PARADIGM pathway analysis of mRNA expression data
Colon/Rectal Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Colon/Rectal Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: PARADIGM pathway analysis of mRNA expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1445JDK
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 47 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
TCGA08_retinoblastoma 132
Syndecan-1-mediated signaling events 73
Signaling events mediated by Stem cell factor receptor (c-Kit) 63
FAS signaling pathway (CD95) 58
BCR signaling pathway 54
FOXM1 transcription factor network 51
Fc-epsilon receptor I signaling in mast cells 47
Glypican 1 network 45
HIF-1-alpha transcription factor network 41
Reelin signaling pathway 32
Results
Summary Table

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
TCGA08_retinoblastoma 132 1061 8 -0.48 0.25 1000 -1000 -0.031 -1000
Syndecan-1-mediated signaling events 73 2498 34 -0.7 0.017 1000 -1000 -0.098 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 63 4982 78 -0.99 0.28 1000 -1000 -0.097 -1000
FAS signaling pathway (CD95) 58 2727 47 -0.41 0.2 1000 -1000 -0.057 -1000
BCR signaling pathway 54 5399 99 -0.48 0.017 1000 -1000 -0.11 -1000
FOXM1 transcription factor network 51 2643 51 -0.69 0.017 1000 -1000 -0.16 -1000
Fc-epsilon receptor I signaling in mast cells 47 4647 97 -0.44 0.064 1000 -1000 -0.11 -1000
Glypican 1 network 45 2164 48 -0.48 0.03 1000 -1000 -0.07 -1000
HIF-1-alpha transcription factor network 41 3166 76 -0.82 0.028 1000 -1000 -0.1 -1000
Reelin signaling pathway 32 1828 56 -0.64 0.017 1000 -1000 -0.11 -1000
IL23-mediated signaling events 31 1905 60 -0.64 0.018 1000 -1000 -0.17 -1000
Osteopontin-mediated events 30 1173 38 -0.48 0.018 1000 -1000 -0.13 -1000
Endothelins 28 2767 96 -0.53 0.084 1000 -1000 -0.09 -1000
Canonical Wnt signaling pathway 27 1393 51 -0.54 0.37 1000 -1000 -0.069 -1000
BMP receptor signaling 26 2182 81 -0.45 0.032 1000 -1000 -0.12 -1000
IL6-mediated signaling events 25 1943 75 -0.49 0.072 1000 -1000 -0.1 -1000
Visual signal transduction: Rods 25 1319 52 -0.45 0.017 1000 -1000 -0.11 -1000
IL4-mediated signaling events 24 2246 91 -0.56 0.38 1000 -1000 -0.15 -1000
Wnt signaling 24 174 7 -0.14 0.014 1000 -1000 -0.03 -1000
Syndecan-2-mediated signaling events 23 1603 69 -0.67 0.053 1000 -1000 -0.073 -1000
Arf6 signaling events 23 1479 62 -0.31 0.018 1000 -1000 -0.083 -1000
TCGA08_p53 23 167 7 -0.16 0.087 1000 -1000 -0.023 -1000
HIF-2-alpha transcription factor network 22 974 43 -0.67 0.38 1000 -1000 -0.098 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 21 1817 85 -0.31 0.023 1000 -1000 -0.094 -1000
Glucocorticoid receptor regulatory network 21 2401 114 -0.69 0.34 1000 -1000 -0.095 -1000
Signaling events mediated by PRL 21 747 34 -0.22 0.11 1000 -1000 -0.079 -1000
Syndecan-3-mediated signaling events 20 729 35 -0.67 0.017 1000 -1000 -0.092 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 18 1225 68 -0.84 0.076 1000 -1000 -0.14 -1000
Presenilin action in Notch and Wnt signaling 17 1045 61 -0.54 0.24 1000 -1000 -0.092 -1000
Aurora A signaling 17 1057 60 -0.69 0.021 1000 -1000 -0.085 -1000
IL1-mediated signaling events 16 1036 62 -0.41 0.082 1000 -1000 -0.12 -1000
TRAIL signaling pathway 15 740 48 -0.15 0.017 1000 -1000 -0.087 -1000
Calcium signaling in the CD4+ TCR pathway 15 473 31 -0.38 0.028 1000 -1000 -0.1 -1000
IGF1 pathway 15 890 57 -0.36 0.077 1000 -1000 -0.13 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 14 802 54 -0.64 0.036 1000 -1000 -0.13 -1000
Signaling events mediated by the Hedgehog family 14 775 52 -0.19 0.16 1000 -1000 -0.1 -1000
PLK1 signaling events 14 1225 85 -0.38 0.02 1000 -1000 -0.07 -1000
EGFR-dependent Endothelin signaling events 14 313 21 -0.21 0.017 1000 -1000 -0.1 -1000
IL12-mediated signaling events 13 1209 87 -0.34 0.031 1000 -1000 -0.14 -1000
p75(NTR)-mediated signaling 13 1644 125 -0.81 0.066 1000 -1000 -0.12 -1000
IL2 signaling events mediated by PI3K 13 774 58 -0.61 0.043 1000 -1000 -0.1 -1000
Regulation of nuclear SMAD2/3 signaling 12 1767 136 -1.1 0.069 1000 -1000 -0.093 -1000
Noncanonical Wnt signaling pathway 12 331 26 -0.14 0.017 1000 -1000 -0.1 -1000
FOXA2 and FOXA3 transcription factor networks 12 590 46 -0.8 0.034 1000 -1000 -0.062 -1000
amb2 Integrin signaling 12 989 82 -0.36 0.017 1000 -1000 -0.1 -1000
S1P1 pathway 12 436 36 -0.14 0.017 1000 -1000 -0.09 -1000
EPHB forward signaling 12 1030 85 -0.26 0.17 1000 -1000 -0.12 -1000
Visual signal transduction: Cones 11 454 38 -0.2 0.025 1000 -1000 -0.092 -1000
Ephrin B reverse signaling 11 556 48 -0.26 0.15 1000 -1000 -0.094 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 10 836 83 -0.41 0.088 1000 -1000 -0.098 -1000
Aurora B signaling 10 699 67 -0.27 0.03 1000 -1000 -0.085 -1000
Thromboxane A2 receptor signaling 9 977 105 -0.49 0.12 1000 -1000 -0.1 -1000
Glypican 2 network 9 36 4 -0.03 0 1000 -1000 -0.028 -1000
Regulation of Telomerase 9 954 102 -0.42 0.062 1000 -1000 -0.14 -1000
Sphingosine 1-phosphate (S1P) pathway 8 224 28 -0.073 0.017 1000 -1000 -0.062 -1000
PLK2 and PLK4 events 8 26 3 -0.006 -0.002 1000 -1000 -0.022 -1000
EPO signaling pathway 8 463 55 -0.57 0.024 1000 -1000 -0.12 -1000
PDGFR-alpha signaling pathway 8 387 44 -0.18 0.033 1000 -1000 -0.095 -1000
ceramide signaling pathway 8 437 49 -0.41 0.085 1000 -1000 -0.063 -1000
TCR signaling in naïve CD8+ T cells 8 744 93 -0.096 0.045 1000 -1000 -0.1 -1000
Syndecan-4-mediated signaling events 8 578 67 -0.48 0.03 1000 -1000 -0.12 -1000
Cellular roles of Anthrax toxin 7 290 39 -0.063 0.017 1000 -1000 -0.036 -1000
Signaling events mediated by PTP1B 7 550 76 -0.6 0.11 1000 -1000 -0.11 -1000
Nectin adhesion pathway 7 448 63 -0.7 0.057 1000 -1000 -0.098 -1000
Ceramide signaling pathway 7 603 76 -0.41 0.09 1000 -1000 -0.071 -1000
RXR and RAR heterodimerization with other nuclear receptor 7 402 52 -0.54 0.1 1000 -1000 -0.079 -1000
Integrins in angiogenesis 7 669 84 -0.48 0.064 1000 -1000 -0.14 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 7 262 33 -0.23 0.038 1000 -1000 -0.091 -1000
Regulation of Androgen receptor activity 7 510 70 -0.59 0.041 1000 -1000 -0.093 -1000
Ras signaling in the CD4+ TCR pathway 7 126 17 -0.088 0.017 1000 -1000 -0.06 -1000
Signaling events mediated by HDAC Class III 6 244 40 -0.27 0.031 1000 -1000 -0.063 -1000
IL27-mediated signaling events 6 336 51 -0.31 0.025 1000 -1000 -0.097 -1000
VEGFR1 specific signals 6 349 56 -0.068 0.04 1000 -1000 -0.1 -1000
E-cadherin signaling in keratinocytes 6 284 43 -0.35 0.045 1000 -1000 -0.085 -1000
E-cadherin signaling events 6 33 5 -0.025 0.017 1000 -1000 -0.06 -1000
Canonical NF-kappaB pathway 5 219 39 -0.21 0.064 1000 -1000 -0.11 -1000
ErbB4 signaling events 5 380 69 -0.49 0.088 1000 -1000 -0.12 -1000
BARD1 signaling events 5 305 57 -0.16 0.052 1000 -1000 -0.089 -1000
a4b1 and a4b7 Integrin signaling 5 26 5 -0.023 0.011 1000 -1000 -0.047 -1000
Signaling mediated by p38-gamma and p38-delta 5 87 15 -0.031 0.039 1000 -1000 -0.032 -1000
Nongenotropic Androgen signaling 5 310 52 -0.068 0.048 1000 -1000 -0.079 -1000
Signaling events mediated by VEGFR1 and VEGFR2 5 664 125 -0.1 0.078 1000 -1000 -0.14 -1000
TCGA08_rtk_signaling 5 154 26 -0.31 0.036 1000 -1000 -0.032 -1000
Stabilization and expansion of the E-cadherin adherens junction 5 415 74 -0.35 0.087 1000 -1000 -0.13 -1000
Class I PI3K signaling events 5 371 73 -0.31 0.033 1000 -1000 -0.073 -1000
Plasma membrane estrogen receptor signaling 5 468 86 -0.35 0.062 1000 -1000 -0.1 -1000
Coregulation of Androgen receptor activity 4 332 76 -0.22 0.063 1000 -1000 -0.085 -1000
IFN-gamma pathway 4 336 68 -0.15 0.056 1000 -1000 -0.11 -1000
Signaling mediated by p38-alpha and p38-beta 4 179 44 -0.2 0.017 1000 -1000 -0.076 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 4 221 45 -0.16 0.089 1000 -1000 -0.1 -1000
Effects of Botulinum toxin 4 119 26 -0.08 0.017 1000 -1000 -0.085 -1000
PDGFR-beta signaling pathway 4 412 97 -0.26 0.066 1000 -1000 -0.12 -1000
Caspase cascade in apoptosis 3 283 74 -0.22 0.061 1000 -1000 -0.056 -1000
Paxillin-independent events mediated by a4b1 and a4b7 3 111 37 -0.13 0.042 1000 -1000 -0.1 -1000
FoxO family signaling 3 230 64 -0.12 0.13 1000 -1000 -0.076 -1000
Regulation of p38-alpha and p38-beta 3 186 54 -0.16 0.037 1000 -1000 -0.073 -1000
IL2 signaling events mediated by STAT5 3 76 22 -0.093 0.11 1000 -1000 -0.049 -1000
S1P3 pathway 3 154 42 -0.066 0.03 1000 -1000 -0.069 -1000
Angiopoietin receptor Tie2-mediated signaling 3 293 88 -0.26 0.099 1000 -1000 -0.14 -1000
Nephrin/Neph1 signaling in the kidney podocyte 2 90 34 -0.033 0.059 1000 -1000 -0.093 -1000
Circadian rhythm pathway 2 53 22 -0.073 0.066 1000 -1000 -0.1 -1000
Ephrin A reverse signaling 2 16 7 -0.006 0.027 1000 -1000 -0.04 -1000
JNK signaling in the CD4+ TCR pathway 2 48 17 -0.086 0.056 1000 -1000 -0.079 -1000
Hedgehog signaling events mediated by Gli proteins 2 190 65 -0.15 0.067 1000 -1000 -0.077 -1000
Arf6 downstream pathway 2 90 43 -0.036 0.037 1000 -1000 -0.057 -1000
Retinoic acid receptors-mediated signaling 2 128 58 -0.069 0.079 1000 -1000 -0.098 -1000
LPA receptor mediated events 2 274 102 -0.32 0.044 1000 -1000 -0.097 -1000
E-cadherin signaling in the nascent adherens junction 2 218 76 -0.054 0.062 1000 -1000 -0.11 -1000
Arf6 trafficking events 2 165 71 -0.17 0.059 1000 -1000 -0.095 -1000
Insulin Pathway 2 165 74 -0.082 0.052 1000 -1000 -0.13 -1000
Neurotrophic factor-mediated Trk receptor signaling 2 313 120 -0.059 0.1 1000 -1000 -0.11 -1000
LPA4-mediated signaling events 1 19 12 -0.002 0.045 1000 -1000 -0.027 -1000
ErbB2/ErbB3 signaling events 1 92 65 -0.017 0.091 1000 -1000 -0.092 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 38 23 -0.02 0.045 1000 -1000 -0.099 -1000
Signaling events mediated by HDAC Class II 1 122 75 -0.083 0.044 1000 -1000 -0.08 -1000
mTOR signaling pathway 1 77 53 -0.007 0.068 1000 -1000 -0.082 -1000
Class I PI3K signaling events mediated by Akt 1 72 68 -0.094 0.062 1000 -1000 -0.096 -1000
Signaling events regulated by Ret tyrosine kinase 1 125 82 -0.041 0.067 1000 -1000 -0.11 -1000
S1P5 pathway 1 29 17 -0.068 0.024 1000 -1000 -0.062 -1000
Paxillin-dependent events mediated by a4b1 1 38 36 -0.023 0.031 1000 -1000 -0.096 -1000
S1P4 pathway 1 45 25 -0.068 0.033 1000 -1000 -0.061 -1000
Arf1 pathway 1 56 54 -0.014 0.048 1000 -1000 -0.07 -1000
Aurora C signaling 0 6 7 -0.006 0.017 1000 -1000 -0.059 -1000
Insulin-mediated glucose transport 0 31 32 -0.054 0.051 1000 -1000 -0.076 -1000
Signaling events mediated by HDAC Class I 0 51 104 -0.025 0.078 1000 -1000 -0.087 -1000
Atypical NF-kappaB pathway 0 11 31 -0.003 0.065 1000 -1000 -0.084 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 14 27 -0.005 0.035 1000 -1000 -0.072 -1000
Rapid glucocorticoid signaling 0 3 20 0 0.017 1000 -1000 -0.057 -1000
Class IB PI3K non-lipid kinase events 0 0 3 -0.017 0.017 1000 -1000 -0.027 -1000
p38 MAPK signaling pathway 0 32 44 -0.012 0.064 1000 -1000 -0.086 -1000
Alternative NF-kappaB pathway 0 3 13 -0.002 0.017 1000 -1000 -0.079 -1000
Total 1643 95907 7203 -38 8.6 131000 -131000 -12 -131000
TCGA08_retinoblastoma

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
CDKN2B -0.48 0.25 -10000 0 -0.61 175 175
CDKN2C 0.034 0.048 -10000 0 -10000 0 0
CDKN2A -0.23 0.34 -10000 0 -0.74 70 70
CCND2 0.22 0.12 0.28 160 -10000 0 160
RB1 -0.23 0.12 -10000 0 -0.28 159 159
CDK4 0.23 0.12 0.28 162 -10000 0 162
CDK6 0.25 0.13 0.3 172 -10000 0 172
G1/S progression 0.23 0.12 0.28 163 -10000 0 163
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.017 0 -9999 0 -10000 0 0
CCL5 -0.14 0.28 -9999 0 -0.64 52 52
SDCBP 0.017 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.41 0.14 -9999 0 -0.44 198 198
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 -0.41 0.17 -9999 0 -0.66 51 51
Syndecan-1/Syntenin -0.39 0.13 -9999 0 -0.61 41 41
MAPK3 -0.35 0.13 -9999 0 -0.57 41 41
HGF/MET -0.24 0.27 -9999 0 -0.54 101 101
TGFB1/TGF beta receptor Type II 0.017 0 -9999 0 -10000 0 0
BSG 0.014 0.044 -9999 0 -0.64 1 1
keratinocyte migration -0.4 0.16 -9999 0 -0.65 51 51
Syndecan-1/RANTES -0.46 0.21 -9999 0 -0.71 75 75
Syndecan-1/CD147 -0.37 0.14 -9999 0 -0.6 44 44
Syndecan-1/Syntenin/PIP2 -0.37 0.13 -9999 0 -0.59 41 41
LAMA5 -0.026 0.17 -9999 0 -0.72 13 13
positive regulation of cell-cell adhesion -0.37 0.12 -9999 0 -0.57 41 41
MMP7 -0.7 0.12 -9999 0 -0.72 216 216
HGF 0.01 0.07 -9999 0 -0.72 2 2
Syndecan-1/CASK -0.4 0.13 -9999 0 -0.43 198 198
Syndecan-1/HGF/MET -0.54 0.22 -9999 0 -0.72 121 121
regulation of cell adhesion -0.33 0.13 -9999 0 -0.56 39 39
HPSE -0.083 0.24 -9999 0 -0.64 34 34
positive regulation of cell migration -0.41 0.14 -9999 0 -0.44 198 198
SDC1 -0.42 0.14 -9999 0 -0.45 198 198
Syndecan-1/Collagen -0.41 0.14 -9999 0 -0.44 198 198
PPIB 0.004 0.098 -9999 0 -0.72 4 4
MET -0.31 0.37 -9999 0 -0.72 99 99
PRKACA 0.017 0 -9999 0 -10000 0 0
MMP9 -0.006 0.13 -9999 0 -0.71 7 7
MAPK1 -0.35 0.13 -9999 0 -0.59 39 39
homophilic cell adhesion -0.41 0.13 -9999 0 -0.44 198 198
MMP1 -0.64 0.23 -9999 0 -0.72 197 197
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.24 0.18 -10000 0 -0.4 100 100
CRKL -0.26 0.2 -10000 0 -0.43 112 112
HRAS -0.21 0.18 -10000 0 -0.5 16 16
mol:PIP3 -0.26 0.19 -10000 0 -0.42 109 109
SPRED1 0.017 0 -10000 0 -10000 0 0
SPRED2 0.017 0 -10000 0 -10000 0 0
GAB1 -0.29 0.2 -10000 0 -0.46 113 113
FOXO3 -0.24 0.19 -10000 0 -0.42 81 81
AKT1 -0.27 0.2 -10000 0 -0.44 115 115
BAD -0.24 0.19 -10000 0 -0.42 81 81
megakaryocyte differentiation -0.33 0.24 -10000 0 -0.51 124 124
GSK3B -0.25 0.19 -10000 0 -0.42 81 81
RAF1 -0.16 0.15 -10000 0 -0.4 13 13
SHC1 0.017 0 -10000 0 -10000 0 0
STAT3 -0.29 0.2 -10000 0 -0.46 111 111
STAT1 -0.8 0.56 -10000 0 -1.3 113 113
HRAS/SPRED1 -0.18 0.12 -10000 0 -0.39 16 16
cell proliferation -0.28 0.2 -10000 0 -0.45 111 111
PIK3CA 0.016 0.001 -10000 0 -10000 0 0
TEC 0.017 0 -10000 0 -10000 0 0
RPS6KB1 -0.29 0.2 -10000 0 -0.46 112 112
HRAS/SPRED2 -0.18 0.12 -10000 0 -0.39 16 16
LYN/TEC/p62DOK -0.27 0.17 -10000 0 -0.42 103 103
MAPK3 -0.11 0.11 -10000 0 -10000 0 0
STAP1 -0.48 0.28 -10000 0 -0.65 150 150
GRAP2 0.017 0 -10000 0 -10000 0 0
JAK2 -0.62 0.39 -10000 0 -0.97 112 112
STAT1 (dimer) -0.77 0.54 -10000 0 -1.2 113 113
mol:Gleevec 0.012 0.008 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.3 0.2 -10000 0 -0.49 82 82
actin filament polymerization -0.29 0.2 -10000 0 -0.46 111 111
LYN 0.017 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.59 0.34 -10000 0 -0.8 149 149
PIK3R1 0.016 0.001 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.24 0.15 -10000 0 -0.51 4 4
PI3K -0.28 0.17 -10000 0 -0.43 109 109
PTEN 0 0.11 -10000 0 -0.63 6 6
SCF/KIT/EPO/EPOR -0.86 0.67 -10000 0 -1.5 111 111
MAPK8 -0.29 0.2 -10000 0 -0.46 111 111
STAT3 (dimer) -0.28 0.2 -10000 0 -0.45 111 111
positive regulation of transcription -0.086 0.097 -10000 0 -10000 0 0
mol:GDP -0.24 0.16 -10000 0 -0.56 16 16
PIK3C2B -0.29 0.2 -10000 0 -0.46 111 111
CBL/CRKL -0.24 0.18 -10000 0 -0.4 100 100
FER -0.3 0.21 -10000 0 -0.48 114 114
SH2B3 -0.29 0.2 -10000 0 -0.46 111 111
PDPK1 -0.23 0.17 -10000 0 -0.39 107 107
SNAI2 -0.3 0.22 -10000 0 -0.48 113 113
positive regulation of cell proliferation -0.52 0.35 -10000 0 -0.82 115 115
KITLG -0.002 0.069 -10000 0 -0.71 2 2
cell motility -0.52 0.35 -10000 0 -0.82 115 115
PTPN6 0.031 0.015 -10000 0 -10000 0 0
EPOR -0.23 0.17 -10000 0 -10000 0 0
STAT5A (dimer) -0.42 0.29 -10000 0 -0.66 114 114
SOCS1 0.014 0.05 -10000 0 -0.72 1 1
cell migration 0.28 0.2 0.45 111 -10000 0 111
SOS1 0.017 0 -10000 0 -10000 0 0
EPO 0.001 0.051 -10000 0 -0.74 1 1
VAV1 -0.042 0.19 -10000 0 -0.64 20 20
GRB10 -0.31 0.23 -10000 0 -0.49 117 117
PTPN11 0.023 0.052 -10000 0 -0.73 1 1
SCF/KIT -0.32 0.2 0.26 1 -0.5 111 112
GO:0007205 0.016 0.01 -10000 0 -10000 0 0
MAP2K1 -0.12 0.12 -10000 0 -10000 0 0
CBL 0.017 0 -10000 0 -10000 0 0
KIT -0.81 0.72 -10000 0 -1.5 111 111
MAP2K2 -0.12 0.12 -10000 0 -10000 0 0
SHC/Grb2/SOS1 -0.27 0.17 -10000 0 -0.43 75 75
STAT5A -0.44 0.3 -10000 0 -0.69 114 114
GRB2 0.017 0 -10000 0 -10000 0 0
response to radiation -0.29 0.21 -10000 0 -0.47 113 113
SHC/GRAP2 0 0 -10000 0 -10000 0 0
PTPRO -0.34 0.25 -10000 0 -0.52 124 124
SH2B2 -0.3 0.2 -10000 0 -0.47 111 111
DOK1 0.014 0.05 -10000 0 -0.72 1 1
MATK -0.29 0.2 -10000 0 -0.46 111 111
CREBBP 0.011 0.021 -10000 0 -10000 0 0
BCL2 -0.99 0.69 -10000 0 -1.5 145 145
FAS signaling pathway (CD95)

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
SPTAN1 0.17 0.13 0.26 145 -0.33 1 146
RFC1 0.17 0.13 0.27 94 -0.33 1 95
PRKDC 0.13 0.19 0.26 131 -0.51 5 136
RIPK1 0.019 0.005 -10000 0 -10000 0 0
CASP7 -0.12 0.26 -10000 0 -0.73 31 31
FASLG/FAS/FADD/FAF1 -0.006 0.18 0.33 2 -0.44 14 16
MAP2K4 -0.067 0.17 -10000 0 -0.47 18 18
mol:ceramide -0.063 0.16 -10000 0 -0.49 16 16
GSN 0.099 0.19 0.26 115 -0.38 8 123
FASLG/FAS/FADD/FAF1/Caspase 8 -0.021 0.17 -10000 0 -0.44 18 18
FAS -0.055 0.19 -10000 0 -0.64 22 22
BID -0.013 0.086 -10000 0 -0.48 7 7
MAP3K1 -0.031 0.19 0.28 1 -0.55 19 20
MAP3K7 0.01 0.009 -10000 0 -10000 0 0
RB1 0.17 0.13 0.26 145 -0.33 1 146
CFLAR 0.019 0.005 -10000 0 -10000 0 0
HGF/MET -0.34 0.32 -10000 0 -0.57 134 134
ARHGDIB 0.17 0.13 0.27 88 -0.33 1 89
FADD 0.01 0.009 -10000 0 -10000 0 0
actin filament polymerization -0.099 0.19 0.38 8 -0.26 115 123
NFKB1 -0.076 0.07 -10000 0 -10000 0 0
MAPK8 -0.097 0.2 -10000 0 -0.53 14 14
DFFA 0.17 0.13 0.26 145 -0.33 1 146
DNA fragmentation during apoptosis 0.17 0.14 0.26 144 -0.39 2 146
FAS/FADD/MET -0.24 0.26 -10000 0 -0.49 111 111
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 0.012 0.07 -10000 0 -0.72 2 2
FAF1 0.01 0.009 -10000 0 -10000 0 0
PARP1 0.17 0.13 0.26 145 -0.33 1 146
DFFB 0.17 0.14 0.26 144 -0.39 2 146
CHUK -0.062 0.059 -10000 0 -10000 0 0
FASLG -0.061 0.2 -10000 0 -0.65 24 24
FAS/FADD -0.046 0.14 -10000 0 -0.46 22 22
HGF 0.01 0.07 -10000 0 -0.72 2 2
LMNA 0.16 0.12 0.34 2 -10000 0 2
CASP6 0.17 0.13 0.26 145 -0.33 1 146
CASP10 0.01 0.009 -10000 0 -10000 0 0
CASP3 0.2 0.15 0.31 145 -0.38 1 146
PTPN13 -0.22 0.34 -10000 0 -0.72 70 70
CASP8 0.003 0.032 0.34 2 -10000 0 2
IL6 -0.23 0.29 -10000 0 -0.54 103 103
MET -0.31 0.37 -10000 0 -0.72 99 99
ICAD/CAD 0.16 0.13 0.34 2 -0.42 1 3
FASLG/FAS/FADD/FAF1/Caspase 10 -0.064 0.16 -10000 0 -0.5 16 16
activation of caspase activity by cytochrome c -0.013 0.086 -10000 0 -0.48 7 7
PAK2 0.17 0.13 0.27 88 -0.33 1 89
BCL2 -0.41 0.31 -10000 0 -0.63 145 145
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.19 0.28 -10000 0 -0.52 85 85
IKBKB -0.096 0.14 -10000 0 -0.28 27 27
AKT1 -0.093 0.17 0.24 2 -0.29 65 67
IKBKG -0.1 0.15 -10000 0 -0.3 28 28
CALM1 -0.32 0.34 -10000 0 -0.66 98 98
PIK3CA 0.017 0 -10000 0 -10000 0 0
MAP3K1 -0.28 0.4 -10000 0 -0.74 89 89
MAP3K7 0.017 0 -10000 0 -10000 0 0
mol:Ca2+ -0.35 0.37 -10000 0 -0.7 104 104
DOK1 0.014 0.05 -10000 0 -0.72 1 1
AP-1 -0.12 0.16 -10000 0 -0.3 74 74
LYN 0.017 0 -10000 0 -10000 0 0
BLNK -0.001 0.11 -10000 0 -0.64 6 6
SHC1 0.017 0 -10000 0 -10000 0 0
BCR complex -0.36 0.38 -10000 0 -0.72 113 113
CD22 -0.38 0.48 -10000 0 -0.91 90 90
CAMK2G -0.28 0.31 -10000 0 -0.6 98 98
CSNK2A1 0.017 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.24 0.26 -10000 0 -0.58 76 76
GO:0007205 -0.36 0.38 -10000 0 -0.72 104 104
SYK 0.014 0.049 -10000 0 -0.72 1 1
ELK1 -0.33 0.35 -10000 0 -0.68 101 101
NFATC1 -0.29 0.38 -10000 0 -0.68 100 100
B-cell antigen/BCR complex -0.36 0.38 -10000 0 -0.72 113 113
PAG1/CSK -0.14 0.21 -10000 0 -0.46 65 65
NFKBIB -0.019 0.049 -10000 0 -10000 0 0
HRAS -0.28 0.32 -10000 0 -0.62 98 98
NFKBIA -0.018 0.048 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta -0.005 0.039 -10000 0 -10000 0 0
RasGAP/Csk -0.35 0.37 -10000 0 -0.79 83 83
mol:GDP -0.33 0.35 -10000 0 -0.67 104 104
PTEN -0.001 0.11 -10000 0 -0.64 6 6
CD79B -0.23 0.32 -10000 0 -0.63 84 84
NF-kappa-B/RelA/I kappa B alpha -0.004 0.039 -10000 0 -10000 0 0
GRB2 0.017 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.31 0.37 -10000 0 -0.68 107 107
PIK3R1 0.017 0 -10000 0 -10000 0 0
mol:IP3 -0.36 0.39 -10000 0 -0.73 104 104
CSK 0.017 0 -10000 0 -10000 0 0
FOS -0.33 0.35 -10000 0 -0.66 107 107
CHUK -0.1 0.15 -10000 0 -0.3 33 33
IBTK 0.017 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.29 0.28 -10000 0 -0.63 79 79
PTPN6 -0.35 0.44 -10000 0 -0.87 85 85
RELA 0.017 0 -10000 0 -10000 0 0
BCL2A1 -0.004 0.039 -10000 0 -0.11 13 13
VAV2 -0.44 0.52 -10000 0 -0.99 99 99
ubiquitin-dependent protein catabolic process -0.012 0.047 -10000 0 -10000 0 0
BTK -0.18 0.43 -10000 0 -1.2 34 34
CD19 -0.48 0.56 -10000 0 -1 101 101
MAP4K1 0.017 0 -10000 0 -10000 0 0
CD72 0.004 0.093 -10000 0 -0.68 4 4
PAG1 -0.17 0.3 -10000 0 -0.64 65 65
MAPK14 -0.22 0.33 -10000 0 -0.6 85 85
SH3BP5 0.014 0.044 -10000 0 -0.64 1 1
PIK3AP1 -0.36 0.39 -10000 0 -0.76 99 99
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.42 0.45 -10000 0 -0.84 105 105
RAF1 -0.26 0.3 -10000 0 -0.57 97 97
RasGAP/p62DOK/SHIP -0.34 0.36 -10000 0 -0.77 84 84
CD79A -0.28 0.32 -10000 0 -0.64 103 103
re-entry into mitotic cell cycle -0.12 0.16 -10000 0 -0.3 75 75
RASA1 0.01 0.07 -10000 0 -0.72 2 2
MAPK3 -0.19 0.25 -10000 0 -0.51 69 69
MAPK1 -0.19 0.24 -10000 0 -0.5 69 69
CD72/SHP1 -0.3 0.42 -10000 0 -0.8 83 83
NFKB1 0.017 0 -10000 0 -10000 0 0
MAPK8 -0.22 0.33 -10000 0 -0.6 85 85
actin cytoskeleton organization -0.32 0.42 -10000 0 -0.76 99 99
NF-kappa-B/RelA -0.002 0.076 -10000 0 -10000 0 0
Calcineurin -0.26 0.26 -10000 0 -0.6 72 72
PI3K -0.29 0.31 -10000 0 -0.64 93 93
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.4 0.4 -10000 0 -0.79 104 104
SOS1 0.017 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.33 0.44 -10000 0 -0.84 87 87
DAPP1 -0.41 0.5 -10000 0 -0.99 87 87
cytokine secretion -0.26 0.34 -10000 0 -0.62 100 100
mol:DAG -0.36 0.39 -10000 0 -0.73 104 104
PLCG2 -0.31 0.33 -10000 0 -0.64 110 110
MAP2K1 -0.22 0.27 -10000 0 -0.55 80 80
B-cell antigen/BCR complex/FcgammaRIIB -0.4 0.43 -10000 0 -0.75 118 118
mol:PI-3-4-5-P3 -0.19 0.2 0.33 2 -0.42 84 86
ETS1 -0.24 0.28 -10000 0 -0.6 69 69
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.28 0.3 -10000 0 -0.67 76 76
B-cell antigen/BCR complex/LYN -0.41 0.52 -10000 0 -0.98 90 90
MALT1 0.017 0 -10000 0 -10000 0 0
TRAF6 0.017 0 -10000 0 -10000 0 0
RAC1 -0.36 0.47 -10000 0 -0.85 99 99
B-cell antigen/BCR complex/LYN/SYK -0.36 0.41 -10000 0 -0.86 83 83
CARD11 -0.35 0.37 -10000 0 -0.7 106 106
FCGR2B -0.13 0.27 -10000 0 -0.64 50 50
PPP3CA 0.017 0 -10000 0 -10000 0 0
BCL10 0.017 0 -10000 0 -10000 0 0
IKK complex -0.023 0.062 -10000 0 -10000 0 0
PTPRC -0.018 0.15 -10000 0 -0.64 12 12
PDPK1 -0.088 0.17 0.23 2 -0.28 64 66
PPP3CB 0.017 0 -10000 0 -10000 0 0
PPP3CC 0.002 0.097 -10000 0 -0.64 5 5
POU2F2 0.004 0.029 -10000 0 -10000 0 0
FOXM1 transcription factor 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
NFATC3 -0.46 0.54 -9999 0 -1.2 60 60
PLK1 0.013 0.054 -9999 0 -10000 0 0
BIRC5 -0.048 0.2 -9999 0 -0.62 20 20
HSPA1B -0.47 0.54 -9999 0 -1.1 76 76
MAP2K1 0.007 0.033 -9999 0 -10000 0 0
BRCA2 -0.55 0.58 -9999 0 -1.2 78 78
FOXM1 -0.63 0.76 -9999 0 -1.5 72 72
XRCC1 -0.46 0.54 -9999 0 -1.1 65 65
FOXM1B/p19 -0.69 0.57 -9999 0 -1.3 94 94
Cyclin D1/CDK4 -0.5 0.52 -9999 0 -1.1 76 76
CDC2 -0.51 0.59 -9999 0 -1.2 66 66
TGFA -0.45 0.5 -9999 0 -1 68 68
SKP2 -0.48 0.57 -9999 0 -1.2 62 62
CCNE1 -0.041 0.19 -9999 0 -0.74 15 15
CKS1B -0.47 0.55 -9999 0 -1.2 61 61
RB1 -0.25 0.22 -9999 0 -0.65 35 35
FOXM1C/SP1 -0.62 0.67 -9999 0 -1.4 79 79
AURKB 0.013 0.054 -9999 0 -10000 0 0
CENPF -0.47 0.55 -9999 0 -1.2 62 62
CDK4 -0.053 0.2 -9999 0 -0.74 18 18
MYC -0.61 0.5 -9999 0 -1.1 91 91
CHEK2 0.007 0.033 -9999 0 -10000 0 0
ONECUT1 -0.5 0.54 -9999 0 -1.1 78 78
CDKN2A -0.22 0.34 -9999 0 -0.73 70 70
LAMA4 -0.46 0.54 -9999 0 -1.2 60 60
FOXM1B/HNF6 -0.6 0.67 -9999 0 -1.4 79 79
FOS -0.54 0.6 -9999 0 -1.2 73 73
SP1 0.011 0.013 -9999 0 -10000 0 0
CDC25B -0.58 0.59 -9999 0 -1.2 88 88
response to radiation -0.016 0.032 -9999 0 -10000 0 0
CENPB -0.46 0.54 -9999 0 -1.2 61 61
CENPA -0.5 0.59 -9999 0 -1.2 69 69
NEK2 -0.56 0.61 -9999 0 -1.2 80 80
HIST1H2BA -0.46 0.54 -9999 0 -1.2 61 61
CCNA2 -0.1 0.26 -9999 0 -0.74 33 33
EP300 0.017 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.57 0.68 -9999 0 -1.5 63 63
CCNB2 -0.46 0.54 -9999 0 -1.1 64 64
CCNB1 -0.52 0.61 -9999 0 -1.3 68 68
ETV5 -0.49 0.56 -9999 0 -1.2 64 64
ESR1 -0.47 0.56 -9999 0 -1.2 63 63
CCND1 -0.5 0.53 -9999 0 -1.1 73 73
GSK3A 0.011 0.025 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.14 0.3 -9999 0 -0.61 55 55
CDK2 -0.071 0.23 -9999 0 -0.73 24 24
G2/M transition of mitotic cell cycle -0.02 0.039 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.55 0.54 -9999 0 -1.2 82 82
GAS1 -0.64 0.65 -9999 0 -1.3 101 101
MMP2 -0.46 0.54 -9999 0 -1.2 60 60
RB1/FOXM1C -0.51 0.55 -9999 0 -1.1 76 76
CREBBP 0.017 0 -9999 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.042 0.19 -9999 0 -0.64 20 20
LAT2 -0.24 0.23 -9999 0 -0.49 88 88
AP1 -0.31 0.29 -9999 0 -0.7 59 59
mol:PIP3 -0.3 0.3 -9999 0 -0.61 93 93
IKBKB -0.14 0.16 -9999 0 -0.3 92 92
AKT1 -0.22 0.24 -9999 0 -0.64 4 4
IKBKG -0.14 0.16 -9999 0 -0.32 48 48
MS4A2 -0.39 0.32 -9999 0 -0.64 137 137
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.015 0.002 -9999 0 -10000 0 0
MAP3K1 -0.21 0.24 -9999 0 -0.59 35 35
mol:Ca2+ -0.21 0.22 -9999 0 -0.43 93 93
LYN 0.007 0.009 -9999 0 -10000 0 0
CBLB -0.24 0.23 -9999 0 -0.48 88 88
SHC1 0.017 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.036 0.12 -9999 0 -0.38 21 21
positive regulation of cell migration -0.013 0.12 -9999 0 -0.47 13 13
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.3 0.28 -9999 0 -0.6 88 88
PTPN13 -0.34 0.29 -9999 0 -0.59 111 111
PTPN11 0.006 0.051 -9999 0 -0.75 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.16 0.2 -9999 0 -0.39 14 14
SYK 0.004 0.05 -9999 0 -0.73 1 1
GRB2 0.016 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.34 0.28 -9999 0 -0.62 99 99
LAT -0.24 0.24 -9999 0 -0.49 88 88
PAK2 -0.24 0.28 -9999 0 -0.51 96 96
NFATC2 -0.1 0.078 -9999 0 -10000 0 0
HRAS -0.28 0.3 -9999 0 -0.57 96 96
GAB2 0.017 0 -9999 0 -10000 0 0
PLA2G1B 0.064 0.028 -9999 0 -10000 0 0
Fc epsilon R1 -0.4 0.31 -9999 0 -0.7 102 102
Antigen/IgE/Fc epsilon R1 -0.37 0.29 -9999 0 -0.64 102 102
mol:GDP -0.3 0.33 -9999 0 -0.62 96 96
JUN 0 0.11 -9999 0 -0.72 5 5
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.015 0.002 -9999 0 -10000 0 0
FOS -0.081 0.23 -9999 0 -0.64 33 33
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.28 0.22 -9999 0 -0.52 88 88
CHUK -0.14 0.16 -9999 0 -0.32 48 48
KLRG1 -0.22 0.22 -9999 0 -0.46 88 88
VAV1 -0.27 0.27 -9999 0 -0.54 90 90
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.24 0.23 -9999 0 -0.48 88 88
negative regulation of mast cell degranulation -0.22 0.18 -9999 0 -0.43 88 88
BTK -0.34 0.34 -9999 0 -0.66 95 95
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.43 0.42 -9999 0 -0.86 98 98
GAB2/PI3K/SHP2 -0.27 0.23 -9999 0 -0.54 88 88
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.28 0.28 -9999 0 -0.6 88 88
RAF1 0.053 0.033 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.41 0.35 -9999 0 -0.78 96 96
FCER1G 0.026 0.011 -9999 0 -10000 0 0
FCER1A -0.29 0.33 -9999 0 -0.65 102 102
Antigen/IgE/Fc epsilon R1/Fyn -0.34 0.28 -9999 0 -0.65 88 88
MAPK3 0.062 0.03 -9999 0 -10000 0 0
MAPK1 0.062 0.029 -9999 0 -10000 0 0
NFKB1 0.017 0 -9999 0 -10000 0 0
MAPK8 -0.057 0.12 -9999 0 -0.66 4 4
DUSP1 -0.039 0.18 -9999 0 -0.64 19 19
NF-kappa-B/RelA -0.096 0.072 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.25 0.24 -9999 0 -0.49 88 88
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.27 0.24 -9999 0 -0.52 84 84
FER -0.25 0.24 -9999 0 -0.5 93 93
RELA 0.017 0 -9999 0 -10000 0 0
ITK -0.057 0.044 -9999 0 -10000 0 0
SOS1 0.017 0 -9999 0 -10000 0 0
PLCG1 -0.32 0.35 -9999 0 -0.65 99 99
cytokine secretion -0.07 0.052 -9999 0 -10000 0 0
SPHK1 -0.29 0.25 -9999 0 -0.5 109 109
PTK2 -0.26 0.24 -9999 0 -0.52 88 88
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.36 0.29 -9999 0 -0.65 99 99
EDG1 -0.013 0.12 -9999 0 -0.48 13 13
mol:DAG -0.3 0.31 -9999 0 -0.61 96 96
MAP2K2 0.058 0.029 -9999 0 -10000 0 0
MAP2K1 0.058 0.029 -9999 0 -10000 0 0
MAP2K7 0.017 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.21 0.18 -9999 0 -0.41 88 88
MAP2K4 -0.006 0.14 -9999 0 -1 4 4
Fc epsilon R1/FcgammaRIIB -0.44 0.37 -9999 0 -0.82 96 96
mol:Choline -0.29 0.28 -9999 0 -0.59 88 88
SHC/Grb2/SOS1 -0.23 0.19 -9999 0 -0.44 88 88
FYN 0.014 0.044 -9999 0 -0.64 1 1
DOK1 0.014 0.05 -9999 0 -0.72 1 1
PXN -0.23 0.23 -9999 0 -0.47 88 88
HCLS1 -0.25 0.26 -9999 0 -0.52 88 88
PRKCB -0.22 0.22 -9999 0 -0.43 93 93
FCGR2B -0.13 0.27 -9999 0 -0.64 50 50
IGHE -0.008 0.008 -9999 0 -10000 0 0
KLRG1/SHIP -0.23 0.19 -9999 0 -0.44 88 88
LCP2 0.003 0.096 -9999 0 -0.7 4 4
PLA2G4A -0.33 0.29 -9999 0 -0.57 114 114
RASA1 0.01 0.07 -9999 0 -0.72 2 2
mol:Phosphatidic acid -0.29 0.28 -9999 0 -0.59 88 88
IKK complex -0.091 0.13 -9999 0 -0.25 5 5
WIPF1 0.014 0.044 -9999 0 -0.64 1 1
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer -0.032 0.11 -10000 0 -0.42 17 17
fibroblast growth factor receptor signaling pathway -0.032 0.11 -10000 0 -0.42 17 17
LAMA1 0.017 0 -10000 0 -10000 0 0
PRNP 0.017 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.28 0.24 -10000 0 -0.47 132 132
SMAD2 0.03 0.084 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ -0.017 0.087 -10000 0 -0.47 8 8
GPC1/Laminin alpha1 -0.019 0.1 -10000 0 -0.54 8 8
TDGF1 -0.48 0.35 -10000 0 -0.72 148 148
CRIPTO/GPC1 -0.38 0.27 -10000 0 -0.55 151 151
APP/GPC1 -0.019 0.1 -10000 0 -0.54 8 8
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.31 0.24 -10000 0 -0.47 151 151
FLT1 -0.02 0.16 -10000 0 -0.72 11 11
GPC1/TGFB/TGFBR1/TGFBR2 -0.016 0.085 -10000 0 -0.46 8 8
SERPINC1 0.014 0.05 -10000 0 -0.72 1 1
FYN -0.31 0.24 -10000 0 -0.47 152 152
FGR -0.31 0.24 -10000 0 -0.47 151 151
positive regulation of MAPKKK cascade -0.26 0.22 -10000 0 -0.54 53 53
SLIT2 -0.35 0.32 -10000 0 -0.64 126 126
GPC1/NRG -0.019 0.1 -10000 0 -0.54 8 8
NRG1 0.017 0 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.081 0.2 -10000 0 -0.53 34 34
LYN -0.31 0.24 -10000 0 -0.47 151 151
mol:Spermine -0.005 0.11 -10000 0 -0.55 8 8
cell growth -0.032 0.11 -10000 0 -0.42 17 17
BMP signaling pathway 0.01 0.14 0.72 8 -10000 0 8
SRC -0.31 0.24 -10000 0 -0.47 151 151
TGFBR1 0.017 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.12 0.27 -10000 0 -0.66 45 45
GPC1 -0.01 0.14 -10000 0 -0.72 8 8
TGFBR1 (dimer) 0.017 0 -10000 0 -10000 0 0
VEGFA -0.053 0.22 -10000 0 -0.72 21 21
BLK -0.41 0.31 -10000 0 -0.56 167 167
HCK -0.34 0.27 -10000 0 -0.5 157 157
FGF2 -0.01 0.13 -10000 0 -0.64 9 9
FGFR1 0.017 0 -10000 0 -10000 0 0
VEGFR1 homodimer -0.02 0.16 -10000 0 -0.72 11 11
TGFBR2 0.017 0 -10000 0 -10000 0 0
cell death -0.019 0.1 -10000 0 -0.54 8 8
ATIII/GPC1 -0.022 0.11 -10000 0 -0.54 9 9
PLA2G2A/GPC1 -0.12 0.22 -10000 0 -0.52 50 50
LCK -0.31 0.25 -10000 0 -0.47 152 152
neuron differentiation -0.019 0.1 -10000 0 -0.54 8 8
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.017 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.017 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.54 0.46 -9999 0 -1.1 59 59
HDAC7 -0.003 0.011 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.38 0.29 -9999 0 -0.83 39 39
SMAD4 0.01 0.075 -9999 0 -0.63 3 3
ID2 -0.53 0.45 -9999 0 -1.1 56 56
AP1 -0.081 0.18 -9999 0 -0.48 37 37
ABCG2 -0.82 0.46 -9999 0 -1.2 109 109
HIF1A -0.075 0.09 -9999 0 -0.87 2 2
TFF3 -0.54 0.45 -9999 0 -1.1 58 58
GATA2 0.018 0.005 -9999 0 -10000 0 0
AKT1 -0.059 0.058 -9999 0 -10000 0 0
response to hypoxia -0.089 0.064 -9999 0 -10000 0 0
MCL1 -0.53 0.45 -9999 0 -1.1 56 56
NDRG1 -0.58 0.48 -9999 0 -1.2 68 68
SERPINE1 -0.59 0.49 -9999 0 -1.2 74 74
FECH -0.54 0.45 -9999 0 -1.1 56 56
FURIN -0.53 0.45 -9999 0 -1.1 56 56
NCOA2 0.019 0.002 -9999 0 -10000 0 0
EP300 -0.053 0.078 -9999 0 -10000 0 0
HMOX1 -0.57 0.48 -9999 0 -1.2 63 63
BHLHE40 -0.54 0.45 -9999 0 -1.1 70 70
BHLHE41 -0.54 0.45 -9999 0 -1.1 70 70
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.072 0.085 -9999 0 -0.54 3 3
ENG -0.04 0.1 -9999 0 -0.51 2 2
JUN 0.001 0.11 -9999 0 -0.72 5 5
RORA -0.54 0.46 -9999 0 -1.2 56 56
ABCB1 -0.6 0.63 -9999 0 -1.3 94 94
TFRC -0.54 0.46 -9999 0 -1.2 57 57
CXCR4 -0.55 0.47 -9999 0 -1.2 58 58
TF -0.53 0.45 -9999 0 -1.1 57 57
CITED2 -0.53 0.45 -9999 0 -1.1 56 56
HIF1A/ARNT -0.63 0.53 -9999 0 -1.2 78 78
LDHA -0.047 0.043 -9999 0 -10000 0 0
ETS1 -0.53 0.45 -9999 0 -1.1 57 57
PGK1 -0.55 0.46 -9999 0 -1.2 60 60
NOS2 -0.54 0.45 -9999 0 -1.1 70 70
ITGB2 -0.54 0.46 -9999 0 -1.1 59 59
ALDOA -0.53 0.45 -9999 0 -1.1 57 57
Cbp/p300/CITED2 -0.52 0.43 -9999 0 -1.1 57 57
FOS -0.08 0.23 -9999 0 -0.64 33 33
HK2 -0.53 0.45 -9999 0 -1.1 57 57
SP1 0.009 0.036 -9999 0 -10000 0 0
GCK -0.072 0.11 -9999 0 -10000 0 0
HK1 -0.53 0.45 -9999 0 -1.1 58 58
NPM1 -0.53 0.45 -9999 0 -1.1 57 57
EGLN1 -0.53 0.45 -9999 0 -1.1 56 56
CREB1 0.028 0 -9999 0 -10000 0 0
PGM1 -0.58 0.47 -9999 0 -1.1 68 68
SMAD3 0.013 0.061 -9999 0 -0.63 2 2
EDN1 -0.099 0.3 -9999 0 -1.3 11 11
IGFBP1 -0.56 0.48 -9999 0 -1.2 66 66
VEGFA -0.37 0.34 -9999 0 -0.99 28 28
HIF1A/JAB1 -0.034 0.066 -9999 0 -0.67 2 2
CP -0.59 0.5 -9999 0 -1.2 66 66
CXCL12 -0.77 0.48 -9999 0 -1.2 101 101
COPS5 0.019 0.001 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.01 0.068 -9999 0 -0.46 5 5
BNIP3 -0.58 0.48 -9999 0 -1.2 71 71
EGLN3 -0.65 0.51 -9999 0 -1.2 77 77
CA9 -0.7 0.48 -9999 0 -1.1 98 98
TERT -0.53 0.45 -9999 0 -1.1 56 56
ENO1 -0.54 0.45 -9999 0 -1.1 57 57
PFKL -0.53 0.45 -9999 0 -1.1 56 56
NCOA1 0.011 0.062 -9999 0 -0.63 2 2
ADM -0.54 0.45 -9999 0 -1.1 56 56
ARNT -0.068 0.049 -9999 0 -10000 0 0
HNF4A 0.023 0 -9999 0 -10000 0 0
ADFP -0.55 0.46 -9999 0 -1.2 61 61
SLC2A1 -0.38 0.34 -9999 0 -0.92 38 38
LEP -0.54 0.45 -9999 0 -1.1 57 57
HIF1A/ARNT/Cbp/p300 -0.4 0.3 -9999 0 -0.83 49 49
EPO -0.24 0.22 -9999 0 -0.82 2 2
CREBBP -0.053 0.078 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/HDAC7 -0.41 0.33 -9999 0 -0.85 56 56
PFKFB3 -0.55 0.47 -9999 0 -1.2 61 61
NT5E -0.55 0.46 -9999 0 -1.2 57 57
Reelin signaling pathway

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
CDK5R1/CDK5 -0.005 0.051 -9999 0 -0.54 2 2
VLDLR -0.12 0.27 -9999 0 -0.64 48 48
CRKL 0.017 0 -9999 0 -10000 0 0
LRPAP1 0.017 0 -9999 0 -10000 0 0
FYN 0.014 0.044 -9999 0 -0.64 1 1
ITGA3 0.014 0.05 -9999 0 -0.72 1 1
RELN/VLDLR/Fyn -0.085 0.16 -9999 0 -0.4 48 48
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.003 0.036 -9999 0 -10000 0 0
AKT1 -0.01 0.12 -9999 0 -10000 0 0
MAP2K7 0.017 0 -9999 0 -10000 0 0
RAPGEF1 0.017 0 -9999 0 -10000 0 0
DAB1 0.017 0 -9999 0 -10000 0 0
RELN/LRP8/DAB1 -0.37 0.14 -9999 0 -0.42 196 196
LRPAP1/LRP8 -0.48 0.17 -9999 0 -0.54 196 196
RELN/LRP8/DAB1/Fyn -0.34 0.13 -9999 0 -0.39 196 196
DAB1/alpha3/beta1 Integrin -0.36 0.17 -9999 0 -0.66 44 44
long-term memory -0.37 0.18 -9999 0 -0.74 30 30
DAB1/LIS1 -0.38 0.18 -9999 0 -0.68 43 43
DAB1/CRLK/C3G -0.36 0.17 -9999 0 -0.66 43 43
PIK3CA 0.017 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.38 0.18 -9999 0 -0.68 43 43
ARHGEF2 0.014 0.05 -9999 0 -0.72 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A 0.017 0 -9999 0 -10000 0 0
CDK5R1 0.017 0 -9999 0 -10000 0 0
RELN 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.017 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.4 0.15 -9999 0 -0.46 196 196
GRIN2A/RELN/LRP8/DAB1/Fyn -0.33 0.12 -9999 0 -0.72 1 1
MAPK8 0.017 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.076 0.15 -9999 0 -0.35 48 48
ITGB1 0.014 0.05 -9999 0 -0.72 1 1
MAP1B -0.38 0.22 -9999 0 -0.71 53 53
RELN/LRP8 -0.4 0.15 -9999 0 -0.46 196 196
GRIN2B/RELN/LRP8/DAB1/Fyn -0.39 0.19 -9999 0 -0.78 30 30
PI3K 0 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.005 0.051 -9999 0 -0.54 2 2
RAP1A -0.33 0.18 -9999 0 -0.6 43 43
PAFAH1B1 0.017 0 -9999 0 -10000 0 0
MAPK8IP1 0.014 0.05 -9999 0 -0.72 1 1
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.086 0.26 -9999 0 -0.72 31 31
NCK2 0.017 0 -9999 0 -10000 0 0
neuron differentiation -0.12 0.069 -9999 0 -0.36 2 2
neuron adhesion -0.3 0.17 -9999 0 -0.56 44 44
LRP8 -0.64 0.24 -9999 0 -0.72 196 196
GSK3B -0.001 0.12 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/Fyn -0.071 0.14 -9999 0 -0.52 2 2
MAP3K11 0.017 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.023 0.12 -9999 0 -10000 0 0
CDK5 0.01 0.07 -9999 0 -0.72 2 2
MAPT 0.014 0.026 -9999 0 -10000 0 0
neuron migration -0.25 0.16 -9999 0 -0.5 43 43
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.12 0.069 -9999 0 -0.36 2 2
RELN/VLDLR -0.44 0.2 -9999 0 -0.76 43 43
IL23-mediated signaling events

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.47 0.49 -10000 0 -1.1 56 56
IL23A -0.59 0.52 -10000 0 -1.3 59 59
NF kappa B1 p50/RelA/I kappa B alpha -0.48 0.45 -10000 0 -1.1 63 63
positive regulation of T cell mediated cytotoxicity -0.49 0.51 -10000 0 -1.2 63 63
ITGA3 -0.46 0.45 -10000 0 -1.1 45 45
IL17F -0.27 0.31 -10000 0 -0.77 21 21
IL12B 0.004 0.077 -10000 0 -0.77 2 2
STAT1 (dimer) -0.49 0.52 -10000 0 -1.2 59 59
CD4 -0.42 0.44 -10000 0 -1.1 34 34
IL23 -0.57 0.48 -10000 0 -1.2 60 60
IL23R -0.078 0.24 -10000 0 -1.6 5 5
IL1B -0.55 0.52 -10000 0 -1.3 51 51
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.44 0.47 -10000 0 -1.1 48 48
TYK2 0.006 0.014 -10000 0 -10000 0 0
STAT4 0.014 0.044 -10000 0 -0.64 1 1
STAT3 0.017 0.001 -10000 0 -10000 0 0
IL18RAP -0.11 0.26 -10000 0 -0.63 43 43
IL12RB1 0.006 0.014 -10000 0 -10000 0 0
PIK3CA 0.017 0.001 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.001 0.017 -10000 0 -10000 0 0
IL23R/JAK2 -0.092 0.25 -10000 0 -1.5 5 5
positive regulation of chronic inflammatory response -0.49 0.51 -10000 0 -1.2 63 63
natural killer cell activation 0.006 0.013 0.078 5 -10000 0 5
JAK2 -0.003 0.11 -10000 0 -0.77 4 4
PIK3R1 0.017 0.001 -10000 0 -10000 0 0
NFKB1 0.013 0.003 -10000 0 -10000 0 0
RELA 0.013 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.54 0.45 -10000 0 -1.1 59 59
ALOX12B -0.42 0.44 -10000 0 -1.1 38 38
CXCL1 -0.64 0.48 -10000 0 -1.2 64 64
T cell proliferation -0.49 0.51 -10000 0 -1.2 63 63
NFKBIA 0.013 0.003 -10000 0 -10000 0 0
IL17A -0.21 0.26 -10000 0 -0.62 6 6
PI3K -0.44 0.45 -10000 0 -1 63 63
IFNG -0.038 0.048 0.16 2 -0.12 2 4
STAT3 (dimer) -0.41 0.43 -10000 0 -1.1 46 46
IL18R1 0.012 0.044 -10000 0 -0.63 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.24 0.26 -10000 0 -0.82 12 12
IL18/IL18R -0.095 0.22 -10000 0 -0.44 59 59
macrophage activation -0.031 0.017 -10000 0 -10000 0 0
TNF -0.52 0.48 -10000 0 -1.2 56 56
STAT3/STAT4 -0.46 0.44 -10000 0 -1 63 63
STAT4 (dimer) -0.46 0.49 -10000 0 -1.2 53 53
IL18 -0.059 0.21 -10000 0 -0.64 25 25
IL19 -0.43 0.45 -10000 0 -1.1 47 47
STAT5A (dimer) -0.46 0.49 -10000 0 -1.2 53 53
STAT1 -0.05 0.21 -10000 0 -0.72 20 20
SOCS3 -0.013 0.15 -10000 0 -0.72 9 9
CXCL9 -0.52 0.52 -10000 0 -1.2 64 64
MPO -0.44 0.45 -10000 0 -1.1 50 50
positive regulation of humoral immune response -0.49 0.51 -10000 0 -1.2 63 63
IL23/IL23R/JAK2/TYK2 -0.52 0.56 -10000 0 -1.2 63 63
IL6 -0.58 0.52 -10000 0 -1.2 71 71
STAT5A 0.017 0 -10000 0 -10000 0 0
IL2 0.018 0.011 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.006 0.013 0.078 5 -10000 0 5
CD3E -0.42 0.44 -10000 0 -1.1 35 35
keratinocyte proliferation -0.49 0.51 -10000 0 -1.2 63 63
NOS2 -0.43 0.44 -10000 0 -1 63 63
Osteopontin-mediated 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
IKK alpha homodimer -0.24 0.22 -9999 0 -0.46 50 50
NF kappa B1 p50/RelA/I kappa B alpha -0.23 0.17 -9999 0 -0.46 52 52
alphaV/beta3 Integrin/Osteopontin/Src -0.36 0.26 -9999 0 -0.54 150 150
AP1 -0.26 0.19 -9999 0 -0.62 26 26
ILK -0.25 0.22 -9999 0 -0.46 46 46
bone resorption -0.22 0.17 -9999 0 -0.68 8 8
PTK2B 0.017 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.24 0.17 -9999 0 -0.78 1 1
ITGAV 0.015 0.05 -9999 0 -0.73 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.022 0.11 -9999 0 -0.54 9 9
alphaV/beta3 Integrin/Osteopontin -0.31 0.22 -9999 0 -0.46 150 150
MAP3K1 -0.26 0.22 -9999 0 -0.46 51 51
JUN 0 0.11 -9999 0 -0.72 5 5
MAPK3 -0.25 0.23 -9999 0 -0.52 52 52
MAPK1 -0.25 0.23 -9999 0 -0.51 50 50
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.017 0 -9999 0 -10000 0 0
MAPK8 -0.23 0.21 -9999 0 -0.6 3 3
ITGB3 0.018 0.005 -9999 0 -10000 0 0
NFKBIA -0.23 0.23 -9999 0 -0.52 52 52
FOS -0.081 0.23 -9999 0 -0.64 33 33
CD44 -0.013 0.15 -9999 0 -0.72 9 9
CHUK 0.017 0 -9999 0 -10000 0 0
PLAU -0.3 0.32 -9999 0 -0.8 51 51
NF kappa B1 p50/RelA -0.24 0.18 -9999 0 -0.5 52 52
BCAR1 0.017 0 -9999 0 -10000 0 0
RELA 0.017 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.002 0.037 -9999 0 -0.55 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.26 0.22 -9999 0 -0.46 51 51
VAV3 -0.28 0.27 -9999 0 -0.74 31 31
MAP3K14 -0.26 0.23 -9999 0 -0.5 51 51
ROCK2 0.017 0 -9999 0 -10000 0 0
SPP1 -0.48 0.35 -9999 0 -0.72 150 150
RAC1 0.017 0 -9999 0 -10000 0 0
Rac1/GTP -0.27 0.22 -9999 0 -0.68 31 31
MMP2 -0.19 0.2 -9999 0 -0.64 7 7
Endothelins

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
AKT1 -0.001 0.28 -10000 0 -0.57 23 23
PTK2B 0.017 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.04 0.18 -10000 0 -0.92 3 3
EDN1 0.073 0.19 -10000 0 -0.62 13 13
EDN3 -0.33 0.32 -10000 0 -0.64 117 117
EDN2 -0.49 0.27 -10000 0 -0.64 173 173
HRAS/GDP -0.062 0.19 -10000 0 -0.56 10 10
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.016 0.16 -10000 0 -0.39 10 10
ADCY4 -0.02 0.21 -10000 0 -0.61 6 6
ADCY5 -0.019 0.21 -10000 0 -0.7 4 4
ADCY6 -0.019 0.21 -10000 0 -0.7 4 4
ADCY7 -0.019 0.21 -10000 0 -0.52 11 11
ADCY1 -0.019 0.21 -10000 0 -0.49 16 16
ADCY2 -0.02 0.21 -10000 0 -0.61 6 6
ADCY3 -0.043 0.23 -10000 0 -0.65 11 11
ADCY8 -0.02 0.21 -10000 0 -0.64 5 5
ADCY9 -0.023 0.21 -10000 0 -0.65 6 6
arachidonic acid secretion -0.095 0.25 -10000 0 -0.62 28 28
ETB receptor/Endothelin-1/Gq/GTP -0.006 0.17 -10000 0 -0.58 10 10
GNAO1 0.017 0 -10000 0 -10000 0 0
HRAS 0.015 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.083 0.32 0.34 117 -0.53 23 140
ETA receptor/Endothelin-1/Gs/GTP 0.077 0.3 0.31 118 -0.5 23 141
mol:GTP 0.001 0.005 -10000 0 -10000 0 0
COL3A1 -0.006 0.29 -10000 0 -1 5 5
EDNRB -0.047 0.18 -10000 0 -0.64 18 18
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0 0.27 -10000 0 -0.81 4 4
CYSLTR1 -0.004 0.28 -10000 0 -0.74 7 7
SLC9A1 0.03 0.15 -10000 0 -0.35 3 3
mol:GDP -0.076 0.2 -10000 0 -0.54 16 16
SLC9A3 -0.38 0.36 -10000 0 -0.69 95 95
RAF1 -0.075 0.21 -10000 0 -0.5 25 25
JUN 0.043 0.17 -10000 0 -0.7 1 1
JAK2 -0.01 0.28 -10000 0 -0.58 25 25
mol:IP3 -0.04 0.17 -10000 0 -0.45 12 12
ETA receptor/Endothelin-1 0.082 0.39 0.39 118 -0.65 24 142
PLCB1 -0.2 0.34 -10000 0 -0.72 65 65
PLCB2 0.015 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.3 0.35 -10000 0 -0.54 138 138
FOS -0.13 0.37 -10000 0 -0.96 33 33
Gai/GDP -0.002 0.1 -10000 0 -10000 0 0
CRK 0.014 0.044 -10000 0 -0.63 1 1
mol:Ca ++ -0.064 0.27 -10000 0 -0.61 22 22
BCAR1 0.017 0 -10000 0 -10000 0 0
PRKCB1 -0.22 0.24 -10000 0 -0.53 55 55
GNAQ 0.002 0.006 -10000 0 -10000 0 0
GNAZ 0.017 0 -10000 0 -10000 0 0
GNAL 0.017 0 -10000 0 -10000 0 0
Gs family/GDP -0.1 0.14 -10000 0 -0.49 14 14
ETA receptor/Endothelin-1/Gq/GTP 0.024 0.18 -10000 0 -0.51 7 7
MAPK14 -0.029 0.15 -10000 0 -0.44 13 13
TRPC6 0.038 0.18 -10000 0 -1 3 3
GNAI2 0.017 0 -10000 0 -10000 0 0
GNAI3 0.017 0 -10000 0 -10000 0 0
GNAI1 -0.068 0.22 -10000 0 -0.64 29 29
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.043 0.16 -10000 0 -0.45 16 16
ETB receptor/Endothelin-2 -0.4 0.21 -10000 0 -0.49 179 179
ETB receptor/Endothelin-3 -0.28 0.27 -10000 0 -0.51 122 122
ETB receptor/Endothelin-1 0.008 0.22 -10000 0 -0.5 28 28
MAPK3 -0.11 0.32 -10000 0 -0.8 34 34
MAPK1 -0.11 0.32 -10000 0 -0.8 34 34
Rac1/GDP -0.062 0.19 -10000 0 -0.53 12 12
cAMP biosynthetic process 0.017 0.19 -10000 0 -0.57 4 4
MAPK8 0.037 0.17 -10000 0 -0.71 2 2
SRC 0.017 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.003 0.13 -10000 0 -0.44 6 6
p130Cas/CRK/Src/PYK2 -0.069 0.2 -10000 0 -0.58 11 11
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.062 0.19 -10000 0 -0.57 9 9
COL1A2 -0.065 0.38 -10000 0 -0.82 30 30
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.42 0.32 -10000 0 -0.55 178 178
mol:DAG -0.04 0.17 -10000 0 -0.45 12 12
MAP2K2 -0.085 0.25 -10000 0 -0.59 34 34
MAP2K1 -0.085 0.25 -10000 0 -0.59 34 34
EDNRA -0.047 0.35 -10000 0 -0.68 49 49
positive regulation of muscle contraction 0.013 0.24 -10000 0 -0.73 4 4
Gq family/GDP -0.097 0.18 -10000 0 -0.56 17 17
HRAS/GTP -0.072 0.18 -10000 0 -0.51 14 14
PRKCH -0.034 0.17 -10000 0 -0.68 5 5
RAC1 0.017 0 -10000 0 -10000 0 0
PRKCA -0.031 0.17 -10000 0 -0.63 5 5
PRKCB -0.039 0.16 -10000 0 -0.43 12 12
PRKCE -0.028 0.16 -10000 0 -0.63 4 4
PRKCD -0.029 0.16 -10000 0 -0.58 5 5
PRKCG -0.036 0.17 -10000 0 -0.58 7 7
regulation of vascular smooth muscle contraction -0.15 0.43 -10000 0 -1.1 33 33
PRKCQ -0.037 0.18 -10000 0 -0.58 9 9
PLA2G4A -0.1 0.27 -10000 0 -0.69 28 28
GNA14 -0.009 0.13 -10000 0 -0.64 9 9
GNA15 -0.006 0.13 -10000 0 -0.72 7 7
GNA12 0.017 0 -10000 0 -10000 0 0
GNA11 -0.001 0.11 -10000 0 -0.63 6 6
Rac1/GTP 0.084 0.32 0.34 118 -0.52 23 141
MMP1 -0.53 0.2 -10000 0 -0.6 197 197
Canonical Wnt 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
HDAC1 0.082 0.052 -10000 0 -10000 0 0
AES 0.071 0.044 -10000 0 -10000 0 0
FBXW11 0.017 0 -10000 0 -10000 0 0
mol:GTP 0.003 0.002 -10000 0 -10000 0 0
LRP6/FZD1 -0.002 0.036 -10000 0 -0.54 1 1
SMAD4 0.008 0.075 -10000 0 -0.64 3 3
DKK2 -0.27 0.36 -10000 0 -0.72 87 87
TLE1 0.069 0.044 -10000 0 -10000 0 0
MACF1 0.018 0.001 -10000 0 -10000 0 0
CTNNB1 0.094 0.11 0.31 10 -10000 0 10
WIF1 -0.092 0.26 -10000 0 -0.72 33 33
beta catenin/RanBP3 0.31 0.2 0.49 106 -10000 0 106
KREMEN2 -0.13 0.29 -10000 0 -0.72 43 43
DKK1 -0.17 0.32 -10000 0 -0.72 56 56
beta catenin/beta TrCP1 0.1 0.099 0.31 9 -10000 0 9
FZD1 0.016 0.003 -10000 0 -10000 0 0
AXIN2 -0.45 0.32 -10000 0 -0.68 141 141
AXIN1 0.019 0.001 -10000 0 -10000 0 0
RAN 0.016 0.05 -10000 0 -0.72 1 1
Axin1/APC/GSK3/beta catenin 0.062 0.058 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.1 0.12 0.31 2 -10000 0 2
Axin1/APC/GSK3 0.14 0.084 0.24 24 -10000 0 24
Axin1/APC/GSK3/beta catenin/Macf1 0.092 0.07 -10000 0 -10000 0 0
HNF1A 0.072 0.046 -10000 0 -10000 0 0
CTBP1 0.073 0.047 -10000 0 -10000 0 0
MYC -0.42 0.33 -10000 0 -0.69 126 126
RANBP3 0.019 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.27 0.28 -10000 0 -0.52 112 112
NKD1 -0.54 0.32 -10000 0 -0.72 167 167
TCF4 0.075 0.047 -10000 0 -10000 0 0
TCF3 0.069 0.065 -10000 0 -0.61 1 1
WNT1/LRP6/FZD1/Axin1 0.001 0.029 -10000 0 -0.41 1 1
Ran/GTP 0.008 0.039 -10000 0 -0.55 1 1
CtBP/CBP/TCF/TLE1/AES 0.37 0.26 0.6 105 -10000 0 105
LEF1 -0.083 0.31 -10000 0 -0.66 48 48
DVL1 0.085 0.049 -10000 0 -10000 0 0
CSNK2A1 0.018 0.001 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.076 0.12 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.2 0.26 -10000 0 -0.51 88 88
LRP6 0.013 0.05 -10000 0 -0.72 1 1
CSNK1A1 0.082 0.051 -10000 0 -10000 0 0
NLK 0.003 0.007 -10000 0 -10000 0 0
CCND1 -0.24 0.25 -10000 0 -0.8 25 25
WNT1 0.016 0.003 -10000 0 -10000 0 0
GSK3A 0.017 0.001 -10000 0 -10000 0 0
GSK3B 0.013 0.05 -10000 0 -0.73 1 1
FRAT1 0.012 0.044 -10000 0 -0.63 1 1
PPP2R5D 0.27 0.14 0.35 167 -10000 0 167
APC 0.034 0.078 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.044 0.093 0.26 33 -10000 0 33
CREBBP 0.072 0.046 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.2 0.19 -9999 0 -0.78 1 1
SMAD6-7/SMURF1 -0.014 0.078 -9999 0 -0.45 7 7
NOG 0.017 0 -9999 0 -10000 0 0
SMAD9 -0.1 0.19 -9999 0 -0.54 31 31
SMAD4 0.008 0.075 -9999 0 -0.64 3 3
SMAD5 -0.15 0.19 -9999 0 -0.48 33 33
BMP7/USAG1 -0.45 0.31 -9999 0 -0.61 164 164
SMAD5/SKI -0.13 0.18 -9999 0 -0.49 22 22
SMAD1 0.023 0.083 -9999 0 -0.55 3 3
BMP2 -0.095 0.24 -9999 0 -0.64 38 38
SMAD1/SMAD1/SMAD4 -0.02 0.076 -9999 0 -0.47 1 1
BMPR1A 0.017 0 -9999 0 -10000 0 0
BMPR1B 0.007 0.085 -9999 0 -0.72 3 3
BMPR1A-1B/BAMBI -0.066 0.16 -9999 0 -0.46 32 32
AHSG 0.017 0 -9999 0 -10000 0 0
CER1 0.014 0.05 -9999 0 -0.72 1 1
BMP2-4/CER1 -0.22 0.28 -9999 0 -0.51 93 93
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.038 0.14 -9999 0 -0.4 4 4
BMP2-4 (homodimer) -0.25 0.31 -9999 0 -0.59 93 93
RGMB 0 0.11 -9999 0 -0.72 5 5
BMP6/BMPR2/BMPR1A-1B -0.14 0.17 -9999 0 -0.76 1 1
RGMA 0.005 0.087 -9999 0 -0.64 4 4
SMURF1 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.062 0.15 -9999 0 -0.37 24 24
BMP2-4/USAG1 -0.36 0.34 -9999 0 -0.59 138 138
SMAD6/SMURF1/SMAD5 -0.13 0.18 -9999 0 -0.49 22 22
SOSTDC1 -0.25 0.32 -9999 0 -0.64 90 90
BMP7/BMPR2/BMPR1A-1B -0.22 0.21 -9999 0 -0.41 117 117
SKI 0.017 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.24 0.32 -9999 0 -0.63 86 86
HFE2 0.017 0 -9999 0 -10000 0 0
ZFYVE16 0.017 0 -9999 0 -10000 0 0
MAP3K7 0.017 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.21 0.27 -9999 0 -0.51 93 93
SMAD5/SMAD5/SMAD4 -0.14 0.18 -9999 0 -0.49 23 23
MAPK1 0.014 0.044 -9999 0 -0.64 1 1
TAK1/TAB family -0.063 0.089 -9999 0 -10000 0 0
BMP7 (homodimer) -0.36 0.37 -9999 0 -0.72 115 115
NUP214 0.017 0 -9999 0 -10000 0 0
BMP6/FETUA -0.18 0.22 -9999 0 -0.46 86 86
SMAD1/SKI 0.032 0.079 -9999 0 -0.51 3 3
SMAD6 -0.003 0.12 -9999 0 -0.72 6 6
CTDSP2 0.008 0.075 -9999 0 -0.64 3 3
BMP2-4/FETUA -0.21 0.27 -9999 0 -0.51 93 93
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
GREM1 -0.033 0.18 -9999 0 -0.72 15 15
BMPR2 (homodimer) 0.017 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.002 0.031 -9999 0 -0.46 1 1
BMPR1A-1B (homodimer) -0.007 0.062 -9999 0 -0.54 3 3
CHRDL1 0.011 0.066 -9999 0 -0.68 2 2
ENDOFIN/SMAD1 0.032 0.079 -9999 0 -0.51 3 3
SMAD6-7/SMURF1/SMAD1 -0.013 0.085 -9999 0 -0.53 1 1
SMAD6/SMURF1 0.017 0 -9999 0 -10000 0 0
BAMBI -0.08 0.25 -9999 0 -0.72 29 29
SMURF2 -0.03 0.18 -9999 0 -0.72 14 14
BMP2-4/CHRDL1 -0.22 0.28 -9999 0 -0.51 94 94
BMP2-4/GREM1 -0.24 0.3 -9999 0 -0.54 99 99
SMAD7 0.014 0.044 -9999 0 -0.64 1 1
SMAD8A/SMAD8A/SMAD4 -0.07 0.19 -9999 0 -0.5 32 32
SMAD1/SMAD6 0.032 0.079 -9999 0 -0.51 3 3
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.37 0.37 -9999 0 -0.72 115 115
BMP6 -0.24 0.32 -9999 0 -0.64 86 86
MAP3K7IP2 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.04 0.13 -9999 0 -0.32 24 24
PPM1A 0.017 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.007 0.13 -9999 0 -0.63 3 3
SMAD7/SMURF1 -0.002 0.031 -9999 0 -0.46 1 1
CTDSPL 0.011 0.062 -9999 0 -0.64 2 2
PPP1CA 0.014 0.05 -9999 0 -0.72 1 1
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.017 0 -9999 0 -10000 0 0
PPP1R15A 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.055 0.14 -9999 0 -0.37 23 23
CHRD 0.017 0 -9999 0 -10000 0 0
BMPR2 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.065 0.16 -9999 0 -0.4 24 24
BMP4 -0.22 0.35 -9999 0 -0.72 73 73
FST 0.017 0 -9999 0 -10000 0 0
BMP2-4/NOG -0.21 0.27 -9999 0 -0.51 93 93
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.2 0.19 -9999 0 -0.78 1 1
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.24 0.22 -9999 0 -0.74 7 7
CRP -0.24 0.22 -9999 0 -0.73 6 6
cell cycle arrest -0.28 0.24 -9999 0 -0.74 22 22
TIMP1 -0.38 0.27 -9999 0 -0.67 77 77
IL6ST 0.012 0.011 -9999 0 -10000 0 0
Rac1/GDP -0.28 0.21 -9999 0 -0.52 67 67
AP1 -0.058 0.15 -9999 0 -0.65 2 2
GAB2 0.021 0.008 -9999 0 -10000 0 0
TNFSF11 -0.3 0.28 -9999 0 -0.81 31 31
HSP90B1 -0.024 0.093 -9999 0 -0.58 4 4
GAB1 0.013 0.062 -9999 0 -0.63 2 2
MAPK14 -0.23 0.22 -9999 0 -0.6 28 28
AKT1 0.065 0.027 -9999 0 -10000 0 0
FOXO1 0.058 0.075 -9999 0 -0.46 1 1
MAP2K6 -0.26 0.22 -9999 0 -0.55 58 58
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
MAP2K4 -0.28 0.22 -9999 0 -0.6 42 42
MITF -0.26 0.2 -9999 0 -0.53 54 54
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.017 0 -9999 0 -10000 0 0
A2M -0.16 0.51 -9999 0 -1.5 29 29
CEBPB 0.008 0.12 -9999 0 -0.71 6 6
GRB2/SOS1/GAB family/SHP2 -0.064 0.092 -9999 0 -10000 0 0
STAT3 -0.29 0.26 -9999 0 -0.78 22 22
STAT1 -0.047 0.09 -9999 0 -0.33 19 19
CEBPD -0.24 0.22 -9999 0 -0.68 14 14
PIK3CA 0.019 0 -9999 0 -10000 0 0
PI3K 0.008 0.013 -9999 0 -10000 0 0
JUN 0 0.11 -9999 0 -0.72 5 5
PIAS3/MITF -0.24 0.2 -9999 0 -0.5 55 55
MAPK11 -0.23 0.22 -9999 0 -0.68 19 19
STAT3 (dimer)/FOXO1 -0.22 0.22 -9999 0 -0.69 14 14
GRB2/SOS1/GAB family -0.22 0.18 -9999 0 -0.52 24 24
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.29 0.22 -9999 0 -0.54 75 75
GRB2 0.019 0.005 -9999 0 -10000 0 0
JAK2 0.004 0.098 -9999 0 -0.72 4 4
LBP -0.18 0.19 -9999 0 -0.72 5 5
PIK3R1 0.018 0 -9999 0 -10000 0 0
JAK1 0.013 0.01 -9999 0 -10000 0 0
MYC -0.4 0.3 -9999 0 -0.75 59 59
FGG -0.24 0.22 -9999 0 -0.77 6 6
macrophage differentiation -0.28 0.24 -9999 0 -0.74 22 22
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.38 0.27 -9999 0 -0.74 62 62
JUNB -0.24 0.21 -9999 0 -0.71 7 7
FOS -0.081 0.23 -9999 0 -0.64 33 33
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.29 0.21 -9999 0 -0.53 71 71
STAT1/PIAS1 -0.26 0.19 -9999 0 -0.49 59 59
GRB2/SOS1/GAB family/SHP2/PI3K 0.047 0.032 -9999 0 -10000 0 0
STAT3 (dimer) -0.29 0.26 -9999 0 -0.78 22 22
PRKCD -0.27 0.22 -9999 0 -0.61 36 36
IL6R -0.34 0.33 -9999 0 -0.64 122 122
SOCS3 -0.21 0.22 -9999 0 -0.8 12 12
gp130 (dimer)/JAK1/JAK1/LMO4 -0.003 0.095 -9999 0 -0.45 8 8
Rac1/GTP -0.29 0.2 -9999 0 -0.51 78 78
HCK -0.044 0.19 -9999 0 -0.63 21 21
MAPKKK cascade -0.014 0.079 -9999 0 -10000 0 0
bone resorption -0.28 0.27 -9999 0 -0.76 31 31
IRF1 -0.25 0.22 -9999 0 -0.78 8 8
mol:GDP -0.29 0.22 -9999 0 -0.54 72 72
SOS1 0.02 0.008 -9999 0 -10000 0 0
VAV1 -0.3 0.22 -9999 0 -0.55 72 72
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.3 0.26 -9999 0 -0.64 61 61
PTPN11 -0.017 0.026 -9999 0 -10000 0 0
IL6/IL6RA -0.49 0.32 -9999 0 -0.63 173 173
gp130 (dimer)/TYK2/TYK2/LMO4 -0.008 0.092 -9999 0 -0.45 8 8
gp130 (dimer)/JAK2/JAK2/LMO4 -0.016 0.13 -9999 0 -0.57 10 10
IL6 -0.33 0.37 -9999 0 -0.73 103 103
PIAS3 0.014 0.05 -9999 0 -0.72 1 1
PTPRE 0.015 0.05 -9999 0 -0.71 1 1
PIAS1 0.017 0 -9999 0 -10000 0 0
RAC1 0.016 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.27 0.19 -9999 0 -0.52 60 60
LMO4 -0.017 0.14 -9999 0 -0.71 9 9
STAT3 (dimer)/PIAS3 -0.29 0.22 -9999 0 -0.72 24 24
MCL1 0.072 0.026 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.017 0 -9999 0 -10000 0 0
GNAT1/GTP 0 0 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.29 0.18 -9999 0 -0.4 160 160
PDE6G/GNAT1/GTP 0 0 -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 0.017 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel -0.25 0.22 -9999 0 -0.61 44 44
mol:Na + -0.14 0.16 -9999 0 -0.62 7 7
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.15 0.2 -9999 0 -0.54 9 9
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.14 0.16 -9999 0 -0.64 7 7
CNGB1 0.017 0 -9999 0 -10000 0 0
RDH5 -0.16 0.29 -9999 0 -0.64 59 59
SAG -0.45 0.29 -9999 0 -0.64 160 160
mol:Ca2+ -0.094 0.18 -9999 0 -0.59 7 7
Na + (4 Units) -0.13 0.14 -9999 0 -0.57 7 7
RGS9 -0.2 0.31 -9999 0 -0.64 74 74
GNB1/GNGT1 -0.24 0.27 -9999 0 -0.54 98 98
GNAT1/GDP -0.12 0.17 -9999 0 -0.72 2 2
GUCY2D 0.017 0 -9999 0 -10000 0 0
GNGT1 -0.31 0.37 -9999 0 -0.72 98 98
GUCY2F 0.008 0.079 -9999 0 -0.66 3 3
GNB5 0.007 0.085 -9999 0 -0.72 3 3
mol:GMP (4 units) -0.1 0.18 -9999 0 -10000 0 0
mol:11-cis-retinal -0.16 0.29 -9999 0 -0.63 59 59
mol:cGMP -0.019 0.08 -9999 0 -10000 0 0
GNB1 0.017 0 -9999 0 -10000 0 0
Rhodopsin -0.12 0.2 -9999 0 -0.46 59 59
SLC24A1 0.017 0 -9999 0 -10000 0 0
CNGA1 -0.29 0.33 -9999 0 -0.64 104 104
Metarhodopsin II 0 0 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.016 0.078 -9999 0 -0.41 7 7
RGS9BP -0.003 0.12 -9999 0 -0.72 6 6
Metarhodopsin II/Transducin -0.08 0.13 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.016 0.08 -9999 0 -0.4 9 9
PDE6A/B -0.18 0.23 -9999 0 -0.46 88 88
mol:Pi -0.15 0.2 -9999 0 -0.53 9 9
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.18 0.21 -9999 0 -0.42 98 98
PDE6B 0.017 0 -9999 0 -10000 0 0
PDE6A -0.24 0.32 -9999 0 -0.64 88 88
PDE6G 0.017 0 -9999 0 -10000 0 0
RHO 0.017 0 -9999 0 -10000 0 0
PDE6 -0.23 0.23 -9999 0 -0.65 37 37
GUCA1A 0.014 0.05 -9999 0 -0.72 1 1
GC2/GCAP Family -0.021 0.088 -9999 0 -0.41 8 8
GUCA1C 0.004 0.093 -9999 0 -0.68 4 4
GUCA1B 0.004 0.098 -9999 0 -0.72 4 4
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.34 0.52 -10000 0 -1.2 39 39
STAT6 (cleaved dimer) -0.44 0.47 -10000 0 -1.1 65 65
IGHG1 -0.1 0.2 -10000 0 -0.55 3 3
IGHG3 -0.34 0.49 -10000 0 -1 58 58
AKT1 -0.14 0.3 -10000 0 -0.68 19 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.11 0.25 -10000 0 -0.71 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.28 -10000 0 -0.7 11 11
THY1 -0.37 0.55 -10000 0 -1.2 44 44
MYB 0.011 0.062 -10000 0 -0.64 2 2
HMGA1 0.017 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.24 0.37 -10000 0 -0.82 37 37
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.15 0.28 -10000 0 -0.67 13 13
SP1 0.023 0.013 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.03 0.024 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.42 0.46 -10000 0 -1.1 62 62
SOCS1 -0.21 0.36 -10000 0 -0.75 31 31
SOCS3 -0.19 0.33 -10000 0 -0.82 22 22
FCER2 -0.28 0.45 -10000 0 -1.1 29 29
PARP14 0.012 0.07 -10000 0 -0.72 2 2
CCL17 -0.36 0.54 -10000 0 -1.2 39 39
GRB2 0.017 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.1 0.23 -10000 0 -0.76 3 3
T cell proliferation -0.34 0.52 -10000 0 -1.1 46 46
IL4R/JAK1 -0.34 0.51 -10000 0 -1.2 41 41
EGR2 -0.36 0.57 -10000 0 -1.2 46 46
JAK2 -0.001 0.1 -10000 0 -0.74 4 4
JAK3 0.016 0.014 -10000 0 -10000 0 0
PIK3R1 0.017 0 -10000 0 -10000 0 0
JAK1 0.012 0.019 -10000 0 -10000 0 0
COL1A2 -0.17 0.31 -10000 0 -0.77 32 32
CCL26 -0.4 0.55 -10000 0 -1.2 49 49
IL4R -0.36 0.55 -10000 0 -1.2 41 41
PTPN6 0.023 0.015 -10000 0 -10000 0 0
IL13RA2 -0.44 0.56 -10000 0 -1.2 52 52
IL13RA1 0.013 0.03 -10000 0 -10000 0 0
IRF4 -0.34 0.63 -10000 0 -1.5 50 50
ARG1 -0.054 0.18 -10000 0 -0.76 4 4
CBL -0.21 0.35 -10000 0 -0.79 33 33
GTF3A -0.38 0.4 -10000 0 -0.81 101 101
PIK3CA 0.017 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.001 0.093 -10000 0 -0.57 4 4
IRF4/BCL6 -0.35 0.56 -10000 0 -1.4 51 51
CD40LG 0.013 0.067 -10000 0 -0.63 2 2
MAPK14 -0.21 0.35 -10000 0 -0.8 33 33
mitosis -0.13 0.28 -10000 0 -0.64 19 19
STAT6 -0.43 0.55 -10000 0 -1.2 55 55
SPI1 0.024 0.013 -10000 0 -10000 0 0
RPS6KB1 -0.12 0.28 -10000 0 -0.64 14 14
STAT6 (dimer) -0.41 0.57 -10000 0 -1.2 55 55
STAT6 (dimer)/PARP14 -0.36 0.55 -10000 0 -1.1 56 56
mast cell activation 0.007 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.15 0.29 -10000 0 -0.66 21 21
FRAP1 -0.14 0.3 -10000 0 -0.68 19 19
LTA -0.34 0.51 -10000 0 -1.2 40 40
FES 0.011 0.066 -10000 0 -0.68 2 2
T-helper 1 cell differentiation 0.38 0.57 1.2 55 -10000 0 55
CCL11 -0.44 0.64 -10000 0 -1.4 59 59
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.15 0.29 -10000 0 -0.67 19 19
IL2RG 0.007 0.078 -10000 0 -0.64 3 3
IL10 -0.34 0.51 -10000 0 -1.1 42 42
IRS1 0.004 0.098 -10000 0 -0.72 4 4
IRS2 0.014 0.05 -10000 0 -0.72 1 1
IL4 -0.049 0.15 -10000 0 -0.81 1 1
IL5 -0.36 0.54 -10000 0 -1.2 47 47
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.27 0.42 -10000 0 -0.88 38 38
COL1A1 -0.56 0.35 -10000 0 -0.9 86 86
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.34 0.52 -10000 0 -1.2 36 36
IL2R gamma/JAK3 0.017 0.063 -10000 0 -0.48 3 3
TFF3 -0.34 0.53 -10000 0 -1.2 41 41
ALOX15 -0.34 0.52 -10000 0 -1.2 41 41
MYBL1 0.004 0.098 -10000 0 -0.72 4 4
T-helper 2 cell differentiation -0.28 0.42 -10000 0 -0.89 46 46
SHC1 0.017 0 -10000 0 -10000 0 0
CEBPB 0.004 0.12 -10000 0 -0.71 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.13 0.27 -10000 0 -0.73 8 8
mol:PI-3-4-5-P3 -0.14 0.3 -10000 0 -0.68 19 19
PI3K -0.15 0.31 -10000 0 -0.72 19 19
DOK2 0.008 0.075 -10000 0 -0.64 3 3
ETS1 0.025 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.091 0.22 -10000 0 -0.71 3 3
ITGB3 -0.34 0.51 -10000 0 -1.2 38 38
PIGR -0.38 0.58 -10000 0 -1.3 45 45
IGHE 0.027 0.069 -10000 0 -10000 0 0
MAPKKK cascade -0.089 0.21 -10000 0 -0.7 3 3
BCL6 0.009 0.066 -10000 0 -0.68 2 2
OPRM1 -0.34 0.51 -10000 0 -1.2 40 40
RETNLB -0.53 0.72 -10000 0 -1.5 68 68
SELP -0.44 0.65 -10000 0 -1.4 57 57
AICDA -0.38 0.57 -10000 0 -1.2 52 52
Wnt 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
Noncanonical Wnts/FZD -0.12 0.18 -9999 0 -0.47 25 25
FZD6 -0.029 0.18 -9999 0 -0.72 14 14
WNT6 0.014 0.05 -9999 0 -0.72 1 1
WNT4 -0.01 0.13 -9999 0 -0.65 9 9
FZD3 -0.14 0.3 -9999 0 -0.72 47 47
WNT5A -0.093 0.26 -9999 0 -0.72 33 33
WNT11 -0.13 0.3 -9999 0 -0.72 45 45
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.027 0.16 -9999 0 -0.46 27 27
EPHB2 -0.003 0.12 -9999 0 -0.71 6 6
Syndecan-2/TACI 0.023 0.065 -9999 0 -0.4 5 5
LAMA1 0.017 0 -9999 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.14 0.19 -9999 0 -0.38 79 79
HRAS 0.017 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.003 0.032 -9999 0 -0.46 1 1
ITGA5 0 0.11 -9999 0 -0.72 5 5
BAX 0.051 0.05 -9999 0 -0.55 1 1
EPB41 0.017 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.002 0.029 -9999 0 -0.41 1 1
LAMA3 0.001 0.1 -9999 0 -0.67 5 5
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.009 0.14 -9999 0 -0.71 8 8
Syndecan-2/MMP2 0.026 0.057 -9999 0 -0.46 3 3
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.19 0.26 -9999 0 -0.55 77 77
dendrite morphogenesis 0.017 0.084 -9999 0 -0.45 7 7
Syndecan-2/GM-CSF -0.24 0.25 -9999 0 -0.46 120 120
determination of left/right symmetry 0.024 0.04 -9999 0 -0.54 1 1
Syndecan-2/PKC delta 0.03 0.034 -9999 0 -0.45 1 1
GNB2L1 0.017 0 -9999 0 -10000 0 0
MAPK3 -0.21 0.23 -9999 0 -0.42 120 120
MAPK1 -0.2 0.23 -9999 0 -0.41 120 120
Syndecan-2/RACK1 -0.002 0.026 -9999 0 -0.38 1 1
NF1 0.017 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.024 0.04 -9999 0 -0.54 1 1
ITGA2 -0.24 0.35 -9999 0 -0.72 77 77
MAPK8 0.044 0.039 -9999 0 -0.45 1 1
Syndecan-2/alpha2/beta1 Integrin -0.14 0.19 -9999 0 -0.64 2 2
Syndecan-2/Kininogen 0.017 0.082 -9999 0 -0.4 8 8
ITGB1 0.014 0.05 -9999 0 -0.72 1 1
SRC 0.048 0.028 -9999 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 -0.002 0.029 -9999 0 -0.42 1 1
extracellular matrix organization 0.03 0.034 -9999 0 -0.45 1 1
actin cytoskeleton reorganization -0.027 0.16 -9999 0 -0.46 27 27
Syndecan-2/Caveolin-2/Ras -0.017 0.08 -9999 0 -0.41 8 8
Syndecan-2/Laminin alpha3 0.02 0.075 -9999 0 -0.42 6 6
Syndecan-2/RasGAP -0.005 0.042 -9999 0 -0.36 2 2
alpha5/beta1 Integrin -0.015 0.087 -9999 0 -0.54 6 6
PRKCD 0.017 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.017 0.085 -9999 0 -0.45 7 7
GO:0007205 0.004 0.008 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.053 0.047 -9999 0 -10000 0 0
RHOA 0.017 0 -9999 0 -10000 0 0
SDCBP 0.017 0 -9999 0 -10000 0 0
TNFRSF13B 0.005 0.087 -9999 0 -0.64 4 4
RASA1 0.01 0.07 -9999 0 -0.72 2 2
alpha2/beta1 Integrin -0.19 0.26 -9999 0 -0.55 77 77
Syndecan-2/Synbindin 0.03 0.034 -9999 0 -0.45 1 1
TGFB1 0.017 0 -9999 0 -10000 0 0
CASP3 0.04 0.041 -9999 0 -0.37 2 2
FN1 -0.07 0.24 -9999 0 -0.72 26 26
Syndecan-2/IL8 -0.42 0.14 -9999 0 -0.46 205 205
SDC2 0.024 0.04 -9999 0 -0.54 1 1
KNG1 -0.004 0.12 -9999 0 -0.65 7 7
Syndecan-2/Neurofibromin 0.03 0.034 -9999 0 -0.45 1 1
TRAPPC4 0.017 0 -9999 0 -10000 0 0
CSF2 -0.38 0.37 -9999 0 -0.72 120 120
Syndecan-2/TGFB1 0.03 0.034 -9999 0 -0.45 1 1
Syndecan-2/Syntenin/PI-4-5-P2 -0.002 0.029 -9999 0 -0.42 1 1
Syndecan-2/Ezrin -0.002 0.029 -9999 0 -0.42 1 1
PRKACA 0.042 0.031 -9999 0 -0.4 1 1
angiogenesis -0.42 0.13 -9999 0 -0.46 205 205
MMP2 0.01 0.07 -9999 0 -0.72 2 2
IL8 -0.67 0.2 -9999 0 -0.72 205 205
calcineurin-NFAT signaling pathway 0.023 0.065 -9999 0 -0.4 5 5
Arf6 signaling events

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
CENTA1/KIF3B -0.004 0.039 -9999 0 -0.41 2 2
ARNO/beta Arrestin1-2 -0.11 0.14 -9999 0 -0.32 24 24
EGFR 0.002 0.099 -9999 0 -0.65 5 5
EPHA2 -0.016 0.15 -9999 0 -0.72 10 10
USP6 0.017 0 -9999 0 -10000 0 0
IQSEC1 0.017 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.15 0.23 -9999 0 -0.5 68 68
ARRB2 0.018 0.041 -9999 0 -0.33 3 3
mol:GTP 0.009 0.007 -9999 0 -10000 0 0
ARRB1 0.008 0.075 -9999 0 -0.64 3 3
FBXO8 0.017 0 -9999 0 -10000 0 0
TSHR 0.017 0 -9999 0 -10000 0 0
EGF -0.18 0.31 -9999 0 -0.68 64 64
somatostatin receptor activity 0 0 -9999 0 -0.001 48 48
ARAP2 0 0 -9999 0 0 53 53
mol:GDP -0.13 0.14 -9999 0 -0.32 57 57
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 50 50
ITGA2B 0.017 0 -9999 0 -10000 0 0
ARF6 0.017 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.018 0.085 -9999 0 -10000 0 0
ADAP1 0 0 -9999 0 0 23 23
KIF13B 0.011 0.062 -9999 0 -0.64 2 2
HGF/MET -0.24 0.27 -9999 0 -0.54 101 101
PXN 0.017 0 -9999 0 -10000 0 0
ARF6/GTP -0.12 0.12 -9999 0 -0.28 51 51
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.13 0.2 -9999 0 -0.47 30 30
ADRB2 -0.22 0.31 -9999 0 -0.64 80 80
receptor agonist activity 0 0 -9999 0 0 49 49
actin filament binding 0 0 -9999 0 -0.001 50 50
SRC 0.017 0 -9999 0 -10000 0 0
ITGB3 0.017 0 -9999 0 -10000 0 0
GNAQ 0 0 -9999 0 -0.001 26 26
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 25 25
ARF6/GDP -0.017 0.058 -9999 0 -10000 0 0
ARF6/GDP/GULP/ACAP1 -0.14 0.17 -9999 0 -0.45 41 41
alphaIIb/beta3 Integrin/paxillin/GIT1 0 0 -9999 0 -10000 0 0
ACAP1 0 0 -9999 0 -10000 0 0
ACAP2 0 0 -9999 0 0 49 49
LHCGR/beta Arrestin2 -0.007 0.056 -9999 0 -0.48 3 3
EFNA1 0.017 0 -9999 0 -10000 0 0
HGF 0.01 0.07 -9999 0 -0.72 2 2
CYTH3 0 0 -9999 0 -0.001 49 49
CYTH2 -0.002 0.002 -9999 0 -0.004 62 62
NCK1 0.017 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 28 28
endosomal lumen acidification 0 0 -9999 0 0 24 24
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.051 0.2 -9999 0 -0.64 23 23
GNAQ/ARNO -0.003 0.003 -9999 0 -0.007 24 24
mol:Phosphatidic acid 0 0 -9999 0 0 49 49
PIP3-E 0.01 0.066 -9999 0 -0.68 2 2
MET -0.31 0.37 -9999 0 -0.72 99 99
GNA14 -0.01 0.13 -9999 0 -0.64 9 9
GNA15 -0.007 0.13 -9999 0 -0.72 7 7
GIT1 0.017 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 45 45
GNA11 -0.001 0.11 -9999 0 -0.64 6 6
LHCGR 0.007 0.082 -9999 0 -0.69 3 3
AGTR1 -0.26 0.32 -9999 0 -0.64 95 95
desensitization of G-protein coupled receptor protein signaling pathway -0.007 0.056 -9999 0 -0.48 3 3
IPCEF1/ARNO -0.093 0.17 -9999 0 -0.38 32 32
alphaIIb/beta3 Integrin 0 0 -9999 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.16 0.26 -10000 0 -0.55 70 70
TP53 -0.058 0.082 -10000 0 -0.27 9 9
Senescence -0.058 0.082 -10000 0 -0.27 9 9
Apoptosis -0.058 0.082 -10000 0 -0.27 9 9
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.087 0.13 0.28 70 -10000 0 70
MDM4 0.017 0 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.041 0.14 -10000 0 -0.62 11 11
oxygen homeostasis -0.014 0.014 -10000 0 -10000 0 0
TCEB2 0.017 0 -10000 0 -10000 0 0
TCEB1 0.01 0.07 -10000 0 -0.72 2 2
VHL/Elongin B/Elongin C/HIF2A -0.14 0.16 -10000 0 -0.48 11 11
EPO -0.27 0.25 -10000 0 -0.7 27 27
FIH (dimer) 0.002 0.009 -10000 0 -10000 0 0
APEX1 0.002 0.013 -10000 0 -10000 0 0
SERPINE1 -0.37 0.37 -10000 0 -0.93 49 49
FLT1 -0.032 0.14 -10000 0 -0.62 10 10
ADORA2A -0.31 0.29 -10000 0 -0.84 27 27
germ cell development -0.31 0.29 -10000 0 -0.82 29 29
SLC11A2 -0.36 0.34 -10000 0 -0.87 47 47
BHLHE40 -0.33 0.3 -10000 0 -0.78 44 44
HIF1AN 0.002 0.008 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.21 0.17 -10000 0 -0.48 41 41
ETS1 0.037 0.008 -10000 0 -10000 0 0
CITED2 -0.015 0.045 -10000 0 -10000 0 0
KDR -0.008 0.043 -10000 0 -10000 0 0
PGK1 -0.33 0.32 -10000 0 -0.9 31 31
SIRT1 0.017 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.39 0.38 -10000 0 -0.86 66 66
EPAS1 -0.18 0.18 -10000 0 -0.44 42 42
SP1 0.026 0.006 -10000 0 -10000 0 0
ABCG2 -0.67 0.31 -10000 0 -0.83 151 151
EFNA1 -0.32 0.3 -10000 0 -0.87 27 27
FXN -0.31 0.3 -10000 0 -0.85 28 28
POU5F1 -0.32 0.31 -10000 0 -0.87 29 29
neuron apoptosis 0.38 0.36 0.82 66 -10000 0 66
EP300 0.017 0 -10000 0 -10000 0 0
EGLN3 -0.25 0.32 -10000 0 -0.65 85 85
EGLN2 0.004 0.01 -10000 0 -10000 0 0
EGLN1 0.002 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.006 0.053 -10000 0 -0.46 3 3
VHL 0.014 0.05 -10000 0 -0.72 1 1
ARNT 0.002 0.013 -10000 0 -10000 0 0
SLC2A1 -0.35 0.34 -10000 0 -0.88 44 44
TWIST1 -0.36 0.35 -10000 0 -0.93 44 44
ELK1 0.018 0.086 -10000 0 -0.72 3 3
HIF2A/ARNT/Cbp/p300 -0.21 0.17 -10000 0 -0.54 16 16
VEGFA -0.35 0.34 -10000 0 -0.89 40 40
CREBBP 0.017 0 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.24 0.27 -10000 0 -0.54 99 99
CRKL -0.048 0.12 -10000 0 -0.52 2 2
mol:PIP3 -0.01 0.095 0.56 6 -10000 0 6
AKT1 0.014 0.064 0.4 6 -10000 0 6
PTK2B 0.017 0 -10000 0 -10000 0 0
RAPGEF1 -0.036 0.11 -10000 0 -0.6 1 1
RANBP10 0.017 0 -10000 0 -10000 0 0
PIK3CA 0.017 0 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.21 0.23 -10000 0 -0.46 101 101
MAP3K5 -0.024 0.11 -10000 0 -0.54 1 1
HGF/MET/CIN85/CBL/ENDOPHILINS -0.19 0.21 -10000 0 -0.42 101 101
AP1 -0.13 0.18 -10000 0 -0.5 37 37
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.017 0 -10000 0 -10000 0 0
apoptosis -0.14 0.27 -10000 0 -0.76 32 32
STAT3 (dimer) -0.051 0.12 -10000 0 -0.38 1 1
GAB1/CRKL/SHP2/PI3K -0.061 0.078 -10000 0 -0.52 2 2
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.038 0.11 -10000 0 -0.6 1 1
PTPN11 0.014 0.05 -10000 0 -0.72 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 -0.033 0.19 -10000 0 -0.72 15 15
PTEN -0.001 0.11 -10000 0 -0.64 6 6
ELK1 -0.11 0.13 0.24 1 -0.26 97 98
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.049 0.064 -10000 0 -0.29 1 1
PAK1 0.023 0.059 0.37 6 -10000 0 6
HGF/MET/RANBP10 -0.21 0.23 -10000 0 -0.46 101 101
HRAS -0.083 0.15 -10000 0 -10000 0 0
DOCK1 -0.039 0.12 -10000 0 -0.54 2 2
GAB1 -0.061 0.12 -10000 0 -0.56 2 2
CRK -0.05 0.12 -10000 0 -0.52 2 2
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.12 0.13 -10000 0 -10000 0 0
JUN 0 0.11 -10000 0 -0.72 5 5
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.11 0.12 -10000 0 -0.25 90 90
PIK3R1 0.017 0 -10000 0 -10000 0 0
cell morphogenesis -0.009 0.12 -10000 0 -10000 0 0
GRB2/SHC -0.084 0.1 -10000 0 -10000 0 0
FOS -0.081 0.23 -10000 0 -0.64 33 33
GLMN 0.006 0.043 -10000 0 -0.23 3 3
cell motility -0.11 0.13 0.23 1 -0.26 97 98
HGF/MET/MUC20 -0.21 0.23 -10000 0 -0.47 101 101
cell migration -0.083 0.099 -10000 0 -10000 0 0
GRB2 0.017 0 -10000 0 -10000 0 0
CBL 0.017 0 -10000 0 -10000 0 0
MET/RANBP10 -0.24 0.27 -10000 0 -0.54 99 99
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.07 0.13 -10000 0 -0.42 1 1
MET/MUC20 -0.25 0.27 -10000 0 -0.55 99 99
RAP1B -0.024 0.11 -10000 0 -0.55 1 1
RAP1A -0.024 0.11 -10000 0 -0.55 1 1
HGF/MET/RANBP9 -0.21 0.23 -10000 0 -0.46 101 101
RAF1 -0.067 0.14 -10000 0 -10000 0 0
STAT3 -0.051 0.12 -10000 0 -0.38 1 1
cell proliferation -0.049 0.14 -10000 0 -10000 0 0
RPS6KB1 -0.023 0.057 -10000 0 -0.22 2 2
MAPK3 -0.1 0.14 0.7 2 -0.24 97 99
MAPK1 -0.11 0.13 0.68 1 -0.24 99 100
RANBP9 0.017 0 -10000 0 -10000 0 0
MAPK8 0 0.1 -10000 0 -0.42 1 1
SRC -0.054 0.12 -10000 0 -0.39 1 1
PI3K -0.084 0.1 -10000 0 -10000 0 0
MET/Glomulin -0.21 0.25 -10000 0 -0.49 99 99
SOS1 0.017 0 -10000 0 -10000 0 0
MAP2K1 -0.053 0.14 -10000 0 -10000 0 0
MET -0.31 0.37 -10000 0 -0.72 99 99
MAP4K1 -0.032 0.11 -10000 0 -0.48 2 2
PTK2 0.014 0.05 -10000 0 -0.72 1 1
MAP2K2 -0.053 0.14 -10000 0 -10000 0 0
BAD 0.023 0.059 0.37 6 -10000 0 6
MAP2K4 -0.018 0.11 -10000 0 -0.44 3 3
SHP2/GRB2/SOS1/GAB1 -0.12 0.13 -10000 0 -0.57 2 2
INPPL1 0.017 0 -10000 0 -10000 0 0
PXN 0.017 0 -10000 0 -10000 0 0
SH3KBP1 0.005 0.087 -10000 0 -0.64 4 4
HGS -0.077 0.12 -10000 0 -10000 0 0
PLCgamma1/PKC -0.037 0.14 -10000 0 -0.55 15 15
HGF 0.01 0.07 -10000 0 -0.72 2 2
RASA1 0.01 0.07 -10000 0 -0.72 2 2
NCK1 0.017 0 -10000 0 -10000 0 0
PTPRJ 0.017 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.092 0.16 -10000 0 -0.52 15 15
PDPK1 0.002 0.074 0.44 6 -10000 0 6
HGF/MET/SHIP -0.21 0.23 -10000 0 -0.47 101 101
Glucocorticoid receptor regulatory network

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
PCK2 0.038 0.12 -10000 0 -0.76 1 1
SMARCC2 0.017 0 -10000 0 -10000 0 0
SMARCC1 0.004 0.098 -10000 0 -0.72 4 4
TBX21 -0.35 0.45 -10000 0 -0.92 81 81
SUMO2 0.017 0.007 -10000 0 -10000 0 0
STAT1 (dimer) -0.039 0.21 -10000 0 -0.72 20 20
FKBP4 0.01 0.07 -10000 0 -0.72 2 2
FKBP5 0.017 0 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.1 0.18 0.35 22 -0.4 2 24
PRL -0.046 0.14 -10000 0 -0.77 1 1
cortisol/GR alpha (dimer)/TIF2 0.29 0.29 0.6 72 -10000 0 72
RELA -0.11 0.073 -10000 0 -10000 0 0
FGG 0.22 0.24 0.59 27 -10000 0 27
GR beta/TIF2 0.11 0.2 0.38 24 -0.44 12 36
IFNG -0.35 0.36 -10000 0 -0.86 60 60
apoptosis 0.068 0.14 0.54 5 -10000 0 5
CREB1 0.029 0.001 -10000 0 -10000 0 0
histone acetylation -0.072 0.14 -10000 0 -0.37 19 19
BGLAP -0.081 0.16 -10000 0 -0.48 6 6
GR/PKAc -0.002 0.24 0.36 8 -0.61 9 17
NF kappa B1 p50/RelA -0.21 0.14 -10000 0 -0.45 26 26
SMARCD1 0.017 0 -10000 0 -10000 0 0
MDM2 0.12 0.093 0.31 26 -10000 0 26
GATA3 0.029 0.027 -10000 0 -10000 0 0
AKT1 0.001 0.018 -10000 0 -10000 0 0
CSF2 -0.29 0.28 -10000 0 -0.65 50 50
GSK3B 0.014 0.05 -10000 0 -0.72 1 1
NR1I3 0.095 0.12 0.55 4 -10000 0 4
CSN2 0.18 0.19 0.47 21 -10000 0 21
BRG1/BAF155/BAF170/BAF60A -0.007 0.054 -10000 0 -0.41 4 4
NFATC1 0.025 0.05 -10000 0 -0.7 1 1
POU2F1 0.027 0.009 -10000 0 -10000 0 0
CDKN1A 0.005 0.19 -10000 0 -1.5 3 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.007 -10000 0 -10000 0 0
SFN 0.011 0.062 -10000 0 -0.64 2 2
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.11 0.17 0.35 19 -0.67 1 20
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.068 0.21 0.53 4 -0.83 8 12
JUN -0.18 0.21 -10000 0 -0.59 25 25
IL4 -0.085 0.17 -10000 0 -0.72 3 3
CDK5R1 0.017 0.005 -10000 0 -10000 0 0
PRKACA 0.017 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.074 0.27 -10000 0 -0.6 16 16
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.11 0.17 0.34 20 -10000 0 20
cortisol/GR alpha (monomer) 0.34 0.36 0.69 83 -0.53 1 84
NCOA2 0.017 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.13 0.24 -10000 0 -0.68 33 33
AP-1/NFAT1-c-4 -0.32 0.28 -10000 0 -0.75 39 39
AFP -0.11 0.16 -10000 0 -0.88 1 1
SUV420H1 0.017 0 -10000 0 -10000 0 0
IRF1 0.15 0.21 0.5 16 -1 2 18
TP53 0.009 0.16 -10000 0 -0.63 12 12
PPP5C 0.014 0.05 -10000 0 -0.72 1 1
KRT17 -0.28 0.29 -10000 0 -0.82 31 31
KRT14 -0.13 0.17 -10000 0 -0.79 4 4
TBP 0.029 0.001 -10000 0 -10000 0 0
CREBBP 0.03 0.031 -10000 0 -10000 0 0
HDAC1 0.009 0.031 -10000 0 -10000 0 0
HDAC2 0.041 0.025 -10000 0 -10000 0 0
AP-1 -0.32 0.29 -10000 0 -0.76 40 40
MAPK14 0.017 0.006 -10000 0 -10000 0 0
MAPK10 0.005 0.093 -10000 0 -0.68 4 4
MAPK11 0.014 0.05 -10000 0 -0.72 1 1
KRT5 -0.26 0.26 -10000 0 -0.79 22 22
interleukin-1 receptor activity 0.025 0.026 -10000 0 -10000 0 0
NCOA1 0.015 0.063 -10000 0 -0.63 2 2
STAT1 -0.039 0.21 -10000 0 -0.72 20 20
CGA -0.081 0.16 -10000 0 -0.49 5 5
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.19 0.23 0.44 76 -10000 0 76
MAPK3 0.011 0.062 -10000 0 -0.64 2 2
MAPK1 0.014 0.044 -10000 0 -0.64 1 1
ICAM1 -0.32 0.32 -10000 0 -0.82 42 42
NFKB1 -0.11 0.073 -10000 0 -10000 0 0
MAPK8 -0.17 0.2 -10000 0 -0.54 28 28
MAPK9 0.017 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.046 0.14 0.55 5 -10000 0 5
BAX 0.019 0.087 -10000 0 -10000 0 0
POMC -0.13 0.19 -10000 0 -1.3 1 1
EP300 0.036 0.036 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.28 0.32 0.6 81 -0.67 1 82
proteasomal ubiquitin-dependent protein catabolic process 0.086 0.07 0.26 6 -10000 0 6
SGK1 0.082 0.073 0.29 5 -10000 0 5
IL13 -0.2 0.23 -10000 0 -0.96 7 7
IL6 -0.49 0.44 -10000 0 -0.92 105 105
PRKACG 0.017 0 -10000 0 -10000 0 0
IL5 -0.21 0.25 -10000 0 -0.82 20 20
IL2 -0.26 0.25 -10000 0 -0.73 24 24
CDK5 0.01 0.07 -10000 0 -0.72 2 2
PRKACB -0.16 0.29 -10000 0 -0.64 60 60
HSP90AA1 0.014 0.05 -10000 0 -0.72 1 1
IL8 -0.69 0.32 -10000 0 -0.83 158 158
CDK5R1/CDK5 -0.003 0.052 -10000 0 -0.54 2 2
NF kappa B1 p50/RelA/PKAc -0.21 0.2 -10000 0 -0.58 30 30
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.28 0.28 0.57 72 -0.5 1 73
SMARCA4 0.017 0 -10000 0 -10000 0 0
chromatin remodeling 0.18 0.2 0.38 64 -0.53 3 67
NF kappa B1 p50/RelA/Cbp -0.12 0.1 -10000 0 -0.52 1 1
JUN (dimer) -0.18 0.2 -10000 0 -0.58 25 25
YWHAH 0.017 0 -10000 0 -10000 0 0
VIPR1 -0.19 0.36 -10000 0 -1.1 29 29
NR3C1 0.16 0.3 0.53 41 -0.56 20 61
NR4A1 0.018 0.084 -10000 0 -0.7 3 3
TIF2/SUV420H1 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.068 0.14 0.54 5 -10000 0 5
cortisol/GR alpha (dimer)/Src-1 0.3 0.3 0.58 83 -0.51 1 84
PBX1 0.015 0.087 -10000 0 -0.63 4 4
POU1F1 0.024 0.045 -10000 0 -0.63 1 1
SELE -0.4 0.4 -10000 0 -0.99 58 58
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.18 0.2 0.38 64 -0.54 3 67
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.28 0.28 0.57 72 -0.5 1 73
mol:cortisol 0.22 0.19 0.42 81 -10000 0 81
MMP1 -0.55 0.22 -10000 0 -0.63 186 186
Signaling events mediated by PRL

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
CCNE1 -0.033 0.19 -10000 0 -0.72 15 15
mol:Halofuginone 0.007 0.001 -10000 0 -10000 0 0
ITGA1 0.01 0.07 -10000 0 -0.72 2 2
CDKN1A 0.031 0.063 -10000 0 -0.39 3 3
PRL-3/alpha Tubulin -0.17 0.25 -10000 0 -0.54 70 70
mol:Ca2+ -0.1 0.29 0.34 35 -0.5 68 103
AGT -0.21 0.34 -10000 0 -0.72 68 68
CCNA2 -0.025 0.17 -10000 0 -0.7 1 1
TUBA1B 0.017 0 -10000 0 -10000 0 0
EGR1 0.008 0.11 -10000 0 -0.48 11 11
CDK2/Cyclin E1 -0.073 0.16 -10000 0 -0.69 6 6
MAPK3 -0.15 0.27 -10000 0 -0.54 72 72
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 -0.15 0.27 -10000 0 -0.54 70 70
PTP4A1 0.031 0.088 -10000 0 -10000 0 0
PTP4A3 -0.22 0.34 -10000 0 -0.72 70 70
PTP4A2 0.017 0 -10000 0 -10000 0 0
ITGB1 -0.15 0.27 -10000 0 -0.54 71 71
SRC 0.017 0 -10000 0 -10000 0 0
RAC1 -0.033 0.11 -10000 0 -0.36 4 4
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.037 0.082 -10000 0 -10000 0 0
RABGGTA 0.017 0 -10000 0 -10000 0 0
BCAR1 0.11 0.16 0.34 70 -10000 0 70
RHOC -0.033 0.11 -10000 0 -0.36 4 4
RHOA -0.033 0.11 -10000 0 -0.36 4 4
cell motility -0.028 0.11 -10000 0 -0.37 4 4
PRL-1/alpha Tubulin 0.037 0.082 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.17 0.26 -10000 0 -0.55 71 71
ROCK1 -0.029 0.12 -10000 0 -0.37 4 4
RABGGTB 0.017 0 -10000 0 -10000 0 0
CDK2 -0.063 0.23 -10000 0 -0.72 24 24
mitosis 0.031 0.088 -10000 0 -10000 0 0
ATF5 0.017 0 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.017 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.12 0.14 -9999 0 -0.56 1 1
Syndecan-3/Neurocan -0.003 0.021 -9999 0 -10000 0 0
POMC 0.014 0.044 -9999 0 -0.64 1 1
EGFR 0.002 0.099 -9999 0 -0.65 5 5
Syndecan-3/EGFR -0.011 0.058 -9999 0 -0.4 3 3
AGRP 0.014 0.05 -9999 0 -0.72 1 1
NCSTN 0.017 0 -9999 0 -10000 0 0
PSENEN 0.017 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.014 0.05 -9999 0 -0.72 1 1
APH1A -0.004 0.12 -9999 0 -0.65 7 7
NCAN 0.017 0 -9999 0 -10000 0 0
long-term memory -0.004 0.027 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.36 0.11 -9999 0 -0.39 205 205
PSEN1 0.017 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.014 0.044 -9999 0 -0.64 1 1
limb bud formation -0.004 0.023 -9999 0 -0.3 1 1
MC4R 0.017 0 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
PTN -0.24 0.32 -9999 0 -0.64 89 89
FGFR/FGF/Syndecan-3 -0.004 0.023 -9999 0 -10000 0 0
neuron projection morphogenesis -0.11 0.13 -9999 0 -0.53 1 1
Syndecan-3/AgRP -0.005 0.033 -9999 0 -0.38 1 1
Syndecan-3/AgRP/MC4R -0.004 0.03 -9999 0 -10000 0 0
Fyn/Cortactin -0.002 0.031 -9999 0 -0.46 1 1
SDC3 -0.004 0.023 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.35 0.1 -9999 0 -0.38 205 205
IL8 -0.67 0.2 -9999 0 -0.72 205 205
Syndecan-3/Fyn/Cortactin -0.004 0.027 -9999 0 -10000 0 0
Syndecan-3/CASK -0.004 0.022 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.002 0.031 -9999 0 -0.46 1 1
Gamma Secretase -0.012 0.061 -9999 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.023 0.026 -10000 0 -10000 0 0
NFATC2 -0.005 0.17 -10000 0 -1 1 1
NFATC3 -0.024 0.094 -10000 0 -10000 0 0
CD40LG -0.52 0.39 -10000 0 -0.99 64 64
ITCH 0.055 0.049 -10000 0 -10000 0 0
CBLB 0.055 0.049 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.19 0.22 -10000 0 -0.89 8 8
JUNB 0.007 0.085 -10000 0 -0.72 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.009 0.049 -10000 0 -10000 0 0
T cell anergy 0.076 0.084 -10000 0 -0.43 2 2
TLE4 0.017 0.14 -10000 0 -1.2 1 1
Jun/NFAT1-c-4/p21SNFT -0.21 0.27 -10000 0 -0.87 19 19
AP-1/NFAT1-c-4 -0.59 0.49 -10000 0 -1.1 71 71
IKZF1 0.008 0.17 -10000 0 -0.96 4 4
T-helper 2 cell differentiation -0.085 0.14 -10000 0 -0.76 2 2
AP-1/NFAT1 -0.16 0.21 -10000 0 -0.61 27 27
CALM1 0.03 0.031 -10000 0 -10000 0 0
EGR2 -0.084 0.36 -10000 0 -1.3 12 12
EGR3 -0.088 0.34 -10000 0 -1.2 10 10
NFAT1/FOXP3 0.017 0.12 -10000 0 -0.8 1 1
EGR1 -0.015 0.15 -10000 0 -0.66 11 11
JUN -0.049 0.12 -10000 0 -0.76 5 5
EGR4 0.002 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.014 0.035 -10000 0 -10000 0 0
GBP3 -0.1 0.34 -10000 0 -0.82 40 40
FOSL1 -0.026 0.17 -10000 0 -0.72 13 13
NFAT1-c-4/MAF/IRF4 -0.28 0.37 -10000 0 -1 29 29
DGKA 0.019 0.12 -10000 0 -0.8 1 1
CREM 0.016 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.12 0.26 -10000 0 -0.85 15 15
CTLA4 0.02 0.13 -10000 0 -0.67 4 4
NFAT1-c-4 (dimer)/EGR1 -0.12 0.29 -10000 0 -0.94 15 15
NFAT1-c-4 (dimer)/EGR4 -0.11 0.26 -10000 0 -0.86 14 14
FOS -0.14 0.24 -10000 0 -0.69 33 33
IFNG -0.32 0.32 -10000 0 -0.72 52 52
T cell activation -0.14 0.17 -10000 0 -0.71 3 3
MAF -0.21 0.31 -10000 0 -0.63 78 78
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.057 0.21 0.71 5 -10000 0 5
TNF -0.085 0.26 -10000 0 -0.86 12 12
FASLG -0.22 0.54 -10000 0 -1.4 33 33
TBX21 -0.19 0.29 -10000 0 -0.63 67 67
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ -0.001 0.11 -10000 0 -0.74 5 5
PTPN1 0.019 0.12 -10000 0 -0.8 1 1
NFAT1-c-4/ICER1 -0.11 0.25 -10000 0 -0.87 13 13
GATA3 0.022 0.002 -10000 0 -10000 0 0
T-helper 1 cell differentiation -0.32 0.32 -10000 0 -0.71 52 52
IL2RA -0.2 0.21 -10000 0 -0.8 10 10
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.016 0.13 -10000 0 -0.8 2 2
E2F1 -0.031 0.18 -10000 0 -0.71 14 14
PPARG -0.001 0.11 -10000 0 -0.63 6 6
SLC3A2 -0.002 0.18 -10000 0 -0.65 10 10
IRF4 -0.13 0.27 -10000 0 -0.63 50 50
PTGS2 -0.61 0.48 -10000 0 -1.1 84 84
CSF2 -0.7 0.49 -10000 0 -1.1 104 104
JunB/Fra1/NFAT1-c-4 -0.12 0.26 -10000 0 -0.86 11 11
IL4 -0.088 0.14 -10000 0 -0.8 2 2
IL5 -0.54 0.41 -10000 0 -1 70 70
IL2 -0.14 0.17 -10000 0 -0.72 3 3
IL3 -0.056 0.052 -10000 0 -10000 0 0
RNF128 0.038 0.13 -10000 0 -0.67 7 7
NFATC1 -0.057 0.21 -10000 0 -0.71 5 5
CDK4 -0.003 0.21 -10000 0 -10000 0 0
PTPRK 0.019 0.12 -10000 0 -0.8 1 1
IL8 -0.84 0.4 -10000 0 -1.1 120 120
POU2F1 0.028 0 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.001 0.007 -10000 0 -10000 0 0
HDAC1 0.028 0.022 -10000 0 -10000 0 0
AES 0.021 0.006 -10000 0 -10000 0 0
FBXW11 0.017 0 -10000 0 -10000 0 0
DTX1 0.017 0 -10000 0 -10000 0 0
LRP6/FZD1 -0.002 0.036 -10000 0 -0.54 1 1
TLE1 0.02 0.005 -10000 0 -10000 0 0
AP1 -0.24 0.2 -10000 0 -0.6 36 36
NCSTN 0.017 0 -10000 0 -10000 0 0
ADAM10 0.018 0.001 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.046 0.099 -10000 0 -10000 0 0
NICD/RBPSUH -0.001 0.007 -10000 0 -10000 0 0
WIF1 -0.093 0.26 -10000 0 -0.72 33 33
NOTCH1 -0.002 0.01 -10000 0 -10000 0 0
PSENEN 0.017 0 -10000 0 -10000 0 0
KREMEN2 -0.13 0.29 -10000 0 -0.72 43 43
DKK1 -0.17 0.32 -10000 0 -0.72 56 56
beta catenin/beta TrCP1 0.12 0.083 -10000 0 -10000 0 0
APH1B 0.013 0.049 -10000 0 -0.72 1 1
APH1A -0.004 0.12 -10000 0 -0.65 7 7
AXIN1 -0.045 0.039 0.29 1 -10000 0 1
CtBP/CBP/TCF1/TLE1/AES 0.093 0.072 -10000 0 -10000 0 0
PSEN1 0.017 0 -10000 0 -10000 0 0
FOS -0.081 0.23 -10000 0 -0.64 33 33
JUN 0 0.11 -10000 0 -0.72 5 5
MAP3K7 0.024 0.008 -10000 0 -10000 0 0
CTNNB1 0.12 0.089 0.28 1 -10000 0 1
MAPK3 0.011 0.062 -10000 0 -0.64 2 2
DKK2/LRP6/Kremen 2 -0.27 0.28 -10000 0 -0.52 112 112
HNF1A 0.021 0.006 -10000 0 -10000 0 0
CTBP1 0.021 0.006 -10000 0 -10000 0 0
MYC -0.32 0.29 -10000 0 -0.57 131 131
NKD1 -0.54 0.32 -10000 0 -0.72 167 167
FZD1 0.017 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.001 0.007 -10000 0 -10000 0 0
apoptosis -0.23 0.2 -10000 0 -0.59 36 36
Delta 1/NOTCHprecursor -0.001 0.007 -10000 0 -10000 0 0
DLL1 0.017 0 -10000 0 -10000 0 0
PPARD -0.011 0.039 -10000 0 -10000 0 0
Gamma Secretase -0.012 0.061 -10000 0 -10000 0 0
APC -0.063 0.099 0.29 1 -0.5 9 10
DVL1 -0.009 0.021 -10000 0 -10000 0 0
CSNK2A1 0.008 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0.024 0.008 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.2 0.26 -10000 0 -0.51 88 88
LRP6 0.013 0.05 -10000 0 -0.72 1 1
CSNK1A1 0.008 0.008 -10000 0 -10000 0 0
NLK 0.052 0.018 -10000 0 -10000 0 0
CCND1 -0.091 0.21 -10000 0 -0.63 19 19
WNT1 0.017 0 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.061 0.073 0.35 1 -10000 0 1
DKK2 -0.27 0.36 -10000 0 -0.72 87 87
NOTCH1 precursor/DVL1 -0.002 0.009 -10000 0 -10000 0 0
GSK3B 0.016 0.049 -10000 0 -0.72 1 1
FRAT1 0.018 0.044 -10000 0 -0.64 1 1
NOTCH/Deltex homolog 1 -0.001 0.007 -10000 0 -10000 0 0
PPP2R5D 0.24 0.14 0.31 167 -10000 0 167
MAPK1 0.014 0.044 -10000 0 -0.64 1 1
WNT1/LRP6/FZD1 -0.063 0.15 -10000 0 -0.41 4 4
RBPJ 0.017 0 -10000 0 -10000 0 0
CREBBP 0.008 0.011 -10000 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0 0.1 -9999 0 -0.44 3 3
BIRC5 -0.06 0.22 -9999 0 -0.72 23 23
NFKBIA 0.01 0.098 -9999 0 -0.42 1 1
CPEB1 -0.021 0.15 -9999 0 -0.64 13 13
AKT1 0.01 0.098 -9999 0 -0.42 1 1
NDEL1 0.017 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.026 0.1 -9999 0 -0.5 5 5
NDEL1/TACC3 -0.02 0.088 -9999 0 -0.48 2 2
GADD45A 0.01 0.07 -9999 0 -0.72 2 2
GSK3B 0.017 0.05 -9999 0 -0.71 1 1
PAK1/Aurora A 0.004 0.095 -9999 0 -0.42 1 1
MDM2 0.017 0 -9999 0 -10000 0 0
JUB -0.69 0.16 -9999 0 -0.72 211 211
TPX2 -0.12 0.25 -9999 0 -0.54 58 58
TP53 0.011 0.083 -9999 0 -0.36 3 3
DLG7 -0.024 0.15 -9999 0 -0.47 16 16
AURKAIP1 0.017 0 -9999 0 -10000 0 0
ARHGEF7 0.017 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.021 0.093 -9999 0 -0.5 2 2
G2/M transition of mitotic cell cycle -0.026 0.1 -9999 0 -0.49 5 5
AURKA -0.003 0.12 -9999 0 -0.5 1 1
AURKB -0.02 0.038 -9999 0 -0.2 1 1
CDC25B -0.24 0.15 -9999 0 -0.37 110 110
G2/M transition checkpoint -0.42 0.12 -9999 0 -0.44 211 211
mRNA polyadenylation -0.039 0.12 -9999 0 -0.39 12 12
Aurora A/CPEB -0.04 0.12 -9999 0 -0.39 12 12
Aurora A/TACC1/TRAP/chTOG -0.011 0.072 -9999 0 -10000 0 0
BRCA1 0.004 0.098 -9999 0 -0.72 4 4
centrosome duplication 0.004 0.095 -9999 0 -0.42 1 1
regulation of centrosome cycle -0.02 0.087 -9999 0 -0.43 3 3
spindle assembly -0.011 0.071 -9999 0 -10000 0 0
TDRD7 0.017 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.062 0.16 -9999 0 -0.63 8 8
CENPA -0.035 0.065 -9999 0 -0.24 13 13
Aurora A/PP2A 0.004 0.095 -9999 0 -0.42 1 1
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.008 0.11 -9999 0 -0.38 3 3
negative regulation of DNA binding 0.011 0.083 -9999 0 -0.36 3 3
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.01 0.07 -9999 0 -0.72 2 2
Ajuba/Aurora A -0.42 0.12 -9999 0 -0.44 211 211
mitotic prometaphase -0.002 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.12 -9999 0 -0.5 1 1
TACC1 0.017 0 -9999 0 -10000 0 0
TACC3 0.007 0.085 -9999 0 -0.72 3 3
Aurora A/Antizyme1 -0.015 0.078 -9999 0 -10000 0 0
Aurora A/RasGAP 0 0.1 -9999 0 -0.44 3 3
OAZ1 0.017 0 -9999 0 -10000 0 0
RAN 0.014 0.05 -9999 0 -0.72 1 1
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.021 0.011 -9999 0 -10000 0 0
GIT1 0.017 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.12 0.25 -9999 0 -0.54 58 58
PPP2R5D 0.017 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.098 0.24 -9999 0 -0.5 48 48
PAK1 0.017 0 -9999 0 -10000 0 0
CKAP5 0.017 0 -9999 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0.017 0 -10000 0 -10000 0 0
ERC1 0.017 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.052 0.088 -10000 0 -0.37 4 4
IRAK/TOLLIP 0.03 0.043 -10000 0 -0.42 2 2
IKBKB 0.014 0.05 -10000 0 -0.72 1 1
IKBKG 0.017 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.41 0.29 -10000 0 -0.57 161 161
IL1A -0.32 0.37 -10000 0 -0.72 100 100
IL1B -0.11 0.25 -10000 0 -0.54 55 55
IRAK/TRAF6/p62/Atypical PKCs -0.013 0.065 -10000 0 -10000 0 0
IL1R2 -0.24 0.32 -10000 0 -0.64 87 87
IL1R1 -0.007 0.12 -10000 0 -0.64 8 8
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.043 0.078 0.2 2 -10000 0 2
TOLLIP 0.017 0 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.017 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.082 0.035 -10000 0 -10000 0 0
JUN 0.056 0.083 -10000 0 -10000 0 0
MAP3K7 0.017 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.11 0.18 -10000 0 -0.74 6 6
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.21 0.22 -10000 0 -0.81 6 6
PIK3R1 0.017 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.19 0.21 -10000 0 -0.77 6 6
IL1 beta fragment/IL1R1/IL1RAP -0.12 0.21 -10000 0 -0.82 6 6
NFKB1 0.017 0 -10000 0 -10000 0 0
MAPK8 0.056 0.065 -10000 0 -10000 0 0
IRAK1 0.021 0.047 -10000 0 -0.47 2 2
IL1RN/IL1R1 -0.17 0.25 -10000 0 -0.53 72 72
IRAK4 0.017 0 -10000 0 -10000 0 0
PRKCI -0.003 0.12 -10000 0 -0.72 6 6
TRAF6 0.017 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.021 0.12 -10000 0 -0.39 4 4
CHUK 0.017 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.12 0.21 -10000 0 -0.82 6 6
IL1 beta/IL1R2 -0.26 0.26 -10000 0 -0.47 125 125
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.003 0.032 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.095 0.16 -10000 0 -0.66 6 6
IRAK3 -0.01 0.14 -10000 0 -0.72 8 8
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.11 0.18 -10000 0 -0.75 6 6
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.082 0.14 -10000 0 -0.43 6 6
IL1 alpha/IL1R1/IL1RAP -0.23 0.25 -10000 0 -0.48 101 101
RELA 0.017 0 -10000 0 -10000 0 0
MAP3K7IP1 0.017 0 -10000 0 -10000 0 0
SQSTM1 0.017 0 -10000 0 -10000 0 0
MYD88 0.017 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.003 0.036 -10000 0 -0.39 2 2
IL1RAP -0.003 0.12 -10000 0 -0.72 6 6
UBE2N 0.017 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.092 0.15 -10000 0 -0.61 7 7
CASP1 -0.032 0.18 -10000 0 -0.67 16 16
IL1RN/IL1R2 -0.33 0.26 -10000 0 -0.52 143 143
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.12 0.19 -10000 0 -0.78 6 6
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.051 0.12 -10000 0 -0.38 6 6
PIK3CA 0.017 0 -10000 0 -10000 0 0
IL1RN -0.2 0.34 -10000 0 -0.72 64 64
TRAF6/TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
MAP2K6 0.047 0.067 -10000 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 -0.042 0.19 -9999 0 -0.64 20 20
positive regulation of NF-kappaB transcription factor activity -0.051 0.15 -9999 0 -0.49 23 23
MAP2K4 0.003 0.12 -9999 0 -0.52 4 4
IKBKB 0.014 0.05 -9999 0 -0.72 1 1
TNFRSF10B -0.083 0.25 -9999 0 -0.72 30 30
TNFRSF10A -0.053 0.22 -9999 0 -0.72 21 21
SMPD1 -0.15 0.23 -9999 0 -0.52 50 50
IKBKG 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.004 0.098 -9999 0 -0.72 4 4
TRAIL/TRAILR2 -0.11 0.23 -9999 0 -0.56 45 45
TRAIL/TRAILR3 -0.1 0.21 -9999 0 -0.52 44 44
TRAIL/TRAILR1 -0.091 0.21 -9999 0 -0.53 38 38
TRAIL/TRAILR4 -0.051 0.15 -9999 0 -0.49 23 23
TRAIL/TRAILR1/DAP3/GTP -0.071 0.16 -9999 0 -0.42 38 38
IKK complex -0.033 0.063 -9999 0 -10000 0 0
RIPK1 0.017 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0 0 -9999 0 -10000 0 0
MAPK3 -0.017 0.15 -9999 0 -0.48 21 21
MAP3K1 -0.044 0.095 -9999 0 -0.42 6 6
TRAILR4 (trimer) 0.004 0.098 -9999 0 -0.72 4 4
TRADD 0.017 0 -9999 0 -10000 0 0
TRAILR1 (trimer) -0.053 0.22 -9999 0 -0.72 21 21
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.12 -9999 0 -0.49 3 3
CFLAR 0.017 0 -9999 0 -10000 0 0
MAPK1 -0.015 0.14 -9999 0 -0.46 21 21
TRAIL/TRAILR1/FADD/TRADD/RIP -0.064 0.15 -9999 0 -0.72 3 3
mol:ceramide -0.15 0.23 -9999 0 -0.51 50 50
FADD 0.017 0 -9999 0 -10000 0 0
MAPK8 0.014 0.12 -9999 0 -0.48 4 4
TRAF2 0.017 0 -9999 0 -10000 0 0
TRAILR3 (trimer) -0.07 0.24 -9999 0 -0.72 26 26
CHUK 0.017 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.078 0.18 -9999 0 -0.45 38 38
DAP3 0.017 0 -9999 0 -10000 0 0
CASP10 -0.08 0.16 -9999 0 -0.59 10 10
JNK cascade -0.051 0.15 -9999 0 -0.49 23 23
TRAIL (trimer) -0.042 0.19 -9999 0 -0.63 20 20
TNFRSF10C -0.07 0.24 -9999 0 -0.72 26 26
TRAIL/TRAILR1/DAP3/GTP/FADD -0.066 0.15 -9999 0 -0.72 3 3
TRAIL/TRAILR2/FADD -0.096 0.2 -9999 0 -0.52 30 30
cell death -0.15 0.23 -9999 0 -0.51 50 50
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.011 0.13 -9999 0 -0.49 5 5
TRAILR2 (trimer) -0.083 0.25 -9999 0 -0.72 30 30
CASP8 0.013 0.044 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.08 0.17 -9999 0 -0.72 5 5
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.004 0.055 -9999 0 -0.5 1 1
NFATC2 -0.002 0.044 -9999 0 -10000 0 0
NFATC3 -0.002 0.044 -9999 0 -10000 0 0
CD40LG -0.21 0.33 -9999 0 -0.74 38 38
PTGS2 -0.3 0.43 -9999 0 -0.86 67 67
JUNB 0.007 0.085 -9999 0 -0.72 3 3
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.013 0.016 -9999 0 -10000 0 0
CaM/Ca2+ -0.013 0.016 -9999 0 -10000 0 0
CALM1 0.01 0.012 -9999 0 -10000 0 0
JUN -0.005 0.11 -9999 0 -0.72 5 5
mol:Ca2+ -0.017 0.015 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.004 -9999 0 -10000 0 0
FOSL1 -0.026 0.17 -9999 0 -0.72 13 13
CREM 0.016 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.12 0.13 -9999 0 -0.55 3 3
FOS -0.087 0.24 -9999 0 -0.65 33 33
IFNG -0.28 0.41 -9999 0 -0.88 53 53
AP-1/NFAT1-c-4 -0.26 0.4 -9999 0 -0.93 38 38
FASLG -0.24 0.36 -9999 0 -0.76 44 44
NFAT1-c-4/ICER1 -0.054 0.068 -9999 0 -0.44 1 1
IL2RA -0.22 0.34 -9999 0 -0.77 39 39
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.38 0.45 -9999 0 -0.86 88 88
JunB/Fra1/NFAT1-c-4 -0.069 0.13 -9999 0 -0.57 9 9
IL4 -0.21 0.33 -9999 0 -0.73 38 38
IL2 0.011 0.013 -9999 0 -10000 0 0
IL3 0.001 0.021 -9999 0 -10000 0 0
FKBP1A 0.017 0 -9999 0 -10000 0 0
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.028 0 -9999 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.017 0 -10000 0 -10000 0 0
PTK2 0.014 0.05 -10000 0 -0.72 1 1
CRKL -0.16 0.18 -10000 0 -0.68 4 4
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.017 0 -10000 0 -10000 0 0
IRS1/Crk -0.17 0.19 -10000 0 -0.68 5 5
IGF-1R heterotetramer/IGF1/PTP1B -0.2 0.18 -10000 0 -0.47 4 4
AKT1 -0.11 0.16 -10000 0 -0.57 4 4
BAD -0.097 0.15 -10000 0 -0.52 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.17 0.19 -10000 0 -0.68 5 5
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.18 0.17 -10000 0 -0.7 5 5
RAF1 -0.087 0.15 -10000 0 -0.49 4 4
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.17 0.16 -10000 0 -0.65 4 4
YWHAZ 0.017 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.2 0.18 -10000 0 -0.36 125 125
PIK3CA 0.017 0 -10000 0 -10000 0 0
RPS6KB1 -0.11 0.16 -10000 0 -0.58 5 5
GNB2L1 0.017 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.079 0.13 -10000 0 -0.41 4 4
PXN 0.017 0 -10000 0 -10000 0 0
PIK3R1 0.017 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.14 0.13 -10000 0 -0.58 4 4
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.15 0.14 -10000 0 -10000 0 0
IGF-1R heterotetramer -0.027 0.04 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.18 0.17 -10000 0 -0.69 4 4
Crk/p130 Cas/Paxillin -0.16 0.15 -10000 0 -0.61 5 5
IGF1R -0.027 0.04 -10000 0 -10000 0 0
IGF1 -0.36 0.33 -10000 0 -0.65 125 125
IRS2/Crk -0.15 0.18 -10000 0 -0.65 6 6
PI3K -0.17 0.15 -10000 0 -0.65 4 4
apoptosis 0.077 0.14 0.44 4 -10000 0 4
HRAS/GDP 0 0 -10000 0 -10000 0 0
PRKCD -0.2 0.22 -10000 0 -0.39 125 125
RAF1/14-3-3 E -0.069 0.13 -10000 0 -10000 0 0
BAD/14-3-3 -0.081 0.14 -10000 0 -0.47 4 4
PRKCZ -0.12 0.16 -10000 0 -0.57 4 4
Crk/p130 Cas/Paxillin/FAK1 -0.11 0.11 -10000 0 -0.5 2 2
PTPN1 0.017 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.22 0.24 -10000 0 -0.42 125 125
BCAR1 0.017 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.2 0.19 -10000 0 -0.63 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.017 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.16 0.18 -10000 0 -0.68 4 4
GRB10 -0.03 0.18 -10000 0 -0.72 14 14
PTPN11 -0.17 0.19 -10000 0 -0.69 5 5
IRS1 -0.19 0.2 -10000 0 -0.36 125 125
IRS2 -0.17 0.19 -10000 0 -0.69 5 5
IGF-1R heterotetramer/IGF1 -0.27 0.24 -10000 0 -0.48 125 125
GRB2 0.017 0 -10000 0 -10000 0 0
PDPK1 -0.13 0.17 -10000 0 -0.61 4 4
YWHAE 0.014 0.05 -10000 0 -0.72 1 1
PRKD1 -0.2 0.23 -10000 0 -0.64 7 7
SHC1 0.017 0 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.017 0 -9999 0 -10000 0 0
VLDLR -0.12 0.27 -9999 0 -0.64 48 48
LRPAP1 0.017 0 -9999 0 -10000 0 0
NUDC 0.017 0 -9999 0 -10000 0 0
RELN/LRP8 -0.4 0.15 -9999 0 -0.46 196 196
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.017 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.35 0.15 -9999 0 -10000 0 0
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 0.017 0 -9999 0 -10000 0 0
IQGAP1 0.017 0 -9999 0 -10000 0 0
PLA2G7 -0.024 0.16 -9999 0 -0.64 14 14
CALM1 0.017 0 -9999 0 -10000 0 0
DYNLT1 0.017 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.48 0.17 -9999 0 -0.54 196 196
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.017 0 -9999 0 -10000 0 0
CDK5R1 0.017 0 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 0.017 0 -9999 0 -10000 0 0
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.084 0.16 -9999 0 -0.39 48 48
YWHAE 0.014 0.05 -9999 0 -0.72 1 1
NDEL1/14-3-3 E -0.25 0.12 -9999 0 -0.61 2 2
MAP1B -0.025 0.087 -9999 0 -0.33 17 17
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.3 0.14 -9999 0 -0.73 2 2
RELN 0.017 0 -9999 0 -10000 0 0
PAFAH/LIS1 0.009 0.1 -9999 0 -10000 0 0
LIS1/CLIP170 0.036 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.19 0.073 -9999 0 -0.46 2 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.034 0.14 -9999 0 -0.56 3 3
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.27 0.13 -9999 0 -0.66 2 2
LIS1/IQGAP1 0.036 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.031 0 -9999 0 -10000 0 0
PAFAH1B3 -0.063 0.23 -9999 0 -0.72 24 24
PAFAH1B2 0.017 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.016 0.061 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.24 0.093 -9999 0 -0.58 2 2
LRP8 -0.64 0.24 -9999 0 -0.72 196 196
NDEL1/Katanin 60 -0.25 0.12 -9999 0 -0.61 2 2
P39/CDK5 -0.3 0.14 -9999 0 -0.73 2 2
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.036 0 -9999 0 -10000 0 0
CDK5 -0.32 0.14 -9999 0 -0.77 2 2
PPP2R5D 0.017 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.017 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.068 0.13 -9999 0 -10000 0 0
RELN/VLDLR -0.44 0.2 -9999 0 -0.76 43 43
CDC42 0 0 -9999 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.016 0.23 -10000 0 -0.69 19 19
IHH 0.02 0.063 -10000 0 -0.79 1 1
SHH Np/Cholesterol/GAS1 -0.16 0.21 -10000 0 -0.4 87 87
LRPAP1 0.017 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.16 0.21 0.4 87 -10000 0 87
SMO/beta Arrestin2 0.046 0.1 -10000 0 -0.7 1 1
SMO 0.04 0.11 -10000 0 -0.75 1 1
AKT1 0.05 0.053 -10000 0 -10000 0 0
ARRB2 0.017 0 -10000 0 -10000 0 0
BOC 0.017 0 -10000 0 -10000 0 0
ADRBK1 0.017 0 -10000 0 -10000 0 0
heart looping 0.04 0.1 -10000 0 -0.74 1 1
STIL -0.048 0.21 -10000 0 -0.63 12 12
DHH N/PTCH2 0 0 -10000 0 -10000 0 0
DHH N/PTCH1 0.04 0.1 -10000 0 -0.7 1 1
PIK3CA 0.017 0 -10000 0 -10000 0 0
DHH 0.017 0 -10000 0 -10000 0 0
PTHLH 0.027 0.21 -10000 0 -1.2 4 4
determination of left/right symmetry 0.04 0.1 -10000 0 -0.74 1 1
PIK3R1 0.017 0 -10000 0 -10000 0 0
skeletal system development 0.028 0.21 -10000 0 -1.1 4 4
IHH N/Hhip -0.087 0.23 -10000 0 -0.51 48 48
DHH N/Hhip -0.1 0.19 -10000 0 -0.46 48 48
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.04 0.1 -10000 0 -0.74 1 1
pancreas development -0.12 0.27 -10000 0 -0.63 48 48
HHAT -0.054 0.2 -10000 0 -0.64 24 24
PI3K 0 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.19 0.31 -10000 0 -0.64 71 71
somite specification 0.04 0.1 -10000 0 -0.74 1 1
SHH Np/Cholesterol/PTCH1 0.004 0.15 -10000 0 -0.57 4 4
SHH Np/Cholesterol/PTCH2 -0.044 0.12 -10000 0 -0.37 26 26
SHH Np/Cholesterol/Megalin -0.045 0.12 -10000 0 -0.37 27 27
SHH -0.029 0.17 -10000 0 -0.48 26 26
catabolic process 0.036 0.11 -10000 0 -0.5 4 4
SMO/Vitamin D3 0.015 0.15 -10000 0 -0.56 4 4
SHH Np/Cholesterol/Hhip -0.12 0.21 -10000 0 -0.42 63 63
LRP2 0.014 0.05 -10000 0 -0.72 1 1
receptor-mediated endocytosis -0.051 0.11 -10000 0 -0.56 3 3
SHH Np/Cholesterol/BOC -0.044 0.12 -10000 0 -0.53 3 3
SHH Np/Cholesterol/CDO -0.044 0.12 -10000 0 -0.53 3 3
mesenchymal cell differentiation 0.12 0.2 0.42 63 -10000 0 63
mol:Vitamin D3 0.009 0.15 -10000 0 -0.57 4 4
IHH N/PTCH2 0.028 0.039 -10000 0 -0.51 1 1
CDON 0.017 0 -10000 0 -10000 0 0
IHH N/PTCH1 0.035 0.11 -10000 0 -0.5 4 4
Megalin/LRPAP1 -0.002 0.036 -10000 0 -0.54 1 1
PTCH2 0.017 0 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.045 0.13 -10000 0 -0.38 26 26
PTCH1 0.036 0.11 -10000 0 -0.5 4 4
HHIP -0.12 0.27 -10000 0 -0.64 48 48
PLK1 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
regulation of centriole-centriole cohesion 0.003 0.048 0.21 11 -10000 0 11
BUB1B -0.098 0.15 -10000 0 -0.38 45 45
PLK1 -0.015 0.042 -10000 0 -0.13 10 10
PLK1S1 -0.008 0.021 -10000 0 -0.092 1 1
KIF2A -0.002 0.038 -10000 0 -10000 0 0
regulation of mitotic centrosome separation -0.015 0.042 -10000 0 -0.13 10 10
GOLGA2 0.017 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.015 0.051 -10000 0 -0.46 2 2
WEE1 -0.05 0.077 -10000 0 -0.34 3 3
cytokinesis -0.033 0.13 -10000 0 -0.38 27 27
PP2A-alpha B56 -0.1 0.13 -10000 0 -0.5 3 3
AURKA -0.02 0.061 -10000 0 -0.17 30 30
PICH/PLK1 -0.38 0.36 -10000 0 -0.72 95 95
CENPE -0.019 0.1 -10000 0 -0.48 9 9
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.001 0.038 -10000 0 -10000 0 0
PPP2CA 0.017 0 -10000 0 -10000 0 0
FZR1 0.017 0 -10000 0 -10000 0 0
TPX2 -0.04 0.077 -10000 0 -0.17 57 57
PAK1 0.015 0.002 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.017 0 -10000 0 -10000 0 0
CLSPN -0.005 0.038 -10000 0 -0.2 5 5
GORASP1 0.017 0 -10000 0 -10000 0 0
metaphase -0.001 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.008 0.021 -10000 0 -0.092 1 1
G2 phase of mitotic cell cycle -0.003 0.004 -10000 0 -0.012 28 28
STAG2 -0.006 0.13 -10000 0 -0.72 7 7
GRASP65/GM130/RAB1/GTP -0.012 0.024 -10000 0 -10000 0 0
spindle elongation -0.015 0.042 -10000 0 -0.13 10 10
ODF2 0.01 0.049 -10000 0 -0.72 1 1
BUB1 -0.13 0.15 -10000 0 -0.56 3 3
TPT1 0 0.021 -10000 0 -10000 0 0
CDC25C -0.011 0.058 -10000 0 -0.23 13 13
CDC25B -0.34 0.37 -10000 0 -0.72 105 105
SGOL1 -0.003 0.048 -10000 0 -0.21 11 11
RHOA 0.017 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.26 0.26 -10000 0 -0.52 82 82
CDC14B 0.013 0.005 -10000 0 -10000 0 0
CDC20 -0.003 0.12 -10000 0 -0.72 6 6
PLK1/PBIP1 -0.05 0.13 -10000 0 -0.42 22 22
mitosis 0.002 0.012 0.033 30 -0.026 1 31
FBXO5 -0.04 0.088 -10000 0 -0.39 9 9
CDC2 -0.062 0.22 -10000 0 -0.73 21 21
NDC80 0.01 0.07 -10000 0 -0.72 2 2
metaphase plate congression -0.003 0.025 -10000 0 -10000 0 0
ERCC6L -0.38 0.33 -10000 0 -0.74 86 86
NLP/gamma Tubulin -0.004 0.022 -10000 0 -0.11 1 1
microtubule cytoskeleton organization 0 0.021 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.002 0.002 -10000 0 -10000 0 0
PPP1R12A 0.016 0.001 -10000 0 -10000 0 0
interphase -0.002 0.002 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.053 0.17 -10000 0 -0.47 31 31
GRASP65/GM130/RAB1/GTP/PLK1 -0.004 0.02 -10000 0 -10000 0 0
RAB1A 0.017 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.01 0.054 -10000 0 -0.43 1 1
mitotic prometaphase -0.002 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.027 -10000 0 -10000 0 0
microtubule-based process -0.055 0.16 -10000 0 -0.47 27 27
Golgi organization -0.015 0.042 -10000 0 -0.13 10 10
Cohesin/SA2 -0.027 0.073 -10000 0 -0.41 7 7
PPP1CB/MYPT1 0 0.002 -10000 0 -10000 0 0
KIF20A -0.073 0.24 -10000 0 -0.72 27 27
APC/C/CDC20 -0.014 0.085 -10000 0 -0.48 6 6
PPP2R1A 0.017 0 -10000 0 -10000 0 0
chromosome segregation -0.05 0.12 -10000 0 -0.42 22 22
PRC1 -0.003 0.12 -10000 0 -0.72 6 6
ECT2 -0.28 0.23 -10000 0 -0.45 137 137
C13orf34 -0.007 0.048 -10000 0 -0.44 1 1
NUDC -0.003 0.025 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.097 0.15 -10000 0 -0.37 45 45
spindle assembly -0.008 0.032 -10000 0 -0.13 1 1
spindle stabilization -0.008 0.021 -10000 0 -0.091 1 1
APC/C/HCDH1 0.02 0.008 -10000 0 -10000 0 0
MKLP2/PLK1 -0.055 0.16 -10000 0 -0.47 27 27
CCNB1 -0.15 0.3 -10000 0 -0.73 48 48
PPP1CB 0.016 0.001 -10000 0 -10000 0 0
BTRC 0.017 0 -10000 0 -10000 0 0
ROCK2 0.006 0.028 -10000 0 -10000 0 0
TUBG1 0 0.021 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.26 0.25 -10000 0 -0.59 56 56
MLF1IP -0.042 0.17 -10000 0 -0.56 22 22
INCENP 0 0.086 -10000 0 -0.73 3 3
EGFR-dependent Endothelin 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
HRAS 0.017 0 -9999 0 -10000 0 0
EGFR 0.002 0.099 -9999 0 -0.65 5 5
EGF/EGFR -0.21 0.22 -9999 0 -0.7 18 18
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.11 0.16 -9999 0 -0.72 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.15 0.31 -9999 0 -0.72 49 49
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.18 0.31 -9999 0 -0.68 64 64
EGF/EGFR dimer/SHC -0.13 0.2 -9999 0 -0.47 30 30
mol:GDP -0.1 0.16 -9999 0 -0.7 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.022 0.16 -9999 0 -0.65 13 13
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.095 0.14 -9999 0 -0.65 1 1
SHC1 0.017 0 -9999 0 -10000 0 0
HRAS/GDP -0.096 0.15 -9999 0 -0.66 1 1
FRAP1 -0.054 0.18 -9999 0 -0.67 1 1
EGF/EGFR dimer -0.15 0.23 -9999 0 -0.5 68 68
SOS1 0.017 0 -9999 0 -10000 0 0
GRB2 0.017 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.15 0.24 -9999 0 -0.53 61 61
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.031 0.097 -10000 0 -0.38 1 1
TBX21 -0.34 0.69 -10000 0 -1.4 67 67
B2M -0.007 0.13 -10000 0 -0.63 9 9
TYK2 0.019 0.021 -10000 0 -10000 0 0
IL12RB1 0.019 0.021 -10000 0 -10000 0 0
GADD45B -0.097 0.37 -10000 0 -0.93 23 23
IL12RB2 0.017 0.057 -10000 0 -0.77 1 1
GADD45G -0.1 0.38 -10000 0 -0.94 24 24
natural killer cell activation -0.001 0.028 -10000 0 -10000 0 0
RELB 0.017 0 -10000 0 -10000 0 0
RELA 0.017 0 -10000 0 -10000 0 0
IL18 -0.053 0.21 -10000 0 -0.64 25 25
IL2RA -0.006 0.13 -10000 0 -0.72 7 7
IFNG -0.15 0.31 -10000 0 -0.72 50 50
STAT3 (dimer) -0.061 0.33 -10000 0 -0.77 23 23
HLA-DRB5 -0.005 0.11 -10000 0 -0.63 7 7
FASLG -0.17 0.52 -10000 0 -1.3 29 29
NF kappa B2 p52/RelB -0.19 0.31 -10000 0 -0.88 29 29
CD4 0.016 0.007 -10000 0 -10000 0 0
SOCS1 0.014 0.05 -10000 0 -0.72 1 1
EntrezGene:6955 0 0.01 -10000 0 -10000 0 0
CD3D -0.011 0.14 -10000 0 -0.64 10 10
CD3E 0.018 0.008 -10000 0 -10000 0 0
CD3G -0.015 0.14 -10000 0 -0.65 11 11
IL12Rbeta2/JAK2 0.017 0.094 -10000 0 -0.55 5 5
CCL3 -0.12 0.39 -10000 0 -0.95 23 23
CCL4 -0.11 0.41 -10000 0 -1.1 19 19
HLA-A 0.005 0.097 -10000 0 -0.63 5 5
IL18/IL18R -0.064 0.25 -10000 0 -0.46 51 51
NOS2 -0.12 0.39 -10000 0 -0.81 39 39
IL12/IL12R/TYK2/JAK2/SPHK2 0.031 0.096 -10000 0 -0.38 1 1
IL1R1 -0.13 0.43 -10000 0 -1.1 26 26
IL4 0.018 0.055 -10000 0 -0.71 1 1
JAK2 0.006 0.1 -10000 0 -0.72 4 4
EntrezGene:6957 0.001 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.003 0.2 -10000 0 -0.74 11 11
RAB7A -0.057 0.32 -10000 0 -0.83 14 14
lysosomal transport -0.051 0.31 -10000 0 -0.78 14 14
FOS -0.18 0.53 -10000 0 -1.3 39 39
STAT4 (dimer) -0.11 0.38 -10000 0 -0.88 28 28
STAT5A (dimer) -0.26 0.31 -10000 0 -0.82 38 38
GZMA -0.12 0.38 -10000 0 -0.88 30 30
GZMB -0.11 0.38 -10000 0 -1 18 18
HLX 0.017 0 -10000 0 -10000 0 0
LCK -0.12 0.41 -10000 0 -0.94 31 31
TCR/CD3/MHC II/CD4 -0.017 0.22 -10000 0 -0.65 17 17
IL2/IL2R -0.019 0.084 -10000 0 -0.41 7 7
MAPK14 -0.093 0.38 -10000 0 -0.9 27 27
CCR5 -0.17 0.52 -10000 0 -1.4 29 29
IL1B -0.12 0.28 -10000 0 -0.71 41 41
STAT6 -0.006 0.12 -10000 0 -0.25 1 1
STAT4 0.014 0.044 -10000 0 -0.64 1 1
STAT3 0.017 0 -10000 0 -10000 0 0
STAT1 -0.05 0.21 -10000 0 -0.72 20 20
NFKB1 0.017 0 -10000 0 -10000 0 0
NFKB2 0.014 0.05 -10000 0 -0.72 1 1
IL12B 0.013 0.071 -10000 0 -0.7 2 2
CD8A 0.002 0.003 -10000 0 -10000 0 0
CD8B 0.019 0.002 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.031 0.097 0.38 1 -10000 0 1
IL2RB 0.014 0.044 -10000 0 -0.64 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.095 0.35 -10000 0 -0.79 28 28
IL2RG 0.008 0.075 -10000 0 -0.64 3 3
IL12 0.007 0.11 -10000 0 -0.51 9 9
STAT5A 0.017 0 -10000 0 -10000 0 0
CD247 -0.014 0.14 -10000 0 -0.64 11 11
IL2 0.017 0 -10000 0 -10000 0 0
SPHK2 0.014 0.044 -10000 0 -0.64 1 1
FRAP1 0.017 0 -10000 0 -10000 0 0
IL12A -0.004 0.13 -10000 0 -0.71 7 7
IL12/IL12R/TYK2/JAK2 -0.13 0.44 -10000 0 -1 29 29
MAP2K3 -0.097 0.38 -10000 0 -0.88 30 30
RIPK2 -0.12 0.29 -10000 0 -0.72 42 42
MAP2K6 -0.11 0.39 -10000 0 -0.92 27 27
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.007 0.075 -10000 0 -0.63 3 3
IL18RAP -0.11 0.26 -10000 0 -0.64 43 43
IL12Rbeta1/TYK2 0.027 0.033 -10000 0 -10000 0 0
EOMES 0.023 0.066 -10000 0 -10000 0 0
STAT1 (dimer) -0.14 0.32 -10000 0 -0.73 30 30
T cell proliferation -0.085 0.3 -10000 0 -0.66 27 27
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.018 0.045 -10000 0 -0.64 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.18 0.26 -10000 0 -0.72 31 31
ATF2 -0.074 0.35 -10000 0 -0.83 25 25
p75(NTR)-mediated 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
Sortilin/TRAF6 -0.002 0.031 -9999 0 -0.46 1 1
Necdin/E2F1 -0.13 0.23 -9999 0 -0.51 57 57
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.009 0.054 -9999 0 -0.39 1 1
NGF (dimer)/p75(NTR)/BEX1 -0.004 0.037 -9999 0 -0.4 2 2
NT-4/5 (dimer)/p75(NTR) 0 0 -9999 0 -10000 0 0
IKBKB 0.014 0.05 -9999 0 -0.72 1 1
AKT1 0.043 0 -9999 0 -10000 0 0
IKBKG 0.017 0 -9999 0 -10000 0 0
BDNF -0.036 0.19 -9999 0 -0.72 16 16
MGDIs/NGR/p75(NTR)/LINGO1 -0.029 0.12 -9999 0 -0.49 13 13
FURIN 0.017 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.035 0.12 -9999 0 -0.45 17 17
LINGO1 0.004 0.098 -9999 0 -0.72 4 4
Sortilin/TRAF6/NRIF -0.011 0.052 -9999 0 -10000 0 0
proBDNF (dimer) -0.036 0.19 -9999 0 -0.72 16 16
NTRK1 0.017 0 -9999 0 -10000 0 0
RTN4R -0.016 0.15 -9999 0 -0.72 10 10
neuron apoptosis 0.028 0.1 -9999 0 -10000 0 0
IRAK1 0.01 0.07 -9999 0 -0.72 2 2
SHC1 0.026 0 -9999 0 -10000 0 0
ARHGDIA 0.017 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.012 0.061 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.017 0.076 -9999 0 -0.35 11 11
MAGEH1 -0.012 0.14 -9999 0 -0.64 10 10
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.076 0.15 -9999 0 -0.36 47 47
Mammalian IAPs/DIABLO -0.02 0.084 -9999 0 -0.37 12 12
proNGF (dimer) 0 0 -9999 0 -10000 0 0
MAGED1 0.014 0.05 -9999 0 -0.72 1 1
APP 0.017 0 -9999 0 -10000 0 0
NT-4/5 (dimer) 0 0 -9999 0 -10000 0 0
ZNF274 0.017 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI 0 0 -9999 0 -10000 0 0
NGF 0 0 -9999 0 -10000 0 0
cell cycle arrest 0 0.029 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.009 0.1 -9999 0 -10000 0 0
NT-4/5 (dimer)/p75(NTR)/TRAF6 0 0 -9999 0 -10000 0 0
NCSTN 0.017 0 -9999 0 -10000 0 0
mol:GTP -0.11 0.18 -9999 0 -0.4 60 60
PSENEN 0.017 0 -9999 0 -10000 0 0
mol:ceramide 0.033 0.026 -9999 0 -0.35 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.002 0.092 -9999 0 -0.39 2 2
p75(NTR)/beta APP 0 0 -9999 0 -10000 0 0
BEX1 0.011 0.062 -9999 0 -0.64 2 2
mol:GDP 0.012 0 -9999 0 -10000 0 0
NGF (dimer) -0.41 0.068 -9999 0 -0.42 216 216
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.026 0.11 -9999 0 -0.44 13 13
PIK3R1 0.017 0 -9999 0 -10000 0 0
RAC1/GTP 0 0 -9999 0 -10000 0 0
MYD88 0.017 0 -9999 0 -10000 0 0
CHUK 0.017 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.11 0.18 -9999 0 -0.4 60 60
RHOB -0.03 0.18 -9999 0 -0.72 14 14
RHOA 0.017 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.036 0.14 -9999 0 -0.54 15 15
NT3 (dimer) 0.01 0.07 -9999 0 -0.72 2 2
TP53 0.014 0.13 -9999 0 -10000 0 0
PRDM4 0.033 0.026 -9999 0 -10000 0 0
BDNF (dimer) -0.81 0.16 -9999 0 -0.81 222 222
PIK3CA 0.017 0 -9999 0 -10000 0 0
SORT1 0.014 0.044 -9999 0 -0.64 1 1
activation of caspase activity -0.009 0.054 -9999 0 -0.38 1 1
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.002 0.024 -9999 0 -0.35 1 1
RHOC 0.017 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 0.054 0.089 -9999 0 -10000 0 0
DIABLO 0.017 0 -9999 0 -10000 0 0
SMPD2 0.033 0.026 -9999 0 -0.35 1 1
APH1B 0.014 0.05 -9999 0 -0.72 1 1
APH1A -0.004 0.12 -9999 0 -0.65 7 7
proNGF (dimer)/p75(NTR)/Sortilin -0.002 0.027 -9999 0 -0.4 1 1
PSEN1 0.017 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.005 0.051 -9999 0 -0.54 2 2
NT3 (dimer)/p75(NTR) -0.005 0.051 -9999 0 -0.54 2 2
MAPK8 0.059 0.081 -9999 0 -10000 0 0
MAPK9 0.059 0.081 -9999 0 -10000 0 0
APAF1 0.01 0.07 -9999 0 -0.72 2 2
NTF3 0.01 0.07 -9999 0 -0.72 2 2
NTF4 0 0 -9999 0 -10000 0 0
NDN -0.12 0.27 -9999 0 -0.64 47 47
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.1 0.16 -9999 0 -0.67 4 4
p75 CTF/Sortilin/TRAF6/NRIF -0.002 0.023 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.11 0.18 -9999 0 -0.39 60 60
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.029 0.099 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.031 0.11 -9999 0 -0.41 16 16
PRKACB -0.16 0.29 -9999 0 -0.64 60 60
proBDNF (dimer)/p75 ECD -0.039 0.14 -9999 0 -0.54 16 16
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.02 0.15 -9999 0 -0.66 12 12
BIRC2 0.017 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.12 0.17 -9999 0 -0.52 23 23
BAD 0.066 0.082 -9999 0 -10000 0 0
RIPK2 -0.12 0.29 -9999 0 -0.72 42 42
NGFR 0.017 0 -9999 0 -10000 0 0
CYCS 0.038 0.045 -9999 0 -0.38 1 1
ADAM17 0.017 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.079 0.16 -9999 0 -0.42 42 42
BCL2L11 0.066 0.082 -9999 0 -10000 0 0
BDNF (dimer)/p75(NTR) -0.039 0.14 -9999 0 -0.54 16 16
PI3K 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.003 0.037 -9999 0 -0.39 2 2
NDNL2 0.014 0.05 -9999 0 -0.72 1 1
YWHAE 0.014 0.05 -9999 0 -0.72 1 1
PRKCI -0.003 0.12 -9999 0 -0.72 6 6
NGF (dimer)/p75(NTR) 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.003 0.037 -9999 0 -0.39 2 2
TRAF6 0.017 0 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
PLG 0.017 0 -9999 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 0.014 0.099 -9999 0 -0.36 1 1
SQSTM1 0.017 0 -9999 0 -10000 0 0
NGFRAP1 0.005 0.087 -9999 0 -0.64 4 4
CASP3 0.066 0.077 -9999 0 -10000 0 0
E2F1 -0.03 0.18 -9999 0 -0.72 14 14
CASP9 0.017 0 -9999 0 -10000 0 0
IKK complex -0.022 0.052 -9999 0 -0.46 1 1
NGF (dimer)/TRKA 0 0 -9999 0 -10000 0 0
MMP7 -0.7 0.12 -9999 0 -0.72 216 216
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.001 0.022 -9999 0 -10000 0 0
MMP3 -0.68 0.18 -9999 0 -0.72 208 208
APAF-1/Caspase 9 -0.018 0.064 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.032 0.062 -10000 0 -10000 0 0
UGCG -0.021 0.025 -10000 0 -10000 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT -0.19 0.17 -10000 0 -0.39 13 13
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.015 0.034 -10000 0 -10000 0 0
mol:DAG 0.043 0.083 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.31 0.2 -10000 0 -0.52 90 90
FRAP1 -0.34 0.27 -10000 0 -0.62 92 92
FOXO3 -0.21 0.19 -10000 0 -0.56 3 3
AKT1 -0.24 0.2 -10000 0 -0.45 86 86
GAB2 0.003 0.007 -10000 0 -10000 0 0
SMPD1 -0.19 0.33 -10000 0 -0.82 47 47
SGMS1 -0.021 0.025 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.012 -10000 0 -10000 0 0
CALM1 0.017 0 -10000 0 -10000 0 0
cell proliferation -0.073 0.11 -10000 0 -10000 0 0
EIF3A 0.017 0 -10000 0 -10000 0 0
PI3K 0.005 0.012 -10000 0 -10000 0 0
RPS6KB1 -0.011 0.038 -10000 0 -10000 0 0
mol:sphingomyelin 0.043 0.083 -10000 0 -10000 0 0
natural killer cell activation -0.009 0.005 -10000 0 -0.014 83 83
JAK3 0.004 0.008 -10000 0 -10000 0 0
PIK3R1 0.003 0.008 -10000 0 -10000 0 0
JAK1 0.003 0.008 -10000 0 -10000 0 0
NFKB1 0.017 0 -10000 0 -10000 0 0
MYC -0.35 0.28 -10000 0 -0.63 90 90
MYB 0.007 0.14 -10000 0 -1.3 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.084 0.12 -10000 0 -0.42 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.002 0.07 -10000 0 -0.4 4 4
mol:PI-3-4-5-P3 -0.083 0.12 -10000 0 -0.41 1 1
Rac1/GDP 0.006 0.014 -10000 0 -10000 0 0
T cell proliferation -0.088 0.11 -10000 0 -0.39 1 1
SHC1 0.003 0.007 -10000 0 -10000 0 0
RAC1 0.016 0.001 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.007 0.007 -10000 0 -0.066 2 2
PRKCZ -0.091 0.11 -10000 0 -0.4 1 1
NF kappa B1 p50/RelA -0.3 0.2 -10000 0 -0.52 88 88
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.006 0.05 -10000 0 -10000 0 0
HSP90AA1 0.014 0.05 -10000 0 -0.72 1 1
RELA 0.017 0 -10000 0 -10000 0 0
IL2RA -0.021 0.13 -10000 0 -0.73 7 7
IL2RB 0.001 0.044 -10000 0 -0.64 1 1
TERT 0.017 0 -10000 0 -10000 0 0
E2F1 0.005 0.071 -10000 0 -0.46 2 2
SOS1 0.003 0.007 -10000 0 -10000 0 0
RPS6 0 0.11 -10000 0 -0.72 5 5
mol:cAMP -0.004 0.003 0.031 2 -10000 0 2
PTPN11 -0.001 0.05 -10000 0 -0.73 1 1
IL2RG -0.005 0.075 -10000 0 -0.64 3 3
actin cytoskeleton organization -0.088 0.11 -10000 0 -0.39 1 1
GRB2 0.003 0.007 -10000 0 -10000 0 0
IL2 0.003 0.008 -10000 0 -10000 0 0
PIK3CA 0.003 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.007 0.018 -10000 0 -10000 0 0
LCK -0.003 0.066 -10000 0 -0.69 2 2
BCL2 -0.61 0.44 -10000 0 -0.93 145 145
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.031 0.017 -10000 0 -10000 0 0
HSPA8 0.008 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.004 0.12 -10000 0 -0.47 7 7
AKT1 -0.043 0.036 -10000 0 -10000 0 0
GSC -0.01 0.12 -10000 0 -0.58 7 7
NKX2-5 0.006 0.055 -10000 0 -0.72 1 1
muscle cell differentiation 0.068 0.13 0.48 5 -10000 0 5
SMAD2-3/SMAD4/SP1 -0.085 0.12 -10000 0 -0.52 2 2
SMAD4 -0.025 0.087 -10000 0 -0.63 3 3
CBFB 0.007 0.085 -10000 0 -0.72 3 3
SAP18 0.012 0.049 -10000 0 -0.72 1 1
Cbp/p300/MSG1 -0.008 0.17 -10000 0 -0.45 28 28
SMAD3/SMAD4/VDR 0 0.08 -10000 0 -10000 0 0
MYC -0.32 0.33 -10000 0 -0.6 131 131
CDKN2B -1.1 0.62 -10000 0 -1.4 175 175
AP1 -0.045 0.17 -10000 0 -0.74 6 6
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.01 0.054 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.26 0.19 -10000 0 -0.54 31 31
SP3 0.02 0.001 -10000 0 -10000 0 0
CREB1 0.017 0 -10000 0 -10000 0 0
FOXH1 0.011 0.026 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.059 0.16 -10000 0 -0.45 24 24
GATA3 0.016 0.039 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 0.021 0.035 -10000 0 -10000 0 0
MEF2C/TIF2 -0.078 0.23 -10000 0 -0.6 34 34
endothelial cell migration 0.042 0.24 0.58 21 -10000 0 21
MAX 0.021 0.014 -10000 0 -10000 0 0
RBBP7 0.015 0.002 -10000 0 -10000 0 0
RBBP4 0.015 0.002 -10000 0 -10000 0 0
RUNX2 0.017 0 -10000 0 -10000 0 0
RUNX3 -0.026 0.16 -10000 0 -0.66 14 14
RUNX1 -0.2 0.34 -10000 0 -0.72 66 66
CTBP1 0.017 0 -10000 0 -10000 0 0
NR3C1 -0.05 0.21 -10000 0 -0.64 24 24
VDR -0.001 0.11 -10000 0 -0.64 6 6
CDKN1A -0.031 0.19 -10000 0 -1.5 3 3
KAT2B 0.005 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.042 0.089 -10000 0 -10000 0 0
DCP1A 0.017 0 -10000 0 -10000 0 0
SKI 0.015 0.002 -10000 0 -10000 0 0
SERPINE1 -0.05 0.24 -10000 0 -0.59 18 18
SMAD3/SMAD4/ATF2 -0.017 0.072 -10000 0 -0.53 1 1
SMAD3/SMAD4/ATF3 -0.026 0.1 -10000 0 -0.54 5 5
SAP30 0.015 0.002 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.069 0.062 -10000 0 -0.49 1 1
JUN -0.027 0.18 -10000 0 -0.74 6 6
SMAD3/SMAD4/IRF7 -0.013 0.071 -10000 0 -0.52 1 1
TFE3 0.021 0.01 -10000 0 -10000 0 0
COL1A2 -0.11 0.25 -10000 0 -0.6 44 44
mesenchymal cell differentiation 0.017 0.072 0.53 1 -10000 0 1
DLX1 0.01 0.07 -10000 0 -0.72 2 2
TCF3 0.014 0.05 -10000 0 -0.72 1 1
FOS -0.08 0.24 -10000 0 -0.64 33 33
SMAD3/SMAD4/Max -0.012 0.079 -10000 0 -0.53 1 1
Cbp/p300/SNIP1 0.005 0.016 -10000 0 -10000 0 0
ZBTB17 0.043 0.023 -10000 0 -10000 0 0
LAMC1 0.011 0.07 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.12 0.22 -10000 0 -0.53 48 48
IRF7 0.022 0.001 -10000 0 -10000 0 0
ESR1 0.004 0.11 -10000 0 -0.64 6 6
HNF4A 0.017 0 -10000 0 -10000 0 0
MEF2C -0.077 0.25 -10000 0 -0.64 34 34
SMAD2-3/SMAD4 -0.061 0.094 -10000 0 -0.45 4 4
Cbp/p300/Src-1 0.047 0.053 -10000 0 -0.39 1 1
IGHV3OR16-13 -0.034 0.046 -10000 0 -10000 0 0
TGIF2/HDAC complex -0.14 0.3 -10000 0 -0.72 48 48
CREBBP 0.027 0.013 -10000 0 -10000 0 0
SKIL 0 0.11 -10000 0 -0.72 5 5
HDAC1 0.015 0.002 -10000 0 -10000 0 0
HDAC2 0.015 0.002 -10000 0 -10000 0 0
SNIP1 0.009 0.008 -10000 0 -10000 0 0
GCN5L2 -0.17 0.32 -10000 0 -0.7 60 60
SMAD3/SMAD4/TFE3 -0.017 0.068 -10000 0 -0.52 1 1
MSG1/HSC70 -0.066 0.18 -10000 0 -0.54 28 28
SMAD2 -0.049 0.049 -10000 0 -10000 0 0
SMAD3 -0.015 0.075 -10000 0 -0.66 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.15 0.19 -10000 0 -0.51 29 29
SMAD2/SMAD2/SMAD4 -0.014 0.05 -10000 0 -0.36 3 3
NCOR1 0.012 0.043 -10000 0 -0.63 1 1
NCOA2 0.017 0 -10000 0 -10000 0 0
NCOA1 0.011 0.062 -10000 0 -0.64 2 2
MYOD/E2A -0.01 0.072 -10000 0 -0.54 4 4
SMAD2-3/SMAD4/SP1/MIZ-1 -0.094 0.12 -10000 0 -0.53 2 2
IFNB1 0.003 0.068 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.095 0.24 -10000 0 -0.63 34 34
CITED1 -0.079 0.24 -10000 0 -0.72 28 28
SMAD2-3/SMAD4/ARC105 -0.041 0.083 -10000 0 -0.51 1 1
RBL1 -0.07 0.24 -10000 0 -0.72 26 26
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.44 0.28 -10000 0 -0.6 145 145
RUNX1-3/PEBPB2 -0.17 0.23 -10000 0 -0.47 79 79
SMAD7 -0.062 0.17 -10000 0 -0.85 3 3
MYC/MIZ-1 -0.18 0.26 -10000 0 -0.53 24 24
SMAD3/SMAD4 0.045 0.19 0.36 3 -0.49 4 7
IL10 -0.007 0.092 -10000 0 -10000 0 0
PIASy/HDAC complex 0.007 0.011 -10000 0 -10000 0 0
PIAS3 0.018 0.051 -10000 0 -0.73 1 1
CDK2 -0.054 0.23 -10000 0 -0.72 24 24
IL5 -0.041 0.19 -10000 0 -0.64 18 18
CDK4 -0.031 0.2 -10000 0 -0.71 18 18
PIAS4 0.007 0.011 -10000 0 -10000 0 0
ATF3 0.004 0.098 -10000 0 -0.72 4 4
SMAD3/SMAD4/SP1 -0.052 0.097 -10000 0 -0.62 1 1
FOXG1 -0.074 0.24 -10000 0 -0.72 27 27
FOXO3 -0.051 0.048 -10000 0 -10000 0 0
FOXO1 -0.071 0.11 -10000 0 -0.56 9 9
FOXO4 -0.05 0.048 -10000 0 -10000 0 0
heart looping -0.075 0.24 -10000 0 -0.63 34 34
CEBPB -0.033 0.13 -10000 0 -0.78 6 6
SMAD3/SMAD4/DLX1 -0.022 0.088 -10000 0 -0.54 3 3
MYOD1 0.007 0.085 -10000 0 -0.72 3 3
SMAD3/SMAD4/HNF4 -0.017 0.072 -10000 0 -0.53 1 1
SMAD3/SMAD4/GATA3 -0.026 0.099 -10000 0 -0.51 1 1
SnoN/SIN3/HDAC complex/NCoR1 0 0.11 -10000 0 -0.72 5 5
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.16 0.22 -10000 0 -0.5 38 38
SMAD3/SMAD4/SP1-3 -0.037 0.08 -10000 0 -0.55 1 1
MED15 0.017 0 -10000 0 -10000 0 0
SP1 -0.015 0.055 -10000 0 -10000 0 0
SIN3B 0.015 0.002 -10000 0 -10000 0 0
SIN3A 0.015 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.053 0.13 -10000 0 -0.44 1 1
ITGB5 -0.009 0.085 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.035 0.057 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.019 0.081 -10000 0 -0.56 2 2
AR 0.014 0.05 -10000 0 -0.72 1 1
negative regulation of cell growth -0.13 0.17 -10000 0 -0.5 20 20
SMAD3/SMAD4/MYOD -0.024 0.091 -10000 0 -0.51 4 4
E2F5 -0.3 0.36 -10000 0 -0.72 94 94
E2F4 0.014 0.05 -10000 0 -0.72 1 1
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.007 0.07 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.27 0.19 -10000 0 -0.53 20 20
TFDP1 -0.043 0.2 -10000 0 -0.72 18 18
SMAD3/SMAD4/AP1 -0.052 0.17 -10000 0 -0.75 6 6
SMAD3/SMAD4/RUNX2 -0.017 0.072 -10000 0 -0.53 1 1
TGIF2 -0.14 0.3 -10000 0 -0.72 48 48
TGIF1 -0.07 0.24 -10000 0 -0.72 26 26
ATF2 0.017 0 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.017 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.12 0.13 -9999 0 -0.45 13 13
mol:DAG -0.098 0.18 -9999 0 -0.55 12 12
PLCG1 -0.1 0.18 -9999 0 -0.57 12 12
YES1 -0.1 0.17 -9999 0 -0.43 25 25
FZD3 -0.14 0.3 -9999 0 -0.72 47 47
FZD6 -0.029 0.18 -9999 0 -0.72 14 14
G protein -0.11 0.12 -9999 0 -0.55 3 3
MAP3K7 -0.064 0.16 -9999 0 -0.51 3 3
mol:Ca2+ -0.095 0.17 -9999 0 -0.53 12 12
mol:IP3 -0.098 0.18 -9999 0 -0.55 12 12
NLK 0.004 0.007 -9999 0 -10000 0 0
GNB1 0.017 0 -9999 0 -10000 0 0
CAMK2A -0.079 0.16 -9999 0 -0.49 12 12
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.12 0.18 -9999 0 -0.47 25 25
CSNK1A1 0.017 0 -9999 0 -10000 0 0
GNAS -0.1 0.17 -9999 0 -0.43 25 25
GO:0007205 -0.093 0.17 -9999 0 -0.52 12 12
WNT6 0.014 0.05 -9999 0 -0.72 1 1
WNT4 -0.01 0.13 -9999 0 -0.65 9 9
NFAT1/CK1 alpha -0.1 0.12 -9999 0 -0.54 3 3
GNG2 0.017 0 -9999 0 -10000 0 0
WNT5A -0.093 0.26 -9999 0 -0.72 33 33
WNT11 -0.13 0.3 -9999 0 -0.72 45 45
CDC42 -0.087 0.16 -9999 0 -0.44 13 13
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.07 0.3 -9999 0 -1.1 8 8
PCK1 -0.73 0.7 -9999 0 -1.3 132 132
HNF4A -0.083 0.31 -9999 0 -1.2 6 6
KCNJ11 -0.058 0.32 -9999 0 -1.1 7 7
AKT1 0.012 0.11 -9999 0 -10000 0 0
response to starvation -0.008 0.022 -9999 0 -10000 0 0
DLK1 -0.058 0.32 -9999 0 -1.1 7 7
NKX2-1 0.034 0.25 -9999 0 -0.8 5 5
ACADM -0.076 0.32 -9999 0 -1.1 10 10
TAT -0.083 0.24 -9999 0 -0.85 7 7
CEBPB -0.014 0.12 -9999 0 -0.72 6 6
CEBPA 0.011 0.013 -9999 0 -10000 0 0
TTR -0.8 0.67 -9999 0 -1.3 129 129
PKLR -0.081 0.31 -9999 0 -1.1 8 8
APOA1 -0.08 0.36 -9999 0 -1.3 9 9
CPT1C -0.075 0.31 -9999 0 -1.1 8 8
ALAS1 -0.006 0.16 -9999 0 -10000 0 0
TFRC -0.074 0.29 -9999 0 -0.98 8 8
FOXF1 -0.008 0.12 -9999 0 -0.64 7 7
NF1 0.027 0.001 -9999 0 -10000 0 0
HNF1A (dimer) 0.02 0.057 -9999 0 -10000 0 0
CPT1A -0.071 0.31 -9999 0 -1.1 9 9
HMGCS1 -0.077 0.31 -9999 0 -1 9 9
NR3C1 -0.045 0.2 -9999 0 -0.62 24 24
CPT1B -0.068 0.3 -9999 0 -1 8 8
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.021 0.027 -9999 0 -10000 0 0
GCK -0.068 0.3 -9999 0 -1 8 8
CREB1 -0.095 0.11 -9999 0 -10000 0 0
IGFBP1 -0.088 0.25 -9999 0 -0.83 10 10
PDX1 -0.018 0.2 -9999 0 -0.81 4 4
UCP2 -0.068 0.3 -9999 0 -1 8 8
ALDOB -0.12 0.42 -9999 0 -1.1 21 21
AFP -0.12 0.16 -9999 0 -0.65 2 2
BDH1 -0.069 0.31 -9999 0 -1.1 8 8
HADH -0.058 0.32 -9999 0 -1.1 7 7
F2 -0.065 0.32 -9999 0 -1.2 6 6
HNF1A 0.02 0.056 -9999 0 -10000 0 0
G6PC -0.076 0.13 -9999 0 -10000 0 0
SLC2A2 -0.062 0.25 -9999 0 -0.77 5 5
INS 0.012 0.038 -9999 0 -10000 0 0
FOXA1 -0.16 0.29 -9999 0 -0.62 62 62
FOXA3 -0.093 0.16 -9999 0 -0.67 7 7
FOXA2 -0.074 0.38 -9999 0 -1.2 10 10
ABCC8 -0.11 0.42 -9999 0 -1.1 20 20
ALB -0.12 0.17 -9999 0 -0.62 5 5
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.023 0.087 -9999 0 -0.54 4 4
alphaM/beta2 Integrin/GPIbA -0.019 0.074 -9999 0 -0.44 6 6
alphaM/beta2 Integrin/proMMP-9 -0.034 0.11 -9999 0 -0.51 8 8
PLAUR 0.014 0.05 -9999 0 -0.72 1 1
HMGB1 0 0.054 -9999 0 -0.74 1 1
alphaM/beta2 Integrin/Talin -0.019 0.074 -9999 0 -0.58 2 2
AGER 0.003 0.02 -9999 0 -10000 0 0
RAP1A 0.017 0 -9999 0 -10000 0 0
SELPLG 0.008 0.075 -9999 0 -0.64 3 3
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.071 0.1 -9999 0 -0.8 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.006 0.13 -9999 0 -0.71 7 7
CYR61 -0.043 0.2 -9999 0 -0.72 18 18
TLN1 0.017 0 -9999 0 -10000 0 0
Rap1/GTP -0.033 0.074 -9999 0 -0.47 2 2
RHOA 0.017 0 -9999 0 -10000 0 0
P-selectin oligomer -0.068 0.22 -9999 0 -0.63 29 29
MYH2 0.002 0.14 -9999 0 -0.55 3 3
MST1R 0.017 0 -9999 0 -10000 0 0
leukocyte activation during inflammatory response -0.008 0.063 -9999 0 -0.64 1 1
APOB 0.017 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.01 0.07 -9999 0 -0.72 2 2
JAM3 0.017 0 -9999 0 -10000 0 0
GP1BA 0.017 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.023 0.087 -9999 0 -0.54 4 4
alphaM/beta2 Integrin -0.002 0.12 -9999 0 -0.48 4 4
JAM3 homodimer 0.017 0 -9999 0 -10000 0 0
ICAM2 0.005 0.09 -9999 0 -0.66 4 4
ICAM1 -0.023 0.17 -9999 0 -0.72 12 12
phagocytosis triggered by activation of immune response cell surface activating receptor -0.002 0.12 -9999 0 -0.48 4 4
cell adhesion -0.019 0.074 -9999 0 -0.44 6 6
NFKB1 -0.071 0.18 -9999 0 -0.8 2 2
THY1 -0.076 0.24 -9999 0 -0.72 28 28
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA -0.012 0.077 -9999 0 -0.57 2 2
IL6 -0.21 0.32 -9999 0 -0.55 104 104
ITGB2 -0.011 0.096 -9999 0 -0.63 5 5
elevation of cytosolic calcium ion concentration -0.14 0.21 -9999 0 -0.46 53 53
alphaM/beta2 Integrin/JAM2/JAM3 -0.22 0.2 -9999 0 -0.74 6 6
JAM2 -0.36 0.32 -9999 0 -0.64 130 130
alphaM/beta2 Integrin/ICAM1 -0.044 0.15 -9999 0 -0.76 3 3
alphaM/beta2 Integrin/uPA/Plg -0.14 0.2 -9999 0 -0.46 53 53
RhoA/GTP 0.002 0.12 -9999 0 -0.39 9 9
positive regulation of phagocytosis -0.054 0.12 -9999 0 -0.68 5 5
Ron/MSP -0.024 0.11 -9999 0 -0.54 10 10
alphaM/beta2 Integrin/uPAR/uPA -0.14 0.21 -9999 0 -0.46 53 53
alphaM/beta2 Integrin/uPAR -0.021 0.081 -9999 0 -0.55 3 3
PLAU -0.19 0.33 -9999 0 -0.72 63 63
PLAT 0.011 0.066 -9999 0 -0.68 2 2
actin filament polymerization 0.003 0.13 -9999 0 -0.52 3 3
MST1 -0.016 0.15 -9999 0 -0.72 10 10
alphaM/beta2 Integrin/lipoprotein(a) -0.008 0.064 -9999 0 -0.65 1 1
TNF -0.053 0.17 -9999 0 -0.71 2 2
RAP1B 0.017 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.16 0.22 -9999 0 -0.5 65 65
fibrinolysis -0.13 0.2 -9999 0 -0.45 53 53
HCK -0.045 0.19 -9999 0 -0.64 21 21
dendritic cell antigen processing and presentation -0.002 0.12 -9999 0 -0.48 4 4
VTN 0.017 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 -0.058 0.15 -9999 0 -0.5 20 20
LPA 0.017 0 -9999 0 -10000 0 0
LRP1 0.017 0 -9999 0 -10000 0 0
cell migration -0.026 0.12 -9999 0 -0.63 6 6
FN1 -0.07 0.24 -9999 0 -0.72 26 26
alphaM/beta2 Integrin/Thy1 -0.079 0.17 -9999 0 -0.49 30 30
MPO -0.03 0.18 -9999 0 -0.72 14 14
KNG1 -0.004 0.12 -9999 0 -0.65 7 7
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 0.013 0.12 -9999 0 -0.42 2 2
ELA2 0.017 0 -9999 0 -10000 0 0
PLG 0.017 0 -9999 0 -10000 0 0
CTGF 0.01 0.07 -9999 0 -0.72 2 2
alphaM/beta2 Integrin/Hck -0.055 0.15 -9999 0 -0.48 22 22
ITGAM -0.003 0.063 -9999 0 -0.63 2 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.059 0.16 -9999 0 -0.76 5 5
HP 0.017 0 -9999 0 -10000 0 0
leukocyte adhesion -0.25 0.19 -9999 0 -0.7 11 11
SELP -0.068 0.22 -9999 0 -0.64 29 29
S1P1 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
VEGFR2 homodimer/VEGFA homodimer -0.068 0.18 -9999 0 -0.56 21 21
PDGFRB 0.013 0.007 -9999 0 -10000 0 0
SPHK1 -0.048 0.087 -9999 0 -0.3 19 19
mol:S1P -0.087 0.14 -9999 0 -0.37 39 39
S1P1/S1P/Gi -0.086 0.2 -9999 0 -0.55 15 15
GNAO1 0.012 0.008 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.13 0.16 -9999 0 -0.52 18 18
PLCG1 -0.096 0.21 -9999 0 -0.55 19 19
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.013 0.007 -9999 0 -10000 0 0
GNAI2 0.012 0.008 -9999 0 -10000 0 0
GNAI3 0.012 0.008 -9999 0 -10000 0 0
GNAI1 -0.073 0.22 -9999 0 -0.64 29 29
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.052 0.23 -9999 0 -0.79 13 13
S1P1/S1P -0.14 0.22 -9999 0 -0.68 21 21
negative regulation of cAMP metabolic process -0.083 0.19 -9999 0 -0.53 15 15
MAPK3 -0.1 0.22 -9999 0 -0.57 15 15
calcium-dependent phospholipase C activity -0.003 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.011 0.043 -9999 0 -10000 0 0
PLCB2 -0.078 0.21 -9999 0 -0.58 21 21
RAC1 0.017 0 -9999 0 -10000 0 0
RhoA/GTP -0.11 0.18 -9999 0 -0.54 21 21
receptor internalization -0.12 0.2 -9999 0 -0.62 21 21
PTGS2 -0.14 0.28 -9999 0 -0.59 34 34
Rac1/GTP -0.11 0.18 -9999 0 -0.54 21 21
RHOA 0.017 0 -9999 0 -10000 0 0
VEGFA -0.059 0.22 -9999 0 -0.73 21 21
negative regulation of T cell proliferation -0.083 0.19 -9999 0 -0.53 15 15
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.012 0.008 -9999 0 -10000 0 0
MAPK1 -0.1 0.22 -9999 0 -0.56 14 14
S1P1/S1P/PDGFB-D/PDGFRB -0.1 0.25 -9999 0 -0.7 21 21
ABCC1 -0.061 0.23 -9999 0 -0.73 23 23
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.014 0.078 -10000 0 -0.45 7 7
cell-cell adhesion 0.17 0.2 0.63 21 -10000 0 21
Ephrin B/EPHB2/RasGAP -0.016 0.076 -10000 0 -10000 0 0
ITSN1 0.017 0 -10000 0 -10000 0 0
PIK3CA 0.017 0 -10000 0 -10000 0 0
SHC1 0.017 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.052 0.14 -10000 0 -0.46 25 25
Ephrin B1/EPHB1 -0.17 0.23 -10000 0 -0.47 82 82
HRAS/GDP -0.16 0.2 -10000 0 -0.63 19 19
Ephrin B/EPHB1/GRB7 -0.16 0.2 -10000 0 -0.78 5 5
Endophilin/SYNJ1 0.038 0.073 -10000 0 -10000 0 0
KRAS 0.017 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.14 0.19 -10000 0 -0.78 1 1
endothelial cell migration -0.068 0.15 -10000 0 -0.39 38 38
GRB2 0.017 0 -10000 0 -10000 0 0
GRB7 -0.01 0.14 -10000 0 -0.72 8 8
PAK1 0.048 0.074 -10000 0 -10000 0 0
HRAS 0.017 0 -10000 0 -10000 0 0
RRAS 0.038 0.074 -10000 0 -10000 0 0
DNM1 0.01 0.07 -10000 0 -0.72 2 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.1 0.2 -10000 0 -0.68 2 2
lamellipodium assembly -0.17 0.2 -10000 0 -0.63 21 21
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.042 0.13 -10000 0 -0.42 1 1
PIK3R1 0.017 0 -10000 0 -10000 0 0
EPHB2 -0.003 0.12 -10000 0 -0.71 6 6
EPHB3 -0.065 0.23 -10000 0 -0.71 25 25
EPHB1 -0.26 0.36 -10000 0 -0.72 82 82
EPHB4 -0.11 0.28 -10000 0 -0.72 38 38
mol:GDP -0.14 0.2 -10000 0 -0.59 19 19
Ephrin B/EPHB2 -0.013 0.069 -10000 0 -0.39 6 6
Ephrin B/EPHB3 -0.046 0.12 -10000 0 -0.39 23 23
JNK cascade -0.12 0.23 -10000 0 -0.75 7 7
Ephrin B/EPHB1 -0.15 0.19 -10000 0 -0.39 82 82
RAP1/GDP -0.11 0.18 -10000 0 -0.51 18 18
EFNB2 0.011 0.066 -10000 0 -0.68 2 2
EFNB3 0.017 0 -10000 0 -10000 0 0
EFNB1 0.017 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.17 0.22 -10000 0 -0.44 85 85
RAP1B 0.017 0 -10000 0 -10000 0 0
RAP1A 0.017 0 -10000 0 -10000 0 0
CDC42/GTP -0.12 0.16 -10000 0 -0.6 6 6
Rap1/GTP -0.12 0.16 -10000 0 -0.6 6 6
axon guidance -0.014 0.078 -10000 0 -0.44 7 7
MAPK3 -0.02 0.12 -10000 0 -10000 0 0
MAPK1 -0.018 0.12 -10000 0 -0.5 1 1
Rac1/GDP -0.09 0.21 -10000 0 -0.54 18 18
actin cytoskeleton reorganization -0.13 0.16 -10000 0 -0.48 23 23
CDC42/GDP -0.09 0.21 -10000 0 -0.54 18 18
PI3K -0.069 0.15 -10000 0 -0.4 38 38
EFNA5 0.014 0.044 -10000 0 -0.64 1 1
Ephrin B2/EPHB4 -0.084 0.18 -10000 0 -0.48 39 39
Ephrin B/EPHB2/Intersectin/N-WASP 0.04 0.054 -10000 0 -10000 0 0
CDC42 0.017 0 -10000 0 -10000 0 0
RAS family/GTP -0.12 0.16 -10000 0 -0.6 7 7
PTK2 0.035 0.07 -10000 0 -0.71 1 1
MAP4K4 -0.12 0.23 -10000 0 -0.76 7 7
SRC 0.017 0 -10000 0 -10000 0 0
KALRN 0.017 0 -10000 0 -10000 0 0
Intersectin/N-WASP -0.002 0.031 -10000 0 -0.46 1 1
neuron projection morphogenesis -0.066 0.19 -10000 0 -0.49 5 5
MAP2K1 -0.029 0.12 -10000 0 -0.38 1 1
WASL 0.014 0.044 -10000 0 -0.64 1 1
Ephrin B1/EPHB1-2/NCK1 -0.16 0.21 -10000 0 -0.82 4 4
cell migration -0.02 0.13 -10000 0 -0.4 1 1
NRAS 0.007 0.085 -10000 0 -0.72 3 3
SYNJ1 0.038 0.074 -10000 0 -10000 0 0
PXN 0.017 0 -10000 0 -10000 0 0
TF 0.048 0.071 -10000 0 -10000 0 0
HRAS/GTP -0.13 0.17 -10000 0 -0.66 5 5
Ephrin B1/EPHB1-2 -0.17 0.22 -10000 0 -0.44 84 84
cell adhesion mediated by integrin -0.012 0.076 0.35 1 -10000 0 1
RAC1 0.017 0 -10000 0 -10000 0 0
mol:GTP -0.14 0.18 -10000 0 -0.72 5 5
RAC1-CDC42/GTP -0.15 0.18 -10000 0 -0.62 13 13
RASA1 0.01 0.07 -10000 0 -0.72 2 2
RAC1-CDC42/GDP -0.11 0.18 -10000 0 -0.51 18 18
ruffle organization -0.13 0.24 -10000 0 -0.64 22 22
NCK1 0.017 0 -10000 0 -10000 0 0
receptor internalization 0.044 0.08 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN -0.013 0.067 -10000 0 -10000 0 0
ROCK1 -0.015 0.14 -10000 0 -0.41 25 25
RAS family/GDP -0.12 0.14 -10000 0 -0.45 20 20
Rac1/GTP -0.18 0.22 -10000 0 -0.69 21 21
Ephrin B/EPHB1/Src/Paxillin -0.047 0.13 -10000 0 -0.42 1 1
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.007 0.051 -9999 0 -0.38 4 4
RGS9BP -0.003 0.12 -9999 0 -0.72 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + -0.14 0.2 -9999 0 -0.41 77 77
mol:ADP 0.013 0.038 -9999 0 -0.55 1 1
GNAT2 0.007 0.085 -9999 0 -0.72 3 3
RGS9-1/Gbeta5/R9AP -0.15 0.2 -9999 0 -0.54 9 9
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.008 0.06 -9999 0 -0.45 4 4
GRK7 0.014 0.05 -9999 0 -0.72 1 1
CNGB3 -0.007 0.13 -9999 0 -0.72 7 7
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.1 0.19 -9999 0 -0.36 77 77
Cone PDE6 -0.12 0.16 -9999 0 -0.71 2 2
Cone Metarhodopsin II -0.002 0.029 -9999 0 -0.44 1 1
Na + (4 Units) -0.12 0.17 -9999 0 -0.46 7 7
GNAT2/GDP -0.13 0.17 -9999 0 -0.72 3 3
GNB5 0.007 0.085 -9999 0 -0.72 3 3
mol:GMP (4 units) 0.025 0.065 -9999 0 -0.4 5 5
Cone Transducin -0.007 0.054 -9999 0 -0.4 4 4
SLC24A2 0.017 0 -9999 0 -10000 0 0
GNB3/GNGT2 -0.002 0.031 -9999 0 -0.46 1 1
GNB3 0.017 0 -9999 0 -10000 0 0
GNAT2/GTP -0.007 0.064 -9999 0 -0.55 3 3
CNGA3 -0.19 0.3 -9999 0 -0.64 71 71
ARR3 0.017 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.14 0.2 -9999 0 -0.41 77 77
mol:Pi -0.15 0.2 -9999 0 -0.53 9 9
Cone CNG Channel -0.12 0.16 -9999 0 -0.66 2 2
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.017 0 -9999 0 -10000 0 0
RGS9 -0.2 0.31 -9999 0 -0.64 74 74
PDE6C 0.014 0.05 -9999 0 -0.72 1 1
GNGT2 0.014 0.044 -9999 0 -0.64 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.014 0.044 -9999 0 -0.64 1 1
Ephrin B reverse 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
EFNB2 0.011 0.066 -10000 0 -0.68 2 2
EPHB2 -0.005 0.12 -10000 0 -0.71 6 6
EFNB1 0.022 0.054 -10000 0 -0.54 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.19 -10000 0 -0.7 7 7
Ephrin B2/EPHB1-2 -0.17 0.22 -10000 0 -0.44 85 85
neuron projection morphogenesis -0.14 0.18 -10000 0 -0.66 7 7
Ephrin B1/EPHB1-2/Tiam1 -0.16 0.21 -10000 0 -0.76 7 7
DNM1 0.009 0.07 -10000 0 -0.72 2 2
cell-cell signaling -0.003 0.004 -10000 0 -10000 0 0
MAP2K4 -0.065 0.15 -10000 0 -0.75 5 5
YES1 -0.094 0.18 -10000 0 -1 4 4
Ephrin B1/EPHB1-2/NCK2 -0.15 0.2 -10000 0 -0.77 5 5
PI3K -0.059 0.15 -10000 0 -0.81 4 4
mol:GDP -0.16 0.21 -10000 0 -0.74 7 7
ITGA2B 0.017 0 -10000 0 -10000 0 0
endothelial cell proliferation -0.084 0.18 -10000 0 -0.48 39 39
FYN -0.095 0.18 -10000 0 -0.91 5 5
MAP3K7 -0.082 0.15 -10000 0 -0.85 4 4
FGR -0.096 0.18 -10000 0 -1 4 4
TIAM1 0.011 0.062 -10000 0 -0.64 2 2
PIK3R1 0.017 0 -10000 0 -10000 0 0
RGS3 0.017 0 -10000 0 -10000 0 0
cell adhesion -0.034 0.14 -10000 0 -0.73 4 4
LYN -0.094 0.18 -10000 0 -1 4 4
Ephrin B1/EPHB1-2/Src Family Kinases -0.089 0.17 -10000 0 -0.97 4 4
Ephrin B1/EPHB1-2 -0.099 0.16 -10000 0 -0.92 4 4
SRC -0.096 0.18 -10000 0 -1 4 4
ITGB3 0.017 0 -10000 0 -10000 0 0
EPHB1 -0.26 0.36 -10000 0 -0.72 82 82
EPHB4 -0.11 0.28 -10000 0 -0.72 38 38
RAC1 0.017 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.084 0.18 -10000 0 -0.48 39 39
alphaIIb/beta3 Integrin 0 0 -10000 0 -10000 0 0
BLK -0.14 0.2 -10000 0 -0.56 21 21
HCK -0.11 0.19 -10000 0 -0.78 8 8
regulation of stress fiber formation 0.15 0.2 0.76 5 -10000 0 5
MAPK8 -0.051 0.14 -10000 0 -0.7 5 5
Ephrin B1/EPHB1-2/RGS3 -0.15 0.2 -10000 0 -0.77 5 5
endothelial cell migration -0.14 0.2 -10000 0 -0.49 41 41
NCK2 0.017 0 -10000 0 -10000 0 0
PTPN13 -0.2 0.32 -10000 0 -0.68 70 70
regulation of focal adhesion formation 0.15 0.2 0.76 5 -10000 0 5
chemotaxis 0.15 0.2 0.76 5 -10000 0 5
PIK3CA 0.017 0 -10000 0 -10000 0 0
Rac1/GTP -0.14 0.19 -10000 0 -0.69 7 7
angiogenesis -0.099 0.16 -10000 0 -0.91 4 4
LCK -0.097 0.18 -10000 0 -1 4 4
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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 0.014 0.05 -10000 0 -0.72 1 1
NFATC1 0.058 0.046 -10000 0 -10000 0 0
NFATC2 0.035 0.047 -10000 0 -0.21 1 1
NFATC3 0.021 0.002 -10000 0 -10000 0 0
YWHAE 0.014 0.05 -10000 0 -0.72 1 1
Calcineurin A alpha-beta B1/CABIN1 -0.1 0.14 -10000 0 -0.45 9 9
Exportin 1/Ran/NUP214 -0.002 0.031 -10000 0 -0.46 1 1
mol:DAG 0.001 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.092 0.091 -10000 0 -0.49 3 3
BCL2/BAX -0.3 0.22 -10000 0 -0.46 146 146
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.002 -10000 0 -10000 0 0
CaM/Ca2+ 0.015 0.002 -10000 0 -10000 0 0
BAX 0.014 0.05 -10000 0 -0.72 1 1
MAPK14 0.017 0.002 -10000 0 -10000 0 0
BAD 0.017 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.089 0.14 -10000 0 -0.52 4 4
Calcineurin A alpha-beta B1/BCL2 -0.41 0.31 -10000 0 -0.63 145 145
FKBP8 0.017 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.088 0.14 0.52 4 -10000 0 4
KPNB1 -0.003 0.12 -10000 0 -0.72 6 6
KPNA2 -0.013 0.15 -10000 0 -0.72 9 9
XPO1 0.017 0 -10000 0 -10000 0 0
SFN 0.011 0.062 -10000 0 -0.64 2 2
MAP3K8 -0.086 0.26 -10000 0 -0.72 31 31
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.005 0.027 -10000 0 -10000 0 0
CABIN1 -0.1 0.14 -10000 0 -0.45 9 9
CALM1 0.018 0.002 -10000 0 -10000 0 0
RAN 0.014 0.05 -10000 0 -0.72 1 1
MAP3K1 0.017 0 -10000 0 -10000 0 0
CAMK4 0.017 0 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.002 -10000 0 -10000 0 0
MAPK3 0.011 0.062 -10000 0 -0.64 2 2
YWHAH 0.017 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.008 0.061 -10000 0 -0.46 4 4
YWHAB 0.017 0 -10000 0 -10000 0 0
MAPK8 0.018 0.002 -10000 0 -10000 0 0
MAPK9 0.017 0 -10000 0 -10000 0 0
YWHAG 0.017 0 -10000 0 -10000 0 0
FKBP1A 0.017 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.001 0.023 -10000 0 -10000 0 0
PRKCH 0.008 0.075 -10000 0 -0.64 3 3
CABIN1/Cbp/p300 0 0 -10000 0 -10000 0 0
CASP3 0.014 0.044 -10000 0 -0.63 1 1
PIM1 0.017 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.09 0.066 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.057 0.024 -10000 0 -10000 0 0
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.017 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.029 0.003 -10000 0 -10000 0 0
BAD/BCL-XL -0.002 0.036 -10000 0 -0.54 1 1
PRKCD 0.017 0 -10000 0 -10000 0 0
NUP214 0.017 0 -10000 0 -10000 0 0
PRKCZ 0.001 0.001 -10000 0 -10000 0 0
PRKCA 0.014 0.05 -10000 0 -0.72 1 1
PRKCG 0.004 0.098 -10000 0 -0.72 4 4
PRKCQ 0 0.11 -10000 0 -0.72 5 5
FKBP38/BCL2 -0.3 0.22 -10000 0 -0.46 145 145
EP300 0.018 0.001 -10000 0 -10000 0 0
PRKCB1 -0.36 0.32 -10000 0 -0.64 127 127
CSNK2A1 0.017 0 -10000 0 -10000 0 0
NFATc/JNK1 0.066 0.045 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.028 0.003 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0 0 -10000 0 -10000 0 0
NFATc/ERK1 0.062 0.054 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.093 0.091 -10000 0 -0.49 3 3
NR4A1 0.073 0.072 -10000 0 -0.57 2 2
GSK3B 0.014 0.05 -10000 0 -0.72 1 1
positive T cell selection 0.021 0.002 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.008 0.021 -10000 0 -10000 0 0
RCH1/ KPNB1 -0.036 0.14 -10000 0 -0.57 14 14
YWHAQ 0.017 0 -10000 0 -10000 0 0
PRKACA 0.017 0.002 -10000 0 -10000 0 0
AKAP5 0.005 0.087 -10000 0 -0.64 4 4
MEF2D 0.018 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.017 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.066 0.045 -10000 0 -10000 0 0
CREBBP 0.018 0.001 -10000 0 -10000 0 0
BCL2 -0.41 0.31 -10000 0 -0.64 145 145
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.014 0.086 -9999 0 -0.42 4 4
STMN1 0.03 0.039 -9999 0 -0.55 1 1
Aurora B/RasGAP/Survivin -0.033 0.16 -9999 0 -0.47 24 24
Chromosomal passenger complex/Cul3 protein complex -0.066 0.15 -9999 0 -0.45 14 14
BIRC5 -0.062 0.23 -9999 0 -0.73 23 23
DES -0.032 0.15 -9999 0 -0.67 11 11
Aurora C/Aurora B/INCENP 0.013 0.054 -9999 0 -0.42 3 3
Aurora B/TACC1 0.015 0.015 -9999 0 -10000 0 0
Aurora B/PP2A 0.016 0.016 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.02 0.029 -9999 0 -0.23 3 3
mitotic metaphase/anaphase transition 0.003 0.006 -9999 0 -10000 0 0
NDC80 0.027 0.055 -9999 0 -0.55 2 2
Cul3 protein complex -0.14 0.19 -9999 0 -0.4 76 76
KIF2C -0.03 0.093 -9999 0 -0.28 17 17
PEBP1 0.012 0.008 -9999 0 -10000 0 0
KIF20A -0.071 0.24 -9999 0 -0.72 27 27
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.011 0.056 -9999 0 -0.55 2 2
SEPT1 0.017 0 -9999 0 -10000 0 0
SMC2 -0.023 0.17 -9999 0 -0.72 12 12
SMC4 0.007 0.085 -9999 0 -0.72 3 3
NSUN2/NPM1/Nucleolin 0.02 0.049 -9999 0 -10000 0 0
PSMA3 0.017 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.001 0.005 -9999 0 -10000 0 0
H3F3B 0.025 0.003 -9999 0 -10000 0 0
AURKB 0.021 0.008 -9999 0 -10000 0 0
AURKC 0.017 0 -9999 0 -10000 0 0
CDCA8 0.007 0.071 -9999 0 -0.74 2 2
cytokinesis -0.09 0.17 -9999 0 -0.57 18 18
Aurora B/Septin1 -0.073 0.16 -9999 0 -0.54 16 16
AURKA -0.084 0.25 -9999 0 -0.72 30 30
INCENP 0.003 0.087 -9999 0 -0.74 3 3
KLHL13 -0.21 0.32 -9999 0 -0.65 76 76
BUB1 -0.27 0.36 -9999 0 -0.72 85 85
hSgo1/Aurora B/Survivin -0.049 0.18 -9999 0 -0.48 30 30
EVI5 0.017 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.12 0.22 -9999 0 -0.6 34 34
SGOL1 -0.02 0.16 -9999 0 -0.72 11 11
CENPA -0.058 0.14 -9999 0 -0.36 28 28
NCAPG 0 0 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.016 0.016 -9999 0 -10000 0 0
NCAPD2 0.01 0.07 -9999 0 -0.72 2 2
Aurora B/PP1-gamma 0.016 0.016 -9999 0 -10000 0 0
RHOA 0.017 0 -9999 0 -10000 0 0
NCAPH -0.01 0.14 -9999 0 -0.72 8 8
NPM1 0.004 0.024 -9999 0 -10000 0 0
RASA1 0.01 0.07 -9999 0 -0.72 2 2
KLHL9 0.017 0 -9999 0 -10000 0 0
mitotic prometaphase -0.003 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.016 -9999 0 -10000 0 0
PPP1CC 0.017 0 -9999 0 -10000 0 0
Centraspindlin -0.14 0.25 -9999 0 -0.64 36 36
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 0.003 0.03 -9999 0 -10000 0 0
MYLK -0.02 0.12 -9999 0 -0.37 25 25
KIF23 -0.088 0.26 -9999 0 -0.73 31 31
VIM 0.021 0.075 -9999 0 -0.47 5 5
RACGAP1 -0.02 0.16 -9999 0 -0.73 10 10
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.006 0.015 -9999 0 -10000 0 0
Chromosomal passenger complex -0.062 0.15 -9999 0 -0.41 22 22
Chromosomal passenger complex/EVI5 -0.02 0.16 -9999 0 -0.79 3 3
TACC1 0.017 0 -9999 0 -10000 0 0
PPP2R5D 0.017 0 -9999 0 -10000 0 0
CUL3 0.017 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.059 0.22 -10000 0 -0.72 22 22
GNB1/GNG2 -0.093 0.063 -10000 0 -0.21 9 9
AKT1 -0.052 0.089 -10000 0 -10000 0 0
EGF -0.18 0.31 -10000 0 -0.68 64 64
mol:TXA2 -0.001 0 -10000 0 -10000 0 0
FGR -0.12 0.095 -10000 0 -10000 0 0
mol:Ca2+ -0.092 0.12 -10000 0 -0.33 7 7
LYN -0.12 0.095 -10000 0 -10000 0 0
RhoA/GTP -0.041 0.039 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.097 0.14 -10000 0 -0.37 5 5
GNG2 0.017 0 -10000 0 -10000 0 0
ARRB2 0.017 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.034 0.11 -10000 0 -0.56 6 6
G beta5/gamma2 -0.12 0.087 -10000 0 -0.29 12 12
PRKCH -0.099 0.14 -10000 0 -0.44 7 7
DNM1 0.01 0.07 -10000 0 -0.72 2 2
TXA2/TP beta/beta Arrestin3 -0.031 0.027 -10000 0 -0.26 1 1
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.49 0.27 -10000 0 -0.64 174 174
G12 family/GTP -0.11 0.096 -10000 0 -0.31 10 10
ADRBK1 0.017 0 -10000 0 -10000 0 0
ADRBK2 0.017 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.12 0.1 0.29 26 -10000 0 26
mol:NADP 0.013 0.049 -10000 0 -0.72 1 1
RAB11A 0.017 0 -10000 0 -10000 0 0
PRKG1 0.017 0 -10000 0 -10000 0 0
mol:IP3 -0.12 0.15 -10000 0 -0.4 11 11
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.15 0.19 -10000 0 -0.54 13 13
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.2 0.17 -10000 0 -0.45 55 55
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.14 0.13 -10000 0 -0.45 19 19
RHOA 0.017 0 -10000 0 -10000 0 0
PTGIR 0.017 0 -10000 0 -10000 0 0
PRKCB1 -0.17 0.18 -10000 0 -0.47 29 29
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.013 0.049 -10000 0 -0.72 1 1
TXA2/TXA2-R family -0.15 0.2 -10000 0 -0.55 13 13
LCK -0.12 0.1 -10000 0 -0.48 2 2
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.17 0.091 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma -0.027 0.038 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.17 0.091 -10000 0 -10000 0 0
MAPK14 -0.058 0.099 -10000 0 -10000 0 0
TGM2/GTP -0.14 0.18 -10000 0 -0.5 11 11
MAPK11 -0.059 0.1 -10000 0 -0.41 1 1
ARHGEF1 -0.045 0.077 -10000 0 -10000 0 0
GNAI2 0.017 0 -10000 0 -10000 0 0
JNK cascade -0.12 0.15 -10000 0 -0.4 13 13
RAB11/GDP 0.018 0.001 -10000 0 -10000 0 0
ICAM1 -0.083 0.13 -10000 0 -0.37 12 12
cAMP biosynthetic process -0.12 0.14 -10000 0 -0.4 8 8
Gq family/GTP/EBP50 0.003 0.085 -10000 0 -0.28 10 10
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.12 0.095 -10000 0 -10000 0 0
GNB5 0.007 0.085 -10000 0 -0.72 3 3
GNB1 0.017 0 -10000 0 -10000 0 0
EGF/EGFR -0.13 0.11 -10000 0 -0.36 10 10
VCAM1 -0.077 0.12 -10000 0 -0.43 5 5
TP beta/Gq family/GDP/G beta5/gamma2 -0.034 0.11 -10000 0 -0.56 6 6
platelet activation -0.08 0.13 -10000 0 -0.34 4 4
PGI2/IP 0 0 -10000 0 -10000 0 0
PRKACA -0.22 0.13 -10000 0 -10000 0 0
Gq family/GDP/G beta5/gamma2 -0.052 0.11 -10000 0 -0.56 6 6
TXA2/TP beta/beta Arrestin2 -0.019 0.03 -10000 0 -0.33 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.2 0.13 -10000 0 -10000 0 0
mol:DAG -0.12 0.16 -10000 0 -0.44 12 12
EGFR 0.002 0.099 -10000 0 -0.65 5 5
TXA2/TP alpha -0.16 0.19 -10000 0 -0.52 13 13
Gq family/GTP 0.001 0.077 -10000 0 -0.25 14 14
YES1 -0.12 0.095 -10000 0 -10000 0 0
GNAI2/GTP -0.15 0.081 -10000 0 -10000 0 0
PGD2/DP -0.37 0.2 -10000 0 -0.48 174 174
SLC9A3R1 0.005 0.087 -10000 0 -0.64 4 4
FYN -0.12 0.098 -10000 0 -0.46 1 1
mol:NO 0.013 0.049 -10000 0 -0.72 1 1
GNA15 -0.006 0.13 -10000 0 -0.72 7 7
PGK/cGMP -0.002 0.031 -10000 0 -0.47 1 1
RhoA/GDP 0.018 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.2 0.14 -10000 0 -0.58 16 16
NOS3 0.013 0.05 -10000 0 -0.72 1 1
RAC1 0.017 0 -10000 0 -10000 0 0
PRKCA -0.097 0.14 -10000 0 -0.39 5 5
PRKCB -0.1 0.14 -10000 0 -0.36 13 13
PRKCE -0.095 0.14 -10000 0 -0.38 7 7
PRKCD -0.098 0.14 -10000 0 -0.4 5 5
PRKCG -0.11 0.15 -10000 0 -0.45 10 10
muscle contraction -0.14 0.18 -10000 0 -0.5 13 13
PRKCZ -0.1 0.14 -10000 0 -0.36 13 13
ARR3 0.017 0 -10000 0 -10000 0 0
TXA2/TP beta -0.18 0.092 -10000 0 -10000 0 0
PRKCQ -0.1 0.14 -10000 0 -0.4 8 8
MAPKKK cascade -0.13 0.17 -10000 0 -0.48 13 13
SELE -0.1 0.15 -10000 0 -0.36 33 33
TP beta/GNAI2/GDP/G beta/gamma -0.16 0.087 -10000 0 -10000 0 0
ROCK1 0.017 0 -10000 0 -10000 0 0
GNA14 -0.01 0.13 -10000 0 -0.64 9 9
chemotaxis -0.16 0.21 -10000 0 -0.6 14 14
GNA12 0.017 0 -10000 0 -10000 0 0
GNA13 0.017 0 -10000 0 -10000 0 0
GNA11 -0.001 0.11 -10000 0 -0.64 6 6
Rac1/GTP 0 0 -10000 0 -10000 0 0
Glypican 2 network

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
MDK -0.023 0.17 -9999 0 -0.72 12 12
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.03 0.12 -9999 0 -0.55 12 12
neuron projection morphogenesis -0.03 0.12 -9999 0 -0.55 12 12
Regulation of Telomerase

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
Telomerase catalytic core complex -0.093 0.15 -9999 0 -10000 0 0
RAD9A 0.017 0 -9999 0 -10000 0 0
AP1 -0.081 0.18 -9999 0 -0.49 37 37
IFNAR2 0.017 0.007 -9999 0 -10000 0 0
AKT1 0.025 0.043 -9999 0 -10000 0 0
ER alpha/Oestrogen -0.013 0.077 -9999 0 -0.47 6 6
NFX1/SIN3/HDAC complex 0.056 0.029 -9999 0 -10000 0 0
EGF -0.18 0.31 -9999 0 -0.67 64 64
SMG5 0.017 0 -9999 0 -10000 0 0
SMG6 0.017 0 -9999 0 -10000 0 0
SP3/HDAC2 0.019 0.015 -9999 0 -10000 0 0
TERT/c-Abl -0.09 0.13 -9999 0 -10000 0 0
SAP18 0.014 0.049 -9999 0 -0.72 1 1
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.39 0.37 -9999 0 -0.72 122 122
WRN 0.017 0 -9999 0 -10000 0 0
SP1 0.018 0.008 -9999 0 -10000 0 0
SP3 0.016 0.005 -9999 0 -10000 0 0
TERF2IP 0.017 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.18 0.2 -9999 0 -0.67 8 8
Mad/Max -0.025 0.1 -9999 0 -0.46 12 12
TERT -0.095 0.15 -9999 0 -10000 0 0
CCND1 -0.12 0.22 -9999 0 -0.73 3 3
MAX 0.016 0.006 -9999 0 -10000 0 0
RBBP7 0.017 0.001 -9999 0 -10000 0 0
RBBP4 0.017 0.001 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.017 0 -9999 0 -10000 0 0
SIN3A 0.017 0.001 -9999 0 -10000 0 0
Telomerase/911 -0.059 0.14 -9999 0 -0.5 1 1
CDKN1B -0.063 0.21 -9999 0 -0.44 51 51
RAD1 -0.013 0.15 -9999 0 -0.72 9 9
XRCC5 0.017 0 -9999 0 -10000 0 0
XRCC6 0.017 0 -9999 0 -10000 0 0
SAP30 0.017 0.001 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.016 0.005 -9999 0 -10000 0 0
JUN 0 0.11 -9999 0 -0.72 5 5
E6 0 0.002 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.013 0.006 -9999 0 -10000 0 0
FOS -0.081 0.23 -9999 0 -0.64 33 33
IFN-gamma/IRF1 -0.12 0.22 -9999 0 -0.52 51 51
PARP2 0.017 0 -9999 0 -10000 0 0
BLM 0.007 0.085 -9999 0 -0.72 3 3
Telomerase -0.063 0.15 -9999 0 -0.37 5 5
IRF1 0.015 0.067 -9999 0 -0.67 2 2
ESR1 0 0.11 -9999 0 -0.64 6 6
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.061 0.033 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.062 0.033 -9999 0 -10000 0 0
HDAC1 0.017 0.001 -9999 0 -10000 0 0
HDAC2 0.017 0.007 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.026 0.047 -9999 0 -0.46 2 2
ABL1 0.017 0 -9999 0 -10000 0 0
MXD1 -0.019 0.15 -9999 0 -0.64 12 12
MRE11A 0.017 0 -9999 0 -10000 0 0
HUS1 0.017 0 -9999 0 -10000 0 0
RPS6KB1 0.014 0.05 -9999 0 -0.72 1 1
TERT/NF kappa B1/14-3-3 -0.064 0.12 -9999 0 -10000 0 0
NR2F2 0.016 0.005 -9999 0 -10000 0 0
MAPK3 0.027 0.047 -9999 0 -0.46 2 2
MAPK1 0.029 0.034 -9999 0 -0.47 1 1
TGFB1/TGF beta receptor Type II 0.017 0.001 -9999 0 -10000 0 0
NFKB1 0.017 0 -9999 0 -10000 0 0
HNRNPC 0.017 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.017 0 -9999 0 -10000 0 0
EGFR 0.002 0.1 -9999 0 -0.65 5 5
mol:Oestrogen 0 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.15 0.23 -9999 0 -0.5 68 68
MYC -0.42 0.36 -9999 0 -0.72 131 131
IL2 0.018 0.008 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.017 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0.05 -9999 0 -0.72 1 1
TGFB1 0.017 0.001 -9999 0 -10000 0 0
TRF2/BLM -0.007 0.058 -9999 0 -0.5 3 3
FRAP1 0.017 0 -9999 0 -10000 0 0
KU/TERT -0.083 0.13 -9999 0 -10000 0 0
SP1/HDAC2 0.029 0.012 -9999 0 -10000 0 0
PINX1 0.014 0.05 -9999 0 -0.72 1 1
Telomerase/EST1A -0.18 0.2 -9999 0 -0.67 8 8
Smad3/Myc -0.26 0.25 -9999 0 -0.46 131 131
911 complex -0.019 0.09 -9999 0 -0.46 9 9
IFNG -0.14 0.3 -9999 0 -0.71 50 50
Telomerase/PinX1 -0.18 0.2 -9999 0 -0.67 8 8
Telomerase/AKT1/mTOR/p70S6K -0.044 0.12 -9999 0 -10000 0 0
SIN3B 0.017 0.001 -9999 0 -10000 0 0
YWHAE 0.014 0.05 -9999 0 -0.72 1 1
Telomerase/EST1B -0.18 0.2 -9999 0 -0.67 8 8
response to DNA damage stimulus 0.005 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.18 0.2 -9999 0 -0.67 8 8
E2F1 -0.03 0.18 -9999 0 -0.72 14 14
ZNFX1 0.014 0.05 -9999 0 -0.72 1 1
PIF1 0.004 0.098 -9999 0 -0.72 4 4
NCL 0.017 0 -9999 0 -10000 0 0
DKC1 -0.2 0.34 -9999 0 -0.72 66 66
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.014 0.044 -9999 0 -0.64 1 1
SPHK1 -0.073 0.24 -9999 0 -0.72 27 27
GNAI2 0.017 0 -9999 0 -10000 0 0
mol:S1P -0.032 0.12 -9999 0 -0.25 49 49
GNAO1 0.017 0 -9999 0 -10000 0 0
mol:Sphinganine-1-P -0.04 0.19 -9999 0 -0.55 27 27
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.037 0.074 -9999 0 -0.42 2 2
GNAI3 0.017 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 -0.021 0.15 -9999 0 -0.64 13 13
S1P1/S1P -0.042 0.14 -9999 0 -0.43 15 15
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 -0.068 0.22 -9999 0 -0.64 29 29
S1P/S1P5/G12 -0.041 0.082 -9999 0 -0.45 2 2
S1P/S1P3/Gq -0.019 0.12 -9999 0 -0.39 9 9
S1P/S1P4/Gi -0.008 0.099 -9999 0 -0.35 5 5
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.017 0 -9999 0 -10000 0 0
GNA14 -0.01 0.13 -9999 0 -0.64 9 9
GNA15 -0.006 0.13 -9999 0 -0.72 7 7
GNA12 0.017 0 -9999 0 -10000 0 0
GNA13 0.017 0 -9999 0 -10000 0 0
GNA11 -0.001 0.11 -9999 0 -0.64 6 6
ABCC1 -0.06 0.22 -9999 0 -0.72 23 23
PLK2 and PLK4 events

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
PLK2 -0.006 0.13 -9999 0 -0.72 7 7
PLK4 -0.003 0.12 -9999 0 -0.72 6 6
regulation of centriole replication -0.002 0.13 -9999 0 -0.54 13 13
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.16 0.18 -9999 0 -0.59 1 1
CRKL -0.01 0.072 -9999 0 -0.42 1 1
mol:DAG -0.054 0.12 -9999 0 -0.46 11 11
HRAS 0.024 0.07 -9999 0 -10000 0 0
MAPK8 0.016 0.039 -9999 0 -0.42 1 1
RAP1A -0.01 0.072 -9999 0 -10000 0 0
GAB1 -0.013 0.08 -9999 0 -10000 0 0
MAPK14 0.016 0.039 -9999 0 -0.42 1 1
EPO 0.004 0.051 -9999 0 -0.74 1 1
PLCG1 -0.056 0.13 -9999 0 -0.47 11 11
EPOR/TRPC2/IP3 Receptors 0.007 0.011 -9999 0 -10000 0 0
RAPGEF1 0.017 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.022 0.1 -9999 0 -0.48 10 10
GAB1/SHC/GRB2/SOS1 -0.014 0.051 -9999 0 -10000 0 0
EPO/EPOR (dimer) 0.008 0.042 -9999 0 -0.56 1 1
IRS2 -0.012 0.078 -9999 0 -0.45 1 1
STAT1 -0.12 0.16 -9999 0 -0.56 11 11
STAT5B -0.064 0.11 -9999 0 -0.47 1 1
cell proliferation 0.019 0.04 -9999 0 -10000 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC -0.015 0.052 -9999 0 -10000 0 0
TEC -0.01 0.072 -9999 0 -10000 0 0
SOCS3 -0.013 0.15 -9999 0 -0.72 9 9
STAT1 (dimer) -0.12 0.16 -9999 0 -0.55 11 11
JAK2 -0.006 0.097 -9999 0 -0.72 4 4
PIK3R1 0.017 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 -0.016 0.081 -9999 0 -0.42 2 2
EPO/EPOR 0.008 0.042 -9999 0 -0.56 1 1
LYN 0.007 0.009 -9999 0 -10000 0 0
TEC/VAV2 -0.005 0.082 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.007 0.011 -9999 0 -10000 0 0
SHC1 0.017 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.015 0.041 -9999 0 -0.48 1 1
mol:IP3 -0.054 0.12 -9999 0 -0.46 11 11
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.026 0.052 -9999 0 -10000 0 0
SH2B3 0.006 0.01 -9999 0 -10000 0 0
NFKB1 0.016 0.039 -9999 0 -0.42 1 1
EPO/EPOR (dimer)/JAK2/SOCS3 -0.013 0.054 -9999 0 -0.43 1 1
PTPN6 -0.022 0.075 -9999 0 -0.42 2 2
TEC/VAV2/GRB2 0.004 0.079 -9999 0 -10000 0 0
EPOR 0.007 0.011 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP -0.015 0.051 -9999 0 -10000 0 0
SOS1 0.017 0 -9999 0 -10000 0 0
PLCG2 -0.31 0.33 -9999 0 -0.64 110 110
CRKL/CBL/C3G 0.01 0.068 -9999 0 -10000 0 0
VAV2 -0.016 0.084 -9999 0 -10000 0 0
CBL -0.01 0.072 -9999 0 -0.42 1 1
SHC/Grb2/SOS1 -0.018 0.044 -9999 0 -10000 0 0
STAT5A -0.064 0.11 -9999 0 -0.47 1 1
GRB2 0.017 0 -9999 0 -10000 0 0
STAT5 (dimer) -0.12 0.17 -9999 0 -0.59 1 1
LYN/PLCgamma2 -0.23 0.23 -9999 0 -0.47 110 110
PTPN11 0.014 0.05 -9999 0 -0.72 1 1
BTK -0.063 0.15 -9999 0 -10000 0 0
BCL2 -0.57 0.47 -9999 0 -0.9 145 145
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.004 0.076 -9999 0 -0.63 3 3
PDGF/PDGFRA/CRKL -0.006 0.051 -9999 0 -0.45 3 3
positive regulation of JUN kinase activity -0.004 0.037 -9999 0 -10000 0 0
CRKL 0.017 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.006 0.051 -9999 0 -0.45 3 3
AP1 -0.18 0.37 -9999 0 -1 35 35
mol:IP3 -0.019 0.16 -9999 0 -0.54 18 18
PLCG1 -0.019 0.16 -9999 0 -0.54 18 18
PDGF/PDGFRA/alphaV Integrin -0.008 0.063 -9999 0 -0.47 4 4
RAPGEF1 0.017 0 -9999 0 -10000 0 0
CRK 0.014 0.044 -9999 0 -0.64 1 1
mol:Ca2+ -0.019 0.16 -9999 0 -0.54 18 18
CAV3 0.017 0 -9999 0 -10000 0 0
CAV1 0.004 0.096 -9999 0 -0.7 4 4
SHC/Grb2/SOS1 -0.004 0.037 -9999 0 -10000 0 0
PDGF/PDGFRA/Shf -0.1 0.22 -9999 0 -0.55 41 41
FOS -0.13 0.39 -9999 0 -1 35 35
JUN -0.023 0.086 -9999 0 -0.57 5 5
oligodendrocyte development -0.008 0.063 -9999 0 -0.47 4 4
GRB2 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.017 0 -9999 0 -10000 0 0
mol:DAG -0.019 0.16 -9999 0 -0.54 18 18
PDGF/PDGFRA 0.004 0.075 -9999 0 -0.63 3 3
actin cytoskeleton reorganization -0.031 0.12 -9999 0 -0.53 13 13
SRF 0.033 0.01 -9999 0 -10000 0 0
SHC1 0.017 0 -9999 0 -10000 0 0
PI3K -0.005 0.042 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk/C3G -0.007 0.05 -9999 0 -0.4 1 1
JAK1 0.022 0.056 -9999 0 -0.44 3 3
ELK1/SRF 0.014 0.13 -9999 0 -0.72 2 2
SHB -0.016 0.15 -9999 0 -0.72 10 10
SHF -0.11 0.28 -9999 0 -0.72 39 39
CSNK2A1 0.013 0.024 -9999 0 -10000 0 0
GO:0007205 -0.016 0.15 -9999 0 -0.51 18 18
SOS1 0.017 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.004 0.037 -9999 0 -10000 0 0
PDGF/PDGFRA/SHB -0.031 0.12 -9999 0 -0.53 13 13
PDGF/PDGFRA/Caveolin-1 -0.016 0.086 -9999 0 -0.49 7 7
ITGAV 0.014 0.05 -9999 0 -0.72 1 1
ELK1 -0.013 0.16 -9999 0 -0.49 19 19
PIK3CA 0.017 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.008 0.06 -9999 0 -0.45 4 4
JAK-STAT cascade 0.022 0.055 -9999 0 -0.44 3 3
cell proliferation -0.1 0.22 -9999 0 -0.55 41 41
ceramide signaling pathway

Figure S59.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S59.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.046 0.093 -10000 0 -0.63 1 1
BAG4 0.017 0 -10000 0 -10000 0 0
BAD 0.012 0.063 -10000 0 -10000 0 0
NFKBIA 0.017 0 -10000 0 -10000 0 0
BIRC3 -0.02 0.15 -10000 0 -0.66 12 12
BAX 0.011 0.071 -10000 0 -0.48 1 1
EnzymeConsortium:3.1.4.12 0.019 0.018 -10000 0 -10000 0 0
IKBKB 0.053 0.092 -10000 0 -0.58 1 1
MAP2K2 0.034 0.054 -10000 0 -10000 0 0
MAP2K1 0.034 0.054 -10000 0 -10000 0 0
SMPD1 -0.032 0.12 -10000 0 -0.26 47 47
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.062 0.069 -10000 0 -10000 0 0
MAP2K4 0.018 0.075 -10000 0 -0.39 2 2
protein ubiquitination 0.056 0.09 -10000 0 -0.59 1 1
EnzymeConsortium:2.7.1.37 0.041 0.055 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAF1 0.025 0.058 -10000 0 -10000 0 0
CRADD 0.011 0.062 -10000 0 -0.64 2 2
mol:ceramide 0.002 0.066 -10000 0 -0.22 4 4
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.017 0 -10000 0 -10000 0 0
MAP3K1 0.013 0.063 -10000 0 -10000 0 0
TRADD 0.017 0 -10000 0 -10000 0 0
RELA/p50 0.017 0 -10000 0 -10000 0 0
MAPK3 0.037 0.055 -10000 0 -10000 0 0
MAPK1 0.037 0.053 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.053 0.071 -10000 0 -10000 0 0
KSR1 0.014 0.062 -10000 0 -10000 0 0
MAPK8 0.028 0.071 -10000 0 -0.35 2 2
TRAF2 0.017 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.055 0.089 -10000 0 -0.58 1 1
TNF R/SODD 0 0 -10000 0 -10000 0 0
TNF 0.017 0 -10000 0 -10000 0 0
CYCS 0.084 0.084 0.16 107 -0.27 1 108
IKBKG 0.055 0.089 -10000 0 -0.58 1 1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.044 0.074 -10000 0 -10000 0 0
RELA 0.017 0 -10000 0 -10000 0 0
RIPK1 0.017 0 -10000 0 -10000 0 0
AIFM1 0.085 0.084 0.16 108 -0.27 1 109
TNF/TNF R/SODD 0 0 -10000 0 -10000 0 0
TNFRSF1A 0.017 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.037 0.02 -10000 0 -10000 0 0
NSMAF 0.054 0.07 -10000 0 -10000 0 0
response to hydrogen peroxide 0.001 0 -10000 0 -10000 0 0
BCL2 -0.41 0.31 -10000 0 -0.64 145 145
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.042 0.13 -10000 0 -0.55 11 11
FYN -0.016 0.22 -10000 0 -0.71 14 14
LAT/GRAP2/SLP76 -0.043 0.14 -10000 0 -0.58 10 10
IKBKB 0.014 0.05 -10000 0 -0.72 1 1
AKT1 0.022 0.15 -10000 0 -0.48 12 12
B2M -0.009 0.13 -10000 0 -0.64 9 9
IKBKG -0.017 0.037 -10000 0 -0.18 1 1
MAP3K8 -0.086 0.26 -10000 0 -0.72 31 31
mol:Ca2+ -0.003 0.021 -10000 0 -0.14 4 4
integrin-mediated signaling pathway 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.006 0.21 -10000 0 -0.74 12 12
TRPV6 -0.01 0.099 -10000 0 -0.74 4 4
CD28 -0.062 0.21 -10000 0 -0.64 27 27
SHC1 0.008 0.2 -10000 0 -0.73 11 11
receptor internalization -0.007 0.21 -10000 0 -0.73 14 14
PRF1 0.013 0.18 -10000 0 -0.7 10 10
KRAS 0.017 0 -10000 0 -10000 0 0
GRB2 0.017 0 -10000 0 -10000 0 0
COT/AKT1 -0.014 0.16 -10000 0 -0.38 19 19
LAT 0.005 0.2 -10000 0 -0.72 11 11
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D -0.011 0.14 -10000 0 -0.64 10 10
CD3E 0.017 0.006 -10000 0 -10000 0 0
CD3G -0.015 0.14 -10000 0 -0.65 11 11
RASGRP2 0.01 0.033 -10000 0 -0.19 4 4
RASGRP1 0.027 0.15 -10000 0 -0.46 12 12
HLA-A 0.003 0.098 -10000 0 -0.64 5 5
RASSF5 0.017 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.036 0.055 -10000 0 -0.14 2 2
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.032 0.066 -10000 0 -0.26 4 4
PRKCA -0.039 0.083 -10000 0 -0.31 12 12
GRAP2 0.017 0 -10000 0 -10000 0 0
mol:IP3 -0.057 0.14 0.28 1 -0.48 14 15
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.001 0.2 -10000 0 -0.71 12 12
ORAI1 0.01 0.05 0.37 4 -10000 0 4
CSK -0.002 0.2 -10000 0 -0.74 11 11
B7 family/CD28 -0.096 0.23 -10000 0 -0.73 20 20
CHUK 0.017 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.012 0.23 -10000 0 -0.84 12 12
PTPN6 0.002 0.2 -10000 0 -0.73 12 12
VAV1 -0.017 0.24 -10000 0 -0.86 13 13
Monovalent TCR/CD3 -0.012 0.2 -10000 0 -0.71 13 13
CBL 0.017 0 -10000 0 -10000 0 0
LCK -0.014 0.22 -10000 0 -0.71 14 14
PAG1 -0.065 0.24 -10000 0 -0.67 18 18
RAP1A 0.017 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.016 0.23 -10000 0 -0.86 12 12
CD80 0.004 0.099 -10000 0 -0.72 4 4
CD86 -0.016 0.14 -10000 0 -0.65 11 11
PDK1/CARD11/BCL10/MALT1 -0.04 0.081 -10000 0 -0.29 9 9
HRAS 0.017 0 -10000 0 -10000 0 0
GO:0035030 -0.015 0.21 -10000 0 -0.61 18 18
CD8A 0.001 0.004 -10000 0 -10000 0 0
CD8B 0.017 0.005 -10000 0 -10000 0 0
PTPRC -0.018 0.15 -10000 0 -0.64 12 12
PDK1/PKC theta 0.023 0.18 -10000 0 -0.61 12 12
CSK/PAG1 -0.056 0.23 -10000 0 -0.68 15 15
SOS1 0.017 0 -10000 0 -10000 0 0
peptide-MHC class I -0.01 0.14 -10000 0 -0.57 11 11
GRAP2/SLP76 -0.05 0.17 -10000 0 -0.69 11 11
STIM1 0.007 0.026 -10000 0 -10000 0 0
RAS family/GTP 0.045 0.07 -10000 0 -0.24 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.011 0.24 -10000 0 -0.8 14 14
mol:DAG -0.055 0.12 -10000 0 -0.42 14 14
RAP1A/GDP 0.018 0.024 -10000 0 -10000 0 0
PLCG1 -0.033 0.19 -10000 0 -0.72 15 15
CD247 -0.014 0.14 -10000 0 -0.64 11 11
cytotoxic T cell degranulation 0.015 0.18 -10000 0 -0.67 10 10
RAP1A/GTP -0.002 0.009 -10000 0 -0.068 3 3
mol:PI-3-4-5-P3 0.014 0.18 -10000 0 -0.59 12 12
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.073 0.17 0.3 1 -0.63 14 15
NRAS 0.007 0.085 -10000 0 -0.72 3 3
ZAP70 0.017 0.001 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.059 0.16 -10000 0 -0.62 13 13
MALT1 0.017 0 -10000 0 -10000 0 0
TRAF6 0.017 0 -10000 0 -10000 0 0
CD8 heterodimer 0.012 0.009 -10000 0 -10000 0 0
CARD11 -0.046 0.21 -10000 0 -0.72 19 19
PRKCB -0.04 0.082 -10000 0 -0.29 14 14
PRKCE -0.038 0.08 -10000 0 -0.29 12 12
PRKCQ 0.009 0.21 -10000 0 -0.71 12 12
LCP2 0.004 0.096 -10000 0 -0.7 4 4
BCL10 0.017 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.025 0.13 -10000 0 -0.4 12 12
IKK complex 0.039 0.058 -10000 0 -0.13 1 1
RAS family/GDP -0.003 0.011 -10000 0 -0.081 3 3
MAP3K14 0.003 0.13 -10000 0 -0.3 13 13
PDPK1 0.027 0.14 -10000 0 -0.45 12 12
TCR/CD3/MHC I/CD8/Fyn -0.01 0.22 -10000 0 -0.84 11 11
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.003 0.12 -9999 0 -0.39 3 3
Syndecan-4/Syndesmos 0.027 0.11 -9999 0 -0.48 4 4
positive regulation of JNK cascade -0.23 0.14 -9999 0 -0.59 15 15
Syndecan-4/ADAM12 -0.12 0.25 -9999 0 -0.61 25 25
CCL5 -0.14 0.28 -9999 0 -0.64 52 52
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.017 0 -9999 0 -10000 0 0
ITGA5 0 0.11 -9999 0 -0.72 5 5
SDCBP 0.017 0 -9999 0 -10000 0 0
PLG 0.013 0.006 -9999 0 -10000 0 0
ADAM12 -0.26 0.36 -9999 0 -0.72 83 83
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.017 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.017 0.042 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.027 0.11 -9999 0 -0.48 4 4
Syndecan-4/CXCL12/CXCR4 -0.24 0.15 -9999 0 -0.64 15 15
Syndecan-4/Laminin alpha3 0.019 0.13 -9999 0 -0.62 3 3
MDK -0.023 0.17 -9999 0 -0.72 12 12
Syndecan-4/FZD7 0.013 0.13 -9999 0 -0.48 4 4
Syndecan-4/Midkine 0.006 0.15 -9999 0 -0.56 4 4
FZD7 -0.009 0.13 -9999 0 -0.7 8 8
Syndecan-4/FGFR1/FGF -0.04 0.09 -9999 0 -10000 0 0
THBS1 0.011 0.066 -9999 0 -0.68 2 2
integrin-mediated signaling pathway 0.019 0.14 -9999 0 -0.56 7 7
positive regulation of MAPKKK cascade -0.23 0.14 -9999 0 -0.59 15 15
Syndecan-4/TACI 0.021 0.12 -9999 0 -0.5 5 5
CXCR4 -0.02 0.16 -9999 0 -0.72 11 11
cell adhesion -0.035 0.094 -9999 0 -0.41 3 3
Syndecan-4/Dynamin 0.027 0.11 -9999 0 -10000 0 0
Syndecan-4/TSP1 0.024 0.12 -9999 0 -0.57 4 4
Syndecan-4/GIPC 0.026 0.12 -9999 0 -0.51 1 1
Syndecan-4/RANTES -0.051 0.18 -9999 0 -0.56 9 9
ITGB1 0.014 0.05 -9999 0 -0.72 1 1
LAMA1 0.017 0 -9999 0 -10000 0 0
LAMA3 0.001 0.1 -9999 0 -0.67 5 5
RAC1 0.017 0 -9999 0 -10000 0 0
PRKCA 0.011 0.058 -9999 0 -0.7 1 1
Syndecan-4/alpha-Actinin 0.027 0.11 -9999 0 -0.48 4 4
TFPI 0.014 0.05 -9999 0 -0.72 1 1
F2 0.019 0.004 -9999 0 -10000 0 0
alpha5/beta1 Integrin -0.015 0.087 -9999 0 -0.54 6 6
positive regulation of cell adhesion 0.03 0.13 -9999 0 -0.65 2 2
ACTN1 0.017 0 -9999 0 -10000 0 0
TNC 0 0.11 -9999 0 -0.72 5 5
Syndecan-4/CXCL12 -0.23 0.16 -9999 0 -0.55 15 15
FGF6 0.014 0.05 -9999 0 -0.72 1 1
RHOA 0.017 0 -9999 0 -10000 0 0
CXCL12 -0.48 0.28 -9999 0 -0.64 168 168
TNFRSF13B 0.005 0.087 -9999 0 -0.64 4 4
FGF2 -0.01 0.13 -9999 0 -0.64 9 9
FGFR1 0.017 0 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2 0.016 0.11 -9999 0 -0.49 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.074 0.24 -9999 0 -0.74 26 26
cell migration -0.006 0.016 -9999 0 -10000 0 0
PRKCD 0.013 0.006 -9999 0 -10000 0 0
vasculogenesis 0.024 0.12 -9999 0 -0.55 4 4
SDC4 0.018 0.12 -9999 0 -0.52 4 4
Syndecan-4/Tenascin C 0.019 0.14 -9999 0 -0.59 7 7
Syndecan-4/PI-4-5-P2/PKC alpha -0.014 0.033 -9999 0 -10000 0 0
Syndecan-4/Syntenin 0.027 0.11 -9999 0 -10000 0 0
MMP9 -0.003 0.13 -9999 0 -0.7 7 7
Rac1/GTP -0.036 0.096 -9999 0 -0.42 3 3
cytoskeleton organization 0.027 0.11 -9999 0 -0.47 4 4
GIPC1 0.014 0.044 -9999 0 -0.64 1 1
Syndecan-4/TFPI 0.026 0.12 -9999 0 -0.53 2 2
Cellular roles of Anthrax toxin

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
ANTXR1 -0.026 0.17 -10000 0 -0.72 13 13
ANTXR2 0.008 0.075 -10000 0 -0.64 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.006 0.022 -10000 0 -0.086 16 16
monocyte activation 0.01 0.066 -10000 0 -0.42 5 5
MAP2K2 -0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.005 0.018 -10000 0 -10000 0 0
MAP2K7 -0.005 0.018 -10000 0 -10000 0 0
MAP2K6 -0.019 0.072 -10000 0 -0.36 9 9
CYAA -0.009 0.11 -10000 0 -0.39 16 16
MAP2K4 -0.011 0.049 -10000 0 -0.35 4 4
IL1B -0.063 0.17 -10000 0 -0.42 41 41
Channel -0.03 0.11 -10000 0 -0.42 16 16
NLRP1 -0.007 0.033 -10000 0 -0.41 1 1
CALM1 0.017 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.007 0.026 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.006 0.022 0.086 16 -10000 0 16
MAPK3 -0.008 0.037 -10000 0 -0.35 2 2
MAPK1 -0.007 0.029 -10000 0 -0.35 1 1
PGR -0.005 0.018 -10000 0 -10000 0 0
PA/Cellular Receptors -0.033 0.12 -10000 0 -0.45 16 16
apoptosis -0.006 0.022 -10000 0 -0.086 16 16
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.007 0.1 -10000 0 -0.38 16 16
macrophage activation 0.017 0.045 -10000 0 -0.32 3 3
TNF 0.017 0 -10000 0 -10000 0 0
VCAM1 0.01 0.067 -10000 0 -0.42 5 5
platelet activation -0.007 0.026 -10000 0 -10000 0 0
MAPKKK cascade -0.011 0.031 0.16 1 -10000 0 1
IL18 -0.026 0.12 -10000 0 -0.35 25 25
negative regulation of macrophage activation -0.006 0.022 -10000 0 -0.086 16 16
LEF -0.006 0.022 -10000 0 -0.086 16 16
CASP1 -0.009 0.025 -10000 0 -0.2 1 1
mol:cAMP -0.007 0.026 -10000 0 -10000 0 0
necrosis -0.006 0.022 -10000 0 -0.086 16 16
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.028 0.1 -10000 0 -0.4 16 16
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.017 0 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.05 0.066 -10000 0 -0.39 2 2
PTP1B/AKT1 -0.089 0.068 -10000 0 -10000 0 0
FYN 0.014 0.044 -10000 0 -0.64 1 1
p210 bcr-abl/PTP1B -0.11 0.076 -10000 0 -0.33 2 2
EGFR -0.006 0.1 -10000 0 -0.66 5 5
EGF/EGFR -0.19 0.18 -10000 0 -0.47 60 60
CSF1 0.017 0 -10000 0 -10000 0 0
AKT1 0.017 0.002 -10000 0 -10000 0 0
INSR 0.008 0.075 -10000 0 -0.64 3 3
PTP1B/N-cadherin -0.11 0.093 -10000 0 -0.46 6 6
Insulin Receptor/Insulin -0.058 0.057 -10000 0 -0.51 1 1
HCK -0.045 0.19 -10000 0 -0.64 21 21
CRK 0.014 0.044 -10000 0 -0.64 1 1
TYK2 -0.096 0.073 -10000 0 -0.33 1 1
EGF -0.19 0.32 -10000 0 -0.68 64 64
YES1 0.017 0 -10000 0 -10000 0 0
CAV1 -0.1 0.1 -10000 0 -0.4 3 3
TXN 0.01 0.007 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.09 0.09 -10000 0 -0.51 4 4
cell migration 0.11 0.076 0.33 2 -10000 0 2
STAT3 0.016 0.001 -10000 0 -10000 0 0
PRLR 0.01 0.098 -10000 0 -0.71 4 4
ITGA2B 0.015 0.001 -10000 0 -10000 0 0
CSF1R 0.017 0 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.026 0.084 -10000 0 -0.52 5 5
FGR 0.017 0 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.096 0.073 -10000 0 -0.33 1 1
Crk/p130 Cas -0.084 0.075 -10000 0 -0.5 1 1
DOK1 -0.073 0.068 -10000 0 -0.38 1 1
JAK2 -0.048 0.062 -10000 0 -0.34 2 2
Jak2/Leptin Receptor/Leptin -0.071 0.12 -10000 0 -0.59 9 9
PIK3R1 0.017 0 -10000 0 -10000 0 0
PTPN1 -0.11 0.077 -10000 0 -0.34 2 2
LYN 0.017 0 -10000 0 -10000 0 0
CDH2 -0.005 0.12 -10000 0 -0.68 7 7
SRC -0.025 0.031 -10000 0 -10000 0 0
ITGB3 0.015 0.001 -10000 0 -10000 0 0
CAT1/PTP1B -0.12 0.12 -10000 0 -0.43 9 9
CAPN1 0.011 0.007 -10000 0 -10000 0 0
CSK 0.017 0 -10000 0 -10000 0 0
PI3K -0.037 0.052 -10000 0 -0.46 1 1
mol:H2O2 0.001 0.007 -10000 0 -10000 0 0
STAT3 (dimer) -0.064 0.12 -10000 0 -0.58 9 9
negative regulation of transcription -0.048 0.061 -10000 0 -0.33 2 2
FCGR2A -0.03 0.18 -10000 0 -0.72 14 14
FER -0.016 0.14 -10000 0 -0.72 8 8
alphaIIb/beta3 Integrin 0 0 -10000 0 -10000 0 0
BLK -0.16 0.29 -10000 0 -0.64 61 61
Insulin Receptor/Insulin/Shc -0.005 0.044 -10000 0 -0.38 3 3
RHOA 0.011 0.007 -10000 0 -10000 0 0
LEPR 0.005 0.086 -10000 0 -0.63 4 4
BCAR1 0.017 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.017 0 -10000 0 -10000 0 0
mol:NADPH -0.003 0.003 -10000 0 -10000 0 0
TRPV6 -0.056 0.16 -10000 0 -0.5 11 11
PRL 0.019 0.049 -10000 0 -0.72 1 1
SOCS3 0.007 0.12 -10000 0 -10000 0 0
SPRY2 0.002 0.11 -10000 0 -0.71 5 5
Insulin Receptor/Insulin/IRS1 -0.014 0.075 -10000 0 -0.43 7 7
CSF1/CSF1R -0.083 0.07 -10000 0 -10000 0 0
Ras protein signal transduction 0.058 0.023 -10000 0 -10000 0 0
IRS1 0.004 0.098 -10000 0 -0.72 4 4
INS 0.017 0.002 -10000 0 -10000 0 0
LEP 0.011 0.062 -10000 0 -0.64 2 2
STAT5B -0.081 0.068 -10000 0 -0.28 3 3
STAT5A -0.081 0.068 -10000 0 -0.28 3 3
GRB2 0.017 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.096 0.073 -10000 0 -0.33 1 1
CSN2 0.062 0.03 -10000 0 -10000 0 0
PIK3CA 0.017 0 -10000 0 -10000 0 0
LAT -0.042 0.069 -10000 0 -0.3 7 7
YBX1 0.025 0.002 -10000 0 -10000 0 0
LCK 0.011 0.066 -10000 0 -0.68 2 2
SHC1 0.017 0 -10000 0 -10000 0 0
NOX4 -0.6 0.27 -10000 0 -0.72 185 185
Nectin adhesion pathway

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
PDGFRB 0.017 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.002 0.036 -9999 0 -0.54 1 1
PTK2 -0.021 0.085 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.015 0.063 -9999 0 -0.29 11 11
CDC42/GDP 0.055 0.1 -9999 0 -0.39 11 11
Rac1/GDP 0.057 0.1 -9999 0 -0.39 11 11
RAP1B 0.017 0 -9999 0 -10000 0 0
RAP1A 0.017 0 -9999 0 -10000 0 0
CTNNB1 0 0.11 -9999 0 -0.72 5 5
CDC42/GTP -0.018 0.076 -9999 0 -0.35 11 11
nectin-3/I-afadin -0.023 0.1 -9999 0 -0.46 11 11
RAPGEF1 0.051 0.11 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.041 0.12 -9999 0 -0.49 11 11
PDGFB-D/PDGFRB 0.017 0 -9999 0 -10000 0 0
TLN1 0.036 0.047 -9999 0 -10000 0 0
Rap1/GTP -0.016 0.065 -9999 0 -10000 0 0
IQGAP1 0.017 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.023 0.1 -9999 0 -0.46 11 11
PVR 0.014 0.05 -9999 0 -0.72 1 1
Necl-5(dimer) 0.014 0.049 -9999 0 -0.72 1 1
mol:GDP 0.051 0.12 -9999 0 -0.48 11 11
MLLT4 0.017 0 -9999 0 -10000 0 0
PIK3CA 0.017 0 -9999 0 -10000 0 0
PI3K -0.015 0.067 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.019 0.074 -9999 0 -0.32 11 11
PVRL1 0.017 0 -9999 0 -10000 0 0
PVRL3 -0.015 0.14 -9999 0 -0.64 11 11
PVRL2 0.014 0.05 -9999 0 -0.72 1 1
PIK3R1 0.017 0 -9999 0 -10000 0 0
CDH1 -0.001 0.11 -9999 0 -0.64 6 6
CLDN1 -0.7 0.14 -9999 0 -0.72 214 214
JAM-A/CLDN1 -0.41 0.11 -9999 0 -0.76 11 11
SRC -0.028 0.12 -9999 0 -0.55 11 11
ITGB3 0.017 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
FARP2 0.047 0.12 -9999 0 -0.46 11 11
RAC1 0.017 0 -9999 0 -10000 0 0
CTNNA1 0.017 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.021 0.089 -9999 0 -0.39 12 12
nectin-1/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2/I-afadin -0.002 0.036 -9999 0 -0.54 1 1
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.019 0.084 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.017 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.015 0.063 -9999 0 -0.29 11 11
alphaV/beta3 Integrin/Talin 0.05 0.051 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.002 0.036 -9999 0 -0.54 1 1
nectin-2(dimer)/I-afadin/I-afadin -0.002 0.036 -9999 0 -0.54 1 1
PIP5K1C 0.026 0.051 -9999 0 -10000 0 0
VAV2 0.037 0.14 -9999 0 -0.5 14 14
RAP1/GDP -0.019 0.077 -9999 0 -0.42 1 1
ITGAV 0.014 0.05 -9999 0 -0.72 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.021 0.089 -9999 0 -0.39 12 12
nectin-3(dimer)/I-afadin/I-afadin -0.023 0.1 -9999 0 -0.46 11 11
Rac1/GTP -0.023 0.09 -9999 0 -0.38 11 11
PTPRM -0.011 0.05 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin -0.017 0.073 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.017 0 -9999 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.018 0.08 -10000 0 -0.46 6 6
MAP4K4 0.045 0.084 -10000 0 -0.58 1 1
BAG4 0.017 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.042 0.056 0.18 1 -10000 0 1
NFKBIA 0.017 0 -10000 0 -10000 0 0
BIRC3 -0.02 0.15 -10000 0 -0.66 12 12
BAX -0.011 0.032 -10000 0 -0.23 1 1
RIPK1 0.017 0 -10000 0 -10000 0 0
AKT1 0.034 0.011 -10000 0 -10000 0 0
BAD -0.03 0.057 -10000 0 -10000 0 0
SMPD1 -0.028 0.13 -10000 0 -0.27 47 47
RB1 -0.03 0.057 -10000 0 -10000 0 0
FADD/Caspase 8 0.066 0.054 -10000 0 -10000 0 0
MAP2K4 -0.025 0.072 -10000 0 -0.38 4 4
NSMAF 0.017 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.018 0.054 -10000 0 -10000 0 0
EGF -0.18 0.31 -10000 0 -0.68 64 64
mol:ceramide -0.044 0.061 0.18 5 -10000 0 5
MADD 0.017 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.02 0.073 -10000 0 -0.46 5 5
ASAH1 0.017 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.03 0.057 -10000 0 -10000 0 0
cell proliferation -0.16 0.14 -10000 0 -0.34 34 34
BID 0.023 0.068 -10000 0 -0.37 2 2
MAP3K1 -0.03 0.057 0.2 1 -10000 0 1
EIF2A -0.055 0.14 -10000 0 -0.42 25 25
TRADD 0.017 0 -10000 0 -10000 0 0
CRADD 0.011 0.062 -10000 0 -0.64 2 2
MAPK3 -0.003 0.052 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.002 0.05 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.032 0.063 -10000 0 -0.47 1 1
FADD 0.053 0.057 -10000 0 -10000 0 0
KSR1 -0.03 0.057 -10000 0 -10000 0 0
MAPK8 -0.022 0.061 0.2 1 -0.25 3 4
PRKRA -0.03 0.057 -10000 0 -10000 0 0
PDGFA 0.002 0.097 -10000 0 -0.64 5 5
TRAF2 0.017 0 -10000 0 -10000 0 0
IGF1 -0.35 0.32 -10000 0 -0.64 125 125
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.044 0.061 0.18 5 -10000 0 5
CTSD 0.014 0.044 -10000 0 -0.64 1 1
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.16 0.16 -10000 0 -0.38 15 15
PRKCD 0.017 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.02 0.073 -10000 0 -0.46 5 5
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.017 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.044 0.06 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0 0 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.018 0.08 -10000 0 -0.46 6 6
MAP2K1 -0.007 0.052 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.017 0 -10000 0 -10000 0 0
CYCS 0.089 0.088 0.29 2 -10000 0 2
TNFRSF1A 0.017 0 -10000 0 -10000 0 0
NFKB1 0.017 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0 0 -10000 0 -10000 0 0
EIF2AK2 -0.031 0.089 -10000 0 -0.45 6 6
TNF-alpha/TNFR1A/FAN 0 0 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.052 0.036 -10000 0 -10000 0 0
MAP2K2 -0.007 0.052 -10000 0 -10000 0 0
SMPD3 0.029 0.072 -10000 0 -0.35 7 7
TNF 0.017 0 -10000 0 -10000 0 0
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.059 0.11 0.23 63 -10000 0 63
NF kappa B1/RelA/I kappa B alpha 0 0 -10000 0 -10000 0 0
AIFM1 0.09 0.09 0.3 3 -10000 0 3
BCL2 -0.41 0.31 -10000 0 -0.64 145 145
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.002 0.035 -9999 0 -10000 0 0
VDR -0.001 0.11 -9999 0 -0.64 6 6
FAM120B 0.017 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.086 0.025 -9999 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.097 0.037 -9999 0 -10000 0 0
MED1 0.007 0.085 -9999 0 -0.72 3 3
mol:9cRA 0.01 0.005 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.028 0.079 -9999 0 -10000 0 0
RXRs/NUR77 0.061 0.044 -9999 0 -10000 0 0
RXRs/PPAR 0.054 0.053 -9999 0 -10000 0 0
NCOR2 0.017 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.013 0.077 -9999 0 -0.47 6 6
RARs/VDR/DNA/Vit D3 -0.014 0.068 -9999 0 -0.39 3 3
RARA 0.014 0.05 -9999 0 -0.72 1 1
NCOA1 0.011 0.062 -9999 0 -0.64 2 2
VDR/VDR/DNA -0.001 0.11 -9999 0 -0.63 6 6
RARs/RARs/DNA/9cRA -0.005 0.045 -9999 0 -0.39 3 3
RARG 0.01 0.07 -9999 0 -0.72 2 2
RPS6KB1 -0.003 0.047 -9999 0 -0.69 1 1
RARs/THRs/DNA/SMRT 0.031 0.074 -9999 0 -10000 0 0
THRA 0.017 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.013 0.077 -9999 0 -0.47 6 6
RXRs/PPAR/9cRA/PGJ2/DNA 0.062 0.014 -9999 0 -10000 0 0
NR1H4 -0.54 0.23 -9999 0 -0.64 190 190
RXRs/LXRs/DNA 0.092 0.018 -9999 0 -10000 0 0
NR1H2 0.026 0.003 -9999 0 -10000 0 0
NR1H3 0.027 0.004 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.05 0.06 -9999 0 -10000 0 0
NR4A1 0.01 0.07 -9999 0 -0.72 2 2
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.2 0.11 -9999 0 -0.4 4 4
RXRG 0.026 0.003 -9999 0 -10000 0 0
RXR alpha/CCPG 0.032 0.003 -9999 0 -10000 0 0
RXRA 0.026 0.003 -9999 0 -10000 0 0
RXRB 0.026 0.004 -9999 0 -10000 0 0
THRB -0.018 0.15 -9999 0 -0.64 12 12
PPARG -0.001 0.11 -9999 0 -0.64 6 6
PPARD 0.017 0 -9999 0 -10000 0 0
TNF 0.1 0.034 -9999 0 -10000 0 0
mol:Oxysterols 0.01 0.005 -9999 0 -10000 0 0
cholesterol transport 0.097 0.036 -9999 0 -10000 0 0
PPARA 0.014 0.044 -9999 0 -0.64 1 1
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.017 0 -9999 0 -10000 0 0
RXRs/NUR77/BCL2 -0.15 0.14 -9999 0 -10000 0 0
SREBF1 0.1 0.049 -9999 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.062 0.014 -9999 0 -10000 0 0
ABCA1 0.099 0.083 -9999 0 -1.1 1 1
RARs/THRs -0.022 0.082 -9999 0 -10000 0 0
RXRs/FXR -0.27 0.14 -9999 0 -0.4 2 2
BCL2 -0.41 0.31 -9999 0 -0.64 145 145
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.051 0.16 -9999 0 -0.54 21 21
alphaV beta3 Integrin -0.018 0.083 -9999 0 -0.46 2 2
PTK2 0.05 0.12 -9999 0 -10000 0 0
IGF1R 0.017 0 -9999 0 -10000 0 0
PI4KB 0.017 0 -9999 0 -10000 0 0
MFGE8 0.017 0 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
CDKN1B -0.008 0.036 -9999 0 -10000 0 0
VEGFA -0.053 0.22 -9999 0 -0.72 21 21
ILK -0.006 0.029 -9999 0 -10000 0 0
ROCK1 0.017 0 -9999 0 -10000 0 0
AKT1 -0.005 0.024 -9999 0 -10000 0 0
PTK2B 0.012 0.13 -9999 0 -10000 0 0
alphaV/beta3 Integrin/JAM-A -0.015 0.067 -9999 0 -10000 0 0
CBL 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.002 0.031 -9999 0 -0.46 1 1
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.2 0.19 -9999 0 -0.76 5 5
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.038 0.063 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Syndecan-1 -0.002 0.031 -9999 0 -0.46 1 1
PI4KA 0.017 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.22 0.2 -9999 0 -0.67 23 23
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.017 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.31 0.22 -9999 0 -0.46 150 150
RPS6KB1 -0.17 0.22 -9999 0 -0.62 24 24
TLN1 0.017 0 -9999 0 -10000 0 0
MAPK3 -0.078 0.13 -9999 0 -0.68 8 8
GPR124 0.01 0.07 -9999 0 -0.72 2 2
MAPK1 -0.077 0.13 -9999 0 -0.68 8 8
PXN 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.017 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.006 0.053 -9999 0 -0.46 3 3
cell adhesion -0.002 0.025 -9999 0 -10000 0 0
ANGPTL3 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.043 0.13 -9999 0 -0.46 21 21
IGF-1R heterotetramer 0.017 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.017 0 -9999 0 -10000 0 0
ITGB3 0.017 0 -9999 0 -10000 0 0
IGF1 -0.35 0.32 -9999 0 -0.64 125 125
RAC1 0.017 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.006 0.052 -9999 0 -0.46 3 3
apoptosis 0.014 0.049 -9999 0 -0.72 1 1
CD47 0.017 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.002 0.031 -9999 0 -0.46 1 1
VCL 0.017 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.044 0.12 -9999 0 -0.46 1 1
CSF1 0.017 0 -9999 0 -10000 0 0
PIK3C2A -0.016 0.065 -9999 0 -0.47 1 1
PI4 Kinase/Pyk2 -0.039 0.11 -9999 0 -0.59 2 2
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.04 0.12 -9999 0 -10000 0 0
FAK1/Vinculin 0.054 0.1 -9999 0 -10000 0 0
alphaV beta3/Integrin/ppsTEM5 -0.006 0.053 -9999 0 -0.46 3 3
RHOA 0.017 0 -9999 0 -10000 0 0
VTN 0.017 0 -9999 0 -10000 0 0
BCAR1 0.017 0 -9999 0 -10000 0 0
FGF2 -0.01 0.13 -9999 0 -0.64 9 9
F11R 0.011 0.099 -9999 0 -0.47 9 9
alphaV/beta3 Integrin/Lactadherin -0.002 0.031 -9999 0 -0.46 1 1
alphaV/beta3 Integrin/TGFBR2 -0.002 0.031 -9999 0 -0.46 1 1
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.002 0.027 -9999 0 -0.41 1 1
HSP90AA1 0.014 0.05 -9999 0 -0.72 1 1
alphaV/beta3 Integrin/Talin -0.002 0.028 -9999 0 -0.42 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.07 0.24 -9999 0 -0.72 26 26
alphaV/beta3 Integrin/Pyk2 -0.037 0.11 -9999 0 -10000 0 0
SDC1 0.017 0 -9999 0 -10000 0 0
VAV3 -0.004 0.14 -9999 0 -0.71 1 1
PTPN11 0.014 0.05 -9999 0 -0.72 1 1
IRS1 0.004 0.098 -9999 0 -0.72 4 4
FAK1/Paxillin 0.054 0.1 -9999 0 -10000 0 0
cell migration 0.064 0.097 -9999 0 -10000 0 0
ITGAV 0.014 0.05 -9999 0 -0.72 1 1
PI3K -0.013 0.058 -9999 0 -10000 0 0
SPP1 -0.48 0.35 -9999 0 -0.72 150 150
KDR 0.017 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.014 0.049 -9999 0 -0.72 1 1
COL4A3 0.01 0.07 -9999 0 -0.72 2 2
angiogenesis -0.034 0.15 -9999 0 -0.7 7 7
Rac1/GTP -0.044 0.11 -9999 0 -0.65 1 1
EDIL3 -0.054 0.2 -9999 0 -0.64 24 24
cell proliferation -0.002 0.03 -9999 0 -0.46 1 1
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.017 0 -9999 0 -10000 0 0
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.017 0 -9999 0 -10000 0 0
TCEB1 0.01 0.07 -9999 0 -0.72 2 2
HIF1A/p53 -0.016 0.1 -9999 0 -0.38 9 9
HIF1A -0.01 0.073 -9999 0 -0.3 4 4
COPS5 0.017 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.005 0.043 -9999 0 -10000 0 0
FIH (dimer) 0.017 0 -9999 0 -10000 0 0
CDKN2A -0.22 0.34 -9999 0 -0.72 70 70
ARNT/IPAS 0 0 -9999 0 -10000 0 0
HIF1AN 0.017 0 -9999 0 -10000 0 0
GNB2L1 0.017 0 -9999 0 -10000 0 0
HIF1A/ARNT 0 0.07 -9999 0 -10000 0 0
CUL2 0.017 0 -9999 0 -10000 0 0
OS9 0.017 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.004 0.043 -9999 0 -0.46 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.001 0.074 -9999 0 -0.35 1 1
PHD1-3/OS9 -0.13 0.17 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C -0.024 0.052 -9999 0 -0.41 1 1
VHL 0.014 0.05 -9999 0 -0.72 1 1
HSP90AA1 0.014 0.05 -9999 0 -0.72 1 1
HIF1A/JAB1 0 0.07 -9999 0 -10000 0 0
EGLN3 -0.23 0.32 -9999 0 -0.64 85 85
EGLN2 0.017 0 -9999 0 -10000 0 0
EGLN1 0.017 0 -9999 0 -10000 0 0
TP53 -0.013 0.15 -9999 0 -0.72 9 9
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.038 0.031 -9999 0 -10000 0 0
ARNT 0.017 0 -9999 0 -10000 0 0
ARD1A -0.006 0.13 -9999 0 -0.72 7 7
RBX1 0.017 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.12 0.19 -9999 0 -0.39 70 70
Regulation of Androgen receptor activity

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
HDAC1 0.032 0 -9999 0 -10000 0 0
SMARCC1 0.002 0.085 -9999 0 -0.55 4 4
REL 0.016 0.001 -9999 0 -10000 0 0
HDAC7 -0.034 0.15 -9999 0 -0.49 10 10
JUN 0.001 0.11 -9999 0 -0.72 5 5
EP300 0.017 0 -9999 0 -10000 0 0
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0 0 -9999 0 -10000 0 0
MAPK14 0 0.1 -9999 0 -0.49 9 9
FOXO1 -0.009 0.13 -9999 0 -0.64 9 9
T-DHT/AR -0.033 0.16 -9999 0 -0.51 10 10
MAP2K6 -0.016 0.13 -9999 0 -0.65 9 9
BRM/BAF57 -0.005 0.051 -9999 0 -0.54 2 2
MAP2K4 -0.001 0.086 -9999 0 -0.64 4 4
SMARCA2 0.018 0.001 -9999 0 -10000 0 0
PDE9A -0.56 0.57 -9999 0 -1.1 111 111
NCOA2 0.018 0 -9999 0 -10000 0 0
CEBPA 0.017 0 -9999 0 -10000 0 0
EHMT2 0.018 0.001 -9999 0 -10000 0 0
cell proliferation 0.014 0.15 -9999 0 -10000 0 0
NR0B1 0 0.11 -9999 0 -0.72 5 5
EGR1 -0.016 0.15 -9999 0 -0.67 11 11
RXRs/9cRA 0 0 -9999 0 -10000 0 0
AR/RACK1/Src 0.031 0.1 -9999 0 -10000 0 0
AR/GR -0.016 0.13 -9999 0 -0.38 11 11
GNB2L1 0.017 0 -9999 0 -10000 0 0
PKN1 0.017 0 -9999 0 -10000 0 0
RCHY1 0.017 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0.001 0 -9999 0 -10000 0 0
MAPK8 0.011 0.067 -9999 0 -0.46 4 4
T-DHT/AR/TIF2/CARM1 0.029 0.1 -9999 0 -10000 0 0
SRC 0.016 0.097 -9999 0 -10000 0 0
NR3C1 -0.054 0.2 -9999 0 -0.64 24 24
KLK3 -0.14 0.12 -9999 0 -0.62 2 2
APPBP2 0.01 0.01 -9999 0 -10000 0 0
TRIM24 0.018 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.035 0.089 -9999 0 -0.42 9 9
TMPRSS2 -0.063 0.11 -9999 0 -1.4 1 1
RXRG 0.017 0 -9999 0 -10000 0 0
mol:9cRA 0 0 -9999 0 -0.006 1 1
RXRA 0.017 0 -9999 0 -10000 0 0
RXRB 0.017 0 -9999 0 -10000 0 0
CARM1 0.018 0 -9999 0 -10000 0 0
NR2C2 0.017 0 -9999 0 -10000 0 0
KLK2 0.04 0.091 -9999 0 -10000 0 0
AR 0.02 0.07 -9999 0 -10000 0 0
SENP1 0.017 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0.05 -9999 0 -0.72 1 1
MDM2 0.015 0.001 -9999 0 -10000 0 0
SRY 0.012 0.05 -9999 0 -0.72 1 1
GATA2 0.017 0 -9999 0 -10000 0 0
MYST2 0.017 0 -9999 0 -10000 0 0
HOXB13 -0.59 0.28 -9999 0 -0.72 183 183
T-DHT/AR/RACK1/Src 0.024 0.1 -9999 0 -10000 0 0
positive regulation of transcription 0.017 0 -9999 0 -10000 0 0
DNAJA1 0.007 0.052 -9999 0 -0.75 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.04 0 -9999 0 -10000 0 0
NCOA1 0.016 0.067 -9999 0 -0.66 2 2
SPDEF -0.19 0.3 -9999 0 -0.64 71 71
T-DHT/AR/TIF2 0.041 0.063 -9999 0 -10000 0 0
T-DHT/AR/Hsp90 0.006 0.11 -9999 0 -0.44 1 1
GSK3B 0.012 0.049 -9999 0 -0.72 1 1
NR2C1 0.003 0.098 -9999 0 -0.72 4 4
mol:T-DHT 0.002 0.1 -9999 0 -0.44 1 1
SIRT1 0.017 0 -9999 0 -10000 0 0
ZMIZ2 0.015 0.001 -9999 0 -10000 0 0
POU2F1 0.019 0.019 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.001 0.12 -9999 0 -0.44 1 1
CREBBP 0.017 0 -9999 0 -10000 0 0
SMARCE1 0.011 0.07 -9999 0 -0.72 2 2
Ras signaling in the CD4+ TCR pathway

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.012 0.16 -9999 0 -0.54 4 4
MAP3K8 -0.088 0.26 -9999 0 -0.72 31 31
FOS 0.004 0.1 -9999 0 -0.42 2 2
PRKCA 0.013 0.051 -9999 0 -0.74 1 1
PTPN7 -0.01 0.14 -9999 0 -0.72 8 8
HRAS 0.017 0.001 -9999 0 -10000 0 0
PRKCB -0.001 0.007 -9999 0 -0.019 32 32
NRAS 0.007 0.086 -9999 0 -0.72 3 3
RAS family/GTP -0.006 0.049 -9999 0 -0.42 3 3
MAPK3 0.008 0.075 -9999 0 -0.42 2 2
MAP2K1 0.011 0.076 -9999 0 -0.51 1 1
ELK1 0.005 0.087 -9999 0 -0.73 3 3
BRAF -0.006 0.025 -9999 0 -0.33 1 1
mol:GTP -0.001 0.002 -9999 0 -0.006 33 33
MAPK1 0.01 0.076 -9999 0 -0.64 1 1
RAF1 -0.006 0.025 -9999 0 -0.33 1 1
KRAS 0.017 0.001 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.017 0 -10000 0 -10000 0 0
HDAC4 0.017 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.002 0.015 -10000 0 -10000 0 0
CDKN1A -0.007 0.097 -10000 0 -0.82 3 3
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.014 0.05 -10000 0 -0.72 1 1
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 -0.01 0.13 -10000 0 -0.64 9 9
FOXO4 0.031 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.017 0 -10000 0 -10000 0 0
TAT 0.017 0 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.008 0.066 -10000 0 -0.55 3 3
PPARGC1A -0.27 0.32 -10000 0 -0.64 99 99
FHL2 0.014 0.05 -10000 0 -0.72 1 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.002 0.018 -10000 0 -10000 0 0
HIST2H4A 0.002 0.015 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.002 0.016 -10000 0 -10000 0 0
SIRT1 0.003 0.024 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.002 0.018 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.001 0.027 -10000 0 -10000 0 0
apoptosis 0 0.035 0.46 1 -10000 0 1
SIRT1/PGC1A -0.18 0.2 -10000 0 -0.4 97 97
p53/SIRT1 -0.017 0.12 0.42 3 -0.55 9 12
SIRT1/FOXO4 0.002 0.02 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.014 0.085 -10000 0 -0.77 1 1
HIST1H1E 0.029 0.026 -10000 0 -10000 0 0
SIRT1/p300 0.002 0.018 -10000 0 -10000 0 0
muscle cell differentiation 0.004 0.057 0.47 3 -10000 0 3
TP53 -0.027 0.15 -10000 0 -0.73 9 9
KU70/SIRT1/BAX 0 0.036 -10000 0 -0.46 1 1
CREBBP 0.017 0 -10000 0 -10000 0 0
MEF2D 0.017 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.002 0.018 -10000 0 -10000 0 0
ACSS2 0.027 0.036 -10000 0 -0.46 1 1
SIRT1/PCAF/MYOD -0.004 0.057 -10000 0 -0.47 3 3
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.028 0.016 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.025 0.12 0.86 1 -10000 0 1
IL27/IL27R/JAK1 -0.057 0.11 -10000 0 -0.82 1 1
TBX21 -0.16 0.27 -10000 0 -0.66 7 7
IL12B 0.008 0.071 -10000 0 -0.73 2 2
IL12A -0.005 0.1 -10000 0 -0.56 7 7
IL6ST 0.009 0.009 -10000 0 -10000 0 0
IL27RA/JAK1 0.003 0.053 -10000 0 -0.53 1 1
IL27 -0.04 0.18 -10000 0 -0.67 16 16
TYK2 0.014 0.008 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.093 0.14 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.025 0.12 0.86 1 -10000 0 1
T cell proliferation during immune response 0.025 0.12 0.86 1 -10000 0 1
MAPKKK cascade -0.025 0.12 -10000 0 -0.86 1 1
STAT3 0.017 0 -10000 0 -10000 0 0
STAT2 0.017 0 -10000 0 -10000 0 0
STAT1 -0.051 0.21 -10000 0 -0.72 20 20
IL12RB1 0.014 0.007 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.072 0.18 -10000 0 -0.64 4 4
IL27/IL27R/JAK2/TYK2 -0.025 0.12 -10000 0 -0.88 1 1
positive regulation of T cell mediated cytotoxicity -0.025 0.12 -10000 0 -0.86 1 1
STAT1 (dimer) -0.14 0.18 -10000 0 -0.9 3 3
JAK2 -0.001 0.1 -10000 0 -0.75 4 4
JAK1 0.015 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.014 0.11 -10000 0 -0.83 1 1
T cell proliferation -0.2 0.24 -10000 0 -0.54 41 41
IL12/IL12R/TYK2/JAK2 -0.008 0.12 -10000 0 -0.56 1 1
IL17A -0.094 0.14 -10000 0 -10000 0 0
mast cell activation 0.025 0.12 0.86 1 -10000 0 1
IFNG -0.012 0.046 -10000 0 -0.098 26 26
T cell differentiation -0.007 0.007 -10000 0 -0.025 1 1
STAT3 (dimer) -0.014 0.11 -10000 0 -0.83 1 1
STAT5A (dimer) -0.014 0.11 -10000 0 -0.83 1 1
STAT4 (dimer) -0.016 0.11 -10000 0 -0.83 1 1
STAT4 0.014 0.044 -10000 0 -0.64 1 1
T cell activation -0.01 0.01 0.084 2 -10000 0 2
IL27R/JAK2/TYK2 -0.024 0.087 -10000 0 -0.92 1 1
GATA3 0.021 0.032 -10000 0 -10000 0 0
IL18 -0.041 0.16 -10000 0 -0.48 25 25
positive regulation of mast cell cytokine production -0.014 0.11 -10000 0 -0.8 1 1
IL27/EBI3 -0.036 0.13 -10000 0 -0.5 16 16
IL27RA -0.01 0.052 -10000 0 -0.59 1 1
IL6 -0.31 0.37 -10000 0 -0.71 103 103
STAT5A 0.017 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.007 0.033 -10000 0 -10000 0 0
IL1B -0.09 0.22 -10000 0 -0.55 41 41
EBI3 0.008 0.009 -10000 0 -10000 0 0
TNF 0.015 0.002 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.011 0.15 -9999 0 -0.62 11 11
VEGFR1 homodimer/NRP1 -0.031 0.14 -9999 0 -0.63 11 11
mol:DAG -0.023 0.21 -9999 0 -0.68 13 13
VEGFR1 homodimer/NRP1/VEGFR 121 -0.067 0.2 -9999 0 -0.72 11 11
CaM/Ca2+ -0.013 0.2 -9999 0 -0.88 6 6
HIF1A 0.005 0.12 -9999 0 -1 2 2
GAB1 0.011 0.062 -9999 0 -0.64 2 2
AKT1 0.04 0.15 -9999 0 -0.87 3 3
PLCG1 -0.024 0.22 -9999 0 -0.69 13 13
NOS3 0.033 0.16 -9999 0 -0.76 4 4
CBL 0.017 0 -9999 0 -10000 0 0
mol:NO 0.034 0.15 -9999 0 -0.71 4 4
FLT1 0.004 0.17 -9999 0 -0.71 11 11
PGF -0.013 0.15 -9999 0 -0.72 9 9
VEGFR1 homodimer/NRP2/VEGFR121 -0.068 0.2 -9999 0 -0.74 11 11
CALM1 0.017 0 -9999 0 -10000 0 0
PIK3CA 0.017 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.04 0.15 -9999 0 -0.68 4 4
endothelial cell proliferation -0.001 0.18 -9999 0 -0.79 6 6
mol:Ca2+ -0.023 0.21 -9999 0 -0.67 13 13
MAPK3 -0.003 0.2 -9999 0 -0.79 7 7
MAPK1 -0.002 0.19 -9999 0 -0.8 6 6
PIK3R1 0.017 0 -9999 0 -10000 0 0
PLGF homodimer -0.013 0.15 -9999 0 -0.72 9 9
PRKACA 0.017 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 0.004 0.096 -9999 0 -0.7 4 4
VEGFA homodimer -0.053 0.22 -9999 0 -0.72 21 21
VEGFR1 homodimer/VEGFA homodimer -0.034 0.22 -9999 0 -0.77 11 11
platelet activating factor biosynthetic process 0.005 0.19 -9999 0 -0.76 7 7
PI3K -0.041 0.15 -9999 0 -1 3 3
PRKCA -0.012 0.2 -9999 0 -0.85 6 6
PRKCB -0.021 0.2 -9999 0 -0.64 13 13
VEGFR1 homodimer/PLGF homodimer -0.008 0.19 -9999 0 -0.6 18 18
VEGFA -0.053 0.22 -9999 0 -0.72 21 21
VEGFB 0.017 0 -9999 0 -10000 0 0
mol:IP3 -0.023 0.21 -9999 0 -0.68 13 13
RASA1 0.02 0.15 -9999 0 -0.56 11 11
NRP2 0.014 0.05 -9999 0 -0.72 1 1
VEGFR1 homodimer 0.005 0.17 -9999 0 -0.71 11 11
VEGFB homodimer 0.017 0 -9999 0 -10000 0 0
NCK1 0.017 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.035 0.15 -9999 0 -0.74 3 3
PTPN11 0.014 0.05 -9999 0 -0.72 1 1
mol:PI-3-4-5-P3 -0.04 0.15 -9999 0 -0.97 3 3
mol:L-citrulline 0.034 0.15 -9999 0 -0.71 4 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.061 0.18 -9999 0 -0.94 5 5
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.066 0.19 -9999 0 -0.99 5 5
CD2AP 0.017 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.041 0.15 -9999 0 -1 3 3
PDPK1 0.026 0.16 -9999 0 -0.91 3 3
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.068 0.19 -9999 0 -0.99 5 5
mol:NADP 0.034 0.15 -9999 0 -0.71 4 4
HSP90AA1 0.014 0.05 -9999 0 -0.72 1 1
ubiquitin-dependent protein catabolic process -0.061 0.18 -9999 0 -0.92 5 5
VEGFR1 homodimer/NRP2 0.009 0.16 -9999 0 -0.66 11 11
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.042 0.081 -9999 0 -10000 0 0
adherens junction organization -0.087 0.068 -9999 0 -0.39 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0.038 0.11 -9999 0 -0.55 2 2
FMN1 0.029 0.067 -9999 0 -0.31 2 2
mol:IP3 -0.026 0.083 -9999 0 -0.44 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.03 0.07 -9999 0 -0.32 2 2
CTNNB1 0 0.11 -9999 0 -0.72 5 5
AKT1 0.045 0.064 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.037 0.09 -9999 0 -0.42 6 6
CTNND1 0.017 0.005 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.04 0.066 -9999 0 -10000 0 0
VASP 0.04 0.067 -9999 0 -10000 0 0
ZYX 0.038 0.072 -9999 0 -10000 0 0
JUB -0.35 0.1 -9999 0 -0.37 211 211
EGFR(dimer) 0.03 0.091 -9999 0 -0.43 3 3
E-cadherin/beta catenin-gamma catenin -0.018 0.091 -9999 0 -0.41 11 11
mol:PI-3-4-5-P3 -0.016 0.049 -9999 0 -10000 0 0
PIK3CA 0.017 0.005 -9999 0 -10000 0 0
PI3K -0.016 0.05 -9999 0 -10000 0 0
FYN 0.043 0.098 -9999 0 -0.5 1 1
mol:Ca2+ -0.026 0.081 -9999 0 -0.42 2 2
JUP 0.017 0.003 -9999 0 -10000 0 0
PIK3R1 0.017 0.005 -9999 0 -10000 0 0
mol:DAG -0.026 0.083 -9999 0 -0.44 2 2
CDH1 -0.001 0.1 -9999 0 -0.63 6 6
RhoA/GDP 0.038 0.11 -9999 0 -0.55 2 2
establishment of polarity of embryonic epithelium 0.04 0.066 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
RHOA 0.017 0 -9999 0 -10000 0 0
EGFR 0.002 0.099 -9999 0 -0.65 5 5
CASR 0.032 0.11 -9999 0 -0.45 4 4
RhoA/GTP -0.023 0.073 -9999 0 -0.38 2 2
AKT2 0.045 0.064 -9999 0 -10000 0 0
actin cable formation 0.039 0.065 -9999 0 -10000 0 0
apoptosis 0.014 0.044 -9999 0 -10000 0 0
CTNNA1 0.017 0.005 -9999 0 -10000 0 0
mol:GDP 0.029 0.12 -9999 0 -0.49 5 5
PIP5K1A 0.04 0.067 -9999 0 -10000 0 0
PLCG1 -0.027 0.085 -9999 0 -0.44 2 2
Rac1/GTP -0.019 0.067 -9999 0 -0.39 3 3
homophilic cell adhesion 0.001 0.003 -9999 0 -10000 0 0
E-cadherin 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
E-cadherin/beta catenin-gamma catenin -0.021 0.091 -9999 0 -0.42 11 11
E-cadherin/beta catenin -0.025 0.11 -9999 0 -0.5 11 11
CTNNB1 0 0.11 -9999 0 -0.72 5 5
JUP 0.017 0 -9999 0 -10000 0 0
CDH1 -0.001 0.11 -9999 0 -0.64 6 6
Canonical NF-kappaB 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
FBXW11 0.022 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.062 0.078 -9999 0 -10000 0 0
ERC1 0.017 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.21 0.3 -9999 0 -0.6 79 79
NFKBIA 0.064 0 -9999 0 -10000 0 0
BIRC2 0.017 0 -9999 0 -10000 0 0
IKBKB 0.014 0.05 -9999 0 -0.72 1 1
RIPK2 -0.12 0.29 -9999 0 -0.72 42 42
IKBKG -0.057 0.08 -9999 0 -10000 0 0
IKK complex/A20 -0.042 0.069 -9999 0 -0.58 1 1
NEMO/A20/RIP2 -0.12 0.29 -9999 0 -0.72 42 42
XPO1 0.017 0 -9999 0 -10000 0 0
NEMO/ATM -0.006 0.1 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.014 0.05 -9999 0 -0.72 1 1
Exportin 1/RanGTP -0.002 0.031 -9999 0 -0.47 1 1
IKK complex/ELKS -0.041 0.067 -9999 0 -0.56 1 1
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.14 0.3 -9999 0 -0.72 47 47
NFKB1 0.022 0 -9999 0 -10000 0 0
RELA 0.022 0 -9999 0 -10000 0 0
MALT1 0.017 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.017 0 -9999 0 -10000 0 0
TNF/TNFR1A 0 0 -9999 0 -10000 0 0
TRAF6 0.017 0 -9999 0 -10000 0 0
PRKCA 0.014 0.05 -9999 0 -0.72 1 1
CHUK 0.017 0 -9999 0 -10000 0 0
UBE2D3 0.017 0 -9999 0 -10000 0 0
TNF 0.017 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.017 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.064 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.022 0 -9999 0 -10000 0 0
TNFRSF1A 0.017 0 -9999 0 -10000 0 0
IKK complex -0.047 0.075 -9999 0 -0.61 1 1
CYLD 0.017 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.044 0.075 -9999 0 -0.53 2 2
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.041 0.058 -10000 0 -10000 0 0
epithelial cell differentiation -0.016 0.058 -10000 0 -10000 0 0
ITCH 0.018 0.006 -10000 0 -10000 0 0
WWP1 0.049 0.022 -10000 0 -10000 0 0
FYN 0.014 0.044 -10000 0 -0.64 1 1
EGFR 0.002 0.099 -10000 0 -0.65 5 5
PRL 0.014 0.05 -10000 0 -0.72 1 1
neuron projection morphogenesis 0.088 0.04 -10000 0 -10000 0 0
PTPRZ1 -0.057 0.21 -10000 0 -0.64 25 25
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0 0.003 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.052 0.018 -10000 0 -10000 0 0
ADAM17 0.018 0.006 -10000 0 -10000 0 0
ErbB4/ErbB4 0.049 0.026 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.045 0.034 -10000 0 -10000 0 0
NCOR1 0.014 0.044 -10000 0 -0.64 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.002 0.021 -10000 0 -10000 0 0
GRIN2B 0.008 0.15 -10000 0 -10000 0 0
ErbB4/ErbB2/betacellulin -0.02 0.079 -10000 0 -0.46 1 1
STAT1 -0.05 0.21 -10000 0 -0.72 20 20
HBEGF 0.007 0.085 -10000 0 -0.72 3 3
PRLR 0.004 0.098 -10000 0 -0.72 4 4
E4ICDs/ETO2 -0.1 0.2 -10000 0 -0.47 1 1
axon guidance 0.056 0.068 -10000 0 -10000 0 0
NEDD4 -0.003 0.12 -10000 0 -0.72 6 6
Prolactin receptor/Prolactin receptor/Prolactin -0.012 0.08 -10000 0 -0.54 5 5
CBFA2T3 -0.22 0.32 -10000 0 -0.64 82 82
ErbB4/ErbB2/HBEGF -0.018 0.078 -10000 0 -10000 0 0
MAPK3 0.08 0.035 -10000 0 -10000 0 0
STAT1 (dimer) 0.005 0.14 -10000 0 -0.42 20 20
MAPK1 0.082 0.027 -10000 0 -10000 0 0
JAK2 0.004 0.098 -10000 0 -0.72 4 4
ErbB4/ErbB2/neuregulin 1 beta -0.013 0.066 -10000 0 -0.46 1 1
NRG1 0.032 0.003 -10000 0 -10000 0 0
NRG3 0.014 0.044 -10000 0 -0.64 1 1
NRG2 0.002 0.097 -10000 0 -0.64 5 5
NRG4 -0.005 0.12 -10000 0 -0.67 7 7
heart development 0.056 0.068 -10000 0 -10000 0 0
neural crest cell migration -0.013 0.065 -10000 0 -0.46 1 1
ERBB2 0.014 0.099 -10000 0 -0.53 7 7
WWOX/E4ICDs 0.047 0.021 -10000 0 -10000 0 0
SHC1 0.017 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.02 0.079 -10000 0 -10000 0 0
apoptosis 0.044 0.052 0.62 1 -10000 0 1
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.038 0.063 -10000 0 -10000 0 0
ErbB4/ErbB2/epiregulin -0.27 0.19 -10000 0 -0.65 10 10
ErbB4/ErbB4/betacellulin/betacellulin 0.038 0.063 -10000 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.019 0.075 -10000 0 -10000 0 0
MDM2 0.054 0.022 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.001 0.004 -10000 0 -10000 0 0
STAT5A 0.063 0.063 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.008 0.048 -10000 0 -10000 0 0
DLG4 0.017 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.003 0.023 -10000 0 -10000 0 0
STAT5A (dimer) -0.017 0.062 -10000 0 -10000 0 0
MAP3K7IP2 0.017 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.059 0.059 -10000 0 -10000 0 0
LRIG1 -0.01 0.13 -10000 0 -0.64 9 9
EREG -0.49 0.34 -10000 0 -0.72 153 153
BTC 0.002 0.097 -10000 0 -0.64 5 5
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.056 0.068 -10000 0 -10000 0 0
ERBB4 0.049 0.026 -10000 0 -10000 0 0
STAT5B 0.017 0 -10000 0 -10000 0 0
YAP1 -0.003 0.026 -10000 0 -10000 0 0
GRB2 0.017 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.023 0.088 -10000 0 -0.46 1 1
glial cell differentiation 0.003 0.023 -10000 0 -10000 0 0
WWOX 0.017 0 -10000 0 -10000 0 0
cell proliferation 0.055 0.089 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0 0 -10000 0 -10000 0 0
ATM 0.017 0 -10000 0 -10000 0 0
UBE2D3 0.017 0 -10000 0 -10000 0 0
PRKDC -0.046 0.21 -10000 0 -0.72 19 19
ATR 0.014 0.05 -10000 0 -0.72 1 1
UBE2L3 0.017 0 -10000 0 -10000 0 0
FANCD2 0.032 0.032 -10000 0 -10000 0 0
protein ubiquitination -0.072 0.17 -10000 0 -0.76 6 6
XRCC5 0.017 0 -10000 0 -10000 0 0
XRCC6 0.017 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.017 0 -10000 0 -10000 0 0
DNA-PK -0.039 0.13 -10000 0 -0.46 19 19
FA complex/FANCD2/Ubiquitin -0.045 0.099 -10000 0 -0.48 6 6
FANCF 0.011 0.062 -10000 0 -0.64 2 2
BRCA1 0.004 0.098 -10000 0 -0.72 4 4
CCNE1 -0.033 0.19 -10000 0 -0.72 15 15
CDK2/Cyclin E1 -0.093 0.22 -10000 0 -0.59 35 35
FANCG -0.016 0.15 -10000 0 -0.72 10 10
BRCA1/BACH1/BARD1 -0.01 0.072 -10000 0 -0.54 4 4
FANCE 0.014 0.05 -10000 0 -0.72 1 1
FANCC 0.017 0 -10000 0 -10000 0 0
NBN 0.017 0 -10000 0 -10000 0 0
FANCA -0.16 0.31 -10000 0 -0.72 52 52
DNA repair 0.013 0.15 -10000 0 -0.6 4 4
BRCA1/BARD1/ubiquitin -0.01 0.072 -10000 0 -0.54 4 4
BARD1/DNA-PK -0.035 0.11 -10000 0 -0.41 19 19
FANCL 0.017 0 -10000 0 -10000 0 0
mRNA polyadenylation 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.052 0.022 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.008 0.061 -10000 0 -0.46 4 4
BRCA1/BARD1/P53 -0.026 0.11 -10000 0 -0.82 1 1
BARD1/CSTF1/BRCA1 -0.008 0.061 -10000 0 -0.46 4 4
BRCA1/BACH1 0.004 0.098 -10000 0 -0.72 4 4
BARD1 0.017 0 -10000 0 -10000 0 0
PCNA -0.01 0.14 -10000 0 -0.72 8 8
BRCA1/BARD1/UbcH5C -0.008 0.061 -10000 0 -0.46 4 4
BRCA1/BARD1/UbcH7 -0.008 0.061 -10000 0 -0.46 4 4
BRCA1/BARD1/RAD51/PCNA -0.022 0.11 -10000 0 -0.49 10 10
BARD1/DNA-PK/P53 -0.048 0.14 -10000 0 -0.78 2 2
BRCA1/BARD1/Ubiquitin -0.01 0.072 -10000 0 -0.54 4 4
BRCA1/BARD1/CTIP -0.007 0.054 -10000 0 -0.41 4 4
FA complex -0.02 0.13 -10000 0 -0.42 9 9
BARD1/EWS -0.002 0.036 -10000 0 -0.54 1 1
RBBP8 0.031 0 -10000 0 -10000 0 0
TP53 -0.013 0.15 -10000 0 -0.72 9 9
TOPBP1 0.017 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.026 0.11 0.81 1 -10000 0 1
BRCA1/BARD1 -0.073 0.17 -10000 0 -0.77 6 6
CSTF1 0.017 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0 0 -10000 0 -10000 0 0
CDK2 -0.063 0.23 -10000 0 -0.72 24 24
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.017 0 -10000 0 -10000 0 0
RAD50 0.017 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.01 0.072 -10000 0 -0.54 4 4
EWSR1 0.014 0.05 -10000 0 -0.72 1 1
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.014 0.05 -9999 0 -0.72 1 1
ITGB7 -0.01 0.13 -9999 0 -0.64 9 9
ITGA4 0.011 0.062 -9999 0 -0.64 2 2
alpha4/beta7 Integrin -0.023 0.1 -9999 0 -0.46 11 11
alpha4/beta1 Integrin -0.007 0.056 -9999 0 -0.49 3 3
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.041 0 -9999 0 -10000 0 0
SNTA1 0.017 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.039 0.033 -9999 0 -0.46 1 1
MAPK12 -0.025 0.14 -9999 0 -0.4 14 14
CCND1 -0.031 0.1 -9999 0 -0.35 10 10
p38 gamma/SNTA1 -0.014 0.13 -9999 0 -0.43 6 6
MAP2K3 0.017 0 -9999 0 -10000 0 0
PKN1 0.017 0 -9999 0 -10000 0 0
G2/M transition checkpoint -0.024 0.14 -9999 0 -0.39 14 14
MAP2K6 -0.026 0.13 -9999 0 -0.38 9 9
MAPT 0.022 0.045 -9999 0 -10000 0 0
MAPK13 0.031 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK -0.026 0.12 -9999 0 -0.31 33 33
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.013 0.038 -10000 0 -0.55 1 1
GNB1/GNG2 -0.002 0.028 -10000 0 -0.42 1 1
regulation of S phase of mitotic cell cycle 0.04 0.018 -10000 0 -10000 0 0
GNAO1 0.017 0 -10000 0 -10000 0 0
HRAS 0.017 0.002 -10000 0 -10000 0 0
SHBG/T-DHT 0 0 -10000 0 -10000 0 0
PELP1 0.017 0.002 -10000 0 -10000 0 0
AKT1 0.016 0.001 -10000 0 -10000 0 0
MAP2K1 0.048 0.053 -10000 0 -10000 0 0
T-DHT/AR -0.001 0.037 -10000 0 -0.55 1 1
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.008 33 33
GNAI2 0.017 0 -10000 0 -10000 0 0
GNAI3 0.017 0 -10000 0 -10000 0 0
GNAI1 -0.068 0.22 -10000 0 -0.64 29 29
mol:GDP -0.002 0.023 -10000 0 -0.34 1 1
cell proliferation 0.029 0.16 -10000 0 -10000 0 0
PIK3CA 0.017 0 -10000 0 -10000 0 0
FOS -0.049 0.32 -10000 0 -0.81 33 33
mol:Ca2+ -0.009 0.023 -10000 0 -0.079 13 13
MAPK3 0.04 0.11 -10000 0 -10000 0 0
MAPK1 0.02 0.088 -10000 0 -0.41 1 1
PIK3R1 0.017 0 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.005 33 33
cAMP biosynthetic process 0.008 0.02 -10000 0 -10000 0 0
GNG2 0.017 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 -10000 0 -0.005 33 33
HRAS/GTP -0.004 0.025 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.017 0.002 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.005 33 33
PI3K 0 0 -10000 0 -10000 0 0
apoptosis -0.014 0.16 0.37 31 -10000 0 31
T-DHT/AR/PELP1 0 0.032 -10000 0 -0.47 1 1
HRAS/GDP -0.001 0.021 -10000 0 -10000 0 0
CREB1 0.011 0.17 -10000 0 -0.4 31 31
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR 0.013 0.049 -10000 0 -0.72 1 1
GNB1 0.017 0 -10000 0 -10000 0 0
RAF1 0.042 0.043 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.001 0.019 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src 0 0.028 -10000 0 -0.42 1 1
MAP2K2 0.048 0.053 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src/PI3K 0.04 0.018 -10000 0 -10000 0 0
GNAZ 0.017 0 -10000 0 -10000 0 0
SHBG 0.017 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.033 0.082 -10000 0 -10000 0 0
mol:T-DHT 0 0.001 -10000 0 -0.003 33 33
RAC1 0.017 0 -10000 0 -10000 0 0
GNRH1 0.015 0.001 -10000 0 -10000 0 0
Gi family/GTP -0.029 0.073 -10000 0 -10000 0 0
CDC42 0.017 0 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin -0.002 0.036 -9999 0 -0.54 1 1
AKT1 0.039 0.17 -9999 0 -0.66 2 2
PTK2B 0.019 0.15 -9999 0 -10000 0 0
VEGFR2 homodimer/Frs2 -0.01 0.068 -9999 0 -0.47 1 1
CAV1 0.004 0.096 -9999 0 -0.7 4 4
CALM1 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.06 0.14 -9999 0 -0.57 7 7
endothelial cell proliferation 0.039 0.18 -9999 0 -0.65 3 3
mol:Ca2+ -0.031 0.24 -9999 0 -0.73 14 14
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.055 0.13 -9999 0 -0.54 6 6
RP11-342D11.1 -0.016 0.2 -9999 0 -0.66 10 10
CDH5 0.017 0 -9999 0 -10000 0 0
VEGFA homodimer -0.045 0.14 -9999 0 -0.5 8 8
SHC1 0.017 0 -9999 0 -10000 0 0
SHC2 -0.02 0.16 -9999 0 -0.72 11 11
HRAS/GDP -0.063 0.14 -9999 0 -0.58 7 7
SH2D2A -0.01 0.14 -9999 0 -0.72 8 8
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.06 0.12 -9999 0 -0.66 3 3
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.074 0.15 -9999 0 -0.57 7 7
VEGFR1 homodimer -0.02 0.16 -9999 0 -0.72 11 11
SHC/GRB2/SOS1 -0.071 0.15 -9999 0 -0.65 7 7
GRB10 -0.027 0.26 -9999 0 -0.78 16 16
PTPN11 0.014 0.05 -9999 0 -0.72 1 1
GRB2 0.017 0 -9999 0 -10000 0 0
PAK1 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.059 0.14 -9999 0 -0.6 4 4
HRAS 0.017 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.039 0.081 -9999 0 -10000 0 0
HIF1A 0.01 0.07 -9999 0 -0.72 2 2
FRS2 0.017 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.054 0.13 -9999 0 -0.53 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.017 0 -9999 0 -10000 0 0
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.062 0.14 -9999 0 -0.57 8 8
mol:GDP -0.069 0.15 -9999 0 -0.63 7 7
mol:NADP 0.031 0.16 -9999 0 -0.56 3 3
eNOS/Hsp90 0.036 0.15 -9999 0 -0.55 2 2
PIK3R1 0.017 0 -9999 0 -10000 0 0
mol:IP3 -0.032 0.25 -9999 0 -0.75 14 14
HIF1A/ARNT -0.005 0.051 -9999 0 -0.54 2 2
SHB -0.016 0.15 -9999 0 -0.72 10 10
VEGFA -0.054 0.22 -9999 0 -0.74 21 21
VEGFC 0.008 0.075 -9999 0 -0.64 3 3
FAK1/Vinculin 0.048 0.14 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.056 0.13 -9999 0 -0.54 6 6
PTPN6 0.017 0 -9999 0 -10000 0 0
EPAS1 0.008 0.11 -9999 0 -0.61 7 7
mol:L-citrulline 0.031 0.16 -9999 0 -0.56 3 3
ITGAV 0.014 0.05 -9999 0 -0.72 1 1
PIK3CA 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.055 0.13 -9999 0 -0.54 6 6
VEGFR2 homodimer/VEGFA homodimer -0.088 0.18 -9999 0 -0.72 10 10
VEGFR2/3 heterodimer -0.01 0.068 -9999 0 -0.47 1 1
VEGFB 0.017 0 -9999 0 -10000 0 0
MAPK11 0.004 0.2 -9999 0 -0.64 10 10
VEGFR2 homodimer 0.03 0.093 -9999 0 -0.56 1 1
FLT1 -0.02 0.16 -9999 0 -0.72 11 11
NEDD4 -0.003 0.12 -9999 0 -0.73 6 6
MAPK3 -0.019 0.22 -9999 0 -0.66 14 14
MAPK1 -0.019 0.22 -9999 0 -0.66 14 14
VEGFA145/NRP2 -0.055 0.17 -9999 0 -0.57 21 21
VEGFR1/2 heterodimer -0.033 0.12 -9999 0 -0.47 2 2
KDR 0.03 0.093 -9999 0 -0.56 1 1
VEGFA165/NRP1/VEGFR2 homodimer -0.08 0.17 -9999 0 -0.65 11 11
SRC 0.017 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.017 0.23 -9999 0 -0.67 14 14
PI3K -0.08 0.16 -9999 0 -0.94 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.06 0.14 -9999 0 -0.58 6 6
FES -0.009 0.22 -9999 0 -0.7 10 10
GAB1 -0.069 0.14 -9999 0 -0.6 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.06 0.14 -9999 0 -0.57 7 7
CTNNB1 0 0.11 -9999 0 -0.72 5 5
SOS1 0.017 0 -9999 0 -10000 0 0
ARNT 0.017 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.032 0.16 -9999 0 -0.57 3 3
VEGFR2 homodimer/VEGFA homodimer/Yes -0.06 0.14 -9999 0 -0.57 7 7
PI3K/GAB1 0.04 0.17 -9999 0 -0.79 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.051 0.12 -9999 0 -0.52 2 2
PRKACA 0.017 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.017 0.072 -9999 0 -10000 0 0
HSP90AA1 0.014 0.05 -9999 0 -0.72 1 1
CDC42 -0.006 0.21 -9999 0 -0.67 10 10
actin cytoskeleton reorganization -0.073 0.15 -9999 0 -0.56 7 7
PTK2 0.04 0.14 -9999 0 -10000 0 0
EDG1 -0.027 0.26 -9999 0 -0.77 17 17
mol:DAG -0.032 0.25 -9999 0 -0.75 14 14
CaM/Ca2+ -0.093 0.19 -9999 0 -0.68 14 14
MAP2K3 0.007 0.2 -9999 0 -0.65 8 8
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.1 0.23 -9999 0 -0.8 16 16
PLCG1 -0.034 0.25 -9999 0 -0.76 14 14
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.072 0.15 -9999 0 -0.56 9 9
IQGAP1 0.017 0 -9999 0 -10000 0 0
YES1 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.062 0.14 -9999 0 -0.57 7 7
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.06 0.14 -9999 0 -0.57 7 7
cell migration 0.078 0.12 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.075 0.14 -9999 0 -0.82 2 2
FYN 0.014 0.044 -9999 0 -0.64 1 1
VEGFB/NRP1 -0.075 0.16 -9999 0 -0.62 10 10
mol:NO 0.031 0.16 -9999 0 -0.56 3 3
PXN 0.017 0 -9999 0 -10000 0 0
HRAS/GTP -0.063 0.14 -9999 0 -0.58 7 7
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.1 0.23 -9999 0 -0.8 16 16
VHL 0.014 0.05 -9999 0 -0.72 1 1
ITGB3 0.017 0 -9999 0 -10000 0 0
NOS3 0.028 0.17 -9999 0 -0.65 3 3
VEGFR2 homodimer/VEGFA homodimer/Sck -0.081 0.17 -9999 0 -0.6 10 10
RAC1 0.017 0 -9999 0 -10000 0 0
PRKCA -0.019 0.23 -9999 0 -0.7 13 13
PRKCB -0.028 0.23 -9999 0 -0.69 14 14
VCL 0.017 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.018 0.2 -9999 0 -0.67 10 10
VEGFR1/2 heterodimer/VEGFA homodimer -0.08 0.18 -9999 0 -0.67 10 10
VEGFA165/NRP2 -0.055 0.17 -9999 0 -0.57 21 21
MAPKKK cascade -0.08 0.18 -9999 0 -0.81 7 7
NRP2 0.014 0.05 -9999 0 -0.72 1 1
VEGFC homodimer 0.008 0.075 -9999 0 -0.63 3 3
NCK1 0.017 0 -9999 0 -10000 0 0
ROCK1 0.017 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.048 0.14 -9999 0 -10000 0 0
MAP3K13 -0.006 0.21 -9999 0 -0.67 10 10
PDPK1 0.026 0.18 -9999 0 -0.69 2 2
TCGA08_rtk_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
PDGFRA 0.008 0.075 -10000 0 -0.64 3 3
HRAS 0.017 0 -10000 0 -10000 0 0
EGFR 0.002 0.099 -10000 0 -0.65 5 5
AKT 0.033 0.038 -10000 0 -10000 0 0
FOXO3 0.017 0 -10000 0 -10000 0 0
AKT1 0.017 0 -10000 0 -10000 0 0
FOXO1 -0.01 0.13 -10000 0 -0.64 9 9
AKT3 0.017 0 -10000 0 -10000 0 0
FOXO4 0.017 0 -10000 0 -10000 0 0
MET -0.31 0.37 -10000 0 -0.72 99 99
PIK3CA 0.017 0 -10000 0 -10000 0 0
PIK3CB 0.014 0.05 -10000 0 -0.72 1 1
NRAS 0.007 0.085 -10000 0 -0.72 3 3
PIK3CG -0.001 0.11 -10000 0 -0.64 6 6
PIK3R3 0.017 0 -10000 0 -10000 0 0
PIK3R2 0.017 0 -10000 0 -10000 0 0
NF1 0.017 0 -10000 0 -10000 0 0
RAS -0.043 0.084 -10000 0 -0.31 4 4
ERBB2 -0.006 0.13 -10000 0 -0.71 7 7
proliferation/survival/translation -0.013 0.054 -10000 0 -10000 0 0
PI3K 0.015 0.068 0.22 4 -0.24 7 11
PIK3R1 0.017 0 -10000 0 -10000 0 0
KRAS 0.017 0 -10000 0 -10000 0 0
FOXO 0.036 0.042 -10000 0 -10000 0 0
AKT2 0.017 0 -10000 0 -10000 0 0
PTEN -0.001 0.11 -10000 0 -0.64 6 6
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.004 0.11 -10000 0 -0.74 1 1
epithelial cell differentiation -0.017 0.076 -10000 0 -0.38 5 5
CYFIP2 0.011 0.062 -10000 0 -0.64 2 2
ENAH 0.062 0.1 -10000 0 -10000 0 0
EGFR 0.002 0.099 -10000 0 -0.65 5 5
EPHA2 -0.016 0.15 -10000 0 -0.72 10 10
MYO6 0.032 0.086 -10000 0 -10000 0 0
CTNNB1 0 0.11 -10000 0 -0.72 5 5
ABI1/Sra1/Nap1 -0.006 0.047 -10000 0 -0.46 1 1
AQP5 -0.033 0.089 -10000 0 -0.57 1 1
CTNND1 0.017 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.033 0.081 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.018 0.11 -10000 0 -0.62 1 1
EGF -0.18 0.31 -10000 0 -0.68 64 64
NCKAP1 0.014 0.05 -10000 0 -0.72 1 1
AQP3 -0.031 0.086 -10000 0 -0.53 1 1
cortical microtubule organization -0.017 0.076 -10000 0 -0.38 5 5
GO:0000145 0.033 0.077 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.017 0.077 -10000 0 -0.39 5 5
MLLT4 0.017 0 -10000 0 -10000 0 0
ARF6/GDP -0.026 0.1 -10000 0 -0.59 5 5
ARF6 0.017 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.018 0.085 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.048 0.079 -10000 0 -10000 0 0
PVRL2 0.014 0.05 -10000 0 -0.72 1 1
ZYX 0.032 0.086 -10000 0 -10000 0 0
ARF6/GTP -0.017 0.077 -10000 0 -10000 0 0
CDH1 -0.001 0.11 -10000 0 -0.64 6 6
EGFR/EGFR/EGF/EGF -0.11 0.16 -10000 0 -0.66 4 4
RhoA/GDP -0.016 0.07 -10000 0 -10000 0 0
actin cytoskeleton organization 0.041 0.082 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.017 0 -10000 0 -10000 0 0
GIT1 0.017 0 -10000 0 -10000 0 0
IGF1R 0.017 0 -10000 0 -10000 0 0
IGF1 -0.35 0.32 -10000 0 -0.64 125 125
DIAPH1 -0.007 0.069 -10000 0 -0.71 2 2
Wnt receptor signaling pathway 0.017 0.076 0.38 5 -10000 0 5
RHOA 0.017 0 -10000 0 -10000 0 0
RhoA/GTP -0.026 0.1 -10000 0 -0.6 5 5
CTNNA1 0.017 0 -10000 0 -10000 0 0
VCL 0.041 0.084 -10000 0 -10000 0 0
EFNA1 0.017 0 -10000 0 -10000 0 0
LPP 0.042 0.082 -10000 0 -10000 0 0
Ephrin A1/EPHA2 -0.031 0.12 -10000 0 -0.7 5 5
SEC6/SEC8 -0.015 0.062 -10000 0 -10000 0 0
MGAT3 0.018 0.11 -10000 0 -0.63 1 1
HGF/MET -0.17 0.18 -10000 0 -0.68 4 4
HGF 0.01 0.07 -10000 0 -0.72 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.004 0.11 -10000 0 -0.75 1 1
actin cable formation 0.087 0.09 -10000 0 -0.41 1 1
KIAA1543 0.042 0.087 -10000 0 -0.6 1 1
KIFC3 0.026 0.11 -10000 0 -0.75 2 2
NCK1 0.017 0 -10000 0 -10000 0 0
EXOC3 0.017 0 -10000 0 -10000 0 0
ACTN1 0.034 0.082 -10000 0 -10000 0 0
NCK1/GIT1 0 0 -10000 0 -10000 0 0
mol:GDP -0.017 0.076 -10000 0 -0.38 5 5
EXOC4 0.017 0 -10000 0 -10000 0 0
STX4 0.034 0.082 -10000 0 -10000 0 0
PIP5K1C 0.034 0.082 -10000 0 -10000 0 0
LIMA1 -0.033 0.17 -10000 0 -0.64 17 17
ABI1 0.017 0 -10000 0 -10000 0 0
ROCK1 -0.023 0.088 -10000 0 -0.5 5 5
adherens junction assembly 0.059 0.1 -10000 0 -0.58 3 3
IGF-1R heterotetramer/IGF1 -0.17 0.16 -10000 0 -0.62 6 6
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.002 0.036 -10000 0 -0.54 1 1
MET -0.31 0.37 -10000 0 -0.72 99 99
PLEKHA7 0.034 0.082 -10000 0 -10000 0 0
mol:GTP -0.018 0.084 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.067 0.077 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.004 0.11 -10000 0 -0.74 1 1
regulation of cell-cell adhesion 0.041 0.082 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.004 0.11 -10000 0 -0.75 1 1
Class I PI3K signaling events

Figure S85.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.003 0.057 0.27 6 -10000 0 6
DAPP1 -0.037 0.16 -10000 0 -0.56 11 11
Src family/SYK family/BLNK-LAT/BTK-ITK -0.037 0.21 -10000 0 -0.61 14 14
mol:DAG -0.036 0.13 0.23 1 -0.28 13 14
HRAS 0.018 0.003 -10000 0 -10000 0 0
RAP1A 0.017 0.003 -10000 0 -10000 0 0
ARF5/GDP 0.033 0.069 -10000 0 -10000 0 0
PLCG2 -0.31 0.33 -10000 0 -0.64 110 110
PLCG1 -0.033 0.19 -10000 0 -0.72 15 15
ARF5 0.017 0 -10000 0 -10000 0 0
mol:GTP 0.002 0.057 -10000 0 -10000 0 0
ARF1/GTP 0.002 0.055 0.25 6 -10000 0 6
RHOA 0.017 0 -10000 0 -10000 0 0
YES1 0.017 0 -10000 0 -10000 0 0
RAP1A/GTP 0.002 0.055 -10000 0 -10000 0 0
ADAP1 0.002 0.054 -10000 0 -10000 0 0
ARAP3 0.002 0.056 -10000 0 -10000 0 0
INPPL1 0.017 0 -10000 0 -10000 0 0
PREX1 0.017 0 -10000 0 -10000 0 0
ARHGEF6 0.011 0.062 -10000 0 -0.64 2 2
ARHGEF7 0.017 0 -10000 0 -10000 0 0
ARF1 0.017 0 -10000 0 -10000 0 0
NRAS 0.008 0.085 -10000 0 -0.72 3 3
FYN 0.014 0.044 -10000 0 -0.64 1 1
ARF6 0.017 0 -10000 0 -10000 0 0
FGR 0.017 0 -10000 0 -10000 0 0
mol:Ca2+ -0.01 0.071 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.011 0.062 -10000 0 -0.64 2 2
ZAP70 0.017 0 -10000 0 -10000 0 0
mol:IP3 -0.019 0.095 -10000 0 -0.28 1 1
LYN 0.017 0 -10000 0 -10000 0 0
ARF1/GDP 0.033 0.069 -10000 0 -10000 0 0
RhoA/GDP -0.002 0.058 0.26 5 -10000 0 5
PDK1/Src/Hsp90 -0.002 0.031 -10000 0 -0.46 1 1
BLNK -0.001 0.11 -10000 0 -0.64 6 6
actin cytoskeleton reorganization 0.055 0.079 -10000 0 -0.4 1 1
SRC 0.017 0 -10000 0 -10000 0 0
PLEKHA2 0.023 0.047 -10000 0 -0.47 2 2
RAC1 0.017 0 -10000 0 -10000 0 0
PTEN -0.016 0.099 -10000 0 -0.61 6 6
HSP90AA1 0.014 0.05 -10000 0 -0.72 1 1
ARF6/GTP 0.003 0.057 -10000 0 -10000 0 0
RhoA/GTP 0.002 0.054 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.02 0.16 -10000 0 -0.45 13 13
BLK -0.16 0.29 -10000 0 -0.64 61 61
PDPK1 0.017 0 -10000 0 -10000 0 0
CYTH1 0.002 0.054 -10000 0 -10000 0 0
HCK -0.045 0.19 -10000 0 -0.64 21 21
CYTH3 0.002 0.054 -10000 0 -10000 0 0
CYTH2 0.002 0.054 -10000 0 -10000 0 0
KRAS 0.018 0.003 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.003 0.039 0.2 6 -10000 0 6
SGK1 0.003 0.04 0.21 6 -10000 0 6
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.072 -10000 0 -0.31 3 3
SOS1 0.017 0 -10000 0 -10000 0 0
SYK 0.014 0.05 -10000 0 -0.72 1 1
ARF6/GDP -0.002 0.058 0.27 5 -10000 0 5
mol:PI-3-4-5-P3 0.004 0.066 0.32 6 -10000 0 6
ARAP3/RAP1A/GTP 0.002 0.056 -10000 0 -10000 0 0
VAV1 -0.042 0.19 -10000 0 -0.64 20 20
mol:PI-3-4-P2 0.015 0 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.027 0.044 -10000 0 -10000 0 0
PLEKHA1 0.027 0 -10000 0 -10000 0 0
Rac1/GDP 0.033 0.069 -10000 0 -10000 0 0
LAT 0.01 0.07 -10000 0 -0.72 2 2
Rac1/GTP 0.029 0.089 -10000 0 -0.51 2 2
ITK 0.002 0.055 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.058 0.17 -10000 0 -0.4 14 14
LCK 0.011 0.066 -10000 0 -0.68 2 2
BTK -0.044 0.13 -10000 0 -0.64 2 2
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 -0.009 0.052 -10000 0 -10000 0 0
ER alpha/Gai/GDP/Gbeta gamma 0.022 0.11 -10000 0 -0.58 3 3
AKT1 0.025 0.14 -10000 0 -0.82 6 6
PIK3CA 0.017 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.021 0.14 -10000 0 -0.84 6 6
mol:Ca2+ -0.092 0.19 -10000 0 -0.43 14 14
IGF1R 0.017 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.015 0.077 -10000 0 -0.42 8 8
SHC1 0.017 0 -10000 0 -10000 0 0
apoptosis -0.026 0.14 0.78 6 -10000 0 6
RhoA/GTP -0.012 0.058 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.028 0.088 -10000 0 -0.58 3 3
regulation of stress fiber formation -0.06 0.058 -10000 0 -10000 0 0
E2/ERA-ERB (dimer) -0.011 0.064 -10000 0 -0.4 6 6
KRAS 0.017 0 -10000 0 -10000 0 0
G13/GTP -0.01 0.059 -10000 0 -0.36 6 6
pseudopodium formation 0.06 0.058 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1 -0.011 0.064 -10000 0 -0.4 6 6
GRB2 0.017 0 -10000 0 -10000 0 0
GNG2 0.017 0 -10000 0 -10000 0 0
GNAO1 0.017 0 -10000 0 -10000 0 0
HRAS 0.017 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.04 0.11 -10000 0 -0.54 6 6
E2/ER beta (dimer) 0 0 -10000 0 -10000 0 0
mol:GDP -0.014 0.071 -10000 0 -0.42 6 6
mol:NADP 0.04 0.11 -10000 0 -0.54 6 6
PIK3R1 0.017 0 -10000 0 -10000 0 0
mol:IP3 -0.096 0.2 -10000 0 -0.44 14 14
IGF-1R heterotetramer 0.017 0 -10000 0 -10000 0 0
PLCB1 -0.11 0.2 -10000 0 -0.38 74 74
PLCB2 0.009 0.11 -10000 0 -0.44 9 9
IGF1 -0.35 0.32 -10000 0 -0.64 125 125
mol:L-citrulline 0.04 0.11 -10000 0 -0.54 6 6
RHOA 0.017 0 -10000 0 -10000 0 0
Gai/GDP -0.03 0.078 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.017 0 -10000 0 -10000 0 0
ESR2 0.017 0 -10000 0 -10000 0 0
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 -0.001 0.11 -10000 0 -0.64 6 6
Gq family/GDP/Gbeta gamma 0.017 0.11 -10000 0 -0.48 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.042 0.056 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.028 0.088 -10000 0 -0.58 3 3
GNAZ 0.017 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.013 0.077 -10000 0 -0.47 6 6
STRN 0.01 0.07 -10000 0 -0.72 2 2
GNAL 0.017 0 -10000 0 -10000 0 0
PELP1 0.017 0 -10000 0 -10000 0 0
MAPK11 0.023 0.033 -10000 0 -0.47 1 1
GNAI2 0.017 0 -10000 0 -10000 0 0
GNAI3 0.017 0 -10000 0 -10000 0 0
GNAI1 -0.068 0.22 -10000 0 -0.64 29 29
HBEGF 0.037 0.11 -10000 0 -0.48 3 3
cAMP biosynthetic process -0.008 0.051 -10000 0 -10000 0 0
SRC 0.032 0.11 -10000 0 -0.54 3 3
PI3K 0 0 -10000 0 -10000 0 0
GNB1 0.017 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.011 0.06 -10000 0 -10000 0 0
SOS1 0.017 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.14 0.14 -10000 0 -0.59 6 6
Gs family/GTP -0.009 0.051 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.006 0.048 -10000 0 -0.42 3 3
vasodilation 0.04 0.11 -10000 0 -0.51 6 6
mol:DAG -0.096 0.2 -10000 0 -0.44 14 14
Gs family/GDP/Gbeta gamma -0.011 0.056 -10000 0 -10000 0 0
MSN 0.062 0.061 -10000 0 -10000 0 0
Gq family/GTP -0.034 0.1 -10000 0 -0.47 9 9
mol:PI-3-4-5-P3 0.022 0.14 -10000 0 -0.8 6 6
NRAS 0.007 0.085 -10000 0 -0.72 3 3
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.04 0.11 0.51 6 -10000 0 6
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.013 0.066 -10000 0 -10000 0 0
NOS3 0.04 0.12 -10000 0 -0.57 6 6
GNA11 -0.001 0.11 -10000 0 -0.64 6 6
MAPKKK cascade 0.047 0.12 -10000 0 -0.62 6 6
E2/ER alpha (dimer)/PELP1/Src -0.03 0.095 -10000 0 -0.52 6 6
ruffle organization 0.06 0.058 -10000 0 -10000 0 0
ROCK2 0.053 0.065 -10000 0