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

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

Summary

There were 49 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 47
TCGA08_p53 37
Ephrin B reverse signaling 33
HIF-1-alpha transcription factor network 32
IL4-mediated signaling events 31
Wnt signaling 30
Fc-epsilon receptor I signaling in mast cells 27
Signaling mediated by p38-alpha and p38-beta 27
Endothelins 26
Syndecan-1-mediated signaling events 24
Results

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
IL23-mediated signaling events 47 2834 60 -0.62 0.036 1000 -1000 -0.055 -1000
TCGA08_p53 37 260 7 -0.086 0.03 1000 -1000 -0.007 -1000
Ephrin B reverse signaling 33 1614 48 -0.24 0.052 1000 -1000 -0.026 -1000
HIF-1-alpha transcription factor network 32 2492 76 -0.28 0.042 1000 -1000 -0.03 -1000
IL4-mediated signaling events 31 2862 91 -0.6 0.48 1000 -1000 -0.066 -1000
Wnt signaling 30 216 7 -0.11 0.033 1000 -1000 -0.013 -1000
Fc-epsilon receptor I signaling in mast cells 27 2695 97 -0.22 0.037 1000 -1000 -0.058 -1000
Signaling mediated by p38-alpha and p38-beta 27 1215 44 -0.16 0.037 1000 -1000 -0.014 -1000
Endothelins 26 2522 96 -0.22 0.041 1000 -1000 -0.043 -1000
Syndecan-1-mediated signaling events 24 819 34 -0.13 0.044 1000 -1000 -0.039 -1000
Thromboxane A2 receptor signaling 23 2423 105 -0.17 0.053 1000 -1000 -0.04 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 22 1517 68 -0.38 0.17 1000 -1000 -0.063 -1000
IL12-mediated signaling events 21 1911 87 -0.34 0.041 1000 -1000 -0.046 -1000
Noncanonical Wnt signaling pathway 21 564 26 -0.11 0.038 1000 -1000 -0.052 -1000
Glypican 1 network 21 1037 48 -0.13 0.046 1000 -1000 -0.021 -1000
IL27-mediated signaling events 21 1095 51 -0.19 0.13 1000 -1000 -0.047 -1000
Glucocorticoid receptor regulatory network 20 2297 114 -0.39 0.22 1000 -1000 -0.057 -1000
Osteopontin-mediated events 19 751 38 -0.17 0.042 1000 -1000 -0.05 -1000
IL1-mediated signaling events 19 1192 62 -0.15 0.085 1000 -1000 -0.035 -1000
Calcium signaling in the CD4+ TCR pathway 19 600 31 -0.21 0.033 1000 -1000 -0.044 -1000
TCGA08_retinoblastoma 19 158 8 -0.03 0.038 1000 -1000 -0.004 -1000
EGFR-dependent Endothelin signaling events 19 417 21 -0.094 0.053 1000 -1000 -0.012 -1000
FOXA2 and FOXA3 transcription factor networks 18 866 46 -0.23 0.045 1000 -1000 -0.058 -1000
Glypican 2 network 18 75 4 -0.006 0 1000 -1000 0 -1000
Presenilin action in Notch and Wnt signaling 17 1047 61 -0.15 0.1 1000 -1000 -0.037 -1000
BMP receptor signaling 17 1406 81 -0.14 0.066 1000 -1000 -0.034 -1000
amb2 Integrin signaling 17 1469 82 -0.16 0.047 1000 -1000 -0.025 -1000
FAS signaling pathway (CD95) 17 826 47 -0.32 0.06 1000 -1000 -0.033 -1000
EPHB forward signaling 17 1475 85 -0.076 0.12 1000 -1000 -0.057 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 17 1329 78 -0.26 0.051 1000 -1000 -0.05 -1000
TCR signaling in naïve CD8+ T cells 16 1507 93 -0.079 0.053 1000 -1000 -0.039 -1000
Canonical Wnt signaling pathway 16 831 51 -0.26 0.11 1000 -1000 -0.039 -1000
Visual signal transduction: Rods 16 834 52 -0.16 0.057 1000 -1000 -0.033 -1000
FOXM1 transcription factor network 16 823 51 -0.24 0.035 1000 -1000 -0.074 -1000
PLK2 and PLK4 events 15 46 3 -0.016 0.031 1000 -1000 -0.001 -1000
Syndecan-2-mediated signaling events 15 1044 69 -0.14 0.045 1000 -1000 -0.029 -1000
IFN-gamma pathway 15 1079 68 -0.11 0.047 1000 -1000 -0.057 -1000
Signaling events mediated by the Hedgehog family 14 778 52 -0.12 0.074 1000 -1000 -0.029 -1000
Arf6 signaling events 14 898 62 -0.094 0.086 1000 -1000 -0.017 -1000
S1P1 pathway 14 513 36 -0.15 0.037 1000 -1000 -0.025 -1000
Cellular roles of Anthrax toxin 13 537 39 -0.063 0.034 1000 -1000 -0.029 -1000
IL6-mediated signaling events 13 1020 75 -0.12 0.049 1000 -1000 -0.035 -1000
BCR signaling pathway 13 1320 99 -0.18 0.047 1000 -1000 -0.046 -1000
a4b1 and a4b7 Integrin signaling 12 61 5 0.003 0.034 1000 -1000 0.011 -1000
Nectin adhesion pathway 12 810 63 -0.054 0.059 1000 -1000 -0.038 -1000
Syndecan-3-mediated signaling events 12 437 35 -0.14 0.054 1000 -1000 -0.034 -1000
LPA receptor mediated events 12 1241 102 -0.14 0.039 1000 -1000 -0.085 -1000
Stabilization and expansion of the E-cadherin adherens junction 12 912 74 -0.094 0.052 1000 -1000 -0.061 -1000
Aurora B signaling 12 833 67 -0.17 0.052 1000 -1000 -0.029 -1000
Caspase cascade in apoptosis 11 865 74 -0.12 0.06 1000 -1000 -0.033 -1000
Syndecan-4-mediated signaling events 11 789 67 -0.058 0.067 1000 -1000 -0.032 -1000
E-cadherin signaling events 11 55 5 0.013 0.037 1000 -1000 0.019 -1000
Ras signaling in the CD4+ TCR pathway 11 201 17 -0.025 0.048 1000 -1000 -0.019 -1000
Sphingosine 1-phosphate (S1P) pathway 10 297 28 -0.039 0.047 1000 -1000 -0.014 -1000
JNK signaling in the CD4+ TCR pathway 10 171 17 -0.036 0.036 1000 -1000 -0.024 -1000
Reelin signaling pathway 10 577 56 -0.077 0.094 1000 -1000 -0.037 -1000
IL2 signaling events mediated by STAT5 10 230 22 -0.082 0.038 1000 -1000 -0.036 -1000
Signaling events mediated by PRL 10 353 34 -0.05 0.054 1000 -1000 -0.038 -1000
Visual signal transduction: Cones 9 352 38 -0.004 0.047 1000 -1000 -0.003 -1000
Signaling events mediated by PTP1B 9 707 76 -0.092 0.061 1000 -1000 -0.032 -1000
IL2 signaling events mediated by PI3K 9 576 58 -0.075 0.051 1000 -1000 -0.029 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 9 424 45 -0.047 0.052 1000 -1000 -0.038 -1000
Nongenotropic Androgen signaling 9 481 52 -0.096 0.059 1000 -1000 -0.029 -1000
E-cadherin signaling in the nascent adherens junction 9 750 76 -0.045 0.077 1000 -1000 -0.055 -1000
Hedgehog signaling events mediated by Gli proteins 8 523 65 -0.11 0.057 1000 -1000 -0.036 -1000
p75(NTR)-mediated signaling 8 1121 125 -0.14 0.082 1000 -1000 -0.038 -1000
Arf6 downstream pathway 8 357 43 -0.034 0.044 1000 -1000 -0.031 -1000
PDGFR-alpha signaling pathway 8 392 44 -0.12 0.075 1000 -1000 -0.04 -1000
Signaling mediated by p38-gamma and p38-delta 8 132 15 -0.017 0.03 1000 -1000 -0.032 -1000
Integrins in angiogenesis 8 698 84 -0.17 0.078 1000 -1000 -0.045 -1000
Regulation of p38-alpha and p38-beta 8 452 54 -0.033 0.067 1000 -1000 -0.02 -1000
Regulation of Androgen receptor activity 8 608 70 -0.11 0.089 1000 -1000 -0.042 -1000
Regulation of nuclear SMAD2/3 signaling 7 1005 136 -0.077 0.059 1000 -1000 -0.046 -1000
mTOR signaling pathway 7 372 53 -0.058 0.04 1000 -1000 -0.036 -1000
Class I PI3K signaling events 7 572 73 -0.059 0.051 1000 -1000 -0.029 -1000
Regulation of Telomerase 7 785 102 -0.2 0.08 1000 -1000 -0.044 -1000
Insulin Pathway 7 544 74 -0.17 0.11 1000 -1000 -0.036 -1000
Plasma membrane estrogen receptor signaling 7 645 86 -0.052 0.11 1000 -1000 -0.053 -1000
VEGFR1 specific signals 7 433 56 -0.007 0.098 1000 -1000 -0.049 -1000
PDGFR-beta signaling pathway 7 684 97 -0.049 0.096 1000 -1000 -0.042 -1000
ErbB4 signaling events 6 467 69 -0.18 0.067 1000 -1000 -0.039 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 6 335 54 -0.077 0.049 1000 -1000 -0.037 -1000
Ceramide signaling pathway 6 487 76 -0.094 0.072 1000 -1000 -0.03 -1000
Paxillin-independent events mediated by a4b1 and a4b7 6 255 37 -0.02 0.07 1000 -1000 -0.031 -1000
Signaling events mediated by HDAC Class III 6 251 40 -0.06 0.064 1000 -1000 -0.032 -1000
RXR and RAR heterodimerization with other nuclear receptor 6 357 52 -0.071 0.097 1000 -1000 -0.024 -1000
HIF-2-alpha transcription factor network 6 265 43 -0.048 0.055 1000 -1000 -0.042 -1000
FoxO family signaling 6 396 64 -0.077 0.051 1000 -1000 -0.041 -1000
Effects of Botulinum toxin 6 167 26 -0.094 0.063 1000 -1000 -0.003 -1000
Signaling events mediated by VEGFR1 and VEGFR2 6 766 125 -0.047 0.098 1000 -1000 -0.048 -1000
Arf6 trafficking events 6 473 71 -0.047 0.039 1000 -1000 -0.023 -1000
S1P3 pathway 6 276 42 -0.032 0.047 1000 -1000 -0.026 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 6 213 33 -0.039 0.077 1000 -1000 -0.025 -1000
EPO signaling pathway 5 316 55 -0.025 0.056 1000 -1000 -0.024 -1000
PLK1 signaling events 5 463 85 -0.022 0.057 1000 -1000 -0.038 -1000
TRAIL signaling pathway 5 279 48 -0.021 0.06 1000 -1000 -0.028 -1000
Signaling events regulated by Ret tyrosine kinase 5 442 82 -0.026 0.071 1000 -1000 -0.058 -1000
Retinoic acid receptors-mediated signaling 5 341 58 -0.1 0.067 1000 -1000 -0.043 -1000
Paxillin-dependent events mediated by a4b1 5 210 36 -0.06 0.064 1000 -1000 -0.026 -1000
Class IB PI3K non-lipid kinase events 5 15 3 -0.027 0.027 1000 -1000 -0.02 -1000
ErbB2/ErbB3 signaling events 4 308 65 -0.094 0.052 1000 -1000 -0.044 -1000
Coregulation of Androgen receptor activity 4 331 76 -0.074 0.059 1000 -1000 -0.017 -1000
BARD1 signaling events 4 237 57 -0.039 0.076 1000 -1000 -0.033 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 4 423 85 -0.19 0.082 1000 -1000 -0.041 -1000
Aurora C signaling 4 30 7 0 0.036 1000 -1000 -0.008 -1000
Class I PI3K signaling events mediated by Akt 4 301 68 -0.054 0.076 1000 -1000 -0.03 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 4 367 83 -0.035 0.074 1000 -1000 -0.021 -1000
TCGA08_rtk_signaling 4 117 26 -0.031 0.059 1000 -1000 -0.007 -1000
IGF1 pathway 4 229 57 -0.024 0.084 1000 -1000 -0.038 -1000
Angiopoietin receptor Tie2-mediated signaling 4 383 88 -0.17 0.11 1000 -1000 -0.066 -1000
Neurotrophic factor-mediated Trk receptor signaling 4 480 120 -0.018 0.095 1000 -1000 -0.042 -1000
S1P4 pathway 4 123 25 -0.014 0.047 1000 -1000 -0.022 -1000
LPA4-mediated signaling events 3 43 12 -0.023 0.018 1000 -1000 -0.028 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 3 75 23 0 0.041 1000 -1000 -0.026 -1000
Ephrin A reverse signaling 3 26 7 -0.001 0.04 1000 -1000 0 -1000
Aurora A signaling 3 238 60 -0.058 0.053 1000 -1000 -0.013 -1000
Insulin-mediated glucose transport 3 101 32 -0.03 0.046 1000 -1000 -0.019 -1000
S1P5 pathway 3 67 17 -0.012 0.037 1000 -1000 -0.009 -1000
ceramide signaling pathway 3 148 49 -0.011 0.052 1000 -1000 -0.034 -1000
Atypical NF-kappaB pathway 3 94 31 -0.012 0.048 1000 -1000 -0.013 -1000
E-cadherin signaling in keratinocytes 3 166 43 -0.045 0.096 1000 -1000 -0.027 -1000
p38 MAPK signaling pathway 3 136 44 0 0.059 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class II 2 176 75 -0.016 0.068 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class I 2 252 104 -0.049 0.083 1000 -1000 -0.025 -1000
Arf1 pathway 2 119 54 -0.001 0.088 1000 -1000 -0.023 -1000
Nephrin/Neph1 signaling in the kidney podocyte 1 62 34 -0.044 0.094 1000 -1000 -0.025 -1000
Circadian rhythm pathway 1 26 22 -0.012 0.076 1000 -1000 -0.036 -1000
Sumoylation by RanBP2 regulates transcriptional repression 1 27 27 0 0.052 1000 -1000 -0.031 -1000
Canonical NF-kappaB pathway 0 38 39 0 0.078 1000 -1000 -0.019 -1000
Rapid glucocorticoid signaling 0 11 20 0 0.046 1000 -1000 -0.002 -1000
Alternative NF-kappaB pathway 0 12 13 0 0.096 1000 -1000 0 -1000
Total 1426 83579 7203 -13 8.5 131000 -131000 -4.2 -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 -0.52 0.61 -10000 0 -1.3 72 72
IL23A -0.57 0.63 -10000 0 -1.3 81 81
NF kappa B1 p50/RelA/I kappa B alpha -0.49 0.59 -10000 0 -1.2 79 79
positive regulation of T cell mediated cytotoxicity -0.54 0.66 -10000 0 -1.3 75 75
ITGA3 -0.5 0.57 -10000 0 -1.2 72 72
IL17F -0.3 0.36 -10000 0 -0.73 73 73
IL12B -0.018 0.074 -10000 0 -0.37 4 4
STAT1 (dimer) -0.52 0.63 -10000 0 -1.3 75 75
CD4 -0.45 0.53 -10000 0 -1.2 61 61
IL23 -0.55 0.6 -10000 0 -1.2 81 81
IL23R -0.14 0.38 -10000 0 -1.3 18 18
IL1B -0.56 0.64 -10000 0 -1.3 79 79
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.46 0.54 -10000 0 -1.2 67 67
TYK2 -0.008 0.043 -10000 0 -10000 0 0
STAT4 0.022 0.079 -10000 0 -0.33 9 9
STAT3 0.036 0.009 -10000 0 -10000 0 0
IL18RAP -0.061 0.18 -10000 0 -0.37 49 49
IL12RB1 -0.01 0.046 -10000 0 -0.25 1 1
PIK3CA 0.036 0.008 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.007 0.056 -10000 0 -0.19 1 1
IL23R/JAK2 -0.15 0.37 -10000 0 -1.3 17 17
positive regulation of chronic inflammatory response -0.54 0.66 -10000 0 -1.3 75 75
natural killer cell activation 0.01 0.018 0.081 11 -10000 0 11
JAK2 -0.027 0.091 -10000 0 -0.3 13 13
PIK3R1 0.029 0.061 -10000 0 -0.48 3 3
NFKB1 0.034 0.006 -10000 0 -10000 0 0
RELA 0.034 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.51 0.56 -10000 0 -1.2 81 81
ALOX12B -0.45 0.54 -10000 0 -1.2 65 65
CXCL1 -0.56 0.62 -10000 0 -1.3 83 83
T cell proliferation -0.54 0.66 -10000 0 -1.3 75 75
NFKBIA 0.027 0.044 -10000 0 -0.31 3 3
IL17A -0.24 0.28 -10000 0 -0.55 77 77
PI3K -0.48 0.6 -10000 0 -1.2 72 72
IFNG -0.03 0.06 0.13 7 -0.13 37 44
STAT3 (dimer) -0.45 0.57 -10000 0 -1.2 72 72
IL18R1 0.003 0.098 -10000 0 -0.28 19 19
IL23/IL23R/JAK2/TYK2/SOCS3 -0.25 0.33 -10000 0 -0.69 54 54
IL18/IL18R -0.066 0.19 -10000 0 -0.36 51 51
macrophage activation -0.024 0.022 -10000 0 -0.047 74 74
TNF -0.52 0.58 -10000 0 -1.2 75 75
STAT3/STAT4 -0.48 0.6 -10000 0 -1.2 74 74
STAT4 (dimer) -0.52 0.63 -10000 0 -1.3 75 75
IL18 -0.027 0.16 -10000 0 -0.43 27 27
IL19 -0.45 0.53 -10000 0 -1.1 69 69
STAT5A (dimer) -0.51 0.63 -10000 0 -1.3 74 74
STAT1 0.017 0.068 -10000 0 -0.21 18 18
SOCS3 0.014 0.09 -10000 0 -0.32 13 13
CXCL9 -0.62 0.66 -10000 0 -1.3 96 96
MPO -0.45 0.54 -10000 0 -1.2 64 64
positive regulation of humoral immune response -0.54 0.66 -10000 0 -1.3 75 75
IL23/IL23R/JAK2/TYK2 -0.59 0.75 -10000 0 -1.5 74 74
IL6 -0.56 0.64 -10000 0 -1.3 82 82
STAT5A 0.029 0.049 -10000 0 -0.26 5 5
IL2 0.028 0.028 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.01 0.018 0.081 11 -10000 0 11
CD3E -0.45 0.53 -10000 0 -1.1 66 66
keratinocyte proliferation -0.54 0.66 -10000 0 -1.3 75 75
NOS2 -0.45 0.53 -10000 0 -1.1 75 75
TCGA08_p53

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
CDKN2A -0.036 0.1 -10000 0 -0.35 17 17
TP53 -0.086 0.13 0.26 2 -0.25 73 75
Senescence -0.086 0.13 0.26 2 -0.25 72 74
Apoptosis -0.086 0.13 0.26 2 -0.25 72 74
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.021 0.079 0.26 17 -10000 0 17
MDM4 0.03 0.053 -10000 0 -0.39 3 3
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 -0.004 0.12 -10000 0 -0.46 13 13
EPHB2 0.007 0.12 -10000 0 -0.48 12 12
EFNB1 0.013 0.047 -10000 0 -0.36 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.003 0.13 -10000 0 -0.3 18 18
Ephrin B2/EPHB1-2 -0.04 0.13 -10000 0 -0.3 34 34
neuron projection morphogenesis -0.021 0.12 -10000 0 -0.28 20 20
Ephrin B1/EPHB1-2/Tiam1 -0.012 0.14 -10000 0 -0.28 30 30
DNM1 0.032 0.037 -10000 0 -0.2 5 5
cell-cell signaling 0.001 0.005 -10000 0 -10000 0 0
MAP2K4 -0.16 0.25 -10000 0 -0.53 65 65
YES1 -0.23 0.37 -10000 0 -0.79 65 65
Ephrin B1/EPHB1-2/NCK2 -0.007 0.14 -10000 0 -0.3 26 26
PI3K -0.14 0.28 -10000 0 -0.52 70 70
mol:GDP -0.013 0.14 -10000 0 -0.28 30 30
ITGA2B 0.036 0.007 -10000 0 -10000 0 0
endothelial cell proliferation 0.01 0.083 -10000 0 -0.29 13 13
FYN -0.24 0.37 -10000 0 -0.78 68 68
MAP3K7 -0.17 0.27 -10000 0 -0.57 65 65
FGR -0.23 0.37 -10000 0 -0.78 66 66
TIAM1 0.029 0.053 -10000 0 -0.39 3 3
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
RGS3 0.037 0.006 -10000 0 -10000 0 0
cell adhesion -0.13 0.25 -10000 0 -0.5 63 63
LYN -0.22 0.36 -10000 0 -0.77 65 65
Ephrin B1/EPHB1-2/Src Family Kinases -0.21 0.33 -10000 0 -0.7 66 66
Ephrin B1/EPHB1-2 -0.18 0.29 -10000 0 -0.61 64 64
SRC -0.22 0.35 -10000 0 -0.75 64 64
ITGB3 0.035 0.018 -10000 0 -0.21 1 1
EPHB1 -0.069 0.16 -10000 0 -0.27 75 75
EPHB4 0.024 0.069 -10000 0 -0.33 7 7
RAC1 0.033 0.012 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.011 0.083 -10000 0 -0.3 13 13
alphaIIb/beta3 Integrin 0.052 0.018 -10000 0 -10000 0 0
BLK -0.24 0.37 -10000 0 -0.78 67 67
HCK -0.23 0.35 -10000 0 -0.76 65 65
regulation of stress fiber formation 0.009 0.14 0.29 26 -10000 0 26
MAPK8 -0.16 0.24 -10000 0 -0.51 66 66
Ephrin B1/EPHB1-2/RGS3 -0.008 0.14 -10000 0 -0.29 29 29
endothelial cell migration -0.096 0.24 0.25 4 -0.48 51 55
NCK2 0.036 0.017 -10000 0 -0.21 1 1
PTPN13 -0.19 0.27 -10000 0 -0.53 74 74
regulation of focal adhesion formation 0.009 0.14 0.29 26 -10000 0 26
chemotaxis 0.009 0.14 0.28 29 -10000 0 29
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.011 0.12 -10000 0 -0.29 19 19
angiogenesis -0.18 0.28 -10000 0 -0.61 64 64
LCK -0.24 0.37 -10000 0 -0.79 67 67
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.22 0.44 -9999 0 -0.92 45 45
HDAC7 -0.001 0.005 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.15 0.4 -9999 0 -0.79 35 35
SMAD4 0.018 0.062 -9999 0 -0.48 3 3
ID2 -0.22 0.46 -9999 0 -0.94 47 47
AP1 -0.081 0.16 -9999 0 -0.36 47 47
ABCG2 -0.23 0.46 -9999 0 -0.94 47 47
HIF1A -0.02 0.1 -9999 0 -0.33 7 7
TFF3 -0.22 0.46 -9999 0 -0.95 46 46
GATA2 0.019 0.059 -9999 0 -0.39 3 3
AKT1 -0.02 0.094 -9999 0 -0.29 4 4
response to hypoxia -0.035 0.072 -9999 0 -0.18 3 3
MCL1 -0.22 0.45 -9999 0 -0.93 45 45
NDRG1 -0.22 0.43 -9999 0 -0.94 42 42
SERPINE1 -0.22 0.44 -9999 0 -0.93 45 45
FECH -0.24 0.44 -9999 0 -0.93 46 46
FURIN -0.22 0.44 -9999 0 -0.91 46 46
NCOA2 0.028 0.052 -9999 0 -0.48 2 2
EP300 -0.038 0.12 -9999 0 -0.3 22 22
HMOX1 -0.23 0.45 -9999 0 -0.94 46 46
BHLHE40 -0.23 0.43 -9999 0 -0.92 45 45
BHLHE41 -0.23 0.43 -9999 0 -0.92 45 45
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.017 0.16 -9999 0 -0.37 9 9
ENG -0.039 0.12 -9999 0 -0.4 5 5
JUN -0.024 0.15 -9999 0 -0.41 26 26
RORA -0.23 0.45 -9999 0 -0.94 46 46
ABCB1 -0.28 0.49 -9999 0 -1.2 47 47
TFRC -0.22 0.45 -9999 0 -0.91 48 48
CXCR4 -0.24 0.47 -9999 0 -0.95 49 49
TF -0.22 0.45 -9999 0 -0.92 46 46
CITED2 -0.22 0.44 -9999 0 -0.92 45 45
HIF1A/ARNT -0.21 0.54 -9999 0 -1.1 41 41
LDHA 0 0.12 -9999 0 -0.95 2 2
ETS1 -0.22 0.45 -9999 0 -0.92 45 45
PGK1 -0.22 0.45 -9999 0 -0.94 43 43
NOS2 -0.23 0.43 -9999 0 -0.92 45 45
ITGB2 -0.23 0.46 -9999 0 -0.94 48 48
ALDOA -0.21 0.44 -9999 0 -0.92 45 45
Cbp/p300/CITED2 -0.23 0.45 -9999 0 -0.95 43 43
FOS -0.07 0.17 -9999 0 -0.33 58 58
HK2 -0.22 0.45 -9999 0 -0.91 46 46
SP1 -0.004 0.069 -9999 0 -0.17 8 8
GCK -0.037 0.2 -9999 0 -1.4 2 2
HK1 -0.21 0.44 -9999 0 -0.91 45 45
NPM1 -0.22 0.44 -9999 0 -0.92 45 45
EGLN1 -0.21 0.44 -9999 0 -0.92 44 44
CREB1 0.042 0.019 -9999 0 -10000 0 0
PGM1 -0.23 0.46 -9999 0 -0.93 48 48
SMAD3 0.026 0.072 -9999 0 -0.43 5 5
EDN1 -0.24 0.43 -9999 0 -1.2 32 32
IGFBP1 -0.23 0.44 -9999 0 -0.92 45 45
VEGFA -0.17 0.31 -9999 0 -0.66 40 40
HIF1A/JAB1 0.004 0.082 -9999 0 -0.25 7 7
CP -0.22 0.45 -9999 0 -0.92 46 46
CXCL12 -0.23 0.46 -9999 0 -0.97 46 46
COPS5 0.03 0.038 -9999 0 -0.48 1 1
SMAD3/SMAD4 0.025 0.073 -9999 0 -0.34 7 7
BNIP3 -0.26 0.47 -9999 0 -0.92 55 55
EGLN3 -0.24 0.47 -9999 0 -0.95 49 49
CA9 -0.27 0.48 -9999 0 -0.96 52 52
TERT -0.22 0.44 -9999 0 -0.92 45 45
ENO1 -0.22 0.44 -9999 0 -0.92 45 45
PFKL -0.22 0.44 -9999 0 -0.92 45 45
NCOA1 0.028 0.07 -9999 0 -0.48 4 4
ADM -0.22 0.46 -9999 0 -0.93 48 48
ARNT -0.019 0.097 -9999 0 -0.55 1 1
HNF4A 0.01 0.072 -9999 0 -0.48 4 4
ADFP -0.23 0.46 -9999 0 -0.93 47 47
SLC2A1 -0.18 0.34 -9999 0 -0.72 36 36
LEP -0.22 0.44 -9999 0 -0.92 45 45
HIF1A/ARNT/Cbp/p300 -0.16 0.4 -9999 0 -0.79 38 38
EPO -0.11 0.27 -9999 0 -0.86 9 9
CREBBP -0.022 0.11 -9999 0 -0.29 9 9
HIF1A/ARNT/Cbp/p300/HDAC7 -0.16 0.39 -9999 0 -0.78 38 38
PFKFB3 -0.21 0.44 -9999 0 -0.92 45 45
NT5E -0.25 0.47 -9999 0 -0.96 48 48
IL4-mediated signaling events

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
BCL2L1 -0.36 0.63 -10000 0 -1.3 50 50
STAT6 (cleaved dimer) -0.44 0.62 -10000 0 -1.3 58 58
IGHG1 -0.11 0.23 -10000 0 -0.48 18 18
IGHG3 -0.4 0.58 -10000 0 -1.2 58 58
AKT1 -0.18 0.36 -10000 0 -0.86 32 32
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.16 0.37 -10000 0 -1 24 24
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.21 0.41 -10000 0 -1 28 28
THY1 -0.42 0.62 -10000 0 -1.3 57 57
MYB -0.002 0.14 -10000 0 -0.48 16 16
HMGA1 0.035 0.036 -10000 0 -0.48 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.24 0.4 -10000 0 -0.86 43 43
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.21 0.4 -10000 0 -0.97 31 31
SP1 0.024 0.049 -10000 0 -0.19 3 3
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.036 0.034 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.42 0.64 -10000 0 -1.3 58 58
SOCS1 -0.25 0.38 -10000 0 -0.79 52 52
SOCS3 -0.22 0.38 -10000 0 -0.99 28 28
FCER2 -0.3 0.48 -10000 0 -1 47 47
PARP14 0.032 0.038 -10000 0 -0.21 5 5
CCL17 -0.46 0.65 -10000 0 -1.4 57 57
GRB2 0.036 0.008 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.15 0.28 -10000 0 -0.74 21 21
T cell proliferation -0.42 0.63 -10000 0 -1.3 56 56
IL4R/JAK1 -0.42 0.61 -10000 0 -1.3 57 57
EGR2 -0.5 0.69 -10000 0 -1.4 66 66
JAK2 -0.026 0.097 -10000 0 -0.32 12 12
JAK3 0.038 0.016 -10000 0 -10000 0 0
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
JAK1 0.015 0.047 -10000 0 -0.49 1 1
COL1A2 -0.19 0.44 -10000 0 -1.5 19 19
CCL26 -0.48 0.67 -10000 0 -1.4 64 64
IL4R -0.45 0.66 -10000 0 -1.4 57 57
PTPN6 0.038 0.026 -10000 0 -10000 0 0
IL13RA2 -0.53 0.71 -10000 0 -1.5 68 68
IL13RA1 -0.019 0.081 -10000 0 -0.33 5 5
IRF4 -0.084 0.32 -10000 0 -1.3 11 11
ARG1 -0.078 0.33 -10000 0 -1.3 10 10
CBL -0.23 0.37 -10000 0 -0.82 43 43
GTF3A -0.01 0.11 -10000 0 -0.46 11 11
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.022 0.11 -10000 0 -0.31 9 9
IRF4/BCL6 -0.084 0.3 -10000 0 -1.2 11 11
CD40LG 0.024 0.078 -10000 0 -0.32 8 8
MAPK14 -0.23 0.39 -10000 0 -0.88 40 40
mitosis -0.17 0.34 -10000 0 -0.8 32 32
STAT6 -0.52 0.81 -10000 0 -1.6 58 58
SPI1 0.018 0.075 -10000 0 -0.24 12 12
RPS6KB1 -0.16 0.33 -10000 0 -0.78 31 31
STAT6 (dimer) -0.52 0.81 -10000 0 -1.6 58 58
STAT6 (dimer)/PARP14 -0.46 0.69 -10000 0 -1.4 58 58
mast cell activation 0.007 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.24 0.41 -10000 0 -0.97 35 35
FRAP1 -0.19 0.36 -10000 0 -0.87 32 32
LTA -0.43 0.61 -10000 0 -1.3 58 58
FES 0.017 0.082 -10000 0 -0.31 11 11
T-helper 1 cell differentiation 0.48 0.73 1.5 58 -10000 0 58
CCL11 -0.49 0.68 -10000 0 -1.4 63 63
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.21 0.4 -10000 0 -0.96 33 33
IL2RG -0.018 0.16 -10000 0 -0.43 26 26
IL10 -0.41 0.61 -10000 0 -1.3 54 54
IRS1 0.018 0.091 -10000 0 -0.37 10 10
IRS2 -0.008 0.12 -10000 0 -0.45 15 15
IL4 -0.058 0.18 -10000 0 -0.98 3 3
IL5 -0.42 0.61 -10000 0 -1.3 56 56
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.3 0.47 -10000 0 -0.94 55 55
COL1A1 -0.28 0.56 -10000 0 -1.5 32 32
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.44 0.64 -10000 0 -1.4 56 56
IL2R gamma/JAK3 0.011 0.12 -10000 0 -0.34 23 23
TFF3 -0.44 0.64 -10000 0 -1.4 58 58
ALOX15 -0.42 0.62 -10000 0 -1.3 58 58
MYBL1 0.025 0.047 -10000 0 -0.28 4 4
T-helper 2 cell differentiation -0.33 0.52 -10000 0 -1.1 54 54
SHC1 0.036 0.007 -10000 0 -10000 0 0
CEBPB 0.013 0.045 -10000 0 -0.5 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.2 0.4 -10000 0 -1 26 26
mol:PI-3-4-5-P3 -0.18 0.36 -10000 0 -0.86 32 32
PI3K -0.2 0.4 -10000 0 -0.96 31 31
DOK2 0.012 0.066 -10000 0 -0.23 13 13
ETS1 0.029 0.057 -10000 0 -0.33 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.14 0.27 -10000 0 -0.71 22 22
ITGB3 -0.41 0.61 -10000 0 -1.3 56 56
PIGR -0.47 0.69 -10000 0 -1.5 60 60
IGHE 0.064 0.086 0.18 42 -0.2 1 43
MAPKKK cascade -0.14 0.26 -10000 0 -0.69 22 22
BCL6 0.008 0.1 -10000 0 -0.32 17 17
OPRM1 -0.42 0.62 -10000 0 -1.3 58 58
RETNLB -0.6 0.74 -10000 0 -1.5 80 80
SELP -0.48 0.7 -10000 0 -1.5 61 61
AICDA -0.42 0.6 -10000 0 -1.3 57 57
Wnt signaling

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
Noncanonical Wnts/FZD -0.11 0.2 -9999 0 -0.37 62 62
FZD6 0.022 0.064 -9999 0 -0.42 4 4
WNT6 0.033 0.033 -9999 0 -0.21 4 4
WNT4 -0.035 0.16 -9999 0 -0.37 37 37
FZD3 -0.03 0.15 -9999 0 -0.38 30 30
WNT5A -0.008 0.14 -9999 0 -0.39 23 23
WNT11 -0.062 0.18 -9999 0 -0.35 56 56
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.03 0.055 -10000 0 -0.35 4 4
LAT2 -0.075 0.16 -10000 0 -0.4 35 35
AP1 -0.12 0.24 -10000 0 -0.54 39 39
mol:PIP3 -0.11 0.23 0.32 3 -0.51 42 45
IKBKB -0.037 0.13 0.24 8 -0.28 30 38
AKT1 -0.1 0.17 0.32 9 -0.43 29 38
IKBKG -0.051 0.13 0.2 7 -0.28 35 42
MS4A2 -0.066 0.19 -10000 0 -0.38 53 53
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.036 0.006 -10000 0 -10000 0 0
MAP3K1 -0.077 0.18 0.24 1 -0.42 35 36
mol:Ca2+ -0.076 0.17 0.29 3 -0.38 38 41
LYN 0.029 0.016 -10000 0 -10000 0 0
CBLB -0.073 0.17 -10000 0 -0.39 36 36
SHC1 0.036 0.007 -10000 0 -10000 0 0
RasGAP/p62DOK 0.036 0.087 -10000 0 -0.26 11 11
positive regulation of cell migration -0.01 0.078 -10000 0 -0.35 10 10
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.11 0.19 0.32 7 -0.38 51 58
PTPN13 -0.13 0.22 -10000 0 -0.59 25 25
PTPN11 0.019 0.061 -10000 0 -0.42 3 3
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.068 0.14 0.3 5 -0.35 26 31
SYK 0.029 0.055 -10000 0 -0.41 3 3
GRB2 0.035 0.008 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.09 0.25 -10000 0 -0.53 41 41
LAT -0.077 0.17 0.2 1 -0.4 37 38
PAK2 -0.083 0.2 0.24 2 -0.46 38 40
NFATC2 -0.019 0.047 -10000 0 -10000 0 0
HRAS -0.089 0.22 0.26 1 -0.49 39 40
GAB2 0.037 0.004 -10000 0 -10000 0 0
PLA2G1B 0.027 0.12 -10000 0 -0.81 4 4
Fc epsilon R1 -0.1 0.21 -10000 0 -0.37 73 73
Antigen/IgE/Fc epsilon R1 -0.091 0.2 -10000 0 -0.33 73 73
mol:GDP -0.099 0.23 0.26 1 -0.53 40 41
JUN -0.017 0.15 -10000 0 -0.41 26 26
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.029 0.062 -10000 0 -0.49 3 3
FOS -0.063 0.17 -10000 0 -0.32 58 58
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.073 0.17 -10000 0 -0.39 39 39
CHUK -0.052 0.13 0.24 3 -0.28 35 38
KLRG1 -0.07 0.15 -10000 0 -0.34 38 38
VAV1 -0.089 0.19 -10000 0 -0.42 41 41
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.072 0.16 -10000 0 -0.39 35 35
negative regulation of mast cell degranulation -0.068 0.14 -10000 0 -0.34 34 34
BTK -0.098 0.25 -10000 0 -0.6 34 34
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.16 0.27 -10000 0 -0.54 56 56
GAB2/PI3K/SHP2 -0.12 0.17 -10000 0 -0.38 50 50
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.08 0.16 -10000 0 -0.32 56 56
RAF1 0.03 0.14 -10000 0 -0.93 4 4
Fc epsilon R1/FcgammaRIIB/SHIP -0.14 0.24 -10000 0 -0.42 74 74
FCER1G 0.028 0.06 -10000 0 -0.33 5 5
FCER1A -0.12 0.22 -10000 0 -0.4 77 77
Antigen/IgE/Fc epsilon R1/Fyn -0.089 0.21 -10000 0 -0.34 72 72
MAPK3 0.027 0.12 -10000 0 -0.82 4 4
MAPK1 0.023 0.12 -10000 0 -0.82 4 4
NFKB1 0.037 0.006 -10000 0 -10000 0 0
MAPK8 -0.12 0.28 -10000 0 -0.71 30 30
DUSP1 0.002 0.1 -10000 0 -0.26 25 25
NF-kappa-B/RelA -0.016 0.087 0.15 5 -0.18 23 28
actin cytoskeleton reorganization -0.059 0.19 -10000 0 -0.49 23 23
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.07 0.21 -10000 0 -0.47 35 35
FER -0.078 0.16 -10000 0 -0.39 37 37
RELA 0.037 0.005 -10000 0 -10000 0 0
ITK -0.021 0.086 -10000 0 -0.43 7 7
SOS1 0.037 0.003 -10000 0 -10000 0 0
PLCG1 -0.039 0.24 0.27 4 -0.5 34 38
cytokine secretion -0.019 0.057 -10000 0 -0.15 1 1
SPHK1 -0.099 0.19 -10000 0 -0.44 41 41
PTK2 -0.062 0.2 -10000 0 -0.52 21 21
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.092 0.26 0.23 2 -0.53 44 46
EDG1 -0.01 0.078 -10000 0 -0.35 10 10
mol:DAG -0.098 0.23 0.34 2 -0.52 38 40
MAP2K2 0.022 0.12 -10000 0 -0.83 4 4
MAP2K1 0.021 0.12 -10000 0 -0.86 4 4
MAP2K7 0.03 0.049 -10000 0 -0.26 5 5
KLRG1/SHP2 -0.058 0.15 -10000 0 -0.35 30 30
MAP2K4 -0.22 0.44 -10000 0 -0.93 59 59
Fc epsilon R1/FcgammaRIIB -0.14 0.26 -10000 0 -0.44 74 74
mol:Choline -0.11 0.18 0.32 7 -0.37 51 58
SHC/Grb2/SOS1 -0.029 0.18 0.28 1 -0.41 27 28
FYN 0.008 0.11 -10000 0 -0.35 16 16
DOK1 0.034 0.039 -10000 0 -0.35 2 2
PXN -0.057 0.18 -10000 0 -0.54 12 12
HCLS1 -0.081 0.18 -10000 0 -0.42 37 37
PRKCB -0.073 0.17 0.26 4 -0.38 39 43
FCGR2B -0.085 0.2 -10000 0 -0.37 64 64
IGHE -0.003 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.069 0.14 -10000 0 -0.35 34 34
LCP2 -0.024 0.16 -10000 0 -0.37 32 32
PLA2G4A -0.16 0.2 -10000 0 -0.39 73 73
RASA1 0.025 0.072 -10000 0 -0.43 5 5
mol:Phosphatidic acid -0.11 0.18 0.32 7 -0.37 51 58
IKK complex -0.027 0.11 0.22 7 -0.22 22 29
WIPF1 0 0 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.16 0.38 -10000 0 -1.1 29 29
MKNK1 0.037 0.005 -10000 0 -10000 0 0
MAPK14 -0.036 0.12 -10000 0 -0.31 30 30
ATF2/c-Jun -0.083 0.2 -10000 0 -0.59 23 23
MAPK11 -0.033 0.12 -10000 0 -0.31 27 27
MITF -0.054 0.16 -10000 0 -0.38 34 34
MAPKAPK5 -0.043 0.14 -10000 0 -0.36 30 30
KRT8 -0.048 0.15 -10000 0 -0.37 32 32
MAPKAPK3 0.037 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.036 0.008 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.053 0.18 -10000 0 -0.4 39 39
CEBPB -0.027 0.098 -10000 0 -0.34 16 16
SLC9A1 -0.048 0.15 -10000 0 -0.39 30 30
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.05 0.15 -10000 0 -0.34 39 39
p38alpha-beta/MNK1 -0.024 0.16 -10000 0 -0.36 30 30
JUN -0.085 0.2 -10000 0 -0.59 23 23
PPARGC1A -0.084 0.18 -10000 0 -0.39 48 48
USF1 -0.063 0.16 -10000 0 -0.34 43 43
RAB5/GDP/GDI1 -0.027 0.11 -10000 0 -0.27 30 30
NOS2 -0.05 0.14 -10000 0 -0.37 30 30
DDIT3 -0.051 0.14 -10000 0 -0.36 34 34
RAB5A 0.037 0.005 -10000 0 -10000 0 0
HSPB1 -0.035 0.13 0.29 8 -0.3 32 40
p38alpha-beta/HBP1 -0.03 0.16 -10000 0 -0.36 32 32
CREB1 -0.049 0.15 -10000 0 -0.38 30 30
RAB5/GDP 0.027 0.004 -10000 0 -10000 0 0
EIF4E -0.046 0.12 -10000 0 -0.33 27 27
RPS6KA4 -0.042 0.14 -10000 0 -0.36 30 30
PLA2G4A -0.15 0.17 -10000 0 -0.36 71 71
GDI1 -0.042 0.14 -10000 0 -0.36 30 30
TP53 -0.095 0.17 -10000 0 -0.44 35 35
RPS6KA5 -0.056 0.15 -10000 0 -0.37 35 35
ESR1 -0.048 0.15 -10000 0 -0.38 31 31
HBP1 0.031 0.05 -10000 0 -0.48 2 2
MEF2C -0.065 0.16 -10000 0 -0.36 40 40
MEF2A -0.042 0.14 -10000 0 -0.38 28 28
EIF4EBP1 -0.057 0.16 -10000 0 -0.41 30 30
KRT19 -0.057 0.14 -10000 0 -0.35 38 38
ELK4 -0.043 0.13 -10000 0 -0.35 30 30
ATF6 -0.041 0.13 -10000 0 -0.36 29 29
ATF1 -0.05 0.15 -10000 0 -0.38 30 30
p38alpha-beta/MAPKAPK2 -0.024 0.15 -10000 0 -0.36 30 30
p38alpha-beta/MAPKAPK3 -0.024 0.16 -10000 0 -0.36 30 30
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 -0.024 0.18 0.27 21 -0.34 30 51
PTK2B 0.028 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.066 0.24 -10000 0 -0.66 17 17
EDN1 -0.032 0.22 0.25 18 -0.46 37 55
EDN3 -0.088 0.19 -10000 0 -0.41 51 51
EDN2 -0.089 0.2 -10000 0 -0.35 70 70
HRAS/GDP -0.076 0.21 0.31 4 -0.46 31 35
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.058 0.17 0.27 1 -0.37 32 33
ADCY4 -0.039 0.16 0.35 1 -0.4 16 17
ADCY5 -0.023 0.14 0.35 1 -0.35 14 15
ADCY6 -0.022 0.14 0.35 1 -0.35 14 15
ADCY7 -0.025 0.15 0.35 1 -0.37 15 16
ADCY1 -0.019 0.14 0.35 1 -0.36 12 13
ADCY2 -0.022 0.14 0.35 1 -0.35 14 15
ADCY3 -0.034 0.16 0.35 1 -0.36 19 20
ADCY8 -0.031 0.13 -10000 0 -0.34 16 16
ADCY9 -0.025 0.15 0.35 1 -0.36 15 16
arachidonic acid secretion -0.17 0.26 -10000 0 -0.61 44 44
ETB receptor/Endothelin-1/Gq/GTP -0.053 0.15 -10000 0 -0.34 33 33
GNAO1 0.037 0.003 -10000 0 -10000 0 0
HRAS 0.033 0.039 -10000 0 -0.35 2 2
ETA receptor/Endothelin-1/G12/GTP 0.041 0.21 0.38 29 -0.39 13 42
ETA receptor/Endothelin-1/Gs/GTP 0.014 0.19 0.35 23 -0.35 16 39
mol:GTP -0.002 0.007 -10000 0 -10000 0 0
COL3A1 -0.035 0.22 -10000 0 -0.57 17 17
EDNRB -0.017 0.13 -10000 0 -0.4 18 18
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.003 0.17 0.31 22 -0.38 10 32
CYSLTR1 -0.028 0.21 0.28 19 -0.5 16 35
SLC9A1 -0.007 0.14 0.2 19 -0.38 11 30
mol:GDP -0.088 0.22 0.3 4 -0.47 34 38
SLC9A3 -0.096 0.32 -10000 0 -0.71 36 36
RAF1 -0.11 0.22 0.28 1 -0.54 31 32
JUN -0.12 0.35 -10000 0 -0.98 25 25
JAK2 -0.027 0.19 0.27 23 -0.4 25 48
mol:IP3 -0.062 0.18 0.28 2 -0.4 33 35
ETA receptor/Endothelin-1 0.024 0.26 0.44 32 -0.39 36 68
PLCB1 -0.038 0.16 -10000 0 -0.4 33 33
PLCB2 0.032 0.02 -10000 0 -0.22 1 1
ETA receptor/Endothelin-3 -0.054 0.16 -10000 0 -0.36 40 40
FOS -0.19 0.36 -10000 0 -0.94 36 36
Gai/GDP -0.003 0.19 -10000 0 -0.87 8 8
CRK 0.029 0.016 -10000 0 -10000 0 0
mol:Ca ++ -0.079 0.22 0.36 2 -0.46 37 39
BCAR1 0.036 0.017 -10000 0 -0.21 1 1
PRKCB1 -0.067 0.18 0.26 3 -0.43 29 32
GNAQ -0.002 0.007 -10000 0 -10000 0 0
GNAZ 0.024 0.064 -10000 0 -0.28 8 8
GNAL 0.025 0.028 -10000 0 -0.21 2 2
Gs family/GDP -0.08 0.2 0.28 3 -0.43 32 35
ETA receptor/Endothelin-1/Gq/GTP -0.039 0.16 -10000 0 -0.35 25 25
MAPK14 -0.068 0.16 -10000 0 -0.39 27 27
TRPC6 -0.071 0.26 -10000 0 -0.72 16 16
GNAI2 0.026 0.072 -10000 0 -0.43 5 5
GNAI3 0.034 0.036 -10000 0 -0.48 1 1
GNAI1 -0.011 0.14 -10000 0 -0.4 23 23
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.069 0.16 -10000 0 -0.36 36 36
ETB receptor/Endothelin-2 -0.062 0.16 -10000 0 -0.4 32 32
ETB receptor/Endothelin-3 -0.07 0.16 -10000 0 -0.39 38 38
ETB receptor/Endothelin-1 -0.035 0.18 -10000 0 -0.37 39 39
MAPK3 -0.16 0.32 -10000 0 -0.79 37 37
MAPK1 -0.17 0.33 -10000 0 -0.8 37 37
Rac1/GDP -0.074 0.2 0.31 4 -0.46 29 33
cAMP biosynthetic process -0.014 0.15 0.27 7 -0.36 15 22
MAPK8 -0.065 0.23 -10000 0 -0.57 22 22
SRC 0.012 0.062 -10000 0 -0.48 3 3
ETB receptor/Endothelin-1/Gi/GTP -0.031 0.14 -10000 0 -0.4 20 20
p130Cas/CRK/Src/PYK2 -0.075 0.24 0.35 4 -0.5 34 38
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.074 0.2 0.31 4 -0.46 29 33
COL1A2 -0.028 0.27 0.38 9 -0.62 25 34
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.04 0.18 -10000 0 -0.36 41 41
mol:DAG -0.062 0.18 0.28 2 -0.4 33 35
MAP2K2 -0.13 0.26 -10000 0 -0.6 37 37
MAP2K1 -0.13 0.26 -10000 0 -0.6 39 39
EDNRA 0.035 0.13 0.24 19 -0.31 13 32
positive regulation of muscle contraction -0.003 0.16 0.25 27 -0.37 13 40
Gq family/GDP -0.08 0.2 -10000 0 -0.46 29 29
HRAS/GTP -0.085 0.2 0.27 3 -0.46 31 34
PRKCH -0.069 0.19 0.32 2 -0.41 34 36
RAC1 0.033 0.012 -10000 0 -10000 0 0
PRKCA -0.06 0.18 0.26 3 -0.42 28 31
PRKCB -0.061 0.18 0.26 2 -0.39 34 36
PRKCE -0.061 0.18 0.26 2 -0.42 27 29
PRKCD -0.06 0.18 0.26 2 -0.41 29 31
PRKCG -0.067 0.18 0.26 2 -0.44 27 29
regulation of vascular smooth muscle contraction -0.22 0.43 -10000 0 -1.1 36 36
PRKCQ -0.079 0.19 0.28 3 -0.4 39 42
PLA2G4A -0.18 0.29 -10000 0 -0.67 44 44
GNA14 -0.024 0.15 -10000 0 -0.37 29 29
GNA15 0.017 0.069 -10000 0 -0.27 10 10
GNA12 0.033 0.012 -10000 0 -10000 0 0
GNA11 0.025 0.056 -10000 0 -0.4 3 3
Rac1/GTP 0.041 0.21 0.38 29 -0.39 13 42
MMP1 -0.22 0.39 0.48 1 -0.89 51 52
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.036 0.017 -10000 0 -0.21 1 1
CCL5 -0.036 0.16 -10000 0 -0.35 40 40
SDCBP 0.031 0.021 -10000 0 -0.21 1 1
FGFR/FGF2/Syndecan-1 -0.079 0.18 0.26 4 -0.36 36 40
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 -0.076 0.13 -10000 0 -0.39 19 19
Syndecan-1/Syntenin -0.065 0.16 0.35 1 -0.36 30 31
MAPK3 -0.076 0.16 0.32 1 -0.4 19 20
HGF/MET 0.044 0.057 -10000 0 -0.38 3 3
TGFB1/TGF beta receptor Type II 0.036 0.017 -10000 0 -0.21 1 1
BSG 0.036 0.007 -10000 0 -10000 0 0
keratinocyte migration -0.075 0.13 -10000 0 -0.38 19 19
Syndecan-1/RANTES -0.1 0.2 0.35 1 -0.4 45 46
Syndecan-1/CD147 -0.062 0.18 0.35 1 -0.36 29 30
Syndecan-1/Syntenin/PIP2 -0.064 0.16 0.32 1 -0.34 30 31
LAMA5 0.012 0.047 -10000 0 -0.28 4 4
positive regulation of cell-cell adhesion -0.063 0.16 0.32 1 -0.34 30 31
MMP7 -0.12 0.22 -10000 0 -0.39 79 79
HGF 0.031 0.043 -10000 0 -0.3 3 3
Syndecan-1/CASK -0.085 0.16 -10000 0 -0.34 37 37
Syndecan-1/HGF/MET -0.063 0.18 -10000 0 -0.37 29 29
regulation of cell adhesion -0.078 0.16 0.32 2 -0.39 18 20
HPSE -0.014 0.13 -10000 0 -0.32 31 31
positive regulation of cell migration -0.079 0.18 0.26 4 -0.36 36 40
SDC1 -0.074 0.17 -10000 0 -0.36 36 36
Syndecan-1/Collagen -0.079 0.18 0.26 4 -0.36 36 40
PPIB 0.029 0.046 -10000 0 -0.28 4 4
MET 0.028 0.055 -10000 0 -0.35 4 4
PRKACA 0.037 0.006 -10000 0 -10000 0 0
MMP9 -0.006 0.094 -10000 0 -0.32 15 15
MAPK1 -0.072 0.16 0.32 1 -0.35 28 29
homophilic cell adhesion -0.08 0.18 0.26 4 -0.36 36 40
MMP1 -0.13 0.21 -10000 0 -0.35 95 95
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.013 0.12 -10000 0 -0.4 16 16
GNB1/GNG2 -0.065 0.079 -10000 0 -0.18 58 58
AKT1 -0.063 0.13 0.24 2 -0.3 24 26
EGF -0.094 0.19 -10000 0 -0.32 79 79
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.02 0.071 0.27 1 -0.25 2 3
mol:Ca2+ -0.083 0.16 0.28 1 -0.3 58 59
LYN -0.017 0.064 0.27 1 -0.25 2 3
RhoA/GTP -0.035 0.068 -10000 0 -0.14 17 17
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.096 0.18 0.31 1 -0.34 57 58
GNG2 0.034 0.011 -10000 0 -10000 0 0
ARRB2 0.026 0.038 -10000 0 -0.48 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 -0.056 0.17 -10000 0 -0.48 24 24
G beta5/gamma2 -0.082 0.1 -10000 0 -0.24 57 57
PRKCH -0.1 0.18 -10000 0 -0.36 58 58
DNM1 0.031 0.037 -10000 0 -0.21 5 5
TXA2/TP beta/beta Arrestin3 0.019 0.023 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.054 0.16 -10000 0 -0.29 58 58
G12 family/GTP -0.09 0.15 -10000 0 -0.31 52 52
ADRBK1 0.037 0.004 -10000 0 -10000 0 0
ADRBK2 0.031 0.043 -10000 0 -0.3 3 3
RhoA/GTP/ROCK1 0.037 0.022 -10000 0 -10000 0 0
mol:GDP 0.053 0.13 0.34 17 -10000 0 17
mol:NADP 0.03 0.053 -10000 0 -0.39 3 3
RAB11A 0.032 0.04 -10000 0 -0.35 2 2
PRKG1 0.036 0.007 -10000 0 -10000 0 0
mol:IP3 -0.11 0.2 -10000 0 -0.38 58 58
cell morphogenesis 0.036 0.022 -10000 0 -10000 0 0
PLCB2 -0.16 0.26 -10000 0 -0.52 59 59
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.028 0.078 0.27 1 -0.28 5 6
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.024 0.078 -10000 0 -0.32 8 8
RHOA 0.037 0.005 -10000 0 -10000 0 0
PTGIR 0.036 0.017 -10000 0 -0.21 1 1
PRKCB1 -0.11 0.2 -10000 0 -0.39 59 59
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.03 0.053 -10000 0 -0.39 3 3
TXA2/TXA2-R family -0.15 0.26 -10000 0 -0.53 58 58
LCK -0.038 0.091 0.27 1 -0.29 9 10
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.001 0.082 -10000 0 -0.29 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.026 0.036 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.006 0.08 -10000 0 -0.28 1 1
MAPK14 -0.062 0.12 0.24 2 -0.23 53 55
TGM2/GTP -0.13 0.2 -10000 0 -0.44 41 41
MAPK11 -0.063 0.12 0.24 2 -0.23 52 54
ARHGEF1 -0.039 0.11 0.19 6 -0.18 40 46
GNAI2 0.026 0.072 -10000 0 -0.43 5 5
JNK cascade -0.11 0.2 -10000 0 -0.39 58 58
RAB11/GDP 0.032 0.04 -10000 0 -0.34 2 2
ICAM1 -0.078 0.15 -10000 0 -0.29 56 56
cAMP biosynthetic process -0.1 0.18 0.29 1 -0.36 59 60
Gq family/GTP/EBP50 -0.008 0.08 -10000 0 -0.23 21 21
actin cytoskeleton reorganization 0.036 0.022 -10000 0 -10000 0 0
SRC -0.014 0.056 -10000 0 -0.25 1 1
GNB5 -0.003 0.13 -10000 0 -0.37 20 20
GNB1 0.038 0 -10000 0 -10000 0 0
EGF/EGFR -0.023 0.12 0.25 4 -0.31 12 16
VCAM1 -0.081 0.16 0.25 1 -0.31 56 57
TP beta/Gq family/GDP/G beta5/gamma2 -0.056 0.17 -10000 0 -0.48 24 24
platelet activation -0.081 0.16 0.3 2 -0.3 56 58
PGI2/IP 0.027 0.011 -10000 0 -0.14 1 1
PRKACA -0.015 0.078 -10000 0 -0.25 17 17
Gq family/GDP/G beta5/gamma2 -0.051 0.15 -10000 0 -0.42 24 24
TXA2/TP beta/beta Arrestin2 -0.017 0.069 -10000 0 -0.33 2 2
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.022 0.068 -10000 0 -0.23 16 16
mol:DAG -0.12 0.22 -10000 0 -0.43 59 59
EGFR 0.016 0.088 -10000 0 -0.42 8 8
TXA2/TP alpha -0.14 0.25 -10000 0 -0.48 59 59
Gq family/GTP -0.02 0.084 -10000 0 -0.24 24 24
YES1 -0.017 0.065 -10000 0 -0.24 2 2
GNAI2/GTP -0.014 0.079 -10000 0 -0.26 3 3
PGD2/DP -0.037 0.11 -10000 0 -0.2 59 59
SLC9A3R1 0.027 0.063 -10000 0 -0.42 4 4
FYN -0.031 0.089 0.27 1 -0.35 6 7
mol:NO 0.03 0.053 -10000 0 -0.39 3 3
GNA15 0.022 0.068 -10000 0 -0.26 10 10
PGK/cGMP 0.043 0.037 -10000 0 -0.3 2 2
RhoA/GDP 0.037 0.005 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.006 0.085 -10000 0 -0.31 4 4
NOS3 0.03 0.053 -10000 0 -0.39 3 3
RAC1 0.033 0.012 -10000 0 -10000 0 0
PRKCA -0.096 0.18 0.28 1 -0.36 57 58
PRKCB -0.097 0.18 -10000 0 -0.36 58 58
PRKCE -0.098 0.18 -10000 0 -0.36 59 59
PRKCD -0.1 0.19 -10000 0 -0.38 58 58
PRKCG -0.11 0.2 -10000 0 -0.39 58 58
muscle contraction -0.14 0.24 -10000 0 -0.49 58 58
PRKCZ -0.095 0.18 0.27 1 -0.34 58 59
ARR3 0.038 0 -10000 0 -10000 0 0
TXA2/TP beta 0 0.083 -10000 0 -0.23 1 1
PRKCQ -0.11 0.19 0.36 1 -0.37 59 60
MAPKKK cascade -0.13 0.23 -10000 0 -0.46 59 59
SELE -0.11 0.19 0.25 1 -0.38 58 59
TP beta/GNAI2/GDP/G beta/gamma 0.014 0.099 0.27 1 -0.28 3 4
ROCK1 0.028 0.017 -10000 0 -10000 0 0
GNA14 -0.018 0.15 -10000 0 -0.37 29 29
chemotaxis -0.17 0.29 -10000 0 -0.62 56 56
GNA12 0.033 0.012 -10000 0 -10000 0 0
GNA13 0.036 0.008 -10000 0 -10000 0 0
GNA11 0.03 0.053 -10000 0 -0.39 3 3
Rac1/GTP 0.024 0.009 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.032 0.035 -10000 0 -0.22 2 2
NFATC2 -0.048 0.17 -10000 0 -0.53 15 15
NFATC3 -0.049 0.11 -10000 0 -0.34 12 12
CD40LG -0.32 0.4 -10000 0 -0.85 56 56
ITCH 0.005 0.063 -10000 0 -10000 0 0
CBLB 0.017 0.083 -10000 0 -0.51 2 2
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.25 0.37 -10000 0 -1 32 32
JUNB 0.02 0.073 -10000 0 -0.25 13 13
CaM/Ca2+/Calcineurin A alpha-beta B1 0.024 0.085 -10000 0 -0.27 15 15
T cell anergy 0.018 0.12 -10000 0 -0.37 12 12
TLE4 -0.04 0.15 -10000 0 -0.59 10 10
Jun/NFAT1-c-4/p21SNFT -0.22 0.32 -10000 0 -0.85 31 31
AP-1/NFAT1-c-4 -0.37 0.44 -10000 0 -0.99 54 54
IKZF1 -0.034 0.12 -10000 0 -0.38 13 13
T-helper 2 cell differentiation -0.086 0.2 -10000 0 -0.66 11 11
AP-1/NFAT1 -0.1 0.18 -10000 0 -0.47 27 27
CALM1 0.029 0.056 -10000 0 -10000 0 0
EGR2 -0.24 0.49 -10000 0 -1.4 31 31
EGR3 -0.22 0.44 -10000 0 -1.2 33 33
NFAT1/FOXP3 -0.023 0.13 -10000 0 -0.46 8 8
EGR1 -0.057 0.17 -10000 0 -0.32 57 57
JUN -0.053 0.16 -10000 0 -0.44 26 26
EGR4 0.001 0.002 -10000 0 -10000 0 0
mol:Ca2+ 0 0.044 -10000 0 -0.16 14 14
GBP3 -0.077 0.23 -10000 0 -0.75 20 20
FOSL1 0.03 0.041 -10000 0 -0.21 6 6
NFAT1-c-4/MAF/IRF4 -0.18 0.33 -10000 0 -0.88 29 29
DGKA -0.036 0.13 -10000 0 -0.5 8 8
CREM 0.033 0.039 -10000 0 -0.35 2 2
NFAT1-c-4/PPARG -0.19 0.33 -10000 0 -0.87 29 29
CTLA4 -0.002 0.14 -10000 0 -0.42 8 8
NFAT1-c-4 (dimer)/EGR1 -0.2 0.34 -10000 0 -0.86 33 33
NFAT1-c-4 (dimer)/EGR4 -0.18 0.31 -10000 0 -0.87 26 26
FOS -0.096 0.17 -10000 0 -0.36 54 54
IFNG -0.33 0.54 -10000 0 -1.2 49 49
T cell activation -0.1 0.22 -10000 0 -0.7 8 8
MAF 0 0.12 -10000 0 -0.34 21 21
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.17 0.28 0.73 36 -10000 0 36
TNF -0.18 0.31 -10000 0 -0.79 33 33
FASLG -0.35 0.61 -10000 0 -1.4 45 45
TBX21 -0.08 0.18 -10000 0 -0.36 53 53
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ -0.021 0.14 -10000 0 -0.37 25 25
PTPN1 -0.033 0.13 -10000 0 -0.54 6 6
NFAT1-c-4/ICER1 -0.17 0.32 -10000 0 -0.88 26 26
GATA3 0.033 0.054 -10000 0 -0.39 3 3
T-helper 1 cell differentiation -0.32 0.51 -10000 0 -1.2 50 50
IL2RA -0.26 0.38 -10000 0 -0.99 34 34
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.036 0.13 -10000 0 -0.5 8 8
E2F1 0.018 0.053 -10000 0 -0.48 2 2
PPARG -0.02 0.16 -10000 0 -0.45 25 25
SLC3A2 -0.034 0.13 -10000 0 -0.48 9 9
IRF4 0.008 0.11 -10000 0 -0.34 17 17
PTGS2 -0.36 0.42 -10000 0 -0.86 67 67
CSF2 -0.36 0.42 -10000 0 -0.88 66 66
JunB/Fra1/NFAT1-c-4 -0.17 0.31 -10000 0 -0.85 26 26
IL4 -0.09 0.2 -10000 0 -0.7 10 10
IL5 -0.32 0.39 -10000 0 -0.84 57 57
IL2 -0.1 0.22 -10000 0 -0.72 8 8
IL3 -0.038 0.14 -10000 0 -0.79 6 6
RNF128 -0.006 0.15 -10000 0 -0.58 13 13
NFATC1 -0.17 0.29 -10000 0 -0.73 36 36
CDK4 0.085 0.17 0.59 8 -10000 0 8
PTPRK -0.04 0.14 -10000 0 -0.55 10 10
IL8 -0.38 0.44 -10000 0 -0.91 66 66
POU2F1 0.033 0.066 -10000 0 -0.37 5 5
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.027 0.12 -10000 0 -0.38 13 13
TBX21 -0.26 0.5 -10000 0 -1.3 36 36
B2M 0.017 0.086 -10000 0 -0.35 10 10
TYK2 0.014 0.039 -10000 0 -10000 0 0
IL12RB1 0.013 0.042 -10000 0 -0.23 1 1
GADD45B -0.17 0.37 -10000 0 -1.1 24 24
IL12RB2 -0.004 0.087 -10000 0 -0.28 14 14
GADD45G -0.18 0.38 -10000 0 -1 26 26
natural killer cell activation -0.008 0.019 -10000 0 -0.042 31 31
RELB 0.035 0.035 -10000 0 -0.48 1 1
RELA 0.037 0.005 -10000 0 -10000 0 0
IL18 -0.022 0.16 -10000 0 -0.43 27 27
IL2RA -0.036 0.16 -10000 0 -0.35 40 40
IFNG -0.11 0.2 -10000 0 -0.33 84 84
STAT3 (dimer) -0.16 0.34 -10000 0 -0.78 40 40
HLA-DRB5 -0.045 0.18 -10000 0 -0.44 35 35
FASLG -0.22 0.45 -10000 0 -1.2 29 29
NF kappa B2 p52/RelB -0.18 0.39 -10000 0 -0.87 41 41
CD4 0.03 0.019 -10000 0 -10000 0 0
SOCS1 0.029 0.063 -10000 0 -0.42 4 4
EntrezGene:6955 -0.003 0.008 -10000 0 -0.025 19 19
CD3D -0.005 0.13 -10000 0 -0.4 18 18
CD3E 0.029 0.026 -10000 0 -0.22 1 1
CD3G -0.03 0.15 -10000 0 -0.36 33 33
IL12Rbeta2/JAK2 -0.003 0.11 -10000 0 -0.37 10 10
CCL3 -0.21 0.42 -10000 0 -1.1 33 33
CCL4 -0.22 0.44 -10000 0 -1.1 34 34
HLA-A 0.001 0.12 -10000 0 -0.39 18 18
IL18/IL18R -0.047 0.19 -10000 0 -0.35 51 51
NOS2 -0.19 0.37 -10000 0 -0.8 44 44
IL12/IL12R/TYK2/JAK2/SPHK2 -0.029 0.12 -10000 0 -0.38 12 12
IL1R1 -0.2 0.39 -10000 0 -1 31 31
IL4 0.041 0.045 -10000 0 -0.34 2 2
JAK2 -0.003 0.086 -10000 0 -0.29 13 13
EntrezGene:6957 -0.002 0.008 -10000 0 -0.024 17 17
TCR/CD3/MHC I/CD8 -0.051 0.2 -10000 0 -0.62 17 17
RAB7A -0.15 0.31 -10000 0 -0.72 36 36
lysosomal transport -0.14 0.29 -10000 0 -0.68 36 36
FOS -0.34 0.56 -10000 0 -1.3 48 48
STAT4 (dimer) -0.17 0.36 -10000 0 -0.86 35 35
STAT5A (dimer) -0.23 0.41 -10000 0 -0.88 48 48
GZMA -0.19 0.37 -10000 0 -0.85 41 41
GZMB -0.27 0.51 -10000 0 -1.2 42 42
HLX 0 0 -10000 0 -10000 0 0
LCK -0.22 0.43 -10000 0 -0.95 44 44
TCR/CD3/MHC II/CD4 -0.097 0.22 -10000 0 -0.53 35 35
IL2/IL2R -0.009 0.18 -10000 0 -0.34 39 39
MAPK14 -0.19 0.4 -10000 0 -0.96 34 34
CCR5 -0.17 0.34 -10000 0 -0.78 40 40
IL1B -0.079 0.19 -10000 0 -0.4 50 50
STAT6 -0.054 0.18 -10000 0 -0.73 8 8
STAT4 0.022 0.079 -10000 0 -0.33 9 9
STAT3 0.036 0.009 -10000 0 -10000 0 0
STAT1 0.017 0.068 -10000 0 -0.21 18 18
NFKB1 0.037 0.006 -10000 0 -10000 0 0
NFKB2 0.035 0.019 -10000 0 -0.21 1 1
IL12B 0.008 0.068 -10000 0 -0.33 5 5
CD8A 0.001 0.004 -10000 0 -0.025 2 2
CD8B 0.001 0.005 -10000 0 -0.039 2 2
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.026 0.12 0.37 13 -10000 0 13
IL2RB 0.02 0.083 -10000 0 -0.38 8 8
proteasomal ubiquitin-dependent protein catabolic process -0.15 0.33 -10000 0 -0.77 35 35
IL2RG -0.02 0.16 -10000 0 -0.44 26 26
IL12 -0.015 0.12 -10000 0 -0.36 15 15
STAT5A 0.029 0.049 -10000 0 -0.26 5 5
CD247 -0.002 0.007 -10000 0 -0.023 17 17
IL2 0.037 0.006 -10000 0 -10000 0 0
SPHK2 0.024 0.08 -10000 0 -0.44 6 6
FRAP1 0.033 0.036 -10000 0 -0.48 1 1
IL12A -0.03 0.13 -10000 0 -0.34 27 27
IL12/IL12R/TYK2/JAK2 -0.22 0.46 -10000 0 -1 41 41
MAP2K3 -0.21 0.42 -10000 0 -0.98 37 37
RIPK2 0.023 0.062 -10000 0 -0.48 3 3
MAP2K6 -0.19 0.4 -10000 0 -0.92 38 38
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.033 0.16 -10000 0 -0.39 32 32
IL18RAP -0.056 0.18 -10000 0 -0.37 49 49
IL12Rbeta1/TYK2 0.024 0.055 -10000 0 -10000 0 0
EOMES 0.007 0.17 -10000 0 -1.3 3 3
STAT1 (dimer) -0.21 0.38 -10000 0 -0.82 48 48
T cell proliferation -0.13 0.27 -10000 0 -0.61 37 37
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.008 0.099 -10000 0 -0.29 19 19
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.14 0.3 -10000 0 -0.69 35 35
ATF2 -0.18 0.35 -10000 0 -0.86 34 34
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.019 0.019 -10000 0 -10000 0 0
GNB1/GNG2 -0.085 0.2 -10000 0 -0.45 33 33
mol:DAG -0.074 0.16 0.23 1 -0.46 23 24
PLCG1 -0.077 0.16 0.24 1 -0.48 23 24
YES1 -0.097 0.19 -10000 0 -0.46 33 33
FZD3 -0.03 0.15 -10000 0 -0.38 30 30
FZD6 0.022 0.064 -10000 0 -0.42 4 4
G protein -0.012 0.21 0.29 8 -0.49 21 29
MAP3K7 -0.069 0.13 0.23 1 -0.43 18 19
mol:Ca2+ -0.071 0.15 0.23 1 -0.44 23 24
mol:IP3 -0.074 0.16 0.23 1 -0.46 23 24
NLK -0.031 0.24 -10000 0 -0.8 19 19
GNB1 0.038 0 -10000 0 -10000 0 0
CAMK2A -0.071 0.14 -10000 0 -0.44 20 20
MAP3K7IP1 0.035 0.009 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.11 0.2 -10000 0 -0.37 62 62
CSNK1A1 0.037 0.006 -10000 0 -10000 0 0
GNAS -0.068 0.18 -10000 0 -0.49 25 25
GO:0007205 -0.075 0.16 0.23 1 -0.46 23 24
WNT6 0.033 0.033 -10000 0 -0.21 4 4
WNT4 -0.035 0.16 -10000 0 -0.37 37 37
NFAT1/CK1 alpha -0.068 0.17 -10000 0 -0.49 21 21
GNG2 0.034 0.011 -10000 0 -10000 0 0
WNT5A -0.008 0.14 -10000 0 -0.39 23 23
WNT11 -0.062 0.18 -10000 0 -0.35 56 56
CDC42 -0.094 0.18 -10000 0 -0.47 29 29
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.017 0.12 -10000 0 -0.33 18 18
fibroblast growth factor receptor signaling pathway 0.017 0.12 -10000 0 -0.33 18 18
LAMA1 0.027 0.017 -10000 0 -10000 0 0
PRNP 0.017 0.08 -10000 0 -0.44 6 6
GPC1/SLIT2 -0.039 0.17 -10000 0 -0.39 33 33
SMAD2 -0.003 0.071 -10000 0 -0.27 12 12
GPC1/PrPc/Cu2+ 0.018 0.078 -10000 0 -0.29 10 10
GPC1/Laminin alpha1 0.021 0.077 -10000 0 -0.34 7 7
TDGF1 -0.063 0.2 -10000 0 -0.46 43 43
CRIPTO/GPC1 -0.044 0.17 -10000 0 -0.35 47 47
APP/GPC1 0.016 0.1 -10000 0 -0.35 12 12
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.055 0.13 0.19 1 -0.3 46 47
FLT1 0.008 0.075 -10000 0 -0.28 11 11
GPC1/TGFB/TGFBR1/TGFBR2 0.046 0.089 -10000 0 -0.3 11 11
SERPINC1 0.027 0.06 -10000 0 -0.3 6 6
FYN -0.068 0.15 0.19 1 -0.31 54 55
FGR -0.057 0.14 0.19 1 -0.31 47 48
positive regulation of MAPKKK cascade -0.042 0.22 0.28 8 -0.42 39 47
SLIT2 -0.062 0.18 -10000 0 -0.36 54 54
GPC1/NRG 0.019 0.087 -10000 0 -0.34 9 9
NRG1 0.024 0.054 -10000 0 -0.39 3 3
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.013 0.073 -10000 0 -0.32 6 6
LYN -0.05 0.13 -10000 0 -0.3 43 43
mol:Spermine -0.006 0.068 -10000 0 -0.35 7 7
cell growth 0.017 0.12 -10000 0 -0.33 18 18
BMP signaling pathway -0.012 0.1 0.35 14 -10000 0 14
SRC -0.047 0.12 0.19 1 -0.31 38 39
TGFBR1 0.028 0.063 -10000 0 -0.42 4 4
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.13 0.23 -10000 0 -0.4 82 82
GPC1 0.012 0.1 -10000 0 -0.35 14 14
TGFBR1 (dimer) 0.028 0.063 -10000 0 -0.41 4 4
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.067 0.14 -10000 0 -0.31 51 51
HCK -0.061 0.14 0.19 1 -0.32 45 46
FGF2 -0.001 0.12 -10000 0 -0.3 24 24
FGFR1 0.024 0.06 -10000 0 -0.3 6 6
VEGFR1 homodimer 0.008 0.075 -10000 0 -0.28 11 11
TGFBR2 0.032 0.05 -10000 0 -0.48 2 2
cell death 0.016 0.1 -10000 0 -0.35 12 12
ATIII/GPC1 0.027 0.087 -10000 0 -0.35 8 8
PLA2G2A/GPC1 -0.098 0.18 -10000 0 -0.36 64 64
LCK -0.078 0.16 0.19 1 -0.32 58 59
neuron differentiation 0.019 0.087 -10000 0 -0.34 9 9
PrPc/Cu2+ 0.013 0.058 -10000 0 -0.35 5 5
APP 0.017 0.086 -10000 0 -0.35 10 10
TGFBR2 (dimer) 0.032 0.05 -10000 0 -0.48 2 2
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.036 0.017 -10000 0 -0.21 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.13 0.21 0.61 22 -10000 0 22
IL27/IL27R/JAK1 -0.14 0.33 -10000 0 -1.2 15 15
TBX21 -0.19 0.25 -10000 0 -0.6 45 45
IL12B 0.02 0.059 -10000 0 -0.32 5 5
IL12A -0.025 0.088 -10000 0 -0.23 27 27
IL6ST 0.019 0.029 -10000 0 -10000 0 0
IL27RA/JAK1 -0.097 0.34 -10000 0 -1.3 15 15
IL27 -0.1 0.2 -10000 0 -0.42 58 58
TYK2 0.016 0.032 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.037 0.13 0.2 20 -0.27 42 62
T-helper 2 cell differentiation 0.13 0.21 0.61 22 -10000 0 22
T cell proliferation during immune response 0.13 0.21 0.61 22 -10000 0 22
MAPKKK cascade -0.13 0.21 -10000 0 -0.61 22 22
STAT3 0.036 0.009 -10000 0 -10000 0 0
STAT2 0.033 0.039 -10000 0 -0.35 2 2
STAT1 0.016 0.069 -10000 0 -0.21 18 18
IL12RB1 0.034 0.018 -10000 0 -0.21 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.18 0.23 -10000 0 -0.58 36 36
IL27/IL27R/JAK2/TYK2 -0.13 0.21 -10000 0 -0.62 22 22
positive regulation of T cell mediated cytotoxicity -0.13 0.21 -10000 0 -0.61 22 22
STAT1 (dimer) -0.19 0.35 0.53 1 -0.92 26 27
JAK2 -0.001 0.082 -10000 0 -0.28 13 13
JAK1 0.034 0.036 -10000 0 -0.48 1 1
STAT2 (dimer) -0.12 0.21 -10000 0 -0.6 22 22
T cell proliferation -0.18 0.23 -10000 0 -0.55 40 40
IL12/IL12R/TYK2/JAK2 -0.061 0.2 -10000 0 -0.85 8 8
IL17A -0.038 0.13 0.2 19 -0.27 42 61
mast cell activation 0.13 0.21 0.61 22 -10000 0 22
IFNG -0.034 0.055 -10000 0 -0.13 43 43
T cell differentiation -0.01 0.01 -10000 0 -0.024 62 62
STAT3 (dimer) -0.12 0.21 -10000 0 -0.59 22 22
STAT5A (dimer) -0.12 0.21 -10000 0 -0.6 22 22
STAT4 (dimer) -0.12 0.22 -10000 0 -0.61 24 24
STAT4 0.022 0.079 -10000 0 -0.33 9 9
T cell activation 0.001 0.034 0.12 15 -10000 0 15
IL27R/JAK2/TYK2 -0.098 0.33 -10000 0 -1.2 15 15
GATA3 0.023 0.16 0.67 3 -1.4 2 5
IL18 -0.031 0.11 -10000 0 -0.3 27 27
positive regulation of mast cell cytokine production -0.11 0.2 -10000 0 -0.57 22 22
IL27/EBI3 -0.064 0.16 -10000 0 -0.36 42 42
IL27RA -0.11 0.35 -10000 0 -1.4 15 15
IL6 -0.11 0.2 -10000 0 -0.35 82 82
STAT5A 0.029 0.049 -10000 0 -0.26 5 5
monocyte differentiation -0.002 0.003 -10000 0 -10000 0 0
IL2 0.035 0.12 0.46 15 -10000 0 15
IL1B -0.057 0.13 -10000 0 -0.27 50 50
EBI3 0.02 0.027 -10000 0 -10000 0 0
TNF -0.001 0.043 -10000 0 -0.18 9 9
Glucocorticoid receptor regulatory network

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
PCK2 0.063 0.11 -10000 0 -0.74 2 2
SMARCC2 0.037 0.005 -10000 0 -10000 0 0
SMARCC1 0.037 0.004 -10000 0 -10000 0 0
TBX21 -0.16 0.26 0.33 1 -0.76 27 28
SUMO2 0.032 0.018 -10000 0 -10000 0 0
STAT1 (dimer) 0.008 0.1 -10000 0 -0.26 25 25
FKBP4 0.033 0.036 -10000 0 -0.48 1 1
FKBP5 0.027 0.065 -10000 0 -0.37 5 5
GR alpha/HSP90/FKBP51/HSP90 0.099 0.1 0.28 27 -0.22 2 29
PRL -0.048 0.099 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.17 0.22 0.51 47 -10000 0 47
RELA -0.085 0.12 -10000 0 -0.26 38 38
FGG 0.14 0.2 0.44 41 -0.52 2 43
GR beta/TIF2 0.096 0.12 0.31 23 -0.34 1 24
IFNG -0.35 0.44 -10000 0 -1.1 50 50
apoptosis -0.013 0.23 0.59 4 -0.6 13 17
CREB1 0.042 0.041 -10000 0 -0.38 2 2
histone acetylation -0.076 0.12 -10000 0 -0.31 28 28
BGLAP -0.066 0.12 -10000 0 -10000 0 0
GR/PKAc 0.098 0.15 0.33 15 -0.27 9 24
NF kappa B1 p50/RelA -0.16 0.22 -10000 0 -0.42 73 73
SMARCD1 0.037 0.004 -10000 0 -10000 0 0
MDM2 0.078 0.087 0.21 48 -10000 0 48
GATA3 0.037 0.058 -10000 0 -0.38 3 3
AKT1 0.027 0.035 0.24 2 -0.2 3 5
CSF2 -0.25 0.45 -10000 0 -1.3 31 31
GSK3B 0.031 0.039 -10000 0 -0.48 1 1
NR1I3 0.001 0.21 0.6 4 -0.62 4 8
CSN2 0.12 0.16 0.37 39 -10000 0 39
BRG1/BAF155/BAF170/BAF60A 0.089 0.037 -10000 0 -0.27 1 1
NFATC1 0.006 0.078 -10000 0 -0.22 20 20
POU2F1 0.032 0.067 -10000 0 -0.38 5 5
CDKN1A -0.1 0.29 -10000 0 -1.5 6 6
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.007 -10000 0 -10000 0 0
SFN 0.02 0.073 -10000 0 -0.3 9 9
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.1 0.11 0.29 21 -0.27 1 22
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.074 0.32 0.54 4 -0.81 27 31
JUN -0.16 0.2 -10000 0 -0.49 38 38
IL4 -0.067 0.14 -10000 0 -0.55 8 8
CDK5R1 0.035 0.008 -10000 0 -10000 0 0
PRKACA 0.037 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.073 0.18 0.22 30 -0.38 31 61
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.098 0.29 26 -10000 0 26
cortisol/GR alpha (monomer) 0.22 0.26 0.6 52 -10000 0 52
NCOA2 0.026 0.051 -10000 0 -0.48 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.1 0.18 -10000 0 -0.38 52 52
AP-1/NFAT1-c-4 -0.24 0.26 -10000 0 -0.61 51 51
AFP -0.19 0.38 -10000 0 -1.5 14 14
SUV420H1 0.037 0.004 -10000 0 -10000 0 0
IRF1 0.082 0.21 0.46 7 -0.71 8 15
TP53 -0.037 0.18 -10000 0 -0.49 28 28
PPP5C 0.036 0.017 -10000 0 -0.21 1 1
KRT17 -0.21 0.27 -10000 0 -0.76 24 24
KRT14 -0.072 0.13 -10000 0 -0.41 9 9
TBP 0.043 0.018 -10000 0 -10000 0 0
CREBBP 0.038 0.043 -10000 0 -0.44 1 1
HDAC1 0.033 0.013 -10000 0 -10000 0 0
HDAC2 0.045 0.046 -10000 0 -0.48 1 1
AP-1 -0.24 0.26 -10000 0 -0.6 55 55
MAPK14 0.036 0.009 -10000 0 -10000 0 0
MAPK10 0.01 0.1 -10000 0 -0.36 13 13
MAPK11 0.03 0.025 -10000 0 -0.21 1 1
KRT5 -0.21 0.27 -10000 0 -0.79 24 24
interleukin-1 receptor activity 0.011 0.026 -10000 0 -10000 0 0
NCOA1 0.029 0.072 -10000 0 -0.41 5 5
STAT1 0.008 0.1 -10000 0 -0.26 25 25
CGA -0.077 0.16 -10000 0 -1.1 2 2
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.088 0.19 0.47 33 -0.39 1 34
MAPK3 0.023 0.075 -10000 0 -0.4 6 6
MAPK1 0.034 0.011 -10000 0 -10000 0 0
ICAM1 -0.22 0.29 -10000 0 -0.62 54 54
NFKB1 -0.084 0.12 -10000 0 -0.26 39 39
MAPK8 -0.11 0.15 -10000 0 -0.4 29 29
MAPK9 0.033 0.037 -10000 0 -0.49 1 1
cortisol/GR alpha (dimer) -0.016 0.24 0.6 4 -0.64 13 17
BAX -0.073 0.18 -10000 0 -1.8 1 1
POMC -0.11 0.23 -10000 0 -1.7 3 3
EP300 0.027 0.095 -10000 0 -0.45 7 7
cortisol/GR alpha (dimer)/p53 0.11 0.24 0.53 34 -0.47 1 35
proteasomal ubiquitin-dependent protein catabolic process 0.048 0.085 0.24 17 -10000 0 17
SGK1 0.035 0.092 0.21 13 -0.24 9 22
IL13 -0.15 0.19 -10000 0 -0.65 10 10
IL6 -0.35 0.48 -10000 0 -1 61 61
PRKACG 0.037 0.005 -10000 0 -10000 0 0
IL5 -0.13 0.16 -10000 0 -0.55 9 9
IL2 -0.19 0.23 -10000 0 -0.62 30 30
CDK5 0.035 0.008 -10000 0 -10000 0 0
PRKACB -0.029 0.16 -10000 0 -0.41 32 32
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.39 0.5 -10000 0 -1.1 60 60
CDK5R1/CDK5 0.05 0.016 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.12 0.21 -10000 0 -0.41 49 49
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.18 0.21 0.49 52 -10000 0 52
SMARCA4 0.032 0.043 -10000 0 -0.3 3 3
chromatin remodeling 0.13 0.13 0.33 46 -10000 0 46
NF kappa B1 p50/RelA/Cbp -0.1 0.2 0.34 1 -0.42 39 40
JUN (dimer) -0.16 0.2 -10000 0 -0.49 38 38
YWHAH 0.033 0.036 -10000 0 -0.48 1 1
VIPR1 -0.13 0.24 -10000 0 -0.73 24 24
NR3C1 0.14 0.16 0.4 42 -10000 0 42
NR4A1 0.014 0.09 -10000 0 -0.42 4 4
TIF2/SUV420H1 0.042 0.044 -10000 0 -0.35 2 2
MAPKKK cascade -0.013 0.23 0.59 4 -0.6 13 17
cortisol/GR alpha (dimer)/Src-1 0.2 0.23 0.53 52 -10000 0 52
PBX1 0.023 0.094 -10000 0 -0.44 8 8
POU1F1 0.04 0.037 -10000 0 -0.48 1 1
SELE -0.38 0.49 -10000 0 -1 68 68
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.13 0.13 0.34 45 -10000 0 45
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.18 0.21 0.49 52 -10000 0 52
mol:cortisol 0.12 0.16 0.33 60 -10000 0 60
MMP1 -0.35 0.52 -10000 0 -1.2 53 53
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.082 0.14 -10000 0 -0.4 10 10
NF kappa B1 p50/RelA/I kappa B alpha -0.082 0.16 0.33 2 -0.42 13 15
alphaV/beta3 Integrin/Osteopontin/Src -0.12 0.18 -10000 0 -0.36 66 66
AP1 -0.15 0.19 -10000 0 -0.46 30 30
ILK -0.091 0.14 -10000 0 -0.36 12 12
bone resorption -0.094 0.14 -10000 0 -0.36 13 13
PTK2B 0.028 0.016 -10000 0 -10000 0 0
PYK2/p130Cas -0.068 0.15 -10000 0 -0.34 12 12
ITGAV 0.022 0.082 -10000 0 -0.4 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.028 0.1 -10000 0 -0.35 14 14
alphaV/beta3 Integrin/Osteopontin -0.086 0.17 -10000 0 -0.3 66 66
MAP3K1 -0.095 0.14 -10000 0 -0.32 23 23
JUN -0.017 0.15 -10000 0 -0.41 26 26
MAPK3 -0.1 0.13 -10000 0 -0.41 10 10
MAPK1 -0.097 0.13 -10000 0 -0.43 9 9
Rac1/GDP 0.024 0.009 -10000 0 -10000 0 0
NFKB1 0.037 0.006 -10000 0 -10000 0 0
MAPK8 -0.096 0.12 -10000 0 -0.35 13 13
ITGB3 0.034 0.025 -10000 0 -0.22 1 1
NFKBIA -0.1 0.15 0.34 1 -0.43 15 16
FOS -0.063 0.17 -10000 0 -0.32 58 58
CD44 0.032 0.05 -10000 0 -0.48 2 2
CHUK 0.031 0.05 -10000 0 -0.48 2 2
PLAU -0.16 0.31 -10000 0 -1.1 16 16
NF kappa B1 p50/RelA -0.082 0.17 -10000 0 -0.46 13 13
BCAR1 0.036 0.017 -10000 0 -0.21 1 1
RELA 0.037 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.042 0.065 -10000 0 -0.34 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.095 0.14 -10000 0 -0.28 66 66
VAV3 -0.15 0.16 -10000 0 -0.36 43 43
MAP3K14 -0.094 0.14 -10000 0 -0.38 10 10
ROCK2 0.007 0.12 -10000 0 -0.46 13 13
SPP1 -0.17 0.22 -10000 0 -0.36 113 113
RAC1 0.033 0.012 -10000 0 -10000 0 0
Rac1/GTP -0.13 0.14 -10000 0 -0.34 37 37
MMP2 -0.15 0.16 -10000 0 -0.44 30 30
IL1-mediated signaling events

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
UBC13/UEV1A 0.027 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0.036 0.007 -10000 0 -10000 0 0
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.032 0.093 -10000 0 -0.26 10 10
IRAK/TOLLIP 0.042 0.021 -10000 0 -10000 0 0
IKBKB 0.033 0.012 -10000 0 -10000 0 0
IKBKG 0.036 0.017 -10000 0 -0.21 1 1
IL1 alpha/IL1R2 -0.12 0.19 -10000 0 -0.37 66 66
IL1A -0.086 0.19 -10000 0 -0.32 74 74
IL1B -0.12 0.19 -10000 0 -0.39 63 63
IRAK/TRAF6/p62/Atypical PKCs 0.065 0.044 -10000 0 -0.24 2 2
IL1R2 -0.072 0.19 -10000 0 -0.36 60 60
IL1R1 0.018 0.081 -10000 0 -0.27 14 14
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.019 0.089 -10000 0 -0.37 1 1
TOLLIP 0.037 0.003 -10000 0 -10000 0 0
TICAM2 0 0 -10000 0 -10000 0 0
MAP3K3 0.035 0.009 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.068 0.033 -10000 0 -0.3 1 1
IKK complex/ELKS 0.026 0.066 -10000 0 -0.35 2 2
JUN -0.043 0.082 -10000 0 -0.43 2 2
MAP3K7 0.034 0.036 -10000 0 -0.48 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.061 0.18 -10000 0 -0.32 59 59
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.009 0.15 -10000 0 -0.28 34 34
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.001 0.15 -10000 0 -0.27 35 35
IL1 beta fragment/IL1R1/IL1RAP -0.084 0.18 -10000 0 -0.33 65 65
NFKB1 0.037 0.006 -10000 0 -10000 0 0
MAPK8 -0.02 0.054 0.19 1 -0.23 9 10
IRAK1 0.019 0.017 -10000 0 -0.19 1 1
IL1RN/IL1R1 -0.019 0.14 -10000 0 -0.24 54 54
IRAK4 0.035 0.036 -10000 0 -0.48 1 1
PRKCI 0.03 0.055 -10000 0 -0.35 4 4
TRAF6 0.037 0.004 -10000 0 -10000 0 0
PI3K 0.047 0.049 -10000 0 -0.35 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.037 0.11 -10000 0 -0.31 13 13
CHUK 0.031 0.05 -10000 0 -0.48 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.084 0.18 -10000 0 -0.33 65 65
IL1 beta/IL1R2 -0.15 0.22 -10000 0 -0.38 88 88
IRAK/TRAF6/TAK1/TAB1/TAB2 0.085 0.042 -10000 0 -0.24 1 1
NF kappa B1 p50/RelA -0.065 0.17 -10000 0 -0.39 23 23
IRAK3 -0.011 0.13 -10000 0 -0.32 29 29
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.069 0.17 -10000 0 -0.31 62 62
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.016 0.1 -10000 0 -0.38 3 3
IL1 alpha/IL1R1/IL1RAP -0.028 0.15 -10000 0 -0.3 38 38
RELA 0.037 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0.035 0.009 -10000 0 -10000 0 0
SQSTM1 0.036 0.018 -10000 0 -0.21 1 1
MYD88 0.037 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.06 0.028 -10000 0 -10000 0 0
IL1RAP 0.032 0.034 -10000 0 -0.21 4 4
UBE2N 0.036 0.007 -10000 0 -10000 0 0
IRAK/TRAF6 -0.075 0.14 -10000 0 -0.37 22 22
CASP1 -0.086 0.2 -10000 0 -0.37 65 65
IL1RN/IL1R2 -0.082 0.2 -10000 0 -0.3 84 84
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.068 0.18 -10000 0 -0.32 61 61
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.001 0.093 -10000 0 -0.37 5 5
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
IL1RN -0.042 0.16 -10000 0 -0.32 49 49
TRAF6/TAK1/TAB1/TAB2 0.082 0.038 -10000 0 -0.25 1 1
MAP2K6 0.004 0.06 -10000 0 -0.24 10 10
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.023 0.052 -9999 0 -0.17 8 8
NFATC2 -0.008 0.029 -9999 0 -10000 0 0
NFATC3 -0.021 0.051 -9999 0 -0.35 1 1
CD40LG -0.16 0.27 -9999 0 -0.56 48 48
PTGS2 -0.2 0.3 -9999 0 -0.57 66 66
JUNB 0.02 0.073 -9999 0 -0.25 13 13
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.035 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.035 -9999 0 -10000 0 0
CALM1 0.014 0.032 -9999 0 -10000 0 0
JUN -0.035 0.15 -9999 0 -0.42 26 26
mol:Ca2+ -0.012 0.014 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.026 -9999 0 -0.29 1 1
FOSL1 0.03 0.041 -9999 0 -0.21 6 6
CREM 0.033 0.039 -9999 0 -0.35 2 2
Jun/NFAT1-c-4/p21SNFT -0.071 0.15 -9999 0 -0.38 23 23
FOS -0.077 0.17 -9999 0 -0.33 58 58
IFNG -0.21 0.31 -9999 0 -0.62 62 62
AP-1/NFAT1-c-4 -0.18 0.32 -9999 0 -0.64 51 51
FASLG -0.18 0.29 -9999 0 -0.6 50 50
NFAT1-c-4/ICER1 -0.023 0.088 -9999 0 -0.38 1 1
IL2RA -0.18 0.3 -9999 0 -0.61 55 55
FKBP12/FK506 0.021 0.027 -9999 0 -0.35 1 1
CSF2 -0.2 0.3 -9999 0 -0.6 57 57
JunB/Fra1/NFAT1-c-4 0.001 0.12 -9999 0 -0.34 3 3
IL4 -0.16 0.26 -9999 0 -0.54 50 50
IL2 -0.002 0.15 -9999 0 -0.94 5 5
IL3 0.006 0.14 -9999 0 -0.76 7 7
FKBP1A 0.028 0.038 -9999 0 -0.48 1 1
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.033 0.066 -9999 0 -0.37 5 5
TCGA08_retinoblastoma

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
CDKN2B 0.008 0.084 -10000 0 -0.26 15 15
CDKN2C 0.038 0.055 -10000 0 -0.37 3 3
CDKN2A -0.03 0.15 -10000 0 -0.32 41 41
CCND2 0 0.086 0.18 19 -0.51 2 21
RB1 0.006 0.084 0.22 7 -0.2 14 21
CDK4 0.015 0.071 0.21 20 -10000 0 20
CDK6 0.012 0.071 0.2 20 -10000 0 20
G1/S progression -0.008 0.092 0.2 14 -0.43 3 17
EGFR-dependent Endothelin signaling events

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
HRAS 0.034 0.039 -10000 0 -0.35 2 2
EGFR 0.016 0.088 -10000 0 -0.42 8 8
EGF/EGFR -0.08 0.15 -10000 0 -0.29 56 56
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.003 0.13 -10000 0 -0.26 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.01 0.092 -10000 0 -0.27 19 19
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF -0.094 0.19 -10000 0 -0.32 79 79
EGF/EGFR dimer/SHC -0.029 0.13 -10000 0 -0.3 32 32
mol:GDP -0.008 0.13 -10000 0 -0.26 31 31
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.063 0.19 -10000 0 -0.36 54 54
GRB2/SOS1 0.053 0.013 -10000 0 -10000 0 0
HRAS/GTP -0.02 0.11 -10000 0 -0.24 32 32
SHC1 0.036 0.007 -10000 0 -10000 0 0
HRAS/GDP -0.009 0.12 -10000 0 -0.25 1 1
FRAP1 -0.025 0.12 0.3 3 -0.48 1 4
EGF/EGFR dimer -0.054 0.15 -10000 0 -0.35 33 33
SOS1 0.037 0.003 -10000 0 -10000 0 0
GRB2 0.036 0.008 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.045 0.15 -10000 0 -0.35 35 35
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 -0.12 0.36 -10000 0 -0.94 24 24
PCK1 -0.23 0.55 -10000 0 -1.4 37 37
HNF4A -0.07 0.42 0.58 8 -1.1 20 28
KCNJ11 -0.092 0.36 -10000 0 -0.96 20 20
AKT1 -0.038 0.21 -10000 0 -0.5 20 20
response to starvation -0.006 0.038 -10000 0 -0.15 9 9
DLK1 -0.1 0.4 -10000 0 -1 22 22
NKX2-1 0.045 0.21 0.41 32 -0.4 7 39
ACADM -0.12 0.38 0.58 1 -0.99 23 24
TAT -0.07 0.24 -10000 0 -0.85 7 7
CEBPB 0.014 0.041 -10000 0 -0.48 1 1
CEBPA 0.011 0.095 -10000 0 -0.38 10 10
TTR -0.2 0.48 -10000 0 -1.2 35 35
PKLR -0.12 0.38 -10000 0 -1 23 23
APOA1 -0.12 0.53 -10000 0 -1.3 26 26
CPT1C -0.12 0.38 -10000 0 -1 24 24
ALAS1 -0.026 0.18 -10000 0 -0.78 1 1
TFRC -0.11 0.38 -10000 0 -1 22 22
FOXF1 0.002 0.13 -10000 0 -0.43 16 16
NF1 0.042 0.011 -10000 0 -10000 0 0
HNF1A (dimer) 0.001 0.035 -10000 0 -0.16 8 8
CPT1A -0.12 0.37 -10000 0 -0.97 24 24
HMGCS1 -0.12 0.38 0.58 1 -0.96 25 26
NR3C1 0.022 0.093 -10000 0 -0.48 6 6
CPT1B -0.12 0.37 -10000 0 -0.96 22 22
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.036 0.017 -10000 0 -0.21 1 1
GCK -0.097 0.38 0.58 2 -0.99 21 23
CREB1 -0.005 0.089 -10000 0 -0.23 18 18
IGFBP1 -0.061 0.25 -10000 0 -1.2 5 5
PDX1 -0.027 0.18 -10000 0 -0.39 18 18
UCP2 -0.14 0.39 -10000 0 -0.94 29 29
ALDOB -0.2 0.48 -10000 0 -1 46 46
AFP -0.14 0.27 -10000 0 -0.91 18 18
BDH1 -0.13 0.4 -10000 0 -1 24 24
HADH -0.091 0.36 -10000 0 -0.87 24 24
F2 -0.08 0.46 -10000 0 -1.2 19 19
HNF1A 0.001 0.035 -10000 0 -0.16 8 8
G6PC 0.011 0.19 -10000 0 -1.1 3 3
SLC2A2 -0.071 0.32 -10000 0 -1.3 8 8
INS 0.03 0.026 0.22 1 -10000 0 1
FOXA1 -0.13 0.23 -10000 0 -0.46 66 66
FOXA3 -0.043 0.18 -10000 0 -0.44 25 25
FOXA2 -0.098 0.41 -10000 0 -1 22 22
ABCC8 -0.099 0.36 -10000 0 -0.96 20 20
ALB -0.12 0.21 -10000 0 -0.7 14 14
Glypican 2 network

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
MDK -0.006 0.13 -9999 0 -0.34 25 25
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.003 0.092 -9999 0 -0.24 25 25
neuron projection morphogenesis -0.003 0.092 -9999 0 -0.24 25 25
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.004 0.18 -10000 0 -0.48 24 24
HDAC1 0.035 0.013 -10000 0 -10000 0 0
AES 0.036 0.009 -10000 0 -10000 0 0
FBXW11 0.037 0.005 -10000 0 -10000 0 0
DTX1 0.037 0.004 -10000 0 -10000 0 0
LRP6/FZD1 0.051 0.02 -10000 0 -10000 0 0
TLE1 0.005 0.12 -10000 0 -0.48 13 13
AP1 -0.13 0.17 -10000 0 -0.33 72 72
NCSTN 0.036 0.008 -10000 0 -10000 0 0
ADAM10 0.025 0.066 -10000 0 -0.37 5 5
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.018 0.12 -10000 0 -0.53 5 5
NICD/RBPSUH -0.025 0.16 -10000 0 -0.46 24 24
WIF1 -0.024 0.11 -10000 0 -0.21 53 53
NOTCH1 -0.023 0.17 -10000 0 -0.49 24 24
PSENEN 0.033 0.039 -10000 0 -0.35 2 2
KREMEN2 -0.064 0.17 -10000 0 -0.31 63 63
DKK1 -0.095 0.19 -10000 0 -0.32 80 80
beta catenin/beta TrCP1 0.075 0.11 0.3 5 -0.32 3 8
APH1B 0.021 0.073 -10000 0 -0.3 9 9
APH1A 0.003 0.11 -10000 0 -0.3 22 22
AXIN1 -0.024 0.095 -10000 0 -0.61 3 3
CtBP/CBP/TCF1/TLE1/AES 0.006 0.08 0.2 2 -0.25 12 14
PSEN1 0.032 0.02 -10000 0 -0.21 1 1
FOS -0.063 0.17 -10000 0 -0.32 58 58
JUN -0.017 0.15 -10000 0 -0.41 26 26
MAP3K7 0.034 0.036 -10000 0 -0.48 1 1
CTNNB1 0.059 0.11 0.3 5 -0.34 3 8
MAPK3 0.025 0.074 -10000 0 -0.39 6 6
DKK2/LRP6/Kremen 2 -0.047 0.15 -10000 0 -0.31 43 43
HNF1A 0 0.003 -10000 0 -10000 0 0
CTBP1 0.036 0.008 -10000 0 -10000 0 0
MYC -0.035 0.31 -10000 0 -1.4 10 10
NKD1 -0.15 0.21 -10000 0 -0.35 103 103
FZD1 0.036 0.008 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.001 0.18 -10000 0 -0.47 24 24
apoptosis -0.13 0.17 -10000 0 -0.33 72 72
Delta 1/NOTCHprecursor 0 0.18 -10000 0 -0.48 24 24
DLL1 0.033 0.039 -10000 0 -0.35 2 2
PPARD 0.032 0.079 -10000 0 -0.74 2 2
Gamma Secretase 0.054 0.1 -10000 0 -0.26 10 10
APC -0.064 0.15 -10000 0 -0.43 26 26
DVL1 0.01 0.086 -10000 0 -0.61 3 3
CSNK2A1 0.031 0.015 -10000 0 -10000 0 0
MAP3K7IP1 0.035 0.01 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.088 0.18 -10000 0 -0.33 56 56
LRP6 0.035 0.018 -10000 0 -0.21 1 1
CSNK1A1 0.037 0.006 -10000 0 -10000 0 0
NLK 0.026 0.028 -10000 0 -0.31 1 1
CCND1 0.006 0.21 -10000 0 -1.3 5 5
WNT1 0.037 0.005 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.014 0.13 0.29 2 -0.46 6 8
DKK2 -0.029 0.15 -10000 0 -0.31 41 41
NOTCH1 precursor/DVL1 -0.006 0.19 -10000 0 -0.6 14 14
GSK3B 0.034 0.036 -10000 0 -0.48 1 1
FRAT1 0.031 0.05 -10000 0 -0.48 2 2
NOTCH/Deltex homolog 1 0.006 0.18 -10000 0 -0.47 24 24
PPP2R5D 0.1 0.11 0.28 51 -0.26 2 53
MAPK1 0.036 0.009 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.041 0.085 -10000 0 -10000 0 0
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.035 0.037 -10000 0 -0.49 1 1
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.032 0.11 -9999 0 -0.27 30 30
SMAD6-7/SMURF1 0.044 0.048 -9999 0 -0.3 1 1
NOG 0.031 0.051 -9999 0 -0.48 2 2
SMAD9 -0.081 0.2 -9999 0 -0.52 34 34
SMAD4 0.017 0.062 -9999 0 -0.48 3 3
SMAD5 -0.041 0.12 -9999 0 -0.41 12 12
BMP7/USAG1 -0.13 0.19 -9999 0 -0.43 56 56
SMAD5/SKI -0.037 0.14 -9999 0 -0.41 14 14
SMAD1 0.006 0.094 -9999 0 -0.45 5 5
BMP2 -0.022 0.15 -9999 0 -0.45 23 23
SMAD1/SMAD1/SMAD4 0.011 0.097 -9999 0 -0.46 3 3
BMPR1A 0.031 0.05 -9999 0 -0.48 2 2
BMPR1B 0.033 0.029 -9999 0 -0.21 3 3
BMPR1A-1B/BAMBI -0.013 0.14 -9999 0 -0.3 33 33
AHSG 0.013 0.11 -9999 0 -0.48 10 10
CER1 0.032 0.04 -9999 0 -0.35 2 2
BMP2-4/CER1 -0.037 0.15 -9999 0 -0.31 41 41
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.04 0.13 -9999 0 -0.35 20 20
BMP2-4 (homodimer) -0.055 0.16 -9999 0 -0.37 40 40
RGMB -0.009 0.11 -9999 0 -0.26 33 33
BMP6/BMPR2/BMPR1A-1B 0.064 0.083 -9999 0 -0.27 8 8
RGMA 0.015 0.096 -9999 0 -0.4 10 10
SMURF1 0.036 0.008 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.058 0.13 -9999 0 -0.34 26 26
BMP2-4/USAG1 -0.13 0.19 -9999 0 -0.36 71 71
SMAD6/SMURF1/SMAD5 -0.037 0.14 -9999 0 -0.41 13 13
SOSTDC1 -0.14 0.22 -9999 0 -0.39 88 88
BMP7/BMPR2/BMPR1A-1B -0.034 0.11 -9999 0 -0.27 29 29
SKI 0.038 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.013 0.096 -9999 0 -0.33 14 14
HFE2 0.029 0.063 -9999 0 -0.42 4 4
ZFYVE16 0.037 0.006 -9999 0 -10000 0 0
MAP3K7 0.034 0.036 -9999 0 -0.48 1 1
BMP2-4/CHRD -0.031 0.15 -9999 0 -0.32 39 39
SMAD5/SMAD5/SMAD4 -0.038 0.14 -9999 0 -0.41 15 15
MAPK1 0.036 0.009 -9999 0 -10000 0 0
TAK1/TAB family -0.012 0.15 -9999 0 -0.33 15 15
BMP7 (homodimer) -0.086 0.18 -9999 0 -0.35 58 58
NUP214 0.034 0.024 -9999 0 -0.21 2 2
BMP6/FETUA 0.017 0.11 -9999 0 -0.37 15 15
SMAD1/SKI 0.016 0.11 -9999 0 -0.44 6 6
SMAD6 0.03 0.046 -9999 0 -0.28 4 4
CTDSP2 0.03 0.055 -9999 0 -0.35 4 4
BMP2-4/FETUA -0.045 0.16 -9999 0 -0.33 46 46
MAP3K7IP1 0.035 0.009 -9999 0 -10000 0 0
GREM1 -0.056 0.18 -9999 0 -0.39 46 46
BMPR2 (homodimer) 0.037 0.004 -9999 0 -10000 0 0
GADD34/PP1CA 0.066 0.039 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) 0.045 0.048 -9999 0 -0.35 2 2
CHRDL1 0.024 0.073 -9999 0 -0.3 9 9
ENDOFIN/SMAD1 0.015 0.11 -9999 0 -0.44 6 6
SMAD6-7/SMURF1/SMAD1 0.027 0.11 -9999 0 -0.46 4 4
SMAD6/SMURF1 0.036 0.008 -9999 0 -10000 0 0
BAMBI -0.07 0.19 -9999 0 -0.35 59 59
SMURF2 0.023 0.066 -9999 0 -0.27 9 9
BMP2-4/CHRDL1 -0.041 0.16 -9999 0 -0.33 42 42
BMP2-4/GREM1 -0.089 0.18 -9999 0 -0.32 67 67
SMAD7 0.022 0.039 -9999 0 -0.48 1 1
SMAD8A/SMAD8A/SMAD4 -0.085 0.21 -9999 0 -0.49 35 35
SMAD1/SMAD6 0.015 0.11 -9999 0 -0.44 6 6
TAK1/SMAD6 0.05 0.031 -9999 0 -0.35 1 1
BMP7 -0.087 0.18 -9999 0 -0.35 58 58
BMP6 0.013 0.096 -9999 0 -0.33 14 14
MAP3K7IP2 0.036 0.007 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.063 0.14 -9999 0 -0.4 21 21
PPM1A 0.033 0.012 -9999 0 -10000 0 0
SMAD1/SMURF2 0.009 0.11 -9999 0 -0.45 6 6
SMAD7/SMURF1 0.033 0.038 -9999 0 -0.35 1 1
CTDSPL 0.017 0.096 -9999 0 -0.4 10 10
PPP1CA 0.031 0.037 -9999 0 -0.21 5 5
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.037 0.004 -9999 0 -10000 0 0
PPP1R15A 0.034 0.029 -9999 0 -0.21 3 3
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.059 0.14 -9999 0 -0.36 26 26
CHRD 0.037 0.004 -9999 0 -10000 0 0
BMPR2 0.037 0.004 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.056 0.14 -9999 0 -0.37 22 22
BMP4 -0.048 0.17 -9999 0 -0.38 43 43
FST 0.018 0.095 -9999 0 -0.42 9 9
BMP2-4/NOG -0.033 0.15 -9999 0 -0.31 39 39
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.027 0.11 -9999 0 -0.26 27 27
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.036 0.16 -10000 0 -0.36 31 31
alphaM/beta2 Integrin/GPIbA -0.028 0.14 -10000 0 -0.34 24 24
alphaM/beta2 Integrin/proMMP-9 -0.03 0.12 -10000 0 -0.36 19 19
PLAUR 0.016 0.094 -10000 0 -0.35 12 12
HMGB1 0.006 0.048 -10000 0 -0.5 1 1
alphaM/beta2 Integrin/Talin -0.02 0.14 -10000 0 -0.34 24 24
AGER 0.009 0.045 -10000 0 -10000 0 0
RAP1A 0.036 0.008 -10000 0 -10000 0 0
SELPLG 0.015 0.095 -10000 0 -0.34 13 13
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.045 0.15 -10000 0 -0.36 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.006 0.094 -10000 0 -0.32 15 15
CYR61 -0.011 0.13 -10000 0 -0.31 29 29
TLN1 0.036 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.014 0.15 -10000 0 -0.45 14 14
RHOA 0.037 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.054 0.18 -10000 0 -0.38 47 47
MYH2 -0.038 0.15 -10000 0 -0.55 13 13
MST1R 0.03 0.061 -10000 0 -0.48 3 3
leukocyte activation during inflammatory response -0.023 0.14 -10000 0 -0.3 32 32
APOB 0.005 0.12 -10000 0 -0.46 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.005 0.11 -10000 0 -0.3 21 21
JAM3 0.028 0.047 -10000 0 -0.21 8 8
GP1BA 0.026 0.028 -10000 0 -0.21 2 2
alphaM/beta2 Integrin/CTGF -0.024 0.14 -10000 0 -0.35 24 24
alphaM/beta2 Integrin -0.039 0.16 -10000 0 -0.44 20 20
JAM3 homodimer 0.028 0.047 -10000 0 -0.21 8 8
ICAM2 0.012 0.1 -10000 0 -0.36 13 13
ICAM1 0.009 0.094 -10000 0 -0.26 20 20
phagocytosis triggered by activation of immune response cell surface activating receptor -0.039 0.15 -10000 0 -0.43 20 20
cell adhesion -0.028 0.14 -10000 0 -0.34 24 24
NFKB1 -0.066 0.23 0.35 2 -0.42 49 51
THY1 0.014 0.098 -10000 0 -0.37 12 12
RhoA/GDP 0.027 0.004 -10000 0 -10000 0 0
Lipoprotein(a) 0.027 0.083 -10000 0 -0.3 13 13
alphaM/beta2 Integrin/LRP/tPA -0.017 0.15 -10000 0 -0.32 29 29
IL6 -0.16 0.33 0.39 1 -0.68 53 54
ITGB2 -0.039 0.14 -10000 0 -0.34 29 29
elevation of cytosolic calcium ion concentration -0.039 0.18 -10000 0 -0.39 34 34
alphaM/beta2 Integrin/JAM2/JAM3 -0.033 0.18 -10000 0 -0.37 33 33
JAM2 -0.011 0.14 -10000 0 -0.38 24 24
alphaM/beta2 Integrin/ICAM1 -0.007 0.16 -10000 0 -0.32 35 35
alphaM/beta2 Integrin/uPA/Plg -0.031 0.18 -10000 0 -0.38 32 32
RhoA/GTP -0.03 0.16 -10000 0 -0.59 11 11
positive regulation of phagocytosis -0.046 0.15 -10000 0 -0.45 19 19
Ron/MSP 0.033 0.076 -10000 0 -0.35 5 5
alphaM/beta2 Integrin/uPAR/uPA -0.038 0.18 -10000 0 -0.39 34 34
alphaM/beta2 Integrin/uPAR -0.031 0.15 -10000 0 -0.33 32 32
PLAU -0.014 0.14 -10000 0 -0.36 27 27
PLAT 0.01 0.1 -10000 0 -0.41 11 11
actin filament polymerization -0.037 0.14 -10000 0 -0.52 13 13
MST1 0.016 0.078 -10000 0 -0.24 16 16
alphaM/beta2 Integrin/lipoprotein(a) -0.02 0.15 -10000 0 -0.31 32 32
TNF -0.071 0.22 -10000 0 -0.54 20 20
RAP1B 0.037 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.046 0.18 -10000 0 -0.39 34 34
fibrinolysis -0.032 0.17 -10000 0 -0.37 32 32
HCK -0.014 0.11 -10000 0 -0.36 18 18
dendritic cell antigen processing and presentation -0.039 0.15 -10000 0 -0.43 20 20
VTN 0.035 0.009 -10000 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 -0.047 0.16 -10000 0 -0.36 35 35
LPA 0.036 0.007 -10000 0 -10000 0 0
LRP1 0.037 0.005 -10000 0 -10000 0 0
cell migration -0.039 0.13 -10000 0 -0.34 25 25
FN1 -0.016 0.13 -10000 0 -0.3 34 34
alphaM/beta2 Integrin/Thy1 -0.031 0.16 -10000 0 -0.39 26 26
MPO 0.022 0.057 -10000 0 -0.21 12 12
KNG1 0.005 0.11 -10000 0 -0.3 20 20
RAP1/GDP 0.047 0.016 -10000 0 -10000 0 0
ROCK1 -0.029 0.14 -10000 0 -0.58 10 10
ELA2 0.033 0.04 -10000 0 -0.35 2 2
PLG 0.034 0.036 -10000 0 -0.48 1 1
CTGF 0.03 0.041 -10000 0 -0.21 6 6
alphaM/beta2 Integrin/Hck -0.034 0.14 -10000 0 -0.38 23 23
ITGAM -0.016 0.11 -10000 0 -0.34 16 16
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.062 0.19 -10000 0 -0.36 47 47
HP 0.033 0.05 -10000 0 -0.48 2 2
leukocyte adhesion -0.038 0.2 -10000 0 -0.52 20 20
SELP -0.054 0.18 -10000 0 -0.38 47 47
FAS signaling pathway (CD95)

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
SPTAN1 0.007 0.062 0.22 9 -0.26 3 12
RFC1 0.005 0.059 0.23 7 -0.28 2 9
PRKDC 0.015 0.074 0.22 18 -0.28 2 20
RIPK1 0.04 0.007 -10000 0 -10000 0 0
CASP7 -0.033 0.15 -10000 0 -0.63 10 10
FASLG/FAS/FADD/FAF1 0.008 0.14 0.21 32 -0.3 19 51
MAP2K4 -0.11 0.19 -10000 0 -0.43 39 39
mol:ceramide -0.073 0.16 -10000 0 -0.43 25 25
GSN 0 0.073 0.22 9 -0.27 5 14
FASLG/FAS/FADD/FAF1/Caspase 8 -0.007 0.14 0.28 1 -0.4 14 15
FAS -0.046 0.17 -10000 0 -0.41 34 34
BID -0.027 0.052 0.27 2 -0.34 4 6
MAP3K1 -0.047 0.13 0.25 2 -0.45 11 13
MAP3K7 0.032 0.036 -10000 0 -0.48 1 1
RB1 0.036 0.1 0.26 32 -0.31 1 33
CFLAR 0.04 0.006 -10000 0 -10000 0 0
HGF/MET -0.071 0.16 -10000 0 -0.3 63 63
ARHGDIB -0.004 0.067 0.22 6 -0.26 7 13
FADD 0.023 0.026 -10000 0 -10000 0 0
actin filament polymerization 0 0.072 0.27 5 -0.22 9 14
NFKB1 -0.051 0.14 -10000 0 -0.73 5 5
MAPK8 -0.15 0.24 -10000 0 -0.5 57 57
DFFA 0.005 0.059 0.23 7 -0.26 3 10
DNA fragmentation during apoptosis 0.004 0.058 0.23 6 -0.28 2 8
FAS/FADD/MET 0.006 0.12 -10000 0 -0.32 23 23
CFLAR/RIP1 0.06 0.012 -10000 0 -10000 0 0
FAIM3 0.029 0.058 -10000 0 -0.32 5 5
FAF1 0.021 0.028 -10000 0 -10000 0 0
PARP1 0.003 0.057 0.23 6 -0.28 2 8
DFFB 0.004 0.058 0.23 6 -0.28 2 8
CHUK -0.05 0.13 -10000 0 -0.68 5 5
FASLG -0.041 0.14 -10000 0 -0.32 38 38
FAS/FADD -0.02 0.13 -10000 0 -0.36 24 24
HGF 0.031 0.043 -10000 0 -0.3 3 3
LMNA -0.001 0.071 0.22 4 -0.29 6 10
CASP6 0.002 0.071 0.23 7 -0.3 6 13
CASP10 0.014 0.064 -10000 0 -0.31 6 6
CASP3 0.005 0.067 0.27 8 -0.27 4 12
PTPN13 -0.16 0.23 -10000 0 -0.39 98 98
CASP8 -0.027 0.056 0.36 2 -0.37 3 5
IL6 -0.32 0.56 -10000 0 -1.3 52 52
MET 0.028 0.055 -10000 0 -0.35 4 4
ICAD/CAD -0.002 0.047 0.27 1 -0.27 2 3
FASLG/FAS/FADD/FAF1/Caspase 10 -0.074 0.16 -10000 0 -0.44 25 25
activation of caspase activity by cytochrome c -0.027 0.052 0.27 2 -0.34 4 6
PAK2 0.004 0.06 0.23 7 -0.26 3 10
BCL2 -0.001 0.097 -10000 0 -0.31 16 16
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.021 0.087 -10000 0 -0.3 14 14
cell-cell adhesion 0.053 0.11 0.29 28 -10000 0 28
Ephrin B/EPHB2/RasGAP 0.01 0.13 -10000 0 -0.29 26 26
ITSN1 0.035 0.009 -10000 0 -10000 0 0
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
SHC1 0.036 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.005 0.13 -10000 0 -0.32 31 31
Ephrin B1/EPHB1 -0.027 0.12 -10000 0 -0.31 21 21
HRAS/GDP -0.037 0.13 -10000 0 -0.37 15 15
Ephrin B/EPHB1/GRB7 -0.014 0.12 -10000 0 -0.27 27 27
Endophilin/SYNJ1 0.033 0.13 -10000 0 -0.26 23 23
KRAS 0.033 0.04 -10000 0 -0.35 2 2
Ephrin B/EPHB1/Src -0.008 0.11 -10000 0 -0.3 18 18
endothelial cell migration 0.025 0.092 -10000 0 -0.27 15 15
GRB2 0.036 0.008 -10000 0 -10000 0 0
GRB7 0.024 0.064 -10000 0 -0.28 8 8
PAK1 0.034 0.14 -10000 0 -0.27 20 20
HRAS 0.034 0.039 -10000 0 -0.35 2 2
RRAS 0.035 0.13 -10000 0 -0.26 24 24
DNM1 0.031 0.037 -10000 0 -0.21 5 5
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.009 0.12 -10000 0 -0.26 26 26
lamellipodium assembly -0.053 0.11 -10000 0 -0.29 28 28
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.008 0.11 -10000 0 -0.42 6 6
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
EPHB2 0.006 0.12 -10000 0 -0.48 12 12
EPHB3 -0.041 0.18 -10000 0 -0.46 34 34
EPHB1 -0.073 0.17 -10000 0 -0.28 75 75
EPHB4 0.024 0.069 -10000 0 -0.33 7 7
mol:GDP -0.017 0.13 0.24 6 -0.4 14 20
Ephrin B/EPHB2 0.007 0.11 -10000 0 -0.27 24 24
Ephrin B/EPHB3 -0.009 0.12 -10000 0 -0.27 34 34
JNK cascade -0.06 0.13 0.31 2 -0.3 35 37
Ephrin B/EPHB1 -0.019 0.12 -10000 0 -0.28 26 26
RAP1/GDP -0.009 0.15 0.31 8 -0.36 14 22
EFNB2 -0.004 0.12 -10000 0 -0.46 13 13
EFNB3 0.029 0.016 -10000 0 -10000 0 0
EFNB1 0.029 0.057 -10000 0 -0.32 5 5
Ephrin B2/EPHB1-2 -0.042 0.13 -10000 0 -0.31 34 34
RAP1B 0.037 0.006 -10000 0 -10000 0 0
RAP1A 0.036 0.008 -10000 0 -10000 0 0
CDC42/GTP -0.046 0.14 -10000 0 -0.36 23 23
Rap1/GTP -0.049 0.12 -10000 0 -0.4 12 12
axon guidance 0.021 0.087 -10000 0 -0.3 14 14
MAPK3 -0.006 0.11 -10000 0 -0.38 8 8
MAPK1 -0.002 0.1 -10000 0 -0.38 6 6
Rac1/GDP -0.024 0.13 0.26 4 -0.37 13 17
actin cytoskeleton reorganization -0.059 0.1 -10000 0 -0.34 13 13
CDC42/GDP -0.017 0.15 0.3 10 -0.36 15 25
PI3K 0.029 0.095 -10000 0 -0.27 15 15
EFNA5 0.03 0.053 -10000 0 -0.39 3 3
Ephrin B2/EPHB4 0.01 0.083 -10000 0 -0.3 13 13
Ephrin B/EPHB2/Intersectin/N-WASP -0.016 0.11 -10000 0 -0.29 23 23
CDC42 0.034 0.019 -10000 0 -0.21 1 1
RAS family/GTP -0.056 0.12 -10000 0 -0.38 14 14
PTK2 0.12 0.23 0.59 40 -10000 0 40
MAP4K4 -0.061 0.13 0.31 2 -0.31 35 37
SRC 0.012 0.062 -10000 0 -0.48 3 3
KALRN 0.037 0.004 -10000 0 -10000 0 0
Intersectin/N-WASP 0.048 0.032 -10000 0 -0.35 1 1
neuron projection morphogenesis -0.018 0.15 0.4 9 -0.38 10 19
MAP2K1 -0.008 0.1 -10000 0 -0.4 6 6
WASL 0.033 0.036 -10000 0 -0.48 1 1
Ephrin B1/EPHB1-2/NCK1 -0.023 0.15 -10000 0 -0.3 34 34
cell migration 0.017 0.14 0.24 11 -0.44 6 17
NRAS 0.021 0.079 -10000 0 -0.33 9 9
SYNJ1 0.033 0.13 -10000 0 -0.26 23 23
PXN 0.037 0.004 -10000 0 -10000 0 0
TF 0.015 0.13 0.18 58 -0.27 19 77
HRAS/GTP -0.04 0.13 -10000 0 -0.42 12 12
Ephrin B1/EPHB1-2 -0.029 0.14 -10000 0 -0.31 30 30
cell adhesion mediated by integrin -0.025 0.13 0.26 14 -0.2 55 69
RAC1 0.033 0.012 -10000 0 -10000 0 0
mol:GTP -0.04 0.14 -10000 0 -0.31 34 34
RAC1-CDC42/GTP -0.076 0.14 -10000 0 -0.4 24 24
RASA1 0.025 0.072 -10000 0 -0.43 5 5
RAC1-CDC42/GDP -0.018 0.13 0.26 4 -0.37 12 16
ruffle organization -0.017 0.16 0.36 12 -0.43 10 22
NCK1 0.027 0.07 -10000 0 -0.48 4 4
receptor internalization 0.015 0.12 0.18 18 -0.45 2 20
Ephrin B/EPHB2/KALRN 0.017 0.12 -10000 0 -0.27 24 24
ROCK1 -0.027 0.11 0.19 1 -0.28 31 32
RAS family/GDP -0.06 0.1 -10000 0 -0.35 13 13
Rac1/GTP -0.052 0.12 -10000 0 -0.43 11 11
Ephrin B/EPHB1/Src/Paxillin -0.018 0.11 -10000 0 -0.3 20 20
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.055 0.14 -10000 0 -0.42 23 23
CRKL -0.056 0.15 -10000 0 -0.43 24 24
HRAS -0.031 0.15 -10000 0 -0.4 23 23
mol:PIP3 -0.037 0.15 -10000 0 -0.4 23 23
SPRED1 0.016 0.098 -10000 0 -0.48 8 8
SPRED2 0.033 0.05 -10000 0 -0.48 2 2
GAB1 -0.055 0.16 -10000 0 -0.46 23 23
FOXO3 -0.061 0.2 0.28 1 -0.44 36 37
AKT1 -0.068 0.21 0.29 1 -0.48 36 37
BAD -0.063 0.2 0.28 1 -0.46 33 34
megakaryocyte differentiation -0.098 0.18 -10000 0 -0.44 33 33
GSK3B -0.062 0.19 0.28 1 -0.46 31 32
RAF1 -0.028 0.12 -10000 0 -0.36 13 13
SHC1 0.036 0.007 -10000 0 -10000 0 0
STAT3 -0.049 0.15 -10000 0 -0.45 21 21
STAT1 -0.14 0.37 -10000 0 -1.1 25 25
HRAS/SPRED1 -0.02 0.14 -10000 0 -0.39 15 15
cell proliferation -0.048 0.15 -10000 0 -0.44 23 23
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
TEC 0.037 0.006 -10000 0 -10000 0 0
RPS6KB1 -0.051 0.17 -10000 0 -0.45 27 27
HRAS/SPRED2 -0.016 0.14 -10000 0 -0.37 15 15
LYN/TEC/p62DOK -0.015 0.16 -10000 0 -0.42 22 22
MAPK3 -0.018 0.097 -10000 0 -0.3 10 10
STAP1 -0.051 0.16 -10000 0 -0.45 24 24
GRAP2 0.021 0.082 -10000 0 -0.4 7 7
JAK2 -0.1 0.3 -10000 0 -0.88 24 24
STAT1 (dimer) -0.13 0.36 -10000 0 -1 25 25
mol:Gleevec 0.002 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.03 0.19 -10000 0 -0.48 24 24
actin filament polymerization -0.049 0.15 -10000 0 -0.44 24 24
LYN 0.032 0.014 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.074 0.22 -10000 0 -0.62 25 25
PIK3R1 0.029 0.061 -10000 0 -0.48 3 3
CBL/CRKL/GRB2 -0.027 0.16 -10000 0 -0.41 22 22
PI3K -0.025 0.18 -10000 0 -0.43 26 26
PTEN 0.031 0.051 -10000 0 -0.48 2 2
SCF/KIT/EPO/EPOR -0.13 0.45 -10000 0 -1.4 23 23
MAPK8 -0.049 0.15 -10000 0 -0.45 23 23
STAT3 (dimer) -0.047 0.15 -10000 0 -0.44 21 21
positive regulation of transcription -0.013 0.081 -10000 0 -0.25 7 7
mol:GDP -0.034 0.16 -10000 0 -0.43 22 22
PIK3C2B -0.052 0.16 -10000 0 -0.45 23 23
CBL/CRKL -0.04 0.15 -10000 0 -0.42 23 23
FER -0.057 0.16 -10000 0 -0.46 24 24
SH2B3 -0.051 0.16 -10000 0 -0.45 24 24
PDPK1 -0.036 0.14 -10000 0 -0.37 24 24
SNAI2 -0.061 0.16 -10000 0 -0.47 25 25
positive regulation of cell proliferation -0.088 0.26 -10000 0 -0.76 24 24
KITLG 0.008 0.091 -10000 0 -0.3 14 14
cell motility -0.088 0.26 -10000 0 -0.76 24 24
PTPN6 0.039 0.011 -10000 0 -10000 0 0
EPOR -0.007 0.15 -10000 0 -0.9 2 2
STAT5A (dimer) -0.072 0.22 -10000 0 -0.63 25 25
SOCS1 0.029 0.063 -10000 0 -0.42 4 4
cell migration 0.051 0.15 0.43 24 -10000 0 24
SOS1 0.037 0.003 -10000 0 -10000 0 0
EPO 0.026 0.033 -10000 0 -0.21 2 2
VAV1 0.003 0.12 -10000 0 -0.42 16 16
GRB10 -0.061 0.16 -10000 0 -0.45 23 23
PTPN11 0.033 0.052 -10000 0 -0.38 3 3
SCF/KIT -0.051 0.16 -10000 0 -0.47 24 24
GO:0007205 0.003 0.008 -10000 0 -10000 0 0
MAP2K1 -0.024 0.1 -10000 0 -0.3 9 9
CBL 0.037 0.005 -10000 0 -10000 0 0
KIT -0.14 0.45 -10000 0 -1.4 24 24
MAP2K2 -0.024 0.099 -10000 0 -0.31 8 8
SHC/Grb2/SOS1 -0.008 0.17 -10000 0 -0.44 21 21
STAT5A -0.077 0.23 -10000 0 -0.65 25 25
GRB2 0.036 0.008 -10000 0 -10000 0 0
response to radiation -0.059 0.16 -10000 0 -0.46 25 25
SHC/GRAP2 0.04 0.064 -10000 0 -0.35 5 5
PTPRO -0.1 0.18 -10000 0 -0.46 33 33
SH2B2 -0.051 0.16 -10000 0 -0.45 24 24
DOK1 0.034 0.039 -10000 0 -0.35 2 2
MATK -0.052 0.15 -10000 0 -0.44 24 24
CREBBP 0.017 0.07 -10000 0 -0.28 3 3
BCL2 -0.26 0.47 -10000 0 -1.3 26 26
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.016 0.16 0.25 4 -0.42 18 22
FYN -0.056 0.19 0.38 1 -0.56 19 20
LAT/GRAP2/SLP76 -0.047 0.19 0.24 1 -0.45 26 27
IKBKB 0.033 0.012 -10000 0 -10000 0 0
AKT1 -0.059 0.15 0.23 1 -0.37 28 29
B2M 0.016 0.087 -10000 0 -0.35 10 10
IKBKG -0.015 0.054 0.14 3 -0.14 8 11
MAP3K8 0.008 0.1 -10000 0 -0.32 18 18
mol:Ca2+ -0.012 0.02 0.089 2 -0.064 9 11
integrin-mediated signaling pathway 0.037 0.048 -10000 0 -0.3 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.079 0.21 0.26 1 -0.54 26 27
TRPV6 0.04 0.25 1.2 10 -10000 0 10
CD28 0 0.12 -10000 0 -0.34 21 21
SHC1 -0.047 0.18 0.24 4 -0.47 22 26
receptor internalization -0.049 0.18 -10000 0 -0.5 23 23
PRF1 -0.058 0.22 -10000 0 -0.8 13 13
KRAS 0.033 0.04 -10000 0 -0.35 2 2
GRB2 0.036 0.008 -10000 0 -10000 0 0
COT/AKT1 -0.047 0.13 0.22 1 -0.31 30 31
LAT -0.055 0.18 0.24 1 -0.5 21 22
EntrezGene:6955 -0.001 0.003 -10000 0 -0.015 3 3
CD3D 0 0.13 -10000 0 -0.4 18 18
CD3E 0.035 0.019 -10000 0 -0.22 1 1
CD3G -0.024 0.15 -10000 0 -0.36 33 33
RASGRP2 0.002 0.035 -10000 0 -0.16 7 7
RASGRP1 -0.031 0.16 0.25 3 -0.38 23 26
HLA-A 0.001 0.13 -10000 0 -0.4 18 18
RASSF5 0.023 0.071 -10000 0 -0.31 8 8
RAP1A/GTP/RAPL 0.038 0.048 -10000 0 -0.3 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.062 0.14 7 -0.13 10 17
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.04 0.07 -10000 0 -0.2 23 23
PRKCA 0.006 0.11 0.16 12 -0.26 15 27
GRAP2 0.021 0.082 -10000 0 -0.4 7 7
mol:IP3 -0.049 0.13 -10000 0 -0.38 19 19
EntrezGene:6957 -0.001 0.004 0.01 1 -0.017 3 4
TCR/CD3/MHC I/CD8 -0.042 0.16 -10000 0 -0.39 27 27
ORAI1 -0.036 0.21 -10000 0 -0.98 10 10
CSK -0.047 0.17 0.25 1 -0.45 24 25
B7 family/CD28 -0.058 0.23 -10000 0 -0.52 27 27
CHUK 0.031 0.05 -10000 0 -0.48 2 2
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.059 0.2 -10000 0 -0.5 25 25
PTPN6 -0.056 0.18 -10000 0 -0.46 24 24
VAV1 -0.065 0.19 0.24 1 -0.5 26 27
Monovalent TCR/CD3 -0.032 0.15 -10000 0 -0.44 22 22
CBL 0.037 0.005 -10000 0 -10000 0 0
LCK -0.062 0.21 0.36 1 -0.55 23 24
PAG1 -0.039 0.18 -10000 0 -0.44 25 25
RAP1A 0.036 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.06 0.2 0.26 1 -0.48 27 28
CD80 0.027 0.047 -10000 0 -0.21 8 8
CD86 -0.047 0.18 -10000 0 -0.38 43 43
PDK1/CARD11/BCL10/MALT1 -0.042 0.089 -10000 0 -0.24 23 23
HRAS 0.034 0.039 -10000 0 -0.35 2 2
GO:0035030 -0.074 0.17 -10000 0 -0.43 28 28
CD8A -0.001 0.004 0.01 1 -0.015 4 5
CD8B -0.001 0.004 0.012 1 -0.013 9 10
PTPRC -0.023 0.15 -10000 0 -0.37 31 31
PDK1/PKC theta -0.061 0.18 0.28 2 -0.45 25 27
CSK/PAG1 -0.036 0.17 -10000 0 -0.48 18 18
SOS1 0.037 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.01 0.12 -10000 0 -0.38 16 16
GRAP2/SLP76 -0.049 0.21 0.26 1 -0.5 27 28
STIM1 0.003 0.12 1.2 2 -10000 0 2
RAS family/GTP 0.009 0.077 0.18 3 -0.18 6 9
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.051 0.19 -10000 0 -0.53 23 23
mol:DAG -0.052 0.11 -10000 0 -0.34 20 20
RAP1A/GDP 0.01 0.031 0.08 2 -0.066 3 5
PLCG1 0.019 0.019 -10000 0 -10000 0 0
CD247 -0.001 0.003 -10000 0 -0.015 3 3
cytotoxic T cell degranulation -0.056 0.21 -10000 0 -0.76 13 13
RAP1A/GTP 0.002 0.014 -10000 0 -0.06 7 7
mol:PI-3-4-5-P3 -0.064 0.17 0.25 1 -0.44 26 27
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.06 0.16 -10000 0 -0.49 19 19
NRAS 0.021 0.079 -10000 0 -0.33 9 9
ZAP70 0.031 0.053 -10000 0 -0.39 3 3
GRB2/SOS1 0.053 0.013 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.059 0.19 -10000 0 -0.47 25 25
MALT1 0.022 0.039 -10000 0 -0.48 1 1
TRAF6 0.037 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0 0.006 0.021 1 -0.018 6 7
CARD11 -0.01 0.099 -10000 0 -0.22 35 35
PRKCB -0.04 0.076 -10000 0 -0.23 22 22
PRKCE 0.009 0.12 0.17 14 -0.26 15 29
PRKCQ -0.067 0.2 0.35 1 -0.5 26 27
LCP2 -0.024 0.15 -10000 0 -0.37 32 32
BCL10 0.034 0.036 -10000 0 -0.48 1 1
regulation of survival gene product expression -0.05 0.13 0.22 1 -0.32 28 29
IKK complex 0.024 0.069 0.13 30 -0.11 4 34
RAS family/GDP -0.005 0.015 -10000 0 -0.056 6 6
MAP3K14 -0.038 0.1 0.19 1 -0.26 23 24
PDPK1 -0.053 0.14 0.23 1 -0.35 27 28
TCR/CD3/MHC I/CD8/Fyn -0.05 0.18 -10000 0 -0.5 22 22
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.051 0.041 0.22 3 -10000 0 3
AES 0.048 0.034 0.2 2 -10000 0 2
FBXW11 0.037 0.005 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.05 0.02 -10000 0 -10000 0 0
SMAD4 0.017 0.062 -10000 0 -0.48 3 3
DKK2 -0.029 0.15 -10000 0 -0.31 41 41
TLE1 0.018 0.13 0.19 5 -0.47 13 18
MACF1 0.037 0.005 -10000 0 -10000 0 0
CTNNB1 0.038 0.09 0.35 3 -10000 0 3
WIF1 -0.024 0.11 -10000 0 -0.21 53 53
beta catenin/RanBP3 0.086 0.18 0.41 42 -10000 0 42
KREMEN2 -0.064 0.17 -10000 0 -0.31 63 63
DKK1 -0.095 0.19 -10000 0 -0.32 80 80
beta catenin/beta TrCP1 0.055 0.091 0.35 3 -10000 0 3
FZD1 0.036 0.008 -10000 0 -10000 0 0
AXIN2 -0.26 0.62 0.68 7 -1.5 40 47
AXIN1 0.03 0.063 -10000 0 -0.41 4 4
RAN 0.037 0.006 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.042 0.089 -10000 0 -0.56 3 3
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.067 0.21 -10000 0 -0.57 17 17
Axin1/APC/GSK3 0.062 0.082 0.27 5 -0.37 1 6
Axin1/APC/GSK3/beta catenin/Macf1 0.026 0.1 0.35 1 -0.47 2 3
HNF1A 0.013 0.035 0.16 6 -10000 0 6
CTBP1 0.049 0.036 0.22 2 -10000 0 2
MYC 0.034 0.45 0.61 41 -1.6 10 51
RANBP3 0.035 0.035 -10000 0 -0.47 1 1
DKK2/LRP6/Kremen 2 -0.046 0.15 -10000 0 -0.31 43 43
NKD1 -0.15 0.21 -10000 0 -0.35 103 103
TCF4 0.033 0.048 0.21 1 -0.2 2 3
TCF3 0.041 0.068 0.2 4 -0.44 3 7
WNT1/LRP6/FZD1/Axin1 0.083 0.054 -10000 0 -0.27 3 3
Ran/GTP 0.028 0.006 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.044 0.24 0.47 41 -0.45 5 46
LEF1 0.016 0.12 0.21 1 -0.32 20 21
DVL1 0.037 0.084 -10000 0 -0.5 3 3
CSNK2A1 0.031 0.015 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.052 0.17 -10000 0 -0.56 10 10
DKK1/LRP6/Kremen 2 -0.088 0.18 -10000 0 -0.33 56 56
LRP6 0.035 0.018 -10000 0 -0.21 1 1
CSNK1A1 0.052 0.04 0.21 5 -10000 0 5
NLK 0.03 0.022 -10000 0 -0.21 1 1
CCND1 -0.052 0.21 -10000 0 -1.3 4 4
WNT1 0.037 0.005 -10000 0 -10000 0 0
GSK3A 0.037 0.004 -10000 0 -10000 0 0
GSK3B 0.035 0.036 -10000 0 -0.48 1 1
FRAT1 0.031 0.05 -10000 0 -0.48 2 2
PPP2R5D 0.11 0.12 0.29 52 -0.23 2 54
APC 0.014 0.08 0.36 1 -0.28 10 11
WNT1/LRP6/FZD1 0.043 0.041 -10000 0 -10000 0 0
CREBBP 0.047 0.052 0.2 5 -0.49 1 6
Visual signal transduction: Rods

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
mol:K + 0.032 0.04 -10000 0 -0.35 2 2
GNAT1/GTP 0.024 0.025 -10000 0 -0.14 5 5
Metarhodopsin II/Arrestin 0.041 0.044 -10000 0 -0.3 2 2
PDE6G/GNAT1/GTP 0.043 0.029 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.031 0.037 -10000 0 -0.21 5 5
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.051 0.15 -10000 0 -0.28 50 50
mol:Na + -0.035 0.14 -10000 0 -0.37 12 12
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.009 0.12 -10000 0 -0.31 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.028 0.15 -10000 0 -0.38 12 12
CNGB1 0.037 0.003 -10000 0 -10000 0 0
RDH5 0.019 0.09 -10000 0 -0.39 9 9
SAG 0.023 0.068 -10000 0 -0.26 10 10
mol:Ca2+ -0.069 0.13 0.33 5 -0.37 12 17
Na + (4 Units) -0.038 0.14 -10000 0 -0.36 12 12
RGS9 0.028 0.051 -10000 0 -0.26 6 6
GNB1/GNGT1 -0.1 0.18 -10000 0 -0.35 64 64
GNAT1/GDP 0.019 0.11 -10000 0 -0.26 21 21
GUCY2D 0.028 0.023 -10000 0 -0.21 1 1
GNGT1 -0.16 0.23 -10000 0 -0.38 102 102
GUCY2F 0.015 0.1 -10000 0 -0.46 10 10
GNB5 -0.003 0.13 -10000 0 -0.37 20 20
mol:GMP (4 units) -0.009 0.099 -10000 0 -0.27 22 22
mol:11-cis-retinal 0.019 0.09 -10000 0 -0.39 9 9
mol:cGMP 0.03 0.1 -10000 0 -0.28 17 17
GNB1 0.038 0 -10000 0 -10000 0 0
Rhodopsin 0.04 0.07 -10000 0 -0.35 6 6
SLC24A1 0.032 0.04 -10000 0 -0.35 2 2
CNGA1 -0.082 0.2 -10000 0 -0.36 64 64
Metarhodopsin II 0.024 0.002 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.051 0.085 -10000 0 -0.28 8 8
RGS9BP 0.004 0.11 -10000 0 -0.3 21 21
Metarhodopsin II/Transducin -0.064 0.12 -10000 0 -0.24 64 64
GCAP Family/Ca ++ 0.05 0.074 -10000 0 -0.28 8 8
PDE6A/B -0.008 0.13 -10000 0 -0.35 23 23
mol:Pi 0.009 0.12 -10000 0 -0.31 21 21
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.068 0.15 -10000 0 -0.27 65 65
PDE6B 0.021 0.076 -10000 0 -0.28 11 11
PDE6A -0.027 0.16 -10000 0 -0.36 35 35
PDE6G 0.035 0.018 -10000 0 -0.21 1 1
RHO 0.037 0.004 -10000 0 -10000 0 0
PDE6 -0.013 0.15 -10000 0 -0.27 41 41
GUCA1A 0.034 0.024 -10000 0 -0.21 2 2
GC2/GCAP Family 0.057 0.11 -10000 0 -0.29 17 17
GUCA1C 0.013 0.1 -10000 0 -0.39 12 12
GUCA1B 0.031 0.046 -10000 0 -0.28 4 4
FOXM1 transcription factor network

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
NFATC3 -0.08 0.42 -9999 0 -1.2 14 14
PLK1 0.03 0.16 -9999 0 -1.3 3 3
BIRC5 -0.008 0.26 -9999 0 -1.1 10 10
HSPA1B -0.079 0.41 -9999 0 -1.1 19 19
MAP2K1 0.029 0.05 -9999 0 -10000 0 0
BRCA2 -0.039 0.45 -9999 0 -1.2 15 15
FOXM1 -0.13 0.59 -9999 0 -1.6 19 19
XRCC1 -0.078 0.41 -9999 0 -1.1 18 18
FOXM1B/p19 -0.13 0.46 -9999 0 -1.2 20 20
Cyclin D1/CDK4 -0.08 0.4 -9999 0 -0.99 21 21
CDC2 -0.087 0.44 -9999 0 -1.2 18 18
TGFA -0.11 0.4 -9999 0 -0.99 21 21
SKP2 -0.081 0.43 -9999 0 -1.2 16 16
CCNE1 0.029 0.058 -9999 0 -0.32 5 5
CKS1B -0.074 0.41 -9999 0 -1.1 17 17
RB1 -0.029 0.23 -9999 0 -1 5 5
FOXM1C/SP1 -0.097 0.48 -9999 0 -1.3 20 20
AURKB -0.18 0.44 -9999 0 -0.92 51 51
CENPF -0.084 0.43 -9999 0 -1.2 16 16
CDK4 0.032 0.028 -9999 0 -10000 0 0
MYC -0.09 0.37 -9999 0 -0.95 20 20
CHEK2 0.027 0.063 -9999 0 -0.53 1 1
ONECUT1 -0.094 0.41 -9999 0 -1 21 21
CDKN2A -0.039 0.15 -9999 0 -0.32 44 44
LAMA4 -0.08 0.42 -9999 0 -1.1 17 17
FOXM1B/HNF6 -0.12 0.48 -9999 0 -1.3 21 21
FOS -0.2 0.56 -9999 0 -1.2 44 44
SP1 0.034 0.022 -9999 0 -0.21 1 1
CDC25B -0.11 0.5 -9999 0 -1.2 29 29
response to radiation 0.004 0.028 -9999 0 -10000 0 0
CENPB -0.06 0.42 -9999 0 -1.2 14 14
CENPA -0.082 0.42 -9999 0 -1.2 17 17
NEK2 -0.08 0.43 -9999 0 -1.2 18 18
HIST1H2BA -0.08 0.41 -9999 0 -1.1 16 16
CCNA2 0.021 0.094 -9999 0 -0.49 7 7
EP300 0.02 0.087 -9999 0 -0.44 7 7
CCNB1/CDK1 -0.11 0.5 -9999 0 -1.6 14 14
CCNB2 -0.088 0.43 -9999 0 -1.2 18 18
CCNB1 -0.092 0.46 -9999 0 -1.3 17 17
ETV5 -0.11 0.45 -9999 0 -1.2 20 20
ESR1 -0.089 0.44 -9999 0 -1.2 17 17
CCND1 -0.096 0.4 -9999 0 -1 21 21
GSK3A 0.029 0.046 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.035 0.1 -9999 0 -0.3 13 13
CDK2 0.023 0.074 -9999 0 -0.29 10 10
G2/M transition of mitotic cell cycle 0.005 0.034 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.092 0.46 -9999 0 -1.2 19 19
GAS1 -0.24 0.59 -9999 0 -1.2 49 49
MMP2 -0.1 0.45 -9999 0 -1.2 21 21
RB1/FOXM1C -0.11 0.39 -9999 0 -1.1 18 18
CREBBP 0.034 0.036 -9999 0 -0.48 1 1
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.013 0.14 -9999 0 -0.33 29 29
PLK4 0.031 0.053 -9999 0 -0.39 3 3
regulation of centriole replication -0.016 0.099 -9999 0 -0.36 14 14
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.011 0.12 -10000 0 -0.38 15 15
EPHB2 0.006 0.12 -10000 0 -0.48 12 12
Syndecan-2/TACI 0.008 0.068 -10000 0 -0.28 10 10
LAMA1 0.027 0.017 -10000 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 0.026 0.11 -10000 0 -0.25 20 20
HRAS 0.034 0.039 -10000 0 -0.35 2 2
Syndecan-2/CASK -0.005 0.062 -10000 0 -0.28 10 10
ITGA5 0.027 0.049 -10000 0 -0.21 9 9
BAX -0.012 0.096 -10000 0 -1.1 1 1
EPB41 0.029 0.046 -10000 0 -0.28 4 4
positive regulation of cell-cell adhesion 0.013 0.063 -10000 0 -0.25 10 10
LAMA3 0.007 0.08 -10000 0 -0.27 14 14
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.009 0.13 -10000 0 -0.32 27 27
Syndecan-2/MMP2 0.004 0.1 -10000 0 -0.32 15 15
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.034 0.085 -10000 0 -0.35 9 9
dendrite morphogenesis -0.003 0.093 -10000 0 -0.28 20 20
Syndecan-2/GM-CSF -0.042 0.13 -10000 0 -0.3 34 34
determination of left/right symmetry -0.005 0.074 -10000 0 -0.28 13 13
Syndecan-2/PKC delta 0.015 0.07 -10000 0 -0.28 10 10
GNB2L1 0.035 0.035 -10000 0 -0.48 1 1
MAPK3 -0.026 0.14 0.2 27 -0.29 34 61
MAPK1 -0.019 0.14 0.2 26 -0.28 32 58
Syndecan-2/RACK1 0.027 0.076 -10000 0 -0.26 11 11
NF1 0.036 0.008 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.005 0.074 -10000 0 -0.28 13 13
ITGA2 0.01 0.11 -10000 0 -0.42 13 13
MAPK8 -0.005 0.068 -10000 0 -0.3 10 10
Syndecan-2/alpha2/beta1 Integrin 0.04 0.099 -10000 0 -0.25 15 15
Syndecan-2/Kininogen 0 0.09 -10000 0 -0.3 15 15
ITGB1 0.036 0.017 -10000 0 -0.21 1 1
SRC 0.012 0.066 -10000 0 -0.26 6 6
Syndecan-2/CASK/Protein 4.1 0.01 0.066 -10000 0 -0.25 11 11
extracellular matrix organization 0.014 0.07 -10000 0 -0.28 10 10
actin cytoskeleton reorganization -0.011 0.12 -10000 0 -0.37 15 15
Syndecan-2/Caveolin-2/Ras 0.004 0.11 -10000 0 -0.32 16 16
Syndecan-2/Laminin alpha3 -0.005 0.08 -10000 0 -0.28 13 13
Syndecan-2/RasGAP 0.037 0.085 -10000 0 -0.26 12 12
alpha5/beta1 Integrin 0.045 0.042 -10000 0 -10000 0 0
PRKCD 0.037 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer -0.003 0.094 -10000 0 -0.28 20 20
GO:0007205 0.002 0.011 -10000 0 -0.14 1 1
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.009 0.058 -10000 0 -0.26 6 6
RHOA 0.037 0.005 -10000 0 -10000 0 0
SDCBP 0.031 0.021 -10000 0 -0.21 1 1
TNFRSF13B 0.029 0.016 -10000 0 -10000 0 0
RASA1 0.025 0.072 -10000 0 -0.43 5 5
alpha2/beta1 Integrin 0.034 0.085 -10000 0 -0.35 9 9
Syndecan-2/Synbindin 0.014 0.07 -10000 0 -0.28 10 10
TGFB1 0.036 0.017 -10000 0 -0.21 1 1
CASP3 0.029 0.093 0.2 31 -0.26 11 42
FN1 -0.016 0.13 -10000 0 -0.3 34 34
Syndecan-2/IL8 -0.071 0.15 -10000 0 -0.32 47 47
SDC2 -0.005 0.075 -10000 0 -0.28 13 13
KNG1 0.005 0.11 -10000 0 -0.3 20 20
Syndecan-2/Neurofibromin 0.015 0.067 -10000 0 -0.28 9 9
TRAPPC4 0.037 0.005 -10000 0 -10000 0 0
CSF2 -0.075 0.18 -10000 0 -0.33 65 65
Syndecan-2/TGFB1 0.014 0.07 -10000 0 -0.28 10 10
Syndecan-2/Syntenin/PI-4-5-P2 0.013 0.064 -10000 0 -0.25 10 10
Syndecan-2/Ezrin 0.014 0.063 -10000 0 -0.25 10 10
PRKACA 0.035 0.092 0.2 35 -0.26 8 43
angiogenesis -0.071 0.15 -10000 0 -0.32 47 47
MMP2 0.005 0.11 -10000 0 -0.3 21 21
IL8 -0.14 0.22 -10000 0 -0.36 94 94
calcineurin-NFAT signaling pathway 0.008 0.068 -10000 0 -0.28 10 10
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.028 0.14 -10000 0 -0.25 44 44
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.031 0.05 -10000 0 -0.48 2 2
STAT1 (dimer)/Cbp/p300 -0.053 0.16 0.32 1 -0.36 26 27
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.022 0.087 -10000 0 -0.31 5 5
antigen processing and presentation of peptide antigen via MHC class I -0.069 0.12 -10000 0 -0.28 28 28
CaM/Ca2+ -0.015 0.14 -10000 0 -0.24 43 43
RAP1A 0.036 0.008 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.053 0.13 -10000 0 -0.26 52 52
AKT1 -0.06 0.11 -10000 0 -0.36 6 6
MAP2K1 -0.064 0.11 0.29 1 -0.28 10 11
MAP3K11 -0.056 0.12 0.3 1 -0.25 40 41
IFNGR1 0.016 0.048 -10000 0 -0.49 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.004 0.1 -10000 0 -0.4 4 4
Rap1/GTP -0.047 0.098 -10000 0 -0.32 5 5
CRKL/C3G 0.047 0.043 -10000 0 -0.35 2 2
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.032 0.14 -10000 0 -0.26 41 41
CEBPB -0.019 0.17 0.31 1 -0.52 8 9
STAT3 0.036 0.009 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.001 0.22 -10000 0 -1.2 5 5
STAT1 -0.065 0.13 0.3 1 -0.26 50 51
CALM1 0.034 0.012 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.11 0.2 -10000 0 -0.34 84 84
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.051 0.13 0.31 1 -0.27 26 27
CEBPB/PTGES2/Cbp/p300 -0.015 0.12 -10000 0 -0.35 8 8
mol:Ca2+ -0.03 0.14 -10000 0 -0.25 44 44
MAPK3 -0.057 0.16 -10000 0 -0.82 5 5
STAT1 (dimer) -0.087 0.17 -10000 0 -0.4 26 26
MAPK1 -0.078 0.2 -10000 0 -0.78 12 12
JAK2 0.002 0.084 -10000 0 -0.29 13 13
PIK3R1 0.029 0.061 -10000 0 -0.48 3 3
JAK1 0.016 0.048 -10000 0 -0.48 1 1
CAMK2D 0.034 0.036 -10000 0 -0.48 1 1
DAPK1 -0.013 0.14 0.26 2 -0.43 9 11
SMAD7 -0.031 0.066 0.14 1 -0.17 14 15
CBL/CRKL/C3G -0.032 0.13 0.31 1 -0.36 5 6
PI3K -0.014 0.14 -10000 0 -0.28 21 21
IFNG -0.11 0.2 -10000 0 -0.34 84 84
apoptosis -0.034 0.14 -10000 0 -0.42 14 14
CAMK2G 0.036 0.008 -10000 0 -10000 0 0
STAT3 (dimer) 0.035 0.009 -10000 0 -10000 0 0
CAMK2A 0.036 0.018 -10000 0 -0.21 1 1
CAMK2B 0.025 0.052 -10000 0 -0.26 6 6
FRAP1 -0.065 0.099 -10000 0 -0.34 7 7
PRKCD -0.062 0.11 0.28 1 -0.36 6 7
RAP1B 0.037 0.006 -10000 0 -10000 0 0
negative regulation of cell growth -0.069 0.12 -10000 0 -0.28 28 28
PTPN2 0.027 0.017 -10000 0 -10000 0 0
EP300 0.02 0.087 -10000 0 -0.44 7 7
IRF1 -0.08 0.16 0.27 2 -0.48 19 21
STAT1 (dimer)/PIASy -0.053 0.13 0.3 1 -0.31 15 16
SOCS1 0.011 0.2 -10000 0 -1.3 5 5
mol:GDP -0.033 0.12 0.29 1 -0.35 5 6
CASP1 -0.068 0.12 -10000 0 -0.26 46 46
PTGES2 0.037 0.006 -10000 0 -10000 0 0
IRF9 -0.004 0.059 0.15 1 -0.17 1 2
mol:PI-3-4-5-P3 -0.038 0.13 -10000 0 -0.27 21 21
RAP1/GDP -0.029 0.11 -10000 0 -0.32 5 5
CBL -0.056 0.12 0.3 1 -0.25 40 41
MAP3K1 -0.058 0.12 0.3 1 -0.25 32 33
PIAS1 0.035 0.009 -10000 0 -10000 0 0
PIAS4 0.035 0.018 -10000 0 -0.21 1 1
antigen processing and presentation of peptide antigen via MHC class II -0.069 0.12 -10000 0 -0.28 28 28
PTPN11 -0.058 0.12 -10000 0 -0.25 44 44
CREBBP 0.034 0.036 -10000 0 -0.48 1 1
RAPGEF1 0.036 0.017 -10000 0 -0.21 1 1
Signaling events mediated by the Hedgehog family

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
TGFB2 0.016 0.12 -10000 0 -0.55 6 6
IHH 0.027 0.094 -10000 0 -0.43 7 7
SHH Np/Cholesterol/GAS1 -0.074 0.14 -10000 0 -0.31 47 47
LRPAP1 0.036 0.007 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.074 0.14 0.31 47 -10000 0 47
SMO/beta Arrestin2 0.007 0.12 -10000 0 -0.4 9 9
SMO -0.007 0.12 -10000 0 -0.34 20 20
AKT1 -0.023 0.16 -10000 0 -0.41 25 25
ARRB2 0.026 0.038 -10000 0 -0.48 1 1
BOC 0.027 0.056 -10000 0 -0.24 8 8
ADRBK1 0.037 0.004 -10000 0 -10000 0 0
heart looping -0.007 0.11 -10000 0 -0.33 20 20
STIL -0.002 0.11 0.35 2 -0.3 8 10
DHH N/PTCH2 0.053 0.011 -10000 0 -10000 0 0
DHH N/PTCH1 0.029 0.075 -10000 0 -0.3 9 9
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
DHH 0.037 0.005 -10000 0 -10000 0 0
PTHLH 0.004 0.16 -10000 0 -0.87 6 6
determination of left/right symmetry -0.007 0.11 -10000 0 -0.33 20 20
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
skeletal system development 0.004 0.16 -10000 0 -0.86 6 6
IHH N/Hhip -0.013 0.16 -10000 0 -0.4 28 28
DHH N/Hhip -0.004 0.13 -10000 0 -0.35 25 25
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.007 0.11 -10000 0 -0.33 20 20
pancreas development -0.034 0.17 -10000 0 -0.41 34 34
HHAT -0.003 0.13 -10000 0 -0.41 19 19
PI3K 0.047 0.049 -10000 0 -0.35 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.12 0.2 -10000 0 -0.33 92 92
somite specification -0.007 0.11 -10000 0 -0.33 20 20
SHH Np/Cholesterol/PTCH1 -0.006 0.093 -10000 0 -0.25 24 24
SHH Np/Cholesterol/PTCH2 0.009 0.083 -10000 0 -0.28 15 15
SHH Np/Cholesterol/Megalin 0.008 0.083 -10000 0 -0.28 15 15
SHH -0.012 0.098 -10000 0 -0.36 15 15
catabolic process 0.008 0.077 -10000 0 -0.33 9 9
SMO/Vitamin D3 -0.016 0.11 -10000 0 -0.33 14 14
SHH Np/Cholesterol/Hhip -0.031 0.13 -10000 0 -0.31 35 35
LRP2 0.035 0.024 -10000 0 -0.21 2 2
receptor-mediated endocytosis -0.016 0.11 -10000 0 -0.34 11 11
SHH Np/Cholesterol/BOC 0.004 0.085 -10000 0 -0.28 15 15
SHH Np/Cholesterol/CDO 0.008 0.083 -10000 0 -0.28 15 15
mesenchymal cell differentiation 0.031 0.13 0.3 35 -10000 0 35
mol:Vitamin D3 0.005 0.11 0.36 2 -0.28 12 14
IHH N/PTCH2 0.046 0.062 -10000 0 -0.32 5 5
CDON 0.035 0.024 -10000 0 -0.21 2 2
IHH N/PTCH1 0.028 0.083 -10000 0 -0.34 9 9
Megalin/LRPAP1 0.052 0.022 -10000 0 -10000 0 0
PTCH2 0.037 0.006 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.004 0.077 -10000 0 -0.27 15 15
PTCH1 0.008 0.078 -10000 0 -0.33 9 9
HHIP -0.034 0.17 -10000 0 -0.41 34 34
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.018 0.024 -10000 0 -0.29 1 1
ARNO/beta Arrestin1-2 -0.003 0.09 -10000 0 -0.24 21 21
EGFR 0.016 0.088 -10000 0 -0.42 8 8
EPHA2 0.013 0.087 -10000 0 -0.28 15 15
USP6 0.029 0.016 -10000 0 -10000 0 0
IQSEC1 0.035 0.018 -10000 0 -0.21 1 1
EGFR/EGFR/EGF/EGF -0.054 0.15 -10000 0 -0.35 33 33
ARRB2 0.009 0.048 -10000 0 -0.36 3 3
mol:GTP 0.001 0.02 0.11 2 -10000 0 2
ARRB1 0.017 0.1 -10000 0 -0.45 9 9
FBXO8 0.036 0.008 -10000 0 -10000 0 0
TSHR 0.031 0.037 -10000 0 -0.48 1 1
EGF -0.094 0.19 -10000 0 -0.32 79 79
somatostatin receptor activity 0 0 0.001 12 -0.001 17 29
ARAP2 0 0 0 12 0 13 25
mol:GDP 0.001 0.076 0.15 4 -0.24 11 15
mol:PI-3-4-5-P3 0 0 0 11 0 15 26
ITGA2B 0.036 0.007 -10000 0 -10000 0 0
ARF6 0.029 0.051 -10000 0 -0.48 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.048 0.097 -10000 0 -0.29 11 11
ADAP1 0 0 0 7 0 6 13
KIF13B 0.026 0.038 -10000 0 -0.48 1 1
HGF/MET 0.044 0.057 -10000 0 -0.38 3 3
PXN 0.037 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.002 0.1 0.2 7 -0.22 17 24
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.031 0.14 -10000 0 -0.3 33 33
ADRB2 0.001 0.12 -10000 0 -0.39 18 18
receptor agonist activity 0 0 0 12 0 10 22
actin filament binding 0 0 0 11 0 17 28
SRC 0.012 0.062 -10000 0 -0.48 3 3
ITGB3 0.035 0.018 -10000 0 -0.21 1 1
GNAQ 0 0 0.001 12 -0.001 10 22
EFA6/PI-4-5-P2 0 0 0.001 14 -0.001 8 22
ARF6/GDP -0.028 0.11 -10000 0 -0.29 23 23
ARF6/GDP/GULP/ACAP1 -0.01 0.12 -10000 0 -0.28 19 19
alphaIIb/beta3 Integrin/paxillin/GIT1 0.086 0.032 -10000 0 -10000 0 0
ACAP1 0 0 0 2 -10000 0 2
ACAP2 0 0 0 13 0 13 26
LHCGR/beta Arrestin2 0.007 0.061 -10000 0 -0.37 3 3
EFNA1 0.023 0.076 -10000 0 -0.37 7 7
HGF 0.031 0.043 -10000 0 -0.3 3 3
CYTH3 0 0 0.001 13 -0.001 13 26
CYTH2 -0.001 0.001 -10000 0 -0.004 20 20
NCK1 0.027 0.07 -10000 0 -0.48 4 4
fibronectin binding 0 0 0 6 0 16 22
endosomal lumen acidification 0 0 0 15 0 10 25
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.047 0.17 -10000 0 -0.34 48 48
GNAQ/ARNO 0.001 0.003 0.008 12 -0.006 9 21
mol:Phosphatidic acid 0 0 0 13 0 13 26
PIP3-E 0.014 0.1 -10000 0 -0.46 10 10
MET 0.028 0.055 -10000 0 -0.35 4 4
GNA14 -0.018 0.15 -10000 0 -0.37 29 29
GNA15 0.022 0.068 -10000 0 -0.26 10 10
GIT1 0.035 0.009 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 12 -0.001 11 23
GNA11 0.03 0.053 -10000 0 -0.39 3 3
LHCGR 0.027 0.062 -10000 0 -0.29 7 7
AGTR1 0.01 0.082 -10000 0 -0.22 23 23
desensitization of G-protein coupled receptor protein signaling pathway 0.007 0.061 -10000 0 -0.36 3 3
IPCEF1/ARNO -0.03 0.12 -10000 0 -0.23 40 40
alphaIIb/beta3 Integrin 0.052 0.018 -10000 0 -10000 0 0
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.012 0.078 -10000 0 -0.29 12 12
PDGFRB 0.035 0.036 -10000 0 -0.48 1 1
SPHK1 -0.082 0.24 -10000 0 -0.74 24 24
mol:S1P -0.059 0.22 -10000 0 -0.64 24 24
S1P1/S1P/Gi -0.057 0.2 -10000 0 -0.47 27 27
GNAO1 0.032 0.019 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 0 0.19 0.28 3 -0.43 20 23
PLCG1 -0.017 0.18 -10000 0 -0.46 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.035 0.036 -10000 0 -0.48 1 1
GNAI2 0.021 0.074 -10000 0 -0.44 5 5
GNAI3 0.031 0.038 -10000 0 -0.48 1 1
GNAI1 -0.013 0.14 -10000 0 -0.4 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.015 0.14 -10000 0 -0.54 12 12
S1P1/S1P -0.052 0.22 -10000 0 -0.56 25 25
negative regulation of cAMP metabolic process -0.054 0.19 -10000 0 -0.46 27 27
MAPK3 -0.094 0.25 0.27 1 -0.58 36 37
calcium-dependent phospholipase C activity -0.001 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.027 0.004 -10000 0 -10000 0 0
KDR 0.024 0.063 -10000 0 -0.21 12 12
PLCB2 -0.044 0.19 -10000 0 -0.5 24 24
RAC1 0.033 0.012 -10000 0 -10000 0 0
RhoA/GTP -0.043 0.18 -10000 0 -0.47 24 24
receptor internalization -0.047 0.2 -10000 0 -0.5 27 27
PTGS2 -0.15 0.38 -10000 0 -1 32 32
Rac1/GTP -0.046 0.17 -10000 0 -0.47 24 24
RHOA 0.037 0.005 -10000 0 -10000 0 0
VEGFA -0.007 0.038 -10000 0 -0.14 15 15
negative regulation of T cell proliferation -0.054 0.19 -10000 0 -0.46 27 27
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.022 0.066 -10000 0 -0.28 8 8
MAPK1 -0.085 0.24 -10000 0 -0.56 35 35
S1P1/S1P/PDGFB-D/PDGFRB -0.029 0.22 -10000 0 -0.56 22 22
ABCC1 0.033 0.043 -10000 0 -0.3 3 3
Cellular roles of Anthrax toxin

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
ANTXR1 -0.016 0.14 -10000 0 -0.35 30 30
ANTXR2 0.016 0.086 -10000 0 -0.29 14 14
negative regulation of myeloid dendritic cell antigen processing and presentation -0.009 0.019 -10000 0 -0.068 18 18
monocyte activation -0.006 0.12 -10000 0 -0.41 16 16
MAP2K2 -0.001 0.11 -10000 0 -0.6 7 7
MAP2K1 -0.01 0.017 -10000 0 -0.097 1 1
MAP2K7 -0.013 0.027 -10000 0 -0.19 2 2
MAP2K6 -0.02 0.055 0.13 1 -0.21 13 14
CYAA -0.036 0.076 -10000 0 -0.26 18 18
MAP2K4 -0.008 0.022 -10000 0 -0.25 1 1
IL1B -0.063 0.097 -10000 0 -0.23 44 44
Channel 0.003 0.099 -10000 0 -0.28 18 18
NLRP1 -0.008 0.018 -10000 0 -0.062 18 18
CALM1 0.034 0.012 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.037 0.13 -10000 0 -0.41 23 23
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.009 0.019 0.068 18 -10000 0 18
MAPK3 -0.016 0.039 -10000 0 -0.26 4 4
MAPK1 -0.01 0.019 -10000 0 -0.11 2 2
PGR -0.012 0.026 -10000 0 -0.15 3 3
PA/Cellular Receptors 0.001 0.11 -10000 0 -0.31 18 18
apoptosis -0.009 0.019 -10000 0 -0.068 18 18
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.005 0.093 -10000 0 -0.27 18 18
macrophage activation -0.015 0.044 0.18 3 -0.26 4 7
TNF 0.024 0.066 -10000 0 -0.27 9 9
VCAM1 -0.005 0.12 -10000 0 -0.41 15 15
platelet activation -0.037 0.13 -10000 0 -0.41 23 23
MAPKKK cascade 0.01 0.031 0.1 7 -10000 0 7
IL18 -0.046 0.081 -10000 0 -0.25 24 24
negative regulation of macrophage activation -0.009 0.019 -10000 0 -0.068 18 18
LEF -0.009 0.019 -10000 0 -0.068 18 18
CASP1 -0.018 0.035 -10000 0 -0.077 52 52
mol:cAMP -0.037 0.13 -10000 0 -0.42 23 23
necrosis -0.009 0.019 -10000 0 -0.068 18 18
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.004 0.094 -10000 0 -0.26 18 18
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 -0.013 0.28 0.5 1 -0.78 12 13
CRP -0.055 0.26 0.51 2 -0.78 13 15
cell cycle arrest -0.081 0.3 -10000 0 -0.84 18 18
TIMP1 -0.043 0.24 -10000 0 -0.71 14 14
IL6ST 0.034 0.023 -10000 0 -10000 0 0
Rac1/GDP -0.064 0.18 0.29 1 -0.53 16 17
AP1 0.009 0.15 -10000 0 -0.48 5 5
GAB2 0.038 0.008 -10000 0 -10000 0 0
TNFSF11 -0.098 0.42 -10000 0 -1 31 31
HSP90B1 0.001 0.088 -10000 0 -1 1 1
GAB1 0.03 0.056 -10000 0 -0.35 4 4
MAPK14 -0.066 0.19 -10000 0 -0.66 12 12
AKT1 0.028 0.087 -10000 0 -0.44 4 4
FOXO1 0.027 0.083 -10000 0 -0.46 3 3
MAP2K6 -0.064 0.18 -10000 0 -0.52 16 16
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.077 0.18 0.31 1 -0.54 17 18
MITF -0.058 0.17 -10000 0 -0.48 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.037 0.006 -10000 0 -10000 0 0
A2M -0.026 0.28 -10000 0 -1.3 9 9
CEBPB 0.016 0.039 -10000 0 -0.48 1 1
GRB2/SOS1/GAB family/SHP2 0.02 0.098 -10000 0 -0.43 3 3
STAT3 -0.09 0.32 -10000 0 -0.91 18 18
STAT1 0.018 0.028 -10000 0 -10000 0 0
CEBPD -0.045 0.26 -10000 0 -0.78 12 12
PIK3CA 0.037 0.009 -10000 0 -10000 0 0
PI3K 0.049 0.049 -10000 0 -0.35 3 3
JUN -0.017 0.15 -10000 0 -0.41 26 26
PIAS3/MITF -0.044 0.17 0.28 1 -0.5 14 15
MAPK11 -0.064 0.19 -10000 0 -0.65 12 12
STAT3 (dimer)/FOXO1 -0.044 0.24 -10000 0 -0.66 16 16
GRB2/SOS1/GAB family 0.007 0.18 -10000 0 -0.46 13 13
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.063 0.15 -10000 0 -0.48 15 15
GRB2 0.036 0.01 -10000 0 -10000 0 0
JAK2 0.017 0.079 -10000 0 -0.27 13 13
LBP 0.043 0.23 -10000 0 -0.56 11 11
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
JAK1 0.033 0.037 -10000 0 -0.47 1 1
MYC -0.06 0.34 0.55 1 -0.95 19 20
FGG -0.072 0.27 -10000 0 -0.83 15 15
macrophage differentiation -0.081 0.3 -10000 0 -0.84 18 18
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.05 0.18 -10000 0 -0.29 57 57
JUNB -0.07 0.26 -10000 0 -0.79 16 16
FOS -0.063 0.17 -10000 0 -0.32 58 58
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.059 0.16 -10000 0 -0.48 15 15
STAT1/PIAS1 -0.031 0.16 0.31 1 -0.49 10 11
GRB2/SOS1/GAB family/SHP2/PI3K 0.037 0.082 -10000 0 -0.36 6 6
STAT3 (dimer) -0.086 0.31 -10000 0 -0.9 18 18
PRKCD -0.065 0.22 0.35 10 -0.6 18 28
IL6R 0.021 0.079 -10000 0 -0.35 8 8
SOCS3 -0.069 0.26 -10000 0 -1.1 9 9
gp130 (dimer)/JAK1/JAK1/LMO4 0.034 0.11 -10000 0 -0.29 13 13
Rac1/GTP -0.065 0.18 -10000 0 -0.54 16 16
HCK -0.014 0.11 -10000 0 -0.36 18 18
MAPKKK cascade 0.044 0.11 -10000 0 -0.54 3 3
bone resorption -0.083 0.39 -10000 0 -0.93 31 31
IRF1 -0.086 0.3 -10000 0 -0.95 16 16
mol:GDP -0.066 0.18 -10000 0 -0.52 17 17
SOS1 0.038 0.007 -10000 0 -10000 0 0
VAV1 -0.067 0.18 -10000 0 -0.53 17 17
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.066 0.21 -10000 0 -0.75 12 12
PTPN11 0.009 0.12 -10000 0 -0.98 3 3
IL6/IL6RA -0.076 0.17 -10000 0 -0.35 49 49
gp130 (dimer)/TYK2/TYK2/LMO4 0.038 0.099 -10000 0 -0.3 12 12
gp130 (dimer)/JAK2/JAK2/LMO4 0.024 0.11 -10000 0 -0.28 21 21
IL6 -0.12 0.2 -10000 0 -0.35 82 82
PIAS3 0.035 0.024 -10000 0 -0.21 2 2
PTPRE 0.022 0.068 -10000 0 -0.34 6 6
PIAS1 0.035 0.009 -10000 0 -10000 0 0
RAC1 0.033 0.013 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.053 0.13 -10000 0 -0.35 18 18
LMO4 -0.013 0.13 -10000 0 -0.33 28 28
STAT3 (dimer)/PIAS3 -0.075 0.3 -10000 0 -0.86 17 17
MCL1 0.026 0.13 -10000 0 -1.1 2 2
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.071 0.16 -10000 0 -0.4 24 24
IKBKB 0.005 0.094 0.27 2 -0.29 2 4
AKT1 -0.034 0.093 0.32 4 -0.25 10 14
IKBKG 0.007 0.08 0.24 1 -0.25 2 3
CALM1 -0.016 0.12 0.22 1 -0.41 13 14
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
MAP3K1 -0.062 0.19 0.28 1 -0.54 21 22
MAP3K7 0.034 0.036 -10000 0 -0.48 1 1
mol:Ca2+ -0.015 0.13 0.23 1 -0.41 15 16
DOK1 0.034 0.039 -10000 0 -0.35 2 2
AP-1 -0.057 0.1 -10000 0 -0.26 17 17
LYN 0.032 0.014 -10000 0 -10000 0 0
BLNK 0.007 0.12 -10000 0 -0.44 13 13
SHC1 0.036 0.007 -10000 0 -10000 0 0
BCR complex 0.012 0.11 -10000 0 -0.32 18 18
CD22 -0.053 0.16 -10000 0 -0.55 15 15
CAMK2G -0.014 0.12 0.33 1 -0.4 11 12
CSNK2A1 0.031 0.015 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.004 0.088 -10000 0 -0.37 2 2
GO:0007205 -0.015 0.14 0.23 1 -0.42 15 16
SYK 0.031 0.053 -10000 0 -0.39 3 3
ELK1 -0.017 0.13 -10000 0 -0.43 12 12
NFATC1 -0.081 0.18 0.34 1 -0.42 31 32
B-cell antigen/BCR complex 0.012 0.11 -10000 0 -0.32 18 18
PAG1/CSK 0.032 0.066 -10000 0 -0.35 5 5
NFKBIB 0.017 0.046 0.15 1 -0.14 4 5
HRAS -0.003 0.11 0.26 1 -0.38 7 8
NFKBIA 0.018 0.045 0.15 1 -0.13 2 3
NF-kappa-B/RelA/I kappa B beta 0.024 0.041 0.16 1 -10000 0 1
RasGAP/Csk -0.03 0.17 -10000 0 -0.3 43 43
mol:GDP -0.011 0.13 0.22 3 -0.42 13 16
PTEN 0.031 0.051 -10000 0 -0.48 2 2
CD79B 0.002 0.11 -10000 0 -0.32 20 20
NF-kappa-B/RelA/I kappa B alpha 0.024 0.04 0.16 1 -10000 0 1
GRB2 0.036 0.008 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.059 0.18 -10000 0 -0.59 14 14
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
mol:IP3 -0.015 0.14 0.24 1 -0.42 15 16
CSK 0.035 0.01 -10000 0 -10000 0 0
FOS -0.056 0.15 -10000 0 -0.4 22 22
CHUK -0.009 0.11 0.24 1 -0.32 13 14
IBTK 0.031 0.046 -10000 0 -0.28 4 4
CARD11/BCL10/MALT1/TAK1 -0.01 0.13 0.26 2 -0.4 11 13
PTPN6 -0.052 0.15 -10000 0 -0.58 12 12
RELA 0.037 0.005 -10000 0 -10000 0 0
BCL2A1 0.006 0.039 -10000 0 -10000 0 0
VAV2 -0.094 0.22 -10000 0 -0.56 31 31
ubiquitin-dependent protein catabolic process 0.021 0.045 0.16 1 -0.13 4 5
BTK -0.054 0.3 -10000 0 -1.2 14 14
CD19 -0.07 0.18 -10000 0 -0.64 14 14
MAP4K1 0.036 0.017 -10000 0 -0.21 1 1
CD72 -0.028 0.15 -10000 0 -0.35 36 36
PAG1 0.016 0.082 -10000 0 -0.4 7 7
MAPK14 -0.052 0.16 0.26 1 -0.48 18 19
SH3BP5 0.02 0.092 -10000 0 -0.48 7 7
PIK3AP1 -0.033 0.14 0.23 1 -0.46 14 15
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.032 0.18 -10000 0 -0.51 19 19
RAF1 -0.004 0.1 0.25 1 -0.36 7 8
RasGAP/p62DOK/SHIP -0.034 0.16 -10000 0 -0.3 43 43
CD79A 0.016 0.082 -10000 0 -0.26 15 15
re-entry into mitotic cell cycle -0.056 0.1 -10000 0 -0.26 18 18
RASA1 0.025 0.072 -10000 0 -0.43 5 5
MAPK3 -0.008 0.1 0.23 1 -0.35 8 9
MAPK1 -0.005 0.089 0.23 1 -0.32 6 7
CD72/SHP1 -0.054 0.18 -10000 0 -0.6 15 15
NFKB1 0.037 0.006 -10000 0 -10000 0 0
MAPK8 -0.051 0.16 0.26 1 -0.47 18 19
actin cytoskeleton organization -0.062 0.2 0.33 3 -0.46 30 33
NF-kappa-B/RelA 0.047 0.078 0.28 1 -10000 0 1
Calcineurin 0.002 0.12 -10000 0 -0.39 11 11
PI3K -0.064 0.15 -10000 0 -0.44 18 18
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.012 0.14 0.24 4 -0.44 15 19
SOS1 0.037 0.003 -10000 0 -10000 0 0
Bam32/HPK1 -0.14 0.36 -10000 0 -0.82 44 44
DAPP1 -0.18 0.4 -10000 0 -0.95 44 44
cytokine secretion -0.075 0.16 0.33 1 -0.39 31 32
mol:DAG -0.015 0.14 0.24 1 -0.42 15 16
PLCG2 -0.009 0.13 -10000 0 -0.33 27 27
MAP2K1 -0.004 0.096 0.24 1 -0.34 7 8
B-cell antigen/BCR complex/FcgammaRIIB -0.049 0.17 -10000 0 -0.31 51 51
mol:PI-3-4-5-P3 -0.059 0.1 -10000 0 -0.31 18 18
ETS1 -0.015 0.11 0.32 1 -0.38 11 12
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.037 0.12 -10000 0 -0.28 15 15
B-cell antigen/BCR complex/LYN -0.047 0.17 -10000 0 -0.51 20 20
MALT1 0.022 0.039 -10000 0 -0.48 1 1
TRAF6 0.037 0.004 -10000 0 -10000 0 0
RAC1 -0.072 0.2 0.33 1 -0.5 30 31
B-cell antigen/BCR complex/LYN/SYK -0.015 0.16 -10000 0 -0.55 11 11
CARD11 -0.01 0.15 0.26 6 -0.43 12 18
FCGR2B -0.085 0.2 -10000 0 -0.37 64 64
PPP3CA 0.036 0.018 -10000 0 -0.21 1 1
BCL10 0.034 0.036 -10000 0 -0.48 1 1
IKK complex 0.005 0.046 0.18 3 -0.12 2 5
PTPRC -0.022 0.15 -10000 0 -0.37 31 31
PDPK1 -0.037 0.089 0.33 4 -0.23 12 16
PPP3CB 0.036 0.008 -10000 0 -10000 0 0
PPP3CC 0.017 0.073 -10000 0 -0.43 5 5
POU2F2 0.019 0.029 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.036 0.017 -9999 0 -0.21 1 1
ITGB7 0.003 0.13 -9999 0 -0.48 14 14
ITGA4 0.01 0.12 -9999 0 -0.46 12 12
alpha4/beta7 Integrin 0.007 0.13 -9999 0 -0.36 24 24
alpha4/beta1 Integrin 0.034 0.087 -9999 0 -0.35 10 10
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.034 0.036 -9999 0 -0.48 1 1
alphaV beta3 Integrin 0.043 0.06 -9999 0 -0.35 4 4
PTK2 -0.023 0.15 -9999 0 -0.4 24 24
positive regulation of JNK cascade 0.002 0.13 -9999 0 -0.32 16 16
CDC42/GDP 0.012 0.19 -9999 0 -0.43 22 22
Rac1/GDP 0.004 0.18 -9999 0 -0.43 21 21
RAP1B 0.037 0.006 -9999 0 -10000 0 0
RAP1A 0.036 0.008 -9999 0 -10000 0 0
CTNNB1 0.014 0.092 -9999 0 -0.3 15 15
CDC42/GTP 0.013 0.16 -9999 0 -0.4 16 16
nectin-3/I-afadin -0.006 0.14 -9999 0 -0.36 27 27
RAPGEF1 -0.014 0.18 -9999 0 -0.44 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.031 0.19 -9999 0 -0.49 26 26
PDGFB-D/PDGFRB 0.034 0.036 -9999 0 -0.48 1 1
TLN1 -0.021 0.067 -9999 0 -0.33 3 3
Rap1/GTP -0.005 0.13 -9999 0 -0.34 15 15
IQGAP1 0.035 0.01 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.057 0.056 -9999 0 -0.27 5 5
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.006 0.14 -9999 0 -0.36 27 27
PVR 0.034 0.039 -9999 0 -0.35 2 2
Necl-5(dimer) 0.034 0.039 -9999 0 -0.35 2 2
mol:GDP -0.009 0.22 -9999 0 -0.51 27 27
MLLT4 0.022 0.086 -9999 0 -0.48 6 6
PIK3CA 0.037 0.006 -9999 0 -10000 0 0
PI3K 0.042 0.14 -9999 0 -0.27 29 29
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.041 0.069 -9999 0 -0.35 6 6
positive regulation of lamellipodium assembly -0.018 0.15 -9999 0 -0.36 22 22
PVRL1 0.036 0.017 -9999 0 -0.21 1 1
PVRL3 -0.026 0.16 -9999 0 -0.4 31 31
PVRL2 0.033 0.042 -9999 0 -0.3 3 3
PIK3R1 0.03 0.061 -9999 0 -0.48 3 3
CDH1 0.013 0.11 -9999 0 -0.48 10 10
CLDN1 -0.029 0.16 -9999 0 -0.41 32 32
JAM-A/CLDN1 -0.011 0.16 -9999 0 -0.3 48 48
SRC -0.054 0.2 -9999 0 -0.53 29 29
ITGB3 0.035 0.018 -9999 0 -0.21 1 1
nectin-1(dimer)/I-afadin/I-afadin 0.041 0.069 -9999 0 -0.35 6 6
FARP2 0.004 0.21 -9999 0 -0.52 17 17
RAC1 0.033 0.012 -9999 0 -10000 0 0
CTNNA1 0.037 0.006 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.015 0.14 -9999 0 -0.32 27 27
nectin-1/I-afadin 0.041 0.069 -9999 0 -0.35 6 6
nectin-2/I-afadin 0.038 0.075 -9999 0 -0.35 7 7
RAC1/GTP/IQGAP1/filamentous actin 0.041 0.02 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.017 0.13 -9999 0 -0.31 27 27
CDC42/GTP/IQGAP1/filamentous actin 0.043 0.021 -9999 0 -10000 0 0
F11R 0.024 0.079 -9999 0 -0.48 5 5
positive regulation of filopodium formation 0.002 0.13 -9999 0 -0.32 16 16
alphaV/beta3 Integrin/Talin -0.02 0.11 -9999 0 -0.34 5 5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.075 -9999 0 -0.35 7 7
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.075 -9999 0 -0.35 7 7
PIP5K1C -0.02 0.074 -9999 0 -0.28 7 7
VAV2 -0.035 0.26 -9999 0 -0.61 22 22
RAP1/GDP 0.022 0.17 -9999 0 -0.4 20 20
ITGAV 0.023 0.082 -9999 0 -0.4 7 7
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.014 0.13 -9999 0 -0.31 28 28
nectin-3(dimer)/I-afadin/I-afadin -0.006 0.14 -9999 0 -0.36 27 27
Rac1/GTP -0.02 0.19 -9999 0 -0.44 21 21
PTPRM -0.019 0.084 -9999 0 -0.22 30 30
E-cadherin/beta catenin/alpha catenin 0.059 0.13 -9999 0 -0.33 16 16
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.034 0.019 -9999 0 -0.21 1 1
Syndecan-3-mediated signaling events

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
CTTN 0.036 0.017 -9999 0 -0.21 1 1
Syndecan-3/Src/Cortactin -0.012 0.15 -9999 0 -0.46 14 14
Syndecan-3/Neurocan -0.027 0.13 -9999 0 -0.47 16 16
POMC 0.022 0.074 -9999 0 -0.29 10 10
EGFR 0.016 0.088 -9999 0 -0.42 8 8
Syndecan-3/EGFR -0.017 0.14 -9999 0 -0.47 16 16
AGRP 0.034 0.029 -9999 0 -0.21 3 3
NCSTN 0.036 0.008 -9999 0 -10000 0 0
PSENEN 0.033 0.039 -9999 0 -0.35 2 2
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.021 0.073 -9999 0 -0.3 9 9
APH1A 0.003 0.11 -9999 0 -0.3 22 22
NCAN 0 0 -9999 0 -10000 0 0
long-term memory 0 0.15 -9999 0 -0.47 16 16
Syndecan-3/IL8 -0.088 0.18 -9999 0 -0.56 17 17
PSEN1 0.032 0.02 -9999 0 -0.21 1 1
Src/Cortactin 0.023 0.052 -9999 0 -0.35 3 3
FYN 0.008 0.11 -9999 0 -0.35 16 16
limb bud formation -0.025 0.13 -9999 0 -0.48 16 16
MC4R 0.025 0.018 -9999 0 -10000 0 0
SRC 0.012 0.062 -9999 0 -0.48 3 3
PTN -0.01 0.14 -9999 0 -0.41 22 22
FGFR/FGF/Syndecan-3 -0.025 0.14 -9999 0 -0.48 16 16
neuron projection morphogenesis -0.032 0.13 -9999 0 -0.45 14 14
Syndecan-3/AgRP -0.004 0.14 -9999 0 -0.47 16 16
Syndecan-3/AgRP/MC4R 0.001 0.14 -9999 0 -0.45 16 16
Fyn/Cortactin 0.03 0.085 -9999 0 -0.35 8 8
SDC3 -0.025 0.14 -9999 0 -0.49 16 16
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.087 0.18 -9999 0 -0.55 17 17
IL8 -0.14 0.22 -9999 0 -0.36 94 94
Syndecan-3/Fyn/Cortactin 0.001 0.16 -9999 0 -0.48 16 16
Syndecan-3/CASK -0.027 0.13 -9999 0 -0.47 16 16
alpha-MSH/MC4R 0.025 0.06 -9999 0 -0.34 3 3
Gamma Secretase 0.054 0.1 -9999 0 -0.26 10 10
LPA receptor 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
GNB1/GNG2 0.032 0.058 -10000 0 -0.22 7 7
NF kappa B1 p50/RelA/I kappa B alpha -0.002 0.091 -10000 0 -0.27 7 7
AP1 -0.071 0.11 -10000 0 -0.24 57 57
mol:PIP3 -0.016 0.069 -10000 0 -0.22 18 18
AKT1 0.019 0.065 -10000 0 -0.36 1 1
PTK2B -0.046 0.095 -10000 0 -0.2 56 56
RHOA 0.016 0.057 0.22 2 -0.27 3 5
PIK3CB 0.033 0.039 -10000 0 -0.35 2 2
mol:Ca2+ -0.021 0.078 0.21 1 -0.24 18 19
MAGI3 0.034 0.036 -10000 0 -0.48 1 1
RELA 0.037 0.005 -10000 0 -10000 0 0
apoptosis 0.005 0.049 -10000 0 -0.22 8 8
HRAS/GDP 0.025 0.028 -10000 0 -0.24 2 2
positive regulation of microtubule depolymerization -0.043 0.088 0.2 2 -0.26 10 12
NF kappa B1 p50/RelA -0.033 0.08 -10000 0 -0.24 17 17
endothelial cell migration -0.008 0.12 -10000 0 -0.32 21 21
ADCY4 -0.028 0.11 -10000 0 -0.33 16 16
ADCY5 -0.01 0.083 -10000 0 -0.3 11 11
ADCY6 -0.011 0.085 -10000 0 -0.3 11 11
ADCY7 -0.014 0.086 -10000 0 -0.3 11 11
ADCY1 -0.015 0.08 -10000 0 -0.3 10 10
ADCY2 -0.012 0.084 -10000 0 -0.29 11 11
ADCY3 -0.02 0.093 -10000 0 -0.29 14 14
ADCY8 -0.013 0.083 -10000 0 -0.29 11 11
ADCY9 -0.015 0.087 -10000 0 -0.3 11 11
GSK3B -0.044 0.093 0.19 2 -0.23 22 24
arachidonic acid secretion -0.013 0.089 -10000 0 -0.29 14 14
GNG2 0.034 0.011 -10000 0 -10000 0 0
TRIP6 -0.016 0.11 -10000 0 -0.42 14 14
GNAO1 0.009 0.054 -10000 0 -0.24 7 7
HRAS 0.034 0.039 -10000 0 -0.35 2 2
NFKBIA -0.028 0.08 -10000 0 -0.28 9 9
GAB1 0.03 0.055 -10000 0 -0.35 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.013 0.25 -10000 0 -0.85 16 16
JUN -0.017 0.15 -10000 0 -0.41 26 26
LPA/LPA2/NHERF2 0.002 0.072 -10000 0 -0.19 21 21
TIAM1 -0.036 0.28 -10000 0 -0.97 18 18
PIK3R1 0.029 0.061 -10000 0 -0.48 3 3
mol:IP3 -0.028 0.075 0.21 1 -0.25 18 19
PLCB3 -0.009 0.082 0.19 2 -0.26 16 18
FOS -0.063 0.17 -10000 0 -0.32 58 58
positive regulation of mitosis -0.013 0.089 -10000 0 -0.29 14 14
LPA/LPA1-2-3 -0.007 0.044 -10000 0 -0.12 21 21
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.036 0.017 -10000 0 -0.21 1 1
stress fiber formation -0.006 0.067 -10000 0 -0.29 4 4
GNAZ 0.001 0.07 -10000 0 -0.3 8 8
EGFR/PI3K-beta/Gab1 -0.007 0.075 -10000 0 -0.23 18 18
positive regulation of dendritic cell cytokine production -0.008 0.044 -10000 0 -0.12 21 21
LPA/LPA2/MAGI-3 0.018 0.033 -10000 0 -0.11 8 8
ARHGEF1 0.039 0.084 0.21 29 -0.21 7 36
GNAI2 0.002 0.071 -10000 0 -0.28 10 10
GNAI3 0.006 0.057 -10000 0 -0.25 8 8
GNAI1 -0.019 0.098 -10000 0 -0.29 22 22
LPA/LPA3 -0.006 0.022 -10000 0 -0.065 21 21
LPA/LPA2 -0.005 0.022 -10000 0 -0.064 21 21
LPA/LPA1 -0.009 0.058 -10000 0 -0.17 21 21
HB-EGF/EGFR -0.014 0.097 -10000 0 -0.34 14 14
HBEGF -0.02 0.087 -10000 0 -0.35 11 11
mol:DAG -0.028 0.075 0.21 1 -0.25 18 19
cAMP biosynthetic process -0.016 0.091 -10000 0 -0.3 12 12
NFKB1 0.037 0.006 -10000 0 -10000 0 0
SRC 0.012 0.062 -10000 0 -0.48 3 3
GNB1 0.038 0 -10000 0 -10000 0 0
LYN 0 0.077 0.23 1 -0.26 4 5
GNAQ -0.003 0.017 -10000 0 -0.087 7 7
LPAR2 0 0.001 -10000 0 -10000 0 0
LPAR3 -0.001 0.001 -10000 0 -10000 0 0
LPAR1 -0.006 0.034 -10000 0 -0.1 21 21
IL8 -0.14 0.24 -10000 0 -0.48 60 60
PTK2 0.011 0.044 -10000 0 -0.21 6 6
Rac1/GDP 0.024 0.009 -10000 0 -10000 0 0
CASP3 0.005 0.049 -10000 0 -0.22 8 8
EGFR 0.015 0.088 -10000 0 -0.42 8 8
PLCG1 -0.002 0.032 -10000 0 -0.13 10 10
PLD2 0.008 0.047 -10000 0 -0.2 7 7
G12/G13 0.031 0.058 -10000 0 -0.22 7 7
PI3K-beta 0.007 0.058 -10000 0 -0.4 1 1
cell migration 0.011 0.089 -10000 0 -0.24 15 15
SLC9A3R2 0.008 0.11 -10000 0 -0.4 14 14
PXN -0.006 0.068 -10000 0 -0.29 4 4
HRAS/GTP -0.013 0.091 -10000 0 -0.29 14 14
RAC1 0.033 0.012 -10000 0 -10000 0 0
MMP9 -0.006 0.094 -10000 0 -0.32 15 15
PRKCE 0.035 0.036 -10000 0 -0.48 1 1
PRKCD -0.023 0.08 0.23 2 -0.24 17 19
Gi(beta/gamma) -0.01 0.09 -10000 0 -0.27 16 16
mol:LPA -0.006 0.034 -10000 0 -0.1 21 21
TRIP6/p130 Cas/FAK1/Paxillin 0.028 0.1 -10000 0 -0.37 5 5
MAPKKK cascade -0.013 0.089 -10000 0 -0.29 14 14
contractile ring contraction involved in cytokinesis 0.015 0.058 0.22 2 -0.27 3 5
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.017 0.08 -10000 0 -0.26 18 18
GNA15 0.004 0.038 -10000 0 -0.22 3 3
GNA12 0.033 0.012 -10000 0 -10000 0 0
GNA13 0.036 0.008 -10000 0 -10000 0 0
MAPT -0.044 0.09 0.2 2 -0.26 11 13
GNA11 0.007 0.034 -10000 0 -0.27 2 2
Rac1/GTP -0.016 0.26 -10000 0 -0.9 16 16
MMP2 -0.008 0.12 -10000 0 -0.32 21 21
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.007 0.071 -10000 0 -0.24 15 15
epithelial cell differentiation 0.045 0.093 -10000 0 -0.26 15 15
CYFIP2 0.012 0.11 -10000 0 -0.46 11 11
ENAH -0.041 0.083 0.28 1 -0.36 5 6
EGFR 0.016 0.088 -10000 0 -0.42 8 8
EPHA2 0.013 0.087 -10000 0 -0.28 15 15
MYO6 -0.008 0.081 -10000 0 -0.25 19 19
CTNNB1 0.014 0.092 -10000 0 -0.3 15 15
ABI1/Sra1/Nap1 0.047 0.089 -10000 0 -0.31 10 10
AQP5 -0.021 0.091 -10000 0 -0.36 9 9
CTNND1 0.037 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.004 0.073 -10000 0 -0.25 15 15
regulation of calcium-dependent cell-cell adhesion -0.04 0.1 -10000 0 -0.25 35 35
EGF -0.094 0.19 -10000 0 -0.32 79 79
NCKAP1 0.023 0.068 -10000 0 -0.26 10 10
AQP3 -0.036 0.11 -10000 0 -0.38 14 14
cortical microtubule organization 0.045 0.093 -10000 0 -0.26 15 15
GO:0000145 -0.026 0.063 -10000 0 -0.24 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.052 0.096 -10000 0 -0.26 15 15
MLLT4 0.022 0.086 -10000 0 -0.48 6 6
ARF6/GDP -0.05 0.087 -10000 0 -0.38 7 7
ARF6 0.029 0.051 -10000 0 -0.48 2 2
Ephrin A1/EPHA2/NCK1/GIT1 0.048 0.097 -10000 0 -0.29 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.014 0.074 -10000 0 -0.28 4 4
PVRL2 0.033 0.042 -10000 0 -0.3 3 3
ZYX -0.006 0.078 -10000 0 -0.25 17 17
ARF6/GTP 0.048 0.1 -10000 0 -0.27 13 13
CDH1 0.013 0.11 -10000 0 -0.48 10 10
EGFR/EGFR/EGF/EGF -0.041 0.14 -10000 0 -0.27 43 43
RhoA/GDP 0.048 0.091 -10000 0 -0.25 15 15
actin cytoskeleton organization -0.03 0.071 0.17 3 -0.24 19 22
IGF-1R heterotetramer 0.031 0.04 -10000 0 -0.35 2 2
GIT1 0.035 0.009 -10000 0 -10000 0 0
IGF1R 0.031 0.04 -10000 0 -0.35 2 2
IGF1 0.016 0.082 -10000 0 -0.26 15 15
DIAPH1 0.027 0.18 -10000 0 -0.62 13 13
Wnt receptor signaling pathway -0.045 0.093 0.26 15 -10000 0 15
RHOA 0.037 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.049 0.086 -10000 0 -0.4 6 6
CTNNA1 0.037 0.006 -10000 0 -10000 0 0
VCL -0.031 0.072 0.17 3 -0.25 19 22
EFNA1 0.023 0.076 -10000 0 -0.37 7 7
LPP -0.026 0.063 -10000 0 -0.24 13 13
Ephrin A1/EPHA2 0.017 0.12 -10000 0 -0.3 20 20
SEC6/SEC8 -0.011 0.092 -10000 0 -0.31 16 16
MGAT3 -0.041 0.1 -10000 0 -0.25 35 35
HGF/MET 0.031 0.098 -10000 0 -0.26 17 17
HGF 0.031 0.043 -10000 0 -0.3 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.007 0.071 -10000 0 -0.24 15 15
actin cable formation -0.025 0.092 0.23 5 -0.3 8 13
KIAA1543 -0.034 0.077 -10000 0 -0.27 17 17
KIFC3 -0.006 0.078 -10000 0 -0.25 16 16
NCK1 0.027 0.07 -10000 0 -0.48 4 4
EXOC3 0.038 0 -10000 0 -10000 0 0
ACTN1 -0.004 0.074 -10000 0 -0.25 15 15
NCK1/GIT1 0.044 0.056 -10000 0 -0.35 4 4
mol:GDP 0.045 0.093 -10000 0 -0.26 15 15
EXOC4 0.036 0.008 -10000 0 -10000 0 0
STX4 -0.029 0.063 -10000 0 -0.25 15 15
PIP5K1C -0.004 0.074 -10000 0 -0.25 15 15
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0.037 0.004 -10000 0 -10000 0 0
ROCK1 -0.035 0.087 0.3 1 -0.4 4 5
adherens junction assembly -0.018 0.09 -10000 0 -0.42 3 3
IGF-1R heterotetramer/IGF1 0.021 0.099 -10000 0 -0.25 19 19
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.075 -10000 0 -0.35 7 7
MET 0.028 0.055 -10000 0 -0.35 4 4
PLEKHA7 -0.003 0.074 -10000 0 -0.25 15 15
mol:GTP 0.046 0.096 -10000 0 -0.29 11 11
establishment of epithelial cell apical/basal polarity -0.032 0.089 -10000 0 -0.39 7 7
cortical actin cytoskeleton stabilization 0.007 0.071 -10000 0 -0.24 15 15
regulation of cell-cell adhesion -0.03 0.071 0.17 3 -0.24 19 22
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.007 0.071 -10000 0 -0.24 15 15
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.02 0.046 -10000 0 -0.097 53 53
STMN1 0.008 0.057 -10000 0 -0.45 3 3
Aurora B/RasGAP/Survivin 0.038 0.09 -10000 0 -0.34 9 9
Chromosomal passenger complex/Cul3 protein complex -0.043 0.12 -10000 0 -0.32 21 21
BIRC5 0.024 0.076 -10000 0 -0.45 5 5
DES -0.17 0.35 -10000 0 -0.69 63 63
Aurora C/Aurora B/INCENP 0.036 0.079 -10000 0 -0.26 11 11
Aurora B/TACC1 0.018 0.07 -10000 0 -0.21 14 14
Aurora B/PP2A 0.038 0.045 -10000 0 -0.35 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.006 0.034 -10000 0 -0.18 6 6
mitotic metaphase/anaphase transition 0.001 0.004 0.012 9 -10000 0 9
NDC80 0.005 0.035 -10000 0 -0.35 2 2
Cul3 protein complex -0.028 0.14 -10000 0 -0.3 29 29
KIF2C -0.009 0.12 -10000 0 -0.68 5 5
PEBP1 -0.001 0.003 -10000 0 -0.018 4 4
KIF20A 0.029 0.071 -10000 0 -0.49 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.029 0.071 -10000 0 -0.35 6 6
SEPT1 0.036 0.017 -10000 0 -0.21 1 1
SMC2 0 0 -10000 0 -10000 0 0
SMC4 0 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.11 0.25 -10000 0 -0.52 53 53
PSMA3 0.03 0.04 -10000 0 -0.35 2 2
G2/M transition of mitotic cell cycle 0.001 0.004 0.008 41 -10000 0 41
H3F3B 0.011 0.043 -10000 0 -0.29 4 4
AURKB 0.024 0.053 -10000 0 -0.5 2 2
AURKC 0.033 0.042 -10000 0 -0.3 3 3
CDCA8 0.033 0.039 -10000 0 -0.52 1 1
cytokinesis -0.021 0.16 -10000 0 -0.44 19 19
Aurora B/Septin1 -0.02 0.17 -10000 0 -0.42 18 18
AURKA 0.001 0.004 0.008 41 -10000 0 41
INCENP 0.015 0.098 -10000 0 -0.41 10 10
KLHL13 -0.096 0.18 -10000 0 -0.29 87 87
BUB1 0.027 0.08 -10000 0 -0.49 5 5
hSgo1/Aurora B/Survivin 0.036 0.082 -10000 0 -0.32 8 8
EVI5 0.03 0.053 -10000 0 -0.39 3 3
RhoA/GTP 0.013 0.15 -10000 0 -0.49 9 9
SGOL1 0.025 0.069 -10000 0 -0.33 7 7
CENPA -0.035 0.13 -10000 0 -0.26 27 27
NCAPG 0 0 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.035 0.055 -10000 0 -0.35 3 3
NCAPD2 0 0 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.038 0.046 -10000 0 -0.35 2 2
RHOA 0.037 0.005 -10000 0 -10000 0 0
NCAPH 0 0 -10000 0 -10000 0 0
NPM1 -0.064 0.19 -10000 0 -0.33 54 54
RASA1 0.025 0.072 -10000 0 -0.43 5 5
KLHL9 0.034 0.036 -10000 0 -0.48 1 1
mitotic prometaphase -0.001 0.003 -10000 0 -0.018 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.055 -10000 0 -0.35 3 3
PPP1CC 0.037 0.004 -10000 0 -10000 0 0
Centraspindlin 0.002 0.16 -10000 0 -0.51 10 10
RhoA/GDP 0.027 0.004 -10000 0 -10000 0 0
NSUN2 -0.051 0.14 -10000 0 -0.29 48 48
MYLK 0.008 0.049 -10000 0 -0.3 5 5
KIF23 0.03 0.052 -10000 0 -0.5 2 2
VIM -0.013 0.095 -10000 0 -0.35 13 13
RACGAP1 0.034 0.037 -10000 0 -0.5 1 1
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.064 0.18 -10000 0 -0.33 52 52
Chromosomal passenger complex -0.028 0.14 -10000 0 -0.43 13 13
Chromosomal passenger complex/EVI5 0.052 0.12 -10000 0 -0.32 14 14
TACC1 0.012 0.088 -10000 0 -0.32 12 12
PPP2R5D 0.036 0.007 -10000 0 -10000 0 0
CUL3 0.033 0.033 -10000 0 -0.21 4 4
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.029 0.14 0.36 1 -0.47 12 13
ACTA1 -0.044 0.14 0.34 3 -0.4 19 22
NUMA1 -0.019 0.15 0.36 1 -0.51 10 11
SPTAN1 -0.042 0.15 0.6 1 -0.4 20 21
LIMK1 -0.056 0.16 0.32 3 -0.41 23 26
BIRC3 -0.011 0.13 -10000 0 -0.31 29 29
BIRC2 0.035 0.018 -10000 0 -0.21 1 1
BAX 0.03 0.048 -10000 0 -0.26 5 5
CASP10 -0.057 0.11 0.21 1 -0.31 27 28
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 -0.02 0.14 0.36 1 -0.46 11 12
DIABLO 0.037 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes -0.042 0.14 0.6 1 -0.39 20 21
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.07 -10000 0 -0.48 4 4
GSN -0.051 0.15 0.6 1 -0.4 20 21
MADD 0.037 0.003 -10000 0 -10000 0 0
TFAP2A 0.027 0.1 -10000 0 -0.66 4 4
BID -0.026 0.075 0.13 1 -0.2 30 31
MAP3K1 -0.004 0.079 0.23 1 -0.58 2 3
TRADD 0.037 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.029 0.085 -10000 0 -0.34 9 9
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.054 0.16 0.37 3 -0.41 23 26
CASP9 0.035 0.01 -10000 0 -10000 0 0
DNA repair -0.005 0.066 0.27 4 -0.2 6 10
neuron apoptosis -0.035 0.22 -10000 0 -0.71 19 19
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.033 0.16 0.37 1 -0.63 7 8
APAF1 0.01 0.11 -10000 0 -0.36 15 15
CASP6 -0.012 0.19 -10000 0 -0.95 7 7
TRAF2 0.035 0.018 -10000 0 -0.21 1 1
ICAD/CAD -0.045 0.13 0.36 1 -0.4 17 18
CASP7 0.02 0.088 0.28 11 -0.37 3 14
KRT18 0.012 0.079 -10000 0 -0.49 4 4
apoptosis -0.043 0.15 0.42 2 -0.45 16 18
DFFA -0.043 0.14 0.38 1 -0.4 19 20
DFFB -0.045 0.14 0.38 1 -0.41 17 18
PARP1 0.004 0.066 0.2 6 -0.27 4 10
actin filament polymerization 0.06 0.16 0.41 23 -0.43 2 25
TNF 0.024 0.066 -10000 0 -0.27 9 9
CYCS -0.008 0.067 0.17 2 -0.28 4 6
SATB1 -0.061 0.2 -10000 0 -0.93 7 7
SLK -0.044 0.14 0.38 1 -0.4 19 20
p15 BID/BAX -0.01 0.08 -10000 0 -0.24 9 9
CASP2 0.021 0.068 0.23 5 -0.32 2 7
JNK cascade 0.004 0.078 0.58 2 -0.23 1 3
CASP3 -0.044 0.15 0.42 1 -0.41 20 21
LMNB2 0.015 0.12 0.29 1 -0.49 6 7
RIPK1 0.037 0.005 -10000 0 -10000 0 0
CASP4 0.021 0.079 -10000 0 -0.33 9 9
Mammalian IAPs/DIABLO 0.037 0.088 -10000 0 -0.26 12 12
negative regulation of DNA binding 0.027 0.1 -10000 0 -0.65 4 4
stress fiber formation -0.044 0.14 0.38 1 -0.39 19 20
GZMB -0.041 0.12 -10000 0 -0.36 22 22
CASP1 -0.058 0.14 -10000 0 -0.34 40 40
LMNB1 -0.01 0.15 0.29 1 -0.63 6 7
APP -0.036 0.22 -10000 0 -0.72 19 19
TNFRSF1A 0.036 0.008 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.005 0.042 -10000 0 -0.35 3 3
VIM -0.039 0.16 0.43 2 -0.45 17 19
LMNA 0.025 0.092 0.29 1 -0.37 5 6
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.021 0.065 -10000 0 -0.33 2 2
LRDD 0.036 0.017 -10000 0 -0.21 1 1
SREBF1 -0.043 0.14 0.38 1 -0.4 19 20
APAF-1/Caspase 9 -0.027 0.18 -10000 0 -0.62 16 16
nuclear fragmentation during apoptosis -0.018 0.15 0.36 1 -0.49 10 11
CFL2 -0.062 0.17 0.43 2 -0.42 23 25
GAS2 -0.12 0.16 -10000 0 -0.4 34 34
positive regulation of apoptosis 0.012 0.12 0.3 1 -0.52 6 7
PRF1 0.005 0.089 -10000 0 -0.23 25 25
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.014 0.12 -10000 0 -0.45 11 11
Syndecan-4/Syndesmos 0.067 0.17 0.36 1 -0.48 11 12
positive regulation of JNK cascade 0.038 0.2 0.36 1 -0.5 18 19
Syndecan-4/ADAM12 0.041 0.19 0.36 1 -0.5 16 17
CCL5 -0.036 0.16 -10000 0 -0.35 40 40
Rac1/GDP 0.024 0.009 -10000 0 -10000 0 0
DNM2 0.037 0.004 -10000 0 -10000 0 0
ITGA5 0.027 0.049 -10000 0 -0.21 9 9
SDCBP 0.031 0.021 -10000 0 -0.21 1 1
PLG 0.003 0.047 -10000 0 -0.46 1 1
ADAM12 -0.024 0.14 -10000 0 -0.3 38 38
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.037 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.022 0.027 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.035 0.16 -10000 0 -0.47 12 12
Syndecan-4/CXCL12/CXCR4 0.04 0.21 0.37 1 -0.52 18 19
Syndecan-4/Laminin alpha3 0.027 0.17 -10000 0 -0.5 12 12
MDK -0.006 0.13 -10000 0 -0.34 25 25
Syndecan-4/FZD7 0.027 0.2 0.36 1 -0.52 15 16
Syndecan-4/Midkine 0.05 0.19 -10000 0 -0.53 12 12
FZD7 -0.058 0.18 -10000 0 -0.36 52 52
Syndecan-4/FGFR1/FGF 0.05 0.19 0.36 1 -0.49 14 15
THBS1 0.018 0.085 -10000 0 -0.36 9 9
integrin-mediated signaling pathway 0.053 0.18 -10000 0 -0.48 14 14
positive regulation of MAPKKK cascade 0.038 0.2 0.36 1 -0.5 18 19
Syndecan-4/TACI 0.045 0.17 0.36 1 -0.47 12 13
CXCR4 -0.026 0.15 -10000 0 -0.32 38 38
cell adhesion -0.004 0.074 0.19 4 -0.3 9 13
Syndecan-4/Dynamin 0.065 0.17 0.36 1 -0.47 12 13
Syndecan-4/TSP1 0.052 0.18 0.36 1 -0.5 13 14
Syndecan-4/GIPC 0.063 0.18 0.36 1 -0.47 12 13
Syndecan-4/RANTES 0.033 0.19 0.36 1 -0.54 13 14
ITGB1 0.036 0.017 -10000 0 -0.21 1 1
LAMA1 0.027 0.017 -10000 0 -10000 0 0
LAMA3 0.007 0.08 -10000 0 -0.27 14 14
RAC1 0.033 0.012 -10000 0 -10000 0 0
PRKCA 0.018 0.13 0.7 7 -0.42 1 8
Syndecan-4/alpha-Actinin 0.052 0.17 -10000 0 -0.47 12 12
TFPI 0.025 0.06 -10000 0 -0.24 10 10
F2 0.037 0.083 -10000 0 -0.4 6 6
alpha5/beta1 Integrin 0.045 0.042 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.019 0.16 -10000 0 -0.49 12 12
ACTN1 0.034 0.012 -10000 0 -10000 0 0
TNC 0.013 0.086 -10000 0 -0.26 18 18
Syndecan-4/CXCL12 0.047 0.19 0.36 1 -0.49 16 17
FGF6 0.029 0.055 -10000 0 -0.35 4 4
RHOA 0.037 0.005 -10000 0 -10000 0 0
CXCL12 -0.015 0.13 -10000 0 -0.31 32 32
TNFRSF13B 0.029 0.016 -10000 0 -10000 0 0
FGF2 -0.001 0.12 -10000 0 -0.3 24 24
FGFR1 0.024 0.06 -10000 0 -0.3 6 6
Syndecan-4/PI-4-5-P2 -0.025 0.12 -10000 0 -0.47 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.045 0.13 -10000 0 -0.3 34 34
cell migration -0.011 0.015 -10000 0 -10000 0 0
PRKCD 0.007 0.034 -10000 0 -10000 0 0
vasculogenesis 0.052 0.18 0.36 1 -0.48 13 14
SDC4 -0.014 0.13 -10000 0 -0.5 12 12
Syndecan-4/Tenascin C 0.053 0.18 -10000 0 -0.5 14 14
Syndecan-4/PI-4-5-P2/PKC alpha -0.018 0.021 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.049 0.16 0.36 1 -0.48 11 12
MMP9 -0.006 0.094 -10000 0 -0.32 15 15
Rac1/GTP -0.004 0.076 0.19 4 -0.31 9 13
cytoskeleton organization 0.067 0.17 0.36 1 -0.46 11 12
GIPC1 0.031 0.053 -10000 0 -0.39 3 3
Syndecan-4/TFPI 0.061 0.18 0.36 1 -0.49 12 13
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.037 0.1 -9999 0 -0.3 14 14
E-cadherin/beta catenin 0.017 0.11 -9999 0 -0.36 15 15
CTNNB1 0.014 0.092 -9999 0 -0.3 15 15
JUP 0.035 0.019 -9999 0 -0.21 1 1
CDH1 0.013 0.11 -9999 0 -0.48 10 10
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.025 0.16 -9999 0 -0.39 16 16
MAP3K8 0.006 0.1 -9999 0 -0.32 18 18
FOS -0.012 0.11 -9999 0 -0.38 5 5
PRKCA 0.025 0.043 -9999 0 -0.36 2 2
PTPN7 0 0.075 -9999 0 -0.21 22 22
HRAS 0.033 0.039 -9999 0 -0.35 2 2
PRKCB -0.003 0.006 -9999 0 -0.012 56 56
NRAS 0.02 0.079 -9999 0 -0.33 9 9
RAS family/GTP 0.048 0.064 -9999 0 -0.26 6 6
MAPK3 0.009 0.088 -9999 0 -0.46 5 5
MAP2K1 -0.005 0.07 -9999 0 -0.34 3 3
ELK1 0.024 0.039 -9999 0 -0.22 3 3
BRAF 0.006 0.043 -9999 0 -0.29 3 3
mol:GTP -0.001 0.002 -9999 0 -0.004 35 35
MAPK1 -0.002 0.11 -9999 0 -0.42 10 10
RAF1 0.005 0.046 -9999 0 -0.28 4 4
KRAS 0.032 0.04 -9999 0 -0.35 2 2
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.024 0.08 -9999 0 -0.44 6 6
SPHK1 -0.036 0.16 -9999 0 -0.32 43 43
GNAI2 0.026 0.072 -9999 0 -0.43 5 5
mol:S1P -0.019 0.099 -9999 0 -0.29 23 23
GNAO1 0.037 0.003 -9999 0 -10000 0 0
mol:Sphinganine-1-P -0.039 0.12 -9999 0 -0.37 23 23
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.012 0.09 -9999 0 -0.22 22 22
GNAI3 0.034 0.036 -9999 0 -0.48 1 1
G12/G13 0.047 0.021 -9999 0 -10000 0 0
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.006 0.12 -9999 0 -0.38 16 16
S1P1/S1P -0.015 0.13 -9999 0 -0.3 28 28
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 -0.011 0.14 -9999 0 -0.4 23 23
S1P/S1P5/G12 -0.002 0.086 -9999 0 -0.23 22 22
S1P/S1P3/Gq -0.02 0.11 -9999 0 -0.32 19 19
S1P/S1P4/Gi -0.015 0.12 -9999 0 -0.38 13 13
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.024 0.064 -9999 0 -0.28 8 8
GNA14 -0.018 0.15 -9999 0 -0.37 29 29
GNA15 0.022 0.068 -9999 0 -0.26 10 10
GNA12 0.033 0.012 -9999 0 -10000 0 0
GNA13 0.036 0.008 -9999 0 -10000 0 0
GNA11 0.03 0.053 -9999 0 -0.39 3 3
ABCC1 0.033 0.042 -9999 0 -0.3 3 3
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.026 0.14 -9999 0 -0.31 24 24
MAP4K1 0.036 0.017 -9999 0 -0.21 1 1
MAP3K8 0.008 0.1 -9999 0 -0.32 18 18
PRKCB 0 0 -9999 0 -10000 0 0
DBNL 0.028 0.035 -9999 0 -0.21 4 4
CRKL 0.031 0.05 -9999 0 -0.48 2 2
MAP3K1 -0.019 0.12 -9999 0 -0.43 11 11
JUN -0.033 0.12 -9999 0 -0.55 7 7
MAP3K7 -0.016 0.12 -9999 0 -0.43 10 10
GRAP2 0.021 0.082 -9999 0 -0.4 7 7
CRK 0.029 0.016 -9999 0 -10000 0 0
MAP2K4 -0.036 0.14 -9999 0 -0.47 14 14
LAT 0.026 0.064 -9999 0 -0.28 8 8
LCP2 -0.024 0.15 -9999 0 -0.37 32 32
MAPK8 -0.005 0.11 -9999 0 -0.63 6 6
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.006 0.12 -9999 0 -0.47 7 7
LAT/GRAP2/SLP76/HPK1/HIP-55 0.029 0.13 -9999 0 -0.3 20 20
Reelin signaling pathway

Figure S56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.052 0.015 -10000 0 -10000 0 0
VLDLR -0.077 0.2 -10000 0 -0.38 59 59
CRKL 0.031 0.05 -10000 0 -0.48 2 2
LRPAP1 0.036 0.007 -10000 0 -10000 0 0
FYN 0.008 0.11 -10000 0 -0.35 16 16
ITGA3 0.021 0.083 -10000 0 -0.38 8 8
RELN/VLDLR/Fyn -0.029 0.15 -10000 0 -0.32 38 38
MAPK8IP1/MKK7/MAP3K11/JNK1 0.094 0.051 -10000 0 -0.26 1 1
AKT1 -0.028 0.094 -10000 0 -0.23 28 28
MAP2K7 0.03 0.049 -10000 0 -0.26 5 5
RAPGEF1 0.036 0.017 -10000 0 -0.21 1 1
DAB1 0.037 0.006 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.049 0.073 -10000 0 -0.27 9 9
LRPAP1/LRP8 0.033 0.084 -10000 0 -0.35 9 9
RELN/LRP8/DAB1/Fyn 0.044 0.1 -10000 0 -0.26 17 17
DAB1/alpha3/beta1 Integrin -0.017 0.14 -10000 0 -0.35 6 6
long-term memory 0.041 0.11 -10000 0 -0.26 18 18
DAB1/LIS1 -0.01 0.13 -10000 0 -0.25 34 34
DAB1/CRLK/C3G -0.013 0.13 -10000 0 -0.37 3 3
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
DAB1/NCK2 0.003 0.14 -10000 0 -0.33 2 2
ARHGEF2 0.035 0.018 -10000 0 -0.21 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.037 0.004 -10000 0 -10000 0 0
CDK5R1 0.036 0.008 -10000 0 -10000 0 0
RELN 0.034 0.019 -10000 0 -0.21 1 1
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
RELN/LRP8/Fyn 0.029 0.11 -10000 0 -0.3 17 17
GRIN2A/RELN/LRP8/DAB1/Fyn 0.06 0.11 -10000 0 -0.26 17 17
MAPK8 0.036 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.007 0.12 -10000 0 -0.27 31 31
ITGB1 0.036 0.017 -10000 0 -0.21 1 1
MAP1B -0.034 0.12 0.33 1 -0.24 40 41
RELN/LRP8 0.049 0.08 -10000 0 -0.3 9 9
GRIN2B/RELN/LRP8/DAB1/Fyn 0.05 0.12 -10000 0 -0.27 19 19
PI3K 0.047 0.049 -10000 0 -0.35 3 3
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.039 0.068 -10000 0 -0.26 9 9
RAP1A -0.051 0.11 0.33 3 -0.35 3 6
PAFAH1B1 0.029 0.016 -10000 0 -10000 0 0
MAPK8IP1 0.035 0.024 -10000 0 -0.21 2 2
CRLK/C3G 0.047 0.043 -10000 0 -0.35 2 2
GRIN2B 0.02 0.071 -10000 0 -0.26 12 12
NCK2 0.036 0.017 -10000 0 -0.21 1 1
neuron differentiation 0.022 0.073 -10000 0 -0.3 3 3
neuron adhesion -0.055 0.12 0.38 3 -0.46 2 5
LRP8 0.012 0.11 -10000 0 -0.42 12 12
GSK3B -0.028 0.096 -10000 0 -0.42 3 3
RELN/VLDLR/DAB1/Fyn -0.011 0.14 -10000 0 -0.28 37 37
MAP3K11 0.037 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.021 0.1 -10000 0 -0.24 32 32
CDK5 0.036 0.008 -10000 0 -10000 0 0
MAPT 0.004 0.081 0.76 2 -0.45 1 3
neuron migration -0.04 0.13 0.26 4 -0.4 4 8
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.021 0.073 -10000 0 -0.3 3 3
RELN/VLDLR -0.011 0.14 -10000 0 -0.28 40 40
IL2 signaling events mediated by STAT5

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
GAB2 0.038 0.005 -10000 0 -10000 0 0
ELF1 -0.008 0.1 -10000 0 -0.36 15 15
CCNA2 0.02 0.092 -10000 0 -0.48 7 7
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
JAK3 0.038 0.004 -10000 0 -10000 0 0
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
JAK1 0.035 0.036 -10000 0 -0.48 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.009 0.17 -10000 0 -0.46 17 17
SHC1 0.037 0.007 -10000 0 -10000 0 0
SP1 -0.013 0.13 -10000 0 -0.33 30 30
IL2RA -0.047 0.19 -10000 0 -0.71 15 15
IL2RB 0.021 0.083 -10000 0 -0.38 8 8
SOS1 0.038 0.003 -10000 0 -10000 0 0
IL2RG -0.019 0.16 -10000 0 -0.44 26 26
G1/S transition of mitotic cell cycle -0.079 0.26 0.3 2 -0.62 37 39
PTPN11 0.032 0.053 -10000 0 -0.39 3 3
CCND2 -0.082 0.26 -10000 0 -0.75 28 28
LCK -0.011 0.14 -10000 0 -0.36 26 26
GRB2 0.036 0.008 -10000 0 -10000 0 0
IL2 0.037 0.006 -10000 0 -10000 0 0
CDK6 0.025 0.067 -10000 0 -0.35 6 6
CCND3 0.012 0.15 -10000 0 -0.55 6 6
Signaling events mediated by PRL

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
CCNE1 0.028 0.058 -10000 0 -0.32 5 5
mol:Halofuginone 0.002 0.021 -10000 0 -0.21 2 2
ITGA1 0.021 0.087 -10000 0 -0.44 7 7
CDKN1A 0.036 0.11 -10000 0 -0.46 4 4
PRL-3/alpha Tubulin -0.007 0.096 -10000 0 -0.3 19 19
mol:Ca2+ -0.041 0.13 0.35 11 -0.36 16 27
AGT -0.05 0.17 -10000 0 -0.33 51 51
CCNA2 0.035 0.14 -10000 0 -0.61 3 3
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 -0.044 0.12 -10000 0 -0.34 26 26
CDK2/Cyclin E1 0.049 0.13 -10000 0 -0.4 6 6
MAPK3 -0.021 0.11 -10000 0 -0.37 18 18
PRL-2 /Rab GGTase beta 0.052 0.014 -10000 0 -10000 0 0
MAPK1 -0.012 0.092 -10000 0 -0.35 14 14
PTP4A1 -0.014 0.099 -10000 0 -0.71 2 2
PTP4A3 -0.011 0.13 -10000 0 -0.43 19 19
PTP4A2 0.036 0.008 -10000 0 -10000 0 0
ITGB1 -0.013 0.097 -10000 0 -0.36 15 15
SRC 0.012 0.062 -10000 0 -0.48 3 3
RAC1 0.002 0.14 -10000 0 -0.49 11 11
Rab GGTase beta/Rab GGTase alpha 0.05 0.018 -10000 0 -10000 0 0
PRL-1/ATF-5 0.054 0.15 -10000 0 -0.61 3 3
RABGGTA 0.034 0.01 -10000 0 -10000 0 0
BCAR1 0.007 0.098 0.36 15 -10000 0 15
RHOC 0.002 0.15 -10000 0 -0.43 17 17
RHOA 0.011 0.14 -10000 0 -0.46 13 13
cell motility -0.01 0.17 -10000 0 -0.45 18 18
PRL-1/alpha Tubulin -0.028 0.093 -10000 0 -0.61 3 3
PRL-3/alpha1 Integrin 0.006 0.11 -10000 0 -0.35 18 18
ROCK1 -0.006 0.17 -10000 0 -0.46 17 17
RABGGTB 0.037 0.006 -10000 0 -10000 0 0
CDK2 0.022 0.074 -10000 0 -0.29 10 10
mitosis -0.016 0.1 -10000 0 -0.64 3 3
ATF5 0.03 0.055 -10000 0 -0.35 4 4
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.042 0.07 -10000 0 -0.25 9 9
RGS9BP 0.004 0.11 -10000 0 -0.3 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.013 0.08 -10000 0 -0.32 7 7
mol:ADP 0.01 0.01 -10000 0 -0.14 1 1
GNAT2 0.013 0.1 -10000 0 -0.41 11 11
RGS9-1/Gbeta5/R9AP 0.009 0.12 -10000 0 -0.31 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.022 0.093 -10000 0 -0.31 14 14
GRK7 0.036 0.017 -10000 0 -0.21 1 1
CNGB3 0.002 0.094 -10000 0 -0.26 21 21
Cone Metarhodopsin II/X-Arrestin 0.028 0 -10000 0 -10000 0 0
mol:Ca2+ 0.027 0.1 0.19 34 -0.3 8 42
Cone PDE6 0.018 0.14 -10000 0 -0.29 25 25
Cone Metarhodopsin II 0.023 0.009 -10000 0 -10000 0 0
Na + (4 Units) 0.027 0.085 -10000 0 -0.3 8 8
GNAT2/GDP 0.011 0.13 -10000 0 -0.29 26 26
GNB5 -0.003 0.13 -10000 0 -0.37 20 20
mol:GMP (4 units) -0.004 0.085 -10000 0 -0.28 15 15
Cone Transducin 0.046 0.075 -10000 0 -0.27 9 9
SLC24A2 0.031 0.046 -10000 0 -0.28 4 4
GNB3/GNGT2 0.047 0.04 -10000 0 -0.35 1 1
GNB3 0.035 0.018 -10000 0 -0.21 1 1
GNAT2/GTP 0.011 0.073 -10000 0 -0.29 11 11
CNGA3 0.021 0.076 -10000 0 -0.28 11 11
ARR3 0.038 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.014 0.08 -10000 0 -0.32 7 7
mol:Pi 0.009 0.12 -10000 0 -0.31 21 21
Cone CNG Channel 0.014 0.12 -10000 0 -0.3 17 17
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.031 0.046 -10000 0 -0.28 4 4
RGS9 0.028 0.051 -10000 0 -0.26 6 6
PDE6C 0.026 0.054 -10000 0 -0.25 7 7
GNGT2 0.031 0.046 -10000 0 -0.28 4 4
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.02 0.092 -10000 0 -0.48 7 7
Signaling events mediated by PTP1B

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
PDGFRB 0.034 0.036 -10000 0 -0.48 1 1
Jak2/Leptin Receptor 0.032 0.13 0.3 1 -0.45 6 7
PTP1B/AKT1 0.025 0.1 0.23 1 -0.29 5 6
FYN 0.008 0.11 -10000 0 -0.35 16 16
p210 bcr-abl/PTP1B 0.02 0.11 0.24 2 -0.28 8 10
EGFR 0.011 0.09 -10000 0 -0.42 8 8
EGF/EGFR -0.013 0.14 -10000 0 -0.3 25 25
CSF1 0.035 0.018 -10000 0 -0.21 1 1
AKT1 0.031 0.031 -10000 0 -0.21 3 3
INSR 0.024 0.076 -10000 0 -0.37 7 7
PTP1B/N-cadherin 0.004 0.11 0.24 1 -0.29 10 11
Insulin Receptor/Insulin 0.043 0.1 -10000 0 -0.31 4 4
HCK -0.014 0.11 -10000 0 -0.36 18 18
CRK 0.029 0.016 -10000 0 -10000 0 0
TYK2 0.019 0.1 0.27 3 -0.29 6 9
EGF -0.092 0.19 -10000 0 -0.32 79 79
YES1 0.028 0.016 -10000 0 -10000 0 0
CAV1 0.03 0.13 0.24 12 -0.34 6 18
TXN 0.036 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.035 0.12 -10000 0 -0.3 8 8
cell migration -0.02 0.11 0.28 8 -0.24 2 10
STAT3 0.036 0.009 -10000 0 -10000 0 0
PRLR 0.009 0.12 -10000 0 -0.44 14 14
ITGA2B 0.035 0.007 -10000 0 -10000 0 0
CSF1R 0.02 0.089 -10000 0 -0.42 8 8
Prolactin Receptor/Prolactin 0.037 0.099 -10000 0 -0.35 12 12
FGR 0.026 0.044 -10000 0 -0.21 7 7
PTP1B/p130 Cas 0.033 0.11 0.24 2 -0.29 6 8
Crk/p130 Cas 0.029 0.11 -10000 0 -0.29 4 4
DOK1 0.022 0.1 0.21 2 -0.29 6 8
JAK2 0.023 0.13 -10000 0 -0.46 6 6
Jak2/Leptin Receptor/Leptin 0.027 0.13 -10000 0 -0.35 3 3
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
PTPN1 0.02 0.11 0.24 2 -0.29 8 10
LYN 0.032 0.014 -10000 0 -10000 0 0
CDH2 -0.003 0.095 -10000 0 -0.28 19 19
SRC 0.019 0.12 -10000 0 -0.48 9 9
ITGB3 0.034 0.018 -10000 0 -0.21 1 1
CAT1/PTP1B 0.021 0.19 0.27 31 -0.47 13 44
CAPN1 0.021 0.073 -10000 0 -0.3 9 9
CSK 0.035 0.01 -10000 0 -10000 0 0
PI3K 0.05 0.11 -10000 0 -0.41 3 3
mol:H2O2 -0.001 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.13 -10000 0 -0.34 4 4
negative regulation of transcription 0.023 0.13 -10000 0 -0.45 6 6
FCGR2A -0.026 0.15 -10000 0 -0.35 34 34
FER 0.023 0.054 -10000 0 -0.21 11 11
alphaIIb/beta3 Integrin 0.05 0.017 -10000 0 -10000 0 0
BLK 0.009 0.088 -10000 0 -0.32 12 12
Insulin Receptor/Insulin/Shc 0.061 0.054 -10000 0 -0.3 3 3
RHOA 0.036 0.005 -10000 0 -10000 0 0
LEPR 0.026 0.062 -10000 0 -0.29 7 7
BCAR1 0.036 0.017 -10000 0 -0.21 1 1
p210 bcr-abl/Grb2 0.036 0.008 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.049 0.23 0.26 2 -0.54 25 27
PRL 0.039 0.025 -10000 0 -0.21 2 2
SOCS3 -0.047 0.3 -10000 0 -1.3 12 12
SPRY2 -0.002 0.11 -10000 0 -0.44 12 12
Insulin Receptor/Insulin/IRS1 0.049 0.09 -10000 0 -0.37 7 7
CSF1/CSF1R 0.036 0.12 0.25 2 -0.31 8 10
Ras protein signal transduction -0.004 0.075 0.43 5 -10000 0 5
IRS1 0.018 0.091 -10000 0 -0.37 10 10
INS 0.037 0.007 -10000 0 -10000 0 0
LEP 0.023 0.066 -10000 0 -0.27 9 9
STAT5B 0.029 0.11 0.22 4 -0.28 5 9
STAT5A 0.027 0.11 0.22 4 -0.3 7 11
GRB2 0.036 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.033 0.11 0.24 2 -0.3 7 9
CSN2 0.013 0.051 -10000 0 -10000 0 0
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
LAT -0.006 0.17 -10000 0 -0.5 20 20
YBX1 0.044 0.052 -10000 0 -0.47 2 2
LCK -0.012 0.14 -10000 0 -0.36 26 26
SHC1 0.036 0.007 -10000 0 -10000 0 0
NOX4 -0.042 0.16 -10000 0 -0.3 49 49
IL2 signaling events mediated by PI3K

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
BCL2L1 0.047 0.15 -10000 0 -0.61 2 2
UGCG 0.007 0.098 -10000 0 -0.65 4 4
AKT1/mTOR/p70S6K/Hsp90/TERT -0.023 0.16 -10000 0 -0.41 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.007 0.097 -10000 0 -0.64 4 4
mol:DAG -0.011 0.015 0.18 1 -10000 0 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.036 0.21 -10000 0 -0.49 28 28
FRAP1 -0.056 0.25 -10000 0 -0.59 28 28
FOXO3 -0.038 0.2 -10000 0 -0.46 29 29
AKT1 -0.042 0.21 -10000 0 -0.5 29 29
GAB2 0.037 0.005 -10000 0 -10000 0 0
SMPD1 0.016 0.069 -10000 0 -0.84 1 1
SGMS1 -0.002 0.037 -10000 0 -0.082 23 23
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 0.004 0.037 -10000 0 -0.3 3 3
CALM1 0.034 0.012 -10000 0 -10000 0 0
cell proliferation 0.006 0.11 -10000 0 -0.28 16 16
EIF3A 0 0 -10000 0 -10000 0 0
PI3K 0.05 0.05 -10000 0 -0.35 3 3
RPS6KB1 -0.01 0.14 -10000 0 -0.76 6 6
mol:sphingomyelin -0.011 0.015 0.18 1 -10000 0 1
natural killer cell activation 0 0.003 -10000 0 -0.012 9 9
JAK3 0.039 0.005 -10000 0 -10000 0 0
PIK3R1 0.031 0.061 -10000 0 -0.48 3 3
JAK1 0.036 0.036 -10000 0 -0.48 1 1
NFKB1 0.037 0.006 -10000 0 -10000 0 0
MYC -0.022 0.27 -10000 0 -0.8 17 17
MYB -0.075 0.35 -10000 0 -1.3 17 17
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.025 0.18 -10000 0 -0.47 20 20
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.008 0.14 -10000 0 -0.65 7 7
mol:PI-3-4-5-P3 -0.024 0.18 -10000 0 -0.46 20 20
Rac1/GDP 0.023 0.039 -10000 0 -0.27 3 3
T cell proliferation -0.024 0.16 -10000 0 -0.42 20 20
SHC1 0.036 0.008 -10000 0 -10000 0 0
RAC1 0.033 0.012 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.001 0.019 -10000 0 -0.067 17 17
PRKCZ -0.026 0.17 -10000 0 -0.44 20 20
NF kappa B1 p50/RelA -0.022 0.22 -10000 0 -0.54 22 22
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.005 0.13 -10000 0 -0.44 12 12
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0.037 0.005 -10000 0 -10000 0 0
IL2RA -0.036 0.16 -10000 0 -0.35 40 40
IL2RB 0.022 0.083 -10000 0 -0.38 8 8
TERT 0.026 0.065 -10000 0 -0.37 5 5
E2F1 -0.023 0.13 -10000 0 -0.42 19 19
SOS1 0.037 0.004 -10000 0 -10000 0 0
RPS6 0.034 0.025 -10000 0 -0.21 2 2
mol:cAMP 0 0.01 0.033 17 -10000 0 17
PTPN11 0.031 0.053 -10000 0 -0.39 3 3
IL2RG -0.018 0.16 -10000 0 -0.44 26 26
actin cytoskeleton organization -0.024 0.16 -10000 0 -0.42 20 20
GRB2 0.035 0.009 -10000 0 -10000 0 0
IL2 0.038 0.007 -10000 0 -10000 0 0
PIK3CA 0.038 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.051 0.051 -10000 0 -0.25 3 3
LCK -0.01 0.14 -10000 0 -0.36 26 26
BCL2 -0.065 0.27 -10000 0 -0.79 21 21
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.028 0.051 -10000 0 -0.48 2 2
Caspase 8 (4 units) -0.014 0.16 -10000 0 -0.44 17 17
NEF -0.015 0.047 -10000 0 -0.17 15 15
NFKBIA 0.018 0.056 -10000 0 -0.31 3 3
BIRC3 -0.02 0.13 -10000 0 -0.48 13 13
CYCS -0.03 0.16 -10000 0 -0.44 18 18
RIPK1 0.037 0.005 -10000 0 -10000 0 0
CD247 -0.015 0.047 -10000 0 -0.17 15 15
MAP2K7 -0.02 0.19 -10000 0 -0.68 11 11
protein ubiquitination 0.017 0.071 0.25 1 -0.32 2 3
CRADD 0.027 0.07 -10000 0 -0.48 4 4
DAXX 0.037 0.004 -10000 0 -10000 0 0
FAS -0.034 0.17 -10000 0 -0.4 34 34
BID -0.045 0.15 -10000 0 -0.42 22 22
NF-kappa-B/RelA/I kappa B alpha 0.04 0.096 -10000 0 -0.27 12 12
TRADD 0.037 0.003 -10000 0 -10000 0 0
MAP3K5 0.013 0.1 -10000 0 -0.36 13 13
CFLAR 0.037 0.004 -10000 0 -10000 0 0
FADD 0.037 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.04 0.097 -10000 0 -0.27 12 12
MAPK8 -0.018 0.17 -10000 0 -0.61 11 11
APAF1 0.01 0.11 -10000 0 -0.36 15 15
TRAF1 0.036 0.018 -10000 0 -0.21 1 1
TRAF2 0.035 0.018 -10000 0 -0.21 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.039 0.16 -10000 0 -0.35 34 34
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.025 0.075 -10000 0 -0.39 1 1
CHUK 0.017 0.075 0.26 1 -0.34 2 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.032 0.15 -10000 0 -0.31 29 29
TCRz/NEF -0.023 0.08 -10000 0 -0.28 15 15
TNF 0.024 0.066 -10000 0 -0.27 9 9
FASLG -0.039 0.16 -10000 0 -0.58 15 15
NFKB1 0.024 0.04 -10000 0 -0.15 1 1
TNFR1A/BAG4/TNF-alpha 0.052 0.064 -10000 0 -0.3 4 4
CASP6 -0.005 0.17 -10000 0 -0.57 12 12
CASP7 -0.046 0.17 -10000 0 -0.52 17 17
RELA 0.024 0.04 -10000 0 -0.15 1 1
CASP2 0.036 0.008 -10000 0 -10000 0 0
CASP3 -0.047 0.17 -10000 0 -0.52 18 18
TNFRSF1A 0.036 0.008 -10000 0 -10000 0 0
TNFR1A/BAG4 0.043 0.044 -10000 0 -0.35 2 2
CASP8 0.03 0.061 -10000 0 -0.48 3 3
CASP9 0.035 0.01 -10000 0 -10000 0 0
MAP3K14 0.022 0.073 -10000 0 -0.36 1 1
APAF-1/Caspase 9 -0.041 0.16 0.21 1 -0.4 25 26
BCL2 -0.033 0.16 -10000 0 -0.59 11 11
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.008 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.053 0.055 -10000 0 -0.26 3 3
regulation of S phase of mitotic cell cycle 0.004 0.059 -10000 0 -0.28 7 7
GNAO1 0.037 0.003 -10000 0 -10000 0 0
HRAS 0.033 0.039 -10000 0 -0.35 2 2
SHBG/T-DHT 0.019 0.011 -10000 0 -10000 0 0
PELP1 0.028 0.016 -10000 0 -10000 0 0
AKT1 0.008 0.017 -10000 0 -0.14 3 3
MAP2K1 0.043 0.1 0.27 1 -0.3 1 2
T-DHT/AR 0.015 0.054 -10000 0 -0.19 12 12
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.008 41 41
GNAI2 0.026 0.072 -10000 0 -0.43 5 5
GNAI3 0.034 0.036 -10000 0 -0.48 1 1
GNAI1 -0.011 0.14 -10000 0 -0.4 23 23
mol:GDP -0.006 0.049 -10000 0 -0.31 4 4
cell proliferation -0.008 0.17 -10000 0 -0.4 17 17
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
FOS -0.096 0.32 -10000 0 -0.8 34 34
mol:Ca2+ -0.007 0.025 -10000 0 -0.074 20 20
MAPK3 0.015 0.14 0.3 1 -0.41 4 5
MAPK1 -0.004 0.12 -10000 0 -0.45 6 6
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
mol:IP3 -0.001 0.002 -10000 0 -0.005 34 34
cAMP biosynthetic process 0.003 0.02 -10000 0 -10000 0 0
GNG2 0.034 0.011 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 34 34
HRAS/GTP 0.014 0.06 -10000 0 -0.26 4 4
actin cytoskeleton reorganization 0.04 0.043 -10000 0 -0.24 3 3
SRC 0.012 0.062 -10000 0 -0.48 3 3
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 34 34
PI3K 0.043 0.042 -10000 0 -0.3 3 3
apoptosis 0.013 0.17 0.35 33 -10000 0 33
T-DHT/AR/PELP1 0.027 0.053 -10000 0 -0.29 3 3
HRAS/GDP 0.051 0.076 -10000 0 -0.32 4 4
CREB1 -0.016 0.18 -10000 0 -0.37 33 33
RAC1-CDC42/GTP 0.05 0.049 -10000 0 -0.24 3 3
AR 0.019 0.078 -10000 0 -0.28 12 12
GNB1 0.038 0 -10000 0 -10000 0 0
RAF1 0.059 0.1 0.28 1 -0.25 4 5
RAC1-CDC42/GDP 0.057 0.076 -10000 0 -0.31 3 3
T-DHT/AR/PELP1/Src 0.019 0.058 -10000 0 -0.27 4 4
MAP2K2 0.043 0.1 -10000 0 -0.3 1 1
T-DHT/AR/PELP1/Src/PI3K 0.004 0.06 -10000 0 -0.28 7 7
GNAZ 0.024 0.064 -10000 0 -0.28 8 8
SHBG 0.029 0.016 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.015 0.095 -10000 0 -0.43 5 5
mol:T-DHT -0.001 0.002 0.002 1 -0.004 31 32
RAC1 0.033 0.012 -10000 0 -10000 0 0
GNRH1 0.002 0.038 -10000 0 -0.22 5 5
Gi family/GTP -0.013 0.093 -10000 0 -0.26 19 19
CDC42 0.034 0.019 -10000 0 -0.21 1 1
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.008 0.15 -10000 0 -0.52 16 16
KLHL20 0.031 0.12 0.22 11 -0.25 18 29
CYFIP2 0.012 0.11 -10000 0 -0.46 11 11
Rac1/GDP 0.052 0.14 0.3 6 -0.4 8 14
ENAH -0.02 0.16 -10000 0 -0.53 16 16
AP1M1 0.035 0.036 -10000 0 -0.48 1 1
RAP1B 0.037 0.006 -10000 0 -10000 0 0
RAP1A 0.036 0.008 -10000 0 -10000 0 0
CTNNB1 0.014 0.093 -10000 0 -0.3 15 15
CDC42/GTP 0.038 0.1 -10000 0 -0.35 7 7
ABI1/Sra1/Nap1 -0.028 0.058 -10000 0 -0.18 21 21
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.016 0.13 -10000 0 -0.27 29 29
RAPGEF1 0.033 0.16 0.32 3 -0.49 11 14
CTNND1 0.037 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.001 0.16 -10000 0 -0.53 16 16
CRK 0.03 0.16 -10000 0 -0.55 11 11
E-cadherin/gamma catenin/alpha catenin 0.051 0.081 -10000 0 -0.3 10 10
alphaE/beta7 Integrin 0.015 0.1 -10000 0 -0.34 14 14
IQGAP1 0.035 0.01 -10000 0 -10000 0 0
NCKAP1 0.023 0.068 -10000 0 -0.26 10 10
Rap1/GTP/I-afadin 0.057 0.056 -10000 0 -0.27 5 5
DLG1 -0.009 0.15 -10000 0 -0.52 16 16
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.01 0.055 -10000 0 -0.27 6 6
MLLT4 0.022 0.086 -10000 0 -0.48 6 6
ARF6/GTP/NME1/Tiam1 0.049 0.061 -10000 0 -0.28 5 5
PI3K -0.01 0.073 -10000 0 -0.38 5 5
ARF6 0.029 0.051 -10000 0 -0.48 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.033 0.086 -10000 0 -0.35 10 10
TIAM1 0.029 0.053 -10000 0 -0.39 3 3
E-cadherin(dimer)/Ca2+ 0.052 0.096 -10000 0 -0.26 15 15
AKT1 0.031 0.069 0.18 5 -0.21 5 10
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
CDH1 0.013 0.11 -10000 0 -0.48 10 10
RhoA/GDP 0.064 0.14 0.29 5 -0.4 8 13
actin cytoskeleton organization 0.032 0.095 0.19 15 -0.18 18 33
CDC42/GDP 0.059 0.14 0.3 6 -0.4 8 14
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.015 0.056 -10000 0 -0.23 10 10
ITGB7 0.003 0.13 -10000 0 -0.48 14 14
RAC1 0.033 0.012 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.056 0.1 -10000 0 -0.28 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin 0.034 0.088 -10000 0 -0.26 15 15
mol:GDP 0.05 0.16 0.3 6 -0.43 11 17
CDC42/GTP/IQGAP1 0.043 0.021 -10000 0 -10000 0 0
JUP 0.035 0.019 -10000 0 -0.21 1 1
p120 catenin/RhoA/GDP 0.074 0.15 0.31 4 -0.42 8 12
RAC1/GTP/IQGAP1 0.041 0.02 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.052 0.029 -10000 0 -0.35 1 1
RHOA 0.037 0.005 -10000 0 -10000 0 0
CDC42 0.034 0.019 -10000 0 -0.21 1 1
CTNNA1 0.037 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.029 0.075 0.15 17 -0.19 5 22
NME1 0.034 0.036 -10000 0 -0.48 1 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.009 0.15 -10000 0 -0.52 16 16
regulation of cell-cell adhesion 0 0.068 -10000 0 -0.3 7 7
WASF2 0.014 0.054 0.11 12 -0.15 3 15
Rap1/GTP 0.074 0.13 0.31 4 -0.4 7 11
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.038 0.12 -10000 0 -0.26 24 24
CCND1 0.032 0.088 0.17 17 -0.24 5 22
VAV2 0.005 0.29 -10000 0 -0.71 24 24
RAP1/GDP 0.077 0.14 0.33 4 -0.41 7 11
adherens junction assembly -0.009 0.14 -10000 0 -0.5 16 16
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.037 0.004 -10000 0 -10000 0 0
PIP5K1C 0.036 0.007 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.018 0.12 -10000 0 -0.25 27 27
E-cadherin/beta catenin -0.003 0.08 -10000 0 -0.34 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.02 0.14 -10000 0 -0.59 11 11
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.045 0.14 -10000 0 -0.4 23 23
E-cadherin/beta catenin/alpha catenin 0.038 0.1 -10000 0 -0.3 15 15
ITGAE 0.027 0.028 -10000 0 -0.21 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.002 0.16 -10000 0 -0.54 16 16
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.036 0.008 -10000 0 -10000 0 0
HDAC2 0.034 0.036 -10000 0 -0.48 1 1
GNB1/GNG2 0.026 0.098 -10000 0 -0.3 12 12
forebrain development -0.057 0.24 -10000 0 -0.67 21 21
GNAO1 0.037 0.003 -10000 0 -10000 0 0
SMO/beta Arrestin2 -0.001 0.1 -10000 0 -0.34 13 13
SMO -0.018 0.13 -10000 0 -0.31 33 33
ARRB2 0.026 0.038 -10000 0 -0.48 1 1
GLI3/SPOP 0.039 0.14 0.28 3 -0.4 7 10
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.035 0.036 -10000 0 -0.48 1 1
GNAI2 0.026 0.072 -10000 0 -0.43 5 5
SIN3/HDAC complex 0.057 0.053 -10000 0 -0.27 1 1
GNAI1 -0.011 0.14 -10000 0 -0.4 23 23
XPO1 0.035 0.014 -10000 0 -10000 0 0
GLI1/Su(fu) -0.061 0.23 -10000 0 -0.85 12 12
SAP30 0.033 0.036 -10000 0 -0.48 1 1
mol:GDP -0.018 0.13 -10000 0 -0.31 33 33
MIM/GLI2A -0.009 0.13 -10000 0 -0.42 16 16
IFT88 0.007 0.098 -10000 0 -0.48 8 8
GNAI3 0.034 0.036 -10000 0 -0.49 1 1
GLI2 0.01 0.084 0.22 1 -0.36 5 6
GLI3 0.027 0.14 0.28 3 -0.42 7 10
CSNK1D 0.036 0.008 -10000 0 -10000 0 0
CSNK1E 0.03 0.053 -10000 0 -0.39 3 3
SAP18 0.026 0.017 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.007 0.098 -10000 0 -0.48 8 8
GNG2 0.034 0.011 -10000 0 -10000 0 0
Gi family/GTP -0.025 0.13 -10000 0 -0.37 15 15
SIN3B 0.037 0.004 -10000 0 -10000 0 0
SIN3A 0.034 0.019 -10000 0 -0.21 1 1
GLI3/Su(fu) 0.025 0.13 0.29 1 -0.42 7 8
GLI2/Su(fu) 0.002 0.1 -10000 0 -0.48 4 4
FOXA2 -0.11 0.36 -10000 0 -0.99 28 28
neural tube patterning -0.057 0.24 -10000 0 -0.67 21 21
SPOP 0.036 0.008 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.008 0.084 -10000 0 -0.64 1 1
GNB1 0.038 0 -10000 0 -10000 0 0
CSNK1G2 0.036 0.008 -10000 0 -10000 0 0
CSNK1G3 0.036 0.007 -10000 0 -10000 0 0
MTSS1 -0.009 0.13 -10000 0 -0.42 16 16
embryonic limb morphogenesis -0.057 0.24 -10000 0 -0.67 21 21
SUFU 0.002 0.071 -10000 0 -0.46 2 2
LGALS3 0.022 0.074 -10000 0 -0.39 6 6
catabolic process 0.041 0.14 0.32 1 -0.38 9 10
GLI3A/CBP 0.008 0.12 -10000 0 -0.37 17 17
KIF3A 0.029 0.061 -10000 0 -0.48 3 3
GLI1 -0.06 0.25 -10000 0 -0.69 21 21
RAB23 0.024 0.071 -10000 0 -0.31 8 8
CSNK1A1 0.037 0.006 -10000 0 -10000 0 0
IFT172 0.006 0.12 -10000 0 -0.48 13 13
RBBP7 0.035 0.024 -10000 0 -0.21 2 2
Su(fu)/Galectin3 0.004 0.096 -10000 0 -0.46 3 3
GNAZ 0.024 0.064 -10000 0 -0.28 8 8
RBBP4 0.033 0.03 -10000 0 -0.21 3 3
CSNK1G1 0.035 0.009 -10000 0 -10000 0 0
PIAS1 0.035 0.009 -10000 0 -10000 0 0
PRKACA 0.037 0.006 -10000 0 -10000 0 0
GLI2/SPOP 0.028 0.085 -10000 0 -0.34 5 5
STK36 0.03 0.045 -10000 0 -0.3 3 3
Gi family/GNB1/GNG2/GDP -0.016 0.12 -10000 0 -0.41 12 12
PTCH1 -0.049 0.21 -10000 0 -0.57 22 22
MIM/GLI1 -0.072 0.27 -10000 0 -0.68 26 26
CREBBP 0.008 0.12 -10000 0 -0.36 17 17
Su(fu)/SIN3/HDAC complex 0.026 0.11 -10000 0 -0.39 8 8
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.052 0.021 -10000 0 -10000 0 0
Necdin/E2F1 -0.003 0.094 -10000 0 -0.35 11 11
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.009 0.13 -10000 0 -0.25 36 36
NGF (dimer)/p75(NTR)/BEX1 0.047 0.019 -10000 0 -10000 0 0
NT-4/5 (dimer)/p75(NTR) 0.026 0.012 -10000 0 -0.14 1 1
IKBKB 0.033 0.012 -10000 0 -10000 0 0
AKT1 0.017 0.044 -10000 0 -0.26 3 3
IKBKG 0.036 0.017 -10000 0 -0.21 1 1
BDNF 0.019 0.083 -10000 0 -0.3 12 12
MGDIs/NGR/p75(NTR)/LINGO1 0.035 0.052 -10000 0 -0.3 3 3
FURIN 0.028 0.049 -10000 0 -0.26 5 5
proBDNF (dimer)/p75(NTR)/Sortilin 0.055 0.068 -10000 0 -0.3 5 5
LINGO1 0 0 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.008 0.083 -10000 0 -0.27 2 2
proBDNF (dimer) 0.019 0.083 -10000 0 -0.3 12 12
NTRK1 0.035 0.019 -10000 0 -0.21 1 1
RTN4R 0.021 0.073 -10000 0 -0.3 9 9
neuron apoptosis -0.034 0.13 -10000 0 -0.48 7 7
IRAK1 0.035 0.024 -10000 0 -0.21 2 2
SHC1 0.019 0.011 -10000 0 -10000 0 0
ARHGDIA 0.036 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.027 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.054 0.1 -10000 0 -0.26 10 10
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.024 0.1 -10000 0 -0.26 17 17
MAGEH1 -0.026 0.15 -10000 0 -0.34 37 37
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.023 0.11 -10000 0 -0.27 21 21
Mammalian IAPs/DIABLO 0.037 0.088 -10000 0 -0.26 12 12
proNGF (dimer) 0 0 -10000 0 -10000 0 0
MAGED1 0.026 0.074 -10000 0 -0.39 6 6
APP 0.017 0.086 -10000 0 -0.35 10 10
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
ZNF274 0.026 0.074 -10000 0 -0.39 6 6
RhoA/GDP/RHOGDI 0.05 0.02 -10000 0 -10000 0 0
NGF 0 0 -10000 0 -10000 0 0
cell cycle arrest -0.009 0.033 0.2 4 -0.2 1 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.026 0.04 -10000 0 -0.28 3 3
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.048 0.015 -10000 0 -10000 0 0
NCSTN 0.036 0.008 -10000 0 -10000 0 0
mol:GTP 0.003 0.11 -10000 0 -0.3 23 23
PSENEN 0.033 0.039 -10000 0 -0.35 2 2
mol:ceramide 0.022 0.029 0.19 4 -0.2 1 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.021 0.037 -10000 0 -0.25 2 2
p75(NTR)/beta APP 0.035 0.067 -10000 0 -0.35 4 4
BEX1 0.036 0.017 -10000 0 -0.21 1 1
mol:GDP 0.003 0.008 -10000 0 -10000 0 0
NGF (dimer) -0.043 0.15 -10000 0 -0.28 53 53
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.053 0.055 -10000 0 -0.27 3 3
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
RAC1/GTP 0.037 0.018 -10000 0 -10000 0 0
MYD88 0.037 0.004 -10000 0 -10000 0 0
CHUK 0.031 0.05 -10000 0 -0.48 2 2
NGF (dimer)/p75(NTR)/PKA 0.003 0.11 -10000 0 -0.3 23 23
RHOB 0.02 0.082 -10000 0 -0.31 11 11
RHOA 0.037 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.021 0.053 -10000 0 -0.35 3 3
NT3 (dimer) 0.013 0.096 -10000 0 -0.33 14 14
TP53 -0.037 0.1 -10000 0 -0.26 34 34
PRDM4 0.023 0.029 0.19 4 -0.2 1 5
BDNF (dimer) -0.14 0.21 -10000 0 -0.34 99 99
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
SORT1 0.035 0.018 -10000 0 -0.21 1 1
activation of caspase activity 0.005 0.12 -10000 0 -0.25 36 36
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.065 0.028 -10000 0 -0.2 1 1
RHOC 0.036 0.008 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.001 0.093 0.24 4 -0.31 3 7
DIABLO 0.037 0.005 -10000 0 -10000 0 0
SMPD2 0.023 0.029 0.19 4 -0.2 1 5
APH1B 0.021 0.073 -10000 0 -0.3 9 9
APH1A 0.003 0.11 -10000 0 -0.3 22 22
proNGF (dimer)/p75(NTR)/Sortilin 0.045 0.024 -10000 0 -0.22 1 1
PSEN1 0.032 0.02 -10000 0 -0.21 1 1
APAF-1/Pro-Caspase 9 0.029 0.085 -10000 0 -0.34 9 9
NT3 (dimer)/p75(NTR) 0.033 0.077 -10000 0 -0.34 7 7
MAPK8 0.008 0.081 0.24 3 -0.31 2 5
MAPK9 0.007 0.08 0.25 2 -0.28 2 4
APAF1 0.01 0.11 -10000 0 -0.36 15 15
NTF3 0.013 0.096 -10000 0 -0.33 14 14
NTF4 0 0 -10000 0 -10000 0 0
NDN -0.027 0.16 -10000 0 -0.37 34 34
RAC1/GDP 0.024 0.009 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.023 0.11 -10000 0 -0.24 26 26
p75 CTF/Sortilin/TRAF6/NRIF 0.082 0.059 -10000 0 -0.27 4 4
RhoA-B-C/GTP 0.002 0.11 -10000 0 -0.3 23 23
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.078 0.087 -10000 0 -0.27 8 8
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.073 0.07 -10000 0 -0.27 5 5
PRKACB -0.029 0.16 -10000 0 -0.41 32 32
proBDNF (dimer)/p75 ECD 0.04 0.066 -10000 0 -0.35 4 4
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.011 0.13 -10000 0 -0.31 29 29
BIRC2 0.035 0.018 -10000 0 -0.21 1 1
neuron projection morphogenesis -0.063 0.1 -10000 0 -0.32 18 18
BAD 0.001 0.088 0.26 1 -0.33 1 2
RIPK2 0.023 0.062 -10000 0 -0.48 3 3
NGFR 0.035 0.018 -10000 0 -0.21 1 1
CYCS 0.008 0.05 -10000 0 -0.25 6 6
ADAM17 0.037 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.052 0.051 -10000 0 -0.3 3 3
BCL2L11 0.001 0.088 0.24 2 -0.33 1 3
BDNF (dimer)/p75(NTR) 0.038 0.067 -10000 0 -0.35 4 4
PI3K 0.061 0.046 -10000 0 -0.27 3 3
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.058 0.041 -10000 0 -0.23 2 2
NDNL2 0.031 0.04 -10000 0 -0.35 2 2
YWHAE 0.029 0.016 -10000 0 -10000 0 0
PRKCI 0.03 0.055 -10000 0 -0.35 4 4
NGF (dimer)/p75(NTR) 0.026 0.012 -10000 0 -0.14 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.057 0.055 -10000 0 -0.26 5 5
TRAF6 0.037 0.004 -10000 0 -10000 0 0
RAC1 0.033 0.012 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PLG 0.034 0.036 -10000 0 -0.48 1 1
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0.015 0.059 -10000 0 -0.28 7 7
SQSTM1 0.036 0.018 -10000 0 -0.21 1 1
NGFRAP1 -0.061 0.2 -10000 0 -0.45 44 44
CASP3 0.001 0.083 0.25 1 -0.3 1 2
E2F1 0.015 0.052 -10000 0 -0.48 2 2
CASP9 0.035 0.01 -10000 0 -10000 0 0
IKK complex 0.062 0.059 -10000 0 -0.43 1 1
NGF (dimer)/TRKA 0.026 0.013 -10000 0 -0.14 1 1
MMP7 -0.12 0.22 -10000 0 -0.39 79 79
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.072 0.058 -10000 0 -0.24 5 5
MMP3 -0.14 0.22 -10000 0 -0.39 90 90
APAF-1/Caspase 9 -0.021 0.086 -10000 0 -0.37 4 4
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.018 0.19 -10000 0 -1.1 6 6
regulation of axonogenesis 0.001 0.066 0.31 7 -10000 0 7
myoblast fusion -0.012 0.08 0.37 8 -10000 0 8
mol:GTP 0.001 0.077 -10000 0 -0.26 10 10
regulation of calcium-dependent cell-cell adhesion -0.034 0.087 0.26 10 -10000 0 10
ARF1/GTP 0.023 0.07 -10000 0 -0.2 9 9
mol:GM1 -0.006 0.056 -10000 0 -0.23 5 5
mol:Choline 0.002 0.047 -10000 0 -0.27 4 4
lamellipodium assembly -0.021 0.12 -10000 0 -0.37 23 23
MAPK3 0 0.088 -10000 0 -0.31 12 12
ARF6/GTP/NME1/Tiam1 0.035 0.088 -10000 0 -0.26 10 10
ARF1 0.036 0.007 -10000 0 -10000 0 0
ARF6/GDP 0.012 0.08 -10000 0 -0.37 8 8
ARF1/GDP 0.004 0.1 -10000 0 -0.31 13 13
ARF6 0.029 0.068 -10000 0 -0.58 2 2
RAB11A 0.032 0.04 -10000 0 -0.35 2 2
TIAM1 0.028 0.054 -10000 0 -0.39 3 3
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.008 0.077 -10000 0 -0.32 8 8
actin filament bundle formation -0.009 0.1 0.3 14 -10000 0 14
KALRN 0.008 0.062 -10000 0 -0.31 7 7
RAB11FIP3/RAB11A 0.044 0.06 -10000 0 -0.38 4 4
RhoA/GDP 0.01 0.1 -10000 0 -0.3 14 14
NME1 0.032 0.038 -10000 0 -0.48 1 1
Rac1/GDP 0.008 0.099 -10000 0 -0.3 12 12
substrate adhesion-dependent cell spreading 0.001 0.077 -10000 0 -0.26 10 10
cortical actin cytoskeleton organization -0.022 0.12 -10000 0 -0.37 23 23
RAC1 0.033 0.012 -10000 0 -10000 0 0
liver development 0.001 0.077 -10000 0 -0.26 10 10
ARF6/GTP 0.001 0.077 -10000 0 -0.26 10 10
RhoA/GTP 0.024 0.07 -10000 0 -0.23 5 5
mol:GDP -0.015 0.1 -10000 0 -0.33 14 14
ARF6/GTP/RAB11FIP3/RAB11A 0.036 0.088 -10000 0 -0.32 6 6
RHOA 0.037 0.005 -10000 0 -10000 0 0
PLD1 0 0.073 -10000 0 -0.26 8 8
RAB11FIP3 0.03 0.061 -10000 0 -0.48 3 3
tube morphogenesis -0.021 0.12 -10000 0 -0.37 23 23
ruffle organization -0.001 0.066 -10000 0 -0.31 7 7
regulation of epithelial cell migration 0.001 0.077 -10000 0 -0.26 10 10
PLD2 0.012 0.046 -10000 0 -0.3 2 2
PIP5K1A -0.001 0.066 -10000 0 -0.31 7 7
mol:Phosphatidic acid 0.002 0.047 -10000 0 -0.27 4 4
Rac1/GTP -0.022 0.12 -10000 0 -0.38 23 23
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.011 0.093 -10000 0 -0.42 8 8
PDGF/PDGFRA/CRKL 0.035 0.079 -10000 0 -0.32 9 9
positive regulation of JUN kinase activity 0.073 0.066 -10000 0 -0.26 6 6
CRKL 0.031 0.05 -10000 0 -0.48 2 2
PDGF/PDGFRA/Caveolin-3 0.04 0.07 -10000 0 -0.34 6 6
AP1 -0.12 0.29 -10000 0 -0.78 28 28
mol:IP3 -0.01 0.05 -10000 0 -0.36 3 3
PLCG1 -0.01 0.05 -10000 0 -0.36 3 3
PDGF/PDGFRA/alphaV Integrin 0.03 0.097 -10000 0 -0.38 10 10
RAPGEF1 0.036 0.017 -10000 0 -0.21 1 1
CRK 0.029 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.01 0.05 -10000 0 -0.36 3 3
CAV3 0.036 0.018 -10000 0 -0.21 1 1
CAV1 0.024 0.064 -10000 0 -0.28 8 8
SHC/Grb2/SOS1 0.075 0.067 -10000 0 -0.26 6 6
PDGF/PDGFRA/Shf -0.027 0.14 -10000 0 -0.29 36 36
FOS -0.12 0.28 -10000 0 -0.77 28 28
JUN -0.05 0.1 -10000 0 -0.37 17 17
oligodendrocyte development 0.03 0.096 -10000 0 -0.38 10 10
GRB2 0.036 0.008 -10000 0 -10000 0 0
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
mol:DAG -0.01 0.05 -10000 0 -0.36 3 3
PDGF/PDGFRA 0.011 0.093 -10000 0 -0.42 8 8
actin cytoskeleton reorganization 0.037 0.072 -10000 0 -0.32 7 7
SRF 0.012 0.031 -10000 0 -0.35 1 1
SHC1 0.036 0.007 -10000 0 -10000 0 0
PI3K 0.056 0.074 -10000 0 -0.29 8 8
PDGF/PDGFRA/Crk/C3G 0.044 0.069 -10000 0 -0.28 6 6
JAK1 -0.003 0.068 -10000 0 -0.34 7 7
ELK1/SRF 0.033 0.089 -10000 0 -0.28 4 4
SHB 0.034 0.025 -10000 0 -0.21 2 2
SHF -0.046 0.16 -10000 0 -0.3 51 51
CSNK2A1 0.028 0.032 -10000 0 -10000 0 0
GO:0007205 -0.007 0.06 0.24 4 -0.38 3 7
SOS1 0.037 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.073 0.066 -10000 0 -0.26 6 6
PDGF/PDGFRA/SHB 0.037 0.072 -10000 0 -0.32 7 7
PDGF/PDGFRA/Caveolin-1 0.029 0.088 -10000 0 -0.38 7 7
ITGAV 0.023 0.082 -10000 0 -0.4 7 7
ELK1 0.002 0.084 0.22 20 -0.31 4 24
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.03 0.069 -10000 0 -0.34 6 6
JAK-STAT cascade -0.003 0.068 -10000 0 -0.34 7 7
cell proliferation -0.027 0.14 -10000 0 -0.29 36 36
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.01 0.037 0.21 1 -0.3 3 4
SNTA1 0.014 0.054 -10000 0 -0.39 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.011 0.042 0.21 1 -0.3 4 5
MAPK12 -0.017 0.09 0.21 9 -0.27 16 25
CCND1 -0.001 0.068 -10000 0 -0.39 4 4
p38 gamma/SNTA1 -0.012 0.087 -10000 0 -0.27 16 16
MAP2K3 0.03 0.015 -10000 0 -10000 0 0
PKN1 0.029 0.063 -10000 0 -0.42 4 4
G2/M transition checkpoint -0.016 0.089 0.21 9 -0.27 16 25
MAP2K6 -0.008 0.097 0.24 9 -0.27 20 29
MAPT -0.007 0.052 -10000 0 -0.23 4 4
MAPK13 0.012 0.036 -10000 0 -0.35 2 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.003 0.072 -10000 0 -0.3 11 11
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.025 0.028 -10000 0 -0.35 1 1
alphaV beta3 Integrin 0.037 0.094 -10000 0 -0.29 11 11
PTK2 0.038 0.1 0.26 4 -0.37 3 7
IGF1R 0.031 0.04 -10000 0 -0.35 2 2
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.017 0.086 -10000 0 -0.35 10 10
SRC 0.012 0.062 -10000 0 -0.48 3 3
CDKN1B 0.016 0.06 -10000 0 -0.39 3 3
VEGFA 0 0 -10000 0 -10000 0 0
ILK 0.022 0.034 -10000 0 -10000 0 0
ROCK1 0.028 0.017 -10000 0 -10000 0 0
AKT1 0.012 0.031 -10000 0 -10000 0 0
PTK2B 0.01 0.048 -10000 0 -0.25 5 5
alphaV/beta3 Integrin/JAM-A 0.043 0.1 -10000 0 -0.27 13 13
CBL 0.037 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.053 0.08 -10000 0 -0.31 8 8
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.049 0.1 -10000 0 -0.3 11 11
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.014 0.048 -10000 0 -0.33 2 2
alphaV/beta3 Integrin/Syndecan-1 0.062 0.064 -10000 0 -0.32 5 5
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.009 0.14 -10000 0 -0.38 12 12
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.089 0.16 -10000 0 -0.3 67 67
RPS6KB1 -0.059 0.11 -10000 0 -0.41 9 9
TLN1 0.036 0.008 -10000 0 -10000 0 0
MAPK3 -0.021 0.14 -10000 0 -0.53 10 10
GPR124 0.021 0.064 -10000 0 -0.28 8 8
MAPK1 -0.017 0.14 -10000 0 -0.56 9 9
PXN 0.037 0.004 -10000 0 -10000 0 0
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
alphaV/beta3 Integrin/Tumstatin 0.06 0.061 -10000 0 -0.3 4 4
cell adhesion 0.026 0.1 -10000 0 -0.28 17 17
ANGPTL3 0.024 0.076 -10000 0 -0.37 7 7
VEGFR2 homodimer/VEGFA homodimer/Src 0.021 0.046 -10000 0 -0.3 3 3
IGF-1R heterotetramer 0.031 0.04 -10000 0 -0.35 2 2
Rac1/GDP 0.024 0.009 -10000 0 -10000 0 0
TGFBR2 0.032 0.05 -10000 0 -0.48 2 2
ITGB3 0.035 0.018 -10000 0 -0.21 1 1
IGF1 0.016 0.082 -10000 0 -0.26 15 15
RAC1 0.033 0.012 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.045 0.075 -10000 0 -0.31 6 6
apoptosis 0.023 0.081 -10000 0 -0.4 7 7
CD47 0.024 0.08 -10000 0 -0.44 6 6
alphaV/beta3 Integrin/CD47 0.053 0.083 -10000 0 -0.33 8 8
VCL 0.034 0.036 -10000 0 -0.48 1 1
alphaV/beta3 Integrin/Del1 0.013 0.13 -10000 0 -0.31 27 27
CSF1 0.035 0.018 -10000 0 -0.21 1 1
PIK3C2A 0.015 0.067 -10000 0 -0.47 3 3
PI4 Kinase/Pyk2 0.006 0.067 -10000 0 -0.23 6 6
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.057 0.058 -10000 0 -0.27 5 5
FAK1/Vinculin 0.057 0.1 0.27 5 -0.3 3 8
alphaV beta3/Integrin/ppsTEM5 0.046 0.076 -10000 0 -0.31 6 6
RHOA 0.037 0.005 -10000 0 -10000 0 0
VTN 0.035 0.009 -10000 0 -10000 0 0
BCAR1 0.036 0.017 -10000 0 -0.21 1 1
FGF2 -0.001 0.12 -10000 0 -0.3 24 24
F11R -0.012 0.09 -10000 0 -0.36 11 11
alphaV/beta3 Integrin/Lactadherin 0.045 0.084 -10000 0 -0.29 10 10
alphaV/beta3 Integrin/TGFBR2 0.059 0.067 -10000 0 -0.3 6 6
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.078 0.065 -10000 0 -0.27 5 5
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.058 0.054 -10000 0 -0.27 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.016 0.13 -10000 0 -0.3 34 34
alphaV/beta3 Integrin/Pyk2 0.039 0.057 -10000 0 -0.25 5 5
SDC1 0.035 0.035 -10000 0 -0.48 1 1
VAV3 -0.046 0.12 -10000 0 -0.27 44 44
PTPN11 0.031 0.053 -10000 0 -0.39 3 3
IRS1 0.018 0.091 -10000 0 -0.37 10 10
FAK1/Paxillin 0.059 0.1 0.27 5 -0.3 3 8
cell migration 0.05 0.097 0.25 6 -0.28 3 9
ITGAV 0.023 0.082 -10000 0 -0.4 7 7
PI3K 0.05 0.11 -10000 0 -0.32 3 3
SPP1 -0.17 0.22 -10000 0 -0.36 113 113
KDR 0.034 0.039 -10000 0 -0.35 2 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.023 0.081 -10000 0 -0.4 7 7
COL4A3 0.032 0.034 -10000 0 -0.21 4 4
angiogenesis -0.019 0.15 -10000 0 -0.56 9 9
Rac1/GTP -0.029 0.11 -10000 0 -0.32 4 4
EDIL3 -0.031 0.16 -10000 0 -0.4 34 34
cell proliferation 0.058 0.067 -10000 0 -0.3 6 6
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.047 0.013 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.037 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.01 0.11 -10000 0 -0.42 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.025 0.038 -10000 0 -0.48 1 1
RAC1-CDC42/GTP/PAK family 0.019 0.027 -10000 0 -0.2 2 2
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.028 0.016 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.035 0.009 -10000 0 -10000 0 0
FYN 0.008 0.11 -10000 0 -0.35 16 16
MAP3K12 0.037 0.006 -10000 0 -10000 0 0
FGR 0.026 0.044 -10000 0 -0.21 7 7
p38 alpha/TAB1 -0.019 0.2 0.27 6 -0.41 28 34
PRKG1 0.036 0.007 -10000 0 -10000 0 0
DUSP8 0.023 0.082 -10000 0 -0.4 7 7
PGK/cGMP/p38 alpha -0.026 0.18 0.22 3 -0.42 25 28
apoptosis -0.018 0.18 0.26 6 -0.39 28 34
RAL/GTP 0.036 0.054 -10000 0 -0.3 5 5
LYN 0.032 0.014 -10000 0 -10000 0 0
DUSP1 0.002 0.1 -10000 0 -0.26 25 25
PAK1 0.032 0.05 -10000 0 -0.48 2 2
SRC 0.012 0.062 -10000 0 -0.48 3 3
RAC1/OSM/MEKK3/MKK3 0.067 0.045 -10000 0 -10000 0 0
TRAF6 0.037 0.004 -10000 0 -10000 0 0
RAC1 0.033 0.012 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.033 0.013 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.04 0.023 -10000 0 -10000 0 0
MAPK11 -0.006 0.19 0.31 11 -0.48 17 28
BLK 0.009 0.088 -10000 0 -0.32 12 12
HCK -0.014 0.11 -10000 0 -0.36 18 18
MAP2K3 0.03 0.015 -10000 0 -10000 0 0
DUSP16 0.024 0.074 -10000 0 -0.39 6 6
DUSP10 0.014 0.098 -10000 0 -0.37 12 12
TRAF6/MEKK3 0.045 0.012 -10000 0 -10000 0 0
MAP3K7IP1 0.035 0.009 -10000 0 -10000 0 0
MAPK14 -0.033 0.21 0.27 7 -0.44 29 36
positive regulation of innate immune response -0.025 0.23 0.33 10 -0.5 24 34
LCK -0.012 0.14 -10000 0 -0.36 26 26
p38alpha-beta/MKP7 -0.018 0.23 0.33 9 -0.52 21 30
p38alpha-beta/MKP5 -0.02 0.23 0.33 8 -0.51 23 31
PGK/cGMP 0.027 0.005 -10000 0 -10000 0 0
PAK2 0.036 0.017 -10000 0 -0.21 1 1
p38alpha-beta/MKP1 -0.022 0.23 0.33 10 -0.49 25 35
CDC42 0.034 0.019 -10000 0 -0.21 1 1
RALB 0.026 0.078 -10000 0 -0.48 5 5
RALA 0.033 0.013 -10000 0 -10000 0 0
PAK3 0.036 0.017 -10000 0 -0.21 1 1
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.019 0.005 -10000 0 -10000 0 0
SMARCC1 0.016 0.064 -10000 0 -0.74 1 1
REL 0.027 0.07 -10000 0 -0.48 4 4
HDAC7 -0.018 0.1 -10000 0 -0.4 10 10
JUN -0.016 0.15 -10000 0 -0.41 26 26
EP300 0.02 0.087 -10000 0 -0.44 7 7
KAT2B 0 0 -10000 0 -10000 0 0
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 -0.002 0.081 -10000 0 -0.35 10 10
FOXO1 0 0 -10000 0 -10000 0 0
T-DHT/AR 0.023 0.13 -10000 0 -0.42 10 10
MAP2K6 0.009 0.11 -10000 0 -0.42 12 12
BRM/BAF57 0.049 0.034 -10000 0 -0.35 1 1
MAP2K4 0.024 0.039 -10000 0 -0.48 1 1
SMARCA2 0.031 0.05 -10000 0 -0.48 2 2
PDE9A -0.095 0.35 -10000 0 -0.98 27 27
NCOA2 0.027 0.051 -10000 0 -0.48 2 2
CEBPA 0.018 0.091 -10000 0 -0.37 10 10
EHMT2 0.038 0.004 -10000 0 -10000 0 0
cell proliferation 0.089 0.16 0.36 14 -0.41 7 21
NR0B1 0.025 0.066 -10000 0 -0.27 9 9
EGR1 -0.057 0.17 -10000 0 -0.32 57 57
RXRs/9cRA 0.059 0.053 -10000 0 -0.27 4 4
AR/RACK1/Src 0.074 0.13 0.29 4 -0.38 7 11
AR/GR 0.004 0.087 -10000 0 -0.27 12 12
GNB2L1 0.036 0.035 -10000 0 -0.48 1 1
PKN1 0.029 0.063 -10000 0 -0.42 4 4
RCHY1 0.029 0.058 -10000 0 -0.32 5 5
epidermal growth factor receptor activity 0.001 0 -10000 0 -10000 0 0
MAPK8 0.01 0.03 -10000 0 -0.34 1 1
T-DHT/AR/TIF2/CARM1 0.02 0.1 -10000 0 -0.37 8 8
SRC 0.029 0.12 0.19 54 -0.34 10 64
NR3C1 0.021 0.087 -10000 0 -0.44 7 7
KLK3 -0.047 0.11 -10000 0 -0.46 1 1
APPBP2 0.032 0.024 -10000 0 -0.2 1 1
TRIM24 0.032 0.05 -10000 0 -0.48 2 2
T-DHT/AR/TIP60 -0.022 0.077 -10000 0 -0.33 10 10
TMPRSS2 -0.022 0.21 -10000 0 -0.88 8 8
RXRG 0.022 0.077 -10000 0 -0.35 8 8
mol:9cRA 0 0 -10000 0 -0.003 1 1
RXRA 0.037 0.006 -10000 0 -10000 0 0
RXRB 0.037 0.004 -10000 0 -10000 0 0
CARM1 0.038 0.004 -10000 0 -10000 0 0
NR2C2 0.037 0.005 -10000 0 -10000 0 0
KLK2 0.052 0.1 0.31 4 -0.46 2 6
AR -0.002 0.063 -10000 0 -0.24 11 11
SENP1 0.037 0.005 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 0.034 0.018 -10000 0 -0.21 1 1
SRY 0.03 0.046 -10000 0 -0.28 4 4
GATA2 0.031 0.053 -10000 0 -0.39 3 3
MYST2 0.036 0.007 -10000 0 -10000 0 0
HOXB13 -0.11 0.2 -10000 0 -0.34 83 83
T-DHT/AR/RACK1/Src 0.077 0.14 0.31 7 -0.4 7 14
positive regulation of transcription 0.031 0.053 -10000 0 -0.39 3 3
DNAJA1 0.032 0.025 -10000 0 -0.23 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.034 -10000 0 -0.32 2 2
NCOA1 0.031 0.078 -10000 0 -0.54 4 4
SPDEF -0.073 0.18 -10000 0 -0.32 66 66
T-DHT/AR/TIF2 -0.002 0.091 -10000 0 -0.36 7 7
T-DHT/AR/Hsp90 -0.022 0.077 -10000 0 -0.33 10 10
GSK3B 0.035 0.036 -10000 0 -0.48 1 1
NR2C1 0.035 0.018 -10000 0 -0.21 1 1
mol:T-DHT -0.014 0.075 0.21 3 -0.32 10 13
SIRT1 0.033 0.04 -10000 0 -0.35 2 2
ZMIZ2 -0.001 0.001 -10000 0 -10000 0 0
POU2F1 0.023 0.079 -10000 0 -0.34 6 6
T-DHT/AR/DAX-1 -0.006 0.1 -10000 0 -0.36 11 11
CREBBP 0.034 0.036 -10000 0 -0.48 1 1
SMARCE1 0.036 0.009 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.019 0.087 -10000 0 -0.44 7 7
HSPA8 0.037 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.02 0.1 -10000 0 -0.28 10 10
AKT1 0.028 0.035 -10000 0 -0.2 3 3
GSC -0.036 0.18 -10000 0 -1.2 2 2
NKX2-5 0.029 0.032 -10000 0 -0.21 1 1
muscle cell differentiation 0.059 0.18 0.49 17 -10000 0 17
SMAD2-3/SMAD4/SP1 0.025 0.13 -10000 0 -0.36 6 6
SMAD4 0.004 0.077 -10000 0 -0.46 3 3
CBFB 0.037 0.003 -10000 0 -10000 0 0
SAP18 0.026 0.017 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.021 0.11 -10000 0 -0.33 12 12
SMAD3/SMAD4/VDR 0.026 0.12 -10000 0 -0.29 11 11
MYC 0.005 0.11 -10000 0 -0.48 10 10
CDKN2B -0.039 0.22 -10000 0 -1.5 4 4
AP1 -0.065 0.18 -10000 0 -0.47 25 25
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.028 0.15 -10000 0 -0.39 22 22
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.052 0.13 -10000 0 -0.36 19 19
SP3 0.037 0.015 -10000 0 -10000 0 0
CREB1 0.037 0.004 -10000 0 -10000 0 0
FOXH1 0.026 0.051 -10000 0 -0.29 3 3
SMAD3/SMAD4/GR 0.012 0.11 -10000 0 -0.34 10 10
GATA3 0.03 0.058 -10000 0 -0.38 3 3
SKI/SIN3/HDAC complex/NCoR1 0.024 0.082 -10000 0 -0.26 8 8
MEF2C/TIF2 -0.005 0.13 0.31 1 -0.49 10 11
endothelial cell migration -0.004 0.14 1.4 2 -10000 0 2
MAX 0.033 0.013 -10000 0 -10000 0 0
RBBP7 0.035 0.024 -10000 0 -0.21 2 2
RBBP4 0.033 0.03 -10000 0 -0.21 3 3
RUNX2 0.036 0.018 -10000 0 -0.21 1 1
RUNX3 -0.019 0.14 -10000 0 -0.35 30 30
RUNX1 0.015 0.089 -10000 0 -0.32 12 12
CTBP1 0.036 0.007 -10000 0 -10000 0 0
NR3C1 0.021 0.088 -10000 0 -0.44 7 7
VDR 0.024 0.08 -10000 0 -0.44 6 6
CDKN1A -0.04 0.22 -10000 0 -1.2 6 6
KAT2B 0 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.028 0.094 -10000 0 -0.36 4 4
DCP1A 0.037 0.005 -10000 0 -10000 0 0
SKI 0.038 0 -10000 0 -10000 0 0
SERPINE1 0.003 0.15 -10000 0 -1.4 2 2
SMAD3/SMAD4/ATF2 0.021 0.092 -10000 0 -0.27 7 7
SMAD3/SMAD4/ATF3 0.01 0.1 -10000 0 -0.3 7 7
SAP30 0.033 0.036 -10000 0 -0.48 1 1
Cbp/p300/PIAS3 0.052 0.074 -10000 0 -0.3 7 7
JUN -0.077 0.17 -10000 0 -0.47 25 25
SMAD3/SMAD4/IRF7 0.023 0.1 -10000 0 -0.32 5 5
TFE3 0.038 0.024 -10000 0 -10000 0 0
COL1A2 -0.06 0.24 -10000 0 -0.83 18 18
mesenchymal cell differentiation -0.02 0.092 0.29 6 -10000 0 6
DLX1 0.028 0.047 -10000 0 -0.21 8 8
TCF3 0.028 0.061 -10000 0 -0.48 3 3
FOS -0.075 0.17 -10000 0 -0.33 58 58
SMAD3/SMAD4/Max 0.021 0.092 -10000 0 -0.26 8 8
Cbp/p300/SNIP1 0.054 0.071 -10000 0 -0.3 7 7
ZBTB17 0.034 0.013 -10000 0 -10000 0 0
LAMC1 -0.006 0.084 -10000 0 -0.45 3 3
TGIF2/HDAC complex/SMAD3/SMAD4 -0.014 0.11 -10000 0 -0.33 19 19
IRF7 0.038 0.022 -10000 0 -10000 0 0
ESR1 0.031 0.065 -10000 0 -0.42 4 4
HNF4A 0.009 0.07 -10000 0 -0.48 4 4
MEF2C -0.018 0.14 0.31 1 -0.51 12 13
SMAD2-3/SMAD4 0.017 0.1 -10000 0 -0.32 4 4
Cbp/p300/Src-1 0.047 0.086 -10000 0 -0.3 11 11
IGHV3OR16-13 0.004 0.028 -10000 0 -10000 0 0
TGIF2/HDAC complex -0.014 0.12 -10000 0 -0.48 14 14
CREBBP 0.034 0.036 -10000 0 -0.48 1 1
SKIL 0.005 0.12 -10000 0 -0.4 16 16
HDAC1 0.036 0.008 -10000 0 -10000 0 0
HDAC2 0.034 0.036 -10000 0 -0.48 1 1
SNIP1 0.037 0.006 -10000 0 -10000 0 0
GCN5L2 0.032 0.037 -10000 0 -0.48 1 1
SMAD3/SMAD4/TFE3 0.025 0.1 -10000 0 -0.33 5 5
MSG1/HSC70 0.019 0.088 -10000 0 -0.35 5 5
SMAD2 0.019 0.048 -10000 0 -0.54 1 1
SMAD3 0.004 0.089 -10000 0 -0.43 5 5
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.011 0.081 -10000 0 -0.34 5 5
SMAD2/SMAD2/SMAD4 -0.073 0.095 -10000 0 -0.22 54 54
NCOR1 0.028 0.016 -10000 0 -10000 0 0
NCOA2 0.026 0.051 -10000 0 -0.48 2 2
NCOA1 0.028 0.07 -10000 0 -0.48 4 4
MYOD/E2A 0.03 0.079 -10000 0 -0.37 5 5
SMAD2-3/SMAD4/SP1/MIZ-1 0.037 0.13 -10000 0 -0.4 3 3
IFNB1 -0.011 0.094 -10000 0 -0.53 4 4
SMAD3/SMAD4/MEF2C -0.006 0.15 -10000 0 -0.51 12 12
CITED1 -0.009 0.11 -10000 0 -0.25 35 35
SMAD2-3/SMAD4/ARC105 0.019 0.092 -10000 0 -0.28 4 4
RBL1 0.012 0.062 -10000 0 -0.48 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.001 0.14 -10000 0 -0.55 7 7
RUNX1-3/PEBPB2 0.012 0.12 -10000 0 -0.3 20 20
SMAD7 -0.061 0.19 -10000 0 -0.55 11 11
MYC/MIZ-1 0.021 0.086 -10000 0 -0.35 10 10
SMAD3/SMAD4 -0.054 0.14 -10000 0 -0.4 18 18
IL10 -0.005 0.079 -10000 0 -0.37 2 2
PIASy/HDAC complex 0.035 0.019 -10000 0 -0.2 1 1
PIAS3 0.034 0.025 -10000 0 -0.21 2 2
CDK2 0.021 0.074 -10000 0 -0.29 10 10
IL5 -0.011 0.09 -10000 0 -0.42 2 2
CDK4 0.036 0.009 -10000 0 -10000 0 0
PIAS4 0.035 0.019 -10000 0 -0.2 1 1
ATF3 0.018 0.07 -10000 0 -0.23 15 15
SMAD3/SMAD4/SP1 0.01 0.13 -10000 0 -0.34 11 11
FOXG1 -0.001 0.003 -10000 0 -10000 0 0
FOXO3 0.007 0.022 -10000 0 -10000 0 0
FOXO1 0.007 0.022 -10000 0 -10000 0 0
FOXO4 0.007 0.022 -10000 0 -10000 0 0
heart looping -0.017 0.13 0.31 1 -0.5 12 13
CEBPB 0.015 0.04 -10000 0 -0.48 1 1
SMAD3/SMAD4/DLX1 0.017 0.097 -10000 0 -0.27 8 8
MYOD1 0.015 0.079 -10000 0 -0.24 17 17
SMAD3/SMAD4/HNF4 0.002 0.09 -10000 0 -0.32 9 9
SMAD3/SMAD4/GATA3 0.02 0.11 -10000 0 -0.38 3 3
SnoN/SIN3/HDAC complex/NCoR1 0.005 0.12 -10000 0 -0.4 16 16
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.008 0.14 -10000 0 -0.3 17 17
SMAD3/SMAD4/SP1-3 0.028 0.13 -10000 0 -0.37 7 7
MED15 0 0 -10000 0 -10000 0 0
SP1 0.015 0.064 -10000 0 -0.21 7 7
SIN3B 0.037 0.004 -10000 0 -10000 0 0
SIN3A 0.034 0.019 -10000 0 -0.21 1 1
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.037 0.12 -10000 0 -0.31 11 11
ITGB5 -0.015 0.11 -10000 0 -0.42 8 8
TGIF/SIN3/HDAC complex/CtBP 0.038 0.071 -10000 0 -0.32 3 3
SMAD3/SMAD4/AR 0.009 0.1 -10000 0 -0.28 9 9
AR 0.02 0.077 -10000 0 -0.28 12 12
negative regulation of cell growth -0.01 0.094 -10000 0 -0.45 4 4
SMAD3/SMAD4/MYOD 0.007 0.11 -10000 0 -0.3 10 10
E2F5 0.008 0.1 -10000 0 -0.46 10 10
E2F4 0.036 0.017 -10000 0 -0.21 1 1
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.045 0.11 -10000 0 -0.28 9 9
SMAD2-3/SMAD4/FOXO1-3a-4 -0.011 0.11 -10000 0 -0.39 13 13
TFDP1 0.023 0.039 -10000 0 -0.48 1 1
SMAD3/SMAD4/AP1 -0.051 0.2 -10000 0 -0.47 25 25
SMAD3/SMAD4/RUNX2 0.021 0.093 -10000 0 -0.3 6 6
TGIF2 -0.014 0.12 -10000 0 -0.48 14 14
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 0.037 0.004 -10000 0 -10000 0 0
mTOR signaling pathway

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
GBL 0.036 0.017 -10000 0 -0.21 1 1
MKNK1 0.037 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.004 0.06 0.25 1 -0.29 7 8
FRAP1 -0.03 0.18 -10000 0 -0.55 19 19
AKT1 -0.008 0.077 0.23 4 -0.3 8 12
INSR 0.023 0.076 -10000 0 -0.37 7 7
Insulin Receptor/Insulin 0.04 0.046 -10000 0 -0.3 3 3
mol:GTP 0.023 0.081 0.25 1 -0.33 3 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.008 0.062 -10000 0 -0.22 8 8
TSC2 0.037 0.005 -10000 0 -10000 0 0
RHEB/GDP 0.013 0.068 -10000 0 -0.3 3 3
TSC1 0.034 0.036 -10000 0 -0.48 1 1
Insulin Receptor/IRS1 0.012 0.088 -10000 0 -0.34 11 11
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.008 0.08 -10000 0 -0.26 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 -0.003 0.11 0.24 2 -0.39 8 10
MAP3K5 -0.007 0.072 0.19 1 -0.28 12 13
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
apoptosis -0.007 0.072 0.19 1 -0.28 12 13
mol:LY294002 0 0 0.001 3 -0.001 7 10
EIF4B -0.003 0.1 0.24 3 -0.35 8 11
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.009 0.099 0.22 2 -0.34 7 9
eIF4E/eIF4G1/eIF4A1 -0.01 0.11 -10000 0 -0.32 17 17
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.033 0.079 -10000 0 -0.28 11 11
mTOR/RHEB/GTP/Raptor/GBL 0.018 0.071 0.25 3 -0.25 3 6
FKBP1A 0.028 0.038 -10000 0 -0.49 1 1
RHEB/GTP 0.031 0.077 0.24 1 -0.3 3 4
mol:Amino Acids 0 0 0.001 3 -0.001 7 10
FKBP12/Rapamycin 0.021 0.028 -10000 0 -0.35 1 1
PDPK1 -0.017 0.059 0.17 3 -0.27 8 11
EIF4E 0.037 0.005 -10000 0 -10000 0 0
ASK1/PP5C -0.018 0.2 -10000 0 -0.56 19 19
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.03 0.043 -10000 0 -10000 0 0
TSC1/TSC2 0.026 0.087 0.27 1 -0.35 3 4
tumor necrosis factor receptor activity 0 0 0.001 7 -0.001 3 10
RPS6 0.034 0.025 -10000 0 -0.21 2 2
PPP5C 0.036 0.017 -10000 0 -0.21 1 1
EIF4G1 0.029 0.057 -10000 0 -0.32 5 5
IRS1 -0.004 0.069 -10000 0 -0.33 9 9
INS 0.036 0.007 -10000 0 -10000 0 0
PTEN 0.031 0.05 -10000 0 -0.48 2 2
PDK2 -0.016 0.056 0.17 3 -0.27 7 10
EIF4EBP1 -0.058 0.32 -10000 0 -1.1 17 17
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
PPP2R5D -0.021 0.16 -10000 0 -0.48 19 19
peptide biosynthetic process 0.011 0.076 0.19 5 -0.33 8 13
RHEB 0.036 0.008 -10000 0 -10000 0 0
EIF4A1 0.029 0.016 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 8 -0.003 8 16
EEF2 0.011 0.076 0.19 5 -0.33 8 13
eIF4E/4E-BP1 -0.036 0.3 -10000 0 -1 17 17
Class I PI3K 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
ARF5/GTP -0.022 0.053 0.22 2 -0.24 7 9
DAPP1 -0.038 0.21 0.24 5 -0.52 23 28
Src family/SYK family/BLNK-LAT/BTK-ITK -0.059 0.25 0.29 1 -0.57 30 31
mol:DAG 0.017 0.11 0.19 36 -0.28 10 46
HRAS 0.034 0.038 -10000 0 -0.33 2 2
RAP1A 0.035 0.014 -10000 0 -10000 0 0
ARF5/GDP 0.042 0.1 -10000 0 -0.28 8 8
PLCG2 -0.009 0.13 -10000 0 -0.33 27 27
PLCG1 0.019 0.019 -10000 0 -10000 0 0
ARF5 0.031 0.05 -10000 0 -0.48 2 2
mol:GTP -0.02 0.05 0.18 2 -0.25 5 7
ARF1/GTP -0.011 0.045 0.19 2 -0.23 5 7
RHOA 0.037 0.005 -10000 0 -10000 0 0
YES1 0.028 0.016 -10000 0 -10000 0 0
RAP1A/GTP -0.014 0.058 0.17 8 -0.25 5 13
ADAP1 -0.02 0.046 0.18 2 -0.24 5 7
ARAP3 -0.02 0.049 0.18 2 -0.24 5 7
INPPL1 0.034 0.039 -10000 0 -0.35 2 2
PREX1 0.001 0.088 -10000 0 -0.39 9 9
ARHGEF6 0.032 0.053 -10000 0 -0.39 3 3
ARHGEF7 0.026 0.018 -10000 0 -10000 0 0
ARF1 0.036 0.007 -10000 0 -10000 0 0
NRAS 0.021 0.08 -10000 0 -0.34 9 9
FYN 0.008 0.11 -10000 0 -0.35 16 16
ARF6 0.029 0.051 -10000 0 -0.48 2 2
FGR 0.026 0.044 -10000 0 -0.21 7 7
mol:Ca2+ 0.015 0.066 0.15 10 -0.14 7 17
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.029 0.053 -10000 0 -0.39 3 3
ZAP70 0.031 0.053 -10000 0 -0.39 3 3
mol:IP3 0.01 0.082 0.17 8 -0.19 9 17
LYN 0.032 0.014 -10000 0 -10000 0 0
ARF1/GDP 0.046 0.1 -10000 0 -0.28 8 8
RhoA/GDP 0.048 0.08 0.24 2 -0.27 1 3
PDK1/Src/Hsp90 0.021 0.046 -10000 0 -0.3 3 3
BLNK 0.007 0.12 -10000 0 -0.44 13 13
actin cytoskeleton reorganization 0.034 0.1 0.24 3 -0.38 4 7
SRC 0.012 0.062 -10000 0 -0.48 3 3
PLEKHA2 -0.006 0.02 -10000 0 -0.3 1 1
RAC1 0.033 0.012 -10000 0 -10000 0 0
PTEN 0.031 0.049 -10000 0 -0.46 2 2
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.02 0.055 0.22 2 -0.24 7 9
RhoA/GTP -0.015 0.058 0.2 2 -0.24 5 7
Src family/SYK family/BLNK-LAT -0.039 0.15 -10000 0 -0.53 14 14
BLK 0.009 0.088 -10000 0 -0.32 12 12
PDPK1 0.034 0.039 -10000 0 -0.35 2 2
CYTH1 -0.02 0.046 0.18 2 -0.24 5 7
HCK -0.014 0.11 -10000 0 -0.36 18 18
CYTH3 -0.02 0.046 0.18 2 -0.24 5 7
CYTH2 -0.02 0.046 0.18 2 -0.24 5 7
KRAS 0.032 0.041 -10000 0 -0.35 2 2
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0 0.045 0.18 1 -0.26 4 5
SGK1 0.001 0.047 0.18 1 -0.27 4 5
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.033 0.099 -10000 0 -0.28 9 9
SOS1 0.037 0.003 -10000 0 -10000 0 0
SYK 0.031 0.053 -10000 0 -0.39 3 3
ARF6/GDP 0.024 0.078 0.22 2 -0.3 2 4
mol:PI-3-4-5-P3 -0.02 0.05 0.23 2 -0.25 5 7
ARAP3/RAP1A/GTP -0.015 0.059 0.17 8 -0.25 5 13
VAV1 0.003 0.12 -10000 0 -0.42 16 16
mol:PI-3-4-P2 0.008 0.026 -10000 0 -0.24 2 2
RAS family/GTP/PI3K Class I 0.051 0.071 -10000 0 -0.25 5 5
PLEKHA1 -0.007 0.021 -10000 0 -0.3 1 1
Rac1/GDP 0.038 0.098 -10000 0 -0.28 7 7
LAT 0.026 0.064 -10000 0 -0.28 8 8
Rac1/GTP 0.002 0.076 -10000 0 -0.42 4 4
ITK -0.028 0.056 0.18 1 -0.24 9 10
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.01 0.14 0.26 9 -0.38 12 21
LCK -0.012 0.14 -10000 0 -0.36 26 26
BTK -0.038 0.076 0.18 2 -0.26 17 19
Regulation of Telomerase

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
Telomerase catalytic core complex -0.052 0.19 -10000 0 -0.9 6 6
RAD9A 0.037 0.004 -10000 0 -10000 0 0
AP1 -0.069 0.17 -10000 0 -0.35 46 46
IFNAR2 0.034 0.021 -10000 0 -0.21 1 1
AKT1 0.024 0.032 -10000 0 -10000 0 0
ER alpha/Oestrogen 0.021 0.051 -10000 0 -0.35 4 4
NFX1/SIN3/HDAC complex 0.038 0.069 -10000 0 -0.3 2 2
EGF -0.093 0.19 -10000 0 -0.32 79 79
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.052 0.033 -10000 0 -0.35 1 1
TERT/c-Abl -0.04 0.19 -10000 0 -0.84 6 6
SAP18 0.026 0.018 -10000 0 -10000 0 0
MRN complex 0.057 0.047 -10000 0 -0.3 2 2
WT1 -0.2 0.22 -10000 0 -0.36 131 131
WRN 0.028 0.022 -10000 0 -0.21 1 1
SP1 0.036 0.022 -10000 0 -0.21 1 1
SP3 0.038 0.004 -10000 0 -10000 0 0
TERF2IP 0.037 0.004 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.032 0.18 -10000 0 -0.74 7 7
Mad/Max 0.043 0.047 -10000 0 -0.17 7 7
TERT -0.054 0.2 -10000 0 -0.94 6 6
CCND1 -0.057 0.21 -10000 0 -0.96 8 8
MAX 0.034 0.012 -10000 0 -10000 0 0
RBBP7 0.036 0.024 -10000 0 -0.21 2 2
RBBP4 0.033 0.03 -10000 0 -0.21 3 3
TERF2 0.032 0.033 -10000 0 -0.43 1 1
PTGES3 0.037 0.005 -10000 0 -10000 0 0
SIN3A 0.034 0.019 -10000 0 -0.21 1 1
Telomerase/911 0.043 0.059 -10000 0 -0.36 2 2
CDKN1B -0.08 0.15 -10000 0 -0.33 42 42
RAD1 0.033 0.04 -10000 0 -0.35 2 2
XRCC5 0.037 0.004 -10000 0 -10000 0 0
XRCC6 0.035 0.009 -10000 0 -10000 0 0
SAP30 0.033 0.036 -10000 0 -0.48 1 1
TRF2/PARP2 0.049 0.048 -10000 0 -0.33 3 3
UBE3A 0.038 0.002 -10000 0 -10000 0 0
JUN -0.016 0.15 -10000 0 -0.41 26 26
E6 0 0.002 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.028 0.008 -10000 0 -10000 0 0
FOS -0.063 0.17 -10000 0 -0.32 58 58
IFN-gamma/IRF1 -0.075 0.18 -10000 0 -0.34 55 55
PARP2 0.032 0.053 -10000 0 -0.39 3 3
BLM 0.023 0.079 -10000 0 -0.48 5 5
Telomerase 0.034 0.045 0.16 1 -10000 0 1
IRF1 0.003 0.11 -10000 0 -0.29 23 23
ESR1 0.027 0.07 -10000 0 -0.48 4 4
KU/TER 0.052 0.015 -10000 0 -10000 0 0
ATM/TRF2 0.047 0.043 -10000 0 -0.28 2 2
ubiquitin-dependent protein catabolic process 0.017 0.058 -10000 0 -0.3 1 1
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.017 0.059 -10000 0 -0.31 1 1
HDAC1 0.036 0.008 -10000 0 -10000 0 0
HDAC2 0.034 0.038 -10000 0 -0.48 1 1
ATM 0.012 0.033 0.2 1 -0.39 1 2
SMAD3 0.01 0.053 -10000 0 -0.33 5 5
ABL1 0.037 0.006 -10000 0 -10000 0 0
MXD1 0.028 0.056 -10000 0 -0.24 8 8
MRE11A 0.037 0.005 -10000 0 -10000 0 0
HUS1 0.029 0.041 -10000 0 -0.35 2 2
RPS6KB1 0.035 0.019 -10000 0 -0.21 1 1
TERT/NF kappa B1/14-3-3 -0.021 0.19 -10000 0 -0.98 4 4
NR2F2 0.033 0.019 -10000 0 -0.21 1 1
MAPK3 0.012 0.053 -10000 0 -0.35 4 4
MAPK1 0.019 0.01 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.036 0.017 -10000 0 -0.21 1 1
NFKB1 0.037 0.006 -10000 0 -10000 0 0
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.012 0.033 0.2 1 -0.39 1 2
NBN 0.028 0.038 -10000 0 -0.48 1 1
EGFR 0.016 0.088 -10000 0 -0.42 8 8
mol:Oestrogen 0 0.001 -10000 0 -10000 0 0
EGF/EGFR -0.053 0.15 -10000 0 -0.35 33 33
MYC 0.005 0.11 -10000 0 -0.48 10 10
IL2 0.037 0.014 -10000 0 -10000 0 0
KU 0.052 0.015 -10000 0 -10000 0 0
RAD50 0.032 0.05 -10000 0 -0.48 2 2
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.036 0.017 -10000 0 -0.21 1 1
TRF2/BLM 0.04 0.066 -10000 0 -0.33 6 6
FRAP1 0.033 0.036 -10000 0 -0.48 1 1
KU/TERT -0.032 0.19 -10000 0 -0.84 6 6
SP1/HDAC2 0.052 0.038 -10000 0 -0.35 1 1
PINX1 0.025 0.042 -10000 0 -0.35 2 2
Telomerase/EST1A -0.042 0.17 -10000 0 -0.75 6 6
Smad3/Myc 0.01 0.085 -10000 0 -0.31 13 13
911 complex 0.058 0.048 -10000 0 -0.3 2 2
IFNG -0.1 0.2 -10000 0 -0.32 85 85
Telomerase/PinX1 -0.039 0.17 -10000 0 -0.76 6 6
Telomerase/AKT1/mTOR/p70S6K 0.019 0.065 -10000 0 -0.4 1 1
SIN3B 0.037 0.005 -10000 0 -10000 0 0
YWHAE 0.029 0.016 -10000 0 -10000 0 0
Telomerase/EST1B -0.042 0.17 -10000 0 -0.75 6 6
response to DNA damage stimulus 0.003 0.023 -10000 0 -0.12 3 3
MRN complex/TRF2/Rap1 0.08 0.061 -10000 0 -0.26 3 3
TRF2/WRN 0.04 0.036 -10000 0 -0.34 1 1
Telomerase/hnRNP C1/C2 -0.042 0.17 -10000 0 -0.75 6 6
E2F1 0.015 0.052 -10000 0 -0.48 2 2
ZNFX1 0 0.001 -10000 0 -10000 0 0
PIF1 0 0 -10000 0 -10000 0 0
NCL 0.027 0.07 -10000 0 -0.48 4 4
DKC1 0.036 0.017 -10000 0 -0.21 1 1
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Insulin Pathway

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
CBL/APS/CAP 0.025 0.11 -10000 0 -0.28 20 20
TC10/GTP 0.012 0.084 -10000 0 -0.24 16 16
Insulin Receptor/Insulin/IRS1/Shp2 0.084 0.11 -10000 0 -0.4 7 7
HRAS 0.034 0.039 -10000 0 -0.35 2 2
APS homodimer 0 0 -10000 0 -10000 0 0
GRB14 -0.17 0.22 -10000 0 -0.36 112 112
FOXO3 -0.02 0.027 -10000 0 -10000 0 0
AKT1 -0.083 0.12 -10000 0 -0.37 11 11
INSR 0.037 0.077 -10000 0 -0.38 6 6
Insulin Receptor/Insulin 0.099 0.11 -10000 0 -0.4 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 -0.002 0.12 -10000 0 -0.4 17 17
SORBS1 -0.018 0.14 -10000 0 -0.36 29 29
CRK 0.029 0.016 -10000 0 -10000 0 0
PTPN1 0.003 0.051 -10000 0 -0.4 2 2
CAV1 0.018 0.082 0.21 2 -0.29 9 11
CBL/APS/CAP/Crk-II/C3G 0.03 0.097 -10000 0 -0.25 16 16
Insulin Receptor/Insulin/IRS1/NCK2 0.086 0.094 -10000 0 -0.33 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.06 0.091 -10000 0 -0.31 9 9
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.064 0.11 -10000 0 -0.54 4 4
RPS6KB1 -0.078 0.11 -10000 0 -0.34 11 11
PARD6A 0.01 0.11 -10000 0 -0.39 14 14
CBL 0.037 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.022 0.074 -10000 0 -0.7 2 2
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.054 0.13 -10000 0 -0.36 10 10
HRAS/GTP 0.013 0.062 -10000 0 -0.32 4 4
Insulin Receptor 0.037 0.077 -10000 0 -0.38 6 6
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.094 0.095 -10000 0 -0.31 7 7
PRKCI 0.007 0.1 -10000 0 -0.63 3 3
Insulin Receptor/Insulin/GRB14/PDK1 -0.07 0.14 -10000 0 -0.28 38 38
SHC1 0.036 0.007 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.044 0.096 -10000 0 -0.54 4 4
PI3K 0.075 0.098 -10000 0 -0.31 9 9
NCK2 0.036 0.017 -10000 0 -0.21 1 1
RHOQ 0.033 0.042 -10000 0 -0.3 3 3
mol:H2O2 0.001 0.008 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.028 -10000 0 -0.24 2 2
AKT2 -0.079 0.13 -10000 0 -0.4 9 9
PRKCZ -0.007 0.08 -10000 0 -0.44 4 4
SH2B2 0 0 -10000 0 -10000 0 0
SHC/SHIP 0.025 0.071 0.19 2 -0.29 7 9
F2RL2 0.015 0.1 -10000 0 -0.48 9 9
TRIP10 0.037 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.075 0.054 -10000 0 -0.25 3 3
TC10/GTP/CIP4/Exocyst 0.046 0.029 -10000 0 -0.3 1 1
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.11 0.062 -10000 0 -0.24 2 2
RAPGEF1 0.036 0.017 -10000 0 -0.21 1 1
RASA1 0.025 0.072 -10000 0 -0.43 5 5
NCK1 0.027 0.07 -10000 0 -0.48 4 4
CBL/APS/CAP/Crk-II 0.019 0.094 -10000 0 -0.27 16 16
TC10/GDP 0.024 0.03 -10000 0 -0.21 3 3
Insulin Receptor/Insulin/SHC/GRB10 0.059 0.11 -10000 0 -0.27 14 14
INPP5D -0.002 0.064 -10000 0 -0.3 7 7
SOS1 0.037 0.003 -10000 0 -10000 0 0
SGK1 -0.01 0.011 -10000 0 -10000 0 0
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.031 0.053 -10000 0 -0.39 3 3
IRS1 0.018 0.091 -10000 0 -0.37 10 10
p62DOK/RasGAP 0.044 0.097 -10000 0 -0.55 4 4
INS 0.048 0.02 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.002 0.064 -10000 0 -0.3 7 7
GRB2 0.036 0.008 -10000 0 -10000 0 0
EIF4EBP1 -0.08 0.11 -10000 0 -0.38 9 9
PTPRA 0.035 0.043 -10000 0 -0.49 1 1
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.046 0.029 -10000 0 -0.3 1 1
PDPK1 0.034 0.039 -10000 0 -0.35 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.036 0.072 -10000 0 -0.41 3 3
Insulin Receptor/Insulin/IRS1 0.065 0.087 -10000 0 -0.32 7 7
Insulin Receptor/Insulin/IRS3 0.065 0.062 -10000 0 -0.34 3 3
Par3/Par6 0.048 0.1 -10000 0 -0.26 19 19
Plasma membrane estrogen 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
GNB1/GNG2 0.07 0.056 -10000 0 -0.26 4 4
ER alpha/Gai/GDP/Gbeta gamma 0.002 0.12 -10000 0 -0.44 9 9
AKT1 0.01 0.17 -10000 0 -0.7 10 10
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.016 0.17 -10000 0 -0.7 10 10
mol:Ca2+ -0.038 0.14 -10000 0 -0.4 18 18
IGF1R 0.031 0.04 -10000 0 -0.35 2 2
E2/ER alpha (dimer)/Striatin 0.04 0.055 -10000 0 -0.3 5 5
SHC1 0.036 0.007 -10000 0 -10000 0 0
apoptosis -0.011 0.16 0.67 10 -10000 0 10
RhoA/GTP 0.018 0.06 -10000 0 -0.24 9 9
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.063 0.13 -10000 0 -0.37 4 4
regulation of stress fiber formation 0.028 0.078 0.3 3 -10000 0 3
E2/ERA-ERB (dimer) 0.037 0.05 -10000 0 -0.3 4 4
KRAS 0.033 0.04 -10000 0 -0.35 2 2
G13/GTP 0.039 0.044 -10000 0 -0.27 4 4
pseudopodium formation -0.028 0.078 -10000 0 -0.3 3 3
E2/ER alpha (dimer)/PELP1 0.033 0.049 -10000 0 -0.29 4 4
GRB2 0.036 0.008 -10000 0 -10000 0 0
GNG2 0.034 0.011 -10000 0 -10000 0 0
GNAO1 0.037 0.003 -10000 0 -10000 0 0
HRAS 0.034 0.039 -10000 0 -0.35 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.009 0.14 -10000 0 -0.43 13 13
E2/ER beta (dimer) 0.024 0.014 -10000 0 -0.14 1 1
mol:GDP 0.006 0.077 -10000 0 -0.33 6 6
mol:NADP 0.009 0.14 -10000 0 -0.43 13 13
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
mol:IP3 -0.048 0.13 -10000 0 -0.42 17 17
IGF-1R heterotetramer 0.031 0.04 -10000 0 -0.35 2 2
PLCB1 -0.052 0.14 -10000 0 -0.32 37 37
PLCB2 -0.027 0.12 -10000 0 -0.41 19 19
IGF1 0.016 0.082 -10000 0 -0.26 15 15
mol:L-citrulline 0.009 0.14 -10000 0 -0.43 13 13
RHOA 0.037 0.005 -10000 0 -10000 0 0
Gai/GDP 0.007 0.16 -10000 0 -0.74 8 8
JNK cascade 0.024 0.014 -10000 0 -0.14 1 1
BCAR1 0.036 0.017 -10000 0 -0.21 1 1
ESR2 0.032 0.02 -10000 0 -0.21 1 1
GNAQ 0 0 -10000 0 -10000 0 0
ESR1 0.027 0.07 -10000 0 -0.48 4 4
Gq family/GDP/Gbeta gamma -0.013 0.16 -10000 0 -0.6 13 13
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.041 0.11 -10000 0 -0.61 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.063 0.13 -10000 0 -0.37 4 4
GNAZ 0.024 0.064 -10000 0 -0.28 8 8
E2/ER alpha (dimer) 0.02 0.051 -10000 0 -0.35 4 4
STRN 0.033 0.042 -10000 0 -0.3 3 3
GNAL 0.025 0.028 -10000 0 -0.21 2 2
PELP1 0.029 0.016 -10000 0 -10000 0 0
MAPK11 0.016 0.015 -10000 0 -10000 0 0
GNAI2 0.026 0.072 -10000 0 -0.43 5 5
GNAI3 0.034 0.036 -10000 0 -0.48 1 1
GNAI1 -0.011 0.14 -10000 0 -0.4 23 23
HBEGF 0.11 0.17 0.33 56 -0.44 3 59
cAMP biosynthetic process 0.023 0.044 -10000 0 -0.23 4 4
SRC 0.065 0.12 -10000 0 -0.38 3 3
PI3K 0.047 0.049 -10000 0 -0.35 3 3
GNB1 0.038 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.045 0.082 -10000 0 -0.35 4 4
SOS1 0.037 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.008 0.075 -10000 0 -0.37 4 4
Gs family/GTP 0.031 0.048 -10000 0 -0.24 4 4
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.052 0.063 -10000 0 -0.26 6 6
vasodilation 0.01 0.13 -10000 0 -0.41 13 13
mol:DAG -0.048 0.13 -10000 0 -0.42 17 17
Gs family/GDP/Gbeta gamma 0.01 0.069 -10000 0 -0.33 4 4
MSN -0.031 0.083 -10000 0 -0.32 3 3
Gq family/GTP -0.022 0.13 -10000 0 -0.41 20 20
mol:PI-3-4-5-P3 0.017 0.16 -10000 0 -0.67 10 10
NRAS 0.021 0.079 -10000 0 -0.33 9 9
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.01 0.13 0.41 13 -10000 0 13
GRB2/SOS1 0.053 0.013 -10000 0 -10000 0 0
RhoA/GDP 0.022 0.082 -10000 0 -0.37 4 4
NOS3 0.008 0.14 -10000 0 -0.45 13 13
GNA11 0.03 0.053 -10000 0 -0.39 3 3
MAPKKK cascade 0.044 0.14 -10000 0 -0.46 10 10
E2/ER alpha (dimer)/PELP1/Src 0.063 0.13 0.28 3 -0.38 4 7
ruffle organization -0.028 0.078 -10000 0 -0.3 3 3
ROCK2 -0.025 0.082 -10000 0 -0.28 1 1
GNA14 -0.018 0.15 -10000 0 -0.37 29 29
GNA15 0.022 0.068 -10000 0 -0.26 10 10
GNA13 0.036 0.008 -10000 0 -10000 0 0
MMP9 0.1 0.18 0.38 56 -0.48 2 58
MMP2 0.053 0.14 0.29 4 -0.46 4 8
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.006 0.097 -10000 0 -0.58 4 4
VEGFR1 homodimer/NRP1 -0.007 0.089 -10000 0 -0.51 5 5
mol:DAG 0.01 0.1 -10000 0 -0.55 4 4
VEGFR1 homodimer/NRP1/VEGFR 121 -0.007 0.083 -10000 0 -0.47 5 5
CaM/Ca2+ 0.019 0.1 -10000 0 -0.52 4 4
HIF1A 0.023 0.071 -10000 0 -0.33 5 5
GAB1 0.03 0.055 -10000 0 -0.35 4 4
AKT1 0.037 0.12 0.32 1 -0.52 4 5
PLCG1 0.01 0.1 -10000 0 -0.55 4 4
NOS3 0.091 0.14 0.31 32 -0.5 4 36
CBL 0.037 0.005 -10000 0 -10000 0 0
mol:NO 0.092 0.14 0.3 32 -0.49 4 36
FLT1 -0.006 0.1 -10000 0 -0.58 5 5
PGF 0.024 0.047 -10000 0 -0.21 8 8
VEGFR1 homodimer/NRP2/VEGFR121 0.005 0.092 -10000 0 -0.5 5 5
CALM1 0.034 0.012 -10000 0 -10000 0 0
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
eNOS/Hsp90 0.083 0.14 0.29 32 -0.47 4 36
endothelial cell proliferation 0.091 0.15 0.32 36 -0.62 3 39
mol:Ca2+ 0.01 0.1 -10000 0 -0.54 4 4
MAPK3 0.003 0.11 0.31 5 -0.58 3 8
MAPK1 0.005 0.1 0.32 4 -0.56 3 7
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
PLGF homodimer 0.024 0.047 -10000 0 -0.21 8 8
PRKACA 0.037 0.006 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.024 0.064 -10000 0 -0.28 8 8
VEGFA homodimer 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.007 0.089 -10000 0 -0.51 5 5
platelet activating factor biosynthetic process 0.072 0.16 0.33 32 -0.57 3 35
PI3K 0.071 0.13 -10000 0 -0.53 4 4
PRKCA 0.005 0.097 -10000 0 -0.58 3 3
PRKCB 0.004 0.096 -10000 0 -0.51 4 4
VEGFR1 homodimer/PLGF homodimer 0.005 0.1 -10000 0 -0.6 4 4
VEGFA 0 0 -10000 0 -10000 0 0
VEGFB 0.034 0.036 -10000 0 -0.48 1 1
mol:IP3 0.01 0.1 -10000 0 -0.55 4 4
RASA1 0.04 0.13 -10000 0 -0.57 4 4
NRP2 0.031 0.046 -10000 0 -0.28 4 4
VEGFR1 homodimer -0.006 0.1 -10000 0 -0.58 5 5
VEGFB homodimer 0.034 0.036 -10000 0 -0.48 1 1
NCK1 0.027 0.07 -10000 0 -0.48 4 4
eNOS/Caveolin-1 0.098 0.14 0.36 1 -0.5 3 4
PTPN11 0.031 0.053 -10000 0 -0.39 3 3
mol:PI-3-4-5-P3 0.068 0.12 -10000 0 -0.52 4 4
mol:L-citrulline 0.092 0.14 0.3 32 -0.49 4 36
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.019 0.091 -10000 0 -0.6 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.004 0.093 -10000 0 -0.51 5 5
CD2AP 0.034 0.036 -10000 0 -0.48 1 1
PI3K/GAB1 0.078 0.13 -10000 0 -0.56 4 4
PDPK1 0.04 0.12 0.34 1 -0.57 3 4
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.005 0.09 -10000 0 -0.54 4 4
mol:NADP 0.092 0.14 0.3 32 -0.49 4 36
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.018 0.09 -10000 0 -0.59 3 3
VEGFR1 homodimer/NRP2 0.005 0.1 -10000 0 -0.54 5 5
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate 0.062 0.17 0.33 1 -0.38 10 11
PDGFB-D/PDGFRB/SLAP 0.03 0.068 -10000 0 -0.35 4 4
PDGFB-D/PDGFRB/APS/CBL 0.048 0.026 -10000 0 -0.29 1 1
AKT1 0.045 0.11 0.33 3 -10000 0 3
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.052 0.16 0.3 1 -0.36 9 10
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
FGR 0.001 0.16 -10000 0 -0.6 11 11
mol:Ca2+ 0.057 0.13 0.29 1 -0.39 3 4
MYC 0.054 0.26 0.39 32 -0.66 15 47
SHC1 0.036 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.063 0.082 -10000 0 -0.25 1 1
LRP1/PDGFRB/PDGFB 0.066 0.038 -10000 0 -0.29 1 1
GRB10 -0.002 0.12 -10000 0 -0.4 17 17
PTPN11 0.031 0.053 -10000 0 -0.39 3 3
GO:0007205 0.056 0.13 0.29 1 -0.4 3 4
PTEN 0.031 0.051 -10000 0 -0.48 2 2
GRB2 0.036 0.008 -10000 0 -10000 0 0
GRB7 0.024 0.064 -10000 0 -0.28 8 8
PDGFB-D/PDGFRB/SHP2 0.048 0.051 -10000 0 -0.35 3 3
PDGFB-D/PDGFRB/GRB10 0.019 0.1 -10000 0 -0.35 13 13
cell cycle arrest 0.029 0.068 -10000 0 -0.35 4 4
HRAS 0.034 0.039 -10000 0 -0.35 2 2
HIF1A 0.033 0.1 0.31 3 -0.28 1 4
GAB1 0.02 0.17 0.33 1 -0.46 11 12
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.037 0.16 0.31 2 -0.41 10 12
PDGFB-D/PDGFRB 0.026 0.045 -10000 0 -0.3 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.053 0.029 -10000 0 -0.35 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.003 0.13 -10000 0 -0.36 11 11
positive regulation of MAPKKK cascade 0.048 0.05 -10000 0 -0.35 3 3
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
mol:IP3 0.057 0.13 0.29 1 -0.4 3 4
E5 0 0.002 -10000 0 -10000 0 0
CSK 0.033 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.042 0.058 -10000 0 -0.35 3 3
SHB 0.034 0.025 -10000 0 -0.21 2 2
BLK -0.044 0.18 -10000 0 -0.51 21 21
PTPN2 0.029 0.018 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.051 0.032 -10000 0 -0.35 1 1
BCAR1 0.036 0.017 -10000 0 -0.21 1 1
VAV2 0.021 0.19 0.3 6 -0.49 12 18
CBL 0.037 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.05 0.042 -10000 0 -0.28 3 3
LCK -0.03 0.2 -10000 0 -0.57 22 22
PDGFRB 0.035 0.036 -10000 0 -0.48 1 1
ACP1 0.038 0 -10000 0 -10000 0 0
HCK -0.049 0.19 -10000 0 -0.61 20 20
ABL1 0.023 0.17 0.29 2 -0.42 14 16
PDGFB-D/PDGFRB/CBL 0.008 0.17 0.31 1 -0.48 12 13
PTPN1 0.016 0.039 -10000 0 -0.49 1 1
SNX15 0.036 0.017 -10000 0 -0.21 1 1
STAT3 0.036 0.009 -10000 0 -10000 0 0
STAT1 0.017 0.068 -10000 0 -0.21 18 18
cell proliferation 0.058 0.25 0.38 33 -0.58 15 48
SLA 0.013 0.077 -10000 0 -0.28 12 12
actin cytoskeleton reorganization 0.096 0.094 0.35 2 -10000 0 2
SRC 0.002 0.095 -10000 0 -0.7 3 3
PI3K -0.012 0.058 -10000 0 -0.25 5 5
PDGFB-D/PDGFRB/GRB7/SHC 0.059 0.057 -10000 0 -0.3 3 3
SH2B2 0 0 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.052 0.16 0.31 1 -0.38 8 9
LYN 0.017 0.083 -10000 0 -0.56 2 2
LRP1 0.037 0.005 -10000 0 -10000 0 0
SOS1 0.037 0.003 -10000 0 -10000 0 0
STAT5B 0.036 0.009 -10000 0 -10000 0 0
STAT5A 0.029 0.049 -10000 0 -0.26 5 5
NCK1-2/p130 Cas 0.041 0.063 -10000 0 -0.25 1 1
SPHK1 -0.033 0.16 -10000 0 -0.32 43 43
EDG1 0.009 0.12 -10000 0 -0.38 16 16
mol:DAG 0.057 0.13 0.29 1 -0.4 3 4
PLCG1 0.057 0.13 0.29 1 -0.41 3 4
NHERF/PDGFRB 0.04 0.097 -10000 0 -0.3 14 14
YES1 -0.042 0.21 -10000 0 -0.57 26 26
cell migration 0.039 0.096 -10000 0 -0.3 14 14
SHC/Grb2/SOS1 0.042 0.059 -10000 0 -10000 0 0
SLC9A3R2 0.008 0.11 -10000 0 -0.4 14 14
SLC9A3R1 0.027 0.063 -10000 0 -0.42 4 4
NHERF1-2/PDGFRB/PTEN 0.05 0.1 -10000 0 -0.27 16 16
FYN -0.01 0.17 -10000 0 -0.67 11 11
DOK1 0.059 0.088 -10000 0 -0.27 2 2
HRAS/GTP 0.025 0.028 -10000 0 -0.24 2 2
PDGFB 0.033 0.025 -10000 0 -0.21 2 2
RAC1 0.035 0.22 0.39 15 -0.45 20 35
PRKCD 0.061 0.086 -10000 0 -0.28 1 1
FER 0.056 0.091 -10000 0 -0.28 1 1
MAPKKK cascade 0.083 0.11 0.3 12 -10000 0 12
RASA1 0.058 0.086 -10000 0 -0.28 1 1
NCK1 0.027 0.07 -10000 0 -0.48 4 4
NCK2 0.036 0.017 -10000 0 -0.21 1 1
p62DOK/Csk 0.08 0.083 -10000 0 -0.26 2 2
PDGFB-D/PDGFRB/SHB 0.049 0.036 -10000 0 -0.35 1 1
chemotaxis 0.024 0.17 0.26 5 -0.4 14 19
STAT1-3-5/STAT1-3-5 0.016 0.065 -10000 0 -0.24 1 1
Bovine Papilomavirus E5/PDGFRB 0.025 0.027 -10000 0 -0.34 1 1
PTPRJ 0.034 0.039 -10000 0 -0.35 2 2
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.045 0.1 -10000 0 -0.61 1 1
epithelial cell differentiation 0.014 0.13 -10000 0 -0.5 3 3
ITCH 0.022 0.023 -10000 0 -10000 0 0
WWP1 0.009 0.1 -10000 0 -1.3 1 1
FYN 0.008 0.11 -10000 0 -0.35 16 16
EGFR 0.016 0.088 -10000 0 -0.42 8 8
PRL 0.035 0.024 -10000 0 -0.21 2 2
neuron projection morphogenesis 0.039 0.079 0.26 3 -0.44 1 4
PTPRZ1 0.01 0.1 -10000 0 -0.34 15 15
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.058 0.08 -10000 0 -0.47 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.035 0.064 -10000 0 -0.53 1 1
ADAM17 0.034 0.017 -10000 0 -10000 0 0
ErbB4/ErbB4 0.011 0.062 -10000 0 -0.67 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.061 0.084 -10000 0 -0.61 1 1
NCOR1 0.028 0.016 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.035 0.088 -10000 0 -0.49 2 2
GRIN2B 0.017 0.089 0.27 1 -0.42 3 4
ErbB4/ErbB2/betacellulin 0.039 0.099 -10000 0 -0.74 1 1
STAT1 0.017 0.068 -10000 0 -0.21 18 18
HBEGF -0.008 0.13 -10000 0 -0.32 27 27
PRLR 0.005 0.12 -10000 0 -0.44 14 14
E4ICDs/ETO2 0.015 0.12 -10000 0 -0.61 1 1
axon guidance 0 0.085 -10000 0 -0.78 1 1
NEDD4 0.005 0.1 -10000 0 -0.39 12 12
Prolactin receptor/Prolactin receptor/Prolactin 0.027 0.097 -10000 0 -0.36 12 12
CBFA2T3 -0.071 0.18 -10000 0 -0.32 65 65
ErbB4/ErbB2/HBEGF 0.037 0.096 -10000 0 -0.37 3 3
MAPK3 0.033 0.075 0.27 1 -0.45 1 2
STAT1 (dimer) 0.057 0.083 -10000 0 -0.6 1 1
MAPK1 0.036 0.067 0.27 1 -0.45 1 2
JAK2 0.017 0.079 -10000 0 -0.27 13 13
ErbB4/ErbB2/neuregulin 1 beta 0.027 0.068 -10000 0 -0.41 2 2
NRG1 0.011 0.039 -10000 0 -0.36 2 2
NRG3 0.025 0.072 -10000 0 -0.43 5 5
NRG2 0.029 0.055 -10000 0 -0.35 4 4
NRG4 0.018 0.073 -10000 0 -0.25 13 13
heart development 0 0.085 -10000 0 -0.78 1 1
neural crest cell migration 0.027 0.068 -10000 0 -0.41 2 2
ERBB2 0.011 0.045 -10000 0 -0.35 2 2
WWOX/E4ICDs 0.067 0.076 -10000 0 -0.61 1 1
SHC1 0.036 0.007 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.05 0.1 -10000 0 -0.88 1 1
apoptosis -0.013 0.11 0.43 5 -10000 0 5
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.062 0.079 -10000 0 -0.61 1 1
ErbB4/ErbB2/epiregulin -0.043 0.15 -10000 0 -0.34 10 10
ErbB4/ErbB4/betacellulin/betacellulin 0.047 0.1 -10000 0 -0.56 2 2
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.061 0.13 -10000 0 -0.4 4 4
MDM2 0.007 0.058 0.26 1 -0.61 1 2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.013 0.051 -10000 0 -0.42 1 1
STAT5A 0.017 0.094 0.34 1 -0.76 1 2
ErbB4/EGFR/neuregulin 1 beta 0.033 0.087 -10000 0 -0.74 1 1
DLG4 0.029 0.016 -10000 0 -10000 0 0
GRB2/SHC 0.051 0.015 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.061 0.076 -10000 0 -0.56 1 1
STAT5A (dimer) 0.029 0.14 -10000 0 -0.55 3 3
MAP3K7IP2 0.036 0.007 -10000 0 -10000 0 0
STAT5B (dimer) 0.041 0.095 -10000 0 -0.76 1 1
LRIG1 -0.016 0.16 -10000 0 -0.46 23 23
EREG -0.18 0.23 -10000 0 -0.38 113 113
BTC -0.004 0.13 -10000 0 -0.38 21 21
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.002 0.083 -10000 0 -0.8 1 1
ERBB4 0.011 0.062 -10000 0 -0.67 1 1
STAT5B 0.036 0.009 -10000 0 -10000 0 0
YAP1 0.006 0.073 -10000 0 -0.48 4 4
GRB2 0.036 0.008 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.047 0.081 -10000 0 -0.59 1 1
glial cell differentiation -0.061 0.075 0.56 1 -10000 0 1
WWOX 0.035 0.036 -10000 0 -0.48 1 1
cell proliferation -0.002 0.11 0.3 1 -0.62 2 3
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.033 0.012 -10000 0 -10000 0 0
VLDLR -0.077 0.2 -10000 0 -0.38 59 59
LRPAP1 0.036 0.007 -10000 0 -10000 0 0
NUDC 0.034 0.011 -10000 0 -10000 0 0
RELN/LRP8 0.049 0.08 -10000 0 -0.3 9 9
CaM/Ca2+ 0.025 0.009 -10000 0 -10000 0 0
KATNA1 0.036 0.007 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.015 0.072 -10000 0 -0.27 9 9
IQGAP1/CaM 0.047 0.021 -10000 0 -10000 0 0
DAB1 0.037 0.006 -10000 0 -10000 0 0
IQGAP1 0.035 0.01 -10000 0 -10000 0 0
PLA2G7 -0.046 0.18 -10000 0 -0.39 42 42
CALM1 0.034 0.012 -10000 0 -10000 0 0
DYNLT1 0.036 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.033 0.084 -10000 0 -0.35 9 9
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 0.036 0.008 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.01 0.007 -10000 0 -10000 0 0
CDK5R2 0.037 0.004 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.01 0.13 -10000 0 -0.3 31 31
YWHAE 0.029 0.016 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.029 0.083 0.34 6 -10000 0 6
MAP1B 0.005 0.013 -10000 0 -10000 0 0
RAC1 0.013 0.011 -10000 0 -10000 0 0
p35/CDK5 0.017 0.06 -10000 0 -10000 0 0
RELN 0.034 0.019 -10000 0 -0.21 1 1
PAFAH/LIS1 -0.013 0.1 -10000 0 -0.29 22 22
LIS1/CLIP170 0.01 0.007 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain 0.018 0.065 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.018 0.11 -10000 0 -0.26 31 31
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.014 0.08 0.33 6 -0.29 3 9
LIS1/IQGAP1 0.028 0.02 -10000 0 -10000 0 0
RHOA 0.014 0.011 -10000 0 -10000 0 0
PAFAH1B1 0.013 0.009 -10000 0 -10000 0 0
PAFAH1B3 0.035 0.036 -10000 0 -0.48 1 1
PAFAH1B2 0.034 0.024 -10000 0 -0.21 2 2
MAP1B/LIS1/Dynein heavy chain 0.016 0.044 -10000 0 -0.23 1 1
NDEL1/Katanin 60/Dynein heavy chain 0.033 0.094 0.35 6 -10000 0 6
LRP8 0.012 0.11 -10000 0 -0.42 12 12
NDEL1/Katanin 60 0.02 0.09 0.34 6 -10000 0 6
P39/CDK5 0.018 0.06 -10000 0 -10000 0 0
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0.02 -10000 0 -10000 0 0
CDK5 -0.02 0.054 0.19 2 -0.26 9 11
PPP2R5D 0.036 0.007 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.009 0.006 -10000 0 -10000 0 0
CSNK2A1 0.031 0.015 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0 0.12 -10000 0 -0.26 28 28
RELN/VLDLR -0.011 0.14 -10000 0 -0.28 40 40
CDC42 0.013 0.013 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.013 0.093 -10000 0 -0.34 13 13
MAP4K4 0.004 0.083 0.22 1 -0.41 3 4
BAG4 0.028 0.051 -10000 0 -0.48 2 2
PKC zeta/ceramide -0.002 0.043 0.14 2 -0.2 1 3
NFKBIA 0.029 0.043 -10000 0 -0.3 3 3
BIRC3 -0.011 0.13 -10000 0 -0.31 29 29
BAX 0.014 0.039 -10000 0 -0.44 1 1
RIPK1 0.037 0.005 -10000 0 -10000 0 0
AKT1 -0.005 0.022 -10000 0 -10000 0 0
BAD -0.004 0.044 -10000 0 -0.21 1 1
SMPD1 0.024 0.051 0.2 2 -0.24 2 4
RB1 0.052 0.097 0.2 52 -0.24 1 53
FADD/Caspase 8 0.017 0.081 -10000 0 -0.44 3 3
MAP2K4 -0.007 0.046 -10000 0 -0.26 1 1
NSMAF 0.028 0.041 -10000 0 -0.35 2 2
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.002 0.047 0.18 2 -0.2 1 3
EGF -0.094 0.19 -10000 0 -0.32 79 79
mol:ceramide -0.001 0.049 0.15 9 -0.22 1 10
MADD 0.037 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.001 0.061 -10000 0 -0.32 5 5
ASAH1 0.028 0.016 -10000 0 -10000 0 0
negative regulation of cell cycle 0.052 0.097 0.2 52 -0.24 1 53
cell proliferation 0.026 0.064 -10000 0 -0.24 2 2
BID 0.03 0.094 -10000 0 -0.74 2 2
MAP3K1 -0.005 0.047 -10000 0 -0.21 1 1
EIF2A -0.008 0.047 0.18 1 -10000 0 1
TRADD 0.037 0.003 -10000 0 -10000 0 0
CRADD 0.027 0.07 -10000 0 -0.48 4 4
MAPK3 0.001 0.048 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.003 0.048 -10000 0 -10000 0 0
Cathepsin D/ceramide 0.013 0.058 0.17 1 -0.26 2 3
FADD 0.01 0.068 -10000 0 -0.46 1 1
KSR1 -0.001 0.047 0.17 2 -0.21 1 3
MAPK8 0 0.052 -10000 0 -0.21 2 2
PRKRA -0.002 0.047 0.17 3 -0.21 1 4
PDGFA 0.002 0.11 -10000 0 -0.29 23 23
TRAF2 0.035 0.018 -10000 0 -0.21 1 1
IGF1 0.016 0.082 -10000 0 -0.26 15 15
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.001 0.049 0.15 9 -0.22 1 10
CTSD 0.033 0.042 -10000 0 -0.3 3 3
regulation of nitric oxide biosynthetic process 0.054 0.01 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.028 0.068 -10000 0 -0.25 2 2
PRKCD 0.037 0.005 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.001 0.061 -10000 0 -0.32 5 5
RelA/NF kappa B1 0.054 0.011 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.034 0.036 -10000 0 -0.48 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.015 0.073 -10000 0 -0.32 4 4
TNFR1A/BAG4/TNF-alpha 0.052 0.064 -10000 0 -0.3 4 4
mol:Sphingosine-1-phosphate -0.013 0.093 -10000 0 -0.34 13 13
MAP2K1 -0.003 0.044 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.037 0.005 -10000 0 -10000 0 0
CYCS 0.053 0.069 0.18 10 -0.19 2 12
TNFRSF1A 0.036 0.008 -10000 0 -10000 0 0
NFKB1 0.037 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.043 0.044 -10000 0 -0.35 2 2
EIF2AK2 -0.005 0.045 0.19 1 -0.2 1 2
TNF-alpha/TNFR1A/FAN 0.051 0.057 -10000 0 -0.3 2 2
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.028 0.089 -10000 0 -0.48 4 4
MAP2K2 -0.004 0.044 -10000 0 -10000 0 0
SMPD3 0.003 0.096 -10000 0 -0.3 16 16
TNF 0.024 0.066 -10000 0 -0.27 9 9
PKC zeta/PAR4 0.025 0.026 -10000 0 -0.35 1 1
mol:PHOSPHOCHOLINE 0.056 0.085 0.22 36 -10000 0 36
NF kappa B1/RelA/I kappa B alpha 0.072 0.048 -10000 0 -0.26 2 2
AIFM1 0.041 0.063 0.17 11 -0.22 1 12
BCL2 -0.002 0.097 -10000 0 -0.31 16 16
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.002 0.1 -10000 0 -0.31 20 20
CRKL 0.031 0.05 -10000 0 -0.48 2 2
Rac1/GDP 0.024 0.009 -10000 0 -10000 0 0
DOCK1 0.023 0.08 -10000 0 -0.44 6 6
ITGA4 0.01 0.12 -10000 0 -0.46 12 12
alpha4/beta7 Integrin/MAdCAM1 0.033 0.13 -10000 0 -0.28 25 25
EPO 0.033 0.025 -10000 0 -0.21 2 2
alpha4/beta7 Integrin 0.007 0.13 -10000 0 -0.36 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.016 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.034 0.087 -10000 0 -0.35 10 10
EPO/EPOR (dimer) 0.048 0.032 -10000 0 -10000 0 0
lamellipodium assembly -0.002 0.11 -10000 0 -0.39 6 6
PIK3CA 0.037 0.006 -10000 0 -10000 0 0
PI3K 0.047 0.049 -10000 0 -0.35 3 3
ARF6 0.029 0.051 -10000 0 -0.48 2 2
JAK2 0.012 0.085 -10000 0 -0.31 11 11
PXN 0.037 0.004 -10000 0 -10000 0 0
PIK3R1 0.03 0.061 -10000 0 -0.48 3 3
MADCAM1 0.018 0.07 -10000 0 -0.23 15 15
cell adhesion 0.031 0.12 -10000 0 -0.28 25 25
CRKL/CBL 0.048 0.041 -10000 0 -0.35 2 2
ITGB1 0.036 0.017 -10000 0 -0.21 1 1
SRC -0.004 0.075 -10000 0 -0.31 10 10
ITGB7 0.003 0.13 -10000 0 -0.48 14 14
RAC1 0.033 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.038 0.12 -10000 0 -0.36 15 15
p130Cas/Crk/Dock1 0.045 0.11 -10000 0 -0.33 4 4
VCAM1 0.013 0.1 -10000 0 -0.39 12 12
RHOA 0.037 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.07 0.082 -10000 0 -0.27 10 10
BCAR1 -0.02 0.067 0.19 2 -0.3 10 12
EPOR 0.034 0.029 -10000 0 -0.21 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.037 0.005 -10000 0 -10000 0 0
GIT1 0.035 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.003 0.11 -10000 0 -0.4 6 6
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.02 0.087 -10000 0 -0.44 7 7
HDAC4 0.033 0.039 -10000 0 -0.35 2 2
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.008 0.029 0.24 2 -10000 0 2
CDKN1A -0.003 0.085 -10000 0 -0.59 3 3
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.03 0.048 -10000 0 -0.26 5 5
FOXO3 0.002 0.069 0.41 6 -10000 0 6
FOXO1 0 0 -10000 0 -10000 0 0
FOXO4 0.005 0.051 -10000 0 -0.27 7 7
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.035 0.009 -10000 0 -10000 0 0
TAT 0.037 0.003 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.003 0.05 -10000 0 -0.16 17 17
PPARGC1A -0.035 0.16 -10000 0 -0.36 39 39
FHL2 0.019 0.091 -10000 0 -0.37 10 10
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.048 0.035 -10000 0 -0.35 1 1
HIST2H4A 0.008 0.029 -10000 0 -0.24 2 2
SIRT1/FOXO3a 0.034 0.051 0.27 7 -10000 0 7
SIRT1 0.032 0.042 -10000 0 -0.35 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.064 0.046 -10000 0 -0.3 2 2
SIRT1/Histone H1b 0.015 0.081 -10000 0 -0.3 10 10
apoptosis -0.06 0.05 0.3 2 -10000 0 2
SIRT1/PGC1A -0.002 0.11 -10000 0 -0.29 23 23
p53/SIRT1 -0.021 0.13 -10000 0 -0.35 27 27
SIRT1/FOXO4 0.018 0.068 0.2 1 -0.26 8 9
FOXO1/FHL2/SIRT1 0.033 0.061 -10000 0 -0.27 7 7
HIST1H1E 0.005 0.071 -10000 0 -0.32 9 9
SIRT1/p300 0.036 0.08 -10000 0 -0.33 8 8
muscle cell differentiation -0.008 0.05 0.27 3 -10000 0 3
TP53 -0.04 0.17 -10000 0 -0.46 29 29
KU70/SIRT1/BAX 0.061 0.05 -10000 0 -0.3 2 2
CREBBP 0.034 0.036 -10000 0 -0.48 1 1
MEF2D 0.036 0.008 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.05 0.034 -10000 0 -0.35 1 1
ACSS2 0.001 0.056 -10000 0 -0.35 5 5
SIRT1/PCAF/MYOD 0.009 0.05 -10000 0 -0.27 3 3
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.01 0.046 -10000 0 -10000 0 0
VDR 0.024 0.08 -10000 0 -0.44 6 6
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.035 0.084 -10000 0 -0.41 3 3
RXRs/LXRs/DNA/Oxysterols 0.041 0.1 -10000 0 -0.43 7 7
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA 0.003 0.01 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.012 0.086 -10000 0 -0.45 2 2
RXRs/NUR77 0.065 0.085 -10000 0 -0.26 4 4
RXRs/PPAR 0.007 0.098 -10000 0 -0.28 12 12
NCOR2 0.033 0.039 -10000 0 -0.35 2 2
VDR/VDR/Vit D3 0.018 0.057 -10000 0 -0.31 6 6
RARs/VDR/DNA/Vit D3 0.059 0.081 -10000 0 -0.26 10 10
RARA 0.034 0.019 -10000 0 -0.21 1 1
NCOA1 0.028 0.07 -10000 0 -0.48 4 4
VDR/VDR/DNA 0.024 0.08 -10000 0 -0.44 6 6
RARs/RARs/DNA/9cRA 0.051 0.058 -10000 0 -0.25 5 5
RARG 0.03 0.055 -10000 0 -0.35 4 4
RPS6KB1 0.018 0.068 0.57 3 -10000 0 3
RARs/THRs/DNA/SMRT 0.016 0.084 -10000 0 -0.52 2 2
THRA 0.016 0.091 -10000 0 -0.37 10 10
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.018 0.057 -10000 0 -0.31 6 6
RXRs/PPAR/9cRA/PGJ2/DNA 0.059 0.072 -10000 0 -0.26 4 4
NR1H4 -0.071 0.18 -10000 0 -0.31 68 68
RXRs/LXRs/DNA 0.097 0.1 -10000 0 -0.38 3 3
NR1H2 0.039 0.018 -10000 0 -10000 0 0
NR1H3 0.031 0.068 -10000 0 -0.43 4 4
RXRs/VDR/DNA/Vit D3 0.066 0.083 -10000 0 -0.25 9 9
NR4A1 0.018 0.066 -10000 0 -0.21 17 17
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.012 0.092 -10000 0 -0.24 24 24
RXRG 0.022 0.079 -10000 0 -0.34 8 8
RXR alpha/CCPG 0.028 0.013 -10000 0 -10000 0 0
RXRA 0.038 0.019 -10000 0 -10000 0 0
RXRB 0.038 0.02 -10000 0 -10000 0 0
THRB 0.024 0.066 -10000 0 -0.27 9 9
PPARG -0.02 0.16 -10000 0 -0.45 25 25
PPARD 0.037 0.004 -10000 0 -10000 0 0
TNF 0.027 0.14 -10000 0 -0.92 3 3
mol:Oxysterols 0.003 0.009 -10000 0 -10000 0 0
cholesterol transport 0.041 0.1 -10000 0 -0.43 7 7
PPARA 0.031 0.04 -10000 0 -0.35 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.023 0.077 -10000 0 -0.35 8 8
RXRs/NUR77/BCL2 -0.006 0.075 -10000 0 -0.27 10 10
SREBF1 0.019 0.12 -10000 0 -0.72 4 4
RXRs/RXRs/DNA/9cRA 0.06 0.072 -10000 0 -0.26 4 4
ABCA1 0.024 0.16 -10000 0 -0.96 4 4
RARs/THRs 0.067 0.1 -10000 0 -0.26 11 11
RXRs/FXR 0.006 0.14 -10000 0 -0.28 24 24
BCL2 -0.002 0.097 -10000 0 -0.31 16 16
HIF-2-alpha transcription factor network

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