Glioblastoma Multiforme: PARADIGM pathway analysis of mRNASeq expression and copy number data
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

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

Summary

There were 37 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
IL23-mediated signaling events 22
Syndecan-1-mediated signaling events 20
Ceramide signaling pathway 15
Signaling mediated by p38-alpha and p38-beta 15
Angiopoietin receptor Tie2-mediated signaling 15
TCR signaling in naïve CD8+ T cells 14
Ephrin A reverse signaling 13
IL4-mediated signaling events 13
Endothelins 13
EGFR-dependent Endothelin signaling events 13
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
IL23-mediated signaling events 22 1365 60 -0.42 0.034 1000 -1000 -0.079 -1000
Syndecan-1-mediated signaling events 20 682 34 -0.11 0.034 1000 -1000 -0.03 -1000
Ceramide signaling pathway 15 1185 76 -0.13 0.052 1000 -1000 -0.028 -1000
Signaling mediated by p38-alpha and p38-beta 15 663 44 -0.086 0.036 1000 -1000 -0.022 -1000
Angiopoietin receptor Tie2-mediated signaling 15 1331 88 -0.18 0.034 1000 -1000 -0.061 -1000
TCR signaling in naïve CD8+ T cells 14 1390 93 -0.3 0.34 1000 -1000 -0.04 -1000
Ephrin A reverse signaling 13 97 7 -0.039 0.007 1000 -1000 -0.016 -1000
IL4-mediated signaling events 13 1217 91 -0.46 0.33 1000 -1000 -0.13 -1000
Endothelins 13 1273 96 -0.16 0.073 1000 -1000 -0.052 -1000
EGFR-dependent Endothelin signaling events 13 278 21 -0.066 0.05 1000 -1000 -0.04 -1000
Syndecan-4-mediated signaling events 13 920 67 -0.1 0.034 1000 -1000 -0.031 -1000
E-cadherin signaling events 13 69 5 -0.037 0.034 1000 -1000 0.02 -1000
Reelin signaling pathway 12 685 56 -0.065 0.062 1000 -1000 -0.027 -1000
Stabilization and expansion of the E-cadherin adherens junction 12 941 74 -0.097 0.077 1000 -1000 -0.074 -1000
IL12-mediated signaling events 11 976 87 -0.28 0.043 1000 -1000 -0.069 -1000
HIF-1-alpha transcription factor network 11 884 76 -0.13 0.049 1000 -1000 -0.063 -1000
Arf6 signaling events 11 725 62 -0.066 0.073 1000 -1000 -0.038 -1000
Caspase cascade in apoptosis 10 745 74 -0.14 0.048 1000 -1000 -0.052 -1000
EPO signaling pathway 10 578 55 -0.009 0.08 1000 -1000 -0.042 -1000
Glucocorticoid receptor regulatory network 10 1248 114 -0.27 0.17 1000 -1000 -0.046 -1000
Signaling events regulated by Ret tyrosine kinase 10 866 82 -0.11 0.034 1000 -1000 -0.041 -1000
Signaling events mediated by the Hedgehog family 9 502 52 -0.066 0.045 1000 -1000 -0.026 -1000
FOXA2 and FOXA3 transcription factor networks 9 447 46 -0.24 0.035 1000 -1000 -0.1 -1000
PDGFR-alpha signaling pathway 9 405 44 -0.05 0.043 1000 -1000 -0.035 -1000
E-cadherin signaling in the nascent adherens junction 9 710 76 -0.048 0.059 1000 -1000 -0.051 -1000
ErbB2/ErbB3 signaling events 8 583 65 -0.088 0.05 1000 -1000 -0.083 -1000
Nephrin/Neph1 signaling in the kidney podocyte 8 296 34 -0.019 0.049 1000 -1000 -0.025 -1000
Visual signal transduction: Cones 8 337 38 -0.065 0.039 1000 -1000 -0.029 -1000
JNK signaling in the CD4+ TCR pathway 8 136 17 -0.15 0.047 1000 -1000 -0.035 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 8 707 85 -0.07 0.096 1000 -1000 -0.052 -1000
p75(NTR)-mediated signaling 8 1041 125 -0.066 0.085 1000 -1000 -0.059 -1000
Glypican 1 network 8 420 48 -0.079 0.063 1000 -1000 -0.033 -1000
HIF-2-alpha transcription factor network 8 348 43 -0.081 0.064 1000 -1000 -0.055 -1000
Effects of Botulinum toxin 8 230 26 -0.043 0.033 1000 -1000 -0.012 -1000
TCGA08_rtk_signaling 8 209 26 -0.066 0.09 1000 -1000 -0.008 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 8 551 68 -0.19 0.035 1000 -1000 -0.072 -1000
E-cadherin signaling in keratinocytes 8 359 43 -0.066 0.039 1000 -1000 -0.026 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 7 417 54 -0.045 0.049 1000 -1000 -0.028 -1000
Thromboxane A2 receptor signaling 7 831 105 -0.066 0.046 1000 -1000 -0.047 -1000
Fc-epsilon receptor I signaling in mast cells 7 703 97 -0.15 0.056 1000 -1000 -0.052 -1000
amb2 Integrin signaling 7 575 82 -0.12 0.049 1000 -1000 -0.031 -1000
FAS signaling pathway (CD95) 7 352 47 -0.18 0.052 1000 -1000 -0.041 -1000
EPHB forward signaling 7 612 85 -0.052 0.083 1000 -1000 -0.051 -1000
TCGA08_retinoblastoma 7 58 8 -0.017 0.076 1000 -1000 -0.005 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 7 251 33 -0.071 0.065 1000 -1000 -0.024 -1000
Visual signal transduction: Rods 7 368 52 -0.061 0.034 1000 -1000 -0.024 -1000
Osteopontin-mediated events 6 240 38 -0.079 0.04 1000 -1000 -0.037 -1000
Noncanonical Wnt signaling pathway 6 168 26 -0.048 0.034 1000 -1000 -0.033 -1000
IL1-mediated signaling events 6 429 62 -0.042 0.063 1000 -1000 -0.039 -1000
RXR and RAR heterodimerization with other nuclear receptor 6 317 52 -0.074 0.083 1000 -1000 -0.048 -1000
Retinoic acid receptors-mediated signaling 6 363 58 -0.078 0.062 1000 -1000 -0.042 -1000
IL2 signaling events mediated by PI3K 6 403 58 -0.24 0.047 1000 -1000 -0.039 -1000
Glypican 2 network 6 27 4 0.003 0.011 1000 -1000 0.022 -1000
Calcium signaling in the CD4+ TCR pathway 6 197 31 -0.07 0.032 1000 -1000 -0.033 -1000
Nongenotropic Androgen signaling 6 345 52 -0.036 0.041 1000 -1000 -0.025 -1000
Signaling events mediated by VEGFR1 and VEGFR2 6 785 125 -0.035 0.063 1000 -1000 -0.038 -1000
Wnt signaling 6 48 7 -0.014 0.028 1000 -1000 -0.013 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 6 536 78 -0.038 0.063 1000 -1000 -0.045 -1000
Signaling events mediated by PTP1B 5 417 76 -0.088 0.044 1000 -1000 -0.037 -1000
BMP receptor signaling 5 435 81 -0.051 0.064 1000 -1000 -0.035 -1000
mTOR signaling pathway 5 285 53 -0.017 0.069 1000 -1000 -0.037 -1000
Nectin adhesion pathway 5 364 63 -0.037 0.06 1000 -1000 -0.052 -1000
Integrins in angiogenesis 5 474 84 -0.05 0.083 1000 -1000 -0.042 -1000
LPA receptor mediated events 5 542 102 -0.15 0.057 1000 -1000 -0.076 -1000
BCR signaling pathway 5 506 99 -0.058 0.07 1000 -1000 -0.067 -1000
LPA4-mediated signaling events 4 48 12 -0.033 0 1000 -1000 -0.021 -1000
Syndecan-2-mediated signaling events 4 324 69 -0.05 0.056 1000 -1000 -0.045 -1000
a4b1 and a4b7 Integrin signaling 4 22 5 0.014 0.028 1000 -1000 0.015 -1000
Class I PI3K signaling events mediated by Akt 4 308 68 -0.027 0.064 1000 -1000 -0.031 -1000
Paxillin-independent events mediated by a4b1 and a4b7 4 162 37 -0.032 0.047 1000 -1000 -0.031 -1000
ceramide signaling pathway 4 197 49 -0.021 0.048 1000 -1000 -0.03 -1000
Ephrin B reverse signaling 4 233 48 -0.025 0.052 1000 -1000 -0.025 -1000
S1P1 pathway 4 171 36 -0.045 0.034 1000 -1000 -0.042 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 4 181 45 -0.076 0.058 1000 -1000 -0.049 -1000
IL27-mediated signaling events 4 204 51 -0.074 0.059 1000 -1000 -0.058 -1000
IL6-mediated signaling events 4 342 75 -0.049 0.071 1000 -1000 -0.067 -1000
Plasma membrane estrogen receptor signaling 4 373 86 -0.034 0.058 1000 -1000 -0.044 -1000
Neurotrophic factor-mediated Trk receptor signaling 4 562 120 -0.062 0.093 1000 -1000 -0.055 -1000
FOXM1 transcription factor network 4 242 51 -0.094 0.064 1000 -1000 -0.12 -1000
S1P4 pathway 4 106 25 0 0.049 1000 -1000 -0.023 -1000
Aurora B signaling 4 319 67 -0.1 0.069 1000 -1000 -0.029 -1000
Regulation of nuclear SMAD2/3 signaling 3 515 136 -0.24 0.11 1000 -1000 -0.038 -1000
Coregulation of Androgen receptor activity 3 290 76 -0.081 0.061 1000 -1000 -0.025 -1000
Arf6 downstream pathway 3 151 43 -0.047 0.05 1000 -1000 -0.025 -1000
Aurora C signaling 3 25 7 0 0.037 1000 -1000 -0.007 -1000
PLK1 signaling events 3 311 85 -0.025 0.053 1000 -1000 -0.029 -1000
TRAIL signaling pathway 3 168 48 -0.047 0.087 1000 -1000 -0.025 -1000
S1P5 pathway 3 52 17 -0.026 0.034 1000 -1000 -0.013 -1000
FoxO family signaling 3 207 64 -0.075 0.071 1000 -1000 -0.054 -1000
Syndecan-3-mediated signaling events 3 121 35 -0.066 0.085 1000 -1000 -0.02 -1000
Canonical Wnt signaling pathway 3 197 51 -0.065 0.1 1000 -1000 -0.044 -1000
IL2 signaling events mediated by STAT5 3 87 22 -0.052 0.035 1000 -1000 -0.034 -1000
Class I PI3K signaling events 3 257 73 -0.031 0.085 1000 -1000 -0.037 -1000
IGF1 pathway 3 224 57 -0.046 0.081 1000 -1000 -0.033 -1000
Insulin Pathway 3 260 74 -0.059 0.074 1000 -1000 -0.044 -1000
VEGFR1 specific signals 3 183 56 -0.029 0.058 1000 -1000 -0.046 -1000
PDGFR-beta signaling pathway 3 306 97 -0.024 0.086 1000 -1000 -0.045 -1000
Regulation of Androgen receptor activity 3 258 70 -0.1 0.044 1000 -1000 -0.046 -1000
ErbB4 signaling events 2 202 69 -0.066 0.046 1000 -1000 -0.039 -1000
Sphingosine 1-phosphate (S1P) pathway 2 56 28 -0.018 0.047 1000 -1000 -0.026 -1000
Cellular roles of Anthrax toxin 2 114 39 -0.032 0.045 1000 -1000 -0.021 -1000
Presenilin action in Notch and Wnt signaling 2 178 61 -0.065 0.086 1000 -1000 -0.037 -1000
Insulin-mediated glucose transport 2 80 32 -0.024 0.068 1000 -1000 -0.031 -1000
IFN-gamma pathway 2 187 68 -0.058 0.067 1000 -1000 -0.052 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 2 235 83 -0.058 0.065 1000 -1000 -0.028 -1000
TCGA08_p53 2 16 7 -0.014 0.027 1000 -1000 -0.015 -1000
Paxillin-dependent events mediated by a4b1 2 95 36 -0.036 0.047 1000 -1000 -0.027 -1000
Atypical NF-kappaB pathway 2 91 31 -0.015 0.045 1000 -1000 -0.026 -1000
Regulation of p38-alpha and p38-beta 2 128 54 -0.057 0.055 1000 -1000 -0.047 -1000
Arf6 trafficking events 2 159 71 -0.059 0.061 1000 -1000 -0.028 -1000
Regulation of Telomerase 2 299 102 -0.1 0.088 1000 -1000 -0.04 -1000
S1P3 pathway 2 105 42 -0.008 0.042 1000 -1000 -0.032 -1000
Class IB PI3K non-lipid kinase events 2 6 3 -0.027 0.027 1000 -1000 -0.024 -1000
Ras signaling in the CD4+ TCR pathway 2 49 17 0 0.058 1000 -1000 -0.029 -1000
Canonical NF-kappaB pathway 1 44 39 -0.015 0.075 1000 -1000 -0.034 -1000
BARD1 signaling events 1 66 57 -0.074 0.086 1000 -1000 -0.035 -1000
PLK2 and PLK4 events 1 4 3 -0.019 0.031 1000 -1000 -0.027 -1000
Hedgehog signaling events mediated by Gli proteins 1 80 65 -0.001 0.075 1000 -1000 -0.041 -1000
Signaling events mediated by HDAC Class III 1 68 40 -0.048 0.049 1000 -1000 -0.033 -1000
Signaling events mediated by HDAC Class I 1 124 104 -0.064 0.078 1000 -1000 -0.034 -1000
Signaling mediated by p38-gamma and p38-delta 1 21 15 -0.023 0.034 1000 -1000 -0.031 -1000
Rapid glucocorticoid signaling 1 24 20 -0.015 0.04 1000 -1000 -0.012 -1000
Signaling events mediated by PRL 1 34 34 -0.03 0.049 1000 -1000 -0.039 -1000
p38 MAPK signaling pathway 1 87 44 -0.014 0.047 1000 -1000 -0.025 -1000
Arf1 pathway 1 63 54 -0.081 0.057 1000 -1000 -0.018 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 15 23 -0.015 0.061 1000 -1000 -0.027 -1000
Signaling events mediated by HDAC Class II 0 39 75 -0.039 0.094 1000 -1000 -0.029 -1000
Circadian rhythm pathway 0 13 22 -0.007 0.064 1000 -1000 -0.025 -1000
Aurora A signaling 0 52 60 -0.022 0.072 1000 -1000 -0.027 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 0 27 -0.017 0.074 1000 -1000 -0.034 -1000
Alternative NF-kappaB pathway 0 0 13 0 0.067 1000 -1000 0 -1000
Total 736 46587 7203 -9.5 8 131000 -131000 -4.9 -131000
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.38 0.51 -10000 0 -1.2 33 33
IL23A -0.36 0.49 -10000 0 -1.2 32 32
NF kappa B1 p50/RelA/I kappa B alpha -0.33 0.5 -10000 0 -1.1 38 38
positive regulation of T cell mediated cytotoxicity -0.39 0.56 -10000 0 -1.2 38 38
ITGA3 -0.35 0.48 -10000 0 -1.2 31 31
IL17F -0.24 0.29 -10000 0 -0.66 39 39
IL12B -0.016 0.044 -10000 0 -10000 0 0
STAT1 (dimer) -0.37 0.54 -10000 0 -1.2 38 38
CD4 -0.33 0.46 -10000 0 -1.1 33 33
IL23 -0.34 0.48 -10000 0 -1.1 34 34
IL23R -0.053 0.07 -10000 0 -0.15 34 34
IL1B -0.36 0.51 -10000 0 -1.2 31 31
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.33 0.45 -10000 0 -1.1 33 33
TYK2 -0.002 0.04 -10000 0 -10000 0 0
STAT4 -0.012 0.12 -10000 0 -0.38 14 14
STAT3 0.034 0 -10000 0 -10000 0 0
IL18RAP -0.008 0.12 -10000 0 -0.38 13 13
IL12RB1 -0.018 0.089 -10000 0 -0.41 6 6
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.007 0.079 -10000 0 -0.3 6 6
IL23R/JAK2 -0.043 0.096 -10000 0 -0.2 17 17
positive regulation of chronic inflammatory response -0.39 0.56 -10000 0 -1.2 38 38
natural killer cell activation 0.005 0.006 0.018 1 -10000 0 1
JAK2 -0.005 0.044 -10000 0 -10000 0 0
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
NFKB1 0.032 0.004 -10000 0 -10000 0 0
RELA 0.032 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.32 0.45 -10000 0 -1 34 34
ALOX12B -0.34 0.46 -10000 0 -1.1 30 30
CXCL1 -0.36 0.49 -10000 0 -1.1 34 34
T cell proliferation -0.39 0.56 -10000 0 -1.2 38 38
NFKBIA 0.03 0.009 -10000 0 -10000 0 0
IL17A -0.18 0.24 -10000 0 -0.52 37 37
PI3K -0.35 0.51 -10000 0 -1.1 38 38
IFNG -0.013 0.025 -10000 0 -0.077 13 13
STAT3 (dimer) -0.33 0.49 -10000 0 -1 38 38
IL18R1 0.016 0.065 -10000 0 -0.38 3 3
IL23/IL23R/JAK2/TYK2/SOCS3 -0.21 0.29 -10000 0 -0.68 30 30
IL18/IL18R 0.021 0.1 -10000 0 -0.24 17 17
macrophage activation -0.017 0.019 -10000 0 -0.043 38 38
TNF -0.37 0.52 -10000 0 -1.2 34 34
STAT3/STAT4 -0.36 0.52 -10000 0 -1.1 41 41
STAT4 (dimer) -0.38 0.55 -10000 0 -1.1 41 41
IL18 0.026 0.059 -10000 0 -0.38 3 3
IL19 -0.33 0.46 -10000 0 -1 39 39
STAT5A (dimer) -0.37 0.54 -10000 0 -1.2 38 38
STAT1 0.033 0.012 -10000 0 -10000 0 0
SOCS3 -0.006 0.11 -10000 0 -0.38 12 12
CXCL9 -0.39 0.51 -10000 0 -1.2 39 39
MPO -0.38 0.51 -10000 0 -1.2 36 36
positive regulation of humoral immune response -0.39 0.56 -10000 0 -1.2 38 38
IL23/IL23R/JAK2/TYK2 -0.42 0.65 -10000 0 -1.3 38 38
IL6 -0.32 0.5 -10000 0 -1.2 30 30
STAT5A 0.034 0 -10000 0 -10000 0 0
IL2 0.004 0.004 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.006 0.018 1 -10000 0 1
CD3E -0.4 0.53 -10000 0 -1.2 40 40
keratinocyte proliferation -0.39 0.56 -10000 0 -1.2 38 38
NOS2 -0.39 0.5 -10000 0 -1.2 37 37
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 0.033 0.007 -10000 0 -10000 0 0
CCL5 0.023 0.061 -10000 0 -0.38 3 3
SDCBP 0.033 0.006 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.11 0.19 -10000 0 -0.37 41 41
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.094 0.19 -10000 0 -0.43 28 28
Syndecan-1/Syntenin -0.088 0.2 0.24 1 -0.42 29 30
MAPK3 -0.096 0.18 -10000 0 -0.44 25 25
HGF/MET -0.02 0.11 -10000 0 -0.31 17 17
TGFB1/TGF beta receptor Type II 0.033 0.007 -10000 0 -10000 0 0
BSG 0.033 0.007 -10000 0 -10000 0 0
keratinocyte migration -0.093 0.19 -10000 0 -0.43 28 28
Syndecan-1/RANTES -0.094 0.2 0.24 1 -0.42 32 33
Syndecan-1/CD147 -0.081 0.2 -10000 0 -0.45 26 26
Syndecan-1/Syntenin/PIP2 -0.086 0.19 0.23 1 -0.41 29 30
LAMA5 0.028 0.035 -10000 0 -0.38 1 1
positive regulation of cell-cell adhesion -0.084 0.18 0.22 1 -0.4 29 30
MMP7 -0.066 0.16 -10000 0 -0.38 28 28
HGF -0.006 0.099 -10000 0 -0.38 9 9
Syndecan-1/CASK -0.1 0.18 -10000 0 -0.36 41 41
Syndecan-1/HGF/MET -0.083 0.19 -10000 0 -0.42 28 28
regulation of cell adhesion -0.094 0.18 0.3 2 -0.43 25 27
HPSE 0.017 0.082 -10000 0 -0.38 6 6
positive regulation of cell migration -0.11 0.19 -10000 0 -0.37 41 41
SDC1 -0.11 0.2 -10000 0 -0.37 41 41
Syndecan-1/Collagen -0.11 0.19 -10000 0 -0.37 41 41
PPIB 0.034 0.005 -10000 0 -10000 0 0
MET -0.026 0.12 -10000 0 -0.38 14 14
PRKACA 0.033 0.007 -10000 0 -10000 0 0
MMP9 -0.034 0.14 -10000 0 -0.38 20 20
MAPK1 -0.097 0.18 -10000 0 -0.44 25 25
homophilic cell adhesion -0.1 0.19 -10000 0 -0.37 41 41
MMP1 -0.066 0.16 -10000 0 -0.38 28 28
Ceramide signaling pathway

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
SPHK2 -0.018 0.048 -10000 0 -0.27 5 5
MAP4K4 -0.019 0.09 -10000 0 -0.29 9 9
BAG4 0.034 0.005 -10000 0 -10000 0 0
PKC zeta/ceramide -0.072 0.14 -10000 0 -0.22 58 58
NFKBIA 0.032 0.009 -10000 0 -10000 0 0
BIRC3 -0.016 0.12 -10000 0 -0.38 14 14
BAX -0.026 0.087 -10000 0 -0.39 6 6
RIPK1 0.033 0.006 -10000 0 -10000 0 0
AKT1 0.005 0.057 0.64 1 -10000 0 1
BAD -0.07 0.12 -10000 0 -0.21 51 51
SMPD1 -0.011 0.062 0.12 1 -0.19 10 11
RB1 -0.069 0.12 0.2 1 -0.2 52 53
FADD/Caspase 8 -0.009 0.088 -10000 0 -0.33 5 5
MAP2K4 -0.07 0.11 0.18 1 -0.2 51 52
NSMAF 0.033 0.006 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.071 0.12 0.18 2 -0.2 51 53
EGF 0.006 0.1 -10000 0 -0.38 9 9
mol:ceramide -0.07 0.13 0.12 3 -0.22 51 54
MADD 0.03 0.035 -10000 0 -0.38 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.017 0.043 -10000 0 -0.27 4 4
ASAH1 0.033 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.069 0.12 0.19 1 -0.2 52 53
cell proliferation -0.047 0.12 -10000 0 -0.3 10 10
BID -0.047 0.19 -10000 0 -0.68 10 10
MAP3K1 -0.069 0.12 0.2 1 -0.21 51 52
EIF2A -0.072 0.11 0.17 1 -0.2 45 46
TRADD 0.031 0.034 -10000 0 -0.38 1 1
CRADD 0.034 0.005 -10000 0 -10000 0 0
MAPK3 -0.063 0.1 0.17 1 -0.28 8 9
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.069 0.11 0.17 1 -0.28 13 14
Cathepsin D/ceramide -0.054 0.13 -10000 0 -0.21 51 51
FADD -0.018 0.088 -10000 0 -0.29 8 8
KSR1 -0.071 0.12 0.19 1 -0.21 53 54
MAPK8 -0.13 0.17 0.18 1 -0.32 47 48
PRKRA -0.07 0.12 -10000 0 -0.21 51 51
PDGFA 0.009 0.075 -10000 0 -0.38 5 5
TRAF2 0.033 0.007 -10000 0 -10000 0 0
IGF1 0.013 0.084 -10000 0 -0.38 6 6
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.069 0.12 0.12 3 -0.22 51 54
CTSD 0.032 0.011 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.05 0.006 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.049 0.13 -10000 0 -0.33 10 10
PRKCD 0.034 0.004 -10000 0 -10000 0 0
PRKCZ -0.011 0.12 -10000 0 -0.38 14 14
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.017 0.043 -10000 0 -0.27 4 4
RelA/NF kappa B1 0.05 0.006 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.02 0.054 -10000 0 -0.38 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.017 0.095 -10000 0 -0.27 12 12
TNFR1A/BAG4/TNF-alpha 0.033 0.078 -10000 0 -0.23 9 9
mol:Sphingosine-1-phosphate -0.018 0.048 -10000 0 -0.27 5 5
MAP2K1 -0.071 0.11 0.17 2 -0.2 45 47
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.034 0.003 -10000 0 -10000 0 0
CYCS -0.019 0.07 0.16 1 -0.26 7 8
TNFRSF1A 0.033 0.007 -10000 0 -10000 0 0
NFKB1 0.034 0.003 -10000 0 -10000 0 0
TNFR1A/BAG4 0.048 0.013 -10000 0 -10000 0 0
EIF2AK2 -0.071 0.11 -10000 0 -0.2 50 50
TNF-alpha/TNFR1A/FAN 0.032 0.078 -10000 0 -0.23 9 9
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.018 0.073 -10000 0 -0.44 2 2
MAP2K2 -0.067 0.1 0.17 2 -0.2 44 46
SMPD3 -0.027 0.1 -10000 0 -0.29 16 16
TNF -0.003 0.1 -10000 0 -0.38 9 9
PKC zeta/PAR4 0.005 0.1 -10000 0 -0.29 14 14
mol:PHOSPHOCHOLINE -0.034 0.092 0.21 6 -0.15 43 49
NF kappa B1/RelA/I kappa B alpha 0.052 0.097 -10000 0 -0.22 14 14
AIFM1 -0.043 0.085 -10000 0 -0.3 7 7
BCL2 0.033 0.007 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.073 0.26 -10000 0 -0.95 10 10
MKNK1 0.033 0.006 -10000 0 -10000 0 0
MAPK14 -0.025 0.12 -10000 0 -0.32 18 18
ATF2/c-Jun -0.03 0.089 -10000 0 -0.28 6 6
MAPK11 -0.025 0.12 -10000 0 -0.32 17 17
MITF -0.034 0.13 -10000 0 -0.37 18 18
MAPKAPK5 -0.031 0.12 -10000 0 -0.36 18 18
KRT8 -0.042 0.14 -10000 0 -0.35 21 21
MAPKAPK3 0.034 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.033 0.007 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.039 0.17 -10000 0 -0.46 18 18
CEBPB -0.03 0.12 -10000 0 -0.36 17 17
SLC9A1 -0.034 0.13 -10000 0 -0.35 19 19
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.029 0.12 -10000 0 -0.35 18 18
p38alpha-beta/MNK1 -0.019 0.14 -10000 0 -0.37 18 18
JUN -0.032 0.087 -10000 0 -0.27 6 6
PPARGC1A -0.039 0.14 -10000 0 -0.36 21 21
USF1 -0.031 0.13 -10000 0 -0.36 18 18
RAB5/GDP/GDI1 -0.021 0.1 -10000 0 -0.27 18 18
NOS2 -0.086 0.28 -10000 0 -0.88 14 14
DDIT3 -0.027 0.12 -10000 0 -0.36 15 15
RAB5A 0.034 0.004 -10000 0 -10000 0 0
HSPB1 0.036 0.15 0.27 32 -0.3 12 44
p38alpha-beta/HBP1 -0.016 0.12 -10000 0 -0.37 12 12
CREB1 -0.049 0.15 -10000 0 -0.4 18 18
RAB5/GDP 0.025 0.003 -10000 0 -10000 0 0
EIF4E -0.037 0.12 0.22 2 -0.34 17 19
RPS6KA4 -0.032 0.13 -10000 0 -0.36 18 18
PLA2G4A -0.038 0.12 0.22 2 -0.34 17 19
GDI1 -0.032 0.13 -10000 0 -0.36 18 18
TP53 -0.058 0.16 -10000 0 -0.46 18 18
RPS6KA5 -0.036 0.14 -10000 0 -0.39 18 18
ESR1 -0.042 0.15 -10000 0 -0.39 20 20
HBP1 0.024 0.016 -10000 0 -10000 0 0
MEF2C -0.032 0.13 -10000 0 -0.37 18 18
MEF2A -0.032 0.13 -10000 0 -0.36 18 18
EIF4EBP1 -0.049 0.15 -10000 0 -0.4 18 18
KRT19 -0.052 0.14 -10000 0 -0.35 26 26
ELK4 -0.033 0.13 -10000 0 -0.38 18 18
ATF6 -0.031 0.13 -10000 0 -0.36 18 18
ATF1 -0.048 0.15 -10000 0 -0.4 18 18
p38alpha-beta/MAPKAPK2 -0.018 0.15 -10000 0 -0.39 17 17
p38alpha-beta/MAPKAPK3 -0.019 0.15 -10000 0 -0.38 18 18
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.14 0.32 -10000 0 -0.8 26 26
NCK1/PAK1/Dok-R -0.081 0.14 -10000 0 -0.39 24 24
NCK1/Dok-R -0.13 0.36 -10000 0 -0.96 22 22
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
mol:beta2-estradiol 0.029 0.08 0.23 20 -10000 0 20
RELA 0.034 0.003 -10000 0 -10000 0 0
SHC1 0.03 0.015 -10000 0 -10000 0 0
Rac/GDP 0.017 0.012 -10000 0 -10000 0 0
F2 0.029 0.081 0.23 20 -10000 0 20
TNIP2 0.034 0.003 -10000 0 -10000 0 0
NF kappa B/RelA -0.11 0.35 -10000 0 -0.92 22 22
FN1 0.033 0.011 -10000 0 -10000 0 0
PLD2 -0.14 0.36 -10000 0 -0.99 22 22
PTPN11 0.034 0.003 -10000 0 -10000 0 0
GRB14 -0.026 0.14 -10000 0 -0.38 20 20
ELK1 -0.14 0.33 -10000 0 -0.91 22 22
GRB7 0.021 0.029 -10000 0 -10000 0 0
PAK1 0.034 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.12 0.35 -10000 0 -0.95 22 22
CDKN1A -0.12 0.28 -10000 0 -0.63 32 32
ITGA5 0.029 0.036 -10000 0 -0.38 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.13 0.36 -10000 0 -0.96 22 22
CRK 0.033 0.006 -10000 0 -10000 0 0
mol:NO -0.065 0.26 0.36 1 -0.59 24 25
PLG -0.14 0.36 -10000 0 -0.99 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.12 0.29 -10000 0 -0.78 22 22
GRB2 0.034 0.005 -10000 0 -10000 0 0
PIK3R1 0.029 0.036 -10000 0 -0.39 1 1
ANGPT2 -0.13 0.32 -10000 0 -0.98 15 15
BMX -0.15 0.36 -10000 0 -0.99 22 22
ANGPT1 -0.16 0.41 -10000 0 -1.2 20 20
tube development -0.13 0.28 -10000 0 -0.67 30 30
ANGPT4 0.021 0.025 -10000 0 -10000 0 0
response to hypoxia -0.011 0.023 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.17 0.38 -10000 0 -1 22 22
alpha5/beta1 Integrin 0.031 0.035 -10000 0 -0.25 1 1
FGF2 0.032 0.035 -10000 0 -0.38 1 1
STAT5A (dimer) -0.15 0.35 -10000 0 -0.78 32 32
mol:L-citrulline -0.065 0.26 0.36 1 -0.59 24 25
AGTR1 -0.026 0.13 -10000 0 -0.37 18 18
MAPK14 -0.15 0.37 -10000 0 -0.98 24 24
Tie2/SHP2 -0.084 0.25 -10000 0 -0.96 8 8
TEK -0.1 0.26 -10000 0 -1.1 8 8
RPS6KB1 -0.13 0.3 -10000 0 -0.79 23 23
Angiotensin II/AT1 -0.017 0.094 -10000 0 -0.26 18 18
Tie2/Ang1/GRB2 -0.14 0.37 -10000 0 -1 22 22
MAPK3 -0.14 0.33 -10000 0 -0.93 22 22
MAPK1 -0.14 0.33 -10000 0 -0.93 22 22
Tie2/Ang1/GRB7 -0.15 0.37 -10000 0 -1 22 22
NFKB1 0.034 0.003 -10000 0 -10000 0 0
MAPK8 -0.14 0.36 -10000 0 -0.99 22 22
PI3K -0.15 0.36 -10000 0 -0.93 23 23
FES -0.14 0.36 -10000 0 -0.97 22 22
Crk/Dok-R -0.13 0.36 -10000 0 -0.97 22 22
Tie2/Ang1/ABIN2 -0.14 0.37 -10000 0 -1 22 22
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.13 0.29 -10000 0 -0.72 26 26
STAT5A 0.034 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.13 0.3 -10000 0 -0.8 22 22
Tie2/Ang2 -0.18 0.4 -10000 0 -0.92 30 30
Tie2/Ang1 -0.15 0.38 -10000 0 -1 22 22
FOXO1 -0.14 0.31 -10000 0 -0.73 30 30
ELF1 0.026 0.035 -10000 0 -10000 0 0
ELF2 -0.14 0.35 -10000 0 -0.97 22 22
mol:Choline -0.14 0.34 -10000 0 -0.96 22 22
cell migration -0.04 0.086 -10000 0 -0.22 23 23
FYN -0.15 0.33 -10000 0 -0.77 30 30
DOK2 0.012 0.084 -10000 0 -0.38 6 6
negative regulation of cell cycle -0.11 0.25 -10000 0 -0.57 32 32
ETS1 -0.001 0.095 -10000 0 -0.24 19 19
PXN -0.11 0.26 0.35 1 -0.66 22 23
ITGB1 0.024 0.016 -10000 0 -10000 0 0
NOS3 -0.088 0.29 0.37 1 -0.67 24 25
RAC1 0.023 0.016 -10000 0 -10000 0 0
TNF -0.039 0.14 -10000 0 -0.32 27 27
MAPKKK cascade -0.14 0.34 -10000 0 -0.96 22 22
RASA1 0.033 0.006 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.14 0.37 -10000 0 -1 22 22
NCK1 0.034 0.005 -10000 0 -10000 0 0
vasculogenesis -0.055 0.24 0.35 1 -0.53 24 25
mol:Phosphatidic acid -0.14 0.34 -10000 0 -0.96 22 22
mol:Angiotensin II -0.001 0.007 -10000 0 -10000 0 0
mol:NADP -0.065 0.26 0.36 1 -0.59 24 25
Rac1/GTP -0.11 0.28 -10000 0 -0.71 23 23
MMP2 -0.15 0.36 -10000 0 -0.99 22 22
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.055 0.2 0.36 1 -0.47 22 23
FYN -0.097 0.24 -10000 0 -0.58 22 22
LAT/GRAP2/SLP76 -0.076 0.2 -10000 0 -0.48 23 23
IKBKB 0.034 0.005 -10000 0 -10000 0 0
AKT1 -0.073 0.16 -10000 0 -0.39 23 23
B2M 0.031 0.013 -10000 0 -10000 0 0
IKBKG -0.004 0.058 0.092 10 -0.12 11 21
MAP3K8 0.018 0.04 -10000 0 -0.38 1 1
mol:Ca2+ -0.01 0.03 0.086 10 -0.067 1 11
integrin-mediated signaling pathway 0.043 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.1 0.23 -10000 0 -0.54 25 25
TRPV6 0.34 0.58 1.2 45 -10000 0 45
CD28 0.021 0.062 -10000 0 -0.39 3 3
SHC1 -0.097 0.23 0.19 1 -0.52 27 28
receptor internalization -0.091 0.22 -10000 0 -0.52 26 26
PRF1 -0.28 0.41 -10000 0 -0.78 54 54
KRAS 0.032 0.008 -10000 0 -10000 0 0
GRB2 0.034 0.005 -10000 0 -10000 0 0
COT/AKT1 -0.056 0.13 -10000 0 -0.32 21 21
LAT -0.098 0.24 0.22 1 -0.56 25 26
EntrezGene:6955 -0.001 0.004 -10000 0 -10000 0 0
CD3D -0.025 0.13 -10000 0 -0.39 17 17
CD3E -0.018 0.13 -10000 0 -0.39 16 16
CD3G -0.03 0.14 -10000 0 -0.39 18 18
RASGRP2 0 0.014 -10000 0 -10000 0 0
RASGRP1 -0.08 0.17 0.22 3 -0.39 25 28
HLA-A 0.026 0.039 -10000 0 -0.4 1 1
RASSF5 0.033 0.007 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.044 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.003 0.059 0.16 5 -0.13 9 14
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.032 0.068 -10000 0 -0.2 15 15
PRKCA -0.045 0.1 0.18 4 -0.26 19 23
GRAP2 0.005 0.095 -10000 0 -0.38 8 8
mol:IP3 -0.066 0.16 0.2 2 -0.38 23 25
EntrezGene:6957 -0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.078 0.2 -10000 0 -0.47 24 24
ORAI1 -0.3 0.48 -10000 0 -1 45 45
CSK -0.096 0.24 0.22 1 -0.57 23 24
B7 family/CD28 -0.066 0.24 -10000 0 -0.5 26 26
CHUK 0.023 0.016 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.11 0.27 -10000 0 -0.6 27 27
PTPN6 -0.097 0.24 0.24 2 -0.53 27 29
VAV1 -0.099 0.24 0.2 2 -0.54 27 29
Monovalent TCR/CD3 -0.065 0.16 -10000 0 -0.32 35 35
CBL 0.034 0.003 -10000 0 -10000 0 0
LCK -0.1 0.26 0.22 2 -0.62 23 25
PAG1 -0.096 0.24 0.22 1 -0.56 24 25
RAP1A 0.034 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.11 0.27 -10000 0 -0.58 28 28
CD80 0.021 0.062 -10000 0 -0.39 3 3
CD86 0.025 0.059 -10000 0 -0.38 3 3
PDK1/CARD11/BCL10/MALT1 -0.031 0.082 -10000 0 -0.23 15 15
HRAS 0.033 0.008 -10000 0 -10000 0 0
GO:0035030 -0.083 0.18 -10000 0 -0.42 27 27
CD8A 0.008 0.092 -10000 0 -0.39 7 7
CD8B -0.013 0.12 -10000 0 -0.39 13 13
PTPRC 0.012 0.089 -10000 0 -0.39 7 7
PDK1/PKC theta -0.086 0.2 0.22 3 -0.46 24 27
CSK/PAG1 -0.093 0.23 -10000 0 -0.59 20 20
SOS1 0.034 0 -10000 0 -10000 0 0
peptide-MHC class I 0.041 0.035 -10000 0 -0.3 1 1
GRAP2/SLP76 -0.084 0.24 -10000 0 -0.54 24 24
STIM1 -0.051 0.15 1 1 -0.99 1 2
RAS family/GTP -0.011 0.076 0.13 4 -0.18 12 16
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.096 0.24 -10000 0 -0.55 26 26
mol:DAG -0.07 0.13 -10000 0 -0.33 24 24
RAP1A/GDP 0.002 0.029 0.071 4 -0.065 2 6
PLCG1 0.028 0.035 -10000 0 -0.38 1 1
CD247 0.022 0.061 -10000 0 -0.39 3 3
cytotoxic T cell degranulation -0.27 0.39 -10000 0 -0.74 54 54
RAP1A/GTP 0.001 0.007 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.084 0.19 -10000 0 -0.46 23 23
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.079 0.2 0.22 2 -0.48 23 25
NRAS 0.034 0.005 -10000 0 -10000 0 0
ZAP70 0.022 0.068 -10000 0 -0.38 4 4
GRB2/SOS1 0.05 0.007 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.08 0.2 -10000 0 -0.46 24 24
MALT1 0.033 0.007 -10000 0 -10000 0 0
TRAF6 0.028 0.048 -10000 0 -0.38 2 2
CD8 heterodimer -0.003 0.13 -10000 0 -0.36 15 15
CARD11 0.017 0.05 -10000 0 -0.38 2 2
PRKCB -0.048 0.1 0.18 3 -0.25 20 23
PRKCE -0.045 0.1 0.18 4 -0.25 19 23
PRKCQ -0.1 0.22 -10000 0 -0.52 25 25
LCP2 0.031 0.034 -10000 0 -0.38 1 1
BCL10 0.033 0.007 -10000 0 -10000 0 0
regulation of survival gene product expression -0.061 0.14 -10000 0 -0.33 23 23
IKK complex -0.014 0.048 0.11 5 -0.11 10 15
RAS family/GDP -0.004 0.013 -10000 0 -10000 0 0
MAP3K14 -0.047 0.098 -10000 0 -0.25 21 21
PDPK1 -0.068 0.15 0.18 3 -0.38 22 25
TCR/CD3/MHC I/CD8/Fyn -0.12 0.3 -10000 0 -0.68 26 26
Ephrin A reverse signaling

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
MAPKKK cascade 0.004 0.091 -10000 0 -0.23 19 19
EFNA5 -0.002 0.11 -10000 0 -0.38 11 11
FYN -0.039 0.067 0.18 1 -0.21 19 20
neuron projection morphogenesis 0.004 0.091 -10000 0 -0.23 19 19
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.004 0.092 -10000 0 -0.23 19 19
EPHA5 0.007 0.1 -10000 0 -0.38 9 9
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.28 0.43 -10000 0 -1.2 18 18
STAT6 (cleaved dimer) -0.3 0.45 -10000 0 -1.2 21 21
IGHG1 -0.1 0.17 -10000 0 -0.44 8 8
IGHG3 -0.28 0.42 -10000 0 -1.1 23 23
AKT1 -0.16 0.28 -10000 0 -0.76 18 18
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.13 0.28 -10000 0 -0.9 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.15 0.26 -10000 0 -0.73 15 15
THY1 -0.3 0.44 -10000 0 -1.2 18 18
MYB -0.008 0.1 -10000 0 -0.38 10 10
HMGA1 0.03 0.036 -10000 0 -0.38 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.2 0.33 -10000 0 -0.87 20 20
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.15 0.28 -10000 0 -0.71 18 18
SP1 0.025 0.033 -10000 0 -10000 0 0
INPP5D 0.022 0.068 -10000 0 -0.38 4 4
SOCS5 0.041 0.022 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.29 0.46 -10000 0 -1.2 20 20
SOCS1 -0.2 0.3 -10000 0 -0.79 19 19
SOCS3 -0.24 0.4 -10000 0 -1.1 21 21
FCER2 -0.26 0.39 -10000 0 -1 21 21
PARP14 0.029 0.036 -10000 0 -0.38 1 1
CCL17 -0.3 0.43 -10000 0 -1.2 19 19
GRB2 0.034 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.12 0.21 -10000 0 -0.55 18 18
T cell proliferation -0.29 0.45 -10000 0 -1.2 20 20
IL4R/JAK1 -0.29 0.44 -10000 0 -1.2 18 18
EGR2 -0.32 0.47 -10000 0 -1.3 20 20
JAK2 -0.008 0.047 -10000 0 -10000 0 0
JAK3 0.013 0.077 -10000 0 -0.38 5 5
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
JAK1 0.009 0.031 -10000 0 -10000 0 0
COL1A2 -0.14 0.31 -10000 0 -1.4 6 6
CCL26 -0.28 0.48 -10000 0 -1.3 22 22
IL4R -0.31 0.46 -10000 0 -1.3 19 19
PTPN6 0.039 0.014 -10000 0 -10000 0 0
IL13RA2 -0.46 0.6 -10000 0 -1.3 45 45
IL13RA1 -0.011 0.06 -10000 0 -0.41 1 1
IRF4 -0.099 0.28 -10000 0 -1.1 9 9
ARG1 -0.19 0.41 -10000 0 -1.3 15 15
CBL -0.2 0.3 -10000 0 -0.82 20 20
GTF3A 0.013 0.047 -10000 0 -0.16 3 3
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.007 0.068 -10000 0 -0.27 1 1
IRF4/BCL6 -0.083 0.27 -10000 0 -1 9 9
CD40LG 0.011 0.081 -10000 0 -0.34 6 6
MAPK14 -0.21 0.35 -10000 0 -0.9 22 22
mitosis -0.15 0.26 -10000 0 -0.71 18 18
STAT6 -0.34 0.5 -10000 0 -1.3 23 23
SPI1 0.016 0.057 -10000 0 -0.18 8 8
RPS6KB1 -0.14 0.26 -10000 0 -0.69 18 18
STAT6 (dimer) -0.34 0.49 -10000 0 -1.3 23 23
STAT6 (dimer)/PARP14 -0.31 0.47 -10000 0 -1.2 22 22
mast cell activation 0.008 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.31 -10000 0 -0.82 18 18
FRAP1 -0.15 0.28 -10000 0 -0.76 18 18
LTA -0.31 0.45 -10000 0 -1.2 21 21
FES 0.033 0.009 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.33 0.48 1.2 23 -10000 0 23
CCL11 -0.28 0.42 -10000 0 -1.1 23 23
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.16 0.3 -10000 0 -0.82 17 17
IL2RG 0.02 0.062 -10000 0 -0.38 3 3
IL10 -0.33 0.48 -10000 0 -1.3 21 21
IRS1 0.02 0.076 -10000 0 -0.38 5 5
IRS2 0.03 0.035 -10000 0 -0.38 1 1
IL4 -0.073 0.1 -10000 0 -0.24 17 17
IL5 -0.3 0.43 -10000 0 -1.2 19 19
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.27 0.4 -10000 0 -0.98 26 26
COL1A1 -0.25 0.48 -10000 0 -1.4 19 19
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.3 0.44 -10000 0 -1.2 18 18
IL2R gamma/JAK3 0.023 0.078 -10000 0 -0.27 8 8
TFF3 -0.37 0.53 -10000 0 -1.3 29 29
ALOX15 -0.3 0.43 -10000 0 -1.2 19 19
MYBL1 0.028 0.048 -10000 0 -0.38 2 2
T-helper 2 cell differentiation -0.25 0.38 -10000 0 -0.98 21 21
SHC1 0.031 0.015 -10000 0 -10000 0 0
CEBPB 0.018 0.044 -10000 0 -0.15 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.14 0.26 -10000 0 -0.72 15 15
mol:PI-3-4-5-P3 -0.15 0.28 -10000 0 -0.76 18 18
PI3K -0.16 0.3 -10000 0 -0.82 18 18
DOK2 0.012 0.084 -10000 0 -0.38 6 6
ETS1 0.04 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.11 0.2 -10000 0 -0.53 15 15
ITGB3 -0.32 0.47 -10000 0 -1.3 20 20
PIGR -0.34 0.49 -10000 0 -1.3 25 25
IGHE 0.018 0.052 0.17 6 -10000 0 6
MAPKKK cascade -0.11 0.2 -10000 0 -0.52 15 15
BCL6 0.034 0.008 -10000 0 -10000 0 0
OPRM1 -0.3 0.43 -10000 0 -1.1 23 23
RETNLB -0.3 0.43 -10000 0 -1.1 23 23
SELP -0.3 0.43 -10000 0 -1.2 18 18
AICDA -0.28 0.42 -10000 0 -1.1 23 23
Endothelins

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
AKT1 0.025 0.14 0.25 23 -0.29 14 37
PTK2B 0.032 0.015 -10000 0 -10000 0 0
mol:Ca2+ -0.14 0.31 -10000 0 -0.78 19 19
EDN1 0.042 0.11 0.22 23 -0.25 8 31
EDN3 -0.052 0.16 -10000 0 -0.38 26 26
EDN2 0.02 0.03 -10000 0 -10000 0 0
HRAS/GDP -0.014 0.18 0.35 3 -0.56 8 11
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.009 0.13 0.25 3 -0.35 10 13
ADCY4 0.005 0.12 0.27 2 -0.3 9 11
ADCY5 -0.012 0.14 0.27 2 -0.31 12 14
ADCY6 0.004 0.12 0.19 1 -0.29 9 10
ADCY7 0.004 0.12 0.27 2 -0.29 9 11
ADCY1 -0.007 0.096 -10000 0 -0.32 6 6
ADCY2 -0.01 0.13 0.27 2 -0.3 13 15
ADCY3 0.005 0.12 0.27 2 -0.29 9 11
ADCY8 -0.003 0.12 0.27 2 -0.3 10 12
ADCY9 0.004 0.12 0.27 2 -0.3 10 12
arachidonic acid secretion -0.047 0.19 0.34 3 -0.57 11 14
ETB receptor/Endothelin-1/Gq/GTP -0.002 0.11 -10000 0 -0.32 10 10
GNAO1 0.011 0.094 -10000 0 -0.38 8 8
HRAS 0.033 0.008 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.047 0.13 0.35 12 -0.26 10 22
ETA receptor/Endothelin-1/Gs/GTP 0.062 0.16 0.32 24 -0.25 17 41
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 0.012 0.18 0.25 25 -0.44 12 37
EDNRB 0.008 0.088 -10000 0 -0.33 8 8
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0.011 0.16 0.25 21 -0.44 11 32
CYSLTR1 0.019 0.17 0.26 24 -0.37 14 38
SLC9A1 0.025 0.095 0.18 24 -0.22 8 32
mol:GDP -0.028 0.18 0.35 3 -0.54 10 13
SLC9A3 -0.091 0.31 -10000 0 -0.76 20 20
RAF1 -0.032 0.18 0.31 3 -0.6 8 11
JUN -0.13 0.27 -10000 0 -0.69 15 15
JAK2 0.015 0.14 0.26 18 -0.29 14 32
mol:IP3 -0.007 0.14 0.2 1 -0.46 8 9
ETA receptor/Endothelin-1 0.073 0.2 0.4 25 -0.33 15 40
PLCB1 0.012 0.083 -10000 0 -0.38 6 6
PLCB2 0.027 0.049 -10000 0 -0.38 2 2
ETA receptor/Endothelin-3 -0.014 0.14 -10000 0 -0.26 30 30
FOS -0.037 0.21 0.41 3 -0.76 8 11
Gai/GDP -0.035 0.23 -10000 0 -0.75 12 12
CRK 0.034 0.006 -10000 0 -10000 0 0
mol:Ca ++ -0.012 0.18 0.23 13 -0.45 14 27
BCAR1 0.033 0.007 -10000 0 -10000 0 0
PRKCB1 -0.012 0.14 0.22 2 -0.45 9 11
GNAQ 0.031 0.016 -10000 0 -10000 0 0
GNAZ 0.027 0.049 -10000 0 -0.38 2 2
GNAL 0.005 0.08 -10000 0 -0.38 5 5
Gs family/GDP -0.028 0.17 0.33 3 -0.47 11 14
ETA receptor/Endothelin-1/Gq/GTP 0.017 0.13 0.21 16 -0.37 9 25
MAPK14 -0.012 0.11 0.2 1 -0.45 5 6
TRPC6 -0.15 0.33 -10000 0 -0.86 18 18
GNAI2 0.034 0.005 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GNAI1 0.014 0.06 -10000 0 -0.38 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.01 0.12 -10000 0 -0.46 6 6
ETB receptor/Endothelin-2 0.018 0.072 -10000 0 -0.28 6 6
ETB receptor/Endothelin-3 -0.034 0.13 -10000 0 -0.29 29 29
ETB receptor/Endothelin-1 0.032 0.12 -10000 0 -0.28 13 13
MAPK3 -0.033 0.2 0.42 3 -0.72 8 11
MAPK1 -0.039 0.21 0.42 3 -0.74 8 11
Rac1/GDP -0.021 0.15 0.31 1 -0.49 8 9
cAMP biosynthetic process -0.013 0.13 0.22 8 -0.34 9 17
MAPK8 -0.16 0.34 -10000 0 -0.67 32 32
SRC 0.029 0.035 -10000 0 -0.38 1 1
ETB receptor/Endothelin-1/Gi/GTP 0 0.1 0.16 8 -0.4 6 14
p130Cas/CRK/Src/PYK2 -0.046 0.2 0.37 4 -0.59 12 16
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.021 0.15 0.31 1 -0.54 7 8
COL1A2 -0.007 0.16 -10000 0 -0.59 7 7
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.042 0.084 -10000 0 -0.16 6 6
mol:DAG -0.007 0.14 0.2 1 -0.46 8 9
MAP2K2 -0.031 0.19 0.48 3 -0.69 7 10
MAP2K1 -0.037 0.18 0.3 3 -0.69 7 10
EDNRA 0.043 0.11 0.22 24 -0.22 8 32
positive regulation of muscle contraction 0.071 0.16 0.27 44 -0.27 7 51
Gq family/GDP -0.01 0.17 -10000 0 -0.52 9 9
HRAS/GTP -0.029 0.17 0.33 3 -0.54 9 12
PRKCH -0.015 0.14 0.22 2 -0.45 9 11
RAC1 0.023 0.016 -10000 0 -10000 0 0
PRKCA -0.016 0.15 0.25 1 -0.47 9 10
PRKCB -0.021 0.15 0.25 1 -0.49 9 10
PRKCE -0.015 0.14 0.25 1 -0.45 9 10
PRKCD -0.014 0.14 0.22 2 -0.45 9 11
PRKCG -0.041 0.16 -10000 0 -0.42 15 15
regulation of vascular smooth muscle contraction -0.045 0.24 0.45 3 -0.9 8 11
PRKCQ -0.025 0.13 -10000 0 -0.47 8 8
PLA2G4A -0.053 0.2 0.35 3 -0.64 11 14
GNA14 0.02 0.054 -10000 0 -0.38 2 2
GNA15 0.013 0.083 -10000 0 -0.38 6 6
GNA12 0.02 0.037 -10000 0 -0.38 1 1
GNA11 0.025 0.05 -10000 0 -0.38 2 2
Rac1/GTP 0.048 0.13 0.35 12 -0.26 9 21
MMP1 -0.16 0.3 0.22 1 -0.76 28 29
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.033 0.008 -9999 0 -10000 0 0
EGFR -0.066 0.15 -9999 0 -0.38 28 28
EGF/EGFR -0.034 0.092 -9999 0 -0.2 31 31
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.026 0.1 -9999 0 -0.21 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.032 0.013 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.006 0.1 -9999 0 -0.38 9 9
EGF/EGFR dimer/SHC -0.038 0.11 -9999 0 -0.24 30 30
mol:GDP -0.027 0.098 -9999 0 -0.21 29 29
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.025 0.051 -9999 0 -0.38 2 2
GRB2/SOS1 0.05 0.007 -9999 0 -10000 0 0
HRAS/GTP -0.03 0.088 -9999 0 -0.2 29 29
SHC1 0.031 0.015 -9999 0 -10000 0 0
HRAS/GDP -0.026 0.094 -9999 0 -0.2 29 29
FRAP1 -0.044 0.08 -9999 0 -0.2 29 29
EGF/EGFR dimer -0.051 0.12 -9999 0 -0.28 31 31
SOS1 0.034 0 -9999 0 -10000 0 0
GRB2 0.034 0.005 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.04 0.043 -9999 0 -0.27 2 2
Syndecan-4-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
PTK2 0.011 0.044 -10000 0 -0.33 1 1
Syndecan-4/Syndesmos -0.058 0.22 -10000 0 -0.45 30 30
positive regulation of JNK cascade -0.06 0.2 -10000 0 -0.43 30 30
Syndecan-4/ADAM12 -0.083 0.22 -10000 0 -0.48 30 30
CCL5 0.023 0.061 -10000 0 -0.38 3 3
Rac1/GDP 0.017 0.012 -10000 0 -10000 0 0
DNM2 0.033 0.007 -10000 0 -10000 0 0
ITGA5 0.029 0.036 -10000 0 -0.38 1 1
SDCBP 0.033 0.006 -10000 0 -10000 0 0
PLG 0 0.01 0.026 4 -0.073 1 5
ADAM12 0 0.088 -10000 0 -0.38 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.034 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.029 0.011 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.089 0.22 -10000 0 -0.48 30 30
Syndecan-4/CXCL12/CXCR4 -0.064 0.22 -10000 0 -0.46 30 30
Syndecan-4/Laminin alpha3 -0.066 0.22 -10000 0 -0.46 30 30
MDK 0.025 0.059 -10000 0 -0.38 3 3
Syndecan-4/FZD7 -0.065 0.23 -10000 0 -0.47 30 30
Syndecan-4/Midkine -0.059 0.23 -10000 0 -0.47 30 30
FZD7 0.012 0.094 -10000 0 -0.38 8 8
Syndecan-4/FGFR1/FGF -0.04 0.21 -10000 0 -0.43 29 29
THBS1 -0.015 0.12 -10000 0 -0.38 13 13
integrin-mediated signaling pathway -0.056 0.21 -10000 0 -0.44 28 28
positive regulation of MAPKKK cascade -0.06 0.2 -10000 0 -0.43 30 30
Syndecan-4/TACI -0.081 0.21 -10000 0 -0.45 30 30
CXCR4 0.029 0.048 -10000 0 -0.38 2 2
cell adhesion 0.005 0.023 -10000 0 -0.17 1 1
Syndecan-4/Dynamin -0.059 0.22 -10000 0 -0.46 29 29
Syndecan-4/TSP1 -0.078 0.24 -10000 0 -0.5 30 30
Syndecan-4/GIPC -0.059 0.22 -10000 0 -0.46 29 29
Syndecan-4/RANTES -0.061 0.22 -10000 0 -0.46 30 30
ITGB1 0.024 0.016 -10000 0 -10000 0 0
LAMA1 -0.036 0.15 -10000 0 -0.38 23 23
LAMA3 0.01 0.079 -10000 0 -0.38 5 5
RAC1 0.023 0.016 -10000 0 -10000 0 0
PRKCA 0.002 0.066 0.67 1 -0.31 1 2
Syndecan-4/alpha-Actinin -0.06 0.22 -10000 0 -0.46 29 29
TFPI 0.01 0.095 -10000 0 -0.38 8 8
F2 -0.001 0.014 0.034 12 -0.045 1 13
alpha5/beta1 Integrin 0.031 0.035 -10000 0 -0.25 1 1
positive regulation of cell adhesion -0.1 0.21 -10000 0 -0.47 30 30
ACTN1 0.031 0.01 -10000 0 -10000 0 0
TNC 0.025 0.059 -10000 0 -0.38 3 3
Syndecan-4/CXCL12 -0.077 0.21 -10000 0 -0.46 30 30
FGF6 0 0 -10000 0 -10000 0 0
RHOA 0.034 0.004 -10000 0 -10000 0 0
CXCL12 0.013 0.052 -10000 0 -0.38 2 2
TNFRSF13B 0 0 -10000 0 -10000 0 0
FGF2 0.031 0.034 -10000 0 -0.38 1 1
FGFR1 0.031 0.034 -10000 0 -0.38 1 1
Syndecan-4/PI-4-5-P2 -0.081 0.21 -10000 0 -0.45 30 30
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.028 0.025 -10000 0 -10000 0 0
cell migration -0.012 0.013 0.013 25 -10000 0 25
PRKCD 0.029 0.023 -10000 0 -10000 0 0
vasculogenesis -0.074 0.23 -10000 0 -0.48 30 30
SDC4 -0.084 0.22 -10000 0 -0.48 30 30
Syndecan-4/Tenascin C -0.059 0.22 -10000 0 -0.46 28 28
Syndecan-4/PI-4-5-P2/PKC alpha -0.023 0.009 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.056 0.22 -10000 0 -0.46 29 29
MMP9 -0.038 0.14 -10000 0 -0.38 20 20
Rac1/GTP 0.005 0.023 -10000 0 -0.18 1 1
cytoskeleton organization -0.055 0.21 -10000 0 -0.44 30 30
GIPC1 0.033 0.008 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.066 0.23 -10000 0 -0.47 30 30
E-cadherin signaling 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
E-cadherin/beta catenin-gamma catenin 0.014 0.11 -9999 0 -0.23 23 23
E-cadherin/beta catenin -0.007 0.12 -9999 0 -0.27 23 23
CTNNB1 0.034 0.004 -9999 0 -10000 0 0
JUP 0.033 0.011 -9999 0 -10000 0 0
CDH1 -0.037 0.15 -9999 0 -0.38 23 23
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.022 0.061 -10000 0 -0.27 5 5
VLDLR 0.023 0.05 -10000 0 -0.38 2 2
CRKL 0.032 0.009 -10000 0 -10000 0 0
LRPAP1 0.034 0.003 -10000 0 -10000 0 0
FYN 0.031 0.01 -10000 0 -10000 0 0
ITGA3 0.013 0.078 -10000 0 -0.38 5 5
RELN/VLDLR/Fyn -0.001 0.092 -10000 0 -0.24 15 15
MAPK8IP1/MKK7/MAP3K11/JNK1 0.062 0.057 -10000 0 -0.2 1 1
AKT1 -0.052 0.12 -10000 0 -0.28 25 25
MAP2K7 0.03 0.035 -10000 0 -0.38 1 1
RAPGEF1 0.03 0.035 -10000 0 -0.38 1 1
DAB1 -0.041 0.15 -10000 0 -0.38 23 23
RELN/LRP8/DAB1 -0.029 0.11 -10000 0 -0.24 26 26
LRPAP1/LRP8 0.049 0.01 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.022 0.11 -10000 0 -0.24 25 25
DAB1/alpha3/beta1 Integrin -0.021 0.12 -10000 0 -0.25 26 26
long-term memory -0.065 0.16 -10000 0 -0.3 37 37
DAB1/LIS1 -0.003 0.12 -10000 0 -0.24 26 26
DAB1/CRLK/C3G -0.014 0.12 -10000 0 -0.24 25 25
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
DAB1/NCK2 -0.002 0.12 -10000 0 -0.24 26 26
ARHGEF2 0.033 0.006 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.046 0.15 -10000 0 -0.38 24 24
CDK5R1 0.012 0.089 -10000 0 -0.38 7 7
RELN -0.033 0.12 -10000 0 -0.38 15 15
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
RELN/LRP8/Fyn 0.002 0.086 -10000 0 -0.23 14 14
GRIN2A/RELN/LRP8/DAB1/Fyn -0.039 0.15 -10000 0 -0.28 34 34
MAPK8 0.023 0.018 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.032 0.12 -10000 0 -0.26 26 26
ITGB1 0.024 0.016 -10000 0 -10000 0 0
MAP1B -0.038 0.12 0.15 19 -0.26 26 45
RELN/LRP8 0.001 0.089 -10000 0 -0.23 15 15
GRIN2B/RELN/LRP8/DAB1/Fyn -0.02 0.14 -10000 0 -0.28 29 29
PI3K 0.045 0.03 -10000 0 -0.27 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.019 0.061 -10000 0 -0.26 5 5
RAP1A -0.017 0.14 0.37 4 -0.34 7 11
PAFAH1B1 0.033 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.028 0.048 -10000 0 -0.38 2 2
CRLK/C3G 0.043 0.03 -10000 0 -0.27 1 1
GRIN2B -0.01 0.11 -10000 0 -0.38 12 12
NCK2 0.034 0.004 -10000 0 -10000 0 0
neuron differentiation -0.035 0.1 -10000 0 -0.29 13 13
neuron adhesion -0.024 0.14 0.36 4 -0.34 7 11
LRP8 0.033 0.006 -10000 0 -10000 0 0
GSK3B -0.045 0.12 -10000 0 -0.27 24 24
RELN/VLDLR/DAB1/Fyn -0.025 0.12 -10000 0 -0.25 25 25
MAP3K11 0.034 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.052 0.12 -10000 0 -0.29 26 26
CDK5 0.023 0.016 -10000 0 -10000 0 0
MAPT -0.014 0.069 -10000 0 -0.34 6 6
neuron migration -0.037 0.15 0.21 15 -0.33 25 40
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.035 0.1 -10000 0 -0.29 13 13
RELN/VLDLR 0.006 0.096 -10000 0 -0.22 16 16
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.015 0.085 -10000 0 -0.2 24 24
epithelial cell differentiation 0.022 0.099 -10000 0 -0.2 23 23
CYFIP2 0.034 0.004 -10000 0 -10000 0 0
ENAH -0.042 0.067 0.42 1 -10000 0 1
EGFR -0.066 0.15 -10000 0 -0.38 28 28
EPHA2 0.028 0.037 -10000 0 -0.38 1 1
MYO6 -0.045 0.067 0.18 2 -0.2 22 24
CTNNB1 0.034 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.047 0.033 -10000 0 -10000 0 0
AQP5 -0.096 0.19 -10000 0 -0.45 30 30
CTNND1 0.034 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.045 0.066 0.17 2 -0.19 20 22
regulation of calcium-dependent cell-cell adhesion -0.05 0.078 0.17 2 -0.2 26 28
EGF 0.006 0.1 -10000 0 -0.38 9 9
NCKAP1 0.034 0.003 -10000 0 -10000 0 0
AQP3 -0.026 0.097 -10000 0 -0.41 3 3
cortical microtubule organization 0.022 0.099 -10000 0 -0.2 23 23
GO:0000145 -0.043 0.062 0.16 2 -0.18 20 22
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.027 0.1 -10000 0 -0.2 23 23
MLLT4 0.031 0.01 -10000 0 -10000 0 0
ARF6/GDP -0.055 0.055 -10000 0 -0.19 20 20
ARF6 0.032 0.009 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.073 0.046 -10000 0 -0.21 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.028 0.061 0.17 1 -10000 0 1
PVRL2 0.033 0.007 -10000 0 -10000 0 0
ZYX -0.036 0.066 0.18 2 -0.19 19 21
ARF6/GTP 0.077 0.049 -10000 0 -0.2 2 2
CDH1 -0.037 0.15 -10000 0 -0.38 23 23
EGFR/EGFR/EGF/EGF -0.051 0.11 -10000 0 -0.23 36 36
RhoA/GDP 0.029 0.097 -10000 0 -0.19 23 23
actin cytoskeleton organization -0.04 0.068 0.16 1 -0.2 22 23
IGF-1R heterotetramer 0.033 0.012 -10000 0 -10000 0 0
GIT1 0.034 0.005 -10000 0 -10000 0 0
IGF1R 0.033 0.012 -10000 0 -10000 0 0
IGF1 0.013 0.084 -10000 0 -0.38 6 6
DIAPH1 -0.097 0.25 -10000 0 -0.58 1 1
Wnt receptor signaling pathway -0.022 0.099 0.2 23 -10000 0 23
RHOA 0.034 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.056 0.055 -10000 0 -0.19 21 21
CTNNA1 0.034 0.004 -10000 0 -10000 0 0
VCL -0.041 0.069 0.16 1 -0.2 22 23
EFNA1 0.03 0.035 -10000 0 -0.38 1 1
LPP -0.048 0.064 0.16 1 -0.19 22 23
Ephrin A1/EPHA2 0.015 0.092 -10000 0 -0.19 21 21
SEC6/SEC8 -0.042 0.058 -10000 0 -0.19 18 18
MGAT3 -0.051 0.079 0.18 2 -0.21 26 28
HGF/MET -0.037 0.12 -10000 0 -0.23 34 34
HGF -0.006 0.099 -10000 0 -0.38 9 9
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.015 0.086 -10000 0 -0.2 24 24
actin cable formation -0.026 0.075 0.33 2 -0.37 1 3
KIAA1543 -0.05 0.068 0.16 1 -0.19 25 26
KIFC3 -0.049 0.063 -10000 0 -0.19 23 23
NCK1 0.034 0.005 -10000 0 -10000 0 0
EXOC3 0.033 0.006 -10000 0 -10000 0 0
ACTN1 -0.047 0.066 0.18 1 -0.19 23 24
NCK1/GIT1 0.049 0.01 -10000 0 -10000 0 0
mol:GDP 0.022 0.099 -10000 0 -0.2 23 23
EXOC4 0.023 0.016 -10000 0 -10000 0 0
STX4 -0.048 0.065 0.18 1 -0.19 23 24
PIP5K1C -0.045 0.066 0.18 2 -0.2 20 22
LIMA1 0.03 0.035 -10000 0 -0.38 1 1
ABI1 0.024 0.016 -10000 0 -10000 0 0
ROCK1 -0.044 0.074 0.45 1 -10000 0 1
adherens junction assembly -0.041 0.081 0.24 1 -0.3 5 6
IGF-1R heterotetramer/IGF1 0.007 0.1 -10000 0 -0.2 27 27
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.044 0.018 -10000 0 -10000 0 0
MET -0.026 0.12 -10000 0 -0.38 14 14
PLEKHA7 -0.052 0.071 0.18 1 -0.2 25 26
mol:GTP 0.07 0.045 -10000 0 -0.21 2 2
establishment of epithelial cell apical/basal polarity 0.01 0.12 0.32 4 -10000 0 4
cortical actin cytoskeleton stabilization -0.015 0.085 -10000 0 -0.2 24 24
regulation of cell-cell adhesion -0.04 0.068 0.16 1 -0.2 22 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.015 0.086 -10000 0 -0.2 24 24
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.043 0.11 -10000 0 -0.32 9 9
TBX21 -0.23 0.41 -10000 0 -1 23 23
B2M 0.027 0.024 -10000 0 -10000 0 0
TYK2 0.004 0.042 -10000 0 -10000 0 0
IL12RB1 -0.013 0.09 -10000 0 -0.4 6 6
GADD45B -0.16 0.31 -10000 0 -0.81 20 20
IL12RB2 -0.004 0.062 -10000 0 -0.38 2 2
GADD45G -0.2 0.39 -10000 0 -0.96 23 23
natural killer cell activation -0.009 0.02 -10000 0 -10000 0 0
RELB 0.033 0.008 -10000 0 -10000 0 0
RELA 0.034 0.003 -10000 0 -10000 0 0
IL18 0.015 0.064 -10000 0 -0.39 3 3
IL2RA -0.027 0.11 -10000 0 -0.38 11 11
IFNG 0.025 0.012 -10000 0 -10000 0 0
STAT3 (dimer) -0.16 0.31 -10000 0 -0.74 24 24
HLA-DRB5 -0.012 0.12 -10000 0 -0.38 13 13
FASLG -0.2 0.37 -10000 0 -0.99 20 20
NF kappa B2 p52/RelB -0.2 0.37 -10000 0 -0.87 26 26
CD4 0.026 0.05 -10000 0 -0.39 2 2
SOCS1 0.021 0.062 -10000 0 -0.38 3 3
EntrezGene:6955 -0.002 0.011 -10000 0 -10000 0 0
CD3D -0.027 0.14 -10000 0 -0.39 17 17
CD3E -0.022 0.13 -10000 0 -0.39 16 16
CD3G -0.031 0.14 -10000 0 -0.39 18 18
IL12Rbeta2/JAK2 0.004 0.064 -10000 0 -0.27 2 2
CCL3 -0.25 0.45 -10000 0 -1.2 23 23
CCL4 -0.24 0.44 -10000 0 -1.1 24 24
HLA-A 0.023 0.042 -10000 0 -0.38 1 1
IL18/IL18R 0.004 0.11 -10000 0 -0.25 17 17
NOS2 -0.23 0.42 -10000 0 -0.99 29 29
IL12/IL12R/TYK2/JAK2/SPHK2 -0.037 0.096 -10000 0 -0.3 7 7
IL1R1 -0.21 0.37 -10000 0 -0.99 20 20
IL4 0.009 0.02 -10000 0 -10000 0 0
JAK2 0.006 0.039 -10000 0 -10000 0 0
EntrezGene:6957 -0.003 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.13 0.34 -10000 0 -0.71 28 28
RAB7A -0.14 0.28 -10000 0 -0.76 15 15
lysosomal transport -0.13 0.27 -10000 0 -0.7 16 16
FOS -0.18 0.38 -10000 0 -1 19 19
STAT4 (dimer) -0.18 0.34 -10000 0 -0.78 27 27
STAT5A (dimer) -0.19 0.37 -10000 0 -0.86 27 27
GZMA -0.28 0.48 -10000 0 -1.1 31 31
GZMB -0.25 0.45 -10000 0 -1.2 24 24
HLX 0.033 0.007 -10000 0 -10000 0 0
LCK -0.23 0.41 -10000 0 -0.94 29 29
TCR/CD3/MHC II/CD4 -0.085 0.19 -10000 0 -0.43 29 29
IL2/IL2R -0.009 0.087 -10000 0 -0.22 16 16
MAPK14 -0.17 0.34 -10000 0 -0.83 23 23
CCR5 -0.18 0.36 -10000 0 -0.99 17 17
IL1B -0.023 0.1 -10000 0 -0.41 8 8
STAT6 -0.058 0.15 -10000 0 -0.54 7 7
STAT4 -0.012 0.12 -10000 0 -0.38 14 14
STAT3 0.034 0 -10000 0 -10000 0 0
STAT1 0.033 0.012 -10000 0 -10000 0 0
NFKB1 0.034 0.003 -10000 0 -10000 0 0
NFKB2 0.023 0.016 -10000 0 -10000 0 0
IL12B -0.003 0.042 -10000 0 -10000 0 0
CD8A 0.004 0.093 -10000 0 -0.39 7 7
CD8B -0.016 0.12 -10000 0 -0.39 13 13
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.043 0.1 0.32 9 -10000 0 9
IL2RB 0.018 0.062 -10000 0 -0.38 3 3
proteasomal ubiquitin-dependent protein catabolic process -0.17 0.31 -10000 0 -0.71 27 27
IL2RG 0.025 0.06 -10000 0 -0.38 3 3
IL12 0.001 0.069 -10000 0 -0.3 2 2
STAT5A 0.034 0 -10000 0 -10000 0 0
CD247 0.018 0.063 -10000 0 -0.39 3 3
IL2 0 0 -10000 0 -10000 0 0
SPHK2 0.033 0.008 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.001 0.064 -10000 0 -0.4 2 2
IL12/IL12R/TYK2/JAK2 -0.23 0.43 -10000 0 -1 27 27
MAP2K3 -0.17 0.35 -10000 0 -0.85 22 22
RIPK2 0.033 0.006 -10000 0 -10000 0 0
MAP2K6 -0.17 0.34 -10000 0 -0.83 23 23
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.017 0.077 -10000 0 -0.38 5 5
IL18RAP -0.018 0.12 -10000 0 -0.39 13 13
IL12Rbeta1/TYK2 0 0.082 -10000 0 -0.29 6 6
EOMES -0.082 0.34 -10000 0 -1.2 12 12
STAT1 (dimer) -0.16 0.3 -10000 0 -0.72 24 24
T cell proliferation -0.14 0.25 -10000 0 -0.56 31 31
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.005 0.066 -10000 0 -0.38 3 3
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.15 0.29 -10000 0 -0.62 29 29
ATF2 -0.16 0.32 -10000 0 -0.76 23 23
HIF-1-alpha transcription factor network

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
PKM2 -0.1 0.32 -10000 0 -0.84 15 15
HDAC7 0.03 0.014 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.068 0.32 -10000 0 -0.66 22 22
SMAD4 0.033 0.008 -10000 0 -10000 0 0
ID2 -0.1 0.32 -10000 0 -0.84 15 15
AP1 0.036 0.045 -10000 0 -0.27 2 2
ABCG2 -0.1 0.32 -10000 0 -0.82 16 16
HIF1A -0.006 0.076 -10000 0 -0.22 2 2
TFF3 -0.12 0.32 -10000 0 -0.8 17 17
GATA2 0.03 0.021 -10000 0 -10000 0 0
AKT1 -0.007 0.085 -10000 0 -0.21 7 7
response to hypoxia -0.023 0.066 -10000 0 -0.18 9 9
MCL1 -0.096 0.31 -10000 0 -0.82 15 15
NDRG1 -0.11 0.33 -10000 0 -0.87 15 15
SERPINE1 -0.096 0.32 -10000 0 -0.84 16 16
FECH -0.1 0.31 -10000 0 -0.83 15 15
FURIN -0.1 0.32 -10000 0 -0.84 15 15
NCOA2 0.017 0.076 -10000 0 -0.38 5 5
EP300 -0.017 0.11 -10000 0 -0.3 12 12
HMOX1 -0.11 0.32 -10000 0 -0.84 15 15
BHLHE40 -0.1 0.32 -10000 0 -0.83 16 16
BHLHE41 -0.099 0.32 -10000 0 -0.85 15 15
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.049 0.12 -10000 0 -10000 0 0
ENG -0.004 0.086 0.28 2 -10000 0 2
JUN 0.033 0.011 -10000 0 -10000 0 0
RORA -0.1 0.32 -10000 0 -0.84 15 15
ABCB1 -0.02 0.17 -10000 0 -1.1 3 3
TFRC -0.099 0.32 -10000 0 -0.84 15 15
CXCR4 -0.1 0.32 -10000 0 -0.85 15 15
TF -0.12 0.34 -10000 0 -0.81 19 19
CITED2 -0.1 0.31 -10000 0 -0.83 15 15
HIF1A/ARNT -0.065 0.41 -10000 0 -1 13 13
LDHA -0.005 0.19 -10000 0 -0.92 5 5
ETS1 -0.099 0.32 -10000 0 -0.84 15 15
PGK1 -0.1 0.32 -10000 0 -0.84 15 15
NOS2 -0.12 0.33 -10000 0 -0.82 17 17
ITGB2 -0.1 0.33 -10000 0 -0.86 15 15
ALDOA -0.1 0.32 -10000 0 -0.83 15 15
Cbp/p300/CITED2 -0.12 0.35 -10000 0 -0.8 22 22
FOS 0.018 0.062 -10000 0 -0.38 3 3
HK2 -0.1 0.32 -10000 0 -0.82 16 16
SP1 0.035 0.021 -10000 0 -10000 0 0
GCK -0.064 0.3 -10000 0 -1.3 7 7
HK1 -0.11 0.31 -10000 0 -0.83 15 15
NPM1 -0.099 0.32 -10000 0 -0.83 15 15
EGLN1 -0.096 0.31 -10000 0 -0.82 15 15
CREB1 0.037 0.017 -10000 0 -10000 0 0
PGM1 -0.096 0.32 -10000 0 -0.83 15 15
SMAD3 0.034 0.005 -10000 0 -10000 0 0
EDN1 -0.045 0.2 -10000 0 -0.74 6 6
IGFBP1 -0.098 0.31 -10000 0 -0.79 16 16
VEGFA -0.11 0.3 -10000 0 -0.64 29 29
HIF1A/JAB1 0.016 0.065 -10000 0 -0.17 1 1
CP -0.11 0.33 -10000 0 -0.87 15 15
CXCL12 -0.12 0.31 -10000 0 -0.86 15 15
COPS5 0.031 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4 0.048 0.014 -10000 0 -10000 0 0
BNIP3 -0.12 0.31 -10000 0 -0.84 15 15
EGLN3 -0.11 0.32 -10000 0 -0.8 17 17
CA9 -0.13 0.35 -10000 0 -0.8 23 23
TERT -0.12 0.33 -10000 0 -0.84 16 16
ENO1 -0.1 0.32 -10000 0 -0.83 15 15
PFKL -0.097 0.32 -10000 0 -0.83 15 15
NCOA1 0.033 0.007 -10000 0 -10000 0 0
ADM -0.12 0.34 -10000 0 -0.88 17 17
ARNT 0.001 0.072 -10000 0 -10000 0 0
HNF4A -0.003 0.019 -10000 0 -10000 0 0
ADFP -0.11 0.31 -10000 0 -0.83 15 15
SLC2A1 -0.098 0.27 -10000 0 -0.6 24 24
LEP -0.09 0.3 -10000 0 -0.81 15 15
HIF1A/ARNT/Cbp/p300 -0.076 0.32 -10000 0 -0.66 24 24
EPO -0.091 0.27 -10000 0 -0.89 9 9
CREBBP -0.012 0.1 -10000 0 -0.28 11 11
HIF1A/ARNT/Cbp/p300/HDAC7 -0.075 0.34 -10000 0 -0.68 24 24
PFKFB3 -0.11 0.31 -10000 0 -0.84 15 15
NT5E -0.1 0.32 -10000 0 -0.81 16 16
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.018 0.057 -10000 0 -0.28 4 4
ARNO/beta Arrestin1-2 0.029 0.14 -10000 0 -0.75 4 4
EGFR -0.066 0.15 -10000 0 -0.38 28 28
EPHA2 0.028 0.037 -10000 0 -0.38 1 1
USP6 0.026 0.04 -10000 0 -0.38 1 1
IQSEC1 0.034 0.003 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.051 0.12 -10000 0 -0.28 31 31
ARRB2 0.012 0.007 -10000 0 -10000 0 0
mol:GTP 0.011 0.04 0.11 1 -0.14 4 5
ARRB1 0.034 0 -10000 0 -10000 0 0
FBXO8 0.033 0.007 -10000 0 -10000 0 0
TSHR -0.034 0.13 -10000 0 -0.38 16 16
EGF 0.006 0.1 -10000 0 -0.38 9 9
somatostatin receptor activity 0 0 0.001 33 -0.001 9 42
ARAP2 0.02 0.075 -10000 0 -0.38 5 5
mol:GDP 0.017 0.11 0.19 26 -0.23 7 33
mol:PI-3-4-5-P3 0 0 0.001 20 -0.001 3 23
ITGA2B 0.007 0.096 -10000 0 -0.38 8 8
ARF6 0.032 0.009 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.073 0.046 -10000 0 -0.21 2 2
ADAP1 0.013 0.052 -10000 0 -0.38 2 2
KIF13B 0.025 0.059 -10000 0 -0.38 3 3
HGF/MET -0.02 0.11 -10000 0 -0.31 17 17
PXN 0.034 0.003 -10000 0 -10000 0 0
ARF6/GTP 0.028 0.14 0.23 30 -0.25 9 39
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.04 0.11 -10000 0 -0.24 31 31
ADRB2 0.023 0.068 -10000 0 -0.38 4 4
receptor agonist activity 0 0 0 19 0 8 27
actin filament binding 0 0 0.001 32 0 9 41
SRC 0.029 0.035 -10000 0 -0.38 1 1
ITGB3 0.015 0.083 -10000 0 -0.38 6 6
GNAQ 0.033 0.007 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 37 -0.001 4 41
ARF6/GDP -0.003 0.14 0.23 1 -0.46 7 8
ARF6/GDP/GULP/ACAP1 0.006 0.14 0.22 14 -0.27 10 24
alphaIIb/beta3 Integrin/paxillin/GIT1 0.051 0.092 -10000 0 -0.23 12 12
ACAP1 0.017 0.077 -10000 0 -0.38 5 5
ACAP2 0.033 0.007 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.022 0.018 -10000 0 -10000 0 0
EFNA1 0.03 0.035 -10000 0 -0.38 1 1
HGF -0.006 0.099 -10000 0 -0.38 9 9
CYTH3 -0.002 0.006 -10000 0 -10000 0 0
CYTH2 -0.002 0.16 -10000 0 -0.95 4 4
NCK1 0.034 0.005 -10000 0 -10000 0 0
fibronectin binding 0 0 0 36 0 7 43
endosomal lumen acidification 0 0 0.001 38 0 9 47
microtubule-based process 0 0 -10000 0 0 2 2
GULP1 -0.032 0.14 -10000 0 -0.38 21 21
GNAQ/ARNO 0.017 0.15 -10000 0 -0.87 4 4
mol:Phosphatidic acid 0 0 0 5 -10000 0 5
PIP3-E 0 0 0 16 0 1 17
MET -0.026 0.12 -10000 0 -0.38 14 14
GNA14 0.022 0.053 -10000 0 -0.38 2 2
GNA15 0.015 0.083 -10000 0 -0.38 6 6
GIT1 0.034 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.001 34 -0.001 7 41
GNA11 0.027 0.048 -10000 0 -0.38 2 2
LHCGR 0.025 0.016 -10000 0 -10000 0 0
AGTR1 -0.023 0.13 -10000 0 -0.38 17 17
desensitization of G-protein coupled receptor protein signaling pathway 0.022 0.018 -10000 0 -10000 0 0
IPCEF1/ARNO -0.045 0.14 -10000 0 -0.8 4 4
alphaIIb/beta3 Integrin 0.014 0.1 -10000 0 -0.29 13 13
Caspase cascade in apoptosis

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
TOP1 -0.035 0.14 -10000 0 -0.39 13 13
ACTA1 -0.071 0.14 0.24 1 -0.35 22 23
NUMA1 -0.032 0.13 -10000 0 -0.38 12 12
SPTAN1 -0.068 0.14 0.33 1 -0.35 23 24
LIMK1 -0.018 0.15 0.2 19 -0.34 18 37
BIRC3 -0.016 0.12 -10000 0 -0.38 14 14
BIRC2 0.034 0.003 -10000 0 -10000 0 0
BAX 0.033 0.008 -10000 0 -10000 0 0
CASP10 -0.03 0.061 -10000 0 -0.25 9 9
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.034 0.003 -10000 0 -10000 0 0
PTK2 -0.034 0.14 -10000 0 -0.37 14 14
DIABLO 0.034 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.067 0.14 0.32 1 -0.34 23 24
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.034 0.005 -10000 0 -10000 0 0
GSN -0.068 0.14 0.33 1 -0.35 22 23
MADD 0.03 0.035 -10000 0 -0.38 1 1
TFAP2A -0.14 0.27 -10000 0 -0.55 37 37
BID -0.012 0.045 -10000 0 -0.17 10 10
MAP3K1 -0.016 0.085 -10000 0 -0.53 2 2
TRADD 0.031 0.034 -10000 0 -0.38 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.048 0.015 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.068 0.14 -10000 0 -0.36 23 23
CASP9 0.032 0.013 -10000 0 -10000 0 0
DNA repair 0.026 0.072 0.22 6 -0.15 2 8
neuron apoptosis 0.022 0.066 -10000 0 -0.71 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.049 0.14 -10000 0 -0.39 17 17
APAF1 0.034 0.004 -10000 0 -10000 0 0
CASP6 -0.003 0.15 -10000 0 -1.1 2 2
TRAF2 0.033 0.007 -10000 0 -10000 0 0
ICAD/CAD -0.066 0.14 0.32 2 -0.36 22 24
CASP7 -0.037 0.11 0.26 6 -0.25 2 8
KRT18 -0.013 0.16 -10000 0 -0.68 7 7
apoptosis -0.049 0.12 -10000 0 -0.44 8 8
DFFA -0.068 0.14 0.18 1 -0.36 23 24
DFFB -0.066 0.14 0.18 1 -0.36 23 24
PARP1 -0.026 0.072 0.15 2 -0.22 6 8
actin filament polymerization 0.014 0.14 0.32 18 -0.22 5 23
TNF -0.003 0.1 -10000 0 -0.38 9 9
CYCS -0.005 0.04 -10000 0 -0.18 1 1
SATB1 -0.008 0.14 -10000 0 -1 2 2
SLK -0.06 0.14 -10000 0 -0.36 22 22
p15 BID/BAX -0.03 0.081 -10000 0 -0.23 14 14
CASP2 0.029 0.097 0.21 24 -0.25 4 28
JNK cascade 0.016 0.084 0.52 2 -10000 0 2
CASP3 -0.071 0.14 0.18 1 -0.37 23 24
LMNB2 0.032 0.1 0.22 2 -0.52 1 3
RIPK1 0.033 0.006 -10000 0 -10000 0 0
CASP4 0.023 0.068 -10000 0 -0.38 4 4
Mammalian IAPs/DIABLO 0.044 0.093 -10000 0 -0.22 14 14
negative regulation of DNA binding -0.14 0.26 -10000 0 -0.54 37 37
stress fiber formation -0.065 0.13 0.18 1 -0.35 22 23
GZMB -0.032 0.072 -10000 0 -0.3 9 9
CASP1 -0.004 0.09 -10000 0 -0.35 8 8
LMNB1 0.03 0.14 0.24 3 -0.78 2 5
APP 0.022 0.067 -10000 0 -0.72 1 1
TNFRSF1A 0.033 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.006 0.005 -10000 0 -10000 0 0
VIM -0.049 0.13 -10000 0 -0.43 9 9
LMNA 0.038 0.099 0.24 3 -0.61 1 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.007 0.08 -10000 0 -0.26 8 8
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.072 0.14 0.18 1 -0.36 23 24
APAF-1/Caspase 9 0.025 0.086 -10000 0 -0.62 2 2
nuclear fragmentation during apoptosis -0.031 0.13 -10000 0 -0.37 12 12
CFL2 -0.016 0.14 0.22 5 -0.33 18 23
GAS2 -0.084 0.15 0.18 1 -0.36 26 27
positive regulation of apoptosis 0.039 0.11 0.23 3 -0.84 1 4
PRF1 0.002 0.077 -10000 0 -0.38 5 5
EPO signaling pathway

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
BCL2L1 0.048 0.078 0.32 1 -10000 0 1
CRKL 0.034 0.097 0.27 7 -10000 0 7
mol:DAG 0.01 0.061 -10000 0 -0.26 6 6
HRAS 0.031 0.1 0.27 9 -10000 0 9
MAPK8 0.005 0.075 0.16 21 -0.2 6 27
RAP1A 0.033 0.094 0.16 33 -10000 0 33
GAB1 0.035 0.099 0.17 32 -10000 0 32
MAPK14 0.027 0.094 0.16 45 -0.2 6 51
EPO 0.005 0.084 -10000 0 -0.39 6 6
PLCG1 0.01 0.062 -10000 0 -0.26 6 6
EPOR/TRPC2/IP3 Receptors 0.036 0.021 -10000 0 -10000 0 0
RAPGEF1 0.03 0.035 -10000 0 -0.38 1 1
EPO/EPOR (dimer)/SOCS3 0.013 0.085 -10000 0 -0.25 10 10
GAB1/SHC/GRB2/SOS1 0.08 0.085 0.3 5 -10000 0 5
EPO/EPOR (dimer) 0.019 0.068 -10000 0 -0.28 6 6
IRS2 0.03 0.095 0.16 31 -10000 0 31
STAT1 0.015 0.063 -10000 0 -0.26 6 6
STAT5B 0.013 0.064 -10000 0 -0.26 6 6
cell proliferation 0.005 0.078 0.17 21 -0.19 6 27
GAB1/SHIP/PIK3R1/SHP2/SHC 0.05 0.075 -10000 0 -10000 0 0
TEC 0.026 0.099 0.17 29 -0.19 1 30
SOCS3 -0.006 0.11 -10000 0 -0.38 12 12
STAT1 (dimer) 0.015 0.062 -10000 0 -0.26 6 6
JAK2 0.032 0.022 -10000 0 -10000 0 0
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
EPO/EPOR (dimer)/JAK2 0.047 0.07 0.24 1 -0.19 6 7
EPO/EPOR 0.019 0.068 -10000 0 -0.28 6 6
LYN 0.029 0.048 -10000 0 -0.38 2 2
TEC/VAV2 0.028 0.079 0.23 2 -0.19 3 5
elevation of cytosolic calcium ion concentration 0.036 0.021 -10000 0 -10000 0 0
SHC1 0.031 0.015 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.033 0.067 -10000 0 -0.22 6 6
mol:IP3 0.01 0.061 -10000 0 -0.26 6 6
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.067 0.099 0.29 4 -0.27 2 6
SH2B3 0.037 0.018 -10000 0 -10000 0 0
NFKB1 0.028 0.095 0.16 46 -0.2 6 52
EPO/EPOR (dimer)/JAK2/SOCS3 -0.009 0.067 -10000 0 -0.24 10 10
PTPN6 0.049 0.088 0.16 45 -0.19 6 51
TEC/VAV2/GRB2 0.049 0.086 0.34 2 -10000 0 2
EPOR 0.036 0.021 -10000 0 -10000 0 0
INPP5D 0.022 0.068 -10000 0 -0.38 4 4
mol:GDP 0.079 0.086 0.3 5 -10000 0 5
SOS1 0.034 0 -10000 0 -10000 0 0
PLCG2 0.03 0.035 -10000 0 -0.38 1 1
CRKL/CBL/C3G 0.063 0.084 0.28 4 -10000 0 4
VAV2 0.029 0.098 0.25 8 -10000 0 8
CBL 0.037 0.099 0.17 34 -10000 0 34
SHC/Grb2/SOS1 0.027 0.056 -10000 0 -10000 0 0
STAT5A 0.013 0.064 -10000 0 -0.26 6 6
GRB2 0.034 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.028 0.067 -10000 0 -10000 0 0
LYN/PLCgamma2 0.042 0.047 -10000 0 -0.27 3 3
PTPN11 0.034 0.003 -10000 0 -10000 0 0
BTK 0.034 0.1 0.17 39 -0.19 2 41
BCL2 0.048 0.077 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.053 0.083 -10000 0 -0.64 1 1
SMARCC2 0.033 0.008 -10000 0 -10000 0 0
SMARCC1 0.035 0.004 -10000 0 -10000 0 0
TBX21 -0.097 0.16 -10000 0 -0.55 11 11
SUMO2 0.029 0.018 -10000 0 -10000 0 0
STAT1 (dimer) 0.037 0.016 -10000 0 -10000 0 0
FKBP4 0.033 0.008 -10000 0 -10000 0 0
FKBP5 0.01 0.094 -10000 0 -0.38 8 8
GR alpha/HSP90/FKBP51/HSP90 0.091 0.094 0.26 8 -0.22 6 14
PRL -0.05 0.074 -10000 0 -0.2 20 20
cortisol/GR alpha (dimer)/TIF2 0.16 0.17 0.42 32 -10000 0 32
RELA -0.03 0.1 -10000 0 -0.22 27 27
FGG 0.12 0.14 0.36 24 -10000 0 24
GR beta/TIF2 0.094 0.094 0.25 17 -0.25 4 21
IFNG -0.14 0.2 -10000 0 -0.59 14 14
apoptosis -0.022 0.17 0.75 1 -0.49 13 14
CREB1 0.03 0.021 -10000 0 -10000 0 0
histone acetylation -0.05 0.084 -10000 0 -0.26 9 9
BGLAP -0.044 0.083 -10000 0 -10000 0 0
GR/PKAc 0.11 0.067 0.24 15 -10000 0 15
NF kappa B1 p50/RelA -0.057 0.18 -10000 0 -0.35 35 35
SMARCD1 0.034 0.007 -10000 0 -10000 0 0
MDM2 0.051 0.06 0.18 17 -10000 0 17
GATA3 0.001 0.072 -10000 0 -0.38 4 4
AKT1 0.03 0.017 0.2 1 -10000 0 1
CSF2 -0.053 0.075 -10000 0 -0.21 18 18
GSK3B 0.028 0.019 -10000 0 -10000 0 0
NR1I3 -0.015 0.16 0.7 1 -0.5 3 4
CSN2 0.1 0.12 0.29 31 -10000 0 31
BRG1/BAF155/BAF170/BAF60A 0.079 0.045 -10000 0 -0.21 2 2
NFATC1 0.032 0.008 -10000 0 -10000 0 0
POU2F1 0.028 0.048 -10000 0 -0.38 2 2
CDKN1A -0.049 0.3 -10000 0 -1.4 7 7
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.006 -10000 0 -10000 0 0
SFN 0.001 0.096 -10000 0 -0.38 8 8
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.082 0.11 0.28 5 -0.21 9 14
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.036 0.19 0.67 1 -0.6 8 9
JUN -0.12 0.16 -10000 0 -0.37 34 34
IL4 -0.062 0.083 -10000 0 -0.22 23 23
CDK5R1 0.011 0.089 -10000 0 -0.38 7 7
PRKACA 0.033 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.015 0.12 0.17 24 -0.26 12 36
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.1 0.095 0.28 6 -0.22 5 11
cortisol/GR alpha (monomer) 0.17 0.19 0.46 33 -10000 0 33
NCOA2 0.019 0.075 -10000 0 -0.38 5 5
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.036 0.09 -10000 0 -0.26 9 9
AP-1/NFAT1-c-4 -0.2 0.22 -10000 0 -0.51 40 40
AFP -0.23 0.38 -10000 0 -1.3 14 14
SUV420H1 0.034 0.004 -10000 0 -10000 0 0
IRF1 0.1 0.096 0.37 5 -10000 0 5
TP53 0.015 0.14 -10000 0 -0.58 7 7
PPP5C 0.033 0.008 -10000 0 -10000 0 0
KRT17 -0.22 0.35 -10000 0 -1 19 19
KRT14 -0.071 0.074 -10000 0 -0.23 16 16
TBP 0.036 0.012 -10000 0 -10000 0 0
CREBBP 0.038 0.006 -10000 0 -10000 0 0
HDAC1 0.032 0.006 -10000 0 -10000 0 0
HDAC2 0.031 0.01 -10000 0 -10000 0 0
AP-1 -0.2 0.23 -10000 0 -0.51 40 40
MAPK14 0.029 0.017 -10000 0 -10000 0 0
MAPK10 0.024 0.05 -10000 0 -0.38 2 2
MAPK11 0.026 0.02 -10000 0 -10000 0 0
KRT5 -0.27 0.4 -10000 0 -0.94 34 34
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.035 0.011 -10000 0 -10000 0 0
STAT1 0.037 0.016 -10000 0 -10000 0 0
CGA -0.06 0.087 -10000 0 -0.36 3 3
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.054 0.075 0.25 6 -10000 0 6
MAPK3 0.029 0.017 -10000 0 -10000 0 0
MAPK1 0.027 0.018 -10000 0 -10000 0 0
ICAM1 -0.13 0.23 -10000 0 -0.69 15 15
NFKB1 -0.03 0.1 -10000 0 -0.22 23 23
MAPK8 -0.081 0.11 -10000 0 -0.29 22 22
MAPK9 0.029 0.017 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.025 0.18 0.75 1 -0.51 13 14
BAX 0 0.097 -10000 0 -10000 0 0
POMC -0.099 0.22 -10000 0 -1.5 3 3
EP300 0.035 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.16 0.17 0.44 24 -10000 0 24
proteasomal ubiquitin-dependent protein catabolic process 0.031 0.064 0.26 6 -10000 0 6
SGK1 0.022 0.08 -10000 0 -10000 0 0
IL13 -0.16 0.2 -10000 0 -0.62 11 11
IL6 -0.15 0.29 -10000 0 -0.83 19 19
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.15 0.17 -10000 0 -0.61 5 5
IL2 -0.15 0.18 -10000 0 -0.4 39 39
CDK5 0.023 0.016 -10000 0 -10000 0 0
PRKACB 0.033 0.007 -10000 0 -10000 0 0
HSP90AA1 0.032 0.009 -10000 0 -10000 0 0
IL8 -0.23 0.38 -10000 0 -0.96 28 28
CDK5R1/CDK5 0.021 0.061 -10000 0 -0.28 5 5
NF kappa B1 p50/RelA/PKAc -0.016 0.15 -10000 0 -0.3 24 24
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.15 0.15 0.41 26 -10000 0 26
SMARCA4 0.026 0.059 -10000 0 -0.38 3 3
chromatin remodeling 0.095 0.1 0.3 15 -10000 0 15
NF kappa B1 p50/RelA/Cbp -0.018 0.16 -10000 0 -0.37 16 16
JUN (dimer) -0.12 0.16 -10000 0 -0.37 34 34
YWHAH 0.031 0.01 -10000 0 -10000 0 0
VIPR1 -0.096 0.16 -10000 0 -0.59 11 11
NR3C1 0.11 0.12 0.31 24 -10000 0 24
NR4A1 0.019 0.074 -10000 0 -0.46 3 3
TIF2/SUV420H1 0.038 0.059 -10000 0 -0.27 5 5
MAPKKK cascade -0.022 0.17 0.75 1 -0.49 13 14
cortisol/GR alpha (dimer)/Src-1 0.17 0.16 0.42 35 -10000 0 35
PBX1 0.034 0.005 -10000 0 -10000 0 0
POU1F1 0 0 -10000 0 -10000 0 0
SELE -0.16 0.28 -10000 0 -0.79 18 18
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.095 0.1 0.31 14 -10000 0 14
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.15 0.15 0.41 26 -10000 0 26
mol:cortisol 0.084 0.11 0.25 32 -10000 0 32
MMP1 -0.24 0.42 -10000 0 -1.1 28 28
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.009 0.04 -10000 0 -0.32 1 1
Crk/p130 Cas/Paxillin -0.086 0.1 -10000 0 -0.27 18 18
JUN -0.037 0.086 -10000 0 -0.31 7 7
HRAS 0.033 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.023 0.1 -10000 0 -0.23 23 23
RAP1A 0.034 0.005 -10000 0 -10000 0 0
FRS2 0.032 0.009 -10000 0 -10000 0 0
RAP1A/GDP 0.025 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.026 0.11 -10000 0 -0.24 24 24
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.034 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0 0.077 -10000 0 -0.21 13 13
RHOA 0.034 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.012 0.1 -10000 0 -0.22 22 22
GRB7 0.021 0.029 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.026 0.11 -10000 0 -0.24 24 24
MAPKKK cascade -0.066 0.11 -10000 0 -0.26 23 23
BCAR1 0.033 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.008 0.088 -10000 0 -0.22 17 17
lamellipodium assembly -0.05 0.094 -10000 0 -0.24 17 17
RET51/GFRalpha1/GDNF/SHC -0.027 0.11 -10000 0 -0.24 23 23
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.001 0.077 -10000 0 -0.21 13 13
RET9/GFRalpha1/GDNF/Shank3 -0.003 0.083 -10000 0 -0.22 14 14
MAPK3 -0.05 0.078 0.17 1 -0.23 13 14
DOK1 0.034 0 -10000 0 -10000 0 0
DOK6 -0.018 0.13 -10000 0 -0.38 15 15
PXN 0.034 0.003 -10000 0 -10000 0 0
neurite development -0.054 0.086 -10000 0 -0.3 10 10
DOK5 0.029 0.035 -10000 0 -0.38 1 1
GFRA1 -0.029 0.12 -10000 0 -0.38 14 14
MAPK8 -0.033 0.089 -10000 0 -0.23 21 21
HRAS/GTP -0.048 0.13 -10000 0 -0.26 25 25
tube development -0.004 0.077 -10000 0 -0.22 13 13
MAPK1 -0.048 0.08 0.17 2 -0.28 6 8
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.032 0.072 -10000 0 -0.2 13 13
Rac1/GDP 0.017 0.012 -10000 0 -10000 0 0
SRC 0.029 0.035 -10000 0 -0.38 1 1
PDLIM7 0.033 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.03 0.14 -10000 0 -0.29 27 27
SHC1 0.031 0.015 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.027 0.11 -10000 0 -0.24 24 24
RET51/GFRalpha1/GDNF/Dok5 -0.026 0.11 -10000 0 -0.25 24 24
PRKCA 0.031 0.034 -10000 0 -0.38 1 1
HRAS/GDP 0.024 0.006 -10000 0 -10000 0 0
CREB1 -0.059 0.11 -10000 0 -0.26 18 18
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.037 0.073 -10000 0 -0.2 14 14
RET51/GFRalpha1/GDNF/Grb7 -0.031 0.11 -10000 0 -0.24 24 24
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.028 0.12 -10000 0 -0.38 14 14
DOK4 0.033 0.01 -10000 0 -10000 0 0
JNK cascade -0.036 0.085 -10000 0 -0.32 6 6
RET9/GFRalpha1/GDNF/FRS2 0.002 0.075 -10000 0 -0.21 12 12
SHANK3 0.023 0.05 -10000 0 -0.38 2 2
RASA1 0.033 0.006 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.019 0.07 -10000 0 -0.2 14 14
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.073 0.11 -10000 0 -0.21 50 50
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.083 0.12 -10000 0 -0.22 45 45
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.034 0.11 -10000 0 -0.25 23 23
PI3K -0.11 0.14 -10000 0 -0.36 19 19
SOS1 0.034 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.004 0.085 -10000 0 -0.22 13 13
GRB10 0.016 0.05 -10000 0 -0.38 2 2
activation of MAPKK activity -0.021 0.077 -10000 0 -0.22 14 14
RET51/GFRalpha1/GDNF/FRS2 -0.021 0.1 -10000 0 -0.23 22 22
GAB1 0.031 0.034 -10000 0 -0.38 1 1
IRS1 0.02 0.076 -10000 0 -0.38 5 5
IRS2 0.03 0.035 -10000 0 -0.38 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.035 0.11 -10000 0 -0.25 24 24
RET51/GFRalpha1/GDNF/PKC alpha -0.027 0.11 -10000 0 -0.25 24 24
GRB2 0.034 0.005 -10000 0 -10000 0 0
PRKACA 0.033 0.007 -10000 0 -10000 0 0
GDNF 0.025 0.021 -10000 0 -10000 0 0
RAC1 0.023 0.016 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.035 0.12 -10000 0 -0.25 27 27
Rac1/GTP -0.056 0.11 -10000 0 -0.29 15 15
RET9/GFRalpha1/GDNF -0.007 0.075 -10000 0 -0.23 13 13
GFRalpha1/GDNF -0.01 0.089 -10000 0 -0.27 13 13
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.002 0.12 -10000 0 -0.5 8 8
IHH 0.023 0.052 -10000 0 -0.16 4 4
SHH Np/Cholesterol/GAS1 -0.01 0.072 -10000 0 -0.22 13 13
LRPAP1 0.034 0.003 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.01 0.072 0.22 13 -10000 0 13
SMO/beta Arrestin2 0.045 0.12 -10000 0 -0.51 3 3
SMO -0.004 0.09 -10000 0 -0.47 4 4
AKT1 -0.003 0.1 -10000 0 -0.38 8 8
ARRB2 0.033 0.006 -10000 0 -10000 0 0
BOC 0.03 0.036 -10000 0 -0.38 1 1
ADRBK1 0.034 0.003 -10000 0 -10000 0 0
heart looping -0.004 0.089 -10000 0 -0.46 4 4
STIL 0.021 0.12 0.18 29 -0.31 7 36
DHH N/PTCH2 0.023 0.076 -10000 0 -0.28 8 8
DHH N/PTCH1 0.009 0.1 -10000 0 -0.31 12 12
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
DHH 0.015 0.071 -10000 0 -0.38 4 4
PTHLH -0.012 0.15 -10000 0 -0.6 8 8
determination of left/right symmetry -0.004 0.089 -10000 0 -0.46 4 4
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
skeletal system development -0.012 0.15 -10000 0 -0.59 8 8
IHH N/Hhip -0.011 0.12 -10000 0 -0.31 18 18
DHH N/Hhip -0.012 0.12 -10000 0 -0.28 20 20
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.004 0.089 -10000 0 -0.46 4 4
pancreas development -0.029 0.14 -10000 0 -0.38 18 18
HHAT 0.027 0.048 -10000 0 -0.38 2 2
PI3K 0.045 0.03 -10000 0 -0.27 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.013 0.072 -10000 0 -0.38 4 4
somite specification -0.004 0.089 -10000 0 -0.46 4 4
SHH Np/Cholesterol/PTCH1 -0.018 0.088 -10000 0 -0.32 7 7
SHH Np/Cholesterol/PTCH2 -0.006 0.068 -10000 0 -0.23 11 11
SHH Np/Cholesterol/Megalin -0.034 0.097 -10000 0 -0.24 25 25
SHH -0.031 0.066 -10000 0 -0.27 10 10
catabolic process 0.001 0.098 -10000 0 -0.36 9 9
SMO/Vitamin D3 -0.014 0.1 -10000 0 -0.46 4 4
SHH Np/Cholesterol/Hhip -0.023 0.079 -10000 0 -0.21 20 20
LRP2 -0.066 0.17 -10000 0 -0.38 31 31
receptor-mediated endocytosis -0.039 0.12 -10000 0 -0.42 9 9
SHH Np/Cholesterol/BOC -0.003 0.06 -10000 0 -0.21 10 10
SHH Np/Cholesterol/CDO -0.004 0.062 -10000 0 -0.21 11 11
mesenchymal cell differentiation 0.023 0.079 0.21 20 -10000 0 20
mol:Vitamin D3 0.028 0.13 0.2 30 -0.32 7 37
IHH N/PTCH2 0.031 0.068 -10000 0 -0.32 4 4
CDON 0.024 0.06 -10000 0 -0.38 3 3
IHH N/PTCH1 0.011 0.1 -10000 0 -0.36 9 9
Megalin/LRPAP1 -0.03 0.13 -10000 0 -0.27 31 31
PTCH2 0.022 0.068 -10000 0 -0.38 4 4
SHH Np/Cholesterol -0.008 0.055 -10000 0 -0.2 10 10
PTCH1 0.001 0.098 -10000 0 -0.36 9 9
HHIP -0.029 0.14 -10000 0 -0.38 18 18
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.14 0.24 -10000 0 -0.8 9 9
PCK1 -0.09 0.14 -10000 0 -0.7 1 1
HNF4A -0.15 0.25 -10000 0 -0.81 10 10
KCNJ11 -0.16 0.3 -10000 0 -0.91 12 12
AKT1 -0.086 0.16 -10000 0 -0.45 9 9
response to starvation -0.001 0.011 -10000 0 -0.12 1 1
DLK1 -0.24 0.38 -10000 0 -0.93 28 28
NKX2-1 -0.079 0.23 -10000 0 -1.2 4 4
ACADM -0.14 0.25 -10000 0 -0.77 10 10
TAT -0.1 0.15 -10000 0 -0.6 2 2
CEBPB 0.031 0.014 -10000 0 -10000 0 0
CEBPA 0.027 0.049 -10000 0 -0.38 2 2
TTR -0.095 0.19 -10000 0 -0.74 5 5
PKLR -0.14 0.24 -10000 0 -0.78 9 9
APOA1 -0.16 0.32 -10000 0 -1.1 7 7
CPT1C -0.14 0.25 -10000 0 -0.74 12 12
ALAS1 -0.072 0.15 -10000 0 -10000 0 0
TFRC -0.12 0.19 -10000 0 -0.66 3 3
FOXF1 0.018 0.084 0.23 3 -0.38 5 8
NF1 0.035 0.034 -10000 0 -0.38 1 1
HNF1A (dimer) 0.004 0.075 -10000 0 -0.19 17 17
CPT1A -0.14 0.25 -10000 0 -0.77 10 10
HMGCS1 -0.14 0.24 -10000 0 -0.8 9 9
NR3C1 0.005 0.074 -10000 0 -0.2 14 14
CPT1B -0.17 0.28 -10000 0 -0.92 12 12
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.003 0.074 -10000 0 -0.19 17 17
GCK -0.12 0.27 -10000 0 -0.88 10 10
CREB1 0.03 0.035 -10000 0 -0.31 1 1
IGFBP1 -0.16 0.37 -10000 0 -1.2 16 16
PDX1 -0.21 0.42 -10000 0 -1.3 18 18
UCP2 -0.15 0.26 -10000 0 -0.84 8 8
ALDOB -0.15 0.28 -10000 0 -0.86 11 11
AFP -0.1 0.26 -10000 0 -0.77 17 17
BDH1 -0.16 0.28 -10000 0 -0.86 12 12
HADH -0.15 0.27 -10000 0 -0.84 9 9
F2 -0.16 0.29 -10000 0 -0.88 11 11
HNF1A 0.004 0.075 -10000 0 -0.19 17 17
G6PC -0.018 0.073 -10000 0 -10000 0 0
SLC2A2 -0.089 0.18 -10000 0 -0.62 1 1
INS 0.012 0.059 0.19 14 -10000 0 14
FOXA1 -0.016 0.097 0.23 3 -0.26 15 18
FOXA3 -0.045 0.13 -10000 0 -0.3 25 25
FOXA2 -0.18 0.3 -10000 0 -0.88 12 12
ABCC8 -0.22 0.38 -10000 0 -0.96 25 25
ALB -0.072 0.19 -10000 0 -0.68 10 10
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.014 0.12 -10000 0 -0.38 15 15
PDGF/PDGFRA/CRKL 0.008 0.093 -10000 0 -0.26 15 15
positive regulation of JUN kinase activity 0.042 0.084 -10000 0 -0.2 13 13
CRKL 0.032 0.009 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.001 0.094 -10000 0 -0.26 15 15
AP1 -0.03 0.15 0.31 1 -0.59 6 7
mol:IP3 -0.037 0.081 -10000 0 -0.29 13 13
PLCG1 -0.037 0.081 -10000 0 -0.29 13 13
PDGF/PDGFRA/alphaV Integrin 0.01 0.094 -10000 0 -0.26 15 15
RAPGEF1 0.03 0.035 -10000 0 -0.38 1 1
CRK 0.033 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.037 0.081 -10000 0 -0.29 13 13
CAV3 0.021 0.027 -10000 0 -10000 0 0
CAV1 0.007 0.076 -10000 0 -0.38 5 5
SHC/Grb2/SOS1 0.043 0.085 -10000 0 -0.2 13 13
PDGF/PDGFRA/Shf 0.009 0.093 -10000 0 -0.26 15 15
FOS -0.05 0.13 -10000 0 -0.59 6 6
JUN -0.022 0.024 -10000 0 -10000 0 0
oligodendrocyte development 0.01 0.094 -10000 0 -0.26 15 15
GRB2 0.034 0.005 -10000 0 -10000 0 0
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
mol:DAG -0.037 0.081 -10000 0 -0.29 13 13
PDGF/PDGFRA -0.014 0.12 -10000 0 -0.38 15 15
actin cytoskeleton reorganization 0.006 0.092 -10000 0 -0.26 15 15
SRF -0.01 0.014 -10000 0 -10000 0 0
SHC1 0.031 0.015 -10000 0 -10000 0 0
PI3K 0.026 0.088 -10000 0 -0.22 15 15
PDGF/PDGFRA/Crk/C3G 0.026 0.087 -10000 0 -0.22 15 15
JAK1 -0.03 0.07 -10000 0 -0.26 12 12
ELK1/SRF -0.013 0.096 0.14 25 -0.24 13 38
SHB 0.031 0.01 -10000 0 -10000 0 0
SHF 0.034 0.005 -10000 0 -10000 0 0
CSNK2A1 0.027 0.025 -10000 0 -10000 0 0
GO:0007205 -0.035 0.092 -10000 0 -0.32 13 13
SOS1 0.034 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.042 0.084 -10000 0 -0.2 13 13
PDGF/PDGFRA/SHB 0.006 0.092 -10000 0 -0.26 15 15
PDGF/PDGFRA/Caveolin-1 0.003 0.082 -10000 0 -0.27 11 11
ITGAV 0.034 0.003 -10000 0 -10000 0 0
ELK1 -0.035 0.079 -10000 0 -0.27 13 13
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.009 0.093 -10000 0 -0.26 15 15
JAK-STAT cascade -0.03 0.07 -10000 0 -0.26 12 12
cell proliferation 0.009 0.093 -10000 0 -0.26 15 15
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.046 0.16 -10000 0 -0.4 24 24
KLHL20 0.021 0.098 0.18 11 -0.23 4 15
CYFIP2 0.034 0.004 -10000 0 -10000 0 0
Rac1/GDP -0.017 0.1 0.22 1 -0.26 19 20
ENAH -0.044 0.16 -10000 0 -0.4 23 23
AP1M1 0.033 0.007 -10000 0 -10000 0 0
RAP1B 0.031 0.01 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CTNNB1 0.034 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.005 0.083 -10000 0 -0.3 1 1
ABI1/Sra1/Nap1 -0.02 0.044 -10000 0 -0.16 4 4
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.024 0.11 -10000 0 -0.22 24 24
RAPGEF1 -0.039 0.15 0.22 1 -0.37 21 22
CTNND1 0.034 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.038 0.17 -10000 0 -0.4 25 25
CRK -0.043 0.15 -10000 0 -0.39 21 21
E-cadherin/gamma catenin/alpha catenin 0.014 0.11 -10000 0 -0.23 23 23
alphaE/beta7 Integrin 0.042 0.04 -10000 0 -0.26 2 2
IQGAP1 0.034 0.005 -10000 0 -10000 0 0
NCKAP1 0.034 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.054 0.026 -10000 0 -10000 0 0
DLG1 -0.046 0.16 -10000 0 -0.4 24 24
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.035 0.046 -10000 0 -0.22 1 1
MLLT4 0.031 0.01 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.059 0.022 -10000 0 -10000 0 0
PI3K -0.044 0.058 -10000 0 -0.28 1 1
ARF6 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.006 0.12 -10000 0 -0.27 23 23
TIAM1 0.033 0.006 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.027 0.1 -10000 0 -0.2 23 23
AKT1 -0.017 0.052 0.15 1 -0.16 1 2
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
CDH1 -0.037 0.15 -10000 0 -0.38 23 23
RhoA/GDP -0.012 0.12 0.22 1 -0.25 21 22
actin cytoskeleton organization 0.019 0.077 0.15 11 -0.17 4 15
CDC42/GDP -0.012 0.12 0.22 1 -0.25 21 22
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.017 0.085 -10000 0 -0.21 24 24
ITGB7 0.026 0.05 -10000 0 -0.38 2 2
RAC1 0.023 0.016 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.029 0.11 -10000 0 -0.21 23 23
E-cadherin/Ca2+/beta catenin/alpha catenin 0.013 0.093 -10000 0 -0.2 23 23
mol:GDP -0.03 0.12 0.22 1 -0.29 21 22
CDC42/GTP/IQGAP1 0.045 0.009 -10000 0 -10000 0 0
JUP 0.033 0.011 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP -0.003 0.12 0.23 1 -0.26 21 22
RAC1/GTP/IQGAP1 0.031 0.022 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.046 0.029 -10000 0 -0.27 1 1
RHOA 0.034 0.004 -10000 0 -10000 0 0
CDC42 0.034 0.005 -10000 0 -10000 0 0
CTNNA1 0.034 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.015 0.054 0.11 10 -0.12 2 12
NME1 0.034 0.009 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.044 0.16 -10000 0 -0.4 24 24
regulation of cell-cell adhesion -0.014 0.066 -10000 0 -0.26 1 1
WASF2 0.008 0.042 0.097 4 -10000 0 4
Rap1/GTP -0.004 0.092 -10000 0 -0.33 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.043 0.11 -10000 0 -0.21 24 24
CCND1 0.017 0.063 0.13 10 -0.14 2 12
VAV2 -0.048 0.21 -10000 0 -0.67 8 8
RAP1/GDP -0.003 0.1 -10000 0 -0.38 1 1
adherens junction assembly -0.042 0.15 -10000 0 -0.38 24 24
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.024 0.016 -10000 0 -10000 0 0
PIP5K1C 0.03 0.035 -10000 0 -0.38 1 1
regulation of heterotypic cell-cell adhesion 0.016 0.1 -10000 0 -0.2 23 23
E-cadherin/beta catenin -0.042 0.11 -10000 0 -0.3 23 23
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.046 0.16 -10000 0 -0.41 21 21
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.034 0.1 -10000 0 -0.35 5 5
E-cadherin/beta catenin/alpha catenin 0.014 0.11 -10000 0 -0.23 23 23
ITGAE 0.032 0.013 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.039 0.17 -10000 0 -0.4 25 25
ErbB2/ErbB3 signaling events

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.013 0.009 -10000 0 -10000 0 0
RAS family/GTP -0.015 0.11 -10000 0 -0.28 9 9
NFATC4 -0.054 0.075 -10000 0 -0.26 5 5
ERBB2IP 0.035 0.005 -10000 0 -10000 0 0
HSP90 (dimer) 0.032 0.009 -10000 0 -10000 0 0
mammary gland morphogenesis -0.057 0.098 -10000 0 -0.24 27 27
JUN -0.016 0.068 0.16 1 -0.41 1 2
HRAS 0.032 0.008 -10000 0 -10000 0 0
DOCK7 -0.072 0.086 -10000 0 -0.23 26 26
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.036 0.12 -10000 0 -0.24 30 30
AKT1 -0.008 0.007 -10000 0 -10000 0 0
BAD -0.012 0.005 -10000 0 -10000 0 0
MAPK10 -0.011 0.075 0.2 4 -0.2 1 5
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.055 0.11 -10000 0 -0.25 27 27
RAF1 -0.053 0.1 0.26 1 -0.31 8 9
ErbB2/ErbB3/neuregulin 2 -0.016 0.11 -10000 0 -0.28 18 18
STAT3 0.03 0.087 -10000 0 -1 1 1
cell migration -0.026 0.069 0.28 2 -0.18 2 4
mol:PI-3-4-5-P3 -0.002 0.002 -10000 0 -10000 0 0
cell proliferation -0.088 0.23 0.48 1 -0.62 19 20
FOS -0.053 0.16 0.42 1 -0.37 22 23
NRAS 0.033 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.057 0.098 -10000 0 -0.24 27 27
MAPK3 -0.065 0.18 0.5 1 -0.5 15 16
MAPK1 -0.084 0.21 0.5 1 -0.56 16 17
JAK2 -0.069 0.086 -10000 0 -0.23 24 24
NF2 0.006 0.016 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.043 0.099 -10000 0 -0.24 25 25
NRG1 -0.041 0.13 -10000 0 -0.38 18 18
GRB2/SOS1 0.05 0.007 -10000 0 -10000 0 0
MAPK8 -0.032 0.095 -10000 0 -0.27 14 14
MAPK9 -0.011 0.074 0.2 4 -0.2 1 5
ERBB2 -0.037 0.042 -10000 0 -0.29 4 4
ERBB3 -0.021 0.12 -10000 0 -0.39 14 14
SHC1 0.031 0.015 -10000 0 -10000 0 0
RAC1 0.023 0.016 -10000 0 -10000 0 0
apoptosis 0.01 0.011 -10000 0 -10000 0 0
STAT3 (dimer) 0.03 0.085 -10000 0 -0.97 1 1
RNF41 -0.017 0.009 -10000 0 -10000 0 0
FRAP1 -0.007 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.045 0.053 -10000 0 -0.18 14 14
ErbB2/ErbB2/HSP90 (dimer) -0.031 0.038 -10000 0 -0.24 4 4
CHRNA1 -0.077 0.21 0.45 1 -0.6 18 19
myelination -0.051 0.089 0.33 2 -0.29 3 5
PPP3CB -0.06 0.082 -10000 0 -0.22 18 18
KRAS 0.032 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.008 0.085 -10000 0 -0.24 9 9
NRG2 0.02 0.075 -10000 0 -0.38 5 5
mol:GDP -0.043 0.098 -10000 0 -0.24 25 25
SOS1 0.034 0.001 -10000 0 -10000 0 0
MAP2K2 -0.057 0.11 0.54 1 -0.33 9 10
SRC 0.029 0.035 -10000 0 -0.38 1 1
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.073 0.085 -10000 0 -0.23 26 26
MAP2K1 -0.069 0.18 0.45 1 -0.52 10 11
heart morphogenesis -0.057 0.098 -10000 0 -0.24 27 27
RAS family/GDP -0.008 0.12 -10000 0 -0.26 10 10
GRB2 0.033 0.005 -10000 0 -10000 0 0
PRKACA 0.016 0.008 -10000 0 -10000 0 0
CHRNE -0.001 0.021 -10000 0 -0.17 1 1
HSP90AA1 0.032 0.009 -10000 0 -10000 0 0
activation of caspase activity 0.008 0.007 -10000 0 -10000 0 0
nervous system development -0.057 0.098 -10000 0 -0.24 27 27
CDC42 0.034 0.005 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.015 0.094 0.28 13 -10000 0 13
KIRREL -0.001 0.12 -10000 0 -0.39 13 13
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.015 0.094 -10000 0 -0.28 13 13
PLCG1 0.028 0.035 -10000 0 -0.38 1 1
ARRB2 0.033 0.006 -10000 0 -10000 0 0
WASL 0.024 0.016 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.032 0.079 -10000 0 -0.21 13 13
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.002 0.055 -10000 0 -0.21 9 9
FYN 0.005 0.072 0.14 11 -0.2 13 24
mol:Ca2+ 0.028 0.083 -10000 0 -0.22 13 13
mol:DAG 0.029 0.084 -10000 0 -0.22 13 13
NPHS2 -0.005 0.012 -10000 0 -10000 0 0
mol:IP3 0.029 0.084 -10000 0 -0.22 13 13
regulation of endocytosis 0.031 0.073 -10000 0 -0.19 13 13
Nephrin/NEPH1/podocin/Cholesterol 0.017 0.071 -10000 0 -0.2 13 13
establishment of cell polarity 0.015 0.094 -10000 0 -0.28 13 13
Nephrin/NEPH1/podocin/NCK1-2 0.049 0.081 -10000 0 -0.19 13 13
Nephrin/NEPH1/beta Arrestin2 0.033 0.075 -10000 0 -0.19 13 13
NPHS1 0.021 0.026 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin 0.015 0.068 -10000 0 -0.2 13 13
TJP1 0.034 0.005 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
NCK2 0.034 0.004 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.03 0.085 -10000 0 -0.22 13 13
CD2AP 0.033 0.007 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.036 0.077 -10000 0 -0.21 12 12
GRB2 0.034 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.019 0.089 0.15 12 -0.2 21 33
cytoskeleton organization -0.015 0.058 0.2 1 -0.23 8 9
Nephrin/NEPH1 0.017 0.066 -10000 0 -0.19 13 13
Nephrin/NEPH1/ZO-1 0.034 0.084 -10000 0 -0.23 13 13
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.036 0.068 -10000 0 -0.2 11 11
RGS9BP 0.021 0.068 -10000 0 -0.38 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.026 0.017 -10000 0 -10000 0 0
mol:Na + 0.001 0.09 -10000 0 -0.23 19 19
mol:ADP -0.017 0.008 -10000 0 -10000 0 0
GNAT2 0.032 0.01 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.016 0.11 -10000 0 -0.24 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.036 0.019 -10000 0 -10000 0 0
GRK7 0.032 0.01 -10000 0 -10000 0 0
CNGB3 0.026 0.013 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.02 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.065 0.088 -10000 0 -0.22 36 36
Cone PDE6 0.014 0.1 -10000 0 -0.21 20 20
Cone Metarhodopsin II 0.035 0.017 -10000 0 -10000 0 0
Na + (4 Units) -0.028 0.11 -10000 0 -0.22 36 36
GNAT2/GDP 0.028 0.099 -10000 0 -0.21 19 19
GNB5 0.034 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.01 0.029 0.18 3 -10000 0 3
Cone Transducin 0.039 0.073 -10000 0 -0.21 11 11
SLC24A2 -0.03 0.13 -10000 0 -0.38 18 18
GNB3/GNGT2 0.021 0.089 -10000 0 -0.27 12 12
GNB3 0 0.11 -10000 0 -0.38 11 11
GNAT2/GTP 0.023 0.007 -10000 0 -10000 0 0
CNGA3 -0.032 0.15 -10000 0 -0.38 22 22
ARR3 0.027 0.006 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.001 0.09 -10000 0 -0.23 19 19
mol:Pi 0.016 0.11 -10000 0 -0.24 20 20
Cone CNG Channel 0.005 0.087 -10000 0 -0.2 18 18
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.03 0.13 -10000 0 -0.38 18 18
RGS9 -0.025 0.14 -10000 0 -0.38 19 19
PDE6C 0.018 0.013 -10000 0 -10000 0 0
GNGT2 0.031 0.034 -10000 0 -0.38 1 1
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.025 0.019 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.047 0.089 -10000 0 -0.26 9 9
MAP4K1 0.03 0.035 -10000 0 -0.38 1 1
MAP3K8 0.018 0.04 -10000 0 -0.38 1 1
PRKCB 0.018 0.07 -10000 0 -0.38 4 4
DBNL 0.024 0.016 -10000 0 -10000 0 0
CRKL 0.032 0.009 -10000 0 -10000 0 0
MAP3K1 0.015 0.064 -10000 0 -0.32 2 2
JUN -0.14 0.26 -10000 0 -0.52 45 45
MAP3K7 0.013 0.059 -10000 0 -0.35 1 1
GRAP2 0.005 0.095 -10000 0 -0.38 8 8
CRK 0.033 0.006 -10000 0 -10000 0 0
MAP2K4 0.001 0.068 0.2 1 -0.3 3 4
LAT 0.027 0.049 -10000 0 -0.38 2 2
LCP2 0.031 0.034 -10000 0 -0.38 1 1
MAPK8 -0.15 0.28 -10000 0 -0.54 47 47
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.024 0.072 -10000 0 -0.24 6 6
LAT/GRAP2/SLP76/HPK1/HIP-55 0.047 0.076 -10000 0 -0.24 5 5
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 -0.006 0.092 -10000 0 -0.27 14 14
CRKL 0.014 0.13 0.29 3 -0.39 5 8
mol:PIP3 0.004 0.006 -10000 0 -10000 0 0
AKT1 0.001 0.035 -10000 0 -10000 0 0
PTK2B 0.032 0.015 -10000 0 -10000 0 0
RAPGEF1 0.012 0.13 0.28 5 -0.38 5 10
RANBP10 0.034 0.005 -10000 0 -10000 0 0
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.007 0.11 -10000 0 -0.27 17 17
MAP3K5 0.017 0.13 0.26 3 -0.41 5 8
HGF/MET/CIN85/CBL/ENDOPHILINS 0.005 0.1 -10000 0 -0.24 17 17
AP1 0.032 0.08 0.16 2 -0.21 2 4
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.031 0.015 -10000 0 -10000 0 0
apoptosis -0.048 0.29 -10000 0 -0.84 16 16
STAT3 (dimer) -0.014 0.083 -10000 0 -0.33 4 4
GAB1/CRKL/SHP2/PI3K 0.046 0.14 0.3 2 -0.37 6 8
INPP5D 0.022 0.068 -10000 0 -0.38 4 4
CBL/CRK 0.03 0.12 0.27 2 -0.39 4 6
PTPN11 0.034 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.028 0.035 -10000 0 -0.38 1 1
PTEN 0.023 0.016 -10000 0 -10000 0 0
ELK1 0.093 0.19 0.35 48 -10000 0 48
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.015 0.07 -10000 0 -0.27 6 6
PAK1 -0.002 0.036 -10000 0 -10000 0 0
HGF/MET/RANBP10 -0.007 0.1 -10000 0 -0.27 17 17
HRAS -0.056 0.19 -10000 0 -0.59 15 15
DOCK1 0.005 0.12 0.28 3 -0.37 5 8
GAB1 0.015 0.12 -10000 0 -0.39 4 4
CRK 0.017 0.12 0.27 2 -0.39 5 7
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.054 0.18 -10000 0 -0.5 20 20
JUN 0.033 0.006 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.029 0.087 -10000 0 -0.23 20 20
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
cell morphogenesis 0.01 0.14 0.32 7 -0.37 4 11
GRB2/SHC 0.025 0.11 0.21 1 -0.23 14 15
FOS 0.018 0.062 -10000 0 -0.38 3 3
GLMN 0.005 0.008 -10000 0 -10000 0 0
cell motility 0.092 0.19 0.35 48 -10000 0 48
HGF/MET/MUC20 -0.015 0.097 -10000 0 -0.26 17 17
cell migration 0.024 0.11 0.21 1 -0.23 14 15
GRB2 0.034 0.005 -10000 0 -10000 0 0
CBL 0.034 0.003 -10000 0 -10000 0 0
MET/RANBP10 -0.006 0.092 -10000 0 -0.27 14 14
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.017 0.087 -10000 0 -0.23 17 17
MET/MUC20 -0.017 0.083 -10000 0 -0.27 14 14
RAP1B 0.019 0.13 0.3 9 -0.35 4 13
RAP1A 0.012 0.12 0.32 4 -0.35 4 8
HGF/MET/RANBP9 -0.007 0.11 -10000 0 -0.27 17 17
RAF1 -0.038 0.2 -10000 0 -0.56 15 15
STAT3 -0.015 0.084 -10000 0 -0.31 5 5
cell proliferation -0.015 0.14 0.29 2 -0.35 19 21
RPS6KB1 -0.001 0.044 0.17 1 -0.24 2 3
MAPK3 0.065 0.18 0.56 2 -10000 0 2
MAPK1 0.096 0.22 0.65 9 -10000 0 9
RANBP9 0.034 0.005 -10000 0 -10000 0 0
MAPK8 -0.07 0.18 0.3 1 -0.46 11 12
SRC -0.02 0.073 -10000 0 -0.29 4 4
PI3K 0.022 0.11 0.21 1 -0.22 20 21
MET/Glomulin -0.015 0.08 -10000 0 -0.24 15 15
SOS1 0.034 0 -10000 0 -10000 0 0
MAP2K1 -0.035 0.18 -10000 0 -0.52 15 15
MET -0.026 0.12 -10000 0 -0.38 14 14
MAP4K1 0.022 0.13 0.28 3 -0.41 6 9
PTK2 0.033 0.008 -10000 0 -10000 0 0
MAP2K2 -0.031 0.18 0.28 2 -0.5 15 17
BAD -0.004 0.033 -10000 0 -10000 0 0
MAP2K4 0.016 0.12 0.25 3 -0.38 5 8
SHP2/GRB2/SOS1/GAB1 -0.007 0.12 -10000 0 -0.32 13 13
INPPL1 0.034 0 -10000 0 -10000 0 0
PXN 0.034 0.003 -10000 0 -10000 0 0
SH3KBP1 0.034 0 -10000 0 -10000 0 0
HGS -0.031 0.081 -10000 0 -0.22 20 20
PLCgamma1/PKC 0.021 0.025 -10000 0 -0.27 1 1
HGF -0.006 0.099 -10000 0 -0.38 9 9
RASA1 0.033 0.006 -10000 0 -10000 0 0
NCK1 0.034 0.005 -10000 0 -10000 0 0
PTPRJ 0.031 0.035 -10000 0 -0.38 1 1
NCK/PLCgamma1 0.029 0.1 -10000 0 -0.2 18 18
PDPK1 0.004 0.035 0.26 1 -10000 0 1
HGF/MET/SHIP -0.013 0.11 -10000 0 -0.27 19 19
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.042 0.046 -10000 0 -0.27 3 3
Necdin/E2F1 -0.018 0.13 -10000 0 -0.28 28 28
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.056 0.098 -10000 0 -0.21 17 17
NGF (dimer)/p75(NTR)/BEX1 0.005 0.11 -10000 0 -0.24 24 24
NT-4/5 (dimer)/p75(NTR) 0.019 0.071 -10000 0 -0.27 7 7
IKBKB 0.034 0.005 -10000 0 -10000 0 0
AKT1 -0.033 0.077 0.2 7 -0.2 16 23
IKBKG 0.034 0.005 -10000 0 -10000 0 0
BDNF 0.005 0.075 -10000 0 -0.38 4 4
MGDIs/NGR/p75(NTR)/LINGO1 0.018 0.11 -10000 0 -0.28 15 15
FURIN 0.034 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.023 0.09 -10000 0 -0.24 12 12
LINGO1 0.006 0.1 -10000 0 -0.38 9 9
Sortilin/TRAF6/NRIF 0.035 0.036 -10000 0 -0.2 2 2
proBDNF (dimer) 0.005 0.075 -10000 0 -0.38 4 4
NTRK1 0.01 0.079 -10000 0 -0.38 5 5
RTN4R 0.017 0.069 -10000 0 -0.38 4 4
neuron apoptosis -0.019 0.11 0.29 2 -0.38 4 6
IRAK1 0.034 0.004 -10000 0 -10000 0 0
SHC1 -0.042 0.065 -10000 0 -0.23 15 15
ARHGDIA 0.034 0 -10000 0 -10000 0 0
RhoA/GTP 0.025 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.085 0.04 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.026 0.11 -10000 0 -0.22 22 22
MAGEH1 0.017 0.082 -10000 0 -0.38 6 6
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.021 0.15 -10000 0 -0.24 42 42
Mammalian IAPs/DIABLO 0.044 0.093 -10000 0 -0.21 14 14
proNGF (dimer) 0 0.1 -10000 0 -0.38 9 9
MAGED1 0.034 0 -10000 0 -10000 0 0
APP 0.033 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.021 0.025 -10000 0 -10000 0 0
ZNF274 0.032 0.009 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.012 0.081 0.17 2 -0.2 16 18
NGF 0 0.1 -10000 0 -0.38 9 9
cell cycle arrest -0.033 0.08 0.37 3 -0.19 1 4
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0 0.083 -10000 0 -0.22 17 17
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.031 0.076 -10000 0 -0.23 9 9
NCSTN 0.034 0.005 -10000 0 -10000 0 0
mol:GTP 0.02 0.095 -10000 0 -0.23 16 16
PSENEN 0.033 0.008 -10000 0 -10000 0 0
mol:ceramide -0.042 0.064 0.18 1 -0.21 17 18
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.019 0.098 -10000 0 -0.37 6 6
p75(NTR)/beta APP 0.029 0.071 -10000 0 -0.27 7 7
BEX1 0.008 0.1 -10000 0 -0.38 9 9
mol:GDP -0.038 0.066 -10000 0 -0.23 16 16
NGF (dimer) -0.026 0.12 -10000 0 -0.23 33 33
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.033 0.11 -10000 0 -0.26 15 15
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
RAC1/GTP 0.013 0.066 -10000 0 -0.2 10 10
MYD88 0.031 0.034 -10000 0 -0.38 1 1
CHUK 0.023 0.016 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.02 0.096 -10000 0 -0.23 16 16
RHOB 0.033 0.009 -10000 0 -10000 0 0
RHOA 0.034 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.042 0.04 -10000 0 -0.27 2 2
NT3 (dimer) 0.021 0.022 -10000 0 -10000 0 0
TP53 -0.037 0.072 0.17 3 -0.22 5 8
PRDM4 -0.044 0.064 0.18 1 -0.21 17 18
BDNF (dimer) -0.044 0.12 -10000 0 -0.24 33 33
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
SORT1 0.031 0.034 -10000 0 -0.38 1 1
activation of caspase activity 0.049 0.095 -10000 0 -0.2 17 17
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.031 0.11 -10000 0 -0.22 18 18
RHOC 0.034 0.005 -10000 0 -10000 0 0
XIAP 0.034 0.003 -10000 0 -10000 0 0
MAPK10 0.001 0.11 0.28 4 -0.27 7 11
DIABLO 0.034 0.004 -10000 0 -10000 0 0
SMPD2 -0.042 0.065 0.18 1 -0.21 17 18
APH1B 0.034 0.005 -10000 0 -10000 0 0
APH1A 0.034 0.005 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.02 0.098 -10000 0 -0.23 17 17
PSEN1 0.032 0.009 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.048 0.015 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.02 0.072 -10000 0 -0.27 7 7
MAPK8 -0.018 0.093 0.31 2 -0.26 8 10
MAPK9 0.004 0.11 0.3 5 -0.27 6 11
APAF1 0.034 0.004 -10000 0 -10000 0 0
NTF3 0.021 0.022 -10000 0 -10000 0 0
NTF4 0.021 0.025 -10000 0 -10000 0 0
NDN -0.055 0.17 -10000 0 -0.38 31 31
RAC1/GDP 0.017 0.012 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.05 0.089 -10000 0 -0.19 16 16
p75 CTF/Sortilin/TRAF6/NRIF 0.074 0.049 -10000 0 -0.21 3 3
RhoA-B-C/GTP 0.019 0.095 -10000 0 -0.23 16 16
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.055 0.094 -10000 0 -0.21 14 14
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.035 0.097 -10000 0 -0.22 14 14
PRKACB 0.033 0.007 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.024 0.062 -10000 0 -0.27 4 4
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.016 0.12 -10000 0 -0.38 14 14
BIRC2 0.034 0.003 -10000 0 -10000 0 0
neuron projection morphogenesis -0.06 0.1 0.22 3 -0.26 20 23
BAD -0.004 0.11 0.26 5 -0.28 6 11
RIPK2 0.033 0.006 -10000 0 -10000 0 0
NGFR 0.01 0.09 -10000 0 -0.38 7 7
CYCS -0.026 0.065 0.35 2 -0.2 10 12
ADAM17 0.034 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.031 0.1 -10000 0 -0.22 17 17
BCL2L11 -0.004 0.11 0.28 5 -0.28 6 11
BDNF (dimer)/p75(NTR) 0.007 0.09 -10000 0 -0.28 11 11
PI3K 0.033 0.098 -10000 0 -0.22 16 16
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.034 0.1 -10000 0 -0.22 17 17
NDNL2 0.034 0.005 -10000 0 -10000 0 0
YWHAE 0.033 0.006 -10000 0 -10000 0 0
PRKCI 0.034 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.002 0.1 -10000 0 -0.27 16 16
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.036 0.1 -10000 0 -0.22 17 17
TRAF6 0.028 0.048 -10000 0 -0.38 2 2
RAC1 0.023 0.016 -10000 0 -10000 0 0
PRKCZ -0.011 0.12 -10000 0 -0.38 14 14
PLG 0 0 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.027 0.089 -10000 0 -0.24 21 21
SQSTM1 0.034 0.004 -10000 0 -10000 0 0
NGFRAP1 0.034 0.003 -10000 0 -10000 0 0
CASP3 -0.001 0.11 0.27 4 -0.26 8 12
E2F1 0.026 0.049 -10000 0 -0.38 2 2
CASP9 0.032 0.013 -10000 0 -10000 0 0
IKK complex -0.007 0.12 -10000 0 -0.37 6 6
NGF (dimer)/TRKA 0.003 0.097 -10000 0 -0.27 14 14
MMP7 -0.066 0.16 -10000 0 -0.38 28 28
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.051 0.1 -10000 0 -0.22 17 17
MMP3 0.003 0.08 -10000 0 -0.38 5 5
APAF-1/Caspase 9 -0.052 0.056 -10000 0 -0.21 3 3
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.064 0.036 -10000 0 -0.23 2 2
fibroblast growth factor receptor signaling pathway 0.063 0.036 -10000 0 -0.23 2 2
LAMA1 -0.036 0.15 -10000 0 -0.38 23 23
PRNP 0.029 0.035 -10000 0 -0.38 1 1
GPC1/SLIT2 -0.013 0.11 -10000 0 -0.28 20 20
SMAD2 -0.018 0.029 0.18 2 -0.21 1 3
GPC1/PrPc/Cu2+ 0.037 0.046 -10000 0 -0.32 2 2
GPC1/Laminin alpha1 -0.008 0.12 -10000 0 -0.27 24 24
TDGF1 -0.009 0.12 -10000 0 -0.38 13 13
CRIPTO/GPC1 0.012 0.1 -10000 0 -0.29 14 14
APP/GPC1 0.047 0.028 -10000 0 -0.27 1 1
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.038 0.067 -10000 0 -0.25 13 13
FLT1 0.028 0.035 -10000 0 -0.38 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.063 0.037 -10000 0 -0.23 2 2
SERPINC1 0.031 0.015 -10000 0 -10000 0 0
FYN -0.035 0.059 -10000 0 -0.23 12 12
FGR -0.042 0.075 -10000 0 -0.26 14 14
positive regulation of MAPKKK cascade -0.029 0.12 0.2 4 -0.33 14 18
SLIT2 -0.038 0.13 -10000 0 -0.38 18 18
GPC1/NRG -0.013 0.11 -10000 0 -0.27 19 19
NRG1 -0.039 0.13 -10000 0 -0.38 18 18
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.023 0.099 -10000 0 -0.24 16 16
LYN -0.042 0.071 -10000 0 -0.25 15 15
mol:Spermine -0.011 0.03 -10000 0 -0.27 2 2
cell growth 0.063 0.036 -10000 0 -0.23 2 2
BMP signaling pathway -0.028 0.048 0.38 2 -10000 0 2
SRC -0.038 0.067 -10000 0 -0.25 13 13
TGFBR1 0.033 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.079 0.16 -10000 0 -0.38 30 30
GPC1 0.029 0.048 -10000 0 -0.38 2 2
TGFBR1 (dimer) 0.033 0.006 -10000 0 -10000 0 0
VEGFA -0.01 0.12 -10000 0 -0.38 14 14
BLK -0.042 0.064 -10000 0 -0.24 14 14
HCK -0.04 0.077 -10000 0 -0.26 14 14
FGF2 0.031 0.034 -10000 0 -0.38 1 1
FGFR1 0.031 0.034 -10000 0 -0.38 1 1
VEGFR1 homodimer 0.028 0.035 -10000 0 -0.38 1 1
TGFBR2 0.034 0.004 -10000 0 -10000 0 0
cell death 0.047 0.028 -10000 0 -0.27 1 1
ATIII/GPC1 0.047 0.016 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.047 0.13 -10000 0 -0.29 30 30
LCK -0.056 0.092 -10000 0 -0.26 22 22
neuron differentiation -0.013 0.11 -10000 0 -0.27 19 19
PrPc/Cu2+ 0.021 0.025 -10000 0 -0.27 1 1
APP 0.033 0.006 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.034 0.004 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.066 0.29 -10000 0 -0.8 17 17
oxygen homeostasis -0.002 0.012 -10000 0 -10000 0 0
TCEB2 0.033 0.006 -10000 0 -10000 0 0
TCEB1 0.033 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.011 0.12 -10000 0 -0.34 5 5
EPO -0.06 0.2 -10000 0 -0.56 11 11
FIH (dimer) 0.011 0.029 -10000 0 -10000 0 0
APEX1 0.014 0.036 -10000 0 -10000 0 0
SERPINE1 -0.05 0.2 -10000 0 -0.54 14 14
FLT1 -0.029 0.22 -10000 0 -0.83 8 8
ADORA2A -0.072 0.19 -10000 0 -0.47 16 16
germ cell development -0.069 0.21 -10000 0 -0.46 22 22
SLC11A2 -0.063 0.2 -10000 0 -0.48 16 16
BHLHE40 -0.063 0.21 -10000 0 -0.5 16 16
HIF1AN 0.011 0.029 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.029 0.15 -10000 0 -0.36 10 10
ETS1 0.04 0.017 -10000 0 -10000 0 0
CITED2 -0.032 0.2 -10000 0 -0.64 13 13
KDR 0.012 0.14 -10000 0 -0.78 4 4
PGK1 -0.061 0.2 -10000 0 -0.48 16 16
SIRT1 0.024 0.016 -10000 0 -10000 0 0
response to hypoxia 0 0.002 -10000 0 -10000 0 0
HIF2A/ARNT -0.036 0.25 -10000 0 -0.54 16 16
EPAS1 -0.023 0.097 -10000 0 -0.31 7 7
SP1 0.031 0.028 -10000 0 -10000 0 0
ABCG2 -0.066 0.21 -10000 0 -0.48 19 19
EFNA1 -0.058 0.2 -10000 0 -0.49 15 15
FXN -0.07 0.19 -10000 0 -0.47 16 16
POU5F1 -0.072 0.22 -10000 0 -0.48 22 22
neuron apoptosis 0.035 0.25 0.53 16 -10000 0 16
EP300 0.031 0.01 -10000 0 -10000 0 0
EGLN3 0.008 0.067 -10000 0 -0.4 3 3
EGLN2 0.018 0.032 -10000 0 -10000 0 0
EGLN1 0.018 0.032 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.064 0.02 -10000 0 -10000 0 0
VHL 0.034 0.005 -10000 0 -10000 0 0
ARNT 0.016 0.035 -10000 0 -10000 0 0
SLC2A1 -0.073 0.2 -10000 0 -0.47 18 18
TWIST1 -0.067 0.2 -10000 0 -0.51 19 19
ELK1 0.038 0.001 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.013 0.16 -10000 0 -0.38 8 8
VEGFA -0.081 0.24 -10000 0 -0.55 21 21
CREBBP 0.034 0.005 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A -0.006 0.007 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.005 0.093 -10000 0 -0.27 14 14
STXBP1 0.03 0.018 -10000 0 -0.064 4 4
ACh/CHRNA1 -0.004 0.084 0.11 4 -0.19 18 22
RAB3GAP2/RIMS1/UNC13B 0.02 0.089 -10000 0 -0.23 14 14
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 -0.017 0.12 -10000 0 -0.38 14 14
mol:ACh 0.022 0.055 0.092 47 -0.1 8 55
RAB3GAP2 0.033 0.007 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.025 0.092 -10000 0 -0.23 8 8
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.004 0.084 0.11 4 -0.19 18 22
UNC13B 0.031 0.011 -10000 0 -10000 0 0
CHRNA1 -0.036 0.13 -10000 0 -0.38 17 17
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.006 0.098 -10000 0 -0.26 16 16
SNAP25 -0.021 0.073 -10000 0 -0.24 14 14
VAMP2 0.005 0.001 -10000 0 -10000 0 0
SYT1 -0.043 0.15 -10000 0 -0.38 22 22
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.017 0.02 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.025 0.092 -10000 0 -0.23 8 8
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.013 0.12 -10000 0 -0.38 15 15
HRAS 0.033 0.008 -10000 0 -10000 0 0
EGFR -0.066 0.15 -10000 0 -0.38 28 28
AKT 0.073 0.14 0.24 36 -0.23 9 45
FOXO3 0.028 0.035 -10000 0 -0.38 1 1
AKT1 0.032 0.009 -10000 0 -10000 0 0
FOXO1 0.031 0.01 -10000 0 -10000 0 0
AKT3 0.033 0.007 -10000 0 -10000 0 0
FOXO4 0.031 0.034 -10000 0 -0.38 1 1
MET -0.026 0.12 -10000 0 -0.38 14 14
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
PIK3CB 0.031 0.034 -10000 0 -0.38 1 1
NRAS 0.034 0.005 -10000 0 -10000 0 0
PIK3CG 0.003 0.088 -10000 0 -0.38 7 7
PIK3R3 0.033 0.006 -10000 0 -10000 0 0
PIK3R2 0.033 0.007 -10000 0 -10000 0 0
NF1 0.031 0.034 -10000 0 -0.38 1 1
RAS -0.013 0.096 -10000 0 -0.24 16 16
ERBB2 0.023 0.068 -10000 0 -0.38 4 4
proliferation/survival/translation -0.027 0.067 0.21 4 -0.21 3 7
PI3K 0.014 0.11 0.21 16 -0.2 15 31
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
KRAS 0.032 0.008 -10000 0 -10000 0 0
FOXO 0.09 0.11 0.23 37 -10000 0 37
AKT2 0.033 0.007 -10000 0 -10000 0 0
PTEN 0.023 0.016 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0 0.081 -10000 0 -0.24 12 12
NFATC2 -0.038 0.18 -10000 0 -0.52 8 8
NFATC3 0.022 0.073 -10000 0 -0.26 4 4
CD40LG -0.091 0.23 -10000 0 -0.86 7 7
ITCH -0.018 0.081 -10000 0 -0.21 20 20
CBLB -0.018 0.083 -10000 0 -0.21 21 21
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.19 0.32 -10000 0 -0.77 28 28
JUNB 0.027 0.038 -10000 0 -0.38 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.018 0.1 -10000 0 -0.24 25 25
T cell anergy -0.058 0.13 -10000 0 -0.36 22 22
TLE4 -0.028 0.12 -10000 0 -0.42 5 5
Jun/NFAT1-c-4/p21SNFT -0.037 0.22 -10000 0 -0.97 5 5
AP-1/NFAT1-c-4 -0.069 0.28 -10000 0 -1.1 6 6
IKZF1 -0.019 0.12 -10000 0 -0.6 4 4
T-helper 2 cell differentiation -0.13 0.22 -10000 0 -0.51 22 22
AP-1/NFAT1 -0.016 0.14 -10000 0 -0.4 6 6
CALM1 -0.001 0.07 -10000 0 -0.16 22 22
EGR2 -0.062 0.26 -10000 0 -1.2 6 6
EGR3 -0.049 0.24 -10000 0 -1.2 5 5
NFAT1/FOXP3 -0.029 0.16 -10000 0 -0.48 8 8
EGR1 0.011 0.078 -10000 0 -0.38 5 5
JUN 0.014 0.036 -10000 0 -10000 0 0
EGR4 -0.02 0.12 -10000 0 -0.36 14 14
mol:Ca2+ -0.021 0.055 -10000 0 -0.14 25 25
GBP3 -0.083 0.23 -10000 0 -0.65 19 19
FOSL1 0.011 0.084 -10000 0 -0.38 6 6
NFAT1-c-4/MAF/IRF4 -0.019 0.22 -10000 0 -0.93 5 5
DGKA -0.027 0.12 -10000 0 -0.45 3 3
CREM 0.024 0.016 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.027 0.22 -10000 0 -1 5 5
CTLA4 -0.06 0.16 -10000 0 -0.51 13 13
NFAT1-c-4 (dimer)/EGR1 -0.036 0.24 -10000 0 -1.1 5 5
NFAT1-c-4 (dimer)/EGR4 -0.056 0.22 -10000 0 -0.98 5 5
FOS 0.001 0.068 -10000 0 -0.39 3 3
IFNG -0.061 0.16 -10000 0 -0.7 3 3
T cell activation -0.025 0.14 -10000 0 -0.5 5 5
MAF 0.033 0.006 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.023 0.14 0.67 5 -10000 0 5
TNF -0.1 0.23 -10000 0 -0.77 10 10
FASLG -0.1 0.3 -10000 0 -1.3 7 7
TBX21 0.008 0.086 -10000 0 -0.38 6 6
BATF3 0.017 0.076 -10000 0 -0.38 5 5
PRKCQ 0.01 0.069 -10000 0 -0.38 4 4
PTPN1 -0.031 0.12 -10000 0 -0.42 5 5
NFAT1-c-4/ICER1 -0.035 0.21 -10000 0 -0.96 5 5
GATA3 0 0.072 -10000 0 -0.38 4 4
T-helper 1 cell differentiation -0.06 0.16 -10000 0 -0.69 3 3
IL2RA -0.16 0.31 -10000 0 -0.84 20 20
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.029 0.12 -10000 0 -0.41 5 5
E2F1 0.019 0.053 -10000 0 -0.38 2 2
PPARG 0.031 0.035 -10000 0 -0.38 1 1
SLC3A2 -0.03 0.12 -10000 0 -0.44 4 4
IRF4 0.022 0.061 -10000 0 -0.38 3 3
PTGS2 -0.093 0.25 -10000 0 -0.84 10 10
CSF2 -0.1 0.21 -10000 0 -0.85 7 7
JunB/Fra1/NFAT1-c-4 -0.026 0.23 -10000 0 -0.94 6 6
IL4 -0.14 0.23 -10000 0 -0.52 23 23
IL5 -0.088 0.23 -10000 0 -0.92 6 6
IL2 -0.025 0.14 -10000 0 -0.51 5 5
IL3 -0.013 0.069 -10000 0 -0.48 2 2
RNF128 -0.07 0.18 -10000 0 -0.47 25 25
NFATC1 -0.023 0.14 -10000 0 -0.67 5 5
CDK4 0.035 0.11 0.55 2 -10000 0 2
PTPRK -0.024 0.11 -10000 0 -0.41 4 4
IL8 -0.12 0.26 -10000 0 -0.81 12 12
POU2F1 0.028 0.048 -10000 0 -0.38 2 2
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.007 0.063 0.2 1 -0.26 2 3
adherens junction organization -0.019 0.087 -10000 0 -0.22 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.006 0.12 0.21 3 -0.27 8 11
FMN1 -0.022 0.091 -10000 0 -0.22 21 21
mol:IP3 -0.005 0.056 -10000 0 -0.22 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.01 0.093 -10000 0 -0.22 21 21
CTNNB1 0.035 0.005 -10000 0 -10000 0 0
AKT1 -0.002 0.07 -10000 0 -0.25 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.022 0.14 -10000 0 -0.32 23 23
CTNND1 0.035 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.012 0.081 -10000 0 -0.21 19 19
VASP -0.017 0.087 -10000 0 -0.22 21 21
ZYX -0.016 0.079 -10000 0 -0.22 18 18
JUB -0.013 0.088 -10000 0 -0.21 21 21
EGFR(dimer) -0.04 0.1 -10000 0 -0.31 12 12
E-cadherin/beta catenin-gamma catenin 0.015 0.1 -10000 0 -0.22 23 23
mol:PI-3-4-5-P3 0.027 0.087 -10000 0 -0.26 1 1
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.027 0.088 -10000 0 -0.26 1 1
FYN -0.016 0.063 -10000 0 -0.23 3 3
mol:Ca2+ -0.005 0.056 -10000 0 -0.22 2 2
JUP 0.035 0.011 -10000 0 -10000 0 0
PIK3R1 0.031 0.036 -10000 0 -0.38 1 1
mol:DAG -0.005 0.056 -10000 0 -0.22 2 2
CDH1 -0.037 0.15 -10000 0 -0.38 23 23
RhoA/GDP 0.039 0.14 0.22 1 -0.27 8 9
establishment of polarity of embryonic epithelium -0.016 0.085 -10000 0 -0.21 21 21
SRC 0.029 0.035 -10000 0 -0.38 1 1
RAC1 0.023 0.016 -10000 0 -10000 0 0
RHOA 0.034 0.004 -10000 0 -10000 0 0
EGFR -0.066 0.15 -10000 0 -0.38 28 28
CASR -0.013 0.054 0.15 1 -0.2 2 3
RhoA/GTP 0.01 0.063 -10000 0 -0.21 2 2
AKT2 -0.002 0.069 -10000 0 -0.24 1 1
actin cable formation -0.028 0.086 -10000 0 -0.25 4 4
apoptosis 0.001 0.07 0.33 1 -0.21 1 2
CTNNA1 0.035 0.005 -10000 0 -10000 0 0
mol:GDP -0.04 0.083 -10000 0 -0.27 9 9
PIP5K1A -0.012 0.082 -10000 0 -0.21 19 19
PLCG1 -0.005 0.057 -10000 0 -0.22 2 2
Rac1/GTP -0.037 0.098 -10000 0 -0.33 8 8
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.032 0.009 -10000 0 -10000 0 0
VLDLR 0.023 0.05 -10000 0 -0.38 2 2
LRPAP1 0.034 0.003 -10000 0 -10000 0 0
NUDC 0.033 0.006 -10000 0 -10000 0 0
RELN/LRP8 0.001 0.089 -10000 0 -0.23 15 15
CaM/Ca2+ 0.023 0.007 -10000 0 -10000 0 0
KATNA1 0.031 0.01 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.005 0.11 0.18 34 -0.21 15 49
IQGAP1/CaM 0.046 0.015 -10000 0 -10000 0 0
DAB1 -0.041 0.15 -10000 0 -0.38 23 23
IQGAP1 0.034 0.005 -10000 0 -10000 0 0
PLA2G7 -0.01 0.12 -10000 0 -0.38 13 13
CALM1 0.032 0.009 -10000 0 -10000 0 0
DYNLT1 0.029 0.017 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.049 0.01 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.031 0.034 -10000 0 -0.38 1 1
CDK5R1 0.012 0.089 -10000 0 -0.38 7 7
LIS1/Poliovirus Protein 3A -0.011 0.004 -10000 0 -10000 0 0
CDK5R2 -0.024 0.13 -10000 0 -0.38 17 17
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.036 0.13 -10000 0 -0.28 26 26
YWHAE 0.033 0.006 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.039 0.17 0.32 29 -0.4 6 35
MAP1B 0.005 0.021 -10000 0 -0.24 1 1
RAC1 0.01 0.008 -10000 0 -10000 0 0
p35/CDK5 -0.04 0.075 0.18 2 -0.23 16 18
RELN -0.033 0.12 -10000 0 -0.38 15 15
PAFAH/LIS1 0.008 0.068 -10000 0 -0.23 10 10
LIS1/CLIP170 0.03 0.024 -10000 0 -0.23 1 1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.019 0.09 -10000 0 -0.33 6 6
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.037 0.13 -10000 0 -0.39 12 12
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.013 0.17 0.31 25 -0.37 8 33
LIS1/IQGAP1 0.032 0.011 -10000 0 -10000 0 0
RHOA 0.014 0.005 -10000 0 -10000 0 0
PAFAH1B1 -0.014 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.033 0.008 -10000 0 -10000 0 0
PAFAH1B2 0.034 0.003 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.028 0.025 -10000 0 -0.17 1 1
NDEL1/Katanin 60/Dynein heavy chain 0.027 0.16 0.32 21 -0.37 6 27
LRP8 0.033 0.006 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.02 0.16 0.32 22 -0.38 6 28
P39/CDK5 -0.045 0.074 0.18 1 -0.22 19 20
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.032 0.011 -10000 0 -10000 0 0
CDK5 -0.033 0.061 0.18 2 -0.2 14 16
PPP2R5D 0.034 0.005 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.026 0.021 -10000 0 -0.2 1 1
CSNK2A1 0.032 0.009 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.022 0.11 -10000 0 -0.23 24 24
RELN/VLDLR 0.006 0.096 -10000 0 -0.22 16 16
CDC42 0.014 0.005 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 0.028 0.02 -10000 0 -10000 0 0
GNB1/GNG2 -0.033 0.064 -10000 0 -0.19 19 19
AKT1 -0.014 0.12 0.29 2 -0.29 11 13
EGF 0.006 0.1 -10000 0 -0.38 9 9
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.01 0.072 0.31 5 -0.29 2 7
mol:Ca2+ -0.015 0.13 0.31 2 -0.32 13 15
LYN -0.009 0.079 0.31 6 -0.29 2 8
RhoA/GTP -0.009 0.05 -10000 0 -0.14 8 8
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.033 0.14 0.31 2 -0.35 19 21
GNG2 0.031 0.012 -10000 0 -10000 0 0
ARRB2 0.033 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.009 0.097 -10000 0 -0.34 10 10
G beta5/gamma2 -0.035 0.087 -10000 0 -0.24 18 18
PRKCH -0.024 0.15 0.31 2 -0.37 14 16
DNM1 0.021 0.061 -10000 0 -0.38 3 3
TXA2/TP beta/beta Arrestin3 0.01 0.024 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.022 0.027 -10000 0 -10000 0 0
G12 family/GTP -0.031 0.11 -10000 0 -0.31 11 11
ADRBK1 0.034 0.003 -10000 0 -10000 0 0
ADRBK2 0.032 0.009 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.044 0.011 -10000 0 -10000 0 0
mol:GDP 0.004 0.1 0.47 2 -0.32 2 4
mol:NADP 0.018 0.05 -10000 0 -0.38 2 2
RAB11A 0.033 0.006 -10000 0 -10000 0 0
PRKG1 0.014 0.06 -10000 0 -0.38 3 3
mol:IP3 -0.025 0.16 0.33 2 -0.41 13 15
cell morphogenesis 0.043 0.011 -10000 0 -10000 0 0
PLCB2 -0.043 0.21 0.38 1 -0.56 13 14
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.01 0.078 0.31 6 -0.29 2 8
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.02 0.058 0.29 2 -0.26 3 5
RHOA 0.034 0.004 -10000 0 -10000 0 0
PTGIR 0.025 0.05 -10000 0 -0.38 2 2
PRKCB1 -0.027 0.16 0.31 2 -0.38 18 20
GNAQ 0.033 0.007 -10000 0 -10000 0 0
mol:L-citrulline 0.018 0.05 -10000 0 -0.38 2 2
TXA2/TXA2-R family -0.051 0.21 0.36 2 -0.53 19 21
LCK -0.019 0.089 0.31 6 -0.24 5 11
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.019 0.056 -10000 0 -0.34 2 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.005 0.077 -10000 0 -0.4 4 4
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.022 0.057 -10000 0 -0.34 2 2
MAPK14 -0.021 0.099 0.25 2 -0.23 19 21
TGM2/GTP -0.03 0.17 -10000 0 -0.44 13 13
MAPK11 -0.023 0.097 0.25 2 -0.23 19 21
ARHGEF1 -0.018 0.063 -10000 0 -0.18 9 9
GNAI2 0.034 0.005 -10000 0 -10000 0 0
JNK cascade -0.032 0.16 0.34 2 -0.39 19 21
RAB11/GDP 0.033 0.008 -10000 0 -10000 0 0
ICAM1 -0.023 0.13 0.27 2 -0.3 19 21
cAMP biosynthetic process -0.026 0.15 0.33 2 -0.37 13 15
Gq family/GTP/EBP50 0.003 0.064 0.25 1 -0.2 11 12
actin cytoskeleton reorganization 0.043 0.011 -10000 0 -10000 0 0
SRC -0.018 0.055 0.29 2 -0.29 2 4
GNB5 0.034 0.005 -10000 0 -10000 0 0
GNB1 0.033 0.008 -10000 0 -10000 0 0
EGF/EGFR 0.002 0.11 0.33 7 -0.23 4 11
VCAM1 -0.027 0.14 0.28 2 -0.33 20 22
TP beta/Gq family/GDP/G beta5/gamma2 -0.009 0.097 -10000 0 -0.34 10 10
platelet activation -0.023 0.13 0.34 2 -0.3 18 20
PGI2/IP 0.019 0.035 -10000 0 -0.27 2 2
PRKACA 0.01 0.041 -10000 0 -0.31 2 2
Gq family/GDP/G beta5/gamma2 -0.007 0.09 -10000 0 -0.31 10 10
TXA2/TP beta/beta Arrestin2 -0.002 0.073 -10000 0 -0.47 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.005 0.05 -10000 0 -0.38 2 2
mol:DAG -0.03 0.17 0.34 2 -0.43 17 19
EGFR -0.066 0.15 -10000 0 -0.38 28 28
TXA2/TP alpha -0.039 0.19 0.38 2 -0.51 13 15
Gq family/GTP 0 0.043 -10000 0 -0.16 9 9
YES1 -0.008 0.077 0.31 6 -0.28 2 8
GNAI2/GTP 0.015 0.052 -10000 0 -0.32 2 2
PGD2/DP 0.017 0.018 -10000 0 -10000 0 0
SLC9A3R1 0.034 0.003 -10000 0 -10000 0 0
FYN -0.007 0.077 0.31 6 -0.27 2 8
mol:NO 0.018 0.05 -10000 0 -0.38 2 2
GNA15 0.015 0.082 -10000 0 -0.38 6 6
PGK/cGMP 0.016 0.051 -10000 0 -0.22 5 5
RhoA/GDP 0.033 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.04 0.061 -10000 0 -0.33 2 2
NOS3 0.018 0.05 -10000 0 -0.38 2 2
RAC1 0.023 0.016 -10000 0 -10000 0 0
PRKCA -0.025 0.15 0.31 2 -0.37 16 18
PRKCB -0.028 0.15 0.31 2 -0.37 18 20
PRKCE -0.025 0.15 0.31 2 -0.36 18 20
PRKCD -0.029 0.16 0.31 2 -0.38 19 21
PRKCG -0.035 0.16 0.35 2 -0.39 19 21
muscle contraction -0.048 0.19 0.34 2 -0.49 19 21
PRKCZ -0.038 0.15 0.31 2 -0.35 19 21
ARR3 0.027 0.006 -10000 0 -10000 0 0
TXA2/TP beta 0.028 0.057 -10000 0 -0.35 2 2
PRKCQ -0.041 0.14 0.29 2 -0.36 19 21
MAPKKK cascade -0.04 0.18 0.34 2 -0.47 17 19
SELE -0.028 0.14 0.28 2 -0.34 19 21
TP beta/GNAI2/GDP/G beta/gamma 0.046 0.059 -10000 0 -0.32 2 2
ROCK1 0.033 0.007 -10000 0 -10000 0 0
GNA14 0.022 0.053 -10000 0 -0.38 2 2
chemotaxis -0.063 0.23 0.38 1 -0.6 20 21
GNA12 0.02 0.037 -10000 0 -0.38 1 1
GNA13 0.034 0.003 -10000 0 -10000 0 0
GNA11 0.027 0.048 -10000 0 -0.38 2 2
Rac1/GTP 0.017 0.012 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.033 0.006 -10000 0 -10000 0 0
LAT2 -0.02 0.081 -10000 0 -0.36 4 4
AP1 -0.056 0.2 -10000 0 -0.54 11 11
mol:PIP3 -0.001 0.14 0.28 7 -0.52 4 11
IKBKB 0.002 0.092 0.25 6 -0.25 4 10
AKT1 -0.054 0.096 0.32 4 -0.26 1 5
IKBKG 0.003 0.092 0.22 6 -0.25 5 11
MS4A2 0.011 0.031 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
MAP3K1 -0.025 0.12 0.28 2 -0.54 5 7
mol:Ca2+ 0.004 0.12 0.26 7 -0.38 4 11
LYN 0.028 0.049 -10000 0 -0.39 2 2
CBLB -0.026 0.096 -10000 0 -0.4 4 4
SHC1 0.031 0.015 -10000 0 -10000 0 0
RasGAP/p62DOK 0.056 0.043 -10000 0 -0.21 3 3
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.022 0.068 -10000 0 -0.38 4 4
PLD2 -0.05 0.094 0.38 3 -0.2 26 29
PTPN13 -0.011 0.12 -10000 0 -0.59 4 4
PTPN11 0.023 0.027 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.026 0.095 0.38 2 -0.33 3 5
SYK 0.018 0.077 -10000 0 -0.39 5 5
GRB2 0.034 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.005 0.13 0.23 1 -0.5 5 6
LAT -0.03 0.099 -10000 0 -0.39 5 5
PAK2 -0.027 0.13 0.21 2 -0.61 5 7
NFATC2 -0.053 0.15 -10000 0 -0.48 15 15
HRAS -0.026 0.15 0.22 2 -0.68 5 7
GAB2 0.029 0.048 -10000 0 -0.38 2 2
PLA2G1B 0.036 0.044 -10000 0 -10000 0 0
Fc epsilon R1 -0.01 0.12 -10000 0 -0.25 26 26
Antigen/IgE/Fc epsilon R1 -0.006 0.11 -10000 0 -0.23 26 26
mol:GDP -0.021 0.16 0.21 1 -0.66 6 7
JUN 0.033 0.006 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.029 0.036 -10000 0 -0.39 1 1
FOS 0.018 0.062 -10000 0 -0.38 3 3
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.021 0.1 -10000 0 -0.42 4 4
CHUK 0.001 0.086 0.22 6 -0.24 5 11
KLRG1 -0.031 0.096 -10000 0 -0.3 7 7
VAV1 -0.03 0.11 -10000 0 -0.48 5 5
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.027 0.096 -10000 0 -0.4 4 4
negative regulation of mast cell degranulation -0.016 0.12 0.21 2 -0.41 6 8
BTK -0.024 0.16 -10000 0 -0.78 5 5
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.046 0.12 -10000 0 -0.27 24 24
GAB2/PI3K/SHP2 -0.068 0.07 -10000 0 -0.21 27 27
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.026 0.098 -10000 0 -0.24 13 13
RAF1 0.038 0.022 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.012 0.14 -10000 0 -0.24 36 36
FCER1G 0.03 0.037 -10000 0 -0.38 1 1
FCER1A -0.051 0.16 -10000 0 -0.39 25 25
Antigen/IgE/Fc epsilon R1/Fyn 0.005 0.11 -10000 0 -0.21 26 26
MAPK3 0.037 0.04 -10000 0 -10000 0 0
MAPK1 0.03 0.052 -10000 0 -10000 0 0
NFKB1 0.034 0.003 -10000 0 -10000 0 0
MAPK8 -0.15 0.3 -10000 0 -0.57 46 46
DUSP1 0.023 0.061 -10000 0 -0.38 3 3
NF-kappa-B/RelA 0.011 0.06 0.14 5 -0.17 3 8
actin cytoskeleton reorganization -0.007 0.13 -10000 0 -0.61 4 4
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.004 0.14 -10000 0 -0.55 6 6
FER -0.03 0.1 -10000 0 -0.45 4 4
RELA 0.034 0.003 -10000 0 -10000 0 0
ITK -0.019 0.085 -10000 0 -0.33 9 9
SOS1 0.034 0 -10000 0 -10000 0 0
PLCG1 -0.009 0.16 0.27 4 -0.68 5 9
cytokine secretion 0.003 0.04 -10000 0 -0.13 2 2
SPHK1 -0.03 0.1 -10000 0 -0.41 5 5
PTK2 -0.009 0.13 -10000 0 -0.64 4 4
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.002 0.13 0.25 3 -0.56 4 7
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.003 0.14 0.29 5 -0.53 4 9
MAP2K2 0.035 0.049 -10000 0 -10000 0 0
MAP2K1 0.028 0.028 -10000 0 -10000 0 0
MAP2K7 0.03 0.035 -10000 0 -0.38 1 1
KLRG1/SHP2 -0.018 0.1 0.18 3 -0.44 3 6
MAP2K4 0.025 0.13 -10000 0 -0.87 3 3
Fc epsilon R1/FcgammaRIIB -0.027 0.14 -10000 0 -0.25 35 35
mol:Choline -0.05 0.093 0.38 3 -0.2 26 29
SHC/Grb2/SOS1 0.024 0.12 -10000 0 -0.43 3 3
FYN 0.031 0.01 -10000 0 -10000 0 0
DOK1 0.034 0 -10000 0 -10000 0 0
PXN -0.01 0.13 0.36 1 -0.59 4 5
HCLS1 -0.026 0.096 -10000 0 -0.4 4 4
PRKCB -0.001 0.11 0.25 6 -0.32 6 12
FCGR2B -0.018 0.12 -10000 0 -0.38 13 13
IGHE -0.002 0.004 -10000 0 -10000 0 0
KLRG1/SHIP -0.017 0.12 0.22 2 -0.42 6 8
LCP2 0.031 0.035 -10000 0 -0.38 1 1
PLA2G4A -0.025 0.094 -10000 0 -0.45 3 3
RASA1 0.033 0.006 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.05 0.093 0.38 3 -0.2 26 29
IKK complex 0.005 0.079 0.22 6 -0.21 2 8
WIPF1 0.034 0.008 -10000 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.026 0.098 -9999 0 -0.31 8 8
alphaM/beta2 Integrin/GPIbA 0.023 0.099 -9999 0 -0.3 9 9
alphaM/beta2 Integrin/proMMP-9 -0.013 0.13 -9999 0 -0.28 22 22
PLAUR 0.026 0.039 -9999 0 -0.38 1 1
HMGB1 0.017 0.033 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.032 0.084 -9999 0 -0.36 4 4
AGER 0.005 0.086 -9999 0 -0.42 5 5
RAP1A 0.034 0.005 -9999 0 -10000 0 0
SELPLG 0.023 0.068 -9999 0 -0.38 4 4
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.006 0.15 -9999 0 -0.3 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.034 0.14 -9999 0 -0.38 20 20
CYR61 0.017 0.07 -9999 0 -0.38 4 4
TLN1 0.03 0.011 -9999 0 -10000 0 0
Rap1/GTP -0.02 0.12 -9999 0 -0.36 8 8
RHOA 0.034 0.004 -9999 0 -10000 0 0
P-selectin oligomer 0.02 0.029 -9999 0 -10000 0 0
MYH2 -0.054 0.13 -9999 0 -0.41 10 10
MST1R 0.007 0.1 -9999 0 -0.38 9 9
leukocyte activation during inflammatory response 0.006 0.099 -9999 0 -0.24 14 14
APOB -0.005 0.1 -9999 0 -0.38 9 9
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.025 0.051 -9999 0 -0.38 2 2
JAM3 0.034 0.004 -9999 0 -10000 0 0
GP1BA 0.022 0.06 -9999 0 -0.38 3 3
alphaM/beta2 Integrin/CTGF 0.027 0.088 -9999 0 -0.29 7 7
alphaM/beta2 Integrin -0.053 0.13 -9999 0 -0.42 11 11
JAM3 homodimer 0.034 0.004 -9999 0 -10000 0 0
ICAM2 0.034 0.003 -9999 0 -10000 0 0
ICAM1 0.014 0.071 -9999 0 -0.38 4 4
phagocytosis triggered by activation of immune response cell surface activating receptor -0.052 0.13 -9999 0 -0.41 11 11
cell adhesion 0.022 0.099 -9999 0 -0.3 9 9
NFKB1 -0.081 0.19 -9999 0 -0.48 24 24
THY1 0.031 0.034 -9999 0 -0.38 1 1
RhoA/GDP 0.025 0.003 -9999 0 -10000 0 0
Lipoprotein(a) 0.009 0.067 -9999 0 -0.23 9 9
alphaM/beta2 Integrin/LRP/tPA 0.043 0.092 -9999 0 -0.26 8 8
IL6 -0.095 0.18 -9999 0 -0.47 22 22
ITGB2 0.005 0.086 -9999 0 -0.42 5 5
elevation of cytosolic calcium ion concentration 0.017 0.096 -9999 0 -0.28 9 9
alphaM/beta2 Integrin/JAM2/JAM3 0.049 0.093 -9999 0 -0.31 6 6
JAM2 0.033 0.006 -9999 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 0.026 0.13 -9999 0 -0.27 19 19
alphaM/beta2 Integrin/uPA/Plg 0.008 0.09 -9999 0 -0.27 10 10
RhoA/GTP -0.056 0.14 -9999 0 -0.43 10 10
positive regulation of phagocytosis -0.022 0.12 -9999 0 -0.41 8 8
Ron/MSP 0.019 0.095 -9999 0 -0.29 12 12
alphaM/beta2 Integrin/uPAR/uPA 0.018 0.097 -9999 0 -0.28 9 9
alphaM/beta2 Integrin/uPAR 0.029 0.087 -9999 0 -0.3 6 6
PLAU 0.01 0.068 -9999 0 -0.38 4 4
PLAT 0.027 0.049 -9999 0 -0.38 2 2
actin filament polymerization -0.052 0.12 -9999 0 -0.39 10 10
MST1 0.02 0.069 -9999 0 -0.38 4 4
alphaM/beta2 Integrin/lipoprotein(a) 0.012 0.1 -9999 0 -0.25 14 14
TNF -0.12 0.22 -9999 0 -0.57 23 23
RAP1B 0.031 0.01 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.008 0.098 -9999 0 -0.29 10 10
fibrinolysis 0.007 0.089 -9999 0 -0.26 10 10
HCK 0.022 0.06 -9999 0 -0.38 3 3
dendritic cell antigen processing and presentation -0.052 0.13 -9999 0 -0.41 11 11
VTN 0.018 0.076 -9999 0 -0.38 5 5
alphaM/beta2 Integrin/CYR61 0.018 0.11 -9999 0 -0.33 9 9
LPA 0.023 0.014 -9999 0 -10000 0 0
LRP1 0.029 0.035 -9999 0 -0.38 1 1
cell migration -0.022 0.12 -9999 0 -0.27 23 23
FN1 0.033 0.011 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 0.031 0.096 -9999 0 -0.33 7 7
MPO -0.015 0.12 -9999 0 -0.38 12 12
KNG1 0 0 -9999 0 -10000 0 0
RAP1/GDP 0.042 0.014 -9999 0 -10000 0 0
ROCK1 -0.055 0.13 -9999 0 -0.47 7 7
ELA2 0 0 -9999 0 -10000 0 0
PLG 0 0 -9999 0 -10000 0 0
CTGF 0.026 0.038 -9999 0 -0.38 1 1
alphaM/beta2 Integrin/Hck 0.027 0.11 -9999 0 -0.52 4 4
ITGAM 0.008 0.074 -9999 0 -0.39 4 4
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.037 0.1 -9999 0 -0.32 7 7
HP -0.064 0.16 -9999 0 -0.38 27 27
leukocyte adhesion -0.002 0.14 -9999 0 -0.32 19 19
SELP 0.02 0.029 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 -0.011 0.046 0.2 3 -0.19 4 7
RFC1 -0.015 0.037 0.16 1 -0.19 4 5
PRKDC -0.015 0.037 0.16 1 -0.19 4 5
RIPK1 0.035 0.007 -10000 0 -10000 0 0
CASP7 -0.18 0.3 -10000 0 -0.61 47 47
FASLG/FAS/FADD/FAF1 -0.035 0.078 0.18 1 -0.27 7 8
MAP2K4 -0.092 0.17 0.21 1 -0.42 21 22
mol:ceramide -0.028 0.095 -10000 0 -0.27 10 10
GSN -0.01 0.05 0.2 4 -0.19 4 8
FASLG/FAS/FADD/FAF1/Caspase 8 -0.036 0.087 -10000 0 -0.32 6 6
FAS 0.013 0.052 -10000 0 -0.39 2 2
BID -0.022 0.033 0.25 2 -10000 0 2
MAP3K1 -0.13 0.21 0.3 1 -0.42 48 49
MAP3K7 0.031 0.01 -10000 0 -10000 0 0
RB1 -0.012 0.043 0.19 2 -0.2 4 6
CFLAR 0.035 0.007 -10000 0 -10000 0 0
HGF/MET -0.007 0.1 -10000 0 -0.27 17 17
ARHGDIB -0.01 0.044 0.2 3 -0.19 3 6
FADD 0.027 0.021 -10000 0 -10000 0 0
actin filament polymerization 0.01 0.049 0.19 4 -0.2 4 8
NFKB1 0.002 0.06 -10000 0 -10000 0 0
MAPK8 -0.11 0.21 -10000 0 -0.59 18 18
DFFA -0.013 0.042 0.19 2 -0.19 4 6
DNA fragmentation during apoptosis -0.011 0.046 0.2 3 -0.19 4 7
FAS/FADD/MET -0.005 0.09 -10000 0 -0.25 14 14
CFLAR/RIP1 0.052 0.01 -10000 0 -10000 0 0
FAIM3 0.027 0.049 -10000 0 -0.38 2 2
FAF1 0.017 0.062 -10000 0 -0.38 3 3
PARP1 -0.013 0.042 0.19 2 -0.19 4 6
DFFB -0.011 0.046 0.2 3 -0.19 4 7
CHUK 0.004 0.039 -10000 0 -10000 0 0
FASLG 0.019 0.043 -10000 0 -0.38 1 1
FAS/FADD 0.024 0.047 -10000 0 -0.28 2 2
HGF -0.006 0.099 -10000 0 -0.38 9 9
LMNA -0.019 0.037 -10000 0 -0.2 1 1
CASP6 -0.016 0.041 -10000 0 -0.19 5 5
CASP10 0.027 0.021 -10000 0 -10000 0 0
CASP3 -0.009 0.038 0.2 1 -0.21 4 5
PTPN13 0.034 0.003 -10000 0 -10000 0 0
CASP8 -0.023 0.041 0.32 2 -10000 0 2
IL6 -0.15 0.4 -10000 0 -1.2 18 18
MET -0.026 0.12 -10000 0 -0.38 14 14
ICAD/CAD -0.01 0.05 0.3 2 -0.18 4 6
FASLG/FAS/FADD/FAF1/Caspase 10 -0.028 0.096 -10000 0 -0.28 10 10
activation of caspase activity by cytochrome c -0.022 0.033 0.25 2 -10000 0 2
PAK2 -0.013 0.042 0.19 2 -0.19 4 6
BCL2 0.033 0.007 -10000 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 0.017 0.078 -10000 0 -0.23 13 13
cell-cell adhesion 0.033 0.046 0.18 11 -10000 0 11
Ephrin B/EPHB2/RasGAP 0.083 0.055 -10000 0 -0.2 3 3
ITSN1 0.033 0.006 -10000 0 -10000 0 0
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
SHC1 0.031 0.015 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.037 0.045 -10000 0 -0.23 4 4
Ephrin B1/EPHB1 0.005 0.086 -10000 0 -0.23 16 16
HRAS/GDP 0.009 0.069 -10000 0 -0.25 2 2
Ephrin B/EPHB1/GRB7 0.044 0.099 -10000 0 -0.21 17 17
Endophilin/SYNJ1 -0.021 0.038 0.17 3 -0.19 3 6
KRAS 0.032 0.008 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.045 0.1 -10000 0 -0.22 16 16
endothelial cell migration 0.045 0.042 -10000 0 -0.2 1 1
GRB2 0.034 0.005 -10000 0 -10000 0 0
GRB7 0.021 0.029 -10000 0 -10000 0 0
PAK1 -0.024 0.048 0.21 4 -10000 0 4
HRAS 0.033 0.008 -10000 0 -10000 0 0
RRAS -0.018 0.048 0.22 4 -0.2 3 7
DNM1 0.021 0.061 -10000 0 -0.38 3 3
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.039 0.064 0.17 2 -0.2 16 18
lamellipodium assembly -0.033 0.046 -10000 0 -0.18 11 11
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.003 0.079 -10000 0 -0.25 4 4
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
EPHB2 0.028 0.048 -10000 0 -0.38 2 2
EPHB3 0.022 0.068 -10000 0 -0.38 4 4
EPHB1 -0.024 0.13 -10000 0 -0.38 16 16
EPHB4 0.021 0.037 -10000 0 -0.38 1 1
mol:GDP -0.011 0.055 0.24 1 -0.24 2 3
Ephrin B/EPHB2 0.065 0.049 -10000 0 -0.2 3 3
Ephrin B/EPHB3 0.06 0.058 -10000 0 -0.2 5 5
JNK cascade -0.039 0.073 0.22 4 -0.21 15 19
Ephrin B/EPHB1 0.027 0.093 -10000 0 -0.2 17 17
RAP1/GDP 0.05 0.1 0.22 22 -0.25 1 23
EFNB2 0.032 0.011 -10000 0 -10000 0 0
EFNB3 0.029 0.036 -10000 0 -0.38 1 1
EFNB1 0.033 0.009 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.017 0.092 -10000 0 -0.22 16 16
RAP1B 0.031 0.01 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.042 0.085 -10000 0 -0.22 4 4
Rap1/GTP -0.005 0.076 -10000 0 -0.2 15 15
axon guidance 0.016 0.078 -10000 0 -0.23 13 13
MAPK3 -0.01 0.072 0.19 2 -0.34 1 3
MAPK1 -0.011 0.069 0.19 1 -0.34 1 2
Rac1/GDP 0.003 0.07 0.24 4 -10000 0 4
actin cytoskeleton reorganization -0.033 0.044 -10000 0 -0.2 2 2
CDC42/GDP 0.049 0.11 0.22 29 -0.25 1 30
PI3K 0.049 0.045 -10000 0 -0.2 1 1
EFNA5 -0.002 0.11 -10000 0 -0.38 11 11
Ephrin B2/EPHB4 0.029 0.03 -10000 0 -0.23 1 1
Ephrin B/EPHB2/Intersectin/N-WASP 0.015 0.039 -10000 0 -0.2 2 2
CDC42 0.034 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.052 0.052 -10000 0 -0.2 15 15
PTK2 0.019 0.12 0.56 7 -10000 0 7
MAP4K4 -0.039 0.074 0.22 4 -0.22 15 19
SRC 0.029 0.035 -10000 0 -0.38 1 1
KALRN 0.033 0.012 -10000 0 -10000 0 0
Intersectin/N-WASP 0.035 0.024 -10000 0 -10000 0 0
neuron projection morphogenesis 0.064 0.17 0.31 42 -10000 0 42
MAP2K1 -0.006 0.073 -10000 0 -0.26 3 3
WASL 0.024 0.016 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.033 0.1 -10000 0 -0.22 16 16
cell migration -0.012 0.09 -10000 0 -0.33 2 2
NRAS 0.034 0.005 -10000 0 -10000 0 0
SYNJ1 -0.021 0.038 0.18 3 -0.2 3 6
PXN 0.034 0.003 -10000 0 -10000 0 0
TF -0.044 0.061 0.16 2 -0.2 14 16
HRAS/GTP 0.025 0.088 -10000 0 -0.2 17 17
Ephrin B1/EPHB1-2 0.019 0.092 -10000 0 -0.22 16 16
cell adhesion mediated by integrin 0.011 0.036 0.2 1 -0.18 2 3
RAC1 0.023 0.016 -10000 0 -10000 0 0
mol:GTP 0.03 0.091 -10000 0 -0.2 17 17
RAC1-CDC42/GTP -0.041 0.058 -10000 0 -0.21 13 13
RASA1 0.033 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.013 0.072 0.25 4 -10000 0 4
ruffle organization 0.062 0.17 0.32 36 -10000 0 36
NCK1 0.034 0.005 -10000 0 -10000 0 0
receptor internalization -0.027 0.044 0.16 3 -10000 0 3
Ephrin B/EPHB2/KALRN 0.082 0.055 -10000 0 -0.2 3 3
ROCK1 -0.014 0.048 0.18 5 -0.21 4 9
RAS family/GDP -0.032 0.042 -10000 0 -0.2 2 2
Rac1/GTP -0.035 0.048 -10000 0 -0.19 11 11
Ephrin B/EPHB1/Src/Paxillin -0.005 0.084 -10000 0 -0.22 16 16
TCGA08_retinoblastoma

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
CDKN2B -0.011 0.032 -10000 0 -10000 0 0
CDKN2C 0.01 0.047 -10000 0 -0.33 2 2
CDKN2A -0.017 0.032 -10000 0 -10000 0 0
CCND2 0 0.01 -10000 0 -10000 0 0
RB1 -0.007 0.039 -10000 0 -0.23 4 4
CDK4 0.003 0.014 -10000 0 -10000 0 0
CDK6 -0.001 0.02 -10000 0 -10000 0 0
G1/S progression 0.076 0.093 0.19 52 -10000 0 52
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.024 0.13 -9999 0 -0.38 17 17
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.033 0.006 -9999 0 -10000 0 0
TCEB1 0.033 0.007 -9999 0 -10000 0 0
HIF1A/p53 -0.05 0.14 -9999 0 -0.29 31 31
HIF1A -0.035 0.11 -9999 0 -0.29 24 24
COPS5 0.034 0.005 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.06 0.052 -9999 0 -10000 0 0
FIH (dimer) 0.023 0.016 -9999 0 -10000 0 0
CDKN2A -0.019 0.034 -9999 0 -10000 0 0
ARNT/IPAS 0.003 0.1 -9999 0 -0.27 17 17
HIF1AN 0.023 0.016 -9999 0 -10000 0 0
GNB2L1 0.034 0.004 -9999 0 -10000 0 0
HIF1A/ARNT -0.051 0.13 -9999 0 -0.29 30 30
CUL2 0.024 0.016 -9999 0 -10000 0 0
OS9 0.029 0.013 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.065 0.018 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.049 0.14 -9999 0 -0.29 31 31
PHD1-3/OS9 0.057 0.056 -9999 0 -0.21 3 3
HIF1A/RACK1/Elongin B/Elongin C -0.032 0.14 -9999 0 -0.28 31 31
VHL 0.034 0.005 -9999 0 -10000 0 0
HSP90AA1 0.032 0.009 -9999 0 -10000 0 0
HIF1A/JAB1 -0.052 0.14 -9999 0 -0.29 31 31
EGLN3 0.023 0.059 -9999 0 -0.38 3 3
EGLN2 0.033 0.007 -9999 0 -10000 0 0
EGLN1 0.033 0.006 -9999 0 -10000 0 0
TP53 0.03 0.035 -9999 0 -0.38 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.027 0.051 -9999 0 -0.45 1 1
ARNT 0.033 0.006 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.03 0.015 -9999 0 -10000 0 0
HIF1A/p19ARF -0.071 0.12 -9999 0 -0.28 31 31
Visual signal transduction: Rods

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
mol:K + 0.034 0.005 -10000 0 -10000 0 0
GNAT1/GTP 0.02 0.013 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.018 0.013 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.032 0.046 -10000 0 -0.22 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.026 0.02 -10000 0 -10000 0 0
GRK1 0.026 0.017 -10000 0 -10000 0 0
CNG Channel 0.003 0.096 -10000 0 -0.22 18 18
mol:Na + -0.023 0.089 -10000 0 -0.2 24 24
mol:ADP 0.026 0.017 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.016 0.11 -10000 0 -0.24 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.015 0.097 -10000 0 -0.2 24 24
CNGB1 0.021 0.028 -10000 0 -10000 0 0
RDH5 0.023 0.06 -10000 0 -0.38 3 3
SAG 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.061 0.07 0.32 1 -10000 0 1
Na + (4 Units) -0.026 0.086 -10000 0 -0.19 24 24
RGS9 -0.025 0.14 -10000 0 -0.38 19 19
GNB1/GNGT1 0.024 0.006 -10000 0 -10000 0 0
GNAT1/GDP 0.023 0.1 -10000 0 -0.21 20 20
GUCY2D 0.024 0.025 -10000 0 -10000 0 0
GNGT1 0 0 -10000 0 -10000 0 0
GUCY2F 0.027 0.009 -10000 0 -10000 0 0
GNB5 0.034 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.003 0.076 -10000 0 -0.21 15 15
mol:11-cis-retinal 0.023 0.06 -10000 0 -0.38 3 3
mol:cGMP -0.01 0.087 -10000 0 -0.21 20 20
GNB1 0.033 0.008 -10000 0 -10000 0 0
Rhodopsin 0.032 0.052 -10000 0 -0.27 3 3
SLC24A1 0.034 0.005 -10000 0 -10000 0 0
CNGA1 0.019 0.068 -10000 0 -0.38 4 4
Metarhodopsin II 0.031 0.022 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0 0.095 -10000 0 -0.22 20 20
RGS9BP 0.021 0.068 -10000 0 -0.38 4 4
Metarhodopsin II/Transducin 0.012 0.01 -10000 0 -10000 0 0
GCAP Family/Ca ++ -0.006 0.085 -10000 0 -0.21 20 20
PDE6A/B 0.016 0.09 -10000 0 -0.27 12 12
mol:Pi 0.016 0.11 -10000 0 -0.24 20 20
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.036 0.017 -10000 0 -10000 0 0
PDE6B 0.026 0.059 -10000 0 -0.38 3 3
PDE6A 0 0.1 -10000 0 -0.38 9 9
PDE6G 0.02 0.076 -10000 0 -0.38 5 5
RHO 0.025 0.024 -10000 0 -10000 0 0
PDE6 0.017 0.14 -10000 0 -0.22 33 33
GUCA1A -0.024 0.12 -10000 0 -0.38 13 13
GC2/GCAP Family 0.003 0.095 -10000 0 -0.22 20 20
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B 0.014 0.088 -10000 0 -0.38 7 7
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.008 0.088 -10000 0 -0.26 10 10
NF kappa B1 p50/RelA/I kappa B alpha -0.025 0.12 -10000 0 -0.46 7 7
alphaV/beta3 Integrin/Osteopontin/Src 0.021 0.089 -10000 0 -0.28 11 11
AP1 0 0.11 -10000 0 -0.39 6 6
ILK -0.015 0.084 -10000 0 -0.25 14 14
bone resorption -0.022 0.11 -10000 0 -0.38 8 8
PTK2B 0.032 0.015 -10000 0 -10000 0 0
PYK2/p130Cas 0.04 0.12 -10000 0 -0.26 16 16
ITGAV 0.033 0.015 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.034 0.069 -10000 0 -0.27 7 7
alphaV/beta3 Integrin/Osteopontin 0.03 0.11 -10000 0 -0.27 15 15
MAP3K1 -0.015 0.085 -10000 0 -0.25 15 15
JUN 0.033 0.006 -10000 0 -10000 0 0
MAPK3 -0.047 0.084 -10000 0 -0.35 6 6
MAPK1 -0.046 0.083 -10000 0 -0.33 7 7
Rac1/GDP 0.017 0.012 -10000 0 -10000 0 0
NFKB1 0.034 0.003 -10000 0 -10000 0 0
MAPK8 -0.037 0.071 -10000 0 -0.3 6 6
ITGB3 0.014 0.085 -10000 0 -0.39 6 6
NFKBIA -0.045 0.12 -10000 0 -0.47 8 8
FOS 0.019 0.061 -10000 0 -0.38 3 3
CD44 0.017 0.082 -10000 0 -0.38 6 6
CHUK 0.023 0.016 -10000 0 -10000 0 0
PLAU -0.079 0.24 -10000 0 -1 8 8
NF kappa B1 p50/RelA 0.003 0.12 -10000 0 -0.39 8 8
BCAR1 0.033 0.007 -10000 0 -10000 0 0
RELA 0.034 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.035 0.07 -10000 0 -0.28 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.022 0.1 -10000 0 -0.29 16 16
VAV3 -0.057 0.096 -10000 0 -0.36 9 9
MAP3K14 -0.015 0.09 -10000 0 -0.26 15 15
ROCK2 0.031 0.034 -10000 0 -0.38 1 1
SPP1 -0.006 0.12 -10000 0 -0.38 12 12
RAC1 0.023 0.016 -10000 0 -10000 0 0
Rac1/GTP -0.02 0.082 -10000 0 -0.3 6 6
MMP2 -0.042 0.093 0.3 1 -0.36 7 8
Noncanonical Wnt signaling pathway

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
NFATC2 -0.011 0.12 -10000 0 -0.38 14 14
GNB1/GNG2 0.016 0.11 -10000 0 -0.36 6 6
mol:DAG -0.014 0.09 0.17 1 -0.37 4 5
PLCG1 -0.015 0.092 0.17 1 -0.38 4 5
YES1 -0.024 0.097 -10000 0 -0.24 21 21
FZD3 0.031 0.034 -10000 0 -0.38 1 1
FZD6 0.02 0.069 -10000 0 -0.38 4 4
G protein 0.024 0.11 -10000 0 -0.38 4 4
MAP3K7 -0.048 0.088 0.16 1 -0.35 5 6
mol:Ca2+ -0.014 0.088 0.17 1 -0.36 4 5
mol:IP3 -0.014 0.09 0.17 1 -0.37 4 5
NLK 0.01 0.065 -10000 0 -0.76 1 1
GNB1 0.033 0.008 -10000 0 -10000 0 0
CAMK2A -0.04 0.097 0.24 1 -0.38 5 6
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.014 0.11 -10000 0 -0.25 21 21
CSNK1A1 0.034 0.004 -10000 0 -10000 0 0
GNAS -0.022 0.091 -10000 0 -0.24 19 19
GO:0007205 -0.02 0.085 0.16 1 -0.31 6 7
WNT6 0.022 0.061 -10000 0 -0.38 3 3
WNT4 0.005 0.091 -10000 0 -0.38 7 7
NFAT1/CK1 alpha -0.005 0.12 0.27 1 -0.42 4 5
GNG2 0.031 0.012 -10000 0 -10000 0 0
WNT5A 0.028 0.048 -10000 0 -0.38 2 2
WNT11 0.003 0.1 -10000 0 -0.38 10 10
CDC42 -0.024 0.097 0.18 3 -0.32 8 11
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.042 0.015 -10000 0 -10000 0 0
PRKCZ -0.011 0.12 -10000 0 -0.38 14 14
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.03 0.035 -10000 0 -0.38 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0 0.089 -10000 0 -0.32 6 6
IRAK/TOLLIP 0.045 0.04 0.17 12 -10000 0 12
IKBKB 0.034 0.005 -10000 0 -10000 0 0
IKBKG 0.034 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.038 0.14 -10000 0 -0.28 34 34
IL1A -0.004 0.11 -10000 0 -0.38 12 12
IL1B -0.038 0.079 -10000 0 -0.32 10 10
IRAK/TRAF6/p62/Atypical PKCs 0.051 0.095 -10000 0 -0.2 13 13
IL1R2 -0.042 0.15 -10000 0 -0.38 23 23
IL1R1 0.019 0.055 -10000 0 -0.38 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.008 0.093 -10000 0 -0.41 5 5
TOLLIP 0.033 0.008 -10000 0 -10000 0 0
TICAM2 0.034 0.004 -10000 0 -10000 0 0
MAP3K3 0.034 0.003 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.021 0.007 -10000 0 -10000 0 0
IKK complex/ELKS -0.029 0.1 -10000 0 -0.42 3 3
JUN -0.019 0.023 0.14 1 -10000 0 1
MAP3K7 0.031 0.01 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.032 0.1 -10000 0 -0.23 14 14
IL1 alpha/IL1R1/IL1RAP/MYD88 0.029 0.11 -10000 0 -0.24 17 17
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.047 0.11 -10000 0 -0.22 17 17
IL1 beta fragment/IL1R1/IL1RAP 0.004 0.097 -10000 0 -0.25 15 15
NFKB1 0.034 0.003 -10000 0 -10000 0 0
MAPK8 -0.017 0.027 0.16 2 -10000 0 2
IRAK1 -0.017 0.007 -10000 0 -10000 0 0
IL1RN/IL1R1 0.008 0.097 -10000 0 -0.29 12 12
IRAK4 0.033 0.008 -10000 0 -10000 0 0
PRKCI 0.034 0.004 -10000 0 -10000 0 0
TRAF6 0.028 0.048 -10000 0 -0.38 2 2
PI3K 0.045 0.03 -10000 0 -0.27 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.006 0.099 -10000 0 -0.36 7 7
CHUK 0.023 0.016 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.004 0.097 -10000 0 -0.25 15 15
IL1 beta/IL1R2 -0.036 0.12 -10000 0 -0.25 32 32
IRAK/TRAF6/TAK1/TAB1/TAB2 0.048 0.041 -10000 0 -0.19 1 1
NF kappa B1 p50/RelA 0.021 0.094 -10000 0 -0.22 14 14
IRAK3 0.025 0.05 -10000 0 -0.38 2 2
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.031 0.1 -10000 0 -0.22 15 15
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.011 0.098 -10000 0 -0.25 17 17
IL1 alpha/IL1R1/IL1RAP 0.015 0.1 -10000 0 -0.24 17 17
RELA 0.034 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.034 0.004 -10000 0 -10000 0 0
MYD88 0.031 0.034 -10000 0 -0.38 1 1
IRAK/TRAF6/MEKK3 0.063 0.044 -10000 0 -0.2 1 1
IL1RAP 0.02 0.069 -10000 0 -0.38 4 4
UBE2N 0.034 0.004 -10000 0 -10000 0 0
IRAK/TRAF6 -0.003 0.08 -10000 0 -0.34 2 2
CASP1 0.017 0.082 -10000 0 -0.38 6 6
IL1RN/IL1R2 -0.038 0.14 -10000 0 -0.29 32 32
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.022 0.1 -10000 0 -0.25 15 15
TMEM189-UBE2V1 0.026 0.01 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.001 0.1 -10000 0 -0.43 5 5
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
IL1RN -0.003 0.11 -10000 0 -0.38 11 11
TRAF6/TAK1/TAB1/TAB2 0.05 0.034 -10000 0 -0.19 1 1
MAP2K6 -0.003 0.058 0.17 13 -0.19 1 14
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.004 0.095 0.33 6 -0.82 1 7
VDR 0.007 0.085 -10000 0 -0.38 6 6
FAM120B 0.031 0.01 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.028 0.12 -10000 0 -0.39 6 6
RXRs/LXRs/DNA/Oxysterols -0.032 0.14 -10000 0 -0.46 10 10
MED1 0.034 0 -10000 0 -10000 0 0
mol:9cRA -0.001 0.012 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.019 0.058 -10000 0 -0.23 3 3
RXRs/NUR77 0.013 0.12 -10000 0 -0.22 25 25
RXRs/PPAR -0.026 0.1 -10000 0 -0.29 9 9
NCOR2 0.031 0.034 -10000 0 -0.38 1 1
VDR/VDR/Vit D3 0.007 0.059 -10000 0 -0.27 6 6
RARs/VDR/DNA/Vit D3 0.048 0.073 -10000 0 -0.2 8 8
RARA 0.034 0 -10000 0 -10000 0 0
NCOA1 0.034 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.007 0.085 -10000 0 -0.38 6 6
RARs/RARs/DNA/9cRA 0.05 0.04 -10000 0 -0.2 2 2
RARG 0.031 0.017 -10000 0 -10000 0 0
RPS6KB1 0.013 0.081 0.62 2 -0.39 1 3
RARs/THRs/DNA/SMRT 0.019 0.059 -10000 0 -0.23 3 3
THRA 0.029 0.048 -10000 0 -0.38 2 2
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.007 0.059 -10000 0 -0.27 6 6
RXRs/PPAR/9cRA/PGJ2/DNA 0 0.11 -10000 0 -0.21 25 25
NR1H4 0.017 0.054 -10000 0 -0.38 2 2
RXRs/LXRs/DNA 0.025 0.13 -10000 0 -0.35 3 3
NR1H2 0.029 0.023 -10000 0 -10000 0 0
NR1H3 0.029 0.025 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.001 0.11 -10000 0 -0.2 30 30
NR4A1 0.027 0.024 -10000 0 -10000 0 0
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.024 0.092 -10000 0 -0.26 9 9
RXRG -0.053 0.16 -10000 0 -0.38 26 26
RXR alpha/CCPG 0.042 0.024 -10000 0 -10000 0 0
RXRA 0.03 0.022 -10000 0 -10000 0 0
RXRB 0.03 0.024 -10000 0 -10000 0 0
THRB 0.025 0.059 -10000 0 -0.38 3 3
PPARG 0.031 0.035 -10000 0 -0.38 1 1
PPARD 0.034 0.004 -10000 0 -10000 0 0
TNF -0.074 0.25 -10000 0 -0.95 10 10
mol:Oxysterols -0.001 0.011 -10000 0 -10000 0 0
cholesterol transport -0.032 0.14 -10000 0 -0.45 10 10
PPARA 0.03 0.011 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.027 0.049 -10000 0 -0.38 2 2
RXRs/NUR77/BCL2 -0.022 0.09 -10000 0 -0.21 26 26
SREBF1 -0.034 0.13 -10000 0 -0.54 3 3
RXRs/RXRs/DNA/9cRA 0.003 0.11 -10000 0 -0.21 25 25
ABCA1 -0.038 0.15 -10000 0 -0.67 5 5
RARs/THRs 0.083 0.07 -10000 0 -0.22 7 7
RXRs/FXR 0.011 0.12 -10000 0 -0.22 27 27
BCL2 0.033 0.007 -10000 0 -10000 0 0
Retinoic acid receptors-mediated 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
HDAC1 0.033 0.006 -10000 0 -10000 0 0
HDAC3 0.034 0.004 -10000 0 -10000 0 0
VDR 0.007 0.085 -10000 0 -0.38 6 6
Cbp/p300/PCAF 0.056 0.041 -10000 0 -0.23 2 2
EP300 0.031 0.01 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.01 0.068 -10000 0 -0.32 3 3
KAT2B 0.028 0.048 -10000 0 -0.38 2 2
MAPK14 0.034 0.005 -10000 0 -10000 0 0
AKT1 -0.019 0.078 0.18 6 -0.24 5 11
RAR alpha/9cRA/Cyclin H -0.029 0.12 -10000 0 -0.34 5 5
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.006 0.063 -10000 0 -0.29 3 3
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.011 0.079 -10000 0 -0.32 4 4
NCOR2 0.031 0.034 -10000 0 -0.38 1 1
VDR/VDR/Vit D3 0.007 0.059 -10000 0 -0.27 6 6
RXRs/RARs/NRIP1/9cRA -0.07 0.16 -10000 0 -0.46 13 13
NCOA2 0.019 0.075 -10000 0 -0.38 5 5
NCOA3 0.031 0.01 -10000 0 -10000 0 0
NCOA1 0.034 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.007 0.085 -10000 0 -0.38 6 6
RARG 0.031 0.017 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.042 0.016 -10000 0 -10000 0 0
MAPK3 0.034 0.004 -10000 0 -10000 0 0
MAPK1 0.032 0.009 -10000 0 -10000 0 0
MAPK8 0.023 0.018 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.073 0.17 -10000 0 -0.43 22 22
RARA -0.025 0.09 -10000 0 -0.23 22 22
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.013 0.068 -10000 0 -0.24 5 5
PRKCA 0.033 0.034 -10000 0 -0.38 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.068 0.16 -10000 0 -0.48 11 11
RXRG -0.073 0.15 -10000 0 -0.3 40 40
RXRA -0.025 0.08 -10000 0 -0.3 5 5
RXRB -0.026 0.11 -10000 0 -0.28 22 22
VDR/Vit D3/DNA 0.007 0.059 -10000 0 -0.27 6 6
RBP1 0.008 0.1 -10000 0 -0.38 9 9
CRBP1/9-cic-RA 0.007 0.07 -10000 0 -0.27 9 9
RARB 0.028 0.05 -10000 0 -0.38 2 2
PRKCG -0.043 0.15 -10000 0 -0.38 22 22
MNAT1 0.032 0.009 -10000 0 -10000 0 0
RAR alpha/RXRs -0.07 0.17 -10000 0 -0.43 22 22
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.06 0.14 -10000 0 -0.36 21 21
proteasomal ubiquitin-dependent protein catabolic process -0.031 0.084 -10000 0 -0.27 6 6
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.07 0.16 -10000 0 -0.49 11 11
positive regulation of DNA binding -0.033 0.11 -10000 0 -0.31 6 6
NRIP1 -0.059 0.15 -10000 0 -0.59 2 2
RXRs/RARs -0.067 0.16 -10000 0 -0.4 24 24
RXRs/RXRs/DNA/9cRA -0.078 0.16 -10000 0 -0.42 23 23
PRKACA 0.033 0.007 -10000 0 -10000 0 0
CDK7 0.033 0.007 -10000 0 -10000 0 0
TFIIH 0.062 0.022 -10000 0 -10000 0 0
RAR alpha/9cRA -0.007 0.099 -10000 0 -0.25 5 5
CCNH 0.033 0.006 -10000 0 -10000 0 0
CREBBP 0.034 0.005 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.056 0.031 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.008 0.097 -10000 0 -0.45 2 2
UGCG -0.002 0.1 -10000 0 -0.58 4 4
AKT1/mTOR/p70S6K/Hsp90/TERT -0.038 0.14 0.24 1 -0.34 16 17
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.002 0.099 -10000 0 -0.58 4 4
mol:DAG -0.24 0.39 -10000 0 -0.81 47 47
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.01 0.11 0.26 1 -0.39 5 6
FRAP1 -0.021 0.12 0.27 1 -0.45 5 6
FOXO3 -0.02 0.11 0.26 1 -0.38 5 6
AKT1 -0.021 0.12 0.28 1 -0.44 6 7
GAB2 0.028 0.048 -10000 0 -0.38 2 2
SMPD1 -0.011 0.13 -10000 0 -0.62 6 6
SGMS1 -0.18 0.3 -10000 0 -0.61 46 46
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 -0.011 0.018 -10000 0 -0.22 1 1
CALM1 0.032 0.009 -10000 0 -10000 0 0
cell proliferation -0.086 0.18 -10000 0 -0.4 28 28
EIF3A 0.023 0.016 -10000 0 -10000 0 0
PI3K 0.047 0.031 -10000 0 -0.27 1 1
RPS6KB1 0 0.083 -10000 0 -0.7 1 1
mol:sphingomyelin -0.24 0.39 -10000 0 -0.81 47 47
natural killer cell activation 0 0.001 -10000 0 -0.01 1 1
JAK3 0.019 0.076 -10000 0 -0.38 5 5
PIK3R1 0.031 0.036 -10000 0 -0.38 1 1
JAK1 0.034 0.007 -10000 0 -10000 0 0
NFKB1 0.034 0.003 -10000 0 -10000 0 0
MYC -0.014 0.13 -10000 0 -0.59 3 3
MYB -0.09 0.34 -10000 0 -1.2 13 13
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.029 0.11 -10000 0 -0.37 8 8
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.022 0.086 -10000 0 -0.63 1 1
mol:PI-3-4-5-P3 -0.029 0.11 -10000 0 -0.36 8 8
Rac1/GDP 0.016 0.023 -10000 0 -0.2 1 1
T cell proliferation -0.045 0.12 0.22 1 -0.35 10 11
SHC1 0.031 0.016 -10000 0 -10000 0 0
RAC1 0.023 0.016 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.004 0.018 -10000 0 -0.06 13 13
PRKCZ -0.047 0.12 0.22 1 -0.36 10 11
NF kappa B1 p50/RelA 0.001 0.12 0.28 1 -0.4 5 6
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.011 0.1 -10000 0 -0.45 5 5
HSP90AA1 0.032 0.009 -10000 0 -10000 0 0
RELA 0.034 0.003 -10000 0 -10000 0 0
IL2RA -0.027 0.11 -10000 0 -0.38 11 11
IL2RB 0.02 0.062 -10000 0 -0.38 3 3
TERT -0.013 0.12 -10000 0 -0.38 14 14
E2F1 -0.022 0.15 -10000 0 -0.48 13 13
SOS1 0.035 0.001 -10000 0 -10000 0 0
RPS6 0.028 0.016 -10000 0 -10000 0 0
mol:cAMP 0.002 0.009 0.031 13 -10000 0 13
PTPN11 0.034 0.003 -10000 0 -10000 0 0
IL2RG 0.026 0.06 -10000 0 -0.38 3 3
actin cytoskeleton organization -0.045 0.12 0.22 1 -0.35 10 11
GRB2 0.034 0.005 -10000 0 -10000 0 0
IL2 0.001 0.001 -10000 0 -10000 0 0
PIK3CA 0.034 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.039 0.038 -10000 0 -0.19 1 1
LCK -0.001 0.11 -10000 0 -0.38 11 11
BCL2 -0.012 0.1 0.42 1 -0.38 4 5
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 0.025 0.059 -9999 0 -0.38 3 3
GPC2 0.003 0.082 -9999 0 -0.38 6 6
GPC2/Midkine 0.011 0.077 -9999 0 -0.27 9 9
neuron projection morphogenesis 0.011 0.077 -9999 0 -0.27 9 9
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0 0.024 -10000 0 -10000 0 0
NFATC2 -0.023 0.072 -10000 0 -0.23 14 14
NFATC3 -0.001 0.026 -10000 0 -10000 0 0
CD40LG -0.053 0.13 0.33 1 -0.37 10 11
PTGS2 -0.056 0.14 0.33 1 -0.45 10 11
JUNB 0.027 0.038 -10000 0 -0.38 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.022 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.022 -10000 0 -10000 0 0
CALM1 0.024 0.022 -10000 0 -10000 0 0
JUN 0.025 0.022 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.007 -10000 0 -0.021 13 13
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.009 -10000 0 -10000 0 0
FOSL1 0.011 0.084 -10000 0 -0.38 6 6
CREM 0.024 0.016 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.008 0.11 -10000 0 -0.24 12 12
FOS 0.011 0.064 -10000 0 -0.39 3 3
IFNG -0.05 0.12 0.33 1 -0.36 8 9
AP-1/NFAT1-c-4 -0.024 0.14 -10000 0 -0.38 10 10
FASLG -0.046 0.12 0.33 1 -0.36 8 9
NFAT1-c-4/ICER1 -0.017 0.077 -10000 0 -0.2 15 15
IL2RA -0.07 0.14 -10000 0 -0.4 16 16
FKBP12/FK506 0.024 0.007 -10000 0 -10000 0 0
CSF2 -0.059 0.1 0.16 5 -0.33 10 15
JunB/Fra1/NFAT1-c-4 -0.007 0.11 -10000 0 -0.22 20 20
IL4 -0.059 0.1 0.16 5 -0.33 10 15
IL2 -0.002 0.006 -10000 0 -0.019 8 8
IL3 0.001 0.075 -10000 0 -0.61 2 2
FKBP1A 0.032 0.009 -10000 0 -10000 0 0
BATF3 0.017 0.076 -10000 0 -0.38 5 5
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.028 0.048 -10000 0 -0.38 2 2
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.007 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.028 0.083 -10000 0 -0.21 15 15
regulation of S phase of mitotic cell cycle -0.002 0.082 -10000 0 -0.23 15 15
GNAO1 0.011 0.094 -10000 0 -0.38 8 8
HRAS 0.032 0.008 -10000 0 -10000 0 0
SHBG/T-DHT 0.006 0.059 -10000 0 -0.22 9 9
PELP1 0.033 0.006 -10000 0 -10000 0 0
AKT1 -0.007 0.003 -10000 0 -10000 0 0
MAP2K1 -0.028 0.075 0.16 9 -0.33 1 10
T-DHT/AR -0.006 0.088 -10000 0 -0.27 15 15
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.008 5 5
GNAI2 0.034 0.005 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GNAI1 0.014 0.06 -10000 0 -0.38 3 3
mol:GDP -0.036 0.11 -10000 0 -0.37 15 15
cell proliferation -0.017 0.1 0.25 4 -0.35 5 9
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
FOS -0.02 0.15 -10000 0 -0.75 5 5
mol:Ca2+ -0.004 0.018 -10000 0 -0.062 9 9
MAPK3 -0.016 0.09 0.25 4 -0.29 4 8
MAPK1 -0.016 0.11 -10000 0 -0.38 9 9
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
mol:IP3 0 0.001 -10000 0 -0.005 5 5
cAMP biosynthetic process -0.014 0.053 -10000 0 -0.21 9 9
GNG2 0.031 0.012 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.005 5 5
HRAS/GTP 0.028 0.084 -10000 0 -0.2 15 15
actin cytoskeleton reorganization 0.031 0.033 -10000 0 -0.2 1 1
SRC 0.029 0.035 -10000 0 -0.38 1 1
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.005 5 5
PI3K 0.041 0.026 -10000 0 -0.23 1 1
apoptosis 0.007 0.099 0.34 7 -0.22 2 9
T-DHT/AR/PELP1 0.015 0.083 -10000 0 -0.23 15 15
HRAS/GDP -0.007 0.12 -10000 0 -0.35 15 15
CREB1 -0.008 0.1 0.23 2 -0.36 7 9
RAC1-CDC42/GTP 0.039 0.039 -10000 0 -0.2 1 1
AR -0.01 0.13 -10000 0 -0.38 15 15
GNB1 0.033 0.008 -10000 0 -10000 0 0
RAF1 -0.023 0.08 0.18 10 -0.34 1 11
RAC1-CDC42/GDP 0 0.11 -10000 0 -0.35 11 11
T-DHT/AR/PELP1/Src 0.029 0.088 -10000 0 -0.22 15 15
MAP2K2 -0.032 0.07 0.16 6 -0.33 1 7
T-DHT/AR/PELP1/Src/PI3K -0.002 0.082 -10000 0 -0.23 15 15
GNAZ 0.027 0.049 -10000 0 -0.38 2 2
SHBG 0.006 0.1 -10000 0 -0.38 9 9
Gi family/GNB1/GNG2/GDP -0.007 0.09 -10000 0 -0.32 9 9
mol:T-DHT 0 0.001 -10000 0 -0.003 5 5
RAC1 0.023 0.016 -10000 0 -10000 0 0
GNRH1 -0.028 0.071 -10000 0 -0.27 12 12
Gi family/GTP -0.014 0.07 -10000 0 -0.26 7 7
CDC42 0.034 0.005 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.035 0.065 -10000 0 -0.27 6 6
AKT1 -0.019 0.14 -10000 0 -0.36 15 15
PTK2B -0.033 0.1 -10000 0 -0.45 3 3
VEGFR2 homodimer/Frs2 0.029 0.059 -10000 0 -0.43 2 2
CAV1 0.007 0.076 -10000 0 -0.38 5 5
CALM1 0.032 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.018 0.1 -10000 0 -0.25 15 15
endothelial cell proliferation -0.005 0.14 0.23 2 -0.38 7 9
mol:Ca2+ -0.005 0.1 0.19 8 -0.45 3 11
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.028 0.1 -10000 0 -0.5 2 2
RP11-342D11.1 -0.026 0.094 0.17 8 -0.39 4 12
CDH5 0.031 0.034 -10000 0 -0.38 1 1
VEGFA homodimer 0.047 0.089 -10000 0 -0.21 13 13
SHC1 0.031 0.015 -10000 0 -10000 0 0
SHC2 0.033 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.095 -10000 0 -0.41 3 3
SH2D2A 0.02 0.069 -10000 0 -0.38 4 4
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.018 0.14 -10000 0 -0.41 7 7
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.015 0.11 -10000 0 -0.27 15 15
VEGFR1 homodimer 0.028 0.035 -10000 0 -0.38 1 1
SHC/GRB2/SOS1 0.057 0.12 -10000 0 -0.44 3 3
GRB10 -0.006 0.1 -10000 0 -0.56 3 3
PTPN11 0.034 0.003 -10000 0 -10000 0 0
GRB2 0.034 0.005 -10000 0 -10000 0 0
PAK1 0.034 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.054 0.12 -10000 0 -0.57 2 2
HRAS 0.033 0.008 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.006 0.11 -10000 0 -0.38 7 7
HIF1A 0.032 0.009 -10000 0 -10000 0 0
FRS2 0.032 0.009 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.026 0.1 -10000 0 -0.5 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.019 0.076 -10000 0 -0.38 5 5
Nck/Pak 0.05 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.015 0.1 -10000 0 -0.25 15 15
mol:GDP 0.033 0.1 -10000 0 -0.42 3 3
mol:NADP 0.004 0.12 -10000 0 -0.39 7 7
eNOS/Hsp90 0.02 0.12 -10000 0 -0.37 7 7
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
mol:IP3 -0.005 0.1 0.19 8 -0.45 3 11
HIF1A/ARNT 0.046 0.015 -10000 0 -10000 0 0
SHB 0.031 0.01 -10000 0 -10000 0 0
VEGFA -0.01 0.12 -10000 0 -0.38 14 14
VEGFC 0.014 0.077 -10000 0 -0.38 5 5
FAK1/Vinculin -0.015 0.13 -10000 0 -0.43 7 7
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.034 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.035 0.12 -10000 0 -0.37 5 5
PTPN6 0.033 0.007 -10000 0 -10000 0 0
EPAS1 0.034 0.049 -10000 0 -0.36 2 2
mol:L-citrulline 0.004 0.12 -10000 0 -0.39 7 7
ITGAV 0.034 0.003 -10000 0 -10000 0 0
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.039 0.11 -10000 0 -0.24 15 15
VEGFR2 homodimer/VEGFA homodimer 0.019 0.11 -10000 0 -0.26 17 17
VEGFR2/3 heterodimer 0.021 0.085 -10000 0 -0.34 6 6
VEGFB 0.034 0.003 -10000 0 -10000 0 0
MAPK11 -0.025 0.11 0.24 2 -0.38 6 8
VEGFR2 homodimer 0.011 0.064 -10000 0 -0.49 2 2
FLT1 0.028 0.035 -10000 0 -0.38 1 1
NEDD4 0.033 0.015 -10000 0 -10000 0 0
MAPK3 -0.014 0.1 -10000 0 -0.41 3 3
MAPK1 -0.014 0.1 -10000 0 -0.41 3 3
VEGFA145/NRP2 0.011 0.099 -10000 0 -0.27 15 15
VEGFR1/2 heterodimer 0.025 0.068 -10000 0 -0.52 2 2
KDR 0.011 0.064 -10000 0 -0.49 2 2
VEGFA165/NRP1/VEGFR2 homodimer 0.02 0.11 -10000 0 -0.39 4 4
SRC 0.029 0.035 -10000 0 -0.38 1 1
platelet activating factor biosynthetic process -0.014 0.11 -10000 0 -0.42 3 3
PI3K -0.013 0.14 -10000 0 -0.34 16 16
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.019 0.1 -10000 0 -0.25 15 15
FES -0.004 0.1 0.19 8 -0.4 4 12
GAB1 -0.017 0.14 -10000 0 -0.36 15 15
VEGFR2 homodimer/VEGFA homodimer/Src 0.014 0.1 -10000 0 -0.25 16 16
CTNNB1 0.034 0.004 -10000 0 -10000 0 0
SOS1 0.034 0 -10000 0 -10000 0 0
ARNT 0.033 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.001 0.12 -10000 0 -0.38 7 7
VEGFR2 homodimer/VEGFA homodimer/Yes 0.018 0.1 -10000 0 -0.25 15 15
PI3K/GAB1 -0.013 0.15 0.26 2 -0.38 15 17
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.054 0.11 -10000 0 -0.49 2 2
PRKACA 0.033 0.007 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.026 0.094 -10000 0 -0.27 10 10
HSP90AA1 0.032 0.009 -10000 0 -10000 0 0
CDC42 -0.004 0.1 0.19 8 -0.4 4 12
actin cytoskeleton reorganization 0.014 0.11 -10000 0 -0.27 15 15
PTK2 -0.014 0.14 0.22 1 -0.46 7 8
EDG1 -0.026 0.094 0.17 8 -0.39 4 12
mol:DAG -0.005 0.1 0.19 8 -0.45 3 11
CaM/Ca2+ 0.009 0.1 -10000 0 -0.42 3 3
MAP2K3 -0.035 0.1 0.17 8 -0.38 6 14
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.063 0.14 0.24 34 -0.58 3 37
PLCG1 -0.005 0.1 0.19 8 -0.46 3 11
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.034 0.11 -10000 0 -0.5 2 2
IQGAP1 0.034 0.005 -10000 0 -10000 0 0
YES1 0.033 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.019 0.1 -10000 0 -0.25 15 15
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.018 0.1 -10000 0 -0.25 15 15
cell migration -0.003 0.13 0.26 1 -0.46 5 6
mol:PI-3-4-5-P3 -0.011 0.13 -10000 0 -0.32 16 16
FYN 0.031 0.01 -10000 0 -10000 0 0
VEGFB/NRP1 0.003 0.099 0.18 8 -0.38 4 12
mol:NO 0.004 0.12 -10000 0 -0.39 7 7
PXN 0.034 0.003 -10000 0 -10000 0 0
HRAS/GTP 0 0.086 -10000 0 -0.4 3 3
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.002 0.1 -10000 0 -0.58 3 3
VHL 0.034 0.005 -10000 0 -10000 0 0
ITGB3 0.015 0.083 -10000 0 -0.38 6 6
NOS3 0.002 0.13 -10000 0 -0.44 7 7
VEGFR2 homodimer/VEGFA homodimer/Sck 0.017 0.1 -10000 0 -0.25 15 15
RAC1 0.023 0.016 -10000 0 -10000 0 0
PRKCA -0.028 0.097 0.17 10 -0.43 3 13
PRKCB -0.032 0.1 0.17 10 -0.38 4 14
VCL 0.023 0.016 -10000 0 -10000 0 0
VEGFA165/NRP1 0.006 0.1 -10000 0 -0.24 17 17
VEGFR1/2 heterodimer/VEGFA homodimer 0.012 0.11 -10000 0 -0.26 15 15
VEGFA165/NRP2 0.011 0.099 -10000 0 -0.27 15 15
MAPKKK cascade -0.005 0.088 -10000 0 -0.46 3 3
NRP2 0.03 0.036 -10000 0 -0.38 1 1
VEGFC homodimer 0.014 0.077 -10000 0 -0.38 5 5
NCK1 0.034 0.005 -10000 0 -10000 0 0
ROCK1 0.033 0.007 -10000 0 -10000 0 0
FAK1/Paxillin 0.003 0.14 -10000 0 -0.43 7 7
MAP3K13 -0.01 0.11 0.19 6 -0.37 7 13
PDPK1 -0.019 0.12 0.22 1 -0.3 14 15
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.014 0.11 -9999 0 -0.25 21 21
FZD6 0.02 0.069 -9999 0 -0.38 4 4
WNT6 0.022 0.061 -9999 0 -0.38 3 3
WNT4 0.005 0.091 -9999 0 -0.38 7 7
FZD3 0.031 0.034 -9999 0 -0.38 1 1
WNT5A 0.028 0.048 -9999 0 -0.38 2 2
WNT11 0.003 0.1 -9999 0 -0.38 10 10
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.003 0.1 0.22 3 -0.38 8 11
CRKL -0.008 0.099 -10000 0 -0.39 8 8
HRAS -0.004 0.11 -10000 0 -0.34 9 9
mol:PIP3 0.053 0.13 0.28 9 -0.36 8 17
SPRED1 0.033 0.007 -10000 0 -10000 0 0
SPRED2 0.031 0.034 -10000 0 -0.38 1 1
GAB1 -0.004 0.1 -10000 0 -0.41 8 8
FOXO3 0.042 0.15 0.28 7 -0.36 9 16
AKT1 0.045 0.15 0.26 7 -0.38 9 16
BAD 0.041 0.14 0.25 6 -0.36 9 15
megakaryocyte differentiation -0.005 0.1 -10000 0 -0.38 9 9
GSK3B 0.042 0.14 0.25 8 -0.36 9 17
RAF1 -0.008 0.094 -10000 0 -0.28 9 9
SHC1 0.031 0.015 -10000 0 -10000 0 0
STAT3 -0.004 0.1 -10000 0 -0.41 8 8
STAT1 -0.033 0.24 -10000 0 -0.97 8 8
HRAS/SPRED1 0.006 0.1 -10000 0 -0.28 9 9
cell proliferation -0.011 0.096 -10000 0 -0.4 8 8
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
TEC 0.014 0.071 -10000 0 -0.38 4 4
RPS6KB1 0.029 0.12 -10000 0 -0.38 8 8
HRAS/SPRED2 0.008 0.1 -10000 0 -0.28 9 9
LYN/TEC/p62DOK 0.038 0.12 -10000 0 -0.38 9 9
MAPK3 -0.003 0.08 0.21 4 -0.24 1 5
STAP1 -0.007 0.1 -10000 0 -0.41 8 8
GRAP2 0.005 0.095 -10000 0 -0.38 8 8
JAK2 -0.022 0.21 -10000 0 -0.79 9 9
STAT1 (dimer) -0.028 0.23 -10000 0 -0.94 8 8
mol:Gleevec -0.001 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.035 0.12 -10000 0 -0.39 8 8
actin filament polymerization -0.012 0.083 -10000 0 -0.33 7 7
LYN 0.028 0.048 -10000 0 -0.38 2 2
STAP1/STAT5A (dimer) -0.016 0.14 -10000 0 -0.55 9 9
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
CBL/CRKL/GRB2 0.025 0.11 -10000 0 -0.37 8 8
PI3K 0.063 0.12 -10000 0 -0.37 7 7
PTEN 0.023 0.016 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.025 0.26 -10000 0 -1.1 8 8
MAPK8 -0.011 0.097 -10000 0 -0.41 8 8
STAT3 (dimer) -0.004 0.1 -10000 0 -0.4 8 8
positive regulation of transcription -0.001 0.07 0.2 4 -0.2 1 5
mol:GDP 0.001 0.11 -10000 0 -0.35 9 9
PIK3C2B -0.009 0.11 -10000 0 -0.43 8 8
CBL/CRKL 0.012 0.1 -10000 0 -0.38 8 8
FER -0.006 0.1 -10000 0 -0.4 8 8
SH2B3 -0.004 0.1 -10000 0 -0.41 8 8
PDPK1 0.05 0.12 0.26 9 -0.34 8 17
SNAI2 -0.007 0.1 -10000 0 -0.41 8 8
positive regulation of cell proliferation -0.018 0.18 -10000 0 -0.67 9 9
KITLG 0.025 0.053 -10000 0 -0.39 2 2
cell motility -0.018 0.18 -10000 0 -0.67 9 9
PTPN6 0.031 0.011 -10000 0 -10000 0 0
EPOR 0.026 0.083 -10000 0 -10000 0 0
STAT5A (dimer) -0.007 0.15 -10000 0 -0.55 9 9
SOCS1 0.021 0.062 -10000 0 -0.38 3 3
cell migration 0.013 0.1 0.38 9 -10000 0 9
SOS1 0.034 0 -10000 0 -10000 0 0
EPO 0.002 0.084 -10000 0 -0.39 6 6
VAV1 0.018 0.076 -10000 0 -0.38 5 5
GRB10 -0.011 0.083 -10000 0 -0.34 7 7
PTPN11 0.032 0.009 -10000 0 -10000 0 0
SCF/KIT 0.001 0.11 -10000 0 -0.42 8 8
GO:0007205 0 0.006 -10000 0 -10000 0 0
MAP2K1 -0.012 0.079 -10000 0 -0.23 8 8
CBL 0.034 0.003 -10000 0 -10000 0 0
KIT -0.038 0.29 -10000 0 -1.1 9 9
MAP2K2 -0.007 0.088 0.27 4 -0.23 8 12
SHC/Grb2/SOS1 0.046 0.12 -10000 0 -0.4 8 8
STAT5A -0.008 0.15 -10000 0 -0.56 9 9
GRB2 0.034 0.005 -10000 0 -10000 0 0
response to radiation -0.006 0.1 -10000 0 -0.4 8 8
SHC/GRAP2 0.025 0.071 -10000 0 -0.27 7 7
PTPRO -0.006 0.1 -10000 0 -0.39 9 9
SH2B2 -0.013 0.085 -10000 0 -0.34 7 7
DOK1 0.034 0 -10000 0 -10000 0 0
MATK -0.014 0.1 -10000 0 -0.39 9 9
CREBBP 0.037 0.038 -10000 0 -0.12 8 8
BCL2 0.02 0.1 -10000 0 -0.62 1 1
Signaling events mediated by PTP1B

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
PDGFRB 0.033 0.012 -10000 0 -10000 0 0
Jak2/Leptin Receptor 0.004 0.13 0.22 2 -0.33 11 13
PTP1B/AKT1 0.029 0.08 0.21 1 -0.26 4 5
FYN 0.031 0.01 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.02 0.081 0.17 4 -0.28 4 8
EGFR -0.068 0.16 -10000 0 -0.39 28 28
EGF/EGFR -0.043 0.1 -10000 0 -0.27 12 12
CSF1 0.034 0.005 -10000 0 -10000 0 0
AKT1 0.033 0.009 -10000 0 -10000 0 0
INSR 0.031 0.035 -10000 0 -0.38 1 1
PTP1B/N-cadherin 0.031 0.081 -10000 0 -0.27 4 4
Insulin Receptor/Insulin 0.031 0.073 -10000 0 -0.25 4 4
HCK 0.022 0.06 -10000 0 -0.38 3 3
CRK 0.033 0.006 -10000 0 -10000 0 0
TYK2 0.022 0.092 0.27 7 -0.28 4 11
EGF -0.002 0.1 -10000 0 -0.38 9 9
YES1 0.033 0.008 -10000 0 -10000 0 0
CAV1 0.034 0.12 0.19 25 -0.34 4 29
TXN 0.034 0.008 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.039 0.096 0.23 1 -0.27 4 5
cell migration -0.02 0.081 0.28 4 -0.17 4 8
STAT3 0.035 0.001 -10000 0 -10000 0 0
PRLR 0.013 0.079 -10000 0 -0.38 5 5
ITGA2B 0.007 0.096 -10000 0 -0.38 8 8
CSF1R 0.022 0.068 -10000 0 -0.38 4 4
Prolactin Receptor/Prolactin 0.013 0.056 -10000 0 -0.26 5 5
FGR 0.03 0.036 -10000 0 -0.38 1 1
PTP1B/p130 Cas 0.029 0.084 0.22 1 -0.28 4 5
Crk/p130 Cas 0.041 0.09 0.23 1 -0.27 4 5
DOK1 0.022 0.076 0.18 3 -0.26 4 7
JAK2 -0.014 0.13 0.21 1 -0.34 14 15
Jak2/Leptin Receptor/Leptin -0.02 0.12 -10000 0 -0.35 11 11
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
PTPN1 0.02 0.081 0.17 4 -0.28 4 8
LYN 0.028 0.048 -10000 0 -0.38 2 2
CDH2 0.033 0.007 -10000 0 -10000 0 0
SRC 0.032 0.059 -10000 0 -0.37 1 1
ITGB3 0.015 0.084 -10000 0 -0.38 6 6
CAT1/PTP1B 0.033 0.12 0.27 9 -0.29 5 14
CAPN1 0.035 0.004 -10000 0 -10000 0 0
CSK 0.033 0.006 -10000 0 -10000 0 0
PI3K 0.044 0.078 -10000 0 -0.24 5 5
mol:H2O2 0.003 0.005 0.01 21 -0.008 1 22
STAT3 (dimer) -0.023 0.13 -10000 0 -0.36 12 12
negative regulation of transcription -0.014 0.13 0.21 1 -0.34 14 15
FCGR2A 0.03 0.036 -10000 0 -0.38 1 1
FER 0.029 0.049 -10000 0 -0.39 2 2
alphaIIb/beta3 Integrin 0.014 0.1 -10000 0 -0.29 13 13
BLK 0.022 0.024 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.04 0.028 -10000 0 -0.23 1 1
RHOA 0.035 0.005 -10000 0 -10000 0 0
LEPR 0.034 0.008 -10000 0 -10000 0 0
BCAR1 0.033 0.007 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.034 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.004 0.009 8 -0.008 3 11
TRPV6 0.017 0.11 0.24 4 -0.29 6 10
PRL 0.001 0.004 0.014 12 -10000 0 12
SOCS3 -0.088 0.35 -10000 0 -1.2 13 13
SPRY2 0.035 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.033 0.055 -10000 0 -0.23 6 6
CSF1/CSF1R 0.041 0.094 -10000 0 -0.26 5 5
Ras protein signal transduction -0.007 0.084 0.55 3 -10000 0 3
IRS1 0.02 0.076 -10000 0 -0.38 5 5
INS 0 0.001 -10000 0 -0.008 2 2
LEP 0.012 0.027 -10000 0 -10000 0 0
STAT5B 0.015 0.083 0.24 1 -0.32 2 3
STAT5A 0.015 0.083 0.2 2 -0.28 3 5
GRB2 0.034 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.033 0.084 0.22 1 -0.28 4 5
CSN2 -0.01 0.033 0.099 1 -0.13 6 7
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
LAT 0.026 0.091 -10000 0 -0.47 4 4
YBX1 0.041 0.008 -10000 0 -10000 0 0
LCK -0.002 0.11 -10000 0 -0.38 11 11
SHC1 0.031 0.015 -10000 0 -10000 0 0
NOX4 0.02 0.084 -10000 0 -0.39 6 6
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.003 0.13 -9999 0 -0.22 31 31
SMAD6-7/SMURF1 0.044 0.034 -9999 0 -10000 0 0
NOG 0.003 0.1 -9999 0 -0.38 10 10
SMAD9 -0.039 0.17 -9999 0 -0.45 20 20
SMAD4 0.033 0.008 -9999 0 -10000 0 0
SMAD5 -0.03 0.1 -9999 0 -0.3 13 13
BMP7/USAG1 -0.004 0.095 -9999 0 -0.29 13 13
SMAD5/SKI -0.023 0.11 -9999 0 -0.31 10 10
SMAD1 0.008 0.068 -9999 0 -0.44 1 1
BMP2 0.025 0.039 -9999 0 -0.38 1 1
SMAD1/SMAD1/SMAD4 0.021 0.065 -9999 0 -0.38 1 1
BMPR1A 0.023 0.016 -9999 0 -10000 0 0
BMPR1B 0.003 0.11 -9999 0 -0.38 11 11
BMPR1A-1B/BAMBI 0.025 0.077 -9999 0 -0.22 11 11
AHSG 0.004 0.1 -9999 0 -0.38 9 9
CER1 0.003 0.079 -9999 0 -0.38 5 5
BMP2-4/CER1 0.026 0.068 -9999 0 -0.23 6 6
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.002 0.078 -9999 0 -0.25 1 1
BMP2-4 (homodimer) 0.036 0.037 -9999 0 -0.27 1 1
RGMB 0.032 0.012 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.036 0.086 -9999 0 -0.22 11 11
RGMA 0.025 0.059 -9999 0 -0.38 3 3
SMURF1 0.023 0.016 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.019 0.079 -9999 0 -0.26 5 5
BMP2-4/USAG1 0.009 0.08 -9999 0 -0.24 11 11
SMAD6/SMURF1/SMAD5 -0.009 0.095 -9999 0 -0.29 10 10
SOSTDC1 -0.018 0.11 -9999 0 -0.38 12 12
BMP7/BMPR2/BMPR1A-1B 0.033 0.093 -9999 0 -0.24 12 12
SKI 0.03 0.035 -9999 0 -0.38 1 1
BMP6 (homodimer) 0.025 0.041 -9999 0 -0.38 1 1
HFE2 0.027 0.01 -9999 0 -10000 0 0
ZFYVE16 0.033 0.006 -9999 0 -10000 0 0
MAP3K7 0.031 0.01 -9999 0 -10000 0 0
BMP2-4/CHRD 0.043 0.061 -9999 0 -0.23 5 5
SMAD5/SMAD5/SMAD4 -0.022 0.11 -9999 0 -0.3 11 11
MAPK1 0.032 0.009 -9999 0 -10000 0 0
TAK1/TAB family 0.008 0.067 -9999 0 -0.23 2 2
BMP7 (homodimer) 0.014 0.082 -9999 0 -0.38 6 6
NUP214 0.033 0.008 -9999 0 -10000 0 0
BMP6/FETUA 0.018 0.082 -9999 0 -0.27 10 10
SMAD1/SKI 0.017 0.079 -9999 0 -0.42 1 1
SMAD6 0.032 0.012 -9999 0 -10000 0 0
CTDSP2 0.029 0.013 -9999 0 -10000 0 0
BMP2-4/FETUA 0.031 0.079 -9999 0 -0.23 10 10
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.042 0.14 -9999 0 -0.38 20 20
BMPR2 (homodimer) 0.034 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.064 0.02 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) 0.013 0.081 -9999 0 -0.26 11 11
CHRDL1 -0.013 0.13 -9999 0 -0.38 15 15
ENDOFIN/SMAD1 0.02 0.077 -9999 0 -0.42 1 1
SMAD6-7/SMURF1/SMAD1 0.032 0.076 -9999 0 -0.41 1 1
SMAD6/SMURF1 0.023 0.016 -9999 0 -10000 0 0
BAMBI 0.02 0.022 -9999 0 -10000 0 0
SMURF2 0.034 0.003 -9999 0 -10000 0 0
BMP2-4/CHRDL1 0.019 0.097 -9999 0 -0.25 15 15
BMP2-4/GREM1 0 0.096 -9999 0 -0.23 17 17
SMAD7 0.033 0.008 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.032 0.18 -9999 0 -0.43 23 23
SMAD1/SMAD6 0.014 0.066 -9999 0 -0.42 1 1
TAK1/SMAD6 0.034 0.024 -9999 0 -10000 0 0
BMP7 0.014 0.082 -9999 0 -0.38 6 6
BMP6 0.025 0.041 -9999 0 -0.38 1 1
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.008 0.065 -9999 0 -0.24 2 2
PPM1A 0.032 0.009 -9999 0 -10000 0 0
SMAD1/SMURF2 0.022 0.077 -9999 0 -0.42 1 1
SMAD7/SMURF1 0.033 0.024 -9999 0 -10000 0 0
CTDSPL 0.034 0.004 -9999 0 -10000 0 0
PPP1CA 0.034 0.003 -9999 0 -10000 0 0
XIAP 0.034 0.003 -9999 0 -10000 0 0
CTDSP1 0.034 0 -9999 0 -10000 0 0
PPP1R15A 0.033 0.008 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.051 0.11 -9999 0 -0.28 17 17
CHRD 0.02 0.075 -9999 0 -0.38 5 5
BMPR2 0.034 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.017 0.076 -9999 0 -0.26 5 5
BMP4 0.029 0.018 -9999 0 -10000 0 0
FST -0.037 0.14 -9999 0 -0.38 21 21
BMP2-4/NOG 0.034 0.082 -9999 0 -0.26 9 9
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.035 0.079 -9999 0 -0.2 9 9
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.033 0.006 -10000 0 -10000 0 0
mol:PIP3 -0.01 0.037 -10000 0 -0.23 3 3
FRAP1 0.046 0.053 0.27 1 -10000 0 1
AKT1 0.038 0.09 0.17 41 -0.2 3 44
INSR 0.03 0.035 -10000 0 -0.38 1 1
Insulin Receptor/Insulin 0.021 0.02 -10000 0 -0.22 1 1
mol:GTP 0.063 0.085 0.19 29 -0.24 2 31
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.009 0.025 -10000 0 -10000 0 0
TSC2 0.031 0.034 -10000 0 -0.38 1 1
RHEB/GDP 0.018 0.043 -10000 0 -0.22 2 2
TSC1 0.033 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.021 0.062 -10000 0 -0.27 6 6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.047 0.047 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.023 0.016 -10000 0 -10000 0 0
RPS6KB1 0.055 0.075 0.21 8 -0.24 1 9
MAP3K5 -0.017 0.072 0.16 2 -0.2 17 19
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
apoptosis -0.017 0.072 0.16 2 -0.2 17 19
mol:LY294002 0 0 -10000 0 -0.002 5 5
EIF4B 0.05 0.074 0.21 10 -0.22 1 11
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.032 0.046 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0.025 0.022 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.043 0.064 -10000 0 -0.25 6 6
mTOR/RHEB/GTP/Raptor/GBL 0.02 0.052 0.19 9 -10000 0 9
FKBP1A 0.032 0.009 -10000 0 -10000 0 0
RHEB/GTP 0.036 0.062 0.26 2 -0.21 2 4
mol:Amino Acids 0 0 -10000 0 -0.002 5 5
FKBP12/Rapamycin 0.024 0.007 -10000 0 -10000 0 0
PDPK1 -0.011 0.039 0.16 2 -0.22 3 5
EIF4E 0.034 0.003 -10000 0 -10000 0 0
ASK1/PP5C -0.007 0.2 -10000 0 -0.54 17 17
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.019 0.03 -10000 0 -10000 0 0
TSC1/TSC2 0.069 0.092 0.2 29 -0.26 2 31
tumor necrosis factor receptor activity 0 0 0.002 5 -10000 0 5
RPS6 0.028 0.016 -10000 0 -10000 0 0
PPP5C 0.033 0.008 -10000 0 -10000 0 0
EIF4G1 0.031 0.034 -10000 0 -0.38 1 1
IRS1 0.002 0.058 -10000 0 -0.31 5 5
INS 0 0 -10000 0 -10000 0 0
PTEN 0.022 0.016 -10000 0 -10000 0 0
PDK2 -0.011 0.04 0.16 2 -0.22 3 5
EIF4EBP1 0.024 0.088 -10000 0 -1 1 1
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
PPP2R5D 0.04 0.051 0.26 1 -10000 0 1
peptide biosynthetic process 0.015 0.018 -10000 0 -0.2 1 1
RHEB 0.024 0.016 -10000 0 -10000 0 0
EIF4A1 0.033 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.001 0.002 33 -10000 0 33
EEF2 0.015 0.018 -10000 0 -0.2 1 1
eIF4E/4E-BP1 0.042 0.083 -10000 0 -0.96 1 1
Nectin adhesion pathway

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
PDGFRB 0.033 0.012 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.035 0.065 -10000 0 -0.27 6 6
PTK2 -0.01 0.12 -10000 0 -0.36 10 10
positive regulation of JNK cascade 0.001 0.12 -10000 0 -0.29 10 10
CDC42/GDP 0.006 0.16 0.3 1 -0.4 13 14
Rac1/GDP 0.004 0.14 0.3 1 -0.39 8 9
RAP1B 0.031 0.01 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CTNNB1 0.034 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.004 0.14 -10000 0 -0.36 10 10
nectin-3/I-afadin 0.021 0.082 -10000 0 -0.27 10 10
RAPGEF1 -0.026 0.16 -10000 0 -0.43 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.034 0.17 -10000 0 -0.48 12 12
PDGFB-D/PDGFRB 0.033 0.012 -10000 0 -10000 0 0
TLN1 -0.014 0.032 -10000 0 -0.19 1 1
Rap1/GTP -0.011 0.12 -10000 0 -0.32 11 11
IQGAP1 0.034 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.054 0.026 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.021 0.082 -10000 0 -0.27 10 10
PVR 0.033 0.008 -10000 0 -10000 0 0
Necl-5(dimer) 0.032 0.008 -10000 0 -10000 0 0
mol:GDP -0.016 0.19 0.31 1 -0.49 13 14
MLLT4 0.031 0.01 -10000 0 -10000 0 0
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
PI3K 0.06 0.085 -10000 0 -0.2 11 11
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.041 0.041 -10000 0 -0.27 2 2
positive regulation of lamellipodium assembly -0.007 0.11 -10000 0 -0.34 8 8
PVRL1 0.027 0.049 -10000 0 -0.38 2 2
PVRL3 0.002 0.1 -10000 0 -0.38 10 10
PVRL2 0.033 0.007 -10000 0 -10000 0 0
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
CDH1 -0.037 0.15 -10000 0 -0.38 23 23
CLDN1 0.02 0.068 -10000 0 -0.38 4 4
JAM-A/CLDN1 0.043 0.089 -10000 0 -0.21 13 13
SRC -0.033 0.19 -10000 0 -0.52 13 13
ITGB3 0.015 0.083 -10000 0 -0.38 6 6
nectin-1(dimer)/I-afadin/I-afadin 0.041 0.041 -10000 0 -0.27 2 2
FARP2 -0.007 0.17 -10000 0 -0.5 4 4
RAC1 0.023 0.016 -10000 0 -10000 0 0
CTNNA1 0.034 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.037 0.075 -10000 0 -0.23 9 9
nectin-1/I-afadin 0.041 0.041 -10000 0 -0.27 2 2
nectin-2/I-afadin 0.044 0.018 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.031 0.022 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.033 0.084 -10000 0 -0.23 12 12
CDC42/GTP/IQGAP1/filamentous actin 0.045 0.009 -10000 0 -10000 0 0
F11R 0.034 0.005 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.001 0.12 -10000 0 -0.29 10 10
alphaV/beta3 Integrin/Talin 0.021 0.078 0.2 5 -0.25 3 8
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.044 0.018 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.044 0.018 -10000 0 -10000 0 0
PIP5K1C -0.006 0.038 -10000 0 -0.15 9 9
VAV2 -0.024 0.21 -10000 0 -0.56 13 13
RAP1/GDP 0.007 0.15 -10000 0 -0.37 13 13
ITGAV 0.034 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.037 0.075 -10000 0 -0.23 9 9
nectin-3(dimer)/I-afadin/I-afadin 0.021 0.082 -10000 0 -0.27 10 10
Rac1/GTP -0.004 0.14 -10000 0 -0.41 8 8
PTPRM 0.001 0.043 -10000 0 -0.16 10 10
E-cadherin/beta catenin/alpha catenin 0.033 0.11 -10000 0 -0.2 23 23
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.034 0.005 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.011 0.097 -10000 0 -0.27 15 15
alphaV beta3 Integrin 0.052 0.066 -10000 0 -0.23 7 7
PTK2 -0.04 0.15 0.46 1 -0.43 9 10
IGF1R 0.033 0.012 -10000 0 -10000 0 0
PI4KB 0.033 0.006 -10000 0 -10000 0 0
MFGE8 0.033 0.009 -10000 0 -10000 0 0
SRC 0.029 0.035 -10000 0 -0.38 1 1
CDKN1B 0.005 0.091 -10000 0 -0.41 6 6
VEGFA -0.01 0.12 -10000 0 -0.38 14 14
ILK 0.006 0.092 -10000 0 -0.42 6 6
ROCK1 0.033 0.007 -10000 0 -10000 0 0
AKT1 -0.009 0.089 -10000 0 -0.4 6 6
PTK2B -0.031 0.09 0.17 13 -0.22 18 31
alphaV/beta3 Integrin/JAM-A 0.05 0.071 -10000 0 -0.2 9 9
CBL 0.034 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.033 0.055 -10000 0 -0.23 6 6
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.058 0.083 -10000 0 -0.22 11 11
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.02 0.1 -10000 0 -0.37 8 8
alphaV/beta3 Integrin/Syndecan-1 0.041 0.081 -10000 0 -0.26 8 8
PI4KA 0.032 0.009 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.044 0.095 -10000 0 -0.21 16 16
PI4 Kinase 0.046 0.015 -10000 0 -10000 0 0
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.027 0.1 -10000 0 -0.26 15 15
RPS6KB1 -0.05 0.061 -10000 0 -0.35 1 1
TLN1 0.03 0.011 -10000 0 -10000 0 0
MAPK3 -0.005 0.086 -10000 0 -0.42 5 5
GPR124 0.03 0.036 -10000 0 -0.38 1 1
MAPK1 -0.007 0.089 -10000 0 -0.43 5 5
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
alphaV/beta3 Integrin/Tumstatin -0.007 0.12 -10000 0 -0.23 27 27
cell adhesion 0.04 0.06 -10000 0 -0.24 6 6
ANGPTL3 0 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.022 0.094 -10000 0 -0.23 16 16
IGF-1R heterotetramer 0.033 0.012 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.012 -10000 0 -10000 0 0
TGFBR2 0.034 0.004 -10000 0 -10000 0 0
ITGB3 0.015 0.083 -10000 0 -0.38 6 6
IGF1 0.013 0.084 -10000 0 -0.38 6 6
RAC1 0.023 0.016 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.051 0.062 -10000 0 -0.23 6 6
apoptosis 0.034 0.003 -10000 0 -10000 0 0
CD47 0.034 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.054 0.061 -10000 0 -0.23 6 6
VCL 0.023 0.016 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.014 0.11 -10000 0 -0.25 19 19
CSF1 0.034 0.005 -10000 0 -10000 0 0
PIK3C2A 0.006 0.092 -10000 0 -0.42 6 6
PI4 Kinase/Pyk2 0 0.094 -10000 0 -0.3 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.033 0.11 -10000 0 -0.22 20 20
FAK1/Vinculin -0.032 0.12 0.44 1 -0.35 8 9
alphaV beta3/Integrin/ppsTEM5 0.052 0.063 -10000 0 -0.23 6 6
RHOA 0.034 0.004 -10000 0 -10000 0 0
VTN 0.018 0.076 -10000 0 -0.38 5 5
BCAR1 0.033 0.007 -10000 0 -10000 0 0
FGF2 0.031 0.034 -10000 0 -0.38 1 1
F11R -0.015 0.002 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.052 0.063 -10000 0 -0.23 6 6
alphaV/beta3 Integrin/TGFBR2 0.053 0.062 -10000 0 -0.23 6 6
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.083 0.022 -10000 0 -10000 0 0
HSP90AA1 0.032 0.009 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.047 0.053 -10000 0 -0.2 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.033 0.011 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.028 0.1 -10000 0 -0.22 18 18
SDC1 0.017 0.064 -10000 0 -0.38 3 3
VAV3 -0.033 0.047 0.18 1 -0.2 9 10
PTPN11 0.034 0.003 -10000 0 -10000 0 0
IRS1 0.02 0.076 -10000 0 -0.38 5 5
FAK1/Paxillin -0.022 0.13 0.44 1 -0.36 8 9
cell migration -0.035 0.11 0.42 1 -0.32 8 9
ITGAV 0.034 0.003 -10000 0 -10000 0 0
PI3K 0.064 0.073 -10000 0 -0.2 9 9
SPP1 -0.005 0.11 -10000 0 -0.38 12 12
KDR 0.029 0.035 -10000 0 -0.38 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.034 0.003 -10000 0 -10000 0 0
COL4A3 -0.042 0.14 -10000 0 -0.38 21 21
angiogenesis -0.007 0.093 -10000 0 -0.45 5 5
Rac1/GTP 0.007 0.054 0.18 1 -0.19 9 10
EDIL3 -0.017 0.13 -10000 0 -0.38 15 15
cell proliferation 0.052 0.062 -10000 0 -0.23 6 6
LPA receptor mediated events

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.049 0.052 -10000 0 -0.2 4 4
NF kappa B1 p50/RelA/I kappa B alpha 0.021 0.081 0.28 4 -10000 0 4
AP1 0.015 0.059 -10000 0 -0.19 6 6
mol:PIP3 -0.044 0.079 -10000 0 -0.2 28 28
AKT1 0.02 0.075 0.23 6 -0.32 1 7
PTK2B 0.009 0.054 0.19 4 -10000 0 4
RHOA 0.031 0.055 0.21 4 -10000 0 4
PIK3CB 0.03 0.035 -10000 0 -0.38 1 1
mol:Ca2+ -0.008 0.039 0.18 1 -10000 0 1
MAGI3 0.034 0.005 -10000 0 -10000 0 0
RELA 0.034 0.003 -10000 0 -10000 0 0
apoptosis 0.006 0.041 -10000 0 -0.21 4 4
HRAS/GDP 0.024 0.006 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.007 0.064 0.22 1 -0.3 1 2
NF kappa B1 p50/RelA 0.006 0.062 -10000 0 -10000 0 0
endothelial cell migration 0.004 0.069 -10000 0 -0.33 5 5
ADCY4 0.014 0.072 -10000 0 -0.24 5 5
ADCY5 0.005 0.091 -10000 0 -0.29 8 8
ADCY6 0.016 0.07 -10000 0 -0.24 5 5
ADCY7 0.015 0.073 -10000 0 -0.25 6 6
ADCY1 -0.006 0.064 -10000 0 -0.27 5 5
ADCY2 0.003 0.088 -10000 0 -0.27 8 8
ADCY3 0.017 0.07 -10000 0 -0.24 5 5
ADCY8 0.006 0.091 -10000 0 -0.31 8 8
ADCY9 0.015 0.074 -10000 0 -0.25 6 6
GSK3B 0.006 0.052 0.21 2 -10000 0 2
arachidonic acid secretion 0.008 0.074 -10000 0 -0.24 6 6
GNG2 0.031 0.013 -10000 0 -10000 0 0
TRIP6 0.016 0.013 -10000 0 -10000 0 0
GNAO1 -0.005 0.071 -10000 0 -0.23 13 13
HRAS 0.033 0.008 -10000 0 -10000 0 0
NFKBIA -0.005 0.073 0.27 4 -10000 0 4
GAB1 0.031 0.034 -10000 0 -0.38 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.035 0.076 -10000 0 -0.8 1 1
JUN 0.033 0.006 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.042 0.021 -10000 0 -10000 0 0
TIAM1 0.037 0.081 -10000 0 -0.92 1 1
PIK3R1 0.029 0.036 -10000 0 -0.38 1 1
mol:IP3 -0.006 0.037 0.19 1 -10000 0 1
PLCB3 0.015 0.043 0.18 6 -0.21 1 7
FOS 0.018 0.062 -10000 0 -0.38 3 3
positive regulation of mitosis 0.008 0.074 -10000 0 -0.24 6 6
LPA/LPA1-2-3 0.041 0.056 -10000 0 -0.21 4 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.033 0.007 -10000 0 -10000 0 0
stress fiber formation 0.02 0.053 0.27 1 -10000 0 1
GNAZ 0.004 0.053 -10000 0 -0.22 7 7
EGFR/PI3K-beta/Gab1 -0.037 0.086 -10000 0 -0.2 28 28
positive regulation of dendritic cell cytokine production 0.039 0.055 -10000 0 -0.21 4 4
LPA/LPA2/MAGI-3 0.043 0.02 -10000 0 -10000 0 0
ARHGEF1 0.057 0.095 0.19 43 -0.2 4 47
GNAI2 0.008 0.045 -10000 0 -0.22 5 5
GNAI3 0.008 0.045 -10000 0 -0.22 5 5
GNAI1 0.003 0.045 -10000 0 -0.23 5 5
LPA/LPA3 0.016 0.022 -10000 0 -0.1 2 2
LPA/LPA2 0.022 0.019 -10000 0 -0.1 2 2
LPA/LPA1 0.016 0.055 -10000 0 -0.26 5 5
HB-EGF/EGFR -0.055 0.11 -10000 0 -0.25 34 34
HBEGF -0.054 0.094 -10000 0 -0.28 20 20
mol:DAG -0.006 0.037 0.19 1 -10000 0 1
cAMP biosynthetic process 0.008 0.093 0.18 2 -0.26 8 10
NFKB1 0.034 0.003 -10000 0 -10000 0 0
SRC 0.029 0.035 -10000 0 -0.38 1 1
GNB1 0.032 0.008 -10000 0 -10000 0 0
LYN 0.002 0.074 0.27 4 -0.35 2 6
GNAQ 0.01 0.019 -10000 0 -10000 0 0
LPAR2 0.032 0.013 -10000 0 -10000 0 0
LPAR3 0.023 0.022 -10000 0 -10000 0 0
LPAR1 0.02 0.064 -10000 0 -0.29 5 5
IL8 -0.15 0.2 0.34 1 -0.41 48 49
PTK2 -0.004 0.054 0.18 6 -0.2 4 10
Rac1/GDP 0.017 0.012 -10000 0 -10000 0 0
CASP3 0.006 0.041 -10000 0 -0.21 4 4
EGFR -0.066 0.15 -10000 0 -0.38 28 28
PLCG1 0.004 0.036 0.15 2 -0.22 1 3
PLD2 -0.002 0.058 0.18 6 -0.2 4 10
G12/G13 0.038 0.055 -10000 0 -0.21 4 4
PI3K-beta 0.01 0.046 -10000 0 -0.35 1 1
cell migration 0.022 0.033 -10000 0 -0.22 1 1
SLC9A3R2 0.034 0.005 -10000 0 -10000 0 0
PXN 0.02 0.053 0.27 1 -10000 0 1
HRAS/GTP 0.008 0.075 -10000 0 -0.24 6 6
RAC1 0.023 0.016 -10000 0 -10000 0 0
MMP9 -0.034 0.14 -10000 0 -0.38 20 20
PRKCE 0.033 0.01 -10000 0 -10000 0 0
PRKCD -0.003 0.066 0.28 5 -10000 0 5
Gi(beta/gamma) 0.017 0.071 0.15 1 -0.23 6 7
mol:LPA 0 0.018 -10000 0 -0.15 2 2
TRIP6/p130 Cas/FAK1/Paxillin 0.052 0.052 -10000 0 -10000 0 0
MAPKKK cascade 0.008 0.074 -10000 0 -0.24 6 6
contractile ring contraction involved in cytokinesis 0.031 0.055 0.21 4 -10000 0 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 0.006 0.027 -10000 0 -0.22 1 1
GNA15 0.003 0.047 -10000 0 -0.23 5 5
GNA12 0.02 0.037 -10000 0 -0.38 1 1
GNA13 0.034 0.003 -10000 0 -10000 0 0
MAPT -0.007 0.066 0.22 1 -0.3 1 2
GNA11 0.008 0.033 -10000 0 -0.22 2 2
Rac1/GTP 0.036 0.08 -10000 0 -0.85 1 1
MMP2 0.004 0.069 -10000 0 -0.33 5 5
BCR 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
JUN -0.005 0.12 0.21 1 -0.38 8 9
IKBKB 0.031 0.088 0.23 3 -0.4 1 4
AKT1 -0.003 0.083 0.22 8 -0.2 5 13
IKBKG 0.027 0.08 0.23 2 -0.24 1 3
CALM1 -0.028 0.097 -10000 0 -0.45 5 5
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
MAP3K1 0.011 0.13 0.26 2 -0.41 6 8
MAP3K7 0.031 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.028 0.1 -10000 0 -0.47 5 5
DOK1 0.034 0 -10000 0 -10000 0 0
AP-1 -0.015 0.078 0.21 1 -0.27 7 8
LYN 0.028 0.048 -10000 0 -0.38 2 2
BLNK 0.015 0.059 -10000 0 -0.38 3 3
SHC1 0.031 0.015 -10000 0 -10000 0 0
BCR complex 0.027 0.068 -10000 0 -0.27 6 6
CD22 -0.044 0.11 -10000 0 -0.42 7 7
CAMK2G -0.019 0.088 -10000 0 -0.46 4 4
CSNK2A1 0.032 0.009 -10000 0 -10000 0 0
INPP5D 0.022 0.068 -10000 0 -0.38 4 4
SHC/GRB2/SOS1 -0.001 0.069 -10000 0 -0.21 10 10
GO:0007205 -0.031 0.11 -10000 0 -0.45 6 6
SYK 0.018 0.076 -10000 0 -0.38 5 5
ELK1 -0.034 0.1 -10000 0 -0.43 6 6
NFATC1 -0.031 0.091 0.22 1 -0.32 7 8
B-cell antigen/BCR complex 0.027 0.068 -10000 0 -0.27 6 6
PAG1/CSK 0.048 0.012 -10000 0 -10000 0 0
NFKBIB 0.032 0.04 0.14 2 -0.14 2 4
HRAS -0.028 0.092 -10000 0 -0.4 5 5
NFKBIA 0.032 0.04 0.14 2 -0.13 2 4
NF-kappa-B/RelA/I kappa B beta 0.036 0.037 0.13 4 -10000 0 4
RasGAP/Csk 0.044 0.1 -10000 0 -0.21 17 17
mol:GDP -0.027 0.11 -10000 0 -0.44 6 6
PTEN 0.023 0.016 -10000 0 -10000 0 0
CD79B 0.02 0.062 -10000 0 -0.38 3 3
NF-kappa-B/RelA/I kappa B alpha 0.036 0.037 0.13 4 -10000 0 4
GRB2 0.034 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.035 0.14 -10000 0 -0.5 8 8
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
mol:IP3 -0.027 0.1 -10000 0 -0.48 5 5
CSK 0.033 0.006 -10000 0 -10000 0 0
FOS -0.035 0.11 -10000 0 -0.42 7 7
CHUK -0.058 0.15 0.23 2 -0.3 26 28
IBTK 0.032 0.009 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.038 0.11 -10000 0 -0.32 4 4
PTPN6 -0.048 0.1 -10000 0 -0.43 6 6
RELA 0.034 0.003 -10000 0 -10000 0 0
BCL2A1 0.021 0.033 0.11 2 -0.11 1 3
VAV2 -0.035 0.12 -10000 0 -0.43 8 8
ubiquitin-dependent protein catabolic process 0.034 0.04 0.14 2 -0.14 2 4
BTK 0.009 0.13 -10000 0 -0.88 3 3
CD19 -0.018 0.091 -10000 0 -0.41 5 5
MAP4K1 0.03 0.035 -10000 0 -0.38 1 1
CD72 0.024 0.039 -10000 0 -0.38 1 1
PAG1 0.033 0.006 -10000 0 -10000 0 0
MAPK14 0.01 0.11 0.25 2 -0.36 6 8
SH3BP5 0.028 0.049 -10000 0 -0.38 2 2
PIK3AP1 -0.014 0.12 -10000 0 -0.54 6 6
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.019 0.17 -10000 0 -0.71 6 6
RAF1 -0.03 0.087 -10000 0 -0.43 4 4
RasGAP/p62DOK/SHIP 0.045 0.1 -10000 0 -0.21 18 18
CD79A 0.017 0.07 -10000 0 -0.38 4 4
re-entry into mitotic cell cycle -0.015 0.078 0.2 1 -0.27 7 8
RASA1 0.033 0.006 -10000 0 -10000 0 0
MAPK3 -0.031 0.075 -10000 0 -0.36 4 4
MAPK1 -0.029 0.077 -10000 0 -0.36 4 4
CD72/SHP1 -0.027 0.11 0.26 2 -0.36 6 8
NFKB1 0.034 0.003 -10000 0 -10000 0 0
MAPK8 0.01 0.11 0.25 2 -0.38 5 7
actin cytoskeleton organization 0.015 0.12 0.26 1 -0.35 7 8
NF-kappa-B/RelA 0.07 0.071 0.26 2 -10000 0 2
Calcineurin 0.001 0.1 -10000 0 -0.39 4 4
PI3K -0.047 0.1 -10000 0 -0.36 7 7
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.011 0.12 0.2 1 -0.44 8 9
SOS1 0.034 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.004 0.2 -10000 0 -0.8 8 8
DAPP1 -0.031 0.23 -10000 0 -0.9 9 9
cytokine secretion -0.029 0.086 0.21 1 -0.3 7 8
mol:DAG -0.027 0.1 -10000 0 -0.48 5 5
PLCG2 0.03 0.035 -10000 0 -0.38 1 1
MAP2K1 -0.031 0.083 -10000 0 -0.4 4 4
B-cell antigen/BCR complex/FcgammaRIIB 0.006 0.1 -10000 0 -0.24 17 17
mol:PI-3-4-5-P3 -0.036 0.067 0.28 1 -0.25 5 6
ETS1 -0.03 0.086 -10000 0 -0.42 4 4
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.034 0.097 -10000 0 -0.23 12 12
B-cell antigen/BCR complex/LYN -0.009 0.11 -10000 0 -0.39 8 8
MALT1 0.033 0.007 -10000 0 -10000 0 0
TRAF6 0.028 0.048 -10000 0 -0.38 2 2
RAC1 0.015 0.12 0.26 1 -0.39 6 7
B-cell antigen/BCR complex/LYN/SYK -0.007 0.14 0.26 1 -0.42 7 8
CARD11 0.01 0.13 -10000 0 -0.38 7 7
FCGR2B -0.018 0.12 -10000 0 -0.38 13 13
PPP3CA 0.034 0.003 -10000 0 -10000 0 0
BCL10 0.033 0.007 -10000 0 -10000 0 0
IKK complex 0.006 0.048 0.16 3 -0.12 5 8
PTPRC 0.013 0.089 -10000 0 -0.38 7 7
PDPK1 -0.028 0.052 0.18 2 -0.18 5 7
PPP3CB 0.023 0.016 -10000 0 -10000 0 0
PPP3CC 0.033 0.006 -10000 0 -10000 0 0
POU2F2 0.026 0.029 0.13 3 -10000 0 3
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.013 0.018 -10000 0 -0.23 1 1
ADCY5 -0.033 0.061 -10000 0 -0.23 13 13
ADCY6 -0.012 0.003 -10000 0 -10000 0 0
ADCY7 -0.013 0.018 -10000 0 -0.23 1 1
ADCY1 -0.014 0.036 -10000 0 -0.23 4 4
ADCY2 -0.032 0.061 -10000 0 -0.23 13 13
ADCY3 -0.012 0.003 -10000 0 -10000 0 0
ADCY8 -0.024 0.049 -10000 0 -0.23 8 8
PRKCE -0.008 0.003 -10000 0 -10000 0 0
ADCY9 -0.013 0.018 -10000 0 -0.23 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.004 0.062 0.16 5 -0.21 2 7
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.025 0.043 -10000 0 -0.22 4 4
EPHB2 0.028 0.048 -10000 0 -0.38 2 2
Syndecan-2/TACI 0.002 0.037 -10000 0 -0.22 4 4
LAMA1 -0.036 0.15 -10000 0 -0.38 23 23
Syndecan-2/alpha2 ITGB1 0.018 0.077 -10000 0 -0.21 11 11
HRAS 0.033 0.008 -10000 0 -10000 0 0
Syndecan-2/CASK 0.002 0.037 -10000 0 -0.22 4 4
ITGA5 0.029 0.036 -10000 0 -0.38 1 1
BAX -0.006 0.017 -10000 0 -10000 0 0
EPB41 0.03 0.035 -10000 0 -0.38 1 1
positive regulation of cell-cell adhesion 0.023 0.038 -10000 0 -0.2 4 4
LAMA3 0.01 0.079 -10000 0 -0.38 5 5
EZR 0.031 0.01 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.016 0.051 -10000 0 -0.38 2 2
Syndecan-2/MMP2 0.02 0.052 -10000 0 -0.22 6 6
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.024 0.055 -10000 0 -0.27 4 4
dendrite morphogenesis 0.021 0.052 -10000 0 -0.23 6 6
Syndecan-2/GM-CSF 0.002 0.037 -10000 0 -0.22 4 4
determination of left/right symmetry 0.003 0.045 -10000 0 -0.26 4 4
Syndecan-2/PKC delta 0.025 0.042 -10000 0 -0.22 4 4
GNB2L1 0.034 0.004 -10000 0 -10000 0 0
MAPK3 0.009 0.046 0.19 4 -0.2 4 8
MAPK1 0.01 0.042 0.19 4 -0.2 3 7
Syndecan-2/RACK1 0.041 0.042 -10000 0 -0.19 4 4
NF1 0.031 0.034 -10000 0 -0.38 1 1
FGFR/FGF/Syndecan-2 0.003 0.045 -10000 0 -0.26 4 4
ITGA2 0.02 0.069 -10000 0 -0.38 4 4
MAPK8 0 0.027 -10000 0 -0.22 2 2
Syndecan-2/alpha2/beta1 Integrin -0.005 0.1 -10000 0 -0.19 30 30
Syndecan-2/Kininogen 0.002 0.037 -10000 0 -0.22 4 4
ITGB1 0.024 0.016 -10000 0 -10000 0 0
SRC -0.017 0.04 0.18 2 -0.19 4 6
Syndecan-2/CASK/Protein 4.1 0.02 0.044 -10000 0 -0.2 5 5
extracellular matrix organization 0.024 0.042 -10000 0 -0.22 4 4
actin cytoskeleton reorganization 0.025 0.043 -10000 0 -0.22 4 4
Syndecan-2/Caveolin-2/Ras 0.025 0.048 -10000 0 -0.2 4 4
Syndecan-2/Laminin alpha3 0.009 0.063 -10000 0 -0.22 9 9
Syndecan-2/RasGAP 0.056 0.044 -10000 0 -0.18 4 4
alpha5/beta1 Integrin 0.031 0.035 -10000 0 -0.25 1 1
PRKCD 0.034 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.021 0.052 -10000 0 -0.23 6 6
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.029 0.044 -10000 0 -0.19 5 5
RHOA 0.034 0.004 -10000 0 -10000 0 0
SDCBP 0.033 0.006 -10000 0 -10000 0 0
TNFRSF13B 0 0 -10000 0 -10000 0 0
RASA1 0.033 0.006 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.024 0.055 -10000 0 -0.27 4 4
Syndecan-2/Synbindin 0.025 0.043 -10000 0 -0.22 4 4
TGFB1 0.033 0.007 -10000 0 -10000 0 0
CASP3 0.013 0.036 0.19 3 -0.2 2 5
FN1 0.033 0.011 -10000 0 -10000 0 0
Syndecan-2/IL8 -0.027 0.11 -10000 0 -0.25 25 25
SDC2 0.003 0.045 -10000 0 -0.26 4 4
KNG1 0 0 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.023 0.047 -10000 0 -0.22 5 5
TRAPPC4 0.034 0.003 -10000 0 -10000 0 0
CSF2 0 0 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.024 0.042 -10000 0 -0.22 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.023 0.039 -10000 0 -0.2 4 4
Syndecan-2/Ezrin 0.04 0.044 -10000 0 -0.19 4 4
PRKACA 0.009 0.05 0.19 4 -0.2 5 9
angiogenesis -0.026 0.11 -10000 0 -0.25 25 25
MMP2 0.025 0.051 -10000 0 -0.38 2 2
IL8 -0.05 0.15 -10000 0 -0.38 24 24
calcineurin-NFAT signaling pathway 0.002 0.037 -10000 0 -0.22 4 4
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.024 0.016 -9999 0 -10000 0 0
ITGB7 0.026 0.05 -9999 0 -0.38 2 2
ITGA4 0.014 0.083 -9999 0 -0.38 6 6
alpha4/beta7 Integrin 0.028 0.075 -9999 0 -0.27 8 8
alpha4/beta1 Integrin 0.019 0.065 -9999 0 -0.27 6 6
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.014 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.048 0.019 -10000 0 -10000 0 0
CDKN1B 0.005 0.082 0.2 2 -0.29 9 11
CDKN1A 0.001 0.078 -10000 0 -0.29 8 8
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.034 0.005 -10000 0 -10000 0 0
FOXO3 0.006 0.073 0.2 1 -0.29 7 8
AKT1 0.006 0.086 -10000 0 -0.3 10 10
BAD 0.034 0.003 -10000 0 -10000 0 0
AKT3 0.015 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.002 0.082 -10000 0 -0.29 10 10
AKT1/ASK1 0.019 0.086 -10000 0 -0.28 9 9
BAD/YWHAZ 0.064 0.02 -10000 0 -10000 0 0
RICTOR 0.034 0.005 -10000 0 -10000 0 0
RAF1 0.034 0.003 -10000 0 -10000 0 0
JNK cascade -0.018 0.084 0.27 9 -10000 0 9
TSC1 0.002 0.078 -10000 0 -0.29 9 9
YWHAZ 0.033 0.006 -10000 0 -10000 0 0
AKT1/RAF1 0.025 0.091 -10000 0 -0.29 10 10
EP300 0.031 0.01 -10000 0 -10000 0 0
mol:GDP 0.006 0.085 -10000 0 -0.3 10 10
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.001 0.082 -10000 0 -0.29 10 10
YWHAQ 0.034 0.003 -10000 0 -10000 0 0
TBC1D4 0.005 0.002 -10000 0 -10000 0 0
MAP3K5 0.025 0.049 -10000 0 -0.38 2 2
MAPKAP1 0.033 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.027 0.067 0.28 2 -10000 0 2
YWHAH 0.031 0.01 -10000 0 -10000 0 0
AKT1S1 0.002 0.079 0.2 1 -0.29 9 10
CASP9 0.003 0.086 0.2 2 -0.29 10 12
YWHAB 0.031 0.01 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.024 0.092 0.25 1 -0.28 10 11
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.056 0.035 -10000 0 -0.23 1 1
YWHAE 0.033 0.006 -10000 0 -10000 0 0
SRC 0.029 0.035 -10000 0 -0.38 1 1
AKT2/p21CIP1 -0.003 0.08 0.24 1 -0.26 9 10
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.007 0.03 -10000 0 -10000 0 0
CHUK 0.004 0.051 -10000 0 -0.29 4 4
BAD/BCL-XL 0.021 0.088 -10000 0 -0.28 10 10
mTORC2 0.041 0.012 -10000 0 -10000 0 0
AKT2 0.016 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.017 0.091 -10000 0 -0.34 4 4
PDPK1 0.033 0.006 -10000 0 -10000 0 0
MDM2 0.016 0.089 0.2 10 -0.29 8 18
MAPKKK cascade -0.025 0.09 0.29 10 -10000 0 10
MDM2/Cbp/p300 0.045 0.1 0.26 3 -0.28 9 12
TSC1/TSC2 0.001 0.091 0.27 4 -0.29 10 14
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.098 0.25 3 -0.26 9 12
glucose import -0.008 0.032 0.21 1 -0.2 3 4
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.016 0.059 0.18 4 -0.17 9 13
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.008 0.032 0.21 1 -0.2 3 4
GSK3A 0.002 0.079 0.2 1 -0.29 9 10
FOXO1 0.001 0.078 -10000 0 -0.29 9 9
GSK3B 0.005 0.08 0.2 1 -0.29 9 10
SFN 0.001 0.096 -10000 0 -0.38 8 8
G1/S transition of mitotic cell cycle 0 0.09 0.25 3 -0.28 10 13
p27Kip1/14-3-3 family 0.039 0.057 -10000 0 -10000 0 0
PRKACA 0.033 0.007 -10000 0 -10000 0 0
KPNA1 0.034 0.005 -10000 0 -10000 0 0
HSP90AA1 0.032 0.009 -10000 0 -10000 0 0
YWHAG 0.023 0.016 -10000 0 -10000 0 0
RHEB 0.023 0.016 -10000 0 -10000 0 0
CREBBP 0.034 0.005 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.016 0.074 -10000 0 -0.28 8 8
CRKL 0.032 0.009 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.012 -10000 0 -10000 0 0
DOCK1 0.022 0.016 -10000 0 -10000 0 0
ITGA4 0.014 0.083 -10000 0 -0.38 6 6
alpha4/beta7 Integrin/MAdCAM1 0.038 0.095 -10000 0 -0.21 15 15
EPO 0.003 0.082 -10000 0 -0.38 6 6
alpha4/beta7 Integrin 0.028 0.075 -10000 0 -0.27 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.019 0.065 -10000 0 -0.27 6 6
EPO/EPOR (dimer) 0.017 0.065 -10000 0 -0.27 6 6
lamellipodium assembly -0.003 0.072 -10000 0 -0.28 5 5
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
PI3K 0.045 0.03 -10000 0 -0.27 1 1
ARF6 0.032 0.009 -10000 0 -10000 0 0
JAK2 -0.009 0.065 -10000 0 -0.21 11 11
PXN 0.034 0.003 -10000 0 -10000 0 0
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
MADCAM1 0.003 0.096 -10000 0 -0.38 8 8
cell adhesion 0.036 0.094 -10000 0 -0.21 15 15
CRKL/CBL 0.047 0.013 -10000 0 -10000 0 0
ITGB1 0.024 0.016 -10000 0 -10000 0 0
SRC -0.029 0.061 0.16 2 -0.21 13 15
ITGB7 0.026 0.05 -10000 0 -0.38 2 2
RAC1 0.023 0.016 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.016 0.089 -10000 0 -0.23 15 15
p130Cas/Crk/Dock1 0.007 0.068 -10000 0 -0.21 1 1
VCAM1 0.008 0.1 -10000 0 -0.38 9 9
RHOA 0.034 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.043 0.069 -10000 0 -0.21 6 6
BCAR1 -0.032 0.058 0.16 2 -0.2 11 13
EPOR 0.032 0.01 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.034 0.003 -10000 0 -10000 0 0
GIT1 0.034 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.003 0.074 -10000 0 -0.28 5 5
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.018 0.1 -10000 0 -0.34 8 8
BAG4 0.034 0.005 -10000 0 -10000 0 0
BAD -0.01 0.041 -10000 0 -0.13 5 5
NFKBIA 0.032 0.009 -10000 0 -10000 0 0
BIRC3 -0.016 0.12 -10000 0 -0.38 14 14
BAX -0.006 0.051 0.18 4 -10000 0 4
EnzymeConsortium:3.1.4.12 -0.003 0.029 0.06 1 -0.081 9 10
IKBKB -0.019 0.1 0.21 1 -0.32 7 8
MAP2K2 -0.014 0.056 0.16 6 -0.24 1 7
MAP2K1 -0.016 0.051 0.16 3 -0.24 1 4
SMPD1 -0.005 0.038 -10000 0 -0.16 4 4
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.012 0.11 -10000 0 -0.33 8 8
MAP2K4 -0.013 0.043 0.23 1 -10000 0 1
protein ubiquitination -0.019 0.1 -10000 0 -0.33 7 7
EnzymeConsortium:2.7.1.37 -0.017 0.056 0.16 2 -0.26 1 3
response to UV 0 0.001 0.002 3 -0.002 2 5
RAF1 -0.014 0.051 0.17 2 -0.2 2 4
CRADD 0.034 0.005 -10000 0 -10000 0 0
mol:ceramide -0.006 0.043 -10000 0 -0.12 9 9
I-kappa-B-alpha/RELA/p50/ubiquitin 0.043 0.012 -10000 0 -10000 0 0
MADD 0.03 0.035 -10000 0 -0.38 1 1
MAP3K1 -0.009 0.045 0.24 1 -0.13 4 5
TRADD 0.031 0.034 -10000 0 -0.38 1 1
RELA/p50 0.034 0.003 -10000 0 -10000 0 0
MAPK3 -0.01 0.052 0.16 1 -0.24 1 2
MAPK1 -0.015 0.059 0.16 1 -0.23 2 3
p50/RELA/I-kappa-B-alpha 0.047 0.013 -10000 0 -10000 0 0
FADD -0.016 0.1 -10000 0 -0.34 7 7
KSR1 -0.011 0.05 0.18 1 -0.16 5 6
MAPK8 -0.009 0.034 0.22 1 -10000 0 1
TRAF2 0.033 0.007 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.021 0.093 -10000 0 -0.32 7 7
TNF R/SODD 0.048 0.013 -10000 0 -10000 0 0
TNF -0.004 0.1 -10000 0 -0.38 9 9
CYCS 0.01 0.051 0.15 3 -0.14 2 5
IKBKG -0.02 0.1 -10000 0 -0.32 8 8
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.013 0.11 -10000 0 -0.33 10 10
RELA 0.034 0.003 -10000 0 -10000 0 0
RIPK1 0.034 0.006 -10000 0 -10000 0 0
AIFM1 -0.009 0.046 0.13 3 -0.14 4 7
TNF/TNF R/SODD 0.033 0.078 -10000 0 -0.23 9 9
TNFRSF1A 0.033 0.007 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.03 0.067 -10000 0 -0.71 1 1
NSMAF -0.014 0.1 0.21 2 -0.33 7 9
response to hydrogen peroxide 0 0.001 0.002 3 -0.002 2 5
BCL2 0.033 0.007 -10000 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.032 0.011 -10000 0 -10000 0 0
EPHB2 0.027 0.049 -10000 0 -0.39 2 2
EFNB1 -0.019 0.039 -10000 0 -0.28 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.083 -10000 0 -0.24 9 9
Ephrin B2/EPHB1-2 0.016 0.092 -10000 0 -0.22 16 16
neuron projection morphogenesis 0.002 0.071 -10000 0 -0.22 9 9
Ephrin B1/EPHB1-2/Tiam1 0.014 0.1 -10000 0 -0.23 17 17
DNM1 0.021 0.061 -10000 0 -0.38 3 3
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 0.001 0.008 -10000 0 -10000 0 0
YES1 0.023 0.02 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK2 0.014 0.1 -10000 0 -0.23 17 17
PI3K 0.048 0.039 -10000 0 -0.32 1 1
mol:GDP 0.012 0.099 -10000 0 -0.22 17 17
ITGA2B 0.007 0.096 -10000 0 -0.38 8 8
endothelial cell proliferation 0.028 0.03 -10000 0 -0.23 1 1
FYN 0.016 0.038 -10000 0 -10000 0 0
MAP3K7 0.004 0.005 -10000 0 -10000 0 0
FGR 0.018 0.048 -10000 0 -0.53 1 1
TIAM1 0.033 0.006 -10000 0 -10000 0 0
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
RGS3 0.033 0.006 -10000 0 -10000 0 0
cell adhesion 0.011 0.075 -10000 0 -0.4 2 2
LYN 0.023 0.018 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/Src Family Kinases 0.009 0.039 -10000 0 -0.46 1 1
Ephrin B1/EPHB1-2 0.009 0.006 -10000 0 -10000 0 0
SRC 0.018 0.048 -10000 0 -0.53 1 1
ITGB3 0.015 0.083 -10000 0 -0.38 6 6
EPHB1 -0.025 0.13 -10000 0 -0.38 16 16
EPHB4 0.021 0.037 -10000 0 -0.38 1 1
RAC1 0.023 0.016 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.029 0.03 -10000 0 -0.23 1 1
alphaIIb/beta3 Integrin 0.014 0.1 -10000 0 -0.29 13 13
BLK 0.02 0.016 -10000 0 -10000 0 0
HCK 0.021 0.022 -10000 0 -10000 0 0
regulation of stress fiber formation -0.012 0.099 0.22 17 -10000 0 17
MAPK8 -0.003 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/RGS3 0.012 0.1 -10000 0 -0.22 18 18
endothelial cell migration 0.052 0.09 0.22 8 -10000 0 8
NCK2 0.034 0.004 -10000 0 -10000 0 0
PTPN13 0.036 0.007 -10000 0 -10000 0 0
regulation of focal adhesion formation -0.012 0.099 0.22 17 -10000 0 17
chemotaxis -0.011 0.099 0.22 18 -10000 0 18
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.012 0.077 -10000 0 -0.23 9 9
angiogenesis 0.009 0.006 -10000 0 -10000 0 0
LCK 0.011 0.044 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.007 0.098 -10000 0 -0.27 15 15
PDGFRB 0.033 0.013 -10000 0 -10000 0 0
SPHK1 0.003 0.092 -10000 0 -0.75 2 2
mol:S1P 0.001 0.085 -10000 0 -0.66 2 2
S1P1/S1P/Gi -0.027 0.11 -10000 0 -0.37 10 10
GNAO1 0.007 0.095 -10000 0 -0.38 8 8
PDGFB-D/PDGFRB/PLCgamma1 0.012 0.13 0.25 6 -0.35 9 15
PLCG1 -0.031 0.1 -10000 0 -0.35 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.033 0.013 -10000 0 -10000 0 0
GNAI2 0.031 0.016 -10000 0 -10000 0 0
GNAI3 0.031 0.015 -10000 0 -10000 0 0
GNAI1 0.012 0.06 -10000 0 -0.39 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.034 0.066 -10000 0 -0.23 15 15
S1P1/S1P -0.015 0.092 -10000 0 -0.43 3 3
negative regulation of cAMP metabolic process -0.026 0.11 -10000 0 -0.36 10 10
MAPK3 -0.041 0.14 0.26 1 -0.49 11 12
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.025 0.003 -10000 0 -10000 0 0
KDR 0.026 0.037 -10000 0 -0.38 1 1
PLCB2 -0.003 0.1 -10000 0 -0.36 4 4
RAC1 0.023 0.016 -10000 0 -10000 0 0
RhoA/GTP -0.01 0.083 -10000 0 -0.37 3 3
receptor internalization -0.015 0.087 -10000 0 -0.4 3 3
PTGS2 -0.045 0.25 -10000 0 -0.91 10 10
Rac1/GTP -0.012 0.065 -10000 0 -0.28 3 3
RHOA 0.034 0.004 -10000 0 -10000 0 0
VEGFA -0.012 0.12 -10000 0 -0.38 14 14
negative regulation of T cell proliferation -0.026 0.11 -10000 0 -0.36 10 10
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.023 0.05 -10000 0 -0.38 2 2
MAPK1 -0.041 0.14 -10000 0 -0.49 11 11
S1P1/S1P/PDGFB-D/PDGFRB -0.002 0.1 -10000 0 -0.36 4 4
ABCC1 0.032 0.034 -10000 0 -0.38 1 1
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.034 0.005 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.005 0.085 -10000 0 -0.25 4 4
NEF 0 0.013 -10000 0 -0.15 1 1
NFKBIA 0.02 0.038 -10000 0 -10000 0 0
BIRC3 -0.035 0.13 -10000 0 -0.43 14 14
CYCS 0.005 0.078 0.18 15 -0.28 3 18
RIPK1 0.033 0.006 -10000 0 -10000 0 0
CD247 0.023 0.062 -10000 0 -0.33 4 4
MAP2K7 -0.014 0.11 -10000 0 -0.46 2 2
protein ubiquitination 0.009 0.055 0.2 1 -0.28 1 2
CRADD 0.034 0.005 -10000 0 -10000 0 0
DAXX 0.034 0.004 -10000 0 -10000 0 0
FAS 0.017 0.05 -10000 0 -0.38 2 2
BID -0.001 0.053 0.15 1 -0.25 5 6
NF-kappa-B/RelA/I kappa B alpha 0.029 0.096 -10000 0 -0.24 14 14
TRADD 0.031 0.034 -10000 0 -0.38 1 1
MAP3K5 0.025 0.049 -10000 0 -0.38 2 2
CFLAR 0.034 0 -10000 0 -10000 0 0
FADD 0.034 0.003 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.029 0.096 -10000 0 -0.24 14 14
MAPK8 -0.007 0.1 -10000 0 -0.43 2 2
APAF1 0.034 0.004 -10000 0 -10000 0 0
TRAF1 0.03 0.017 -10000 0 -10000 0 0
TRAF2 0.033 0.007 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.007 0.052 -10000 0 -0.26 5 5
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.02 0.064 -10000 0 -0.35 1 1
CHUK 0.009 0.057 0.21 1 -0.28 2 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.058 0.07 -10000 0 -0.26 3 3
TCRz/NEF 0.02 0.049 -10000 0 -0.26 4 4
TNF -0.003 0.1 -10000 0 -0.38 9 9
FASLG 0.005 0.056 -10000 0 -0.29 4 4
NFKB1 0.023 0.038 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.033 0.078 -10000 0 -0.23 9 9
CASP6 0.007 0.1 -10000 0 -0.48 2 2
CASP7 -0.076 0.17 -10000 0 -0.46 15 15
RELA 0.022 0.039 -10000 0 -0.098 12 12
CASP2 0.024 0.016 -10000 0 -10000 0 0
CASP3 -0.047 0.14 -10000 0 -0.44 15 15
TNFRSF1A 0.033 0.007 -10000 0 -10000 0 0
TNFR1A/BAG4 0.048 0.013 -10000 0 -10000 0 0
CASP8 0.034 0 -10000 0 -10000 0 0
CASP9 0.032 0.013 -10000 0 -10000 0 0
MAP3K14 0.016 0.067 -10000 0 -0.33 1 1
APAF-1/Caspase 9 -0.005 0.1 -10000 0 -0.28 10 10
BCL2 -0.011 0.099 0.26 1 -0.46 1 2
IL27-mediated 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
TGFB1 0.033 0.007 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.01 0.091 0.35 1 -10000 0 1
IL27/IL27R/JAK1 0.055 0.11 -10000 0 -10000 0 0
TBX21 -0.004 0.14 0.4 8 -0.35 6 14
IL12B 0.026 0.011 -10000 0 -10000 0 0
IL12A -0.006 0.032 -10000 0 -0.27 2 2
IL6ST 0.013 0.096 -10000 0 -0.38 8 8
IL27RA/JAK1 0.029 0.054 -10000 0 -10000 0 0
IL27 0.026 0.041 -10000 0 -0.39 1 1
TYK2 0.034 0.007 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.021 0.1 0.17 30 -0.29 7 37
T-helper 2 cell differentiation 0.01 0.091 0.35 1 -10000 0 1
T cell proliferation during immune response 0.01 0.091 0.35 1 -10000 0 1
MAPKKK cascade -0.01 0.091 -10000 0 -0.35 1 1
STAT3 0.034 0 -10000 0 -10000 0 0
STAT2 0.033 0.008 -10000 0 -10000 0 0
STAT1 0.034 0.013 -10000 0 -10000 0 0
IL12RB1 0.015 0.082 -10000 0 -0.38 6 6
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.002 0.13 0.39 8 -10000 0 8
IL27/IL27R/JAK2/TYK2 -0.01 0.091 -10000 0 -0.36 1 1
positive regulation of T cell mediated cytotoxicity -0.01 0.091 -10000 0 -0.35 1 1
STAT1 (dimer) 0.059 0.15 0.52 6 -10000 0 6
JAK2 0.03 0.013 -10000 0 -10000 0 0
JAK1 0.034 0.008 -10000 0 -10000 0 0
STAT2 (dimer) 0.011 0.1 0.37 1 -10000 0 1
T cell proliferation -0.016 0.088 -10000 0 -0.48 2 2
IL12/IL12R/TYK2/JAK2 0.021 0.11 -10000 0 -0.8 2 2
IL17A 0.022 0.098 0.18 29 -0.3 6 35
mast cell activation 0.01 0.091 0.35 1 -10000 0 1
IFNG 0.002 0.03 0.091 2 -0.088 6 8
T cell differentiation -0.001 0.003 0.013 1 -10000 0 1
STAT3 (dimer) 0.012 0.11 0.37 1 -10000 0 1
STAT5A (dimer) 0.012 0.11 0.37 1 -0.34 1 2
STAT4 (dimer) -0.007 0.12 0.37 1 -0.34 1 2
STAT4 -0.012 0.12 -10000 0 -0.38 14 14
T cell activation -0.005 0.004 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.038 0.07 -10000 0 -10000 0 0
GATA3 -0.074 0.29 0.72 1 -1.2 8 9
IL18 -0.009 0.038 -10000 0 -0.27 3 3
positive regulation of mast cell cytokine production 0.012 0.11 0.37 1 -0.34 1 2
IL27/EBI3 0.035 0.063 -10000 0 -0.27 5 5
IL27RA 0.002 0.018 -10000 0 -10000 0 0
IL6 -0.01 0.09 -10000 0 -0.38 7 7
STAT5A 0.034 0 -10000 0 -10000 0 0
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.006 0.017 -10000 0 -10000 0 0
IL1B -0.02 0.06 -10000 0 -0.27 8 8
EBI3 0.024 0.068 -10000 0 -0.38 4 4
TNF -0.023 0.063 -10000 0 -0.27 9 9
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.063 0.16 0.46 3 -0.66 1 4
CRP 0.05 0.15 0.48 1 -0.58 2 3
cell cycle arrest 0.051 0.16 0.51 1 -0.66 2 3
TIMP1 0.039 0.23 0.49 1 -0.91 6 7
IL6ST 0.002 0.096 -10000 0 -0.35 9 9
Rac1/GDP 0 0.1 0.27 1 -0.37 6 7
AP1 0.05 0.096 -10000 0 -0.46 1 1
GAB2 0.028 0.048 -10000 0 -0.38 2 2
TNFSF11 0.046 0.15 0.48 1 -0.66 1 2
HSP90B1 0.048 0.074 -10000 0 -0.7 1 1
GAB1 0.031 0.034 -10000 0 -0.38 1 1
MAPK14 -0.031 0.16 -10000 0 -0.54 11 11
AKT1 0.036 0.047 -10000 0 -0.35 1 1
FOXO1 0.03 0.047 -10000 0 -0.34 1 1
MAP2K6 -0.022 0.13 -10000 0 -0.43 9 9
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 0.001 0.12 0.33 4 -0.38 6 10
MITF -0.011 0.1 -10000 0 -0.35 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.033 0.007 -10000 0 -10000 0 0
A2M -0.006 0.18 -10000 0 -1.1 4 4
CEBPB 0.028 0.023 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.036 0.07 -10000 0 -0.4 1 1
STAT3 0.049 0.16 0.52 1 -0.69 2 3
STAT1 0.022 0.021 -10000 0 -10000 0 0
CEBPD 0.039 0.2 0.48 1 -1 3 4
PIK3CA 0.034 0.006 -10000 0 -10000 0 0
PI3K 0.046 0.03 -10000 0 -0.27 1 1
JUN 0.033 0.006 -10000 0 -10000 0 0
PIAS3/MITF 0.028 0.12 0.21 7 -0.36 6 13
MAPK11 -0.04 0.17 -10000 0 -0.58 11 11
STAT3 (dimer)/FOXO1 0.002 0.11 -10000 0 -0.5 2 2
GRB2/SOS1/GAB family 0.044 0.12 -10000 0 -0.35 5 5
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.015 0.099 -10000 0 -0.36 7 7
GRB2 0.034 0.005 -10000 0 -10000 0 0
JAK2 0.03 0.012 -10000 0 -10000 0 0
LBP -0.029 0.31 0.42 3 -0.81 17 20
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
JAK1 0.025 0.028 -10000 0 -0.1 1 1
MYC 0.053 0.17 0.43 3 -0.8 2 5
FGG 0.045 0.15 0.48 1 -0.66 1 2
macrophage differentiation 0.051 0.16 0.51 1 -0.66 2 3
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.022 0.1 -10000 0 -0.25 11 11
JUNB 0.048 0.16 0.43 2 -0.75 2 4
FOS 0.018 0.061 -10000 0 -0.38 3 3
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.019 0.097 -10000 0 -0.37 7 7
STAT1/PIAS1 0.023 0.097 -10000 0 -0.33 3 3
GRB2/SOS1/GAB family/SHP2/PI3K 0.043 0.046 -10000 0 -0.37 1 1
STAT3 (dimer) 0.051 0.16 0.52 1 -0.69 2 3
PRKCD 0.071 0.18 0.33 31 -0.44 5 36
IL6R 0.023 0.045 -10000 0 -0.41 1 1
SOCS3 -0.049 0.32 0.49 2 -1 13 15
gp130 (dimer)/JAK1/JAK1/LMO4 0.035 0.085 -10000 0 -0.22 9 9
Rac1/GTP -0.003 0.1 -10000 0 -0.38 6 6
HCK 0.022 0.06 -10000 0 -0.38 3 3
MAPKKK cascade 0.051 0.073 -10000 0 -0.52 1 1
bone resorption 0.047 0.15 0.48 1 -0.62 1 2
IRF1 0.043 0.16 0.48 1 -0.78 2 3
mol:GDP -0.014 0.11 -10000 0 -0.38 7 7
SOS1 0.034 0.001 -10000 0 -10000 0 0
VAV1 -0.015 0.11 -10000 0 -0.38 7 7
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.031 0.17 -10000 0 -0.46 14 14
PTPN11 0.023 0.022 -10000 0 -10000 0 0
IL6/IL6RA 0.004 0.081 -10000 0 -0.33 6 6
gp130 (dimer)/TYK2/TYK2/LMO4 0.036 0.078 -10000 0 -0.22 9 9
gp130 (dimer)/JAK2/JAK2/LMO4 0.034 0.077 -10000 0 -0.22 8 8
IL6 -0.012 0.092 -10000 0 -0.39 7 7
PIAS3 0.034 0.004 -10000 0 -10000 0 0
PTPRE 0.014 0.058 -10000 0 -0.37 3 3
PIAS1 0.034 0.005 -10000 0 -10000 0 0
RAC1 0.023 0.016 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.009 0.067 -10000 0 -0.23 9 9
LMO4 0.025 0.031 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0.016 0.13 -10000 0 -0.65 2 2
MCL1 0.04 0.042 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.037 0.066 -10000 0 -0.2 5 5
ER alpha/Gai/GDP/Gbeta gamma -0.014 0.1 -10000 0 -0.34 7 7
AKT1 -0.034 0.2 -10000 0 -0.61 16 16
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.028 0.21 -10000 0 -0.62 16 16
mol:Ca2+ -0.008 0.066 0.18 5 -0.29 2 7
IGF1R 0.033 0.012 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.035 0.041 -10000 0 -0.23 3 3
SHC1 0.031 0.015 -10000 0 -10000 0 0
apoptosis 0.031 0.2 0.58 16 -10000 0 16
RhoA/GTP 0.022 0.036 -10000 0 -0.19 3 3
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.021 0.12 0.25 3 -0.33 6 9
regulation of stress fiber formation 0.021 0.063 0.31 1 -0.3 2 3
E2/ERA-ERB (dimer) 0.017 0.056 -10000 0 -0.23 5 5
KRAS 0.032 0.008 -10000 0 -10000 0 0
G13/GTP 0.034 0.038 -10000 0 -0.2 3 3
pseudopodium formation -0.021 0.063 0.3 2 -0.31 1 3
E2/ER alpha (dimer)/PELP1 0.034 0.042 -10000 0 -0.23 3 3
GRB2 0.034 0.005 -10000 0 -10000 0 0
GNG2 0.031 0.012 -10000 0 -10000 0 0
GNAO1 0.011 0.094 -10000 0 -0.38 8 8
HRAS 0.033 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.006 0.15 0.27 1 -0.48 7 8
E2/ER beta (dimer) 0.01 0.04 -10000 0 -0.27 2 2
mol:GDP -0.013 0.078 -10000 0 -0.3 5 5
mol:NADP -0.006 0.15 0.27 1 -0.48 7 8
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
mol:IP3 -0.013 0.057 -10000 0 -0.3 2 2
IGF-1R heterotetramer 0.033 0.012 -10000 0 -10000 0 0
PLCB1 -0.006 0.058 -10000 0 -0.33 1 1
PLCB2 -0.002 0.062 -10000 0 -0.33 3 3
IGF1 0.013 0.084 -10000 0 -0.38 6 6
mol:L-citrulline -0.006 0.15 0.27 1 -0.48 7 8
RHOA 0.034 0.004 -10000 0 -10000 0 0
Gai/GDP -0.022 0.18 -10000 0 -0.57 13 13
JNK cascade 0.01 0.04 -10000 0 -0.27 2 2
BCAR1 0.033 0.007 -10000 0 -10000 0 0
ESR2 0.012 0.058 -10000 0 -0.38 2 2
GNAQ 0.033 0.007 -10000 0 -10000 0 0
ESR1 0.021 0.06 -10000 0 -0.38 3 3
Gq family/GDP/Gbeta gamma 0.005 0.1 -10000 0 -0.38 7 7
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.038 0.049 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.024 0.12 0.25 3 -0.33 5 8
GNAZ 0.027 0.049 -10000 0 -0.38 2 2
E2/ER alpha (dimer) 0.016 0.042 -10000 0 -0.27 3 3
STRN 0.034 0 -10000 0 -10000 0 0
GNAL 0.005 0.08 -10000 0 -0.38 5 5
PELP1 0.033 0.006 -10000 0 -10000 0 0
MAPK11 0.003 0.032 -10000 0 -0.23 2 2
GNAI2 0.034 0.005 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
GNAI1 0.014 0.06 -10000 0 -0.38 3 3
HBEGF -0.002 0.15 0.32 9 -0.39 8 17
cAMP biosynthetic process 0 0.06 -10000 0 -0.19 10 10
SRC -0.012 0.1 0.21 3 -0.35 6 9
PI3K 0.045 0.03 -10000 0 -0.27 1 1
GNB1 0.033 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.029 0.085 -10000 0 -0.27 5 5
SOS1 0.034 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.02 0.086 -10000 0 -0.27 7 7
Gs family/GTP 0.005 0.064 -10000 0 -0.19 10 10
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.058 0.022 -10000 0 -10000 0 0
vasodilation -0.004 0.14 0.27 1 -0.46 7 8
mol:DAG -0.013 0.057 -10000 0 -0.3 2 2
Gs family/GDP/Gbeta gamma -0.017 0.084 -10000 0 -0.28 7 7
MSN -0.023 0.065 0.31 2 -0.33 1 3
Gq family/GTP 0.008 0.065 -10000 0 -0.37 2 2
mol:PI-3-4-5-P3 -0.026 0.2 -10000 0 -0.6 16 16
NRAS 0.034 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.004 0.14 0.46 7 -0.27 1 8
GRB2/SOS1 0.05 0.007 -10000 0 -10000 0 0
RhoA/GDP 0 0.083 -10000 0 -0.29 5 5
NOS3 -0.007 0.15 0.27 1 -0.51 7 8
GNA11 0.027 0.048 -10000 0 -0.38 2 2
MAPKKK cascade 0 0.15 -10000 0 -0.47 8 8
E2/ER alpha (dimer)/PELP1/Src 0.017 0.12 0.27 3 -0.34 6 9
ruffle organization -0.021 0.063 0.3 2 -0.31 1 3
ROCK2 -0.017 0.063 0.28 3 -10000 0 3
GNA14 0.022 0.053 -10000 0 -0.38 2 2
GNA15 0.015 0.082 -10000 0 -0.38 6 6
GNA13 0.034 0.003 -10000 0 -10000 0 0
MMP9 -0.022 0.14 0.37 4 -0.4 8 12
MMP2 0.002 0.12 0.26 4 -0.35 5 9
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.032 0.009 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 0.018 0.03 -10000 0 -10000 0 0
NT3 (dimer)/TRKC 0.03 0.057 -10000 0 -0.29 4 4
NT3 (dimer)/TRKB 0.015 0.1 -10000 0 -0.24 17 17
SHC/Grb2/SOS1/GAB1/PI3K 0.026 0.035 -10000 0 -0.29 1 1
RAPGEF1 0.03 0.035 -10000 0 -0.38 1 1
BDNF 0.005 0.075 -10000 0 -0.38 4 4
PIK3CA 0.033 0.006 -10000 0 -10000 0 0
DYNLT1 0.029 0.017 -10000 0 -10000 0 0
NTRK1 0.01 0.079 -10000 0 -0.38 5 5
NTRK2 0.001 0.1 -10000 0 -0.38 10 10
NTRK3 0.022 0.068 -10000 0 -0.38 4 4
NT-4/5 (dimer)/TRKB 0.015 0.096 -10000 0 -0.24 16 16
neuron apoptosis 0.015 0.12 0.35 8 -10000 0 8
SHC 2-3/Grb2 -0.017 0.12 -10000 0 -0.38 8 8
SHC1 0.031 0.015 -10000 0 -10000 0 0
SHC2 -0.012 0.084 -10000 0 -0.38 2 2
SHC3 -0.041 0.14 -10000 0 -0.47 11 11
STAT3 (dimer) 0.037 0.016 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.022 0.086 -10000 0 -0.24 12 12
RIN/GDP -0.011 0.079 -10000 0 -0.24 4 4
GIPC1 0.033 0.008 -10000 0 -10000 0 0
KRAS 0.032 0.008 -10000 0 -10000 0 0
DNAJA3 -0.027 0.079 -10000 0 -0.22 19 19
RIN/GTP -0.041 0.11 -10000 0 -0.27 27 27
CCND1 0.016 0.018 -10000 0 -10000 0 0
MAGED1 0.034 0 -10000 0 -10000 0 0
PTPN11 0.034 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.021 0.025 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.063 0.023 -10000 0 -10000 0 0
GRB2 0.034 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.009 0.1 -10000 0 -0.25 17 17
TRKA/NEDD4-2 0.027 0.065 -10000 0 -0.28 5 5
ELMO1 0.02 0.038 -10000 0 -0.38 1 1
RhoG/GTP/ELMO1/DOCK1 0.022 0.031 -10000 0 -0.23 1 1
NGF 0 0.1 -10000 0 -0.38 9 9
HRAS 0.033 0.008 -10000 0 -10000 0 0
DOCK1 0.022 0.016 -10000 0 -10000 0 0
GAB2 0.029 0.048 -10000 0 -0.38 2 2
RIT2 -0.062 0.16 -10000 0 -0.38 27 27
RIT1 0.033 0.006 -10000 0 -10000 0 0
FRS2 0.032 0.009 -10000 0 -10000 0 0
DNM1 0.021 0.061 -10000 0 -0.38 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.033 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.005 0.078 -10000 0 -0.24 13 13
mol:GDP 0.013 0.09 0.38 2 -0.31 2 4
NGF (dimer) 0 0.1 -10000 0 -0.38 9 9
RhoG/GDP 0.015 0.026 -10000 0 -0.27 1 1
RIT1/GDP 0.022 0.073 0.27 3 -0.21 2 5
TIAM1 0.033 0.006 -10000 0 -10000 0 0
PIK3R1 0.03 0.036 -10000 0 -0.38 1 1
BDNF (dimer)/TRKB 0.016 0.094 -10000 0 -0.24 14 14
KIDINS220/CRKL/C3G 0.043 0.03 -10000 0 -0.27 1 1
SHC/RasGAP 0.046 0.018 -10000 0 -10000 0 0
FRS2 family/SHP2 0.065 0.018 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.079 0.029 -10000 0 -10000 0 0
RIT1/GTP 0.025 0.004 -10000 0 -10000 0 0
NT3 (dimer) 0.021 0.022 -10000 0 -10000 0 0
RAP1/GDP 0.013 0.054 -10000 0 -10000 0 0
KIDINS220/CRKL 0.032 0.009 -10000 0 -10000 0 0
BDNF (dimer) 0.005 0.075 -10000 0 -0.38 4 4
ubiquitin-dependent protein catabolic process 0.019 0.092 -10000 0 -0.23 14 14
Schwann cell development -0.013 0.017 -10000 0 -10000 0 0
EHD4 0.033 0.006 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.08 0.026 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.022 0.056 -10000 0 -0.42 1 1
RAP1B 0.031 0.01 -10000 0 -10000 0 0
RAP1A 0.034 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.006 0.1 -10000 0 -0.25 16 16
ABL1 0.033 0.008 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.05 0.007 -10000 0 -10000 0 0
Rap1/GTP 0.011 0.081 -10000 0 -0.35 3 3
STAT3 0.037 0.016 -10000 0 -10000 0 0
axon guidance -0.006 0.092 -10000 0 -0.24 16 16
MAPK3 -0.04 0.08 0.18 6 -0.23 17 23
MAPK1 -0.039 0.081 0.18 6 -0.23 17 23
CDC42/GDP 0.018 0.064 0.21 1 -0.21 2 3
NTF3 0.021 0.022 -10000 0 -10000 0 0
NTF4 0.021 0.025 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.023 0.09 -10000 0 -0.23 13 13
PI3K 0.045 0.03 -10000 0 -0.27 1 1
FRS3 0.034 0.004 -10000 0 -10000 0 0
FAIM 0.034 0.005 -10000 0 -10000 0 0
GAB1 0.031 0.034 -10000 0 -0.38 1 1
RASGRF1 -0.048 0.095 -10000 0 -0.24 22 22
SOS1 0.034 0 -10000 0 -10000 0 0
MCF2L -0.029 0.048 -10000 0 -0.24 7 7
RGS19 0.031 0.01 -10000 0 -10000 0 0
CDC42 0.034 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.019 0.061 -10000 0 -10000 0 0
Rac1/GDP 0.015 0.061 0.3 2 -0.21 1 3
NGF (dimer)/TRKA/GRIT 0.006 0.082 -10000 0 -0.23 14 14
neuron projection morphogenesis 0.006 0.082 -10000 0 -10000 0 0
NGF (dimer)/TRKA/NEDD4-2 0.019 0.092 -10000 0 -0.23 14 14
MAP2K1 -0.013 0.045 0.18 8 -10000 0 8
NGFR 0.01 0.09 -10000 0 -0.38 7 7
NGF (dimer)/TRKA/GIPC/GAIP -0.013 0.087 -10000 0 -0.38 3 3
RAS family/GTP/PI3K 0.02 0.029 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.093 0.03 -10000 0 -10000 0 0
NRAS 0.034 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.05 0.007 -10000 0 -10000 0 0
PRKCI 0.034 0.004 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.023 0.016 -10000 0 -10000 0 0
PRKCZ -0.011 0.12 -10000 0 -0.38 14 14
MAPKKK cascade -0.025 0.16 -10000 0 -0.49 14 14
RASA1 0.033 0.006 -10000 0 -10000 0 0
TRKA/c-Abl 0.027 0.064 -10000 0 -0.27 5 5
SQSTM1 0.034 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.026 0.09 -10000 0 -0.21 12 12
NGF (dimer)/TRKA/p62/Atypical PKCs 0.028 0.12 -10000 0 -0.22 24 24
MATK 0.006 0.095 -10000 0 -0.38 8 8
NEDD4L 0.032 0.011 -10000 0 -10000 0 0
RAS family/GDP -0.008 0.037 -10000 0 -0.15 2 2
NGF (dimer)/TRKA -0.021 0.086 -10000 0 -0.23 20 20
Rac1/GTP -0.02 0.058 -10000 0 -0.22 1 1
FRS2 family/SHP2/CRK family 0.088 0.037 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.017 0.32 -9999 0 -1.2 6 6
PLK1 -0.008 0.31 -9999 0 -1.4 7 7
BIRC5 0.028 0.2 -9999 0 -1.4 3 3
HSPA1B -0.001 0.35 -9999 0 -1.2 8 8
MAP2K1 0.035 0.042 -9999 0 -10000 0 0
BRCA2 0.017 0.32 -9999 0 -1.3 5 5
FOXM1 -0.021 0.52 -9999 0 -2.2 6 6
XRCC1 0.022 0.32 -9999 0 -1.3 5 5
FOXM1B/p19 -0.094 0.27 -9999 0 -1.3 5 5
Cyclin D1/CDK4 -0.007 0.3 -9999 0 -1.1 6 6
CDC2 0.015 0.34 -9999 0 -1.3 6 6
TGFA -0.008 0.33 -9999 0 -0.96 9 9
SKP2 0.018 0.32 -9999 0 -1.3 5 5
CCNE1 0.032 0.016 -9999 0 -10000 0 0
CKS1B 0.023 0.32 -9999 0 -1.3 5 5
RB1 -0.001 0.22 -9999 0 -0.72 8 8
FOXM1C/SP1 0.013 0.38 -9999 0 -1.5 6 6
AURKB -0.027 0.32 -9999 0 -1.1 11 11
CENPF 0.011 0.35 -9999 0 -1.4 6 6
CDK4 0.024 0.027 -9999 0 -10000 0 0
MYC 0.018 0.28 -9999 0 -0.98 7 7
CHEK2 0.034 0.042 -9999 0 -10000 0 0
ONECUT1 0.005 0.32 -9999 0 -1.1 6 6
CDKN2A -0.02 0.034 -9999 0 -10000 0 0
LAMA4 0.011 0.33 -9999 0 -1.2 6 6
FOXM1B/HNF6 -0.01 0.39 -9999 0 -1.5 6 6
FOS -0.009 0.37 -9999 0 -1.2 10 10
SP1 0.034 0.008 -9999 0 -10000 0 0
CDC25B 0.03 0.32 -9999 0 -1.2 6 6
response to radiation 0.009 0.02 -9999 0 -10000 0 0
CENPB 0.03 0.32 -9999 0 -1.3 5 5
CENPA 0.007 0.34 -9999 0 -1.3 6 6
NEK2 0.01 0.35 -9999 0 -1.4 6 6
HIST1H2BA 0.018 0.32 -9999 0 -1.2 6 6
CCNA2 0.03 0.051 -9999 0 -0.4 2 2
EP300 0.031 0.01 -9999 0 -10000 0 0
CCNB1/CDK1 -0.002 0.4 -9999 0 -1.5 7 7
CCNB2 0.013 0.33 -9999 0 -1.3 6 6
CCNB1 0.011 0.35 -9999 0 -1.3 7 7
ETV5 0.013 0.33 -9999 0 -1.2 6 6
ESR1 0 0.35 -9999 0 -1.2 8 8
CCND1 0.011 0.31 -9999 0 -1.1 6 6
GSK3A 0.031 0.038 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.064 0.057 -9999 0 -0.27 2 2
CDK2 0.033 0.016 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.01 0.023 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 0.019 0.36 -9999 0 -1.4 6 6
GAS1 -0.002 0.35 -9999 0 -1.2 8 8
MMP2 0.012 0.33 -9999 0 -1.2 7 7
RB1/FOXM1C -0.026 0.32 -9999 0 -1.2 6 6
CREBBP 0.034 0.005 -9999 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.011 0.094 -10000 0 -0.38 8 8
CDC42/GTP 0.035 0.074 -10000 0 -0.31 2 2
PLCG1 0.011 0.07 -10000 0 -0.25 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.034 0.005 -10000 0 -10000 0 0
GNAI3 0.034 0.005 -10000 0 -10000 0 0
G12/G13 0.032 0.035 -10000 0 -0.27 1 1
cell migration 0.033 0.072 -10000 0 -0.3 2 2
S1PR5 0.009 0.084 -10000 0 -0.38 6 6
S1PR4 0.029 0.036 -10000 0 -0.38 1 1
MAPK3 0.014 0.067 -10000 0 -0.32 2 2
MAPK1 0.016 0.066 -10000 0 -0.32 2 2
S1P/S1P5/Gi 0.014 0.086 -10000 0 -0.25 10 10
GNAI1 0.014 0.06 -10000 0 -0.38 3 3
CDC42/GDP 0.025 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.018 0.049 -10000 0 -0.23 4 4
RHOA 0.049 0.1 0.19 49 -0.2 1 50
S1P/S1P4/Gi 0.023 0.071 -10000 0 -0.25 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.027 0.049 -10000 0 -0.38 2 2
S1P/S1P4/G12/G13 0.04 0.038 -10000 0 -0.21 1 1
GNA12 0.02 0.037 -10000 0 -0.38 1 1
GNA13 0.034 0.003 -10000 0 -10000 0 0
CDC42 0.034 0.005 -10000 0 -10000 0 0
Aurora B 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
Condensin I complex 0 0.11 -10000 0 -0.42 7 7
STMN1 -0.022 0.058 -10000 0 -0.28 7 7
Aurora B/RasGAP/Survivin 0.048 0.089 -10000 0 -0.33 7 7
Chromosomal passenger complex/Cul3 protein complex -0.028 0.094 -10000 0 -0.33 8 8
BIRC5 0.024 0.064 -10000 0 -0.42 3 3
DES -0.1 0.31 -10000 0 -0.69 29 29
Aurora C/Aurora B/INCENP 0.038 0.079 -10000 0 -0.22 12 12
Aurora B/TACC1 0.032 0.059 -10000 0 -0.23 7 7
Aurora B/PP2A 0.034 0.07 -10000 0 -0.28 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.003 0.031 -10000 0 -0.14 7 7
mitotic metaphase/anaphase transition 0 0.004 -10000 0 -10000 0 0
NDC80 -0.026 0.081 -10000 0 -0.37 7 7
Cul3 protein complex 0.044 0.039 -10000 0 -0.22 1 1
KIF2C -0.013 0.18 -10000 0 -0.88 5 5
PEBP1 0.032 0.012 -10000 0 -10000 0 0
KIF20A 0.017 0.083 -10000 0 -0.38 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.034 0.07 -10000 0 -0.28 7 7
SEPT1 0.031 0.034 -10000 0 -0.38 1 1
SMC2 0.033 0.006 -10000 0 -10000 0 0
SMC4 0.034 0.005 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.027 0.18 -10000 0 -0.64 11 11
PSMA3 0.032 0.009 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 -10000 0 -10000 0 0
H3F3B 0.003 0.062 -10000 0 -0.28 7 7
AURKB 0.015 0.092 -10000 0 -0.4 7 7
AURKC 0.022 0.06 -10000 0 -0.38 3 3
CDCA8 0.026 0.053 -10000 0 -0.42 2 2
cytokinesis -0.022 0.19 -10000 0 -0.72 8 8
Aurora B/Septin1 0.011 0.19 0.36 1 -0.67 8 9
AURKA 0.029 0.036 -10000 0 -0.39 1 1
INCENP 0.026 0.051 -10000 0 -0.39 2 2
KLHL13 0.032 0.034 -10000 0 -0.38 1 1
BUB1 0.02 0.076 -10000 0 -0.38 5 5
hSgo1/Aurora B/Survivin 0.038 0.11 -10000 0 -0.36 9 9
EVI5 0.033 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.026 0.18 -10000 0 -0.6 8 8
SGOL1 0.017 0.082 -10000 0 -0.38 6 6
CENPA -0.012 0.17 -10000 0 -0.57 9 9
NCAPG 0.02 0.075 -10000 0 -0.38 5 5
Aurora B/HC8 Proteasome 0.032 0.07 -10000 0 -0.28 7 7
NCAPD2 0.033 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.035 0.07 -10000 0 -0.28 7 7
RHOA 0.034 0.004 -10000 0 -10000 0 0
NCAPH 0.023 0.068 -10000 0 -0.38 4 4
NPM1 -0.016 0.14 -10000 0 -0.46 11 11
RASA1 0.033 0.006 -10000 0 -10000 0 0
KLHL9 0.023 0.016 -10000 0 -10000 0 0
mitotic prometaphase -0.001 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.07 -10000 0 -0.28 7 7
PPP1CC 0.034 0.003 -10000 0 -10000 0 0
Centraspindlin 0.015 0.2 -10000 0 -0.66 8 8
RhoA/GDP 0.025 0.003 -10000 0 -10000 0 0
NSUN2 -0.016 0.14 -10000 0 -0.44 12 12
MYLK -0.002 0.071 -10000 0 -0.28 9 9
KIF23 0.023 0.07 -10000 0 -0.4 4 4
VIM -0.018 0.059 -10000 0 -0.28 7 7
RACGAP1 0.032 0.012 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.01 0.12 -10000 0 -0.4 11 11
Chromosomal passenger complex -0.016 0.18 -10000 0 -0.59 9 9
Chromosomal passenger complex/EVI5 0.069 0.12 -10000 0 -0.33 9 9
TACC1 0.034 0.005 -10000 0 -10000 0 0
PPP2R5D 0.034 0.005 -10000 0 -10000 0 0
CUL3 0.034 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.026 0.03 -10000 0 -10000 0 0
HSPA8 0.033 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.044 0.077 0.23 1 -0.28 3 4
AKT1 0.025 0.024 -10000 0 -0.096 3 3
GSC -0.12 0.4 -10000 0 -1.3 13 13
NKX2-5 -0.066 0.17 -10000 0 -0.38 34 34
muscle cell differentiation 0.003 0.098 0.37 2 -10000 0 2
SMAD2-3/SMAD4/SP1 0.047 0.11 -10000 0 -0.31 5 5
SMAD4 0.014 0.058 -10000 0 -0.2 2 2
CBFB 0.034 0.004 -10000 0 -10000 0 0
SAP18 0.032 0.009 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.024 0.098 -10000 0 -0.24 14 14
SMAD3/SMAD4/VDR 0.059 0.1 -10000 0 -0.27 6 6
MYC 0.033 0.036 -10000 0 -0.38 1 1
CDKN2B -0.24 0.28 -10000 0 -1.2 7 7
AP1 0.03 0.058 -10000 0 -0.25 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.015 0.067 -10000 0 -0.31 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.03 0.11 -10000 0 -0.43 7 7
SP3 0.035 0 -10000 0 -10000 0 0
CREB1 0.034 0 -10000 0 -10000 0 0
FOXH1 0.009 0.08 -10000 0 -0.29 7 7
SMAD3/SMAD4/GR 0.059 0.061 -10000 0 -10000 0 0
GATA3 -0.009 0.075 -10000 0 -0.31 6 6
SKI/SIN3/HDAC complex/NCoR1 0.017 0.053 -10000 0 -0.25 2 2
MEF2C/TIF2 -0.048 0.13 0.32 1 -0.37 8 9
endothelial cell migration 0.11 0.39 1.3 15 -10000 0 15
MAX 0.036 0.018 -10000 0 -10000 0 0
RBBP7 0.034 0.001 -10000 0 -10000 0 0
RBBP4 0.033 0.006 -10000 0 -10000 0 0
RUNX2 0.024 0.051 -10000 0 -0.38 2 2
RUNX3 0.031 0.035 -10000 0 -0.38 1 1
RUNX1 0.026 0.05 -10000 0 -0.38 2 2
CTBP1 0.034 0.003 -10000 0 -10000 0 0
NR3C1 0.039 0.016 -10000 0 -10000 0 0
VDR 0.007 0.085 -10000 0 -0.38 6 6
CDKN1A -0.035 0.26 0.36 1 -1.2 7 8
KAT2B 0.024 0.054 -10000 0 -0.4 2 2
SMAD2/SMAD2/SMAD4/FOXH1 0.026 0.11 -10000 0 -0.28 15 15
DCP1A 0.034 0.004 -10000 0 -10000 0 0
SKI 0.03 0.035 -10000 0 -0.38 1 1
SERPINE1 -0.12 0.4 -10000 0 -1.3 15 15
SMAD3/SMAD4/ATF2 0.049 0.064 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.041 0.078 -10000 0 -0.31 3 3
SAP30 0.033 0.007 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.055 0.057 0.21 1 -10000 0 1
JUN 0.012 0.052 -10000 0 -0.24 1 1
SMAD3/SMAD4/IRF7 0.046 0.064 -10000 0 -0.19 1 1
TFE3 0.023 0.039 -10000 0 -0.15 2 2
COL1A2 -0.015 0.14 -10000 0 -0.73 5 5
mesenchymal cell differentiation -0.042 0.076 0.28 3 -10000 0 3
DLX1 -0.011 0.11 -10000 0 -0.38 11 11
TCF3 0.033 0.007 -10000 0 -10000 0 0
FOS 0.019 0.064 -10000 0 -0.38 3 3
SMAD3/SMAD4/Max 0.057 0.061 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.051 0.041 -10000 0 -10000 0 0
ZBTB17 0.033 0.035 -10000 0 -0.38 1 1
LAMC1 -0.002 0.073 -10000 0 -0.44 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.047 0.062 -10000 0 -10000 0 0
IRF7 0.031 0.014 -10000 0 -10000 0 0
ESR1 0.023 0.062 -10000 0 -0.38 3 3
HNF4A 0 0 -10000 0 -10000 0 0
MEF2C -0.058 0.12 0.33 1 -0.36 7 8
SMAD2-3/SMAD4 0.036 0.084 -10000 0 -0.21 5 5
Cbp/p300/Src-1 0.053 0.046 -10000 0 -10000 0 0
IGHV3OR16-13 0.011 0.014 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.031 0.01 -10000 0 -10000 0 0
CREBBP 0.028 0.025 -10000 0 -10000 0 0
SKIL 0.034 0.004 -10000 0 -10000 0 0
HDAC1 0.033 0.006 -10000 0 -10000 0 0
HDAC2 0.031 0.01 -10000 0 -10000 0 0
SNIP1 0.033 0.008 -10000 0 -10000 0 0
GCN5L2 0 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.044 0.082 -10000 0 -0.23 4 4
MSG1/HSC70 0.016 0.095 -10000 0 -0.27 14 14
SMAD2 0.017 0.049 -10000 0 -0.14 8 8
SMAD3 0.025 0.047 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.016 0.051 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.008 0.055 0.19 1 -0.31 2 3
NCOR1 0.034 0.004 -10000 0 -10000 0 0
NCOA2 0.019 0.075 -10000 0 -0.38 5 5
NCOA1 0.034 0.004 -10000 0 -10000 0 0
MYOD/E2A 0.039 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.054 0.12 -10000 0 -0.3 5 5
IFNB1 -0.013 0.033 -10000 0 -0.16 1 1
SMAD3/SMAD4/MEF2C -0.028 0.13 -10000 0 -0.34 8 8
CITED1 -0.009 0.12 -10000 0 -0.38 14 14
SMAD2-3/SMAD4/ARC105 0.049 0.085 -10000 0 -0.23 1 1
RBL1 0.032 0.008 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.017 0.12 -10000 0 -0.58 5 5
RUNX1-3/PEBPB2 0.057 0.047 -10000 0 -0.23 3 3
SMAD7 0.01 0.089 -10000 0 -0.52 1 1
MYC/MIZ-1 0.048 0.042 -10000 0 -0.27 2 2
SMAD3/SMAD4 -0.025 0.19 0.29 8 -0.51 15 23
IL10 -0.025 0.1 -10000 0 -0.36 9 9
PIASy/HDAC complex 0.026 0.042 -10000 0 -0.38 1 1
PIAS3 0.029 0.02 -10000 0 -10000 0 0
CDK2 0.028 0.024 -10000 0 -10000 0 0
IL5 -0.02 0.069 -10000 0 -0.25 3 3
CDK4 0.025 0.025 -10000 0 -10000 0 0
PIAS4 0.026 0.042 -10000 0 -0.38 1 1
ATF3 0.022 0.061 -10000 0 -0.38 3 3
SMAD3/SMAD4/SP1 0.043 0.094 -10000 0 -0.29 6 6
FOXG1 -0.004 0.12 -10000 0 -0.38 13 13
FOXO3 -0.004 0.033 -10000 0 -0.17 3 3
FOXO1 -0.001 0.022 -10000 0 -0.12 1 1
FOXO4 -0.004 0.035 -10000 0 -0.18 3 3
heart looping -0.057 0.12 0.32 1 -0.36 7 8
CEBPB 0.028 0.017 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.016 0.1 -10000 0 -0.24 12 12
MYOD1 0.023 0.017 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.031 0.054 -10000 0 -0.16 1 1
SMAD3/SMAD4/GATA3 0.01 0.091 -10000 0 -0.25 10 10
SnoN/SIN3/HDAC complex/NCoR1 0.034 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.069 0.082 -10000 0 -0.22 3 3
SMAD3/SMAD4/SP1-3 0.065 0.093 -10000 0 -0.28 4 4
MED15 0.032 0.009 -10000 0 -10000 0 0
SP1 0.019 0.049 -10000 0 -0.18 3 3
SIN3B 0.033 0.007 -10000 0 -10000 0 0
SIN3A 0.034 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.013 0.16 -10000 0 -0.24 42 42
ITGB5 -0.002 0.072 0.35 1 -0.29 2 3
TGIF/SIN3/HDAC complex/CtBP 0.018 0.053 -10000 0 -0.25 2 2
SMAD3/SMAD4/AR 0.017 0.11 -10000 0 -0.26 15 15
AR -0.01 0.13 -10000 0 -0.38 15 15
negative regulation of cell growth 0.014 0.06 -10000 0 -0.3 1 1
SMAD3/SMAD4/MYOD 0.041 0.064 -10000 0 -10000 0 0
E2F5 0.033 0.006 -10000 0 -10000 0 0
E2F4 0.034 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.048 0.1 -10000 0 -0.28 4 4
SMAD2-3/SMAD4/FOXO1-3a-4 -0.013 0.094 -10000 0 -0.44 5 5
TFDP1 0.024 0.059 -10000 0 -0.38 3 3
SMAD3/SMAD4/AP1 0.051 0.071 -10000 0 -0.25 1 1
SMAD3/SMAD4/RUNX2 0.042 0.076 -10000 0 -0.28 3 3
TGIF2 0.031 0.01 -10000 0 -10000 0 0
TGIF1 0.032 0.008 -10000 0 -10000 0 0
ATF2 0.034 0 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.033 0.007 -10000 0 -10000 0 0
SVIL 0.021 0.022 -10000 0 -10000 0 0
ZNF318 0.034 0.005 -10000 0 -10000 0 0
JMJD2C 0 0 -10000 0 -10000 0 0
T-DHT/AR/Ubc9 0 0.092 -10000 0 -0.24 15 15
CARM1 0.033 0.007 -10000 0 -10000 0 0
PRDX1 0.033 0.006 -10000 0 -10000 0 0
PELP1 0.033 0.006 -10000 0 -10000 0 0
CTNNB1 0.034 0.004 -10000 0 -10000 0 0
AKT1 0.032 0.009 -10000 0 -10000 0 0
PTK2B 0.032 0.015 -10000 0 -10000 0 0
MED1 0.034 0 -10000 0 -10000 0 0
MAK 0.017 0.064 -10000 0 -0.38 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.018 0.05 -10000 0 -0.38 2 2
GSN 0.032 0.011 -10000 0 -10000 0 0
NCOA2 0.019 0.075 -10000 0 -0.38 5 5
NCOA6 0.029 0.035 -10000 0 -0.38 1 1
DNA-PK 0.061 0.023 -10000 0 -10000 0 0
NCOA4 0.024 0.016 -10000 0 -10000 0 0
PIAS3 0.034 0.004 -10000 0 -10000 0 0
cell proliferation -0.025 0.12 -10000 0 -0.55 7 7
XRCC5 0.034 0 -10000 0 -10000 0 0
UBE3A 0.034 0.005 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.006 0.098 -10000 0 -0.24 18 18
FHL2 -0.027 0.15 -10000 0 -0.79 5 5
RANBP9 0.034 0.005 -10000 0 -10000 0 0
JMJD1A -0.01 0.045 -10000 0 -0.14 16 16
CDK6 -0.001 0.093 -10000 0 -0.38 8 8
TGFB1I1 0.034 0.004 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.002 0.093 -10000 0 -0.23 16 16
XRCC6 0.031 0.01 -10000 0 -10000 0 0
T-DHT/AR -0.023 0.1 -10000 0 -0.21 26 26
CTDSP1 0.034 0 -10000 0 -10000 0 0
CTDSP2 0.029 0.013 -10000 0 -10000 0 0
BRCA1 0.034 0.003 -10000 0 -10000 0 0
TCF4 0.033 0.007 -10000 0 -10000 0 0
CDKN2A -0.019 0.034 -10000 0 -10000 0 0
SRF 0.027 0.036 -10000 0 -0.15 4 4
NKX3-1 -0.045 0.17 -10000 0 -0.85 5 5
KLK3 0.018 0.039 0.15 4 -10000 0 4
TMF1 0.034 0.004 -10000 0 -10000 0 0
HNRNPA1 0.033 0.007 -10000 0 -10000 0 0
AOF2 0 0 -10000 0 -10000 0 0
APPL1 -0.014 0.004 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 0 0.093 -10000 0 -0.24 15 15
AR -0.024 0.13 -10000 0 -0.39 15 15
UBA3 0.034 0.004 -10000 0 -10000 0 0
PATZ1 0.031 0.01 -10000 0 -10000 0 0
PAWR 0.02 0.054 -10000 0 -0.38 2 2
PRKDC 0.034 0.005 -10000 0 -10000 0 0
PA2G4 0.032 0.008 -10000 0 -10000 0 0
UBE2I 0.034 0.005 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.002 0.084 -10000 0 -0.22 15 15
RPS6KA3 0.034 0 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.009 0.088 -10000 0 -0.24 15 15
LATS2 0.032 0.009 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.001 0.084 -10000 0 -0.21 16 16
Cyclin D3/CDK11 p58 0.025 0.004 -10000 0 -10000 0 0
VAV3 0.005 0.1 -10000 0 -0.38 10 10
KLK2 -0.021 0.041 -10000 0 -0.11 16 16
CASP8 0.034 0 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.014 0.11 -10000 0 -0.28 13 13
TMPRSS2 -0.081 0.23 -10000 0 -0.8 13 13
CCND1 0.031 0.018 -10000 0 -10000 0 0
PIAS1 0.034 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.007 0.02 -10000 0 -10000 0 0
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.03 0.035 -10000 0 -0.38 1 1
T-DHT/AR/CDK6 -0.015 0.092 -10000 0 -0.24 18 18
CMTM2 0.026 0.05 -10000 0 -0.38 2 2
SNURF 0.025 0.059 -10000 0 -0.38 3 3
ZMIZ1 0.012 0.044 -10000 0 -0.38 1 1
CCND3 0.034 0.005 -10000 0 -10000 0 0
TGIF1 0.032 0.008 -10000 0 -10000 0 0
FKBP4 0.033 0.008 -10000 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR 0.008 0.088 -10000 0 -1 1 1
regulation of axonogenesis 0.006 0.069 0.26 9 -10000 0 9
myoblast fusion -0.02 0.038 0.39 1 -10000 0 1
mol:GTP 0.012 0.05 -10000 0 -0.16 11 11
regulation of calcium-dependent cell-cell adhesion -0.047 0.053 0.23 1 -10000 0 1
ARF1/GTP 0.031 0.047 -10000 0 -0.17 1 1
mol:GM1 0.001 0.036 -10000 0 -0.16 1 1
mol:Choline -0.001 0.039 -10000 0 -0.3 1 1
lamellipodium assembly -0.004 0.076 -10000 0 -0.36 6 6
MAPK3 0.014 0.045 -10000 0 -0.33 1 1
ARF6/GTP/NME1/Tiam1 0.048 0.054 -10000 0 -0.23 1 1
ARF1 0.033 0.007 -10000 0 -10000 0 0
ARF6/GDP 0.02 0.038 -10000 0 -0.39 1 1
ARF1/GDP 0.012 0.075 -10000 0 -0.26 6 6
ARF6 0.038 0.019 -10000 0 -0.14 1 1
RAB11A 0.033 0.006 -10000 0 -10000 0 0
TIAM1 0.033 0.01 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.041 -10000 0 -0.33 1 1
actin filament bundle formation -0.019 0.074 0.26 6 -10000 0 6
KALRN 0.012 0.029 -10000 0 -0.29 1 1
RAB11FIP3/RAB11A 0.049 0.01 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.075 -10000 0 -0.26 6 6
NME1 0.033 0.011 -10000 0 -10000 0 0
Rac1/GDP 0.015 0.06 -10000 0 -0.28 3 3
substrate adhesion-dependent cell spreading 0.012 0.05 -10000 0 -0.16 11 11
cortical actin cytoskeleton organization -0.004 0.077 -10000 0 -0.37 6 6
RAC1 0.023 0.016 -10000 0 -10000 0 0
liver development 0.012 0.05 -10000 0 -0.16 11 11
ARF6/GTP 0.012 0.05 -10000 0 -0.16 11 11
RhoA/GTP 0.034 0.046 -10000 0 -0.17 1 1
mol:GDP -0.006 0.071 -10000 0 -0.28 6 6
ARF6/GTP/RAB11FIP3/RAB11A 0.05 0.05 -10000 0 -0.15 1 1
RHOA 0.034 0.004 -10000 0 -10000 0 0
PLD1 0.009 0.048 -10000 0 -0.26 2 2
RAB11FIP3 0.034 0.005 -10000 0 -10000 0 0
tube morphogenesis -0.004 0.076 -10000