14 56 63
actin cytoskeleton reorganization -0.051 0.2 -10000 0 -0.72 31 31
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.016 0.13 0.26 3 -0.28 77 80
FER -0.015 0.093 -10000 0 -0.21 74 74
RELA 0.041 0.006 -10000 0 0 10 10
ITK -0.002 0.058 -10000 0 -0.28 17 17
SOS1 0.038 0.013 -10000 0 0 57 57
PLCG1 -0.028 0.15 0.28 3 -0.38 60 63
cytokine secretion -0.003 0.047 0.09 6 -0.1 61 67
SPHK1 -0.017 0.098 0.21 3 -0.21 83 86
PTK2 -0.055 0.22 -10000 0 -0.78 31 31
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.018 0.14 -10000 0 -0.3 77 77
EDG1 -0.01 0.002 -10000 0 -10000 0 0
mol:DAG -0.036 0.13 0.33 3 -0.32 64 67
MAP2K2 0.003 0.15 -10000 0 -0.91 14 14
MAP2K1 0.004 0.15 -10000 0 -0.91 14 14
MAP2K7 0.038 0.011 -10000 0 0 44 44
KLRG1/SHP2 0.013 0.091 0.2 34 -0.22 34 68
MAP2K4 -0.073 0.32 -10000 0 -0.89 74 74
Fc epsilon R1/FcgammaRIIB 0.036 0.099 -10000 0 -0.13 121 121
mol:Choline -0.011 0.079 0.29 19 -0.16 5 24
SHC/Grb2/SOS1 0.023 0.13 -10000 0 -0.22 73 73
FYN 0.034 0.016 -10000 0 0 102 102
DOK1 0.04 0.009 -10000 0 0 24 24
PXN -0.054 0.2 -10000 0 -0.7 31 31
HCLS1 -0.01 0.098 0.2 6 -0.24 59 65
PRKCB -0.025 0.1 0.24 6 -0.25 59 65
FCGR2B 0.03 0.019 -10000 0 0 158 158
IGHE 0 0.006 0.048 2 -10000 0 2
KLRG1/SHIP -0.02 0.075 0.13 1 -0.21 40 41
LCP2 0.034 0.016 -10000 0 0 100 100
PLA2G4A -0.006 0.092 0.17 12 -0.22 62 74
RASA1 0.036 0.014 -10000 0 0 73 73
mol:Phosphatidic acid -0.011 0.079 0.29 19 -0.16 5 24
IKK complex -0.016 0.072 0.21 9 -0.17 38 47
WIPF1 0 0 -10000 0 -10000 0 0
FoxO family 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
G6PC -0.001 0.064 -10000 0 -10000 0 0
PLK1 -0.15 0.38 -10000 0 -0.94 77 77
CDKN1B -0.043 0.2 0.4 3 -0.37 96 99
FOXO3 -0.14 0.36 -10000 0 -0.58 171 171
KAT2B -0.008 0.029 0.047 2 -0.046 177 179
FOXO1/SIRT1 0.016 0.077 -10000 0 -0.23 16 16
CAT -0.16 0.4 0.49 4 -0.86 103 107
CTNNB1 0.039 0.01 -10000 0 0 32 32
AKT1 0.013 0.055 -10000 0 -0.064 148 148
FOXO1 -0.004 0.069 -10000 0 -0.26 9 9
MAPK10 0 0.047 0.18 8 -0.12 27 35
mol:GTP 0 0.003 -10000 0 -10000 0 0
FOXO4 -0.024 0.12 0.23 4 -0.31 55 59
response to oxidative stress -0.006 0.03 0.061 1 -0.053 101 102
FOXO3A/SIRT1 -0.13 0.35 0.41 1 -0.56 176 177
XPO1 0.039 0.011 -10000 0 0 39 39
EP300 0.038 0.015 -10000 0 -10000 0 0
BCL2L11 0.01 0.11 -10000 0 -0.87 7 7
FOXO1/SKP2 0.013 0.073 -10000 0 -0.24 14 14
mol:GDP -0.006 0.03 0.061 1 -0.053 101 102
RAN 0.041 0.006 -10000 0 0 11 11
GADD45A -0.075 0.28 -10000 0 -0.77 53 53
YWHAQ 0.04 0.009 -10000 0 0 26 26
FOXO1/14-3-3 family 0.016 0.12 0.24 1 -0.35 34 35
MST1 0.012 0.056 -10000 0 -0.063 187 187
CSNK1D 0.04 0.009 -10000 0 0 30 30
CSNK1E 0.038 0.012 -10000 0 0 54 54
FOXO4/14-3-3 family 0.008 0.13 -10000 0 -0.4 32 32
YWHAB 0.038 0.011 -10000 0 0 44 44
MAPK8 0.001 0.053 0.19 13 -0.12 30 43
MAPK9 0 0.053 0.19 12 -0.13 29 41
YWHAG 0.04 0.009 -10000 0 0 26 26
YWHAE 0.038 0.012 -10000 0 0 50 50
YWHAZ 0.034 0.016 -10000 0 0 104 104
SIRT1 0.037 0.019 0.12 2 -0.035 25 27
SOD2 -0.12 0.3 -10000 0 -0.67 95 95
RBL2 -0.13 0.34 -10000 0 -0.81 73 73
RAL/GDP 0.031 0.056 -10000 0 -0.099 46 46
CHUK 0.012 0.054 -10000 0 -0.063 168 168
Ran/GTP 0.027 0.019 -10000 0 -0.052 12 12
CSNK1G2 0.037 0.014 -10000 0 0 68 68
RAL/GTP 0.031 0.057 -10000 0 -0.089 55 55
CSNK1G1 0.04 0.008 -10000 0 0 21 21
FASLG 0.018 0.065 -10000 0 -1.2 1 1
SKP2 0.036 0.014 -10000 0 0 73 73
USP7 0.038 0.012 -10000 0 0 49 49
IKBKB 0.011 0.054 -10000 0 -0.062 175 175
CCNB1 -0.18 0.43 -10000 0 -1 97 97
FOXO1-3a-4/beta catenin -0.057 0.2 -10000 0 -0.39 93 93
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.073 -10000 0 -0.24 14 14
CSNK1A1 0.04 0.009 -10000 0 0 24 24
SGK1 -0.008 0.029 0.047 2 -0.046 177 179
CSNK1G3 0.039 0.01 -10000 0 0 37 37
Ran/GTP/Exportin 1 0.046 0.038 -10000 0 -0.099 29 29
ZFAND5 -0.018 0.1 0.21 4 -0.26 55 59
SFN 0.035 0.015 -10000 0 0 84 84
CDK2 0.04 0.014 -10000 0 -10000 0 0
FOXO3A/14-3-3 -0.002 0.14 -10000 0 -0.34 48 48
CREBBP 0.041 0.013 -10000 0 -10000 0 0
FBXO32 -0.19 0.54 0.52 3 -1.1 137 140
BCL6 -0.12 0.35 -10000 0 -0.91 65 65
RALB 0.04 0.009 -10000 0 0 27 27
RALA 0.04 0.01 -10000 0 0 29 29
YWHAH 0.038 0.012 -10000 0 0 54 54
IL2 signaling events mediated by STAT5

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
GAB2 0.031 0.019 -10000 0 0 144 144
ELF1 0.047 0.024 -10000 0 -0.26 2 2
CCNA2 0.032 0.018 -10000 0 0 135 135
PIK3CA 0.031 0.019 -10000 0 0 150 150
JAK3 0.038 0.013 -10000 0 -0.001 57 57
PIK3R1 0.034 0.017 -10000 0 -0.001 108 108
JAK1 0.039 0.011 -10000 0 -0.002 38 38
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.001 0.14 -10000 0 -0.34 44 44
SHC1 0.04 0.01 -10000 0 -0.001 30 30
SP1 0.044 0.043 -10000 0 -0.27 9 9
IL2RA 0.019 0.032 -10000 0 -0.49 2 2
IL2RB 0.037 0.015 -10000 0 -0.001 72 72
SOS1 0.038 0.014 -10000 0 -0.001 59 59
IL2RG 0.028 0.02 -10000 0 0 182 182
G1/S transition of mitotic cell cycle -0.042 0.18 0.29 4 -0.51 37 41
PTPN11 0.04 0.011 -10000 0 -0.004 33 33
CCND2 0.011 0.062 -10000 0 -0.49 8 8
LCK 0.04 0.011 -10000 0 -0.004 32 32
GRB2 0.041 0.008 -10000 0 -0.004 16 16
IL2 0.038 0.013 -10000 0 -0.002 50 50
CDK6 0.032 0.018 -10000 0 0 128 128
CCND3 0.004 0.14 -10000 0 -0.55 14 14
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.037 0.014 -10000 0 0 70 70
GNB1/GNG2 0.013 0.12 0.23 2 -0.26 46 48
mol:DAG -0.007 0.1 0.21 6 -0.25 42 48
PLCG1 -0.008 0.1 0.21 6 -0.26 42 48
YES1 -0.017 0.096 0.2 1 -0.27 44 45
FZD3 0.029 0.019 -10000 0 0 166 166
FZD6 0.029 0.019 -10000 0 0 173 173
G protein 0.029 0.13 0.25 43 -0.26 41 84
MAP3K7 -0.029 0.085 0.17 10 -0.23 41 51
mol:Ca2+ -0.007 0.1 0.2 6 -0.25 42 48
mol:IP3 -0.007 0.1 0.21 6 -0.25 42 48
NLK -0.029 0.26 -10000 0 -0.85 49 49
GNB1 0.041 0.005 -10000 0 0 7 7
CAMK2A -0.018 0.092 0.18 7 -0.24 41 48
MAP3K7IP1 0.038 0.012 -10000 0 0 51 51
Noncanonical Wnts/FZD -0.019 0.096 -10000 0 -0.2 94 94
CSNK1A1 0.04 0.009 -10000 0 0 24 24
GNAS -0.011 0.1 0.2 19 -0.28 37 56
GO:0007205 -0.014 0.097 0.19 7 -0.25 44 51
WNT6 0.041 0.006 -10000 0 0 12 12
WNT4 0.04 0.008 -10000 0 0 19 19
NFAT1/CK1 alpha 0.004 0.12 0.3 8 -0.27 42 50
GNG2 0.039 0.01 -10000 0 0 34 34
WNT5A 0.035 0.015 -10000 0 0 90 90
WNT11 0.033 0.017 -10000 0 0 122 122
CDC42 -0.02 0.094 0.2 4 -0.26 43 47
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.01 0.1 -10000 0 -0.13 142 142
SMAD6-7/SMURF1 0.07 0.039 -10000 0 -0.14 8 8
NOG 0.038 0.012 -10000 0 0 49 49
SMAD9 0.003 0.12 -10000 0 -0.42 39 39
SMAD4 0.038 0.012 -10000 0 0 49 49
SMAD5 -0.006 0.1 0.29 1 -0.28 42 43
BMP7/USAG1 -0.02 0.084 -10000 0 -0.16 132 132
SMAD5/SKI 0.009 0.11 0.29 1 -0.28 44 45
SMAD1 0.002 0.096 -10000 0 -0.3 31 31
BMP2 0.039 0.01 -10000 0 0 32 32
SMAD1/SMAD1/SMAD4 0.026 0.1 -10000 0 -0.3 27 27
BMPR1A 0.037 0.014 -10000 0 0 67 67
BMPR1B 0.031 0.019 -10000 0 0 148 148
BMPR1A-1B/BAMBI 0.007 0.088 -10000 0 -0.14 121 121
AHSG 0.034 0.017 -10000 0 0 108 108
CER1 0.038 0.012 -10000 0 0 47 47
BMP2-4/CER1 0.061 0.044 -10000 0 -0.12 11 11
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.012 0.11 0.19 1 -0.26 62 63
BMP2-4 (homodimer) 0.048 0.035 -10000 0 -0.14 11 11
RGMB 0.039 0.011 -10000 0 0 43 43
BMP6/BMPR2/BMPR1A-1B 0.05 0.085 -10000 0 -0.13 80 80
RGMA 0.039 0.01 -10000 0 0 34 34
SMURF1 0.04 0.008 -10000 0 0 19 19
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0 0.082 0.17 2 -0.24 36 38
BMP2-4/USAG1 0.021 0.071 -10000 0 -0.12 76 76
SMAD6/SMURF1/SMAD5 0.007 0.11 -10000 0 -0.28 43 43
SOSTDC1 0.022 0.021 -10000 0 0 257 257
BMP7/BMPR2/BMPR1A-1B 0.008 0.1 -10000 0 -0.14 153 153
SKI 0.042 0.003 -10000 0 0 3 3
BMP6 (homodimer) 0.037 0.013 -10000 0 0 63 63
HFE2 0.041 0.005 -10000 0 0 9 9
ZFYVE16 0.035 0.016 -10000 0 0 95 95
MAP3K7 0.038 0.012 -10000 0 0 47 47
BMP2-4/CHRD 0.055 0.045 -10000 0 -0.12 8 8
SMAD5/SMAD5/SMAD4 0.006 0.11 0.29 1 -0.27 46 47
MAPK1 0.039 0.011 -10000 0 0 43 43
TAK1/TAB family 0.027 0.12 -10000 0 -0.24 44 44
BMP7 (homodimer) 0.022 0.021 -10000 0 0 267 267
NUP214 0.039 0.01 -10000 0 0 32 32
BMP6/FETUA 0.044 0.028 -10000 0 -10000 0 0
SMAD1/SKI 0.023 0.1 -10000 0 -0.29 32 32
SMAD6 0.039 0.01 -10000 0 0 31 31
CTDSP2 0.039 0.011 -10000 0 0 42 42
BMP2-4/FETUA 0.055 0.045 -10000 0 -0.12 8 8
MAP3K7IP1 0.038 0.012 -10000 0 0 51 51
GREM1 0.034 0.016 -10000 0 0 98 98
BMPR2 (homodimer) 0.039 0.01 -10000 0 0 31 31
GADD34/PP1CA 0.056 0.056 -10000 0 -0.12 35 35
BMPR1A-1B (homodimer) 0.016 0.079 -10000 0 -0.15 90 90
CHRDL1 0.026 0.02 -10000 0 0 209 209
ENDOFIN/SMAD1 0.018 0.1 -10000 0 -0.3 29 29
SMAD6-7/SMURF1/SMAD1 0.048 0.11 -10000 0 -0.3 27 27
SMAD6/SMURF1 0.04 0.008 -10000 0 0 19 19
BAMBI 0.029 0.019 -10000 0 0 173 173
SMURF2 0.039 0.01 -10000 0 0 33 33
BMP2-4/CHRDL1 0.021 0.077 -10000 0 -0.12 100 100
BMP2-4/GREM1 0.054 0.049 -10000 0 -0.12 16 16
SMAD7 0.038 0.012 -10000 0 0 46 46
SMAD8A/SMAD8A/SMAD4 0.017 0.13 -10000 0 -0.39 45 45
SMAD1/SMAD6 0.023 0.1 -10000 0 -0.3 29 29
TAK1/SMAD6 0.051 0.036 -10000 0 -0.14 15 15
BMP7 0.022 0.021 -10000 0 0 267 267
BMP6 0.037 0.013 -10000 0 0 63 63
MAP3K7IP2 0.037 0.013 -10000 0 0 63 63
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.002 0.085 0.17 1 -0.24 38 39
PPM1A 0.041 0.007 -10000 0 0 16 16
SMAD1/SMURF2 0.021 0.1 -10000 0 -0.3 32 32
SMAD7/SMURF1 0.053 0.028 -10000 0 -0.14 7 7
CTDSPL 0.041 0.006 -10000 0 0 12 12
PPP1CA 0.041 0.006 -10000 0 0 13 13
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0.041 0.006 -10000 0 0 13 13
PPP1R15A 0.039 0.011 -10000 0 0 41 41
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.001 0.088 0.17 1 -0.23 43 44
CHRD 0.033 0.017 -10000 0 0 113 113
BMPR2 0.039 0.01 -10000 0 0 31 31
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.004 0.088 -10000 0 -0.24 39 39
BMP4 0.036 0.014 -10000 0 0 71 71
FST 0.033 0.017 -10000 0 0 122 122
BMP2-4/NOG 0.06 0.049 -10000 0 -0.12 20 20
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.017 0.11 -10000 0 -0.13 148 148
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.039 0.011 -9999 0 0 39 39
ITGB7 0.039 0.011 -9999 0 0 39 39
ITGA4 0.035 0.015 -9999 0 0 90 90
alpha4/beta7 Integrin 0.032 0.066 -9999 0 -0.14 65 65
alpha4/beta1 Integrin 0.032 0.065 -9999 0 -0.14 64 64
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.013 0.15 0.25 17 -0.33 59 76
FYN -0.03 0.18 0.24 16 -0.4 78 94
LAT/GRAP2/SLP76 -0.003 0.15 0.28 2 -0.33 68 70
IKBKB 0.038 0.011 -10000 0 0 44 44
AKT1 -0.015 0.14 0.22 10 -0.31 72 82
B2M 0.037 0.016 -10000 0 -0.002 75 75
IKBKG -0.002 0.05 0.12 11 -0.11 55 66
MAP3K8 0.04 0.008 -10000 0 0 22 22
mol:Ca2+ -0.014 0.014 0.043 9 -0.043 45 54
integrin-mediated signaling pathway 0.045 0.035 -10000 0 -0.11 22 22
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.026 0.18 0.24 10 -0.42 73 83
TRPV6 0.081 0.33 1.3 40 -10000 0 40
CD28 0.041 0.007 -10000 0 0 16 16
SHC1 -0.011 0.16 0.22 22 -0.36 66 88
receptor internalization -0.015 0.14 0.17 3 -0.33 74 77
PRF1 -0.01 0.21 -10000 0 -0.81 25 25
KRAS 0.034 0.016 -10000 0 0 103 103
GRB2 0.041 0.007 -10000 0 0 14 14
COT/AKT1 0.005 0.12 0.22 9 -0.26 70 79
LAT -0.017 0.16 0.23 10 -0.36 70 80
EntrezGene:6955 0.001 0.003 -10000 0 -0.022 3 3
CD3D 0.035 0.018 -10000 0 -0.001 105 105
CD3E 0.037 0.016 -10000 0 -0.001 81 81
CD3G 0.032 0.02 -10000 0 -0.002 134 134
RASGRP2 0.008 0.019 -10000 0 -0.14 2 2
RASGRP1 -0.023 0.15 0.22 11 -0.3 88 99
HLA-A 0.038 0.015 -10000 0 -0.002 67 67
RASSF5 0.039 0.01 -10000 0 0 33 33
RAP1A/GTP/RAPL 0.045 0.035 -10000 0 -0.11 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.06 0.15 16 -0.11 36 52
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.02 0.064 -10000 0 -0.16 76 76
PRKCA -0.01 0.082 0.18 14 -0.19 57 71
GRAP2 0.038 0.013 -10000 0 0 55 55
mol:IP3 -0.016 0.11 -10000 0 -0.26 69 69
EntrezGene:6957 0.001 0.004 -10000 0 -0.022 2 2
TCR/CD3/MHC I/CD8 -0.01 0.12 -10000 0 -0.36 43 43
ORAI1 -0.076 0.28 -10000 0 -1.1 40 40
CSK -0.014 0.16 0.23 11 -0.36 67 78
B7 family/CD28 0.027 0.16 0.33 1 -0.36 61 62
CHUK 0.038 0.012 -10000 0 0 52 52
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.023 0.17 0.2 4 -0.37 78 82
PTPN6 -0.011 0.16 0.2 32 -0.34 71 103
VAV1 -0.017 0.16 0.22 13 -0.38 68 81
Monovalent TCR/CD3 -0.004 0.082 -10000 0 -0.2 65 65
CBL 0.04 0.008 -10000 0 0 23 23
LCK -0.018 0.17 0.23 16 -0.38 74 90
PAG1 -0.009 0.16 0.21 32 -0.36 68 100
RAP1A 0.039 0.01 -10000 0 0 35 35
TCR/CD3/MHC I/CD8/LCK -0.022 0.16 0.2 4 -0.36 80 84
CD80 0.039 0.01 -10000 0 0 35 35
CD86 0.035 0.016 -10000 0 0 101 101
PDK1/CARD11/BCL10/MALT1 -0.007 0.084 -10000 0 -0.19 69 69
HRAS 0.04 0.009 -10000 0 0 29 29
GO:0035030 -0.013 0.13 0.19 16 -0.3 65 81
CD8A 0.042 0.01 -10000 0 -0.016 14 14
CD8B 0.001 0.004 -10000 0 -0.022 4 4
PTPRC 0.025 0.021 -10000 0 0 227 227
PDK1/PKC theta -0.021 0.16 0.25 9 -0.36 72 81
CSK/PAG1 -0.008 0.16 0.24 20 -0.37 61 81
SOS1 0.038 0.013 -10000 0 0 57 57
peptide-MHC class I 0.037 0.07 -10000 0 -0.18 44 44
GRAP2/SLP76 -0.001 0.17 0.25 5 -0.36 73 78
STIM1 -0.021 0.074 1.1 1 -10000 0 1
RAS family/GTP 0.01 0.077 0.18 4 -0.16 49 53
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.017 0.15 0.17 3 -0.34 74 77
mol:DAG -0.028 0.09 -10000 0 -0.24 71 71
RAP1A/GDP 0.01 0.033 0.079 12 -0.06 40 52
PLCG1 0.039 0.011 -10000 0 0 39 39
CD247 0.001 0.003 -10000 0 -0.022 3 3
cytotoxic T cell degranulation -0.008 0.2 -10000 0 -0.77 25 25
RAP1A/GTP 0.003 0.011 -10000 0 -0.045 8 8
mol:PI-3-4-5-P3 -0.018 0.16 0.22 11 -0.36 72 83
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.01 0.14 0.22 1 -0.32 68 69
NRAS 0.039 0.01 -10000 0 0 31 31
ZAP70 0.041 0.006 -10000 0 0 11 11
GRB2/SOS1 0.048 0.046 -10000 0 -0.14 26 26
LAT/GRAP2/SLP76/VAV1 -0.012 0.14 0.26 3 -0.33 71 74
MALT1 0.036 0.015 -10000 0 0 80 80
TRAF6 0.04 0.009 -10000 0 0 24 24
CD8 heterodimer 0.031 0.012 -10000 0 -0.038 7 7
CARD11 0.037 0.013 -10000 0 0 60 60
PRKCB -0.028 0.061 -10000 0 -0.17 71 71
PRKCE -0.007 0.083 0.18 16 -0.2 51 67
PRKCQ -0.023 0.17 0.23 9 -0.39 74 83
LCP2 0.034 0.016 -10000 0 0 100 100
BCL10 0.041 0.006 -10000 0 0 12 12
regulation of survival gene product expression -0.009 0.12 0.21 10 -0.27 72 82
IKK complex 0.003 0.049 0.14 15 -0.093 25 40
RAS family/GDP -0.002 0.014 -10000 0 -0.036 35 35
MAP3K14 -0.002 0.093 0.16 13 -0.2 69 82
PDPK1 -0.015 0.13 0.21 13 -0.3 72 85
TCR/CD3/MHC I/CD8/Fyn -0.038 0.2 -10000 0 -0.46 72 72
EPO signaling pathway

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
BCL2L1 0.029 0.14 0.33 2 -0.52 20 22
CRKL 0.028 0.089 0.18 122 -0.16 1 123
mol:DAG 0.044 0.073 0.21 5 -0.22 18 23
HRAS 0.022 0.099 0.26 41 -0.18 3 44
MAPK8 0.014 0.08 0.18 87 -0.14 2 89
RAP1A 0.027 0.088 0.18 121 -0.17 2 123
GAB1 0.025 0.086 0.18 113 -0.16 1 114
MAPK14 0.015 0.083 0.18 90 -0.14 2 92
EPO 0.046 0.016 0.083 6 -0.037 8 14
PLCG1 0.044 0.074 0.21 5 -0.22 18 23
EPOR/TRPC2/IP3 Receptors 0.04 0.019 0.087 4 -0.003 81 85
RAPGEF1 0.04 0.008 -10000 0 0 22 22
EPO/EPOR (dimer)/SOCS3 0.064 0.051 -10000 0 -0.13 16 16
GAB1/SHC/GRB2/SOS1 0.072 0.083 0.24 32 -0.16 6 38
EPO/EPOR (dimer) 0.057 0.032 -10000 0 -0.15 2 2
IRS2 0.027 0.088 0.18 118 -0.16 1 119
STAT1 0.035 0.095 0.25 3 -0.21 46 49
STAT5B 0.047 0.076 0.22 5 -0.2 22 27
cell proliferation 0.008 0.079 0.17 90 -0.13 2 92
GAB1/SHIP/PIK3R1/SHP2/SHC 0.036 0.061 0.16 2 -0.13 8 10
TEC 0.02 0.083 0.18 101 -0.17 8 109
SOCS3 0.037 0.014 -10000 0 0 67 67
STAT1 (dimer) 0.035 0.093 0.25 3 -0.21 46 49
JAK2 0.038 0.021 0.081 9 -0.001 112 121
PIK3R1 0.034 0.016 -10000 0 0 106 106
EPO/EPOR (dimer)/JAK2 0.065 0.069 0.24 29 -0.1 28 57
EPO/EPOR 0.057 0.032 -10000 0 -0.15 2 2
LYN 0.036 0.018 -10000 0 -0.004 92 92
TEC/VAV2 0.035 0.078 0.22 28 -0.15 14 42
elevation of cytosolic calcium ion concentration 0.04 0.019 0.087 4 -0.003 81 85
SHC1 0.04 0.009 -10000 0 0 29 29
EPO/EPOR (dimer)/LYN 0.062 0.061 -10000 0 -0.11 31 31
mol:IP3 0.044 0.073 0.21 5 -0.22 18 23
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.046 0.074 0.21 43 -0.13 4 47
SH2B3 0 0.008 0.033 11 -10000 0 11
NFKB1 0.011 0.077 0.19 73 -0.17 6 79
EPO/EPOR (dimer)/JAK2/SOCS3 0.013 0.05 0.21 2 -0.16 30 32
PTPN6 0.036 0.068 0.18 79 -0.1 26 105
TEC/VAV2/GRB2 0.053 0.086 0.23 32 -0.17 11 43
EPOR 0.04 0.019 0.087 4 -0.003 81 85
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.071 0.082 0.24 32 -0.16 6 38
SOS1 0.038 0.013 -10000 0 0 57 57
PLCG2 0.036 0.015 -10000 0 0 83 83
CRKL/CBL/C3G 0.073 0.078 0.24 41 -0.15 4 45
VAV2 0.026 0.088 0.18 115 -0.16 2 117
CBL 0.028 0.091 0.18 126 -0.23 1 127
SHC/Grb2/SOS1 0.037 0.056 0.17 1 -0.14 11 12
STAT5A 0.046 0.079 0.22 5 -0.21 25 30
GRB2 0.041 0.007 -10000 0 0 14 14
STAT5 (dimer) 0.062 0.091 0.28 3 -0.28 13 16
LYN/PLCgamma2 0.038 0.05 -10000 0 -0.13 33 33
PTPN11 0.04 0.009 -10000 0 0 29 29
BTK 0.027 0.089 0.18 120 -0.17 6 126
BCL2 0.031 0.12 0.33 2 -0.38 20 22
FAS signaling pathway (CD95)

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
SPTAN1 -0.025 0.062 0.2 4 -0.21 38 42
RFC1 -0.023 0.061 0.17 3 -0.22 37 40
PRKDC -0.019 0.071 0.2 17 -0.21 41 58
RIPK1 0.038 0.012 -10000 0 0 48 48
CASP7 0 0.12 -10000 0 -0.58 21 21
FASLG/FAS/FADD/FAF1 0.021 0.082 0.15 101 -0.17 38 139
MAP2K4 0.001 0.12 0.27 5 -0.33 35 40
mol:ceramide 0.017 0.095 -10000 0 -0.28 25 25
GSN -0.025 0.062 0.2 3 -0.21 40 43
FASLG/FAS/FADD/FAF1/Caspase 8 0.026 0.091 0.2 18 -0.24 20 38
FAS 0.035 0.018 -10000 0 -0.002 104 104
BID -0.034 0.024 0.23 2 -0.13 12 14
MAP3K1 -0.002 0.11 0.24 8 -0.37 30 38
MAP3K7 0.039 0.012 -10000 0 0 47 47
RB1 -0.026 0.062 0.16 3 -0.21 37 40
CFLAR 0.04 0.008 -10000 0 0 21 21
HGF/MET -0.014 0.092 -10000 0 -0.14 165 165
ARHGDIB -0.014 0.073 0.22 22 -0.22 27 49
FADD 0.041 0.012 -10000 0 -0.009 28 28
actin filament polymerization 0.025 0.061 0.21 40 -0.2 3 43
NFKB1 -0.053 0.24 -10000 0 -0.64 73 73
MAPK8 -0.002 0.12 0.3 3 -0.37 30 33
DFFA -0.022 0.068 0.2 9 -0.21 44 53
DNA fragmentation during apoptosis -0.023 0.062 0.18 6 -0.21 41 47
FAS/FADD/MET 0.017 0.089 -10000 0 -0.13 126 126
CFLAR/RIP1 0.052 0.032 -10000 0 -0.15 8 8
FAIM3 0.04 0.009 -10000 0 0 24 24
FAF1 0.041 0.014 -10000 0 -0.009 33 33
PARP1 -0.02 0.071 0.21 17 -0.21 39 56
DFFB -0.023 0.062 0.18 6 -0.21 41 47
CHUK -0.06 0.22 -10000 0 -0.61 72 72
FASLG 0.041 0.013 -10000 0 -0.013 28 28
FAS/FADD 0.037 0.061 -10000 0 -0.13 59 59
HGF 0.04 0.009 -10000 0 0 29 29
LMNA -0.02 0.068 0.19 14 -0.22 31 45
CASP6 -0.018 0.061 0.14 2 -0.24 26 28
CASP10 0.037 0.017 -10000 0 -0.004 75 75
CASP3 -0.023 0.066 0.16 4 -0.23 44 48
PTPN13 0.021 0.021 -10000 0 0 276 276
CASP8 -0.031 0.02 0.26 2 -10000 0 2
IL6 -0.047 0.25 -10000 0 -0.77 33 33
MET 0.027 0.02 -10000 0 0 195 195
ICAD/CAD -0.025 0.064 0.2 12 -0.2 43 55
FASLG/FAS/FADD/FAF1/Caspase 10 0.016 0.096 -10000 0 -0.29 25 25
activation of caspase activity by cytochrome c -0.034 0.024 0.23 2 -0.13 12 14
PAK2 -0.025 0.061 0.14 2 -0.21 42 44
BCL2 0.036 0.014 -10000 0 0 76 76
EPHB forward signaling

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
Ephrin A5/EPHB2 0.035 0.048 -10000 0 -0.12 43 43
cell-cell adhesion 0.041 0.041 0.12 82 -10000 0 82
Ephrin B/EPHB2/RasGAP 0.052 0.097 -10000 0 -0.12 104 104
ITSN1 0.041 0.007 -10000 0 0 16 16
PIK3CA 0.03 0.019 -10000 0 0 150 150
SHC1 0.04 0.009 -10000 0 0 29 29
Ephrin B1/EPHB3 0.037 0.038 -10000 0 -0.11 22 22
Ephrin B1/EPHB1 0.048 0.024 -10000 0 -0.11 5 5
HRAS/GDP -0.017 0.11 -10000 0 -0.18 128 128
Ephrin B/EPHB1/GRB7 0.057 0.09 -10000 0 -0.12 85 85
Endophilin/SYNJ1 -0.025 0.06 0.19 12 -0.2 6 18
KRAS 0.034 0.016 -10000 0 0 103 103
Ephrin B/EPHB1/Src 0.062 0.088 -10000 0 -0.12 79 79
endothelial cell migration 0.021 0.076 -10000 0 -0.11 99 99
GRB2 0.041 0.007 -10000 0 0 14 14
GRB7 0.037 0.013 -10000 0 0 62 62
PAK1 -0.018 0.073 0.18 29 -0.2 11 40
HRAS 0.04 0.009 -10000 0 0 29 29
RRAS -0.026 0.059 0.19 9 -0.2 12 21
DNM1 0.039 0.01 -10000 0 0 36 36
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.011 0.073 0.19 36 -0.18 5 41
lamellipodium assembly -0.041 0.041 -10000 0 -0.12 82 82
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.007 0.072 -10000 0 -0.23 12 12
PIK3R1 0.034 0.016 -10000 0 0 106 106
EPHB2 0.039 0.011 -10000 0 0 38 38
EPHB3 0.032 0.018 -10000 0 0 133 133
EPHB1 0.038 0.013 -10000 0 0 57 57
EPHB4 0.04 0.009 -10000 0 0 27 27
mol:GDP -0.042 0.097 0.19 14 -0.23 71 85
Ephrin B/EPHB2 0.048 0.081 -10000 0 -0.11 97 97
Ephrin B/EPHB3 0.035 0.077 -10000 0 -0.11 89 89
JNK cascade -0.004 0.098 0.28 49 -0.18 3 52
Ephrin B/EPHB1 0.049 0.075 -10000 0 -0.11 82 82
RAP1/GDP -0.025 0.12 0.31 4 -0.22 82 86
EFNB2 0.031 0.018 -10000 0 0 141 141
EFNB3 0.037 0.013 -10000 0 0 64 64
EFNB1 0.041 0.007 -10000 0 0 15 15
Ephrin B2/EPHB1-2 0.035 0.068 -10000 0 -0.11 77 77
RAP1B 0.038 0.013 -10000 0 0 57 57
RAP1A 0.039 0.01 -10000 0 0 35 35
CDC42/GTP 0.029 0.099 -10000 0 -0.16 84 84
Rap1/GTP -0.046 0.051 0.062 2 -0.2 15 17
axon guidance 0.034 0.048 -10000 0 -0.11 43 43
MAPK3 -0.003 0.069 0.2 7 -0.22 11 18
MAPK1 -0.002 0.068 0.19 7 -0.22 12 19
Rac1/GDP -0.029 0.11 0.26 8 -0.21 76 84
actin cytoskeleton reorganization -0.051 0.06 -10000 0 -0.16 72 72
CDC42/GDP -0.029 0.11 0.27 6 -0.22 78 84
PI3K 0.025 0.08 -10000 0 -0.12 99 99
EFNA5 0.034 0.016 -10000 0 0 103 103
Ephrin B2/EPHB4 0.023 0.061 -10000 0 -0.11 83 83
Ephrin B/EPHB2/Intersectin/N-WASP 0.001 0.079 -10000 0 -0.15 97 97
CDC42 0.04 0.008 -10000 0 0 22 22
RAS family/GTP -0.041 0.049 -10000 0 -0.19 15 15
PTK2 0.16 0.26 0.56 166 -0.18 1 167
MAP4K4 -0.004 0.099 0.28 49 -0.19 3 52
SRC 0.039 0.01 -10000 0 0 31 31
KALRN 0.038 0.012 -10000 0 0 53 53
Intersectin/N-WASP 0.057 0.023 -10000 0 -0.14 5 5
neuron projection morphogenesis -0.018 0.094 0.29 21 -0.21 15 36
MAP2K1 -0.001 0.066 0.21 2 -0.22 12 14
WASL 0.04 0.008 -10000 0 0 23 23
Ephrin B1/EPHB1-2/NCK1 0.076 0.065 -10000 0 -0.12 40 40
cell migration -0.009 0.09 0.26 7 -0.25 17 24
NRAS 0.039 0.01 -10000 0 0 31 31
SYNJ1 -0.025 0.06 0.19 12 -0.2 6 18
PXN 0.041 0.007 -10000 0 0 14 14
TF -0.029 0.054 0.17 11 -0.2 6 17
HRAS/GTP 0.032 0.081 -10000 0 -0.12 87 87
Ephrin B1/EPHB1-2 0.062 0.043 -10000 0 -0.11 18 18
cell adhesion mediated by integrin 0.01 0.065 0.17 12 -0.22 15 27
RAC1 0.039 0.01 -10000 0 0 35 35
mol:GTP 0.036 0.083 -10000 0 -0.12 89 89
RAC1-CDC42/GTP -0.041 0.046 -10000 0 -0.19 11 11
RASA1 0.036 0.014 -10000 0 0 73 73
RAC1-CDC42/GDP -0.018 0.11 0.28 6 -0.21 75 81
ruffle organization -0.021 0.082 0.22 17 -0.24 2 19
NCK1 0.036 0.014 -10000 0 0 77 77
receptor internalization -0.03 0.055 0.17 11 -0.19 7 18
Ephrin B/EPHB2/KALRN 0.059 0.093 -10000 0 -0.12 86 86
ROCK1 0.02 0.088 0.19 107 -10000 0 107
RAS family/GDP -0.056 0.063 -10000 0 -0.16 108 108
Rac1/GTP -0.04 0.047 0.051 3 -0.18 13 16
Ephrin B/EPHB1/Src/Paxillin 0.004 0.073 -10000 0 -0.15 79 79
Paxillin-independent events mediated by a4b1 and a4b7

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 0.068 0.14 13 -0.19 54 67
CRKL 0.039 0.01 -10000 0 0 35 35
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
DOCK1 0.037 0.013 -10000 0 0 63 63
ITGA4 0.035 0.015 -10000 0 0 90 90
alpha4/beta7 Integrin/MAdCAM1 0.065 0.074 -10000 0 -0.11 67 67
EPO 0.04 0.007 -10000 0 0 18 18
alpha4/beta7 Integrin 0.032 0.066 -10000 0 -0.14 65 65
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.038 0.011 -10000 0 0 45 45
alpha4/beta1 Integrin 0.032 0.065 -10000 0 -0.14 64 64
EPO/EPOR (dimer) 0.052 0.025 -10000 0 -0.14 2 2
lamellipodium assembly 0.016 0.11 0.21 1 -0.34 20 21
PIK3CA 0.03 0.019 -10000 0 0 150 150
PI3K 0.024 0.062 -10000 0 -0.15 47 47
ARF6 0.04 0.007 -10000 0 0 18 18
JAK2 0.006 0.066 -10000 0 -0.18 51 51
PXN 0.041 0.007 -10000 0 0 14 14
PIK3R1 0.034 0.016 -10000 0 0 106 106
MADCAM1 0.037 0.014 -10000 0 0 69 69
cell adhesion 0.063 0.073 -10000 0 -0.11 67 67
CRKL/CBL 0.055 0.02 -10000 0 -0.14 1 1
ITGB1 0.039 0.011 -10000 0 0 39 39
SRC -0.018 0.091 0.18 38 -0.19 39 77
ITGB7 0.039 0.011 -10000 0 0 39 39
RAC1 0.039 0.01 -10000 0 0 35 35
alpha4/beta1 Integrin/VCAM1 -0.006 0.095 -10000 0 -0.14 152 152
p130Cas/Crk/Dock1 0.012 0.1 0.22 21 -0.18 44 65
VCAM1 0.02 0.021 -10000 0 0 287 287
RHOA 0.041 0.007 -10000 0 0 14 14
alpha4/beta1 Integrin/Paxillin/GIT1 0.07 0.073 -10000 0 -0.11 63 63
BCAR1 -0.019 0.082 0.2 23 -0.18 39 62
EPOR 0.036 0.014 -10000 0 0 75 75
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.04 0.008 -10000 0 0 23 23
GIT1 0.04 0.008 -10000 0 0 23 23
Rac1/GTP 0.016 0.11 0.21 1 -0.36 20 21
HIF-2-alpha transcription factor network

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
MMP14 -0.054 0.3 -10000 0 -0.86 64 64
oxygen homeostasis 0.003 0.011 0.035 14 -0.025 3 17
TCEB2 0.04 0.008 -10000 0 0 22 22
TCEB1 0.038 0.012 -10000 0 0 49 49
VHL/Elongin B/Elongin C/HIF2A 0.04 0.13 0.29 9 -0.22 60 69
EPO 0.027 0.18 0.37 6 -0.34 41 47
FIH (dimer) 0.04 0.024 0.088 2 -0.035 35 37
APEX1 0.033 0.033 -10000 0 -0.035 78 78
SERPINE1 -0.008 0.16 0.36 8 -0.32 65 73
FLT1 -0.048 0.26 -10000 0 -0.71 70 70
ADORA2A 0.005 0.17 0.33 20 -0.31 59 79
germ cell development 0.008 0.18 0.36 14 -0.33 62 76
SLC11A2 0.01 0.19 0.35 14 -0.33 68 82
BHLHE40 0.012 0.18 0.33 21 -0.31 67 88
HIF1AN 0.04 0.023 0.088 2 -0.035 34 36
HIF2A/ARNT/SIRT1 0.04 0.16 0.32 8 -0.25 62 70
ETS1 0.043 0.026 0.12 1 -0.11 5 6
CITED2 0.015 0.15 -10000 0 -0.63 24 24
KDR -0.041 0.26 -10000 0 -0.71 66 66
PGK1 0.012 0.19 0.36 15 -0.34 71 86
SIRT1 0.041 0.008 -10000 0 0 19 19
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.062 0.23 0.46 1 -0.35 64 65
EPAS1 0.005 0.11 0.22 18 -0.22 72 90
SP1 0.034 0.049 -10000 0 -0.11 54 54
ABCG2 0.012 0.18 0.35 13 -0.32 64 77
EFNA1 0.002 0.19 0.35 13 -0.37 64 77
FXN 0.006 0.17 0.34 18 -0.31 63 81
POU5F1 0.006 0.18 0.36 13 -0.34 64 77
neuron apoptosis -0.061 0.22 0.34 64 -0.46 1 65
EP300 0.036 0.014 -10000 0 0 72 72
EGLN3 0.028 0.027 0.084 1 -0.034 22 23
EGLN2 0.04 0.023 0.09 2 -0.033 31 33
EGLN1 0.039 0.024 0.088 2 -0.035 34 36
VHL/Elongin B/Elongin C 0.069 0.039 -10000 0 -0.12 10 10
VHL 0.04 0.009 -10000 0 0 27 27
ARNT 0.035 0.033 -10000 0 -0.035 84 84
SLC2A1 -0.012 0.18 0.34 12 -0.33 78 90
TWIST1 0.004 0.17 0.34 17 -0.32 50 67
ELK1 0.047 0.013 -10000 0 -0.088 3 3
HIF2A/ARNT/Cbp/p300 0.04 0.16 0.33 10 -0.26 58 68
VEGFA 0.012 0.18 0.33 21 -0.31 67 88
CREBBP 0.038 0.012 -10000 0 0 49 49
E-cadherin 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
E-cadherin/beta catenin-gamma catenin 0.048 0.065 -9999 0 -0.12 49 49
E-cadherin/beta catenin 0.04 0.051 -9999 0 -0.14 35 35
CTNNB1 0.039 0.01 -9999 0 0 32 32
JUP 0.037 0.014 -9999 0 0 67 67
CDH1 0.035 0.016 -9999 0 0 96 96
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.04 0.15 -10000 0 -0.34 97 97
KLHL20 -0.015 0.1 0.2 13 -0.23 51 64
CYFIP2 0.038 0.011 -10000 0 0 45 45
Rac1/GDP -0.012 0.11 0.24 8 -0.25 48 56
ENAH -0.038 0.14 -10000 0 -0.33 95 95
AP1M1 0.036 0.015 -10000 0 0 78 78
RAP1B 0.038 0.013 -10000 0 0 57 57
RAP1A 0.039 0.01 -10000 0 0 35 35
CTNNB1 0.039 0.01 -10000 0 0 32 32
CDC42/GTP 0.002 0.08 0.16 4 -0.2 34 38
ABI1/Sra1/Nap1 -0.032 0.053 -10000 0 -0.16 60 60
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.068 0.068 -10000 0 -0.11 44 44
RAPGEF1 -0.037 0.13 0.28 3 -0.31 84 87
CTNND1 0.041 0.007 -10000 0 0 17 17
regulation of calcium-dependent cell-cell adhesion -0.03 0.16 -10000 0 -0.34 101 101
CRK -0.034 0.14 0.21 4 -0.32 86 90
E-cadherin/gamma catenin/alpha catenin 0.05 0.065 -10000 0 -0.14 42 42
alphaE/beta7 Integrin 0.05 0.038 -10000 0 -0.13 17 17
IQGAP1 0.037 0.014 -10000 0 0 67 67
NCKAP1 0.039 0.01 -10000 0 0 33 33
Rap1/GTP/I-afadin 0.042 0.065 -10000 0 -0.11 64 64
DLG1 -0.044 0.15 -10000 0 -0.34 102 102
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.034 0.048 -10000 0 -0.15 53 53
MLLT4 0.033 0.017 -10000 0 0 110 110
ARF6/GTP/NME1/Tiam1 0.046 0.062 -10000 0 -0.11 57 57
PI3K -0.04 0.063 -10000 0 -0.19 53 53
ARF6 0.04 0.007 -10000 0 0 18 18
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.038 0.052 -10000 0 -0.15 30 30
TIAM1 0.037 0.014 -10000 0 0 70 70
E-cadherin(dimer)/Ca2+ 0.063 0.072 -10000 0 -0.13 51 51
AKT1 -0.008 0.062 0.15 18 -0.16 18 36
PIK3R1 0.034 0.016 -10000 0 0 106 106
CDH1 0.035 0.016 -10000 0 0 96 96
RhoA/GDP -0.013 0.11 0.22 5 -0.25 50 55
actin cytoskeleton organization -0.009 0.076 0.16 14 -0.17 50 64
CDC42/GDP -0.012 0.11 0.25 7 -0.25 48 55
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.002 0.073 -10000 0 -0.19 55 55
ITGB7 0.039 0.011 -10000 0 0 39 39
RAC1 0.039 0.01 -10000 0 0 35 35
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.068 0.078 -10000 0 -0.14 51 51
E-cadherin/Ca2+/beta catenin/alpha catenin 0.046 0.056 -10000 0 -0.11 48 48
mol:GDP -0.031 0.11 0.24 7 -0.28 50 57
CDC42/GTP/IQGAP1 0.04 0.046 -10000 0 -0.11 40 40
JUP 0.037 0.014 -10000 0 0 67 67
p120 catenin/RhoA/GDP -0.001 0.12 0.23 4 -0.26 50 54
RAC1/GTP/IQGAP1 0.038 0.046 -10000 0 -0.11 40 40
PIP5K1C/AP1M1 0.048 0.027 -10000 0 -0.14 1 1
RHOA 0.041 0.007 -10000 0 0 14 14
CDC42 0.04 0.008 -10000 0 0 22 22
CTNNA1 0.039 0.01 -10000 0 0 36 36
positive regulation of S phase of mitotic cell cycle -0.015 0.059 0.12 4 -0.12 93 97
NME1 0.035 0.015 -10000 0 0 87 87
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.039 0.15 -10000 0 -0.34 93 93
regulation of cell-cell adhesion -0.009 0.065 -10000 0 -0.15 53 53
WASF2 -0.006 0.042 0.098 12 -0.093 44 56
Rap1/GTP 0.001 0.087 0.2 9 -0.24 26 35
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.072 0.082 -10000 0 -0.12 49 49
CCND1 -0.019 0.071 0.14 4 -0.15 93 97
VAV2 -0.047 0.21 -10000 0 -0.62 45 45
RAP1/GDP 0 0.098 0.23 8 -0.26 29 37
adherens junction assembly -0.039 0.14 -10000 0 -0.33 93 93
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.04 0.009 -10000 0 0 28 28
PIP5K1C 0.037 0.013 -10000 0 0 63 63
regulation of heterotypic cell-cell adhesion 0.046 0.076 0.22 6 -0.13 58 64
E-cadherin/beta catenin 0.007 0.04 0.15 1 -0.23 12 13
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.038 0.14 -10000 0 -0.33 94 94
PIK3CA 0.03 0.019 -10000 0 0 150 150
Rac1/GTP -0.054 0.13 -10000 0 -0.35 63 63
E-cadherin/beta catenin/alpha catenin 0.052 0.065 -10000 0 -0.13 48 48
ITGAE 0.039 0.01 -10000 0 0 34 34
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.031 0.16 -10000 0 -0.34 101 101
IL12-mediated 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
IL12/IL12R/TYK2/JAK2/SOCS1 0.032 0.1 0.22 16 -0.26 24 40
TBX21 -0.026 0.28 -10000 0 -0.72 47 47
B2M 0.038 0.014 -10000 0 -10000 0 0
TYK2 0.025 0.044 -10000 0 -0.058 38 38
IL12RB1 0.025 0.045 -10000 0 -0.058 43 43
GADD45B -0.057 0.35 -10000 0 -0.93 56 56
IL12RB2 0.028 0.045 -10000 0 -0.058 34 34
GADD45G -0.029 0.3 -10000 0 -0.84 41 41
natural killer cell activation 0.002 0.021 0.048 10 -0.038 50 60
RELB 0.04 0.009 -10000 0 0 25 25
RELA 0.041 0.006 -10000 0 0 10 10
IL18 0.03 0.025 -10000 0 -0.042 20 20
IL2RA 0.038 0.012 -10000 0 0 49 49
IFNG 0.037 0.013 -10000 0 0 59 59
STAT3 (dimer) -0.022 0.28 0.41 1 -0.64 63 64
HLA-DRB5 0.019 0.028 -10000 0 -0.008 262 262
FASLG -0.023 0.28 0.53 1 -0.76 42 43
NF kappa B2 p52/RelB -0.011 0.29 0.42 1 -0.68 57 58
CD4 0.025 0.028 -10000 0 -0.012 186 186
SOCS1 0.038 0.012 -10000 0 0 52 52
EntrezGene:6955 -0.001 0.01 -10000 0 -0.026 55 55
CD3D 0.027 0.03 -10000 0 -0.04 66 66
CD3E 0.028 0.029 -10000 0 -0.037 68 68
CD3G 0.026 0.029 -10000 0 -0.041 56 56
IL12Rbeta2/JAK2 0.031 0.073 -10000 0 -0.15 29 29
CCL3 -0.042 0.32 -10000 0 -0.9 48 48
CCL4 -0.026 0.28 -10000 0 -0.67 57 57
HLA-A 0.038 0.014 -10000 0 -10000 0 0
IL18/IL18R 0.061 0.081 -10000 0 -0.12 73 73
NOS2 -0.023 0.27 0.45 1 -0.6 65 66
IL12/IL12R/TYK2/JAK2/SPHK2 0.031 0.1 0.22 16 -0.25 24 40
IL1R1 -0.1 0.43 -10000 0 -0.99 91 91
IL4 0.019 0.044 0.099 1 -0.063 15 16
JAK2 0.023 0.042 -10000 0 -0.058 39 39
EntrezGene:6957 -0.001 0.009 -10000 0 -0.025 20 20
TCR/CD3/MHC I/CD8 -0.012 0.11 -10000 0 -0.46 21 21
RAB7A -0.029 0.27 -10000 0 -0.61 71 71
lysosomal transport -0.025 0.26 0.39 1 -0.58 71 72
FOS -0.18 0.51 -10000 0 -1.1 117 117
STAT4 (dimer) -0.017 0.29 0.42 2 -0.67 60 62
STAT5A (dimer) -0.019 0.28 0.42 1 -0.68 55 56
GZMA -0.05 0.34 -10000 0 -0.95 51 51
GZMB -0.033 0.31 0.56 1 -0.86 47 48
HLX 0 0 -10000 0 -10000 0 0
LCK -0.032 0.29 0.42 3 -0.71 56 59
TCR/CD3/MHC II/CD4 -0.07 0.2 -10000 0 -0.38 133 133
IL2/IL2R 0.046 0.082 -10000 0 -0.11 92 92
MAPK14 -0.045 0.32 -10000 0 -0.74 70 70
CCR5 -0.017 0.25 0.42 1 -0.55 67 68
IL1B 0.023 0.042 -10000 0 -0.059 30 30
STAT6 0.011 0.14 -10000 0 -0.61 13 13
STAT4 0.04 0.009 -10000 0 0 28 28
STAT3 0.038 0.012 -10000 0 0 52 52
STAT1 0.034 0.017 -10000 0 0 108 108
NFKB1 0.035 0.015 -10000 0 0 85 85
NFKB2 0.04 0.008 -10000 0 0 23 23
IL12B 0.028 0.045 -10000 0 -0.057 43 43
CD8A 0.042 0.005 -10000 0 -10000 0 0
CD8B 0.001 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.032 0.1 0.25 24 -0.22 16 40
IL2RB 0.037 0.014 -10000 0 0 70 70
proteasomal ubiquitin-dependent protein catabolic process -0.011 0.27 0.42 2 -0.62 60 62
IL2RG 0.028 0.02 -10000 0 0 181 181
IL12 0.024 0.071 -10000 0 -0.15 31 31
STAT5A 0.038 0.012 -10000 0 0 50 50
CD247 -0.001 0.009 -10000 0 -0.025 20 20
IL2 0.038 0.012 -10000 0 0 47 47
SPHK2 0.04 0.008 -10000 0 0 23 23
FRAP1 0.04 0.009 -10000 0 0 24 24
IL12A 0.02 0.04 -10000 0 -0.058 31 31
IL12/IL12R/TYK2/JAK2 -0.043 0.29 -10000 0 -0.75 57 57
MAP2K3 -0.048 0.34 -10000 0 -0.77 69 69
RIPK2 0.032 0.018 -10000 0 0 125 125
MAP2K6 -0.052 0.32 -10000 0 -0.72 72 72
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.023 0.029 -10000 0 -0.011 205 205
IL18RAP 0.04 0.019 -10000 0 -0.042 24 24
IL12Rbeta1/TYK2 0.039 0.057 -10000 0 -0.091 2 2
EOMES 0.003 0.079 -10000 0 -0.59 4 4
STAT1 (dimer) -0.039 0.29 0.42 1 -0.66 65 66
T cell proliferation -0.016 0.24 0.37 2 -0.51 65 67
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.04 0.019 -10000 0 -0.042 23 23
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.029 0.25 -10000 0 -0.56 66 66
ATF2 -0.042 0.3 0.58 1 -0.69 72 73
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 0.007 0.051 -10000 0 -0.15 39 39
EPHB2 0.039 0.011 -10000 0 0 38 38
Syndecan-2/TACI 0.025 0.041 -10000 0 -0.11 38 38
LAMA1 0.034 0.017 -10000 0 0 108 108
Syndecan-2/alpha2 ITGB1 0.039 0.086 0.19 37 -0.12 81 118
HRAS 0.04 0.009 -10000 0 0 29 29
Syndecan-2/CASK 0.001 0.028 -10000 0 -0.098 39 39
ITGA5 0.037 0.013 -10000 0 0 58 58
BAX 0.021 0.067 -10000 0 -10000 0 0
EPB41 0.039 0.01 -10000 0 0 33 33
positive regulation of cell-cell adhesion 0.016 0.046 -10000 0 -0.098 66 66
LAMA3 0.031 0.018 -10000 0 0 147 147
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.033 0.017 -10000 0 0 111 111
Syndecan-2/MMP2 0.007 0.052 -10000 0 -0.16 39 39
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.034 0.057 -10000 0 -0.14 44 44
dendrite morphogenesis 0.025 0.043 -10000 0 -0.12 37 37
Syndecan-2/GM-CSF 0.026 0.041 -10000 0 -0.11 38 38
determination of left/right symmetry 0.01 0.007 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.024 0.041 -10000 0 -0.11 37 37
GNB2L1 0.041 0.005 -10000 0 0 7 7
MAPK3 0.01 0.075 0.2 64 -10000 0 64
MAPK1 0.011 0.075 0.2 64 -10000 0 64
Syndecan-2/RACK1 0.041 0.047 -10000 0 -0.094 41 41
NF1 0.034 0.016 -10000 0 0 98 98
FGFR/FGF/Syndecan-2 0.01 0.007 -10000 0 -10000 0 0
ITGA2 0.033 0.017 -10000 0 0 122 122
MAPK8 0 0.02 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.052 0.077 0.19 42 -0.11 52 94
Syndecan-2/Kininogen 0.022 0.039 -10000 0 -0.11 34 34
ITGB1 0.039 0.011 -10000 0 0 39 39
SRC 0.007 0.074 0.19 68 -10000 0 68
Syndecan-2/CASK/Protein 4.1 0.023 0.037 -10000 0 -0.094 41 41
extracellular matrix organization 0.024 0.041 -10000 0 -0.11 35 35
actin cytoskeleton reorganization 0.007 0.051 -10000 0 -0.15 39 39
Syndecan-2/Caveolin-2/Ras 0.03 0.059 -10000 0 -0.11 59 59
Syndecan-2/Laminin alpha3 0.019 0.044 -10000 0 -0.13 32 32
Syndecan-2/RasGAP 0.063 0.069 -10000 0 -0.097 51 51
alpha5/beta1 Integrin 0.045 0.046 -10000 0 -0.14 28 28
PRKCD 0.038 0.013 -10000 0 0 55 55
Syndecan-2 dimer 0.025 0.043 -10000 0 -0.12 37 37
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.038 0.058 0.2 1 -10000 0 1
RHOA 0.041 0.007 -10000 0 0 14 14
SDCBP 0.036 0.014 -10000 0 0 77 77
TNFRSF13B 0.039 0.011 -10000 0 0 38 38
RASA1 0.036 0.014 -10000 0 0 73 73
alpha2/beta1 Integrin 0.034 0.057 -10000 0 -0.14 44 44
Syndecan-2/Synbindin 0.021 0.042 -10000 0 -0.11 37 37
TGFB1 0.037 0.013 -10000 0 0 61 61
CASP3 0.004 0.07 0.2 50 -0.18 1 51
FN1 0.021 0.021 -10000 0 0 273 273
Syndecan-2/IL8 0.018 0.043 -10000 0 -0.12 35 35
SDC2 0.01 0.007 -10000 0 -10000 0 0
KNG1 0.034 0.017 -10000 0 0 108 108
Syndecan-2/Neurofibromin 0.022 0.042 -10000 0 -0.12 34 34
TRAPPC4 0.034 0.016 -10000 0 0 98 98
CSF2 0.04 0.009 -10000 0 0 24 24
Syndecan-2/TGFB1 0.024 0.042 -10000 0 -0.11 35 35
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.046 -10000 0 -0.098 66 66
Syndecan-2/Ezrin 0.024 0.038 -10000 0 -0.094 42 42
PRKACA 0.001 0.071 0.2 46 -0.18 3 49
angiogenesis 0.018 0.043 -10000 0 -0.12 35 35
MMP2 0.021 0.021 -10000 0 0 269 269
IL8 0.031 0.018 -10000 0 0 137 137
calcineurin-NFAT signaling pathway 0.025 0.041 -10000 0 -0.11 38 38
Retinoic acid receptors-mediated signaling

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
HDAC1 0.038 0.012 -10000 0 0 54 54
HDAC3 0.041 0.006 -10000 0 0 12 12
VDR 0.037 0.013 -10000 0 0 58 58
Cbp/p300/PCAF 0.04 0.043 -10000 0 -0.14 24 24
EP300 0.036 0.014 -10000 0 0 72 72
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.012 0.096 0.18 1 -0.26 48 49
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.04 0.009 -10000 0 0 28 28
AKT1 0.011 0.092 0.21 19 -0.21 27 46
RAR alpha/9cRA/Cyclin H -0.003 0.12 -10000 0 -0.25 70 70
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.002 0.078 -10000 0 -0.21 48 48
CDC2 0.026 0.024 -10000 0 -0.005 192 192
response to UV -0.001 0.008 -10000 0 -0.026 43 43
RAR alpha/Jnk1 0.017 0.069 -10000 0 -0.16 45 45
NCOR2 0.04 0.009 -10000 0 0 26 26
VDR/VDR/Vit D3 0.022 0.032 -10000 0 -0.13 23 23
RXRs/RARs/NRIP1/9cRA -0.039 0.19 -10000 0 -0.5 61 61
NCOA2 0.037 0.014 -10000 0 0 69 69
NCOA3 0.036 0.014 -10000 0 0 77 77
NCOA1 0.04 0.009 -10000 0 0 28 28
VDR/VDR/DNA 0.037 0.013 -10000 0 0 58 58
RARG 0.035 0.021 -10000 0 -0.018 69 69
RAR gamma1/9cRA 0.042 0.033 -10000 0 -0.11 15 15
MAPK3 0.035 0.022 -10000 0 -0.026 60 60
MAPK1 0.039 0.011 -10000 0 0 43 43
MAPK8 0.034 0.024 -10000 0 -0.026 70 70
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.014 0.14 -10000 0 -0.32 77 77
RARA 0.006 0.054 -10000 0 -0.16 42 42
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.004 0.081 -10000 0 -0.25 37 37
PRKCA 0.03 0.032 -10000 0 -0.072 36 36
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.046 0.2 -10000 0 -0.55 61 61
RXRG 0.014 0.059 -10000 0 -0.19 31 31
RXRA -0.027 0.096 -10000 0 -0.24 52 52
RXRB 0.011 0.061 -10000 0 -0.2 35 35
VDR/Vit D3/DNA 0.022 0.032 -10000 0 -0.13 23 23
RBP1 0.03 0.019 -10000 0 0 159 159
CRBP1/9-cic-RA 0.002 0.057 -10000 0 -0.13 89 89
RARB 0.032 0.026 -10000 0 -0.015 117 117
PRKCG 0.035 0.032 -10000 0 -0.071 45 45
MNAT1 0.04 0.008 -10000 0 0 22 22
RAR alpha/RXRs -0.016 0.16 0.28 3 -0.36 75 78
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.01 0.13 0.23 1 -0.29 64 65
proteasomal ubiquitin-dependent protein catabolic process -0.012 0.1 0.17 3 -0.27 47 50
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.046 0.2 -10000 0 -0.55 61 61
positive regulation of DNA binding -0.01 0.11 -10000 0 -0.23 74 74
NRIP1 -0.083 0.32 -10000 0 -0.98 55 55
RXRs/RARs -0.028 0.17 -10000 0 -0.39 78 78
RXRs/RXRs/DNA/9cRA -0.032 0.14 -10000 0 -0.32 82 82
PRKACA 0.035 0.015 -10000 0 0 87 87
CDK7 0.035 0.016 -10000 0 0 94 94
TFIIH 0.059 0.055 -10000 0 -0.14 25 25
RAR alpha/9cRA 0.035 0.087 -10000 0 -0.22 20 20
CCNH 0.037 0.014 -10000 0 0 69 69
CREBBP 0.038 0.012 -10000 0 0 49 49
RAR gamma2/9cRA 0.043 0.062 -10000 0 -0.13 36 36
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.067 0.065 -10000 0 -0.1 53 53
ER alpha/Gai/GDP/Gbeta gamma -0.022 0.13 -10000 0 -0.34 43 43
AKT1 -0.089 0.27 -10000 0 -0.64 101 101
PIK3CA 0.03 0.019 -10000 0 0 150 150
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.089 0.28 -10000 0 -0.65 102 102
mol:Ca2+ -0.007 0.071 0.18 9 -0.28 24 33
IGF1R 0.033 0.017 -10000 0 0 116 116
E2/ER alpha (dimer)/Striatin 0.035 0.05 -10000 0 -0.11 49 49
SHC1 0.04 0.009 -10000 0 0 29 29
apoptosis 0.085 0.26 0.61 101 -10000 0 101
RhoA/GTP 0.014 0.048 -10000 0 -0.11 57 57
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.006 0.14 -10000 0 -0.29 64 64
regulation of stress fiber formation 0.015 0.07 0.16 14 -0.15 62 76
E2/ERA-ERB (dimer) 0.037 0.046 -10000 0 -0.11 42 42
KRAS 0.034 0.016 -10000 0 0 103 103
G13/GTP 0.033 0.046 -10000 0 -0.1 51 51
pseudopodium formation -0.015 0.07 0.15 62 -0.16 14 76
E2/ER alpha (dimer)/PELP1 0.036 0.046 -10000 0 -0.11 42 42
GRB2 0.041 0.007 -10000 0 0 14 14
GNG2 0.039 0.01 -10000 0 0 34 34
GNAO1 0.034 0.016 -10000 0 0 101 101
HRAS 0.04 0.009 -10000 0 0 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.037 0.16 -10000 0 -0.38 79 79
E2/ER beta (dimer) 0.03 0.005 -10000 0 -10000 0 0
mol:GDP -0.005 0.079 0.14 3 -0.22 55 58
mol:NADP -0.037 0.16 -10000 0 -0.38 79 79
PIK3R1 0.034 0.016 -10000 0 0 106 106
mol:IP3 -0.005 0.07 0.18 6 -0.29 25 31
IGF-1R heterotetramer 0.033 0.017 -10000 0 0 116 116
PLCB1 0.003 0.069 -10000 0 -0.3 24 24
PLCB2 0.004 0.067 -10000 0 -0.28 26 26
IGF1 0.036 0.015 -10000 0 0 82 82
mol:L-citrulline -0.037 0.16 -10000 0 -0.38 79 79
RHOA 0.041 0.007 -10000 0 0 14 14
Gai/GDP -0.017 0.19 -10000 0 -0.58 55 55
JNK cascade 0.03 0.005 -10000 0 -10000 0 0
BCAR1 0.036 0.014 -10000 0 0 74 74
ESR2 0.041 0.007 -10000 0 0 17 17
GNAQ 0.038 0.012 -10000 0 0 50 50
ESR1 0.035 0.016 -10000 0 0 92 92
Gq family/GDP/Gbeta gamma -0.04 0.23 -10000 0 -0.63 67 67
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.024 0.1 -10000 0 -0.65 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.007 0.14 -10000 0 -0.29 66 66
GNAZ 0.039 0.011 -10000 0 0 38 38
E2/ER alpha (dimer) 0.016 0.042 -10000 0 -0.13 42 42
STRN 0.039 0.01 -10000 0 0 31 31
GNAL 0.04 0.009 -10000 0 0 27 27
PELP1 0.04 0.009 -10000 0 0 29 29
MAPK11 0.014 0.008 0.069 1 -10000 0 1
GNAI2 0.041 0.006 -10000 0 0 13 13
GNAI3 0.038 0.012 -10000 0 0 46 46
GNAI1 0.035 0.016 -10000 0 0 94 94
HBEGF -0.017 0.14 0.31 15 -0.34 46 61
cAMP biosynthetic process 0.032 0.038 -10000 0 -0.092 39 39
SRC -0.022 0.13 0.24 3 -0.34 43 46
PI3K 0.024 0.062 -10000 0 -0.15 47 47
GNB1 0.041 0.005 -10000 0 0 7 7
G13/GDP/Gbeta gamma 0.04 0.095 -10000 0 -0.2 54 54
SOS1 0.038 0.013 -10000 0 0 57 57
IGF-1R heterotetramer/IGF1 -0.038 0.1 -10000 0 -0.25 65 65
Gs family/GTP 0.041 0.043 -10000 0 -0.093 39 39
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.054 0.05 -10000 0 -0.11 28 28
vasodilation -0.035 0.15 -10000 0 -0.36 79 79
mol:DAG -0.005 0.07 0.18 6 -0.29 25 31
Gs family/GDP/Gbeta gamma 0.003 0.081 -10000 0 -0.21 50 50
MSN -0.017 0.072 0.15 60 -0.17 15 75
Gq family/GTP 0.017 0.073 -10000 0 -0.28 26 26
mol:PI-3-4-5-P3 -0.085 0.27 -10000 0 -0.62 104 104
NRAS 0.039 0.01 -10000 0 0 31 31
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.035 0.15 0.36 79 -10000 0 79
GRB2/SOS1 0.048 0.046 -10000 0 -0.14 26 26
RhoA/GDP 0.013 0.09 -10000 0 -0.21 57 57
NOS3 -0.039 0.17 -10000 0 -0.4 78 78
GNA11 0.037 0.013 -10000 0 0 63 63
MAPKKK cascade -0.027 0.18 -10000 0 -0.46 76 76
E2/ER alpha (dimer)/PELP1/Src -0.012 0.14 0.25 1 -0.3 69 70
ruffle organization -0.015 0.07 0.15 62 -0.16 14 76
ROCK2 -0.008 0.082 0.18 70 -0.17 8 78
GNA14 0.039 0.01 -10000 0 0 33 33
GNA15 0.037 0.014 -10000 0 0 69 69
GNA13 0.04 0.009 -10000 0 0 28 28
MMP9 -0.018 0.14 0.35 17 -0.33 45 62
MMP2 -0.019 0.13 0.25 5 -0.35 38 43
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.047 0.14 -10000 0 -0.34 62 62
IKBKB 0.018 0.097 0.26 9 -0.26 20 29
AKT1 0.024 0.093 0.23 44 -0.18 9 53
IKBKG 0.02 0.078 0.23 1 -0.26 12 13
CALM1 -0.011 0.12 0.2 9 -0.35 38 47
PIK3CA 0.03 0.019 -10000 0 0 150 150
MAP3K1 -0.046 0.16 -10000 0 -0.46 45 45
MAP3K7 0.038 0.012 -10000 0 0 47 47
mol:Ca2+ -0.01 0.12 0.21 4 -0.36 41 45
DOK1 0.04 0.009 -10000 0 0 24 24
AP-1 -0.023 0.093 -10000 0 -0.22 55 55
LYN 0.035 0.015 -10000 0 0 83 83
BLNK 0.037 0.014 -10000 0 0 67 67
SHC1 0.04 0.009 -10000 0 0 29 29
BCR complex 0.053 0.024 -10000 0 -0.13 3 3
CD22 -0.011 0.087 -10000 0 -0.26 38 38
CAMK2G -0.014 0.11 0.2 12 -0.34 37 49
CSNK2A1 0.039 0.011 -10000 0 0 40 40
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.021 0.063 -10000 0 -0.13 58 58
GO:0007205 -0.011 0.13 0.21 4 -0.37 42 46
SYK 0.037 0.014 -10000 0 0 67 67
ELK1 -0.015 0.12 0.22 3 -0.36 41 44
NFATC1 -0.025 0.11 0.22 3 -0.28 48 51
B-cell antigen/BCR complex 0.053 0.024 -10000 0 -0.13 3 3
PAG1/CSK 0.052 0.027 -10000 0 -0.14 5 5
NFKBIB 0.011 0.067 0.13 2 -0.13 84 86
HRAS -0.009 0.098 0.25 3 -0.28 39 42
NFKBIA 0.014 0.062 0.12 3 -0.12 72 75
NF-kappa-B/RelA/I kappa B beta 0.02 0.059 0.12 5 -0.1 78 83
RasGAP/Csk 0.056 0.088 -10000 0 -0.11 84 84
mol:GDP -0.01 0.12 0.21 4 -0.36 41 45
PTEN 0.039 0.011 -10000 0 0 39 39
CD79B 0.04 0.008 -10000 0 0 19 19
NF-kappa-B/RelA/I kappa B alpha 0.022 0.056 0.12 5 -0.1 68 73
GRB2 0.041 0.007 -10000 0 0 14 14
PI3K/BCAP/CD19 -0.026 0.15 -10000 0 -0.41 42 42
PIK3R1 0.034 0.016 -10000 0 0 106 106
mol:IP3 -0.007 0.12 0.21 4 -0.38 39 43
CSK 0.04 0.008 -10000 0 0 22 22
FOS -0.016 0.12 0.22 6 -0.34 44 50
CHUK -0.003 0.12 0.23 1 -0.29 53 54
IBTK 0.037 0.014 -10000 0 0 66 66
CARD11/BCL10/MALT1/TAK1 0.014 0.12 -10000 0 -0.31 41 41
PTPN6 -0.003 0.089 0.18 29 -0.26 28 57
RELA 0.041 0.006 -10000 0 0 10 10
BCL2A1 0.014 0.044 0.1 5 -0.078 72 77
VAV2 -0.021 0.11 -10000 0 -0.31 51 51
ubiquitin-dependent protein catabolic process 0.015 0.065 0.13 1 -0.12 84 85
BTK -0.036 0.25 -10000 0 -1.1 31 31
CD19 -0.019 0.095 -10000 0 -0.28 41 41
MAP4K1 0.039 0.011 -10000 0 0 43 43
CD72 0.04 0.008 -10000 0 0 20 20
PAG1 0.038 0.013 -10000 0 0 55 55
MAPK14 -0.038 0.15 0.31 1 -0.4 44 45
SH3BP5 0.04 0.008 -10000 0 0 23 23
PIK3AP1 -0.009 0.12 0.24 4 -0.38 39 43
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.018 0.17 -10000 0 -0.53 39 39
RAF1 -0.013 0.093 0.24 5 -0.27 37 42
RasGAP/p62DOK/SHIP 0.044 0.078 -10000 0 -0.11 87 87
CD79A 0.037 0.013 -10000 0 0 57 57
re-entry into mitotic cell cycle -0.023 0.092 -10000 0 -0.21 56 56
RASA1 0.036 0.014 -10000 0 0 73 73
MAPK3 -0.019 0.083 0.23 6 -0.26 32 38
MAPK1 -0.017 0.082 0.22 7 -0.25 31 38
CD72/SHP1 0.025 0.12 0.29 22 -0.26 29 51
NFKB1 0.035 0.015 -10000 0 0 85 85
MAPK8 -0.043 0.14 -10000 0 -0.39 46 46
actin cytoskeleton organization -0.023 0.11 0.24 3 -0.29 50 53
NF-kappa-B/RelA 0.032 0.12 0.24 1 -0.22 79 80
Calcineurin 0.013 0.12 0.25 2 -0.3 41 43
PI3K -0.01 0.075 -10000 0 -0.25 19 19
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.001 0.12 0.22 4 -0.37 39 43
SOS1 0.038 0.013 -10000 0 0 57 57
Bam32/HPK1 -0.054 0.25 -10000 0 -0.68 64 64
DAPP1 -0.077 0.27 -10000 0 -0.76 63 63
cytokine secretion -0.023 0.1 0.21 3 -0.27 47 50
mol:DAG -0.007 0.12 0.21 4 -0.38 39 43
PLCG2 0.036 0.015 -10000 0 0 83 83
MAP2K1 -0.016 0.089 0.24 6 -0.27 34 40
B-cell antigen/BCR complex/FcgammaRIIB 0.038 0.071 -10000 0 -0.12 73 73
mol:PI-3-4-5-P3 0.01 0.093 0.22 34 -0.23 10 44
ETS1 -0.012 0.11 0.24 9 -0.32 38 47
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.07 0.083 -10000 0 -0.12 50 50
B-cell antigen/BCR complex/LYN -0.012 0.1 -10000 0 -0.29 42 42
MALT1 0.036 0.015 -10000 0 0 80 80
TRAF6 0.04 0.009 -10000 0 0 24 24
RAC1 -0.023 0.11 0.25 3 -0.3 48 51
B-cell antigen/BCR complex/LYN/SYK 0.053 0.11 0.31 20 -0.24 17 37
CARD11 -0.011 0.12 0.22 8 -0.36 40 48
FCGR2B 0.03 0.019 -10000 0 0 158 158
PPP3CA 0.037 0.013 -10000 0 0 63 63
BCL10 0.041 0.006 -10000 0 0 12 12
IKK complex 0.018 0.052 0.14 22 -0.11 18 40
PTPRC 0.025 0.021 -10000 0 0 227 227
PDPK1 0.014 0.082 0.2 46 -0.16 9 55
PPP3CB 0.04 0.009 -10000 0 0 30 30
PPP3CC 0.033 0.017 -10000 0 0 114 114
POU2F2 0.013 0.043 0.11 3 -0.075 76 79
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.039 0.087 0.25 1 -0.14 63 64
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.039 0.01 -10000 0 0 35 35
STAT1 (dimer)/Cbp/p300 0.007 0.12 0.3 5 -0.21 81 86
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.04 0.08 -10000 0 -0.15 62 62
antigen processing and presentation of peptide antigen via MHC class I -0.025 0.093 -10000 0 -0.2 82 82
CaM/Ca2+ 0.042 0.088 0.23 1 -0.14 61 62
RAP1A 0.039 0.01 -10000 0 0 35 35
STAT1 (dimer)/SHP2 0.002 0.095 0.21 10 -0.19 60 70
AKT1 0.009 0.11 0.23 38 -0.22 30 68
MAP2K1 -0.024 0.07 0.14 31 -0.18 33 64
MAP3K11 -0.017 0.077 0.19 14 -0.18 23 37
IFNGR1 0.034 0.022 0.083 1 -0.037 16 17
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.011 0.1 -10000 0 -0.29 40 40
Rap1/GTP -0.043 0.057 0.07 8 -0.18 44 52
CRKL/C3G 0.056 0.018 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.061 0.09 -10000 0 -0.14 57 57
CEBPB -0.025 0.17 0.28 1 -0.43 56 57
STAT3 0.038 0.012 -10000 0 0 52 52
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.045 0.16 -10000 0 -0.77 16 16
STAT1 -0.024 0.085 0.21 12 -0.21 44 56
CALM1 0.04 0.009 -10000 0 0 30 30
IFN-gamma (dimer) 0.032 0.025 0.082 2 -0.039 43 45
PIK3CA 0.03 0.019 -10000 0 0 150 150
STAT1 (dimer)/PIAS1 -0.007 0.095 0.24 7 -0.2 51 58
CEBPB/PTGES2/Cbp/p300 -0.009 0.12 -10000 0 -0.29 56 56
mol:Ca2+ 0.036 0.084 0.23 1 -0.14 63 64
MAPK3 -0.017 0.14 -10000 0 -0.65 14 14
STAT1 (dimer) -0.022 0.13 0.19 1 -0.28 81 82
MAPK1 -0.05 0.21 0.43 1 -0.74 38 39
JAK2 0.032 0.022 -10000 0 -0.038 20 20
PIK3R1 0.034 0.016 -10000 0 0 106 106
JAK1 0.036 0.023 0.082 1 -0.038 34 35
CAMK2D 0.036 0.015 -10000 0 0 81 81
DAPK1 -0.023 0.16 -10000 0 -0.49 46 46
SMAD7 -0.002 0.072 0.16 34 -0.13 46 80
CBL/CRKL/C3G 0.031 0.088 0.24 9 -0.17 31 40
PI3K 0.021 0.092 0.21 1 -0.2 43 44
IFNG 0.032 0.025 0.082 2 -0.039 44 46
apoptosis -0.02 0.15 -10000 0 -0.42 54 54
CAMK2G 0.04 0.008 -10000 0 0 23 23
STAT3 (dimer) 0.038 0.012 -10000 0 0 52 52
CAMK2A 0.041 0.006 -10000 0 0 11 11
CAMK2B 0.04 0.007 -10000 0 0 18 18
FRAP1 0 0.1 0.2 44 -0.21 33 77
PRKCD 0.007 0.11 0.24 36 -0.23 31 67
RAP1B 0.038 0.013 -10000 0 0 57 57
negative regulation of cell growth -0.025 0.093 -10000 0 -0.2 82 82
PTPN2 0.04 0.008 -10000 0 0 23 23
EP300 0.036 0.014 -10000 0 0 72 72
IRF1 -0.043 0.1 0.22 10 -0.25 69 79
STAT1 (dimer)/PIASy -0.025 0.091 0.21 11 -0.22 33 44
SOCS1 0 0.19 -10000 0 -1.1 16 16
mol:GDP 0.027 0.083 0.22 9 -0.16 31 40
CASP1 -0.021 0.082 0.17 17 -0.17 96 113
PTGES2 0.04 0.009 -10000 0 0 25 25
IRF9 -0.007 0.053 0.12 11 -0.12 49 60
mol:PI-3-4-5-P3 0.007 0.082 -10000 0 -0.18 54 54
RAP1/GDP 0.018 0.087 0.24 1 -0.18 44 45
CBL -0.015 0.077 0.17 33 -0.18 21 54
MAP3K1 -0.016 0.074 0.16 28 -0.18 27 55
PIAS1 0.04 0.009 -10000 0 0 28 28
PIAS4 0.037 0.013 -10000 0 0 56 56
antigen processing and presentation of peptide antigen via MHC class II -0.025 0.093 -10000 0 -0.2 82 82
PTPN11 -0.01 0.078 0.17 47 -0.18 24 71
CREBBP 0.038 0.012 -10000 0 0 49 49
RAPGEF1 0.04 0.008 -10000 0 0 22 22
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.014 0.17 -10000 0 -0.71 19 19
UGCG -0.006 0.15 -10000 0 -0.7 20 20
AKT1/mTOR/p70S6K/Hsp90/TERT -0.02 0.18 0.28 3 -0.38 76 79
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.004 0.14 -10000 0 -0.69 20 20
mol:DAG -0.007 0.031 0.17 15 -10000 0 15
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.037 0.22 0.37 1 -0.47 87 88
FRAP1 -0.055 0.26 0.39 1 -0.54 89 90
FOXO3 -0.053 0.25 0.29 3 -0.52 94 97
AKT1 -0.062 0.28 0.26 2 -0.57 94 96
GAB2 0.029 0.021 -10000 0 -0.003 155 155
SMPD1 0 0.12 -10000 0 -0.58 19 19
SGMS1 -0.003 0.038 0.061 12 -0.077 80 92
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 -0.02 0.035 -10000 0 -0.12 51 51
CALM1 0.04 0.009 -10000 0 0 30 30
cell proliferation 0.005 0.18 0.23 20 -0.33 76 96
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.021 0.064 -10000 0 -0.14 54 54
RPS6KB1 -0.023 0.2 -10000 0 -0.84 27 27
mol:sphingomyelin -0.007 0.031 0.17 15 -10000 0 15
natural killer cell activation -0.001 0.004 -10000 0 -0.014 28 28
JAK3 0.035 0.022 -10000 0 -0.046 22 22
PIK3R1 0.031 0.024 -10000 0 -0.04 26 26
JAK1 0.037 0.02 -10000 0 -0.043 22 22
NFKB1 0.035 0.015 -10000 0 0 85 85
MYC -0.03 0.35 0.38 18 -0.81 77 95
MYB -0.048 0.3 -10000 0 -1.1 40 40
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.027 0.17 0.25 3 -0.36 88 91
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.005 0.19 -10000 0 -0.78 27 27
mol:PI-3-4-5-P3 -0.025 0.17 0.27 4 -0.35 87 91
Rac1/GDP 0.008 0.045 -10000 0 -0.11 47 47
T cell proliferation -0.028 0.16 0.25 4 -0.34 85 89
SHC1 0.037 0.016 -10000 0 -0.013 48 48
RAC1 0.039 0.01 -10000 0 0 35 35
positive regulation of cyclin-dependent protein kinase activity 0.001 0.02 0.032 40 -0.064 40 80
PRKCZ -0.031 0.17 0.25 4 -0.35 87 91
NF kappa B1 p50/RelA -0.03 0.24 0.4 1 -0.48 88 89
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.004 0.12 -10000 0 -0.34 41 41
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0.041 0.006 -10000 0 0 10 10
IL2RA 0.036 0.018 -10000 0 -0.009 68 68
IL2RB 0.034 0.022 -10000 0 -0.045 22 22
TERT 0.037 0.014 -10000 0 0 67 67
E2F1 -0.003 0.13 -10000 0 -0.41 43 43
SOS1 0.035 0.018 -10000 0 -0.008 77 77
RPS6 0.038 0.011 -10000 0 0 44 44
mol:cAMP -0.001 0.01 0.032 37 -0.017 39 76
PTPN11 0.035 0.02 -10000 0 -0.017 62 62
IL2RG 0.025 0.026 -10000 0 -0.041 28 28
actin cytoskeleton organization -0.028 0.16 0.25 4 -0.34 85 89
GRB2 0.038 0.016 -10000 0 -0.019 35 35
IL2 0.035 0.024 -10000 0 -0.04 36 36
PIK3CA 0.028 0.024 -10000 0 -0.043 22 22
Rac1/GTP 0.032 0.062 -10000 0 -0.11 47 47
LCK 0.036 0.023 -10000 0 -0.04 37 37
BCL2 -0.032 0.2 0.4 1 -0.49 60 61
Circadian rhythm pathway

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
chromatin modification -0.049 0.3 -10000 0 -1 48 48
CLOCK 0.031 0.031 -10000 0 -0.069 40 40
TIMELESS/CRY2 -0.05 0.31 -10000 0 -1 48 48
DEC1/BMAL1 0.044 0.048 -10000 0 -0.085 52 52
ATR 0.035 0.016 -10000 0 0 92 92
NR1D1 -0.017 0.11 -10000 0 -0.38 45 45
ARNTL 0.032 0.031 -10000 0 -0.068 42 42
TIMELESS -0.081 0.32 -10000 0 -1.1 48 48
NPAS2 0.027 0.031 -10000 0 -0.068 37 37
CRY2 0.041 0.004 -10000 0 0 6 6
mol:CO 0.001 0.041 0.13 48 -10000 0 48
CHEK1 0.033 0.017 -10000 0 0 118 118
mol:HEME -0.001 0.041 -10000 0 -0.13 48 48
PER1 0.039 0.01 -10000 0 0 36 36
BMAL/CLOCK/NPAS2 0.033 0.096 -10000 0 -0.13 114 114
BMAL1/CLOCK -0.041 0.2 -10000 0 -0.59 50 50
S phase of mitotic cell cycle -0.049 0.3 -10000 0 -1 48 48
TIMELESS/CHEK1/ATR -0.051 0.31 -10000 0 -1.1 48 48
mol:NADPH -0.001 0.041 -10000 0 -0.13 48 48
PER1/TIMELESS -0.053 0.31 -10000 0 -1 48 48
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.04 0.008 -10000 0 0 23 23
Class I PI3K signaling 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
ARF5/GTP -0.012 0.073 0.15 80 -0.18 5 85
DAPP1 -0.006 0.1 0.22 6 -0.26 36 42
Src family/SYK family/BLNK-LAT/BTK-ITK -0.011 0.14 -10000 0 -0.36 46 46
mol:DAG 0.005 0.075 0.18 18 -0.18 19 37
HRAS 0.041 0.013 0.079 3 -0.004 33 36
RAP1A 0.041 0.012 0.069 4 -0.001 36 40
ARF5/GDP 0.016 0.097 0.2 1 -0.24 40 41
PLCG2 0.036 0.015 -10000 0 0 83 83
PLCG1 0.039 0.011 -10000 0 0 39 39
ARF5 0.038 0.011 -10000 0 0 44 44
mol:GTP -0.012 0.067 0.14 79 -0.18 4 83
ARF1/GTP 0.002 0.064 0.14 84 -0.17 4 88
RHOA 0.041 0.007 -10000 0 0 14 14
YES1 0.037 0.013 -10000 0 0 59 59
RAP1A/GTP -0.006 0.078 0.16 83 -0.18 4 87
ADAP1 -0.014 0.061 0.13 72 -0.18 4 76
ARAP3 -0.012 0.066 0.14 79 -0.18 4 83
INPPL1 0.04 0.009 -10000 0 0 29 29
PREX1 0.037 0.013 -10000 0 0 58 58
ARHGEF6 0.037 0.013 -10000 0 0 64 64
ARHGEF7 0.04 0.009 -10000 0 0 30 30
ARF1 0.038 0.012 -10000 0 0 51 51
NRAS 0.042 0.011 0.068 3 0 31 34
FYN 0.034 0.016 -10000 0 0 102 102
ARF6 0.04 0.007 -10000 0 0 18 18
FGR 0.041 0.007 -10000 0 0 16 16
mol:Ca2+ 0.001 0.047 0.18 9 -0.12 5 14
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.037 0.014 -10000 0 0 70 70
ZAP70 0.041 0.006 -10000 0 0 11 11
mol:IP3 -0.003 0.058 0.22 8 -0.16 9 17
LYN 0.036 0.015 -10000 0 0 83 83
ARF1/GDP 0.017 0.097 0.2 1 -0.25 36 37
RhoA/GDP 0.036 0.085 0.19 47 -0.17 21 68
PDK1/Src/Hsp90 0.05 0.022 -10000 0 -0.11 5 5
BLNK 0.037 0.014 -10000 0 0 67 67
actin cytoskeleton reorganization 0.009 0.094 0.23 17 -0.26 20 37
SRC 0.039 0.01 -10000 0 0 31 31
PLEKHA2 -0.014 0.006 -10000 0 -10000 0 0
RAC1 0.039 0.01 -10000 0 0 35 35
PTEN 0.031 0.028 -10000 0 -0.03 79 79
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.01 0.075 0.15 85 -0.18 4 89
RhoA/GTP -0.009 0.08 0.16 87 -0.18 5 92
Src family/SYK family/BLNK-LAT 0.001 0.098 -10000 0 -0.28 30 30
BLK 0.033 0.017 -10000 0 0 115 115
PDPK1 0.04 0.009 -10000 0 0 27 27
CYTH1 -0.014 0.061 0.13 72 -0.18 4 76
HCK 0.036 0.015 -10000 0 0 79 79
CYTH3 -0.014 0.061 0.13 72 -0.18 4 76
CYTH2 -0.014 0.061 0.13 72 -0.18 4 76
KRAS 0.034 0.018 0.091 1 -0.001 106 107
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.011 0.044 0.15 3 -0.16 9 12
SGK1 0.011 0.043 0.12 1 -0.17 9 10
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.094 0.2 2 -0.25 40 42
SOS1 0.038 0.013 -10000 0 0 57 57
SYK 0.037 0.014 -10000 0 0 67 67
ARF6/GDP 0.003 0.08 0.17 60 -0.18 15 75
mol:PI-3-4-5-P3 -0.014 0.064 0.14 72 -0.18 4 76
ARAP3/RAP1A/GTP -0.006 0.078 0.17 83 -0.18 4 87
VAV1 0.037 0.014 -10000 0 0 67 67
mol:PI-3-4-P2 -0.01 0.002 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.044 0.065 0.22 28 -0.12 38 66
PLEKHA1 -0.015 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.1 0.21 2 -0.24 40 42
LAT 0.041 0.006 -10000 0 0 13 13
Rac1/GTP -0.005 0.1 -10000 0 -0.27 49 49
ITK -0.013 0.066 0.13 79 -0.18 5 84
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.001 0.092 0.21 14 -0.23 26 40
LCK 0.04 0.009 -10000 0 0 28 28
BTK -0.013 0.069 0.13 80 -0.19 8 88
Caspase cascade in apoptosis

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
TOP1 -0.015 0.14 0.26 3 -0.32 57 60
ACTA1 0.004 0.086 0.21 14 -0.23 20 34
NUMA1 -0.018 0.14 0.26 3 -0.35 42 45
SPTAN1 -0.002 0.085 0.21 11 -0.24 17 28
LIMK1 0.001 0.085 0.22 11 -0.24 16 27
BIRC3 0.026 0.02 -10000 0 0 213 213
BIRC2 0.036 0.014 -10000 0 0 73 73
BAX 0.04 0.008 -10000 0 0 20 20
CASP10 -0.011 0.025 0.057 54 -10000 0 54
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.037 0.17 0.26 3 -0.38 75 78
DIABLO 0.037 0.013 -10000 0 0 64 64
apoptotic nuclear changes -0.002 0.085 0.21 11 -0.24 17 28
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.041 0.006 -10000 0 0 12 12
GSN -0.003 0.085 0.21 12 -0.25 17 29
MADD 0.041 0.006 -10000 0 0 12 12
TFAP2A -0.031 0.21 -10000 0 -0.59 50 50
BID 0.006 0.034 0.13 20 -0.094 25 45
MAP3K1 -0.029 0.14 -10000 0 -0.37 71 71
TRADD 0.036 0.014 -10000 0 0 76 76
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.051 0.042 -10000 0 -0.15 20 20
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.007 0.1 0.23 43 -0.23 24 67
CASP9 0.04 0.009 -10000 0 0 26 26
DNA repair -0.012 0.08 0.25 27 -0.16 19 46
neuron apoptosis -0.035 0.2 -10000 0 -0.63 46 46
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.016 0.12 0.25 5 -0.32 32 37
APAF1 0.039 0.01 -10000 0 0 33 33
CASP6 -0.11 0.34 -10000 0 -0.85 91 91
TRAF2 0.04 0.009 -10000 0 0 25 25
ICAD/CAD -0.001 0.084 0.21 17 -0.23 15 32
CASP7 0.013 0.11 0.18 82 -0.28 23 105
KRT18 -0.016 0.15 -10000 0 -0.62 23 23
apoptosis -0.043 0.16 0.25 7 -0.38 80 87
DFFA 0.002 0.083 0.2 14 -0.23 16 30
DFFB 0.002 0.085 0.22 14 -0.24 16 30
PARP1 0.012 0.081 0.16 19 -0.26 27 46
actin filament polymerization 0.004 0.083 0.24 13 -0.23 13 26
TNF 0.04 0.009 -10000 0 0 25 25
CYCS 0.001 0.07 0.14 19 -0.21 33 52
SATB1 -0.11 0.32 -10000 0 -0.81 91 91
SLK -0.002 0.085 0.22 10 -0.25 16 26
p15 BID/BAX 0.032 0.05 0.16 3 -0.3 4 7
CASP2 0.005 0.087 0.24 18 -0.24 29 47
JNK cascade 0.029 0.14 0.37 71 -10000 0 71
CASP3 0.006 0.089 0.19 26 -0.23 20 46
LMNB2 -0.051 0.21 0.25 4 -0.42 98 102
RIPK1 0.038 0.012 -10000 0 0 48 48
CASP4 0.034 0.017 -10000 0 0 107 107
Mammalian IAPs/DIABLO 0.014 0.09 -10000 0 -0.13 127 127
negative regulation of DNA binding -0.03 0.2 -10000 0 -0.58 50 50
stress fiber formation -0.003 0.084 0.21 10 -0.24 16 26
GZMB -0.016 0.009 0 131 -10000 0 131
CASP1 -0.011 0.069 -10000 0 -0.2 66 66
LMNB1 -0.05 0.2 0.26 5 -0.42 82 87
APP -0.036 0.2 -10000 0 -0.64 46 46
TNFRSF1A 0.036 0.015 -10000 0 0 82 82
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.01 0.002 0 28 -10000 0 28
VIM -0.038 0.17 0.26 9 -0.38 81 90
LMNA -0.019 0.15 0.26 5 -0.32 84 89
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.006 0.085 -10000 0 -0.25 32 32
LRDD 0.039 0.01 -10000 0 0 34 34
SREBF1 0 0.084 0.21 10 -0.24 16 26
APAF-1/Caspase 9 0.026 0.15 -10000 0 -0.69 18 18
nuclear fragmentation during apoptosis -0.018 0.13 0.26 3 -0.35 42 45
CFL2 -0.004 0.084 0.23 13 -0.25 13 26
GAS2 0.004 0.088 0.22 18 -0.25 15 33
positive regulation of apoptosis -0.044 0.19 0.24 9 -0.38 98 107
PRF1 0.037 0.013 -10000 0 0 60 60
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.016 0.16 -10000 0 -0.44 53 53
HDAC1 0.043 0.025 0.084 104 -0.003 59 163
AES 0.038 0.016 0.08 15 0 71 86
FBXW11 0.04 0.008 -10000 0 0 23 23
DTX1 0.041 0.005 -10000 0 0 9 9
LRP6/FZD1 0.041 0.049 -10000 0 -0.14 31 31
TLE1 0.039 0.015 0.076 13 -0.001 53 66
AP1 -0.007 0.084 0.15 1 -0.18 93 94
NCSTN 0.04 0.008 -10000 0 0 21 21
ADAM10 0.039 0.011 -10000 0 0 39 39
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.066 0.21 -10000 0 -0.68 39 39
NICD/RBPSUH -0.011 0.14 -10000 0 -0.44 53 53
WIF1 0.039 0.01 -10000 0 0 31 31
NOTCH1 -0.004 0.15 -10000 0 -0.46 52 52
PSENEN 0.035 0.015 -10000 0 0 88 88
KREMEN2 0.04 0.009 -10000 0 0 26 26
DKK1 0.039 0.011 -10000 0 0 41 41
beta catenin/beta TrCP1 0.017 0.091 0.31 1 -0.33 13 14
APH1B 0.035 0.015 -10000 0 0 86 86
APH1A 0.041 0.006 -10000 0 0 11 11
AXIN1 0.003 0.061 -10000 0 -0.32 4 4
CtBP/CBP/TCF1/TLE1/AES 0.013 0.095 0.18 82 -0.18 48 130
PSEN1 0.039 0.01 -10000 0 0 34 34
FOS 0.026 0.02 -10000 0 0 205 205
JUN 0.036 0.015 -10000 0 0 80 80
MAP3K7 0.041 0.015 0.068 14 0 47 61
CTNNB1 0 0.085 0.3 1 -0.33 13 14
MAPK3 0.041 0.007 -10000 0 0 17 17
DKK2/LRP6/Kremen 2 0.056 0.053 -10000 0 -0.12 28 28
HNF1A 0.002 0.008 0.037 18 -10000 0 18
CTBP1 0.039 0.016 0.079 18 -0.001 59 77
MYC -0.15 0.42 -10000 0 -1.2 73 73
NKD1 0.039 0.012 -10000 0 0 50 50
FZD1 0.04 0.007 -10000 0 0 17 17
NOTCH1 precursor/Deltex homolog 1 0.015 0.16 -10000 0 -0.44 53 53
apoptosis -0.006 0.083 0.15 1 -0.18 93 94
Delta 1/NOTCHprecursor 0.011 0.15 -10000 0 -0.44 53 53
DLL1 0.037 0.013 -10000 0 0 60 60
PPARD 0.009 0.076 -10000 0 -1 2 2
Gamma Secretase 0.071 0.087 -10000 0 -0.12 68 68
APC -0.02 0.12 -10000 0 -0.42 32 32
DVL1 0.019 0.058 -10000 0 -0.29 13 13
CSNK2A1 0.038 0.011 -10000 0 0 40 40
MAP3K7IP1 0.041 0.015 0.068 15 0 51 66
DKK1/LRP6/Kremen 2 0.056 0.053 -10000 0 -0.12 27 27
LRP6 0.034 0.016 -10000 0 0 103 103
CSNK1A1 0.039 0.009 -10000 0 0 24 24
NLK 0.026 0.043 -10000 0 -0.22 12 12
CCND1 -0.16 0.44 -10000 0 -1.2 82 82
WNT1 0.041 0.007 -10000 0 0 15 15
Axin1/APC/beta catenin 0.002 0.1 0.27 3 -0.36 17 20
DKK2 0.038 0.012 -10000 0 0 49 49
NOTCH1 precursor/DVL1 0.014 0.15 -10000 0 -0.4 46 46
GSK3B 0.04 0.01 -10000 0 0 29 29
FRAT1 0.041 0.01 -10000 0 0 25 25
NOTCH/Deltex homolog 1 0.021 0.16 -10000 0 -0.44 53 53
PPP2R5D 0.021 0.054 -10000 0 -0.29 12 12
MAPK1 0.039 0.011 -10000 0 0 43 43
WNT1/LRP6/FZD1 0.075 0.061 -10000 0 -0.11 30 30
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.03 0.024 -10000 0 -0.017 82 82
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.037 0.013 -10000 0 0 63 63
Caspase 8 (4 units) 0.035 0.094 -10000 0 -0.24 28 28
NEF 0.003 0.005 -10000 0 -0.1 1 1
NFKBIA 0.026 0.042 0.084 6 -0.068 78 84
BIRC3 -0.057 0.1 0.2 4 -0.28 87 91
CYCS -0.006 0.069 0.19 11 -0.25 18 29
RIPK1 0.038 0.012 -10000 0 0 48 48
CD247 0.003 0.005 -10000 0 -0.1 1 1
MAP2K7 -0.008 0.17 -10000 0 -0.56 36 36
protein ubiquitination -0.001 0.098 0.24 6 -0.27 31 37
CRADD 0.041 0.006 -10000 0 0 12 12
DAXX 0.04 0.007 -10000 0 0 18 18
FAS 0.034 0.016 -10000 0 0 98 98
BID 0.002 0.064 0.16 3 -0.26 16 19
NF-kappa-B/RelA/I kappa B alpha 0.028 0.11 -10000 0 -0.18 118 118
TRADD 0.036 0.014 -10000 0 0 76 76
MAP3K5 0.037 0.014 -10000 0 0 70 70
CFLAR 0.04 0.008 -10000 0 0 21 21
FADD 0.04 0.008 -10000 0 0 21 21
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.028 0.11 -10000 0 -0.18 118 118
MAPK8 -0.012 0.16 -10000 0 -0.54 34 34
APAF1 0.039 0.01 -10000 0 0 33 33
TRAF1 0.04 0.008 -10000 0 0 19 19
TRAF2 0.04 0.009 -10000 0 0 25 25
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.011 0.067 -10000 0 -0.17 50 50
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.006 0.11 -10000 0 -0.32 33 33
CHUK -0.003 0.1 0.24 7 -0.29 32 39
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.075 0.085 -10000 0 -0.13 58 58
TCRz/NEF 0.01 0.008 -10000 0 -0.17 1 1
TNF 0.04 0.009 -10000 0 0 25 25
FASLG 0.022 0.014 -10000 0 -0.3 1 1
NFKB1 0.027 0.041 0.084 7 -0.071 64 71
TNFR1A/BAG4/TNF-alpha 0.059 0.046 -10000 0 -0.12 15 15
CASP6 -0.047 0.23 -10000 0 -0.54 87 87
CASP7 -0.045 0.2 0.31 6 -0.4 109 115
RELA 0.027 0.044 0.08 7 -0.066 95 102
CASP2 0.038 0.012 -10000 0 0 48 48
CASP3 -0.057 0.2 0.32 5 -0.41 114 119
TNFRSF1A 0.036 0.015 -10000 0 0 82 82
TNFR1A/BAG4 0.044 0.038 -10000 0 -0.13 14 14
CASP8 0.04 0.009 -10000 0 0 28 28
CASP9 0.04 0.009 -10000 0 0 26 26
MAP3K14 0.006 0.11 0.26 6 -0.31 29 35
APAF-1/Caspase 9 -0.027 0.11 0.19 1 -0.25 91 92
BCL2 -0.014 0.14 -10000 0 -0.5 32 32
Arf6 signaling events

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
CENTA1/KIF3B 0.022 0.011 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 0.044 0.031 -10000 0 -0.082 11 11
EGFR 0.036 0.014 -10000 0 0 73 73
EPHA2 0.039 0.01 -10000 0 0 34 34
USP6 0.04 0.009 -10000 0 0 30 30
IQSEC1 0.041 0.007 -10000 0 0 17 17
EGFR/EGFR/EGF/EGF 0.04 0.051 -10000 0 -0.13 37 37
ARRB2 0.016 0.017 -10000 0 -0.2 3 3
mol:GTP 0.001 0.014 -10000 0 -0.061 9 9
ARRB1 0.038 0.012 -10000 0 0 47 47
FBXO8 0.037 0.014 -10000 0 0 70 70
TSHR 0.037 0.013 -10000 0 0 60 60
EGF 0.038 0.012 -10000 0 0 52 52
somatostatin receptor activity 0 0 0 7 -0.001 43 50
ARAP2 0 0 0 11 0 36 47
mol:GDP 0.012 0.073 0.15 2 -0.18 40 42
mol:PI-3-4-5-P3 0 0 0 7 0 37 44
ITGA2B 0.04 0.009 -10000 0 0 29 29
ARF6 0.041 0.007 -10000 0 0 18 18
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.077 -10000 0 -0.12 61 61
ADAP1 0 0 0 6 0 27 33
KIF13B 0.033 0.017 -10000 0 0 111 111
HGF/MET 0.013 0.075 -10000 0 -0.14 104 104
PXN 0.041 0.007 -10000 0 0 14 14
ARF6/GTP 0.014 0.083 0.18 7 -0.21 42 49
EGFR/EGFR/EGF/EGF/ARFGEP100 0.059 0.054 -10000 0 -0.12 35 35
ADRB2 0.041 0.006 -10000 0 0 11 11
receptor agonist activity 0 0 0 10 0 36 46
actin filament binding 0 0 0 5 0 45 50
SRC 0.039 0.01 -10000 0 0 31 31
ITGB3 0.033 0.017 -10000 0 0 120 120
GNAQ 0.038 0.012 -10000 0 0 50 50
EFA6/PI-4-5-P2 0 0 0.001 11 -0.001 33 44
ARF6/GDP 0.011 0.076 0.19 9 -0.24 24 33
ARF6/GDP/GULP/ACAP1 0.027 0.086 -10000 0 -0.2 35 35
alphaIIb/beta3 Integrin/paxillin/GIT1 0.081 0.058 -10000 0 -0.11 34 34
ACAP1 0 0 0 4 0 1 5
ACAP2 0 0 0 5 0 36 41
LHCGR/beta Arrestin2 0.032 0.024 -10000 0 -0.065 26 26
EFNA1 0.034 0.016 -10000 0 0 101 101
HGF 0.04 0.009 -10000 0 0 29 29
CYTH3 0 0 0.001 12 -0.001 35 47
CYTH2 0 0.001 0.003 4 -0.004 40 44
NCK1 0.036 0.014 -10000 0 0 77 77
fibronectin binding 0 0 0 9 0 36 45
endosomal lumen acidification 0 0 0 11 0 22 33
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.032 0.018 -10000 0 0 130 130
GNAQ/ARNO 0.026 0.009 -10000 0 0 50 50
mol:Phosphatidic acid 0 0 0 5 0 36 41
PIP3-E 0.038 0.013 -10000 0 0 57 57
MET 0.027 0.02 -10000 0 0 195 195
GNA14 0.039 0.01 -10000 0 0 33 33
GNA15 0.037 0.014 -10000 0 0 69 69
GIT1 0.04 0.008 -10000 0 0 23 23
mol:PI-4-5-P2 0 0 0.001 13 -0.001 40 53
GNA11 0.037 0.013 -10000 0 0 63 63
LHCGR 0.04 0.009 -10000 0 0 25 25
AGTR1 0.037 0.014 -10000 0 0 69 69
desensitization of G-protein coupled receptor protein signaling pathway 0.032 0.024 -10000 0 -0.065 26 26
IPCEF1/ARNO 0.053 0.045 -10000 0 -0.087 34 34
alphaIIb/beta3 Integrin 0.039 0.05 -10000 0 -0.14 34 34
Reelin signaling pathway

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
CDK5R1/CDK5 0.047 0.04 -10000 0 -0.14 19 19
VLDLR 0.032 0.018 -10000 0 0 129 129
CRKL 0.039 0.01 -10000 0 0 35 35
LRPAP1 0.036 0.015 -10000 0 0 79 79
FYN 0.034 0.016 -10000 0 0 102 102
ITGA3 0.034 0.016 -10000 0 0 101 101
RELN/VLDLR/Fyn 0.032 0.067 -10000 0 -0.13 51 51
MAPK8IP1/MKK7/MAP3K11/JNK1 0.094 0.062 -10000 0 -0.11 18 18
AKT1 -0.001 0.075 -10000 0 -0.17 60 60
MAP2K7 0.038 0.011 -10000 0 0 44 44
RAPGEF1 0.04 0.008 -10000 0 0 22 22
DAB1 0.04 0.009 -10000 0 0 25 25
RELN/LRP8/DAB1 0.059 0.039 -10000 0 -0.1 6 6
LRPAP1/LRP8 0.041 0.053 -10000 0 -0.14 37 37
RELN/LRP8/DAB1/Fyn 0.066 0.056 -10000 0 -0.1 32 32
DAB1/alpha3/beta1 Integrin 0.028 0.083 -10000 0 -0.12 87 87
long-term memory 0.073 0.072 0.22 9 -0.11 30 39
DAB1/LIS1 0.057 0.083 -10000 0 -0.11 58 58
DAB1/CRLK/C3G 0.045 0.073 -10000 0 -0.12 54 54
PIK3CA 0.03 0.019 -10000 0 0 150 150
DAB1/NCK2 0.062 0.083 -10000 0 -0.11 57 57
ARHGEF2 0.039 0.01 -10000 0 0 34 34
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.033 0.017 -10000 0 0 110 110
CDK5R1 0.04 0.009 -10000 0 0 27 27
RELN 0.034 0.016 -10000 0 0 104 104
PIK3R1 0.034 0.016 -10000 0 0 106 106
RELN/LRP8/Fyn 0.045 0.057 -10000 0 -0.12 33 33
GRIN2A/RELN/LRP8/DAB1/Fyn 0.075 0.07 -10000 0 -0.11 33 33
MAPK8 0.04 0.009 -10000 0 0 29 29
RELN/VLDLR/DAB1 0.042 0.054 -10000 0 -0.1 37 37
ITGB1 0.039 0.011 -10000 0 0 39 39
MAP1B -0.002 0.064 0.22 23 -0.2 5 28
RELN/LRP8 0.049 0.056 -10000 0 -0.12 30 30
GRIN2B/RELN/LRP8/DAB1/Fyn 0.076 0.069 -10000 0 -0.11 28 28
PI3K 0.024 0.062 -10000 0 -0.15 47 47
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.03 0.066 -10000 0 -0.14 67 67
RAP1A -0.004 0.097 0.31 26 -0.18 4 30
PAFAH1B1 0.039 0.011 -10000 0 0 40 40
MAPK8IP1 0.039 0.01 -10000 0 0 31 31
CRLK/C3G 0.056 0.018 -10000 0 -10000 0 0
GRIN2B 0.037 0.014 -10000 0 0 68 68
NCK2 0.041 0.006 -10000 0 0 10 10
neuron differentiation 0.022 0.059 0.17 1 -0.24 6 7
neuron adhesion -0.012 0.1 0.28 32 -0.25 1 33
LRP8 0.039 0.011 -10000 0 0 39 39
GSK3B -0.005 0.076 0.18 9 -0.16 61 70
RELN/VLDLR/DAB1/Fyn 0.05 0.068 -10000 0 -0.12 50 50
MAP3K11 0.041 0.006 -10000 0 0 12 12
RELN/VLDLR/DAB1/P13K -0.004 0.068 -10000 0 -0.16 64 64
CDK5 0.036 0.014 -10000 0 0 77 77
MAPT -0.009 0.034 0.68 1 -10000 0 1
neuron migration 0.001 0.098 0.24 34 -0.23 19 53
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.021 0.057 0.17 1 -0.23 5 6
RELN/VLDLR 0.052 0.074 -10000 0 -0.11 60 60
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.003 0.07 -10000 0 -0.19 52 52
epithelial cell differentiation 0.056 0.068 -10000 0 -0.13 51 51
CYFIP2 0.038 0.011 -10000 0 0 45 45
ENAH -0.034 0.072 0.21 14 -0.2 7 21
EGFR 0.036 0.014 -10000 0 0 73 73
EPHA2 0.039 0.01 -10000 0 0 34 34
MYO6 -0.03 0.048 0.18 8 -0.21 17 25
CTNNB1 0.039 0.01 -10000 0 0 32 32
ABI1/Sra1/Nap1 0.061 0.058 -10000 0 -0.12 39 39
AQP5 -0.076 0.14 0.17 6 -0.36 99 105
CTNND1 0.041 0.007 -10000 0 0 17 17
mol:PI-4-5-P2 -0.03 0.044 0.18 7 -0.2 12 19
regulation of calcium-dependent cell-cell adhesion -0.028 0.045 0.19 8 -0.2 12 20
EGF 0.038 0.012 -10000 0 0 52 52
NCKAP1 0.039 0.01 -10000 0 0 33 33
AQP3 -0.023 0.057 0.18 3 -0.29 14 17
cortical microtubule organization 0.056 0.068 -10000 0 -0.13 51 51
GO:0000145 -0.029 0.04 0.16 7 -0.19 12 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.063 0.072 -10000 0 -0.13 51 51
MLLT4 0.033 0.017 -10000 0 0 110 110
ARF6/GDP -0.051 0.048 -10000 0 -0.2 26 26
ARF6 0.04 0.007 -10000 0 0 18 18
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.077 -10000 0 -0.12 61 61
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.016 0.05 0.21 6 -0.2 18 24
PVRL2 0.039 0.011 -10000 0 0 43 43
ZYX -0.027 0.042 0.19 7 -0.2 8 15
ARF6/GTP 0.067 0.083 -10000 0 -0.12 62 62
CDH1 0.035 0.016 -10000 0 0 96 96
EGFR/EGFR/EGF/EGF 0.037 0.075 -10000 0 -0.12 73 73
RhoA/GDP 0.056 0.072 -10000 0 -0.12 54 54
actin cytoskeleton organization -0.032 0.049 0.16 7 -0.23 17 24
IGF-1R heterotetramer 0.033 0.017 -10000 0 0 116 116
GIT1 0.04 0.008 -10000 0 0 23 23
IGF1R 0.033 0.017 -10000 0 0 116 116
IGF1 0.036 0.015 -10000 0 0 82 82
DIAPH1 -0.002 0.22 -10000 0 -0.56 70 70
Wnt receptor signaling pathway -0.056 0.068 0.13 51 -10000 0 51
RHOA 0.041 0.007 -10000 0 0 14 14
RhoA/GTP -0.051 0.047 -10000 0 -0.19 27 27
CTNNA1 0.039 0.01 -10000 0 0 36 36
VCL -0.033 0.05 0.16 7 -0.23 17 24
EFNA1 0.034 0.016 -10000 0 0 101 101
LPP -0.029 0.044 0.18 7 -0.2 14 21
Ephrin A1/EPHA2 0.032 0.077 -10000 0 -0.13 75 75
SEC6/SEC8 -0.045 0.043 -10000 0 -0.15 42 42
MGAT3 -0.029 0.046 0.19 8 -0.2 12 20
HGF/MET 0.016 0.087 -10000 0 -0.12 124 124
HGF 0.04 0.009 -10000 0 0 29 29
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.003 0.07 -10000 0 -0.19 52 52
actin cable formation 0.002 0.098 0.24 31 -0.23 21 52
KIAA1543 -0.033 0.043 0.16 7 -0.2 13 20
KIFC3 -0.032 0.042 0.18 6 -0.2 12 18
NCK1 0.036 0.014 -10000 0 0 77 77
EXOC3 0.041 0.005 -10000 0 0 7 7
ACTN1 -0.031 0.05 0.19 9 -0.21 16 25
NCK1/GIT1 0.044 0.047 -10000 0 -0.14 30 30
mol:GDP 0.056 0.068 -10000 0 -0.13 51 51
EXOC4 0.038 0.012 -10000 0 0 51 51
STX4 -0.029 0.034 0.035 8 -0.12 51 59
PIP5K1C -0.03 0.044 0.18 7 -0.2 12 19
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0.04 0.009 -10000 0 0 28 28
ROCK1 -0.027 0.086 0.23 17 -0.23 6 23
adherens junction assembly -0.053 0.14 -10000 0 -0.44 40 40
IGF-1R heterotetramer/IGF1 0.024 0.082 -10000 0 -0.13 87 87
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.05 -10000 0 -0.14 31 31
MET 0.027 0.02 -10000 0 0 195 195
PLEKHA7 -0.031 0.046 0.18 8 -0.2 14 22
mol:GTP 0.059 0.075 -10000 0 -0.12 61 61
establishment of epithelial cell apical/basal polarity -0.037 0.056 0.13 27 -0.2 15 42
cortical actin cytoskeleton stabilization 0.003 0.07 -10000 0 -0.19 52 52
regulation of cell-cell adhesion -0.032 0.049 0.16 7 -0.23 17 24
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.003 0.07 -10000 0 -0.19 52 52
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.007 0.038 -10000 0 -0.12 56 56
STMN1 -0.011 0.016 0.03 11 -10000 0 11
Aurora B/RasGAP/Survivin 0.046 0.074 -10000 0 -0.16 49 49
Chromosomal passenger complex/Cul3 protein complex -0.005 0.091 -10000 0 -0.24 46 46
BIRC5 0.037 0.015 -10000 0 -0.002 62 62
DES -0.04 0.27 -10000 0 -0.81 57 57
Aurora C/Aurora B/INCENP 0.064 0.047 -10000 0 -0.12 27 27
Aurora B/TACC1 0.037 0.04 -10000 0 -0.1 28 28
Aurora B/PP2A 0.044 0.049 -10000 0 -0.14 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 -0.01 0.062 -10000 0 -0.16 74 74
mitotic metaphase/anaphase transition 0.002 0.006 0.013 107 -10000 0 107
NDC80 -0.004 0.01 0.02 10 -10000 0 10
Cul3 protein complex 0.049 0.06 -10000 0 -0.12 42 42
KIF2C -0.057 0.19 -10000 0 -0.49 79 79
PEBP1 -0.001 0.003 -10000 0 -0.011 36 36
KIF20A 0.032 0.018 -10000 0 0 132 132
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.036 0.057 -10000 0 -0.14 44 44
SEPT1 0.041 0.007 -10000 0 0 16 16
SMC2 0 0 -10000 0 -10000 0 0
SMC4 0 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.035 0.19 -10000 0 -0.56 57 57
PSMA3 0.038 0.012 -10000 0 0 54 54
G2/M transition of mitotic cell cycle -0.001 0.003 0.009 28 -0.008 16 44
H3F3B 0.002 0.056 -10000 0 -0.2 39 39
AURKB 0.038 0.016 -10000 0 0 76 76
AURKC 0.042 0.002 -10000 0 0 1 1
CDCA8 0.036 0.016 -10000 0 -0.004 71 71
cytokinesis -0.03 0.18 0.2 1 -0.44 67 68
Aurora B/Septin1 -0.003 0.19 0.22 1 -0.38 80 81
AURKA -0.001 0.003 0.009 28 -0.008 16 44
INCENP 0.039 0.016 -10000 0 -0.029 27 27
KLHL13 0.033 0.017 -10000 0 0 118 118
BUB1 0.037 0.015 0.064 1 0 74 75
hSgo1/Aurora B/Survivin 0.041 0.078 -10000 0 -0.15 62 62
EVI5 0.039 0.011 -10000 0 0 37 37
RhoA/GTP 0.004 0.17 -10000 0 -0.35 71 71
SGOL1 0.036 0.014 -10000 0 0 73 73
CENPA -0.014 0.11 -10000 0 -0.3 56 56
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.034 0.064 -10000 0 -0.14 57 57
NCAPD2 0 0 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.037 0.062 -10000 0 -0.14 54 54
RHOA 0.041 0.007 -10000 0 0 14 14
NCAPH 0 0 -10000 0 -10000 0 0
NPM1 -0.021 0.13 -10000 0 -0.33 71 71
RASA1 0.036 0.014 -10000 0 0 73 73
KLHL9 0.039 0.011 -10000 0 0 43 43
mitotic prometaphase -0.001 0.003 -10000 0 -0.011 36 36
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.064 -10000 0 -0.14 57 57
PPP1CC 0.039 0.01 -10000 0 0 37 37
Centraspindlin -0.009 0.17 -10000 0 -0.38 71 71
RhoA/GDP 0.029 0.014 -10000 0 -0.13 4 4
NSUN2 -0.009 0.12 -10000 0 -0.33 60 60
MYLK 0.001 0.057 -10000 0 -0.2 40 40
KIF23 0.035 0.017 -10000 0 0 99 99
VIM -0.01 0.016 0.038 11 -10000 0 11
RACGAP1 0.037 0.014 -10000 0 -0.004 53 53
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.024 0.12 -10000 0 -0.32 80 80
Chromosomal passenger complex -0.034 0.14 -10000 0 -0.34 68 68
Chromosomal passenger complex/EVI5 0.066 0.097 -10000 0 -0.17 57 57
TACC1 0.035 0.016 -10000 0 0 91 91
PPP2R5D 0.04 0.009 -10000 0 0 27 27
CUL3 0.04 0.008 -10000 0 0 22 22
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.026 0.2 -10000 0 -0.77 33 33
epithelial cell differentiation -0.027 0.19 -10000 0 -0.68 35 35
ITCH 0.039 0.038 0.11 5 -0.097 28 33
WWP1 -0.063 0.27 -10000 0 -1.1 32 32
FYN 0.034 0.016 -10000 0 0 102 102
EGFR 0.036 0.014 -10000 0 0 73 73
PRL 0.039 0.011 -10000 0 0 39 39
neuron projection morphogenesis -0.043 0.16 0.28 7 -0.58 33 40
PTPRZ1 0.039 0.01 -10000 0 0 36 36
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.006 0.18 -10000 0 -0.62 34 34
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.033 0.18 -10000 0 -0.66 36 36
ADAM17 0.038 0.035 0.1 2 -0.087 25 27
ErbB4/ErbB4 -0.05 0.21 -10000 0 -0.83 33 33
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.029 0.2 -10000 0 -0.75 33 33
NCOR1 0.038 0.013 -10000 0 0 57 57
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.027 0.18 -10000 0 -0.61 38 38
GRIN2B -0.033 0.16 0.28 2 -0.58 37 39
ErbB4/ErbB2/betacellulin -0.028 0.18 -10000 0 -0.65 36 36
STAT1 0.034 0.017 -10000 0 0 108 108
HBEGF 0.04 0.009 -10000 0 0 29 29
PRLR 0.035 0.015 -10000 0 0 84 84
E4ICDs/ETO2 -0.03 0.2 -10000 0 -0.77 33 33
axon guidance -0.054 0.22 -10000 0 -0.86 35 35
NEDD4 0.038 0.039 0.1 6 -0.087 36 42
Prolactin receptor/Prolactin receptor/Prolactin 0.049 0.025 -10000 0 -10000 0 0
CBFA2T3 0.036 0.015 -10000 0 0 81 81
ErbB4/ErbB2/HBEGF -0.02 0.18 -10000 0 -0.65 36 36
MAPK3 -0.024 0.16 0.29 7 -0.6 33 40
STAT1 (dimer) -0.034 0.21 -10000 0 -0.77 34 34
MAPK1 -0.024 0.16 0.29 7 -0.6 33 40
JAK2 0.034 0.017 -10000 0 0 108 108
ErbB4/ErbB2/neuregulin 1 beta -0.031 0.17 -10000 0 -0.64 36 36
NRG1 -0.007 0.032 0.045 18 -0.11 20 38
NRG3 0.035 0.016 -10000 0 0 91 91
NRG2 0.041 0.006 -10000 0 0 12 12
NRG4 0.029 0.019 -10000 0 0 168 168
heart development -0.054 0.22 -10000 0 -0.86 35 35
neural crest cell migration -0.031 0.17 -10000 0 -0.63 36 36
ERBB2 -0.008 0.032 0.048 24 -0.1 24 48
WWOX/E4ICDs -0.028 0.2 -10000 0 -0.77 33 33
SHC1 0.04 0.009 -10000 0 0 29 29
ErbB4/EGFR/neuregulin 4 -0.036 0.2 -10000 0 -0.72 34 34
apoptosis 0.03 0.19 0.66 39 -10000 0 39
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.025 0.2 -10000 0 -0.77 33 33
ErbB4/ErbB2/epiregulin -0.02 0.18 -10000 0 -0.64 36 36
ErbB4/ErbB4/betacellulin/betacellulin -0.034 0.2 -10000 0 -0.77 33 33
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.003 0.19 -10000 0 -0.65 34 34
MDM2 -0.042 0.19 0.27 8 -0.77 30 38
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.02 0.16 -10000 0 -0.6 34 34
STAT5A -0.055 0.22 -10000 0 -0.83 35 35
ErbB4/EGFR/neuregulin 1 beta -0.026 0.18 -10000 0 -0.65 35 35
DLG4 0.04 0.009 -10000 0 0 29 29
GRB2/SHC 0.057 0.022 -10000 0 -0.14 4 4
E4ICDs/TAB2/NCoR1 -0.019 0.2 -10000 0 -0.74 34 34
STAT5A (dimer) -0.023 0.21 -10000 0 -0.76 35 35
MAP3K7IP2 0.037 0.013 -10000 0 0 63 63
STAT5B (dimer) -0.036 0.23 -10000 0 -0.83 35 35
LRIG1 0.033 0.017 -10000 0 0 118 118
EREG 0.038 0.012 -10000 0 0 48 48
BTC 0.033 0.017 -10000 0 0 113 113
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.058 0.23 -10000 0 -0.87 35 35
ERBB4 -0.049 0.21 -10000 0 -0.84 33 33
STAT5B 0.039 0.011 -10000 0 0 41 41
YAP1 0.007 0.1 -10000 0 -0.52 17 17
GRB2 0.041 0.007 -10000 0 0 14 14
ErbB4/ErbB2/neuregulin 4 -0.032 0.18 -10000 0 -0.65 36 36
glial cell differentiation 0.019 0.2 0.73 34 -10000 0 34
WWOX 0.037 0.014 -10000 0 0 69 69
cell proliferation -0.07 0.21 -10000 0 -0.7 45 45
Regulation of Telomerase

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
Telomerase catalytic core complex -0.031 0.18 -10000 0 -0.52 28 28
RAD9A 0.041 0.004 -10000 0 0 6 6
AP1 0.002 0.084 -10000 0 -0.15 114 114
IFNAR2 0.03 0.027 -10000 0 -0.033 70 70
AKT1 0.013 0.038 -10000 0 -0.16 5 5
ER alpha/Oestrogen 0.013 0.043 -10000 0 -0.13 42 42
NFX1/SIN3/HDAC complex 0 0.086 0.17 5 -0.26 32 37
EGF 0.038 0.012 -10000 0 0 52 52
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.044 0.043 -10000 0 -0.13 6 6
TERT/c-Abl -0.021 0.18 -10000 0 -0.49 31 31
SAP18 0.039 0.01 -10000 0 0 31 31
MRN complex 0.049 0.07 -10000 0 -0.15 48 48
WT1 0.029 0.027 -10000 0 -0.033 67 67
WRN 0.033 0.017 -10000 0 0 119 119
SP1 0.032 0.031 -10000 0 -0.041 78 78
SP3 0.04 0.009 -10000 0 -0.004 18 18
TERF2IP 0.036 0.014 -10000 0 0 73 73
Telomerase/Nucleolin -0.019 0.18 -10000 0 -0.44 41 41
Mad/Max 0.055 0.024 -10000 0 -10000 0 0
TERT -0.034 0.19 -10000 0 -0.53 28 28
CCND1 -0.11 0.37 -10000 0 -0.97 81 81
MAX 0.04 0.009 -10000 0 -0.005 19 19
RBBP7 0.04 0.009 -10000 0 0 25 25
RBBP4 0.038 0.011 -10000 0 0 45 45
TERF2 0.034 0.021 0.094 43 0 78 121
PTGES3 0.038 0.013 -10000 0 0 56 56
SIN3A 0.039 0.01 -10000 0 0 31 31
Telomerase/911 0.024 0.082 -10000 0 -0.28 22 22
CDKN1B -0.002 0.081 0.2 3 -0.18 69 72
RAD1 0.038 0.013 -10000 0 0 56 56
XRCC5 0.039 0.011 -10000 0 0 38 38
XRCC6 0.037 0.014 -10000 0 0 69 69
SAP30 0.038 0.013 -10000 0 0 55 55
TRF2/PARP2 0.049 0.035 -10000 0 -0.13 9 9
UBE3A 0.041 0.007 -10000 0 -0.004 9 9
JUN 0.035 0.015 -10000 0 0 81 81
E6 0 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.023 0.027 -10000 0 -0.048 39 39
FOS 0.026 0.021 -10000 0 -0.001 209 209
IFN-gamma/IRF1 0.025 0.081 -10000 0 -0.16 81 81
PARP2 0.04 0.009 -10000 0 0 30 30
BLM 0.037 0.014 -10000 0 0 67 67
Telomerase 0.004 0.063 0.13 1 -0.26 19 20
IRF1 0.029 0.04 0.11 1 -0.14 20 21
ESR1 0.035 0.016 -10000 0 0 92 92
KU/TER 0.042 0.054 -10000 0 -0.16 31 31
ATM/TRF2 0.036 0.055 -10000 0 -0.14 40 40
ubiquitin-dependent protein catabolic process 0.002 0.087 0.18 6 -0.27 28 34
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.002 0.089 0.18 6 -0.28 27 33
HDAC1 0.038 0.012 -10000 0 0 54 54
HDAC2 0.029 0.03 -10000 0 -0.04 74 74
ATM 0.009 0.065 -10000 0 -0.24 31 31
SMAD3 -0.013 0.016 0.025 69 -10000 0 69
ABL1 0.039 0.011 -10000 0 0 41 41
MXD1 0.04 0.01 -10000 0 -0.005 20 20
MRE11A 0.038 0.012 -10000 0 0 51 51
HUS1 0.04 0.008 -10000 0 0 20 20
RPS6KB1 0.039 0.01 -10000 0 0 36 36
TERT/NF kappa B1/14-3-3 -0.01 0.19 -10000 0 -0.51 27 27
NR2F2 0.039 0.013 0.07 1 0 38 39
MAPK3 -0.016 0.015 0.022 50 -0.041 5 55
MAPK1 -0.015 0.015 0.022 46 -0.041 6 52
TGFB1/TGF beta receptor Type II 0.037 0.013 -10000 0 0 61 61
NFKB1 0.035 0.015 -10000 0 0 85 85
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.065 -10000 0 -0.24 31 31
NBN 0.035 0.016 -10000 0 0 96 96
EGFR 0.036 0.015 -10000 0 0 74 74
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR 0.04 0.052 -10000 0 -0.14 37 37
MYC 0.021 0.021 -10000 0 0 272 272
IL2 0.03 0.031 -10000 0 -0.042 74 74
KU 0.042 0.054 -10000 0 -0.16 31 31
RAD50 0.039 0.011 -10000 0 0 38 38
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.037 0.013 -10000 0 0 61 61
TRF2/BLM 0.043 0.044 -10000 0 -0.13 21 21
FRAP1 0.04 0.009 -10000 0 0 24 24
KU/TERT -0.014 0.19 -10000 0 -0.48 34 34
SP1/HDAC2 0.042 0.051 -10000 0 -0.098 24 24
PINX1 0.033 0.017 -10000 0 0 121 121
Telomerase/EST1A -0.027 0.17 -10000 0 -0.44 39 39
Smad3/Myc 0.015 0.038 -10000 0 -0.14 19 19
911 complex 0.071 0.037 -10000 0 -0.12 9 9
IFNG 0.034 0.035 0.11 2 -0.11 24 26
Telomerase/PinX1 -0.026 0.17 -10000 0 -0.44 39 39
Telomerase/AKT1/mTOR/p70S6K -0.003 0.1 -10000 0 -0.29 39 39
SIN3B 0.037 0.014 -10000 0 0 67 67
YWHAE 0.038 0.012 -10000 0 0 50 50
Telomerase/EST1B -0.027 0.17 -10000 0 -0.44 39 39
response to DNA damage stimulus 0.002 0.035 0.063 3 -0.11 47 50
MRN complex/TRF2/Rap1 0.066 0.08 -10000 0 -0.13 36 36
TRF2/WRN 0.038 0.04 -10000 0 -0.11 19 19
Telomerase/hnRNP C1/C2 -0.027 0.17 -10000 0 -0.44 39 39
E2F1 0.031 0.027 -10000 0 -0.033 70 70
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.04 0.009 -10000 0 0 30 30
DKC1 0.04 0.008 -10000 0 0 20 20
telomeric DNA binding 0 0 -10000 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.009 0.054 0.17 50 -0.092 3 53
BUB1B -0.026 0.083 0.12 1 -0.22 66 67
PLK1 -0.002 0.037 0.074 5 -0.098 42 47
PLK1S1 -0.001 0.02 0.045 5 -0.052 44 49
KIF2A -0.002 0.033 0.067 4 -0.089 42 46
regulation of mitotic centrosome separation -0.002 0.037 0.075 4 -0.098 42 46
GOLGA2 0.04 0.009 -10000 0 0 26 26
Hec1/SPC24 -0.01 0.025 -10000 0 -0.08 47 47
WEE1 -0.013 0.089 -10000 0 -0.32 31 31
cytokinesis -0.038 0.13 0.14 4 -0.29 96 100
PP2A-alpha B56 -0.005 0.25 -10000 0 -0.69 61 61
AURKA -0.002 0.022 0.049 8 -0.063 33 41
PICH/PLK1 -0.033 0.069 0.067 3 -0.16 109 112
CENPE -0.008 0.035 0.15 2 -0.13 19 21
RhoA/GTP 0.029 0.014 -10000 0 -0.13 4 4
positive regulation of microtubule depolymerization -0.002 0.033 0.067 4 -0.088 42 46
PPP2CA 0.04 0.009 -10000 0 0 26 26
FZR1 0.038 0.013 -10000 0 0 57 57
TPX2 -0.025 0.098 -10000 0 -0.24 87 87
PAK1 0.037 0.014 -10000 0 0 66 66
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.04 0.008 -10000 0 0 23 23
CLSPN 0.009 0.037 -10000 0 -0.26 7 7
GORASP1 0.041 0.006 -10000 0 0 11 11
metaphase 0 0.004 0.016 12 -0.013 26 38
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.001 0.02 0.045 5 -0.052 44 49
G2 phase of mitotic cell cycle -0.001 0.003 0.012 13 -10000 0 13
STAG2 0.039 0.01 -10000 0 0 35 35
GRASP65/GM130/RAB1/GTP 0.015 0.071 -10000 0 -0.58 6 6
spindle elongation -0.002 0.037 0.075 4 -0.098 42 46
ODF2 0.04 0.009 -10000 0 0 27 27
BUB1 -0.043 0.25 -10000 0 -0.73 61 61
TPT1 -0.004 0.055 -10000 0 -0.18 41 41
CDC25C -0.008 0.089 -10000 0 -0.33 36 36
CDC25B 0.025 0.03 -10000 0 -0.031 104 104
SGOL1 -0.009 0.054 0.093 3 -0.17 50 53
RHOA 0.041 0.007 -10000 0 0 14 14
CCNB1/CDK1 0.005 0.13 -10000 0 -0.2 128 128
CDC14B -0.01 0.005 0.011 24 -10000 0 24
CDC20 0.034 0.016 -10000 0 0 104 104
PLK1/PBIP1 -0.003 0.032 -10000 0 -0.1 34 34
mitosis -0.001 0.003 0.013 7 -0.012 4 11
FBXO5 -0.016 0.063 0.11 4 -0.17 59 63
CDC2 0.028 0.022 -10000 0 -0.029 18 18
NDC80 0 0 -10000 0 -10000 0 0
metaphase plate congression 0.002 0.053 -10000 0 -0.25 19 19
ERCC6L -0.03 0.099 -10000 0 -0.2 125 125
NLP/gamma Tubulin -0.002 0.032 0.066 3 -0.088 45 48
microtubule cytoskeleton organization -0.004 0.055 -10000 0 -0.18 41 41
G2/M transition DNA damage checkpoint 0 0.002 0.012 9 -10000 0 9
PPP1R12A 0.04 0.01 -10000 0 0 29 29
interphase 0 0.002 0.012 9 -10000 0 9
PLK1/PRC1-2 0.013 0.083 -10000 0 -0.15 91 91
GRASP65/GM130/RAB1/GTP/PLK1 0.05 0.06 -10000 0 -0.12 32 32
RAB1A 0.04 0.009 -10000 0 0 29 29
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.001 0.026 0.059 11 -0.066 39 50
mitotic prometaphase -0.002 0.004 0.018 18 -10000 0 18
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.069 -10000 0 -0.24 24 24
microtubule-based process 0.014 0.051 -10000 0 -0.14 37 37
Golgi organization -0.002 0.037 0.075 4 -0.098 42 46
Cohesin/SA2 0.013 0.047 -10000 0 -0.098 59 59
PPP1CB/MYPT1 0.05 0.041 -10000 0 -0.14 21 21
KIF20A 0.032 0.018 -10000 0 0 132 132
APC/C/CDC20 0.016 0.051 -10000 0 -0.13 39 39
PPP2R1A 0.039 0.011 -10000 0 0 42 42
chromosome segregation -0.003 0.032 -10000 0 -0.1 34 34
PRC1 0.036 0.015 -10000 0 0 82 82
ECT2 0.035 0.11 0.21 136 -0.14 55 191
C13orf34 -0.001 0.029 0.063 8 -0.076 40 48
NUDC 0.002 0.053 -10000 0 -0.25 19 19
regulation of attachment of spindle microtubules to kinetochore -0.026 0.082 0.12 1 -0.21 66 67
spindle assembly -0.002 0.034 0.071 11 -0.09 39 50
spindle stabilization -0.001 0.02 0.045 5 -0.052 44 49
APC/C/HCDH1 0.032 0.014 -10000 0 -0.11 1 1
MKLP2/PLK1 0.014 0.051 -10000 0 -0.14 37 37
CCNB1 0.026 0.027 -10000 0 -0.03 60 60
PPP1CB 0.04 0.01 -10000 0 0 32 32
BTRC 0.04 0.008 -10000 0 0 22 22
ROCK2 -0.006 0.094 -10000 0 -0.32 40 40
TUBG1 -0.002 0.054 -10000 0 -0.2 31 31
G2/M transition of mitotic cell cycle -0.036 0.1 0.13 12 -0.21 121 133
MLF1IP -0.008 0.007 0.011 32 -10000 0 32
INCENP 0.041 0.005 -10000 0 0 6 6
Canonical NF-kappaB 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
FBXW11 0.036 0.027 0.09 2 -0.069 30 32
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.009 0.13 0.24 4 -0.27 68 72
ERC1 0 0 -10000 0 -10000 0 0
RIP2/NOD2 0.015 0.041 -10000 0 -0.13 40 40
NFKBIA -0.035 0.067 0.24 4 -0.28 29 33
BIRC2 0.036 0.014 -10000 0 0 73 73
IKBKB 0.038 0.011 -10000 0 0 44 44
RIPK2 0.032 0.018 -10000 0 0 125 125
IKBKG -0.006 0.11 -10000 0 -0.3 48 48
IKK complex/A20 0.032 0.12 -10000 0 -0.28 42 42
NEMO/A20/RIP2 0.032 0.017 -10000 0 0 125 125
XPO1 0.039 0.011 -10000 0 0 39 39
NEMO/ATM 0.003 0.13 -10000 0 -0.31 52 52
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.041 0.006 -10000 0 0 11 11
Exportin 1/RanGTP 0.047 0.036 -10000 0 -0.11 24 24
IKK complex/ELKS 0.005 0.11 -10000 0 -0.28 48 48
BCL10/MALT1/TRAF6 0.063 0.049 -10000 0 -0.13 20 20
NOD2 0 0 -10000 0 -10000 0 0
NFKB1 0.032 0.028 0.083 1 -0.072 24 25
RELA 0.036 0.028 0.097 1 -0.068 33 34
MALT1 0.036 0.015 -10000 0 0 80 80
cIAP1/UbcH5C 0.039 0.053 -10000 0 -0.14 38 38
ATM 0.036 0.014 -10000 0 0 72 72
TNF/TNFR1A 0.047 0.038 -10000 0 -0.14 15 15
TRAF6 0.04 0.009 -10000 0 0 24 24
PRKCA 0.035 0.016 -10000 0 0 91 91
CHUK 0.038 0.012 -10000 0 0 52 52
UBE2D3 0.038 0.012 -10000 0 0 50 50
TNF 0.04 0.009 -10000 0 0 25 25
NF kappa B1 p50/RelA 0.057 0.081 -10000 0 -0.15 60 60
BCL10 0.041 0.006 -10000 0 0 12 12
proteasomal ubiquitin-dependent protein catabolic process -0.035 0.066 0.24 4 -0.28 29 33
beta TrCP1/SCF ubiquitin ligase complex 0.036 0.027 0.09 2 -0.069 30 32
TNFRSF1A 0.036 0.015 -10000 0 0 82 82
IKK complex 0.018 0.13 -10000 0 -0.31 46 46
CYLD 0.038 0.012 -10000 0 0 51 51
IKK complex/PKC alpha 0.022 0.13 -10000 0 -0.3 47 47
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.038 0.012 -10000 0 0 50 50
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.04 0.008 -10000 0 0 22 22
TCEB1 0.038 0.012 -10000 0 0 49 49
HIF1A/p53 0 0.087 0.22 1 -0.27 35 36
HIF1A -0.002 0.074 0.16 4 -0.31 18 22
COPS5 0.035 0.015 -10000 0 0 84 84
VHL/Elongin B/Elongin C/RBX1/CUL2 0.085 0.071 -10000 0 -0.12 29 29
FIH (dimer) 0.04 0.009 -10000 0 0 25 25
CDKN2A 0.028 0.019 -10000 0 0 176 176
ARNT/IPAS 0.054 0.025 -10000 0 -0.14 4 4
HIF1AN 0.04 0.009 -10000 0 0 25 25
GNB2L1 0.041 0.005 -10000 0 0 7 7
HIF1A/ARNT 0.013 0.086 0.22 1 -0.29 24 25
CUL2 0.039 0.011 -10000 0 0 38 38
OS9 0.039 0.01 -10000 0 0 37 37
RACK1/Elongin B/Elongin C 0.071 0.037 -10000 0 -0.12 10 10
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.006 0.074 0.15 4 -0.29 22 26
PHD1-3/OS9 0.052 0.081 -10000 0 -0.11 88 88
HIF1A/RACK1/Elongin B/Elongin C 0.047 0.091 -10000 0 -0.29 20 20
VHL 0.04 0.009 -10000 0 0 27 27
HSP90AA1 0 0 -10000 0 -10000 0 0
HIF1A/JAB1 0.011 0.081 0.22 1 -0.28 24 25
EGLN3 0.028 0.02 -10000 0 0 185 185
EGLN2 0.04 0.009 -10000 0 0 27 27
EGLN1 0.039 0.01 -10000 0 0 35 35
TP53 0.027 0.02 -10000 0 0 200 200
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.023 0.13 -10000 0 -0.55 23 23
ARNT 0.041 0.006 -10000 0 0 13 13
ARD1A 0.04 0.009 -10000 0 0 30 30
RBX1 0.037 0.014 -10000 0 0 68 68
HIF1A/p19ARF 0.003 0.084 -10000 0 -0.28 29 29
Signaling events mediated by PRL

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
CCNE1 0.028 0.02 -10000 0 0 188 188
mol:Halofuginone 0.002 0.022 -10000 0 -0.17 9 9
ITGA1 0.032 0.018 -10000 0 0 131 131
CDKN1A 0.02 0.078 -10000 0 -0.36 17 17
PRL-3/alpha Tubulin 0.01 0.038 -10000 0 -0.13 35 35
mol:Ca2+ -0.003 0.071 0.26 34 -10000 0 34
AGT 0.038 0.011 -10000 0 0 44 44
CCNA2 -0.016 0.087 -10000 0 -0.62 7 7
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 0.007 0.043 -10000 0 -0.32 9 9
CDK2/Cyclin E1 0.026 0.096 -10000 0 -0.35 17 17
MAPK3 -0.012 0.01 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.032 0.068 -10000 0 -0.14 70 70
MAPK1 -0.011 0.01 -10000 0 -10000 0 0
PTP4A1 -0.003 0.076 -10000 0 -0.61 7 7
PTP4A3 0.025 0.021 -10000 0 0 228 228
PTP4A2 0.04 0.009 -10000 0 0 30 30
ITGB1 -0.011 0.01 -10000 0 -10000 0 0
SRC 0.039 0.01 -10000 0 0 31 31
RAC1 -0.008 0.11 -10000 0 -0.36 44 44
Rab GGTase beta/Rab GGTase alpha 0.035 0.063 -10000 0 -0.14 62 62
PRL-1/ATF-5 0.016 0.095 -10000 0 -0.54 9 9
RABGGTA 0.04 0.009 -10000 0 0 26 26
BCAR1 -0.003 0.069 0.26 32 -10000 0 32
RHOC -0.006 0.11 -10000 0 -0.36 42 42
RHOA -0.008 0.11 -10000 0 -0.36 45 45
cell motility 0.01 0.12 0.29 1 -0.35 38 39
PRL-1/alpha Tubulin -0.018 0.078 -10000 0 -0.54 9 9
PRL-3/alpha1 Integrin 0.009 0.067 -10000 0 -0.15 68 68
ROCK1 0.009 0.12 0.3 1 -0.36 38 39
RABGGTB 0.036 0.015 -10000 0 0 83 83
CDK2 0.038 0.013 -10000 0 0 56 56
mitosis -0.002 0.076 -10000 0 -0.61 7 7
ATF5 0.038 0.012 -10000 0 0 52 52
Regulation of Androgen receptor activity

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
HDAC1 -0.017 0.007 -10000 0 -10000 0 0
SMARCC1 -0.012 0.17 -10000 0 -1.1 13 13
REL 0.04 0.007 -10000 0 0 18 18
HDAC7 -0.045 0.093 0.18 15 -0.22 72 87
JUN 0.036 0.015 -10000 0 0 80 80
EP300 0.036 0.014 -10000 0 0 72 72
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.012 0.021 0.063 13 -10000 0 13
FOXO1 0 0 -10000 0 -10000 0 0
T-DHT/AR -0.002 0.12 0.28 6 -0.22 87 93
MAP2K6 0.028 0.025 -10000 0 -0.034 49 49
BRM/BAF57 0.031 0.059 -10000 0 -0.13 53 53
MAP2K4 0.031 0.024 -10000 0 -0.015 106 106
SMARCA2 0.032 0.018 -10000 0 0 135 135
PDE9A -0.086 0.32 -10000 0 -0.83 83 83
NCOA2 0.037 0.014 -10000 0 0 69 69
CEBPA 0.037 0.013 -10000 0 0 65 65
EHMT2 0.041 0.007 -10000 0 0 17 17
cell proliferation -0.015 0.12 0.29 10 -0.3 34 44
NR0B1 0.039 0.011 -10000 0 0 38 38
EGR1 0.028 0.02 -10000 0 0 192 192
RXRs/9cRA 0.07 0.027 -10000 0 -0.1 3 3
AR/RACK1/Src -0.014 0.092 0.21 24 -0.22 22 46
AR/GR -0.011 0.093 0.21 2 -0.19 85 87
GNB2L1 0.042 0.005 -10000 0 0 7 7
PKN1 0.034 0.016 -10000 0 0 98 98
RCHY1 0.036 0.014 -10000 0 0 75 75
epidermal growth factor receptor activity 0 0 0.003 1 -10000 0 1
MAPK8 -0.013 0.021 0.052 6 -0.059 1 7
T-DHT/AR/TIF2/CARM1 0.004 0.088 0.24 6 -0.21 25 31
SRC -0.017 0.064 0.17 38 -0.15 7 45
NR3C1 0.038 0.011 -10000 0 0 44 44
KLK3 0.005 0.072 -10000 0 -10000 0 0
APPBP2 0.03 0.027 -10000 0 -0.034 67 67
TRIM24 0.039 0.012 -10000 0 0 44 44
T-DHT/AR/TIP60 -0.036 0.059 0.089 3 -0.16 63 66
TMPRSS2 0.013 0.12 -10000 0 -0.57 13 13
RXRG 0.036 0.015 -10000 0 0 84 84
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.04 0.01 -10000 0 0 31 31
RXRB 0.041 0.007 -10000 0 0 16 16
CARM1 0.037 0.014 -10000 0 0 70 70
NR2C2 0.041 0.007 -10000 0 0 16 16
KLK2 -0.001 0.073 0.25 3 -0.26 7 10
AR -0.018 0.078 0.15 11 -0.18 74 85
SENP1 0.039 0.01 -10000 0 0 37 37
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 0.038 0.01 -10000 0 0 35 35
SRY 0.041 0.002 -10000 0 0 2 2
GATA2 0.039 0.01 -10000 0 0 34 34
MYST2 0.04 0.009 -10000 0 0 25 25
HOXB13 0.04 0.01 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.017 0.094 0.22 27 -0.22 23 50
positive regulation of transcription 0.039 0.01 -10000 0 0 34 34
DNAJA1 0.03 0.026 -10000 0 -0.034 65 65
proteasomal ubiquitin-dependent protein catabolic process -0.002 0.091 0.17 23 -0.25 52 75
NCOA1 0.041 0.034 0.12 5 -0.18 11 16
SPDEF 0.037 0.015 -10000 0 0 74 74
T-DHT/AR/TIF2 -0.011 0.096 0.2 10 -0.26 43 53
T-DHT/AR/Hsp90 -0.035 0.059 0.097 2 -0.16 62 64
GSK3B 0.04 0.009 -10000 0 0 29 29
NR2C1 0.039 0.011 -10000 0 0 40 40
mol:T-DHT -0.023 0.052 0.19 14 -0.16 8 22
SIRT1 0.04 0.008 -10000 0 0 19 19
ZMIZ2 -0.001 0.001 -10000 0 -0.012 2 2
POU2F1 0.033 0.057 0.12 3 -0.11 71 74
T-DHT/AR/DAX-1 -0.021 0.082 0.2 20 -0.21 25 45
CREBBP 0.038 0.012 -10000 0 0 49 49
SMARCE1 0.039 0.011 -10000 0 0 42 42
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.046 0.051 -10000 0 -0.14 35 35
Necdin/E2F1 0.045 0.041 -10000 0 -0.14 17 17
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.072 0.06 -10000 0 -0.11 41 41
NGF (dimer)/p75(NTR)/BEX1 0.022 0.053 -10000 0 -0.11 61 61
NT-4/5 (dimer)/p75(NTR) 0.029 0.009 -10000 0 -0.13 1 1
IKBKB 0.038 0.011 -10000 0 0 44 44
AKT1 0.014 0.09 0.19 98 -0.18 6 104
IKBKG 0.042 0.003 -10000 0 0 2 2
BDNF 0.04 0.009 -10000 0 0 24 24
MGDIs/NGR/p75(NTR)/LINGO1 0.049 0.021 -10000 0 -0.11 3 3
FURIN 0.039 0.01 -10000 0 0 32 32
proBDNF (dimer)/p75(NTR)/Sortilin 0.066 0.048 -10000 0 -0.12 25 25
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.019 0.072 -10000 0 -0.13 79 79
proBDNF (dimer) 0.04 0.009 -10000 0 0 24 24
NTRK1 0.039 0.01 -10000 0 0 33 33
RTN4R 0.038 0.012 -10000 0 0 50 50
neuron apoptosis -0.058 0.13 0.31 1 -0.36 46 47
IRAK1 0.04 0.008 -10000 0 0 19 19
SHC1 0.017 0.009 0.069 7 -0.11 1 8
ARHGDIA 0.038 0.013 -10000 0 0 56 56
RhoA/GTP 0.029 0.014 -10000 0 -0.13 4 4
Gamma Secretase 0.072 0.087 -10000 0 -0.12 68 68
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.056 0.057 -10000 0 -0.11 49 49
MAGEH1 0.038 0.011 -10000 0 0 44 44
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.053 0.054 -10000 0 -0.1 40 40
Mammalian IAPs/DIABLO 0.012 0.089 -10000 0 -0.13 127 127
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.04 0.009 -10000 0 0 25 25
APP 0.038 0.012 -10000 0 0 47 47
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.042 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.047 0.028 0.19 1 -0.11 8 9
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.017 0.04 0.2 3 -0.11 13 16
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.009 0.063 -10000 0 -0.16 51 51
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.05 0.024 -10000 0 -0.11 8 8
NCSTN 0.04 0.008 -10000 0 0 21 21
mol:GTP 0.045 0.035 -10000 0 -0.11 23 23
PSENEN 0.035 0.015 -10000 0 0 88 88
mol:ceramide -0.021 0.027 0.19 3 -0.1 25 28
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.011 0.093 -10000 0 -0.32 22 22
p75(NTR)/beta APP 0.048 0.043 -10000 0 -0.14 24 24
BEX1 0.027 0.02 -10000 0 0 202 202
mol:GDP -0.008 0.004 -10000 0 -0.1 1 1
NGF (dimer) -0.004 0.074 -10000 0 -0.1 171 171
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.064 0.037 -10000 0 -0.1 8 8
PIK3R1 0.034 0.016 -10000 0 0 106 106
RAC1/GTP 0.044 0.016 -10000 0 -0.06 2 2
MYD88 0.041 0.007 -10000 0 0 15 15
CHUK 0.038 0.012 -10000 0 0 52 52
NGF (dimer)/p75(NTR)/PKA 0.045 0.035 -10000 0 -0.11 23 23
RHOB 0.04 0.008 -10000 0 0 22 22
RHOA 0.041 0.007 -10000 0 0 14 14
MAGE-G1/E2F1 0.053 0.024 -10000 0 -0.14 2 2
NT3 (dimer) 0.031 0.018 -10000 0 0 144 144
TP53 -0.023 0.047 0.21 9 -0.18 12 21
PRDM4 -0.022 0.027 0.19 3 -0.1 25 28
BDNF (dimer) 0.019 0.091 -10000 0 -0.11 164 164
PIK3CA 0.03 0.019 -10000 0 0 150 150
SORT1 0.038 0.012 -10000 0 0 46 46
activation of caspase activity 0.065 0.057 -10000 0 -0.11 41 41
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.062 0.049 -10000 0 -0.11 33 33
RHOC 0.041 0.006 -10000 0 0 13 13
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.016 0.056 0.24 5 -0.21 10 15
DIABLO 0.037 0.013 -10000 0 0 64 64
SMPD2 -0.021 0.027 0.19 3 -0.1 25 28
APH1B 0.035 0.015 -10000 0 0 86 86
APH1A 0.041 0.006 -10000 0 0 11 11
proNGF (dimer)/p75(NTR)/Sortilin 0.044 0.037 -10000 0 -0.11 26 26
PSEN1 0.039 0.01 -10000 0 0 34 34
APAF-1/Pro-Caspase 9 0.051 0.042 -10000 0 -0.15 20 20
NT3 (dimer)/p75(NTR) 0.041 0.038 -10000 0 -0.15 10 10
MAPK8 -0.019 0.064 0.25 6 -0.24 12 18
MAPK9 -0.02 0.061 0.24 5 -0.23 10 15
APAF1 0.039 0.01 -10000 0 0 33 33
NTF3 0.031 0.018 -10000 0 0 144 144
NTF4 0 0 -10000 0 -10000 0 0
NDN 0.036 0.014 -10000 0 0 76 76
RAC1/GDP 0.029 0.01 -10000 0 -0.13 1 1
RhoA-B-C/GDP 0.073 0.051 -10000 0 -0.1 28 28
p75 CTF/Sortilin/TRAF6/NRIF 0.075 0.076 -10000 0 -0.13 57 57
RhoA-B-C/GTP 0.044 0.035 -10000 0 -0.11 23 23
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.098 0.065 -10000 0 -0.11 31 31
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.084 0.058 -10000 0 -0.12 31 31
PRKACB 0.038 0.012 -10000 0 0 49 49
proBDNF (dimer)/p75 ECD 0.046 0.048 -10000 0 -0.14 31 31
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.026 0.02 -10000 0 0 213 213
BIRC2 0.036 0.014 -10000 0 0 73 73
neuron projection morphogenesis -0.019 0.05 0.14 5 -0.16 24 29
BAD -0.024 0.067 0.26 4 -0.21 20 24
RIPK2 0.032 0.018 -10000 0 0 125 125
NGFR 0.04 0.009 -10000 0 0 26 26
CYCS -0.026 0.033 0.19 2 -0.18 5 7
ADAM17 0.038 0.013 -10000 0 0 56 56
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.049 0.056 -10000 0 -0.11 43 43
BCL2L11 -0.024 0.067 0.26 4 -0.22 17 21
BDNF (dimer)/p75(NTR) 0.057 0.018 -10000 0 -0.11 1 1
PI3K 0.036 0.06 -10000 0 -0.12 48 48
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.061 0.046 -10000 0 -0.1 27 27
NDNL2 0.039 0.011 -10000 0 0 40 40
YWHAE 0.038 0.012 -10000 0 0 50 50
PRKCI 0.027 0.02 -10000 0 0 193 193
NGF (dimer)/p75(NTR) 0.029 0.009 -10000 0 -0.13 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.06 0.052 -10000 0 -0.11 38 38
TRAF6 0.04 0.009 -10000 0 0 24 24
RAC1 0.039 0.01 -10000 0 0 35 35
PRKCZ 0.042 0 -10000 0 -10000 0 0
PLG 0.038 0.012 -10000 0 0 50 50
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.013 0.044 0.16 6 -0.16 25 31
SQSTM1 0.038 0.012 -10000 0 0 48 48
NGFRAP1 0.041 0.007 -10000 0 0 15 15
CASP3 -0.026 0.071 0.26 4 -0.23 25 29
E2F1 0.039 0.011 -10000 0 0 41 41
CASP9 0.04 0.009 -10000 0 0 26 26
IKK complex 0.046 0.1 -10000 0 -0.25 22 22
NGF (dimer)/TRKA 0.029 0.007 -10000 0 -10000 0 0
MMP7 0.016 0.02 -10000 0 0 336 336
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.079 0.054 -10000 0 -0.1 33 33
MMP3 0.038 0.013 -10000 0 0 56 56
APAF-1/Caspase 9 -0.056 0.061 -10000 0 -0.2 50 50
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.038 0.19 0.33 11 -0.98 21 32
VDR 0.037 0.013 -10000 0 0 58 58
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.024 0.09 -10000 0 -0.23 45 45
RXRs/LXRs/DNA/Oxysterols 0.017 0.12 -10000 0 -0.34 54 54
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA 0.001 0.016 0.057 1 -0.047 48 49
RARs/THRs/DNA/Src-1 -0.004 0.094 -10000 0 -0.18 110 110
RXRs/NUR77 0.079 0.072 0.3 1 -0.11 36 37
RXRs/PPAR 0.027 0.054 -10000 0 -0.16 11 11
NCOR2 0.04 0.009 -10000 0 0 26 26
VDR/VDR/Vit D3 0.022 0.032 -10000 0 -0.13 23 23
RARs/VDR/DNA/Vit D3 0.064 0.069 -10000 0 -0.11 59 59
RARA 0.039 0.01 -10000 0 0 34 34
NCOA1 0.04 0.009 -10000 0 0 28 28
VDR/VDR/DNA 0.037 0.013 -10000 0 0 58 58
RARs/RARs/DNA/9cRA 0.052 0.053 -10000 0 -0.1 46 46
RARG 0.04 0.009 -10000 0 0 27 27
RPS6KB1 -0.018 0.1 0.56 5 -0.42 22 27
RARs/THRs/DNA/SMRT -0.002 0.09 -10000 0 -0.17 107 107
THRA 0.039 0.011 -10000 0 0 39 39
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.022 0.032 -10000 0 -0.13 23 23
RXRs/PPAR/9cRA/PGJ2/DNA 0.07 0.078 0.31 12 -0.15 34 46
NR1H4 0.041 0.007 -10000 0 0 15 15
RXRs/LXRs/DNA 0.094 0.1 0.32 1 -0.2 34 35
NR1H2 0.034 0.032 -10000 0 -0.058 51 51
NR1H3 0.035 0.034 -10000 0 -0.065 52 52
RXRs/VDR/DNA/Vit D3 0.072 0.072 0.28 1 -0.12 16 17
NR4A1 0.034 0.016 -10000 0 0 99 99
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.023 0.041 0.16 1 -0.15 4 5
RXRG 0.032 0.031 0.099 1 -0.055 44 45
RXR alpha/CCPG 0.026 0.022 -10000 0 -0.074 2 2
RXRA 0.035 0.031 0.099 1 -0.056 50 51
RXRB 0.036 0.034 0.1 1 -0.062 55 56
THRB 0.034 0.017 -10000 0 0 107 107
PPARG 0.039 0.01 -10000 0 0 34 34
PPARD 0.04 0.008 -10000 0 0 23 23
TNF 0.009 0.12 -10000 0 -0.51 8 8
mol:Oxysterols 0 0.014 0.027 1 -0.04 58 59
cholesterol transport 0.017 0.12 -10000 0 -0.34 54 54
PPARA 0.034 0.016 -10000 0 0 98 98
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.036 0.015 -10000 0 0 78 78
RXRs/NUR77/BCL2 0.021 0.047 -10000 0 -0.14 23 23
SREBF1 0.007 0.12 -10000 0 -0.55 6 6
RXRs/RXRs/DNA/9cRA 0.07 0.077 0.3 12 -0.15 34 46
ABCA1 -0.036 0.26 -10000 0 -0.79 56 56
RARs/THRs 0.07 0.092 -10000 0 -0.12 82 82
RXRs/FXR 0.088 0.068 0.3 1 -0.12 3 4
BCL2 0.036 0.014 -10000 0 0 76 76
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.049 0.023 -10000 0 -0.11 5 5
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.038 0.012 -10000 0 0 48 48
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.034 0.016 -10000 0 0 98 98
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.037 0.013 -10000 0 0 59 59
RAC1-CDC42/GTP/PAK family 0.008 0.048 -10000 0 -0.15 32 32
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.037 0.013 -10000 0 0 59 59
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.04 0.008 -10000 0 0 19 19
FYN 0.034 0.016 -10000 0 0 102 102
MAP3K12 0.041 0.006 -10000 0 0 13 13
FGR 0.041 0.007 -10000 0 0 16 16
p38 alpha/TAB1 0.001 0.12 0.19 2 -0.26 53 55
PRKG1 0.04 0.009 -10000 0 0 30 30
DUSP8 0.04 0.009 -10000 0 0 27 27
PGK/cGMP/p38 alpha -0.003 0.11 -10000 0 -0.26 53 53
apoptosis 0 0.11 0.18 2 -0.25 53 55
RAL/GTP 0.046 0.037 -10000 0 -0.11 25 25
LYN 0.036 0.015 -10000 0 0 83 83
DUSP1 0.027 0.02 -10000 0 0 202 202
PAK1 0.037 0.014 -10000 0 0 66 66
SRC 0.039 0.01 -10000 0 0 31 31
RAC1/OSM/MEKK3/MKK3 0.09 0.04 -10000 0 -0.11 1 1
TRAF6 0.04 0.009 -10000 0 0 24 24
RAC1 0.039 0.01 -10000 0 0 35 35
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 0.041 0.007 -10000 0 0 16 16
RAC1-CDC42/GTP 0.05 0.022 -10000 0 -0.14 3 3
MAPK11 -0.028 0.12 0.2 2 -0.29 63 65
BLK 0.033 0.017 -10000 0 0 115 115
HCK 0.036 0.015 -10000 0 0 79 79
MAP2K3 0.039 0.011 -10000 0 0 43 43
DUSP16 0.035 0.015 -10000 0 0 84 84
DUSP10 0.034 0.017 -10000 0 0 107 107
TRAF6/MEKK3 0.048 0.022 -10000 0 -0.098 8 8
MAP3K7IP1 0.038 0.012 -10000 0 0 51 51
MAPK14 -0.01 0.12 0.19 3 -0.28 53 56
positive regulation of innate immune response -0.024 0.14 0.23 2 -0.34 56 58
LCK 0.04 0.009 -10000 0 0 28 28
p38alpha-beta/MKP7 -0.013 0.14 0.24 2 -0.33 53 55
p38alpha-beta/MKP5 -0.017 0.14 0.24 2 -0.33 54 56
PGK/cGMP 0.029 0.007 -10000 0 -10000 0 0
PAK2 0.04 0.009 -10000 0 0 24 24
p38alpha-beta/MKP1 -0.028 0.14 0.25 1 -0.33 60 61
CDC42 0.04 0.008 -10000 0 0 22 22
RALB 0.04 0.009 -10000 0 0 27 27
RALA 0.04 0.009 -10000 0 0 29 29
PAK3 0.037 0.013 -10000 0 0 62 62
EGFR-dependent Endothelin signaling events

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
HRAS 0.04 0.009 -10000 0 0 29 29
EGFR 0.036 0.014 -10000 0 0 73 73
EGF/EGFR 0.044 0.059 -10000 0 -0.099 55 55
EGF/EGFR dimer/SHC/GRB2/SOS1 0.081 0.077 -10000 0 -0.12 44 44
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.035 0.015 -10000 0 0 86 86
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.038 0.012 -10000 0 0 52 52
EGF/EGFR dimer/SHC 0.057 0.055 -10000 0 -0.12 33 33
mol:GDP 0.073 0.072 -10000 0 -0.12 44 44
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.034 0.016 -10000 0 0 100 100
GRB2/SOS1 0.048 0.046 -10000 0 -0.14 26 26
HRAS/GTP 0.049 0.06 -10000 0 -0.11 42 42
SHC1 0.04 0.009 -10000 0 0 29 29
HRAS/GDP 0.069 0.072 -10000 0 -0.12 42 42
FRAP1 -0.016 0.074 0.2 39 -0.18 4 43
EGF/EGFR dimer 0.04 0.051 -10000 0 -0.13 37 37
SOS1 0.038 0.013 -10000 0 0 57 57
GRB2 0.041 0.007 -10000 0 0 14 14
ETA receptor/Endothelin-1 0.037 0.047 -10000 0 -0.14 25 25
ErbB2/ErbB3 signaling events

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
USP8 -0.013 0.01 0.019 20 -10000 0 20
RAS family/GTP 0.017 0.1 0.26 3 -0.21 28 31
NFATC4 -0.018 0.081 0.24 20 -0.18 4 24
ERBB2IP 0.036 0.015 -10000 0 -0.001 72 72
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.001 0.08 0.24 2 -0.16 50 52
JUN 0.008 0.086 0.21 4 -10000 0 4
HRAS 0.04 0.009 -10000 0 0 29 29
DOCK7 -0.024 0.083 0.23 15 -0.21 10 25
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.036 0.08 0.21 21 -0.12 69 90
AKT1 -0.005 0.012 0.021 29 -10000 0 29
BAD -0.015 0.007 0.012 12 -10000 0 12
MAPK10 -0.008 0.07 0.19 24 -0.16 2 26
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0 0.086 0.26 2 -0.17 50 52
RAF1 0.008 0.11 0.26 27 -0.23 27 54
ErbB2/ErbB3/neuregulin 2 0.028 0.076 0.18 38 -0.12 78 116
STAT3 -0.021 0.24 -10000 0 -0.92 37 37
cell migration -0.008 0.073 0.21 23 -0.19 9 32
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.03 0.23 0.41 3 -0.58 47 50
FOS -0.034 0.22 0.36 7 -0.4 125 132
NRAS 0.039 0.01 -10000 0 0 31 31
mol:Ca2+ -0.001 0.08 0.24 2 -0.16 50 52
MAPK3 -0.011 0.19 0.37 4 -0.49 40 44
MAPK1 -0.023 0.2 0.37 4 -0.49 48 52
JAK2 -0.023 0.079 0.25 9 -0.23 7 16
NF2 0.005 0.071 -10000 0 -0.72 5 5
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.002 0.073 0.18 3 -0.17 64 67
NRG1 0.035 0.016 -10000 0 0 90 90
GRB2/SOS1 0.048 0.046 -10000 0 -0.14 26 26
MAPK8 -0.019 0.11 0.23 5 -0.22 76 81
MAPK9 -0.011 0.071 0.19 24 -0.17 5 29
ERBB2 -0.024 0.04 0.26 9 -10000 0 9
ERBB3 0.033 0.018 -10000 0 0 124 124
SHC1 0.04 0.009 -10000 0 0 29 29
RAC1 0.039 0.01 -10000 0 0 35 35
apoptosis 0.005 0.027 0.18 1 -0.21 7 8
STAT3 (dimer) -0.017 0.24 -10000 0 -0.9 37 37
RNF41 -0.017 0.016 0.047 11 -0.12 3 14
FRAP1 -0.014 0.007 0.012 12 -10000 0 12
RAC1-CDC42/GTP -0.031 0.056 0.087 24 -0.14 47 71
ErbB2/ErbB2/HSP90 (dimer) -0.024 0.015 0.018 3 -0.12 5 8
CHRNA1 0.005 0.15 0.34 7 -0.36 33 40
myelination -0.01 0.097 0.26 33 -0.2 4 37
PPP3CB -0.021 0.079 0.22 12 -0.2 4 16
KRAS 0.034 0.016 -10000 0 0 103 103
RAC1-CDC42/GDP 0.021 0.099 0.21 3 -0.17 64 67
NRG2 0.041 0.006 -10000 0 0 12 12
mol:GDP -0.002 0.072 0.18 3 -0.17 64 67
SOS1 0.038 0.013 -10000 0 0 57 57
MAP2K2 -0.006 0.11 0.25 22 -0.23 37 59
SRC 0.039 0.01 -10000 0 0 31 31
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.022 0.085 0.23 15 -0.21 10 25
MAP2K1 -0.017 0.19 0.38 1 -0.54 27 28
heart morphogenesis -0.001 0.08 0.24 2 -0.16 50 52
RAS family/GDP 0.026 0.1 0.26 3 -0.22 24 27
GRB2 0.041 0.007 -10000 0 0 14 14
PRKACA 0.009 0.078 -10000 0 -0.72 6 6
CHRNE 0.007 0.023 0.074 1 -10000 0 1
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity 0.005 0.012 -10000 0 -0.021 29 29
nervous system development -0.001 0.08 0.24 2 -0.16 50 52
CDC42 0.04 0.008 -10000 0 0 22 22
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.026 0.2 -10000 0 -0.8 33 33
regulation of axonogenesis -0.002 0.051 0.21 22 -10000 0 22
myoblast fusion -0.012 0.1 0.35 36 -0.17 2 38
mol:GTP 0.017 0.066 -10000 0 -0.2 44 44
regulation of calcium-dependent cell-cell adhesion -0.034 0.088 0.15 81 -10000 0 81
ARF1/GTP 0.038 0.059 -10000 0 -0.16 40 40
mol:GM1 0.003 0.047 -10000 0 -0.15 44 44
mol:Choline 0.001 0.039 0.092 1 -0.15 27 28
lamellipodium assembly -0.013 0.12 -10000 0 -0.4 44 44
MAPK3 0.011 0.084 -10000 0 -0.28 40 40
ARF6/GTP/NME1/Tiam1 0.035 0.089 -10000 0 -0.15 81 81
ARF1 0.038 0.012 -10000 0 0 51 51
ARF6/GDP 0.012 0.1 0.18 2 -0.35 36 38
ARF1/GDP 0.015 0.1 -10000 0 -0.3 44 44
ARF6 0.043 0.045 -10000 0 -0.13 33 33
RAB11A 0.04 0.009 -10000 0 0 24 24
TIAM1 0.032 0.023 -10000 0 -0.013 99 99
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.013 0.077 -10000 0 -0.27 34 34
actin filament bundle formation -0.026 0.11 0.31 46 -10000 0 46
KALRN 0.004 0.074 -10000 0 -0.26 36 36
RAB11FIP3/RAB11A 0.058 0.023 -10000 0 -0.14 6 6
RhoA/GDP 0.027 0.11 -10000 0 -0.31 46 46
NME1 0.031 0.024 -10000 0 -0.047 30 30
Rac1/GDP 0.026 0.11 -10000 0 -0.31 45 45
substrate adhesion-dependent cell spreading 0.017 0.066 -10000 0 -0.2 44 44
cortical actin cytoskeleton organization -0.013 0.12 -10000 0 -0.41 44 44
RAC1 0.039 0.01 -10000 0 0 35 35
liver development 0.017 0.066 -10000 0 -0.2 44 44
ARF6/GTP 0.017 0.066 -10000 0 -0.2 44 44
RhoA/GTP 0.041 0.063 -10000 0 -0.16 44 44
mol:GDP -0.003 0.096 -10000 0 -0.34 37 37
ARF6/GTP/RAB11FIP3/RAB11A 0.061 0.066 -10000 0 -0.14 49 49
RHOA 0.041 0.007 -10000 0 0 14 14
PLD1 0.009 0.048 -10000 0 -0.17 30 30
RAB11FIP3 0.042 0.003 -10000 0 0 3 3
tube morphogenesis -0.013 0.12 -10000 0 -0.4 44 44
ruffle organization 0.002 0.051 -10000 0 -0.21 22 22
regulation of epithelial cell migration 0.017 0.066 -10000 0 -0.2 44 44
PLD2 0.016 0.048 -10000 0 -0.15 40 40
PIP5K1A 0.002 0.051 -10000 0 -0.21 22 22
mol:Phosphatidic acid 0.001 0.039 0.092 1 -0.15 27 28
Rac1/GTP -0.013 0.12 -10000 0 -0.41 44 44
S1P3 pathway

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
PDGFRB 0.037 0.013 -10000 0 0 64 64
mol:S1P 0.001 0.007 -10000 0 -0.028 23 23
S1P1/S1P/Gi 0.007 0.08 -10000 0 -0.26 23 23
GNAO1 0.033 0.024 -10000 0 -0.05 19 19
S1P/S1P3/G12/G13 0.046 0.032 -10000 0 -0.066 24 24
AKT1 0.015 0.1 -10000 0 -0.45 21 21
AKT3 -0.02 0.23 -10000 0 -0.9 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.037 0.013 -10000 0 0 64 64
GNAI2 0.04 0.02 -10000 0 -0.031 35 35
GNAI3 0.038 0.02 -10000 0 -0.014 65 65
GNAI1 0.034 0.022 -10000 0 -0.007 111 111
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.001 0.007 -10000 0 -0.03 23 23
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.041 0.007 -10000 0 0 15 15
mol:Ca2+ 0.001 0.1 0.16 1 -0.27 46 47
MAPK3 -0.008 0.094 0.21 1 -0.26 48 49
MAPK1 -0.004 0.089 -10000 0 -0.26 40 40
JAK2 -0.018 0.11 0.19 7 -0.29 51 58
CXCR4 -0.01 0.099 0.19 3 -0.28 47 50
FLT1 0.04 0.022 -10000 0 -0.059 18 18
RhoA/GDP 0.029 0.014 -10000 0 -0.13 4 4
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
SRC -0.002 0.098 0.22 15 -0.26 43 58
S1P/S1P3/Gi 0.001 0.1 0.16 1 -0.27 45 46
RAC1 0.039 0.01 -10000 0 0 35 35
RhoA/GTP 0.011 0.1 -10000 0 -0.26 45 45
VEGFA 0.003 0.01 0.017 98 -0.037 22 120
S1P/S1P2/Gi -0.001 0.087 0.14 1 -0.19 73 74
VEGFR1 homodimer/VEGFA homodimer 0.036 0.032 -10000 0 -0.089 23 23
RHOA 0.041 0.007 -10000 0 0 14 14
S1P/S1P3/Gq 0.017 0.04 -10000 0 -0.15 26 26
GNAQ 0.038 0.012 -10000 0 0 50 50
GNAZ 0.038 0.02 -10000 0 -0.016 58 58
G12/G13 0.053 0.03 -10000 0 -0.14 9 9
GNA14 0.039 0.01 -10000 0 0 33 33
GNA15 0.037 0.014 -10000 0 0 69 69
GNA12 0.039 0.01 -10000 0 0 36 36
GNA13 0.04 0.009 -10000 0 0 28 28
GNA11 0.037 0.013 -10000 0 0 63 63
Rac1/GTP 0.01 0.1 -10000 0 -0.25 45 45
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.039 0.01 -10000 0 0 35 35
RAS family/GTP/Tiam1 0.012 0.06 -10000 0 -0.21 14 14
NT3 (dimer)/TRKC 0.04 0.036 -10000 0 -0.14 9 9
NT3 (dimer)/TRKB 0.055 0.046 -10000 0 -0.12 10 10
SHC/Grb2/SOS1/GAB1/PI3K -0.001 0.08 -10000 0 -0.19 61 61
RAPGEF1 0.04 0.008 -10000 0 0 22 22
BDNF 0.04 0.009 -10000 0 0 24 24
PIK3CA 0.03 0.019 -10000 0 0 150 150
DYNLT1 0.035 0.015 -10000 0 0 84 84
NTRK1 0.039 0.01 -10000 0 0 33 33
NTRK2 0.039 0.011 -10000 0 0 39 39
NTRK3 0.038 0.012 -10000 0 0 50 50
NT-4/5 (dimer)/TRKB 0.05 0.018 -10000 0 -0.087 1 1
neuron apoptosis -0.029 0.1 0.24 32 -0.23 2 34
SHC 2-3/Grb2 0.03 0.11 0.24 2 -0.26 32 34
SHC1 0.04 0.009 -10000 0 0 29 29
SHC2 0.003 0.12 0.21 2 -0.36 46 48
SHC3 0.026 0.082 0.21 2 -0.4 12 14
STAT3 (dimer) 0.003 0.11 -10000 0 -0.27 75 75
NT3 (dimer)/TRKA 0.054 0.047 -10000 0 -0.13 10 10
RIN/GDP 0.048 0.083 0.22 25 -0.19 20 45
GIPC1 0.035 0.015 -10000 0 0 89 89
KRAS 0.034 0.016 -10000 0 0 103 103
DNAJA3 0.009 0.051 0.15 10 -0.14 12 22
RIN/GTP 0.029 0.008 -10000 0 -10000 0 0
CCND1 -0.048 0.17 -10000 0 -0.49 73 73
MAGED1 0.04 0.009 -10000 0 0 25 25
PTPN11 0.04 0.009 -10000 0 0 29 29
RICS 0.037 0.014 -10000 0 0 69 69
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.065 0.05 -10000 0 -0.12 25 25
GRB2 0.041 0.007 -10000 0 0 14 14
NGF (dimer)/TRKA/MATK 0.048 0.02 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.046 0.039 -10000 0 -0.14 16 16
ELMO1 0.035 0.015 -10000 0 0 87 87
RhoG/GTP/ELMO1/DOCK1 0.034 0.047 -10000 0 -0.11 42 42
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.04 0.009 -10000 0 0 29 29
DOCK1 0.037 0.013 -10000 0 0 63 63
GAB2 0.031 0.018 -10000 0 0 142 142
RIT2 0.039 0.011 -10000 0 0 38 38
RIT1 0.038 0.011 -10000 0 0 44 44
FRS2 0.039 0.01 -10000 0 0 37 37
DNM1 0.039 0.01 -10000 0 0 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.038 0.011 -10000 0 0 45 45
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.026 0.061 0.17 8 -0.15 16 24
mol:GDP 0.044 0.1 0.26 25 -0.28 20 45
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.022 0.03 -10000 0 -0.13 19 19
RIT1/GDP 0.044 0.082 0.22 21 -0.19 22 43
TIAM1 0.037 0.014 -10000 0 0 70 70
PIK3R1 0.034 0.016 -10000 0 0 106 106
BDNF (dimer)/TRKB 0.07 0.033 -10000 0 -0.12 1 1
KIDINS220/CRKL/C3G 0.056 0.018 -10000 0 -10000 0 0
SHC/RasGAP 0.047 0.039 -10000 0 -0.13 17 17
FRS2 family/SHP2 0.067 0.05 -10000 0 -0.12 26 26
SHC/GRB2/SOS1/GAB1 0.079 0.061 -10000 0 -0.12 30 30
RIT1/GTP 0.025 0.026 -10000 0 -0.13 15 15
NT3 (dimer) 0.031 0.018 -10000 0 0 144 144
RAP1/GDP 0.033 0.071 0.17 17 -0.17 24 41
KIDINS220/CRKL 0.039 0.01 -10000 0 0 35 35
BDNF (dimer) 0.04 0.009 -10000 0 0 24 24
ubiquitin-dependent protein catabolic process 0.041 0.034 -10000 0 -0.11 16 16
Schwann cell development -0.007 0.011 -10000 0 -0.044 10 10
EHD4 0.039 0.011 -10000 0 0 38 38
FRS2 family/GRB2/SOS1 0.082 0.06 -10000 0 -0.12 29 29
FRS2 family/SHP2/CRK family/C3G/GAB2 0.007 0.081 -10000 0 -0.24 26 26
RAP1B 0.038 0.013 -10000 0 0 57 57
RAP1A 0.039 0.01 -10000 0 0 35 35
CDC42/GTP 0.067 0.053 0.18 26 -0.11 9 35
ABL1 0.039 0.011 -10000 0 0 41 41
SH2B family/GRB2/SOS1 0.048 0.046 -10000 0 -0.14 26 26
Rap1/GTP 0.009 0.11 -10000 0 -0.27 50 50
STAT3 0.003 0.11 -10000 0 -0.27 75 75
axon guidance 0.046 0.041 -10000 0 -0.11 9 9
MAPK3 -0.009 0.045 0.19 25 -10000 0 25
MAPK1 -0.008 0.045 0.19 25 -10000 0 25
CDC42/GDP 0.05 0.084 0.22 30 -0.2 19 49
NTF3 0.031 0.018 -10000 0 0 144 144
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.049 0.021 -10000 0 -0.11 2 2
PI3K 0.024 0.062 -10000 0 -0.15 47 47
FRS3 0.04 0.008 -10000 0 0 23 23
FAIM 0.038 0.012 -10000 0 0 48 48
GAB1 0.038 0.012 -10000 0 0 49 49
RASGRF1 0.009 0.052 0.15 10 -0.15 12 22
SOS1 0.038 0.013 -10000 0 0 57 57
MCF2L 0.004 0.06 0.18 38 -0.12 9 47
RGS19 0.036 0.015 -10000 0 0 80 80
CDC42 0.04 0.008 -10000 0 0 22 22
RAS family/GTP 0.036 0.12 0.32 2 -0.38 22 24
Rac1/GDP 0.048 0.084 0.22 28 -0.19 20 48
NGF (dimer)/TRKA/GRIT 0.042 0.036 -10000 0 -0.11 20 20
neuron projection morphogenesis -0.049 0.24 -10000 0 -0.83 40 40
NGF (dimer)/TRKA/NEDD4-2 0.042 0.034 -10000 0 -0.11 16 16
MAP2K1 -0.011 0.073 0.2 46 -0.19 3 49
NGFR 0.04 0.009 -10000 0 0 26 26
NGF (dimer)/TRKA/GIPC/GAIP 0.014 0.04 -10000 0 -0.15 23 23
RAS family/GTP/PI3K -0.004 0.071 -10000 0 -0.19 51 51
FRS2 family/SHP2/GRB2/SOS1 0.091 0.075 -10000 0 -0.13 39 39
NRAS 0.039 0.01 -10000 0 0 31 31
GRB2/SOS1 0.048 0.046 -10000 0 -0.14 26 26
PRKCI 0.027 0.02 -10000 0 0 193 193
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.039 0.01 -10000 0 0 35 35
PRKCZ 0.042 0 -10000 0 -10000 0 0
MAPKKK cascade 0.026 0.045 -10000 0 -0.45 2 2
RASA1 0.036 0.014 -10000 0 0 73 73
TRKA/c-Abl 0.051 0.034 -10000 0 -0.14 12 12
SQSTM1 0.038 0.012 -10000 0 0 48 48
BDNF (dimer)/TRKB/GIPC 0.07 0.059 -10000 0 -0.11 21 21
NGF (dimer)/TRKA/p62/Atypical PKCs 0.048 0.069 -10000 0 -0.11 54 54
MATK 0.037 0.013 -10000 0 0 58 58
NEDD4L 0.035 0.015 -10000 0 0 84 84
RAS family/GDP -0.008 0.037 -10000 0 -0.14 20 20
NGF (dimer)/TRKA 0.015 0.051 0.16 6 -0.15 13 19
Rac1/GTP -0.004 0.048 -10000 0 -0.15 14 14
FRS2 family/SHP2/CRK family 0.089 0.068 -10000 0 -0.12 24 24
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.031 0.11 0.25 3 -0.28 27 30
CaM/Ca2+ 0.028 0.016 -10000 0 -0.13 5 5
AKT1 0.039 0.011 -10000 0 0 38 38
AKT2 0.038 0.011 -10000 0 0 45 45
STXBP4 0.038 0.011 -10000 0 0 44 44
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.02 0.11 0.24 4 -0.29 29 33
YWHAZ 0.034 0.016 -10000 0 0 104 104
CALM1 0.04 0.009 -10000 0 0 30 30
YWHAQ 0.04 0.009 -10000 0 0 26 26
TBC1D4 -0.018 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.038 0.012 -10000 0 0 54 54
YWHAB 0.038 0.011 -10000 0 0 44 44
SNARE/Synip 0.045 0.029 -10000 0 -0.11 9 9
YWHAG 0.04 0.009 -10000 0 0 26 26
ASIP 0.038 0.012 -10000 0 0 51 51
PRKCI 0.027 0.02 -10000 0 0 193 193
AS160/CaM/Ca2+ 0.028 0.016 -10000 0 -0.13 5 5
RHOQ 0.039 0.01 -10000 0 0 35 35
GYS1 0.009 0.029 0.25 4 -0.17 6 10
PRKCZ 0.042 0 -10000 0 -10000 0 0
TRIP10 0.038 0.012 -10000 0 0 48 48
TC10/GTP/CIP4/Exocyst 0.046 0.029 -10000 0 -0.11 12 12
AS160/14-3-3 0.022 0.081 0.2 1 -0.26 21 22
VAMP2 0.037 0.013 -10000 0 0 62 62
SLC2A4 0.019 0.12 0.24 4 -0.32 28 32
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0.023 0.026 -10000 0 -0.2 6 6
SFN 0.035 0.015 -10000 0 0 84 84
LNPEP 0.035 0.015 -10000 0 0 87 87
YWHAE 0.038 0.012 -10000 0 0 50 50
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0.04 0.009 -10000 0 0 24 24
MKNK1 0.04 0.009 -10000 0 0 25 25
mol:PIP3 -0.014 0.038 0.2 1 -0.18 11 12
FRAP1 0.028 0.1 -10000 0 -0.42 20 20
AKT1 0.016 0.081 0.17 95 -0.18 9 104
INSR 0.038 0.012 -10000 0 0 53 53
Insulin Receptor/Insulin 0.048 0.023 -10000 0 -0.11 4 4
mol:GTP 0.051 0.09 0.24 28 -0.16 11 39
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.005 0.052 -10000 0 -0.19 27 27
TSC2 0.039 0.01 -10000 0 0 33 33
RHEB/GDP 0.028 0.069 0.16 6 -0.16 14 20
TSC1 0.04 0.009 -10000 0 0 27 27
Insulin Receptor/IRS1 0.033 0.033 -10000 0 -0.23 7 7
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.013 0.071 -10000 0 -0.22 24 24
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.029 0.11 0.25 18 -0.32 26 44
MAP3K5 -0.009 0.067 0.2 5 -0.22 47 52
PIK3R1 0.034 0.017 -10000 0 0 106 106
apoptosis -0.01 0.067 0.2 5 -0.22 48 53
mol:LY294002 0 0 -10000 0 -0.001 7 7
EIF4B 0.024 0.1 0.25 17 -0.29 25 42
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.036 0.098 0.23 15 -0.28 24 39
eIF4E/eIF4G1/eIF4A1 0.012 0.062 -10000 0 -0.26 19 19
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.028 0.053 -10000 0 -0.16 15 15
mTOR/RHEB/GTP/Raptor/GBL 0.026 0.075 0.2 20 -0.17 25 45
FKBP1A 0.039 0.011 -10000 0 0 39 39
RHEB/GTP 0.05 0.085 0.23 18 -0.16 14 32
mol:Amino Acids 0 0 -10000 0 -0.001 7 7
FKBP12/Rapamycin 0.029 0.013 -10000 0 -0.13 2 2
PDPK1 0.005 0.074 0.16 87 -0.17 11 98
EIF4E 0.038 0.011 -10000 0 0 44 44
ASK1/PP5C 0.011 0.2 -10000 0 -0.56 53 53
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.001 0.12 -10000 0 -0.44 20 20
TSC1/TSC2 0.056 0.096 0.26 28 -0.18 8 36
tumor necrosis factor receptor activity 0 0 0.001 7 -10000 0 7
RPS6 0.038 0.011 -10000 0 0 44 44
PPP5C 0.04 0.009 -10000 0 0 27 27
EIF4G1 0.032 0.017 -10000 0 0 124 124
IRS1 0.01 0.03 -10000 0 -0.24 7 7
INS 0.04 0.009 -10000 0 0 30 30
PTEN 0.038 0.011 -10000 0 0 39 39
PDK2 0.005 0.073 0.16 84 -0.18 10 94
EIF4EBP1 -0.049 0.3 -10000 0 -1.1 43 43
PIK3CA 0.031 0.019 -10000 0 0 150 150
PPP2R5D 0.029 0.1 0.28 3 -0.38 19 22
peptide biosynthetic process -0.014 0.031 0.19 10 -10000 0 10
RHEB 0.037 0.013 -10000 0 0 62 62
EIF4A1 0.039 0.01 -10000 0 0 35 35
mol:Rapamycin 0 0.001 0.004 42 -0.002 3 45
EEF2 -0.014 0.031 0.19 10 -10000 0 10
eIF4E/4E-BP1 -0.029 0.28 -10000 0 -0.99 43 43
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.017 0.055 -10000 0 -0.13 51 51
TRAF2/ASK1 0.044 0.035 -10000 0 -0.11 20 20
ATM 0.036 0.014 -10000 0 0 72 72
MAP2K3 -0.043 0.16 -10000 0 -0.35 82 82
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.044 0.14 0.21 2 -0.36 62 64
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.037 0.013 -10000 0 0 58 58
TXN 0.009 0.003 -10000 0 -10000 0 0
CALM1 0.04 0.009 -10000 0 0 30 30
GADD45A 0.036 0.014 -10000 0 0 71 71
GADD45B 0.034 0.016 -10000 0 0 100 100
MAP3K1 0.036 0.015 -10000 0 0 78 78
MAP3K6 0.04 0.008 -10000 0 0 21 21
MAP3K7 0.038 0.012 -10000 0 0 47 47
MAP3K4 0.038 0.012 -10000 0 0 50 50
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.048 0.041 -10000 0 -0.14 20 20
TAK1/TAB family 0.015 0.066 0.19 5 -0.27 19 24
RAC1/OSM/MEKK3 0.072 0.026 -10000 0 -0.1 1 1
TRAF2 0.04 0.009 -10000 0 0 25 25
RAC1/OSM/MEKK3/MKK3 -0.011 0.14 -10000 0 -0.3 75 75
TRAF6 0.008 0.043 -10000 0 -0.2 23 23
RAC1 0.039 0.01 -10000 0 0 35 35
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.04 0.007 -10000 0 0 18 18
CCM2 0.041 0.007 -10000 0 0 16 16
CaM/Ca2+/CAMKIIB 0.051 0.019 -10000 0 -0.11 3 3
MAPK11 0.032 0.018 -10000 0 0 132 132
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.061 0.044 -10000 0 -0.1 22 22
OSM/MEKK3 0.058 0.015 -10000 0 -10000 0 0
TAOK1 0.004 0.053 -10000 0 -0.2 35 35
TAOK2 0.005 0.052 -10000 0 -0.2 34 34
TAOK3 0.001 0.057 -10000 0 -0.2 42 42
MAP3K7IP1 0.038 0.012 -10000 0 0 51 51
MAPK14 0.04 0.009 -10000 0 0 28 28
MAP3K7IP2 0.037 0.013 -10000 0 0 63 63
MAP3K5 0.037 0.014 -10000 0 0 70 70
MAP3K10 0.039 0.011 -10000 0 0 39 39
MAP3K3 0.04 0.008 -10000 0 0 19 19
TRX/ASK1 0.022 0.047 0.11 1 -0.15 33 34
GADD45/MTK1/MTK1 0.054 0.068 -10000 0 -0.11 56 56
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.038 0.011 -10000 0 0 44 44
VLDLR 0.032 0.018 -10000 0 0 129 129
LRPAP1 0.036 0.015 -10000 0 0 79 79
NUDC 0.04 0.009 -10000 0 0 25 25
RELN/LRP8 0.049 0.056 -10000 0 -0.12 30 30
CaM/Ca2+ 0.028 0.016 -10000 0 -0.13 5 5
KATNA1 0.037 0.013 -10000 0 0 64 64
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.003 0.068 0.21 33 -0.19 1 34
IQGAP1/CaM 0.041 0.055 -10000 0 -0.14 43 43
DAB1 0.04 0.009 -10000 0 0 25 25
IQGAP1 0.037 0.014 -10000 0 0 67 67
PLA2G7 0.03 0.019 -10000 0 0 152 152
CALM1 0.04 0.009 -10000 0 0 30 30
DYNLT1 0.035 0.015 -10000 0 0 84 84
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.041 0.053 -10000 0 -0.14 37 37
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 0.04 0.009 -10000 0 0 27 27
LIS1/Poliovirus Protein 3A -0.016 0.013 -10000 0 -0.12 6 6
CDK5R2 0.041 0.006 -10000 0 0 10 10
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.043 0.059 -10000 0 -0.12 37 37
YWHAE 0.038 0.012 -10000 0 0 50 50
NDEL1/14-3-3 E 0.034 0.087 0.27 38 -0.17 7 45
MAP1B -0.002 0.049 0.18 3 -0.18 33 36
RAC1 0.01 0.041 -10000 0 -0.59 1 1
p35/CDK5 -0.01 0.068 0.19 30 -0.18 1 31
RELN 0.034 0.016 -10000 0 0 104 104
PAFAH/LIS1 0.025 0.028 -10000 0 -0.15 6 6
LIS1/CLIP170 -0.016 0.013 -10000 0 -0.12 6 6
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.024 0.077 0.2 17 -0.19 10 27
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.004 0.099 -10000 0 -0.22 67 67
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.006 0.084 0.23 49 -0.16 4 53
LIS1/IQGAP1 0.031 0.027 -10000 0 -0.15 6 6
RHOA 0.011 0.045 0.12 17 -0.12 30 47
PAFAH1B1 -0.018 0.007 -10000 0 -10000 0 0
PAFAH1B3 0.035 0.015 -10000 0 0 89 89
PAFAH1B2 0.04 0.009 -10000 0 0 29 29
MAP1B/LIS1/Dynein heavy chain 0.011 0.061 -10000 0 -0.15 38 38
NDEL1/Katanin 60/Dynein heavy chain 0.04 0.091 0.29 26 -0.18 8 34
LRP8 0.039 0.011 -10000 0 0 39 39
NDEL1/Katanin 60 0.031 0.081 0.25 36 -0.17 8 44
P39/CDK5 -0.009 0.072 0.2 34 -0.18 1 35
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.034 0.025 -10000 0 -0.15 6 6
CDK5 -0.011 0.053 0.19 19 -0.18 1 20
PPP2R5D 0.04 0.009 -10000 0 0 27 27
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.013 0.011 -10000 0 -0.1 6 6
CSNK2A1 0.039 0.011 -10000 0 0 40 40
RELN/VLDLR/DAB1/LIS1 0.055 0.064 0.2 15 -0.11 36 51
RELN/VLDLR 0.052 0.074 -10000 0 -0.11 60 60
CDC42 0.01 0.047 0.12 1 -0.45 3 4
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.019 0.015 0.057 14 -10000 0 14
SNTA1 0.039 0.01 -10000 0 0 35 35
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.018 0.016 0.057 14 -10000 0 14
MAPK12 -0.009 0.041 0.21 5 -0.16 16 21
CCND1 -0.039 0.13 -10000 0 -0.37 72 72
p38 gamma/SNTA1 0.024 0.071 0.22 11 -0.17 30 41
MAP2K3 0.039 0.011 -10000 0 0 43 43
PKN1 0.034 0.016 -10000 0 0 98 98
G2/M transition checkpoint -0.009 0.041 0.21 5 -0.16 16 21
MAP2K6 0.003 0.045 0.24 5 -0.17 21 26
MAPT 0.002 0.054 0.15 12 -0.2 13 25
MAPK13 -0.017 0.008 0 96 -10000 0 96
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.003 0.05 -10000 0 -0.2 31 31
Syndecan-3-mediated 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
CTTN 0.039 0.01 -9999 0 0 34 34
Syndecan-3/Src/Cortactin 0.028 0.093 -9999 0 -0.38 12 12
Syndecan-3/Neurocan 0.002 0.064 -9999 0 -0.42 12 12
POMC 0.04 0.007 -9999 0 0 18 18
EGFR 0.036 0.014 -9999 0 0 73 73
Syndecan-3/EGFR 0.03 0.072 -9999 0 -0.42 12 12
AGRP 0.036 0.014 -9999 0 0 74 74
NCSTN 0.04 0.008 -9999 0 0 21 21
PSENEN 0.035 0.015 -9999 0 0 88 88
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.035 0.015 -9999 0 0 86 86
APH1A 0.041 0.006 -9999 0 0 11 11
NCAN 0 0 -9999 0 -10000 0 0
long-term memory 0.038 0.079 -9999 0 -0.39 12 12
Syndecan-3/IL8 0.023 0.072 -9999 0 -0.43 12 12
PSEN1 0.039 0.01 -9999 0 0 34 34
Src/Cortactin 0.053 0.031 -9999 0 -0.14 10 10
FYN 0.034 0.016 -9999 0 0 102 102
limb bud formation 0.003 0.067 -9999 0 -0.43 12 12
MC4R 0 0 -9999 0 -10000 0 0
SRC 0.039 0.01 -9999 0 0 31 31
PTN 0.023 0.021 -9999 0 0 244 244
FGFR/FGF/Syndecan-3 0.003 0.067 -9999 0 -0.44 12 12
neuron projection morphogenesis -0.013 0.069 -9999 0 -0.37 12 12
Syndecan-3/AgRP 0.03 0.071 -9999 0 -0.42 12 12
Syndecan-3/AgRP/MC4R 0.028 0.069 -9999 0 -0.41 12 12
Fyn/Cortactin 0.037 0.055 -9999 0 -0.14 43 43
SDC3 0.003 0.068 -9999 0 -0.44 12 12
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.023 0.071 -9999 0 -0.42 12 12
IL8 0.031 0.018 -9999 0 0 137 137
Syndecan-3/Fyn/Cortactin 0.04 0.08 -9999 0 -0.4 12 12
Syndecan-3/CASK 0.002 0.064 -9999 0 -0.42 12 12
alpha-MSH/MC4R 0.03 0.005 -9999 0 -10000 0 0
Gamma Secretase 0.072 0.087 -9999 0 -0.12 68 68
PDGFR-beta signaling pathway

Figure S87.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.06 0.1 0.31 15 -0.31 9 24
PDGFB-D/PDGFRB/SLAP 0.032 0.038 -10000 0 -0.14 10 10
PDGFB-D/PDGFRB/APS/CBL 0.047 0.024 -10000 0 -0.11 4 4
AKT1 0.021 0.1 0.26 39 -10000 0 39
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.044 0.093 0.28 14 -0.33 10 24
PIK3CA 0.03 0.019 -10000 0 0 150 150
FGR 0.022 0.09 0.29 6 -0.39 12 18
mol:Ca2+ 0.025 0.086 0.26 11 -0.36 10 21
MYC 0.007 0.28 0.35 20 -0.66 72 92
SHC1 0.04 0.009 -10000 0 0 29 29
HRAS/GDP 0.037 0.058 0.19 39 -0.11 15 54
LRP1/PDGFRB/PDGFB 0.055 0.056 -10000 0 -0.12 35 35
GRB10 0.04 0.008 -10000 0 0 23 23
PTPN11 0.04 0.009 -10000 0 0 29 29
GO:0007205 0.025 0.087 0.26 11 -0.37 10 21
PTEN 0.039 0.011 -10000 0 0 39 39
GRB2 0.041 0.007 -10000 0 0 14 14
GRB7 0.037 0.013 -10000 0 0 62 62
PDGFB-D/PDGFRB/SHP2 0.046 0.043 -10000 0 -0.14 22 22
PDGFB-D/PDGFRB/GRB10 0.051 0.034 -10000 0 -0.15 9 9
cell cycle arrest 0.031 0.038 -10000 0 -0.14 10 10
HRAS 0.04 0.009 -10000 0 0 29 29
HIF1A 0.008 0.093 0.23 36 -0.21 4 40
GAB1 0.021 0.1 0.28 8 -0.3 15 23
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.024 0.11 0.29 19 -0.27 16 35
PDGFB-D/PDGFRB 0.058 0.051 -10000 0 -0.13 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.048 0.042 -10000 0 -0.14 21 21
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.053 0.12 0.31 15 -0.25 31 46
positive regulation of MAPKKK cascade 0.046 0.043 -10000 0 -0.14 22 22
PIK3R1 0.034 0.016 -10000 0 0 106 106
mol:IP3 0.025 0.087 0.27 11 -0.37 10 21
E5 0 0.002 -10000 0 -10000 0 0
CSK 0.04 0.01 -10000 0 -0.003 24 24
PDGFB-D/PDGFRB/GRB7 0.047 0.035 -10000 0 -0.14 10 10
SHB 0.041 0.007 -10000 0 0 16 16
BLK -0.036 0.16 0.33 3 -0.37 88 91
PTPN2 0.039 0.015 -10000 0 -0.013 39 39
PDGFB-D/PDGFRB/SNX15 0.054 0.025 -10000 0 -0.14 3 3
BCAR1 0.036 0.014 -10000 0 0 74 74
VAV2 0.01 0.13 0.3 9 -0.34 36 45
CBL 0.04 0.008 -10000 0 0 23 23
PDGFB-D/PDGFRB/DEP1 0.047 0.041 -10000 0 -0.13 19 19
LCK 0.028 0.075 0.3 5 -0.39 5 10
PDGFRB 0.036 0.019 0.068 1 -0.007 81 82
ACP1 0.04 0.009 -10000 0 0 26 26
HCK 0.014 0.096 0.33 3 -0.45 14 17
ABL1 0.018 0.091 0.26 14 -0.25 16 30
PDGFB-D/PDGFRB/CBL 0.022 0.1 0.29 5 -0.36 12 17
PTPN1 0.037 0.017 -10000 0 -0.008 62 62
SNX15 0.041 0.005 -10000 0 0 7 7
STAT3 0.038 0.012 -10000 0 0 52 52
STAT1 0.034 0.017 -10000 0 0 108 108
cell proliferation 0.015 0.26 0.32 30 -0.59 72 102
SLA 0.026 0.02 -10000 0 0 205 205
actin cytoskeleton reorganization 0.007 0.093 0.22 64 -0.18 1 65
SRC 0.026 0.057 0.33 3 -10000 0 3
PI3K -0.028 0.036 -10000 0 -0.14 10 10
PDGFB-D/PDGFRB/GRB7/SHC 0.064 0.042 -10000 0 -0.12 10 10
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.044 0.095 0.29 14 -0.34 10 24
LYN 0 0.12 0.27 7 -0.42 33 40
LRP1 0.036 0.014 -10000 0 0 73 73
SOS1 0.038 0.013 -10000 0 0 57 57
STAT5B 0.039 0.011 -10000 0 0 41 41
STAT5A 0.038 0.012 -10000 0 0 50 50
NCK1-2/p130 Cas 0.074 0.076 -10000 0 -0.12 20 20
SPHK1 0.042 0.008 0.062 1 0 16 17
EDG1 0.042 0.008 -10000 0 0 15 15
mol:DAG 0.025 0.087 0.27 11 -0.37 10 21
PLCG1 0.025 0.088 0.27 10 -0.38 10 20
NHERF/PDGFRB 0.062 0.046 -10000 0 -0.12 18 18
YES1 -0.001 0.13 0.27 3 -0.43 35 38
cell migration 0.059 0.048 -10000 0 -0.12 18 18
SHC/Grb2/SOS1 0.085 0.072 -10000 0 -0.14 11 11
SLC9A3R2 0.038 0.012 -10000 0 0 51 51
SLC9A3R1 0.038 0.012 -10000 0 0 47 47
NHERF1-2/PDGFRB/PTEN 0.078 0.058 -10000 0 -0.11 28 28
FYN -0.015 0.14 0.3 2 -0.38 54 56
DOK1 0.005 0.067 0.19 51 -10000 0 51
HRAS/GTP 0.029 0.007 -10000 0 -10000 0 0
PDGFB 0.038 0.012 -10000 0 0 54 54
RAC1 -0.031 0.24 0.3 12 -0.53 75 87
PRKCD 0.003 0.066 0.2 45 -10000 0 45
FER 0.004 0.065 0.19 48 -10000 0 48
MAPKKK cascade -0.003 0.081 0.26 21 -0.18 3 24
RASA1 0.003 0.062 0.19 41 -10000 0 41
NCK1 0.036 0.014 -10000 0 0 77 77
NCK2 0.041 0.006 -10000 0 0 10 10
p62DOK/Csk 0.054 0.055 0.2 52 -0.11 11 63
PDGFB-D/PDGFRB/SHB 0.053 0.026 -10000 0 -0.14 3 3
chemotaxis 0.018 0.089 0.26 14 -0.24 16 30
STAT1-3-5/STAT1-3-5 0.051 0.08 -10000 0 -0.16 15 15
Bovine Papilomavirus E5/PDGFRB 0.025 0.019 -10000 0 -0.13 3 3
PTPRJ 0.039 0.01 -10000 0 0 36 36
Aurora A 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
Aurora A/GADD45A 0.042 0.041 0.17 2 -0.16 9 11
BIRC5 0.037 0.013 -10000 0 0 58 58
NFKBIA -0.004 0.028 0.25 1 -0.18 6 7
CPEB1 0.039 0.01 -10000 0 0 37 37
AKT1 -0.002 0.043 0.26 10 -0.18 7 17
NDEL1 0.039 0.01 -10000 0 0 33 33
Aurora A/BRCA1 0.027 0.049 0.15 2 -0.1 50 52
NDEL1/TACC3 0.045 0.052 0.17 1 -0.16 7 8
GADD45A 0.036 0.014 -10000 0 0 71 71
GSK3B 0.038 0.012 0.091 14 0 29 43
PAK1/Aurora A 0.043 0.04 0.17 2 -0.17 8 10
MDM2 0.039 0.01 -10000 0 0 35 35
JUB 0.037 0.013 -10000 0 0 58 58
TPX2 -0.015 0.009 -10000 0 -10000 0 0
TP53 -0.043 0.12 0.16 1 -0.24 133 134
DLG7 -0.002 0.025 0.25 1 -0.17 3 4
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 0.04 0.009 -10000 0 0 30 30
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.048 0.055 0.18 1 -0.17 7 8
G2/M transition of mitotic cell cycle 0.027 0.049 0.15 2 -0.1 50 52
AURKA 0.01 0.03 0.13 12 -0.2 7 19
AURKB 0.001 0.061 -10000 0 -0.2 41 41
CDC25B 0.005 0.047 -10000 0 -0.22 19 19
G2/M transition checkpoint 0.034 0.044 0.15 2 -0.11 30 32
mRNA polyadenylation 0.039 0.035 0.15 2 -0.14 9 11
Aurora A/CPEB 0.039 0.036 0.15 2 -0.14 9 11
Aurora A/TACC1/TRAP/chTOG 0.056 0.075 0.21 2 -0.18 14 16
BRCA1 0.034 0.016 -10000 0 0 99 99
centrosome duplication 0.043 0.04 0.17 2 -0.17 8 10
regulation of centrosome cycle 0.044 0.051 0.17 1 -0.16 7 8
spindle assembly 0.054 0.073 0.21 2 -0.17 14 16
TDRD7 0.035 0.015 -10000 0 0 87 87
Aurora A/RasGAP/Survivin 0.045 0.072 0.2 4 -0.15 12 16
CENPA 0.009 0.052 -10000 0 -0.32 11 11
Aurora A/PP2A 0.046 0.038 0.17 2 -0.16 8 10
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.013 0.058 0.16 5 -0.2 16 21
negative regulation of DNA binding -0.043 0.11 0.16 1 -0.24 133 134
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.057 0.017 -10000 0 -10000 0 0
RASA1 0.036 0.014 -10000 0 0 73 73
Ajuba/Aurora A 0.034 0.044 0.15 2 -0.11 30 32
mitotic prometaphase 0.003 0.024 0.074 56 -10000 0 56
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.03 0.13 12 -0.2 7 19
TACC1 0.035 0.016 -10000 0 0 91 91
TACC3 0.033 0.017 -10000 0 0 112 112
Aurora A/Antizyme1 0.029 0.044 0.15 1 -0.1 34 35
Aurora A/RasGAP 0.042 0.042 0.17 2 -0.17 9 11
OAZ1 0.033 0.017 -10000 0 0 110 110
RAN 0.041 0.006 -10000 0 0 11 11
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.034 0.017 0.091 12 0 87 99
GIT1 0.04 0.008 -10000 0 0 23 23
GIT1/beta-PIX/PAK1 0.066 0.043 -10000 0 -0.12 15 15
Importin alpha/Importin beta/TPX2 -0.015 0.009 -10000 0 -10000 0 0
PPP2R5D 0.04 0.009 -10000 0 0 27 27
Aurora A/TPX2 0.018 0.036 0.15 1 -0.21 8 9
PAK1 0.037 0.014 -10000 0 0 66 66
CKAP5 0.038 0.011 -10000 0 0 45 45
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.022 0.13 0.24 4 -0.37 41 45
BAG4 0.037 0.013 -10000 0 0 63 63
BAD -0.008 0.047 0.17 5 -0.14 29 34
NFKBIA 0.037 0.014 -10000 0 0 66 66
BIRC3 0.026 0.02 -10000 0 0 213 213
BAX -0.006 0.048 0.15 9 -0.14 27 36
EnzymeConsortium:3.1.4.12 -0.003 0.032 0.074 3 -0.085 36 39
IKBKB -0.021 0.13 0.22 13 -0.37 37 50
MAP2K2 -0.01 0.039 0.16 2 -0.15 7 9
MAP2K1 -0.013 0.045 0.18 7 -0.15 7 14
SMPD1 -0.003 0.037 0.097 1 -0.11 34 35
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.013 0.14 0.24 9 -0.37 42 51
MAP2K4 -0.009 0.041 -10000 0 -0.14 11 11
protein ubiquitination -0.027 0.13 0.24 2 -0.38 38 40
EnzymeConsortium:2.7.1.37 -0.013 0.044 0.15 4 -0.16 5 9
response to UV 0 0 0.002 7 -0.002 4 11
RAF1 -0.01 0.043 0.15 4 -0.14 16 20
CRADD 0.041 0.006 -10000 0 0 12 12
mol:ceramide -0.004 0.046 0.12 1 -0.13 36 37
I-kappa-B-alpha/RELA/p50/ubiquitin 0.042 0.043 -10000 0 -0.11 36 36
MADD 0.041 0.006 -10000 0 0 12 12
MAP3K1 -0.008 0.044 -10000 0 -0.14 27 27
TRADD 0.036 0.014 -10000 0 0 76 76
RELA/p50 0.041 0.006 -10000 0 0 10 10
MAPK3 -0.008 0.043 0.16 4 -0.16 6 10
MAPK1 -0.012 0.052 0.16 5 -0.17 19 24
p50/RELA/I-kappa-B-alpha 0.045 0.051 -10000 0 -0.14 36 36
FADD -0.017 0.13 0.24 9 -0.38 38 47
KSR1 -0.007 0.042 0.12 1 -0.13 26 27
MAPK8 -0.016 0.043 0.18 2 -0.16 6 8
TRAF2 0.04 0.009 -10000 0 0 25 25
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.03 0.13 0.22 4 -0.36 43 47
TNF R/SODD 0.044 0.038 -10000 0 -0.13 14 14
TNF 0.04 0.009 -10000 0 0 25 25
CYCS -0.006 0.049 0.12 10 -0.14 22 32
IKBKG -0.029 0.13 0.22 4 -0.37 38 42
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.017 0.14 -10000 0 -0.39 39 39
RELA 0.041 0.006 -10000 0 0 10 10
RIPK1 0.038 0.012 -10000 0 0 48 48
AIFM1 -0.006 0.047 0.12 11 -0.14 21 32
TNF/TNF R/SODD 0.059 0.046 -10000 0 -0.12 15 15
TNFRSF1A 0.036 0.015 -10000 0 0 82 82
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.018 0.13 -10000 0 -0.65 19 19
NSMAF -0.013 0.14 0.24 16 -0.4 35 51
response to hydrogen peroxide 0 0 0.002 7 -0.002 4 11
BCL2 0.036 0.014 -10000 0 0 76 76
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.039 0.01 0 34 -9999 0 34
PI3K Class IB/PDE3B 0.039 0.01 -9999 0 0 34 34
PDE3B 0.039 0.01 -9999 0 0 34 34
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.038 0.012 -10000 0 0 49 49
SMAD2 0.009 0.051 0.2 4 -0.22 4 8
SMAD3 0.013 0.054 0.22 2 -0.17 18 20
SMAD3/SMAD4 -0.016 0.16 -10000 0 -0.4 77 77
SMAD4/Ubc9/PIASy 0.066 0.042 -10000 0 -0.13 10 10
SMAD2/SMAD2/SMAD4 0.047 0.085 0.27 1 -0.21 3 4
PPM1A 0.041 0.007 -10000 0 0 16 16
CALM1 0.04 0.009 -10000 0 0 30 30
SMAD2/SMAD4 0.028 0.05 0.22 2 -0.18 6 8
MAP3K1 0.036 0.015 -10000 0 0 78 78
TRAP-1/SMAD4 0.048 0.043 -10000 0 -0.14 23 23
MAPK3 0.041 0.007 -10000 0 0 17 17
MAPK1 0.039 0.011 -10000 0 0 43 43
NUP214 0.039 0.01 -10000 0 0 32 32
CTDSP1 0.041 0.006 -10000 0 0 13 13
CTDSP2 0.039 0.011 -10000 0 0 42 42
CTDSPL 0.041 0.006 -10000 0 0 12 12
KPNB1 0.04 0.009 -10000 0 0 29 29
TGFBRAP1 0.04 0.008 -10000 0 0 22 22
UBE2I 0.04 0.009 -10000 0 0 26 26
NUP153 0.037 0.014 -10000 0 0 69 69
KPNA2 0.035 0.015 -10000 0 0 84 84
PIAS4 0.038 0.013 -10000 0 0 56 56
Ephrin A reverse signaling

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
MAPKKK cascade 0.037 0.042 -10000 0 -0.11 32 32
EFNA5 0.034 0.016 -10000 0 0 103 103
FYN -0.013 0.036 0.18 7 -10000 0 7
neuron projection morphogenesis 0.037 0.042 -10000 0 -0.11 32 32
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.037 0.042 -10000 0 -0.11 32 32
EPHA5 0.04 0.009 -10000 0 0 26 26
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.04 0.25 0.48 1 -0.58 53 54
PCK1 -0.1 0.41 -10000 0 -1.1 76 76
HNF4A -0.075 0.35 0.57 3 -0.77 88 91
KCNJ11 -0.009 0.24 0.53 1 -0.57 27 28
AKT1 0.003 0.17 -10000 0 -0.34 28 28
response to starvation -0.015 0.044 -10000 0 -0.12 77 77
DLK1 0 0.24 0.64 3 -0.57 26 29
NKX2-1 -0.007 0.15 0.37 2 -0.32 28 30
ACADM -0.055 0.27 0.54 1 -0.6 69 70
TAT -0.028 0.19 -10000 0 -0.66 13 13
CEBPB 0.04 0.017 -10000 0 -0.064 2 2
CEBPA 0.041 0.016 -10000 0 -0.066 1 1
TTR 0.036 0.17 -10000 0 -0.92 4 4
PKLR -0.027 0.25 0.43 7 -0.55 49 56
APOA1 -0.13 0.48 -10000 0 -1.1 95 95
CPT1C -0.031 0.24 -10000 0 -0.59 43 43
ALAS1 -0.007 0.18 -10000 0 -0.74 6 6
TFRC -0.059 0.37 -10000 0 -0.93 69 69
FOXF1 0.036 0.015 -10000 0 -10000 0 0
NF1 0.039 0.02 -10000 0 -0.16 1 1
HNF1A (dimer) 0.009 0.001 -10000 0 -10000 0 0
CPT1A -0.045 0.27 0.45 4 -0.59 68 72
HMGCS1 -0.037 0.26 0.5 3 -0.6 57 60
NR3C1 0.048 0.014 -10000 0 -10000 0 0
CPT1B -0.038 0.24 -10000 0 -0.59 43 43
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.041 0.006 -10000 0 -10000 0 0
GCK -0.034 0.24 0.49 2 -0.55 53 55
CREB1 0.02 0.096 -10000 0 -0.21 77 77
IGFBP1 -0.002 0.15 -10000 0 -0.5 4 4
PDX1 0.01 0.14 0.4 1 -0.3 26 27
UCP2 -0.059 0.31 0.47 10 -0.66 80 90
ALDOB -0.008 0.23 -10000 0 -0.56 28 28
AFP 0.014 0.05 -10000 0 -0.23 1 1
BDH1 -0.058 0.27 -10000 0 -0.59 75 75
HADH -0.009 0.23 -10000 0 -0.5 47 47
F2 -0.039 0.31 -10000 0 -0.75 40 40
HNF1A 0.009 0.001 -10000 0 -10000 0 0
G6PC 0.026 0.09 -10000 0 -10000 0 0
SLC2A2 0.029 0.17 -10000 0 -10000 0 0
INS 0.03 0.013 0.18 1 -10000 0 1
FOXA1 0.056 0.016 -10000 0 -10000 0 0
FOXA3 0.02 0.12 -10000 0 -0.21 101 101
FOXA2 0.01 0.29 -10000 0 -0.6 40 40
ABCC8 -0.008 0.24 0.53 1 -0.56 28 29
ALB 0.014 0.051 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.016 0.009 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.061 0.061 0.18 72 -0.11 18 90
CDKN1B 0.016 0.09 0.21 31 -0.31 25 56
CDKN1A 0.009 0.086 0.21 17 -0.3 29 46
FRAP1 0.04 0.009 -10000 0 0 24 24
PRKDC 0.038 0.011 -10000 0 0 44 44
FOXO3 0.006 0.08 -10000 0 -0.3 32 32
AKT1 0.006 0.081 -10000 0 -0.32 30 30
BAD 0.041 0.005 -10000 0 0 9 9
AKT3 0.004 0.045 -10000 0 -0.2 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.006 0.08 -10000 0 -0.3 32 32
AKT1/ASK1 0.027 0.089 -10000 0 -0.29 34 34
BAD/YWHAZ 0.055 0.044 -10000 0 -0.12 7 7
RICTOR 0.037 0.014 -10000 0 0 66 66
RAF1 0.04 0.008 -10000 0 0 20 20
JNK cascade -0.026 0.086 0.28 34 -10000 0 34
TSC1 0.002 0.079 0.23 2 -0.3 29 31
YWHAZ 0.034 0.016 -10000 0 0 104 104
AKT1/RAF1 0.034 0.094 -10000 0 -0.31 32 32
EP300 0.036 0.014 -10000 0 0 72 72
mol:GDP 0.006 0.082 -10000 0 -0.31 32 32
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0 0.081 -10000 0 -0.3 33 33
YWHAQ 0.04 0.009 -10000 0 0 26 26
TBC1D4 0.006 0.031 0.24 5 -0.17 6 11
MAP3K5 0.037 0.014 -10000 0 0 70 70
MAPKAP1 0.04 0.009 -10000 0 0 25 25
negative regulation of cell cycle -0.029 0.082 0.32 10 -0.22 4 14
YWHAH 0.038 0.012 -10000 0 0 54 54
AKT1S1 0.007 0.084 0.23 11 -0.31 28 39
CASP9 0.001 0.079 -10000 0 -0.31 30 30
YWHAB 0.038 0.011 -10000 0 0 44 44
p27Kip1/KPNA1 0.036 0.11 0.28 7 -0.31 29 36
GBL 0.04 0.009 -10000 0 0 24 24
PDK1/Src/Hsp90 0.05 0.022 -10000 0 -0.11 5 5
YWHAE 0.038 0.012 -10000 0 0 50 50
SRC 0.039 0.01 -10000 0 0 31 31
AKT2/p21CIP1 0.012 0.079 0.21 17 -0.28 26 43
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.022 0.092 -10000 0 -0.35 25 25
CHUK -0.001 0.081 -10000 0 -0.31 31 31
BAD/BCL-XL 0.028 0.087 -10000 0 -0.3 28 28
mTORC2 0.078 0.062 -10000 0 -0.12 32 32
AKT2 0.015 0.023 -10000 0 -0.2 6 6
FOXO1-3a-4/14-3-3 family 0.03 0.1 0.25 4 -0.36 13 17
PDPK1 0.04 0.009 -10000 0 0 27 27
MDM2 0.005 0.088 0.2 13 -0.31 32 45
MAPKKK cascade -0.034 0.092 0.3 32 -10000 0 32
MDM2/Cbp/p300 0.039 0.11 0.34 3 -0.31 32 35
TSC1/TSC2 -0.003 0.082 0.29 4 -0.3 32 36
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.1 0.33 3 -0.3 32 35
glucose import -0.004 0.035 0.21 10 -0.16 6 16
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.022 0.087 0.28 1 -0.35 8 9
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.004 0.033 0.21 9 -0.16 6 15
GSK3A 0.003 0.081 0.27 2 -0.31 30 32
FOXO1 0.006 0.08 -10000 0 -0.3 32 32
GSK3B 0.007 0.089 0.22 15 -0.3 32 47
SFN 0.035 0.015 -10000 0 0 84 84
G1/S transition of mitotic cell cycle 0.007 0.096 0.32 9 -0.3 31 40
p27Kip1/14-3-3 family 0.021 0.078 -10000 0 -0.37 8 8
PRKACA 0.035 0.015 -10000 0 0 87 87
KPNA1 0.039 0.01 -10000 0 0 36 36
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG 0.04 0.009 -10000 0 0 26 26
RHEB 0.037 0.013 -10000 0 0 62 62
CREBBP 0.038 0.012 -10000 0 0 49 49
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.07 0.067 -10000 0 -0.11 45 45
MAP4K1 0.039 0.011 -10000 0 0 43 43
MAP3K8 0.04 0.008 -10000 0 0 22 22
PRKCB 0 0 -10000 0 -10000 0 0
DBNL 0.04 0.007 -10000 0 0 18 18
CRKL 0.039 0.01 -10000 0 0 35 35
MAP3K1 0.005 0.061 -10000 0 -0.23 17 17
JUN -0.005 0.11 0.24 6 -0.51 22 28
MAP3K7 0.005 0.063 0.21 5 -0.22 18 23
GRAP2 0.038 0.013 -10000 0 0 55 55
CRK 0.038 0.011 -10000 0 0 45 45
MAP2K4 -0.005 0.077 -10000 0 -0.28 23 23
LAT 0.041 0.006 -10000 0 0 13 13
LCP2 0.034 0.016 -10000 0 0 100 100
MAPK8 -0.002 0.11 -10000 0 -0.55 22 22
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.016 0.066 -10000 0 -0.21 19 19
LAT/GRAP2/SLP76/HPK1/HIP-55 0.078 0.077 -10000 0 -0.11 46 46
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.038 0.012 -10000 0 0 54 54
HDAC2 0.038 0.012 -10000 0 0 48 48
GNB1/GNG2 0.071 0.042 -10000 0 -0.12 18 18
forebrain development 0.016 0.11 -10000 0 -0.38 28 28
GNAO1 0.034 0.016 -10000 0 0 101 101
SMO/beta Arrestin2 0.055 0.025 -10000 0 -0.14 4 4
SMO 0.04 0.01 -10000 0 -0.001 32 32
ARRB2 0.039 0.011 -10000 0 0 37 37
GLI3/SPOP 0.023 0.13 0.25 4 -0.35 30 34
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0.04 0.009 -10000 0 0 29 29
GNAI2 0.041 0.006 -10000 0 0 13 13
SIN3/HDAC complex 0.074 0.055 -10000 0 -0.12 11 11
GNAI1 0.035 0.016 -10000 0 0 94 94
XPO1 0.039 0.012 -10000 0 -0.002 42 42
GLI1/Su(fu) 0.024 0.11 -10000 0 -0.41 22 22
SAP30 0.038 0.013 -10000 0 0 55 55
mol:GDP 0.04 0.01 -10000 0 -0.001 32 32
MIM/GLI2A 0.031 0.026 -10000 0 -0.12 2 2
IFT88 0.037 0.014 -10000 0 0 67 67
GNAI3 0.038 0.012 -10000 0 0 46 46
GLI2 0.017 0.073 0.21 2 -0.25 13 15
GLI3 0.006 0.12 0.23 7 -0.37 28 35
CSNK1D 0.04 0.009 -10000 0 0 30 30
CSNK1E 0.038 0.012 -10000 0 0 54 54
SAP18 0.039 0.01 -10000 0 0 31 31
embryonic digit morphogenesis 0.037 0.014 -10000 0 0 67 67
GNG2 0.039 0.01 -10000 0 0 34 34
Gi family/GTP 0.002 0.076 -10000 0 -0.25 28 28
SIN3B 0.037 0.014 -10000 0 0 67 67
SIN3A 0.039 0.01 -10000 0 0 31 31
GLI3/Su(fu) 0.019 0.12 0.26 3 -0.32 37 40
GLI2/Su(fu) 0.026 0.081 0.2 2 -0.25 19 21
FOXA2 0.023 0.098 -10000 0 -0.55 13 13
neural tube patterning 0.016 0.11 -10000 0 -0.38 28 28
SPOP 0.04 0.009 -10000 0 0 26 26
Su(fu)/PIAS1 0.041 0.059 0.21 1 -0.18 27 28
GNB1 0.041 0.005 -10000 0 0 7 7
CSNK1G2 0.037 0.014 -10000 0 0 68 68
CSNK1G3 0.039 0.01 -10000 0 0 37 37
MTSS1 0.031 0.026 -10000 0 -0.12 2 2
embryonic limb morphogenesis 0.016 0.11 -10000 0 -0.38 28 28
SUFU 0.023 0.039 -10000 0 -0.24 10 10
LGALS3 0.037 0.014 -10000 0 0 68 68
catabolic process 0.029 0.13 0.3 1 -0.37 24 25
GLI3A/CBP 0.047 0.015 -10000 0 -10000 0 0
KIF3A 0.038 0.012 -10000 0 0 48 48
GLI1 0.015 0.11 -10000 0 -0.38 28 28
RAB23 0.041 0.007 -10000 0 0 16 16
CSNK1A1 0.04 0.009 -10000 0 0 24 24
IFT172 0.039 0.01 -10000 0 0 32 32
RBBP7 0.04 0.009 -10000 0 0 25 25
Su(fu)/Galectin3 0.038 0.058 0.21 1 -0.18 25 26
GNAZ 0.039 0.011 -10000 0 0 38 38
RBBP4 0.038 0.011 -10000 0 0 45 45
CSNK1G1 0.04 0.008 -10000 0 0 21 21
PIAS1 0.04 0.009 -10000 0 0 28 28
PRKACA 0.035 0.015 -10000 0 0 87 87
GLI2/SPOP 0.035 0.08 0.21 1 -0.25 14 15
STK36 0.04 0.011 -10000 0 -0.003 32 32
Gi family/GNB1/GNG2/GDP 0 0.085 -10000 0 -0.26 30 30
PTCH1 0.016 0.099 -10000 0 -0.35 28 28
MIM/GLI1 0.027 0.098 -10000 0 -0.38 14 14
CREBBP 0.047 0.015 -10000 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.004 0.11 0.18 7 -0.31 36 43
Ceramide 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
SPHK2 -0.019 0.005 0 40 -10000 0 40
MAP4K4 -0.002 0.081 0.2 3 -0.25 28 31
BAG4 0.037 0.013 -10000 0 0 63 63
PKC zeta/ceramide 0.032 0.031 -10000 0 -0.17 9 9
NFKBIA 0.037 0.014 -10000 0 0 66 66
BIRC3 0.026 0.02 -10000 0 0 213 213
BAX 0.013 0.054 -10000 0 -0.34 12 12
RIPK1 0.038 0.012 -10000 0 0 48 48
AKT1 0.003 0.12 0.67 18 -10000 0 18
BAD 0.001 0.03 0.18 4 -0.18 8 12
SMPD1 0.01 0.061 0.16 15 -0.18 25 40
RB1 -0.006 0.038 0.22 2 -0.18 8 10
FADD/Caspase 8 -0.005 0.11 0.24 7 -0.31 35 42
MAP2K4 -0.006 0.028 -10000 0 -0.18 8 8
NSMAF 0.038 0.013 -10000 0 0 55 55
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.005 0.032 0.17 6 -0.18 8 14
EGF 0.038 0.012 -10000 0 0 52 52
mol:ceramide 0.006 0.027 -10000 0 -0.19 8 8
MADD 0.041 0.006 -10000 0 0 12 12
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.016 0.009 0 135 -10000 0 135
ASAH1 0.033 0.017 -10000 0 0 121 121
negative regulation of cell cycle -0.006 0.038 0.22 2 -0.18 8 10
cell proliferation 0.026 0.05 0.19 4 -0.18 8 12
BID 0.02 0.097 -10000 0 -0.49 8 8
MAP3K1 -0.002 0.028 -10000 0 -0.18 8 8
EIF2A 0.011 0.08 0.18 77 -0.2 9 86
TRADD 0.036 0.014 -10000 0 0 76 76
CRADD 0.041 0.006 -10000 0 0 12 12
MAPK3 -0.003 0.037 0.17 5 -0.19 7 12
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.009 0.043 0.17 5 -0.18 8 13
Cathepsin D/ceramide 0.029 0.032 -10000 0 -0.17 9 9
FADD -0.001 0.084 0.22 6 -0.25 27 33
KSR1 -0.001 0.026 -10000 0 -0.18 8 8
MAPK8 0.008 0.047 -10000 0 -0.21 14 14
PRKRA 0.004 0.047 0.2 19 -0.18 8 27
PDGFA 0.04 0.007 -10000 0 0 18 18
TRAF2 0.04 0.009 -10000 0 0 25 25
IGF1 0.036 0.015 -10000 0 0 82 82
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.006 0.027 -10000 0 -0.19 8 8
CTSD 0.038 0.012 -10000 0 0 53 53
regulation of nitric oxide biosynthetic process 0.043 0.05 -10000 0 -0.14 35 35
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.029 0.054 0.2 4 -0.19 8 12
PRKCD 0.038 0.013 -10000 0 0 55 55
PRKCZ 0.042 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.016 0.009 0 135 -10000 0 135
RelA/NF kappa B1 0.043 0.05 -10000 0 -0.14 35 35
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.041 0.007 -10000 0 0 16 16
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.005 0.086 -10000 0 -0.26 27 27
TNFR1A/BAG4/TNF-alpha 0.059 0.046 -10000 0 -0.12 15 15
mol:Sphingosine-1-phosphate -0.019 0.005 0 40 -10000 0 40
MAP2K1 -0.009 0.035 0.17 10 -0.17 7 17
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.041 0.006 -10000 0 0 10 10
CYCS 0.009 0.049 0.14 4 -0.18 10 14
TNFRSF1A 0.036 0.015 -10000 0 0 82 82
NFKB1 0.035 0.015 -10000 0 0 85 85
TNFR1A/BAG4 0.044 0.038 -10000 0 -0.13 14 14
EIF2AK2 0 0.059 0.19 32 -0.18 12 44
TNF-alpha/TNFR1A/FAN 0.059 0.052 -10000 0 -0.14 20 20
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.006 0.14 -10000 0 -0.38 52 52
MAP2K2 -0.008 0.032 0.16 6 -0.18 8 14
SMPD3 -0.003 0.1 0.17 10 -0.28 52 62
TNF 0.04 0.009 -10000 0 0 25 25
PKC zeta/PAR4 0.06 0.013 -10000 0 -0.14 1 1
mol:PHOSPHOCHOLINE 0.004 0.034 0.12 3 -0.14 8 11
NF kappa B1/RelA/I kappa B alpha 0.081 0.082 -10000 0 -0.12 59 59
AIFM1 0.01 0.042 0.13 4 -0.18 9 13
BCL2 0.036 0.014 -10000 0 0 76 76
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.007 0.083 0.22 34 -10000 0 34
GNAI2 0.041 0.006 -10000 0 0 13 13
S1P/S1P5/G12 0.026 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.034 0.016 -10000 0 0 101 101
RhoA/GTP 0.008 0.085 -10000 0 -0.23 34 34
negative regulation of cAMP metabolic process -0.005 0.077 -10000 0 -0.18 66 66
GNAZ 0.039 0.011 -10000 0 0 38 38
GNAI3 0.038 0.012 -10000 0 0 46 46
GNA12 0.039 0.01 -10000 0 0 36 36
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.005 0.077 -10000 0 -0.18 66 66
RhoA/GDP 0.029 0.014 -10000 0 -0.13 4 4
RHOA 0.041 0.007 -10000 0 0 14 14
GNAI1 0.035 0.016 -10000 0 0 94 94
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.053 0.092 -10000 0 -0.21 32 32
Ran/GTP/Exportin 1/HDAC1 -0.03 0.033 -10000 0 -0.12 47 47
NF kappa B1 p50/RelA/I kappa B alpha 0.027 0.1 0.24 1 -0.3 27 28
SUMO1 0.041 0.006 -10000 0 0 13 13
ZFPM1 0.035 0.016 -10000 0 0 92 92
NPC/RanGAP1/SUMO1/Ubc9 0.009 0.034 -10000 0 -0.14 25 25
FKBP3 0.039 0.01 -10000 0 0 34 34
Histones 0.069 0.086 0.24 1 -0.21 17 18
YY1/LSF 0.013 0.082 -10000 0 -0.23 40 40
SMG5 0 0 -10000 0 -10000 0 0
RAN 0.041 0.006 -10000 0 0 11 11
I kappa B alpha/HDAC3 0.017 0.06 -10000 0 -0.18 37 37
I kappa B alpha/HDAC1 0.031 0.09 0.22 1 -0.23 46 47
SAP18 0.039 0.01 -10000 0 0 31 31
RELA 0.018 0.085 0.22 3 -0.27 23 26
HDAC1/Smad7 0.062 0.053 -10000 0 -0.12 31 31
RANGAP1 0.038 0.013 -10000 0 0 55 55
HDAC3/TR2 0.048 0.059 0.22 1 -0.2 16 17
NuRD/MBD3 Complex 0.009 0.1 -10000 0 -0.28 34 34
NF kappa B1 p50/RelA 0.024 0.1 0.25 1 -0.28 31 32
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.039 0.01 -10000 0 0 34 34
GATA1 0.042 0.002 -10000 0 0 1 1
Mad/Max 0.059 0.014 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.004 0.11 -10000 0 -0.27 43 43
RBBP7 0.04 0.009 -10000 0 0 25 25
NPC 0.02 0.022 -10000 0 -0.085 23 23
RBBP4 0.038 0.011 -10000 0 0 45 45
MAX 0.041 0.007 -10000 0 0 16 16
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.04 0.008 -10000 0 0 23 23
NFKBIA 0.009 0.07 -10000 0 -0.27 29 29
KAT2B 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.005 0.092 -10000 0 -0.28 30 30
SIN3 complex 0.074 0.055 -10000 0 -0.12 11 11
SMURF1 0.04 0.008 -10000 0 0 19 19
CHD3 0.038 0.012 -10000 0 0 49 49
SAP30 0.038 0.013 -10000 0 0 55 55
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.038 0.013 -10000 0 0 57 57
YY1/HDAC3 0.018 0.076 -10000 0 -0.24 26 26
YY1/HDAC2 0.016 0.076 -10000 0 -0.21 38 38
YY1/HDAC1 0.013 0.078 -10000 0 -0.22 37 37
NuRD/MBD2 Complex (MeCP1) 0.011 0.099 -10000 0 -0.29 32 32
PPARG 0.031 0.068 0.2 6 -0.21 25 31
HDAC8/hEST1B 0.042 0.036 -10000 0 -0.11 20 20
UBE2I 0.04 0.009 -10000 0 0 26 26
beta TrCP1/SCF ubiquitin ligase complex 0.04 0.008 -10000 0 0 23 23
TNFRSF1A 0.036 0.015 -10000 0 0 82 82
HDAC3/SMRT (N-CoR2) 0.049 0.058 0.22 1 -0.2 15 16
MBD3L2 0.039 0.011 -10000 0 0 41 41
ubiquitin-dependent protein catabolic process 0.061 0.052 -10000 0 -0.12 31 31
CREBBP 0.038 0.012 -10000 0 0 49 49
NuRD/MBD3/MBD3L2 Complex 0.008 0.1 0.19 8 -0.27 43 51
HDAC1 0.038 0.012 -10000 0 0 54 54
HDAC3 0.022 0.036 -10000 0 -0.3 4 4
HDAC2 0.038 0.012 -10000 0 0 48 48
YY1 0.006 0.056 -10000 0 -0.24 23 23
HDAC8 0.04 0.009 -10000 0 0 26 26
SMAD7 0.038 0.012 -10000 0 0 46 46
NCOR2 0.04 0.009 -10000 0 0 26 26
MXD1 0.041 0.007 -10000 0 0 17 17
STAT3 0.01 0.064 -10000 0 -0.25 29 29
NFKB1 0.035 0.015 -10000 0 0 85 85
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.04 0.009 -10000 0 0 30 30
YY1/LSF/HDAC1 0.023 0.091 -10000 0 -0.22 43 43
YY1/SAP30/HDAC1 0.025 0.084 -10000 0 -0.2 38 38
EP300 0.036 0.014 -10000 0 0 72 72
STAT3 (dimer non-phopshorylated) 0.01 0.064 -10000 0 -0.24 29 29
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.07 -10000 0 -0.27 29 29
histone deacetylation 0.011 0.098 -10000 0 -0.28 32 32
STAT3 (dimer non-phopshorylated)/HDAC3 0.022 0.082 -10000 0 -0.28 20 20
nuclear export -0.041 0.036 0.11 20 -10000 0 20
PRKACA 0.035 0.015 -10000 0 0 87 87
GATAD2B 0.038 0.012 -10000 0 0 49 49
GATAD2A 0.037 0.013 -10000 0 0 59 59
GATA2/HDAC3 0.048 0.057 0.22 1 -0.2 15 16
GATA1/HDAC1 0.05 0.043 -10000 0 -0.14 26 26
GATA1/HDAC3 0.052 0.058 0.22 1 -0.21 15 16
CHD4 0.036 0.014 -10000 0 0 77 77
TNF-alpha/TNFR1A 0.047 0.038 -10000 0 -0.14 15 15
SIN3/HDAC complex/Mad/Max 0.009 0.093 -10000 0 -0.3 26 26
NuRD Complex 0.004 0.1 0.19 8 -0.27 40 48
positive regulation of chromatin silencing 0.066 0.083 0.23 1 -0.21 17 18
SIN3B 0.037 0.014 -10000 0 0 67 67
MTA2 0.041 0.005 -10000 0 0 9 9
SIN3A 0.039 0.01 -10000 0 0 31 31
XPO1 0.039 0.011 -10000 0 0 39 39
SUMO1/HDAC1 0.037 0.064 -10000 0 -0.18 22 22
HDAC complex 0.072 0.077 -10000 0 -0.14 54 54
GATA1/Fog1 0.052 0.023 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.057 0.061 -10000 0 -0.13 43 43
TNF 0.04 0.009 -10000 0 0 25 25
negative regulation of cell growth 0.009 0.092 -10000 0 -0.3 26 26
NuRD/MBD2/PRMT5 Complex 0.011 0.099 -10000 0 -0.29 32 32
Ran/GTP/Exportin 1 0.038 0.07 0.18 1 -0.18 33 34
NF kappa B/RelA/I kappa B alpha 0.017 0.082 -10000 0 -0.29 24 24
SIN3/HDAC complex/NCoR1 -0.001 0.096 0.17 1 -0.27 38 39
TFCP2 0.039 0.011 -10000 0 0 38 38
NR2C1 0.039 0.011 -10000 0 0 40 40
MBD3 0.036 0.014 -10000 0 0 72 72
MBD2 0.039 0.011 -10000 0 0 42 42
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.034 0.016 -10000 0 0 101 101
CDC42/GTP 0.008 0.084 -10000 0 -0.22 33 33
PLCG1 -0.013 0.071 -10000 0 -0.18 66 66
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.041 0.006 -10000 0 0 13 13
GNAI3 0.038 0.012 -10000 0 0 46 46
G12/G13 0.053 0.03 -10000 0 -0.14 9 9
cell migration 0.007 0.082 -10000 0 -0.22 33 33
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
MAPK3 -0.013 0.073 -10000 0 -0.18 65 65
MAPK1 -0.007 0.064 -10000 0 -0.17 57 57
S1P/S1P5/Gi -0.005 0.077 -10000 0 -0.18 66 66
GNAI1 0.035 0.016 -10000 0 0 94 94
CDC42/GDP 0.029 0.013 -10000 0 -0.13 3 3
S1P/S1P5/G12 0.026 0.007 -10000 0 -10000 0 0
RHOA -0.012 0.037 0.18 16 -0.17 1 17
S1P/S1P4/Gi -0.005 0.077 -10000 0 -0.18 66 66
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.039 0.011 -10000 0 0 38 38
S1P/S1P4/G12/G13 0.046 0.024 -10000 0 -0.098 9 9
GNA12 0.039 0.01 -10000 0 0 36 36
GNA13 0.04 0.009 -10000 0 0 28 28
CDC42 0.04 0.008 -10000 0 0 22 22
Regulation of nuclear SMAD2/3 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
EP300 0.037 0.016 0.079 2 -0.057 3 5
HSPA8 0.039 0.01 -10000 0 0 34 34
SMAD3/SMAD4/ER alpha 0.065 0.091 0.26 10 -0.17 17 27
AKT1 0.04 0.017 -10000 0 -0.098 5 5
GSC 0.007 0.097 -10000 0 -0.96 3 3
NKX2-5 0.039 0.017 -10000 0 -0.053 13 13
muscle cell differentiation -0.041 0.1 0.26 27 -10000 0 27
SMAD2-3/SMAD4/SP1 0.071 0.12 -10000 0 -0.2 10 10
SMAD4 0.036 0.046 -10000 0 -0.1 14 14
CBFB 0.036 0.015 -10000 0 0 83 83
SAP18 0.039 0.01 -10000 0 0 31 31
Cbp/p300/MSG1 0.06 0.056 -10000 0 -0.15 22 22
SMAD3/SMAD4/VDR 0.074 0.1 -10000 0 -0.21 13 13
MYC 0.021 0.022 0.12 4 -0.044 2 6
CDKN2B -0.047 0.17 -10000 0 -0.88 10 10
AP1 0.004 0.091 -10000 0 -0.23 37 37
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.001 0.13 0.19 6 -0.31 52 58
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.012 0.063 -10000 0 -0.2 34 34
SP3 0.036 0.024 0.08 3 -0.036 49 52
CREB1 0.04 0.008 -10000 0 0 19 19
FOXH1 0.041 0.019 -10000 0 -0.058 17 17
SMAD3/SMAD4/GR 0.054 0.079 -10000 0 -0.14 25 25
GATA3 0.042 0.012 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 0.003 0.096 0.17 6 -0.27 37 43
MEF2C/TIF2 0.023 0.067 0.26 6 -0.22 15 21
endothelial cell migration -0.032 0.1 1.2 3 -10000 0 3
MAX 0.029 0.027 0.098 3 -0.03 93 96
RBBP7 0.04 0.009 -10000 0 0 25 25
RBBP4 0.038 0.011 -10000 0 0 45 45
RUNX2 0.039 0.011 -10000 0 0 42 42
RUNX3 0.039 0.01 -10000 0 0 31 31
RUNX1 0.039 0.01 -10000 0 0 33 33
CTBP1 0.037 0.013 -10000 0 0 58 58
NR3C1 0.027 0.028 0.098 3 -0.036 77 80
VDR 0.037 0.013 -10000 0 0 58 58
CDKN1A 0.012 0.077 -10000 0 -0.63 3 3
KAT2B 0 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.081 0.06 -10000 0 -0.27 2 2
DCP1A 0.04 0.008 -10000 0 0 20 20
SKI 0.042 0.003 -10000 0 0 3 3
SERPINE1 0.031 0.1 -10000 0 -1.2 3 3
SMAD3/SMAD4/ATF2 0.063 0.074 -10000 0 -0.16 16 16
SMAD3/SMAD4/ATF3 0.061 0.068 -10000 0 -0.13 11 11
SAP30 0.038 0.013 -10000 0 0 55 55
Cbp/p300/PIAS3 0.062 0.058 0.18 1 -0.14 27 28
JUN -0.001 0.086 0.18 5 -0.23 35 40
SMAD3/SMAD4/IRF7 0.071 0.07 -10000 0 -0.14 9 9
TFE3 0.039 0.033 0.11 1 -0.082 35 36
COL1A2 -0.091 0.25 -10000 0 -0.62 102 102
mesenchymal cell differentiation -0.064 0.069 0.13 11 -10000 0 11
DLX1 0.04 0.008 -10000 0 0 22 22
TCF3 0.036 0.015 -10000 0 0 83 83
FOS 0.025 0.029 -10000 0 -0.051 25 25
SMAD3/SMAD4/Max 0.063 0.067 -10000 0 -0.14 7 7
Cbp/p300/SNIP1 0.058 0.056 -10000 0 -0.14 23 23
ZBTB17 0.039 0.011 0.1 4 -0.042 4 8
LAMC1 0.009 0.073 -10000 0 -0.26 24 24
TGIF2/HDAC complex/SMAD3/SMAD4 0.062 0.074 -10000 0 -0.14 20 20
IRF7 0.04 0.011 0.087 1 -10000 0 1
ESR1 0.046 0.037 0.12 89 0 92 181
HNF4A 0.039 0.01 -10000 0 0 35 35
MEF2C -0.003 0.06 0.22 11 -0.23 15 26
SMAD2-3/SMAD4 0.071 0.073 -10000 0 -0.15 4 4
Cbp/p300/Src-1 0.059 0.061 -10000 0 -0.14 31 31
IGHV3OR16-13 0.009 0.061 -10000 0 -0.43 10 10
TGIF2/HDAC complex 0.038 0.012 -10000 0 0 48 48
CREBBP 0.038 0.013 -10000 0 -0.045 2 2
SKIL 0.025 0.02 -10000 0 0 221 221
HDAC1 0.038 0.012 -10000 0 0 54 54
HDAC2 0.038 0.012 -10000 0 0 48 48
SNIP1 0.039 0.011 -10000 0 0 40 40
GCN5L2 0.039 0.013 -10000 0 -0.045 3 3
SMAD3/SMAD4/TFE3 0.078 0.083 -10000 0 -0.16 22 22
MSG1/HSC70 0.053 0.027 -10000 0 -0.14 5 5
SMAD2 0.039 0.025 -10000 0 -0.064 20 20
SMAD3 0.036 0.045 -10000 0 -0.1 15 15
SMAD3/E2F4-5/DP1/p107/SMAD4 0.019 0.066 0.18 1 -0.19 21 22
SMAD2/SMAD2/SMAD4 -0.01 0.061 0.17 7 -0.18 41 48
NCOR1 0.037 0.013 -10000 0 0 57 57
NCOA2 0.037 0.014 -10000 0 0 69 69
NCOA1 0.04 0.009 -10000 0 0 28 28
MYOD/E2A 0.051 0.025 -10000 0 -0.14 1 1
SMAD2-3/SMAD4/SP1/MIZ-1 0.081 0.12 -10000 0 -0.23 4 4
IFNB1 0.013 0.051 0.27 3 -0.16 2 5
SMAD3/SMAD4/MEF2C 0.051 0.083 0.29 1 -0.22 15 16
CITED1 0.039 0.01 -10000 0 0 35 35
SMAD2-3/SMAD4/ARC105 0.068 0.067 -10000 0 -0.13 3 3
RBL1 0.038 0.012 -10000 0 0 51 51
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.023 0.075 -10000 0 -0.4 7 7
RUNX1-3/PEBPB2 0.063 0.044 -10000 0 -0.11 15 15
SMAD7 -0.001 0.14 -10000 0 -0.39 24 24
MYC/MIZ-1 0.017 0.058 0.2 4 -0.14 49 53
SMAD3/SMAD4 -0.006 0.11 0.26 1 -0.33 33 34
IL10 0.022 0.061 0.22 19 -10000 0 19
PIASy/HDAC complex 0.037 0.015 -10000 0 -0.038 5 5
PIAS3 0.04 0.01 -10000 0 -0.004 26 26
CDK2 0.038 0.014 -10000 0 -0.043 3 3
IL5 0.023 0.061 0.22 17 -10000 0 17
CDK4 0.038 0.015 -10000 0 -0.045 3 3
PIAS4 0.037 0.015 -10000 0 -0.038 5 5
ATF3 0.037 0.014 -10000 0 0 68 68
SMAD3/SMAD4/SP1 0.054 0.11 -10000 0 -0.18 28 28
FOXG1 -0.001 0.001 -10000 0 -10000 0 0
FOXO3 0.01 0.012 -10000 0 -0.11 5 5
FOXO1 0.01 0.012 -10000 0 -0.11 5 5
FOXO4 0.01 0.012 -10000 0 -0.11 5 5
heart looping -0.003 0.06 0.22 11 -0.23 15 26
CEBPB 0.036 0.017 -10000 0 -0.061 5 5
SMAD3/SMAD4/DLX1 0.069 0.066 -10000 0 -0.14 7 7
MYOD1 0.04 0.008 -10000 0 0 19 19
SMAD3/SMAD4/HNF4 0.066 0.067 -10000 0 -0.14 7 7
SMAD3/SMAD4/GATA3 0.077 0.071 -10000 0 -0.17 1 1
SnoN/SIN3/HDAC complex/NCoR1 0.025 0.02 -10000 0 0 221 221
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.086 0.084 -10000 0 -0.18 1 1
SMAD3/SMAD4/SP1-3 0.069 0.12 -10000 0 -0.21 24 24
MED15 0 0 -10000 0 -10000 0 0
SP1 0.018 0.066 -10000 0 -0.099 126 126
SIN3B 0.037 0.014 -10000 0 0 67 67
SIN3A 0.039 0.01 -10000 0 0 31 31
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.1 0.073 -10000 0 -0.17 12 12
ITGB5 -0.005 0.094 0.21 15 -0.26 32 47
TGIF/SIN3/HDAC complex/CtBP 0.006 0.091 -10000 0 -0.27 33 33
SMAD3/SMAD4/AR 0.042 0.09 -10000 0 -0.14 46 46
AR 0.033 0.017 -10000 0 0 119 119
negative regulation of cell growth 0.017 0.077 -10000 0 -0.25 20 20
SMAD3/SMAD4/MYOD 0.069 0.067 -10000 0 -0.14 7 7
E2F5 0.037 0.014 -10000 0 0 70 70
E2F4 0.036 0.015 -10000 0 0 79 79
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.097 0.081 -10000 0 -0.16 5 5
SMAD2-3/SMAD4/FOXO1-3a-4 0.025 0.052 -10000 0 -0.29 7 7
TFDP1 0.038 0.012 -10000 0 0 53 53
SMAD3/SMAD4/AP1 0.033 0.11 -10000 0 -0.24 35 35
SMAD3/SMAD4/RUNX2 0.065 0.069 -10000 0 -0.14 11 11
TGIF2 0.038 0.012 -10000 0 0 48 48
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0.039 0.01 -10000 0 0 34 34
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.038 0.012 -10000 0 0 47 47
NFATC1 0.02 0.1 0.24 2 -0.34 14 16
NFATC2 0.026 0.058 0.16 12 -0.21 11 23
NFATC3 0.025 0.016 -10000 0 -10000 0 0
YWHAE 0.038 0.012 -10000 0 0 50 50
Calcineurin A alpha-beta B1/CABIN1 -0.002 0.085 0.18 3 -0.26 26 29
Exportin 1/Ran/NUP214 0.067 0.052 -10000 0 -0.12 33 33
mol:DAG 0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.029 0.097 -10000 0 -0.23 23 23
BCL2/BAX 0.051 0.026 -10000 0 -0.14 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.029 0.019 -10000 0 -0.13 5 5
CaM/Ca2+ 0.029 0.019 -10000 0 -0.13 5 5
BAX 0.04 0.008 -10000 0 0 20 20
MAPK14 0.04 0.009 -10000 0 0 28 28
BAD 0.041 0.005 -10000 0 0 9 9
CABIN1/MEF2D 0.014 0.089 -10000 0 -0.25 24 24
Calcineurin A alpha-beta B1/BCL2 0.036 0.014 -10000 0 0 76 76
FKBP8 0.036 0.014 -10000 0 0 73 73
activation-induced cell death of T cells -0.014 0.088 0.25 24 -0.19 1 25
KPNB1 0.04 0.009 -10000 0 0 29 29
KPNA2 0.035 0.015 -10000 0 0 84 84
XPO1 0.039 0.011 -10000 0 0 39 39
SFN 0.035 0.015 -10000 0 0 84 84
MAP3K8 0.041 0.008 -10000 0 0 22 22
NFAT4/CK1 alpha 0.027 0.045 0.19 1 -0.16 9 10
MEF2D/NFAT1/Cbp/p300 0.072 0.089 0.24 3 -0.18 16 19
CABIN1 -0.002 0.085 0.18 3 -0.27 26 29
CALM1 0.04 0.01 -10000 0 0 30 30
RAN 0.041 0.006 -10000 0 0 11 11
MAP3K1 0.036 0.015 -10000 0 0 78 78
CAMK4 0.037 0.013 -10000 0 0 65 65
mol:Ca2+ 0.001 0.004 -10000 0 -10000 0 0
MAPK3 0.041 0.007 -10000 0 0 17 17
YWHAH 0.038 0.012 -10000 0 0 54 54
Calcineurin A alpha-beta B1/AKAP79/PKA 0.05 0.026 -10000 0 -0.14 2 2
YWHAB 0.038 0.011 -10000 0 0 44 44
MAPK8 0.04 0.01 -10000 0 0 29 29
MAPK9 0.039 0.011 -10000 0 0 39 39
YWHAG 0.04 0.009 -10000 0 0 26 26
FKBP1A 0.039 0.011 -10000 0 0 39 39
NFAT1-c-4/YWHAQ 0.036 0.11 0.26 1 -0.31 17 18
PRKCH 0.039 0.011 -10000 0 0 41 41
CABIN1/Cbp/p300 0.043 0.052 -10000 0 -0.16 24 24
CASP3 0.037 0.014 -10000 0 0 70 70
PIM1 0.038 0.011 -10000 0 0 44 44
Calcineurin A alpha-beta B1/FKBP12/FK506 0.027 0.011 -10000 0 -0.1 2 2
apoptosis 0.02 0.037 -10000 0 -0.2 11 11
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.026 0.077 -10000 0 -0.26 18 18
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.039 0.011 -10000 0 0 38 38
JNK2/NFAT4 0.025 0.068 -10000 0 -0.14 68 68
BAD/BCL-XL 0.053 0.032 -10000 0 -0.14 11 11
PRKCD 0.038 0.013 -10000 0 0 55 55
NUP214 0.04 0.01 -10000 0 0 32 32
PRKCZ 0.043 0.002 -10000 0 -10000 0 0
PRKCA 0.035 0.016 -10000 0 0 91 91
PRKCG 0.041 0.005 -10000 0 0 7 7
PRKCQ 0.035 0.016 -10000 0 0 93 93
FKBP38/BCL2 0.046 0.03 -10000 0 -0.14 3 3
EP300 0.037 0.015 -10000 0 0 73 73
PRKCB1 0.038 0.012 -10000 0 0 48 48
CSNK2A1 0.039 0.011 -10000 0 0 40 40
NFATc/JNK1 0.034 0.11 0.26 2 -0.33 15 17
CaM/Ca2+/FKBP38 0.047 0.027 -10000 0 -0.13 4 4
FKBP12/FK506 0.028 0.012 -10000 0 -0.13 2 2
CSNK1A1 0.017 0.017 0.092 6 -0.091 4 10
CaM/Ca2+/CAMK IV 0.047 0.028 -10000 0 -0.11 7 7
NFATc/ERK1 0.035 0.1 0.26 1 -0.33 13 14
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.026 0.098 -10000 0 -0.23 27 27
NR4A1 0.016 0.073 0.2 17 -0.22 21 38
GSK3B 0.04 0.01 -10000 0 0 29 29
positive T cell selection 0.025 0.016 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.023 0.047 0.12 7 -0.19 11 18
RCH1/ KPNB1 0.036 0.063 -10000 0 -0.14 58 58
YWHAQ 0.04 0.009 -10000 0 0 26 26
PRKACA 0.036 0.016 -10000 0 0 87 87
AKAP5 0.04 0.007 -10000 0 0 18 18
MEF2D 0.041 0.009 -10000 0 0 24 24
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.034 0.016 -10000 0 0 104 104
NFATc/p38 alpha 0.036 0.1 0.26 1 -0.32 14 15
CREBBP 0.039 0.013 -10000 0 -0.001 50 50
BCL2 0.036 0.014 -10000 0 0 76 76
Coregulation of Androgen receptor activity

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
NRIP1 0.037 0.015 -9999 0 -10000 0 0
SVIL 0.037 0.015 -9999 0 -10000 0 0
ZNF318 0.037 0.009 -9999 0 -0.035 2 2
JMJD2C 0.042 0.016 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 0.037 0.061 -9999 0 -0.11 67 67
CARM1 0.037 0.014 -9999 0 0 70 70
PRDX1 0.039 0.01 -9999 0 0 36 36
PELP1 0.039 0.009 -9999 0 0 29 29
CTNNB1 0.04 0.01 -9999 0 -10000 0 0
AKT1 0.038 0.01 -9999 0 0 38 38
PTK2B 0.034 0.017 -9999 0 -10000 0 0
MED1 -0.001 0 -9999 0 -10000 0 0
MAK 0.033 0.015 -9999 0 -0.034 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.04 0.01 -9999 0 -10000 0 0
GSN 0.04 0.011 -9999 0 -10000 0 0
NCOA2 0.037 0.014 -9999 0 0 69 69
NCOA6 0.04 0.011 -9999 0 -10000 0 0
DNA-PK 0.051 0.066 -9999 0 -0.14 45 45
NCOA4 0.04 0.009 -9999 0 0 24 24
PIAS3 0.041 0.009 -9999 0 -10000 0 0
cell proliferation 0.018 0.048 -9999 0 -0.42 6 6
XRCC5 0.038 0.01 -9999 0 0 38 38
UBE3A 0.043 0.005 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.038 0.062 -9999 0 -0.11 73 73
FHL2 0.025 0.069 -9999 0 -0.61 5 5
RANBP9 0.039 0.013 -9999 0 -10000 0 0
JMJD1A 0.052 0.019 -9999 0 -0.14 1 1
CDK6 0.032 0.018 -9999 0 0 128 128
TGFB1I1 0.042 0.007 -9999 0 -10000 0 0
T-DHT/AR/CyclinD1 0.013 0.078 -9999 0 -0.12 125 125
XRCC6 0.036 0.014 -9999 0 0 69 69
T-DHT/AR 0.036 0.057 -9999 0 -0.1 69 69
CTDSP1 0.041 0.006 -9999 0 0 13 13
CTDSP2 0.037 0.011 -9999 0 -10000 0 0
BRCA1 0.035 0.016 -9999 0 -10000 0 0
TCF4 0.036 0.013 -9999 0 0 59 59
CDKN2A 0.028 0.019 -9999 0 0 176 176
SRF 0.043 0.021 -9999 0 -0.14 4 4
NKX3-1 0.014 0.082 -9999 0 -0.3 27 27
KLK3 0.003 0.049 -9999 0 -10000 0 0
TMF1 0.039 0.011 -9999 0 0 38 38
HNRNPA1 -0.001 0 -9999 0 -10000 0 0
AOF2 0.041 0.009 -9999 0 -10000 0 0
APPL1 -0.011 0.003 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 0.034 0.065 -9999 0 -0.11 86 86
AR 0.037 0.02 -9999 0 -0.043 1 1
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 -0.001 0 -9999 0 -10000 0 0
PAWR 0.041 0.007 -9999 0 0 16 16
PRKDC 0.038 0.011 -9999 0 0 44 44
PA2G4 0.039 0.008 -9999 0 0 24 24
UBE2I 0.04 0.009 -9999 0 0 26 26
T-DHT/AR/Cyclin D3/CDK11 p58 0.035 0.057 -9999 0 -0.095 77 77
RPS6KA3 0.038 0.014 -9999 0 -10000 0 0
T-DHT/AR/ARA70 0.035 0.065 -9999 0 -0.11 86 86
LATS2 0.039 0.009 -9999 0 0 25 25
T-DHT/AR/PRX1 0.032 0.059 -9999 0 -0.098 79 79
Cyclin D3/CDK11 p58 0.028 0.016 -9999 0 -0.13 5 5
VAV3 0.034 0.017 -9999 0 -10000 0 0
KLK2 0.021 0.064 -9999 0 -0.3 16 16
CASP8 0.039 0.009 -9999 0 0 28 28
T-DHT/AR/TIF2/CARM1 0.045 0.071 -9999 0 -0.11 67 67
TMPRSS2 0.013 0.091 -9999 0 -0.31 35 35
CCND1 0.031 0.019 -9999 0 0 144 144
PIAS1 0.041 0.01 -9999 0 -10000 0 0
mol:T-DHT 0.005 0.005 -9999 0 -0.033 1 1
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.04 0.013 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.017 0.076 -9999 0 -0.12 118 118
CMTM2 0.036 0.014 -9999 0 0 75 75
SNURF 0.041 0.006 -9999 0 0 10 10
ZMIZ1 0.005 0.005 -9999 0 -0.033 1 1
CCND3 0.039 0.01 -9999 0 0 33 33
TGIF1 -0.001 0 -9999 0 -10000 0 0
FKBP4 0.037 0.015 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.04 0.008 -10000 0 0 23 23
SPHK1 0.041 0.007 -10000 0 0 16 16
GNAI2 0.041 0.006 -10000 0 0 13 13
mol:S1P 0.015 0.028 -10000 0 -0.17 11 11
GNAO1 0.034 0.016 -10000 0 0 101 101
mol:Sphinganine-1-P -0.019 0.005 -10000 0 -10000 0 0
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.051 0.046 -10000 0 -0.16 12 12
GNAI3 0.038 0.012 -10000 0 0 46 46
G12/G13 0.053 0.03 -10000 0 -0.14 9 9
S1PR3 0 0 -10000 0 -10000 0 0
S1PR2 0 0 -10000 0 -10000 0 0
EDG1 0.041 0.007 -10000 0 0 15 15
S1P1/S1P 0.037 0.04 -10000 0 -0.12 29 29
S1PR5 0 0 -10000 0 -10000 0 0
S1PR4 0 0 -10000 0 -10000 0 0
GNAI1 0.035 0.016 -10000 0 0 94 94
S1P/S1P5/G12 0.032 0.036 -10000 0 -0.11 25 25
S1P/S1P3/Gq 0.015 0.078 0.17 1 -0.26 36 37
S1P/S1P4/Gi -0.008 0.085 -10000 0 -0.2 66 66
GNAQ 0.038 0.012 -10000 0 0 50 50
GNAZ 0.039 0.011 -10000 0 0 38 38
GNA14 0.039 0.01 -10000 0 0 33 33
GNA15 0.037 0.014 -10000 0 0 69 69
GNA12 0.039 0.01 -10000 0 0 36 36
GNA13 0.04 0.009 -10000 0 0 28 28
GNA11 0.037 0.013 -10000 0 0 63 63
ABCC1 0.04 0.009 -10000 0 0 24 24
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.055 0.051 -10000 0 -0.11 23 23
fibroblast growth factor receptor signaling pathway 0.055 0.05 -10000 0 -0.11 23 23
LAMA1 0.034 0.017 -10000 0 0 108 108
PRNP 0.037 0.013 -10000 0 0 59 59
GPC1/SLIT2 0.018 0.072 -10000 0 -0.14 90 90
SMAD2 -0.021 0.036 0.19 8 -0.19 1 9
GPC1/PrPc/Cu2+ 0.041 0.041 -10000 0 -0.11 32 32
GPC1/Laminin alpha1 0.046 0.032 -10000 0 -0.14 6 6
TDGF1 0.041 0.006 -10000 0 0 12 12
CRIPTO/GPC1 0.057 0.018 -10000 0 -0.14 1 1
APP/GPC1 0.047 0.044 -10000 0 -0.14 25 25
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.017 0.028 0.19 7 -0.12 1 8
FLT1 0.039 0.01 -10000 0 0 36 36
GPC1/TGFB/TGFBR1/TGFBR2 0.068 0.043 -10000 0 -0.12 17 17
SERPINC1 0.04 0.008 -10000 0 0 23 23
FYN -0.015 0.029 0.19 7 -0.12 1 8
FGR -0.018 0.028 0.19 7 -0.12 1 8
positive regulation of MAPKKK cascade 0.005 0.074 0.21 18 -0.22 12 30
SLIT2 0.028 0.02 -10000 0 0 181 181
GPC1/NRG 0.049 0.026 -10000 0 -0.14 1 1
NRG1 0.035 0.015 -10000 0 0 90 90
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.049 0.024 -10000 0 -0.11 6 6
LYN -0.017 0.025 0.19 5 -0.12 1 6
mol:Spermine -0.01 0.002 -10000 0 -10000 0 0
cell growth 0.055 0.05 -10000 0 -0.11 23 23
BMP signaling pathway -0.04 0.009 0 29 -10000 0 29
SRC -0.018 0.028 0.19 7 -0.12 1 8
TGFBR1 0.04 0.008 -10000 0 0 22 22
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.037 0.014 -10000 0 0 67 67
GPC1 0.04 0.009 -10000 0 0 29 29
TGFBR1 (dimer) 0.04 0.008 -10000 0 0 22 22
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.016 0.024 0.19 4 -0.12 1 5
HCK -0.016 0.027 0.19 6 -10000 0 6
FGF2 0.038 0.012 -10000 0 0 46 46
FGFR1 0.033 0.017 -10000 0 0 121 121
VEGFR1 homodimer 0.039 0.01 -10000 0 0 36 36
TGFBR2 0.039 0.011 -10000 0 0 38 38
cell death 0.047 0.044 -10000 0 -0.14 25 25
ATIII/GPC1 0.056 0.019 -10000 0 -0.14 1 1
PLA2G2A/GPC1 0.051 0.027 -10000 0 -0.14 3 3
LCK -0.018 0.028 0.19 7 -10000 0 7
neuron differentiation 0.049 0.026 -10000 0 -0.14 1 1
PrPc/Cu2+ 0.02 0.037 -10000 0 -0.13 31 31
APP 0.038 0.012 -10000 0 0 47 47
TGFBR2 (dimer) 0.039 0.011 -10000 0 0 38 38
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.015 0.088 -10000 0 -0.38 23 23
Crk/p130 Cas/Paxillin 0.005 0.039 -10000 0 -0.18 5 5
JUN 0.002 0.062 0.18 5 -0.23 11 16
HRAS 0.04 0.009 -10000 0 0 29 29
RET51/GFRalpha1/GDNF/GRB10 0.089 0.04 -10000 0 -0.11 5 5
RAP1A 0.039 0.01 -10000 0 0 35 35
FRS2 0.039 0.01 -10000 0 0 37 37
RAP1A/GDP 0.024 0.03 -10000 0 -0.13 21 21
RET51/GFRalpha1/GDNF/DOK1 0.089 0.04 -10000 0 -0.11 5 5
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.04 0.009 -10000 0 0 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.038 0.011 -10000 0 0 45 45
RET9/GFRalpha1/GDNF/Enigma 0.062 0.035 -10000 0 -0.1 2 2
RHOA 0.041 0.007 -10000 0 0 14 14
RAP1A/GTP 0.074 0.051 -10000 0 -0.1 15 15
GRB7 0.037 0.013 -10000 0 0 62 62
RET51/GFRalpha1/GDNF 0.077 0.047 -10000 0 -0.11 3 3
MAPKKK cascade 0.048 0.045 -10000 0 -0.15 4 4
BCAR1 0.036 0.014 -10000 0 0 74 74
RET9/GFRalpha1/GDNF/IRS1 0.063 0.036 -10000 0 -0.1 5 5
lamellipodium assembly 0.029 0.051 -10000 0 -0.18 4 4
RET51/GFRalpha1/GDNF/SHC 0.088 0.039 -10000 0 -0.11 2 2
PIK3CA 0.03 0.019 -10000 0 0 150 150
RET9/GFRalpha1/GDNF/SHC 0.062 0.035 -10000 0 -0.1 2 2
RET9/GFRalpha1/GDNF/Shank3 0.066 0.032 -10000 0 -0.1 1 1
MAPK3 -0.008 0.065 0.18 42 -10000 0 42
DOK1 0.04 0.009 -10000 0 0 24 24
DOK6 0.037 0.013 -10000 0 0 61 61
PXN 0.041 0.007 -10000 0 0 14 14
neurite development 0.002 0.06 0.17 39 -0.21 4 43
DOK5 0.022 0.021 -10000 0 0 266 266
GFRA1 0.037 0.013 -10000 0 0 64 64
MAPK8 0.011 0.06 -10000 0 -0.16 34 34
HRAS/GTP 0.08 0.048 -10000 0 -0.15 4 4
tube development 0.063 0.029 0.24 4 -0.1 2 6
MAPK1 -0.008 0.063 0.18 41 -10000 0 41
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.021 0.048 -10000 0 -0.17 25 25
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
SRC 0.039 0.01 -10000 0 0 31 31
PDLIM7 0.039 0.01 -10000 0 0 35 35
RET51/GFRalpha1/GDNF/Dok6 0.091 0.055 -10000 0 -0.11 1 1
SHC1 0.04 0.009 -10000 0 0 29 29
RET51/GFRalpha1/GDNF/Dok4 0.085 0.041 -10000 0 -0.11 1 1
RET51/GFRalpha1/GDNF/Dok5 0.041 0.079 -10000 0 -0.11 82 82
PRKCA 0.035 0.016 -10000 0 0 91 91
HRAS/GDP 0.029 0.007 -10000 0 -10000 0 0
CREB1 0.035 0.064 -10000 0 -0.38 5 5
PIK3R1 0.034 0.016 -10000 0 0 106 106
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.024 0.034 -10000 0 -0.15 10 10
RET51/GFRalpha1/GDNF/Grb7 0.084 0.045 -10000 0 -0.11 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.04 0.007 -10000 0 0 18 18
DOK4 0.038 0.012 -10000 0 0 50 50
JNK cascade 0.002 0.061 0.18 5 -0.23 11 16
RET9/GFRalpha1/GDNF/FRS2 0.06 0.04 -10000 0 -0.1 10 10
SHANK3 0.042 0.002 -10000 0 0 1 1
RASA1 0.036 0.014 -10000 0 0 73 73
NCK1 0.036 0.014 -10000 0 0 77 77
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.023 0.038 -10000 0 -0.14 21 21
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.026 0.051 -10000 0 -0.27 6 6
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.016 0.058 -10000 0 -0.16 34 34
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.028 0.043 -10000 0 -0.15 22 22
PI3K 0.041 0.064 0.26 5 -0.24 3 8
SOS1 0.038 0.013 -10000 0 0 57 57
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.085 0.033 -10000 0 -0.1 2 2
GRB10 0.04 0.008 -10000 0 0 23 23
activation of MAPKK activity 0.029 0.054 0.16 1 -0.3 6 7
RET51/GFRalpha1/GDNF/FRS2 0.086 0.045 -10000 0 -0.11 10 10
GAB1 0.038 0.012 -10000 0 0 49 49
IRS1 0.04 0.008 -10000 0 0 22 22
IRS2 0.039 0.01 -10000 0 0 36 36
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.03 0.037 -10000 0 -0.15 10 10
RET51/GFRalpha1/GDNF/PKC alpha 0.076 0.058 -10000 0 -0.11 29 29
GRB2 0.041 0.007 -10000 0 0 14 14
PRKACA 0.035 0.015 -10000 0 0 87 87
GDNF 0.039 0.011 -10000 0 0 40 40
RAC1 0.039 0.01 -10000 0 0 35 35
RET51/GFRalpha1/GDNF/IRS1 0.09 0.039 -10000 0 -0.11 5 5
Rac1/GTP 0.04 0.063 0.2 3 -0.23 3 6
RET9/GFRalpha1/GDNF 0.046 0.023 -10000 0 -0.11 1 1
GFRalpha1/GDNF 0.051 0.025 -10000 0 -0.14 1 1
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.055 0.027 -10000 0 -0.16 5 5
FBXW11 0.04 0.008 -10000 0 0 23 23
NF kappa B1 p50/c-Rel 0.027 0.037 -10000 0 -0.12 27 27
NF kappa B1 p50/RelA/I kappa B alpha 0.021 0.076 0.19 1 -0.22 21 22
NFKBIA 0.006 0.062 -10000 0 -0.25 9 9
MAPK14 0.04 0.009 -10000 0 0 28 28
NF kappa B1 p105/p50 0.026 0.039 -10000 0 -0.12 28 28
ARRB2 0.014 0.028 -10000 0 -0.2 9 9
REL 0.04 0.007 -10000 0 0 18 18
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.025 0.038 -10000 0 -0.12 28 28
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.039 -10000 0 -0.12 29 29
PIK3CA 0.03 0.019 -10000 0 0 150 150
NF kappa B1 p50 dimer 0.02 0.04 -10000 0 -0.14 29 29
PIK3R1 0.034 0.016 -10000 0 0 106 106
NFKB1 -0.016 0.009 -10000 0 -10000 0 0
RELA 0.041 0.006 -10000 0 0 10 10
positive regulation of anti-apoptosis 0.013 0.051 0.14 2 -0.17 13 15
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.024 0.082 -10000 0 -0.22 21 21
SRC 0.039 0.01 -10000 0 0 31 31
PI3K 0.024 0.062 -10000 0 -0.15 47 47
NF kappa B1 p50/RelA 0.013 0.052 0.14 2 -0.17 13 15
IKBKB 0.038 0.011 -10000 0 0 44 44
beta TrCP1/SCF ubiquitin ligase complex 0.04 0.008 -10000 0 0 23 23
SYK 0.037 0.014 -10000 0 0 67 67
I kappa B alpha/PIK3R1 0.018 0.068 0.19 1 -0.24 12 13
cell death 0.02 0.076 -10000 0 -0.22 21 21
NF kappa B1 p105/c-Rel 0.027 0.037 -10000 0 -0.12 27 27
LCK 0.04 0.009 -10000 0 0 28 28
BCL3 0.039 0.011 -10000 0 0 39 39
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin 0.014 0.079 -10000 0 -0.15 92 92
AKT1 0.011 0.1 0.28 9 -0.31 18 27
PTK2B -0.011 0.08 0.2 26 -0.31 7 33
VEGFR2 homodimer/Frs2 0.032 0.058 -10000 0 -0.37 4 4
CAV1 0.036 0.015 -10000 0 0 80 80
CALM1 0.04 0.009 -10000 0 0 30 30
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.031 0.058 -10000 0 -0.36 4 4
endothelial cell proliferation 0.033 0.095 0.26 16 -0.31 7 23
mol:Ca2+ 0.02 0.064 0.2 24 -0.29 7 31
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.047 0.079 -10000 0 -0.22 19 19
RP11-342D11.1 -0.005 0.058 0.17 25 -0.35 4 29
CDH5 0.036 0.015 -10000 0 0 79 79
VEGFA homodimer 0.065 0.049 -10000 0 -0.11 32 32
SHC1 0.04 0.009 -10000 0 0 29 29
SHC2 0.037 0.014 -10000 0 0 69 69
HRAS/GDP 0.039 0.067 -10000 0 -0.26 8 8
SH2D2A 0.04 0.009 -10000 0 0 30 30
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.05 0.082 0.31 1 -0.37 6 7
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.034 0.053 -10000 0 -0.31 4 4
VEGFR1 homodimer 0.039 0.01 -10000 0 0 36 36
SHC/GRB2/SOS1 0.072 0.084 -10000 0 -0.26 9 9
GRB10 0.02 0.069 0.28 1 -0.34 8 9
PTPN11 0.04 0.009 -10000 0 0 29 29
GRB2 0.041 0.007 -10000 0 0 14 14
PAK1 0.037 0.014 -10000 0 0 66 66
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.051 0.089 -10000 0 -0.21 21 21
HRAS 0.04 0.009 -10000 0 0 29 29
VEGF/Rho/ROCK1/Integrin Complex -0.014 0.11 -10000 0 -0.26 78 78
HIF1A 0.039 0.011 -10000 0 0 43 43
FRS2 0.039 0.01 -10000 0 0 37 37
oxygen and reactive oxygen species metabolic process 0.045 0.077 -10000 0 -0.21 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.04 0.008 -10000 0 0 21 21
Nck/Pak 0.036 0.056 -10000 0 -0.14 43 43
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.023 0.061 -10000 0 -0.29 6 6
mol:GDP 0.056 0.075 -10000 0 -0.25 9 9
mol:NADP 0.038 0.079 0.31 4 -0.34 7 11
eNOS/Hsp90 0.035 0.074 0.29 4 -0.32 7 11
PIK3R1 0.034 0.016 -10000 0 0 106 106
mol:IP3 0.02 0.065 0.2 24 -0.29 7 31
HIF1A/ARNT 0.049 0.045 -10000 0 -0.14 25 25
SHB 0.041 0.007 -10000 0 0 16 16
VEGFA 0.002 0.005 -10000 0 -0.041 6 6
VEGFC 0.036 0.015 -10000 0 0 78 78
FAK1/Vinculin 0.013 0.13 0.28 9 -0.29 43 52
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.041 0.007 -10000 0 0 14 14
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.024 0.088 -10000 0 -0.21 33 33
PTPN6 0.037 0.013 -10000 0 0 63 63
EPAS1 0.043 0.031 -10000 0 -0.27 3 3
mol:L-citrulline 0.038 0.079 0.31 4 -0.34 7 11
ITGAV 0.033 0.017 -10000 0 0 115 115
PIK3CA 0.03 0.019 -10000 0 0 150 150
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.055 0.07 -10000 0 -0.31 5 5
VEGFR2 homodimer/VEGFA homodimer 0.043 0.061 -10000 0 -0.29 7 7
VEGFR2/3 heterodimer 0.033 0.057 -10000 0 -0.37 4 4
VEGFB 0.039 0.011 -10000 0 0 42 42
MAPK11 -0.001 0.071 0.25 9 -0.31 8 17
VEGFR2 homodimer 0.022 0.044 -10000 0 -0.43 4 4
FLT1 0.039 0.01 -10000 0 0 36 36
NEDD4 0.041 0.014 -10000 0 -0.058 5 5
MAPK3 -0.002 0.071 0.23 11 -0.28 7 18
MAPK1 -0.002 0.072 0.23 12 -0.32 6 18
VEGFA145/NRP2 0.016 0.045 -10000 0 -0.12 50 50
VEGFR1/2 heterodimer 0.032 0.058 -10000 0 -0.31 6 6
KDR 0.022 0.044 -10000 0 -0.43 4 4
VEGFA165/NRP1/VEGFR2 homodimer 0.033 0.073 -10000 0 -0.21 19 19
SRC 0.039 0.01 -10000 0 0 31 31
platelet activating factor biosynthetic process -0.001 0.073 0.24 10 -0.31 6 16
PI3K 0.012 0.081 0.25 1 -0.32 8 9
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.025 0.062 -10000 0 -0.26 9 9
FES 0.021 0.065 0.2 25 -0.27 7 32
GAB1 0.017 0.083 0.26 3 -0.31 16 19
VEGFR2 homodimer/VEGFA homodimer/Src 0.034 0.053 -10000 0 -0.31 4 4
CTNNB1 0.039 0.01 -10000 0 0 32 32
SOS1 0.038 0.013 -10000 0 0 57 57
ARNT 0.041 0.006 -10000 0 0 13 13
eNOS/Caveolin-1 0.044 0.082 0.33 3 -0.34 7 10
VEGFR2 homodimer/VEGFA homodimer/Yes 0.027 0.062 -10000 0 -0.28 7 7
PI3K/GAB1 0.024 0.11 0.26 7 -0.31 20 27
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.05 0.084 -10000 0 -0.21 12 12
PRKACA 0.035 0.015 -10000 0 0 87 87
VEGFR2/3 heterodimer/VEGFC homodimer 0.051 0.068 -10000 0 -0.32 5 5
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 0.021 0.065 0.2 24 -0.28 7 31
actin cytoskeleton reorganization 0.034 0.052 -10000 0 -0.31 4 4
PTK2 -0.004 0.11 0.26 4 -0.31 35 39
EDG1 0.02 0.062 0.24 2 -0.36 4 6
mol:DAG 0.02 0.065 0.2 24 -0.29 7 31
CaM/Ca2+ 0.035 0.066 0.25 2 -0.27 7 9
MAP2K3 -0.007 0.061 0.18 24 -0.36 4 28
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.047 0.072 0.24 5 -0.34 8 13
PLCG1 0.021 0.065 0.2 24 -0.29 7 31
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.06 0.064 -10000 0 -0.29 4 4
IQGAP1 0.037 0.014 -10000 0 0 67 67
YES1 0.037 0.013 -10000 0 0 59 59
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.03 0.061 -10000 0 -0.3 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.033 0.053 -10000 0 -0.34 4 4
cell migration 0.001 0.13 0.26 10 -0.34 38 48
mol:PI-3-4-5-P3 0.012 0.078 0.24 1 -0.3 8 9
FYN 0.034 0.016 -10000 0 0 102 102
VEGFB/NRP1 0.026 0.062 0.24 3 -0.24 9 12
mol:NO 0.038 0.079 0.31 4 -0.34 7 11
PXN 0.041 0.007 -10000 0 0 14 14
HRAS/GTP 0.018 0.056 -10000 0 -0.24 9 9
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.025 0.06 -10000 0 -0.34 8 8
VHL 0.04 0.009 -10000 0 0 27 27
ITGB3 0.033 0.017 -10000 0 0 120 120
NOS3 0.038 0.084 0.33 3 -0.38 7 10
VEGFR2 homodimer/VEGFA homodimer/Sck 0.031 0.055 -10000 0 -0.35 4 4
RAC1 0.039 0.01 -10000 0 0 35 35
PRKCA -0.007 0.066 0.18 28 -0.36 4 32
PRKCB -0.006 0.061 0.18 27 -0.36 4 31
VCL 0.039 0.01 -10000 0 0 35 35
VEGFA165/NRP1 0.011 0.055 0.17 21 -0.27 7 28
VEGFR1/2 heterodimer/VEGFA homodimer 0.033 0.057 -10000 0 -0.3 6 6
VEGFA165/NRP2 0.016 0.045 -10000 0 -0.12 50 50
MAPKKK cascade -0.022 0.07 0.2 23 -0.35 6 29
NRP2 0.035 0.016 -10000 0 0 94 94
VEGFC homodimer 0.036 0.015 -10000 0 0 78 78
NCK1 0.036 0.014 -10000 0 0 77 77
ROCK1 0.04 0.007 -10000 0 0 18 18
FAK1/Paxillin 0.016 0.13 0.28 9 -0.29 39 48
MAP3K13 0.015 0.062 0.2 21 -0.27 8 29
PDPK1 -0.003 0.067 0.24 1 -0.28 7 8
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.049 0.045 0.15 18 -10000 0 18
KIRREL 0.041 0.017 0.082 2 -0.037 2 4
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.049 0.045 -10000 0 -0.15 18 18
PLCG1 0.039 0.011 -10000 0 0 39 39
ARRB2 0.039 0.01 -10000 0 0 37 37
WASL 0.04 0.008 -10000 0 0 23 23
Nephrin/NEPH1/podocin/CD2AP 0.073 0.071 0.21 1 -0.12 39 40
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.031 0.057 -10000 0 -0.14 30 30
FYN 0.002 0.063 0.17 56 -0.13 17 73
mol:Ca2+ 0.076 0.063 0.2 1 -0.13 24 25
mol:DAG 0.077 0.064 0.21 1 -0.13 24 25
NPHS2 0.042 0.02 0.081 2 -0.043 19 21
mol:IP3 0.077 0.064 0.21 1 -0.13 24 25
regulation of endocytosis 0.054 0.058 -10000 0 -0.12 20 20
Nephrin/NEPH1/podocin/Cholesterol 0.063 0.048 0.17 3 -0.11 18 21
establishment of cell polarity 0.049 0.045 -10000 0 -0.15 18 18
Nephrin/NEPH1/podocin/NCK1-2 0.085 0.078 -10000 0 -0.11 37 37
Nephrin/NEPH1/beta Arrestin2 0.057 0.06 -10000 0 -0.12 20 20
NPHS1 0.04 0.022 0.085 8 -0.044 17 25
Nephrin/NEPH1/podocin 0.055 0.056 0.22 1 -0.12 19 20
TJP1 0.037 0.013 -10000 0 0 65 65
NCK1 0.036 0.014 -10000 0 0 77 77
NCK2 0.041 0.006 -10000 0 0 10 10
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.079 0.065 0.21 1 -0.13 24 25
CD2AP 0.037 0.013 -10000 0 0 63 63
Nephrin/NEPH1/podocin/GRB2 0.085 0.058 0.21 1 -0.12 18 19
GRB2 0.041 0.007 -10000 0 0 14 14
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.005 0.071 0.17 68 -0.12 3 71
cytoskeleton organization 0.013 0.053 0.28 3 -0.16 12 15
Nephrin/NEPH1 0.042 0.034 -10000 0 -0.096 18 18
Nephrin/NEPH1/ZO-1 0.054 0.062 -10000 0 -0.13 36 36
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.054 -10000 0 -0.18 24 24
VEGFR1 homodimer/NRP1 0.008 0.047 -10000 0 -0.39 5 5
mol:DAG -0.024 0.041 0.2 2 -0.31 6 8
VEGFR1 homodimer/NRP1/VEGFR 121 0.007 0.042 -10000 0 -0.36 5 5
CaM/Ca2+ 0.026 0.053 0.2 2 -0.28 7 9
HIF1A 0.045 0.034 -10000 0 -0.28 5 5
GAB1 0.038 0.012 -10000 0 0 49 49
AKT1 0 0.09 0.21 8 -0.26 18 26
PLCG1 -0.024 0.041 0.2 2 -0.31 6 8
NOS3 0.025 0.07 0.29 4 -0.26 10 14
CBL 0.04 0.008 -10000 0 0 23 23
mol:NO 0.026 0.071 0.28 5 -0.26 10 15
FLT1 0.018 0.044 -10000 0 -0.49 4 4
PGF 0.04 0.009 -10000 0 0 25 25
VEGFR1 homodimer/NRP2/VEGFR121 0.017 0.062 -10000 0 -0.31 8 8
CALM1 0.04 0.009 -10000 0 0 30 30
PIK3CA 0.03 0.019 -10000 0 0 150 150
eNOS/Hsp90 0.02 0.068 0.28 4 -0.25 10 14
endothelial cell proliferation -0.005 0.064 0.24 4 -0.3 10 14
mol:Ca2+ -0.024 0.041 0.2 2 -0.31 6 8
MAPK3 -0.03 0.053 0.17 10 -0.25 9 19
MAPK1 -0.029 0.051 0.18 7 -0.25 9 16
PIK3R1 0.034 0.016 -10000 0 0 106 106
PLGF homodimer 0.04 0.009 -10000 0 0 25 25
PRKACA 0.035 0.015 -10000 0 0 87 87
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.036 0.015 -10000 0 0 80 80
VEGFA homodimer 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.008 0.047 -10000 0 -0.39 5 5
platelet activating factor biosynthetic process -0.03 0.054 0.16 15 -0.25 8 23
PI3K 0.039 0.081 -10000 0 -0.19 26 26
PRKCA -0.021 0.047 0.21 5 -0.26 8 13
PRKCB -0.022 0.037 0.18 2 -0.29 6 8
VEGFR1 homodimer/PLGF homodimer 0.034 0.055 -10000 0 -0.17 28 28
VEGFA 0 0 -10000 0 -10000 0 0
VEGFB 0.039 0.011 -10000 0 0 42 42
mol:IP3 -0.024 0.041 0.2 2 -0.31 6 8
RASA1 -0.021 0.046 0.2 3 -0.32 7 10
NRP2 0.035 0.016 -10000 0 0 94 94
VEGFR1 homodimer 0.018 0.044 -10000 0 -0.49 4 4
VEGFB homodimer 0.039 0.011 -10000 0 0 42 42
NCK1 0.036 0.014 -10000 0 0 77 77
eNOS/Caveolin-1 0.041 0.081 0.32 3 -0.26 10 13
PTPN11 0.04 0.009 -10000 0 0 29 29
mol:PI-3-4-5-P3 0.037 0.079 -10000 0 -0.19 26 26
mol:L-citrulline 0.026 0.071 0.28 5 -0.26 10 15
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.041 0.066 -10000 0 -0.27 10 10
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.023 0.058 -10000 0 -0.28 10 10
CD2AP 0.037 0.013 -10000 0 0 63 63
PI3K/GAB1 0.044 0.088 -10000 0 -0.23 18 18
PDPK1 0 0.091 0.17 88 -0.24 16 104
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.027 0.056 -10000 0 -0.16 29 29
mol:NADP 0.026 0.071 0.28 5 -0.26 10 15
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.039 0.065 -10000 0 -0.26 10 10
VEGFR1 homodimer/NRP2 0.027 0.058 -10000 0 -0.18 28 28
Alternative NF-kappaB pathway

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
IKK alpha homodimer 0.047 0.045 -9999 0 -0.14 27 27
FBXW11 0.04 0.008 -9999 0 0 23 23
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.04 0.008 -9999 0 0 23 23
CHUK 0.038 0.012 -9999 0 0 52 52
NF kappa B2 p100/RelB 0.095 0.066 -9999 0 -0.12 29 29
NFKB1 0.035 0.015 -9999 0 0 85 85
MAP3K14 0.04 0.009 -9999 0 0 27 27
NF kappa B1 p50/RelB 0.042 0.05 -9999 0 -0.14 34 34
RELB 0.04 0.009 -9999 0 0 25 25
NFKB2 0.04 0.008 -9999 0 0 23 23
NF kappa B2 p52/RelB 0.051 0.021 -9999 0 -0.14 3 3
regulation of B cell activation 0.05 0.021 -9999 0 -0.14 3 3
Insulin 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
CBL/APS/CAP 0.06 0.04 -10000 0 -0.11 9 9
TC10/GTP 0.05 0.037 -10000 0 -0.1 11 11
Insulin Receptor/Insulin/IRS1/Shp2 0.087 0.058 -10000 0 -0.12 22 22
HRAS 0.04 0.009 -10000 0 0 29 29
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 0.038 0.012 -10000 0 0 54 54
FOXO3 -0.005 0.009 0.02 8 -0.036 6 14
AKT1 0.015 0.098 0.23 38 -10000 0 38
INSR 0.041 0.015 0.082 8 -10000 0 8
Insulin Receptor/Insulin 0.083 0.052 0.24 28 -0.1 3 31
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.04 0.008 -10000 0 0 23 23
SORBS1 0.039 0.011 -10000 0 0 39 39
CRK 0.038 0.011 -10000 0 0 45 45
PTPN1 -0.006 0.041 0.15 32 -10000 0 32
CAV1 -0.008 0.041 0.17 17 -10000 0 17
CBL/APS/CAP/Crk-II/C3G 0.081 0.042 -10000 0 -0.11 6 6
Insulin Receptor/Insulin/IRS1/NCK2 0.093 0.047 -10000 0 -0.11 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.04 0.065 -10000 0 -0.11 45 45
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.023 0.096 -10000 0 -0.33 29 29
RPS6KB1 0.004 0.09 0.2 38 -0.18 9 47
PARD6A 0.036 0.015 -10000 0 0 80 80
CBL 0.04 0.008 -10000 0 0 23 23
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.022 0.082 -10000 0 -0.69 7 7
PIK3R1 0.034 0.016 -10000 0 0 106 106
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.049 0.083 0.21 20 -0.19 10 30
HRAS/GTP -0.027 0.032 -10000 0 -0.15 2 2
Insulin Receptor 0.041 0.015 0.081 8 -10000 0 8
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.1 0.06 -10000 0 -0.11 9 9
PRKCI -0.007 0.13 -10000 0 -0.38 57 57
Insulin Receptor/Insulin/GRB14/PDK1 0.019 0.053 -10000 0 -0.12 42 42
SHC1 0.04 0.009 -10000 0 0 29 29
negative regulation of MAPKKK cascade 0.046 0.085 -10000 0 -0.56 7 7
PI3K 0.05 0.073 -10000 0 -0.12 41 41
NCK2 0.041 0.006 -10000 0 0 10 10
RHOQ 0.039 0.01 -10000 0 0 35 35
mol:H2O2 -0.002 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.029 0.007 -10000 0 -10000 0 0
AKT2 0.014 0.095 0.22 37 -10000 0 37
PRKCZ 0.036 0.09 -10000 0 -0.34 19 19
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP -0.009 0.039 0.16 16 -10000 0 16
F2RL2 0.036 0.014 -10000 0 0 76 76
TRIP10 0.038 0.012 -10000 0 0 48 48
Insulin Receptor/Insulin/Shc 0.069 0.037 -10000 0 -0.098 5 5
TC10/GTP/CIP4/Exocyst 0.046 0.029 -10000 0 -0.11 12 12
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.092 0.071 -10000 0 -0.12 22 22
RAPGEF1 0.04 0.008 -10000 0 0 22 22
RASA1 0.036 0.014 -10000 0 0 73 73
NCK1 0.036 0.014 -10000 0 0 77 77
CBL/APS/CAP/Crk-II 0.066 0.035 -10000 0 -0.12 6 6
TC10/GDP 0.027 0.02 -10000 0 -0.13 8 8
Insulin Receptor/Insulin/SHC/GRB10 0.088 0.052 -10000 0 -0.11 11 11
INPP5D -0.013 0.019 0.048 18 -0.094 7 25
SOS1 0.038 0.013 -10000 0 0 57 57
SGK1 -0.004 0.004 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.04 0.009 -10000 0 0 29 29
IRS1 0.04 0.008 -10000 0 0 22 22
p62DOK/RasGAP 0.046 0.086 -10000 0 -0.56 7 7
INS 0.044 0.013 0.083 13 0 30 43
mol:PI-3-4-P2 -0.013 0.018 0.048 18 -0.093 7 25
GRB2 0.041 0.007 -10000 0 0 14 14
EIF4EBP1 0.003 0.081 0.19 34 -0.17 3 37
PTPRA 0.042 0.013 0.082 5 0 34 39
PIK3CA 0.03 0.019 -10000 0 0 150 150
TC10/GTP/CIP4 0.046 0.029 -10000 0 -0.11 12 12
PDPK1 0.04 0.009 -10000 0 0 27 27
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.027 0.059 -10000 0 -0.2 9 9
Insulin Receptor/Insulin/IRS1 0.07 0.037 -10000 0 -0.099 8 8
Insulin Receptor/Insulin/IRS3 0.058 0.03 -10000 0 -0.14 3 3
Par3/Par6 0.066 0.051 -10000 0 -0.1 14 14
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.09 0.049 -10000 0 -0.11 20 20
HDAC3 0.041 0.006 -10000 0 0 12 12
Ran/GTP/Exportin 1/HDAC4 -0.027 0.024 -10000 0 -0.12 33 33
GATA1/HDAC4 0.06 0.011 -10000 0 -10000 0 0
GATA1/HDAC5 0.059 0.014 -10000 0 -10000 0 0
GATA2/HDAC5 0.055 0.02 -10000 0 -10000 0 0
HDAC5/BCL6/BCoR 0.052 0.057 -10000 0 -0.12 33 33
HDAC9 0.035 0.016 -10000 0 0 92 92
Glucocorticoid receptor/Hsp90/HDAC6 0.044 0.039 -10000 0 -0.11 30 30
HDAC4/ANKRA2 0.049 0.033 -10000 0 -0.14 9 9
HDAC5/YWHAB 0.052 0.029 -10000 0 -0.14 7 7
NPC/RanGAP1/SUMO1/Ubc9 0.009 0.034 -10000 0 -0.14 25 25
GATA2 0.039 0.01 -10000 0 0 34 34
HDAC4/RFXANK 0.047 0.04 -10000 0 -0.14 19 19
BCOR 0.041 0.005 -10000 0 0 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.032 0.018 -10000 0 0 131 131
HDAC5 0.04 0.009 -10000 0 0 30 30
GNB1/GNG2 0.053 0.038 -10000 0 -0.14 19 19
Histones -0.006 0.07 -10000 0 -0.19 38 38
ADRBK1 0.041 0.005 -10000 0 0 7 7
HDAC4 0.041 0.007 -10000 0 0 17 17
XPO1 0.039 0.011 -10000 0 0 39 39
HDAC5/ANKRA2 0.048 0.033 -10000 0 -0.13 9 9
HDAC4/Ubc9 0.057 0.018 -10000 0 -0.14 1 1
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.053 0.029 -10000 0 -0.14 7 7
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0.041 0.007 -10000 0 0 15 15
HDAC5/RFXANK 0.046 0.041 -10000 0 -0.14 20 20
CAMK4 0.037 0.013 -10000 0 0 65 65
Tubulin/HDAC6 0.05 0.018 -10000 0 -10000 0 0
SUMO1 0.041 0.006 -10000 0 0 13 13
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.038 0.011 -10000 0 0 44 44
GATA1 0.042 0.002 -10000 0 0 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.038 0.012 -10000 0 0 50 50
NR3C1 0.038 0.011 -10000 0 0 44 44
SUMO1/HDAC4 0.04 0.061 -10000 0 -0.18 15 15
SRF 0.039 0.011 -10000 0 0 40 40
HDAC4/YWHAB 0.054 0.028 -10000 0 -0.14 7 7
Tubulin 0.028 0.009 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.053 0.029 -10000 0 -0.14 7 7
GNB1 0.041 0.005 -10000 0 0 7 7
RANGAP1 0.038 0.013 -10000 0 0 55 55
BCL6/BCoR 0.037 0.052 -10000 0 -0.14 33 33
HDAC4/HDAC3/SMRT (N-CoR2) 0.075 0.03 -10000 0 -0.12 5 5
HDAC4/SRF 0.068 0.035 -10000 0 -0.12 1 1
HDAC4/ER alpha 0.04 0.054 -10000 0 -0.14 41 41
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.006 0.07 -10000 0 -0.19 38 38
cell motility 0.05 0.017 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.04 0.009 -10000 0 0 26 26
HDAC7/HDAC3 0.03 0.01 -10000 0 -0.13 2 2
BCL6 0.031 0.018 -10000 0 0 141 141
HDAC4/CaMK II delta B 0.04 0.007 -10000 0 0 17 17
Hsp90/HDAC6 0.03 0.005 -10000 0 -10000 0 0
ESR1 0.035 0.016 -10000 0 0 92 92
HDAC6/HDAC11 0.056 0.026 -10000 0 -0.14 7 7
Ran/GTP/Exportin 1 0.038 0.07 0.18 1 -0.18 33 34
NPC 0.02 0.022 -10000 0 -0.085 23 23
MEF2C 0.036 0.014 -10000 0 0 77 77
RAN 0.041 0.006 -10000 0 0 11 11
HDAC4/MEF2C 0.094 0.062 -10000 0 -0.11 18 18
GNG2 0.039 0.01 -10000 0 0 34 34
NCOR2 0.04 0.009 -10000 0 0 26 26
TUBB2A 0.038 0.012 -10000 0 0 47 47
HDAC11 0.04 0.008 -10000 0 0 23 23
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 0.04 0.009 -10000 0 0 30 30
ANKRA2 0.035 0.015 -10000 0 0 86 86
RFXANK 0.036 0.014 -10000 0 0 77 77
nuclear import -0.037 0.04 0.18 13 -10000 0 13
Glucocorticoid receptor regulatory network

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
PCK2 -0.021 0.075 -10000 0 -0.57 3 3
SMARCC2 0.04 0.009 -10000 0 0 24 24
SMARCC1 0.04 0.008 -10000 0 0 20 20
TBX21 0.04 0.059 0.41 1 -0.28 1 2
SUMO2 0.037 0.015 -10000 0 -0.03 20 20
STAT1 (dimer) 0.022 0.064 -10000 0 -0.18 46 46
FKBP4 0.036 0.015 -10000 0 0 82 82
FKBP5 0.03 0.019 -10000 0 0 150 150
GR alpha/HSP90/FKBP51/HSP90 -0.035 0.074 -10000 0 -0.21 21 21
PRL 0.048 0.07 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 -0.059 0.12 0.42 3 -0.35 1 4
RELA 0.013 0.097 -10000 0 -0.17 114 114
FGG -0.055 0.11 0.41 2 -0.32 1 3
GR beta/TIF2 -0.034 0.08 0.3 1 -0.22 9 10
IFNG 0.047 0.11 -10000 0 -0.43 1 1
apoptosis -0.052 0.17 -10000 0 -0.44 50 50
CREB1 0.048 0.009 -10000 0 -10000 0 0
histone acetylation 0.024 0.082 0.28 11 -0.34 8 19
BGLAP 0.045 0.082 -10000 0 -0.88 2 2
GR/PKAc 0.032 0.085 0.31 1 -0.16 25 26
NF kappa B1 p50/RelA 0.011 0.17 -10000 0 -0.3 112 112
SMARCD1 0.04 0.008 -10000 0 0 20 20
MDM2 -0.013 0.047 0.14 3 -0.24 7 10
GATA3 0.05 0.014 -10000 0 -10000 0 0
AKT1 0.035 0.016 0.17 2 -0.052 6 8
CSF2 0.014 0.055 -10000 0 -10000 0 0
GSK3B 0.037 0.016 -10000 0 -0.03 17 17
NR1I3 -0.041 0.16 -10000 0 -0.46 10 10
CSN2 -0.05 0.098 0.34 2 -0.3 2 4
BRG1/BAF155/BAF170/BAF60A 0.075 0.066 -10000 0 -0.13 32 32
NFATC1 0.043 0.017 -10000 0 -10000 0 0
POU2F1 0.045 0.01 -10000 0 -10000 0 0
CDKN1A -0.038 0.12 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.004 -10000 0 -10000 0 0
SFN 0.035 0.015 -10000 0 0 84 84
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.025 0.081 -10000 0 -0.2 29 29
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.1 0.28 -10000 0 -0.71 89 89
JUN 0.042 0.099 0.35 10 -0.28 4 14
IL4 0.043 0.059 0.32 1 -0.3 1 2
CDK5R1 0.039 0.009 -10000 0 0 27 27
PRKACA 0.035 0.015 -10000 0 0 87 87
cortisol/GR alpha (monomer)/AP-1 -0.041 0.068 0.2 11 -0.22 22 33
GR alpha/HSP90/FKBP51/HSP90/PP5C -0.018 0.081 -10000 0 -0.19 23 23
cortisol/GR alpha (monomer) -0.072 0.13 0.44 4 -0.38 2 6
NCOA2 0.037 0.014 -10000 0 0 69 69
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.033 0.053 -10000 0 -0.12 27 27
AP-1/NFAT1-c-4 0.04 0.14 -10000 0 -0.38 17 17
AFP 0.032 0.095 -10000 0 -10000 0 0
SUV420H1 0.039 0.01 -10000 0 0 31 31
IRF1 -0.1 0.22 0.29 1 -0.56 90 91
TP53 0.037 0.028 -10000 0 -10000 0 0
PPP5C 0.04 0.009 -10000 0 0 27 27
KRT17 0.03 0.16 -10000 0 -0.72 12 12
KRT14 0.021 0.18 0.5 8 -1.1 12 20
TBP 0.044 0.028 -10000 0 -0.32 2 2
CREBBP 0.031 0.057 0.34 14 -10000 0 14
HDAC1 0.033 0.012 -10000 0 -0.059 2 2
HDAC2 0.037 0.011 -10000 0 -10000 0 0
AP-1 0.04 0.14 -10000 0 -0.38 17 17
MAPK14 0.036 0.016 -10000 0 -0.03 20 20
MAPK10 0.032 0.021 -10000 0 -0.03 32 32
MAPK11 0.029 0.021 -10000 0 -0.03 16 16
KRT5 -0.005 0.26 -10000 0 -0.83 44 44
interleukin-1 receptor activity -0.001 0 -10000 0 -10000 0 0
NCOA1 0.04 0.012 -10000 0 -0.068 2 2
STAT1 0.022 0.064 -10000 0 -0.18 46 46
CGA 0.046 0.066 0.3 1 -0.3 1 2
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.06 0.11 0.31 3 -0.36 35 38
MAPK3 0.036 0.019 -10000 0 -0.03 36 36
MAPK1 0.035 0.018 -10000 0 -0.03 22 22
ICAM1 -0.078 0.32 -10000 0 -0.77 92 92
NFKB1 0.006 0.11 -10000 0 -0.2 108 108
MAPK8 0.05 0.083 0.57 1 -0.28 2 3
MAPK9 0.035 0.018 -10000 0 -0.011 62 62
cortisol/GR alpha (dimer) -0.054 0.18 -10000 0 -0.44 57 57
BAX -0.046 0.12 -10000 0 -10000 0 0
POMC 0.055 0.098 0.47 3 -10000 0 3
EP300 0.028 0.048 0.32 10 -10000 0 10
cortisol/GR alpha (dimer)/p53 -0.076 0.13 0.42 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process -0.024 0.051 0.26 7 -0.22 7 14
SGK1 -0.022 0.11 0.33 11 -0.32 37 48
IL13 0.05 0.094 -10000 0 -10000 0 0
IL6 0.012 0.16 -10000 0 -0.64 17 17
PRKACG 0.041 0.006 -10000 0 0 12 12
IL5 0.048 0.097 -10000 0 -10000 0 0
IL2 0.037 0.12 -10000 0 -0.54 5 5
CDK5 0.035 0.014 -10000 0 0 77 77
PRKACB 0.038 0.012 -10000 0 0 49 49
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.01 0.22 -10000 0 -0.79 34 34
CDK5R1/CDK5 0.045 0.04 -10000 0 -0.13 19 19
NF kappa B1 p50/RelA/PKAc 0.041 0.15 -10000 0 -0.22 86 86
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.043 0.11 0.38 4 -0.32 1 5
SMARCA4 0.035 0.016 -10000 0 0 91 91
chromatin remodeling -0.03 0.093 0.28 4 -0.29 22 26
NF kappa B1 p50/RelA/Cbp 0.026 0.16 0.41 7 -0.25 100 107
JUN (dimer) 0.042 0.099 0.35 10 -0.28 4 14
YWHAH 0.038 0.012 -10000 0 0 54 54
VIPR1 0.041 0.058 0.4 1 -0.28 1 2
NR3C1 -0.047 0.094 0.33 2 -0.31 6 8
NR4A1 0.038 0.018 -10000 0 -10000 0 0
TIF2/SUV420H1 0.042 0.052 -10000 0 -0.14 36 36
MAPKKK cascade -0.052 0.17 -10000 0 -0.44 50 50
cortisol/GR alpha (dimer)/Src-1 -0.055 0.13 0.41 4 -0.35 1 5
PBX1 0.044 0.013 -10000 0 -10000 0 0
POU1F1 0.046 0.009 -10000 0 -10000 0 0
SELE 0.023 0.12 -10000 0 -0.39 5 5
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.03 0.093 0.28 4 -0.29 23 27
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.043 0.11 0.38 4 -0.32 1 5
mol:cortisol -0.043 0.067 0.28 2 -10000 0 2
MMP1 0.013 0.17 -10000 0 -0.8 18 18
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.02 0.023 0.22 2 -0.093 3 5
NFATC2 0.021 0.023 0.23 2 -0.11 3 5
NFATC3 0.021 0.023 0.21 2 -0.093 3 5
CD40LG 0.032 0.1 0.29 21 -0.23 2 23
PTGS2 0.013 0.091 0.33 10 -0.28 6 16
JUNB 0.03 0.019 -10000 0 0 162 162
CaM/Ca2+/Calcineurin A alpha-beta B1 0.032 0.017 -10000 0 -0.13 3 3
CaM/Ca2+ 0.032 0.017 -10000 0 -0.13 3 3
CALM1 0.041 0.011 -10000 0 -0.001 31 31
JUN 0.038 0.016 0.098 1 0 81 82
mol:Ca2+ 0.001 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.027 0.011 -10000 0 -0.1 2 2
FOSL1 0.041 0.007 -10000 0 0 15 15
CREM 0.04 0.008 -10000 0 0 22 22
Jun/NFAT1-c-4/p21SNFT 0.055 0.069 0.24 8 -0.18 1 9
FOS 0.028 0.022 0.098 1 0 205 206
IFNG 0.022 0.095 0.31 13 -0.24 1 14
AP-1/NFAT1-c-4 0.084 0.12 0.34 1 -0.23 4 5
FASLG 0.029 0.1 0.32 14 -0.24 2 16
NFAT1-c-4/ICER1 0.053 0.057 0.21 8 -0.16 1 9
IL2RA 0.028 0.1 0.32 16 -0.25 2 18
FKBP12/FK506 0.028 0.012 -10000 0 -0.13 2 2
CSF2 0.031 0.1 0.29 20 -0.24 1 21
JunB/Fra1/NFAT1-c-4 0.047 0.074 0.23 6 -0.18 3 9
IL4 0.03 0.1 0.3 19 -0.24 1 20
IL2 -0.042 0.24 -10000 0 -0.86 42 42
IL3 0.028 0.12 -10000 0 -0.59 18 18
FKBP1A 0.039 0.011 -10000 0 0 39 39
BATF3 0 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.045 0.01 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.015 0.17 -10000 0 -0.7 13 13
NCK1/PAK1/Dok-R -0.031 0.073 -10000 0 -0.34 14 14
NCK1/Dok-R 0.049 0.099 -10000 0 -0.87 2 2
PIK3CA 0.03 0.018 -10000 0 0 150 150
mol:beta2-estradiol -0.009 0.008 -10000 0 -10000 0 0
RELA 0.041 0.006 -10000 0 0 10 10
SHC1 0.04 0.01 -10000 0 0 29 29
Rac/GDP 0.029 0.01 -10000 0 -0.13 1 1
F2 0.01 0.038 -10000 0 -0.083 1 1
TNIP2 0.038 0.012 -10000 0 0 48 48
NF kappa B/RelA 0.074 0.1 -10000 0 -0.84 2 2
FN1 0.021 0.021 -10000 0 0 273 273
PLD2 0.032 0.079 -10000 0 -0.9 2 2
PTPN11 0.04 0.009 -10000 0 0 29 29
GRB14 0.038 0.012 -10000 0 0 54 54
ELK1 0.032 0.08 -10000 0 -0.84 2 2
GRB7 0.037 0.013 -10000 0 0 62 62
PAK1 0.037 0.014 -10000 0 0 66 66
Tie2/Ang1/alpha5/beta1 Integrin 0.036 0.12 -10000 0 -0.86 2 2
CDKN1A 0.013 0.19 -10000 0 -0.62 39 39
ITGA5 0.037 0.013 -10000 0 0 58 58
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.053 0.098 -10000 0 -0.87 2 2
CRK 0.038 0.011 -10000 0 0 45 45
mol:NO 0.029 0.15 -10000 0 -0.54 12 12
PLG 0.03 0.077 -10000 0 -0.9 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.026 0.14 -10000 0 -0.75 6 6
GRB2 0.041 0.007 -10000 0 0 14 14
PIK3R1 0.034 0.017 -10000 0 0 106 106
ANGPT2 -0.045 0.29 -10000 0 -1 38 38
BMX 0.031 0.079 -10000 0 -0.9 2 2
ANGPT1 0.03 0.057 -10000 0 -10000 0 0
tube development -0.003 0.21 -10000 0 -0.7 39 39
ANGPT4 0.036 0.02 -10000 0 -0.015 68 68
response to hypoxia 0.001 0.008 0.037 2 -0.062 2 4
Tie2/Ang1/GRB14 0.053 0.091 -10000 0 -0.91 2 2
alpha5/beta1 Integrin 0.045 0.046 -10000 0 -0.14 28 28
FGF2 0.038 0.012 -10000 0 0 46 46
STAT5A (dimer) 0.013 0.24 -10000 0 -0.79 39 39
mol:L-citrulline 0.029 0.15 -10000 0 -0.54 12 12
AGTR1 0.032 0.025 -10000 0 -0.016 103 103
MAPK14 0.04 0.13 -10000 0 -1 4 4
Tie2/SHP2 0.036 0.11 -10000 0 -0.76 3 3
TEK 0.028 0.11 -10000 0 -1 2 2
RPS6KB1 0.015 0.16 -10000 0 -0.7 9 9
Angiotensin II/AT1 0.025 0.024 -10000 0 -0.056 34 34
Tie2/Ang1/GRB2 0.058 0.093 -10000 0 -0.91 2 2
MAPK3 0.027 0.077 -10000 0 -0.85 2 2
MAPK1 0.027 0.076 -10000 0 -0.85 2 2
Tie2/Ang1/GRB7 0.054 0.091 -10000 0 -0.91 2 2
NFKB1 0.035 0.015 -10000 0 0 85 85
MAPK8 0.031 0.081 -10000 0 -0.9 2 2
PI3K 0.017 0.16 -10000 0 -0.93 6 6
FES 0.043 0.11 -10000 0 -1 2 2
Crk/Dok-R 0.057 0.096 -10000 0 -0.87 2 2
Tie2/Ang1/ABIN2 0.055 0.092 -10000 0 -0.91 2 2
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.019 0.16 -10000 0 -0.63 13 13
STAT5A 0.038 0.012 -10000 0 0 50 50
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.061 0.18 -10000 0 -0.73 6 6
Tie2/Ang2 -0.014 0.27 -10000 0 -0.95 39 39
Tie2/Ang1 0.042 0.084 -10000 0 -0.94 2 2
FOXO1 0.015 0.19 -10000 0 -0.6 38 38
ELF1 0.047 0.019 -10000 0 -0.13 2 2
ELF2 0.039 0.08 -10000 0 -0.9 2 2
mol:Choline 0.032 0.078 -10000 0 -0.87 2 2
cell migration -0.018 0.048 -10000 0 -0.19 14 14
FYN -0.011 0.23 -10000 0 -0.8 39 39
DOK2 0.032 0.018 -10000 0 0 130 130
negative regulation of cell cycle 0.017 0.18 -10000 0 -0.56 39 39
ETS1 0.042 0.021 -10000 0 -10000 0 0
PXN 0.061 0.17 0.4 1 -0.57 8 9
ITGB1 0.039 0.011 -10000 0 0 39 39
NOS3 0.025 0.16 -10000 0 -0.61 12 12
RAC1 0.039 0.01 -10000 0 0 35 35
TNF 0.049 0.014 -10000 0 -10000 0 0
MAPKKK cascade 0.032 0.078 -10000 0 -0.87 2 2
RASA1 0.036 0.014 -10000 0 0 73 73
Tie2/Ang1/Shc 0.058 0.093 -10000 0 -0.91 2 2
NCK1 0.036 0.014 -10000 0 0 77 77
vasculogenesis 0.03 0.14 0.36 2 -0.49 12 14
mol:Phosphatidic acid 0.032 0.078 -10000 0 -0.87 2 2
mol:Angiotensin II 0 0.008 -10000 0 -0.033 30 30
mol:NADP 0.029 0.15 -10000 0 -0.54 12 12
Rac1/GTP 0.027 0.15 -10000 0 -0.74 6 6
MMP2 0.032 0.088 -10000 0 -0.9 2 2
Signaling events mediated by HDAC Class III

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
EP300 0.036 0.014 -10000 0 0 72 72
HDAC4 0.041 0.007 -10000 0 0 17 17
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.013 0.004 -10000 0 -10000 0 0
CDKN1A 0.025 0.069 0.29 22 -10000 0 22
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.04 0.008 -10000 0 0 20 20
FOXO3 0.003 0.043 0.25 16 -10000 0 16
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.005 0.033 -10000 0 -0.18 17 17
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.037 0.014 -10000 0 0 69 69
TAT 0.036 0.014 -10000 0 0 72 72
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.01 0.002 -10000 0 -10000 0 0
PPARGC1A 0.038 0.013 -10000 0 0 55 55
FHL2 0.04 0.008 -10000 0 0 21 21
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.046 0.041 -10000 0 -0.17 15 15
HIST2H4A -0.013 0.004 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.037 0.049 0.2 18 -0.21 6 24
SIRT1 0.037 0.007 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.072 0.033 -10000 0 -0.12 8 8
SIRT1/Histone H1b 0.006 0.088 -10000 0 -0.2 63 63
apoptosis -0.064 0.045 0.14 15 -10000 0 15
SIRT1/PGC1A 0.045 0.026 -10000 0 -0.11 8 8
p53/SIRT1 -0.008 0.089 -10000 0 -0.15 157 157
SIRT1/FOXO4 0.01 0.074 -10000 0 -0.16 71 71
FOXO1/FHL2/SIRT1 0.045 0.025 -10000 0 -0.1 12 12
HIST1H1E -0.003 0.068 -10000 0 -0.2 49 49
SIRT1/p300 0.044 0.043 -10000 0 -0.14 24 24
muscle cell differentiation -0.018 0.024 0.11 9 -0.21 2 11
TP53 0.024 0.018 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.065 0.046 -10000 0 -0.14 15 15
CREBBP 0.038 0.012 -10000 0 0 49 49
MEF2D 0.04 0.009 -10000 0 0 24 24
HIV-1 Tat/SIRT1 0.048 0.03 -10000 0 -0.13 8 8
ACSS2 -0.021 0.009 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.018 0.024 0.21 2 -0.11 9 11
IL27-mediated signaling events

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
TGFB1 0.037 0.013 -10000 0 0 61 61
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.003 0.1 0.41 12 -10000 0 12
IL27/IL27R/JAK1 0.079 0.11 -10000 0 -0.89 2 2
TBX21 0.006 0.1 0.35 5 -0.56 2 7
IL12B 0.042 0.008 -10000 0 0 20 20
IL12A -0.006 0.006 0.012 25 -10000 0 25
IL6ST 0.036 0.018 -10000 0 -0.031 1 1
IL27RA/JAK1 0.051 0.099 -10000 0 -1 2 2
IL27 0.043 0.009 -10000 0 -0.037 2 2
TYK2 0.039 0.016 -10000 0 -0.038 2 2
T-helper cell lineage commitment 0.007 0.062 0.2 23 -0.18 29 52
T-helper 2 cell differentiation -0.003 0.1 0.41 12 -10000 0 12
T cell proliferation during immune response -0.003 0.1 0.41 12 -10000 0 12
MAPKKK cascade 0.003 0.1 -10000 0 -0.41 12 12
STAT3 0.038 0.012 -10000 0 0 52 52
STAT2 0.039 0.011 -10000 0 0 43 43
STAT1 0.034 0.017 -10000 0 0 108 108
IL12RB1 0.039 0.012 -10000 0 0 49 49
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.003 0.099 -10000 0 -0.52 2 2
IL27/IL27R/JAK2/TYK2 0.003 0.1 -10000 0 -0.42 12 12
positive regulation of T cell mediated cytotoxicity 0.003 0.1 -10000 0 -0.41 12 12
STAT1 (dimer) 0.06 0.13 -10000 0 -0.78 2 2
JAK2 0.035 0.019 -10000 0 -0.037 1 1
JAK1 0.039 0.01 -10000 0 0 36 36
STAT2 (dimer) 0.02 0.12 -10000 0 -0.4 15 15
T cell proliferation 0.004 0.1 0.34 1 -0.39 12 13
IL12/IL12R/TYK2/JAK2 0.012 0.17 -10000 0 -0.7 26 26
IL17A 0.009 0.057 0.2 21 -0.17 25 46
mast cell activation -0.003 0.1 0.41 12 -10000 0 12
IFNG 0.013 0.03 0.1 2 -0.1 4 6
T cell differentiation -0.001 0.003 0.014 1 -0.02 3 4
STAT3 (dimer) 0.025 0.12 -10000 0 -0.39 14 14
STAT5A (dimer) 0.024 0.12 -10000 0 -0.42 12 12
STAT4 (dimer) 0.024 0.12 -10000 0 -0.4 13 13
STAT4 0.04 0.009 -10000 0 0 28 28
T cell activation -0.008 0.011 0.12 1 -0.046 31 32
IL27R/JAK2/TYK2 0.05 0.095 -10000 0 -0.93 2 2
GATA3 0.018 0.12 0.63 21 -10000 0 21
IL18 -0.006 0.006 0.01 31 -10000 0 31
positive regulation of mast cell cytokine production 0.024 0.12 -10000 0 -0.39 14 14
IL27/EBI3 0.058 0.023 -10000 0 -10000 0 0
IL27RA 0.024 0.1 -10000 0 -1.1 2 2
IL6 0.033 0.017 -10000 0 0 114 114
STAT5A 0.038 0.012 -10000 0 0 50 50
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.009 0.036 0.48 2 -10000 0 2
IL1B -0.007 0.006 0.002 148 -10000 0 148
EBI3 0.039 0.015 -10000 0 -0.037 1 1
TNF -0.008 0.005 0.006 63 -10000 0 63
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.038 0.012 -10000 0 0 54 54
Ran/GTP/Exportin 1/HDAC4 -0.029 0.033 -10000 0 -0.14 34 34
MDM2/SUMO1 0.039 0.061 -10000 0 -0.18 16 16
HDAC4 0.041 0.007 -10000 0 0 17 17
Ran/GTP/Exportin 1/HDAC1 -0.031 0.04 -10000 0 -0.14 47 47
SUMO1 0.041 0.006 -10000 0 0 13 13
NPC/RanGAP1/SUMO1 0.008 0.032 -10000 0 -0.14 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0 0.04 -10000 0 -0.17 15 15
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.041 0.006 -10000 0 0 11 11
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.04 0.009 -10000 0 0 30 30
SUMO1/HDAC4 0.04 0.061 -10000 0 -0.18 15 15
SUMO1/HDAC1 0.037 0.064 -10000 0 -0.18 22 22
RANGAP1 0.038 0.013 -10000 0 0 55 55
MDM2/SUMO1/SUMO1 0.083 0.055 -10000 0 -0.13 18 18
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.009 0.034 -10000 0 -0.14 25 25
Ran/GTP 0.023 0.057 0.17 1 -0.15 35 36
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.039 0.01 -10000 0 0 35 35
UBE2I 0.04 0.009 -10000 0 0 26 26
Ran/GTP/Exportin 1 0.019 0.067 0.2 13 -0.18 33 46
NPC 0.02 0.022 -10000 0 -0.085 23 23
PIAS2 0.038 0.012 -10000 0 0 52 52
PIAS1 0.04 0.009 -10000 0 0 28 28
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.063 0.036 -9999 0 -0.098 17 17
MAPK9 0.009 0.003 -9999 0 0 39 39
adrenocorticotropin secretion -0.01 0.003 0 45 -10000 0 45
GNB1/GNG2 0.048 0.032 -9999 0 -0.11 19 19
GNB1 0.041 0.005 -9999 0 0 7 7
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.009 0.002 -9999 0 0 28 28
Gs family/GTP 0.025 0.006 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0.002 0.001 -9999 0 -10000 0 0
GNAL 0.04 0.009 -9999 0 0 27 27
GNG2 0.039 0.01 -9999 0 0 34 34
CRH 0.038 0.011 -9999 0 0 45 45
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.009 0.002 -9999 0 0 29 29
MAPK11 0.007 0.004 -9999 0 0 132 132
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.011 0.069 0.26 7 -0.36 4 11
CRKL 0.013 0.063 0.22 2 -0.37 4 6
HRAS 0.03 0.08 0.25 2 -0.28 10 12
mol:PIP3 0.025 0.088 0.27 4 -0.32 10 14
SPRED1 0.035 0.015 -10000 0 0 89 89
SPRED2 0.04 0.009 -10000 0 0 26 26
GAB1 0.018 0.061 -10000 0 -0.33 6 6
FOXO3 0.022 0.093 0.27 2 -0.36 16 18
AKT1 0.022 0.098 0.3 1 -0.38 16 17
BAD 0.018 0.094 0.28 1 -0.36 16 17
megakaryocyte differentiation 0.023 0.06 0.22 7 -0.28 4 11
GSK3B 0.023 0.1 0.32 9 -0.36 16 25
RAF1 0.022 0.075 0.25 8 -0.24 10 18
SHC1 0.04 0.009 -10000 0 0 29 29
STAT3 0.019 0.063 0.28 2 -0.33 6 8
STAT1 0.031 0.11 -10000 0 -0.77 4 4
HRAS/SPRED1 0.035 0.084 0.26 3 -0.27 8 11
cell proliferation 0.019 0.063 0.25 2 -0.34 5 7
PIK3CA 0.03 0.019 -10000 0 0 150 150
TEC 0.033 0.017 -10000 0 0 114 114
RPS6KB1 0.022 0.099 0.26 1 -0.34 16 17
HRAS/SPRED2 0.042 0.084 0.25 4 -0.25 9 13
LYN/TEC/p62DOK 0.042 0.098 -10000 0 -0.29 8 8
MAPK3 0.018 0.065 0.22 7 -0.24 6 13
STAP1 0.023 0.062 0.26 1 -0.32 6 7
GRAP2 0.038 0.013 -10000 0 0 55 55
JAK2 0.027 0.11 -10000 0 -0.58 6 6
STAT1 (dimer) 0.031 0.12 0.38 1 -0.68 5 6
mol:Gleevec -0.002 0.003 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.063 0.093 0.3 1 -0.33 6 7
actin filament polymerization 0.024 0.063 0.26 1 -0.32 6 7
LYN 0.036 0.015 -10000 0 0 83 83
STAP1/STAT5A (dimer) 0.016 0.1 0.3 1 -0.46 7 8
PIK3R1 0.034 0.017 -10000 0 0 106 106
CBL/CRKL/GRB2 0.046 0.084 0.42 1 -0.37 4 5
PI3K 0.025 0.1 -10000 0 -0.33 16 16
PTEN 0.039 0.011 -10000 0 0 39 39
SCF/KIT/EPO/EPOR 0.059 0.13 -10000 0 -1.3 2 2
MAPK8 0.019 0.063 0.25 2 -0.34 5 7
STAT3 (dimer) 0.02 0.066 0.23 7 -0.32 6 13
positive regulation of transcription 0.018 0.058 0.2 9 -0.19 6 15
mol:GDP 0.039 0.086 0.26 2 -0.28 9 11
PIK3C2B 0.02 0.068 0.25 4 -0.33 6 10
CBL/CRKL 0.031 0.077 0.3 3 -0.37 4 7
FER 0.02 0.063 0.26 1 -0.33 6 7
SH2B3 0.023 0.062 0.26 1 -0.32 6 7
PDPK1 0.023 0.086 0.26 9 -0.29 10 19
SNAI2 0.024 0.067 0.25 3 -0.32 6 9
positive regulation of cell proliferation 0.02 0.11 0.34 1 -0.54 6 7
KITLG 0.043 0.015 -10000 0 -0.041 3 3
cell motility 0.02 0.11 0.34 1 -0.54 6 7
PTPN6 0.034 0.016 -10000 0 -0.005 74 74
EPOR 0.013 0.16 -10000 0 -0.56 28 28
STAT5A (dimer) 0.021 0.1 0.31 1 -0.44 9 10
SOCS1 0.038 0.012 -10000 0 0 52 52
cell migration -0.018 0.062 0.38 4 -0.26 1 5
SOS1 0.038 0.013 -10000 0 0 57 57
EPO 0.043 0.011 -10000 0 -0.035 3 3
VAV1 0.037 0.014 -10000 0 0 67 67
GRB10 0.018 0.065 0.26 1 -0.32 6 7
PTPN11 0.037 0.011 -10000 0 -0.004 33 33
SCF/KIT 0.026 0.066 0.28 1 -0.34 6 7
GO:0007205 -0.002 0.004 -10000 0 -10000 0 0
MAP2K1 0.016 0.068 0.22 12 -0.22 5 17
CBL 0.04 0.008 -10000 0 0 23 23
KIT 0.018 0.16 -10000 0 -0.54 19 19
MAP2K2 0.014 0.063 0.23 6 -0.22 6 12
SHC/Grb2/SOS1 0.066 0.094 0.3 1 -0.31 6 7
STAT5A 0.023 0.1 0.31 1 -0.45 9 10
GRB2 0.041 0.007 -10000 0 0 14 14
response to radiation 0.026 0.07 0.22 9 -0.32 6 15
SHC/GRAP2 0.053 0.023 -10000 0 -0.14 1 1
PTPRO 0.021 0.056 0.25 2 -0.29 4 6
SH2B2 0.023 0.062 0.26 1 -0.32 6 7
DOK1 0.04 0.009 -10000 0 0 24 24
MATK 0.018 0.062 0.26 1 -0.38 4 5
CREBBP 0.059 0.029 0.14 5 -0.15 3 8
BCL2 -0.017 0.22 -10000 0 -0.61 49 49
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.023 0.048 0.15 68 -10000 0 68
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.013 0.032 0.13 2 -0.19 1 3
AP2 0.038 0.045 -10000 0 -0.14 22 22
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.052 0.019 -10000 0 -0.11 1 1
CLTB 0.04 0.009 -10000 0 0 25 25
coatomer protein complex/ARF1/GTP/ER cargo protein 0.019 0.03 -10000 0 -0.15 14 14
CD4 0.032 0.018 -10000 0 0 128 128
CLTA 0.04 0.008 -10000 0 0 20 20
mol:GTP -0.003 0.002 0.012 6 -0.02 1 7
ARFGAP1 -0.009 0.004 0 78 -10000 0 78
mol:PI-4-5-P2 0.01 0.016 -10000 0 -10000 0 0
ARF1/GTP 0.023 0.012 0.079 1 -0.14 1 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.026 0.058 0.17 64 -0.14 8 72
mol:Choline 0.01 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.038 0.012 -10000 0 0 51 51
DDEF1 0.005 0.012 -10000 0 -10000 0 0
ARF1/GDP 0.006 0.011 -10000 0 -0.077 4 4
AP2M1 0.032 0.018 -10000 0 0 135 135
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.01 0.016 0.049 16 -0.1 2 18
Rac/GTP 0.029 0.011 -10000 0 -0.13 1 1
ARF1/GTP/GGA3/ARF-GAP1 0.044 0.026 -10000 0 -0.1 1 1
ARFIP2 0.035 0.018 -10000 0 -0.04 24 24
COPA 0.04 0.009 -10000 0 0 26 26
RAC1 0.039 0.01 -10000 0 0 35 35
ARF1/GTP/coatomer protein complex 0.013 0.039 0.14 1 -0.19 11 12
ARF1/GTP/ARHGAP10 0.024 0.01 -10000 0 -0.11 1 1
GGA3 0.04 0.007 -10000 0 0 18 18
ARF1/GTP/Membrin 0.023 0.048 -10000 0 -0.22 19 19
AP2A1 0.039 0.011 -10000 0 0 41 41
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.01 0.034 -10000 0 -0.17 13 13
ARF1/GDP/Membrin 0.025 0.055 -10000 0 -0.25 19 19
Arfaptin 2/Rac/GDP 0.05 0.019 -10000 0 -0.058 3 3
CYTH2 -0.003 0.002 0.012 6 -0.02 1 7
ARF1/GTP/GGA3 0.048 0.021 -10000 0 -0.12 2 2
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.029 0.01 -10000 0 -0.13 1 1
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 0.007 0.057 -10000 0 -0.34 7 7
PLD2 0.01 0.016 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.009 0.004 0 78 -10000 0 78
PIP5K1A 0.01 0.016 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.018 0.025 -10000 0 -0.075 18 18
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.01 0.016 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.009 0.004 0 78 -10000 0 78
GOSR2 0.011 0.052 -10000 0 -0.31 14 14
USO1 0.004 0.008 0.04 25 -0.029 1 26
GBF1 0.004 0.073 -10000 0 -0.34 23 23
ARF1/GTP/Arfaptin 2 0.05 0.02 -10000 0 -0.12 1 1
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.037 0.062 -10000 0 -0.13 40 40
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.047 0.012 -10000 0 -0.072 4 4
NFATC2 0.046 0.18 0.4 6 -0.39 39 45
NFATC3 0.069 0.067 0.29 26 -0.26 2 28
CD40LG 0.081 0.15 0.49 5 -0.48 4 9
ITCH 0.024 0.051 0.2 6 -0.21 17 23
CBLB 0.02 0.061 0.2 7 -0.26 19 26
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment 0.044 0.14 0.37 2 -0.51 8 10
JUNB 0.03 0.019 -10000 0 0 162 162
CaM/Ca2+/Calcineurin A alpha-beta B1 0.044 0.048 -10000 0 -0.18 21 21
T cell anergy 0.003 0.067 0.25 6 -0.28 17 23
TLE4 0.009 0.16 0.28 6 -0.41 50 56
Jun/NFAT1-c-4/p21SNFT 0.081 0.15 -10000 0 -0.46 3 3
AP-1/NFAT1-c-4 0.09 0.19 -10000 0 -0.54 2 2
IKZF1 0.022 0.11 0.22 19 -0.26 39 58
T-helper 2 cell differentiation 0.033 0.14 0.45 2 -0.47 3 5
AP-1/NFAT1 0.036 0.15 0.32 2 -0.25 43 45
CALM1 0.043 0.034 -10000 0 -0.12 18 18
EGR2 0.059 0.16 0.57 8 -0.83 3 11
EGR3 0.052 0.14 0.56 7 -0.51 2 9
NFAT1/FOXP3 0.058 0.14 0.33 3 -0.27 38 41
EGR1 0.028 0.021 -10000 0 -0.036 2 2
JUN 0.04 0.026 0.14 2 -0.059 3 5
EGR4 0.041 0.009 -10000 0 -0.004 19 19
mol:Ca2+ 0.005 0.021 -10000 0 -0.099 21 21
GBP3 -0.02 0.21 0.3 9 -0.45 92 101
FOSL1 0.041 0.007 -10000 0 0 15 15
NFAT1-c-4/MAF/IRF4 0.094 0.15 -10000 0 -0.46 3 3
DGKA 0.026 0.13 0.3 8 -0.3 34 42
CREM 0.039 0.009 -10000 0 -0.002 23 23
NFAT1-c-4/PPARG 0.084 0.14 -10000 0 -0.5 2 2
CTLA4 0.025 0.1 0.23 1 -0.23 36 37
NFAT1-c-4 (dimer)/EGR1 0.062 0.15 -10000 0 -0.51 3 3
NFAT1-c-4 (dimer)/EGR4 0.09 0.15 -10000 0 -0.48 3 3
FOS 0.029 0.029 0.14 2 -0.044 4 6
IFNG 0.035 0.13 -10000 0 -0.49 6 6
T cell activation 0.05 0.12 0.6 1 -10000 0 1
MAF 0.036 0.015 -10000 0 0 78 78
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.06 0.13 0.56 3 -0.51 22 25
TNF 0.046 0.13 0.46 2 -0.49 3 5
FASLG 0.049 0.17 0.69 1 -1 3 4
TBX21 0.047 0.013 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.037 0.018 -10000 0 -0.12 1 1
PTPN1 0.025 0.12 0.27 2 -0.28 33 35
NFAT1-c-4/ICER1 0.084 0.15 -10000 0 -0.48 3 3
GATA3 0.041 0.012 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.038 0.13 -10000 0 -0.48 6 6
IL2RA 0.05 0.15 0.39 1 -0.48 9 10
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.021 0.12 0.27 3 -0.31 33 36
E2F1 0.032 0.05 -10000 0 -0.18 27 27
PPARG 0.039 0.01 -10000 0 0 34 34
SLC3A2 0.023 0.13 0.28 6 -0.3 39 45
IRF4 0.041 0.008 -10000 0 0 18 18
PTGS2 0.054 0.14 0.68 1 -0.5 4 5
CSF2 0.077 0.15 0.49 5 -0.48 4 9
JunB/Fra1/NFAT1-c-4 0.077 0.15 -10000 0 -0.46 3 3
IL4 0.033 0.14 0.45 2 -0.5 2 4
IL5 0.076 0.15 0.48 4 -0.48 4 8
IL2 0.05 0.12 0.6 1 -10000 0 1
IL3 0.038 0.073 -10000 0 -0.43 6 6
RNF128 0.024 0.043 0.2 7 -0.16 19 26
NFATC1 0.061 0.13 0.51 22 -0.57 3 25
CDK4 -0.075 0.29 0.46 2 -1.2 28 30
PTPRK 0.01 0.15 0.28 3 -0.4 46 49
IL8 0.047 0.14 0.54 4 -0.47 4 8
POU2F1 0.046 0.01 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.037 0.018 -10000 0 -0.13 3 3
PDGFRB 0.037 0.014 -10000 0 0 64 64
SPHK1 0.016 0.068 -10000 0 -0.61 6 6
mol:S1P 0.013 0.063 0.21 3 -0.51 6 9
S1P1/S1P/Gi 0.021 0.087 -10000 0 -0.3 24 24
GNAO1 0.034 0.018 -10000 0 -0.036 7 7
PDGFB-D/PDGFRB/PLCgamma1 0.008 0.1 0.25 1 -0.28 30 31
PLCG1 0.006 0.089 0.21 2 -0.29 25 27
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.037 0.014 -10000 0 0 64 64
GNAI2 0.041 0.012 -10000 0 -0.015 22 22
GNAI3 0.038 0.015 -10000 0 -0.006 55 55
GNAI1 0.035 0.018 -10000 0 -0.002 101 101
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.027 0.026 0.2 8 -0.12 3 11
S1P1/S1P 0.022 0.058 0.19 4 -0.32 7 11
negative regulation of cAMP metabolic process 0.022 0.086 -10000 0 -0.3 24 24
MAPK3 0.008 0.1 -10000 0 -0.42 17 17
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.029 0.01 -10000 0 -0.13 1 1
RhoA/GDP 0.029 0.014 -10000 0 -0.13 4 4
KDR 0.043 0.011 -10000 0 -10000 0 0
PLCB2 0.017 0.057 -10000 0 -0.28 7 7
RAC1 0.039 0.01 -10000 0 0 35 35
RhoA/GTP 0.023 0.053 -10000 0 -0.26 9 9
receptor internalization 0.021 0.055 0.18 4 -0.3 7 11
PTGS2 -0.002 0.15 -10000 0 -0.86 10 10
Rac1/GTP 0.022 0.053 -10000 0 -0.26 8 8
RHOA 0.041 0.007 -10000 0 0 14 14
VEGFA 0.004 0.002 -10000 0 -10000 0 0
negative regulation of T cell proliferation 0.022 0.086 -10000 0 -0.3 24 24
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.039 0.014 -10000 0 -0.006 47 47
MAPK1 0.009 0.1 -10000 0 -0.46 15 15
S1P1/S1P/PDGFB-D/PDGFRB 0.033 0.07 0.22 2 -0.25 9 11
ABCC1 0.04 0.009 -10000 0 0 24 24
Effects of Botulinum toxin

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
STX1A -0.01 0.002 0 12 -10000 0 12
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.057 0.02 -10000 0 -0.14 2 2
STXBP1 0.039 0.011 -10000 0 0 39 39
ACh/CHRNA1 0.028 0.024 0.092 1 -0.049 31 32
RAB3GAP2/RIMS1/UNC13B 0.071 0.04 -10000 0 -0.12 14 14
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 0.041 0.007 -10000 0 0 16 16
mol:ACh 0.003 0.022 0.074 22 -0.086 4 26
RAB3GAP2 0.039 0.01 -10000 0 0 35 35
STX1A/SNAP25/VAMP2 0.057 0.055 0.18 1 -0.14 5 6
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.028 0.024 0.091 1 -0.049 31 32
UNC13B 0.04 0.009 -10000 0 0 25 25
CHRNA1 0.037 0.013 -10000 0 0 62 62
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.03 0.023 0.092 1 -0.051 27 28
SNAP25 0.006 0.002 -10000 0 0 57 57
VAMP2 0.005 0.002 -10000 0 0 62 62
SYT1 0.038 0.011 -10000 0 0 45 45
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.034 0.011 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.057 0.055 0.18 1 -0.14 5 6
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.04 0.009 -10000 0 0 26 26
CLTC 0.015 0.089 0.22 2 -0.47 11 13
calcium ion-dependent exocytosis 0.015 0.047 0.18 2 -0.17 12 14
Dynamin 2/GTP 0.021 0.041 -10000 0 -0.11 41 41
EXOC4 0.038 0.012 -10000 0 0 51 51
CD59 0.01 0.061 -10000 0 -0.35 11 11
CPE 0.011 0.013 -10000 0 -0.11 4 4
CTNNB1 0.039 0.01 -10000 0 0 32 32
membrane fusion 0.004 0.035 0.11 5 -0.14 13 18
CTNND1 -0.004 0.074 0.18 61 -0.2 3 64
DNM2 0.036 0.014 -10000 0 0 72 72
mol:PI-4-5-P2 0.017 0.056 0.18 5 -0.23 12 17
TSHR 0.014 0.015 -10000 0 -0.11 7 7
INS 0.004 0.1 -10000 0 -0.45 26 26
BIN1 0.041 0.007 -10000 0 0 17 17
mol:Choline 0.004 0.035 0.11 5 -0.14 13 18
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.014 -10000 0 -0.11 5 5
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.04 0.007 -10000 0 0 18 18
mol:Ca2+ 0.021 0.04 -10000 0 -0.11 41 41
JUP 0.009 0.064 -10000 0 -0.36 11 11
ASAP2/amphiphysin II 0.048 0.023 -10000 0 -0.098 11 11
ARF6/GTP 0.028 0.019 -10000 0 -0.13 8 8
CDH1 0.008 0.064 -10000 0 -0.38 10 10
clathrin-independent pinocytosis 0.028 0.019 -10000 0 -0.13 8 8
MAPK8IP3 0.04 0.009 -10000 0 0 26 26
positive regulation of endocytosis 0.028 0.019 -10000 0 -0.13 8 8
EXOC2 0.041 0.006 -10000 0 0 12 12
substrate adhesion-dependent cell spreading 0.008 0.1 -10000 0 -0.28 45 45
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.039 0.011 -10000 0 0 40 40
regulation of calcium-dependent cell-cell adhesion -0.035 0.086 0.36 12 -10000 0 12
positive regulation of phagocytosis 0.015 0.015 -10000 0 -0.11 7 7
ARF6/GTP/JIP3 0.05 0.024 -10000 0 -0.11 8 8
ACAP1 0.004 0.035 0.11 5 -0.17 10 15
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.014 0.061 -10000 0 -0.34 11 11
clathrin heavy chain/ACAP1 0.015 0.078 0.21 6 -0.37 11 17
JIP4/KLC1 0.044 0.031 -10000 0 -0.098 20 20
EXOC1 0.038 0.012 -10000 0 0 52 52
exocyst 0.008 0.1 -10000 0 -0.28 45 45
RALA/GTP 0.027 0.021 -10000 0 -0.13 9 9
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.046 0.034 -10000 0 -0.11 20 20
receptor recycling 0.028 0.019 -10000 0 -0.13 8 8
CTNNA1 -0.005 0.072 0.18 57 -0.2 3 60
NME1 0.014 0.014 -10000 0 -0.11 5 5
clathrin coat assembly 0.014 0.089 0.22 2 -0.46 11 13
IL2RA 0.014 0.06 0.22 1 -0.33 10 11
VAMP3 0.015 0.015 -10000 0 -0.11 7 7
GLUT4/clathrin heavy chain/ACAP1 0.039 0.081 -10000 0 -0.35 11 11
EXOC6 0.038 0.013 -10000 0 0 56 56
PLD1 0.001 0.049 0.11 6 -0.2 28 34
PLD2 0.015 0.03 -10000 0 -0.19 5 5
EXOC5 0.04 0.009 -10000 0 0 26 26
PIP5K1C 0.012 0.049 0.16 3 -0.23 10 13
SDC1 0.011 0.061 -10000 0 -0.35 10 10
ARF6/GDP 0.026 0.039 -10000 0 -0.12 34 34
EXOC7 0.041 0.005 -10000 0 0 9 9
E-cadherin/beta catenin 0.038 0.09 -10000 0 -0.37 12 12
mol:Phosphatidic acid 0.004 0.035 0.11 5 -0.14 13 18
endocytosis -0.046 0.023 0.098 11 -10000 0 11
SCAMP2 0.04 0.009 -10000 0 0 25 25
ADRB2 0.008 0.088 0.21 4 -0.43 12 16
EXOC3 0.041 0.005 -10000 0 0 7 7
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.027 0.044 0.19 4 -0.11 41 45
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 0.008 0.085 0.21 1 -0.43 12 13
RALA 0.04 0.009 -10000 0 0 29 29
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.02 0.092 -10000 0 -0.4 11 11
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.016 0.12 -10000 0 -0.85 9 9
MKNK1 0.04 0.009 -10000 0 0 25 25
MAPK14 0.041 0.054 0.17 1 -0.26 10 11
ATF2/c-Jun -0.018 0.1 -10000 0 -0.31 43 43
MAPK11 0.032 0.054 -10000 0 -0.28 9 9
MITF 0.02 0.061 -10000 0 -0.3 14 14
MAPKAPK5 0.019 0.058 -10000 0 -0.27 16 16
KRT8 0.016 0.062 -10000 0 -0.23 25 25
MAPKAPK3 0.041 0.006 -10000 0 0 12 12
MAPKAPK2 0.04 0.008 -10000 0 0 21 21
p38alpha-beta/CK2 0.042 0.078 -10000 0 -0.31 14 14
CEBPB 0.022 0.053 -10000 0 -0.3 9 9
SLC9A1 0.021 0.056 -10000 0 -0.28 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 0.015 0.073 0.23 1 -0.24 26 27
p38alpha-beta/MNK1 0.054 0.077 -10000 0 -0.32 10 10
JUN -0.021 0.1 -10000 0 -0.31 44 44
PPARGC1A 0.022 0.054 -10000 0 -0.28 12 12
USF1 0.019 0.058 -10000 0 -0.26 16 16
RAB5/GDP/GDI1 0.007 0.077 -10000 0 -0.21 22 22
NOS2 0.015 0.055 -10000 0 -0.28 14 14
DDIT3 0.017 0.061 -10000 0 -0.23 23 23
RAB5A 0.041 0.006 -10000 0 0 13 13
HSPB1 0.003 0.052 0.28 3 -0.24 14 17
p38alpha-beta/HBP1 0.046 0.084 -10000 0 -0.22 23 23
CREB1 -0.003 0.097 -10000 0 -0.3 18 18
RAB5/GDP 0.029 0.012 -10000 0 -0.13 3 3
EIF4E -0.007 0.066 0.2 22 -0.3 9 31
RPS6KA4 0.021 0.056 -10000 0 -0.28 13 13
PLA2G4A -0.009 0.062 0.23 10 -0.3 12 22
GDI1 0.018 0.061 -10000 0 -0.26 20 20
TP53 0.002 0.063 -10000 0 -0.36 12 12
RPS6KA5 0.019 0.059 -10000 0 -0.27 16 16
ESR1 0.008 0.075 -10000 0 -0.22 42 42
HBP1 0.038 0.012 -10000 0 0 50 50
MEF2C 0.015 0.068 -10000 0 -0.29 19 19
MEF2A 0.019 0.057 -10000 0 -0.26 16 16
EIF4EBP1 0.002 0.09 -10000 0 -0.29 17 17
KRT19 0.008 0.08 -10000 0 -0.23 42 42
ELK4 0.02 0.056 -10000 0 -0.28 14 14
ATF6 0.019 0.057 -10000 0 -0.26 16 16
ATF1 -0.002 0.096 -10000 0 -0.3 18 18
p38alpha-beta/MAPKAPK2 0.054 0.077 -10000 0 -0.29 11 11
p38alpha-beta/MAPKAPK3 0.056 0.076 -10000 0 -0.33 9 9
Aurora C 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
INCENP 0.041 0.004 -9999 0 0 6 6
Aurora C/Aurora B/INCENP 0.064 0.045 -9999 0 -0.1 27 27
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.005 0.065 -9999 0 -0.39 14 14
AURKB 0.036 0.014 -9999 0 0 75 75
AURKC 0.042 0.002 -9999 0 0 1 1
Glypican 2 network

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
MDK 0.04 0.009 -9999 0 0 25 25
GPC2 0.04 0.008 -9999 0 0 20 20
GPC2/Midkine 0.054 0.032 -9999 0 -0.14 13 13
neuron projection morphogenesis 0.054 0.032 -9999 0 -0.14 13 13
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.062 0.028 -10000 0 -0.098 1 1
RGS9BP 0.037 0.013 -10000 0 0 60 60
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.05 0.017 -10000 0 -10000 0 0
mol:ADP -0.01 0.003 -10000 0 -10000 0 0
GNAT2 0.041 0.005 -10000 0 0 9 9
RGS9-1/Gbeta5/R9AP 0.067 0.035 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.05 0.018 -10000 0 -10000 0 0
GRK7 0.038 0.012 -10000 0 0 49 49
CNGB3 0.038 0.012 -10000 0 0 54 54
Cone Metarhodopsin II/X-Arrestin 0.031 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.057 0.19 43 -10000 0 43
Cone PDE6 0.087 0.057 -10000 0 -0.11 1 1
Cone Metarhodopsin II 0.024 0.008 -10000 0 -10000 0 0
Na + (4 Units) 0.065 0.03 -10000 0 -10000 0 0
GNAT2/GDP 0.079 0.039 -10000 0 -0.1 1 1
GNB5 0.04 0.009 -10000 0 0 28 28
mol:GMP (4 units) -0.002 0.06 0.19 48 -10000 0 48
Cone Transducin 0.067 0.03 -10000 0 -0.1 1 1
SLC24A2 0.038 0.011 -10000 0 0 44 44
GNB3/GNGT2 0.053 0.023 -10000 0 -0.14 1 1
GNB3 0.037 0.013 -10000 0 0 63 63
GNAT2/GTP 0.03 0.004 -10000 0 -10000 0 0
CNGA3 0.041 0.005 -10000 0 0 7 7
ARR3 0.042 0.002 -10000 0 0 1 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.05 0.018 -10000 0 -10000 0 0
mol:Pi 0.066 0.035 -10000 0 -0.12 1 1
Cone CNG Channel 0.078 0.046 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.038 0.011 -10000 0 0 44 44
RGS9 0.039 0.011 -10000 0 0 40 40
PDE6C 0.04 0.009 -10000 0 0 24 24
GNGT2 0.04 0.008 -10000 0 0 23 23
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.037 0.013 -10000 0 0 58 58
Visual signal transduction: Rods

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
mol:K + 0.04 0.008 -10000 0 0 19 19
GNAT1/GTP 0.03 0.005 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.053 0.013 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.049 0.021 -10000 0 -0.11 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.041 0.007 -10000 0 0 15 15
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel 0.068 0.037 -10000 0 -0.11 2 2
mol:Na + 0.069 0.042 -10000 0 -0.11 1 1
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.067 0.035 -10000 0 -0.12 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.086 0.05 -10000 0 -0.11 1 1
CNGB1 0.038 0.012 -10000 0 0 48 48
RDH5 0.037 0.014 -10000 0 0 68 68
SAG 0.041 0.006 -10000 0 0 11 11
mol:Ca2+ -0.018 0.081 0.34 19 -10000 0 19
Na + (4 Units) 0.056 0.038 -10000 0 -0.11 1 1
RGS9 0.039 0.011 -10000 0 0 40 40
GNB1/GNGT1 0.057 0.023 -10000 0 -0.14 5 5
GNAT1/GDP 0.079 0.039 -10000 0 -0.1 1 1
GUCY2D 0.039 0.01 -10000 0 0 32 32
GNGT1 0.04 0.009 -10000 0 0 28 28
GUCY2F 0.042 0.002 -10000 0 0 1 1
GNB5 0.04 0.009 -10000 0 0 28 28
mol:GMP (4 units) 0.04 0.025 0.17 14 -0.1 2 16
mol:11-cis-retinal 0.037 0.014 -10000 0 0 68 68
mol:cGMP 0.077 0.033 0.2 2 -0.11 1 3
GNB1 0.041 0.005 -10000 0 0 7 7
Rhodopsin 0.05 0.03 -10000 0 -0.14 7 7
SLC24A1 0.04 0.008 -10000 0 0 19 19
CNGA1 0.04 0.008 -10000 0 0 21 21
Metarhodopsin II 0.026 0.005 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.093 0.037 -10000 0 -0.11 1 1
RGS9BP 0.037 0.013 -10000 0 0 60 60
Metarhodopsin II/Transducin 0.024 0.019 -10000 0 -0.14 6 6
GCAP Family/Ca ++ 0.073 0.024 -10000 0 -0.1 1 1
PDE6A/B 0.059 0.013 -10000 0 -10000 0 0
mol:Pi 0.066 0.035 -10000 0 -0.12 1 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.073 0.027 -10000 0 -0.1 5 5
PDE6B 0.041 0.004 -10000 0 0 6 6
PDE6A 0.04 0.007 -10000 0 0 18 18
PDE6G 0.038 0.013 -10000 0 0 57 57
RHO 0.04 0.008 -10000 0 0 23 23
PDE6 0.095 0.055 -10000 0 -0.15 2 2
GUCA1A 0.04 0.009 -10000 0 0 24 24
GC2/GCAP Family 0.098 0.031 -10000 0 -0.11 1 1
GUCA1C 0.04 0.009 -10000 0 0 28 28
GUCA1B 0.04 0.008 -10000 0 0 23 23
Methods & Data
Input

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

  • Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/1269872/2.GDAC_MergeDataFiles.Finished/OV.exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.data.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/OV/1282598/1.GetReducedSegments.Finished/OV.RS.tsv

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

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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)
Meta

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