Ovarian Serous Cystadenocarcinoma: Paradigm Report
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 66 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
Syndecan-1-mediated signaling events 139
TCGA08_retinoblastoma 137
FOXM1 transcription factor network 129
HIF-1-alpha transcription factor network 128
TCGA08_p53 105
Glypican 2 network 100
IGF1 pathway 96
Syndecan-4-mediated signaling events 94
amb2 Integrin signaling 86
LPA receptor mediated events 82
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
Syndecan-1-mediated signaling events 139 4755 34 -0.2 0.023 1000 -1000 -0.008 -1000
TCGA08_retinoblastoma 137 1098 8 -0.07 0.051 1000 -1000 -0.001 -1000
FOXM1 transcription factor network 129 6596 51 -0.62 0.02 1000 -1000 -0.11 -1000
HIF-1-alpha transcription factor network 128 9763 76 -0.32 0.029 1000 -1000 -0.036 -1000
TCGA08_p53 105 741 7 -0.11 0.053 1000 -1000 0 -1000
Glypican 2 network 100 402 4 -0.065 0 1000 -1000 0 -1000
IGF1 pathway 96 5490 57 -0.1 0.061 1000 -1000 -0.035 -1000
Syndecan-4-mediated signaling events 94 6321 67 -0.2 0.039 1000 -1000 -0.02 -1000
amb2 Integrin signaling 86 7111 82 -0.14 0.027 1000 -1000 -0.03 -1000
LPA receptor mediated events 82 8438 102 -0.14 0.02 1000 -1000 -0.051 -1000
Wnt signaling 80 560 7 -0.083 0.02 1000 -1000 -0.001 -1000
PLK2 and PLK4 events 79 238 3 -0.067 0.018 1000 -1000 0.002 -1000
Osteopontin-mediated events 77 2947 38 -0.21 0.02 1000 -1000 -0.013 -1000
TRAIL signaling pathway 71 3436 48 -0.093 0.034 1000 -1000 -0.006 -1000
Fc-epsilon receptor I signaling in mast cells 70 6873 97 -0.11 0.023 1000 -1000 -0.036 -1000
Syndecan-2-mediated signaling events 69 4817 69 -0.15 0.024 1000 -1000 -0.008 -1000
Noncanonical Wnt signaling pathway 67 1746 26 -0.083 0.021 1000 -1000 -0.026 -1000
Endothelins 67 6459 96 -0.25 0.02 1000 -1000 -0.007 -1000
Nongenotropic Androgen signaling 65 3411 52 -0.19 0.098 1000 -1000 -0.023 -1000
Thromboxane A2 receptor signaling 59 6253 105 -0.16 0.042 1000 -1000 -0.037 -1000
Signaling events mediated by PRL 59 2031 34 -0.084 0.035 1000 -1000 -0.004 -1000
Ephrin B reverse signaling 58 2831 48 -0.16 0.053 1000 -1000 -0.018 -1000
IL23-mediated signaling events 58 3484 60 -0.39 0.033 1000 -1000 -0.006 -1000
FOXA2 and FOXA3 transcription factor networks 57 2631 46 -0.42 0.041 1000 -1000 -0.012 -1000
Nectin adhesion pathway 57 3629 63 -0.081 0.036 1000 -1000 -0.033 -1000
EPHB forward signaling 57 4897 85 -0.089 0.053 1000 -1000 -0.033 -1000
PDGFR-alpha signaling pathway 55 2424 44 -0.21 0.02 1000 -1000 0 -1000
Ras signaling in the CD4+ TCR pathway 54 934 17 -0.06 0.014 1000 -1000 -0.003 -1000
BCR signaling pathway 53 5280 99 -0.11 0.027 1000 -1000 -0.038 -1000
Integrins in angiogenesis 50 4237 84 -0.1 0.024 1000 -1000 -0.038 -1000
IL2 signaling events mediated by PI3K 49 2890 58 -0.16 0.02 1000 -1000 -0.015 -1000
Class I PI3K signaling events 45 3323 73 -0.049 0.04 1000 -1000 -0.013 -1000
Reelin signaling pathway 43 2459 56 -0.054 0.057 1000 -1000 -0.004 -1000
Arf6 downstream pathway 42 1811 43 -0.081 0.029 1000 -1000 -0.008 -1000
ErbB2/ErbB3 signaling events 40 2662 65 -0.11 0.021 1000 -1000 -0.027 -1000
BARD1 signaling events 40 2310 57 -0.096 0.031 1000 -1000 -0.017 -1000
IL6-mediated signaling events 40 3029 75 -0.17 0.041 1000 -1000 -0.009 -1000
PLK1 signaling events 39 3392 85 -0.082 0.023 1000 -1000 -0.024 -1000
Canonical Wnt signaling pathway 39 1994 51 -0.4 0.21 1000 -1000 -0.023 -1000
Aurora B signaling 39 2616 67 -0.072 0.023 1000 -1000 -0.011 -1000
IL1-mediated signaling events 38 2398 62 -0.057 0.028 1000 -1000 -0.032 -1000
Stabilization and expansion of the E-cadherin adherens junction 37 2749 74 -0.07 0.026 1000 -1000 -0.036 -1000
E-cadherin signaling in the nascent adherens junction 37 2847 76 -0.08 0.029 1000 -1000 -0.038 -1000
Coregulation of Androgen receptor activity 36 2774 76 -0.14 0.028 1000 -1000 -0.019 -1000
Signaling events mediated by PTP1B 36 2762 76 -0.11 0.046 1000 -1000 -0.025 -1000
mTOR signaling pathway 36 1919 53 -0.079 0.026 1000 -1000 -0.029 -1000
Syndecan-3-mediated signaling events 36 1293 35 -0.14 0.032 1000 -1000 -0.021 -1000
Regulation of nuclear SMAD2/3 signaling 35 4778 136 -0.16 0.04 1000 -1000 -0.023 -1000
Aurora A signaling 35 2125 60 -0.06 0.033 1000 -1000 -0.006 -1000
IL4-mediated signaling events 35 3212 91 -0.23 0.049 1000 -1000 -0.098 -1000
HIF-2-alpha transcription factor network 35 1537 43 -0.088 0.036 1000 -1000 -0.08 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 34 1867 54 -0.047 0.02 1000 -1000 -0.037 -1000
Regulation of Telomerase 34 3494 102 -0.28 0.031 1000 -1000 -0.043 -1000
FoxO family signaling 33 2129 64 -0.12 0.025 1000 -1000 -0.016 -1000
p75(NTR)-mediated signaling 32 4009 125 -0.15 0.045 1000 -1000 -0.037 -1000
IFN-gamma pathway 32 2218 68 -0.091 0.038 1000 -1000 -0.037 -1000
Paxillin-independent events mediated by a4b1 and a4b7 32 1201 37 -0.14 0.051 1000 -1000 -0.007 -1000
E-cadherin signaling in keratinocytes 32 1395 43 -0.035 0.02 1000 -1000 -0.009 -1000
Signaling events mediated by HDAC Class III 31 1275 40 -0.094 0.029 1000 -1000 -0.012 -1000
IL2 signaling events mediated by STAT5 31 697 22 -0.052 0.02 1000 -1000 -0.005 -1000
Signaling mediated by p38-gamma and p38-delta 30 454 15 -0.095 0.027 1000 -1000 -0.002 -1000
FAS signaling pathway (CD95) 29 1404 47 -0.084 0.037 1000 -1000 -0.013 -1000
Presenilin action in Notch and Wnt signaling 28 1727 61 -0.36 0.076 1000 -1000 -0.031 -1000
Caspase cascade in apoptosis 27 2020 74 -0.068 0.038 1000 -1000 -0.02 -1000
Glucocorticoid receptor regulatory network 27 3145 114 -0.2 0.046 1000 -1000 -0.031 -1000
S1P5 pathway 27 474 17 -0.021 0.018 1000 -1000 -0.005 -1000
TCGA08_rtk_signaling 26 689 26 -0.035 0.048 1000 -1000 -0.004 -1000
Insulin Pathway 25 1873 74 -0.046 0.048 1000 -1000 -0.031 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 24 570 23 -0.034 0.027 1000 -1000 -0.004 -1000
Signaling events mediated by HDAC Class II 24 1856 75 -0.073 0.043 1000 -1000 -0.019 -1000
Circadian rhythm pathway 24 534 22 -0.065 0.031 1000 -1000 -0.007 -1000
BMP receptor signaling 24 2019 81 -0.053 0.029 1000 -1000 -0.042 -1000
Class I PI3K signaling events mediated by Akt 24 1684 68 -0.066 0.04 1000 -1000 -0.01 -1000
E-cadherin signaling events 24 122 5 0.002 0.018 1000 -1000 0.001 -1000
ErbB4 signaling events 23 1600 69 -0.07 0.027 1000 -1000 -0.041 -1000
Ceramide signaling pathway 23 1786 76 -0.07 0.021 1000 -1000 -0.01 -1000
Retinoic acid receptors-mediated signaling 23 1363 58 -0.097 0.041 1000 -1000 -0.035 -1000
Paxillin-dependent events mediated by a4b1 22 824 36 -0.14 0.054 1000 -1000 -0.012 -1000
Atypical NF-kappaB pathway 22 704 31 -0.029 0.02 1000 -1000 -0.001 -1000
TCR signaling in naïve CD8+ T cells 22 2075 93 -0.059 0.031 1000 -1000 -0.032 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 22 1027 45 -0.063 0.039 1000 -1000 -0.034 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 22 732 33 -0.096 0.034 1000 -1000 -0.006 -1000
Neurotrophic factor-mediated Trk receptor signaling 22 2664 120 -0.18 0.053 1000 -1000 -0.034 -1000
IL12-mediated signaling events 21 1902 87 -0.29 0.048 1000 -1000 -0.074 -1000
Insulin-mediated glucose transport 21 687 32 -0.066 0.021 1000 -1000 -0.005 -1000
Plasma membrane estrogen receptor signaling 21 1837 86 -0.07 0.045 1000 -1000 -0.037 -1000
Glypican 1 network 20 973 48 -0.058 0.035 1000 -1000 -0.006 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 19 1683 85 -0.18 0.042 1000 -1000 -0.034 -1000
Sumoylation by RanBP2 regulates transcriptional repression 19 534 27 -0.02 0.041 1000 -1000 -0.022 -1000
Canonical NF-kappaB pathway 18 705 39 -0.027 0.047 1000 -1000 -0.005 -1000
EPO signaling pathway 18 1024 55 -0.029 0.059 1000 -1000 -0.036 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 18 1279 68 -0.1 0.087 1000 -1000 -0.044 -1000
EGFR-dependent Endothelin signaling events 18 379 21 -0.009 0.041 1000 -1000 0 -1000
PDGFR-beta signaling pathway 18 1806 97 -0.12 0.032 1000 -1000 -0.039 -1000
Cellular roles of Anthrax toxin 17 663 39 -0.11 0.019 1000 -1000 -0.009 -1000
Signaling events regulated by Ret tyrosine kinase 17 1426 82 -0.084 0.047 1000 -1000 -0.036 -1000
JNK signaling in the CD4+ TCR pathway 16 288 17 -0.014 0.02 1000 -1000 -0.006 -1000
Regulation of Androgen receptor activity 16 1134 70 -0.097 0.049 1000 -1000 -0.014 -1000
Signaling events mediated by HDAC Class I 15 1660 104 -0.026 0.035 1000 -1000 -0.018 -1000
Regulation of p38-alpha and p38-beta 15 859 54 -0.049 0.035 1000 -1000 -0.02 -1000
S1P4 pathway 15 386 25 -0.021 0.029 1000 -1000 0 -1000
ceramide signaling pathway 14 732 49 -0.051 0.027 1000 -1000 -0.004 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 14 1166 83 -0.066 0.06 1000 -1000 -0.005 -1000
Calcium signaling in the CD4+ TCR pathway 14 438 31 -0.11 0.085 1000 -1000 -0.041 -1000
S1P3 pathway 14 623 42 -0.02 0.029 1000 -1000 -0.009 -1000
S1P1 pathway 13 486 36 -0.021 0.036 1000 -1000 -0.029 -1000
Signaling events mediated by VEGFR1 and VEGFR2 12 1586 125 -0.056 0.06 1000 -1000 -0.038 -1000
Arf6 trafficking events 12 864 71 -0.026 0.029 1000 -1000 -0.009 -1000
Hedgehog signaling events mediated by Gli proteins 11 715 65 -0.021 0.067 1000 -1000 -0.013 -1000
Sphingosine 1-phosphate (S1P) pathway 10 281 28 -0.021 0.034 1000 -1000 -0.002 -1000
Signaling events mediated by the Hedgehog family 10 530 52 -0.03 0.071 1000 -1000 -0.006 -1000
Aurora C signaling 10 70 7 0 0.026 1000 -1000 -0.005 -1000
Signaling mediated by p38-alpha and p38-beta 10 483 44 -0.026 0.038 1000 -1000 0 -1000
Effects of Botulinum toxin 10 272 26 -0.02 0.029 1000 -1000 -0.001 -1000
p38 MAPK signaling pathway 10 466 44 -0.019 0.034 1000 -1000 -0.03 -1000
IL27-mediated signaling events 9 468 51 -0.023 0.031 1000 -1000 -0.02 -1000
VEGFR1 specific signals 9 505 56 -0.056 0.051 1000 -1000 -0.005 -1000
Arf1 pathway 9 513 54 0 0.029 1000 -1000 -0.003 -1000
Alternative NF-kappaB pathway 9 120 13 -0.003 0.052 1000 -1000 0 -1000
Nephrin/Neph1 signaling in the kidney podocyte 8 284 34 -0.018 0.04 1000 -1000 -0.006 -1000
Ephrin A reverse signaling 8 59 7 -0.008 0.027 1000 -1000 0 -1000
Angiopoietin receptor Tie2-mediated signaling 8 732 88 -0.057 0.06 1000 -1000 -0.046 -1000
Arf6 signaling events 7 468 62 -0.05 0.057 1000 -1000 0 -1000
RXR and RAR heterodimerization with other nuclear receptor 4 257 52 0 0.058 1000 -1000 -0.013 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 4 378 78 -0.032 0.065 1000 -1000 -0.033 -1000
Rapid glucocorticoid signaling 3 74 20 0 0.02 1000 -1000 -0.001 -1000
Visual signal transduction: Rods 3 187 52 -0.001 0.043 1000 -1000 -0.03 -1000
LPA4-mediated signaling events 2 26 12 0 0.018 1000 -1000 -0.003 -1000
Visual signal transduction: Cones 0 16 38 0 0.049 1000 -1000 0 -1000
a4b1 and a4b7 Integrin signaling 0 0 5 0.02 0.029 1000 -1000 0.004 -1000
Class IB PI3K non-lipid kinase events 0 0 3 -0.02 0.02 1000 -1000 -0.004 -1000
Total 4594 256368 7203 -13 5 131000 -131000 -2.6 -131000
Syndecan-1-mediated signaling 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
TGFB1 0.017 0.024 -9999 0 -0.2 6 6
CCL5 -0.078 0.15 -9999 0 -0.28 175 175
SDCBP 0.009 0.061 -9999 0 -0.34 16 16
FGFR/FGF2/Syndecan-1 -0.17 0.16 -9999 0 -0.33 217 217
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.17 0.16 -9999 0 -0.32 233 233
Syndecan-1/Syntenin -0.16 0.16 -9999 0 -0.32 220 220
MAPK3 -0.16 0.16 -9999 0 -0.34 180 180
HGF/MET 0.023 0.031 -9999 0 -0.25 1 1
TGFB1/TGF beta receptor Type II 0.017 0.023 -9999 0 -0.2 6 6
BSG -0.012 0.097 -9999 0 -0.29 55 55
keratinocyte migration -0.17 0.16 -9999 0 -0.31 233 233
Syndecan-1/RANTES -0.2 0.18 -9999 0 -0.34 267 267
Syndecan-1/CD147 -0.17 0.16 -9999 0 -0.34 202 202
Syndecan-1/Syntenin/PIP2 -0.16 0.16 -9999 0 -0.31 220 220
LAMA5 -0.006 0.091 -9999 0 -0.3 43 43
positive regulation of cell-cell adhesion -0.15 0.16 -9999 0 -0.3 220 220
MMP7 -0.15 0.17 -9999 0 -0.29 297 297
HGF 0.019 0.014 -9999 0 -0.2 2 2
Syndecan-1/CASK -0.16 0.16 -9999 0 -0.32 217 217
Syndecan-1/HGF/MET -0.15 0.16 -9999 0 -0.35 151 151
regulation of cell adhesion -0.15 0.16 -9999 0 -0.33 186 186
HPSE -0.034 0.12 -9999 0 -0.26 103 103
positive regulation of cell migration -0.17 0.16 -9999 0 -0.33 217 217
SDC1 -0.17 0.17 -9999 0 -0.34 217 217
Syndecan-1/Collagen -0.17 0.16 -9999 0 -0.33 217 217
PPIB -0.002 0.089 -9999 0 -0.36 31 31
MET 0.012 0.041 -9999 0 -0.2 19 19
PRKACA 0.02 0 -9999 0 -10000 0 0
MMP9 -0.12 0.16 -9999 0 -0.28 245 245
MAPK1 -0.16 0.16 -9999 0 -0.34 190 190
homophilic cell adhesion -0.17 0.16 -9999 0 -0.33 217 217
MMP1 -0.043 0.1 -9999 0 -0.2 152 152
TCGA08_retinoblastoma

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
CDKN2B 0.018 0.009 -10000 0 -10000 0 0
CDKN2C -0.042 0.12 -10000 0 -0.24 134 134
CDKN2A -0.07 0.16 -10000 0 -0.33 143 143
CCND2 0.041 0.075 0.14 161 -10000 0 161
RB1 -0.045 0.087 -10000 0 -0.16 161 161
CDK4 0.047 0.096 0.18 161 -0.14 15 176
CDK6 0.051 0.088 0.17 162 -10000 0 162
G1/S progression 0.045 0.087 0.16 161 -10000 0 161
FOXM1 transcription factor network

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
NFATC3 -0.38 0.57 -9999 0 -1.2 149 149
PLK1 -0.008 0.14 -9999 0 -1.4 4 4
BIRC5 -0.13 0.42 -9999 0 -1.4 52 52
HSPA1B -0.38 0.57 -9999 0 -1.1 173 173
MAP2K1 0.004 0.045 -9999 0 -0.31 3 3
BRCA2 -0.38 0.57 -9999 0 -1.2 150 150
FOXM1 -0.62 1 -9999 0 -1.8 173 173
XRCC1 -0.38 0.57 -9999 0 -1.1 160 160
FOXM1B/p19 -0.52 0.6 -9999 0 -1.2 191 191
Cyclin D1/CDK4 -0.44 0.56 -9999 0 -1.1 202 202
CDC2 -0.43 0.65 -9999 0 -1.3 163 163
TGFA -0.36 0.5 -9999 0 -1 167 167
SKP2 -0.38 0.57 -9999 0 -1.1 159 159
CCNE1 -0.07 0.15 -9999 0 -0.31 145 145
CKS1B -0.4 0.6 -9999 0 -1.2 172 172
RB1 -0.31 0.38 -9999 0 -0.79 155 155
FOXM1C/SP1 -0.49 0.71 -9999 0 -1.4 181 181
AURKB -0.034 0.24 -9999 0 -1.4 15 15
CENPF -0.42 0.61 -9999 0 -1.2 177 177
CDK4 -0.009 0.083 -9999 0 -0.33 31 31
MYC -0.38 0.52 -9999 0 -0.99 195 195
CHEK2 -0.016 0.09 -9999 0 -0.29 41 41
ONECUT1 -0.41 0.56 -9999 0 -1.1 174 174
CDKN2A -0.083 0.17 -9999 0 -0.36 143 143
LAMA4 -0.38 0.57 -9999 0 -1.1 159 159
FOXM1B/HNF6 -0.52 0.73 -9999 0 -1.4 174 174
FOS -0.51 0.64 -9999 0 -1.2 221 221
SP1 0.017 0.01 -9999 0 -10000 0 0
CDC25B -0.42 0.61 -9999 0 -1.2 169 169
response to radiation -0.011 0.031 -9999 0 -10000 0 0
CENPB -0.38 0.57 -9999 0 -1.1 159 159
CENPA -0.39 0.59 -9999 0 -1.2 161 161
NEK2 -0.38 0.58 -9999 0 -1.2 161 161
HIST1H2BA -0.38 0.57 -9999 0 -1.1 173 173
CCNA2 -0.056 0.14 -9999 0 -0.3 123 123
EP300 0.015 0.044 -9999 0 -0.36 7 7
CCNB1/CDK1 -0.51 0.76 -9999 0 -1.5 161 161
CCNB2 -0.4 0.6 -9999 0 -1.2 163 163
CCNB1 -0.43 0.64 -9999 0 -1.3 163 163
ETV5 -0.4 0.58 -9999 0 -1.2 163 163
ESR1 -0.38 0.57 -9999 0 -1.1 159 159
CCND1 -0.45 0.57 -9999 0 -1.1 201 201
GSK3A 0.007 0.032 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.068 0.14 -9999 0 -0.26 148 148
CDK2 0.012 0.033 -9999 0 -0.21 11 11
G2/M transition of mitotic cell cycle -0.013 0.037 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.43 0.64 -9999 0 -1.2 174 174
GAS1 -0.42 0.62 -9999 0 -1.2 170 170
MMP2 -0.5 0.64 -9999 0 -1.2 206 206
RB1/FOXM1C -0.47 0.58 -9999 0 -1.1 195 195
CREBBP 0.02 0 -9999 0 -10000 0 0
HIF-1-alpha transcription factor network

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.28 0.49 -9999 0 -0.84 180 180
HDAC7 -0.002 0.009 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.18 0.39 -9999 0 -0.72 133 133
SMAD4 -0.026 0.12 -9999 0 -0.33 72 72
ID2 -0.29 0.5 -9999 0 -0.88 175 175
AP1 -0.083 0.14 -9999 0 -0.22 250 250
ABCG2 -0.27 0.48 -9999 0 -0.83 180 180
HIF1A -0.028 0.082 -9999 0 -0.19 24 24
TFF3 -0.28 0.48 -9999 0 -0.85 180 180
GATA2 0.015 0.032 -9999 0 -0.2 11 11
AKT1 -0.039 0.11 -9999 0 -0.32 35 35
response to hypoxia -0.041 0.076 -9999 0 -0.13 134 134
MCL1 -0.27 0.48 -9999 0 -0.82 181 181
NDRG1 -0.29 0.5 -9999 0 -0.86 185 185
SERPINE1 -0.28 0.48 -9999 0 -0.83 181 181
FECH -0.27 0.48 -9999 0 -0.83 180 180
FURIN -0.27 0.48 -9999 0 -0.83 179 179
NCOA2 0.021 0.014 -9999 0 -0.2 2 2
EP300 -0.027 0.11 -9999 0 -0.28 36 36
HMOX1 -0.29 0.5 -9999 0 -0.86 185 185
BHLHE40 -0.28 0.48 -9999 0 -0.83 180 180
BHLHE41 -0.28 0.48 -9999 0 -0.83 180 180
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.002 0.13 -9999 0 -0.24 55 55
ENG -0.012 0.11 -9999 0 -0.24 41 41
JUN -0.011 0.099 -9999 0 -0.31 51 51
RORA -0.28 0.48 -9999 0 -0.83 183 183
ABCB1 -0.055 0.083 -9999 0 -0.36 3 3
TFRC -0.29 0.5 -9999 0 -0.85 184 184
CXCR4 -0.3 0.5 -9999 0 -0.86 194 194
TF -0.27 0.48 -9999 0 -0.84 174 174
CITED2 -0.29 0.49 -9999 0 -0.85 185 185
HIF1A/ARNT -0.29 0.61 -9999 0 -1.1 149 149
LDHA -0.067 0.24 -9999 0 -1.1 23 23
ETS1 -0.27 0.48 -9999 0 -0.83 179 179
PGK1 -0.29 0.5 -9999 0 -0.86 183 183
NOS2 -0.28 0.48 -9999 0 -0.83 180 180
ITGB2 -0.31 0.51 -9999 0 -0.86 195 195
ALDOA -0.27 0.48 -9999 0 -0.84 178 178
Cbp/p300/CITED2 -0.28 0.5 -9999 0 -0.91 162 162
FOS -0.11 0.16 -9999 0 -0.29 233 233
HK2 -0.27 0.48 -9999 0 -0.83 179 179
SP1 0.029 0.005 -9999 0 -10000 0 0
GCK -0.032 0.15 -9999 0 -0.49 5 5
HK1 -0.27 0.48 -9999 0 -0.83 180 180
NPM1 -0.27 0.48 -9999 0 -0.84 179 179
EGLN1 -0.28 0.48 -9999 0 -0.83 183 183
CREB1 0.021 0.051 -9999 0 -0.36 9 9
PGM1 -0.28 0.5 -9999 0 -0.85 184 184
SMAD3 0.02 0.017 -9999 0 -0.2 3 3
EDN1 -0.06 0.15 -9999 0 -0.49 13 13
IGFBP1 -0.27 0.48 -9999 0 -0.83 178 178
VEGFA -0.19 0.36 -9999 0 -0.65 152 152
HIF1A/JAB1 -0.008 0.078 -9999 0 -0.27 23 23
CP -0.31 0.51 -9999 0 -0.89 184 184
CXCL12 -0.32 0.5 -9999 0 -0.86 198 198
COPS5 0.008 0.069 -9999 0 -0.33 21 21
SMAD3/SMAD4 -0.003 0.087 -9999 0 -0.21 75 75
BNIP3 -0.29 0.5 -9999 0 -0.88 175 175
EGLN3 -0.28 0.48 -9999 0 -0.83 182 182
CA9 -0.28 0.48 -9999 0 -0.84 180 180
TERT -0.27 0.48 -9999 0 -0.83 179 179
ENO1 -0.28 0.49 -9999 0 -0.86 171 171
PFKL -0.27 0.48 -9999 0 -0.83 181 181
NCOA1 0.006 0.071 -9999 0 -0.34 22 22
ADM -0.31 0.51 -9999 0 -0.87 194 194
ARNT -0.026 0.075 -9999 0 -0.14 29 29
HNF4A 0.023 0.007 -9999 0 -10000 0 0
ADFP -0.3 0.5 -9999 0 -0.87 190 190
SLC2A1 -0.2 0.38 -9999 0 -0.67 164 164
LEP -0.27 0.48 -9999 0 -0.83 179 179
HIF1A/ARNT/Cbp/p300 -0.19 0.4 -9999 0 -0.74 134 134
EPO -0.11 0.29 -9999 0 -0.62 62 62
CREBBP -0.023 0.11 -9999 0 -0.27 28 28
HIF1A/ARNT/Cbp/p300/HDAC7 -0.2 0.41 -9999 0 -0.76 138 138
PFKFB3 -0.3 0.5 -9999 0 -0.85 191 191
NT5E -0.3 0.49 -9999 0 -0.87 183 183
TCGA08_p53

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
CDKN2A -0.057 0.12 -10000 0 -0.25 143 143
TP53 -0.11 0.13 -10000 0 -0.3 153 153
Senescence -0.11 0.13 -10000 0 -0.3 153 153
Apoptosis -0.11 0.13 -10000 0 -0.3 153 153
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.053 0.083 0.19 139 -10000 0 139
MDM4 0.02 0 -10000 0 -10000 0 0
Glypican 2 network

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
MDK -0.065 0.15 -9999 0 -0.32 134 134
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.044 0.1 -9999 0 -0.22 134 134
neuron projection morphogenesis -0.043 0.1 -9999 0 -0.22 134 134
IGF1 pathway

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
NCK2 0.012 0.051 -10000 0 -0.34 11 11
PTK2 0.001 0.08 -10000 0 -0.33 29 29
CRKL -0.071 0.12 -10000 0 -0.22 167 167
GRB2/SOS1/SHC 0.021 0.035 -10000 0 -0.17 17 17
HRAS 0.014 0.04 -10000 0 -0.27 10 10
IRS1/Crk -0.074 0.12 -10000 0 -0.22 174 174
IGF-1R heterotetramer/IGF1/PTP1B -0.062 0.12 -10000 0 -0.23 158 158
AKT1 -0.076 0.12 -10000 0 -0.28 115 115
BAD -0.069 0.12 -10000 0 -0.26 117 117
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.075 0.12 -10000 0 -0.22 174 174
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.069 0.12 -10000 0 -0.22 167 167
RAF1 -0.067 0.14 -10000 0 -0.41 43 43
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.066 0.12 -10000 0 -0.21 173 173
YWHAZ 0.005 0.074 -10000 0 -0.35 22 22
IGF-1R heterotetramer/IGF1/IRS1 -0.082 0.13 -10000 0 -0.25 167 167
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
RPS6KB1 -0.07 0.12 -10000 0 -0.26 107 107
GNB2L1 0.015 0.044 -10000 0 -0.36 7 7
positive regulation of MAPKKK cascade -0.061 0.12 0.21 2 -0.32 55 57
PXN 0.019 0.01 -10000 0 -0.2 1 1
PIK3R1 -0.011 0.097 -10000 0 -0.3 52 52
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.009 0.037 -10000 0 -0.24 11 11
HRAS/GTP -0.071 0.094 -10000 0 -0.2 159 159
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.039 0.1 -10000 0 -0.18 160 160
IGF-1R heterotetramer -0.071 0.16 -10000 0 -0.36 115 115
IGF-1R heterotetramer/IGF1/IRS/Nck -0.069 0.12 -10000 0 -0.22 173 173
Crk/p130 Cas/Paxillin -0.059 0.11 -10000 0 -0.21 161 161
IGF1R -0.071 0.16 -10000 0 -0.36 115 115
IGF1 -0.085 0.15 -10000 0 -0.29 166 166
IRS2/Crk -0.092 0.14 -10000 0 -0.24 209 209
PI3K -0.083 0.14 -10000 0 -0.24 189 189
apoptosis 0.061 0.12 0.24 122 -10000 0 122
HRAS/GDP 0.011 0.028 -10000 0 -0.18 10 10
PRKCD -0.086 0.15 -10000 0 -0.29 163 163
RAF1/14-3-3 E -0.053 0.12 -10000 0 -0.33 48 48
BAD/14-3-3 -0.064 0.12 -10000 0 -0.25 122 122
PRKCZ -0.076 0.12 -10000 0 -0.27 106 106
Crk/p130 Cas/Paxillin/FAK1 -0.076 0.1 -10000 0 -0.24 121 121
PTPN1 0.014 0.046 -10000 0 -0.33 9 9
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.086 0.15 -10000 0 -0.31 155 155
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.045 0.11 -10000 0 -0.2 158 158
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.071 0.12 -10000 0 -0.22 173 173
GRB10 0.01 0.053 -10000 0 -0.25 20 20
PTPN11 -0.07 0.12 -10000 0 -0.22 167 167
IRS1 -0.081 0.12 -10000 0 -0.25 167 167
IRS2 -0.1 0.14 -10000 0 -0.25 213 213
IGF-1R heterotetramer/IGF1 -0.097 0.15 -10000 0 -0.29 167 167
GRB2 0.012 0.053 -10000 0 -0.35 11 11
PDPK1 -0.078 0.12 -10000 0 -0.28 106 106
YWHAE 0.013 0.048 -10000 0 -0.3 12 12
PRKD1 -0.092 0.16 -10000 0 -0.3 160 160
SHC1 0.017 0.027 -10000 0 -0.23 6 6
Syndecan-4-mediated signaling events

Figure S8.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S8.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.11 0.23 -10000 0 -0.47 128 128
Syndecan-4/Syndesmos -0.15 0.24 -10000 0 -0.47 155 155
positive regulation of JNK cascade -0.19 0.24 -10000 0 -0.5 167 167
Syndecan-4/ADAM12 -0.14 0.24 -10000 0 -0.47 155 155
CCL5 -0.078 0.15 -10000 0 -0.28 175 175
Rac1/GDP 0.013 0.023 -10000 0 -0.25 4 4
DNM2 0.02 0 -10000 0 -10000 0 0
ITGA5 0.005 0.061 -10000 0 -0.23 33 33
SDCBP 0.009 0.061 -10000 0 -0.34 16 16
PLG 0.023 0.007 -10000 0 -10000 0 0
ADAM12 0.018 0.021 -10000 0 -0.2 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.006 0.016 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.15 0.24 -10000 0 -0.47 155 155
Syndecan-4/CXCL12/CXCR4 -0.2 0.26 -10000 0 -0.54 167 167
Syndecan-4/Laminin alpha3 -0.2 0.26 -10000 0 -0.54 159 159
MDK -0.065 0.15 -10000 0 -0.32 134 134
Syndecan-4/FZD7 -0.16 0.26 -10000 0 -0.5 157 157
Syndecan-4/Midkine -0.17 0.25 -10000 0 -0.5 156 156
FZD7 -0.048 0.14 -10000 0 -0.3 114 114
Syndecan-4/FGFR1/FGF -0.12 0.23 -10000 0 -0.43 155 155
THBS1 -0.017 0.096 -10000 0 -0.25 74 74
integrin-mediated signaling pathway -0.17 0.24 -10000 0 -0.49 157 157
positive regulation of MAPKKK cascade -0.19 0.24 -10000 0 -0.5 167 167
Syndecan-4/TACI -0.14 0.24 -10000 0 -0.47 155 155
CXCR4 -0.064 0.15 -10000 0 -0.31 135 135
cell adhesion -0.019 0.096 -10000 0 -0.22 85 85
Syndecan-4/Dynamin -0.14 0.24 -10000 0 -0.47 155 155
Syndecan-4/TSP1 -0.15 0.25 -10000 0 -0.49 155 155
Syndecan-4/GIPC -0.14 0.24 -10000 0 -0.47 155 155
Syndecan-4/RANTES -0.17 0.26 -10000 0 -0.52 157 157
ITGB1 0.02 0 -10000 0 -10000 0 0
LAMA1 0 0 -10000 0 -10000 0 0
LAMA3 -0.15 0.16 -10000 0 -0.29 292 292
RAC1 0.017 0.033 -10000 0 -0.36 4 4
PRKCA 0.039 0.043 0.15 8 -0.19 2 10
Syndecan-4/alpha-Actinin -0.15 0.25 -10000 0 -0.49 156 156
TFPI 0.015 0.032 -10000 0 -0.2 11 11
F2 0.012 0.012 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.019 0.043 -10000 0 -0.24 5 5
positive regulation of cell adhesion -0.19 0.25 -10000 0 -0.52 159 159
ACTN1 -0.005 0.091 -10000 0 -0.33 38 38
TNC -0.09 0.15 -10000 0 -0.27 205 205
Syndecan-4/CXCL12 -0.18 0.26 -10000 0 -0.52 157 157
FGF6 0.02 0 -10000 0 -10000 0 0
RHOA -0.008 0.1 -10000 0 -0.36 39 39
CXCL12 -0.09 0.15 -10000 0 -0.28 200 200
TNFRSF13B 0.02 0 -10000 0 -10000 0 0
FGF2 0.019 0.01 -10000 0 -0.2 1 1
FGFR1 0.012 0.041 -10000 0 -0.2 19 19
Syndecan-4/PI-4-5-P2 -0.15 0.24 -10000 0 -0.47 155 155
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.053 0.14 -10000 0 -0.3 126 126
cell migration -0.003 0.007 -10000 0 -10000 0 0
PRKCD -0.001 0.086 -10000 0 -0.3 39 39
vasculogenesis -0.15 0.24 -10000 0 -0.47 155 155
SDC4 -0.15 0.26 -10000 0 -0.5 155 155
Syndecan-4/Tenascin C -0.18 0.26 -10000 0 -0.52 157 157
Syndecan-4/PI-4-5-P2/PKC alpha -0.006 0.012 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.14 0.24 -10000 0 -0.47 157 157
MMP9 -0.12 0.16 -10000 0 -0.28 245 245
Rac1/GTP -0.02 0.098 -10000 0 -0.23 85 85
cytoskeleton organization -0.14 0.23 -10000 0 -0.45 157 157
GIPC1 0.015 0.037 -10000 0 -0.26 9 9
Syndecan-4/TFPI -0.14 0.24 -10000 0 -0.47 155 155
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.088 0.14 -9999 0 -0.24 196 196
alphaM/beta2 Integrin/GPIbA -0.016 0.094 -9999 0 -0.19 103 103
alphaM/beta2 Integrin/proMMP-9 -0.094 0.14 -9999 0 -0.24 214 214
PLAUR -0.03 0.12 -9999 0 -0.32 79 79
HMGB1 0.018 0.025 -9999 0 -0.37 2 2
alphaM/beta2 Integrin/Talin -0.02 0.099 -9999 0 -0.2 106 106
AGER 0.02 0.008 -9999 0 -10000 0 0
RAP1A 0.015 0.039 -9999 0 -0.32 7 7
SELPLG 0.019 0.01 -9999 0 -0.2 1 1
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.005 0.094 -9999 0 -0.25 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.12 0.16 -9999 0 -0.28 245 245
CYR61 -0.089 0.16 -9999 0 -0.3 186 186
TLN1 0.012 0.049 -9999 0 -0.29 13 13
Rap1/GTP -0.088 0.14 -9999 0 -0.35 96 96
RHOA -0.008 0.1 -9999 0 -0.36 39 39
P-selectin oligomer 0.018 0.021 -9999 0 -0.2 5 5
MYH2 -0.092 0.16 -9999 0 -0.34 116 116
MST1R 0.009 0.047 -9999 0 -0.2 25 25
leukocyte activation during inflammatory response -0.004 0.079 -9999 0 -0.15 103 103
APOB 0.019 0.01 -9999 0 -0.2 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.11 0.16 -9999 0 -0.29 223 223
JAM3 -0.003 0.078 -9999 0 -0.25 45 45
GP1BA 0.02 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.084 0.14 -9999 0 -0.24 197 197
alphaM/beta2 Integrin -0.094 0.17 -9999 0 -0.41 92 92
JAM3 homodimer -0.003 0.078 -9999 0 -0.25 45 45
ICAM2 0.008 0.051 -9999 0 -0.2 29 29
ICAM1 -0.032 0.12 -9999 0 -0.27 98 98
phagocytosis triggered by activation of immune response cell surface activating receptor -0.093 0.17 -9999 0 -0.41 92 92
cell adhesion -0.016 0.093 -9999 0 -0.19 103 103
NFKB1 -0.014 0.11 -9999 0 -0.28 40 40
THY1 -0.088 0.16 -9999 0 -0.31 174 174
RhoA/GDP -0.005 0.069 -9999 0 -0.25 39 39
Lipoprotein(a) 0.027 0.006 -9999 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA -0.065 0.13 -9999 0 -0.21 201 201
IL6 -0.016 0.11 -9999 0 -0.28 36 36
ITGB2 -0.073 0.15 -9999 0 -0.31 150 150
elevation of cytosolic calcium ion concentration -0.08 0.17 -9999 0 -0.29 168 168
alphaM/beta2 Integrin/JAM2/JAM3 -0.022 0.1 -9999 0 -0.18 123 123
JAM2 0.003 0.059 -9999 0 -0.2 40 40
alphaM/beta2 Integrin/ICAM1 -0.03 0.12 -9999 0 -0.26 75 75
alphaM/beta2 Integrin/uPA/Plg -0.057 0.13 -9999 0 -0.24 151 151
RhoA/GTP -0.1 0.17 -9999 0 -0.36 120 120
positive regulation of phagocytosis -0.079 0.16 -9999 0 -0.33 120 120
Ron/MSP 0.011 0.055 -9999 0 -0.26 6 6
alphaM/beta2 Integrin/uPAR/uPA -0.08 0.17 -9999 0 -0.29 168 168
alphaM/beta2 Integrin/uPAR -0.042 0.14 -9999 0 -0.26 128 128
PLAU -0.086 0.15 -9999 0 -0.28 193 193
PLAT -0.096 0.16 -9999 0 -0.3 194 194
actin filament polymerization -0.089 0.15 -9999 0 -0.33 116 116
MST1 0.003 0.063 -9999 0 -0.23 36 36
alphaM/beta2 Integrin/lipoprotein(a) -0.002 0.082 -9999 0 -0.15 103 103
TNF -0.014 0.11 -9999 0 -0.28 37 37
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.075 0.14 -9999 0 -0.27 155 155
fibrinolysis -0.057 0.13 -9999 0 -0.24 151 151
HCK -0.004 0.072 -9999 0 -0.21 56 56
dendritic cell antigen processing and presentation -0.093 0.17 -9999 0 -0.41 92 92
VTN 0.02 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 -0.079 0.13 -9999 0 -0.22 200 200
LPA 0.02 0 -9999 0 -10000 0 0
LRP1 0.016 0.027 -9999 0 -0.2 8 8
cell migration -0.14 0.15 -9999 0 -0.26 284 284
FN1 -0.057 0.14 -9999 0 -0.31 126 126
alphaM/beta2 Integrin/Thy1 -0.078 0.13 -9999 0 -0.23 196 196
MPO 0.02 0 -9999 0 -10000 0 0
KNG1 0.02 0 -9999 0 -10000 0 0
RAP1/GDP 0.011 0.023 -9999 0 -0.21 5 5
ROCK1 -0.094 0.16 -9999 0 -0.34 118 118
ELA2 0.02 0 -9999 0 -10000 0 0
PLG 0.02 0 -9999 0 -10000 0 0
CTGF -0.099 0.16 -9999 0 -0.3 202 202
alphaM/beta2 Integrin/Hck -0.029 0.11 -9999 0 -0.2 138 138
ITGAM 0.02 0.008 -9999 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.002 0.089 -9999 0 -0.16 108 108
HP -0.14 0.16 -9999 0 -0.28 298 298
leukocyte adhesion -0.062 0.13 -9999 0 -0.28 85 85
SELP 0.018 0.021 -9999 0 -0.2 5 5
LPA receptor mediated 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
GNB1/GNG2 -0.047 0.092 -10000 0 -0.2 121 121
NF kappa B1 p50/RelA/I kappa B alpha -0.016 0.1 -10000 0 -0.27 49 49
AP1 -0.1 0.12 -10000 0 -0.21 251 251
mol:PIP3 -0.05 0.066 -10000 0 -0.15 120 120
AKT1 -0.042 0.11 -10000 0 -0.25 70 70
PTK2B -0.028 0.069 -10000 0 -0.15 113 113
RHOA -0.041 0.11 -10000 0 -0.39 39 39
PIK3CB 0.018 0.021 -10000 0 -0.2 5 5
mol:Ca2+ 0.008 0.029 -10000 0 -10000 0 0
MAGI3 0 0 -10000 0 -10000 0 0
RELA 0.018 0.021 -10000 0 -0.26 3 3
apoptosis -0.046 0.088 -10000 0 -0.2 113 113
HRAS/GDP 0.011 0.028 -10000 0 -0.18 10 10
positive regulation of microtubule depolymerization -0.02 0.072 -10000 0 -0.23 17 17
NF kappa B1 p50/RelA -0.049 0.069 -10000 0 -0.23 37 37
endothelial cell migration -0.13 0.2 -10000 0 -0.34 223 223
ADCY4 -0.055 0.11 -10000 0 -0.23 121 121
ADCY5 -0.055 0.11 -10000 0 -0.23 121 121
ADCY6 -0.051 0.11 -10000 0 -0.23 121 121
ADCY7 -0.059 0.12 -10000 0 -0.24 130 130
ADCY1 -0.051 0.11 -10000 0 -0.23 121 121
ADCY2 -0.051 0.11 -10000 0 -0.23 121 121
ADCY3 -0.055 0.11 -10000 0 -0.23 121 121
ADCY8 -0.054 0.11 -10000 0 -0.23 126 126
ADCY9 -0.051 0.11 -10000 0 -0.23 121 121
GSK3B -0.028 0.077 -10000 0 -0.15 125 125
arachidonic acid secretion -0.047 0.11 -10000 0 -0.22 123 123
GNG2 0 0.001 0.001 76 -10000 0 76
TRIP6 -0.011 0.078 -10000 0 -0.32 29 29
GNAO1 -0.052 0.093 -10000 0 -0.21 113 113
HRAS 0.014 0.04 -10000 0 -0.27 10 10
NFKBIA -0.026 0.094 -10000 0 -0.28 43 43
GAB1 0.02 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.004 0.15 -10000 0 -0.9 15 15
JUN -0.011 0.099 -10000 0 -0.31 51 51
LPA/LPA2/NHERF2 -0.011 0.036 -10000 0 -10000 0 0
TIAM1 -0.018 0.18 -10000 0 -1.1 15 15
PIK3R1 -0.011 0.097 -10000 0 -0.3 52 52
mol:IP3 0.008 0.029 -10000 0 -10000 0 0
PLCB3 -0.002 0.032 -10000 0 -10000 0 0
FOS -0.11 0.16 -10000 0 -0.29 233 233
positive regulation of mitosis -0.047 0.11 -10000 0 -0.22 123 123
LPA/LPA1-2-3 -0.053 0.081 -10000 0 -0.14 223 223
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -0.001 27 27
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation -0.03 0.08 -10000 0 -0.16 119 119
GNAZ -0.051 0.092 -10000 0 -0.2 113 113
EGFR/PI3K-beta/Gab1 -0.051 0.068 -10000 0 -0.16 117 117
positive regulation of dendritic cell cytokine production -0.053 0.08 -10000 0 -0.14 223 223
LPA/LPA2/MAGI-3 -0.022 0.033 -10000 0 -0.058 223 223
ARHGEF1 -0.027 0.078 -10000 0 -0.16 115 115
GNAI2 -0.054 0.098 -10000 0 -0.21 119 119
GNAI3 -0.055 0.098 -10000 0 -0.21 122 122
GNAI1 -0.071 0.11 -10000 0 -0.23 139 139
LPA/LPA3 -0.028 0.041 -10000 0 -0.073 223 223
LPA/LPA2 -0.028 0.041 -10000 0 -0.073 223 223
LPA/LPA1 -0.072 0.11 -10000 0 -0.19 223 223
HB-EGF/EGFR -0.05 0.096 -10000 0 -0.2 125 125
HBEGF -0.072 0.11 -10000 0 -0.24 123 123
mol:DAG 0.008 0.029 -10000 0 -10000 0 0
cAMP biosynthetic process -0.05 0.11 -10000 0 -0.22 124 124
NFKB1 -0.003 0.088 -10000 0 -0.34 34 34
SRC 0.02 0 -10000 0 -10000 0 0
GNB1 0.009 0.065 -10000 0 -0.36 16 16
LYN -0.044 0.12 -10000 0 -0.29 78 78
GNAQ -0.013 0.034 -10000 0 -10000 0 0
LPAR2 0 0.001 -10000 0 -0.001 38 38
LPAR3 0 0 -10000 0 -0.002 36 36
LPAR1 -0.044 0.064 -10000 0 -0.12 223 223
IL8 -0.14 0.17 -10000 0 -0.34 160 160
PTK2 -0.049 0.087 -10000 0 -0.18 128 128
Rac1/GDP 0.013 0.023 -10000 0 -0.25 4 4
CASP3 -0.046 0.088 -10000 0 -0.2 113 113
EGFR 0.018 0.017 -10000 0 -0.2 3 3
PLCG1 -0.004 0.033 -10000 0 -0.11 2 2
PLD2 -0.04 0.078 -10000 0 -0.17 113 113
G12/G13 -0.032 0.087 -10000 0 -0.18 115 115
PI3K-beta -0.067 0.095 -10000 0 -0.28 63 63
cell migration -0.012 0.066 -10000 0 -0.23 23 23
SLC9A3R2 0.02 0 -10000 0 -10000 0 0
PXN -0.031 0.081 -10000 0 -0.16 118 118
HRAS/GTP -0.048 0.11 -10000 0 -0.22 123 123
RAC1 0.017 0.033 -10000 0 -0.36 4 4
MMP9 -0.12 0.16 -10000 0 -0.28 245 245
PRKCE 0.02 0 -10000 0 -10000 0 0
PRKCD 0.002 0.047 -10000 0 -0.15 31 31
Gi(beta/gamma) -0.053 0.11 -10000 0 -0.23 124 124
mol:LPA -0.044 0.064 -10000 0 -0.12 223 223
TRIP6/p130 Cas/FAK1/Paxillin -0.042 0.1 -10000 0 -0.2 131 131
MAPKKK cascade -0.047 0.11 -10000 0 -0.22 123 123
contractile ring contraction involved in cytokinesis -0.041 0.11 -10000 0 -0.38 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.013 0.034 -10000 0 -0.16 1 1
GNA15 -0.014 0.035 -10000 0 -0.11 6 6
GNA12 0.019 0.017 -10000 0 -0.2 3 3
GNA13 0.02 0 -10000 0 -10000 0 0
MAPT -0.021 0.074 -10000 0 -0.23 17 17
GNA11 -0.013 0.034 -10000 0 -10000 0 0
Rac1/GTP 0.004 0.16 -10000 0 -0.95 15 15
MMP2 -0.13 0.2 -10000 0 -0.34 223 223
Wnt 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
Noncanonical Wnts/FZD -0.083 0.15 -9999 0 -0.37 83 83
FZD6 -0.057 0.15 -9999 0 -0.32 121 121
WNT6 0.02 0 -9999 0 -10000 0 0
WNT4 0.017 0.025 -9999 0 -0.2 7 7
FZD3 -0.05 0.14 -9999 0 -0.29 120 120
WNT5A -0.069 0.14 -9999 0 -0.28 160 160
WNT11 -0.009 0.075 -9999 0 -0.2 69 69
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.067 0.15 -9999 0 -0.3 149 149
PLK4 0.018 0.021 -9999 0 -0.2 5 5
regulation of centriole replication -0.037 0.1 -9999 0 -0.24 84 84
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.036 0.12 -9999 0 -0.29 72 72
NF kappa B1 p50/RelA/I kappa B alpha -0.06 0.18 -9999 0 -0.4 86 86
alphaV/beta3 Integrin/Osteopontin/Src -0.05 0.14 -9999 0 -0.28 123 123
AP1 -0.15 0.21 -9999 0 -0.41 164 164
ILK -0.038 0.12 -9999 0 -0.29 71 71
bone resorption -0.044 0.13 -9999 0 -0.28 88 88
PTK2B 0.02 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.036 0.12 -9999 0 -0.25 97 97
ITGAV -0.024 0.12 -9999 0 -0.35 59 59
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0 0.077 -9999 0 -0.25 36 36
alphaV/beta3 Integrin/Osteopontin -0.034 0.13 -9999 0 -0.25 121 121
MAP3K1 -0.038 0.12 -9999 0 -0.27 78 78
JUN -0.013 0.099 -9999 0 -0.31 51 51
MAPK3 -0.047 0.13 -9999 0 -0.29 91 91
MAPK1 -0.058 0.14 -9999 0 -0.3 108 108
Rac1/GDP 0.013 0.023 -9999 0 -0.25 4 4
NFKB1 -0.003 0.088 -9999 0 -0.34 34 34
MAPK8 -0.037 0.11 -9999 0 -0.26 78 78
ITGB3 0.015 0.021 -9999 0 -0.23 2 2
NFKBIA -0.069 0.17 -9999 0 -0.35 117 117
FOS -0.12 0.16 -9999 0 -0.29 233 233
CD44 -0.021 0.11 -9999 0 -0.28 73 73
CHUK 0.006 0.068 -9999 0 -0.33 21 21
PLAU -0.21 0.42 -9999 0 -1.1 88 88
NF kappa B1 p50/RelA -0.063 0.18 -9999 0 -0.36 111 111
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0.018 0.021 -9999 0 -0.26 3 3
alphaV beta3 Integrin -0.007 0.087 -9999 0 -0.24 58 58
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.051 0.13 -9999 0 -0.24 147 147
VAV3 -0.11 0.15 -9999 0 -0.28 200 200
MAP3K14 -0.042 0.12 -9999 0 -0.28 83 83
ROCK2 0.018 0.017 -9999 0 -0.2 3 3
SPP1 -0.049 0.14 -9999 0 -0.35 95 95
RAC1 0.017 0.033 -9999 0 -0.36 4 4
Rac1/GTP -0.11 0.14 -9999 0 -0.28 164 164
MMP2 -0.17 0.22 -9999 0 -0.42 184 184
TRAIL signaling pathway

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
TNFSF10 -0.093 0.16 -9999 0 -0.31 186 186
positive regulation of NF-kappaB transcription factor activity -0.051 0.12 -9999 0 -0.24 120 120
MAP2K4 -0.015 0.093 -9999 0 -0.24 17 17
IKBKB 0.017 0.025 -9999 0 -0.2 7 7
TNFRSF10B 0.019 0.014 -9999 0 -0.2 2 2
TNFRSF10A 0 0 -9999 0 -10000 0 0
SMPD1 -0.024 0.069 -9999 0 -0.14 120 120
IKBKG 0.02 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.019 0.01 -9999 0 -0.2 1 1
TRAIL/TRAILR2 -0.051 0.12 -9999 0 -0.2 187 187
TRAIL/TRAILR3 -0.05 0.12 -9999 0 -0.2 186 186
TRAIL/TRAILR1 -0.063 0.11 -9999 0 -0.21 186 186
TRAIL/TRAILR4 -0.051 0.12 -9999 0 -0.24 120 120
TRAIL/TRAILR1/DAP3/GTP -0.036 0.088 -9999 0 -0.15 188 188
IKK complex 0.001 0.074 -9999 0 -0.32 16 16
RIPK1 0.019 0.014 -9999 0 -0.2 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.013 0.02 -9999 0 -0.25 3 3
MAPK3 -0.053 0.11 -9999 0 -0.2 186 186
MAP3K1 -0.019 0.095 -9999 0 -0.24 13 13
TRAILR4 (trimer) 0.019 0.01 -9999 0 -0.2 1 1
TRADD 0.02 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.024 0.09 -9999 0 -0.18 125 125
CFLAR 0.012 0.052 -9999 0 -0.3 14 14
MAPK1 -0.069 0.13 -9999 0 -0.22 209 209
TRAIL/TRAILR1/FADD/TRADD/RIP -0.017 0.09 -9999 0 -0.16 127 127
mol:ceramide -0.024 0.069 -9999 0 -0.14 120 120
FADD 0.013 0.046 -9999 0 -0.28 12 12
MAPK8 -0.008 0.089 -9999 0 -0.25 10 10
TRAF2 0.02 0 -9999 0 -10000 0 0
TRAILR3 (trimer) 0.02 0 -9999 0 -10000 0 0
CHUK 0.006 0.068 -9999 0 -0.33 21 21
TRAIL/TRAILR1/FADD -0.044 0.1 -9999 0 -0.17 191 191
DAP3 0.018 0.029 -9999 0 -0.36 3 3
CASP10 -0.049 0.1 -9999 0 -0.23 126 126
JNK cascade -0.051 0.12 -9999 0 -0.24 120 120
TRAIL (trimer) -0.093 0.16 -9999 0 -0.31 186 186
TNFRSF10C 0.02 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD -0.027 0.089 -9999 0 -0.17 127 127
TRAIL/TRAILR2/FADD -0.033 0.1 -9999 0 -0.2 126 126
cell death -0.024 0.069 -9999 0 -0.14 120 120
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.017 0.09 -9999 0 -0.17 125 125
TRAILR2 (trimer) 0.019 0.014 -9999 0 -0.2 2 2
CASP8 0.034 0.086 -9999 0 -0.78 4 4
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.007 0.093 -9999 0 -0.16 127 127
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A -0.006 0.087 -9999 0 -0.28 45 45
LAT2 -0.052 0.14 -9999 0 -0.26 127 127
AP1 -0.086 0.17 -9999 0 -0.35 116 116
mol:PIP3 -0.038 0.14 -9999 0 -0.31 76 76
IKBKB -0.016 0.085 -9999 0 -0.19 64 64
AKT1 -0.064 0.12 -9999 0 -0.26 109 109
IKBKG -0.015 0.085 -9999 0 -0.19 65 65
MS4A2 0.023 0.008 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA -0.012 0.1 -9999 0 -0.33 48 48
MAP3K1 -0.038 0.13 -9999 0 -0.28 80 80
mol:Ca2+ -0.027 0.11 -9999 0 -0.24 75 75
LYN -0.032 0.13 -9999 0 -0.35 76 76
CBLB -0.052 0.13 -9999 0 -0.26 127 127
SHC1 0.017 0.027 -9999 0 -0.23 6 6
RasGAP/p62DOK -0.003 0.078 -9999 0 -0.18 64 64
positive regulation of cell migration 0.011 0.015 -9999 0 -0.13 6 6
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.04 0.092 -9999 0 -0.18 116 116
PTPN13 -0.11 0.21 -9999 0 -0.46 106 106
PTPN11 0.017 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.058 0.13 -9999 0 -0.28 94 94
SYK -0.031 0.12 -9999 0 -0.32 79 79
GRB2 0.012 0.053 -9999 0 -0.35 11 11
LAT/PLCgamma1/GRB2/SLP76/GADs -0.068 0.12 -9999 0 -0.27 119 119
LAT -0.052 0.14 -9999 0 -0.26 127 127
PAK2 -0.047 0.14 -9999 0 -0.3 86 86
NFATC2 -0.018 0.027 -9999 0 -10000 0 0
HRAS -0.052 0.14 -9999 0 -0.33 86 86
GAB2 -0.03 0.12 -9999 0 -0.31 81 81
PLA2G1B 0.019 0.12 -9999 0 -0.9 9 9
Fc epsilon R1 -0.024 0.093 -9999 0 -0.18 119 119
Antigen/IgE/Fc epsilon R1 -0.018 0.083 -9999 0 -0.16 119 119
mol:GDP -0.056 0.15 -9999 0 -0.3 124 124
JUN -0.011 0.099 -9999 0 -0.31 51 51
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 -0.012 0.098 -9999 0 -0.3 52 52
FOS -0.11 0.16 -9999 0 -0.29 233 233
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.06 0.14 -9999 0 -0.28 127 127
CHUK -0.02 0.088 -9999 0 -0.19 74 74
KLRG1 -0.048 0.12 -9999 0 -0.29 78 78
VAV1 -0.055 0.13 -9999 0 -0.26 127 127
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.052 0.13 -9999 0 -0.26 127 127
negative regulation of mast cell degranulation -0.045 0.11 -9999 0 -0.28 72 72
BTK -0.058 0.15 -9999 0 -0.34 83 83
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.078 0.15 -9999 0 -0.34 106 106
GAB2/PI3K/SHP2 -0.087 0.11 -9999 0 -0.27 106 106
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.067 0.15 -9999 0 -0.31 116 116
RAF1 0.011 0.13 -9999 0 -1 9 9
Fc epsilon R1/FcgammaRIIB/SHIP -0.069 0.14 -9999 0 -0.25 178 178
FCER1G -0.083 0.16 -9999 0 -0.31 165 165
FCER1A 0.012 0.039 -9999 0 -0.2 17 17
Antigen/IgE/Fc epsilon R1/Fyn -0.041 0.1 -9999 0 -0.19 135 135
MAPK3 0.02 0.12 -9999 0 -0.91 9 9
MAPK1 0.013 0.13 -9999 0 -0.92 9 9
NFKB1 -0.003 0.088 -9999 0 -0.34 34 34
MAPK8 0.009 0.066 -9999 0 -0.44 6 6
DUSP1 -0.026 0.11 -9999 0 -0.25 91 91
NF-kappa-B/RelA -0.024 0.055 -9999 0 -0.15 58 58
actin cytoskeleton reorganization -0.08 0.2 -9999 0 -0.47 85 85
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.059 0.15 -9999 0 -0.33 95 95
FER -0.054 0.14 -9999 0 -0.26 128 128
RELA 0.018 0.021 -9999 0 -0.26 3 3
ITK -0.003 0.036 -9999 0 -10000 0 0
SOS1 0 0 -9999 0 -10000 0 0
PLCG1 -0.05 0.14 -9999 0 -0.33 84 84
cytokine secretion -0.02 0.038 -9999 0 -0.13 31 31
SPHK1 -0.055 0.13 -9999 0 -0.26 128 128
PTK2 -0.085 0.21 -9999 0 -0.51 79 79
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.069 0.13 -9999 0 -0.28 119 119
EDG1 0.011 0.015 -9999 0 -0.13 6 6
mol:DAG -0.045 0.14 -9999 0 -0.32 83 83
MAP2K2 0.015 0.12 -9999 0 -0.93 9 9
MAP2K1 0.015 0.12 -9999 0 -0.93 9 9
MAP2K7 0.02 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.038 0.11 -9999 0 -0.29 61 61
MAP2K4 0.015 0.098 -9999 0 -0.9 6 6
Fc epsilon R1/FcgammaRIIB -0.074 0.15 -9999 0 -0.27 178 178
mol:Choline -0.04 0.091 -9999 0 -0.18 116 116
SHC/Grb2/SOS1 -0.042 0.14 -9999 0 -0.3 86 86
FYN -0.049 0.13 -9999 0 -0.28 122 122
DOK1 0.02 0 -9999 0 -10000 0 0
PXN -0.072 0.2 -9999 0 -0.47 78 78
HCLS1 -0.086 0.18 -9999 0 -0.35 139 139
PRKCB -0.03 0.11 -9999 0 -0.24 82 82
FCGR2B -0.11 0.16 -9999 0 -0.29 225 225
IGHE -0.001 0.004 -9999 0 -10000 0 0
KLRG1/SHIP -0.046 0.12 -9999 0 -0.29 72 72
LCP2 -0.014 0.095 -9999 0 -0.26 66 66
PLA2G4A -0.092 0.15 -9999 0 -0.3 143 143
RASA1 -0.01 0.1 -9999 0 -0.35 44 44
mol:Phosphatidic acid -0.04 0.091 -9999 0 -0.18 116 116
IKK complex -0.005 0.071 -9999 0 -0.16 47 47
WIPF1 0.016 0.03 -9999 0 -0.2 10 10
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.058 0.12 -9999 0 -0.23 147 147
EPHB2 0.016 0.029 -9999 0 -0.2 9 9
Syndecan-2/TACI -0.015 0.081 -9999 0 -0.19 75 75
LAMA1 0 0 -9999 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.077 0.11 -9999 0 -0.19 219 219
HRAS 0.014 0.04 -9999 0 -0.27 10 10
Syndecan-2/CASK -0.028 0.078 -9999 0 -0.2 75 75
ITGA5 0.005 0.061 -9999 0 -0.23 33 33
BAX -0.004 0.079 -9999 0 -0.37 1 1
EPB41 0.02 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.018 0.081 -9999 0 -0.18 84 84
LAMA3 -0.15 0.16 -9999 0 -0.29 292 292
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.017 0.1 -9999 0 -0.3 61 61
Syndecan-2/MMP2 -0.085 0.13 -9999 0 -0.24 171 171
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.024 0.028 -9999 0 -10000 0 0
dendrite morphogenesis -0.017 0.082 -9999 0 -0.19 76 76
Syndecan-2/GM-CSF -0.015 0.081 -9999 0 -0.19 75 75
determination of left/right symmetry -0.032 0.096 -9999 0 -0.19 134 134
Syndecan-2/PKC delta -0.029 0.096 -9999 0 -0.21 102 102
GNB2L1 0.015 0.044 -9999 0 -0.36 7 7
MAPK3 -0.007 0.072 -9999 0 -0.17 75 75
MAPK1 -0.019 0.085 -9999 0 -0.18 98 98
Syndecan-2/RACK1 -0.006 0.077 -9999 0 -0.16 84 84
NF1 0.02 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.032 0.096 -9999 0 -0.19 134 134
ITGA2 0.012 0.04 -9999 0 -0.2 18 18
MAPK8 -0.012 0.082 -9999 0 -0.19 75 75
Syndecan-2/alpha2/beta1 Integrin -0.004 0.073 -9999 0 -0.16 77 77
Syndecan-2/Kininogen -0.015 0.081 -9999 0 -0.19 75 75
ITGB1 0.02 0 -9999 0 -10000 0 0
SRC -0.004 0.07 -9999 0 -0.15 79 79
Syndecan-2/CASK/Protein 4.1 -0.013 0.073 -9999 0 -0.17 75 75
extracellular matrix organization -0.016 0.082 -9999 0 -0.19 76 76
actin cytoskeleton reorganization -0.057 0.12 -9999 0 -0.23 147 147
Syndecan-2/Caveolin-2/Ras -0.023 0.099 -9999 0 -0.2 104 104
Syndecan-2/Laminin alpha3 -0.11 0.12 -9999 0 -0.24 213 213
Syndecan-2/RasGAP -0.011 0.089 -9999 0 -0.16 110 110
alpha5/beta1 Integrin 0.019 0.043 -9999 0 -0.24 5 5
PRKCD -0.005 0.09 -9999 0 -0.32 39 39
Syndecan-2 dimer -0.017 0.082 -9999 0 -0.19 76 76
GO:0007205 0.003 0.008 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.006 0.086 -9999 0 -0.27 16 16
RHOA -0.008 0.1 -9999 0 -0.36 39 39
SDCBP 0.009 0.061 -9999 0 -0.34 16 16
TNFRSF13B 0.02 0 -9999 0 -10000 0 0
RASA1 -0.01 0.1 -9999 0 -0.35 44 44
alpha2/beta1 Integrin 0.024 0.028 -9999 0 -10000 0 0
Syndecan-2/Synbindin -0.022 0.091 -9999 0 -0.2 87 87
TGFB1 0.017 0.024 -9999 0 -0.2 6 6
CASP3 -0.021 0.09 -9999 0 -0.19 102 102
FN1 -0.057 0.14 -9999 0 -0.31 126 126
Syndecan-2/IL8 -0.056 0.12 -9999 0 -0.24 123 123
SDC2 -0.032 0.096 -9999 0 -0.19 134 134
KNG1 0.02 0 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin -0.015 0.081 -9999 0 -0.19 75 75
TRAPPC4 0.007 0.067 -9999 0 -0.34 19 19
CSF2 0.02 0 -9999 0 -10000 0 0
Syndecan-2/TGFB1 -0.016 0.082 -9999 0 -0.19 76 76
Syndecan-2/Syntenin/PI-4-5-P2 -0.018 0.081 -9999 0 -0.18 84 84
Syndecan-2/Ezrin -0.027 0.091 -9999 0 -0.19 104 104
PRKACA -0.007 0.072 -9999 0 -0.17 75 75
angiogenesis -0.056 0.12 -9999 0 -0.24 123 123
MMP2 -0.11 0.16 -9999 0 -0.29 223 223
IL8 -0.055 0.13 -9999 0 -0.27 139 139
calcineurin-NFAT signaling pathway -0.015 0.081 -9999 0 -0.19 75 75
Noncanonical Wnt signaling pathway

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
NFATC2 0 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.073 0.15 -9999 0 -0.34 89 89
mol:DAG -0.063 0.14 -9999 0 -0.31 89 89
PLCG1 -0.065 0.14 -9999 0 -0.32 89 89
YES1 -0.082 0.15 -9999 0 -0.34 96 96
FZD3 -0.05 0.14 -9999 0 -0.29 120 120
FZD6 -0.057 0.15 -9999 0 -0.32 121 121
G protein -0.066 0.14 -9999 0 -0.32 90 90
MAP3K7 -0.05 0.12 -9999 0 -0.28 84 84
mol:Ca2+ -0.061 0.13 -9999 0 -0.3 89 89
mol:IP3 -0.063 0.14 -9999 0 -0.31 89 89
NLK 0.021 0.019 -9999 0 -10000 0 0
GNB1 0.008 0.065 -9999 0 -0.36 16 16
CAMK2A -0.053 0.12 -9999 0 -0.28 89 89
MAP3K7IP1 0.019 0.01 -9999 0 -0.2 1 1
Noncanonical Wnts/FZD -0.083 0.15 -9999 0 -0.37 83 83
CSNK1A1 0.017 0.033 -9999 0 -0.36 4 4
GNAS -0.074 0.14 -9999 0 -0.34 84 84
GO:0007205 -0.062 0.13 -9999 0 -0.31 89 89
WNT6 0.02 0 -9999 0 -10000 0 0
WNT4 0.017 0.025 -9999 0 -0.2 7 7
NFAT1/CK1 alpha -0.063 0.14 -9999 0 -0.32 93 93
GNG2 0 0 -9999 0 -10000 0 0
WNT5A -0.069 0.14 -9999 0 -0.28 160 160
WNT11 -0.009 0.075 -9999 0 -0.2 69 69
CDC42 -0.072 0.14 -9999 0 -0.32 95 95
Endothelins

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
AKT1 -0.094 0.17 -9999 0 -0.32 156 156
PTK2B 0.02 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.006 0.13 -9999 0 -0.48 16 16
EDN1 -0.063 0.13 -9999 0 -0.25 142 142
EDN3 0.016 0.029 -9999 0 -0.2 9 9
EDN2 0.008 0.051 -9999 0 -0.2 29 29
HRAS/GDP -0.04 0.13 -9999 0 -0.3 62 62
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.02 0.09 -9999 0 -0.21 42 42
ADCY4 -0.074 0.13 -9999 0 -0.27 132 132
ADCY5 -0.074 0.13 -9999 0 -0.27 132 132
ADCY6 -0.065 0.13 -9999 0 -0.26 130 130
ADCY7 -0.072 0.14 -9999 0 -0.27 140 140
ADCY1 -0.065 0.13 -9999 0 -0.26 131 131
ADCY2 -0.065 0.13 -9999 0 -0.26 131 131
ADCY3 -0.074 0.13 -9999 0 -0.27 132 132
ADCY8 -0.073 0.14 -9999 0 -0.27 140 140
ADCY9 -0.065 0.13 -9999 0 -0.26 130 130
arachidonic acid secretion -0.12 0.23 -9999 0 -0.45 142 142
ETB receptor/Endothelin-1/Gq/GTP -0.009 0.071 -9999 0 -0.21 16 16
GNAO1 0.015 0.033 -9999 0 -0.2 12 12
HRAS 0.013 0.04 -9999 0 -0.27 10 10
ETA receptor/Endothelin-1/G12/GTP -0.059 0.17 -9999 0 -0.3 133 133
ETA receptor/Endothelin-1/Gs/GTP -0.056 0.16 -9999 0 -0.28 131 131
mol:GTP -0.002 0.006 -9999 0 -10000 0 0
COL3A1 -0.16 0.25 -9999 0 -0.46 201 201
EDNRB -0.018 0.075 -9999 0 -0.22 50 50
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.083 0.16 -9999 0 -0.33 128 128
CYSLTR1 -0.094 0.16 -9999 0 -0.3 171 171
SLC9A1 -0.044 0.1 -9999 0 -0.21 107 107
mol:GDP -0.048 0.14 -9999 0 -0.32 61 61
SLC9A3 -0.033 0.14 -9999 0 -0.4 22 22
RAF1 -0.083 0.18 -9999 0 -0.36 128 128
JUN -0.047 0.27 -9999 0 -1 33 33
JAK2 -0.086 0.16 -9999 0 -0.31 149 149
mol:IP3 -0.024 0.095 -9999 0 -0.23 44 44
ETA receptor/Endothelin-1 -0.094 0.21 -9999 0 -0.36 169 169
PLCB1 0.017 0.017 -9999 0 -0.21 3 3
PLCB2 0.017 0.005 -9999 0 -10000 0 0
ETA receptor/Endothelin-3 -0.028 0.088 -9999 0 -0.17 83 83
FOS -0.21 0.39 -9999 0 -0.9 123 123
Gai/GDP -0.001 0.12 -9999 0 -0.66 14 14
CRK 0.01 0.053 -9999 0 -0.25 20 20
mol:Ca ++ -0.084 0.18 -9999 0 -0.38 118 118
BCAR1 0 0 -9999 0 -10000 0 0
PRKCB1 -0.023 0.097 -9999 0 -0.24 44 44
GNAQ 0.018 0.008 -9999 0 -10000 0 0
GNAZ 0.017 0.025 -9999 0 -0.2 7 7
GNAL 0.02 0 -9999 0 -10000 0 0
Gs family/GDP -0.037 0.12 -9999 0 -0.3 54 54
ETA receptor/Endothelin-1/Gq/GTP -0.028 0.1 -9999 0 -0.23 60 60
MAPK14 0.002 0.062 -9999 0 -0.22 4 4
TRPC6 -0.007 0.14 -9999 0 -0.5 16 16
GNAI2 0.012 0.054 -9999 0 -0.36 11 11
GNAI3 0.01 0.06 -9999 0 -0.35 14 14
GNAI1 -0.021 0.11 -9999 0 -0.28 74 74
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.004 0.066 -9999 0 -0.22 7 7
ETB receptor/Endothelin-2 -0.005 0.06 -9999 0 -0.17 23 23
ETB receptor/Endothelin-3 0.001 0.054 -9999 0 -0.18 16 16
ETB receptor/Endothelin-1 -0.056 0.13 -9999 0 -0.25 126 126
MAPK3 -0.17 0.33 -9999 0 -0.73 127 127
MAPK1 -0.18 0.34 -9999 0 -0.76 127 127
Rac1/GDP -0.038 0.13 -9999 0 -0.3 60 60
cAMP biosynthetic process -0.054 0.12 -9999 0 -0.25 108 108
MAPK8 -0.018 0.15 -9999 0 -0.47 33 33
SRC 0.02 0 -9999 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.025 0.094 -9999 0 -0.29 33 33
p130Cas/CRK/Src/PYK2 -0.026 0.14 -9999 0 -0.38 35 35
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.037 0.13 -9999 0 -0.3 60 60
COL1A2 -0.16 0.31 -9999 0 -0.64 136 136
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.034 0.092 -9999 0 -0.18 90 90
mol:DAG -0.024 0.095 -9999 0 -0.23 44 44
MAP2K2 -0.12 0.24 -9999 0 -0.52 129 129
MAP2K1 -0.12 0.24 -9999 0 -0.52 130 130
EDNRA -0.061 0.12 -9999 0 -0.23 161 161
positive regulation of muscle contraction -0.074 0.15 -9999 0 -0.29 141 141
Gq family/GDP -0.03 0.12 -9999 0 -0.29 47 47
HRAS/GTP -0.049 0.12 -9999 0 -0.28 74 74
PRKCH -0.023 0.096 -9999 0 -0.24 43 43
RAC1 0.017 0.033 -9999 0 -0.36 4 4
PRKCA -0.021 0.094 -9999 0 -0.24 39 39
PRKCB -0.028 0.095 -9999 0 -0.24 45 45
PRKCE -0.02 0.094 -9999 0 -0.23 39 39
PRKCD -0.032 0.1 -9999 0 -0.25 53 53
PRKCG -0.022 0.095 -9999 0 -0.24 41 41
regulation of vascular smooth muscle contraction -0.25 0.46 -9999 0 -1.1 123 123
PRKCQ -0.045 0.11 -9999 0 -0.25 75 75
PLA2G4A -0.13 0.25 -9999 0 -0.49 142 142
GNA14 0.017 0.013 -9999 0 -0.22 1 1
GNA15 0.016 0.024 -9999 0 -0.21 6 6
GNA12 0.018 0.017 -9999 0 -0.2 3 3
GNA11 0.018 0.006 -9999 0 -10000 0 0
Rac1/GTP -0.06 0.17 -9999 0 -0.3 132 132
MMP1 0 0.13 -9999 0 -10000 0 0
Nongenotropic Androgen 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
PTK2 -0.001 0.055 -10000 0 -0.22 29 29
GNB1/GNG2 -0.009 0.069 -10000 0 -0.17 64 64
regulation of S phase of mitotic cell cycle -0.022 0.093 -10000 0 -0.2 95 95
GNAO1 0.015 0.033 -10000 0 -0.2 12 12
HRAS 0.013 0.041 -10000 0 -0.27 10 10
SHBG/T-DHT 0.013 0 -10000 0 -10000 0 0
PELP1 0.016 0.025 -10000 0 -0.2 7 7
AKT1 0.001 0.048 -10000 0 -0.19 30 30
MAP2K1 -0.023 0.076 -10000 0 -0.19 43 43
T-DHT/AR -0.022 0.078 -10000 0 -0.18 101 101
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.005 224 224
GNAI2 0.012 0.054 -10000 0 -0.36 11 11
GNAI3 0.01 0.06 -10000 0 -0.35 14 14
GNAI1 -0.022 0.11 -10000 0 -0.28 74 74
mol:GDP -0.047 0.095 -10000 0 -0.31 46 46
cell proliferation -0.09 0.18 -10000 0 -0.38 133 133
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
FOS -0.19 0.33 -10000 0 -0.75 129 129
mol:Ca2+ -0.007 0.022 -10000 0 -0.055 67 67
MAPK3 -0.054 0.13 -10000 0 -0.25 129 129
MAPK1 -0.06 0.14 -10000 0 -0.25 138 138
PIK3R1 -0.011 0.097 -10000 0 -0.3 52 52
mol:IP3 -0.001 0.002 -10000 0 -0.003 230 230
cAMP biosynthetic process 0.009 0.016 0.079 5 -10000 0 5
GNG2 0 0 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.003 230 230
HRAS/GTP -0.008 0.064 -10000 0 -0.16 57 57
actin cytoskeleton reorganization 0 0.067 -10000 0 -0.16 69 69
SRC 0.019 0.002 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.003 230 230
PI3K -0.01 0.082 -10000 0 -0.21 66 66
apoptosis 0.098 0.19 0.38 141 -10000 0 141
T-DHT/AR/PELP1 -0.008 0.069 -10000 0 -0.17 63 63
HRAS/GDP -0.028 0.1 -10000 0 -0.28 51 51
CREB1 -0.1 0.2 -10000 0 -0.42 138 138
RAC1-CDC42/GTP 0.006 0.071 -10000 0 -0.16 69 69
AR -0.034 0.11 -10000 0 -0.26 101 101
GNB1 0.008 0.065 -10000 0 -0.36 16 16
RAF1 -0.019 0.069 -10000 0 -0.16 66 66
RAC1-CDC42/GDP -0.013 0.099 -10000 0 -0.29 42 42
T-DHT/AR/PELP1/Src 0.003 0.065 -10000 0 -0.18 36 36
MAP2K2 -0.023 0.076 -10000 0 -0.19 42 42
T-DHT/AR/PELP1/Src/PI3K -0.022 0.094 -10000 0 -0.2 95 95
GNAZ 0.017 0.025 -10000 0 -0.2 7 7
SHBG 0.02 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.006 0.1 -10000 0 -0.36 30 30
mol:T-DHT -0.001 0.001 -10000 0 -0.003 106 106
RAC1 0.017 0.033 -10000 0 -0.36 4 4
GNRH1 0.012 0.001 -10000 0 -10000 0 0
Gi family/GTP -0.011 0.073 -10000 0 -0.18 60 60
CDC42 0.019 0.01 -10000 0 -0.2 1 1
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.011 0.04 -9999 0 -0.2 18 18
GNB1/GNG2 -0.061 0.077 -9999 0 -0.17 163 163
AKT1 -0.044 0.12 -9999 0 -0.2 169 169
EGF 0.019 0.01 -9999 0 -0.2 1 1
mol:TXA2 0 0.001 -9999 0 -10000 0 0
FGR 0.035 0.029 -9999 0 -10000 0 0
mol:Ca2+ -0.065 0.16 -9999 0 -0.28 162 162
LYN 0.031 0.04 -9999 0 -0.25 6 6
RhoA/GTP -0.044 0.059 -9999 0 -0.13 169 169
mol:PGI2 0 0 -9999 0 -10000 0 0
SYK -0.091 0.18 -9999 0 -0.33 165 165
GNG2 0 0 -9999 0 -10000 0 0
ARRB2 0.018 0.021 -9999 0 -0.2 5 5
TP alpha/Gq family/GDP/G beta5/gamma2 0.037 0.015 -9999 0 -10000 0 0
G beta5/gamma2 -0.077 0.099 -9999 0 -0.22 163 163
PRKCH -0.081 0.18 -9999 0 -0.33 162 162
DNM1 0.019 0.01 -9999 0 -0.2 1 1
TXA2/TP beta/beta Arrestin3 0.016 0.013 -9999 0 -10000 0 0
mol:GTP 0 0.001 -9999 0 -0.002 162 162
PTGDR 0.02 0 -9999 0 -10000 0 0
G12 family/GTP -0.1 0.13 -9999 0 -0.29 162 162
ADRBK1 0.019 0.01 -9999 0 -0.2 1 1
ADRBK2 0.017 0.025 -9999 0 -0.2 7 7
RhoA/GTP/ROCK1 0.008 0.065 -9999 0 -0.21 42 42
mol:GDP 0.018 0.089 -9999 0 -10000 0 0
mol:NADP 0.01 0.044 -9999 0 -0.2 22 22
RAB11A 0.012 0.052 -9999 0 -0.32 12 12
PRKG1 0.02 0 -9999 0 -10000 0 0
mol:IP3 -0.085 0.19 -9999 0 -0.35 162 162
cell morphogenesis 0.008 0.064 -9999 0 -0.21 42 42
PLCB2 -0.12 0.24 -9999 0 -0.47 162 162
mol:cGMP 0 0.001 -9999 0 -10000 0 0
BLK 0.038 0.025 -9999 0 -10000 0 0
mol:PDG2 0 0 -9999 0 -10000 0 0
HCK 0.03 0.035 -9999 0 -10000 0 0
RHOA -0.008 0.1 -9999 0 -0.36 39 39
PTGIR 0.02 0 -9999 0 -10000 0 0
PRKCB1 -0.088 0.19 -9999 0 -0.36 162 162
GNAQ 0.02 0 -9999 0 -10000 0 0
mol:L-citrulline 0.01 0.044 -9999 0 -0.2 22 22
TXA2/TXA2-R family -0.13 0.26 -9999 0 -0.5 162 162
LCK 0.037 0.026 -9999 0 -10000 0 0
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.04 0.023 -9999 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.021 0.08 -9999 0 -0.43 16 16
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.039 0.025 -9999 0 -10000 0 0
MAPK14 -0.054 0.12 -9999 0 -0.22 164 164
TGM2/GTP -0.093 0.21 -9999 0 -0.38 162 162
MAPK11 -0.054 0.12 -9999 0 -0.22 164 164
ARHGEF1 -0.032 0.097 -9999 0 -0.17 162 162
GNAI2 0.012 0.054 -9999 0 -0.36 11 11
JNK cascade -0.092 0.2 -9999 0 -0.37 162 162
RAB11/GDP 0.012 0.051 -9999 0 -0.32 12 12
ICAM1 -0.075 0.16 -9999 0 -0.3 163 163
cAMP biosynthetic process -0.078 0.17 -9999 0 -0.32 162 162
Gq family/GTP/EBP50 0.019 0.047 -9999 0 -0.18 25 25
actin cytoskeleton reorganization 0.008 0.064 -9999 0 -0.21 42 42
SRC 0.038 0.024 -9999 0 -10000 0 0
GNB5 0.013 0.037 -9999 0 -0.2 15 15
GNB1 0.008 0.065 -9999 0 -0.36 16 16
EGF/EGFR 0.021 0.062 -9999 0 -0.18 13 13
VCAM1 -0.1 0.19 -9999 0 -0.38 163 163
TP beta/Gq family/GDP/G beta5/gamma2 0.037 0.015 -9999 0 -10000 0 0
platelet activation -0.067 0.16 -9999 0 -0.29 162 162
PGI2/IP 0.014 0.001 -9999 0 -10000 0 0
PRKACA 0.024 0.002 -9999 0 -10000 0 0
Gq family/GDP/G beta5/gamma2 0.037 0.014 -9999 0 -10000 0 0
TXA2/TP beta/beta Arrestin2 0.012 0.022 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TBXA2R 0.028 0.003 -9999 0 -10000 0 0
mol:DAG -0.1 0.21 -9999 0 -0.4 162 162
EGFR 0.018 0.017 -9999 0 -0.2 3 3
TXA2/TP alpha -0.11 0.23 -9999 0 -0.43 162 162
Gq family/GTP 0.014 0.014 -9999 0 -10000 0 0
YES1 0.035 0.031 -9999 0 -0.25 2 2
GNAI2/GTP -0.003 0.018 -9999 0 -10000 0 0
PGD2/DP 0.014 0.001 -9999 0 -10000 0 0
SLC9A3R1 -0.007 0.09 -9999 0 -0.29 46 46
FYN 0.023 0.041 -9999 0 -0.26 3 3
mol:NO 0.01 0.044 -9999 0 -0.2 22 22
GNA15 0.017 0.024 -9999 0 -0.2 6 6
PGK/cGMP 0.021 0.025 -9999 0 -0.1 22 22
RhoA/GDP -0.008 0.098 -9999 0 -0.36 39 39
TP alpha/TGM2/GDP/G beta/gamma 0.037 0.034 -9999 0 -10000 0 0
NOS3 0.01 0.044 -9999 0 -0.2 22 22
RAC1 0.017 0.033 -9999 0 -0.36 4 4
PRKCA -0.079 0.18 -9999 0 -0.33 162 162
PRKCB -0.083 0.18 -9999 0 -0.34 162 162
PRKCE -0.08 0.18 -9999 0 -0.34 162 162
PRKCD -0.095 0.2 -9999 0 -0.37 165 165
PRKCG -0.09 0.19 -9999 0 -0.36 162 162
muscle contraction -0.12 0.24 -9999 0 -0.46 162 162
PRKCZ -0.08 0.18 -9999 0 -0.33 162 162
ARR3 0.02 0 -9999 0 -10000 0 0
TXA2/TP beta 0.042 0.013 -9999 0 -10000 0 0
PRKCQ -0.093 0.18 -9999 0 -0.35 163 163
MAPKKK cascade -0.11 0.22 -9999 0 -0.42 162 162
SELE -0.068 0.15 -9999 0 -0.28 163 163
TP beta/GNAI2/GDP/G beta/gamma 0.037 0.042 -9999 0 -0.29 3 3
ROCK1 0.016 0.034 -9999 0 -0.33 5 5
GNA14 0.019 0.01 -9999 0 -0.2 1 1
chemotaxis -0.16 0.3 -9999 0 -0.6 162 162
GNA12 0.018 0.017 -9999 0 -0.2 3 3
GNA13 0.02 0 -9999 0 -10000 0 0
GNA11 0.02 0 -9999 0 -10000 0 0
Rac1/GTP 0.012 0.023 -9999 0 -0.25 4 4
Signaling events mediated by PRL

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
CCNE1 -0.067 0.15 -10000 0 -0.3 145 145
mol:Halofuginone -0.002 0.04 -10000 0 -0.19 21 21
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A -0.018 0.15 -10000 0 -0.44 42 42
PRL-3/alpha Tubulin -0.017 0.096 -10000 0 -0.19 113 113
mol:Ca2+ 0.035 0.11 0.31 62 -0.14 23 85
AGT 0.004 0.057 -10000 0 -0.2 38 38
CCNA2 -0.072 0.18 -10000 0 -0.7 29 29
TUBA1B 0.018 0.023 -10000 0 -0.36 2 2
EGR1 -0.059 0.12 -10000 0 -0.27 110 110
CDK2/Cyclin E1 -0.047 0.16 -10000 0 -0.41 50 50
MAPK3 -0.021 0.091 -10000 0 -0.19 113 113
PRL-2 /Rab GGTase beta 0.012 0.071 -10000 0 -0.25 33 33
MAPK1 -0.036 0.11 -10000 0 -0.2 145 145
PTP4A1 -0.048 0.17 -10000 0 -0.78 22 22
PTP4A3 -0.046 0.13 -10000 0 -0.29 113 113
PTP4A2 0.011 0.057 -10000 0 -0.35 13 13
ITGB1 -0.021 0.091 -10000 0 -0.19 113 113
SRC 0.02 0 -10000 0 -10000 0 0
RAC1 -0.053 0.18 -10000 0 -0.44 80 80
Rab GGTase beta/Rab GGTase alpha 0.014 0.061 -10000 0 -0.22 33 33
PRL-1/ATF-5 -0.038 0.16 -10000 0 -0.73 22 22
RABGGTA 0.014 0.042 -10000 0 -0.28 10 10
BCAR1 0.035 0.1 0.21 113 -10000 0 113
RHOC -0.061 0.19 -10000 0 -0.45 87 87
RHOA -0.084 0.22 -10000 0 -0.47 108 108
cell motility -0.073 0.2 -10000 0 -0.44 94 94
PRL-1/alpha Tubulin -0.037 0.16 -10000 0 -0.71 23 23
PRL-3/alpha1 Integrin -0.03 0.091 -10000 0 -0.2 113 113
ROCK1 -0.074 0.2 -10000 0 -0.44 94 94
RABGGTB 0.004 0.074 -10000 0 -0.33 24 24
CDK2 0.015 0.032 -10000 0 -0.2 11 11
mitosis -0.048 0.17 -10000 0 -0.77 22 22
ATF5 0.016 0.03 -10000 0 -0.2 10 10
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 -0.089 0.16 -10000 0 -0.32 175 175
EPHB2 0.017 0.029 -10000 0 -0.2 9 9
EFNB1 0.025 0.008 -10000 0 -0.12 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.045 0.047 -10000 0 -0.14 16 16
Ephrin B2/EPHB1-2 -0.023 0.092 -10000 0 -0.18 123 123
neuron projection morphogenesis 0.029 0.04 -10000 0 -0.14 16 16
Ephrin B1/EPHB1-2/Tiam1 0.041 0.047 -10000 0 -0.16 15 15
DNM1 0.02 0.01 -10000 0 -0.2 1 1
cell-cell signaling 0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.097 0.21 -10000 0 -0.52 101 101
YES1 -0.15 0.3 -10000 0 -0.77 99 99
Ephrin B1/EPHB1-2/NCK2 0.05 0.034 -10000 0 -0.15 9 9
PI3K -0.11 0.22 -10000 0 -0.53 109 109
mol:GDP 0.04 0.046 -10000 0 -0.16 15 15
ITGA2B 0.02 0 -10000 0 -10000 0 0
endothelial cell proliferation -0.037 0.097 -10000 0 -0.17 175 175
FYN -0.16 0.3 -10000 0 -0.79 99 99
MAP3K7 -0.11 0.22 -10000 0 -0.56 101 101
FGR -0.14 0.3 -10000 0 -0.76 99 99
TIAM1 -0.003 0.079 -10000 0 -0.26 44 44
PIK3R1 -0.011 0.097 -10000 0 -0.3 52 52
RGS3 0.019 0.01 -10000 0 -0.2 1 1
cell adhesion -0.09 0.21 -10000 0 -0.49 103 103
LYN -0.16 0.3 -10000 0 -0.78 99 99
Ephrin B1/EPHB1-2/Src Family Kinases -0.13 0.28 -10000 0 -0.71 99 99
Ephrin B1/EPHB1-2 -0.12 0.23 -10000 0 -0.6 99 99
SRC -0.14 0.3 -10000 0 -0.76 99 99
ITGB3 0.019 0.014 -10000 0 -0.2 2 2
EPHB1 0.019 0.017 -10000 0 -0.2 3 3
EPHB4 0.02 0 -10000 0 -10000 0 0
RAC1 0.017 0.033 -10000 0 -0.36 4 4
Ephrin B2/EPHB4 -0.037 0.097 -10000 0 -0.17 175 175
alphaIIb/beta3 Integrin 0.029 0.009 -10000 0 -10000 0 0
BLK -0.14 0.3 -10000 0 -0.76 99 99
HCK -0.14 0.3 -10000 0 -0.76 99 99
regulation of stress fiber formation -0.048 0.033 0.15 9 -10000 0 9
MAPK8 -0.087 0.2 -10000 0 -0.49 101 101
Ephrin B1/EPHB1-2/RGS3 0.053 0.021 -10000 0 -10000 0 0
endothelial cell migration -0.12 0.2 -10000 0 -0.46 119 119
NCK2 0.012 0.051 -10000 0 -0.34 11 11
PTPN13 -0.1 0.19 -10000 0 -0.36 179 179
regulation of focal adhesion formation -0.048 0.033 0.15 9 -10000 0 9
chemotaxis -0.051 0.02 -10000 0 -10000 0 0
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
Rac1/GTP 0.038 0.044 -10000 0 -0.14 16 16
angiogenesis -0.11 0.23 -10000 0 -0.6 99 99
LCK -0.14 0.3 -10000 0 -0.76 99 99
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.33 0.55 -9999 0 -1.2 131 131
IL23A -0.18 0.36 -9999 0 -0.95 45 45
NF kappa B1 p50/RelA/I kappa B alpha -0.18 0.37 -9999 0 -0.78 107 107
positive regulation of T cell mediated cytotoxicity -0.2 0.38 -9999 0 -0.81 112 112
ITGA3 -0.19 0.37 -9999 0 -0.94 63 63
IL17F -0.14 0.26 -9999 0 -0.55 109 109
IL12B 0.01 0.032 -9999 0 -10000 0 0
STAT1 (dimer) -0.2 0.38 -9999 0 -0.79 115 115
CD4 -0.17 0.35 -9999 0 -0.86 58 58
IL23 -0.17 0.35 -9999 0 -0.91 46 46
IL23R -0.032 0.08 -9999 0 -0.15 56 56
IL1B -0.18 0.36 -9999 0 -0.95 49 49
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.17 0.35 -9999 0 -0.86 57 57
TYK2 -0.012 0.083 -9999 0 -0.27 42 42
STAT4 0.018 0.019 -9999 0 -0.2 4 4
STAT3 0.004 0.075 -9999 0 -0.35 23 23
IL18RAP 0.021 0.001 -9999 0 -10000 0 0
IL12RB1 0.011 0.024 -9999 0 -10000 0 0
PIK3CA -0.011 0.1 -9999 0 -0.33 48 48
IL12Rbeta1/TYK2 0.001 0.062 -9999 0 -0.2 33 33
IL23R/JAK2 -0.029 0.1 -9999 0 -0.19 35 35
positive regulation of chronic inflammatory response -0.2 0.38 -9999 0 -0.81 112 112
natural killer cell activation 0.003 0.007 -9999 0 -10000 0 0
JAK2 0.008 0.035 -9999 0 -0.2 3 3
PIK3R1 -0.011 0.097 -9999 0 -0.3 52 52
NFKB1 -0.004 0.089 -9999 0 -0.34 34 34
RELA 0.017 0.022 -9999 0 -0.26 3 3
positive regulation of dendritic cell antigen processing and presentation -0.17 0.34 -9999 0 -0.87 46 46
ALOX12B -0.17 0.34 -9999 0 -0.86 58 58
CXCL1 -0.29 0.5 -9999 0 -1.2 110 110
T cell proliferation -0.2 0.38 -9999 0 -0.81 112 112
NFKBIA -0.006 0.092 -9999 0 -0.32 40 40
IL17A -0.096 0.23 -9999 0 -0.48 76 76
PI3K -0.2 0.36 -9999 0 -0.77 114 114
IFNG 0.007 0.017 -9999 0 -10000 0 0
STAT3 (dimer) -0.18 0.36 -9999 0 -0.76 109 109
IL18R1 0.02 0.017 -9999 0 -0.2 3 3
IL23/IL23R/JAK2/TYK2/SOCS3 -0.096 0.23 -9999 0 -0.51 60 60
IL18/IL18R 0.033 0.05 -9999 0 -0.19 8 8
macrophage activation -0.013 0.016 -9999 0 -0.042 40 40
TNF -0.18 0.36 -9999 0 -0.9 58 58
STAT3/STAT4 -0.18 0.36 -9999 0 -0.76 113 113
STAT4 (dimer) -0.18 0.37 -9999 0 -0.78 112 112
IL18 -0.005 0.079 -9999 0 -0.22 59 59
IL19 -0.17 0.35 -9999 0 -0.86 58 58
STAT5A (dimer) -0.18 0.37 -9999 0 -0.78 112 112
STAT1 -0.024 0.11 -9999 0 -0.3 74 74
SOCS3 0.02 0 -9999 0 -10000 0 0
CXCL9 -0.39 0.57 -9999 0 -1.2 161 161
MPO -0.17 0.34 -9999 0 -0.86 58 58
positive regulation of humoral immune response -0.2 0.38 -9999 0 -0.81 112 112
IL23/IL23R/JAK2/TYK2 -0.2 0.39 -9999 0 -0.83 112 112
IL6 -0.18 0.35 -9999 0 -0.88 58 58
STAT5A 0.019 0.014 -9999 0 -0.2 2 2
IL2 0.025 0.005 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.003 0.007 -9999 0 -10000 0 0
CD3E -0.17 0.34 -9999 0 -0.86 58 58
keratinocyte proliferation -0.2 0.38 -9999 0 -0.81 112 112
NOS2 -0.18 0.34 -9999 0 -0.73 112 112
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.2 0.34 -10000 0 -0.72 113 113
PCK1 -0.41 0.54 -10000 0 -1.2 167 167
HNF4A -0.29 0.42 -10000 0 -0.82 176 176
KCNJ11 -0.14 0.29 -10000 0 -0.65 86 86
AKT1 -0.081 0.17 -10000 0 -0.37 76 76
response to starvation -0.033 0.049 -10000 0 -0.16 17 17
DLK1 -0.16 0.31 -10000 0 -0.72 78 78
NKX2-1 -0.068 0.15 -10000 0 -10000 0 0
ACADM -0.19 0.33 -10000 0 -0.71 108 108
TAT -0.12 0.21 -10000 0 -0.65 29 29
CEBPB 0.013 0.066 -10000 0 -0.35 17 17
CEBPA 0.008 0.068 -10000 0 -0.22 43 43
TTR -0.069 0.15 -10000 0 -0.79 3 3
PKLR -0.17 0.3 -10000 0 -0.69 82 82
APOA1 -0.42 0.59 -10000 0 -1.2 182 182
CPT1C -0.18 0.3 -10000 0 -0.63 116 116
ALAS1 -0.081 0.27 -10000 0 -1.4 15 15
TFRC -0.2 0.4 -10000 0 -1.1 68 68
FOXF1 0.01 0.022 -10000 0 -0.21 5 5
NF1 0.023 0.026 -10000 0 -0.2 1 1
HNF1A (dimer) 0.041 0.001 -10000 0 -10000 0 0
CPT1A -0.17 0.3 -10000 0 -0.66 95 95
HMGCS1 -0.17 0.3 -10000 0 -0.66 98 98
NR3C1 0 0.11 -10000 0 -0.35 49 49
CPT1B -0.17 0.3 -10000 0 -0.66 99 99
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.028 0 -10000 0 -10000 0 0
GCK -0.17 0.3 -10000 0 -0.68 87 87
CREB1 -0.047 0.092 -10000 0 -0.19 117 117
IGFBP1 -0.1 0.19 -10000 0 -0.64 21 21
PDX1 -0.029 0.15 -10000 0 -10000 0 0
UCP2 -0.21 0.35 -10000 0 -0.8 101 101
ALDOB -0.12 0.29 -10000 0 -0.71 64 64
AFP -0.002 0.045 -10000 0 -0.34 1 1
BDH1 -0.22 0.35 -10000 0 -0.75 121 121
HADH -0.15 0.33 -10000 0 -0.76 81 81
F2 -0.22 0.37 -10000 0 -0.91 68 68
HNF1A 0.041 0.001 -10000 0 -10000 0 0
G6PC -0.011 0.094 -10000 0 -10000 0 0
SLC2A2 -0.052 0.18 -10000 0 -10000 0 0
INS 0.011 0.027 0.19 5 -10000 0 5
FOXA1 0.017 0.008 -10000 0 -0.16 1 1
FOXA3 -0.039 0.092 -10000 0 -0.19 92 92
FOXA2 -0.15 0.34 -10000 0 -0.75 84 84
ABCC8 -0.12 0.29 -10000 0 -0.71 64 64
ALB -0.002 0.045 -10000 0 -0.34 1 1
Nectin adhesion pathway

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
PDGFRB 0.01 0.045 -9999 0 -0.2 23 23
alphaV beta3 Integrin 0.001 0.082 -9999 0 -0.24 51 51
PTK2 -0.065 0.16 -9999 0 -0.34 113 113
positive regulation of JNK cascade -0.052 0.11 -9999 0 -0.27 97 97
CDC42/GDP -0.032 0.16 -9999 0 -0.36 97 97
Rac1/GDP -0.031 0.16 -9999 0 -0.36 97 97
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0.015 0.039 -9999 0 -0.32 7 7
CTNNB1 0.012 0.054 -9999 0 -0.36 11 11
CDC42/GTP -0.034 0.15 -9999 0 -0.33 97 97
nectin-3/I-afadin -0.042 0.11 -9999 0 -0.24 97 97
RAPGEF1 -0.051 0.17 -9999 0 -0.4 98 98
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.065 0.19 -9999 0 -0.46 98 98
PDGFB-D/PDGFRB 0.01 0.045 -9999 0 -0.2 23 23
TLN1 -0.048 0.11 -9999 0 -0.27 82 82
Rap1/GTP -0.059 0.11 -9999 0 -0.29 99 99
IQGAP1 -0.01 0.1 -9999 0 -0.33 46 46
Rap1/GTP/I-afadin 0.023 0.021 -9999 0 -0.18 5 5
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.042 0.11 -9999 0 -0.24 97 97
PVR 0.02 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.02 0 -9999 0 -10000 0 0
mol:GDP -0.051 0.19 -9999 0 -0.44 97 97
MLLT4 0.02 0 -9999 0 -10000 0 0
PIK3CA -0.011 0.1 -9999 0 -0.33 48 48
PI3K -0.033 0.11 -9999 0 -0.27 39 39
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.029 0 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.054 0.11 -9999 0 -0.29 97 97
PVRL1 0.02 0 -9999 0 -10000 0 0
PVRL3 -0.081 0.15 -9999 0 -0.29 174 174
PVRL2 0.002 0.076 -9999 0 -0.3 30 30
PIK3R1 -0.011 0.097 -9999 0 -0.3 52 52
CDH1 0.009 0.061 -9999 0 -0.34 16 16
CLDN1 -0.044 0.12 -9999 0 -0.25 125 125
JAM-A/CLDN1 -0.051 0.12 -9999 0 -0.22 151 151
SRC -0.074 0.21 -9999 0 -0.5 97 97
ITGB3 0.019 0.014 -9999 0 -0.2 2 2
nectin-1(dimer)/I-afadin/I-afadin 0.029 0 -9999 0 -10000 0 0
FARP2 -0.053 0.19 -9999 0 -0.43 97 97
RAC1 0.017 0.033 -9999 0 -0.36 4 4
CTNNA1 0.01 0.059 -9999 0 -0.36 13 13
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.021 0.094 -9999 0 -0.2 97 97
nectin-1/I-afadin 0.029 0 -9999 0 -10000 0 0
nectin-2/I-afadin 0.017 0.054 -9999 0 -0.24 18 18
RAC1/GTP/IQGAP1/filamentous actin 0.007 0.062 -9999 0 -0.2 41 41
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.021 0.094 -9999 0 -0.2 97 97
CDC42/GTP/IQGAP1/filamentous actin 0.009 0.06 -9999 0 -0.2 37 37
F11R -0.001 0.085 -9999 0 -0.34 32 32
positive regulation of filopodium formation -0.052 0.11 -9999 0 -0.27 97 97
alphaV/beta3 Integrin/Talin -0.045 0.12 -9999 0 -0.25 95 95
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.017 0.054 -9999 0 -0.24 18 18
nectin-2(dimer)/I-afadin/I-afadin 0.017 0.054 -9999 0 -0.24 18 18
PIP5K1C -0.054 0.12 -9999 0 -0.3 75 75
VAV2 -0.053 0.19 -9999 0 -0.44 97 97
RAP1/GDP -0.061 0.13 -9999 0 -0.34 97 97
ITGAV -0.02 0.12 -9999 0 -0.34 59 59
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.031 0.1 -9999 0 -0.21 113 113
nectin-3(dimer)/I-afadin/I-afadin -0.042 0.11 -9999 0 -0.24 97 97
Rac1/GTP -0.036 0.15 -9999 0 -0.35 97 97
PTPRM -0.067 0.13 -9999 0 -0.24 157 157
E-cadherin/beta catenin/alpha catenin 0.036 0.067 -9999 0 -0.31 6 6
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.019 0.01 -9999 0 -0.2 1 1
EPHB forward signaling

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
Ephrin A5/EPHB2 0.025 0.016 -10000 0 -0.1 9 9
cell-cell adhesion 0.041 0.059 0.24 16 -10000 0 16
Ephrin B/EPHB2/RasGAP -0.02 0.1 -10000 0 -0.17 151 151
ITSN1 0.019 0.019 -10000 0 -0.28 2 2
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
SHC1 0.017 0.027 -10000 0 -0.23 6 6
Ephrin B1/EPHB3 -0.004 0.07 -10000 0 -0.2 43 43
Ephrin B1/EPHB1 0.026 0.01 -10000 0 -0.1 3 3
HRAS/GDP -0.045 0.079 -10000 0 -0.2 99 99
Ephrin B/EPHB1/GRB7 -0.013 0.096 -10000 0 -0.16 139 139
Endophilin/SYNJ1 -0.016 0.076 -10000 0 -0.14 123 123
KRAS -0.007 0.087 -10000 0 -0.27 49 49
Ephrin B/EPHB1/Src -0.003 0.089 -10000 0 -0.15 123 123
endothelial cell migration -0.044 0.11 -10000 0 -0.19 169 169
GRB2 0.012 0.053 -10000 0 -0.35 11 11
GRB7 0 0.077 -10000 0 -0.28 35 35
PAK1 -0.015 0.08 -10000 0 -0.14 128 128
HRAS 0.014 0.04 -10000 0 -0.27 10 10
RRAS -0.025 0.088 -10000 0 -0.17 128 128
DNM1 0.019 0.01 -10000 0 -0.2 1 1
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.019 0.082 -10000 0 -0.15 124 124
lamellipodium assembly -0.041 0.059 -10000 0 -0.24 16 16
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.015 0.091 -10000 0 -0.29 5 5
PIK3R1 -0.011 0.097 -10000 0 -0.3 52 52
EPHB2 0.016 0.029 -10000 0 -0.2 9 9
EPHB3 -0.033 0.12 -10000 0 -0.28 95 95
EPHB1 0.018 0.017 -10000 0 -0.2 3 3
EPHB4 0.02 0 -10000 0 -10000 0 0
mol:GDP -0.019 0.11 -10000 0 -0.22 106 106
Ephrin B/EPHB2 -0.014 0.088 -10000 0 -0.16 123 123
Ephrin B/EPHB3 -0.038 0.11 -10000 0 -0.18 158 158
JNK cascade 0.019 0.052 -10000 0 -0.15 36 36
Ephrin B/EPHB1 -0.013 0.087 -10000 0 -0.16 123 123
RAP1/GDP -0.011 0.1 -10000 0 -0.2 100 100
EFNB2 -0.089 0.16 -10000 0 -0.32 175 175
EFNB3 0.017 0.024 -10000 0 -0.2 6 6
EFNB1 0.02 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.025 0.091 -10000 0 -0.18 123 123
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.015 0.039 -10000 0 -0.32 7 7
CDC42/GTP -0.017 0.097 -10000 0 -0.29 15 15
Rap1/GTP -0.045 0.068 -10000 0 -0.25 27 27
axon guidance 0.024 0.016 -10000 0 -0.1 9 9
MAPK3 -0.003 0.081 -10000 0 -0.26 5 5
MAPK1 -0.014 0.091 -10000 0 -0.26 18 18
Rac1/GDP -0.008 0.11 -10000 0 -0.21 98 98
actin cytoskeleton reorganization -0.052 0.075 -10000 0 -0.21 66 66
CDC42/GDP -0.008 0.11 -10000 0 -0.21 97 97
PI3K -0.042 0.11 -10000 0 -0.19 169 169
EFNA5 0.02 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.038 0.097 -10000 0 -0.17 175 175
Ephrin B/EPHB2/Intersectin/N-WASP -0.015 0.088 -10000 0 -0.17 123 123
CDC42 0.019 0.01 -10000 0 -0.2 1 1
RAS family/GTP -0.063 0.085 -10000 0 -0.25 63 63
PTK2 -0.017 0.075 -10000 0 -0.32 29 29
MAP4K4 0.019 0.052 -10000 0 -0.15 36 36
SRC 0.02 0 -10000 0 -10000 0 0
KALRN 0.019 0.01 -10000 0 -0.2 1 1
Intersectin/N-WASP 0.029 0.013 -10000 0 -0.18 2 2
neuron projection morphogenesis 0 0.088 -10000 0 -0.22 21 21
MAP2K1 -0.009 0.086 -10000 0 -0.26 6 6
WASL 0.02 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.038 0.046 -10000 0 -0.17 16 16
cell migration -0.012 0.096 -10000 0 -0.25 14 14
NRAS -0.03 0.12 -10000 0 -0.29 87 87
SYNJ1 -0.016 0.077 -10000 0 -0.14 123 123
PXN 0.019 0.01 -10000 0 -0.2 1 1
TF -0.013 0.074 -10000 0 -0.14 125 125
HRAS/GTP -0.016 0.087 -10000 0 -0.26 18 18
Ephrin B1/EPHB1-2 0.036 0.018 -10000 0 -10000 0 0
cell adhesion mediated by integrin 0.053 0.078 0.18 126 -10000 0 126
RAC1 0.017 0.033 -10000 0 -0.36 4 4
mol:GTP -0.015 0.094 -10000 0 -0.15 126 126
RAC1-CDC42/GTP -0.054 0.073 -10000 0 -0.24 45 45
RASA1 -0.01 0.1 -10000 0 -0.35 44 44
RAC1-CDC42/GDP -0.001 0.11 -10000 0 -0.2 98 98
ruffle organization -0.01 0.088 -10000 0 -0.24 26 26
NCK1 0.002 0.074 -10000 0 -0.28 32 32
receptor internalization -0.011 0.073 -10000 0 -0.13 123 123
Ephrin B/EPHB2/KALRN -0.004 0.091 -10000 0 -0.15 123 123
ROCK1 -0.001 0.063 -10000 0 -0.18 47 47
RAS family/GDP -0.056 0.081 -10000 0 -0.22 66 66
Rac1/GTP -0.043 0.062 -10000 0 -0.25 16 16
Ephrin B/EPHB1/Src/Paxillin -0.014 0.087 -10000 0 -0.17 122 122
PDGFR-alpha signaling pathway

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
PDGFRA -0.032 0.11 -10000 0 -0.32 67 67
PDGF/PDGFRA/CRKL -0.004 0.077 -10000 0 -0.24 45 45
positive regulation of JUN kinase activity 0.006 0.066 -10000 0 -0.18 54 54
CRKL 0.019 0.01 -10000 0 -0.2 1 1
PDGF/PDGFRA/Caveolin-3 -0.004 0.077 -10000 0 -0.24 45 45
AP1 -0.2 0.34 -10000 0 -0.69 153 153
mol:IP3 -0.022 0.081 -10000 0 -0.24 53 53
PLCG1 -0.022 0.081 -10000 0 -0.24 53 53
PDGF/PDGFRA/alphaV Integrin -0.032 0.11 -10000 0 -0.26 92 92
RAPGEF1 0.02 0 -10000 0 -10000 0 0
CRK 0.01 0.053 -10000 0 -0.25 20 20
mol:Ca2+ -0.021 0.081 -10000 0 -0.24 53 53
CAV3 0.02 0 -10000 0 -10000 0 0
CAV1 -0.056 0.14 -10000 0 -0.3 129 129
SHC/Grb2/SOS1 0.007 0.067 -10000 0 -0.18 54 54
PDGF/PDGFRA/Shf -0.02 0.075 -10000 0 -0.21 67 67
FOS -0.21 0.33 -10000 0 -0.75 130 130
JUN -0.021 0.1 0.3 24 -0.24 47 71
oligodendrocyte development -0.032 0.11 -10000 0 -0.26 92 92
GRB2 0.012 0.053 -10000 0 -0.35 11 11
PIK3R1 -0.011 0.097 -10000 0 -0.3 52 52
mol:DAG -0.022 0.081 -10000 0 -0.24 53 53
PDGF/PDGFRA -0.032 0.11 -10000 0 -0.31 67 67
actin cytoskeleton reorganization -0.006 0.078 -10000 0 -0.22 56 56
SRF 0.015 0.061 -10000 0 -0.21 33 33
SHC1 0.017 0.027 -10000 0 -0.23 6 6
PI3K -0.025 0.11 -10000 0 -0.23 97 97
PDGF/PDGFRA/Crk/C3G 0.006 0.073 -10000 0 -0.2 48 48
JAK1 -0.022 0.093 -10000 0 -0.24 77 77
ELK1/SRF 0.003 0.071 -10000 0 -0.19 53 53
SHB 0.017 0.025 -10000 0 -0.2 7 7
SHF 0 0 -10000 0 -10000 0 0
CSNK2A1 0.009 0.088 -10000 0 -0.31 35 35
GO:0007205 -0.026 0.088 -10000 0 -0.28 45 45
SOS1 0 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.006 0.066 -10000 0 -0.18 54 54
PDGF/PDGFRA/SHB -0.006 0.078 -10000 0 -0.22 56 56
PDGF/PDGFRA/Caveolin-1 -0.056 0.13 -10000 0 -0.27 130 130
ITGAV -0.02 0.12 -10000 0 -0.34 59 59
ELK1 -0.026 0.082 -10000 0 -0.25 43 43
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
PDGF/PDGFRA/Crk -0.011 0.086 -10000 0 -0.21 71 71
JAK-STAT cascade -0.022 0.093 -10000 0 -0.24 77 77
cell proliferation -0.02 0.075 -10000 0 -0.21 67 67
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.06 0.15 -9999 0 -0.3 124 124
MAP3K8 -0.011 0.086 -9999 0 -0.25 56 56
FOS -0.033 0.098 -9999 0 -0.28 26 26
PRKCA 0.013 0.016 -9999 0 -0.22 2 2
PTPN7 0.013 0.014 -9999 0 -0.23 1 1
HRAS 0.014 0.04 -9999 0 -0.27 10 10
PRKCB -0.005 0.007 -9999 0 -0.012 233 233
NRAS -0.031 0.12 -9999 0 -0.29 87 87
RAS family/GTP -0.014 0.084 -9999 0 -0.2 67 67
MAPK3 0 0.045 -9999 0 -10000 0 0
MAP2K1 -0.011 0.055 -9999 0 -0.19 17 17
ELK1 0.012 0.016 -9999 0 -0.23 1 1
BRAF 0 0.032 -9999 0 -0.16 1 1
mol:GTP -0.001 0.002 -9999 0 -0.004 228 228
MAPK1 -0.023 0.11 -9999 0 -0.46 23 23
RAF1 -0.006 0.058 -9999 0 -0.38 9 9
KRAS -0.007 0.087 -9999 0 -0.27 49 49
BCR signaling 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
JUN -0.019 0.11 0.2 3 -0.28 57 60
IKBKB 0.001 0.076 0.2 6 -0.23 16 22
AKT1 -0.018 0.089 0.18 26 -0.19 60 86
IKBKG 0.001 0.073 0.2 1 -0.23 13 14
CALM1 -0.026 0.12 0.19 18 -0.29 67 85
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
MAP3K1 -0.03 0.13 -10000 0 -0.4 42 42
MAP3K7 0.002 0.072 -10000 0 -0.27 32 32
mol:Ca2+ -0.033 0.13 0.19 18 -0.3 69 87
DOK1 0.02 0 -10000 0 -10000 0 0
AP-1 -0.03 0.092 0.18 7 -0.19 85 92
LYN -0.031 0.13 -10000 0 -0.34 76 76
BLNK -0.033 0.12 -10000 0 -0.28 97 97
SHC1 0.017 0.027 -10000 0 -0.23 6 6
BCR complex 0.027 0.02 -10000 0 -10000 0 0
CD22 -0.049 0.13 -10000 0 -0.31 82 82
CAMK2G -0.019 0.12 0.19 18 -0.27 65 83
CSNK2A1 -0.003 0.088 -10000 0 -0.33 35 35
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.053 0.091 -10000 0 -0.3 45 45
GO:0007205 -0.034 0.13 0.19 18 -0.31 69 87
SYK -0.029 0.12 -10000 0 -0.32 79 79
ELK1 -0.026 0.12 0.19 18 -0.29 66 84
NFATC1 -0.029 0.1 -10000 0 -0.31 46 46
B-cell antigen/BCR complex 0.027 0.02 -10000 0 -10000 0 0
PAG1/CSK 0.005 0.049 -10000 0 -0.24 20 20
NFKBIB 0.005 0.044 0.1 3 -0.14 29 32
HRAS -0.023 0.12 0.18 6 -0.27 68 74
NFKBIA 0.008 0.039 0.1 3 -0.13 23 26
NF-kappa-B/RelA/I kappa B beta 0.01 0.043 0.1 3 -0.14 29 32
RasGAP/Csk -0.036 0.1 -10000 0 -0.17 172 172
mol:GDP -0.03 0.12 0.19 18 -0.29 68 86
PTEN -0.018 0.11 -10000 0 -0.35 55 55
CD79B 0.019 0.01 -10000 0 -0.2 1 1
NF-kappa-B/RelA/I kappa B alpha 0.011 0.041 0.1 3 -0.13 29 32
GRB2 0.012 0.053 -10000 0 -0.35 11 11
PI3K/BCAP/CD19 -0.063 0.16 0.24 1 -0.4 77 78
PIK3R1 -0.011 0.097 -10000 0 -0.3 52 52
mol:IP3 -0.034 0.13 0.19 18 -0.31 69 87
CSK 0.006 0.07 -10000 0 -0.35 20 20
FOS -0.072 0.14 0.19 10 -0.31 98 108
CHUK -0.009 0.09 0.2 1 -0.28 30 31
IBTK 0.011 0.057 -10000 0 -0.33 14 14
CARD11/BCL10/MALT1/TAK1 -0.032 0.12 -10000 0 -0.28 68 68
PTPN6 -0.045 0.13 -10000 0 -0.4 47 47
RELA 0.018 0.021 -10000 0 -0.26 3 3
BCL2A1 0.006 0.032 -10000 0 -0.12 9 9
VAV2 -0.045 0.13 -10000 0 -0.41 45 45
ubiquitin-dependent protein catabolic process 0.009 0.043 0.1 3 -0.13 29 32
BTK 0.009 0.009 -10000 0 -10000 0 0
CD19 -0.046 0.13 -10000 0 -0.32 79 79
MAP4K1 0.003 0.059 -10000 0 -0.2 41 41
CD72 0.02 0 -10000 0 -10000 0 0
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 -0.02 0.12 -10000 0 -0.35 39 39
SH3BP5 -0.009 0.097 -10000 0 -0.32 46 46
PIK3AP1 -0.037 0.14 0.2 18 -0.34 66 84
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.051 0.17 -10000 0 -0.36 106 106
RAF1 -0.019 0.11 0.2 3 -0.27 61 64
RasGAP/p62DOK/SHIP -0.031 0.092 -10000 0 -0.16 156 156
CD79A 0.016 0.027 -10000 0 -0.2 8 8
re-entry into mitotic cell cycle -0.03 0.092 0.18 7 -0.2 82 89
RASA1 -0.01 0.1 -10000 0 -0.35 44 44
MAPK3 -0.005 0.098 0.2 2 -0.26 39 41
MAPK1 -0.015 0.1 0.24 1 -0.27 44 45
CD72/SHP1 -0.034 0.13 -10000 0 -0.38 45 45
NFKB1 -0.003 0.088 -10000 0 -0.34 34 34
MAPK8 -0.019 0.12 -10000 0 -0.35 41 41
actin cytoskeleton organization -0.035 0.12 -10000 0 -0.36 46 46
NF-kappa-B/RelA 0.018 0.092 0.2 3 -0.23 44 47
Calcineurin -0.024 0.12 -10000 0 -0.31 51 51
PI3K -0.07 0.11 -10000 0 -0.31 76 76
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.039 0.14 0.21 18 -0.36 66 84
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.038 0.15 -10000 0 -0.53 35 35
DAPP1 -0.045 0.16 -10000 0 -0.57 35 35
cytokine secretion -0.027 0.099 0.19 1 -0.29 46 47
mol:DAG -0.034 0.13 0.19 18 -0.31 69 87
PLCG2 -0.002 0.078 -10000 0 -0.26 42 42
MAP2K1 -0.013 0.11 0.24 1 -0.28 44 45
B-cell antigen/BCR complex/FcgammaRIIB -0.04 0.099 -10000 0 -0.2 124 124
mol:PI-3-4-5-P3 -0.04 0.1 0.2 31 -0.24 58 89
ETS1 -0.012 0.11 0.18 18 -0.25 64 82
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.024 0.12 -10000 0 -0.2 135 135
B-cell antigen/BCR complex/LYN -0.053 0.14 -10000 0 -0.33 79 79
MALT1 0.008 0.057 -10000 0 -0.24 25 25
TRAF6 0.019 0.017 -10000 0 -0.36 1 1
RAC1 -0.037 0.13 -10000 0 -0.38 46 46
B-cell antigen/BCR complex/LYN/SYK -0.042 0.14 -10000 0 -0.34 69 69
CARD11 -0.032 0.12 0.18 18 -0.29 69 87
FCGR2B -0.11 0.16 -10000 0 -0.29 225 225
PPP3CA -0.013 0.11 -10000 0 -0.35 48 48
BCL10 0.001 0.082 -10000 0 -0.36 26 26
IKK complex 0.008 0.039 0.11 9 -0.095 11 20
PTPRC -0.059 0.14 -10000 0 -0.28 139 139
PDPK1 -0.015 0.079 0.17 27 -0.17 54 81
PPP3CB 0.009 0.061 -10000 0 -0.34 16 16
PPP3CC 0.02 0 -10000 0 -10000 0 0
POU2F2 0.01 0.032 -10000 0 -0.12 8 8
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.006 0.07 -9999 0 -0.24 29 29
alphaV beta3 Integrin 0.015 0.071 -9999 0 -0.2 52 52
PTK2 0.008 0.12 -9999 0 -0.36 28 28
IGF1R -0.055 0.15 -9999 0 -0.33 115 115
PI4KB 0.018 0.019 -9999 0 -0.2 4 4
MFGE8 -0.053 0.14 -9999 0 -0.3 124 124
SRC 0.02 0 -9999 0 -10000 0 0
CDKN1B -0.022 0.13 -9999 0 -0.38 58 58
VEGFA -0.009 0.092 -9999 0 -0.28 51 51
ILK 0.018 0.051 -9999 0 -0.35 6 6
ROCK1 0.016 0.034 -9999 0 -0.33 5 5
AKT1 0.015 0.059 -9999 0 -0.29 10 10
PTK2B 0.003 0.073 -9999 0 -0.16 79 79
alphaV/beta3 Integrin/JAM-A 0.021 0.078 -9999 0 -0.17 73 73
CBL 0.02 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.015 0.071 -9999 0 -0.2 51 51
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.074 0.13 -9999 0 -0.23 185 185
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.001 0.09 -9999 0 -0.32 17 17
alphaV/beta3 Integrin/Syndecan-1 -0.031 0.11 -9999 0 -0.22 117 117
PI4KA -0.008 0.09 -9999 0 -0.28 50 50
IGF-1R heterotetramer/IGF1/IRS1 -0.1 0.14 -9999 0 -0.31 139 139
PI4 Kinase 0.009 0.064 -9999 0 -0.24 23 23
PIK3CA -0.011 0.1 -9999 0 -0.33 48 48
alphaV/beta3 Integrin/Osteopontin -0.022 0.11 -9999 0 -0.23 114 114
RPS6KB1 -0.094 0.14 -9999 0 -0.29 139 139
TLN1 0.012 0.049 -9999 0 -0.29 13 13
MAPK3 -0.049 0.15 -9999 0 -0.43 57 57
GPR124 0.013 0.037 -9999 0 -0.2 15 15
MAPK1 -0.056 0.16 -9999 0 -0.44 60 60
PXN 0.019 0.01 -9999 0 -0.2 1 1
PIK3R1 -0.011 0.097 -9999 0 -0.3 52 52
alphaV/beta3 Integrin/Tumstatin 0.015 0.071 -9999 0 -0.2 51 51
cell adhesion -0.026 0.12 -9999 0 -0.21 131 131
ANGPTL3 0.02 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.02 0.06 -9999 0 -0.2 29 29
IGF-1R heterotetramer -0.054 0.15 -9999 0 -0.33 115 115
Rac1/GDP 0.013 0.023 -9999 0 -0.25 4 4
TGFBR2 0.012 0.05 -9999 0 -0.31 12 12
ITGB3 0.019 0.014 -9999 0 -0.2 2 2
IGF1 -0.07 0.14 -9999 0 -0.27 166 166
RAC1 0.017 0.033 -9999 0 -0.36 4 4
regulation of cell-matrix adhesion 0.011 0.072 -9999 0 -0.2 51 51
apoptosis -0.02 0.11 -9999 0 -0.34 59 59
CD47 -0.003 0.09 -9999 0 -0.35 34 34
alphaV/beta3 Integrin/CD47 0.002 0.094 -9999 0 -0.22 72 72
VCL 0.018 0.023 -9999 0 -0.36 2 2
alphaV/beta3 Integrin/Del1 0.015 0.071 -9999 0 -0.2 51 51
CSF1 0.019 0.014 -9999 0 -0.2 2 2
PIK3C2A 0.011 0.032 -9999 0 -10000 0 0
PI4 Kinase/Pyk2 -0.027 0.051 -9999 0 -0.23 11 11
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.009 0.085 -9999 0 -0.18 79 79
FAK1/Vinculin 0.018 0.11 -9999 0 -0.3 28 28
alphaV beta3/Integrin/ppsTEM5 0.012 0.073 -9999 0 -0.2 51 51
RHOA -0.008 0.1 -9999 0 -0.36 39 39
VTN 0.02 0 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 0.019 0.01 -9999 0 -0.2 1 1
F11R 0.01 0.06 -9999 0 -0.24 26 26
alphaV/beta3 Integrin/Lactadherin -0.028 0.11 -9999 0 -0.22 117 117
alphaV/beta3 Integrin/TGFBR2 0.011 0.078 -9999 0 -0.2 57 57
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.016 0.064 -9999 0 -0.18 51 51
HSP90AA1 0.02 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.012 0.069 -9999 0 -0.18 60 60
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.057 0.14 -9999 0 -0.31 126 126
alphaV/beta3 Integrin/Pyk2 0.012 0.077 -9999 0 -0.16 79 79
SDC1 -0.059 0.14 -9999 0 -0.3 135 135
VAV3 -0.066 0.1 -9999 0 -0.19 168 168
PTPN11 0.02 0 -9999 0 -10000 0 0
IRS1 -0.046 0.13 -9999 0 -0.28 118 118
FAK1/Paxillin 0.019 0.11 -9999 0 -0.29 28 28
cell migration 0.024 0.1 -9999 0 -0.27 27 27
ITGAV -0.02 0.12 -9999 0 -0.34 59 59
PI3K 0.001 0.1 -9999 0 -0.3 28 28
SPP1 -0.044 0.14 -9999 0 -0.34 95 95
KDR 0.015 0.033 -9999 0 -0.2 12 12
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 -0.02 0.12 -9999 0 -0.34 59 59
COL4A3 0.02 0 -9999 0 -10000 0 0
angiogenesis -0.049 0.16 -9999 0 -0.47 54 54
Rac1/GTP -0.053 0.097 -9999 0 -0.17 172 172
EDIL3 0.02 0 -9999 0 -10000 0 0
cell proliferation 0.011 0.078 -9999 0 -0.2 57 57
IL2 signaling events mediated by PI3K

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 0.015 0.087 -10000 0 -10000 0 0
UGCG -0.042 0.19 -10000 0 -0.75 34 34
AKT1/mTOR/p70S6K/Hsp90/TERT -0.027 0.15 -10000 0 -0.31 82 82
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.042 0.19 -10000 0 -0.74 34 34
mol:DAG -0.1 0.3 -10000 0 -0.94 59 59
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.044 0.19 -10000 0 -0.36 118 118
FRAP1 -0.058 0.21 -10000 0 -0.42 118 118
FOXO3 -0.063 0.21 -10000 0 -0.42 118 118
AKT1 -0.071 0.22 -10000 0 -0.45 119 119
GAB2 -0.032 0.12 -10000 0 -0.31 81 81
SMPD1 0.006 0.037 -10000 0 -10000 0 0
SGMS1 -0.076 0.24 -10000 0 -0.72 59 59
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 -0.018 0.079 -10000 0 -0.21 66 66
CALM1 0.019 0.019 -10000 0 -0.28 2 2
cell proliferation -0.11 0.27 -10000 0 -0.43 148 148
EIF3A 0.009 0.063 -10000 0 -0.36 15 15
PI3K -0.013 0.098 -10000 0 -0.25 66 66
RPS6KB1 -0.01 0.069 -10000 0 -10000 0 0
mol:sphingomyelin -0.1 0.3 -10000 0 -0.94 59 59
natural killer cell activation -0.002 0.004 -10000 0 -0.009 114 114
JAK3 0.02 0.004 -10000 0 -10000 0 0
PIK3R1 -0.011 0.098 -10000 0 -0.3 52 52
JAK1 0.002 0.081 -10000 0 -0.37 25 25
NFKB1 -0.003 0.088 -10000 0 -0.34 34 34
MYC -0.16 0.39 -10000 0 -0.93 106 106
MYB -0.099 0.34 -10000 0 -1.2 47 47
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.033 0.16 -10000 0 -0.33 79 79
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.006 0.076 -10000 0 -0.32 1 1
mol:PI-3-4-5-P3 -0.032 0.15 -10000 0 -0.32 79 79
Rac1/GDP -0.006 0.076 -10000 0 -0.19 69 69
T cell proliferation -0.03 0.14 -10000 0 -0.3 79 79
SHC1 0.015 0.028 -10000 0 -0.24 6 6
RAC1 0.017 0.033 -10000 0 -0.36 4 4
positive regulation of cyclin-dependent protein kinase activity -0.005 0.021 -10000 0 -0.039 127 127
PRKCZ -0.032 0.15 -10000 0 -0.31 79 79
NF kappa B1 p50/RelA -0.043 0.2 -10000 0 -0.38 121 121
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.007 0.093 -10000 0 -0.34 16 16
HSP90AA1 0.02 0 -10000 0 -10000 0 0
RELA 0.018 0.021 -10000 0 -0.26 3 3
IL2RA 0.018 0.004 -10000 0 -10000 0 0
IL2RB 0.002 0.062 -10000 0 -0.2 44 44
TERT 0.02 0 -10000 0 -10000 0 0
E2F1 -0.028 0.13 -10000 0 -0.43 47 47
SOS1 -0.001 0.004 -10000 0 -0.009 111 111
RPS6 0.018 0.029 -10000 0 -0.36 3 3
mol:cAMP 0.002 0.01 0.018 127 -10000 0 127
PTPN11 0.018 0.005 -10000 0 -10000 0 0
IL2RG -0.006 0.073 -10000 0 -0.2 64 64
actin cytoskeleton organization -0.03 0.14 -10000 0 -0.3 79 79
GRB2 0.011 0.053 -10000 0 -0.35 11 11
IL2 0.02 0.005 -10000 0 -10000 0 0
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
Rac1/GTP 0.001 0.077 -10000 0 -0.18 69 69
LCK 0.016 0.031 -10000 0 -0.2 10 10
BCL2 -0.034 0.17 -10000 0 -0.39 58 58
Class I PI3K 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
ARF5/GTP 0.003 0.089 0.2 36 -0.17 72 108
DAPP1 -0.013 0.092 -10000 0 -0.28 26 26
Src family/SYK family/BLNK-LAT/BTK-ITK -0.042 0.15 -10000 0 -0.36 67 67
mol:DAG -0.006 0.089 0.18 25 -0.18 51 76
HRAS 0.014 0.04 -10000 0 -0.27 10 10
RAP1A 0.015 0.04 -10000 0 -0.32 7 7
ARF5/GDP 0.012 0.063 -10000 0 -0.19 31 31
PLCG2 -0.002 0.078 -10000 0 -0.26 42 42
PLCG1 0.02 0 -10000 0 -10000 0 0
ARF5 0.009 0.059 -10000 0 -0.31 17 17
mol:GTP -0.013 0.084 0.19 39 -0.18 60 99
ARF1/GTP -0.003 0.084 0.19 34 -0.18 60 94
RHOA -0.008 0.1 -10000 0 -0.36 39 39
YES1 0 0.082 -10000 0 -0.33 30 30
RAP1A/GTP 0.001 0.086 0.19 37 -0.18 60 97
ADAP1 -0.013 0.08 0.18 39 -0.17 60 99
ARAP3 -0.013 0.083 0.19 39 -0.18 60 99
INPPL1 0.014 0.041 -10000 0 -0.29 9 9
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 -0.002 0.079 -10000 0 -0.27 41 41
ARHGEF7 0.017 0.027 -10000 0 -0.28 4 4
ARF1 0.014 0.046 -10000 0 -0.36 8 8
NRAS -0.029 0.12 -10000 0 -0.29 87 87
FYN -0.049 0.13 -10000 0 -0.28 122 122
ARF6 0.017 0.033 -10000 0 -0.36 4 4
FGR 0.012 0.04 -10000 0 -0.2 18 18
mol:Ca2+ -0.002 0.045 -10000 0 -0.12 16 16
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.003 0.079 -10000 0 -0.26 44 44
ZAP70 0.02 0 -10000 0 -10000 0 0
mol:IP3 -0.006 0.06 -10000 0 -0.14 41 41
LYN -0.031 0.13 -10000 0 -0.34 76 76
ARF1/GDP 0.013 0.061 -10000 0 -0.21 22 22
RhoA/GDP 0 0.1 0.2 32 -0.26 31 63
PDK1/Src/Hsp90 0.04 0 -10000 0 -10000 0 0
BLNK -0.033 0.12 -10000 0 -0.28 97 97
actin cytoskeleton reorganization 0.004 0.093 0.2 32 -0.24 30 62
SRC 0.02 0 -10000 0 -10000 0 0
PLEKHA2 0.01 0.032 -10000 0 -0.2 5 5
RAC1 0.017 0.033 -10000 0 -0.36 4 4
PTEN -0.015 0.11 -10000 0 -0.32 55 55
HSP90AA1 0.02 0 -10000 0 -10000 0 0
ARF6/GTP 0.007 0.086 0.2 37 -0.17 62 99
RhoA/GTP -0.005 0.099 0.19 36 -0.18 88 124
Src family/SYK family/BLNK-LAT -0.041 0.14 -10000 0 -0.36 60 60
BLK 0.019 0.014 -10000 0 -0.2 2 2
PDPK1 0.02 0 -10000 0 -10000 0 0
CYTH1 -0.013 0.08 0.18 39 -0.17 60 99
HCK -0.004 0.072 -10000 0 -0.21 56 56
CYTH3 -0.013 0.08 0.18 39 -0.17 60 99
CYTH2 -0.013 0.08 0.18 39 -0.17 60 99
KRAS -0.007 0.087 -10000 0 -0.27 49 49
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.018 0.057 0.15 34 -0.18 6 40
SGK1 0.017 0.055 0.15 37 -0.17 8 45
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.004 0.059 -10000 0 -0.2 27 27
SOS1 0 0 -10000 0 -10000 0 0
SYK -0.029 0.12 -10000 0 -0.32 79 79
ARF6/GDP 0.007 0.085 0.2 33 -0.24 19 52
mol:PI-3-4-5-P3 -0.011 0.088 0.2 41 -0.18 60 101
ARAP3/RAP1A/GTP 0.001 0.087 0.19 37 -0.18 60 97
VAV1 0.015 0.032 -10000 0 -0.2 11 11
mol:PI-3-4-P2 0.009 0.028 -10000 0 -0.2 9 9
RAS family/GTP/PI3K Class I 0.009 0.089 0.19 37 -0.18 60 97
PLEKHA1 0.006 0.047 -10000 0 -0.2 23 23
Rac1/GDP 0.014 0.059 -10000 0 -0.18 28 28
LAT 0.019 0.014 -10000 0 -0.2 2 2
Rac1/GTP 0.007 0.075 -10000 0 -0.25 34 34
ITK 0.004 0.083 0.2 36 -0.17 58 94
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.014 0.12 0.21 19 -0.25 53 72
LCK 0.016 0.03 -10000 0 -0.2 10 10
BTK 0.004 0.083 0.2 36 -0.17 60 96
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.016 0.054 -9999 0 -0.18 35 35
VLDLR -0.046 0.13 -9999 0 -0.28 117 117
CRKL 0.019 0.01 -9999 0 -0.2 1 1
LRPAP1 -0.004 0.087 -9999 0 -0.31 38 38
FYN -0.049 0.13 -9999 0 -0.28 122 122
ITGA3 0.002 0.07 -9999 0 -0.26 35 35
RELN/VLDLR/Fyn -0.054 0.12 -9999 0 -0.23 137 137
MAPK8IP1/MKK7/MAP3K11/JNK1 0.057 0.019 -9999 0 -0.15 3 3
AKT1 -0.035 0.11 -9999 0 -0.21 118 118
MAP2K7 0.02 0 -9999 0 -10000 0 0
RAPGEF1 0.02 0 -9999 0 -10000 0 0
DAB1 0.02 0 -9999 0 -10000 0 0
RELN/LRP8/DAB1 0.009 0.062 -9999 0 -0.19 24 24
LRPAP1/LRP8 -0.007 0.083 -9999 0 -0.25 37 37
RELN/LRP8/DAB1/Fyn -0.016 0.091 -9999 0 -0.18 93 93
DAB1/alpha3/beta1 Integrin -0.024 0.091 -9999 0 -0.25 33 33
long-term memory -0.003 0.089 -9999 0 -0.24 20 20
DAB1/LIS1 -0.015 0.096 -9999 0 -0.2 56 56
DAB1/CRLK/C3G -0.016 0.086 -9999 0 -0.26 21 21
PIK3CA -0.011 0.1 -9999 0 -0.33 48 48
DAB1/NCK2 -0.016 0.099 -9999 0 -0.2 54 54
ARHGEF2 0.019 0.01 -9999 0 -0.2 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A 0.016 0.029 -9999 0 -0.2 9 9
CDK5R1 0.02 0 -9999 0 -10000 0 0
RELN -0.006 0.072 -9999 0 -0.2 63 63
PIK3R1 -0.011 0.097 -9999 0 -0.3 52 52
RELN/LRP8/Fyn -0.032 0.1 -9999 0 -0.22 93 93
GRIN2A/RELN/LRP8/DAB1/Fyn -0.008 0.094 -9999 0 -0.18 95 95
MAPK8 0.02 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.012 0.081 -9999 0 -0.18 72 72
ITGB1 0.02 0 -9999 0 -10000 0 0
MAP1B -0.051 0.1 -9999 0 -0.19 158 158
RELN/LRP8 -0.006 0.083 -9999 0 -0.21 49 49
GRIN2B/RELN/LRP8/DAB1/Fyn -0.006 0.093 -9999 0 -0.18 93 93
PI3K -0.014 0.098 -9999 0 -0.25 66 66
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.017 0.049 -9999 0 -0.24 11 11
RAP1A -0.01 0.084 -9999 0 -0.25 23 23
PAFAH1B1 0.015 0.033 -9999 0 -0.2 12 12
MAPK8IP1 0.019 0.01 -9999 0 -0.2 1 1
CRLK/C3G 0.029 0.007 -9999 0 -10000 0 0
GRIN2B 0.02 0 -9999 0 -10000 0 0
NCK2 0.012 0.051 -9999 0 -0.34 11 11
neuron differentiation 0.009 0.067 -9999 0 -0.24 9 9
neuron adhesion -0.006 0.086 -9999 0 -0.22 35 35
LRP8 -0.009 0.084 -9999 0 -0.24 60 60
GSK3B -0.035 0.11 -9999 0 -0.3 51 51
RELN/VLDLR/DAB1/Fyn -0.035 0.1 -9999 0 -0.19 137 137
MAP3K11 0.017 0.032 -9999 0 -0.3 5 5
RELN/VLDLR/DAB1/P13K -0.035 0.11 -9999 0 -0.21 115 115
CDK5 0 0.077 -9999 0 -0.28 35 35
MAPT 0.017 0.016 -9999 0 -10000 0 0
neuron migration -0.046 0.12 -9999 0 -0.26 83 83
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.009 0.068 -9999 0 -0.24 9 9
RELN/VLDLR -0.028 0.11 -9999 0 -0.2 119 119
Arf6 downstream 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
PLAUR -0.081 0.31 -10000 0 -0.96 56 56
regulation of axonogenesis -0.009 0.061 0.35 5 -10000 0 5
myoblast fusion 0.023 0.13 0.39 56 -10000 0 56
mol:GTP -0.012 0.078 -10000 0 -0.23 52 52
regulation of calcium-dependent cell-cell adhesion 0.009 0.093 0.23 69 -10000 0 69
ARF1/GTP 0.003 0.071 -10000 0 -0.19 56 56
mol:GM1 -0.008 0.059 -10000 0 -0.18 52 52
mol:Choline 0.01 0.053 -10000 0 -0.26 5 5
lamellipodium assembly -0.025 0.15 -10000 0 -0.43 58 58
MAPK3 -0.008 0.11 -10000 0 -0.3 58 58
ARF6/GTP/NME1/Tiam1 -0.009 0.094 -10000 0 -0.23 69 69
ARF1 0.014 0.046 -10000 0 -0.36 8 8
ARF6/GDP -0.023 0.13 -10000 0 -0.39 56 56
ARF1/GDP -0.015 0.13 -10000 0 -0.36 59 59
ARF6 0.004 0.054 -10000 0 -0.14 50 50
RAB11A 0.012 0.052 -10000 0 -0.32 12 12
TIAM1 -0.006 0.081 -10000 0 -0.26 44 44
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.024 0.12 -10000 0 -0.3 79 79
actin filament bundle formation 0.029 0.14 0.36 70 -10000 0 70
KALRN -0.012 0.1 -10000 0 -0.3 56 56
RAB11FIP3/RAB11A 0.023 0.038 -10000 0 -0.24 9 9
RhoA/GDP -0.029 0.14 -10000 0 -0.36 70 70
NME1 -0.003 0.01 -10000 0 -10000 0 0
Rac1/GDP -0.017 0.13 -10000 0 -0.36 58 58
substrate adhesion-dependent cell spreading -0.012 0.078 -10000 0 -0.23 52 52
cortical actin cytoskeleton organization -0.025 0.15 -10000 0 -0.43 58 58
RAC1 0.017 0.033 -10000 0 -0.36 4 4
liver development -0.012 0.078 -10000 0 -0.23 52 52
ARF6/GTP -0.012 0.079 -10000 0 -0.23 52 52
RhoA/GTP -0.012 0.091 -10000 0 -0.21 85 85
mol:GDP -0.023 0.13 -10000 0 -0.39 58 58
ARF6/GTP/RAB11FIP3/RAB11A 0.015 0.065 -10000 0 -0.23 15 15
RHOA -0.008 0.1 -10000 0 -0.36 39 39
PLD1 0.003 0.061 -10000 0 -0.17 52 52
RAB11FIP3 0.019 0.014 -10000 0 -0.2 2 2
tube morphogenesis -0.025 0.15 -10000 0 -0.43 58 58
ruffle organization 0.009 0.061 -10000 0 -0.35 5 5
regulation of epithelial cell migration -0.012 0.078 -10000 0 -0.23 52 52
PLD2 0.004 0.061 -10000 0 -0.17 52 52
PIP5K1A 0.009 0.061 -10000 0 -0.35 5 5
mol:Phosphatidic acid 0.01 0.053 -10000 0 -0.26 5 5
Rac1/GTP -0.025 0.15 -10000 0 -0.43 58 58
ErbB2/ErbB3 signaling events

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
USP8 -0.001 0.063 -10000 0 -0.22 35 35
RAS family/GTP -0.03 0.11 -10000 0 -0.24 82 82
NFATC4 -0.004 0.077 0.18 10 -0.22 20 30
ERBB2IP 0.005 0.073 -10000 0 -0.35 22 22
HSP90 (dimer) 0.02 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.018 0.09 0.21 6 -0.21 47 53
JUN -0.001 0.072 -10000 0 -10000 0 0
HRAS 0.014 0.04 -10000 0 -0.27 10 10
DOCK7 -0.02 0.085 0.19 9 -0.2 48 57
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.001 0.087 0.22 13 -0.18 80 93
AKT1 0.001 0.049 -10000 0 -0.19 30 30
BAD 0.005 0.049 -10000 0 -0.19 24 24
MAPK10 0.002 0.056 0.14 10 -0.15 24 34
mol:GTP -0.001 0.001 -10000 0 -0.004 29 29
ErbB2/ErbB3/neuregulin 1 beta -0.017 0.098 0.21 9 -0.23 47 56
RAF1 -0.031 0.12 -10000 0 -0.25 81 81
ErbB2/ErbB3/neuregulin 2 -0.011 0.086 0.22 13 -0.19 80 93
STAT3 -0.012 0.19 -10000 0 -0.97 21 21
cell migration 0.006 0.06 0.16 9 -0.16 20 29
mol:PI-3-4-5-P3 -0.001 0.002 0.003 10 -0.004 90 100
cell proliferation -0.092 0.23 -10000 0 -0.54 71 71
FOS -0.11 0.22 -10000 0 -0.44 148 148
NRAS -0.03 0.12 -10000 0 -0.29 87 87
mol:Ca2+ -0.018 0.09 0.21 6 -0.21 47 53
MAPK3 -0.059 0.18 -10000 0 -0.48 49 49
MAPK1 -0.075 0.19 -10000 0 -0.49 63 63
JAK2 -0.01 0.088 0.2 10 -0.22 34 44
NF2 0.016 0.01 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.015 0.09 -10000 0 -0.21 83 83
NRG1 0.019 0.002 -10000 0 -10000 0 0
GRB2/SOS1 0.009 0.037 -10000 0 -0.24 11 11
MAPK8 -0.012 0.099 0.19 9 -0.22 83 92
MAPK9 0.001 0.058 0.14 9 -0.16 26 35
ERBB2 0.008 0.064 0.32 20 -10000 0 20
ERBB3 -0.059 0.15 -10000 0 -0.31 127 127
SHC1 0.017 0.027 -10000 0 -0.23 6 6
RAC1 0.017 0.033 -10000 0 -0.36 4 4
apoptosis 0.001 0.057 0.26 19 -10000 0 19
STAT3 (dimer) -0.011 0.19 -10000 0 -0.94 21 21
RNF41 0.003 0.058 -10000 0 -0.19 38 38
FRAP1 0.008 0.04 -10000 0 -0.2 14 14
RAC1-CDC42/GTP -0.028 0.053 -10000 0 -0.21 18 18
ErbB2/ErbB2/HSP90 (dimer) 0.021 0.043 0.23 20 -10000 0 20
CHRNA1 -0.041 0.14 -10000 0 -0.36 46 46
myelination -0.001 0.078 0.19 10 -0.23 18 28
PPP3CB -0.012 0.086 0.19 10 -0.26 20 30
KRAS -0.007 0.087 -10000 0 -0.27 49 49
RAC1-CDC42/GDP 0.006 0.085 -10000 0 -0.17 82 82
NRG2 0.018 0.017 -10000 0 -0.2 3 3
mol:GDP -0.015 0.089 -10000 0 -0.21 83 83
SOS1 0 0.001 -10000 0 -0.003 14 14
MAP2K2 -0.031 0.12 -10000 0 -0.25 80 80
SRC 0.02 0 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -0.004 17 17
PTPN11 -0.01 0.088 0.2 10 -0.23 30 40
MAP2K1 -0.071 0.18 -10000 0 -0.45 58 58
heart morphogenesis -0.018 0.09 0.21 6 -0.21 47 53
RAS family/GDP -0.025 0.12 -10000 0 -0.24 81 81
GRB2 0.012 0.053 -10000 0 -0.35 11 11
PRKACA 0.001 0.006 -10000 0 -10000 0 0
CHRNE 0.009 0.019 -10000 0 -0.079 1 1
HSP90AA1 0.02 0 -10000 0 -10000 0 0
activation of caspase activity -0.001 0.049 0.19 30 -10000 0 30
nervous system development -0.018 0.09 0.21 6 -0.21 47 53
CDC42 0.019 0.01 -10000 0 -0.2 1 1
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.013 0.064 -10000 0 -0.24 29 29
ATM 0.012 0.046 -10000 0 -0.26 14 14
UBE2D3 0.01 0.059 -10000 0 -0.36 13 13
PRKDC -0.006 0.091 -10000 0 -0.31 41 41
ATR 0.014 0.046 -10000 0 -0.36 8 8
UBE2L3 0.013 0.047 -10000 0 -0.28 13 13
FANCD2 0.011 0.044 -10000 0 -0.26 13 13
protein ubiquitination -0.008 0.093 -10000 0 -0.17 109 109
XRCC5 0.008 0.066 -10000 0 -0.36 17 17
XRCC6 0.018 0.025 -10000 0 -0.31 3 3
M/R/N Complex 0.031 0.042 -10000 0 -0.2 15 15
MRE11A 0.02 0 -10000 0 -10000 0 0
DNA-PK 0.017 0.076 -10000 0 -0.23 39 39
FA complex/FANCD2/Ubiquitin 0.002 0.1 -10000 0 -0.34 36 36
FANCF -0.004 0.088 -10000 0 -0.32 37 37
BRCA1 0.018 0.017 -10000 0 -0.2 3 3
CCNE1 -0.067 0.15 -10000 0 -0.3 145 145
CDK2/Cyclin E1 -0.035 0.1 -10000 0 -0.19 156 156
FANCG -0.011 0.099 -10000 0 -0.31 50 50
BRCA1/BACH1/BARD1 0.016 0.057 -10000 0 -0.24 22 22
FANCE 0.015 0.032 -10000 0 -0.2 11 11
FANCC 0.02 0 -10000 0 -10000 0 0
NBN 0.008 0.063 -10000 0 -0.31 19 19
FANCA 0.02 0 -10000 0 -10000 0 0
DNA repair 0.003 0.1 -10000 0 -0.31 35 35
BRCA1/BARD1/ubiquitin 0.016 0.057 -10000 0 -0.24 22 22
BARD1/DNA-PK 0.019 0.09 -10000 0 -0.22 54 54
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.013 0.064 0.24 29 -10000 0 29
BRCA1/BARD1/CTIP/M/R/N Complex 0.012 0.073 -10000 0 -0.3 15 15
BRCA1/BACH1/BARD1/TopBP1 0.015 0.075 -10000 0 -0.22 45 45
BRCA1/BARD1/P53 -0.029 0.11 -10000 0 -0.18 168 168
BARD1/CSTF1/BRCA1 0.025 0.056 -10000 0 -0.2 29 29
BRCA1/BACH1 0.018 0.017 -10000 0 -0.2 3 3
BARD1 0.002 0.079 -10000 0 -0.33 28 28
PCNA -0.006 0.091 -10000 0 -0.32 40 40
BRCA1/BARD1/UbcH5C 0.023 0.061 -10000 0 -0.2 34 34
BRCA1/BARD1/UbcH7 0.024 0.056 -10000 0 -0.2 28 28
BRCA1/BARD1/RAD51/PCNA 0.026 0.073 -10000 0 -0.19 46 46
BARD1/DNA-PK/P53 -0.034 0.12 -10000 0 -0.18 188 188
BRCA1/BARD1/Ubiquitin 0.016 0.057 -10000 0 -0.24 22 22
BRCA1/BARD1/CTIP 0.008 0.081 -10000 0 -0.2 61 61
FA complex 0.009 0.074 -10000 0 -0.2 35 35
BARD1/EWS 0.016 0.056 -10000 0 -0.22 28 28
RBBP8 -0.007 0.081 -10000 0 -0.24 47 47
TP53 -0.096 0.17 -10000 0 -0.34 175 175
TOPBP1 -0.002 0.087 -10000 0 -0.34 33 33
G1/S transition of mitotic cell cycle 0.03 0.11 0.18 168 -10000 0 168
BRCA1/BARD1 -0.005 0.096 -10000 0 -0.17 109 109
CSTF1 0.014 0.045 -10000 0 -0.34 8 8
BARD1/EWS-Fli1 0.002 0.055 -10000 0 -0.23 28 28
CDK2 0.015 0.032 -10000 0 -0.2 11 11
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.019 0.01 -10000 0 -0.2 1 1
RAD50 0.017 0.029 -10000 0 -0.27 5 5
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.016 0.057 -10000 0 -0.24 22 22
EWSR1 0.02 0 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.052 0.31 -10000 0 -0.8 53 53
CRP -0.052 0.31 -10000 0 -0.81 52 52
cell cycle arrest -0.082 0.38 -10000 0 -0.98 58 58
TIMP1 -0.076 0.33 -10000 0 -0.79 75 75
IL6ST 0.02 0.026 -10000 0 -0.24 4 4
Rac1/GDP 0.022 0.12 0.26 1 -0.32 28 29
AP1 -0.049 0.19 -10000 0 -0.44 72 72
GAB2 -0.027 0.12 -10000 0 -0.31 81 81
TNFSF11 -0.052 0.31 -10000 0 -0.8 54 54
HSP90B1 -0.008 0.24 -10000 0 -1.2 20 20
GAB1 0.022 0.004 -10000 0 -10000 0 0
MAPK14 0.035 0.067 -10000 0 -0.3 2 2
AKT1 -0.006 0.13 -10000 0 -0.36 35 35
FOXO1 -0.019 0.14 -10000 0 -0.37 43 43
MAP2K6 0.026 0.083 0.24 1 -0.25 26 27
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 0.016 0.16 -10000 0 -0.37 39 39
MITF 0.016 0.1 0.26 1 -0.29 30 31
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 -0.002 0.078 -10000 0 -0.26 42 42
A2M -0.14 0.42 -10000 0 -1.3 61 61
CEBPB 0.016 0.068 -10000 0 -0.36 17 17
GRB2/SOS1/GAB family/SHP2 0.008 0.12 0.23 8 -0.34 48 56
STAT3 -0.096 0.42 -10000 0 -1.1 58 58
STAT1 -0.06 0.25 -10000 0 -0.89 43 43
CEBPD -0.069 0.35 -10000 0 -0.92 58 58
PIK3CA -0.01 0.1 -10000 0 -0.33 48 48
PI3K -0.012 0.098 -10000 0 -0.25 66 66
JUN -0.011 0.099 -10000 0 -0.31 51 51
PIAS3/MITF 0.018 0.1 0.24 1 -0.28 28 29
MAPK11 0.036 0.067 -10000 0 -0.3 2 2
STAT3 (dimer)/FOXO1 -0.087 0.35 -10000 0 -0.75 85 85
GRB2/SOS1/GAB family 0.025 0.096 0.21 5 -0.26 26 31
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK 0.018 0.081 -10000 0 -0.24 30 30
GRB2 0.014 0.053 -10000 0 -0.35 11 11
JAK2 0.018 0.017 -10000 0 -0.2 3 3
LBP -0.027 0.26 -10000 0 -0.68 43 43
PIK3R1 -0.01 0.098 -10000 0 -0.3 52 52
JAK1 0.004 0.083 -10000 0 -0.37 25 25
MYC -0.17 0.46 -10000 0 -0.96 125 125
FGG -0.052 0.31 -10000 0 -0.82 52 52
macrophage differentiation -0.082 0.38 -10000 0 -0.98 58 58
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.041 0.061 -10000 0 -0.19 12 12
JUNB -0.082 0.36 -10000 0 -0.93 62 62
FOS -0.11 0.16 -10000 0 -0.29 233 233
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.016 0.11 0.27 1 -0.31 29 30
STAT1/PIAS1 -0.004 0.15 0.28 1 -0.34 59 60
GRB2/SOS1/GAB family/SHP2/PI3K -0.008 0.12 -10000 0 -0.27 80 80
STAT3 (dimer) -0.094 0.41 -10000 0 -1.1 58 58
PRKCD -0.004 0.22 -10000 0 -0.48 56 56
IL6R 0.017 0.033 -10000 0 -0.2 12 12
SOCS3 0.041 0.056 -10000 0 -10000 0 0
gp130 (dimer)/JAK1/JAK1/LMO4 0.028 0.074 -10000 0 -0.21 39 39
Rac1/GTP 0.018 0.13 -10000 0 -0.34 31 31
HCK -0.004 0.072 -10000 0 -0.21 56 56
MAPKKK cascade -0.011 0.17 -10000 0 -0.48 55 55
bone resorption -0.045 0.3 -10000 0 -0.75 54 54
IRF1 -0.12 0.42 -10000 0 -1 81 81
mol:GDP 0.017 0.11 0.26 1 -0.3 28 29
SOS1 0.003 0.006 -10000 0 -10000 0 0
VAV1 0.017 0.11 0.26 1 -0.3 28 29
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.03 0.081 -10000 0 -0.29 26 26
PTPN11 0.021 0.023 -10000 0 -10000 0 0
IL6/IL6RA 0.013 0.054 -10000 0 -0.13 35 35
gp130 (dimer)/TYK2/TYK2/LMO4 0.023 0.067 -10000 0 -0.21 29 29
gp130 (dimer)/JAK2/JAK2/LMO4 0.035 0.046 -10000 0 -0.2 15 15
IL6 -0.002 0.07 -10000 0 -0.2 59 59
PIAS3 0.005 0.059 -10000 0 -0.22 32 32
PTPRE 0.01 0.045 -10000 0 -0.23 15 15
PIAS1 0.016 0.038 -10000 0 -0.34 6 6
RAC1 0.017 0.033 -10000 0 -0.37 4 4
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.011 0.073 0.23 1 -0.24 23 24
LMO4 0.011 0.065 -10000 0 -0.34 17 17
STAT3 (dimer)/PIAS3 -0.078 0.36 -10000 0 -0.93 59 59
MCL1 0.003 0.12 -10000 0 -0.48 10 10
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0 0.009 0.032 18 -10000 0 18
BUB1B -0.028 0.11 -10000 0 -0.32 58 58
PLK1 0.002 0.031 -10000 0 -0.1 29 29
PLK1S1 0.001 0.015 -10000 0 -0.051 18 18
KIF2A -0.013 0.07 -10000 0 -0.19 61 61
regulation of mitotic centrosome separation 0.002 0.031 -10000 0 -0.1 29 29
GOLGA2 0.009 0.06 -10000 0 -0.3 18 18
Hec1/SPC24 -0.02 0.081 -10000 0 -0.18 98 98
WEE1 -0.015 0.094 -10000 0 -0.28 32 32
cytokinesis -0.054 0.16 -10000 0 -0.41 80 80
PP2A-alpha B56 0.022 0.062 -10000 0 -0.36 3 3
AURKA -0.003 0.059 -10000 0 -0.26 24 24
PICH/PLK1 -0.042 0.14 -10000 0 -0.26 132 132
CENPE 0.005 0.036 -10000 0 -0.12 24 24
RhoA/GTP -0.005 0.069 -10000 0 -0.25 39 39
positive regulation of microtubule depolymerization -0.013 0.069 -10000 0 -0.19 61 61
PPP2CA 0.001 0.081 -10000 0 -0.36 26 26
FZR1 0.02 0 -10000 0 -10000 0 0
TPX2 -0.031 0.096 -10000 0 -0.25 82 82
PAK1 0.009 0.046 -10000 0 -0.2 24 24
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.02 0 -10000 0 -10000 0 0
CLSPN 0.009 0.017 -10000 0 -0.11 1 1
GORASP1 0.012 0.052 -10000 0 -0.32 12 12
metaphase -0.001 0.002 -10000 0 -0.014 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.001 0.015 -10000 0 -0.051 18 18
G2 phase of mitotic cell cycle -0.001 0.003 -10000 0 -0.012 21 21
STAG2 0.014 0.047 -10000 0 -0.35 9 9
GRASP65/GM130/RAB1/GTP -0.009 0.1 -10000 0 -0.52 14 14
spindle elongation 0.002 0.031 -10000 0 -0.1 29 29
ODF2 0.014 0.032 -10000 0 -0.2 11 11
BUB1 0.014 0.03 -10000 0 -10000 0 0
TPT1 0.008 0.015 -10000 0 -0.1 1 1
CDC25C 0.011 0.017 -10000 0 -0.11 1 1
CDC25B -0.034 0.13 -10000 0 -0.32 82 82
SGOL1 0 0.009 -10000 0 -0.032 18 18
RHOA -0.008 0.1 -10000 0 -0.36 39 39
CCNB1/CDK1 -0.056 0.17 -10000 0 -0.33 128 128
CDC14B 0.011 0.011 -10000 0 -0.14 3 3
CDC20 -0.037 0.13 -10000 0 -0.34 86 86
PLK1/PBIP1 -0.022 0.075 -10000 0 -0.17 96 96
mitosis 0 0.007 0.03 22 -0.014 6 28
FBXO5 -0.019 0.078 -10000 0 -0.23 50 50
CDC2 -0.044 0.14 -10000 0 -0.33 95 95
NDC80 -0.05 0.14 -10000 0 -0.32 111 111
metaphase plate congression 0.003 0.049 -10000 0 -0.31 11 11
ERCC6L -0.053 0.16 -10000 0 -0.31 131 131
NLP/gamma Tubulin 0 0.028 -10000 0 -0.1 23 23
microtubule cytoskeleton organization 0.008 0.015 -10000 0 -0.1 1 1
G2/M transition DNA damage checkpoint -0.001 0.001 -10000 0 -0.008 1 1
PPP1R12A 0.013 0.049 -10000 0 -0.34 10 10
interphase -0.001 0.001 -10000 0 -0.008 1 1
PLK1/PRC1-2 -0.034 0.12 -10000 0 -0.24 118 118
GRASP65/GM130/RAB1/GTP/PLK1 0.018 0.063 -10000 0 -0.17 43 43
RAB1A 0.004 0.076 -10000 0 -0.36 22 22
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.002 0.046 -10000 0 -0.13 45 45
mitotic prometaphase 0 0.003 0.022 10 -0.009 3 13
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.048 -10000 0 -0.2 1 1
microtubule-based process -0.02 0.085 -10000 0 -0.18 99 99
Golgi organization 0.002 0.031 -10000 0 -0.1 29 29
Cohesin/SA2 0.009 0.034 -10000 0 -0.14 16 16
PPP1CB/MYPT1 0.021 0.044 -10000 0 -0.25 12 12
KIF20A -0.049 0.14 -10000 0 -0.31 113 113
APC/C/CDC20 -0.014 0.083 -10000 0 -0.2 80 80
PPP2R1A 0.01 0.06 -10000 0 -0.35 14 14
chromosome segregation -0.022 0.074 -10000 0 -0.17 96 96
PRC1 -0.038 0.13 -10000 0 -0.32 90 90
ECT2 -0.019 0.08 -10000 0 -0.19 82 82
C13orf34 -0.001 0.044 -10000 0 -0.12 44 44
NUDC 0.003 0.049 -10000 0 -0.31 11 11
regulation of attachment of spindle microtubules to kinetochore -0.028 0.11 -10000 0 -0.32 58 58
spindle assembly 0.001 0.028 -10000 0 -0.085 29 29
spindle stabilization 0.001 0.015 -10000 0 -0.051 18 18
APC/C/HCDH1 0.023 0.009 -10000 0 -0.1 3 3
MKLP2/PLK1 -0.02 0.086 -10000 0 -0.18 99 99
CCNB1 -0.039 0.14 -10000 0 -0.34 86 86
PPP1CB 0.016 0.033 -10000 0 -0.29 6 6
BTRC 0.02 0 -10000 0 -10000 0 0
ROCK2 0.003 0.052 -10000 0 -0.18 22 22
TUBG1 -0.001 0.048 -10000 0 -0.26 16 16
G2/M transition of mitotic cell cycle -0.082 0.15 -10000 0 -0.32 128 128
MLF1IP -0.036 0.099 -10000 0 -0.23 105 105
INCENP 0.019 0.001 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.049 0.075 0.2 35 -0.3 12 47
AES 0.042 0.068 0.17 32 -0.3 12 44
FBXW11 0.02 0 -10000 0 -10000 0 0
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.015 0.047 -10000 0 -0.14 40 40
SMAD4 -0.027 0.12 -10000 0 -0.33 72 72
DKK2 0.003 0.059 -10000 0 -0.2 40 40
TLE1 0.043 0.066 0.17 28 -0.32 10 38
MACF1 -0.01 0.1 -10000 0 -0.32 48 48
CTNNB1 0.037 0.076 0.2 1 -0.3 8 9
WIF1 0.011 0.045 -10000 0 -0.2 23 23
beta catenin/RanBP3 0.15 0.19 0.39 182 -0.31 1 183
KREMEN2 0.016 0.029 -10000 0 -0.2 9 9
DKK1 0.011 0.044 -10000 0 -0.2 22 22
beta catenin/beta TrCP1 0.048 0.073 0.2 1 -0.28 7 8
FZD1 0.013 0.038 -10000 0 -0.2 16 16
AXIN2 -0.11 0.15 -10000 0 -0.27 203 203
AXIN1 0.02 0.001 -10000 0 -10000 0 0
RAN 0.004 0.078 -10000 0 -0.36 24 24
Axin1/APC/GSK3/beta catenin 0.031 0.13 -10000 0 -0.57 21 21
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.031 0.14 0.24 16 -0.38 30 46
Axin1/APC/GSK3 0.029 0.075 -10000 0 -0.25 24 24
Axin1/APC/GSK3/beta catenin/Macf1 0.035 0.084 -10000 0 -0.32 22 22
HNF1A 0.052 0.045 0.18 35 -10000 0 35
CTBP1 0.038 0.084 0.18 34 -0.32 20 54
MYC -0.32 0.55 -10000 0 -1.4 103 103
RANBP3 0.02 0.01 -10000 0 -0.2 1 1
DKK2/LRP6/Kremen 2 0.022 0.052 -10000 0 -0.2 11 11
NKD1 0 0 -10000 0 -10000 0 0
TCF4 0.016 0.12 0.18 33 -0.29 56 89
TCF3 0.052 0.045 0.18 35 -10000 0 35
WNT1/LRP6/FZD1/Axin1 0.039 0.039 -10000 0 -0.17 7 7
Ran/GTP 0.006 0.054 -10000 0 -0.24 24 24
CtBP/CBP/TCF/TLE1/AES 0.21 0.26 0.5 202 -0.32 3 205
LEF1 0.047 0.056 0.18 34 -0.17 10 44
DVL1 0.025 0.088 -10000 0 -0.26 36 36
CSNK2A1 -0.003 0.088 -10000 0 -0.33 35 35
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.047 0.15 -10000 0 -0.36 53 53
DKK1/LRP6/Kremen 2 0.026 0.046 -10000 0 -0.2 7 7
LRP6 0.007 0.058 -10000 0 -0.25 24 24
CSNK1A1 0.054 0.058 0.2 34 -0.31 3 37
NLK 0.007 0.038 -10000 0 -0.21 15 15
CCND1 -0.4 0.59 -10000 0 -1.3 145 145
WNT1 0.019 0.001 -10000 0 -10000 0 0
GSK3A 0.019 0.001 -10000 0 -10000 0 0
GSK3B 0.002 0.077 -10000 0 -0.34 25 25
FRAT1 0.018 0.014 -10000 0 -0.2 2 2
PPP2R5D 0.025 0.045 -10000 0 -0.16 11 11
APC 0.03 0.032 -10000 0 -0.15 7 7
WNT1/LRP6/FZD1 0.025 0.052 -10000 0 -0.18 15 15
CREBBP 0.052 0.045 0.18 35 -10000 0 35
Aurora B 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
Condensin I complex -0.047 0.17 -9999 0 -0.33 102 102
STMN1 -0.008 0.091 -9999 0 -0.24 58 58
Aurora B/RasGAP/Survivin -0.021 0.11 -9999 0 -0.24 94 94
Chromosomal passenger complex/Cul3 protein complex -0.022 0.12 -9999 0 -0.3 68 68
BIRC5 -0.033 0.13 -9999 0 -0.32 84 84
DES -0.016 0.19 -9999 0 -1.1 15 15
Aurora C/Aurora B/INCENP 0.023 0.047 -9999 0 -0.2 16 16
Aurora B/TACC1 0.008 0.057 -9999 0 -0.24 17 17
Aurora B/PP2A 0.014 0.055 -9999 0 -0.18 33 33
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.004 0.058 -9999 0 -0.18 47 47
mitotic metaphase/anaphase transition 0 0.004 -9999 0 -10000 0 0
NDC80 -0.037 0.12 -9999 0 -0.29 86 86
Cul3 protein complex 0.017 0.046 -9999 0 -0.2 22 22
KIF2C -0.06 0.22 -9999 0 -0.51 77 77
PEBP1 0.014 0.041 -9999 0 -0.37 6 6
KIF20A -0.05 0.14 -9999 0 -0.31 113 113
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.006 0.089 -9999 0 -0.25 56 56
SEPT1 0 0 -9999 0 -10000 0 0
SMC2 -0.002 0.083 -9999 0 -0.3 36 36
SMC4 -0.004 0.088 -9999 0 -0.32 37 37
NSUN2/NPM1/Nucleolin -0.022 0.16 -9999 0 -0.74 19 19
PSMA3 0.01 0.06 -9999 0 -0.35 14 14
G2/M transition of mitotic cell cycle 0 0.003 -9999 0 -10000 0 0
H3F3B 0.003 0.06 -9999 0 -0.26 24 24
AURKB -0.001 0.078 -9999 0 -0.28 36 36
AURKC 0.016 0.029 -9999 0 -0.2 9 9
CDCA8 -0.024 0.12 -9999 0 -0.32 70 70
cytokinesis -0.072 0.25 -9999 0 -0.62 71 71
Aurora B/Septin1 -0.064 0.23 -9999 0 -0.57 71 71
AURKA 0 0.082 -9999 0 -0.33 30 30
INCENP 0.018 0.006 -9999 0 -10000 0 0
KLHL13 0 0 -9999 0 -10000 0 0
BUB1 0.018 0.022 -9999 0 -0.2 5 5
hSgo1/Aurora B/Survivin -0.013 0.087 -9999 0 -0.23 62 62
EVI5 0.019 0.01 -9999 0 -0.2 1 1
RhoA/GTP -0.066 0.22 -9999 0 -0.51 82 82
SGOL1 0 0 -9999 0 -10000 0 0
CENPA -0.039 0.19 -9999 0 -0.5 58 58
NCAPG -0.019 0.11 -9999 0 -0.29 69 69
Aurora B/HC8 Proteasome 0.008 0.068 -9999 0 -0.25 29 29
NCAPD2 -0.041 0.13 -9999 0 -0.32 98 98
Aurora B/PP1-gamma 0.012 0.062 -9999 0 -0.22 30 30
RHOA -0.008 0.1 -9999 0 -0.36 39 39
NCAPH 0.003 0.073 -9999 0 -0.3 27 27
NPM1 -0.008 0.11 -9999 0 -0.5 23 23
RASA1 -0.01 0.1 -9999 0 -0.35 44 44
KLHL9 0.003 0.078 -9999 0 -0.34 25 25
mitotic prometaphase -0.001 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.068 -9999 0 -0.25 29 29
PPP1CC 0.015 0.04 -9999 0 -0.36 6 6
Centraspindlin -0.066 0.24 -9999 0 -0.56 75 75
RhoA/GDP -0.005 0.069 -9999 0 -0.25 39 39
NSUN2 -0.011 0.089 -9999 0 -0.52 15 15
MYLK -0.042 0.11 -9999 0 -0.28 90 90
KIF23 -0.044 0.14 -9999 0 -0.31 103 103
VIM -0.024 0.1 -9999 0 -0.24 92 92
RACGAP1 -0.023 0.12 -9999 0 -0.36 60 60
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.015 0.12 -9999 0 -0.46 32 32
Chromosomal passenger complex -0.044 0.18 -9999 0 -0.46 63 63
Chromosomal passenger complex/EVI5 -0.004 0.13 -9999 0 -0.28 78 78
TACC1 0.007 0.052 -9999 0 -0.21 29 29
PPP2R5D 0.019 0.014 -9999 0 -0.2 2 2
CUL3 0.02 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.004 0.05 -9999 0 -0.24 22 22
PRKCZ 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0.01 0.057 -9999 0 -0.3 17 17
ERC1 -0.027 0.12 -9999 0 -0.31 77 77
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.028 0.12 -9999 0 -0.34 55 55
IRAK/TOLLIP 0.006 0.069 -9999 0 -0.18 58 58
IKBKB 0.017 0.025 -9999 0 -0.2 7 7
IKBKG 0.02 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 0.007 0.055 -9999 0 -0.25 2 2
IL1A 0.016 0.027 -9999 0 -0.2 8 8
IL1B -0.042 0.11 -9999 0 -0.25 97 97
IRAK/TRAF6/p62/Atypical PKCs 0 0.088 -9999 0 -0.17 99 99
IL1R2 -0.009 0.075 -9999 0 -0.2 70 70
IL1R1 0.015 0.033 -9999 0 -0.22 10 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.024 0.11 -9999 0 -0.35 37 37
TOLLIP 0.017 0.024 -9999 0 -0.2 6 6
TICAM2 0 0 -9999 0 -10000 0 0
MAP3K3 0.018 0.017 -9999 0 -0.2 3 3
TAK1/TAB1/TAB2 0.024 0.059 -9999 0 -0.22 22 22
IKK complex/ELKS -0.006 0.12 -9999 0 -0.3 56 56
JUN 0.023 0.059 -9999 0 -0.27 12 12
MAP3K7 0.002 0.072 -9999 0 -0.27 32 32
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.036 0.12 -9999 0 -0.29 50 50
IL1 alpha/IL1R1/IL1RAP/MYD88 0.018 0.075 -9999 0 -0.18 49 49
PIK3R1 -0.011 0.097 -9999 0 -0.3 52 52
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.027 0.072 -9999 0 -0.17 49 49
IL1 beta fragment/IL1R1/IL1RAP -0.028 0.1 -9999 0 -0.19 119 119
NFKB1 -0.003 0.088 -9999 0 -0.34 34 34
MAPK8 0.026 0.057 -9999 0 -0.29 8 8
IRAK1 -0.006 0.073 -9999 0 -0.21 58 58
IL1RN/IL1R1 0.026 0.025 -9999 0 -0.24 1 1
IRAK4 0.018 0.017 -9999 0 -0.2 3 3
PRKCI -0.009 0.093 -9999 0 -0.3 48 48
TRAF6 0.019 0.017 -9999 0 -0.36 1 1
PI3K -0.014 0.098 -9999 0 -0.25 66 66
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.022 0.12 -9999 0 -0.34 50 50
CHUK 0.006 0.068 -9999 0 -0.33 21 21
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.028 0.1 -9999 0 -0.19 119 119
IL1 beta/IL1R2 -0.039 0.098 -9999 0 -0.21 106 106
IRAK/TRAF6/TAK1/TAB1/TAB2 0.021 0.082 -9999 0 -0.28 16 16
NF kappa B1 p50/RelA -0.044 0.12 -9999 0 -0.29 64 64
IRAK3 0.019 0.01 -9999 0 -0.2 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.016 0.092 -9999 0 -0.16 119 119
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.014 0.072 -9999 0 -0.19 49 49
IL1 alpha/IL1R1/IL1RAP 0.017 0.061 -9999 0 -0.2 25 25
RELA 0.018 0.021 -9999 0 -0.26 3 3
MAP3K7IP1 0.019 0.01 -9999 0 -0.2 1 1
SQSTM1 -0.002 0.083 -9999 0 -0.3 37 37
MYD88 0 0.084 -9999 0 -0.36 27 27
IRAK/TRAF6/MEKK3 0.018 0.066 -9999 0 -0.16 59 59
IL1RAP -0.012 0.094 -9999 0 -0.27 58 58
UBE2N 0.005 0.073 -9999 0 -0.34 22 22
IRAK/TRAF6 -0.051 0.079 -9999 0 -0.26 48 48
CASP1 -0.057 0.15 -9999 0 -0.32 122 122
IL1RN/IL1R2 0.009 0.052 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.024 0.12 -9999 0 -0.2 123 123
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.001 0.11 -9999 0 -0.36 33 33
PIK3CA -0.011 0.1 -9999 0 -0.33 48 48
IL1RN 0.019 0.014 -9999 0 -0.2 2 2
TRAF6/TAK1/TAB1/TAB2 0.028 0.066 -9999 0 -0.32 9 9
MAP2K6 0.022 0.06 -9999 0 -0.31 8 8
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.006 0.1 -10000 0 -0.23 78 78
epithelial cell differentiation 0.022 0.066 -10000 0 -0.18 49 49
CYFIP2 -0.003 0.086 -10000 0 -0.31 38 38
ENAH 0.003 0.089 -10000 0 -0.23 46 46
EGFR 0.018 0.017 -10000 0 -0.2 3 3
EPHA2 -0.003 0.079 -10000 0 -0.25 45 45
MYO6 0.008 0.078 -10000 0 -0.32 19 19
CTNNB1 0.012 0.054 -10000 0 -0.36 11 11
ABI1/Sra1/Nap1 0.02 0.064 -10000 0 -0.2 39 39
AQP5 0.01 0.093 -10000 0 -0.4 17 17
CTNND1 0.006 0.07 -10000 0 -0.36 19 19
mol:PI-4-5-P2 0.018 0.06 -10000 0 -0.16 49 49
regulation of calcium-dependent cell-cell adhesion 0.018 0.06 -10000 0 -0.16 49 49
EGF 0.019 0.01 -10000 0 -0.2 1 1
NCKAP1 0.019 0.01 -10000 0 -0.2 1 1
AQP3 0.011 0.093 -10000 0 -0.39 18 18
cortical microtubule organization 0.022 0.066 -10000 0 -0.18 49 49
GO:0000145 0.013 0.056 -10000 0 -0.16 49 49
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.026 0.068 -10000 0 -0.18 49 49
MLLT4 0.02 0 -10000 0 -10000 0 0
ARF6/GDP -0.031 0.068 -10000 0 -0.27 27 27
ARF6 0.017 0.033 -10000 0 -0.36 4 4
Ephrin A1/EPHA2/NCK1/GIT1 0.012 0.084 -10000 0 -0.19 61 61
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.004 0.1 -10000 0 -0.35 26 26
PVRL2 0.002 0.076 -10000 0 -0.3 30 30
ZYX 0.013 0.07 -10000 0 -0.19 49 49
ARF6/GTP 0.018 0.082 -10000 0 -0.18 63 63
CDH1 0.009 0.061 -10000 0 -0.34 16 16
EGFR/EGFR/EGF/EGF 0.02 0.058 -10000 0 -0.28 7 7
RhoA/GDP 0.011 0.086 -10000 0 -0.19 75 75
actin cytoskeleton organization 0.011 0.077 -10000 0 -0.32 18 18
IGF-1R heterotetramer -0.054 0.15 -10000 0 -0.33 115 115
GIT1 0.019 0.01 -10000 0 -0.2 1 1
IGF1R -0.055 0.15 -10000 0 -0.33 115 115
IGF1 -0.07 0.14 -10000 0 -0.27 166 166
DIAPH1 0.002 0.16 -10000 0 -0.58 38 38
Wnt receptor signaling pathway -0.022 0.066 0.18 49 -10000 0 49
RHOA -0.008 0.1 -10000 0 -0.36 39 39
RhoA/GTP -0.039 0.081 -10000 0 -0.29 37 37
CTNNA1 0.01 0.059 -10000 0 -0.36 13 13
VCL 0.011 0.078 -10000 0 -0.33 18 18
EFNA1 -0.009 0.097 -10000 0 -0.31 47 47
LPP 0.014 0.073 -10000 0 -0.35 12 12
Ephrin A1/EPHA2 -0.002 0.082 -10000 0 -0.3 18 18
SEC6/SEC8 -0.02 0.056 -10000 0 -0.3 12 12
MGAT3 0.018 0.061 -10000 0 -0.16 49 49
HGF/MET 0.017 0.061 -10000 0 -0.28 9 9
HGF 0.019 0.014 -10000 0 -0.2 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.006 0.1 -10000 0 -0.24 78 78
actin cable formation 0.005 0.1 -10000 0 -0.26 42 42
KIAA1543 0.006 0.056 -10000 0 -0.16 49 49
KIFC3 0.018 0.061 -10000 0 -0.16 49 49
NCK1 0.002 0.074 -10000 0 -0.28 32 32
EXOC3 0.016 0.036 -10000 0 -0.26 8 8
ACTN1 0.013 0.071 -10000 0 -0.19 49 49
NCK1/GIT1 0.016 0.053 -10000 0 -0.18 33 33
mol:GDP 0.022 0.066 -10000 0 -0.18 49 49
EXOC4 0 0 -10000 0 -10000 0 0
STX4 0.016 0.066 -10000 0 -0.17 49 49
PIP5K1C 0.018 0.061 -10000 0 -0.16 49 49
LIMA1 -0.019 0.11 -10000 0 -0.31 63 63
ABI1 0.009 0.062 -10000 0 -0.35 15 15
ROCK1 0.003 0.093 -10000 0 -0.26 38 38
adherens junction assembly 0.022 0.057 -10000 0 -0.28 6 6
IGF-1R heterotetramer/IGF1 -0.051 0.11 -10000 0 -0.28 59 59
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.017 0.054 -10000 0 -0.24 18 18
MET 0.012 0.041 -10000 0 -0.2 19 19
PLEKHA7 0.006 0.058 -10000 0 -0.17 49 49
mol:GTP 0.01 0.083 -10000 0 -0.19 61 61
establishment of epithelial cell apical/basal polarity 0.022 0.073 -10000 0 -0.29 15 15
cortical actin cytoskeleton stabilization -0.006 0.1 -10000 0 -0.23 78 78
regulation of cell-cell adhesion 0.011 0.077 -10000 0 -0.32 18 18
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.006 0.1 -10000 0 -0.24 78 78
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.01 0.1 -9999 0 -0.41 26 26
KLHL20 -0.026 0.089 -9999 0 -0.21 42 42
CYFIP2 -0.003 0.086 -9999 0 -0.31 38 38
Rac1/GDP 0.026 0.077 -9999 0 -0.26 27 27
ENAH 0.002 0.11 -9999 0 -0.43 27 27
AP1M1 0 0 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 0 112 112
RAP1A 0.015 0.039 -9999 0 -0.32 7 7
CTNNB1 0.012 0.054 -9999 0 -0.36 11 11
CDC42/GTP -0.015 0.047 -9999 0 -0.25 12 12
ABI1/Sra1/Nap1 -0.038 0.05 -9999 0 -0.14 59 59
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.021 0.08 -9999 0 -0.2 50 50
RAPGEF1 0.016 0.096 -9999 0 -0.37 26 26
CTNND1 0.006 0.07 -9999 0 -0.36 19 19
regulation of calcium-dependent cell-cell adhesion 0.006 0.11 -9999 0 -0.43 25 25
CRK 0.01 0.1 -9999 0 -0.4 26 26
E-cadherin/gamma catenin/alpha catenin 0.017 0.072 -9999 0 -0.21 46 46
alphaE/beta7 Integrin 0.006 0.072 -9999 0 -0.24 35 35
IQGAP1 -0.01 0.1 -9999 0 -0.33 46 46
NCKAP1 0.019 0.01 -9999 0 -0.2 1 1
Rap1/GTP/I-afadin 0.022 0.021 -9999 0 -0.18 5 5
DLG1 0.009 0.1 -9999 0 -0.42 25 25
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.022 0.047 -9999 0 -0.19 28 28
MLLT4 0.02 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.011 0.045 -9999 0 -0.18 19 19
PI3K -0.028 0.061 -9999 0 -0.24 28 28
ARF6 0.017 0.033 -9999 0 -0.36 4 4
mol:Ca2+ 0 0 -9999 0 0 208 208
E-cadherin/gamma catenin 0.009 0.072 -9999 0 -0.26 34 34
TIAM1 -0.003 0.079 -9999 0 -0.26 44 44
E-cadherin(dimer)/Ca2+ 0.024 0.068 -9999 0 -0.18 49 49
AKT1 0.007 0.055 -9999 0 -0.16 31 31
PIK3R1 -0.011 0.097 -9999 0 -0.3 52 52
CDH1 0.009 0.061 -9999 0 -0.34 16 16
RhoA/GDP 0.023 0.089 -9999 0 -0.29 31 31
actin cytoskeleton organization -0.018 0.067 -9999 0 -0.15 42 42
CDC42/GDP 0.029 0.075 -9999 0 -0.25 26 26
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.001 0.084 -9999 0 -0.23 56 56
ITGB7 0.02 0 -9999 0 -10000 0 0
RAC1 0.017 0.033 -9999 0 -0.36 4 4
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.027 0.072 -9999 0 -0.19 49 49
E-cadherin/Ca2+/beta catenin/alpha catenin 0.02 0.053 -9999 0 -0.17 35 35
mol:GDP 0.02 0.083 -9999 0 -0.29 26 26
CDC42/GTP/IQGAP1 0.009 0.06 -9999 0 -0.2 37 37
JUP 0.002 0.079 -9999 0 -0.35 26 26
p120 catenin/RhoA/GDP 0.019 0.097 -9999 0 -0.3 32 32
RAC1/GTP/IQGAP1 0.007 0.062 -9999 0 -0.2 41 41
PIP5K1C/AP1M1 0.014 0.009 -9999 0 -0.13 2 2
RHOA -0.008 0.1 -9999 0 -0.36 39 39
CDC42 0.019 0.01 -9999 0 -0.2 1 1
CTNNA1 0.01 0.059 -9999 0 -0.36 13 13
positive regulation of S phase of mitotic cell cycle -0.043 0.087 -9999 0 -0.16 159 159
NME1 0 0 -9999 0 -0.001 218 218
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.007 0.11 -9999 0 -0.43 26 26
regulation of cell-cell adhesion -0.014 0.041 -9999 0 -0.22 12 12
WASF2 -0.021 0.027 -9999 0 -0.078 59 59
Rap1/GTP 0.019 0.066 -9999 0 -0.28 12 12
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.02 0.085 -9999 0 -0.3 11 11
CCND1 -0.054 0.11 -9999 0 -0.2 159 159
VAV2 0.014 0.1 -9999 0 -0.42 19 19
RAP1/GDP 0.018 0.07 -9999 0 -0.3 11 11
adherens junction assembly 0.007 0.11 -9999 0 -0.42 26 26
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.009 0.062 -9999 0 -0.35 15 15
PIP5K1C 0.019 0.014 -9999 0 -0.2 2 2
regulation of heterotypic cell-cell adhesion 0.019 0.089 -9999 0 -0.3 18 18
E-cadherin/beta catenin 0.008 0.049 -9999 0 -0.28 13 13
mol:GTP 0 0 -9999 0 -0.001 218 218
SRC 0.009 0.1 -9999 0 -0.42 25 25
PIK3CA -0.011 0.1 -9999 0 -0.33 48 48
Rac1/GTP -0.08 0.11 -9999 0 -0.34 42 42
E-cadherin/beta catenin/alpha catenin 0.022 0.062 -9999 0 -0.21 35 35
ITGAE -0.014 0.1 -9999 0 -0.3 56 56
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.005 0.11 -9999 0 -0.44 25 25
Coregulation of Androgen receptor activity

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
NRIP1 -0.036 0.13 -9999 0 -0.31 92 92
SVIL -0.005 0.092 -9999 0 -0.3 44 44
ZNF318 0.012 0.029 -9999 0 -0.21 9 9
JMJD2C 0.028 0 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.002 0.075 -9999 0 -0.2 43 43
CARM1 0.012 0.052 -9999 0 -0.32 12 12
PRDX1 0.013 0.049 -9999 0 -0.36 9 9
PELP1 0.016 0.025 -9999 0 -0.2 7 7
CTNNB1 0.013 0.054 -9999 0 -0.36 11 11
AKT1 0.002 0.071 -9999 0 -0.28 30 30
PTK2B 0.021 0 -9999 0 -10000 0 0
MED1 0.001 0.08 -9999 0 -0.35 26 26
MAK -0.001 0.059 -9999 0 -0.21 41 41
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.015 0.044 -9999 0 -0.25 13 13
GSN -0.005 0.091 -9999 0 -0.29 46 46
NCOA2 0.019 0.014 -9999 0 -0.2 2 2
NCOA6 0.006 0.074 -9999 0 -0.35 22 22
DNA-PK 0.013 0.076 -9999 0 -0.23 39 39
NCOA4 0.014 0.046 -9999 0 -0.36 8 8
PIAS3 0.006 0.059 -9999 0 -0.22 32 32
cell proliferation -0.014 0.042 -9999 0 -0.23 2 2
XRCC5 0.007 0.066 -9999 0 -0.36 17 17
UBE3A 0.019 0.033 -9999 0 -0.36 4 4
T-DHT/AR/SNURF -0.013 0.072 -9999 0 -0.14 101 101
FHL2 -0.1 0.3 -9999 0 -0.83 72 72
RANBP9 0.009 0.067 -9999 0 -0.32 20 20
JMJD1A 0.019 0.084 -9999 0 -0.34 27 27
CDK6 0.02 0 -9999 0 -10000 0 0
TGFB1I1 -0.045 0.13 -9999 0 -0.29 116 116
T-DHT/AR/CyclinD1 -0.078 0.12 -9999 0 -0.22 192 192
XRCC6 0.017 0.025 -9999 0 -0.31 3 3
T-DHT/AR -0.011 0.12 -9999 0 -0.23 75 75
CTDSP1 0.017 0.037 -9999 0 -0.36 5 5
CTDSP2 0.013 0.038 -9999 0 -0.29 8 8
BRCA1 0.02 0.017 -9999 0 -0.2 3 3
TCF4 -0.019 0.11 -9999 0 -0.32 59 59
CDKN2A -0.082 0.17 -9999 0 -0.36 143 143
SRF 0.003 0.05 -9999 0 -10000 0 0
NKX3-1 0.006 0.11 -9999 0 -0.52 13 13
KLK3 0.012 0.048 -9999 0 -10000 0 0
TMF1 0.01 0.06 -9999 0 -0.32 16 16
HNRNPA1 0.017 0.023 -9999 0 -0.37 2 2
AOF2 0.009 0.065 -9999 0 -0.32 19 19
APPL1 -0.002 0.076 -9999 0 -0.27 35 35
T-DHT/AR/Caspase 8 -0.006 0.077 -9999 0 -0.2 47 47
AR -0.033 0.12 -9999 0 -0.26 101 101
UBA3 0.001 0 -9999 0 -10000 0 0
PATZ1 0.017 0.019 -9999 0 -0.21 4 4
PAWR 0.02 0 -9999 0 -10000 0 0
PRKDC -0.006 0.091 -9999 0 -0.32 41 41
PA2G4 0.012 0.044 -9999 0 -0.3 10 10
UBE2I 0.02 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.019 0.09 -9999 0 -0.2 81 81
RPS6KA3 0.005 0.072 -9999 0 -0.28 30 30
T-DHT/AR/ARA70 -0.005 0.081 -9999 0 -0.21 50 50
LATS2 -0.001 0 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.005 0.072 -9999 0 -0.18 52 52
Cyclin D3/CDK11 p58 -0.01 0.072 -9999 0 -0.21 58 58
VAV3 -0.14 0.16 -9999 0 -0.28 295 295
KLK2 0.02 0.047 -9999 0 -10000 0 0
CASP8 0.015 0.037 -9999 0 -0.3 7 7
T-DHT/AR/TIF2/CARM1 0.008 0.076 -9999 0 -0.18 47 47
TMPRSS2 0.006 0.11 -9999 0 -0.42 26 26
CCND1 -0.12 0.16 -9999 0 -0.3 230 230
PIAS1 0.018 0.038 -9999 0 -0.34 6 6
mol:T-DHT -0.001 0.021 -9999 0 -0.058 49 49
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.023 0 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.003 0.075 -9999 0 -0.2 43 43
CMTM2 0 0 -9999 0 -10000 0 0
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 -0.011 0.1 -9999 0 -0.33 47 47
CCND3 -0.016 0.1 -9999 0 -0.31 58 58
TGIF1 0.005 0.064 -9999 0 -0.28 25 25
FKBP4 -0.009 0.1 -9999 0 -0.32 49 49
Signaling events mediated by PTP1B

Figure S45.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S45.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.01 0.045 -10000 0 -0.2 23 23
Jak2/Leptin Receptor -0.002 0.056 -10000 0 -0.21 1 1
PTP1B/AKT1 -0.038 0.094 -10000 0 -0.26 49 49
FYN -0.049 0.13 -10000 0 -0.28 122 122
p210 bcr-abl/PTP1B -0.046 0.09 -10000 0 -0.27 34 34
EGFR 0.018 0.017 -10000 0 -0.21 3 3
EGF/EGFR -0.026 0.08 -10000 0 -0.23 32 32
CSF1 0.019 0.014 -10000 0 -0.2 2 2
AKT1 0.003 0.072 -10000 0 -0.28 30 30
INSR 0.019 0.014 -10000 0 -0.2 2 2
PTP1B/N-cadherin -0.067 0.11 -10000 0 -0.26 103 103
Insulin Receptor/Insulin -0.018 0.089 -10000 0 -0.25 38 38
HCK -0.004 0.072 -10000 0 -0.21 56 56
CRK 0.01 0.053 -10000 0 -0.25 20 20
TYK2 -0.047 0.094 -10000 0 -0.25 52 52
EGF 0.019 0.01 -10000 0 -0.21 1 1
YES1 0 0.082 -10000 0 -0.33 30 30
CAV1 -0.046 0.096 -10000 0 -0.25 63 63
TXN 0.007 0.064 -10000 0 -0.34 17 17
PTP1B/IRS1/GRB2 -0.055 0.11 -10000 0 -0.28 75 75
cell migration 0.046 0.09 0.27 34 -10000 0 34
STAT3 0.004 0.076 -10000 0 -0.35 23 23
PRLR 0.024 0.003 -10000 0 -10000 0 0
ITGA2B 0.019 0.001 -10000 0 -10000 0 0
CSF1R -0.036 0.12 -10000 0 -0.29 95 95
Prolactin Receptor/Prolactin 0.037 0.018 -10000 0 -10000 0 0
FGR 0.012 0.04 -10000 0 -0.2 18 18
PTP1B/p130 Cas -0.044 0.085 -10000 0 -0.22 55 55
Crk/p130 Cas -0.037 0.088 -10000 0 -0.21 60 60
DOK1 -0.028 0.082 -10000 0 -0.25 30 30
JAK2 -0.005 0.054 -10000 0 -0.22 1 1
Jak2/Leptin Receptor/Leptin -0.005 0.085 -10000 0 -0.23 28 28
PIK3R1 -0.011 0.097 -10000 0 -0.3 52 52
PTPN1 -0.046 0.091 -10000 0 -0.28 34 34
LYN -0.031 0.13 -10000 0 -0.34 76 76
CDH2 -0.073 0.15 -10000 0 -0.3 157 157
SRC -0.013 0.098 -10000 0 -0.5 18 18
ITGB3 0.018 0.014 -10000 0 -0.2 2 2
CAT1/PTP1B -0.054 0.12 -10000 0 -0.29 69 69
CAPN1 0.006 0.069 -10000 0 -0.36 18 18
CSK 0.006 0.07 -10000 0 -0.35 20 20
PI3K -0.032 0.11 -10000 0 -0.27 61 61
mol:H2O2 0.001 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.002 0.08 -10000 0 -0.24 18 18
negative regulation of transcription -0.005 0.053 -10000 0 -0.22 1 1
FCGR2A -0.061 0.15 -10000 0 -0.31 134 134
FER 0.013 0.034 -10000 0 -0.2 13 13
alphaIIb/beta3 Integrin 0.027 0.01 -10000 0 -10000 0 0
BLK 0.019 0.014 -10000 0 -0.2 2 2
Insulin Receptor/Insulin/Shc 0.037 0.019 -10000 0 -0.21 1 1
RHOA -0.01 0.1 -10000 0 -0.37 39 39
LEPR 0.012 0.039 -10000 0 -0.2 17 17
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.012 0.053 -10000 0 -0.35 11 11
mol:NADPH -0.001 0.001 -10000 0 -10000 0 0
TRPV6 -0.029 0.12 -10000 0 -0.3 45 45
PRL 0.021 0.025 -10000 0 -0.2 7 7
SOCS3 0.017 0.012 -10000 0 -10000 0 0
SPRY2 -0.11 0.16 -10000 0 -0.29 219 219
Insulin Receptor/Insulin/IRS1 -0.001 0.079 -10000 0 -0.2 55 55
CSF1/CSF1R -0.048 0.11 -10000 0 -0.26 68 68
Ras protein signal transduction 0.02 0.049 0.12 1 -0.26 11 12
IRS1 -0.046 0.13 -10000 0 -0.28 118 118
INS 0.019 0.002 -10000 0 -10000 0 0
LEP 0.019 0.014 -10000 0 -0.2 2 2
STAT5B -0.024 0.075 -10000 0 -0.22 28 28
STAT5A -0.024 0.075 -10000 0 -0.23 27 27
GRB2 0.012 0.053 -10000 0 -0.35 11 11
PDGFB-D/PDGFRB -0.038 0.089 -10000 0 -0.26 34 34
CSN2 0.039 0.024 -10000 0 -10000 0 0
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
LAT -0.08 0.18 -10000 0 -0.49 85 85
YBX1 0.017 0.068 -10000 0 -0.33 19 19
LCK 0.016 0.03 -10000 0 -0.2 10 10
SHC1 0.017 0.027 -10000 0 -0.23 6 6
NOX4 -0.036 0.1 -10000 0 -0.22 128 128
mTOR signaling pathway

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
GBL 0.013 0.04 -10000 0 -0.23 14 14
MKNK1 0.007 0.068 -10000 0 -0.35 19 19
mol:PIP3 -0.026 0.12 0.22 35 -0.22 99 134
FRAP1 0.008 0.11 -10000 0 -0.59 13 13
AKT1 -0.017 0.11 0.2 35 -0.23 69 104
INSR 0.019 0.014 -10000 0 -0.2 2 2
Insulin Receptor/Insulin 0.026 0.008 -10000 0 -0.1 2 2
mol:GTP -0.017 0.09 0.17 3 -0.23 44 47
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.024 0.055 -10000 0 -0.18 42 42
TSC2 -0.001 0.082 -10000 0 -0.3 36 36
RHEB/GDP -0.034 0.067 -10000 0 -0.21 41 41
TSC1 0.015 0.041 -10000 0 -0.29 9 9
Insulin Receptor/IRS1 -0.018 0.094 -10000 0 -0.29 55 55
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.023 0.059 -10000 0 -0.2 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.009 0.063 -10000 0 -0.36 15 15
RPS6KB1 0.009 0.085 0.23 1 -0.29 11 12
MAP3K5 0.004 0.04 -10000 0 -0.25 9 9
PIK3R1 -0.011 0.098 -10000 0 -0.3 52 52
apoptosis 0.004 0.04 -10000 0 -0.25 9 9
mol:LY294002 0 0 0.001 19 -0.001 56 75
EIF4B 0.013 0.081 0.17 30 -0.25 14 44
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.018 0.08 -10000 0 -0.25 17 17
eIF4E/eIF4G1/eIF4A1 -0.022 0.068 -10000 0 -0.32 20 20
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.032 0.11 -10000 0 -0.23 111 111
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.065 0.16 32 -0.17 11 43
FKBP1A 0.011 0.059 -10000 0 -0.37 13 13
RHEB/GTP -0.01 0.081 -10000 0 -0.23 33 33
mol:Amino Acids 0 0 0.001 19 -0.001 56 75
FKBP12/Rapamycin 0.008 0.042 -10000 0 -0.26 13 13
PDPK1 -0.018 0.11 0.2 35 -0.24 63 98
EIF4E -0.001 0.087 -10000 0 -0.35 31 31
ASK1/PP5C 0.017 0.11 -10000 0 -0.5 19 19
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.003 0.094 -10000 0 -0.38 30 30
TSC1/TSC2 -0.006 0.11 0.21 32 -0.25 44 76
tumor necrosis factor receptor activity 0 0 0.001 56 -0.001 19 75
RPS6 0.018 0.029 -10000 0 -0.36 3 3
PPP5C 0.016 0.027 -10000 0 -0.2 8 8
EIF4G1 -0.001 0.087 -10000 0 -0.36 30 30
IRS1 -0.032 0.098 -10000 0 -0.31 55 55
INS 0.02 0 -10000 0 -10000 0 0
PTEN -0.018 0.11 -10000 0 -0.35 55 55
PDK2 -0.019 0.11 0.2 35 -0.24 65 100
EIF4EBP1 -0.079 0.32 -10000 0 -1.1 45 45
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
PPP2R5D 0.014 0.096 0.22 1 -0.52 13 14
peptide biosynthetic process 0.024 0.024 -10000 0 -0.18 7 7
RHEB 0.02 0 -10000 0 -10000 0 0
EIF4A1 0.016 0.038 -10000 0 -0.34 6 6
mol:Rapamycin 0 0.001 0.003 44 -0.003 24 68
EEF2 0.024 0.024 -10000 0 -0.18 7 7
eIF4E/4E-BP1 -0.074 0.3 -10000 0 -1.1 45 45
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.017 0.029 -9999 0 -0.27 5 5
Syndecan-3/Src/Cortactin -0.06 0.14 -9999 0 -0.48 37 37
Syndecan-3/Neurocan -0.007 0.13 -9999 0 -0.53 28 28
POMC 0.018 0.019 -9999 0 -0.2 4 4
EGFR 0.018 0.017 -9999 0 -0.2 3 3
Syndecan-3/EGFR -0.007 0.13 -9999 0 -0.53 28 28
AGRP 0.02 0 -9999 0 -10000 0 0
NCSTN 0.01 0.06 -9999 0 -0.34 15 15
PSENEN -0.005 0.084 -9999 0 -0.28 44 44
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.015 0.033 -9999 0 -0.2 12 12
APH1A 0.015 0.04 -9999 0 -0.3 8 8
NCAN 0.02 0 -9999 0 -10000 0 0
long-term memory -0.028 0.14 -9999 0 -0.42 41 41
Syndecan-3/IL8 -0.041 0.14 -9999 0 -0.49 38 38
PSEN1 0.013 0.046 -9999 0 -0.32 10 10
Src/Cortactin 0.027 0.02 -9999 0 -0.17 5 5
FYN -0.049 0.13 -9999 0 -0.28 122 122
limb bud formation -0.035 0.12 -9999 0 -0.55 28 28
MC4R 0.008 0.05 -9999 0 -0.2 28 28
SRC 0.02 0 -9999 0 -10000 0 0
PTN -0.14 0.17 -9999 0 -0.3 272 272
FGFR/FGF/Syndecan-3 -0.035 0.12 -9999 0 -0.56 28 28
neuron projection morphogenesis -0.057 0.14 -9999 0 -0.46 36 36
Syndecan-3/AgRP -0.007 0.13 -9999 0 -0.53 28 28
Syndecan-3/AgRP/MC4R -0.001 0.12 -9999 0 -0.51 28 28
Fyn/Cortactin -0.02 0.095 -9999 0 -0.18 126 126
SDC3 -0.036 0.13 -9999 0 -0.56 28 28
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.04 0.14 -9999 0 -0.48 38 38
IL8 -0.055 0.13 -9999 0 -0.27 139 139
Syndecan-3/Fyn/Cortactin -0.028 0.14 -9999 0 -0.44 40 40
Syndecan-3/CASK -0.034 0.12 -9999 0 -0.54 28 28
alpha-MSH/MC4R 0.02 0.036 -9999 0 -10000 0 0
Gamma Secretase 0.032 0.069 -9999 0 -0.17 46 46
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.014 0.044 -10000 0 -0.37 7 7
HSPA8 -0.016 0.11 -10000 0 -0.36 51 51
SMAD3/SMAD4/ER alpha 0.04 0.1 0.22 33 -0.2 43 76
AKT1 0.006 0.071 -10000 0 -0.28 30 30
GSC -0.001 0.024 -10000 0 -10000 0 0
NKX2-5 0.021 0.01 -10000 0 -0.2 1 1
muscle cell differentiation 0.001 0.13 0.33 58 -10000 0 58
SMAD2-3/SMAD4/SP1 0.008 0.13 -10000 0 -0.29 47 47
SMAD4 -0.026 0.13 -10000 0 -0.33 73 73
CBFB 0.018 0.025 -10000 0 -0.31 3 3
SAP18 0.016 0.037 -10000 0 -0.36 5 5
Cbp/p300/MSG1 0.032 0.034 -10000 0 -0.2 7 7
SMAD3/SMAD4/VDR 0.026 0.087 -10000 0 -0.21 31 31
MYC -0.075 0.16 -10000 0 -0.32 144 144
CDKN2B 0.037 0.054 -10000 0 -10000 0 0
AP1 -0.059 0.16 -10000 0 -0.33 102 102
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.003 0.13 -10000 0 -0.38 37 37
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.003 0.11 -10000 0 -0.33 32 32
SP3 0.011 0.057 -10000 0 -0.36 12 12
CREB1 0.013 0.049 -10000 0 -0.36 9 9
FOXH1 0.02 0.017 -10000 0 -0.2 3 3
SMAD3/SMAD4/GR -0.007 0.12 -10000 0 -0.23 92 92
GATA3 0.023 0.028 -10000 0 -0.19 9 9
SKI/SIN3/HDAC complex/NCoR1 0.015 0.08 -10000 0 -0.3 18 18
MEF2C/TIF2 0.033 0.073 -10000 0 -0.27 12 12
endothelial cell migration 0.005 0.083 -10000 0 -10000 0 0
MAX 0.02 0.012 -10000 0 -0.21 1 1
RBBP7 0.006 0.069 -10000 0 -0.34 20 20
RBBP4 -0.012 0.1 -10000 0 -0.34 47 47
RUNX2 0.02 0 -10000 0 -10000 0 0
RUNX3 -0.058 0.13 -10000 0 -0.25 154 154
RUNX1 0.02 0 -10000 0 -10000 0 0
CTBP1 0.006 0.07 -10000 0 -0.33 22 22
NR3C1 -0.014 0.11 -10000 0 -0.36 49 49
VDR 0.019 0.014 -10000 0 -0.2 2 2
CDKN1A -0.04 0.24 -10000 0 -1.2 18 18
KAT2B -0.001 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.014 0.092 -10000 0 -0.21 65 65
DCP1A 0.012 0.051 -10000 0 -0.34 11 11
SKI 0.02 0 -10000 0 -10000 0 0
SERPINE1 -0.005 0.083 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 0.013 0.09 -10000 0 -0.21 49 49
SMAD3/SMAD4/ATF3 -0.048 0.13 -10000 0 -0.25 125 125
SAP30 0.019 0.014 -10000 0 -0.2 2 2
Cbp/p300/PIAS3 0.025 0.047 -10000 0 -0.22 10 10
JUN -0.062 0.16 -10000 0 -0.32 102 102
SMAD3/SMAD4/IRF7 -0.025 0.13 -10000 0 -0.23 116 116
TFE3 0.012 0.04 -10000 0 -0.2 12 12
COL1A2 -0.16 0.31 -10000 0 -0.78 103 103
mesenchymal cell differentiation -0.013 0.089 0.19 65 -10000 0 65
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.02 0 -10000 0 -10000 0 0
FOS -0.12 0.17 -10000 0 -0.29 233 233
SMAD3/SMAD4/Max 0.014 0.092 -10000 0 -0.2 63 63
Cbp/p300/SNIP1 0.034 0.031 -10000 0 -0.2 7 7
ZBTB17 0.018 0.001 -10000 0 -10000 0 0
LAMC1 -0.001 0.12 -10000 0 -0.38 33 33
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.11 -10000 0 -0.24 66 66
IRF7 -0.05 0.14 -10000 0 -0.3 121 121
ESR1 0.032 0.028 -10000 0 -10000 0 0
HNF4A 0.02 0 -10000 0 -10000 0 0
MEF2C 0.023 0.075 -10000 0 -0.28 13 13
SMAD2-3/SMAD4 0.012 0.11 -10000 0 -0.25 54 54
Cbp/p300/Src-1 0.027 0.054 -10000 0 -0.21 23 23
IGHV3OR16-13 -0.017 0.083 -10000 0 -0.64 9 9
TGIF2/HDAC complex -0.003 0.089 -10000 0 -0.34 34 34
CREBBP 0.019 0.003 -10000 0 -10000 0 0
SKIL 0.016 0.027 -10000 0 -0.2 8 8
HDAC1 0.012 0.052 -10000 0 -0.32 12 12
HDAC2 0.004 0.071 -10000 0 -0.29 28 28
SNIP1 0.017 0.027 -10000 0 -0.2 8 8
GCN5L2 0.016 0.027 -10000 0 -0.23 6 6
SMAD3/SMAD4/TFE3 0.007 0.11 -10000 0 -0.24 55 55
MSG1/HSC70 0 0.084 -10000 0 -0.25 51 51
SMAD2 0.011 0.068 -10000 0 -0.33 20 20
SMAD3 0.013 0.044 -10000 0 -0.22 7 7
SMAD3/E2F4-5/DP1/p107/SMAD4 0.004 0.092 -10000 0 -0.22 65 65
SMAD2/SMAD2/SMAD4 -0.02 0.085 0.12 2 -0.23 64 66
NCOR1 0.014 0.046 -10000 0 -0.36 8 8
NCOA2 0.019 0.014 -10000 0 -0.2 2 2
NCOA1 0.005 0.071 -10000 0 -0.34 22 22
MYOD/E2A 0.029 0.011 -10000 0 -0.12 3 3
SMAD2-3/SMAD4/SP1/MIZ-1 0.021 0.12 -10000 0 -0.27 43 43
IFNB1 -0.019 0.11 -10000 0 -0.25 46 46
SMAD3/SMAD4/MEF2C 0.038 0.09 -10000 0 -0.28 14 14
CITED1 0.014 0.036 -10000 0 -0.2 14 14
SMAD2-3/SMAD4/ARC105 0.024 0.1 -10000 0 -0.25 38 38
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.003 0.12 -10000 0 -0.38 23 23
RUNX1-3/PEBPB2 -0.008 0.08 -10000 0 -0.2 49 49
SMAD7 -0.096 0.26 -10000 0 -0.59 86 86
MYC/MIZ-1 -0.041 0.11 -10000 0 -0.25 103 103
SMAD3/SMAD4 -0.013 0.096 -10000 0 -0.33 24 24
IL10 0.023 0.076 -10000 0 -0.26 10 10
PIASy/HDAC complex 0.021 0.003 -10000 0 -10000 0 0
PIAS3 0.005 0.059 -10000 0 -0.22 32 32
CDK2 0.014 0.032 -10000 0 -0.21 11 11
IL5 0.023 0.076 -10000 0 -0.24 13 13
CDK4 -0.001 0.081 -10000 0 -0.32 31 31
PIAS4 0.021 0.003 -10000 0 -10000 0 0
ATF3 -0.079 0.15 -10000 0 -0.28 180 180
SMAD3/SMAD4/SP1 -0.007 0.13 -10000 0 -0.27 58 58
FOXG1 0.014 0.036 -10000 0 -0.2 14 14
FOXO3 0.011 0.062 -10000 0 -0.25 21 21
FOXO1 -0.012 0.09 -10000 0 -0.25 53 53
FOXO4 0.017 0.049 -10000 0 -0.24 14 14
heart looping 0.023 0.074 -10000 0 -0.28 13 13
CEBPB 0.01 0.066 -10000 0 -0.35 17 17
SMAD3/SMAD4/DLX1 0.001 0.087 -10000 0 -0.2 69 69
MYOD1 0.018 0.017 -10000 0 -0.2 3 3
SMAD3/SMAD4/HNF4 0.013 0.09 -10000 0 -0.21 48 48
SMAD3/SMAD4/GATA3 0.025 0.094 -10000 0 -0.24 25 25
SnoN/SIN3/HDAC complex/NCoR1 0.016 0.027 -10000 0 -0.2 8 8
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.007 0.1 -10000 0 -0.21 63 63
SMAD3/SMAD4/SP1-3 0.006 0.13 -10000 0 -0.3 46 46
MED15 0.018 0.021 -10000 0 -0.2 5 5
SP1 -0.004 0.055 -10000 0 -0.17 11 11
SIN3B 0.016 0.03 -10000 0 -0.2 10 10
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.034 0.087 -10000 0 -0.25 24 24
ITGB5 -0.009 0.13 -10000 0 -0.36 38 38
TGIF/SIN3/HDAC complex/CtBP 0.006 0.089 -10000 0 -0.31 22 22
SMAD3/SMAD4/AR -0.019 0.11 -10000 0 -0.22 90 90
AR -0.032 0.11 -10000 0 -0.26 101 101
negative regulation of cell growth -0.03 0.14 -10000 0 -0.32 76 76
SMAD3/SMAD4/MYOD 0.013 0.09 -10000 0 -0.21 50 50
E2F5 0.019 0.01 -10000 0 -0.2 1 1
E2F4 0.02 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.029 0.092 -10000 0 -0.24 34 34
SMAD2-3/SMAD4/FOXO1-3a-4 -0.004 0.12 -10000 0 -0.33 42 42
TFDP1 0.002 0.076 -10000 0 -0.31 28 28
SMAD3/SMAD4/AP1 -0.047 0.17 -10000 0 -0.33 102 102
SMAD3/SMAD4/RUNX2 0.013 0.09 -10000 0 -0.19 65 65
TGIF2 -0.003 0.089 -10000 0 -0.34 34 34
TGIF1 0.006 0.064 -10000 0 -0.28 25 25
ATF2 0.019 0.014 -10000 0 -0.2 2 2
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.003 0.091 -9999 0 -0.22 61 61
BIRC5 -0.031 0.12 -9999 0 -0.3 84 84
NFKBIA 0.004 0.086 -9999 0 -0.24 50 50
CPEB1 0.011 0.043 -9999 0 -0.2 21 21
AKT1 0.009 0.079 -9999 0 -0.24 38 38
NDEL1 0.015 0.042 -9999 0 -0.32 8 8
Aurora A/BRCA1 0.016 0.064 -9999 0 -0.22 25 25
NDEL1/TACC3 0.008 0.096 -9999 0 -0.24 55 55
GADD45A -0.019 0.11 -9999 0 -0.3 65 65
GSK3B 0.006 0.078 -9999 0 -0.34 25 25
PAK1/Aurora A 0.013 0.074 -9999 0 -0.25 25 25
MDM2 0.02 0 -9999 0 -10000 0 0
JUB 0 0 -9999 0 -10000 0 0
TPX2 -0.032 0.12 -9999 0 -0.27 94 94
TP53 -0.06 0.15 -9999 0 -0.28 149 149
DLG7 -0.028 0.11 -9999 0 -0.26 75 75
AURKAIP1 0.013 0.052 -9999 0 -0.36 10 10
ARHGEF7 0.017 0.027 -9999 0 -0.28 4 4
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.008 0.1 -9999 0 -0.25 55 55
G2/M transition of mitotic cell cycle 0.016 0.063 -9999 0 -0.22 25 25
AURKA 0.011 0.083 -9999 0 -0.31 24 24
AURKB -0.011 0.096 -9999 0 -0.26 48 48
CDC25B -0.022 0.13 -9999 0 -0.32 73 73
G2/M transition checkpoint 0.004 0.061 -9999 0 -0.23 24 24
mRNA polyadenylation 0.012 0.065 -9999 0 -0.22 25 25
Aurora A/CPEB 0.012 0.066 -9999 0 -0.22 25 25
Aurora A/TACC1/TRAP/chTOG 0.007 0.1 -9999 0 -0.34 23 23
BRCA1 0.018 0.017 -9999 0 -0.2 3 3
centrosome duplication 0.013 0.073 -9999 0 -0.25 25 25
regulation of centrosome cycle 0.007 0.095 -9999 0 -0.23 55 55
spindle assembly 0.006 0.1 -9999 0 -0.33 23 23
TDRD7 -0.027 0.12 -9999 0 -0.31 77 77
Aurora A/RasGAP/Survivin -0.002 0.1 -9999 0 -0.3 35 35
CENPA -0.019 0.12 -9999 0 -0.36 48 48
Aurora A/PP2A 0.018 0.07 -9999 0 -0.25 25 25
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process -0.034 0.11 -9999 0 -0.3 51 51
negative regulation of DNA binding -0.06 0.15 -9999 0 -0.28 149 149
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.027 0.02 -9999 0 -0.17 5 5
RASA1 -0.01 0.1 -9999 0 -0.35 44 44
Ajuba/Aurora A 0.004 0.061 -9999 0 -0.23 24 24
mitotic prometaphase 0.001 0.013 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.083 -9999 0 -0.31 24 24
TACC1 0.007 0.052 -9999 0 -0.21 29 29
TACC3 -0.017 0.11 -9999 0 -0.32 58 58
Aurora A/Antizyme1 0.024 0.077 -9999 0 -0.23 35 35
Aurora A/RasGAP 0.003 0.091 -9999 0 -0.24 53 53
OAZ1 0.017 0.033 -9999 0 -0.36 4 4
RAN 0.003 0.078 -9999 0 -0.36 24 24
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.022 0.014 -9999 0 -10000 0 0
GIT1 0.019 0.01 -9999 0 -0.2 1 1
GIT1/beta-PIX/PAK1 0.033 0.032 -9999 0 -0.2 2 2
Importin alpha/Importin beta/TPX2 -0.032 0.12 -9999 0 -0.27 94 94
PPP2R5D 0.019 0.014 -9999 0 -0.2 2 2
Aurora A/TPX2 -0.015 0.11 -9999 0 -0.24 90 90
PAK1 0.01 0.046 -9999 0 -0.2 24 24
CKAP5 0.013 0.052 -9999 0 -0.36 10 10
IL4-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
BCL2L1 -0.039 0.38 -10000 0 -0.92 46 46
STAT6 (cleaved dimer) -0.16 0.28 -10000 0 -0.85 59 59
IGHG1 0.006 0.22 -10000 0 -0.67 18 18
IGHG3 -0.051 0.36 -10000 0 -0.86 54 54
AKT1 -0.005 0.24 -10000 0 -0.64 27 27
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.027 0.18 -10000 0 -0.53 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.016 0.25 -10000 0 -0.62 32 32
THY1 -0.23 0.62 -10000 0 -1.2 126 126
MYB -0.047 0.13 -10000 0 -0.26 127 127
HMGA1 0.019 0.01 -10000 0 -0.2 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 0.013 0.25 -10000 0 -0.53 31 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP 0.003 0.24 -10000 0 -0.72 17 17
SP1 0.005 0.047 -10000 0 -0.15 12 12
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.005 0.053 -10000 0 -0.3 13 13
STAT6 (dimer)/ETS1 -0.034 0.36 -10000 0 -0.88 49 49
SOCS1 0.005 0.29 -10000 0 -0.62 48 48
SOCS3 0.029 0.21 -10000 0 -0.54 4 4
FCER2 -0.004 0.3 -10000 0 -0.72 24 24
PARP14 0.002 0.001 -10000 0 -10000 0 0
CCL17 -0.038 0.38 -10000 0 -0.94 43 43
GRB2 0.012 0.053 -10000 0 -0.35 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP 0.017 0.2 -10000 0 -0.54 16 16
T cell proliferation -0.059 0.38 -10000 0 -0.94 52 52
IL4R/JAK1 -0.061 0.4 -10000 0 -0.98 52 52
EGR2 -0.059 0.42 -10000 0 -1 53 53
JAK2 0.028 0.044 -10000 0 -0.18 3 3
JAK3 0.023 0.005 -10000 0 -10000 0 0
PIK3R1 -0.011 0.097 -10000 0 -0.3 52 52
JAK1 0.01 0.084 -10000 0 -0.36 25 25
COL1A2 -0.2 0.56 -10000 0 -1.3 103 103
CCL26 -0.048 0.38 -10000 0 -0.89 54 54
IL4R -0.05 0.42 -10000 0 -1 49 49
PTPN6 0.01 0.052 -10000 0 -0.33 11 11
IL13RA2 -0.047 0.38 -10000 0 -0.94 45 45
IL13RA1 -0.022 0.13 -10000 0 -0.33 74 74
IRF4 0.049 0.1 -10000 0 -10000 0 0
ARG1 0.036 0.16 -10000 0 -0.59 8 8
CBL 0.015 0.23 -10000 0 -0.5 31 31
GTF3A -0.009 0.068 -10000 0 -0.28 17 17
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
IL13RA1/JAK2 0.01 0.11 -10000 0 -0.23 61 61
IRF4/BCL6 0.037 0.1 -10000 0 -10000 0 0
CD40LG 0.03 0.001 -10000 0 -10000 0 0
MAPK14 0.021 0.23 -10000 0 -0.5 26 26
mitosis -0.002 0.23 -10000 0 -0.6 27 27
STAT6 -0.047 0.42 -10000 0 -0.99 54 54
SPI1 0.027 0.01 -10000 0 -0.2 1 1
RPS6KB1 0.003 0.23 -10000 0 -0.58 26 26
STAT6 (dimer) -0.047 0.42 -10000 0 -0.99 54 54
STAT6 (dimer)/PARP14 -0.062 0.38 -10000 0 -0.93 54 54
mast cell activation -0.004 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 0.018 0.21 -10000 0 -0.51 15 15
FRAP1 -0.005 0.24 -10000 0 -0.64 27 27
LTA -0.038 0.38 -10000 0 -0.94 43 43
FES 0.016 0.027 -10000 0 -0.2 8 8
T-helper 1 cell differentiation 0.045 0.42 0.97 54 -10000 0 54
CCL11 -0.057 0.36 -10000 0 -0.89 47 47
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.022 0.21 -10000 0 -0.51 15 15
IL2RG -0.003 0.073 -10000 0 -0.2 64 64
IL10 -0.038 0.38 -10000 0 -0.94 42 42
IRS1 -0.046 0.13 -10000 0 -0.28 118 118
IRS2 -0.046 0.13 -10000 0 -0.3 112 112
IL4 0.04 0.13 -10000 0 -10000 0 0
IL5 -0.038 0.38 -10000 0 -0.92 46 46
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.039 0.38 -10000 0 -0.83 60 60
COL1A1 -0.22 0.59 -10000 0 -1.4 102 102
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.06 0.4 -10000 0 -1 46 46
IL2R gamma/JAK3 0.019 0.052 -10000 0 -0.14 1 1
TFF3 -0.053 0.38 -10000 0 -0.94 46 46
ALOX15 -0.038 0.38 -10000 0 -0.94 43 43
MYBL1 -0.001 0.072 -10000 0 -0.23 44 44
T-helper 2 cell differentiation -0.031 0.34 -10000 0 -0.76 53 53
SHC1 0.017 0.027 -10000 0 -0.23 6 6
CEBPB 0.015 0.067 -10000 0 -0.36 17 17
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.01 0.25 -10000 0 -0.67 25 25
mol:PI-3-4-5-P3 -0.005 0.24 -10000 0 -0.64 27 27
PI3K -0.008 0.25 -10000 0 -0.68 27 27
DOK2 0 0 -10000 0 -10000 0 0
ETS1 0.015 0.019 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 0.018 0.2 -10000 0 -0.54 17 17
ITGB3 -0.039 0.38 -10000 0 -0.93 45 45
PIGR -0.04 0.38 -10000 0 -0.94 43 43
IGHE -0.014 0.071 0.18 8 -0.24 16 24
MAPKKK cascade 0.019 0.19 -10000 0 -0.53 17 17
BCL6 -0.007 0.091 -10000 0 -0.31 42 42
OPRM1 -0.038 0.38 -10000 0 -0.92 46 46
RETNLB -0.048 0.38 -10000 0 -0.89 54 54
SELP -0.039 0.38 -10000 0 -0.94 43 43
AICDA -0.042 0.36 -10000 0 -0.91 43 43
HIF-2-alpha transcription factor network

Figure S51.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S51.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.007 0.028 -10000 0 -10000 0 0
oxygen homeostasis -0.003 0.014 -10000 0 -10000 0 0
TCEB2 0.019 0.014 -10000 0 -0.2 2 2
TCEB1 0.012 0.051 -10000 0 -0.34 11 11
VHL/Elongin B/Elongin C/HIF2A 0.009 0.095 -10000 0 -0.27 23 23
EPO -0.02 0.22 -10000 0 -0.48 52 52
FIH (dimer) 0.017 0.014 -10000 0 -10000 0 0
APEX1 0.004 0.069 -10000 0 -0.34 18 18
SERPINE1 -0.047 0.24 -10000 0 -0.5 68 68
FLT1 0.011 0.03 -10000 0 -10000 0 0
ADORA2A -0.036 0.23 -10000 0 -0.5 60 60
germ cell development -0.041 0.23 -10000 0 -0.44 83 83
SLC11A2 -0.042 0.24 -10000 0 -0.52 68 68
BHLHE40 -0.043 0.23 -10000 0 -0.46 83 83
HIF1AN 0.017 0.014 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.003 0.15 -10000 0 -0.35 29 29
ETS1 0.036 0.005 -10000 0 -10000 0 0
CITED2 -0.083 0.28 -10000 0 -1.1 40 40
KDR 0.008 0.042 -10000 0 -10000 0 0
PGK1 -0.057 0.27 -10000 0 -0.56 81 81
SIRT1 0.007 0.068 -10000 0 -0.35 19 19
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.027 0.29 -10000 0 -0.52 83 83
EPAS1 -0.003 0.1 -10000 0 -0.27 27 27
SP1 0.028 0 -10000 0 -10000 0 0
ABCG2 -0.035 0.24 -10000 0 -0.51 61 61
EFNA1 -0.049 0.26 -10000 0 -0.53 78 78
FXN -0.04 0.23 -10000 0 -0.5 62 62
POU5F1 -0.043 0.23 -10000 0 -0.46 83 83
neuron apoptosis 0.026 0.28 0.51 83 -10000 0 83
EP300 0.015 0.044 -10000 0 -0.36 7 7
EGLN3 -0.007 0.07 -10000 0 -0.2 57 57
EGLN2 0.013 0.035 -10000 0 -0.23 9 9
EGLN1 -0.002 0.08 -10000 0 -0.31 32 32
VHL/Elongin B/Elongin C 0.022 0.031 -10000 0 -0.17 13 13
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.016 0.019 -10000 0 -10000 0 0
SLC2A1 -0.072 0.26 -10000 0 -0.52 95 95
TWIST1 -0.088 0.27 -10000 0 -0.5 109 109
ELK1 0.02 0.025 -10000 0 -0.2 1 1
HIF2A/ARNT/Cbp/p300 0.009 0.15 -10000 0 -0.34 25 25
VEGFA -0.048 0.26 -10000 0 -0.53 75 75
CREBBP 0.02 0 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.015 0.039 -9999 0 -0.32 7 7
VLDLR -0.046 0.13 -9999 0 -0.28 117 117
LRPAP1 -0.004 0.087 -9999 0 -0.31 38 38
NUDC 0.012 0.053 -9999 0 -0.35 11 11
RELN/LRP8 -0.006 0.083 -9999 0 -0.21 49 49
CaM/Ca2+ 0.014 0.013 -9999 0 -0.19 2 2
KATNA1 0.005 0.071 -9999 0 -0.32 23 23
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.02 0.088 -9999 0 -0.19 82 82
IQGAP1/CaM 0.007 0.072 -9999 0 -0.24 38 38
DAB1 0.02 0 -9999 0 -10000 0 0
IQGAP1 -0.01 0.1 -9999 0 -0.33 46 46
PLA2G7 -0.003 0.068 -9999 0 -0.2 55 55
CALM1 0.019 0.019 -9999 0 -0.28 2 2
DYNLT1 0.008 0.063 -9999 0 -0.31 19 19
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.007 0.083 -9999 0 -0.25 37 37
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.018 0.017 -9999 0 -0.2 3 3
CDK5R1 0.02 0 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.002 0.053 -9999 0 -0.2 28 28
CDK5R2 0.02 0 -9999 0 -10000 0 0
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.015 0.09 -9999 0 -0.2 72 72
YWHAE 0.013 0.048 -9999 0 -0.3 12 12
NDEL1/14-3-3 E 0 0.093 -9999 0 -0.28 25 25
MAP1B -0.047 0.1 -9999 0 -0.25 93 93
RAC1 0.003 0.055 -9999 0 -0.25 9 9
p35/CDK5 -0.011 0.087 -9999 0 -0.28 19 19
RELN -0.006 0.072 -9999 0 -0.2 63 63
PAFAH/LIS1 0.004 0.066 -9999 0 -0.2 31 31
LIS1/CLIP170 0.016 0.055 -9999 0 -0.2 28 28
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.035 0.077 -9999 0 -0.27 35 35
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.023 0.11 -9999 0 -0.23 89 89
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.007 0.091 -9999 0 -0.29 23 23
LIS1/IQGAP1 -0.001 0.082 -9999 0 -0.21 64 64
RHOA -0.024 0.13 -9999 0 -0.3 68 68
PAFAH1B1 0.005 0.064 -9999 0 -0.24 28 28
PAFAH1B3 -0.01 0.095 -9999 0 -0.29 52 52
PAFAH1B2 0.018 0.017 -9999 0 -0.2 3 3
MAP1B/LIS1/Dynein heavy chain -0.02 0.091 -9999 0 -0.28 34 34
NDEL1/Katanin 60/Dynein heavy chain 0.003 0.096 -9999 0 -0.27 26 26
LRP8 -0.009 0.084 -9999 0 -0.24 60 60
NDEL1/Katanin 60 -0.003 0.096 -9999 0 -0.27 31 31
P39/CDK5 -0.011 0.087 -9999 0 -0.28 19 19
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.012 0.064 -9999 0 -0.21 36 36
CDK5 -0.022 0.089 -9999 0 -0.18 100 100
PPP2R5D 0.019 0.014 -9999 0 -0.2 2 2
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.014 0.046 -9999 0 -0.16 28 28
CSNK2A1 -0.003 0.088 -9999 0 -0.33 35 35
RELN/VLDLR/DAB1/LIS1 -0.008 0.092 -9999 0 -0.17 101 101
RELN/VLDLR -0.028 0.11 -9999 0 -0.2 119 119
CDC42 0.005 0.046 -9999 0 -0.18 5 5
Regulation of Telomerase

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
Telomerase catalytic core complex -0.11 0.21 -10000 0 -0.46 104 104
RAD9A 0.016 0.036 -10000 0 -0.26 8 8
AP1 -0.087 0.14 -10000 0 -0.22 250 250
IFNAR2 0.012 0.039 -10000 0 -0.34 6 6
AKT1 0.008 0.056 -10000 0 -0.3 14 14
ER alpha/Oestrogen 0.012 0.005 -10000 0 -10000 0 0
NFX1/SIN3/HDAC complex 0 0.084 -10000 0 -0.23 42 42
EGF 0.018 0.01 -10000 0 -0.21 1 1
SMG5 0.019 0.014 -10000 0 -0.2 2 2
SMG6 0.019 0.01 -10000 0 -0.2 1 1
SP3/HDAC2 0.006 0.068 -10000 0 -0.22 37 37
TERT/c-Abl -0.11 0.21 -10000 0 -0.46 97 97
SAP18 0.015 0.037 -10000 0 -0.36 5 5
MRN complex 0.031 0.042 -10000 0 -0.2 15 15
WT1 -0.038 0.13 -10000 0 -0.34 82 82
WRN 0.01 0.053 -10000 0 -0.24 21 21
SP1 0.014 0.012 -10000 0 -10000 0 0
SP3 0.01 0.055 -10000 0 -0.35 12 12
TERF2IP 0.008 0.06 -10000 0 -0.28 20 20
Telomerase/Nucleolin -0.12 0.18 -10000 0 -0.44 84 84
Mad/Max 0.024 0.013 -10000 0 -0.14 1 1
TERT -0.12 0.22 -10000 0 -0.48 89 89
CCND1 -0.28 0.47 -10000 0 -1.1 136 136
MAX 0.017 0.011 -10000 0 -0.21 1 1
RBBP7 0.006 0.069 -10000 0 -0.34 20 20
RBBP4 -0.013 0.1 -10000 0 -0.34 47 47
TERF2 -0.002 0.078 -10000 0 -0.29 37 37
PTGES3 0.009 0.063 -10000 0 -0.36 15 15
SIN3A -0.001 0.002 -10000 0 -10000 0 0
Telomerase/911 0.003 0.11 -10000 0 -0.4 26 26
CDKN1B -0.054 0.17 -10000 0 -0.32 130 130
RAD1 0.006 0.066 -10000 0 -0.29 24 24
XRCC5 0.008 0.066 -10000 0 -0.36 17 17
XRCC6 0.018 0.025 -10000 0 -0.31 3 3
SAP30 0.018 0.014 -10000 0 -0.21 2 2
TRF2/PARP2 0.001 0.081 -10000 0 -0.23 54 54
UBE3A 0.015 0.034 -10000 0 -0.37 4 4
JUN -0.013 0.099 -10000 0 -0.31 51 51
E6 -0.002 0.004 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.009 0.025 -10000 0 -0.26 4 4
FOS -0.12 0.16 -10000 0 -0.29 233 233
IFN-gamma/IRF1 -0.038 0.13 -10000 0 -0.26 122 122
PARP2 0 0.078 -10000 0 -0.3 33 33
BLM -0.004 0.083 -10000 0 -0.28 43 43
Telomerase 0.008 0.07 -10000 0 -0.35 10 10
IRF1 -0.056 0.14 -10000 0 -0.31 107 107
ESR1 0.019 0.002 -10000 0 -10000 0 0
KU/TER 0.02 0.052 -10000 0 -0.26 17 17
ATM/TRF2 0.015 0.051 -10000 0 -0.15 40 40
ubiquitin-dependent protein catabolic process 0.006 0.081 -10000 0 -0.28 23 23
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.006 0.083 -10000 0 -0.28 23 23
HDAC1 0.011 0.052 -10000 0 -0.32 12 12
HDAC2 -0.002 0.072 -10000 0 -0.29 28 28
ATM 0.005 0.052 0.17 29 -0.28 5 34
SMAD3 0.024 0.019 -10000 0 -10000 0 0
ABL1 -0.009 0.099 -10000 0 -0.34 44 44
MXD1 0.018 0.004 -10000 0 -10000 0 0
MRE11A 0.02 0 -10000 0 -10000 0 0
HUS1 0.02 0 -10000 0 -10000 0 0
RPS6KB1 0.019 0.014 -10000 0 -0.2 2 2
TERT/NF kappa B1/14-3-3 -0.088 0.2 -10000 0 -0.46 59 59
NR2F2 -0.025 0.12 -10000 0 -0.32 77 77
MAPK3 0.021 0.008 -10000 0 -10000 0 0
MAPK1 0.005 0.06 -10000 0 -0.22 32 32
TGFB1/TGF beta receptor Type II 0.018 0.023 -10000 0 -0.2 6 6
NFKB1 -0.003 0.088 -10000 0 -0.34 34 34
HNRNPC 0.015 0.04 -10000 0 -0.36 6 6
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.005 0.052 0.17 29 -0.28 5 34
NBN 0.008 0.063 -10000 0 -0.31 19 19
EGFR 0.017 0.017 -10000 0 -0.21 3 3
mol:Oestrogen -0.001 0.003 -10000 0 -10000 0 0
EGF/EGFR 0.025 0.016 -10000 0 -0.14 4 4
MYC -0.073 0.15 -10000 0 -0.32 144 144
IL2 0.014 0.012 -10000 0 -10000 0 0
KU 0.02 0.052 -10000 0 -0.26 17 17
RAD50 0.017 0.029 -10000 0 -0.27 5 5
HSP90AA1 0.02 0 -10000 0 -10000 0 0
TGFB1 0.018 0.023 -10000 0 -0.2 6 6
TRF2/BLM -0.002 0.081 -10000 0 -0.23 53 53
FRAP1 0.02 0 -10000 0 -10000 0 0
KU/TERT -0.096 0.21 -10000 0 -0.45 89 89
SP1/HDAC2 0.01 0.054 -10000 0 -0.19 28 28
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A -0.11 0.17 -10000 0 -0.42 80 80
Smad3/Myc -0.021 0.093 -10000 0 -0.2 103 103
911 complex 0.029 0.045 -10000 0 -0.2 16 16
IFNG 0.005 0.05 -10000 0 -0.2 2 2
Telomerase/PinX1 -0.12 0.17 -10000 0 -0.42 85 85
Telomerase/AKT1/mTOR/p70S6K -0.003 0.1 -10000 0 -0.41 17 17
SIN3B 0.015 0.03 -10000 0 -0.2 10 10
YWHAE 0.013 0.048 -10000 0 -0.3 12 12
Telomerase/EST1B -0.11 0.17 -10000 0 -0.43 80 80
response to DNA damage stimulus 0.006 0.017 0.06 29 -0.097 5 34
MRN complex/TRF2/Rap1 0.031 0.071 -10000 0 -0.17 49 49
TRF2/WRN 0.006 0.069 -10000 0 -0.21 42 42
Telomerase/hnRNP C1/C2 -0.12 0.18 -10000 0 -0.43 80 80
E2F1 0.016 0.009 -10000 0 -10000 0 0
ZNFX1 -0.001 0.002 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.007 0.069 -10000 0 -0.36 18 18
DKC1 0.009 0.06 -10000 0 -0.32 17 17
telomeric DNA binding 0 0 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.022 0.063 -9999 0 -10000 0 0
PLK1 -0.031 0.23 -9999 0 -0.73 28 28
CDKN1B -0.061 0.21 -9999 0 -0.42 100 100
FOXO3 -0.034 0.22 -9999 0 -0.46 91 91
KAT2B -0.002 0.021 -9999 0 -0.045 75 75
FOXO1/SIRT1 0.01 0.072 -9999 0 -0.27 9 9
CAT -0.067 0.34 -9999 0 -1.1 39 39
CTNNB1 0.012 0.054 -9999 0 -0.36 11 11
AKT1 0.003 0.076 -9999 0 -0.29 30 30
FOXO1 0.014 0.07 -9999 0 -0.23 7 7
MAPK10 0.008 0.062 -9999 0 -0.17 42 42
mol:GTP 0 0.004 -9999 0 -10000 0 0
FOXO4 -0.001 0.17 -9999 0 -0.44 43 43
response to oxidative stress 0.001 0.022 -9999 0 -0.048 41 41
FOXO3A/SIRT1 -0.057 0.21 -9999 0 -0.45 94 94
XPO1 0.019 0.01 -9999 0 -0.21 1 1
EP300 0.017 0.044 -9999 0 -0.36 7 7
BCL2L11 0.025 0.032 -9999 0 -10000 0 0
FOXO1/SKP2 0.02 0.067 -9999 0 -0.25 6 6
mol:GDP 0.001 0.022 -9999 0 -0.048 41 41
RAN 0.003 0.079 -9999 0 -0.36 24 24
GADD45A -0.07 0.29 -9999 0 -0.83 55 55
YWHAQ 0.013 0.049 -9999 0 -0.36 9 9
FOXO1/14-3-3 family -0.01 0.16 -9999 0 -0.4 51 51
MST1 0.001 0.067 -9999 0 -0.23 36 36
CSNK1D 0.01 0.059 -9999 0 -0.33 15 15
CSNK1E 0.01 0.057 -9999 0 -0.3 17 17
FOXO4/14-3-3 family -0.063 0.22 -9999 0 -0.5 73 73
YWHAB 0.015 0.041 -9999 0 -0.34 7 7
MAPK8 0.012 0.058 -9999 0 -0.18 36 36
MAPK9 0.007 0.067 -9999 0 -0.19 41 41
YWHAG 0 0 -9999 0 -10000 0 0
YWHAE 0.013 0.048 -9999 0 -0.3 12 12
YWHAZ 0.005 0.074 -9999 0 -0.35 22 22
SIRT1 0.002 0.068 -9999 0 -0.35 19 19
SOD2 -0.11 0.35 -9999 0 -0.83 87 87
RBL2 -0.027 0.24 -9999 0 -0.86 27 27
RAL/GDP 0.011 0.065 -9999 0 -0.21 38 38
CHUK 0.004 0.072 -9999 0 -0.33 21 21
Ran/GTP 0.003 0.055 -9999 0 -0.25 24 24
CSNK1G2 0.02 0 -9999 0 -10000 0 0
RAL/GTP 0.013 0.063 -9999 0 -0.19 38 38
CSNK1G1 0.02 0 -9999 0 -10000 0 0
FASLG 0.025 0.032 -9999 0 -10000 0 0
SKP2 0.015 0.033 -9999 0 -0.2 12 12
USP7 0.014 0.042 -9999 0 -0.3 9 9
IKBKB 0.015 0.033 -9999 0 -0.2 7 7
CCNB1 -0.12 0.43 -9999 0 -1.2 73 73
FOXO1-3a-4/beta catenin -0.026 0.21 -9999 0 -0.39 81 81
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.067 -9999 0 -0.25 6 6
CSNK1A1 0.017 0.033 -9999 0 -0.36 4 4
SGK1 -0.002 0.021 -9999 0 -0.045 75 75
CSNK1G3 0.003 0.074 -9999 0 -0.3 29 29
Ran/GTP/Exportin 1 0.017 0.049 -9999 0 -0.2 25 25
ZFAND5 0.006 0.17 -9999 0 -0.59 24 24
SFN -0.066 0.15 -9999 0 -0.31 141 141
CDK2 0.018 0.032 -9999 0 -0.2 11 11
FOXO3A/14-3-3 -0.056 0.21 -9999 0 -0.5 70 70
CREBBP 0.023 0.002 -9999 0 -10000 0 0
FBXO32 -0.031 0.2 -9999 0 -0.42 91 91
BCL6 -0.056 0.3 -9999 0 -0.99 39 39
RALB 0.008 0.067 -9999 0 -0.36 17 17
RALA 0.004 0.074 -9999 0 -0.33 25 25
YWHAH -0.027 0.12 -9999 0 -0.32 73 73
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.027 0.022 -10000 0 -0.24 3 3
Necdin/E2F1 -0.057 0.11 -10000 0 -0.24 108 108
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.034 0.049 -10000 0 -0.17 24 24
NGF (dimer)/p75(NTR)/BEX1 -0.055 0.088 -10000 0 -0.2 90 90
NT-4/5 (dimer)/p75(NTR) 0.013 0.016 -10000 0 -0.13 6 6
IKBKB 0.017 0.025 -10000 0 -0.2 7 7
AKT1 -0.006 0.081 -10000 0 -0.19 75 75
IKBKG 0.02 0 -10000 0 -10000 0 0
BDNF 0.012 0.04 -10000 0 -0.2 18 18
MGDIs/NGR/p75(NTR)/LINGO1 0.012 0.013 -10000 0 -0.11 6 6
FURIN 0.02 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.033 0.032 -10000 0 -0.2 2 2
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.02 0.053 -10000 0 -0.32 8 8
proBDNF (dimer) 0.012 0.04 -10000 0 -0.2 18 18
NTRK1 0.02 0 -10000 0 -10000 0 0
RTN4R 0 0 -10000 0 -10000 0 0
neuron apoptosis -0.029 0.12 -10000 0 -0.43 17 17
IRAK1 -0.013 0.1 -10000 0 -0.33 50 50
SHC1 0.018 0.021 -10000 0 -0.21 2 2
ARHGDIA 0.019 0.01 -10000 0 -0.2 1 1
RhoA/GTP -0.005 0.069 -10000 0 -0.25 39 39
Gamma Secretase 0.032 0.069 -10000 0 -0.17 46 46
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.011 0.068 -10000 0 -0.18 56 56
MAGEH1 -0.024 0.12 -10000 0 -0.33 67 67
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.032 0.089 -10000 0 -0.18 113 113
Mammalian IAPs/DIABLO -0.013 0.087 -10000 0 -0.19 80 80
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.004 0.073 -10000 0 -0.32 24 24
APP 0.002 0.078 -10000 0 -0.34 26 26
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.005 0.071 -10000 0 -0.31 25 25
RhoA/GDP/RHOGDI 0.017 0.052 -10000 0 -0.16 39 39
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest 0.045 0.051 0.12 84 -0.17 11 95
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.001 0.099 -10000 0 -0.25 57 57
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.025 0.017 -10000 0 -0.2 1 1
NCSTN 0.01 0.06 -10000 0 -0.34 15 15
mol:GTP 0.004 0.066 -10000 0 -0.2 45 45
PSENEN -0.005 0.084 -10000 0 -0.28 44 44
mol:ceramide 0.025 0.018 -10000 0 -0.17 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.006 0.091 -10000 0 -0.34 19 19
p75(NTR)/beta APP 0.015 0.057 -10000 0 -0.21 32 32
BEX1 -0.12 0.15 -10000 0 -0.26 271 271
mol:GDP 0.007 0.012 -10000 0 -0.11 6 6
NGF (dimer) -0.057 0.092 -10000 0 -0.18 165 165
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.024 0.013 -10000 0 -10000 0 0
PIK3R1 -0.011 0.097 -10000 0 -0.3 52 52
RAC1/GTP 0.021 0.02 -10000 0 -0.12 10 10
MYD88 0 0.084 -10000 0 -0.36 27 27
CHUK 0.006 0.068 -10000 0 -0.33 21 21
NGF (dimer)/p75(NTR)/PKA 0.004 0.066 -10000 0 -0.2 45 45
RHOB -0.039 0.13 -10000 0 -0.29 101 101
RHOA -0.008 0.1 -10000 0 -0.36 39 39
MAGE-G1/E2F1 0.015 0 -10000 0 -10000 0 0
NT3 (dimer) -0.024 0.089 -10000 0 -0.2 105 105
TP53 0.01 0.059 -10000 0 -0.24 16 16
PRDM4 0.021 0.032 -10000 0 -0.18 11 11
BDNF (dimer) -0.053 0.098 -10000 0 -0.17 175 175
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
SORT1 0.017 0.027 -10000 0 -0.28 4 4
activation of caspase activity 0.03 0.048 -10000 0 -0.17 24 24
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.035 0.022 -10000 0 -0.18 3 3
RHOC 0.01 0.06 -10000 0 -0.35 14 14
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 0.031 0.057 -10000 0 -0.26 7 7
DIABLO 0.005 0.074 -10000 0 -0.35 22 22
SMPD2 0.025 0.018 -10000 0 -0.18 2 2
APH1B 0.015 0.033 -10000 0 -0.2 12 12
APH1A 0.015 0.04 -10000 0 -0.3 8 8
proNGF (dimer)/p75(NTR)/Sortilin 0.024 0.021 -10000 0 -0.2 2 2
PSEN1 0.013 0.046 -10000 0 -0.32 10 10
APAF-1/Pro-Caspase 9 0.027 0.021 -10000 0 -0.24 2 2
NT3 (dimer)/p75(NTR) -0.002 0.062 -10000 0 -10000 0 0
MAPK8 0.033 0.055 -10000 0 -0.25 7 7
MAPK9 0.028 0.063 -10000 0 -0.26 10 10
APAF1 0.02 0 -10000 0 -10000 0 0
NTF3 -0.024 0.089 -10000 0 -0.2 105 105
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.1 0.16 -10000 0 -0.28 220 220
RAC1/GDP 0.013 0.023 -10000 0 -0.25 4 4
RhoA-B-C/GDP -0.019 0.1 -10000 0 -0.18 132 132
p75 CTF/Sortilin/TRAF6/NRIF 0.04 0.045 -10000 0 -0.17 20 20
RhoA-B-C/GTP 0.004 0.065 -10000 0 -0.2 45 45
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.044 0.049 -10000 0 -0.16 21 21
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.044 0.032 -10000 0 -0.17 3 3
PRKACB -0.016 0.11 -10000 0 -0.33 55 55
proBDNF (dimer)/p75 ECD 0.023 0.03 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.05 0.13 -10000 0 -0.27 131 131
BIRC2 0.011 0.055 -10000 0 -0.35 12 12
neuron projection morphogenesis -0.006 0.096 0.15 48 -0.25 34 82
BAD 0.033 0.06 -10000 0 -0.28 7 7
RIPK2 0.007 0.061 -10000 0 -0.25 26 26
NGFR 0.017 0.024 -10000 0 -0.2 6 6
CYCS 0.02 0.045 -10000 0 -0.16 29 29
ADAM17 0.018 0.017 -10000 0 -0.2 3 3
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.029 0.037 -10000 0 -0.18 9 9
BCL2L11 0.034 0.06 -10000 0 -0.28 7 7
BDNF (dimer)/p75(NTR) 0.023 0.032 -10000 0 -10000 0 0
PI3K 0.003 0.078 -10000 0 -0.18 67 67
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.023 0.019 -10000 0 -0.18 2 2
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0.013 0.048 -10000 0 -0.3 12 12
PRKCI -0.009 0.093 -10000 0 -0.3 48 48
NGF (dimer)/p75(NTR) 0.013 0.016 -10000 0 -0.13 6 6
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.027 0.045 -10000 0 -0.18 21 21
TRAF6 0.019 0.017 -10000 0 -0.36 1 1
RAC1 0.017 0.033 -10000 0 -0.36 4 4
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.02 0 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.021 0.042 -10000 0 -0.17 17 17
SQSTM1 -0.002 0.083 -10000 0 -0.3 37 37
NGFRAP1 0.008 0.067 -10000 0 -0.36 17 17
CASP3 0.034 0.058 -10000 0 -0.26 7 7
E2F1 0.02 0 -10000 0 -10000 0 0
CASP9 0.017 0.03 -10000 0 -0.26 6 6
IKK complex 0.014 0.079 -10000 0 -0.27 20 20
NGF (dimer)/TRKA 0.015 0 -10000 0 -10000 0 0
MMP7 -0.15 0.17 -10000 0 -0.29 297 297
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.036 0.043 -10000 0 -0.16 20 20
MMP3 0.017 0.025 -10000 0 -0.2 7 7
APAF-1/Caspase 9 -0.03 0.056 -10000 0 -0.22 24 24
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.019 0.075 -10000 0 -0.18 54 54
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.019 0.01 -10000 0 -0.2 1 1
STAT1 (dimer)/Cbp/p300 -0.008 0.14 -10000 0 -0.28 82 82
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.011 0.081 -10000 0 -0.22 54 54
antigen processing and presentation of peptide antigen via MHC class I -0.068 0.11 -10000 0 -0.26 111 111
CaM/Ca2+ 0.021 0.071 -10000 0 -0.18 41 41
RAP1A 0.015 0.039 -10000 0 -0.32 7 7
STAT1 (dimer)/SHP2 -0.009 0.1 -10000 0 -0.25 54 54
AKT1 -0.011 0.1 -10000 0 -0.26 52 52
MAP2K1 0.016 0.065 -10000 0 -0.2 24 24
MAP3K11 0.012 0.069 -10000 0 -0.17 55 55
IFNGR1 -0.008 0.097 -10000 0 -0.33 42 42
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.029 0.039 -10000 0 -0.22 1 1
Rap1/GTP -0.014 0.043 -10000 0 -0.18 19 19
CRKL/C3G 0.029 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.031 0.073 -10000 0 -0.17 57 57
CEBPB 0.026 0.11 -10000 0 -0.36 20 20
STAT3 0.004 0.075 -10000 0 -0.35 23 23
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.038 0.065 -10000 0 -10000 0 0
STAT1 -0.01 0.096 -10000 0 -0.24 56 56
CALM1 0.019 0.019 -10000 0 -0.28 2 2
IFN-gamma (dimer) 0.018 0.016 -10000 0 -0.2 2 2
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
STAT1 (dimer)/PIAS1 -0.005 0.099 -10000 0 -0.27 44 44
CEBPB/PTGES2/Cbp/p300 -0.038 0.097 -10000 0 -0.36 31 31
mol:Ca2+ 0.017 0.074 -10000 0 -0.18 54 54
MAPK3 0.029 0.066 -10000 0 -0.31 1 1
STAT1 (dimer) -0.091 0.15 -10000 0 -0.35 111 111
MAPK1 -0.008 0.18 -10000 0 -0.81 23 23
JAK2 0.017 0.019 -10000 0 -0.21 3 3
PIK3R1 -0.011 0.098 -10000 0 -0.3 52 52
JAK1 0.001 0.082 -10000 0 -0.37 25 25
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 0.033 0.085 -10000 0 -0.38 6 6
SMAD7 -0.019 0.095 -10000 0 -0.2 82 82
CBL/CRKL/C3G 0.031 0.065 -10000 0 -0.2 18 18
PI3K -0.007 0.099 -10000 0 -0.24 50 50
IFNG 0.018 0.016 -10000 0 -0.2 2 2
apoptosis 0.02 0.074 0.24 2 -0.26 11 13
CAMK2G 0.018 0.021 -10000 0 -0.2 5 5
STAT3 (dimer) 0.004 0.075 -10000 0 -0.35 23 23
CAMK2A 0.02 0 -10000 0 -10000 0 0
CAMK2B 0.018 0.017 -10000 0 -0.2 3 3
FRAP1 -0.005 0.095 -10000 0 -0.24 48 48
PRKCD -0.014 0.1 -10000 0 -0.25 60 60
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.068 0.11 -10000 0 -0.26 111 111
PTPN2 0.018 0.029 -10000 0 -0.36 3 3
EP300 0.014 0.044 -10000 0 -0.37 7 7
IRF1 -0.025 0.16 -10000 0 -0.38 78 78
STAT1 (dimer)/PIASy -0.007 0.096 -10000 0 -0.26 42 42
SOCS1 0.024 0.003 -10000 0 -10000 0 0
mol:GDP 0.028 0.062 -10000 0 -0.19 18 18
CASP1 -0.032 0.12 -10000 0 -0.23 112 112
PTGES2 0.02 0 -10000 0 -10000 0 0
IRF9 0.012 0.09 -10000 0 -0.24 48 48
mol:PI-3-4-5-P3 -0.037 0.08 -10000 0 -0.24 50 50
RAP1/GDP -0.012 0.044 -10000 0 -0.19 19 19
CBL 0.012 0.066 -10000 0 -0.17 54 54
MAP3K1 0.012 0.067 -10000 0 -0.17 46 46
PIAS1 0.016 0.038 -10000 0 -0.34 6 6
PIAS4 0.019 0 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.068 0.11 -10000 0 -0.26 111 111
PTPN11 0.005 0.069 -10000 0 -0.18 54 54
CREBBP 0.019 0.002 -10000 0 -10000 0 0
RAPGEF1 0.02 0 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.025 0.045 -9999 0 -0.19 22 22
CRKL 0.019 0.01 -9999 0 -0.2 1 1
Rac1/GDP 0.013 0.023 -9999 0 -0.25 4 4
DOCK1 0.011 0.053 -9999 0 -0.27 17 17
ITGA4 0.02 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin/MAdCAM1 0.035 0.057 -9999 0 -0.17 39 39
EPO 0.02 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.029 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.01 0.053 -9999 0 -0.25 20 20
alpha4/beta1 Integrin 0.029 0 -9999 0 -10000 0 0
EPO/EPOR (dimer) 0.027 0.019 -9999 0 -10000 0 0
lamellipodium assembly -0.007 0.1 -9999 0 -0.26 47 47
PIK3CA -0.011 0.1 -9999 0 -0.33 48 48
PI3K -0.014 0.098 -9999 0 -0.25 66 66
ARF6 0.017 0.033 -9999 0 -0.36 4 4
JAK2 0.037 0.012 -9999 0 -10000 0 0
PXN 0.019 0.01 -9999 0 -0.2 1 1
PIK3R1 -0.011 0.097 -9999 0 -0.3 52 52
MADCAM1 0.02 0 -9999 0 -10000 0 0
cell adhesion 0.033 0.056 -9999 0 -0.17 39 39
CRKL/CBL 0.029 0.007 -9999 0 -10000 0 0
ITGB1 0.02 0 -9999 0 -10000 0 0
SRC -0.046 0.088 -9999 0 -0.17 155 155
ITGB7 0.02 0 -9999 0 -10000 0 0
RAC1 0.017 0.033 -9999 0 -0.36 4 4
alpha4/beta1 Integrin/VCAM1 -0.054 0.1 -9999 0 -0.2 155 155
p130Cas/Crk/Dock1 -0.031 0.086 -9999 0 -0.23 16 16
VCAM1 -0.14 0.17 -9999 0 -0.3 261 261
RHOA -0.008 0.1 -9999 0 -0.36 39 39
alpha4/beta1 Integrin/Paxillin/GIT1 0.051 0.008 -9999 0 -10000 0 0
BCAR1 -0.044 0.08 -9999 0 -0.16 155 155
EPOR 0.016 0.027 -9999 0 -0.2 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.02 0 -9999 0 -10000 0 0
GIT1 0.019 0.01 -9999 0 -0.2 1 1
Rac1/GTP -0.008 0.1 -9999 0 -0.27 47 47
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.008 0.12 -10000 0 -0.34 38 38
adherens junction organization -0.003 0.1 -10000 0 -0.27 54 54
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.009 0.098 -10000 0 -0.28 32 32
FMN1 -0.003 0.098 -10000 0 -0.26 54 54
mol:IP3 -0.005 0.097 -10000 0 -0.3 32 32
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.003 0.1 -10000 0 -0.27 54 54
CTNNB1 0.012 0.055 -10000 0 -0.37 11 11
AKT1 -0.006 0.11 -10000 0 -0.31 41 41
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.006 0.11 -10000 0 -0.4 30 30
CTNND1 0.006 0.071 -10000 0 -0.36 19 19
mol:PI-4-5-P2 0.003 0.097 -10000 0 -0.31 32 32
VASP 0.001 0.1 -10000 0 -0.32 32 32
ZYX -0.009 0.11 -10000 0 -0.34 38 38
JUB -0.003 0.098 -10000 0 -0.26 54 54
EGFR(dimer) 0.007 0.1 -10000 0 -0.32 31 31
E-cadherin/beta catenin-gamma catenin 0.019 0.066 -10000 0 -0.19 45 45
mol:PI-3-4-5-P3 -0.003 0.11 -10000 0 -0.32 35 35
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
PI3K -0.003 0.11 -10000 0 -0.32 35 35
FYN -0.035 0.14 -10000 0 -0.33 81 81
mol:Ca2+ -0.005 0.096 -10000 0 -0.29 32 32
JUP 0.002 0.079 -10000 0 -0.35 26 26
PIK3R1 -0.011 0.098 -10000 0 -0.3 52 52
mol:DAG -0.005 0.097 -10000 0 -0.3 32 32
CDH1 0.009 0.061 -10000 0 -0.33 16 16
RhoA/GDP -0.002 0.11 -10000 0 -0.29 44 44
establishment of polarity of embryonic epithelium 0.002 0.1 -10000 0 -0.31 32 32
SRC 0.02 0 -10000 0 -10000 0 0
RAC1 0.017 0.033 -10000 0 -0.36 4 4
RHOA -0.008 0.1 -10000 0 -0.36 39 39
EGFR 0.018 0.017 -10000 0 -0.2 3 3
CASR 0.001 0.091 -10000 0 -0.28 31 31
RhoA/GTP -0.007 0.1 -10000 0 -0.28 44 44
AKT2 0 0.1 -10000 0 -0.3 34 34
actin cable formation 0.001 0.098 -10000 0 -0.31 32 32
apoptosis 0.008 0.11 0.32 38 -10000 0 38
CTNNA1 0.01 0.06 -10000 0 -0.37 13 13
mol:GDP 0 0.099 -10000 0 -0.3 31 31
PIP5K1A 0.002 0.099 -10000 0 -0.31 32 32
PLCG1 -0.005 0.099 -10000 0 -0.3 32 32
Rac1/GTP 0.013 0.097 -10000 0 -0.3 32 32
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.015 0.044 -10000 0 -0.36 7 7
HDAC4 0.002 0.074 -10000 0 -0.28 33 33
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.005 0.052 0.24 19 -0.13 14 33
CDKN1A 0.014 0.12 -10000 0 -0.58 16 16
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.014 0.036 -10000 0 -0.2 14 14
FOXO3 -0.004 0.05 0.34 7 -0.19 8 15
FOXO1 -0.023 0.11 -10000 0 -0.29 74 74
FOXO4 0.022 0.028 -10000 0 -0.22 7 7
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.018 0.025 -10000 0 -0.31 3 3
TAT 0.02 0 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.011 0.011 -10000 0 -0.13 3 3
PPARGC1A 0.014 0.034 -10000 0 -0.2 13 13
FHL2 -0.049 0.14 -10000 0 -0.31 114 114
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.02 0.056 -10000 0 -0.25 19 19
HIST2H4A 0.005 0.052 0.13 14 -0.24 19 33
SIRT1/FOXO3a 0.003 0.052 0.16 20 -0.18 23 43
SIRT1 0.009 0.075 0.19 14 -0.35 19 33
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.023 0.066 -10000 0 -0.21 30 30
SIRT1/Histone H1b 0.023 0.052 0.16 14 -0.19 23 37
apoptosis -0.028 0.052 0.2 19 -10000 0 19
SIRT1/PGC1A 0.017 0.049 0.13 14 -0.2 17 31
p53/SIRT1 -0.059 0.15 0.36 14 -0.26 155 169
SIRT1/FOXO4 0.024 0.052 0.16 14 -0.19 23 37
FOXO1/FHL2/SIRT1 -0.028 0.1 -10000 0 -0.2 118 118
HIST1H1E 0.021 0.029 -10000 0 -0.22 7 7
SIRT1/p300 0.018 0.063 0.15 14 -0.26 23 37
muscle cell differentiation -0.013 0.045 0.2 17 -0.13 13 30
TP53 -0.094 0.18 0.19 14 -0.34 173 187
KU70/SIRT1/BAX 0.029 0.053 -10000 0 -0.2 19 19
CREBBP 0.02 0 -10000 0 -10000 0 0
MEF2D 0.02 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.022 0.053 0.15 14 -0.25 17 31
ACSS2 0.005 0.052 0.13 14 -0.24 19 33
SIRT1/PCAF/MYOD 0.013 0.045 0.13 13 -0.2 17 30
IL2 signaling events mediated by STAT5

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
GAB2 -0.03 0.12 -9999 0 -0.31 81 81
ELF1 0.009 0.088 -9999 0 -0.35 30 30
CCNA2 -0.052 0.14 -9999 0 -0.29 123 123
PIK3CA -0.012 0.1 -9999 0 -0.33 48 48
JAK3 0.019 0.004 -9999 0 -10000 0 0
PIK3R1 -0.011 0.098 -9999 0 -0.3 52 52
JAK1 0.002 0.081 -9999 0 -0.37 25 25
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.022 0.18 -9999 0 -0.46 56 56
SHC1 0.017 0.027 -9999 0 -0.23 6 6
SP1 0.014 0.045 -9999 0 -10000 0 0
IL2RA 0.02 0.062 -9999 0 -0.24 30 30
IL2RB 0.001 0.063 -9999 0 -0.21 44 44
SOS1 0 0.003 -9999 0 -10000 0 0
IL2RG -0.007 0.072 -9999 0 -0.2 64 64
G1/S transition of mitotic cell cycle -0.031 0.13 -9999 0 -0.33 69 69
PTPN11 0.019 0.004 -9999 0 -10000 0 0
CCND2 0.007 0.074 -9999 0 -10000 0 0
LCK 0.015 0.03 -9999 0 -0.2 10 10
GRB2 0.012 0.053 -9999 0 -0.35 11 11
IL2 0.019 0.004 -9999 0 -10000 0 0
CDK6 0.02 0 -9999 0 -10000 0 0
CCND3 -0.05 0.27 -9999 0 -0.84 48 48
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.006 0.063 -9999 0 -0.2 40 40
SNTA1 0.019 0.01 -9999 0 -0.2 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 -0.013 0.082 -9999 0 -0.2 72 72
MAPK12 0.017 0.039 -9999 0 -0.18 16 16
CCND1 -0.095 0.17 -9999 0 -0.39 134 134
p38 gamma/SNTA1 0.027 0.038 -9999 0 -0.17 16 16
MAP2K3 0.018 0.029 -9999 0 -0.36 3 3
PKN1 -0.003 0.08 -9999 0 -0.26 44 44
G2/M transition checkpoint 0.017 0.039 -9999 0 -0.18 16 16
MAP2K6 0.012 0.044 -9999 0 -0.21 16 16
MAPT 0.009 0.053 -9999 0 -0.16 40 40
MAPK13 -0.005 0.078 -9999 0 -0.25 40 40
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.006 0.051 -9999 0 -0.26 16 16
FAS signaling pathway (CD95)

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
SPTAN1 -0.005 0.051 -10000 0 -0.21 29 29
RFC1 -0.002 0.045 -10000 0 -0.2 23 23
PRKDC -0.009 0.056 -10000 0 -0.21 34 34
RIPK1 0.019 0.014 -10000 0 -0.2 2 2
CASP7 -0.014 0.15 -10000 0 -0.64 26 26
FASLG/FAS/FADD/FAF1 0.03 0.098 0.18 81 -0.23 35 116
MAP2K4 0.012 0.1 -10000 0 -0.39 18 18
mol:ceramide 0.018 0.085 -10000 0 -0.3 21 21
GSN -0.01 0.054 -10000 0 -0.21 30 30
FASLG/FAS/FADD/FAF1/Caspase 8 0.037 0.1 -10000 0 -0.32 17 17
FAS -0.017 0.11 -10000 0 -0.3 61 61
BID -0.022 0.073 -10000 0 -0.22 54 54
MAP3K1 0.002 0.11 -10000 0 -0.42 26 26
MAP3K7 0.002 0.072 -10000 0 -0.27 32 32
RB1 0.004 0.029 -10000 0 -0.2 9 9
CFLAR 0.011 0.052 -10000 0 -0.3 14 14
HGF/MET -0.028 0.097 -10000 0 -0.2 108 108
ARHGDIB -0.024 0.074 -10000 0 -0.2 75 75
FADD 0.013 0.047 -10000 0 -0.28 12 12
actin filament polymerization 0.01 0.054 0.2 30 -10000 0 30
NFKB1 -0.024 0.16 -10000 0 -0.7 28 28
MAPK8 0.017 0.1 -10000 0 -0.42 13 13
DFFA -0.004 0.049 -10000 0 -0.21 24 24
DNA fragmentation during apoptosis 0.004 0.029 -10000 0 -0.2 8 8
FAS/FADD/MET 0.01 0.077 -10000 0 -0.21 43 43
CFLAR/RIP1 0.023 0.038 -10000 0 -0.19 16 16
FAIM3 0.017 0.023 -10000 0 -0.2 6 6
FAF1 0.009 0.063 -10000 0 -0.32 18 18
PARP1 0.002 0.036 -10000 0 -0.22 12 12
DFFB 0.004 0.029 -10000 0 -0.21 8 8
CHUK -0.023 0.16 -10000 0 -0.66 28 28
FASLG 0.02 0.004 -10000 0 -10000 0 0
FAS/FADD -0.001 0.084 -10000 0 -0.21 69 69
HGF 0.019 0.014 -10000 0 -0.2 2 2
LMNA -0.002 0.054 -10000 0 -0.2 30 30
CASP6 -0.004 0.047 -10000 0 -0.2 23 23
CASP10 0.02 0.003 -10000 0 -10000 0 0
CASP3 -0.004 0.032 -10000 0 -0.24 8 8
PTPN13 -0.084 0.15 -10000 0 -0.29 179 179
CASP8 -0.003 0.027 -10000 0 -0.21 7 7
IL6 -0.011 0.13 -10000 0 -0.59 11 11
MET 0.012 0.041 -10000 0 -0.2 19 19
ICAD/CAD 0.003 0.046 -10000 0 -0.2 20 20
FASLG/FAS/FADD/FAF1/Caspase 10 0.018 0.086 -10000 0 -0.3 21 21
activation of caspase activity by cytochrome c -0.022 0.072 -10000 0 -0.22 54 54
PAK2 -0.001 0.041 -10000 0 -0.2 19 19
BCL2 0.019 0.01 -10000 0 -0.2 1 1
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.004 0.045 -10000 0 -0.55 3 3
HDAC1 0.027 0.057 -10000 0 -0.31 12 12
AES 0.015 0.057 -10000 0 -0.31 15 15
FBXW11 0.02 0 -10000 0 -10000 0 0
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.016 0.048 -10000 0 -0.15 40 40
TLE1 0.016 0.052 -10000 0 -0.31 12 12
AP1 -0.069 0.12 -10000 0 -0.23 154 154
NCSTN 0.009 0.06 -10000 0 -0.34 15 15
ADAM10 0.011 0.048 -10000 0 -0.23 20 20
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.083 0.15 -10000 0 -0.42 25 25
NICD/RBPSUH 0.029 0.054 -10000 0 -0.54 3 3
WIF1 0.01 0.045 -10000 0 -0.2 23 23
NOTCH1 0.021 0.051 -10000 0 -0.57 3 3
PSENEN -0.005 0.085 -10000 0 -0.28 44 44
KREMEN2 0.016 0.029 -10000 0 -0.2 9 9
DKK1 0.011 0.044 -10000 0 -0.2 22 22
beta catenin/beta TrCP1 -0.016 0.091 -10000 0 -0.3 31 31
APH1B 0.015 0.033 -10000 0 -0.2 12 12
APH1A 0.015 0.04 -10000 0 -0.3 8 8
AXIN1 0.009 0.039 0.19 16 -0.19 2 18
CtBP/CBP/TCF1/TLE1/AES 0.076 0.1 0.25 53 -0.24 16 69
PSEN1 0.013 0.047 -10000 0 -0.32 10 10
FOS -0.11 0.16 -10000 0 -0.29 233 233
JUN -0.011 0.099 -10000 0 -0.31 51 51
MAP3K7 0.009 0.072 -10000 0 -0.27 32 32
CTNNB1 -0.027 0.093 -10000 0 -0.32 31 31
MAPK3 0.02 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.021 0.052 -10000 0 -0.2 11 11
HNF1A 0.025 0.01 -10000 0 -10000 0 0
CTBP1 0.011 0.071 -10000 0 -0.32 22 22
MYC -0.27 0.52 -10000 0 -1.3 103 103
NKD1 0.002 0.002 -10000 0 -10000 0 0
FZD1 0.013 0.038 -10000 0 -0.2 16 16
NOTCH1 precursor/Deltex homolog 1 0.019 0.048 -10000 0 -0.54 3 3
apoptosis -0.068 0.12 -10000 0 -0.23 154 154
Delta 1/NOTCHprecursor 0.019 0.048 -10000 0 -0.54 3 3
DLL1 0 0 -10000 0 -10000 0 0
PPARD -0.016 0.05 -10000 0 -10000 0 0
Gamma Secretase 0.029 0.069 -10000 0 -0.17 46 46
APC 0.009 0.039 0.19 13 -10000 0 13
DVL1 -0.004 0.11 -10000 0 -0.35 42 42
CSNK2A1 -0.005 0.088 -10000 0 -0.33 35 35
MAP3K7IP1 0.026 0.013 -10000 0 -0.19 1 1
DKK1/LRP6/Kremen 2 0.025 0.046 -10000 0 -0.2 7 7
LRP6 0.007 0.058 -10000 0 -0.25 24 24
CSNK1A1 0.015 0.033 -10000 0 -0.37 4 4
NLK 0.032 0.054 -10000 0 -0.22 14 14
CCND1 -0.36 0.56 -10000 0 -1.3 133 133
WNT1 0.019 0 -10000 0 -10000 0 0
Axin1/APC/beta catenin -0.006 0.096 0.22 4 -0.31 30 34
DKK2 0.003 0.059 -10000 0 -0.2 40 40
NOTCH1 precursor/DVL1 0.015 0.1 -10000 0 -0.44 11 11
GSK3B 0.004 0.077 -10000 0 -0.34 25 25
FRAT1 0.022 0.014 -10000 0 -0.2 2 2
NOTCH/Deltex homolog 1 -0.004 0.045 -10000 0 -0.55 3 3
PPP2R5D 0.005 0.049 -10000 0 -0.16 25 25
MAPK1 -0.004 0.086 -10000 0 -0.29 41 41
WNT1/LRP6/FZD1 0.033 0.047 -10000 0 -0.17 12 12
RBPJ 0.014 0.045 -10000 0 -0.34 8 8
CREBBP 0.012 0.011 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.029 0.09 0.19 22 -0.31 12 34
ACTA1 0.028 0.075 0.21 37 -0.2 1 38
NUMA1 0.034 0.071 0.2 14 -0.26 6 20
SPTAN1 0.026 0.082 0.21 40 -0.23 6 46
LIMK1 0.034 0.074 0.21 42 -0.19 1 43
BIRC3 -0.051 0.13 -10000 0 -0.27 131 131
BIRC2 0.012 0.055 -10000 0 -0.35 12 12
BAX 0.014 0.036 -10000 0 -0.2 14 14
CASP10 0.004 0.061 -10000 0 -0.2 30 30
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.022 0.1 0.19 19 -0.32 21 40
DIABLO 0.005 0.074 -10000 0 -0.35 22 22
apoptotic nuclear changes 0.026 0.082 0.21 40 -0.22 6 46
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.019 0.01 -10000 0 -0.2 1 1
GSN 0.022 0.082 0.21 35 -0.2 4 39
MADD 0.019 0.01 -10000 0 -0.2 1 1
TFAP2A 0.019 0.042 -10000 0 -10000 0 0
BID -0.018 0.077 -10000 0 -0.22 56 56
MAP3K1 0.025 0.038 -10000 0 -10000 0 0
TRADD 0.02 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.027 0.021 -10000 0 -0.24 2 2
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.009 0.078 0.2 16 -0.2 7 23
CASP9 0.017 0.03 -10000 0 -0.26 6 6
DNA repair -0.025 0.061 0.31 5 -0.17 41 46
neuron apoptosis -0.001 0.13 -10000 0 -0.62 22 22
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.038 0.074 0.21 34 -0.29 2 36
APAF1 0.02 0 -10000 0 -10000 0 0
CASP6 0.018 0.14 -10000 0 -0.78 14 14
TRAF2 0.02 0 -10000 0 -10000 0 0
ICAD/CAD 0.032 0.081 0.21 40 -0.28 4 44
CASP7 0.017 0.1 0.22 43 -0.31 24 67
KRT18 -0.007 0.13 -10000 0 -0.54 26 26
apoptosis 0.014 0.1 0.23 20 -0.34 14 34
DFFA 0.028 0.084 0.21 42 -0.27 5 47
DFFB 0.034 0.075 0.21 42 -0.19 1 43
PARP1 0.025 0.061 0.17 41 -0.32 5 46
actin filament polymerization -0.033 0.07 0.18 1 -0.2 42 43
TNF 0.001 0.063 -10000 0 -0.2 46 46
CYCS -0.002 0.048 -10000 0 -0.26 9 9
SATB1 -0.017 0.15 -10000 0 -0.79 14 14
SLK 0.027 0.082 0.21 37 -0.25 6 43
p15 BID/BAX -0.008 0.072 -10000 0 -0.19 55 55
CASP2 0.02 0.067 -10000 0 -0.31 11 11
JNK cascade -0.025 0.037 -10000 0 -10000 0 0
CASP3 0.03 0.08 0.22 42 -0.19 2 44
LMNB2 0.029 0.062 -10000 0 -0.25 16 16
RIPK1 0.019 0.014 -10000 0 -0.2 2 2
CASP4 -0.027 0.12 -10000 0 -0.33 72 72
Mammalian IAPs/DIABLO -0.013 0.087 -10000 0 -0.19 80 80
negative regulation of DNA binding 0.019 0.042 -10000 0 -10000 0 0
stress fiber formation 0.027 0.081 0.21 37 -0.25 6 43
GZMB -0.004 0.074 -10000 0 -0.25 30 30
CASP1 -0.068 0.18 -10000 0 -0.4 105 105
LMNB1 0.009 0.1 -10000 0 -0.27 49 49
APP -0.001 0.13 -10000 0 -0.63 22 22
TNFRSF1A 0.007 0.066 -10000 0 -0.32 20 20
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0.025 -10000 0 -0.2 7 7
VIM 0.016 0.1 0.23 23 -0.35 13 36
LMNA 0.022 0.083 -10000 0 -0.3 25 25
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.015 0.071 -10000 0 -0.33 11 11
LRDD 0.02 0 -10000 0 -10000 0 0
SREBF1 0.031 0.077 0.21 41 -0.2 4 45
APAF-1/Caspase 9 0.016 0.073 0.35 4 -0.75 2 6
nuclear fragmentation during apoptosis 0.034 0.07 0.19 17 -0.25 6 23
CFL2 0.033 0.071 0.2 42 -0.18 1 43
GAS2 0.032 0.074 0.21 38 -0.19 1 39
positive regulation of apoptosis 0.02 0.081 -10000 0 -0.32 19 19
PRF1 0.006 0.054 -10000 0 -0.2 33 33
Glucocorticoid receptor regulatory network

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
PCK2 -0.044 0.18 0.3 4 -0.8 24 28
SMARCC2 -0.001 0.086 -10000 0 -0.34 31 31
SMARCC1 0.002 0.078 -10000 0 -0.34 26 26
TBX21 0.04 0.053 -10000 0 -10000 0 0
SUMO2 0.018 0.006 -10000 0 -10000 0 0
STAT1 (dimer) -0.039 0.13 -10000 0 -0.28 103 103
FKBP4 -0.011 0.1 -10000 0 -0.32 49 49
FKBP5 0.01 0.045 -10000 0 -0.2 23 23
GR alpha/HSP90/FKBP51/HSP90 0.007 0.08 -10000 0 -0.24 30 30
PRL 0.034 0.069 -10000 0 -0.44 1 1
cortisol/GR alpha (dimer)/TIF2 -0.012 0.12 0.35 4 -0.44 8 12
RELA -0.015 0.077 -10000 0 -0.22 31 31
FGG -0.006 0.12 0.33 3 -0.45 8 11
GR beta/TIF2 -0.003 0.088 -10000 0 -0.29 29 29
IFNG -0.039 0.13 -10000 0 -0.5 2 2
apoptosis -0.047 0.19 0.49 6 -0.48 35 41
CREB1 0.024 0.05 -10000 0 -0.36 9 9
histone acetylation 0.044 0.064 0.25 4 -0.26 4 8
BGLAP 0.026 0.11 -10000 0 -1 4 4
GR/PKAc 0.007 0.091 -10000 0 -0.23 38 38
NF kappa B1 p50/RelA -0.037 0.15 -10000 0 -0.33 80 80
SMARCD1 0.02 0 -10000 0 -10000 0 0
MDM2 0.008 0.038 0.15 1 -10000 0 1
GATA3 0.034 0.029 -10000 0 -0.19 9 9
AKT1 0.005 0.07 0.16 3 -0.27 26 29
CSF2 0.039 0.054 -10000 0 -10000 0 0
GSK3B 0.002 0.077 -10000 0 -0.34 25 25
NR1I3 -0.03 0.17 0.47 6 -0.47 13 19
CSN2 -0.006 0.11 0.29 4 -0.4 8 12
BRG1/BAF155/BAF170/BAF60A 0.017 0.092 -10000 0 -0.22 58 58
NFATC1 0.031 0 -10000 0 -10000 0 0
POU2F1 0.026 0.019 -10000 0 -0.36 1 1
CDKN1A -0.097 0.26 -10000 0 -1.3 18 18
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.002 0.006 -10000 0 -10000 0 0
SFN -0.066 0.15 -10000 0 -0.31 141 141
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.023 0.12 -10000 0 -0.25 73 73
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.12 0.32 0.45 6 -0.78 93 99
JUN -0.008 0.12 -10000 0 -0.33 17 17
IL4 0.046 0.05 -10000 0 -10000 0 0
CDK5R1 0.019 0.003 -10000 0 -10000 0 0
PRKACA 0.02 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.1 0.12 -10000 0 -0.28 114 114
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.02 0.077 -10000 0 -0.23 22 22
cortisol/GR alpha (monomer) -0.027 0.14 0.38 4 -0.5 9 13
NCOA2 0.019 0.014 -10000 0 -0.2 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.13 0.17 -10000 0 -0.31 235 235
AP-1/NFAT1-c-4 -0.1 0.2 -10000 0 -0.47 67 67
AFP 0.009 0.097 -10000 0 -10000 0 0
SUV420H1 0.002 0.08 -10000 0 -0.35 26 26
IRF1 -0.11 0.3 -10000 0 -0.81 75 75
TP53 -0.096 0.19 -10000 0 -0.36 165 165
PPP5C 0.016 0.027 -10000 0 -0.2 8 8
KRT17 -0.2 0.4 -10000 0 -1 93 93
KRT14 -0.022 0.11 -10000 0 -10000 0 0
TBP 0.018 0.051 -10000 0 -0.24 15 15
CREBBP 0.028 0.037 -10000 0 -10000 0 0
HDAC1 0.004 0.052 -10000 0 -0.33 12 12
HDAC2 0.001 0.071 -10000 0 -0.29 28 28
AP-1 -0.1 0.21 -10000 0 -0.48 67 67
MAPK14 0.017 0.018 -10000 0 -0.2 3 3
MAPK10 0.009 0.045 -10000 0 -0.21 22 22
MAPK11 0.018 0.006 -10000 0 -10000 0 0
KRT5 -0.083 0.21 -10000 0 -0.97 14 14
interleukin-1 receptor activity -0.002 0 -10000 0 -10000 0 0
NCOA1 0.004 0.073 -10000 0 -0.34 22 22
STAT1 -0.039 0.13 -10000 0 -0.28 102 102
CGA 0.041 0.064 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.032 0.11 -10000 0 -0.35 28 28
MAPK3 0.018 0.007 -10000 0 -10000 0 0
MAPK1 -0.006 0.086 -10000 0 -0.3 41 41
ICAM1 -0.078 0.27 -10000 0 -0.9 43 43
NFKB1 -0.036 0.12 -10000 0 -0.35 44 44
MAPK8 0.024 0.083 0.27 3 -10000 0 3
MAPK9 0.006 0.063 -10000 0 -0.3 21 21
cortisol/GR alpha (dimer) -0.05 0.19 0.49 6 -0.5 36 42
BAX -0.064 0.15 -10000 0 -0.53 1 1
POMC 0.04 0.081 -10000 0 -10000 0 0
EP300 0.023 0.056 -10000 0 -0.35 7 7
cortisol/GR alpha (dimer)/p53 -0.076 0.16 0.36 3 -0.44 25 28
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.082 0.25 54 -10000 0 54
SGK1 0.019 0.055 -10000 0 -0.28 6 6
IL13 -0.009 0.1 -10000 0 -10000 0 0
IL6 -0.021 0.12 -10000 0 -0.4 7 7
PRKACG 0.02 0 -10000 0 -10000 0 0
IL5 -0.005 0.093 -10000 0 -10000 0 0
IL2 -0.038 0.13 -10000 0 -0.5 2 2
CDK5 -0.001 0.077 -10000 0 -0.28 35 35
PRKACB -0.016 0.11 -10000 0 -0.33 55 55
HSP90AA1 0.02 0 -10000 0 -10000 0 0
IL8 -0.1 0.31 -10000 0 -0.92 59 59
CDK5R1/CDK5 0.013 0.055 -10000 0 -0.18 35 35
NF kappa B1 p50/RelA/PKAc -0.01 0.13 -10000 0 -0.34 38 38
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.014 0.12 0.34 5 -0.4 10 15
SMARCA4 -0.004 0.087 -10000 0 -0.31 39 39
chromatin remodeling -0.021 0.13 0.25 2 -0.39 30 32
NF kappa B1 p50/RelA/Cbp 0 0.14 -10000 0 -0.35 32 32
JUN (dimer) -0.008 0.12 -10000 0 -0.33 17 17
YWHAH -0.027 0.12 -10000 0 -0.32 73 73
VIPR1 0.036 0.063 -10000 0 -0.26 5 5
NR3C1 -0.02 0.12 0.23 2 -0.41 32 34
NR4A1 0.025 0.021 -10000 0 -10000 0 0
TIF2/SUV420H1 0.016 0.058 -10000 0 -0.24 24 24
MAPKKK cascade -0.047 0.19 0.49 6 -0.48 35 41
cortisol/GR alpha (dimer)/Src-1 -0.019 0.14 0.36 4 -0.44 13 17
PBX1 0 0.092 -10000 0 -0.29 47 47
POU1F1 0.027 0.009 -10000 0 -10000 0 0
SELE -0.006 0.11 -10000 0 -0.42 4 4
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.021 0.13 0.25 2 -0.39 30 32
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.014 0.12 0.34 5 -0.4 10 15
mol:cortisol -0.015 0.064 0.2 5 -0.23 1 6
MMP1 -0.069 0.11 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0 0.086 0.18 82 -10000 0 82
GNAI2 0.012 0.054 -10000 0 -0.36 11 11
S1P/S1P5/G12 0.013 0.009 -10000 0 -0.11 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.015 0.033 -10000 0 -0.2 12 12
RhoA/GTP 0.001 0.088 -10000 0 -0.18 82 82
negative regulation of cAMP metabolic process 0.004 0.071 -10000 0 -0.19 54 54
GNAZ 0.017 0.025 -10000 0 -0.2 7 7
GNAI3 0.01 0.06 -10000 0 -0.35 14 14
GNA12 0.018 0.017 -10000 0 -0.2 3 3
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.004 0.071 -10000 0 -0.19 54 54
RhoA/GDP -0.005 0.069 -10000 0 -0.25 39 39
RHOA -0.008 0.1 -10000 0 -0.36 39 39
GNAI1 -0.021 0.11 -10000 0 -0.28 74 74
TCGA08_rtk_signaling

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
PDGFRA -0.021 0.11 -10000 0 -0.3 67 67
HRAS 0.014 0.04 -10000 0 -0.27 10 10
EGFR 0.018 0.017 -10000 0 -0.2 3 3
AKT 0.035 0.06 -10000 0 -0.22 12 12
FOXO3 0.01 0.054 -10000 0 -0.28 17 17
AKT1 0.003 0.071 -10000 0 -0.28 30 30
FOXO1 -0.023 0.11 -10000 0 -0.29 74 74
AKT3 0.02 0 -10000 0 -10000 0 0
FOXO4 0.02 0 -10000 0 -10000 0 0
MET 0.012 0.041 -10000 0 -0.2 19 19
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
PIK3CB 0.018 0.021 -10000 0 -0.2 5 5
NRAS -0.03 0.12 -10000 0 -0.29 87 87
PIK3CG 0.02 0 -10000 0 -10000 0 0
PIK3R3 0.009 0.051 -10000 0 -0.22 23 23
PIK3R2 0.019 0.014 -10000 0 -0.2 2 2
NF1 0.02 0 -10000 0 -10000 0 0
RAS -0.01 0.07 -10000 0 -0.21 30 30
ERBB2 0.017 0.025 -10000 0 -0.2 7 7
proliferation/survival/translation -0.035 0.068 0.2 17 -0.18 10 27
PI3K 0.018 0.069 0.16 31 -0.2 21 52
PIK3R1 -0.011 0.097 -10000 0 -0.3 52 52
KRAS -0.007 0.087 -10000 0 -0.27 49 49
FOXO 0.048 0.04 0.16 18 -10000 0 18
AKT2 0.019 0.014 -10000 0 -0.2 2 2
PTEN -0.018 0.11 -10000 0 -0.35 55 55
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.006 0.059 -9999 0 -0.14 55 55
TC10/GTP 0.022 0.036 -9999 0 -0.15 17 17
Insulin Receptor/Insulin/IRS1/Shp2 0.014 0.077 -9999 0 -0.18 55 55
HRAS 0.014 0.04 -9999 0 -0.27 10 10
APS homodimer 0 0 -9999 0 -10000 0 0
GRB14 0.003 0.059 -9999 0 -0.2 41 41
FOXO3 -0.003 0.085 -9999 0 -0.66 8 8
AKT1 -0.014 0.088 -9999 0 -0.25 33 33
INSR 0.02 0.015 -9999 0 -0.2 2 2
Insulin Receptor/Insulin 0.048 0.06 -9999 0 -0.36 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.01 0.053 -9999 0 -0.25 20 20
SORBS1 0.02 0 -9999 0 -10000 0 0
CRK 0.01 0.053 -9999 0 -0.25 20 20
PTPN1 0.027 0.056 -9999 0 -0.35 9 9
CAV1 -0.036 0.097 -9999 0 -0.18 133 133
CBL/APS/CAP/Crk-II/C3G 0.042 0.028 -9999 0 -0.16 6 6
Insulin Receptor/Insulin/IRS1/NCK2 0.01 0.083 -9999 0 -0.18 62 62
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.018 0.09 -9999 0 -0.17 114 114
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.013 0.075 -9999 0 -0.28 15 15
RPS6KB1 -0.008 0.083 -9999 0 -0.23 33 33
PARD6A 0.019 0.01 -9999 0 -0.2 1 1
CBL 0.02 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.002 0.012 -9999 0 -10000 0 0
PIK3R1 -0.011 0.097 -9999 0 -0.3 52 52
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.01 0.086 -9999 0 -0.22 41 41
HRAS/GTP -0.024 0.048 -9999 0 -0.14 70 70
Insulin Receptor 0.02 0.015 -9999 0 -0.2 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.018 0.08 -9999 0 -0.16 68 68
PRKCI -0.015 0.13 -9999 0 -0.47 38 38
Insulin Receptor/Insulin/GRB14/PDK1 -0.043 0.066 -9999 0 -0.24 28 28
SHC1 0.017 0.027 -9999 0 -0.23 6 6
negative regulation of MAPKKK cascade 0.012 0.067 -9999 0 -0.31 7 7
PI3K -0.013 0.095 -9999 0 -0.17 114 114
NCK2 0.012 0.051 -9999 0 -0.34 11 11
RHOQ 0.008 0.06 -9999 0 -0.28 21 21
mol:H2O2 -0.001 0.006 -9999 0 -10000 0 0
HRAS/GDP 0.011 0.028 -9999 0 -0.18 10 10
AKT2 -0.009 0.081 -9999 0 -0.23 26 26
PRKCZ -0.017 0.065 -9999 0 -0.43 11 11
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP 0 0.063 -9999 0 -0.15 59 59
F2RL2 0.02 0 -9999 0 -10000 0 0
TRIP10 0.013 0.04 -9999 0 -0.21 16 16
Insulin Receptor/Insulin/Shc 0.037 0.019 -9999 0 -0.22 1 1
TC10/GTP/CIP4/Exocyst 0.016 0.042 -9999 0 -0.2 12 12
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.043 0.034 -9999 0 -0.16 11 11
RAPGEF1 0.02 0 -9999 0 -10000 0 0
RASA1 -0.01 0.1 -9999 0 -0.35 44 44
NCK1 0.002 0.074 -9999 0 -0.28 32 32
CBL/APS/CAP/Crk-II 0.033 0.029 -9999 0 -0.18 6 6
TC10/GDP 0.007 0.041 -9999 0 -0.19 21 21
Insulin Receptor/Insulin/SHC/GRB10 0.044 0.038 -9999 0 -0.18 9 9
INPP5D -0.011 0.062 -9999 0 -0.17 56 56
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.005 0.007 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.02 0 -9999 0 -10000 0 0
IRS1 -0.046 0.13 -9999 0 -0.28 118 118
p62DOK/RasGAP 0.013 0.068 -9999 0 -0.31 7 7
INS 0.021 0.006 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.011 0.061 -9999 0 -0.16 56 56
GRB2 0.012 0.053 -9999 0 -0.35 11 11
EIF4EBP1 -0.018 0.092 -9999 0 -0.23 57 57
PTPRA 0.014 0.052 -9999 0 -0.3 13 13
PIK3CA -0.011 0.1 -9999 0 -0.33 48 48
TC10/GTP/CIP4 0.016 0.042 -9999 0 -0.2 12 12
PDPK1 0.02 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.002 0.072 -9999 0 -0.18 65 65
Insulin Receptor/Insulin/IRS1 0.002 0.074 -9999 0 -0.18 56 56
Insulin Receptor/Insulin/IRS3 0.03 0.014 -9999 0 -0.12 2 2
Par3/Par6 0.037 0.039 -9999 0 -0.16 13 13
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 -0.027 0.12 -9999 0 -0.33 72 72
SMAD2 0.006 0.046 -9999 0 -0.19 20 20
SMAD3 0.027 0.052 -9999 0 -0.44 1 1
SMAD3/SMAD4 -0.034 0.18 -9999 0 -0.45 74 74
SMAD4/Ubc9/PIASy 0.011 0.075 -9999 0 -0.2 58 58
SMAD2/SMAD2/SMAD4 -0.005 0.11 -9999 0 -0.3 43 43
PPM1A 0.02 0 -9999 0 -10000 0 0
CALM1 0.019 0.019 -9999 0 -0.28 2 2
SMAD2/SMAD4 -0.005 0.078 -9999 0 -0.2 64 64
MAP3K1 0.017 0.025 -9999 0 -0.2 7 7
TRAP-1/SMAD4 -0.004 0.087 -9999 0 -0.22 72 72
MAPK3 0.02 0 -9999 0 -10000 0 0
MAPK1 -0.004 0.086 -9999 0 -0.29 41 41
NUP214 0.02 0 -9999 0 -10000 0 0
CTDSP1 0.016 0.037 -9999 0 -0.36 5 5
CTDSP2 0.015 0.038 -9999 0 -0.28 8 8
CTDSPL 0.019 0.01 -9999 0 -0.2 1 1
KPNB1 0.012 0.054 -9999 0 -0.36 11 11
TGFBRAP1 0.02 0 -9999 0 -10000 0 0
UBE2I 0.02 0 -9999 0 -10000 0 0
NUP153 -0.003 0.088 -9999 0 -0.32 36 36
KPNA2 -0.018 0.11 -9999 0 -0.35 55 55
PIAS4 0.02 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.03 0.039 -10000 0 -0.18 16 16
HDAC3 0.011 0.055 -10000 0 -0.35 12 12
Ran/GTP/Exportin 1/HDAC4 -0.019 0.051 -10000 0 -0.15 60 60
GATA1/HDAC4 0.017 0.052 -10000 0 -0.24 15 15
GATA1/HDAC5 0.027 0.019 -10000 0 -0.12 8 8
GATA2/HDAC5 0.024 0.028 -10000 0 -0.12 19 19
HDAC5/BCL6/BCoR 0.016 0.069 -10000 0 -0.2 41 41
HDAC9 -0.041 0.13 -10000 0 -0.28 108 108
Glucocorticoid receptor/Hsp90/HDAC6 0.019 0.067 -10000 0 -0.2 46 46
HDAC4/ANKRA2 0.009 0.067 -10000 0 -0.19 51 51
HDAC5/YWHAB 0.024 0.035 -10000 0 -0.24 6 6
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.051 -10000 0 -0.18 33 33
GATA2 0.015 0.032 -10000 0 -0.2 11 11
HDAC4/RFXANK -0.004 0.085 -10000 0 -0.2 79 79
BCOR 0.009 0.06 -10000 0 -0.3 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0.016 0.027 -10000 0 -0.2 8 8
GNB1/GNG2 0.007 0.045 -10000 0 -0.25 16 16
Histones -0.001 0.067 -10000 0 -0.16 69 69
ADRBK1 0.019 0.01 -10000 0 -0.2 1 1
HDAC4 0.002 0.074 -10000 0 -0.28 33 33
XPO1 0.019 0.01 -10000 0 -0.2 1 1
HDAC5/ANKRA2 0.019 0.046 -10000 0 -0.17 27 27
HDAC4/Ubc9 0.017 0.052 -10000 0 -0.24 15 15
HDAC7 0 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.022 0.041 -10000 0 -0.26 9 9
TUBA1B 0.018 0.023 -10000 0 -0.36 2 2
HDAC6 0.019 0.01 -10000 0 -0.2 1 1
HDAC5/RFXANK 0.006 0.071 -10000 0 -0.2 56 56
CAMK4 0.019 0.01 -10000 0 -0.2 1 1
Tubulin/HDAC6 -0.017 0.094 -10000 0 -0.2 94 94
SUMO1 0.013 0.049 -10000 0 -0.36 9 9
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.015 0.041 -10000 0 -0.34 7 7
GATA1 0.02 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.013 0.048 -10000 0 -0.3 12 12
NR3C1 -0.014 0.11 -10000 0 -0.36 49 49
SUMO1/HDAC4 0.019 0.064 -10000 0 -0.21 24 24
SRF 0.02 0 -10000 0 -10000 0 0
HDAC4/YWHAB 0.013 0.059 -10000 0 -0.24 21 21
Tubulin -0.037 0.11 -10000 0 -0.25 94 94
HDAC4/14-3-3 E 0.012 0.064 -10000 0 -0.27 20 20
GNB1 0.008 0.065 -10000 0 -0.36 16 16
RANGAP1 0.018 0.017 -10000 0 -0.2 3 3
BCL6/BCoR 0.004 0.077 -10000 0 -0.25 39 39
HDAC4/HDAC3/SMRT (N-CoR2) 0.024 0.055 -10000 0 -0.2 26 26
HDAC4/SRF 0.029 0.045 -10000 0 -0.2 15 15
HDAC4/ER alpha 0.017 0.052 -10000 0 -0.18 33 33
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.001 0.067 -10000 0 -0.16 69 69
cell motility -0.018 0.093 -10000 0 -0.2 94 94
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.02 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0.009 0.038 -10000 0 -0.24 12 12
BCL6 -0.006 0.091 -10000 0 -0.31 42 42
HDAC4/CaMK II delta B 0.002 0.074 -10000 0 -0.28 33 33
Hsp90/HDAC6 0.029 0.007 -10000 0 -10000 0 0
ESR1 0.02 0 -10000 0 -10000 0 0
HDAC6/HDAC11 0.029 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.023 0.066 -10000 0 -0.17 49 49
NPC 0.002 0.041 -10000 0 -0.18 26 26
MEF2C 0.018 0.019 -10000 0 -0.2 4 4
RAN 0.003 0.078 -10000 0 -0.36 24 24
HDAC4/MEF2C 0.043 0.05 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
NCOR2 0.02 0 -10000 0 -10000 0 0
TUBB2A -0.073 0.15 -10000 0 -0.3 157 157
HDAC11 0.02 0 -10000 0 -10000 0 0
HSP90AA1 0.02 0 -10000 0 -10000 0 0
RANBP2 0 0.084 -10000 0 -0.35 29 29
ANKRA2 0.009 0.06 -10000 0 -0.3 19 19
RFXANK -0.01 0.098 -10000 0 -0.32 48 48
nuclear import -0.018 0.064 0.24 26 -10000 0 26
Circadian rhythm pathway

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
chromatin modification -0.055 0.3 -10000 0 -1.1 41 41
CLOCK 0.006 0.068 -10000 0 -0.36 17 17
TIMELESS/CRY2 -0.053 0.31 -10000 0 -1.1 40 40
DEC1/BMAL1 0.026 0.02 -10000 0 -10000 0 0
ATR 0.014 0.046 -10000 0 -0.36 8 8
NR1D1 0.004 0.11 -10000 0 -0.57 1 1
ARNTL 0.015 0.028 -10000 0 -0.2 6 6
TIMELESS -0.065 0.33 -10000 0 -1.2 40 40
NPAS2 0.014 0.032 -10000 0 -0.21 8 8
CRY2 0.02 0 -10000 0 -10000 0 0
mol:CO 0 0.041 0.14 40 -10000 0 40
CHEK1 -0.013 0.093 -10000 0 -0.26 64 64
mol:HEME 0 0.041 -10000 0 -0.14 40 40
PER1 0.017 0.025 -10000 0 -0.2 7 7
BMAL/CLOCK/NPAS2 0.031 0.065 -10000 0 -0.2 18 18
BMAL1/CLOCK -0.003 0.17 -10000 0 -0.54 42 42
S phase of mitotic cell cycle -0.055 0.3 -10000 0 -1.1 41 41
TIMELESS/CHEK1/ATR -0.057 0.31 -10000 0 -1.1 41 41
mol:NADPH 0 0.041 -10000 0 -0.14 40 40
PER1/TIMELESS -0.054 0.31 -10000 0 -1.1 40 40
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.02 0 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.011 0.082 -9999 0 -0.18 54 54
SMAD6-7/SMURF1 0.017 0.066 -9999 0 -0.2 42 42
NOG 0 0 -9999 0 -10000 0 0
SMAD9 0.023 0.026 -9999 0 -10000 0 0
SMAD4 -0.027 0.12 -9999 0 -0.33 72 72
SMAD5 0.016 0.068 -9999 0 -0.27 10 10
BMP7/USAG1 -0.016 0.077 -9999 0 -0.25 14 14
SMAD5/SKI 0.027 0.066 -9999 0 -0.26 9 9
SMAD1 -0.012 0.13 -9999 0 -0.3 76 76
BMP2 0.016 0.03 -9999 0 -0.2 10 10
SMAD1/SMAD1/SMAD4 -0.053 0.12 -9999 0 -0.36 46 46
BMPR1A 0.002 0.08 -9999 0 -0.36 25 25
BMPR1B 0.015 0.032 -9999 0 -0.2 11 11
BMPR1A-1B/BAMBI 0.002 0.069 -9999 0 -0.2 26 26
AHSG 0.02 0 -9999 0 -10000 0 0
CER1 0.02 0 -9999 0 -10000 0 0
BMP2-4/CER1 0.025 0.043 -9999 0 -0.2 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA 0.011 0.066 -9999 0 -0.24 11 11
BMP2-4 (homodimer) 0.012 0.05 -9999 0 -0.25 2 2
RGMB 0 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.022 0.073 -9999 0 -0.18 49 49
RGMA 0 0 -9999 0 -10000 0 0
SMURF1 0.02 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0.004 0.057 -9999 0 -0.16 47 47
BMP2-4/USAG1 -0.006 0.072 -9999 0 -0.21 20 20
SMAD6/SMURF1/SMAD5 0.027 0.066 -9999 0 -0.26 9 9
SOSTDC1 -0.034 0.096 -9999 0 -0.2 129 129
BMP7/BMPR2/BMPR1A-1B 0.02 0.074 -9999 0 -0.18 48 48
SKI 0.02 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.011 0.044 -9999 0 -0.2 22 22
HFE2 0 0 -9999 0 -10000 0 0
ZFYVE16 0.015 0.038 -9999 0 -0.25 10 10
MAP3K7 0.002 0.072 -9999 0 -0.27 32 32
BMP2-4/CHRD 0.025 0.043 -9999 0 -0.2 2 2
SMAD5/SMAD5/SMAD4 0.015 0.082 -9999 0 -0.31 19 19
MAPK1 -0.004 0.086 -9999 0 -0.29 41 41
TAK1/TAB family 0.028 0.07 -9999 0 -0.29 10 10
BMP7 (homodimer) 0.006 0.053 -9999 0 -0.2 32 32
NUP214 0.02 0 -9999 0 -10000 0 0
BMP6/FETUA 0.023 0.03 -9999 0 -10000 0 0
SMAD1/SKI -0.001 0.12 -9999 0 -0.28 76 76
SMAD6 0.02 0 -9999 0 -10000 0 0
CTDSP2 0.015 0.038 -9999 0 -0.28 8 8
BMP2-4/FETUA 0.025 0.043 -9999 0 -0.2 2 2
MAP3K7IP1 0.019 0.01 -9999 0 -0.2 1 1
GREM1 -0.02 0.086 -9999 0 -0.2 96 96
BMPR2 (homodimer) 0 0.084 -9999 0 -0.34 30 30
GADD34/PP1CA 0.026 0.051 -9999 0 -0.21 17 17
BMPR1A-1B (homodimer) 0.014 0.06 -9999 0 -0.24 24 24
CHRDL1 0 0 -9999 0 -10000 0 0
ENDOFIN/SMAD1 -0.002 0.13 -9999 0 -0.29 76 76
SMAD6-7/SMURF1/SMAD1 0.001 0.14 -9999 0 -0.4 29 29
SMAD6/SMURF1 0.02 0 -9999 0 -10000 0 0
BAMBI -0.022 0.087 -9999 0 -0.2 100 100
SMURF2 0.009 0.061 -9999 0 -0.31 18 18
BMP2-4/CHRDL1 0.013 0.041 -9999 0 -0.21 2 2
BMP2-4/GREM1 0.002 0.066 -9999 0 -0.2 15 15
SMAD7 -0.018 0.11 -9999 0 -0.32 60 60
SMAD8A/SMAD8A/SMAD4 0.022 0.048 -9999 0 -0.23 11 11
SMAD1/SMAD6 -0.001 0.12 -9999 0 -0.28 76 76
TAK1/SMAD6 0.017 0.051 -9999 0 -0.24 14 14
BMP7 0.006 0.053 -9999 0 -0.2 32 32
BMP6 0.011 0.044 -9999 0 -0.2 22 22
MAP3K7IP2 0.01 0.057 -9999 0 -0.3 17 17
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.002 0.082 -9999 0 -0.28 24 24
PPM1A 0.02 0 -9999 0 -10000 0 0
SMAD1/SMURF2 -0.005 0.13 -9999 0 -0.3 77 77
SMAD7/SMURF1 0.003 0.077 -9999 0 -0.24 42 42
CTDSPL 0.019 0.01 -9999 0 -0.2 1 1
PPP1CA 0.01 0.061 -9999 0 -0.36 14 14
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.016 0.037 -9999 0 -0.36 5 5
PPP1R15A 0.011 0.043 -9999 0 -0.2 21 21
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS 0.001 0.062 -9999 0 -0.24 14 14
CHRD 0.02 0 -9999 0 -10000 0 0
BMPR2 0 0.084 -9999 0 -0.34 30 30
BMP2-4/BMPR2/BMPR1A-1B/RGM 0.004 0.064 -9999 0 -0.18 47 47
BMP4 -0.001 0.065 -9999 0 -0.2 50 50
FST -0.014 0.08 -9999 0 -0.2 81 81
BMP2-4/NOG 0.013 0.041 -9999 0 -0.21 2 2
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.029 0.071 -9999 0 -0.29 5 5
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.024 0.011 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.031 0.049 -10000 0 -0.18 25 25
CDKN1B -0.014 0.13 -10000 0 -0.42 42 42
CDKN1A -0.003 0.11 -10000 0 -0.37 41 41
FRAP1 0.02 0 -10000 0 -10000 0 0
PRKDC -0.006 0.091 -10000 0 -0.31 41 41
FOXO3 0.001 0.11 -10000 0 -0.36 41 41
AKT1 0 0.11 -10000 0 -0.38 41 41
BAD 0.013 0.045 -10000 0 -0.29 11 11
AKT3 0.02 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.006 0.11 -10000 0 -0.36 41 41
AKT1/ASK1 0.005 0.11 -10000 0 -0.36 42 42
BAD/YWHAZ 0.027 0.054 -10000 0 -0.2 25 25
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0.012 0.052 -10000 0 -0.32 12 12
JNK cascade -0.004 0.11 0.35 42 -10000 0 42
TSC1 0.003 0.11 -10000 0 -0.36 41 41
YWHAZ 0.005 0.074 -10000 0 -0.35 22 22
AKT1/RAF1 0.009 0.11 -10000 0 -0.36 41 41
EP300 0.015 0.044 -10000 0 -0.36 7 7
mol:GDP 0 0.11 -10000 0 -0.37 41 41
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.004 0.11 -10000 0 -0.36 42 42
YWHAQ 0.013 0.049 -10000 0 -0.36 9 9
TBC1D4 0.022 0.015 -10000 0 -10000 0 0
MAP3K5 0.008 0.056 -10000 0 -0.25 23 23
MAPKAP1 0.018 0.023 -10000 0 -0.36 2 2
negative regulation of cell cycle 0.028 0.12 0.33 55 -10000 0 55
YWHAH -0.027 0.12 -10000 0 -0.32 73 73
AKT1S1 -0.001 0.11 -10000 0 -0.36 41 41
CASP9 0.004 0.11 -10000 0 -0.36 41 41
YWHAB 0.015 0.041 -10000 0 -0.34 7 7
p27Kip1/KPNA1 -0.003 0.13 -10000 0 -0.39 41 41
GBL 0.013 0.04 -10000 0 -0.23 14 14
PDK1/Src/Hsp90 0.04 0 -10000 0 -10000 0 0
YWHAE 0.013 0.048 -10000 0 -0.3 12 12
SRC 0.02 0 -10000 0 -10000 0 0
AKT2/p21CIP1 0.005 0.1 -10000 0 -0.32 41 41
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.024 0.043 -10000 0 -0.42 2 2
CHUK 0 0.11 -10000 0 -0.36 42 42
BAD/BCL-XL 0.022 0.11 -10000 0 -0.33 41 41
mTORC2 0.034 0.025 -10000 0 -0.18 4 4
AKT2 0.019 0.006 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family -0.034 0.16 -10000 0 -0.38 71 71
PDPK1 0.02 0 -10000 0 -10000 0 0
MDM2 0.006 0.11 -10000 0 -0.36 41 41
MAPKKK cascade -0.009 0.11 0.35 41 -10000 0 41
MDM2/Cbp/p300 0.024 0.1 -10000 0 -0.32 41 41
TSC1/TSC2 0 0.11 -10000 0 -0.36 41 41
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.099 -10000 0 -0.31 41 41
glucose import 0.026 0.013 -10000 0 -10000 0 0
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.019 0.068 -10000 0 -0.29 6 6
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.026 0.013 -10000 0 -10000 0 0
GSK3A 0.006 0.11 -10000 0 -0.36 41 41
FOXO1 -0.013 0.12 -10000 0 -0.36 45 45
GSK3B -0.002 0.12 -10000 0 -0.37 41 41
SFN -0.066 0.15 -10000 0 -0.31 141 141
G1/S transition of mitotic cell cycle 0.004 0.11 -10000 0 -0.35 41 41
p27Kip1/14-3-3 family -0.039 0.16 -10000 0 -0.47 43 43
PRKACA 0.02 0 -10000 0 -10000 0 0
KPNA1 0.017 0.033 -10000 0 -0.36 4 4
HSP90AA1 0.02 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.02 0 -10000 0 -10000 0 0
CREBBP 0.02 0 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.018 0.07 -9999 0 -0.2 45 45
E-cadherin/beta catenin 0.016 0.057 -9999 0 -0.24 24 24
CTNNB1 0.012 0.054 -9999 0 -0.36 11 11
JUP 0.002 0.079 -9999 0 -0.35 26 26
CDH1 0.009 0.061 -9999 0 -0.34 16 16
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.023 0.17 -10000 0 -0.64 31 31
epithelial cell differentiation -0.043 0.15 -10000 0 -0.67 26 26
ITCH 0.018 0.038 -10000 0 -0.22 7 7
WWP1 -0.041 0.28 -10000 0 -1.3 26 26
FYN -0.049 0.13 -10000 0 -0.28 122 122
EGFR 0.018 0.017 -10000 0 -0.2 3 3
PRL 0.017 0.025 -10000 0 -0.2 7 7
neuron projection morphogenesis 0.006 0.13 -10000 0 -0.51 27 27
PTPRZ1 0.014 0.036 -10000 0 -0.2 14 14
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.012 0.14 -10000 0 -0.56 26 26
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.014 0.15 -10000 0 -0.64 26 26
ADAM17 0.02 0.031 -10000 0 -0.19 3 3
ErbB4/ErbB4 -0.034 0.18 -10000 0 -0.7 31 31
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.036 0.16 -10000 0 -0.64 31 31
NCOR1 0.014 0.046 -10000 0 -0.36 8 8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.036 0.16 -10000 0 -0.62 28 28
GRIN2B -0.03 0.15 -10000 0 -0.58 28 28
ErbB4/ErbB2/betacellulin -0.008 0.15 -10000 0 -0.61 26 26
STAT1 -0.024 0.11 -10000 0 -0.3 74 74
HBEGF 0.018 0.021 -10000 0 -0.2 5 5
PRLR 0.02 0 -10000 0 -10000 0 0
E4ICDs/ETO2 -0.023 0.17 -10000 0 -0.64 31 31
axon guidance -0.051 0.19 -10000 0 -0.78 29 29
NEDD4 0.021 0.029 -10000 0 -0.17 2 2
Prolactin receptor/Prolactin receptor/Prolactin 0.027 0.017 -10000 0 -0.12 7 7
CBFA2T3 0.019 0.01 -10000 0 -0.2 1 1
ErbB4/ErbB2/HBEGF -0.006 0.14 -10000 0 -0.6 26 26
MAPK3 0.009 0.13 -10000 0 -0.52 26 26
STAT1 (dimer) -0.045 0.18 -10000 0 -0.62 34 34
MAPK1 0.002 0.14 -10000 0 -0.53 27 27
JAK2 0.018 0.017 -10000 0 -0.2 3 3
ErbB4/ErbB2/neuregulin 1 beta -0.008 0.14 -10000 0 -0.6 26 26
NRG1 0.025 0.019 -10000 0 -10000 0 0
NRG3 0 0 -10000 0 -10000 0 0
NRG2 0.018 0.017 -10000 0 -0.2 3 3
NRG4 0 0 -10000 0 -10000 0 0
heart development -0.051 0.19 -10000 0 -0.78 29 29
neural crest cell migration -0.008 0.14 -10000 0 -0.59 26 26
ERBB2 0.023 0.026 -10000 0 -10000 0 0
WWOX/E4ICDs -0.023 0.17 -10000 0 -0.64 31 31
SHC1 0.017 0.027 -10000 0 -0.23 6 6
ErbB4/EGFR/neuregulin 4 -0.022 0.16 -10000 0 -0.67 26 26
apoptosis 0.024 0.15 0.66 26 -10000 0 26
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.023 0.17 -10000 0 -0.64 31 31
ErbB4/ErbB2/epiregulin -0.006 0.14 -10000 0 -0.6 26 26
ErbB4/ErbB4/betacellulin/betacellulin -0.026 0.17 -10000 0 -0.65 31 31
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.007 0.15 -10000 0 -0.61 26 26
MDM2 -0.025 0.17 -10000 0 -0.71 26 26
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.003 0.13 -10000 0 -0.56 26 26
STAT5A -0.044 0.18 -10000 0 -0.77 28 28
ErbB4/EGFR/neuregulin 1 beta -0.004 0.14 -10000 0 -0.6 26 26
DLG4 0.02 0 -10000 0 -10000 0 0
GRB2/SHC 0.022 0.042 -10000 0 -0.2 17 17
E4ICDs/TAB2/NCoR1 -0.018 0.16 -10000 0 -0.66 27 27
STAT5A (dimer) -0.014 0.18 -10000 0 -0.74 26 26
MAP3K7IP2 0.01 0.057 -10000 0 -0.3 17 17
STAT5B (dimer) -0.042 0.18 -10000 0 -0.76 28 28
LRIG1 -0.07 0.15 -10000 0 -0.31 148 148
EREG 0.017 0.024 -10000 0 -0.2 6 6
BTC 0.013 0.038 -10000 0 -0.2 16 16
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.051 0.2 -10000 0 -0.79 29 29
ERBB4 -0.034 0.18 -10000 0 -0.7 31 31
STAT5B 0.02 0 -10000 0 -10000 0 0
YAP1 -0.031 0.15 -10000 0 -0.56 36 36
GRB2 0.012 0.053 -10000 0 -0.35 11 11
ErbB4/ErbB2/neuregulin 4 -0.017 0.14 -10000 0 -0.6 26 26
glial cell differentiation 0.018 0.16 0.66 27 -10000 0 27
WWOX 0.019 0.01 -10000 0 -0.2 1 1
cell proliferation -0.01 0.15 -10000 0 -0.63 26 26
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.002 0.064 -10000 0 -0.16 63 63
MAP4K4 0.007 0.077 -10000 0 -0.27 17 17
BAG4 0.015 0.033 -10000 0 -0.2 12 12
PKC zeta/ceramide 0.001 0.024 0.093 20 -10000 0 20
NFKBIA -0.006 0.091 -10000 0 -0.32 40 40
BIRC3 -0.05 0.13 -10000 0 -0.27 131 131
BAX 0.009 0.017 -10000 0 -10000 0 0
RIPK1 0.019 0.014 -10000 0 -0.2 2 2
AKT1 -0.001 0.065 -10000 0 -0.26 30 30
BAD 0.005 0.033 0.11 19 -0.14 10 29
SMPD1 0.01 0.042 -10000 0 -0.17 15 15
RB1 0.008 0.027 0.11 20 -0.18 1 21
FADD/Caspase 8 0.017 0.085 -10000 0 -0.36 13 13
MAP2K4 0.01 0.033 0.11 20 -0.17 6 26
NSMAF 0.006 0.069 -10000 0 -0.32 22 22
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.01 0.033 0.11 19 -0.17 8 27
EGF 0.019 0.01 -10000 0 -0.2 1 1
mol:ceramide 0.002 0.028 0.11 21 -10000 0 21
MADD 0.019 0.01 -10000 0 -0.2 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.002 0.071 -10000 0 -0.24 29 29
ASAH1 0.013 0.049 -10000 0 -0.32 11 11
negative regulation of cell cycle 0.008 0.027 0.11 20 -0.18 1 21
cell proliferation -0.007 0.076 -10000 0 -0.22 21 21
BID -0.051 0.22 -10000 0 -0.68 53 53
MAP3K1 0.007 0.028 0.11 20 -0.095 6 26
EIF2A 0.004 0.045 0.1 19 -0.16 28 47
TRADD 0.02 0 -10000 0 -10000 0 0
CRADD 0.019 0.01 -10000 0 -0.2 1 1
MAPK3 0.02 0.032 0.11 19 -0.15 8 27
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.014 0.041 -10000 0 -0.16 8 8
Cathepsin D/ceramide 0.007 0.042 0.11 18 -0.18 14 32
FADD 0.012 0.072 -10000 0 -0.29 13 13
KSR1 0.008 0.026 0.11 20 -10000 0 20
MAPK8 0.013 0.028 0.11 20 -0.1 6 26
PRKRA -0.002 0.048 0.11 19 -0.17 29 48
PDGFA -0.013 0.093 -10000 0 -0.26 63 63
TRAF2 0.02 0 -10000 0 -10000 0 0
IGF1 -0.07 0.14 -10000 0 -0.27 166 166
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process 0.002 0.028 0.11 20 -10000 0 20
CTSD 0.001 0.076 -10000 0 -0.3 31 31
regulation of nitric oxide biosynthetic process 0.012 0.064 -10000 0 -0.24 29 29
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.007 0.081 -10000 0 -0.24 21 21
PRKCD -0.005 0.09 -10000 0 -0.32 39 39
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.002 0.071 -10000 0 -0.24 29 29
RelA/NF kappa B1 0.012 0.064 -10000 0 -0.24 29 29
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.02 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.01 0.073 -10000 0 -0.31 11 11
TNFR1A/BAG4/TNF-alpha 0.018 0.058 -10000 0 -0.2 19 19
mol:Sphingosine-1-phosphate 0.002 0.064 -10000 0 -0.16 63 63
MAP2K1 0.015 0.033 0.11 6 -0.16 9 15
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.018 0.021 -10000 0 -0.26 3 3
CYCS 0.005 0.029 -10000 0 -0.16 8 8
TNFRSF1A 0.007 0.066 -10000 0 -0.32 20 20
NFKB1 -0.003 0.088 -10000 0 -0.34 34 34
TNFR1A/BAG4 0.017 0.052 -10000 0 -0.18 32 32
EIF2AK2 0.004 0.047 0.11 19 -0.16 28 47
TNF-alpha/TNFR1A/FAN 0.013 0.071 -10000 0 -0.22 29 29
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.097 -10000 0 -0.46 14 14
MAP2K2 0.016 0.032 -10000 0 -0.16 8 8
SMPD3 0.013 0.046 -10000 0 -0.21 11 11
TNF 0.001 0.063 -10000 0 -0.2 46 46
PKC zeta/PAR4 0.015 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.004 0.028 0.1 20 -10000 0 20
NF kappa B1/RelA/I kappa B alpha 0.021 0.071 -10000 0 -0.18 52 52
AIFM1 -0.011 0.053 -10000 0 -0.16 52 52
BCL2 0.019 0.01 -10000 0 -0.2 1 1
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.012 0.052 -10000 0 -0.32 12 12
HDAC3 0.011 0.055 -10000 0 -0.35 12 12
VDR 0.019 0.014 -10000 0 -0.2 2 2
Cbp/p300/PCAF 0.024 0.026 -10000 0 -0.2 7 7
EP300 0.015 0.044 -10000 0 -0.36 7 7
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.034 0.035 -10000 0 -0.23 2 2
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.018 0.017 -10000 0 -0.2 3 3
AKT1 0.041 0.076 0.2 76 -0.19 10 86
RAR alpha/9cRA/Cyclin H -0.009 0.12 -10000 0 -0.34 37 37
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.025 0.05 -10000 0 -0.28 5 5
CDC2 -0.042 0.13 -10000 0 -0.32 95 95
response to UV -0.003 0.009 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.02 0.029 -10000 0 -10000 0 0
NCOR2 0.02 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.014 0.009 -10000 0 -0.13 2 2
RXRs/RARs/NRIP1/9cRA -0.015 0.19 -10000 0 -0.51 64 64
NCOA2 0.019 0.014 -10000 0 -0.2 2 2
NCOA3 0.016 0.037 -10000 0 -0.3 7 7
NCOA1 0.005 0.071 -10000 0 -0.34 22 22
VDR/VDR/DNA 0.019 0.014 -10000 0 -0.2 2 2
RARG 0.018 0.007 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.025 0.005 -10000 0 -10000 0 0
MAPK3 0.018 0.005 -10000 0 -10000 0 0
MAPK1 -0.004 0.086 -10000 0 -0.29 41 41
MAPK8 0.017 0.01 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.003 0.12 -10000 0 -0.3 64 64
RARA 0.021 0.033 -10000 0 -10000 0 0
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.031 0.032 -10000 0 -0.21 2 2
PRKCA 0.014 0.025 -10000 0 -0.2 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.029 0.21 -10000 0 -0.58 64 64
RXRG 0.017 0.039 -10000 0 -0.17 2 2
RXRA -0.008 0.09 -10000 0 -0.3 14 14
RXRB 0.021 0.033 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.014 0.009 -10000 0 -0.13 2 2
RBP1 -0.055 0.14 -10000 0 -0.32 118 118
CRBP1/9-cic-RA -0.037 0.1 -10000 0 -0.22 118 118
RARB 0.018 0.016 -10000 0 -0.2 2 2
PRKCG 0.015 0.02 -10000 0 -10000 0 0
MNAT1 0.014 0.042 -10000 0 -0.28 10 10
RAR alpha/RXRs 0.016 0.14 -10000 0 -0.33 59 59
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.022 0.1 -10000 0 -0.27 15 15
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.039 -10000 0 -0.17 2 2
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.029 0.21 -10000 0 -0.58 64 64
positive regulation of DNA binding -0.045 0.091 -10000 0 -0.32 37 37
NRIP1 -0.097 0.39 -10000 0 -1.2 64 64
RXRs/RARs -0.009 0.15 -10000 0 -0.4 64 64
RXRs/RXRs/DNA/9cRA -0.013 0.12 -10000 0 -0.32 64 64
PRKACA 0.02 0 -10000 0 -10000 0 0
CDK7 -0.015 0.11 -10000 0 -0.35 50 50
TFIIH 0.003 0.1 -10000 0 -0.26 60 60
RAR alpha/9cRA 0.019 0.085 -10000 0 -0.28 26 26
CCNH -0.003 0.088 -10000 0 -0.34 34 34
CREBBP 0.02 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.01 0.078 -10000 0 -0.32 18 18
Paxillin-dependent events mediated by a4b1

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
CRKL 0.019 0.01 -9999 0 -0.2 1 1
Rac1/GDP 0.01 0.032 -9999 0 -0.36 4 4
DOCK1 0.011 0.053 -9999 0 -0.27 17 17
ITGA4 0.02 0 -9999 0 -10000 0 0
RAC1 0.017 0.033 -9999 0 -0.36 4 4
alpha4/beta7 Integrin 0.029 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.01 0.053 -9999 0 -0.25 20 20
alpha4/beta1 Integrin 0.04 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin/Paxillin 0.043 0.005 -9999 0 -10000 0 0
lamellipodium assembly -0.01 0.13 -9999 0 -0.32 67 67
PIK3CA -0.011 0.1 -9999 0 -0.33 48 48
PI3K -0.014 0.098 -9999 0 -0.25 66 66
ARF6 0.017 0.033 -9999 0 -0.36 4 4
TLN1 0.012 0.049 -9999 0 -0.29 13 13
PXN 0.024 0.006 -9999 0 -10000 0 0
PIK3R1 -0.011 0.097 -9999 0 -0.3 52 52
ARF6/GTP 0.048 0.017 -9999 0 -10000 0 0
cell adhesion 0.048 0.027 -9999 0 -0.15 8 8
CRKL/CBL 0.029 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.043 0.005 -9999 0 -10000 0 0
ITGB1 0.02 0 -9999 0 -10000 0 0
ITGB7 0.02 0 -9999 0 -10000 0 0
ARF6/GDP 0.01 0.032 -9999 0 -0.36 4 4
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.029 0.09 -9999 0 -0.15 155 155
p130Cas/Crk/Dock1 0.016 0.045 -9999 0 -0.2 16 16
VCAM1 -0.14 0.17 -9999 0 -0.3 261 261
alpha4/beta1 Integrin/Paxillin/Talin 0.05 0.027 -9999 0 -0.15 8 8
alpha4/beta1 Integrin/Paxillin/GIT1 0.054 0.007 -9999 0 -10000 0 0
BCAR1 0 0 -9999 0 -10000 0 0
mol:GDP -0.052 0.007 -9999 0 -10000 0 0
CBL 0.02 0 -9999 0 -10000 0 0
PRKACA 0.02 0 -9999 0 -10000 0 0
GIT1 0.019 0.01 -9999 0 -0.2 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.05 0.027 -9999 0 -0.15 8 8
Rac1/GTP -0.013 0.14 -9999 0 -0.36 67 67
Atypical NF-kappaB 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
BCL3/RelA 0.027 0.019 -9999 0 -0.14 6 6
FBXW11 0.02 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.018 0.054 -9999 0 -0.2 28 28
NF kappa B1 p50/RelA/I kappa B alpha 0.009 0.089 -9999 0 -0.29 23 23
NFKBIA -0.005 0.082 -9999 0 -0.19 75 75
MAPK14 0.018 0.017 -9999 0 -0.2 3 3
NF kappa B1 p105/p50 0.018 0.054 -9999 0 -0.2 28 28
ARRB2 0.018 0.012 -9999 0 -10000 0 0
REL 0.019 0.01 -9999 0 -0.2 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.017 0.054 -9999 0 -0.2 28 28
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.017 0.055 -9999 0 -0.2 29 29
PIK3CA -0.011 0.1 -9999 0 -0.33 48 48
NF kappa B1 p50 dimer 0.007 0.063 -9999 0 -0.24 28 28
PIK3R1 -0.011 0.097 -9999 0 -0.3 52 52
NFKB1 0.007 0.063 -9999 0 -0.24 28 28
RELA 0.018 0.021 -9999 0 -0.26 3 3
positive regulation of anti-apoptosis 0.007 0.063 -9999 0 -0.26 4 4
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.014 0.087 -9999 0 -0.28 23 23
SRC 0.02 0 -9999 0 -10000 0 0
PI3K -0.014 0.098 -9999 0 -0.25 66 66
NF kappa B1 p50/RelA 0.007 0.063 -9999 0 -0.26 4 4
IKBKB 0.017 0.025 -9999 0 -0.2 7 7
beta TrCP1/SCF ubiquitin ligase complex 0.02 0 -9999 0 -10000 0 0
SYK -0.029 0.12 -9999 0 -0.32 79 79
I kappa B alpha/PIK3R1 -0.002 0.087 -9999 0 -0.19 77 77
cell death 0.013 0.084 -9999 0 -0.27 23 23
NF kappa B1 p105/c-Rel 0.018 0.054 -9999 0 -0.2 28 28
LCK 0.016 0.03 -9999 0 -0.2 10 10
BCL3 0.018 0.017 -9999 0 -0.2 3 3
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.02 0.092 -10000 0 -0.31 24 24
FYN -0.019 0.14 -10000 0 -0.36 49 49
LAT/GRAP2/SLP76 0.017 0.1 -10000 0 -0.3 30 30
IKBKB 0.017 0.025 -10000 0 -0.2 7 7
AKT1 0.023 0.089 -10000 0 -0.28 25 25
B2M -0.001 0.089 -10000 0 -0.37 30 30
IKBKG 0.018 0.036 -10000 0 -0.1 13 13
MAP3K8 -0.008 0.086 -10000 0 -0.25 56 56
mol:Ca2+ -0.002 0.007 -10000 0 -0.034 9 9
integrin-mediated signaling pathway 0.011 0.023 -10000 0 -0.18 7 7
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.02 0.11 -10000 0 -0.36 25 25
TRPV6 0.005 0.012 -10000 0 -0.21 1 1
CD28 0.02 0.001 -10000 0 -10000 0 0
SHC1 0.018 0.1 -10000 0 -0.32 28 28
receptor internalization 0.021 0.083 -10000 0 -0.3 18 18
PRF1 0.019 0.086 -10000 0 -10000 0 0
KRAS -0.007 0.087 -10000 0 -0.27 49 49
GRB2 0.012 0.053 -10000 0 -0.35 11 11
COT/AKT1 0.021 0.082 -10000 0 -0.24 27 27
LAT 0.019 0.1 -10000 0 -0.32 28 28
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D -0.008 0.081 -10000 0 -0.22 64 64
CD3E 0.02 0.003 -10000 0 -10000 0 0
CD3G 0.015 0.037 -10000 0 -0.21 14 14
RASGRP2 0.011 0.012 -10000 0 -10000 0 0
RASGRP1 -0.004 0.12 -10000 0 -0.27 63 63
HLA-A -0.004 0.095 -10000 0 -0.37 34 34
RASSF5 0 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.011 0.023 -10000 0 -0.18 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.043 -10000 0 -0.099 29 29
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.016 0.038 -10000 0 -0.15 29 29
PRKCA 0.022 0.059 -10000 0 -0.17 22 22
GRAP2 0.02 0 -10000 0 -10000 0 0
mol:IP3 -0.025 0.061 0.12 1 -0.25 24 25
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.012 0.077 -10000 0 -0.28 19 19
ORAI1 -0.001 0.014 0.14 1 -0.14 4 5
CSK 0.015 0.1 -10000 0 -0.34 28 28
B7 family/CD28 0.031 0.094 -10000 0 -0.29 23 23
CHUK 0.006 0.068 -10000 0 -0.33 21 21
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.013 0.11 -10000 0 -0.36 28 28
PTPN6 0.012 0.1 -10000 0 -0.34 29 29
VAV1 0.017 0.1 -10000 0 -0.33 28 28
Monovalent TCR/CD3 0.018 0.043 -10000 0 -0.16 19 19
CBL 0.02 0 -10000 0 -10000 0 0
LCK -0.001 0.12 -10000 0 -0.38 36 36
PAG1 0.013 0.1 -10000 0 -0.33 28 28
RAP1A 0.015 0.039 -10000 0 -0.32 7 7
TCR/CD3/MHC I/CD8/LCK 0.011 0.11 -10000 0 -0.35 28 28
CD80 0.02 0.001 -10000 0 -10000 0 0
CD86 0.01 0.047 -10000 0 -0.2 25 25
PDK1/CARD11/BCL10/MALT1 -0.02 0.046 -10000 0 -0.18 29 29
HRAS 0.014 0.04 -10000 0 -0.27 10 10
GO:0035030 0.021 0.081 -10000 0 -0.26 23 23
CD8A 0.001 0.003 -10000 0 -10000 0 0
CD8B 0.019 0.017 -10000 0 -0.21 3 3
PTPRC -0.059 0.14 -10000 0 -0.29 139 139
PDK1/PKC theta 0.02 0.1 -10000 0 -0.31 28 28
CSK/PAG1 0.013 0.1 -10000 0 -0.33 28 28
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0 0.1 -10000 0 -0.32 48 48
GRAP2/SLP76 0.015 0.11 -10000 0 -0.35 29 29
STIM1 0.003 0.019 -10000 0 -0.21 4 4
RAS family/GTP 0.003 0.068 -10000 0 -0.15 53 53
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.021 0.085 -10000 0 -0.31 18 18
mol:DAG -0.023 0.055 -10000 0 -0.21 31 31
RAP1A/GDP 0.008 0.021 -10000 0 -0.055 20 20
PLCG1 0.02 0 -10000 0 -10000 0 0
CD247 0.019 0.02 -10000 0 -0.21 4 4
cytotoxic T cell degranulation 0.019 0.085 -10000 0 -10000 0 0
RAP1A/GTP -0.001 0.006 -10000 0 -0.059 5 5
mol:PI-3-4-5-P3 0.022 0.099 -10000 0 -0.31 25 25
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.029 0.073 -10000 0 -0.31 24 24
NRAS -0.03 0.12 -10000 0 -0.29 87 87
ZAP70 0.02 0 -10000 0 -10000 0 0
GRB2/SOS1 0.009 0.037 -10000 0 -0.24 11 11
LAT/GRAP2/SLP76/VAV1 -0.027 0.077 -10000 0 -0.31 25 25
MALT1 0.008 0.057 -10000 0 -0.24 25 25
TRAF6 0.019 0.017 -10000 0 -0.36 1 1
CD8 heterodimer 0.015 0.012 -10000 0 -0.13 3 3
CARD11 0 0 -10000 0 -10000 0 0
PRKCB -0.017 0.041 -10000 0 -0.16 31 31
PRKCE 0.023 0.059 -10000 0 -0.17 22 22
PRKCQ 0.014 0.11 -10000 0 -0.33 31 31
LCP2 -0.014 0.095 -10000 0 -0.26 66 66
BCL10 0.001 0.082 -10000 0 -0.36 26 26
regulation of survival gene product expression 0.023 0.08 -10000 0 -0.24 25 25
IKK complex 0.028 0.036 -10000 0 -0.076 6 6
RAS family/GDP -0.009 0.015 -10000 0 -0.041 74 74
MAP3K14 0.024 0.067 -10000 0 -0.18 26 26
PDPK1 0.026 0.085 -10000 0 -0.26 24 24
TCR/CD3/MHC I/CD8/Fyn 0.004 0.12 -10000 0 -0.45 23 23
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.015 0.033 -9999 0 -0.2 12 12
Caspase 8 (4 units) 0.024 0.086 -9999 0 -0.33 17 17
NEF 0.006 0 -9999 0 -10000 0 0
NFKBIA -0.019 0.1 -9999 0 -0.35 40 40
BIRC3 -0.054 0.17 -9999 0 -0.42 68 68
CYCS 0.002 0.095 -9999 0 -0.33 23 23
RIPK1 0.019 0.014 -9999 0 -0.2 2 2
CD247 0.024 0.019 -9999 0 -0.2 4 4
MAP2K7 0.03 0.075 -9999 0 -0.4 8 8
protein ubiquitination 0.032 0.065 -9999 0 -0.24 7 7
CRADD 0.019 0.01 -9999 0 -0.2 1 1
DAXX 0.015 0.034 -9999 0 -0.24 9 9
FAS -0.017 0.11 -9999 0 -0.3 61 61
BID -0.001 0.096 -9999 0 -0.32 25 25
NF-kappa-B/RelA/I kappa B alpha -0.022 0.13 -9999 0 -0.25 97 97
TRADD 0.02 0 -9999 0 -10000 0 0
MAP3K5 0.008 0.056 -9999 0 -0.25 23 23
CFLAR 0.012 0.052 -9999 0 -0.3 14 14
FADD 0.013 0.046 -9999 0 -0.28 12 12
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.022 0.13 -9999 0 -0.26 97 97
MAPK8 0.035 0.071 -9999 0 -0.37 8 8
APAF1 0.02 0 -9999 0 -10000 0 0
TRAF1 0.02 0 -9999 0 -10000 0 0
TRAF2 0.02 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.017 0.076 -9999 0 -0.34 12 12
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.03 0.071 -9999 0 -0.29 10 10
CHUK 0.032 0.068 -9999 0 -0.26 7 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.025 0.08 -9999 0 -0.19 49 49
TCRz/NEF 0.026 0.013 -9999 0 -10000 0 0
TNF 0.001 0.063 -9999 0 -0.2 46 46
FASLG 0.031 0.01 -9999 0 -10000 0 0
NFKB1 -0.016 0.095 -9999 0 -0.36 34 34
TNFR1A/BAG4/TNF-alpha 0.018 0.058 -9999 0 -0.2 19 19
CASP6 0.006 0.15 -9999 0 -0.6 25 25
CASP7 -0.036 0.19 -9999 0 -0.48 67 67
RELA 0.005 0.038 -9999 0 -0.3 3 3
CASP2 0.02 0 -9999 0 -10000 0 0
CASP3 -0.028 0.18 -9999 0 -0.48 61 61
TNFRSF1A 0.007 0.066 -9999 0 -0.32 20 20
TNFR1A/BAG4 0.017 0.052 -9999 0 -0.18 32 32
CASP8 0.016 0.037 -9999 0 -0.3 7 7
CASP9 0.017 0.03 -9999 0 -0.26 6 6
MAP3K14 0.034 0.067 -9999 0 -0.29 7 7
APAF-1/Caspase 9 -0.063 0.12 -9999 0 -0.29 86 86
BCL2 0.039 0.068 -9999 0 -0.34 8 8
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.017 0.025 -9999 0 -0.2 7 7
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.019 0.014 -9999 0 -0.2 2 2
TCEB1 0.012 0.051 -9999 0 -0.34 11 11
HIF1A/p53 -0.002 0.071 -9999 0 -0.21 29 29
HIF1A 0.012 0.045 -9999 0 -0.22 7 7
COPS5 0.006 0.068 -9999 0 -0.33 21 21
VHL/Elongin B/Elongin C/RBX1/CUL2 0.031 0.059 -9999 0 -0.19 31 31
FIH (dimer) 0.02 0 -9999 0 -10000 0 0
CDKN2A -0.081 0.17 -9999 0 -0.36 143 143
ARNT/IPAS 0.027 0.017 -9999 0 -10000 0 0
HIF1AN 0.02 0 -9999 0 -10000 0 0
GNB2L1 0.015 0.044 -9999 0 -0.36 7 7
HIF1A/ARNT 0.024 0.045 -9999 0 -0.2 7 7
CUL2 0.007 0.068 -9999 0 -0.35 19 19
OS9 0.01 0.057 -9999 0 -0.32 15 15
RACK1/Elongin B/Elongin C 0.032 0.041 -9999 0 -0.2 16 16
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.024 0.045 -9999 0 -0.2 7 7
PHD1-3/OS9 0.019 0.07 -9999 0 -0.2 29 29
HIF1A/RACK1/Elongin B/Elongin C 0.034 0.055 -9999 0 -0.25 5 5
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0.02 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.02 0.054 -9999 0 -0.26 10 10
EGLN3 -0.004 0.069 -9999 0 -0.2 57 57
EGLN2 0.016 0.032 -9999 0 -0.22 9 9
EGLN1 0.001 0.078 -9999 0 -0.3 32 32
TP53 -0.096 0.17 -9999 0 -0.34 175 175
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.014 0.097 -9999 0 -0.44 16 16
ARNT 0.02 0 -9999 0 -10000 0 0
ARD1A -0.001 0.08 -9999 0 -0.28 38 38
RBX1 0.011 0.055 -9999 0 -0.32 14 14
HIF1A/p19ARF 0.003 0.072 -9999 0 -0.24 25 25
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.019 0.01 -10000 0 -0.2 1 1
RAS family/GTP/Tiam1 -0.022 0.095 -10000 0 -0.22 77 77
NT3 (dimer)/TRKC -0.001 0.061 -10000 0 -10000 0 0
NT3 (dimer)/TRKB 0.012 0.055 -10000 0 -0.2 2 2
SHC/Grb2/SOS1/GAB1/PI3K -0.001 0.082 -10000 0 -0.2 73 73
RAPGEF1 0.02 0 -10000 0 -10000 0 0
BDNF 0.012 0.04 -10000 0 -0.2 18 18
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
DYNLT1 0.008 0.063 -10000 0 -0.31 19 19
NTRK1 0.02 0 -10000 0 -10000 0 0
NTRK2 0.018 0.017 -10000 0 -0.2 3 3
NTRK3 0.02 0 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB 0.025 0.018 -10000 0 -0.21 1 1
neuron apoptosis -0.034 0.051 0.22 2 -10000 0 2
SHC 2-3/Grb2 0.036 0.053 -10000 0 -0.24 2 2
SHC1 0.017 0.027 -10000 0 -0.23 6 6
SHC2 0.021 0.048 -10000 0 -0.24 2 2
SHC3 0.021 0.048 -10000 0 -0.24 2 2
STAT3 (dimer) -0.089 0.15 -10000 0 -0.31 150 150
NT3 (dimer)/TRKA 0.013 0.054 -10000 0 -10000 0 0
RIN/GDP 0.032 0.048 -10000 0 -0.18 10 10
GIPC1 0.015 0.037 -10000 0 -0.26 9 9
KRAS -0.007 0.087 -10000 0 -0.27 49 49
DNAJA3 0.005 0.058 0.2 11 -0.23 4 15
RIN/GTP 0.015 0 -10000 0 -10000 0 0
CCND1 -0.18 0.27 -10000 0 -0.58 150 150
MAGED1 0.004 0.073 -10000 0 -0.32 24 24
PTPN11 0.02 0 -10000 0 -10000 0 0
RICS 0.003 0.067 -10000 0 -0.25 33 33
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.021 0.035 -10000 0 -0.17 17 17
GRB2 0.012 0.053 -10000 0 -0.35 11 11
NGF (dimer)/TRKA/MATK 0.027 0 -10000 0 -10000 0 0
TRKA/NEDD4-2 0.026 0.023 -10000 0 -0.24 1 1
ELMO1 0.008 0.051 -10000 0 -0.2 29 29
RhoG/GTP/ELMO1/DOCK1 0.015 0.042 -10000 0 -0.22 7 7
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.014 0.04 -10000 0 -0.27 10 10
DOCK1 0.011 0.053 -10000 0 -0.27 17 17
GAB2 -0.03 0.12 -10000 0 -0.31 81 81
RIT2 0.02 0 -10000 0 -10000 0 0
RIT1 -0.018 0.1 -10000 0 -0.29 66 66
FRS2 0.019 0.01 -10000 0 -0.2 1 1
DNM1 0.019 0.01 -10000 0 -0.2 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.01 0.053 -10000 0 -0.25 20 20
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.008 0.058 0.19 13 -0.18 3 16
mol:GDP 0.031 0.065 -10000 0 -0.28 10 10
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.007 0.033 -10000 0 -0.13 29 29
RIT1/GDP 0.022 0.059 -10000 0 -0.19 15 15
TIAM1 -0.003 0.079 -10000 0 -0.26 44 44
PIK3R1 -0.011 0.097 -10000 0 -0.3 52 52
BDNF (dimer)/TRKB 0.031 0.038 -10000 0 -0.2 7 7
KIDINS220/CRKL/C3G 0.029 0.007 -10000 0 -10000 0 0
SHC/RasGAP 0.006 0.075 -10000 0 -0.23 48 48
FRS2 family/SHP2 0.04 0.008 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.032 0.033 -10000 0 -0.18 11 11
RIT1/GTP -0.011 0.072 -10000 0 -0.2 66 66
NT3 (dimer) -0.024 0.089 -10000 0 -0.2 105 105
RAP1/GDP -0.007 0.027 -10000 0 -0.16 10 10
KIDINS220/CRKL 0.019 0.01 -10000 0 -0.2 1 1
BDNF (dimer) 0.012 0.04 -10000 0 -0.2 18 18
ubiquitin-dependent protein catabolic process 0.024 0.019 -10000 0 -0.2 1 1
Schwann cell development -0.007 0.012 -10000 0 -10000 0 0
EHD4 0.014 0.046 -10000 0 -0.33 9 9
FRS2 family/GRB2/SOS1 0.034 0.03 -10000 0 -0.18 10 10
FRS2 family/SHP2/CRK family/C3G/GAB2 0.019 0.062 -10000 0 -0.22 4 4
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.015 0.039 -10000 0 -0.32 7 7
CDC42/GTP 0.019 0.05 -10000 0 -0.21 3 3
ABL1 -0.009 0.099 -10000 0 -0.34 44 44
SH2B family/GRB2/SOS1 0.009 0.037 -10000 0 -0.24 11 11
Rap1/GTP 0.033 0.041 -10000 0 -0.23 5 5
STAT3 -0.089 0.15 -10000 0 -0.31 150 150
axon guidance -0.015 0.03 -10000 0 -0.2 3 3
MAPK3 0.027 0 -10000 0 -10000 0 0
MAPK1 0.015 0.045 -10000 0 -0.18 23 23
CDC42/GDP 0.032 0.048 -10000 0 -0.18 10 10
NTF3 -0.024 0.089 -10000 0 -0.2 105 105
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.01 0.057 -10000 0 -0.2 30 30
PI3K -0.014 0.098 -10000 0 -0.25 66 66
FRS3 0.019 0.01 -10000 0 -0.2 1 1
FAIM -0.01 0.096 -10000 0 -0.3 49 49
GAB1 0.02 0 -10000 0 -10000 0 0
RASGRF1 0.008 0.055 0.2 13 -0.19 2 15
SOS1 0 0 -10000 0 -10000 0 0
MCF2L 0 0.054 -10000 0 -0.2 3 3
RGS19 0.015 0.04 -10000 0 -0.36 6 6
CDC42 0.019 0.01 -10000 0 -0.2 1 1
RAS family/GTP 0.013 0.099 -10000 0 -0.34 31 31
Rac1/GDP 0.031 0.049 -10000 0 -0.18 10 10
NGF (dimer)/TRKA/GRIT 0.017 0.039 -10000 0 -0.2 9 9
neuron projection morphogenesis -0.08 0.2 -10000 0 -0.59 46 46
NGF (dimer)/TRKA/NEDD4-2 0.024 0.019 -10000 0 -0.2 1 1
MAP2K1 0.027 0.031 -10000 0 -0.16 13 13
NGFR 0.017 0.024 -10000 0 -0.2 6 6
NGF (dimer)/TRKA/GIPC/GAIP 0.025 0.043 -10000 0 -0.18 22 22
RAS family/GTP/PI3K -0.034 0.12 -10000 0 -0.24 116 116
FRS2 family/SHP2/GRB2/SOS1 0.043 0.029 -10000 0 -0.16 10 10
NRAS -0.03 0.12 -10000 0 -0.29 87 87
GRB2/SOS1 0.009 0.037 -10000 0 -0.24 11 11
PRKCI -0.009 0.093 -10000 0 -0.3 48 48
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.017 0.033 -10000 0 -0.36 4 4
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade -0.007 0.1 -10000 0 -0.42 29 29
RASA1 -0.01 0.1 -10000 0 -0.35 44 44
TRKA/c-Abl 0.009 0.07 -10000 0 -0.24 36 36
SQSTM1 -0.002 0.083 -10000 0 -0.3 37 37
BDNF (dimer)/TRKB/GIPC 0.037 0.047 -10000 0 -0.17 16 16
NGF (dimer)/TRKA/p62/Atypical PKCs 0.01 0.065 -10000 0 -0.18 48 48
MATK 0.02 0 -10000 0 -10000 0 0
NEDD4L 0.015 0.033 -10000 0 -0.22 10 10
RAS family/GDP -0.02 0.042 -10000 0 -0.16 28 28
NGF (dimer)/TRKA 0.002 0.058 0.2 15 -0.19 3 18
Rac1/GTP -0.027 0.057 -10000 0 -0.2 33 33
FRS2 family/SHP2/CRK family 0.053 0.031 -10000 0 -0.15 6 6
IL12-mediated signaling events

Figure S84.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S84.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.028 0.069 -10000 0 -0.23 9 9
TBX21 -0.018 0.21 -10000 0 -0.6 13 13
B2M -0.002 0.088 -10000 0 -0.36 30 30
TYK2 -0.004 0.082 -10000 0 -0.27 42 42
IL12RB1 0.018 0.02 -10000 0 -10000 0 0
GADD45B 0.002 0.19 -10000 0 -0.68 10 10
IL12RB2 0.016 0.031 -10000 0 -0.21 6 6
GADD45G 0.009 0.17 -10000 0 -0.55 6 6
natural killer cell activation -0.001 0.019 -10000 0 -10000 0 0
RELB 0.02 0 -10000 0 -10000 0 0
RELA 0.018 0.021 -10000 0 -0.26 3 3
IL18 -0.003 0.079 -10000 0 -0.22 59 59
IL2RA 0.02 0 -10000 0 -10000 0 0
IFNG 0.019 0.014 -10000 0 -0.2 2 2
STAT3 (dimer) 0.001 0.21 -10000 0 -0.57 26 26
HLA-DRB5 -0.005 0.008 -10000 0 -10000 0 0
FASLG -0.018 0.21 -10000 0 -0.63 10 10
NF kappa B2 p52/RelB -0.017 0.2 -10000 0 -0.46 50 50
CD4 0.007 0.041 -10000 0 -0.21 18 18
SOCS1 0.02 0 -10000 0 -10000 0 0
EntrezGene:6955 -0.006 0.01 -10000 0 -10000 0 0
CD3D -0.016 0.081 -10000 0 -0.23 64 64
CD3E 0.014 0.009 -10000 0 -10000 0 0
CD3G 0.007 0.038 -10000 0 -0.22 14 14
IL12Rbeta2/JAK2 0.026 0.038 -10000 0 -0.16 4 4
CCL3 -0.027 0.21 -10000 0 -0.47 53 53
CCL4 -0.14 0.45 -10000 0 -1.1 82 82
HLA-A -0.005 0.093 -10000 0 -0.36 34 34
IL18/IL18R 0.048 0.061 -10000 0 -0.19 9 9
NOS2 -0.013 0.19 -10000 0 -0.42 49 49
IL12/IL12R/TYK2/JAK2/SPHK2 0.028 0.069 -10000 0 -0.22 10 10
IL1R1 -0.021 0.22 -10000 0 -0.65 13 13
IL4 0.02 0.02 -10000 0 -10000 0 0
JAK2 0.017 0.025 -10000 0 -0.2 3 3
EntrezGene:6957 -0.005 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.007 0.08 -10000 0 -0.25 38 38
RAB7A 0.013 0.22 -10000 0 -0.98 14 14
lysosomal transport 0.015 0.21 -10000 0 -0.9 14 14
FOS -0.29 0.52 -10000 0 -1.2 132 132
STAT4 (dimer) 0.015 0.2 -10000 0 -0.57 17 17
STAT5A (dimer) -0.018 0.2 -10000 0 -0.46 51 51
GZMA -0.029 0.22 -10000 0 -0.57 19 19
GZMB -0.032 0.22 -10000 0 -0.61 12 12
HLX 0.018 0.017 -10000 0 -0.2 3 3
LCK -0.023 0.22 -10000 0 -0.49 56 56
TCR/CD3/MHC II/CD4 -0.079 0.12 -10000 0 -0.25 144 144
IL2/IL2R 0.027 0.061 -10000 0 -0.18 28 28
MAPK14 0.016 0.19 -10000 0 -0.65 12 12
CCR5 0.003 0.18 -10000 0 -0.61 9 9
IL1B -0.002 0.072 -10000 0 -0.22 47 47
STAT6 0.004 0.1 -10000 0 -0.5 6 6
STAT4 0.018 0.019 -10000 0 -0.2 4 4
STAT3 0.004 0.075 -10000 0 -0.35 23 23
STAT1 -0.024 0.11 -10000 0 -0.3 74 74
NFKB1 -0.003 0.088 -10000 0 -0.34 34 34
NFKB2 0.02 0 -10000 0 -10000 0 0
IL12B 0.018 0.02 -10000 0 -10000 0 0
CD8A 0 0 -10000 0 -10000 0 0
CD8B 0.018 0.017 -10000 0 -0.2 3 3
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.028 0.069 0.23 9 -10000 0 9
IL2RB 0.001 0.063 -10000 0 -0.21 44 44
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.19 -10000 0 -0.53 17 17
IL2RG -0.007 0.072 -10000 0 -0.2 64 64
IL12 0.023 0.042 -10000 0 -0.14 6 6
STAT5A 0.019 0.014 -10000 0 -0.2 2 2
CD247 0.012 0.021 -10000 0 -0.21 4 4
IL2 0.02 0 -10000 0 -10000 0 0
SPHK2 0.02 0 -10000 0 -10000 0 0
FRAP1 0.02 0 -10000 0 -10000 0 0
IL12A 0.01 0.046 -10000 0 -0.2 20 20
IL12/IL12R/TYK2/JAK2 -0.027 0.23 -10000 0 -0.52 53 53
MAP2K3 0.012 0.19 -10000 0 -0.62 12 12
RIPK2 0.007 0.061 -10000 0 -0.25 26 26
MAP2K6 0.013 0.18 -10000 0 -0.61 11 11
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.092 0.16 -10000 0 -0.33 164 164
IL18RAP 0.023 0.006 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.011 0.063 -10000 0 -0.21 27 27
EOMES -0.002 0.027 0.064 2 -10000 0 2
STAT1 (dimer) -0.017 0.22 -10000 0 -0.55 37 37
T cell proliferation 0.014 0.16 -10000 0 -0.47 15 15
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.022 0.018 -10000 0 -0.21 3 3
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.051 0.12 -10000 0 -0.52 15 15
ATF2 0.021 0.18 -10000 0 -0.61 12 12
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.002 0.074 -9999 0 -0.24 24 24
CaM/Ca2+ 0.014 0.013 -9999 0 -0.19 2 2
AKT1 0.003 0.071 -9999 0 -0.28 30 30
AKT2 0.019 0.014 -9999 0 -0.2 2 2
STXBP4 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.012 0.078 -9999 0 -0.23 43 43
YWHAZ 0.005 0.074 -9999 0 -0.35 22 22
CALM1 0.019 0.019 -9999 0 -0.28 2 2
YWHAQ 0.013 0.049 -9999 0 -0.36 9 9
TBC1D4 0.011 0.052 -9999 0 -0.24 14 14
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH -0.027 0.12 -9999 0 -0.32 73 73
YWHAB 0.015 0.041 -9999 0 -0.34 7 7
SNARE/Synip 0.021 0.036 -9999 0 -0.2 14 14
YWHAG 0 0 -9999 0 -10000 0 0
ASIP 0.019 0.01 -9999 0 -0.2 1 1
PRKCI -0.009 0.093 -9999 0 -0.3 48 48
AS160/CaM/Ca2+ 0.014 0.013 -9999 0 -0.19 2 2
RHOQ 0.008 0.06 -9999 0 -0.28 21 21
GYS1 0.007 0.075 -9999 0 -0.23 38 38
PRKCZ 0 0 -9999 0 -10000 0 0
TRIP10 0.013 0.04 -9999 0 -0.21 16 16
TC10/GTP/CIP4/Exocyst 0.016 0.042 -9999 0 -0.2 12 12
AS160/14-3-3 -0.037 0.14 -9999 0 -0.36 56 56
VAMP2 0.02 0 -9999 0 -10000 0 0
SLC2A4 -0.014 0.085 -9999 0 -0.24 45 45
STX4 0.01 0.06 -9999 0 -0.35 14 14
GSK3B 0.007 0.074 -9999 0 -0.26 34 34
SFN -0.066 0.15 -9999 0 -0.31 141 141
LNPEP 0.018 0.021 -9999 0 -0.2 5 5
YWHAE 0.013 0.048 -9999 0 -0.3 12 12
Plasma membrane estrogen receptor signaling

Figure S86.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S86.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.029 0.034 -10000 0 -0.16 16 16
ER alpha/Gai/GDP/Gbeta gamma 0.011 0.092 -10000 0 -0.31 28 28
AKT1 -0.009 0.14 -10000 0 -0.48 37 37
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.011 0.14 -10000 0 -0.49 37 37
mol:Ca2+ 0.045 0.01 -10000 0 -10000 0 0
IGF1R -0.055 0.15 -10000 0 -0.33 115 115
E2/ER alpha (dimer)/Striatin 0.027 0 -10000 0 -10000 0 0
SHC1 0.017 0.027 -10000 0 -0.23 6 6
apoptosis 0.009 0.14 0.46 37 -10000 0 37
RhoA/GTP -0.035 0.069 -10000 0 -0.17 94 94
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.015 0.061 -10000 0 -0.31 13 13
regulation of stress fiber formation 0.004 0.08 0.23 39 -10000 0 39
E2/ERA-ERB (dimer) 0.027 0 -10000 0 -10000 0 0
KRAS -0.007 0.087 -10000 0 -0.27 49 49
G13/GTP 0.025 0 -10000 0 -10000 0 0
pseudopodium formation -0.004 0.08 -10000 0 -0.23 39 39
E2/ER alpha (dimer)/PELP1 0.025 0.014 -10000 0 -10000 0 0
GRB2 0.012 0.053 -10000 0 -0.35 11 11
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 0.015 0.033 -10000 0 -0.2 12 12
HRAS 0.014 0.04 -10000 0 -0.27 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.015 0.08 -10000 0 -0.29 21 21
E2/ER beta (dimer) 0.015 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.041 -10000 0 -0.16 6 6
mol:NADP 0.015 0.08 -10000 0 -0.29 21 21
PIK3R1 -0.011 0.097 -10000 0 -0.3 52 52
mol:IP3 0.045 0.011 -10000 0 -10000 0 0
IGF-1R heterotetramer -0.054 0.15 -10000 0 -0.33 115 115
PLCB1 0.042 0.011 -10000 0 -10000 0 0
PLCB2 0.042 0.009 -10000 0 -10000 0 0
IGF1 -0.07 0.14 -10000 0 -0.27 166 166
mol:L-citrulline 0.015 0.08 -10000 0 -0.29 21 21
RHOA -0.008 0.1 -10000 0 -0.36 39 39
Gai/GDP 0.008 0.12 -10000 0 -0.6 14 14
JNK cascade 0.015 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.02 0 -10000 0 -10000 0 0
GNAQ 0.02 0 -10000 0 -10000 0 0
ESR1 0.02 0 -10000 0 -10000 0 0
Gq family/GDP/Gbeta gamma 0.03 0.063 -10000 0 -0.32 16 16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.023 0.091 -10000 0 -0.58 11 11
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.027 0.075 -10000 0 -0.33 11 11
GNAZ 0.017 0.025 -10000 0 -0.2 7 7
E2/ER alpha (dimer) 0.015 0 -10000 0 -10000 0 0
STRN 0.02 0 -10000 0 -10000 0 0
GNAL 0.02 0 -10000 0 -10000 0 0
PELP1 0.017 0.025 -10000 0 -0.2 7 7
MAPK11 0.021 0 -10000 0 -10000 0 0
GNAI2 0.012 0.054 -10000 0 -0.36 11 11
GNAI3 0.01 0.06 -10000 0 -0.35 14 14
GNAI1 -0.021 0.11 -10000 0 -0.28 74 74
HBEGF -0.038 0.11 -10000 0 -0.36 29 29
cAMP biosynthetic process 0.023 0 -10000 0 -10000 0 0
SRC 0.017 0.088 -10000 0 -0.35 17 17
PI3K -0.014 0.098 -10000 0 -0.25 66 66
GNB1 0.008 0.065 -10000 0 -0.36 16 16
G13/GDP/Gbeta gamma 0.019 0.046 -10000 0 -0.2 4 4
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.052 0.078 -10000 0 -0.27 40 40
Gs family/GTP 0.029 0 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.006 0.085 -10000 0 -0.2 67 67
vasodilation 0.016 0.078 -10000 0 -0.28 21 21
mol:DAG 0.045 0.011 -10000 0 -10000 0 0
Gs family/GDP/Gbeta gamma -0.01 0.032 -10000 0 -0.19 4 4
MSN -0.005 0.085 -10000 0 -0.24 39 39
Gq family/GTP 0.039 0.009 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.011 0.14 -10000 0 -0.48 37 37
NRAS -0.03 0.12 -10000 0 -0.29 87 87
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.016 0.078 0.28 21 -10000 0 21
GRB2/SOS1 0.009 0.037 -10000 0 -0.24 11 11
RhoA/GDP 0.013 0.062 -10000 0 -0.23 14 14
NOS3 0.015 0.082 -10000 0 -0.3 21 21
GNA11 0.02 0 -10000 0 -10000 0 0
MAPKKK cascade 0.036 0.063 -10000 0 -0.39 5 5
E2/ER alpha (dimer)/PELP1/Src 0.025 0.077 -10000 0 -0.32 13 13
ruffle organization -0.004 0.08 -10000 0 -0.23 39 39
ROCK2 -0.001 0.08 -10000 0 -0.26 23 23
GNA14 0.019 0.01 -10000 0 -0.2 1 1
GNA15 0.017 0.024 -10000 0 -0.2 6 6
GNA13 0.02 0 -10000 0 -10000 0 0
MMP9 -0.035 0.11 -10000 0 -0.38 25 25
MMP2 -0.03 0.11 -10000 0 -0.35 34 34
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.035 0.026 -10000 0 -10000 0 0
fibroblast growth factor receptor signaling pathway 0.034 0.026 -10000 0 -10000 0 0
LAMA1 0 0 -10000 0 -10000 0 0
PRNP -0.018 0.11 -10000 0 -0.34 57 57
GPC1/SLIT2 -0.026 0.099 -10000 0 -0.19 137 137
SMAD2 0.023 0.046 -10000 0 -0.18 23 23
GPC1/PrPc/Cu2+ 0.004 0.067 -10000 0 -0.18 59 59
GPC1/Laminin alpha1 0.014 0.009 -10000 0 -0.13 2 2
TDGF1 0.013 0.037 -10000 0 -0.2 15 15
CRIPTO/GPC1 0.025 0.027 -10000 0 -0.12 17 17
APP/GPC1 0.016 0.056 -10000 0 -0.22 28 28
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.014 0.052 -10000 0 -0.2 24 24
FLT1 0.02 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.035 0.032 -10000 0 -0.2 8 8
SERPINC1 0.02 0 -10000 0 -10000 0 0
FYN -0.013 0.078 -10000 0 -0.2 62 62
FGR 0.022 0.03 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.003 0.074 -10000 0 -0.22 20 20
SLIT2 -0.058 0.14 -10000 0 -0.29 136 136
GPC1/NRG 0.029 0.009 -10000 0 -0.12 2 2
NRG1 0.02 0 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.022 0.056 -10000 0 -0.2 25 25
LYN -0.004 0.078 -10000 0 -0.2 64 64
mol:Spermine 0.012 0.009 -10000 0 -0.13 2 2
cell growth 0.034 0.026 -10000 0 -10000 0 0
BMP signaling pathway -0.019 0.014 0.2 2 -10000 0 2
SRC 0.026 0.022 -10000 0 -10000 0 0
TGFBR1 0.02 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.005 0.056 -10000 0 -0.2 36 36
GPC1 0.019 0.014 -10000 0 -0.2 2 2
TGFBR1 (dimer) 0.02 0 -10000 0 -10000 0 0
VEGFA -0.009 0.092 -10000 0 -0.28 51 51
BLK 0.025 0.023 -10000 0 -10000 0 0
HCK 0.013 0.045 -10000 0 -0.2 4 4
FGF2 0.019 0.01 -10000 0 -0.2 1 1
FGFR1 0.012 0.041 -10000 0 -0.2 19 19
VEGFR1 homodimer 0.02 0 -10000 0 -10000 0 0
TGFBR2 0.012 0.05 -10000 0 -0.31 12 12
cell death 0.016 0.056 -10000 0 -0.22 28 28
ATIII/GPC1 0.029 0.009 -10000 0 -0.12 2 2
PLA2G2A/GPC1 0.019 0.039 -10000 0 -0.12 38 38
LCK 0.024 0.027 -10000 0 -10000 0 0
neuron differentiation 0.029 0.009 -10000 0 -0.12 2 2
PrPc/Cu2+ -0.011 0.077 -10000 0 -0.23 57 57
APP 0.002 0.078 -10000 0 -0.34 26 26
TGFBR2 (dimer) 0.012 0.05 -10000 0 -0.31 12 12
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.015 0.056 -10000 0 -0.25 16 16
CRKL 0.032 0.028 -10000 0 -10000 0 0
mol:PIP3 0.013 0.1 0.31 55 -10000 0 55
AKT1 0.013 0.081 0.23 54 -0.2 13 67
PTK2B 0.02 0 -10000 0 -10000 0 0
RAPGEF1 0.037 0.027 -10000 0 -10000 0 0
RANBP10 0.018 0.017 -10000 0 -0.2 3 3
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
HGF/MET/SHIP2 0.032 0.036 -10000 0 -0.2 6 6
MAP3K5 0.037 0.04 -10000 0 -10000 0 0
HGF/MET/CIN85/CBL/ENDOPHILINS 0.034 0.024 -10000 0 -0.18 1 1
AP1 -0.07 0.12 -10000 0 -0.19 239 239
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.017 0.027 -10000 0 -0.23 6 6
apoptosis -0.18 0.32 -10000 0 -0.72 139 139
STAT3 (dimer) 0.015 0.074 -10000 0 -0.3 9 9
GAB1/CRKL/SHP2/PI3K 0.03 0.071 -10000 0 -0.32 2 2
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.038 0.039 -10000 0 -0.24 1 1
PTPN11 0.02 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.02 0 -10000 0 -10000 0 0
PTEN -0.018 0.11 -10000 0 -0.35 55 55
ELK1 0.005 0.051 0.23 23 -10000 0 23
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.026 0.017 -10000 0 -0.15 2 2
PAK1 0.014 0.077 0.22 54 -0.18 13 67
HGF/MET/RANBP10 0.034 0.028 -10000 0 -0.2 1 1
HRAS 0.021 0.091 -10000 0 -0.49 15 15
DOCK1 0.033 0.035 -10000 0 -10000 0 0
GAB1 0.027 0.03 -10000 0 -10000 0 0
CRK 0.028 0.039 -10000 0 -0.26 1 1
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.022 0.077 -10000 0 -0.41 15 15
JUN -0.011 0.099 -10000 0 -0.31 51 51
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.015 0.015 -10000 0 -10000 0 0
PIK3R1 -0.011 0.097 -10000 0 -0.3 52 52
cell morphogenesis 0.021 0.086 -10000 0 -0.28 17 17
GRB2/SHC 0.033 0.033 -10000 0 -0.15 12 12
FOS -0.11 0.16 -10000 0 -0.29 233 233
GLMN 0 0.028 -10000 0 -0.21 8 8
cell motility 0.005 0.051 0.22 23 -10000 0 23
HGF/MET/MUC20 0.022 0.026 -10000 0 -0.21 1 1
cell migration 0.032 0.032 -10000 0 -0.15 12 12
GRB2 0.012 0.053 -10000 0 -0.35 11 11
CBL 0.02 0 -10000 0 -10000 0 0
MET/RANBP10 0.023 0.03 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.014 0.074 -10000 0 -0.31 7 7
MET/MUC20 0.009 0.027 -10000 0 -0.13 19 19
RAP1B 0.035 0.026 -10000 0 -10000 0 0
RAP1A 0.039 0.031 -10000 0 -10000 0 0
HGF/MET/RANBP9 0.027 0.049 -10000 0 -0.2 17 17
RAF1 0.023 0.09 -10000 0 -0.47 15 15
STAT3 0.015 0.075 -10000 0 -0.3 9 9
cell proliferation 0.028 0.062 -10000 0 -0.26 7 7
RPS6KB1 0.014 0.015 -10000 0 -10000 0 0
MAPK3 -0.013 0.019 -10000 0 -10000 0 0
MAPK1 0.019 0.14 0.69 23 -10000 0 23
RANBP9 0.007 0.066 -10000 0 -0.32 20 20
MAPK8 0.042 0.046 -10000 0 -10000 0 0
SRC 0.018 0.069 -10000 0 -0.29 7 7
PI3K 0.008 0.07 -10000 0 -0.26 7 7
MET/Glomulin 0.01 0.033 -10000 0 -0.13 27 27
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.028 0.085 -10000 0 -0.43 15 15
MET 0.012 0.041 -10000 0 -0.2 19 19
MAP4K1 0.037 0.033 -10000 0 -10000 0 0
PTK2 0.001 0.08 -10000 0 -0.33 29 29
MAP2K2 0.028 0.085 -10000 0 -0.44 15 15
BAD 0.015 0.079 0.22 53 -0.19 17 70
MAP2K4 0.039 0.041 -10000 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 -0.006 0.021 -10000 0 -10000 0 0
INPPL1 0.014 0.041 -10000 0 -0.29 9 9
PXN 0.019 0.01 -10000 0 -0.2 1 1
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS 0.011 0.042 -10000 0 -0.16 26 26
PLCgamma1/PKC 0.015 0 -10000 0 -10000 0 0
HGF 0.019 0.014 -10000 0 -0.2 2 2
RASA1 -0.01 0.1 -10000 0 -0.35 44 44
NCK1 0.002 0.074 -10000 0 -0.28 32 32
PTPRJ 0.02 0 -10000 0 -10000 0 0
NCK/PLCgamma1 0.031 0.039 -10000 0 -0.15 16 16
PDPK1 0.017 0.084 0.26 55 -10000 0 55
HGF/MET/SHIP 0.022 0.026 -10000 0 -0.21 1 1
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.012 0.052 -9999 0 -0.32 12 12
Ran/GTP/Exportin 1/HDAC4 -0.02 0.055 -9999 0 -0.16 60 60
MDM2/SUMO1 0.027 0.053 -9999 0 -0.28 9 9
HDAC4 0.002 0.074 -9999 0 -0.28 33 33
Ran/GTP/Exportin 1/HDAC1 -0.017 0.051 -9999 0 -0.16 55 55
SUMO1 0.013 0.049 -9999 0 -0.36 9 9
NPC/RanGAP1/SUMO1 0.006 0.052 -9999 0 -0.18 33 33
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.016 0.048 -9999 0 -0.16 33 33
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.003 0.078 -9999 0 -0.36 24 24
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0.084 -9999 0 -0.35 29 29
SUMO1/HDAC4 0.019 0.064 -9999 0 -0.21 24 24
SUMO1/HDAC1 0.023 0.058 -9999 0 -0.22 18 18
RANGAP1 0.018 0.017 -9999 0 -0.2 3 3
MDM2/SUMO1/SUMO1 0.041 0.042 -9999 0 -0.18 13 13
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.011 0.051 -9999 0 -0.18 33 33
Ran/GTP 0.013 0.066 -9999 0 -0.18 49 49
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.02 0 -9999 0 -10000 0 0
UBE2I 0.02 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.018 0.065 -9999 0 -0.17 49 49
NPC 0.002 0.041 -9999 0 -0.18 26 26
PIAS2 0.013 0.038 -9999 0 -0.2 16 16
PIAS1 0.016 0.038 -9999 0 -0.34 6 6
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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
FBXW11 0.017 0.022 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.029 0.1 -9999 0 -0.29 30 30
ERC1 -0.027 0.12 -9999 0 -0.31 77 77
RIP2/NOD2 0.017 0.049 -9999 0 -0.25 10 10
NFKBIA 0.003 0.12 -9999 0 -0.36 40 40
BIRC2 0.011 0.055 -9999 0 -0.35 12 12
IKBKB 0.017 0.025 -9999 0 -0.2 7 7
RIPK2 0.007 0.061 -9999 0 -0.25 26 26
IKBKG 0.029 0.06 -9999 0 -0.28 9 9
IKK complex/A20 0.039 0.073 -9999 0 -0.29 9 9
NEMO/A20/RIP2 0.007 0.061 -9999 0 -0.25 26 26
XPO1 0.019 0.01 -9999 0 -0.2 1 1
NEMO/ATM 0.036 0.061 -9999 0 -0.28 8 8
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.003 0.078 -9999 0 -0.36 24 24
Exportin 1/RanGTP 0.017 0.047 -9999 0 -0.2 23 23
IKK complex/ELKS 0.018 0.078 -9999 0 -0.32 7 7
BCL10/MALT1/TRAF6 0.021 0.061 -9999 0 -0.2 33 33
NOD2 0.014 0.034 -9999 0 -0.2 13 13
NFKB1 -0.006 0.093 -9999 0 -0.35 34 34
RELA 0.015 0.03 -9999 0 -0.25 3 3
MALT1 0.008 0.057 -9999 0 -0.24 25 25
cIAP1/UbcH5C 0.017 0.06 -9999 0 -0.26 23 23
ATM 0.012 0.046 -9999 0 -0.26 14 14
TNF/TNFR1A 0.007 0.063 -9999 0 -0.24 17 17
TRAF6 0.019 0.017 -9999 0 -0.36 1 1
PRKCA 0.019 0.014 -9999 0 -0.2 2 2
CHUK 0.006 0.068 -9999 0 -0.33 21 21
UBE2D3 0.01 0.059 -9999 0 -0.36 13 13
TNF 0.001 0.063 -9999 0 -0.2 46 46
NF kappa B1 p50/RelA 0.022 0.086 -9999 0 -0.22 52 52
BCL10 0.001 0.082 -9999 0 -0.36 26 26
proteasomal ubiquitin-dependent protein catabolic process 0.003 0.11 -9999 0 -0.36 40 40
beta TrCP1/SCF ubiquitin ligase complex 0.017 0.022 -9999 0 -10000 0 0
TNFRSF1A 0.007 0.066 -9999 0 -0.32 20 20
IKK complex 0.041 0.068 -9999 0 -0.28 8 8
CYLD 0.018 0.017 -9999 0 -0.2 3 3
IKK complex/PKC alpha 0.047 0.067 -9999 0 -0.44 2 2
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.024 0.12 -10000 0 -0.4 20 20
CRKL 0.037 0.045 -10000 0 -0.23 4 4
mol:DAG 0.019 0.1 -10000 0 -0.36 18 18
HRAS 0.043 0.053 -10000 0 -0.27 7 7
MAPK8 0.01 0.073 -10000 0 -0.18 64 64
RAP1A 0.036 0.046 -10000 0 -0.23 4 4
GAB1 0.037 0.045 -10000 0 -0.23 4 4
MAPK14 0.009 0.073 -10000 0 -0.18 64 64
EPO 0.022 0.005 -10000 0 -10000 0 0
PLCG1 0.019 0.1 -10000 0 -0.36 18 18
EPOR/TRPC2/IP3 Receptors 0.019 0.028 -10000 0 -0.21 8 8
RAPGEF1 0.02 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.042 0.018 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.041 0.053 -10000 0 -0.27 7 7
EPO/EPOR (dimer) 0.031 0.022 -10000 0 -0.16 2 2
IRS2 0.021 0.062 -10000 0 -0.24 15 15
STAT1 0.006 0.13 -10000 0 -0.38 34 34
STAT5B 0.024 0.1 -10000 0 -0.36 18 18
cell proliferation 0.013 0.067 -10000 0 -0.16 64 64
GAB1/SHIP/PIK3R1/SHP2/SHC -0.014 0.04 -10000 0 -0.23 8 8
TEC 0.037 0.045 -10000 0 -0.23 4 4
SOCS3 0.02 0 -10000 0 -10000 0 0
STAT1 (dimer) 0.006 0.13 -10000 0 -0.38 34 34
JAK2 0.02 0.017 -10000 0 -0.2 3 3
PIK3R1 -0.011 0.097 -10000 0 -0.3 52 52
EPO/EPOR (dimer)/JAK2 0.059 0.056 -10000 0 -0.25 4 4
EPO/EPOR 0.031 0.022 -10000 0 -0.16 2 2
LYN -0.029 0.13 -10000 0 -0.34 76 76
TEC/VAV2 0.049 0.046 -10000 0 -0.22 4 4
elevation of cytosolic calcium ion concentration 0.019 0.028 -10000 0 -0.21 8 8
SHC1 0.017 0.027 -10000 0 -0.23 6 6
EPO/EPOR (dimer)/LYN 0.017 0.089 -10000 0 -0.21 64 64
mol:IP3 0.019 0.1 -10000 0 -0.36 18 18
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.001 0.087 -10000 0 -0.23 31 31
SH2B3 0.003 0.079 -10000 0 -0.3 33 33
NFKB1 -0.002 0.096 -10000 0 -0.22 77 77
EPO/EPOR (dimer)/JAK2/SOCS3 0.026 0.04 0.22 19 -10000 0 19
PTPN6 0.032 0.045 -10000 0 -0.25 4 4
TEC/VAV2/GRB2 0.053 0.056 -10000 0 -0.27 6 6
EPOR 0.019 0.028 -10000 0 -0.21 8 8
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.041 0.053 -10000 0 -0.27 7 7
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 -0.002 0.078 -10000 0 -0.26 42 42
CRKL/CBL/C3G 0.057 0.046 -10000 0 -0.22 3 3
VAV2 0.037 0.045 -10000 0 -0.23 4 4
CBL 0.037 0.045 -10000 0 -0.23 4 4
SHC/Grb2/SOS1 -0.011 0.041 -10000 0 -0.29 7 7
STAT5A 0.024 0.1 -10000 0 -0.36 18 18
GRB2 0.012 0.053 -10000 0 -0.35 11 11
STAT5 (dimer) 0.049 0.099 -10000 0 -0.32 17 17
LYN/PLCgamma2 -0.019 0.11 -10000 0 -0.27 73 73
PTPN11 0.02 0 -10000 0 -10000 0 0
BTK 0.036 0.046 -10000 0 -0.23 4 4
BCL2 0.024 0.12 -10000 0 -0.39 22 22
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.028 0.001 -10000 0 -10000 0 0
NFATC2 0.058 0.12 0.31 8 -0.39 8 16
NFATC3 0.027 0.069 0.24 16 -0.23 8 24
CD40LG 0.019 0.19 -10000 0 -0.67 12 12
ITCH 0.041 0.038 -10000 0 -0.45 1 1
CBLB 0.042 0.026 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment 0.062 0.12 -10000 0 -0.49 3 3
JUNB -0.025 0.11 -10000 0 -0.29 77 77
CaM/Ca2+/Calcineurin A alpha-beta B1 0.041 0.032 -10000 0 -0.22 2 2
T cell anergy 0.031 0.045 -10000 0 -0.3 1 1
TLE4 0.056 0.083 -10000 0 -0.3 6 6
Jun/NFAT1-c-4/p21SNFT 0.072 0.16 -10000 0 -0.61 11 11
AP-1/NFAT1-c-4 0.048 0.23 -10000 0 -0.75 12 12
IKZF1 0.057 0.08 -10000 0 -0.29 5 5
T-helper 2 cell differentiation 0.053 0.09 -10000 0 -10000 0 0
AP-1/NFAT1 -0.009 0.16 -10000 0 -0.27 82 82
CALM1 0.03 0.026 -10000 0 -0.26 2 2
EGR2 0.055 0.22 0.52 10 -1.1 11 21
EGR3 0.065 0.16 0.52 9 -0.52 10 19
NFAT1/FOXP3 0.07 0.084 -10000 0 -0.29 5 5
EGR1 -0.085 0.15 -10000 0 -0.28 185 185
JUN -0.005 0.1 -10000 0 -0.3 51 51
EGR4 0.02 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.012 0.017 -10000 0 -0.14 1 1
GBP3 0.042 0.078 0.21 8 -0.26 8 16
FOSL1 0.017 0.027 -10000 0 -0.2 8 8
NFAT1-c-4/MAF/IRF4 0.087 0.15 -10000 0 -0.61 10 10
DGKA 0.055 0.083 -10000 0 -0.29 6 6
CREM 0.018 0.014 -10000 0 -0.21 2 2
NFAT1-c-4/PPARG 0.073 0.15 -10000 0 -0.65 10 10
CTLA4 0.059 0.063 -10000 0 -0.23 5 5
NFAT1-c-4 (dimer)/EGR1 0.026 0.19 -10000 0 -0.75 12 12
NFAT1-c-4 (dimer)/EGR4 0.08 0.16 -10000 0 -0.65 10 10
FOS -0.1 0.16 -10000 0 -0.28 233 233
IFNG 0.057 0.086 -10000 0 -10000 0 0
T cell activation 0.024 0.13 -10000 0 -0.58 11 11
MAF 0.013 0.039 -10000 0 -0.2 17 17
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.061 0.15 0.52 10 -0.51 15 25
TNF 0.019 0.18 -10000 0 -0.64 15 15
FASLG 0.042 0.19 -10000 0 -0.92 10 10
TBX21 0.027 0.004 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ -0.029 0.12 -10000 0 -0.3 89 89
PTPN1 0.05 0.11 -10000 0 -0.5 10 10
NFAT1-c-4/ICER1 0.072 0.15 -10000 0 -0.65 10 10
GATA3 0.02 0.029 -10000 0 -0.2 9 9
T-helper 1 cell differentiation 0.057 0.085 -10000 0 -10000 0 0
IL2RA 0.058 0.12 -10000 0 -0.44 5 5
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.053 0.097 -10000 0 -0.44 8 8
E2F1 0.018 0.039 -10000 0 -0.21 8 8
PPARG 0.014 0.036 -10000 0 -0.2 14 14
SLC3A2 0.054 0.085 -10000 0 -0.29 6 6
IRF4 0.02 0.01 -10000 0 -0.2 1 1
PTGS2 0.013 0.2 -10000 0 -0.64 15 15
CSF2 0.019 0.19 -10000 0 -0.67 12 12
JunB/Fra1/NFAT1-c-4 0.063 0.17 -10000 0 -0.68 11 11
IL4 0.053 0.091 -10000 0 -10000 0 0
IL5 0.019 0.19 -10000 0 -0.67 12 12
IL2 0.023 0.13 -10000 0 -0.58 11 11
IL3 0.004 0.032 -10000 0 -10000 0 0
RNF128 0.036 0.042 -10000 0 -10000 0 0
NFATC1 0.061 0.15 0.51 15 -0.52 10 25
CDK4 -0.084 0.28 -10000 0 -1.3 22 22
PTPRK 0.003 0.21 -10000 0 -0.57 58 58
IL8 -0.013 0.22 -10000 0 -0.6 26 26
POU2F1 0.028 0.017 -10000 0 -0.36 1 1
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.014 0.04 -9999 0 -0.27 10 10
EGFR 0.018 0.017 -9999 0 -0.2 3 3
EGF/EGFR 0.013 0.051 -9999 0 -0.16 12 12
EGF/EGFR dimer/SHC/GRB2/SOS1 0.041 0.033 -9999 0 -0.16 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.009 0.075 -9999 0 -0.2 69 69
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.019 0.01 -9999 0 -0.2 1 1
EGF/EGFR dimer/SHC 0.038 0.021 -9999 0 -0.2 2 2
mol:GDP 0.037 0.032 -9999 0 -0.16 12 12
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.006 0.072 -9999 0 -0.2 63 63
GRB2/SOS1 0.009 0.037 -9999 0 -0.24 11 11
HRAS/GTP 0.024 0.034 -9999 0 -0.15 15 15
SHC1 0.017 0.027 -9999 0 -0.23 6 6
HRAS/GDP 0.035 0.037 -9999 0 -0.16 15 15
FRAP1 0.032 0.029 -9999 0 -0.14 12 12
EGF/EGFR dimer 0.028 0.013 -9999 0 -0.12 4 4
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0.012 0.053 -9999 0 -0.35 11 11
ETA receptor/Endothelin-1 -0.008 0.071 -9999 0 -0.14 121 121
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.017 0.069 -9999 0 -0.27 7 7
PDGFB-D/PDGFRB/SLAP 0.011 0.057 -9999 0 -0.25 12 12
PDGFB-D/PDGFRB/APS/CBL 0.021 0.026 -9999 0 -10000 0 0
AKT1 -0.011 0.093 -9999 0 -0.25 37 37
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.013 0.065 -9999 0 -0.28 8 8
PIK3CA -0.011 0.1 -9999 0 -0.33 48 48
FGR -0.003 0.048 -9999 0 -0.26 4 4
mol:Ca2+ 0.008 0.059 -9999 0 -0.3 7 7
MYC -0.12 0.32 -9999 0 -0.77 104 104
SHC1 0.017 0.027 -9999 0 -0.23 6 6
HRAS/GDP 0.015 0.065 -9999 0 -0.19 23 23
LRP1/PDGFRB/PDGFB 0.032 0.034 -9999 0 -0.2 4 4
GRB10 0.01 0.053 -9999 0 -0.25 20 20
PTPN11 0.02 0 -9999 0 -10000 0 0
GO:0007205 0.008 0.06 -9999 0 -0.3 7 7
PTEN -0.018 0.11 -9999 0 -0.35 55 55
GRB2 0.012 0.053 -9999 0 -0.35 11 11
GRB7 0 0.077 -9999 0 -0.28 35 35
PDGFB-D/PDGFRB/SHP2 0.022 0.031 -9999 0 -0.13 6 6
PDGFB-D/PDGFRB/GRB10 0.015 0.05 -9999 0 -0.16 35 35
cell cycle arrest 0.011 0.057 -9999 0 -0.25 12 12
HRAS 0.014 0.04 -9999 0 -0.27 10 10
HIF1A -0.005 0.087 -9999 0 -0.25 30 30
GAB1 -0.009 0.092 -9999 0 -0.38 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.005 0.088 -9999 0 -0.34 9 9
PDGFB-D/PDGFRB 0.024 0.047 -9999 0 -0.21 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.01 0.066 -9999 0 -0.27 22 22
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.004 0.093 -9999 0 -0.28 11 11
positive regulation of MAPKKK cascade 0.022 0.031 -9999 0 -0.13 6 6
PIK3R1 -0.011 0.097 -9999 0 -0.3 52 52
mol:IP3 0.008 0.06 -9999 0 -0.3 7 7
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.006 0.07 -9999 0 -0.35 20 20
PDGFB-D/PDGFRB/GRB7 0.008 0.066 -9999 0 -0.28 17 17
SHB 0.017 0.025 -9999 0 -0.2 7 7
BLK -0.001 0.045 -9999 0 -0.32 1 1
PTPN2 0.016 0.029 -9999 0 -0.37 3 3
PDGFB-D/PDGFRB/SNX15 0.022 0.031 -9999 0 -0.13 2 2
BCAR1 0 0 -9999 0 -10000 0 0
VAV2 -0.028 0.13 -9999 0 -0.34 37 37
CBL 0.02 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.022 0.031 -9999 0 -0.13 3 3
LCK -0.001 0.046 -9999 0 -0.26 4 4
PDGFRB 0.009 0.046 -9999 0 -0.21 23 23
ACP1 0.002 0.078 -9999 0 -0.33 27 27
HCK -0.012 0.061 -9999 0 -0.37 7 7
ABL1 -0.006 0.079 -9999 0 -0.33 9 9
PDGFB-D/PDGFRB/CBL -0.01 0.093 -9999 0 -0.38 9 9
PTPN1 0.013 0.046 -9999 0 -0.33 9 9
SNX15 0.02 0 -9999 0 -10000 0 0
STAT3 0.004 0.075 -9999 0 -0.35 23 23
STAT1 -0.024 0.11 -9999 0 -0.3 74 74
cell proliferation -0.11 0.28 -9999 0 -0.67 104 104
SLA 0.003 0.067 -9999 0 -0.25 33 33
actin cytoskeleton reorganization 0.024 0.058 -9999 0 -0.27 7 7
SRC 0.001 0.045 -9999 0 -0.32 1 1
PI3K -0.043 0.071 -9999 0 -0.28 24 24
PDGFB-D/PDGFRB/GRB7/SHC 0.021 0.061 -9999 0 -0.24 18 18
SH2B2 0 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 0.013 0.067 -9999 0 -0.28 8 8
LYN -0.065 0.18 -9999 0 -0.51 66 66
LRP1 0.016 0.027 -9999 0 -0.2 8 8
SOS1 0 0 -9999 0 -10000 0 0
STAT5B 0.02 0 -9999 0 -10000 0 0
STAT5A 0.019 0.014 -9999 0 -0.2 2 2
NCK1-2/p130 Cas 0.022 0.063 -9999 0 -0.22 16 16
SPHK1 0.012 0.042 -9999 0 -0.2 19 19
EDG1 0.017 0.024 -9999 0 -0.2 6 6
mol:DAG 0.008 0.06 -9999 0 -0.3 7 7
PLCG1 0.008 0.061 -9999 0 -0.31 7 7
NHERF/PDGFRB 0.018 0.06 -9999 0 -0.2 25 25
YES1 -0.025 0.12 -9999 0 -0.48 28 28
cell migration 0.017 0.06 -9999 0 -0.2 25 25
SHC/Grb2/SOS1 0.029 0.05 -9999 0 -0.17 19 19
SLC9A3R2 0.02 0 -9999 0 -10000 0 0
SLC9A3R1 -0.007 0.09 -9999 0 -0.29 46 46
NHERF1-2/PDGFRB/PTEN 0.009 0.084 -9999 0 -0.18 71 71
FYN -0.065 0.16 -9999 0 -0.48 63 63
DOK1 0.024 0.037 -9999 0 -0.18 10 10
HRAS/GTP 0.011 0.028 -9999 0 -0.18 10 10
PDGFB 0.02 0 -9999 0 -10000 0 0
RAC1 -0.06 0.2 -9999 0 -0.43 106 106
PRKCD 0.01 0.064 -9999 0 -0.2 35 35
FER 0.02 0.041 -9999 0 -0.18 10 10
MAPKKK cascade -0.003 0.042 -9999 0 -0.2 7 7
RASA1 0.007 0.068 -9999 0 -0.19 47 47
NCK1 0.002 0.074 -9999 0 -0.28 32 32
NCK2 0.012 0.051 -9999 0 -0.34 11 11
p62DOK/Csk 0.03 0.053 -9999 0 -0.29 5 5
PDGFB-D/PDGFRB/SHB 0.02 0.036 -9999 0 -0.25 1 1
chemotaxis -0.006 0.077 -9999 0 -0.32 9 9
STAT1-3-5/STAT1-3-5 0.007 0.074 -9999 0 -0.26 15 15
Bovine Papilomavirus E5/PDGFRB 0.007 0.03 -9999 0 -0.13 23 23
PTPRJ 0.02 0 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.013 0.037 -10000 0 -0.2 15 15
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0.004 -10000 0 -0.024 15 15
monocyte activation -0.11 0.17 -10000 0 -0.37 155 155
MAP2K2 0.014 0.005 -10000 0 -10000 0 0
MAP2K1 0.007 0.011 -10000 0 -0.12 3 3
MAP2K7 0.008 0.004 -10000 0 -10000 0 0
MAP2K6 0.008 0.006 -10000 0 -0.088 1 1
CYAA 0.004 0.016 -10000 0 -0.089 15 15
MAP2K4 0.005 0.021 -10000 0 -0.15 9 9
IL1B -0.008 0.038 -10000 0 -0.13 16 16
Channel 0.01 0.018 -10000 0 -0.096 15 15
NLRP1 0.008 0.006 -10000 0 -0.088 1 1
CALM1 0.019 0.019 -10000 0 -0.28 2 2
negative regulation of phagocytosis 0.012 0.022 -10000 0 -0.49 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0.004 0.024 15 -10000 0 15
MAPK3 0.008 0.004 -10000 0 -10000 0 0
MAPK1 -0.003 0.041 -10000 0 -0.14 41 41
PGR 0.006 0.013 -10000 0 -0.091 9 9
PA/Cellular Receptors 0.01 0.02 -10000 0 -0.11 15 15
apoptosis -0.001 0.004 -10000 0 -0.024 15 15
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.01 0.016 -10000 0 -0.084 15 15
macrophage activation 0.003 0.039 -10000 0 -0.16 25 25
TNF 0.001 0.063 -10000 0 -0.2 46 46
VCAM1 -0.11 0.17 -10000 0 -0.38 155 155
platelet activation 0.012 0.022 -10000 0 -0.49 1 1
MAPKKK cascade -0.01 0.008 -10000 0 -10000 0 0
IL18 -0.011 0.042 -10000 0 -0.15 16 16
negative regulation of macrophage activation -0.001 0.004 -10000 0 -0.024 15 15
LEF -0.001 0.004 -10000 0 -0.024 15 15
CASP1 0.005 0.009 -10000 0 -0.16 1 1
mol:cAMP 0.012 0.023 -10000 0 -0.49 1 1
necrosis -0.001 0.004 -10000 0 -0.024 15 15
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.01 0.017 -10000 0 -0.089 15 15
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.019 0.15 -9999 0 -0.45 57 57
Crk/p130 Cas/Paxillin -0.04 0.073 -9999 0 -0.25 39 39
JUN 0.011 0.079 -9999 0 -0.28 16 16
HRAS 0.014 0.04 -9999 0 -0.27 10 10
RET51/GFRalpha1/GDNF/GRB10 0.041 0.039 -9999 0 -0.2 7 7
RAP1A 0.015 0.039 -9999 0 -0.32 7 7
FRS2 0.019 0.01 -9999 0 -0.2 1 1
RAP1A/GDP 0.012 0.027 -9999 0 -0.22 7 7
RET51/GFRalpha1/GDNF/DOK1 0.047 0.023 -9999 0 -0.18 1 1
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.02 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.01 0.053 -9999 0 -0.25 20 20
RET9/GFRalpha1/GDNF/Enigma 0.037 0.012 -9999 0 -10000 0 0
RHOA -0.008 0.1 -9999 0 -0.36 39 39
RAP1A/GTP 0.042 0.028 -9999 0 -0.15 7 7
GRB7 0 0.077 -9999 0 -0.28 35 35
RET51/GFRalpha1/GDNF 0.047 0.023 -9999 0 -0.18 1 1
MAPKKK cascade 0.025 0.044 -9999 0 -0.2 3 3
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.001 0.072 -9999 0 -0.18 55 55
lamellipodium assembly -0.039 0.071 -9999 0 -0.23 40 40
RET51/GFRalpha1/GDNF/SHC 0.045 0.027 -9999 0 -0.17 2 2
PIK3CA -0.011 0.1 -9999 0 -0.33 48 48
RET9/GFRalpha1/GDNF/SHC 0.036 0.018 -9999 0 -0.18 1 1
RET9/GFRalpha1/GDNF/Shank3 0.025 0.01 -9999 0 -10000 0 0
MAPK3 0.036 0.025 -9999 0 -10000 0 0
DOK1 0.02 0 -9999 0 -10000 0 0
DOK6 0 0 -9999 0 -10000 0 0
PXN 0.019 0.01 -9999 0 -0.2 1 1
neurite development 0.031 0.063 -9999 0 -0.24 23 23
DOK5 -0.084 0.16 -9999 0 -0.31 170 170
GFRA1 0.018 0.019 -9999 0 -0.2 4 4
MAPK8 0.02 0.067 -9999 0 -0.29 8 8
HRAS/GTP 0.032 0.044 -9999 0 -10000 0 0
tube development 0.025 0.028 -9999 0 -0.16 10 10
MAPK1 0.03 0.039 -9999 0 -0.3 4 4
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.031 0.03 -9999 0 -0.18 10 10
Rac1/GDP 0.013 0.023 -9999 0 -0.25 4 4
SRC 0.02 0 -9999 0 -10000 0 0
PDLIM7 0.019 0.01 -9999 0 -0.2 1 1
RET51/GFRalpha1/GDNF/Dok6 0.043 0.021 -9999 0 -0.16 1 1
SHC1 0.017 0.027 -9999 0 -0.23 6 6
RET51/GFRalpha1/GDNF/Dok4 0.047 0.024 -9999 0 -0.18 2 2
RET51/GFRalpha1/GDNF/Dok5 -0.012 0.093 -9999 0 -0.17 115 115
PRKCA 0.019 0.014 -9999 0 -0.2 2 2
HRAS/GDP 0.011 0.028 -9999 0 -0.18 10 10
CREB1 0.027 0.042 -9999 0 -0.19 11 11
PIK3R1 -0.011 0.097 -9999 0 -0.3 52 52
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.03 0.031 -9999 0 -0.18 11 11
RET51/GFRalpha1/GDNF/Grb7 0.036 0.05 -9999 0 -0.18 18 18
mol:GDP 0 0 -9999 0 -10000 0 0
RET 0.014 0.034 -9999 0 -0.2 13 13
DOK4 0.019 0.01 -9999 0 -0.2 1 1
JNK cascade 0.011 0.078 -9999 0 -0.27 16 16
RET9/GFRalpha1/GDNF/FRS2 0.037 0.012 -9999 0 -10000 0 0
SHANK3 0 0 -9999 0 -10000 0 0
RASA1 -0.01 0.1 -9999 0 -0.35 44 44
NCK1 0.002 0.074 -9999 0 -0.28 32 32
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.023 0.031 -9999 0 -0.18 11 11
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.036 0.033 -9999 0 -0.18 10 10
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.016 0.072 -9999 0 -0.32 8 8
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.028 0.034 -9999 0 -0.18 11 11
PI3K -0.024 0.12 -9999 0 -0.34 38 38
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.031 0.029 -9999 0 -0.16 10 10
GRB10 0.01 0.053 -9999 0 -0.25 20 20
activation of MAPKK activity 0.034 0.04 -9999 0 -0.24 10 10
RET51/GFRalpha1/GDNF/FRS2 0.047 0.024 -9999 0 -0.18 1 1
GAB1 0.02 0 -9999 0 -10000 0 0
IRS1 -0.046 0.13 -9999 0 -0.28 118 118
IRS2 -0.046 0.13 -9999 0 -0.3 112 112
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.035 0.034 -9999 0 -0.24 1 1
RET51/GFRalpha1/GDNF/PKC alpha 0.047 0.024 -9999 0 -0.18 1 1
GRB2 0.012 0.053 -9999 0 -0.35 11 11
PRKACA 0.02 0 -9999 0 -10000 0 0
GDNF 0.02 0 -9999 0 -10000 0 0
RAC1 0.017 0.033 -9999 0 -0.36 4 4
RET51/GFRalpha1/GDNF/IRS1 0.01 0.077 -9999 0 -0.17 58 58
Rac1/GTP -0.016 0.1 -9999 0 -0.28 37 37
RET9/GFRalpha1/GDNF 0.026 0.011 -9999 0 -10000 0 0
GFRalpha1/GDNF 0.028 0.013 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.022 0.066 -9999 0 -0.19 27 27
MAP4K1 0.003 0.059 -9999 0 -0.2 41 41
MAP3K8 -0.008 0.086 -9999 0 -0.25 56 56
PRKCB 0 0 -9999 0 -10000 0 0
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0.019 0.01 -9999 0 -0.2 1 1
MAP3K1 0.02 0.052 -9999 0 -0.21 9 9
JUN 0.008 0.05 -9999 0 -0.2 5 5
MAP3K7 0.013 0.061 -9999 0 -0.23 13 13
GRAP2 0.02 0 -9999 0 -10000 0 0
CRK 0.01 0.053 -9999 0 -0.25 20 20
MAP2K4 0.015 0.06 -9999 0 -0.22 12 12
LAT 0.019 0.014 -9999 0 -0.2 2 2
LCP2 -0.014 0.095 -9999 0 -0.26 66 66
MAPK8 0.017 0.018 -9999 0 -10000 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.016 0.055 -9999 0 -0.22 9 9
LAT/GRAP2/SLP76/HPK1/HIP-55 0.02 0.061 -9999 0 -0.18 27 27
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.008 0.036 -9999 0 -0.22 12 12
SMARCC1 -0.028 0.26 -9999 0 -1.2 22 22
REL 0.018 0.01 -9999 0 -0.21 1 1
HDAC7 0.006 0.087 -9999 0 -0.23 21 21
JUN -0.011 0.099 -9999 0 -0.31 51 51
EP300 0.015 0.044 -9999 0 -0.36 7 7
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0 0 -9999 0 -10000 0 0
MAPK14 0.022 0.018 -9999 0 -0.15 1 1
FOXO1 -0.022 0.11 -9999 0 -0.29 74 74
T-DHT/AR 0.021 0.1 -9999 0 -0.24 21 21
MAP2K6 0.019 0.011 -9999 0 -0.2 1 1
BRM/BAF57 0.023 0.038 -9999 0 -0.24 5 5
MAP2K4 0.014 0.043 -9999 0 -0.31 9 9
SMARCA2 0.015 0.036 -9999 0 -0.2 14 14
PDE9A -0.097 0.34 -9999 0 -0.96 70 70
NCOA2 0.02 0.014 -9999 0 -0.2 2 2
CEBPA 0 0.067 -9999 0 -0.22 43 43
EHMT2 0.02 0.01 -9999 0 -0.2 1 1
cell proliferation 0.043 0.093 -9999 0 -0.25 4 4
NR0B1 0.011 0.044 -9999 0 -0.2 22 22
EGR1 -0.084 0.15 -9999 0 -0.28 185 185
RXRs/9cRA 0.036 0.022 -9999 0 -10000 0 0
AR/RACK1/Src 0.037 0.049 -9999 0 -10000 0 0
AR/GR -0.002 0.087 -9999 0 -0.2 72 72
GNB2L1 0.015 0.044 -9999 0 -0.36 7 7
PKN1 -0.003 0.08 -9999 0 -0.26 44 44
RCHY1 -0.001 0.084 -9999 0 -0.32 33 33
epidermal growth factor receptor activity 0.001 0 -9999 0 -10000 0 0
MAPK8 0.02 0.032 -9999 0 -0.24 6 6
T-DHT/AR/TIF2/CARM1 0.04 0.055 -9999 0 -0.2 2 2
SRC 0.029 0.031 -9999 0 -10000 0 0
NR3C1 -0.014 0.11 -9999 0 -0.36 49 49
KLK3 0.009 0.054 -9999 0 -0.44 2 2
APPBP2 0.01 0.056 -9999 0 -0.31 15 15
TRIM24 0.018 0.034 -9999 0 -0.33 5 5
T-DHT/AR/TIP60 0.014 0.045 -9999 0 -0.17 9 9
TMPRSS2 0.021 0.066 -9999 0 -0.48 1 1
RXRG 0.012 0.04 -9999 0 -0.2 18 18
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.02 0.01 -9999 0 -0.2 1 1
RXRB 0.02 0 -9999 0 -10000 0 0
CARM1 0.013 0.052 -9999 0 -0.32 12 12
NR2C2 0.02 0.01 -9999 0 -0.2 1 1
KLK2 0.049 0.047 -9999 0 -10000 0 0
AR 0 0.079 -9999 0 -0.21 56 56
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0.02 0 -9999 0 -10000 0 0
MDM2 0.018 0 -9999 0 -10000 0 0
SRY 0.018 0 -9999 0 -10000 0 0
GATA2 0.015 0.032 -9999 0 -0.2 11 11
MYST2 0.013 0.046 -9999 0 -0.32 10 10
HOXB13 0.021 0.01 -9999 0 -0.2 1 1
T-DHT/AR/RACK1/Src 0.034 0.048 -9999 0 -0.17 2 2
positive regulation of transcription 0.015 0.032 -9999 0 -0.2 11 11
DNAJA1 -0.003 0.088 -9999 0 -0.36 30 30
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.066 -9999 0 -0.24 33 33
NCOA1 0.003 0.088 -9999 0 -0.38 22 22
SPDEF 0.011 0.047 -9999 0 -0.2 25 25
T-DHT/AR/TIF2 0.022 0.063 -9999 0 -0.23 13 13
T-DHT/AR/Hsp90 0.026 0.048 -9999 0 -0.18 3 3
GSK3B 0.003 0.077 -9999 0 -0.34 25 25
NR2C1 0.019 0 -9999 0 -10000 0 0
mol:T-DHT 0.025 0.034 -9999 0 -0.16 6 6
SIRT1 0.007 0.068 -9999 0 -0.35 19 19
ZMIZ2 0.018 0.01 -9999 0 -0.21 1 1
POU2F1 0.018 0.04 -9999 0 -0.36 1 1
T-DHT/AR/DAX-1 0.022 0.053 -9999 0 -0.17 12 12
CREBBP 0.02 0 -9999 0 -10000 0 0
SMARCE1 0.015 0.042 -9999 0 -0.28 10 10
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 0.024 0.077 -9999 0 -0.26 21 21
Ran/GTP/Exportin 1/HDAC1 -0.016 0.047 -9999 0 -0.15 55 55
NF kappa B1 p50/RelA/I kappa B alpha 0.014 0.095 -9999 0 -0.31 25 25
SUMO1 0.013 0.049 -9999 0 -0.36 9 9
ZFPM1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.011 0.051 -9999 0 -0.18 33 33
FKBP3 0.01 0.058 -9999 0 -0.34 14 14
Histones 0.021 0.065 -9999 0 -0.25 13 13
YY1/LSF 0.023 0.046 -9999 0 -0.2 20 20
SMG5 0.019 0.014 -9999 0 -0.2 2 2
RAN 0.003 0.078 -9999 0 -0.36 24 24
I kappa B alpha/HDAC3 0.007 0.078 -9999 0 -0.21 50 50
I kappa B alpha/HDAC1 0.008 0.085 -9999 0 -0.26 38 38
SAP18 0.016 0.037 -9999 0 -0.36 5 5
RELA 0.023 0.053 -9999 0 -0.18 23 23
HDAC1/Smad7 0.013 0.073 -9999 0 -0.2 51 51
RANGAP1 0.018 0.017 -9999 0 -0.2 3 3
HDAC3/TR2 0.024 0.052 -9999 0 -0.26 11 11
NuRD/MBD3 Complex 0.006 0.089 -9999 0 -0.3 24 24
NF kappa B1 p50/RelA 0.025 0.066 -9999 0 -0.3 13 13
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.015 0.032 -9999 0 -0.2 11 11
GATA1 0.02 0 -9999 0 -10000 0 0
Mad/Max 0.029 0.007 -9999 0 -0.12 1 1
NuRD/MBD3 Complex/GATA1/Fog1 0.012 0.091 -9999 0 -0.3 24 24
RBBP7 0.006 0.069 -9999 0 -0.34 20 20
NPC 0.002 0.041 -9999 0 -0.18 26 26
RBBP4 -0.012 0.1 -9999 0 -0.34 47 47
MAX 0.019 0.01 -9999 0 -0.2 1 1
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.02 0 -9999 0 -10000 0 0
NFKBIA 0.002 0.088 -9999 0 -0.33 29 29
KAT2B 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.007 0.089 -9999 0 -0.36 17 17
SIN3 complex 0.034 0.027 -9999 0 -0.18 5 5
SMURF1 0.02 0 -9999 0 -10000 0 0
CHD3 0.019 0.01 -9999 0 -0.2 1 1
SAP30 0.019 0.014 -9999 0 -0.2 2 2
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.014 0.046 -9999 0 -0.36 8 8
YY1/HDAC3 0.026 0.054 -9999 0 -0.24 13 13
YY1/HDAC2 0.02 0.049 -9999 0 -0.2 22 22
YY1/HDAC1 0.025 0.042 -9999 0 -0.2 16 16
NuRD/MBD2 Complex (MeCP1) 0.006 0.089 -9999 0 -0.3 24 24
PPARG 0.02 0.064 -9999 0 -0.24 22 22
HDAC8/hEST1B 0.026 0.008 -9999 0 -10000 0 0
UBE2I 0.02 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0 -9999 0 -10000 0 0
TNFRSF1A 0.007 0.066 -9999 0 -0.32 20 20
HDAC3/SMRT (N-CoR2) 0.024 0.052 -9999 0 -0.26 11 11
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.012 0.072 -9999 0 -0.2 51 51
CREBBP 0.02 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.008 0.093 -9999 0 -0.31 24 24
HDAC1 0.012 0.052 -9999 0 -0.32 12 12
HDAC3 0.015 0.056 -9999 0 -0.3 11 11
HDAC2 0.004 0.071 -9999 0 -0.29 28 28
YY1 0.021 0.035 -9999 0 -0.26 7 7
HDAC8 0 0 -9999 0 -10000 0 0
SMAD7 -0.018 0.11 -9999 0 -0.32 60 60
NCOR2 0.02 0 -9999 0 -10000 0 0
MXD1 0.02 0 -9999 0 -10000 0 0
STAT3 0.015 0.062 -9999 0 -0.25 28 28
NFKB1 -0.003 0.088 -9999 0 -0.34 34 34
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0 0.084 -9999 0 -0.35 29 29
YY1/LSF/HDAC1 0.03 0.051 -9999 0 -0.17 30 30
YY1/SAP30/HDAC1 0.035 0.04 -9999 0 -0.18 16 16
EP300 0.015 0.044 -9999 0 -0.36 7 7
STAT3 (dimer non-phopshorylated) 0.015 0.062 -9999 0 -0.25 28 28
proteasomal ubiquitin-dependent protein catabolic process 0.002 0.088 -9999 0 -0.33 29 29
histone deacetylation 0.006 0.088 -9999 0 -0.3 24 24
STAT3 (dimer non-phopshorylated)/HDAC3 0.021 0.067 -9999 0 -0.24 17 17
nuclear export -0.026 0.008 -9999 0 -10000 0 0
PRKACA 0.02 0 -9999 0 -10000 0 0
GATAD2B 0 0 -9999 0 -10000 0 0
GATAD2A -0.004 0.09 -9999 0 -0.32 38 38
GATA2/HDAC3 0.022 0.054 -9999 0 -0.26 11 11
GATA1/HDAC1 0.024 0.037 -9999 0 -0.21 12 12
GATA1/HDAC3 0.024 0.052 -9999 0 -0.26 11 11
CHD4 0.012 0.053 -9999 0 -0.35 11 11
TNF-alpha/TNFR1A 0.007 0.063 -9999 0 -0.24 17 17
SIN3/HDAC complex/Mad/Max 0.016 0.078 -9999 0 -0.31 17 17
NuRD Complex 0.013 0.092 -9999 0 -0.3 24 24
positive regulation of chromatin silencing 0.02 0.064 -9999 0 -0.24 13 13
SIN3B 0.016 0.03 -9999 0 -0.2 10 10
MTA2 0.02 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
XPO1 0.019 0.01 -9999 0 -0.2 1 1
SUMO1/HDAC1 0.023 0.058 -9999 0 -0.22 18 18
HDAC complex 0.013 0.094 -9999 0 -0.21 68 68
GATA1/Fog1 0.015 0 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.02 0.066 -9999 0 -0.21 33 33
TNF 0.001 0.063 -9999 0 -0.2 46 46
negative regulation of cell growth 0.016 0.078 -9999 0 -0.3 17 17
NuRD/MBD2/PRMT5 Complex 0.006 0.089 -9999 0 -0.3 24 24
Ran/GTP/Exportin 1 0.023 0.066 -9999 0 -0.17 49 49
NF kappa B/RelA/I kappa B alpha 0.015 0.079 -9999 0 -0.31 16 16
SIN3/HDAC complex/NCoR1 0.008 0.087 -9999 0 -0.33 18 18
TFCP2 0.009 0.061 -9999 0 -0.34 16 16
NR2C1 0.02 0 -9999 0 -10000 0 0
MBD3 0.019 0.01 -9999 0 -0.2 1 1
MBD2 0.02 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.026 0.012 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.019 0.014 -9999 0 -0.2 2 2
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.019 0.01 -9999 0 -0.2 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.014 0.044 -9999 0 -0.31 9 9
RAC1-CDC42/GTP/PAK family 0.019 0.035 -9999 0 -0.16 15 15
response to UV 0 0 -9999 0 -10000 0 0
YES1 0 0.082 -9999 0 -0.33 30 30
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.018 0.017 -9999 0 -0.2 3 3
FYN -0.049 0.13 -9999 0 -0.28 122 122
MAP3K12 0.018 0.017 -9999 0 -0.2 3 3
FGR 0.012 0.04 -9999 0 -0.2 18 18
p38 alpha/TAB1 0.019 0.073 -9999 0 -0.2 19 19
PRKG1 0.02 0 -9999 0 -10000 0 0
DUSP8 0.018 0.017 -9999 0 -0.2 3 3
PGK/cGMP/p38 alpha -0.014 0.054 -9999 0 -0.2 19 19
apoptosis 0.018 0.07 -9999 0 -0.19 19 19
RAL/GTP 0.01 0.058 -9999 0 -0.19 42 42
LYN -0.031 0.13 -9999 0 -0.34 76 76
DUSP1 -0.026 0.11 -9999 0 -0.25 91 91
PAK1 0.01 0.046 -9999 0 -0.2 24 24
SRC 0.02 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.035 0.026 -9999 0 -0.18 7 7
TRAF6 0.019 0.017 -9999 0 -0.36 1 1
RAC1 0.017 0.033 -9999 0 -0.36 4 4
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.025 0.02 -9999 0 -0.2 4 4
MAPK11 0.005 0.094 -9999 0 -0.27 27 27
BLK 0.019 0.014 -9999 0 -0.2 2 2
HCK -0.004 0.072 -9999 0 -0.21 56 56
MAP2K3 0.018 0.029 -9999 0 -0.36 3 3
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 -0.001 0.071 -9999 0 -0.23 46 46
TRAF6/MEKK3 0.024 0.012 -9999 0 -0.18 1 1
MAP3K7IP1 0.019 0.01 -9999 0 -0.2 1 1
MAPK14 0.011 0.077 -9999 0 -0.22 20 20
positive regulation of innate immune response 0.008 0.1 -9999 0 -0.3 24 24
LCK 0.016 0.03 -9999 0 -0.2 10 10
p38alpha-beta/MKP7 0.007 0.1 -9999 0 -0.28 24 24
p38alpha-beta/MKP5 0.01 0.11 -9999 0 -0.29 24 24
PGK/cGMP 0.015 0 -9999 0 -10000 0 0
PAK2 0.009 0.059 -9999 0 -0.31 17 17
p38alpha-beta/MKP1 0.002 0.11 -9999 0 -0.31 27 27
CDC42 0.019 0.01 -9999 0 -0.2 1 1
RALB 0.008 0.066 -9999 0 -0.36 17 17
RALA 0.004 0.074 -9999 0 -0.33 25 25
PAK3 0.011 0.044 -9999 0 -0.2 22 22
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.015 0.033 -9999 0 -0.2 12 12
CDC42/GTP 0.013 0.066 -9999 0 -0.23 17 17
PLCG1 0.009 0.067 -9999 0 -0.24 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.012 0.054 -9999 0 -0.36 11 11
GNAI3 0.01 0.06 -9999 0 -0.35 14 14
G12/G13 0.029 0.011 -9999 0 -0.12 3 3
cell migration 0.013 0.065 -9999 0 -0.23 17 17
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 0.009 0.067 -9999 0 -0.24 17 17
MAPK1 -0.001 0.082 -9999 0 -0.22 39 39
S1P/S1P5/Gi 0.004 0.071 -9999 0 -0.19 54 54
GNAI1 -0.021 0.11 -9999 0 -0.28 74 74
CDC42/GDP 0.014 0.006 -9999 0 -0.13 1 1
S1P/S1P5/G12 0.013 0.009 -9999 0 -0.11 3 3
RHOA 0.012 0.05 -9999 0 -0.16 39 39
S1P/S1P4/Gi 0.004 0.071 -9999 0 -0.19 54 54
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.017 0.025 -9999 0 -0.2 7 7
S1P/S1P4/G12/G13 0.025 0.009 -9999 0 -0.09 3 3
GNA12 0.018 0.017 -9999 0 -0.2 3 3
GNA13 0.02 0 -9999 0 -10000 0 0
CDC42 0.019 0.01 -9999 0 -0.2 1 1
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.001 0.11 -9999 0 -0.47 16 16
BAG4 0.015 0.033 -9999 0 -0.2 12 12
BAD 0.013 0.04 -9999 0 -0.15 16 16
NFKBIA -0.006 0.091 -9999 0 -0.32 40 40
BIRC3 -0.051 0.13 -9999 0 -0.27 131 131
BAX 0.014 0.035 -9999 0 -0.14 11 11
EnzymeConsortium:3.1.4.12 0.005 0.025 -9999 0 -0.11 11 11
IKBKB 0.006 0.11 -9999 0 -0.43 17 17
MAP2K2 0.024 0.037 -9999 0 -0.15 7 7
MAP2K1 0.024 0.037 -9999 0 -0.15 8 8
SMPD1 0.011 0.025 -9999 0 -0.1 11 11
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 0.013 0.11 -9999 0 -0.49 14 14
MAP2K4 0.018 0.037 -9999 0 -0.13 17 17
protein ubiquitination 0.006 0.11 -9999 0 -0.41 19 19
EnzymeConsortium:2.7.1.37 0.027 0.037 -9999 0 -0.17 4 4
response to UV 0 0 -9999 0 -0.002 2 2
RAF1 0.02 0.038 -9999 0 -0.14 19 19
CRADD 0.019 0.01 -9999 0 -0.2 1 1
mol:ceramide 0.011 0.035 -9999 0 -0.15 11 11
I-kappa-B-alpha/RELA/p50/ubiquitin 0.011 0.055 -9999 0 -0.17 43 43
MADD 0.019 0.01 -9999 0 -0.2 1 1
MAP3K1 0.015 0.035 -9999 0 -0.13 13 13
TRADD 0.02 0 -9999 0 -10000 0 0
RELA/p50 0.018 0.021 -9999 0 -0.26 3 3
MAPK3 0.027 0.036 -9999 0 -0.17 4 4
MAPK1 0.023 0.041 -9999 0 -0.19 5 5
p50/RELA/I-kappa-B-alpha 0.01 0.066 -9999 0 -0.21 43 43
FADD 0.006 0.11 -9999 0 -0.51 13 13
KSR1 0.017 0.033 -9999 0 -0.14 11 11
MAPK8 0.023 0.035 -9999 0 -0.13 6 6
TRAF2 0.02 0.001 -9999 0 -10000 0 0
response to radiation 0 0 -9999 0 -0.001 1 1
CHUK 0.002 0.11 -9999 0 -0.43 18 18
TNF R/SODD 0.017 0.052 -9999 0 -0.18 32 32
TNF 0.001 0.063 -9999 0 -0.2 46 46
CYCS 0.012 0.037 -9999 0 -0.14 12 12
IKBKG 0.007 0.11 -9999 0 -0.45 15 15
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.003 0.11 -9999 0 -0.52 13 13
RELA 0.018 0.021 -9999 0 -0.26 3 3
RIPK1 0.019 0.014 -9999 0 -0.2 2 2
AIFM1 0.002 0.052 -9999 0 -0.19 20 20
TNF/TNF R/SODD 0.018 0.058 -9999 0 -0.2 19 19
TNFRSF1A 0.007 0.066 -9999 0 -0.32 20 20
response to heat 0 0 -9999 0 -0.001 1 1
CASP8 0.019 0.085 -9999 0 -0.78 5 5
NSMAF 0.004 0.11 -9999 0 -0.53 13 13
response to hydrogen peroxide 0 0 -9999 0 -0.002 2 2
BCL2 0.019 0.01 -9999 0 -0.2 1 1
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.018 0.017 -10000 0 -0.2 3 3
NFATC1 0.008 0.12 -10000 0 -0.35 36 36
NFATC2 0.021 0.036 -10000 0 -0.11 4 4
NFATC3 0.017 0.008 -10000 0 -0.15 1 1
YWHAE 0.013 0.048 -10000 0 -0.3 12 12
Calcineurin A alpha-beta B1/CABIN1 0.009 0.068 -10000 0 -0.25 11 11
Exportin 1/Ran/NUP214 0.03 0.048 -10000 0 -0.2 23 23
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.033 0.062 -10000 0 -0.28 5 5
BCL2/BAX 0.025 0.025 -10000 0 -0.12 15 15
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.013 -10000 0 -0.19 2 2
CaM/Ca2+ 0.015 0.013 -10000 0 -0.19 2 2
BAX 0.014 0.036 -10000 0 -0.2 14 14
MAPK14 0.019 0.017 -10000 0 -0.2 3 3
BAD 0.013 0.045 -10000 0 -0.29 11 11
CABIN1/MEF2D 0.019 0.066 -10000 0 -0.23 11 11
Calcineurin A alpha-beta B1/BCL2 0.019 0.01 -10000 0 -0.2 1 1
FKBP8 0.02 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.019 0.066 0.23 11 -10000 0 11
KPNB1 0.012 0.054 -10000 0 -0.36 11 11
KPNA2 -0.018 0.11 -10000 0 -0.35 55 55
XPO1 0.019 0.01 -10000 0 -0.2 1 1
SFN -0.066 0.15 -10000 0 -0.31 141 141
MAP3K8 -0.008 0.086 -10000 0 -0.25 56 56
NFAT4/CK1 alpha 0.033 0.023 -10000 0 -0.16 5 5
MEF2D/NFAT1/Cbp/p300 0.06 0.043 -10000 0 -10000 0 0
CABIN1 0.009 0.069 -10000 0 -0.25 11 11
CALM1 0.019 0.019 -10000 0 -0.28 2 2
RAN 0.003 0.078 -10000 0 -0.36 24 24
MAP3K1 0.017 0.025 -10000 0 -0.2 7 7
CAMK4 0.019 0.01 -10000 0 -0.2 1 1
mol:Ca2+ 0.001 0.001 -10000 0 -10000 0 0
MAPK3 0.02 0 -10000 0 -10000 0 0
YWHAH -0.027 0.12 -10000 0 -0.32 73 73
Calcineurin A alpha-beta B1/AKAP79/PKA 0.03 0 -10000 0 -10000 0 0
YWHAB 0.015 0.041 -10000 0 -0.34 7 7
MAPK8 0.02 0 -10000 0 -10000 0 0
MAPK9 0.007 0.063 -10000 0 -0.3 21 21
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0.01 0.059 -10000 0 -0.36 13 13
NFAT1-c-4/YWHAQ 0.031 0.1 -10000 0 -0.36 21 21
PRKCH 0.013 0.037 -10000 0 -0.2 15 15
CABIN1/Cbp/p300 0.027 0.031 -10000 0 -0.24 7 7
CASP3 0.016 0.036 -10000 0 -0.31 6 6
PIM1 0.011 0.045 -10000 0 -0.21 21 21
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.034 -10000 0 -0.21 13 13
apoptosis 0.015 0.032 -10000 0 -0.25 6 6
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.03 0.13 -10000 0 -0.37 47 47
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.02 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.021 0.033 -10000 0 -0.17 12 12
BAD/BCL-XL 0.024 0.034 -10000 0 -0.18 14 14
PRKCD -0.005 0.09 -10000 0 -0.32 39 39
NUP214 0.02 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.019 0.014 -10000 0 -0.2 2 2
PRKCG 0.02 0 -10000 0 -10000 0 0
PRKCQ -0.034 0.12 -10000 0 -0.3 89 89
FKBP38/BCL2 0.029 0.007 -10000 0 -10000 0 0
EP300 0.015 0.043 -10000 0 -0.36 7 7
PRKCB1 0.014 0.036 -10000 0 -0.2 14 14
CSNK2A1 -0.003 0.088 -10000 0 -0.33 35 35
NFATc/JNK1 0.019 0.11 -10000 0 -0.39 24 24
CaM/Ca2+/FKBP38 0.027 0.011 -10000 0 -0.2 1 1
FKBP12/FK506 0.008 0.041 -10000 0 -0.25 13 13
CSNK1A1 0.02 0.022 -10000 0 -0.18 6 6
CaM/Ca2+/CAMK IV 0.027 0.013 -10000 0 -0.2 1 1
NFATc/ERK1 0.018 0.11 -10000 0 -0.39 24 24
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.029 0.066 -10000 0 -0.27 7 7
NR4A1 0.051 0.039 -10000 0 -0.18 2 2
GSK3B 0.004 0.077 -10000 0 -0.34 25 25
positive T cell selection 0.017 0.008 -10000 0 -0.15 1 1
NFAT1/CK1 alpha 0.024 0.034 -10000 0 -0.2 5 5
RCH1/ KPNB1 -0.003 0.09 -10000 0 -0.25 60 60
YWHAQ 0.013 0.049 -10000 0 -0.36 9 9
PRKACA 0.02 0 -10000 0 -10000 0 0
AKAP5 0.02 0 -10000 0 -10000 0 0
MEF2D 0.02 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.005 0.074 -10000 0 -0.35 22 22
NFATc/p38 alpha 0.018 0.11 -10000 0 -0.39 24 24
CREBBP 0.02 0 -10000 0 -10000 0 0
BCL2 0.019 0.01 -10000 0 -0.2 1 1
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.034 0.012 -9999 0 -0.18 1 1
NFATC2 0.021 0.012 -9999 0 -0.14 2 2
NFATC3 0.034 0.012 -9999 0 -0.18 1 1
CD40LG 0.054 0.09 -9999 0 -10000 0 0
PTGS2 0.047 0.1 -9999 0 -0.25 10 10
JUNB -0.025 0.11 -9999 0 -0.29 77 77
CaM/Ca2+/Calcineurin A alpha-beta B1 0.021 0.013 -9999 0 -0.18 2 2
CaM/Ca2+ 0.021 0.013 -9999 0 -0.18 2 2
CALM1 0.022 0.019 -9999 0 -0.28 2 2
JUN -0.006 0.098 -9999 0 -0.3 51 51
mol:Ca2+ 0.003 0.003 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.034 -9999 0 -0.21 13 13
FOSL1 0.016 0.027 -9999 0 -0.2 8 8
CREM 0.018 0.014 -9999 0 -0.2 2 2
Jun/NFAT1-c-4/p21SNFT 0.073 0.053 -9999 0 -0.18 2 2
FOS -0.11 0.16 -9999 0 -0.28 233 233
IFNG 0.053 0.091 -9999 0 -10000 0 0
AP-1/NFAT1-c-4 0.085 0.12 -9999 0 -10000 0 0
FASLG 0.054 0.09 -9999 0 -10000 0 0
NFAT1-c-4/ICER1 0.061 0.018 -9999 0 -10000 0 0
IL2RA 0.054 0.09 -9999 0 -10000 0 0
FKBP12/FK506 0.008 0.041 -9999 0 -0.25 13 13
CSF2 0.054 0.09 -9999 0 -10000 0 0
JunB/Fra1/NFAT1-c-4 0.052 0.061 -9999 0 -0.16 4 4
IL4 0.054 0.09 -9999 0 -10000 0 0
IL2 0.004 0.007 -9999 0 -10000 0 0
IL3 0.015 0.032 -9999 0 -0.61 1 1
FKBP1A 0.01 0.059 -9999 0 -0.36 13 13
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.027 0.017 -9999 0 -0.36 1 1
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.01 0.045 -9999 0 -0.2 23 23
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.014 0.076 -9999 0 -0.2 47 47
GNAO1 0.017 0.033 -9999 0 -0.2 12 12
S1P/S1P3/G12/G13 0.028 0.009 -9999 0 -0.088 3 3
AKT1 0.012 0.081 -9999 0 -0.43 14 14
AKT3 0.026 0.068 -9999 0 -0.44 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.045 -9999 0 -0.2 23 23
GNAI2 0.014 0.054 -9999 0 -0.36 11 11
GNAI3 0.012 0.06 -9999 0 -0.35 14 14
GNAI1 -0.02 0.11 -9999 0 -0.28 74 74
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.002 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.017 0.024 -9999 0 -0.2 6 6
mol:Ca2+ 0.016 0.071 -9999 0 -0.25 17 17
MAPK3 0.02 0.067 -9999 0 -0.28 10 10
MAPK1 0.009 0.082 -9999 0 -0.3 17 17
JAK2 0.008 0.082 -9999 0 -0.29 22 22
CXCR4 -0.018 0.1 -9999 0 -0.3 33 33
FLT1 0.023 0.001 -9999 0 -10000 0 0
RhoA/GDP -0.005 0.069 -9999 0 -0.25 39 39
Rac1/GDP 0.013 0.023 -9999 0 -0.25 4 4
SRC 0.02 0.067 -9999 0 -0.28 10 10
S1P/S1P3/Gi 0.016 0.071 -9999 0 -0.25 17 17
RAC1 0.017 0.033 -9999 0 -0.36 4 4
RhoA/GTP 0.011 0.088 -9999 0 -0.32 19 19
VEGFA -0.006 0.092 -9999 0 -0.28 51 51
S1P/S1P2/Gi 0.011 0.071 -9999 0 -0.18 54 54
VEGFR1 homodimer/VEGFA homodimer 0.018 0.067 -9999 0 -0.23 29 29
RHOA -0.008 0.1 -9999 0 -0.36 39 39
S1P/S1P3/Gq 0.029 0.009 -9999 0 -10000 0 0
GNAQ 0.02 0 -9999 0 -10000 0 0
GNAZ 0.019 0.025 -9999 0 -0.2 7 7
G12/G13 0.029 0.011 -9999 0 -0.12 3 3
GNA14 0.019 0.01 -9999 0 -0.2 1 1
GNA15 0.017 0.024 -9999 0 -0.2 6 6
GNA12 0.018 0.017 -9999 0 -0.2 3 3
GNA13 0.02 0 -9999 0 -10000 0 0
GNA11 0.02 0 -9999 0 -10000 0 0
Rac1/GTP 0.022 0.067 -9999 0 -0.28 10 10
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.017 0.073 -9999 0 -0.24 31 31
PDGFRB 0.011 0.045 -9999 0 -0.2 23 23
SPHK1 -0.001 0.017 -9999 0 -10000 0 0
mol:S1P 0.018 0.034 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.03 0.079 -9999 0 -0.31 12 12
GNAO1 0.015 0.033 -9999 0 -0.2 12 12
PDGFB-D/PDGFRB/PLCgamma1 0.029 0.08 -9999 0 -0.28 11 11
PLCG1 0.032 0.075 -9999 0 -0.3 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.011 0.045 -9999 0 -0.2 23 23
GNAI2 0.012 0.055 -9999 0 -0.37 11 11
GNAI3 0.011 0.06 -9999 0 -0.36 14 14
GNAI1 -0.021 0.11 -9999 0 -0.28 74 74
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.02 0.064 -9999 0 -0.25 8 8
S1P1/S1P 0.029 0.059 -9999 0 -0.28 4 4
negative regulation of cAMP metabolic process 0.03 0.078 -9999 0 -0.31 12 12
MAPK3 0.036 0.081 -9999 0 -0.31 10 10
calcium-dependent phospholipase C activity 0 0.001 -9999 0 -10000 0 0
Rac1/GDP 0.013 0.023 -9999 0 -0.25 4 4
RhoA/GDP -0.005 0.069 -9999 0 -0.25 39 39
KDR 0.019 0.036 -9999 0 -0.21 12 12
PLCB2 0.033 0.055 -9999 0 -0.25 4 4
RAC1 0.017 0.033 -9999 0 -0.36 4 4
RhoA/GTP -0.019 0.047 -9999 0 -0.23 10 10
receptor internalization 0.027 0.056 -9999 0 -0.26 4 4
PTGS2 0.027 0.094 -9999 0 -0.4 4 4
Rac1/GTP -0.011 0.036 -9999 0 -0.24 5 5
RHOA -0.008 0.1 -9999 0 -0.36 39 39
VEGFA -0.004 0.092 -9999 0 -0.28 51 51
negative regulation of T cell proliferation 0.03 0.078 -9999 0 -0.31 12 12
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.018 0.025 -9999 0 -0.2 7 7
MAPK1 0.027 0.091 -9999 0 -0.32 16 16
S1P1/S1P/PDGFB-D/PDGFRB 0.036 0.069 -9999 0 -0.29 5 5
ABCC1 0.012 0.053 -9999 0 -0.31 14 14
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.001 0.082 -9999 0 -0.24 51 51
AKT1 0.031 0.12 -9999 0 -0.34 15 15
PTK2B 0.021 0.077 -9999 0 -0.26 9 9
VEGFR2 homodimer/Frs2 0.039 0.037 -9999 0 -0.26 1 1
CAV1 -0.056 0.14 -9999 0 -0.3 129 129
CALM1 0.019 0.019 -9999 0 -0.28 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.039 0.067 -9999 0 -0.25 6 6
endothelial cell proliferation 0.053 0.087 -9999 0 -0.3 6 6
mol:Ca2+ 0.041 0.067 -9999 0 -0.3 4 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.032 0.085 -9999 0 -0.26 13 13
RP11-342D11.1 0.031 0.065 -9999 0 -0.26 8 8
CDH5 0.016 0.032 -9999 0 -0.22 9 9
VEGFA homodimer 0.023 0.055 -9999 0 -0.18 28 28
SHC1 0.017 0.027 -9999 0 -0.23 6 6
SHC2 0.018 0.021 -9999 0 -0.2 5 5
HRAS/GDP -0.016 0.044 -9999 0 -0.27 7 7
SH2D2A 0.011 0.042 -9999 0 -0.2 20 20
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.06 0.075 -9999 0 -0.4 2 2
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.035 0.07 -9999 0 -0.25 8 8
VEGFR1 homodimer 0.02 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 0.047 0.071 -9999 0 -0.3 4 4
GRB10 0.037 0.085 -9999 0 -0.38 11 11
PTPN11 0.02 0 -9999 0 -10000 0 0
GRB2 0.012 0.053 -9999 0 -0.35 11 11
PAK1 0.01 0.046 -9999 0 -0.2 24 24
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.036 0.089 -9999 0 -0.29 12 12
HRAS 0.014 0.04 -9999 0 -0.27 10 10
VEGF/Rho/ROCK1/Integrin Complex 0.005 0.1 -9999 0 -0.34 19 19
HIF1A 0.016 0.034 -9999 0 -0.33 5 5
FRS2 0.019 0.01 -9999 0 -0.2 1 1
oxygen and reactive oxygen species metabolic process 0.03 0.084 -9999 0 -0.25 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.019 0.01 -9999 0 -0.2 1 1
Nck/Pak 0.01 0.061 -9999 0 -0.16 55 55
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.003 0.099 -9999 0 -0.28 22 22
mol:GDP 0.035 0.065 -9999 0 -0.3 4 4
mol:NADP 0.051 0.063 -9999 0 -0.26 1 1
eNOS/Hsp90 0.059 0.061 -9999 0 -0.24 1 1
PIK3R1 -0.011 0.097 -9999 0 -0.3 52 52
mol:IP3 0.042 0.068 -9999 0 -0.31 4 4
HIF1A/ARNT 0.027 0.024 -9999 0 -0.24 4 4
SHB 0.017 0.025 -9999 0 -0.2 7 7
VEGFA -0.006 0.091 -9999 0 -0.28 51 51
VEGFC -0.01 0.081 -9999 0 -0.22 67 67
FAK1/Vinculin 0.024 0.11 -9999 0 -0.34 17 17
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA -0.008 0.1 -9999 0 -0.36 39 39
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.028 0.087 -9999 0 -0.28 9 9
PTPN6 0.012 0.051 -9999 0 -0.34 11 11
EPAS1 0.027 0.036 -9999 0 -0.22 7 7
mol:L-citrulline 0.051 0.063 -9999 0 -0.26 1 1
ITGAV -0.02 0.12 -9999 0 -0.34 59 59
PIK3CA -0.011 0.1 -9999 0 -0.33 48 48
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.045 0.069 -9999 0 -0.3 2 2
VEGFR2 homodimer/VEGFA homodimer 0.049 0.077 -9999 0 -0.29 8 8
VEGFR2/3 heterodimer 0.039 0.037 -9999 0 -0.26 1 1
VEGFB 0.019 0.019 -9999 0 -0.28 2 2
MAPK11 0.042 0.07 -9999 0 -0.31 4 4
VEGFR2 homodimer 0.034 0.044 -9999 0 -0.25 5 5
FLT1 0.02 0 -9999 0 -10000 0 0
NEDD4 0.022 0.017 -9999 0 -0.21 2 2
MAPK3 0.04 0.061 -9999 0 -0.28 4 4
MAPK1 0.035 0.063 -9999 0 -0.28 5 5
VEGFA145/NRP2 0.011 0.066 -9999 0 -0.24 27 27
VEGFR1/2 heterodimer 0.04 0.036 -9999 0 -0.26 1 1
KDR 0.035 0.044 -9999 0 -0.25 5 5
VEGFA165/NRP1/VEGFR2 homodimer 0.052 0.071 -9999 0 -0.32 4 4
SRC 0.02 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.039 0.063 -9999 0 -0.29 4 4
PI3K 0.039 0.097 -9999 0 -0.32 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.029 0.079 -9999 0 -0.26 11 11
FES 0.04 0.069 -9999 0 -0.31 4 4
GAB1 0.045 0.077 -9999 0 -0.34 2 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.039 0.066 -9999 0 -0.25 6 6
CTNNB1 0.012 0.054 -9999 0 -0.36 11 11
SOS1 0 0 -9999 0 -10000 0 0
ARNT 0.02 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.036 0.081 -9999 0 -0.26 7 7
VEGFR2 homodimer/VEGFA homodimer/Yes 0.028 0.082 -9999 0 -0.29 12 12
PI3K/GAB1 0.039 0.11 -9999 0 -0.36 6 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.043 0.078 -9999 0 -0.25 8 8
PRKACA 0.02 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.033 0.056 -9999 0 -0.24 3 3
HSP90AA1 0.02 0 -9999 0 -10000 0 0
CDC42 0.042 0.069 -9999 0 -0.31 4 4
actin cytoskeleton reorganization 0.034 0.069 -9999 0 -0.25 8 8
PTK2 0.015 0.11 -9999 0 -0.35 17 17
EDG1 0.041 0.071 -9999 0 -0.32 6 6
mol:DAG 0.042 0.068 -9999 0 -0.31 4 4
CaM/Ca2+ 0.047 0.064 -9999 0 -0.28 4 4
MAP2K3 0.043 0.065 -9999 0 -0.29 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.052 0.091 -9999 0 -0.38 11 11
PLCG1 0.042 0.068 -9999 0 -0.31 4 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.048 0.066 -9999 0 -0.3 3 3
IQGAP1 -0.01 0.1 -9999 0 -0.33 46 46
YES1 0 0.082 -9999 0 -0.33 30 30
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.039 0.066 -9999 0 -0.25 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.035 0.074 -9999 0 -0.3 7 7
cell migration 0.029 0.12 -9999 0 -0.36 19 19
mol:PI-3-4-5-P3 0.038 0.093 -9999 0 -0.31 6 6
FYN -0.049 0.13 -9999 0 -0.28 122 122
VEGFB/NRP1 0.04 0.064 -9999 0 -0.29 4 4
mol:NO 0.051 0.063 -9999 0 -0.26 1 1
PXN 0.019 0.01 -9999 0 -0.2 1 1
HRAS/GTP -0.016 0.044 -9999 0 -0.27 7 7
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.047 0.089 -9999 0 -0.38 11 11
VHL 0 0 -9999 0 -10000 0 0
ITGB3 0.019 0.014 -9999 0 -0.2 2 2
NOS3 0.053 0.066 -9999 0 -0.29 1 1
VEGFR2 homodimer/VEGFA homodimer/Sck 0.038 0.068 -9999 0 -0.25 7 7
RAC1 0.017 0.033 -9999 0 -0.36 4 4
PRKCA 0.043 0.063 -9999 0 -0.28 4 4
PRKCB 0.036 0.062 -9999 0 -0.29 4 4
VCL 0.018 0.023 -9999 0 -0.36 2 2
VEGFA165/NRP1 0.038 0.069 -9999 0 -0.26 8 8
VEGFR1/2 heterodimer/VEGFA homodimer 0.039 0.066 -9999 0 -0.25 6 6
VEGFA165/NRP2 0.011 0.066 -9999 0 -0.24 27 27
MAPKKK cascade 0.052 0.083 -9999 0 -0.3 14 14
NRP2 0.019 0.014 -9999 0 -0.2 2 2
VEGFC homodimer -0.01 0.081 -9999 0 -0.22 67 67
NCK1 0.002 0.074 -9999 0 -0.28 32 32
ROCK1 0.016 0.034 -9999 0 -0.33 5 5
FAK1/Paxillin 0.024 0.1 -9999 0 -0.33 18 18
MAP3K13 0.042 0.068 -9999 0 -0.31 4 4
PDPK1 0.039 0.086 -9999 0 -0.3 4 4
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.02 0 -10000 0 -10000 0 0
CLTC 0.019 0.053 -10000 0 -0.53 4 4
calcium ion-dependent exocytosis 0.011 0.06 -10000 0 -0.23 22 22
Dynamin 2/GTP 0.02 0.017 -10000 0 -0.18 4 4
EXOC4 0 0 -10000 0 -10000 0 0
CD59 0.004 0.07 -10000 0 -0.42 7 7
CPE -0.026 0.085 -10000 0 -0.2 87 87
CTNNB1 0.012 0.054 -10000 0 -0.36 11 11
membrane fusion 0.01 0.061 -10000 0 -0.19 40 40
CTNND1 0.017 0.041 -10000 0 -0.18 20 20
DNM2 0.02 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.019 0.047 -10000 0 -0.38 4 4
TSHR 0.016 0.027 -10000 0 -0.12 17 17
INS 0.019 0.014 -10000 0 -10000 0 0
BIN1 0.002 0.07 -10000 0 -0.26 33 33
mol:Choline 0.01 0.061 -10000 0 -0.19 40 40
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.007 0.019 -10000 0 -0.21 4 4
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.017 0.033 -10000 0 -0.36 4 4
mol:Ca2+ 0.02 0.017 -10000 0 -0.18 4 4
JUP 0.008 0.061 -10000 0 -0.41 6 6
ASAP2/amphiphysin II 0.015 0.042 -10000 0 -0.19 16 16
ARF6/GTP 0.013 0.023 -10000 0 -0.25 4 4
CDH1 0.011 0.062 -10000 0 -0.49 5 5
clathrin-independent pinocytosis 0.013 0.023 -10000 0 -0.25 4 4
MAPK8IP3 0.02 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0.013 0.023 -10000 0 -0.25 4 4
EXOC2 0.01 0.046 -10000 0 -0.2 24 24
substrate adhesion-dependent cell spreading 0.021 0.041 -10000 0 -0.25 2 2
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.018 0.021 -10000 0 -0.2 5 5
regulation of calcium-dependent cell-cell adhesion -0.024 0.057 0.48 4 -10000 0 4
positive regulation of phagocytosis -0.003 0.07 -10000 0 -0.2 60 60
ARF6/GTP/JIP3 0.025 0.02 -10000 0 -0.2 4 4
ACAP1 0.009 0.057 -10000 0 -0.24 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.016 0.051 -10000 0 -0.5 4 4
clathrin heavy chain/ACAP1 0.019 0.058 -10000 0 -0.46 4 4
JIP4/KLC1 0.029 0.042 -10000 0 -0.18 20 20
EXOC1 0.007 0.068 -10000 0 -0.35 19 19
exocyst 0.021 0.041 -10000 0 -0.25 2 2
RALA/GTP 0.004 0.051 -10000 0 -0.22 25 25
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.024 0.023 -10000 0 -0.2 4 4
receptor recycling 0.013 0.023 -10000 0 -0.25 4 4
CTNNA1 0.019 0.033 -10000 0 -0.16 17 17
NME1 0.007 0.019 -10000 0 -0.21 4 4
clathrin coat assembly 0.019 0.052 -10000 0 -0.52 4 4
IL2RA 0.016 0.051 -10000 0 -0.5 4 4
VAMP3 -0.003 0.07 -10000 0 -0.2 60 60
GLUT4/clathrin heavy chain/ACAP1 0.023 0.055 -10000 0 -0.43 4 4
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 0.009 0.054 -10000 0 -0.23 19 19
PLD2 0.009 0.054 -10000 0 -0.23 19 19
EXOC5 0.017 0.025 -10000 0 -0.2 7 7
PIP5K1C 0.019 0.047 -10000 0 -0.38 4 4
SDC1 -0.015 0.079 -10000 0 -0.32 14 14
ARF6/GDP 0.013 0.019 -10000 0 -0.21 4 4
EXOC7 0.018 0.025 -10000 0 -0.31 3 3
E-cadherin/beta catenin 0.026 0.06 -10000 0 -0.5 4 4
mol:Phosphatidic acid 0.01 0.061 -10000 0 -0.19 40 40
endocytosis -0.014 0.041 0.19 16 -10000 0 16
SCAMP2 0.004 0.073 -10000 0 -0.32 24 24
ADRB2 0.024 0.05 -10000 0 -0.49 4 4
EXOC3 0.016 0.036 -10000 0 -0.26 8 8
ASAP2 0 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.02 0.017 -10000 0 -0.18 4 4
KLC1 0.007 0.066 -10000 0 -0.33 19 19
AVPR2 0.025 0.049 -10000 0 -0.49 4 4
RALA 0.004 0.074 -10000 0 -0.33 25 25
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.025 0.074 -10000 0 -0.33 13 13
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.012 0.052 -9999 0 -0.32 12 12
HDAC2 0.003 0.071 -9999 0 -0.29 28 28
GNB1/GNG2 0.02 0.041 -9999 0 -0.21 16 16
forebrain development 0.051 0.036 -9999 0 -10000 0 0
GNAO1 0.015 0.033 -9999 0 -0.2 12 12
SMO/beta Arrestin2 0.03 0.02 -9999 0 -10000 0 0
SMO 0.02 0.019 -9999 0 -0.2 4 4
ARRB2 0.019 0.022 -9999 0 -0.2 5 5
GLI3/SPOP 0.024 0.056 -9999 0 -0.23 10 10
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
GSK3B 0.003 0.076 -9999 0 -0.34 25 25
GNAI2 0.013 0.054 -9999 0 -0.36 11 11
SIN3/HDAC complex 0.032 0.027 -9999 0 -0.18 5 5
GNAI1 -0.021 0.11 -9999 0 -0.28 74 74
XPO1 0.022 0.01 -9999 0 -0.2 1 1
GLI1/Su(fu) 0.048 0.033 -9999 0 -10000 0 0
SAP30 0.019 0.014 -9999 0 -0.2 2 2
mol:GDP 0.02 0.019 -9999 0 -0.2 4 4
MIM/GLI2A 0.026 0.012 -9999 0 -10000 0 0
IFT88 0.015 0.033 -9999 0 -0.22 10 10
GNAI3 0.011 0.06 -9999 0 -0.35 14 14
GLI2 0.025 0.072 -9999 0 -0.31 13 13
GLI3 0.016 0.05 -9999 0 -0.23 7 7
CSNK1D 0.01 0.059 -9999 0 -0.33 15 15
CSNK1E 0.01 0.057 -9999 0 -0.3 17 17
SAP18 0.016 0.037 -9999 0 -0.36 5 5
embryonic digit morphogenesis 0.015 0.033 -9999 0 -0.22 10 10
GNG2 0 0 -9999 0 -10000 0 0
Gi family/GTP 0.015 0.072 -9999 0 -0.25 19 19
SIN3B 0.015 0.03 -9999 0 -0.2 10 10
SIN3A 0 0 -9999 0 -10000 0 0
GLI3/Su(fu) 0.021 0.05 -9999 0 -0.21 6 6
GLI2/Su(fu) 0.03 0.064 -9999 0 -0.26 13 13
FOXA2 0.027 0.055 -9999 0 -10000 0 0
neural tube patterning 0.051 0.036 -9999 0 -10000 0 0
SPOP 0.01 0.059 -9999 0 -0.33 15 15
Su(fu)/PIAS1 0.022 0.022 -9999 0 -0.18 5 5
GNB1 0.008 0.065 -9999 0 -0.36 16 16
CSNK1G2 0.02 0 -9999 0 -10000 0 0
CSNK1G3 0.003 0.074 -9999 0 -0.3 29 29
MTSS1 0.026 0.012 -9999 0 -10000 0 0
embryonic limb morphogenesis 0.051 0.036 -9999 0 -10000 0 0
SUFU 0.012 0.01 -9999 0 -10000 0 0
LGALS3 -0.016 0.11 -9999 0 -0.35 52 52
catabolic process 0.037 0.087 -9999 0 -0.33 16 16
GLI3A/CBP 0.032 0.002 -9999 0 -10000 0 0
KIF3A 0.017 0.025 -9999 0 -0.2 7 7
GLI1 0.052 0.035 -9999 0 -10000 0 0
RAB23 0.015 0.032 -9999 0 -0.2 11 11
CSNK1A1 0.017 0.033 -9999 0 -0.36 4 4
IFT172 0 0 -9999 0 -10000 0 0
RBBP7 0.006 0.069 -9999 0 -0.34 20 20
Su(fu)/Galectin3 0.005 0.059 -9999 0 -0.18 48 48
GNAZ 0.018 0.025 -9999 0 -0.2 7 7
RBBP4 -0.012 0.1 -9999 0 -0.34 47 47
CSNK1G1 0.02 0 -9999 0 -10000 0 0
PIAS1 0.016 0.038 -9999 0 -0.34 6 6
PRKACA 0.02 0 -9999 0 -10000 0 0
GLI2/SPOP 0.03 0.077 -9999 0 -0.3 18 18
STK36 0.003 0.002 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.011 0.082 -9999 0 -0.33 16 16
PTCH1 0.057 0.034 -9999 0 -10000 0 0
MIM/GLI1 0.067 0.05 -9999 0 -10000 0 0
CREBBP 0.032 0.002 -9999 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.007 0.09 -9999 0 -0.22 50 50
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.02 0 -9999 0 -10000 0 0
SPHK1 0.012 0.041 -9999 0 -0.2 19 19
GNAI2 0.012 0.054 -9999 0 -0.36 11 11
mol:S1P 0.017 0.035 -9999 0 -0.22 9 9
GNAO1 0.015 0.033 -9999 0 -0.2 12 12
mol:Sphinganine-1-P 0.019 0.027 -9999 0 -0.12 19 19
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.034 0.029 -9999 0 -0.15 9 9
GNAI3 0.01 0.06 -9999 0 -0.35 14 14
G12/G13 0.029 0.011 -9999 0 -0.12 3 3
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.017 0.024 -9999 0 -0.2 6 6
S1P1/S1P 0.024 0.033 -9999 0 -0.18 10 10
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 -0.021 0.11 -9999 0 -0.28 74 74
S1P/S1P5/G12 0.023 0.029 -9999 0 -0.16 10 10
S1P/S1P3/Gq 0.034 0.018 -9999 0 -10000 0 0
S1P/S1P4/Gi 0.01 0.072 -9999 0 -0.18 54 54
GNAQ 0.02 0 -9999 0 -10000 0 0
GNAZ 0.017 0.025 -9999 0 -0.2 7 7
GNA14 0.019 0.01 -9999 0 -0.2 1 1
GNA15 0.017 0.024 -9999 0 -0.2 6 6
GNA12 0.018 0.017 -9999 0 -0.2 3 3
GNA13 0.02 0 -9999 0 -10000 0 0
GNA11 0.02 0 -9999 0 -10000 0 0
ABCC1 0.011 0.053 -9999 0 -0.31 14 14
Signaling events mediated by the Hedgehog family

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
TGFB2 0.065 0.016 -10000 0 -10000 0 0
IHH 0.034 0.01 -10000 0 -0.18 1 1
SHH Np/Cholesterol/GAS1 0.003 0.066 -10000 0 -0.18 58 58
LRPAP1 -0.004 0.087 -10000 0 -0.31 38 38
dorsoventral neural tube patterning -0.003 0.066 0.18 58 -10000 0 58
SMO/beta Arrestin2 0.071 0.014 -10000 0 -10000 0 0
SMO 0.064 0.011 -10000 0 -10000 0 0
AKT1 0.012 0.12 -10000 0 -0.44 20 20
ARRB2 0.018 0.021 -10000 0 -0.2 5 5
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0.019 0.01 -10000 0 -0.2 1 1
heart looping 0.064 0.011 -10000 0 -10000 0 0
STIL 0.05 0.027 -10000 0 -0.21 1 1
DHH N/PTCH2 0.015 0 -10000 0 -10000 0 0
DHH N/PTCH1 0.046 0.009 -10000 0 -10000 0 0
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
DHH 0 0 -10000 0 -10000 0 0
PTHLH 0.067 0.015 -10000 0 -10000 0 0
determination of left/right symmetry 0.064 0.011 -10000 0 -10000 0 0
PIK3R1 -0.011 0.097 -10000 0 -0.3 52 52
skeletal system development 0.067 0.015 -10000 0 -10000 0 0
IHH N/Hhip 0.022 0.005 -10000 0 -0.091 1 1
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.064 0.011 -10000 0 -10000 0 0
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.019 0.014 -10000 0 -0.2 2 2
PI3K -0.014 0.098 -10000 0 -0.25 66 66
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.03 0.12 -10000 0 -0.32 78 78
somite specification 0.064 0.011 -10000 0 -10000 0 0
SHH Np/Cholesterol/PTCH1 0.059 0.011 -10000 0 -10000 0 0
SHH Np/Cholesterol/PTCH2 0.03 0.007 -10000 0 -10000 0 0
SHH Np/Cholesterol/Megalin 0.014 0.04 -10000 0 -0.18 1 1
SHH 0.024 0.009 -10000 0 -10000 0 0
catabolic process 0.056 0.011 -10000 0 -10000 0 0
SMO/Vitamin D3 0.069 0.01 -10000 0 -10000 0 0
SHH Np/Cholesterol/Hhip 0.016 0.006 -10000 0 -10000 0 0
LRP2 -0.011 0.077 -10000 0 -0.2 74 74
receptor-mediated endocytosis 0.063 0.023 -10000 0 -10000 0 0
SHH Np/Cholesterol/BOC 0.016 0.006 -10000 0 -10000 0 0
SHH Np/Cholesterol/CDO 0.03 0.007 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.016 0.006 -10000 0 -10000 0 0
mol:Vitamin D3 0.063 0.011 -10000 0 -10000 0 0
IHH N/PTCH2 0.038 0.005 -10000 0 -10000 0 0
CDON 0.02 0 -10000 0 -10000 0 0
IHH N/PTCH1 0.062 0.011 -10000 0 -10000 0 0
Megalin/LRPAP1 -0.008 0.078 -10000 0 -0.25 26 26
PTCH2 0.02 0 -10000 0 -10000 0 0
SHH Np/Cholesterol 0.018 0.007 -10000 0 -10000 0 0
PTCH1 0.056 0.011 -10000 0 -10000 0 0
HHIP 0 0 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.02 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.026 0.045 -9999 0 -0.18 16 16
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.008 0.061 -9999 0 -0.45 9 9
AURKB 0 0.075 -9999 0 -0.27 36 36
AURKC 0.016 0.029 -9999 0 -0.2 9 9
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.024 0.061 -9999 0 -10000 0 0
MKNK1 0.007 0.068 -9999 0 -0.35 19 19
MAPK14 0.018 0.038 -9999 0 -0.19 3 3
ATF2/c-Jun 0.001 0.13 -9999 0 -0.46 37 37
MAPK11 0.019 0.035 -9999 0 -10000 0 0
MITF 0.025 0.041 -9999 0 -10000 0 0
MAPKAPK5 0.03 0.036 -9999 0 -10000 0 0
KRT8 -0.001 0.092 -9999 0 -0.25 53 53
MAPKAPK3 0.016 0.036 -9999 0 -0.31 6 6
MAPKAPK2 0.02 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 0.026 0.047 -9999 0 -0.21 2 2
CEBPB 0.022 0.059 -9999 0 -0.24 16 16
SLC9A1 0.028 0.041 -9999 0 -0.27 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.027 0.056 -9999 0 -0.24 2 2
p38alpha-beta/MNK1 0.029 0.059 -9999 0 -0.22 17 17
JUN 0 0.13 -9999 0 -0.46 37 37
PPARGC1A 0.027 0.039 -9999 0 -10000 0 0
USF1 0.02 0.036 -9999 0 -0.16 2 2
RAB5/GDP/GDI1 0.024 0.042 -9999 0 -0.22 9 9
NOS2 0.02 0.035 -9999 0 -0.16 2 2
DDIT3 0.019 0.057 -9999 0 -0.25 10 10
RAB5A 0.017 0.033 -9999 0 -0.36 4 4
HSPB1 0.017 0.06 -9999 0 -0.2 30 30
p38alpha-beta/HBP1 0.038 0.039 -9999 0 -10000 0 0
CREB1 0.032 0.04 -9999 0 -10000 0 0
RAB5/GDP 0.013 0.023 -9999 0 -0.25 4 4
EIF4E 0.013 0.065 -9999 0 -0.18 45 45
RPS6KA4 0.03 0.036 -9999 0 -10000 0 0
PLA2G4A -0.026 0.089 -9999 0 -0.18 89 89
GDI1 0.025 0.05 -9999 0 -0.28 6 6
TP53 0.006 0.059 -9999 0 -0.21 14 14
RPS6KA5 0.028 0.038 -9999 0 -10000 0 0
ESR1 0.03 0.036 -9999 0 -10000 0 0
HBP1 0.02 0 -9999 0 -10000 0 0
MEF2C 0.029 0.037 -9999 0 -0.2 1 1
MEF2A 0.027 0.045 -9999 0 -0.24 5 5
EIF4EBP1 0.02 0.055 -9999 0 -0.21 1 1
KRT19 -0.005 0.092 -9999 0 -0.24 60 60
ELK4 0.03 0.036 -9999 0 -10000 0 0
ATF6 0.029 0.039 -9999 0 -0.23 2 2
ATF1 0.023 0.051 -9999 0 -10000 0 0
p38alpha-beta/MAPKAPK2 0.038 0.039 -9999 0 -10000 0 0
p38alpha-beta/MAPKAPK3 0.035 0.045 -9999 0 -0.2 5 5
Effects of Botulinum toxin

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
STX1A 0.01 0.017 -9999 0 -0.13 7 7
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.021 0.044 -9999 0 -0.18 22 22
STXBP1 -0.02 0.11 -9999 0 -0.3 66 66
ACh/CHRNA1 0.018 0.012 -9999 0 -0.11 1 1
RAB3GAP2/RIMS1/UNC13B 0.029 0.048 -9999 0 -0.2 19 19
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0.02 0 -9999 0 -10000 0 0
mol:ACh 0.006 0.012 -9999 0 -0.06 7 7
RAB3GAP2 0.014 0.047 -9999 0 -0.35 9 9
STX1A/SNAP25/VAMP2 0.017 0.06 -9999 0 -0.22 8 8
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction 0.018 0.012 -9999 0 -0.11 1 1
UNC13B 0.007 0.062 -9999 0 -0.28 22 22
CHRNA1 0.019 0.01 -9999 0 -0.2 1 1
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 0.011 0.032 -9999 0 -0.12 29 29
SNAP25 0.002 0.022 -9999 0 -10000 0 0
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 0.008 0.051 -9999 0 -0.2 29 29
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.001 0.066 -9999 0 -0.2 43 43
STX1A/SNAP25 fragment 1/VAMP2 0.017 0.06 -9999 0 -0.22 8 8
p38 MAPK signaling 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
TRAF6/ASK1 0.014 0.041 -9999 0 -0.19 16 16
TRAF2/ASK1 0.02 0.033 -9999 0 -0.13 23 23
ATM 0.012 0.046 -9999 0 -0.26 14 14
MAP2K3 0.033 0.053 -9999 0 -0.27 10 10
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.034 0.048 -9999 0 -0.23 10 10
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.02 0 -9999 0 -10000 0 0
TXN 0.002 0.045 -9999 0 -0.27 14 14
CALM1 0.019 0.019 -9999 0 -0.28 2 2
GADD45A -0.019 0.11 -9999 0 -0.3 65 65
GADD45B 0.009 0.05 -9999 0 -0.22 24 24
MAP3K1 0.017 0.025 -9999 0 -0.2 7 7
MAP3K6 0.012 0.041 -9999 0 -0.2 19 19
MAP3K7 0.002 0.072 -9999 0 -0.27 32 32
MAP3K4 0.006 0.067 -9999 0 -0.3 23 23
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 0.016 0.049 -9999 0 -0.25 8 8
TAK1/TAB family 0 0.064 -9999 0 -0.39 10 10
RAC1/OSM/MEKK3 0.023 0.02 -9999 0 -0.14 7 7
TRAF2 0.02 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.006 0.033 -9999 0 -0.21 10 10
TRAF6 0.013 0.04 -9999 0 -0.26 11 11
RAC1 0.017 0.033 -9999 0 -0.36 4 4
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B 0.018 0.017 -9999 0 -0.2 3 3
CCM2 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.025 0.015 -9999 0 -0.2 1 1
MAPK11 0.02 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.031 0.033 -9999 0 -0.18 7 7
OSM/MEKK3 0.014 0.011 -9999 0 -0.13 3 3
TAOK1 0.006 0.029 -9999 0 -0.27 5 5
TAOK2 0.015 0.029 -9999 0 -0.26 5 5
TAOK3 0.014 0.034 -9999 0 -0.26 7 7
MAP3K7IP1 0.019 0.01 -9999 0 -0.2 1 1
MAPK14 0.018 0.017 -9999 0 -0.2 3 3
MAP3K7IP2 0.01 0.057 -9999 0 -0.3 17 17
MAP3K5 0.008 0.056 -9999 0 -0.25 23 23
MAP3K10 0.02 0 -9999 0 -10000 0 0
MAP3K3 0.018 0.017 -9999 0 -0.2 3 3
TRX/ASK1 0.009 0.05 -9999 0 -0.22 19 19
GADD45/MTK1/MTK1 0.014 0.071 -9999 0 -0.16 60 60
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.027 0.023 -10000 0 -0.19 6 6
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.02 0.046 -10000 0 -10000 0 0
IL27/IL27R/JAK1 0.031 0.053 -10000 0 -10000 0 0
TBX21 0.019 0.064 -10000 0 -10000 0 0
IL12B 0.021 0.001 -10000 0 -10000 0 0
IL12A 0.007 0.028 -10000 0 -0.13 20 20
IL6ST 0.018 0.024 -10000 0 -0.25 4 4
IL27RA/JAK1 0.011 0.053 -10000 0 -10000 0 0
IL27 0 0.002 -10000 0 -10000 0 0
TYK2 -0.001 0.08 -10000 0 -0.26 42 42
T-helper cell lineage commitment 0.031 0.032 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.02 0.046 -10000 0 -10000 0 0
T cell proliferation during immune response -0.02 0.046 -10000 0 -10000 0 0
MAPKKK cascade 0.02 0.046 -10000 0 -10000 0 0
STAT3 0.004 0.075 -10000 0 -0.35 23 23
STAT2 0.02 0 -10000 0 -10000 0 0
STAT1 -0.023 0.11 -10000 0 -0.3 74 74
IL12RB1 0.02 0 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.02 0.067 -10000 0 -0.31 2 2
IL27/IL27R/JAK2/TYK2 0.02 0.046 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity 0.02 0.046 -10000 0 -10000 0 0
STAT1 (dimer) 0.017 0.078 -10000 0 -10000 0 0
JAK2 0.018 0.017 -10000 0 -0.2 3 3
JAK1 0.002 0.081 -10000 0 -0.36 25 25
STAT2 (dimer) 0.03 0.045 -10000 0 -10000 0 0
T cell proliferation 0.019 0.052 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 0.025 0.14 -10000 0 -0.79 15 15
IL17A 0.031 0.032 -10000 0 -10000 0 0
mast cell activation -0.02 0.046 -10000 0 -10000 0 0
IFNG 0.01 0.014 -10000 0 -10000 0 0
T cell differentiation -0.001 0.002 -10000 0 -10000 0 0
STAT3 (dimer) 0.023 0.059 -10000 0 -0.33 3 3
STAT5A (dimer) 0.03 0.045 -10000 0 -10000 0 0
STAT4 (dimer) 0.029 0.046 -10000 0 -10000 0 0
STAT4 0.018 0.019 -10000 0 -0.2 4 4
T cell activation -0.007 0.008 0.035 19 -10000 0 19
IL27R/JAK2/TYK2 0.031 0.056 -10000 0 -10000 0 0
GATA3 0.003 0.026 -10000 0 -10000 0 0
IL18 -0.005 0.052 -10000 0 -0.15 59 59
positive regulation of mast cell cytokine production 0.022 0.059 -10000 0 -0.32 3 3
IL27/EBI3 0.013 0.016 -10000 0 -0.13 6 6
IL27RA 0.009 0.035 -10000 0 -10000 0 0
IL6 0.005 0.069 -10000 0 -0.19 59 59
STAT5A 0.019 0.014 -10000 0 -0.2 2 2
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.001 0.026 -10000 0 -10000 0 0
IL1B -0.001 0.044 -10000 0 -0.14 47 47
EBI3 0.017 0.023 -10000 0 -0.2 6 6
TNF 0 0.041 -10000 0 -0.13 46 46
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.038 0.023 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.024 0.019 -9999 0 -0.19 4 4
mol:DAG 0.037 0.022 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.02 0.053 -9999 0 -0.35 1 1
CaM/Ca2+ 0.046 0.024 -9999 0 -10000 0 0
HIF1A 0.027 0.034 -9999 0 -0.32 5 5
GAB1 0.02 0 -9999 0 -10000 0 0
AKT1 0.016 0.089 -9999 0 -0.32 17 17
PLCG1 0.037 0.023 -9999 0 -10000 0 0
NOS3 0.042 0.043 -9999 0 -0.26 1 1
CBL 0.02 0 -9999 0 -10000 0 0
mol:NO 0.042 0.042 -9999 0 -0.25 1 1
FLT1 0.033 0.024 -9999 0 -0.23 4 4
PGF 0.016 0.029 -9999 0 -0.2 9 9
VEGFR1 homodimer/NRP2/VEGFR121 0.033 0.055 -9999 0 -0.34 1 1
CALM1 0.019 0.019 -9999 0 -0.28 2 2
PIK3CA -0.011 0.1 -9999 0 -0.33 48 48
eNOS/Hsp90 0.051 0.043 -9999 0 -0.24 1 1
endothelial cell proliferation 0.036 0.026 -9999 0 -10000 0 0
mol:Ca2+ 0.037 0.022 -9999 0 -10000 0 0
MAPK3 0.041 0.02 -9999 0 -10000 0 0
MAPK1 0.031 0.045 -9999 0 -0.3 1 1
PIK3R1 -0.011 0.097 -9999 0 -0.3 52 52
PLGF homodimer 0.016 0.029 -9999 0 -0.2 9 9
PRKACA 0.02 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.056 0.14 -9999 0 -0.3 129 129
VEGFA homodimer -0.009 0.092 -9999 0 -0.28 51 51
VEGFR1 homodimer/VEGFA homodimer 0.022 0.058 -9999 0 -0.38 1 1
platelet activating factor biosynthetic process 0.035 0.043 -9999 0 -0.28 1 1
PI3K 0.024 0.078 -9999 0 -0.28 7 7
PRKCA 0.039 0.021 -9999 0 -10000 0 0
PRKCB 0.031 0.02 -9999 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer 0.037 0.026 -9999 0 -10000 0 0
VEGFA -0.009 0.092 -9999 0 -0.28 51 51
VEGFB 0.019 0.019 -9999 0 -0.28 2 2
mol:IP3 0.037 0.022 -9999 0 -10000 0 0
RASA1 0.023 0.058 -9999 0 -0.34 1 1
NRP2 0.019 0.014 -9999 0 -0.2 2 2
VEGFR1 homodimer 0.033 0.024 -9999 0 -0.23 4 4
VEGFB homodimer 0.019 0.019 -9999 0 -0.28 2 2
NCK1 0.002 0.074 -9999 0 -0.28 32 32
eNOS/Caveolin-1 0.029 0.066 -9999 0 -0.27 4 4
PTPN11 0.02 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.023 0.077 -9999 0 -0.28 7 7
mol:L-citrulline 0.042 0.042 -9999 0 -0.25 1 1
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.036 0.069 -9999 0 -0.32 6 6
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.023 0.067 -9999 0 -0.3 2 2
CD2AP 0.004 0.075 -9999 0 -0.34 24 24
PI3K/GAB1 0.032 0.076 -9999 0 -0.27 7 7
PDPK1 0.018 0.068 -9999 0 -0.26 7 7
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.033 0.055 -9999 0 -0.34 1 1
mol:NADP 0.042 0.042 -9999 0 -0.25 1 1
HSP90AA1 0.02 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.034 0.068 -9999 0 -0.32 6 6
VEGFR1 homodimer/NRP2 0.038 0.022 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.02 0.022 -10000 0 -0.29 1 1
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.018 0.036 -10000 0 -0.23 8 8
AP2 0.01 0.033 -10000 0 -0.24 9 9
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.014 0.052 -10000 0 -0.19 32 32
CLTB 0.017 0.027 -10000 0 -0.28 4 4
coatomer protein complex/ARF1/GTP/ER cargo protein 0.021 0.044 -10000 0 -0.24 12 12
CD4 0.012 0.04 -10000 0 -0.2 18 18
CLTA 0.016 0.034 -10000 0 -0.33 5 5
mol:GTP 0 0.003 -10000 0 -10000 0 0
ARFGAP1 0.012 0.011 -10000 0 -0.25 1 1
mol:PI-4-5-P2 0.015 0.028 0.13 23 -10000 0 23
ARF1/GTP 0.008 0.025 -10000 0 -0.19 8 8
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.022 0.037 -10000 0 -0.21 12 12
mol:Choline 0.015 0.029 0.14 23 -10000 0 23
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.013 0.047 -10000 0 -0.37 8 8
DDEF1 0.015 0.029 0.14 23 -10000 0 23
ARF1/GDP 0.01 0.013 -10000 0 -0.22 1 1
AP2M1 0.014 0.047 -10000 0 -0.35 9 9
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.013 0.031 -10000 0 -0.2 11 11
Rac/GTP 0.013 0.024 -10000 0 -0.26 4 4
ARF1/GTP/GGA3/ARF-GAP1 0.029 0.025 -10000 0 -0.16 9 9
ARFIP2 0 0.076 -10000 0 -0.31 29 29
COPA 0.018 0.023 -10000 0 -0.24 4 4
RAC1 0.017 0.033 -10000 0 -0.36 4 4
ARF1/GTP/coatomer protein complex 0.021 0.043 -10000 0 -0.25 10 10
ARF1/GTP/ARHGAP10 0.009 0.027 -10000 0 -0.21 8 8
GGA3 0.02 0 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.016 0.024 -10000 0 -0.17 8 8
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.023 0.041 -10000 0 -0.22 12 12
ARF1/GDP/Membrin 0.018 0.023 -10000 0 -0.17 7 7
Arfaptin 2/Rac/GDP 0.014 0.052 -10000 0 -0.19 32 32
CYTH2 0 0.003 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.022 0.028 -10000 0 -0.2 8 8
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.013 0.023 -10000 0 -0.25 4 4
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.023 0.049 -10000 0 -0.23 14 14
PLD2 0.015 0.029 0.14 23 -10000 0 23
ARF-GAP1/v-SNARE 0.012 0.011 -10000 0 -0.25 1 1
PIP5K1A 0.015 0.028 0.13 23 -10000 0 23
ARF1/GTP/Membrin/GBF1/p115 0.015 0.027 -10000 0 -0.18 8 8
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.015 0.029 0.14 23 -10000 0 23
KDEL Receptor/Ligand/ARF-GAP1 0.012 0.011 -10000 0 -0.25 1 1
GOSR2 0.017 0.015 -10000 0 -10000 0 0
USO1 0.009 0.055 -10000 0 -0.37 10 10
GBF1 0.017 0.015 -10000 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.012 0.055 -10000 0 -0.19 36 36
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.019 0.036 -10000 0 -0.13 27 27
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.02 0.048 -9999 0 -0.22 21 21
FBXW11 0.02 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0 -9999 0 -10000 0 0
CHUK 0.006 0.068 -9999 0 -0.33 21 21
NF kappa B2 p100/RelB 0.052 0.037 -9999 0 -0.15 16 16
NFKB1 -0.003 0.088 -9999 0 -0.34 34 34
MAP3K14 0.02 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.013 0.062 -9999 0 -0.24 28 28
RELB 0.02 0 -9999 0 -10000 0 0
NFKB2 0.02 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.027 0 -9999 0 -10000 0 0
regulation of B cell activation 0.026 0 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.018 0.039 0.18 9 -10000 0 9
KIRREL 0.008 0.05 -10000 0 -0.22 25 25
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.018 0.039 -10000 0 -0.18 9 9
PLCG1 0.02 0 -10000 0 -10000 0 0
ARRB2 0.018 0.021 -10000 0 -0.2 5 5
WASL 0.02 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.03 0.057 -10000 0 -0.2 22 22
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.022 0.051 -10000 0 -0.23 9 9
FYN 0.01 0.041 -10000 0 -0.18 9 9
mol:Ca2+ 0.038 0.031 -10000 0 -0.2 2 2
mol:DAG 0.039 0.031 -10000 0 -0.2 2 2
NPHS2 0.018 0.007 -10000 0 -10000 0 0
mol:IP3 0.039 0.031 -10000 0 -0.2 2 2
regulation of endocytosis 0.013 0.059 -10000 0 -0.21 4 4
Nephrin/NEPH1/podocin/Cholesterol 0.027 0.03 -10000 0 -0.18 3 3
establishment of cell polarity 0.018 0.039 -10000 0 -0.18 9 9
Nephrin/NEPH1/podocin/NCK1-2 0.035 0.062 -10000 0 -0.19 26 26
Nephrin/NEPH1/beta Arrestin2 0.015 0.06 -10000 0 -0.21 4 4
NPHS1 0.016 0.023 -10000 0 -0.21 5 5
Nephrin/NEPH1/podocin 0.006 0.061 -10000 0 -0.18 9 9
TJP1 0.01 0.057 -10000 0 -0.32 15 15
NCK1 0.002 0.074 -10000 0 -0.28 32 32
NCK2 0.012 0.051 -10000 0 -0.34 11 11
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.04 0.032 -10000 0 -0.2 2 2
CD2AP 0.004 0.075 -10000 0 -0.34 24 24
Nephrin/NEPH1/podocin/GRB2 0.035 0.045 -10000 0 -0.2 12 12
GRB2 0.012 0.053 -10000 0 -0.35 11 11
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.018 0.029 -10000 0 -0.18 2 2
cytoskeleton organization 0.023 0.05 -10000 0 -0.24 6 6
Nephrin/NEPH1 0.017 0.027 -10000 0 -0.19 2 2
Nephrin/NEPH1/ZO-1 0.024 0.049 -10000 0 -0.22 13 13
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.026 0 -9999 0 -10000 0 0
EFNA5 0.02 0 -9999 0 -10000 0 0
FYN -0.008 0.069 -9999 0 -0.18 59 59
neuron projection morphogenesis 0.026 0 -9999 0 -10000 0 0
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0.027 0 -9999 0 -10000 0 0
EPHA5 0.02 0 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.041 0.11 -9999 0 -0.86 1 1
NCK1/PAK1/Dok-R -0.019 0.047 -9999 0 -0.38 2 2
NCK1/Dok-R 0.048 0.067 -9999 0 -0.85 1 1
PIK3CA -0.011 0.1 -9999 0 -0.33 48 48
mol:beta2-estradiol -0.009 0.014 -9999 0 -10000 0 0
RELA 0.018 0.021 -9999 0 -0.26 3 3
SHC1 0.018 0.027 -9999 0 -0.23 6 6
Rac/GDP 0.013 0.023 -9999 0 -0.25 4 4
F2 0.008 0.015 -9999 0 -10000 0 0
TNIP2 0.013 0.047 -9999 0 -0.28 13 13
NF kappa B/RelA 0.06 0.08 -9999 0 -0.79 1 1
FN1 -0.057 0.14 -9999 0 -0.31 126 126
PLD2 0.058 0.055 -9999 0 -0.88 1 1
PTPN11 0.02 0 -9999 0 -10000 0 0
GRB14 0.003 0.059 -9999 0 -0.2 41 41
ELK1 0.056 0.06 -9999 0 -0.83 1 1
GRB7 0 0.077 -9999 0 -0.28 35 35
PAK1 0.01 0.046 -9999 0 -0.2 24 24
Tie2/Ang1/alpha5/beta1 Integrin 0.034 0.099 -9999 0 -0.82 1 1
CDKN1A 0.038 0.16 -9999 0 -0.76 17 17
ITGA5 0.005 0.061 -9999 0 -0.23 33 33
mol:GTP 0 0 -9999 0 -10000 0 0
RasGAP/Dok-R 0.042 0.079 -9999 0 -0.99 1 1
CRK 0.01 0.053 -9999 0 -0.25 20 20
mol:NO 0.042 0.097 -9999 0 -0.64 1 1
PLG 0.058 0.055 -9999 0 -0.88 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
chemokinesis 0.051 0.099 -9999 0 -0.82 1 1
GRB2 0.012 0.053 -9999 0 -0.35 11 11
PIK3R1 -0.011 0.098 -9999 0 -0.3 52 52
ANGPT2 0.032 0.057 -9999 0 -10000 0 0
BMX 0.058 0.055 -9999 0 -0.88 1 1
ANGPT1 0.031 0.04 -9999 0 -10000 0 0
tube development 0.027 0.11 -9999 0 -0.54 4 4
ANGPT4 0.021 0.001 -9999 0 -10000 0 0
response to hypoxia 0.004 0.005 -9999 0 -10000 0 0
Tie2/Ang1/GRB14 0.052 0.068 -9999 0 -0.88 1 1
alpha5/beta1 Integrin 0.019 0.043 -9999 0 -0.24 5 5
FGF2 0.018 0.01 -9999 0 -0.2 1 1
STAT5A (dimer) 0.053 0.13 -9999 0 -0.56 17 17
mol:L-citrulline 0.042 0.097 -9999 0 -0.64 1 1
AGTR1 0.019 0.02 -9999 0 -0.21 4 4
MAPK14 0.057 0.074 -9999 0 -1.1 1 1
Tie2/SHP2 0.038 0.081 -9999 0 -0.9 1 1
TEK 0.034 0.09 -9999 0 -0.7 2 2
RPS6KB1 0.045 0.1 -9999 0 -0.84 1 1
Angiotensin II/AT1 0.017 0.014 -9999 0 -0.14 4 4
Tie2/Ang1/GRB2 0.057 0.064 -9999 0 -0.88 1 1
MAPK3 0.06 0.053 -9999 0 -0.82 1 1
MAPK1 0.053 0.06 -9999 0 -0.82 1 1
Tie2/Ang1/GRB7 0.052 0.072 -9999 0 -0.88 1 1
NFKB1 -0.003 0.088 -9999 0 -0.34 34 34
MAPK8 0.058 0.055 -9999 0 -0.88 1 1
PI3K 0.042 0.11 -9999 0 -0.99 1 1
FES 0.057 0.073 -9999 0 -1.1 1 1
Crk/Dok-R 0.051 0.064 -9999 0 -0.85 1 1
Tie2/Ang1/ABIN2 0.057 0.065 -9999 0 -0.88 1 1
blood circulation 0 0 -9999 0 -10000 0 0
negative regulation of caspase activity 0.041 0.1 -9999 0 -0.77 1 1
STAT5A 0.019 0.014 -9999 0 -0.21 2 2
mol:ROS 0 0 -9999 0 -10000 0 0
PTK2 0.039 0.11 -9999 0 -0.69 2 2
Tie2/Ang2 0.047 0.11 -9999 0 -0.85 1 1
Tie2/Ang1 0.056 0.058 -9999 0 -0.93 1 1
FOXO1 0.037 0.11 -9999 0 -0.63 2 2
ELF1 0.008 0.089 -9999 0 -0.36 30 30
ELF2 0.057 0.055 -9999 0 -0.88 1 1
mol:Choline 0.058 0.054 -9999 0 -0.85 1 1
cell migration -0.016 0.034 -9999 0 -0.19 4 4
FYN 0.027 0.12 -9999 0 -0.64 3 3
DOK2 0 0 -9999 0 -10000 0 0
negative regulation of cell cycle 0.039 0.15 -9999 0 -0.67 17 17
ETS1 0.028 0.014 -9999 0 -10000 0 0
PXN 0.043 0.1 -9999 0 -0.58 2 2
ITGB1 0.02 0 -9999 0 -10000 0 0
NOS3 0.042 0.1 -9999 0 -0.73 1 1
RAC1 0.017 0.033 -9999 0 -0.36 4 4
TNF 0.01 0.064 -9999 0 -0.19 46 46
MAPKKK cascade 0.058 0.054 -9999 0 -0.85 1 1
RASA1 -0.01 0.1 -9999 0 -0.35 44 44
Tie2/Ang1/Shc 0.059 0.065 -9999 0 -0.89 1 1
NCK1 0.002 0.074 -9999 0 -0.28 32 32
vasculogenesis 0.042 0.092 -9999 0 -0.57 1 1
mol:Phosphatidic acid 0.058 0.054 -9999 0 -0.85 1 1
mol:Angiotensin II 0.001 0.002 -9999 0 -10000 0 0
mol:NADP 0.042 0.097 -9999 0 -0.64 1 1
Rac1/GTP 0.043 0.099 -9999 0 -0.78 1 1
MMP2 0.017 0.083 -9999 0 -0.88 1 1
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.008 0.025 -9999 0 -0.11 22 22
ARNO/beta Arrestin1-2 0.03 0.009 -9999 0 -10000 0 0
EGFR 0.019 0.017 -9999 0 -0.2 3 3
EPHA2 -0.003 0.079 -9999 0 -0.25 45 45
USP6 0.019 0.01 -9999 0 -0.2 1 1
IQSEC1 0.02 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.028 0.013 -9999 0 -0.12 4 4
ARRB2 0.019 0.009 -9999 0 -10000 0 0
mol:GTP 0.004 0.007 -9999 0 -0.059 1 1
ARRB1 0.019 0.01 -9999 0 -0.2 1 1
FBXO8 0 0 -9999 0 -10000 0 0
TSHR 0.014 0.034 -9999 0 -0.2 13 13
EGF 0.019 0.01 -9999 0 -0.2 1 1
somatostatin receptor activity 0 0 -9999 0 -10000 0 0
ARAP2 0 0 -9999 0 -10000 0 0
mol:GDP 0.04 0.009 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
ITGA2B 0.02 0 -9999 0 -10000 0 0
ARF6 0.017 0.033 -9999 0 -0.36 4 4
Ephrin A1/EPHA2/NCK1/GIT1 0.012 0.084 -9999 0 -0.19 61 61
ADAP1 0 0 -9999 0 -10000 0 0
KIF13B 0.01 0.046 -9999 0 -0.21 22 22
HGF/MET 0.024 0.031 -9999 0 -0.25 1 1
PXN 0.019 0.01 -9999 0 -0.2 1 1
ARF6/GTP 0.057 0.016 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF/ARFGEP100 0.039 0.011 -9999 0 -10000 0 0
ADRB2 0.019 0.014 -9999 0 -0.2 2 2
receptor agonist activity 0 0 -9999 0 -10000 0 0
actin filament binding 0 0 -9999 0 -10000 0 0
SRC 0.02 0 -9999 0 -10000 0 0
ITGB3 0.019 0.014 -9999 0 -0.2 2 2
GNAQ 0.02 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF6/GDP 0.034 0.038 -9999 0 -0.25 4 4
ARF6/GDP/GULP/ACAP1 0.024 0.06 -9999 0 -0.2 4 4
alphaIIb/beta3 Integrin/paxillin/GIT1 0.05 0.012 -9999 0 -0.18 1 1
ACAP1 0 0 -9999 0 -10000 0 0
ACAP2 0 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 0.021 0.009 -9999 0 -10000 0 0
EFNA1 -0.009 0.097 -9999 0 -0.31 47 47
HGF 0.019 0.014 -9999 0 -0.2 2 2
CYTH3 0 0 -9999 0 -10000 0 0
CYTH2 0 0 -9999 0 -10000 0 0
NCK1 0.002 0.074 -9999 0 -0.28 32 32
fibronectin binding 0 0 -9999 0 -10000 0 0
endosomal lumen acidification 0 0 -9999 0 -10000 0 0
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.05 0.13 -9999 0 -0.27 130 130
GNAQ/ARNO 0.015 0.001 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0.006 0.054 -9999 0 -0.2 33 33
MET 0.012 0.041 -9999 0 -0.2 19 19
GNA14 0.019 0.01 -9999 0 -0.2 1 1
GNA15 0.017 0.024 -9999 0 -0.2 6 6
GIT1 0.019 0.01 -9999 0 -0.2 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
GNA11 0.02 0 -9999 0 -10000 0 0
LHCGR 0.02 0 -9999 0 -10000 0 0
AGTR1 0.018 0.019 -9999 0 -0.2 4 4
desensitization of G-protein coupled receptor protein signaling pathway 0.021 0.009 -9999 0 -10000 0 0
IPCEF1/ARNO 0.03 0.026 -9999 0 -10000 0 0
alphaIIb/beta3 Integrin 0.029 0.009 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.029 0.025 -9999 0 -10000 0 0
VDR 0.019 0.014 -9999 0 -0.2 2 2
FAM120B 0 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.031 0.082 -9999 0 -0.3 5 5
RXRs/LXRs/DNA/Oxysterols 0.029 0.11 -9999 0 -0.36 25 25
MED1 0.002 0.08 -9999 0 -0.35 26 26
mol:9cRA 0.002 0.014 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.034 0.039 -9999 0 -0.17 18 18
RXRs/NUR77 0.05 0.041 -9999 0 -0.16 2 2
RXRs/PPAR 0.041 0.027 -9999 0 -10000 0 0
NCOR2 0.02 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0.014 0.009 -9999 0 -0.13 2 2
RARs/VDR/DNA/Vit D3 0.046 0.01 -9999 0 -10000 0 0
RARA 0.02 0 -9999 0 -10000 0 0
NCOA1 0.005 0.071 -9999 0 -0.34 22 22
VDR/VDR/DNA 0.019 0.014 -9999 0 -0.2 2 2
RARs/RARs/DNA/9cRA 0.036 0.011 -9999 0 -10000 0 0
RARG 0.02 0 -9999 0 -10000 0 0
RPS6KB1 0.007 0.024 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.042 0.007 -9999 0 -10000 0 0
THRA 0.019 0.01 -9999 0 -0.2 1 1
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0.014 0.009 -9999 0 -0.13 2 2
RXRs/PPAR/9cRA/PGJ2/DNA 0.04 0.051 -9999 0 -0.22 1 1
NR1H4 0.019 0.014 -9999 0 -0.2 2 2
RXRs/LXRs/DNA 0.052 0.078 -9999 0 -0.25 5 5
NR1H2 0.02 0.029 -9999 0 -0.24 5 5
NR1H3 0.004 0.076 -9999 0 -0.29 32 32
RXRs/VDR/DNA/Vit D3 0.047 0.037 -9999 0 -0.15 1 1
NR4A1 0.018 0.019 -9999 0 -0.2 4 4
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.024 0.05 -9999 0 -0.21 6 6
RXRG 0.014 0.042 -9999 0 -0.2 18 18
RXR alpha/CCPG 0.016 0.012 -9999 0 -0.17 1 1
RXRA 0.021 0.017 -9999 0 -0.25 1 1
RXRB 0.022 0.014 -9999 0 -10000 0 0
THRB 0.019 0.014 -9999 0 -0.2 2 2
PPARG 0.014 0.036 -9999 0 -0.2 14 14
PPARD 0.02 0 -9999 0 -10000 0 0
TNF 0.027 0.11 -9999 0 -0.55 1 1
mol:Oxysterols 0.002 0.012 -9999 0 -10000 0 0
cholesterol transport 0.029 0.11 -9999 0 -0.36 25 25
PPARA 0.02 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.019 0.014 -9999 0 -0.2 2 2
RXRs/NUR77/BCL2 0.034 0.018 -9999 0 -10000 0 0
SREBF1 0.031 0.11 -9999 0 -0.78 2 2
RXRs/RXRs/DNA/9cRA 0.041 0.051 -9999 0 -0.22 1 1
ABCA1 0.005 0.22 -9999 0 -0.94 24 24
RARs/THRs 0.058 0.012 -9999 0 -10000 0 0
RXRs/FXR 0.051 0.04 -9999 0 -0.16 2 2
BCL2 0.019 0.01 -9999 0 -0.2 1 1
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.035 0.044 -10000 0 -10000 0 0
CRKL 0.037 0.038 -10000 0 -10000 0 0
HRAS 0.052 0.049 -10000 0 -0.3 2 2
mol:PIP3 0.017 0.07 0.28 1 -0.23 3 4
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.02 0 -10000 0 -10000 0 0
GAB1 0.033 0.039 -10000 0 -10000 0 0
FOXO3 0.023 0.082 -10000 0 -0.38 14 14
AKT1 0.022 0.083 -10000 0 -0.4 14 14
BAD 0.025 0.082 -10000 0 -0.38 14 14
megakaryocyte differentiation 0.029 0.042 -10000 0 -10000 0 0
GSK3B 0.02 0.087 -10000 0 -0.38 14 14
RAF1 0.05 0.046 -10000 0 -0.29 1 1
SHC1 0.017 0.027 -10000 0 -0.23 6 6
STAT3 0.026 0.053 -10000 0 -0.25 3 3
STAT1 0.053 0.062 -10000 0 -10000 0 0
HRAS/SPRED1 0.044 0.043 -10000 0 -0.25 2 2
cell proliferation 0.032 0.039 -10000 0 -10000 0 0
PIK3CA -0.011 0.1 -10000 0 -0.33 48 48
TEC 0.019 0.01 -10000 0 -0.2 1 1
RPS6KB1 0.032 0.046 -10000 0 -0.26 1 1
HRAS/SPRED2 0.055 0.045 -10000 0 -0.29 1 1
LYN/TEC/p62DOK 0.032 0.074 -10000 0 -0.25 9 9
MAPK3 0.049 0.039 -10000 0 -0.22 1 1
STAP1 0.032 0.039 -10000 0 -10000 0 0
GRAP2 0.02 0 -10000 0 -10000 0 0
JAK2 0.049 0.057 -10000 0 -10000 0 0
STAT1 (dimer) 0.053 0.062 -10000 0 -10000 0 0
mol:Gleevec -0.002 0.002 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.05 0.047 -10000 0 -10000 0 0
actin filament polymerization 0.026 0.039 -10000 0 -10000 0 0
LYN -0.031 0.13 -10000 0 -0.34 76 76
STAP1/STAT5A (dimer) 0.048 0.047 -10000 0 -10000 0 0
PIK3R1 -0.011 0.098 -10000 0 -0.3 52 52
CBL/CRKL/GRB2 0.052 0.043 -10000 0 -10000 0 0
PI3K 0.024 0.081 -10000 0 -0.29 5 5
PTEN -0.018 0.11 -10000 0 -0.35 55 55
SCF/KIT/EPO/EPOR 0.065 0.066 -10000 0 -10000 0 0
MAPK8 0.032 0.039 -10000 0 -10000 0 0
STAT3 (dimer) 0.025 0.053 -10000 0 -0.24 3 3
positive regulation of transcription 0.045 0.035 -10000 0 -0.18 1 1
mol:GDP 0.052 0.045 -10000 0 -10000 0 0
PIK3C2B 0.023 0.052 -10000 0 -10000 0 0
CBL/CRKL 0.047 0.038 -10000 0 -10000 0 0
FER 0.03 0.041 -10000 0 -10000 0 0
SH2B3 0.024 0.052 -10000 0 -0.25 1 1
PDPK1 0.021 0.067 0.27 1 -0.22 3 4
SNAI2 -0.01 0.07 -10000 0 -0.26 4 4
positive regulation of cell proliferation 0.044 0.059 -10000 0 -10000 0 0
KITLG 0.024 0.005 -10000 0 -10000 0 0
cell motility 0.044 0.059 -10000 0 -10000 0 0
PTPN6 0.01 0.05 -10000 0 -0.33 11 11
EPOR 0.05 0.039 -10000 0 -10000 0 0
STAT5A (dimer) 0.045 0.049 -10000 0 -10000 0 0
SOCS1 0.02 0 -10000 0 -10000 0 0
cell migration -0.032 0.039 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.022 0.003 -10000 0 -10000 0 0
VAV1 0.015 0.032 -10000 0 -0.2 11 11
GRB10 0.028 0.046 -10000 0 -0.25 2 2
PTPN11 0.018 0.002 -10000 0 -10000 0 0
SCF/KIT 0.028 0.041 -10000 0 -10000 0 0
GO:0007205 -0.002 0.003 -10000 0 -10000 0 0
MAP2K1 0.047 0.042 -10000 0 -0.23 1 1
CBL 0.02 0 -10000 0 -10000 0 0
KIT 0.045 0.055 -10000 0 -10000 0 0
MAP2K2 0.048 0.041 -10000 0 -0.23 1 1
SHC/Grb2/SOS1 0.037 0.044 -10000 0 -10000 0 0
STAT5A 0.045 0.049 -10000 0 -10000 0 0
GRB2 0.012 0.053 -10000 0 -0.35 11 11
response to radiation -0.011 0.071 -10000 0 -0.25 4 4
SHC/GRAP2 0.027 0.019 -10000 0 -0.24 1 1
PTPRO 0.03 0.043 -10000 0 -10000 0 0
SH2B2 0.026 0.039 -10000 0 -10000 0 0
DOK1 0.02 0 -10000 0 -10000 0 0
MATK 0.032 0.039 -10000 0 -10000 0 0
CREBBP 0.044 0.013 -10000 0 -10000 0 0
BCL2 0.052 0.033 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.018 0.033 -9999 0 -0.17 16 16
MAPK9 0.002 0.043 -9999 0 -0.19 21 21
adrenocorticotropin secretion 0.012 0.006 -9999 0 -0.13 1 1
GNB1/GNG2 0.007 0.038 -9999 0 -0.21 16 16
GNB1 0.008 0.065 -9999 0 -0.36 16 16
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 0.007 -9999 0 -0.088 3 3
Gs family/GTP 0.013 0 -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 0 -9999 0 -10000 0 0
GNAL 0.02 0 -9999 0 -10000 0 0
GNG2 0 0 -9999 0 -10000 0 0
CRH 0.019 0.01 -9999 0 -0.2 1 1
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.01 0 -9999 0 -10000 0 0
MAPK11 0.01 0 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.02 0 -9999 0 -10000 0 0
GNAT1/GTP 0.015 0 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin 0.027 0 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP 0.026 0.011 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.02 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel 0.034 0.022 -9999 0 -10000 0 0
mol:Na + 0.03 0.015 -9999 0 -10000 0 0
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.023 0.021 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel 0.038 0.016 -9999 0 -10000 0 0
CNGB1 0.02 0 -9999 0 -10000 0 0
RDH5 0.012 0.04 -9999 0 -0.2 18 18
SAG 0.02 0 -9999 0 -10000 0 0
mol:Ca2+ 0.038 0.015 -9999 0 -10000 0 0
Na + (4 Units) -0.001 0.008 -9999 0 -10000 0 0
RGS9 0.02 0 -9999 0 -10000 0 0
GNB1/GNGT1 0.018 0.052 -9999 0 -0.25 16 16
GNAT1/GDP 0.032 0.018 -9999 0 -10000 0 0
GUCY2D 0.019 0.01 -9999 0 -0.2 1 1
GNGT1 0.015 0.033 -9999 0 -0.2 12 12
GUCY2F 0.02 0 -9999 0 -10000 0 0
GNB5 0.013 0.037 -9999 0 -0.2 15 15
mol:GMP (4 units) 0.034 0.018 -9999 0 -10000 0 0
mol:11-cis-retinal 0.012 0.04 -9999 0 -0.2 18 18
mol:cGMP 0.028 0.005 -9999 0 -10000 0 0
GNB1 0.008 0.065 -9999 0 -0.36 16 16
Rhodopsin 0.024 0.028 -9999 0 -0.12 18 18
SLC24A1 0.02 0 -9999 0 -10000 0 0
CNGA1 0.014 0.036 -9999 0 -0.2 14 14
Metarhodopsin II 0.013 0 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.025 0.005 -9999 0 -0.09 1 1
RGS9BP 0 0 -9999 0 -10000 0 0
Metarhodopsin II/Transducin 0.021 0.038 -9999 0 -0.19 16 16
GCAP Family/Ca ++ 0.013 0 -9999 0 -10000 0 0
PDE6A/B 0.026 0.022 -9999 0 -0.12 11 11
mol:Pi 0.023 0.021 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.029 0.041 -9999 0 -0.18 16 16
PDE6B 0.016 0.029 -9999 0 -0.2 9 9
PDE6A 0.019 0.014 -9999 0 -0.2 2 2
PDE6G 0.018 0.019 -9999 0 -0.2 4 4
RHO 0.02 0 -9999 0 -10000 0 0
PDE6 0.043 0.025 -9999 0 -10000 0 0
GUCA1A 0 0 -9999 0 -10000 0 0
GC2/GCAP Family 0.025 0 -9999 0 -10000 0 0
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.02 0 -9999 0 -10000 0 0
LPA4-mediated signaling events

Figure S128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.009 0 -9999 0 -10000 0 0
ADCY5 0.009 0 -9999 0 -10000 0 0
ADCY6 0.018 0.005 -9999 0 -10000 0 0
ADCY7 0.005 0.05 -9999 0 -0.2 26 26
ADCY1 0.018 0 -9999 0 -10000 0 0
ADCY2 0.018 0 -9999 0 -10000 0 0
ADCY3 0.009 0 -9999 0 -10000 0 0
ADCY8 0.008 0.033 -9999 0 -10000 0 0
PRKCE 0.012 0 -9999 0 -10000 0 0
ADCY9 0.017 0.009 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process 0.018 0.019 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.023 0 -9999 0 -10000 0 0
RGS9BP 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + 0.026 0.005 -9999 0 -10000 0 0
mol:ADP 0 0 -9999 0 -10000 0 0
GNAT2 0.02 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.023 0.021 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.027 0 -9999 0 -10000 0 0
GRK7 0 0 -9999 0 -10000 0 0
CNGB3 0.02 0 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ 0.027 0.005 -9999 0 -10000 0 0
Cone PDE6 0.044 0.019 -9999 0 -10000 0 0
Cone Metarhodopsin II 0 0 -9999 0 -10000 0 0
Na + (4 Units) 0.037 0.005 -9999 0 -10000 0 0
GNAT2/GDP 0.032 0.018 -9999 0 -10000 0 0
GNB5 0.013 0.037 -9999 0 -0.2 15 15
mol:GMP (4 units) 0.027 0 -9999 0 -10000 0 0
Cone Transducin 0.025 0 -9999 0 -10000 0 0
SLC24A2 0.02 0 -9999 0 -10000 0 0
GNB3/GNGT2 0.015 0 -9999 0 -10000 0 0
GNB3 0.02 0 -9999 0 -10000 0 0
GNAT2/GTP 0.015 0 -9999 0 -10000 0 0
CNGA3 0.019 0.01 -9999 0 -0.2 1 1
ARR3 0.02 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.027 0.006 -9999 0 -10000 0 0
mol:Pi 0.023 0.021 -9999 0 -10000 0 0
Cone CNG Channel 0.049 0.005 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.02 0 -9999 0 -10000 0 0
RGS9 0.02 0 -9999 0 -10000 0 0
PDE6C 0.02 0 -9999 0 -10000 0 0
GNGT2 0 0 -9999 0 -10000 0 0
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.02 0 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.02 0 -9999 0 -9999 0 0
ITGB7 0.02 0 -9999 0 -9999 0 0
ITGA4 0.02 0 -9999 0 -9999 0 0
alpha4/beta7 Integrin 0.029 0 -9999 0 -9999 0 0
alpha4/beta1 Integrin 0.029 0 -9999 0 -9999 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.02 0 -9999 0 -9999 0 0
PI3K Class IB/PDE3B 0.02 0 -9999 0 -9999 0 0
PDE3B 0.02 0 -9999 0 -9999 0 0
Methods & Data
Input

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

  • Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/484198/1.GDAC_MergeDataFiles.Finished/OV.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

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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

  • Maintainer = TCGA GDAC Team

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