PARADIGM pathway analysis of mRNASeq expression data
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C11N8056
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C11N8056
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 38 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
TCGA08_retinoblastoma 234
Syndecan-1-mediated signaling events 199
IL4-mediated signaling events 142
Syndecan-4-mediated signaling events 138
Osteopontin-mediated events 109
HIF-1-alpha transcription factor network 101
Glypican 2 network 89
amb2 Integrin signaling 75
IL23-mediated signaling events 75
Syndecan-2-mediated signaling events 70
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 520 . Pathway is significant if Significance.Ratio > 0.05 .

  • 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. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 520 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
TCGA08_retinoblastoma 0.4500 234 1873 8 -0.34 0.15 1000 -1000 -0.024 -1000
Syndecan-1-mediated signaling events 0.3827 199 6798 34 -0.71 0.014 1000 -1000 -0.081 -1000
IL4-mediated signaling events 0.2731 142 12952 91 -1.4 1.2 1000 -1000 -0.2 -1000
Syndecan-4-mediated signaling events 0.2654 138 9286 67 -0.68 0.09 1000 -1000 -0.12 -1000
Osteopontin-mediated events 0.2096 109 4142 38 -0.44 0.014 1000 -1000 -0.13 -1000
HIF-1-alpha transcription factor network 0.1942 101 7737 76 -1 0.022 1000 -1000 -0.22 -1000
Glypican 2 network 0.1712 89 356 4 -0.15 -0.15 1000 -1000 -0.052 -1000
amb2 Integrin signaling 0.1442 75 6231 82 -0.58 0.014 1000 -1000 -0.11 -1000
IL23-mediated signaling events 0.1442 75 4515 60 -0.73 0.014 1000 -1000 -0.2 -1000
Syndecan-2-mediated signaling events 0.1346 70 4856 69 -0.42 0.022 1000 -1000 -0.066 -1000
TCGA08_p53 0.1327 69 488 7 -0.26 0.13 1000 -1000 -0.018 -1000
Endothelins 0.1135 59 5752 96 -0.56 0.016 1000 -1000 -0.099 -1000
p75(NTR)-mediated signaling 0.0942 49 6140 125 -0.53 0.014 1000 -1000 -0.12 -1000
FOXA2 and FOXA3 transcription factor networks 0.0827 43 2023 46 -0.5 0.021 1000 -1000 -0.14 -1000
Visual signal transduction: Rods 0.0827 43 2277 52 -0.42 0.014 1000 -1000 -0.11 -1000
Effects of Botulinum toxin 0.0808 42 1115 26 -0.22 0.014 1000 -1000 -0.074 -1000
Calcium signaling in the CD4+ TCR pathway 0.0750 39 1224 31 -0.48 0.014 1000 -1000 -0.11 -1000
Glypican 1 network 0.0712 37 1804 48 -0.37 0.033 1000 -1000 -0.061 -1000
Coregulation of Androgen receptor activity 0.0692 36 2757 76 -0.5 0.041 1000 -1000 -0.055 -1000
Signaling events mediated by the Hedgehog family 0.0692 36 1920 52 -0.45 0.064 1000 -1000 -0.083 -1000
BMP receptor signaling 0.0692 36 2991 81 -0.34 0.047 1000 -1000 -0.11 -1000
Caspase cascade in apoptosis 0.0673 35 2654 74 -0.14 0.049 1000 -1000 -0.062 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0673 35 2417 68 -0.53 0.038 1000 -1000 -0.16 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0673 35 2796 78 -0.15 0.039 1000 -1000 -0.091 -1000
Signaling events regulated by Ret tyrosine kinase 0.0654 34 2800 82 -0.18 0.014 1000 -1000 -0.1 -1000
PDGFR-beta signaling pathway 0.0654 34 3316 97 -0.12 0.014 1000 -1000 -0.1 -1000
IL12-mediated signaling events 0.0615 32 2867 87 -0.26 0.087 1000 -1000 -0.17 -1000
Visual signal transduction: Cones 0.0596 31 1204 38 -0.18 0.014 1000 -1000 -0.084 -1000
Glucocorticoid receptor regulatory network 0.0596 31 3628 114 -0.64 0.25 1000 -1000 -0.087 -1000
TCR signaling in naïve CD8+ T cells 0.0596 31 2915 93 -0.27 0.15 1000 -1000 -0.11 -1000
EPHB forward signaling 0.0596 31 2700 85 -0.28 0.13 1000 -1000 -0.12 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0596 31 3723 120 -0.25 0.11 1000 -1000 -0.1 -1000
LPA4-mediated signaling events 0.0577 30 363 12 -0.11 0.02 1000 -1000 -0.031 -1000
Thromboxane A2 receptor signaling 0.0558 29 3143 105 -0.1 0.021 1000 -1000 -0.088 -1000
Canonical Wnt signaling pathway 0.0558 29 1506 51 -0.37 0.11 1000 -1000 -0.078 -1000
Nongenotropic Androgen signaling 0.0558 29 1513 52 -0.15 0.043 1000 -1000 -0.073 -1000
ErbB4 signaling events 0.0538 28 1948 69 -0.32 0.066 1000 -1000 -0.12 -1000
BCR signaling pathway 0.0519 27 2752 99 -0.15 0.034 1000 -1000 -0.11 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0500 26 908 34 -0.062 0.014 1000 -1000 -0.083 -1000
IL27-mediated signaling events 0.0500 26 1352 51 -0.19 0.063 1000 -1000 -0.12 -1000
Presenilin action in Notch and Wnt signaling 0.0462 24 1510 61 -0.37 0.039 1000 -1000 -0.089 -1000
Ephrin B reverse signaling 0.0462 24 1197 48 -0.2 0.17 1000 -1000 -0.1 -1000
Signaling mediated by p38-gamma and p38-delta 0.0462 24 361 15 -0.14 0.024 1000 -1000 -0.055 -1000
Regulation of nuclear SMAD2/3 signaling 0.0442 23 3182 136 -0.36 0.36 1000 -1000 -0.096 -1000
IL1-mediated signaling events 0.0442 23 1469 62 -0.24 0.071 1000 -1000 -0.14 -1000
Syndecan-3-mediated signaling events 0.0442 23 830 35 -0.21 0.014 1000 -1000 -0.085 -1000
Integrins in angiogenesis 0.0442 23 2009 84 -0.44 0.015 1000 -1000 -0.12 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0442 23 783 33 -0.34 0.037 1000 -1000 -0.087 -1000
Wnt signaling 0.0404 21 150 7 -0.075 0.009 1000 -1000 -0.041 -1000
LPA receptor mediated events 0.0404 21 2184 102 -0.58 0.03 1000 -1000 -0.11 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0404 21 1923 88 -0.35 0.069 1000 -1000 -0.12 -1000
Arf6 signaling events 0.0365 19 1184 62 -0.16 0.04 1000 -1000 -0.077 -1000
Signaling events mediated by PTP1B 0.0365 19 1474 76 -0.14 0.028 1000 -1000 -0.1 -1000
Reelin signaling pathway 0.0365 19 1105 56 -0.24 0.014 1000 -1000 -0.099 -1000
ErbB2/ErbB3 signaling events 0.0346 18 1186 65 -0.32 0.026 1000 -1000 -0.089 -1000
Ephrin A reverse signaling 0.0346 18 131 7 -0.024 0 1000 -1000 -0.04 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0327 17 949 54 -0.31 0.028 1000 -1000 -0.12 -1000
IFN-gamma pathway 0.0327 17 1187 68 -0.2 0.038 1000 -1000 -0.12 -1000
EGFR-dependent Endothelin signaling events 0.0327 17 374 21 -0.1 0.014 1000 -1000 -0.082 -1000
Regulation of Androgen receptor activity 0.0327 17 1255 70 -0.51 0.033 1000 -1000 -0.082 -1000
PDGFR-alpha signaling pathway 0.0308 16 720 44 -0.13 0.031 1000 -1000 -0.073 -1000
Signaling mediated by p38-alpha and p38-beta 0.0308 16 747 44 -0.17 0.014 1000 -1000 -0.07 -1000
Signaling events mediated by HDAC Class III 0.0288 15 635 40 -0.19 0.078 1000 -1000 -0.054 -1000
TRAIL signaling pathway 0.0288 15 746 48 -0.081 0.016 1000 -1000 -0.087 -1000
Regulation of Telomerase 0.0288 15 1576 102 -0.16 0.044 1000 -1000 -0.13 -1000
Noncanonical Wnt signaling pathway 0.0269 14 382 26 -0.081 0.014 1000 -1000 -0.097 -1000
Fc-epsilon receptor I signaling in mast cells 0.0269 14 1372 97 -0.2 0.035 1000 -1000 -0.12 -1000
S1P1 pathway 0.0269 14 510 36 -0.12 0.014 1000 -1000 -0.063 -1000
Plasma membrane estrogen receptor signaling 0.0269 14 1288 86 -0.29 0.033 1000 -1000 -0.099 -1000
VEGFR1 specific signals 0.0269 14 814 56 -0.13 0.039 1000 -1000 -0.097 -1000
EPO signaling pathway 0.0250 13 754 55 -0.075 0.027 1000 -1000 -0.12 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0250 13 498 37 -0.081 0.014 1000 -1000 -0.069 -1000
Retinoic acid receptors-mediated signaling 0.0250 13 758 58 -0.17 0.028 1000 -1000 -0.1 -1000
Signaling events mediated by PRL 0.0250 13 444 34 -0.1 0.033 1000 -1000 -0.069 -1000
Cellular roles of Anthrax toxin 0.0231 12 506 39 -0.046 0.019 1000 -1000 -0.042 -1000
Nectin adhesion pathway 0.0231 12 780 63 -0.12 0.039 1000 -1000 -0.091 -1000
IL6-mediated signaling events 0.0231 12 947 75 -0.11 0.063 1000 -1000 -0.11 -1000
IGF1 pathway 0.0231 12 690 57 -0.087 0.021 1000 -1000 -0.11 -1000
FAS signaling pathway (CD95) 0.0212 11 560 47 -0.089 0.014 1000 -1000 -0.061 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0212 11 876 74 -0.3 0.081 1000 -1000 -0.1 -1000
FOXM1 transcription factor network 0.0212 11 580 51 -0.35 0.16 1000 -1000 -0.22 -1000
IL2 signaling events mediated by PI3K 0.0192 10 614 58 -0.17 0.061 1000 -1000 -0.1 -1000
Rapid glucocorticoid signaling 0.0192 10 205 20 -0.061 0.014 1000 -1000 -0.047 -1000
Ras signaling in the CD4+ TCR pathway 0.0192 10 183 17 -0.025 0.028 1000 -1000 -0.053 -1000
Aurora B signaling 0.0192 10 707 67 -0.32 0.031 1000 -1000 -0.091 -1000
JNK signaling in the CD4+ TCR pathway 0.0173 9 167 17 -0.036 0.037 1000 -1000 -0.076 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0173 9 513 52 -0.21 0.033 1000 -1000 -0.08 -1000
S1P3 pathway 0.0173 9 395 42 -0.12 0.037 1000 -1000 -0.066 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0154 8 227 28 -0.072 0.018 1000 -1000 -0.065 -1000
Circadian rhythm pathway 0.0154 8 189 22 -0.13 0.045 1000 -1000 -0.087 -1000
Ceramide signaling pathway 0.0154 8 629 76 -0.1 0.034 1000 -1000 -0.081 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0154 8 401 45 -0.081 0.037 1000 -1000 -0.11 -1000
p38 MAPK signaling pathway 0.0154 8 369 44 -0.16 0.018 1000 -1000 -0.091 -1000
a4b1 and a4b7 Integrin signaling 0.0135 7 39 5 -0.015 0.011 1000 -1000 -0.043 -1000
Arf6 downstream pathway 0.0135 7 333 43 -0.039 0.022 1000 -1000 -0.045 -1000
Paxillin-dependent events mediated by a4b1 0.0135 7 253 36 -0.063 0.024 1000 -1000 -0.081 -1000
Class IB PI3K non-lipid kinase events 0.0135 7 21 3 -0.004 0.004 1000 -1000 -0.03 -1000
BARD1 signaling events 0.0115 6 368 57 -0.025 0.055 1000 -1000 -0.085 -1000
Aurora A signaling 0.0115 6 390 60 -0.074 0.031 1000 -1000 -0.073 -1000
HIF-2-alpha transcription factor network 0.0115 6 300 43 -0.25 0.032 1000 -1000 -0.14 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0115 6 849 125 -0.11 0.094 1000 -1000 -0.11 -1000
IL2 signaling events mediated by STAT5 0.0115 6 149 22 -0.036 0.051 1000 -1000 -0.068 -1000
Insulin Pathway 0.0115 6 511 74 -0.2 0.038 1000 -1000 -0.12 -1000
S1P4 pathway 0.0115 6 156 25 -0.032 0.024 1000 -1000 -0.067 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0096 5 446 85 -0.07 0.058 1000 -1000 -0.084 -1000
Regulation of p38-alpha and p38-beta 0.0096 5 270 54 -0.1 0.038 1000 -1000 -0.087 -1000
Hedgehog signaling events mediated by Gli proteins 0.0077 4 295 65 -0.094 0.062 1000 -1000 -0.086 -1000
Aurora C signaling 0.0077 4 32 7 -0.015 0.003 1000 -1000 -0.059 -1000
Arf6 trafficking events 0.0077 4 297 71 -0.25 0.046 1000 -1000 -0.089 -1000
PLK1 signaling events 0.0058 3 320 85 -0.019 0.035 1000 -1000 -0.061 -1000
ceramide signaling pathway 0.0058 3 194 49 -0.025 0.046 1000 -1000 -0.074 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0058 3 287 83 -0.083 0.065 1000 -1000 -0.096 -1000
TCGA08_rtk_signaling 0.0058 3 84 26 -0.031 0.047 1000 -1000 -0.03 -1000
Class I PI3K signaling events 0.0058 3 275 73 -0.1 0.04 1000 -1000 -0.09 -1000
E-cadherin signaling in keratinocytes 0.0058 3 143 43 -0.017 0.047 1000 -1000 -0.077 -1000
E-cadherin signaling events 0.0058 3 18 5 -0.006 0.012 1000 -1000 -0.051 -1000
Canonical NF-kappaB pathway 0.0038 2 91 39 -0.028 0.085 1000 -1000 -0.11 -1000
Signaling events mediated by HDAC Class II 0.0038 2 157 75 -0.031 0.033 1000 -1000 -0.071 -1000
S1P5 pathway 0.0038 2 44 17 -0.014 0.024 1000 -1000 -0.066 -1000
E-cadherin signaling in the nascent adherens junction 0.0038 2 176 76 -0.017 0.058 1000 -1000 -0.1 -1000
Alternative NF-kappaB pathway 0.0038 2 30 13 -0.007 0.014 1000 -1000 -0.086 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0019 1 40 23 -0.015 0.049 1000 -1000 -0.082 -1000
PLK2 and PLK4 events 0.0019 1 4 3 0.011 0.023 1000 -1000 -0.024 -1000
Insulin-mediated glucose transport 0.0019 1 32 32 -0.078 0.048 1000 -1000 -0.082 -1000
Signaling events mediated by HDAC Class I 0.0019 1 156 104 -0.13 0.061 1000 -1000 -0.086 -1000
FoxO family signaling 0.0019 1 101 64 -0.025 0.16 1000 -1000 -0.1 -1000
Atypical NF-kappaB pathway 0.0019 1 37 31 -0.005 0.048 1000 -1000 -0.058 -1000
mTOR signaling pathway 0.0000 0 42 53 -0.003 0.034 1000 -1000 -0.08 -1000
Class I PI3K signaling events mediated by Akt 0.0000 0 19 68 -0.12 0.062 1000 -1000 -0.089 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.032 1000 -1000 -0.071 -1000
Arf1 pathway 0.0000 0 12 54 -0.004 0.036 1000 -1000 -0.045 -1000
Total NA 3232 183938 7203 -28 7 131000 -131000 -12 -131000
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B -0.11 0.23 -10000 0 -0.54 111 111
CDKN2C 0.01 0.15 -10000 0 -0.74 19 19
CDKN2A -0.34 0.39 -10000 0 -0.76 238 238
CCND2 0.13 0.13 0.23 300 -0.15 1 301
RB1 -0.14 0.14 -10000 0 -0.24 300 300
CDK4 0.15 0.15 0.26 305 -10000 0 305
CDK6 0.15 0.14 0.25 299 -10000 0 299
G1/S progression 0.14 0.15 0.24 300 -10000 0 300
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.009 0.062 -9999 0 -0.81 3 3
CCL5 -0.11 0.29 -9999 0 -0.8 77 77
SDCBP 0.014 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.48 0.2 -9999 0 -0.58 374 374
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.45 0.19 -9999 0 -0.55 374 374
Syndecan-1/Syntenin -0.45 0.19 -9999 0 -0.55 374 374
MAPK3 -0.4 0.17 -9999 0 -0.61 145 145
HGF/MET -0.027 0.11 -9999 0 -0.49 28 28
TGFB1/TGF beta receptor Type II 0.009 0.062 -9999 0 -0.81 3 3
BSG 0.014 0 -9999 0 -10000 0 0
keratinocyte migration -0.44 0.19 -9999 0 -0.54 374 374
Syndecan-1/RANTES -0.51 0.25 -9999 0 -0.62 390 390
Syndecan-1/CD147 -0.43 0.18 -9999 0 -0.53 342 342
Syndecan-1/Syntenin/PIP2 -0.44 0.18 -9999 0 -0.53 374 374
LAMA5 0.014 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.42 0.18 -9999 0 -0.52 374 374
MMP7 -0.27 0.39 -9999 0 -0.8 183 183
HGF -0.015 0.14 -9999 0 -0.65 22 22
Syndecan-1/CASK -0.46 0.19 -9999 0 -0.56 374 374
Syndecan-1/HGF/MET -0.44 0.19 -9999 0 -0.55 357 357
regulation of cell adhesion -0.38 0.17 -9999 0 -0.58 145 145
HPSE 0.009 0.052 -9999 0 -0.58 4 4
positive regulation of cell migration -0.48 0.2 -9999 0 -0.58 374 374
SDC1 -0.48 0.2 -9999 0 -0.58 374 374
Syndecan-1/Collagen -0.48 0.2 -9999 0 -0.58 374 374
PPIB 0.014 0 -9999 0 -10000 0 0
MET 0.005 0.08 -9999 0 -0.73 6 6
PRKACA 0.014 0 -9999 0 -10000 0 0
MMP9 -0.58 0.37 -9999 0 -0.81 374 374
MAPK1 -0.4 0.17 -9999 0 -0.61 145 145
homophilic cell adhesion -0.47 0.19 -9999 0 -0.57 374 374
MMP1 -0.71 0.26 -9999 0 -0.81 460 460
IL4-mediated signaling events

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
BCL2L1 -1 0.5 -10000 0 -1.4 334 334
STAT6 (cleaved dimer) -1.1 0.52 -10000 0 -1.4 370 370
IGHG1 -0.33 0.13 -10000 0 -0.47 121 121
IGHG3 -1 0.48 -10000 0 -1.3 358 358
AKT1 -0.4 0.18 -10000 0 -0.75 39 39
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.29 0.16 -10000 0 -0.73 28 28
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.41 0.18 -10000 0 -0.79 26 26
THY1 -1.1 0.55 -10000 0 -1.5 341 341
MYB -0.047 0.18 -10000 0 -0.6 51 51
HMGA1 0.014 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.51 0.23 -10000 0 -0.94 51 51
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.41 0.18 -10000 0 -0.77 25 25
SP1 0.014 0.011 -10000 0 -10000 0 0
INPP5D 0.011 0.037 -10000 0 -0.58 2 2
SOCS5 0.035 0.01 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -1.1 0.52 -10000 0 -1.4 351 351
SOCS1 -0.64 0.27 -10000 0 -0.84 255 255
SOCS3 -0.42 0.2 -10000 0 -0.81 40 40
FCER2 -0.74 0.35 -10000 0 -1 213 213
PARP14 0.009 0.062 -10000 0 -0.81 3 3
CCL17 -1.1 0.51 -10000 0 -1.4 338 338
GRB2 0.014 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.33 0.15 -10000 0 -0.74 19 19
T cell proliferation -1.1 0.53 -10000 0 -1.4 339 339
IL4R/JAK1 -1 0.5 -10000 0 -1.4 336 336
EGR2 -1.1 0.51 -10000 0 -1.4 328 328
JAK2 -0.032 0.032 -10000 0 -0.62 1 1
JAK3 -0.014 0.17 -10000 0 -0.81 22 22
PIK3R1 0.011 0.037 -10000 0 -0.58 2 2
JAK1 0.001 0.005 -10000 0 -10000 0 0
COL1A2 -0.48 0.35 -10000 0 -0.93 192 192
CCL26 -1.1 0.52 -10000 0 -1.4 328 328
IL4R -1.1 0.55 -10000 0 -1.5 336 336
PTPN6 0.035 0.007 -10000 0 -10000 0 0
IL13RA2 -1.1 0.52 -10000 0 -1.4 332 332
IL13RA1 -0.031 0.019 -10000 0 -10000 0 0
IRF4 -0.27 0.32 -10000 0 -0.93 87 87
ARG1 -0.59 0.6 -10000 0 -1.4 171 171
CBL -0.48 0.22 -10000 0 -0.9 48 48
GTF3A 0.006 0.018 -10000 0 -10000 0 0
PIK3CA 0.014 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.043 0.031 -10000 0 -0.46 1 1
IRF4/BCL6 -0.25 0.3 -10000 0 -0.87 86 86
CD40LG -0.057 0.2 -10000 0 -0.59 65 65
MAPK14 -0.47 0.22 -10000 0 -0.9 48 48
mitosis -0.38 0.18 -10000 0 -0.71 38 38
STAT6 -1.3 0.7 -10000 0 -1.7 351 351
SPI1 -0.021 0.075 -10000 0 -0.75 3 3
RPS6KB1 -0.36 0.17 -10000 0 -0.71 28 28
STAT6 (dimer) -1.3 0.7 -10000 0 -1.7 351 351
STAT6 (dimer)/PARP14 -1.2 0.59 -10000 0 -1.5 349 349
mast cell activation 0.021 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.39 0.18 -10000 0 -0.81 33 33
FRAP1 -0.4 0.18 -10000 0 -0.74 40 40
LTA -1.1 0.51 -10000 0 -1.4 339 339
FES 0.014 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 1.2 0.62 1.6 351 -10000 0 351
CCL11 -1.2 0.49 -10000 0 -1.4 377 377
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.39 0.18 -10000 0 -0.8 32 32
IL2RG -0.005 0.14 -10000 0 -0.78 17 17
IL10 -1.1 0.5 -10000 0 -1.4 336 336
IRS1 0.01 0.045 -10000 0 -0.58 3 3
IRS2 0.011 0.037 -10000 0 -0.58 2 2
IL4 -0.2 0.074 -10000 0 -10000 0 0
IL5 -1.1 0.5 -10000 0 -1.4 326 326
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.77 0.32 -10000 0 -0.97 320 320
COL1A1 -0.66 0.37 -10000 0 -0.95 316 316
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -1.1 0.54 -10000 0 -1.5 320 320
IL2R gamma/JAK3 -0.023 0.18 -10000 0 -0.67 35 35
TFF3 -1.3 0.59 -10000 0 -1.6 378 378
ALOX15 -1.1 0.54 -10000 0 -1.5 343 343
MYBL1 -0.002 0.11 -10000 0 -0.81 10 10
T-helper 2 cell differentiation -0.78 0.33 -10000 0 -1 330 330
SHC1 0.014 0 -10000 0 -10000 0 0
CEBPB -0.016 0.05 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.39 0.17 -10000 0 -0.74 28 28
mol:PI-3-4-5-P3 -0.4 0.18 -10000 0 -0.74 40 40
PI3K -0.42 0.2 -10000 0 -0.8 40 40
DOK2 0.008 0.067 -10000 0 -0.75 4 4
ETS1 0.03 0.063 -10000 0 -0.8 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.31 0.14 -10000 0 -0.69 22 22
ITGB3 -1.1 0.51 -10000 0 -1.4 332 332
PIGR -1.4 0.61 -10000 0 -1.7 396 396
IGHE 0.05 0.044 0.27 3 -10000 0 3
MAPKKK cascade -0.3 0.14 -10000 0 -0.68 22 22
BCL6 0.013 0.002 -10000 0 -10000 0 0
OPRM1 -1.1 0.5 -10000 0 -1.4 334 334
RETNLB -1.1 0.51 -10000 0 -1.4 337 337
SELP -1.1 0.55 -10000 0 -1.5 338 338
AICDA -1 0.48 -10000 0 -1.3 338 338
Syndecan-4-mediated signaling events

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
PTK2 -0.21 0.23 -9999 0 -0.46 228 228
Syndecan-4/Syndesmos -0.38 0.26 -9999 0 -0.62 225 225
positive regulation of JNK cascade -0.39 0.22 -9999 0 -0.58 261 261
Syndecan-4/ADAM12 -0.68 0.35 -9999 0 -0.91 337 337
CCL5 -0.11 0.29 -9999 0 -0.8 77 77
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.014 0 -9999 0 -10000 0 0
ITGA5 -0.24 0.38 -9999 0 -0.81 164 164
SDCBP 0.014 0 -9999 0 -10000 0 0
PLG 0.001 0.079 -9999 0 -0.79 5 5
ADAM12 -0.58 0.37 -9999 0 -0.81 375 375
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.12 0.062 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.56 0.34 -9999 0 -0.81 300 300
Syndecan-4/CXCL12/CXCR4 -0.4 0.26 -9999 0 -0.62 261 261
Syndecan-4/Laminin alpha3 -0.49 0.34 -9999 0 -0.76 273 273
MDK -0.024 0.17 -9999 0 -0.8 24 24
Syndecan-4/FZD7 -0.39 0.26 -9999 0 -0.63 228 228
Syndecan-4/Midkine -0.4 0.26 -9999 0 -0.64 238 238
FZD7 0.001 0.098 -9999 0 -0.78 8 8
Syndecan-4/FGFR1/FGF -0.37 0.23 -9999 0 -0.58 236 236
THBS1 -0.012 0.14 -9999 0 -0.73 18 18
integrin-mediated signaling pathway -0.44 0.3 -9999 0 -0.7 251 251
positive regulation of MAPKKK cascade -0.39 0.22 -9999 0 -0.58 261 261
Syndecan-4/TACI -0.42 0.28 -9999 0 -0.67 253 253
CXCR4 -0.015 0.15 -9999 0 -0.81 18 18
cell adhesion -0.18 0.21 -9999 0 -0.39 229 229
Syndecan-4/Dynamin -0.38 0.26 -9999 0 -0.62 225 225
Syndecan-4/TSP1 -0.39 0.27 -9999 0 -0.64 228 228
Syndecan-4/GIPC -0.38 0.26 -9999 0 -0.62 225 225
Syndecan-4/RANTES -0.44 0.3 -9999 0 -0.69 261 261
ITGB1 0.012 0.036 -9999 0 -0.81 1 1
LAMA1 -0.35 0.41 -9999 0 -0.8 231 231
LAMA3 -0.21 0.37 -9999 0 -0.8 144 144
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCA 0.09 0.07 -9999 0 -0.66 2 2
Syndecan-4/alpha-Actinin -0.38 0.26 -9999 0 -0.62 225 225
TFPI 0.007 0.072 -9999 0 -0.72 5 5
F2 -0.084 0.25 -9999 0 -0.81 53 53
alpha5/beta1 Integrin -0.2 0.29 -9999 0 -0.62 165 165
positive regulation of cell adhesion -0.63 0.38 -9999 0 -0.87 327 327
ACTN1 0.012 0.036 -9999 0 -0.81 1 1
TNC -0.14 0.32 -9999 0 -0.81 98 98
Syndecan-4/CXCL12 -0.41 0.25 -9999 0 -0.63 254 254
FGF6 0.003 0.005 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
CXCL12 -0.05 0.18 -9999 0 -0.58 56 56
TNFRSF13B -0.072 0.25 -9999 0 -0.81 53 53
FGF2 -0.008 0.12 -9999 0 -0.63 17 17
FGFR1 0.003 0.091 -9999 0 -0.77 7 7
Syndecan-4/PI-4-5-P2 -0.39 0.25 -9999 0 -0.63 225 225
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.34 0.41 -9999 0 -0.8 228 228
cell migration -0.039 0.02 -9999 0 -10000 0 0
PRKCD 0.026 0.011 -9999 0 -10000 0 0
vasculogenesis -0.38 0.25 -9999 0 -0.61 228 228
SDC4 -0.41 0.27 -9999 0 -0.67 225 225
Syndecan-4/Tenascin C -0.46 0.33 -9999 0 -0.74 251 251
Syndecan-4/PI-4-5-P2/PKC alpha -0.091 0.048 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.38 0.26 -9999 0 -0.62 225 225
MMP9 -0.57 0.37 -9999 0 -0.8 374 374
Rac1/GTP -0.19 0.21 -9999 0 -0.4 229 229
cytoskeleton organization -0.36 0.24 -9999 0 -0.6 225 225
GIPC1 0.014 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.38 0.26 -9999 0 -0.62 228 228
Osteopontin-mediated 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
IKK alpha homodimer -0.28 0.27 -9999 0 -0.56 164 164
NF kappa B1 p50/RelA/I kappa B alpha -0.28 0.23 -9999 0 -0.57 150 150
alphaV/beta3 Integrin/Osteopontin/Src -0.35 0.32 -9999 0 -0.63 287 287
AP1 -0.32 0.32 -9999 0 -0.8 97 97
ILK -0.28 0.28 -9999 0 -0.57 164 164
bone resorption -0.22 0.25 -9999 0 -0.74 20 20
PTK2B 0.012 0.026 -9999 0 -0.58 1 1
PYK2/p130Cas -0.27 0.24 -9999 0 -0.52 149 149
ITGAV 0.004 0.077 -9999 0 -0.77 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.008 0.057 -9999 0 -0.42 10 10
alphaV/beta3 Integrin/Osteopontin -0.33 0.29 -9999 0 -0.58 291 291
MAP3K1 -0.29 0.29 -9999 0 -0.53 291 291
JUN 0.013 0.002 -9999 0 -10000 0 0
MAPK3 -0.3 0.29 -9999 0 -0.62 164 164
MAPK1 -0.3 0.29 -9999 0 -0.62 164 164
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 -0.27 0.28 -9999 0 -0.56 166 166
ITGB3 -0.019 0.15 -9999 0 -0.74 21 21
NFKBIA -0.29 0.28 -9999 0 -0.63 152 152
FOS -0.063 0.2 -9999 0 -0.58 67 67
CD44 0.012 0.026 -9999 0 -0.58 1 1
CHUK 0.014 0 -9999 0 -10000 0 0
PLAU -0.44 0.39 -9999 0 -0.92 163 163
NF kappa B1 p50/RelA -0.3 0.24 -9999 0 -0.61 149 149
BCAR1 0.014 0 -9999 0 -10000 0 0
RELA 0.014 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.029 0.13 -9999 0 -0.59 25 25
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.28 0.28 -9999 0 -0.52 291 291
VAV3 -0.28 0.28 -9999 0 -0.51 291 291
MAP3K14 -0.3 0.29 -9999 0 -0.54 291 291
ROCK2 0.003 0.077 -9999 0 -0.58 9 9
SPP1 -0.44 0.41 -9999 0 -0.82 285 285
RAC1 0.014 0 -9999 0 -10000 0 0
Rac1/GTP -0.27 0.24 -9999 0 -0.51 184 184
MMP2 -0.28 0.31 -9999 0 -0.8 90 90
HIF-1-alpha transcription factor network

Figure S6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.69 0.47 -9999 0 -1.2 148 148
HDAC7 0.014 0.003 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.47 0.32 -9999 0 -0.93 57 57
SMAD4 0.014 0.026 -9999 0 -0.57 1 1
ID2 -0.69 0.47 -9999 0 -1.2 150 150
AP1 -0.05 0.14 -9999 0 -0.41 67 67
ABCG2 -0.69 0.48 -9999 0 -1.3 151 151
HIF1A -0.084 0.061 -9999 0 -0.72 1 1
TFF3 -0.82 0.53 -9999 0 -1.3 216 216
GATA2 0.011 0.058 -9999 0 -0.74 3 3
AKT1 -0.085 0.063 -9999 0 -10000 0 0
response to hypoxia -0.11 0.065 -9999 0 -10000 0 0
MCL1 -0.69 0.47 -9999 0 -1.2 148 148
NDRG1 -0.69 0.48 -9999 0 -1.3 147 147
SERPINE1 -0.91 0.55 -9999 0 -1.4 265 265
FECH -0.69 0.47 -9999 0 -1.2 148 148
FURIN -0.69 0.47 -9999 0 -1.2 152 152
NCOA2 -0.035 0.16 -9999 0 -0.58 42 42
EP300 -0.09 0.092 -9999 0 -0.42 3 3
HMOX1 -0.69 0.47 -9999 0 -1.2 150 150
BHLHE40 -0.69 0.47 -9999 0 -1.2 148 148
BHLHE41 -0.7 0.48 -9999 0 -1.3 151 151
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.068 0.057 -9999 0 -10000 0 0
ENG -0.045 0.072 -9999 0 -10000 0 0
JUN 0.014 0.001 -9999 0 -10000 0 0
RORA -0.69 0.48 -9999 0 -1.3 148 148
ABCB1 -0.2 0.31 -9999 0 -1.4 30 30
TFRC -0.7 0.48 -9999 0 -1.3 155 155
CXCR4 -0.7 0.48 -9999 0 -1.3 153 153
TF -0.86 0.53 -9999 0 -1.3 235 235
CITED2 -0.69 0.47 -9999 0 -1.2 148 148
HIF1A/ARNT -0.79 0.59 -9999 0 -1.4 217 217
LDHA -0.069 0.044 -9999 0 -10000 0 0
ETS1 -0.69 0.47 -9999 0 -1.3 148 148
PGK1 -0.69 0.47 -9999 0 -1.2 148 148
NOS2 -0.75 0.49 -9999 0 -1.3 172 172
ITGB2 -0.7 0.48 -9999 0 -1.3 153 153
ALDOA -0.69 0.47 -9999 0 -1.2 148 148
Cbp/p300/CITED2 -0.67 0.48 -9999 0 -1.3 133 133
FOS -0.062 0.2 -9999 0 -0.58 67 67
HK2 -0.69 0.47 -9999 0 -1.2 148 148
SP1 0.022 0.005 -9999 0 -10000 0 0
GCK -0.18 0.22 -9999 0 -0.8 40 40
HK1 -0.69 0.47 -9999 0 -1.2 149 149
NPM1 -0.69 0.47 -9999 0 -1.2 149 149
EGLN1 -0.69 0.47 -9999 0 -1.2 148 148
CREB1 0.022 0 -9999 0 -10000 0 0
PGM1 -0.69 0.47 -9999 0 -1.2 149 149
SMAD3 0.014 0.026 -9999 0 -0.57 1 1
EDN1 -0.09 0.17 -9999 0 -1.4 5 5
IGFBP1 -0.7 0.48 -9999 0 -1.3 154 154
VEGFA -0.4 0.3 -9999 0 -1 20 20
HIF1A/JAB1 -0.043 0.035 -9999 0 -0.54 1 1
CP -0.81 0.54 -9999 0 -1.3 207 207
CXCL12 -0.72 0.49 -9999 0 -1.3 154 154
COPS5 0.013 0.005 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.002 0.025 -9999 0 -0.41 2 2
BNIP3 -0.69 0.47 -9999 0 -1.2 152 152
EGLN3 -0.71 0.49 -9999 0 -1.3 152 152
CA9 -1 0.49 -9999 0 -1.3 325 325
TERT -0.77 0.52 -9999 0 -1.3 187 187
ENO1 -0.69 0.47 -9999 0 -1.2 148 148
PFKL -0.69 0.47 -9999 0 -1.2 148 148
NCOA1 0.013 0.002 -9999 0 -10000 0 0
ADM -0.69 0.48 -9999 0 -1.2 152 152
ARNT -0.082 0.053 -9999 0 -10000 0 0
HNF4A -0.071 0.24 -9999 0 -0.81 51 51
ADFP -0.7 0.47 -9999 0 -1.2 176 176
SLC2A1 -0.4 0.3 -9999 0 -1 24 24
LEP -0.74 0.51 -9999 0 -1.3 173 173
HIF1A/ARNT/Cbp/p300 -0.49 0.34 -9999 0 -0.92 83 83
EPO -0.4 0.32 -9999 0 -0.98 72 72
CREBBP -0.089 0.09 -9999 0 -0.37 2 2
HIF1A/ARNT/Cbp/p300/HDAC7 -0.46 0.33 -9999 0 -1 35 35
PFKFB3 -0.69 0.47 -9999 0 -1.2 149 149
NT5E -0.75 0.52 -9999 0 -1.3 178 178
Glypican 2 network

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
MDK -0.024 0.17 -9999 0 -0.8 24 24
GPC2 -0.15 0.33 -9999 0 -0.81 104 104
GPC2/Midkine -0.15 0.29 -9999 0 -0.68 114 114
neuron projection morphogenesis -0.15 0.29 -9999 0 -0.68 114 114
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.12 0.26 -9999 0 -0.63 94 94
alphaM/beta2 Integrin/GPIbA -0.067 0.2 -9999 0 -0.69 45 45
alphaM/beta2 Integrin/proMMP-9 -0.43 0.3 -9999 0 -0.59 377 377
PLAUR -0.032 0.19 -9999 0 -0.81 29 29
HMGB1 0.011 0.016 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.053 0.18 -9999 0 -0.67 38 38
AGER -0.001 0.095 -9999 0 -0.8 7 7
RAP1A 0.014 0 -9999 0 -10000 0 0
SELPLG 0.014 0 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.072 0.19 -9999 0 -0.63 41 41
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.58 0.37 -9999 0 -0.81 374 374
CYR61 0.005 0.084 -9999 0 -0.77 6 6
TLN1 0.01 0.051 -9999 0 -0.81 2 2
Rap1/GTP -0.16 0.15 -9999 0 -0.48 53 53
RHOA 0.014 0 -9999 0 -10000 0 0
P-selectin oligomer -0.084 0.22 -9999 0 -0.58 86 86
MYH2 -0.36 0.25 -9999 0 -0.57 254 254
MST1R 0.004 0.073 -9999 0 -0.58 8 8
leukocyte activation during inflammatory response -0.069 0.19 -9999 0 -0.55 62 62
APOB -0.017 0.15 -9999 0 -0.8 18 18
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.091 0.27 -9999 0 -0.81 66 66
JAM3 0.012 0.036 -9999 0 -0.81 1 1
GP1BA -0.014 0.14 -9999 0 -0.74 18 18
alphaM/beta2 Integrin/CTGF -0.058 0.19 -9999 0 -0.66 41 41
alphaM/beta2 Integrin -0.18 0.19 -9999 0 -0.43 155 155
JAM3 homodimer 0.012 0.036 -9999 0 -0.81 1 1
ICAM2 0.011 0.037 -9999 0 -0.58 2 2
ICAM1 -0.026 0.18 -9999 0 -0.81 25 25
phagocytosis triggered by activation of immune response cell surface activating receptor -0.18 0.19 -9999 0 -0.42 155 155
cell adhesion -0.067 0.2 -9999 0 -0.69 45 45
NFKB1 -0.03 0.22 -9999 0 -0.83 21 21
THY1 -0.22 0.37 -9999 0 -0.81 147 147
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.03 0.12 -9999 0 -0.54 29 29
alphaM/beta2 Integrin/LRP/tPA -0.063 0.19 -9999 0 -0.59 52 52
IL6 -0.06 0.29 -9999 0 -0.78 64 64
ITGB2 -0.013 0.14 -9999 0 -0.79 15 15
elevation of cytosolic calcium ion concentration -0.28 0.32 -9999 0 -0.57 255 255
alphaM/beta2 Integrin/JAM2/JAM3 -0.054 0.17 -9999 0 -0.63 37 37
JAM2 0 0.089 -9999 0 -0.58 12 12
alphaM/beta2 Integrin/ICAM1 -0.073 0.21 -9999 0 -0.61 56 56
alphaM/beta2 Integrin/uPA/Plg -0.27 0.29 -9999 0 -0.54 257 257
RhoA/GTP -0.22 0.22 -9999 0 -0.52 144 144
positive regulation of phagocytosis -0.14 0.17 -9999 0 -0.57 46 46
Ron/MSP -0.013 0.078 -9999 0 -0.47 14 14
alphaM/beta2 Integrin/uPAR/uPA -0.28 0.33 -9999 0 -0.58 255 255
alphaM/beta2 Integrin/uPAR -0.08 0.23 -9999 0 -0.67 59 59
PLAU -0.35 0.41 -9999 0 -0.81 230 230
PLAT -0.014 0.15 -9999 0 -0.8 18 18
actin filament polymerization -0.34 0.23 -9999 0 -0.54 254 254
MST1 0.005 0.08 -9999 0 -0.73 6 6
alphaM/beta2 Integrin/lipoprotein(a) -0.07 0.19 -9999 0 -0.56 62 62
TNF -0.035 0.25 -9999 0 -0.76 38 38
RAP1B 0.012 0.036 -9999 0 -0.81 1 1
alphaM/beta2 Integrin/uPA -0.28 0.31 -9999 0 -0.58 252 252
fibrinolysis -0.26 0.29 -9999 0 -0.53 257 257
HCK 0.006 0.076 -9999 0 -0.76 5 5
dendritic cell antigen processing and presentation -0.18 0.19 -9999 0 -0.42 155 155
VTN -0.039 0.2 -9999 0 -0.81 33 33
alphaM/beta2 Integrin/CYR61 -0.057 0.19 -9999 0 -0.67 41 41
LPA -0.009 0.12 -9999 0 -0.81 11 11
LRP1 0.012 0.026 -9999 0 -0.58 1 1
cell migration -0.45 0.35 -9999 0 -0.61 380 380
FN1 -0.35 0.41 -9999 0 -0.81 228 228
alphaM/beta2 Integrin/Thy1 -0.2 0.31 -9999 0 -0.62 164 164
MPO -0.022 0.14 -9999 0 -0.59 30 30
KNG1 -0.023 0.15 -9999 0 -0.81 18 18
RAP1/GDP -0.001 0.024 -9999 0 -0.54 1 1
ROCK1 -0.2 0.21 -9999 0 -0.49 136 136
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.006 0.079 -9999 0 -0.81 5 5
CTGF 0.001 0.088 -9999 0 -0.62 10 10
alphaM/beta2 Integrin/Hck -0.056 0.18 -9999 0 -0.66 40 40
ITGAM -0.04 0.2 -9999 0 -0.8 32 32
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.097 0.2 -9999 0 -0.64 36 36
HP -0.21 0.29 -9999 0 -0.58 190 190
leukocyte adhesion -0.17 0.25 -9999 0 -0.76 45 45
SELP -0.084 0.22 -9999 0 -0.58 86 86
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.56 0.44 -10000 0 -1.2 111 111
IL23A -0.56 0.43 -10000 0 -1.2 108 108
NF kappa B1 p50/RelA/I kappa B alpha -0.55 0.42 -10000 0 -1.1 131 131
positive regulation of T cell mediated cytotoxicity -0.61 0.49 -10000 0 -1.3 133 133
ITGA3 -0.55 0.42 -10000 0 -1.2 108 108
IL17F -0.37 0.27 -10000 0 -0.74 86 86
IL12B -0.074 0.24 -10000 0 -0.85 44 44
STAT1 (dimer) -0.6 0.48 -10000 0 -1.2 145 145
CD4 -0.53 0.41 -10000 0 -1.1 103 103
IL23 -0.56 0.43 -10000 0 -1.2 113 113
IL23R -0.083 0.091 -10000 0 -0.69 6 6
IL1B -0.57 0.45 -10000 0 -1.2 113 113
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.73 0.43 -10000 0 -1.2 196 196
TYK2 -0.005 0.039 -10000 0 -0.85 1 1
STAT4 -0.008 0.13 -10000 0 -0.79 14 14
STAT3 0.014 0 -10000 0 -10000 0 0
IL18RAP -0.013 0.14 -10000 0 -0.73 18 18
IL12RB1 -0.066 0.22 -10000 0 -0.83 39 39
PIK3CA 0.014 0 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.057 0.17 -10000 0 -0.65 40 40
IL23R/JAK2 -0.1 0.097 -10000 0 -0.74 4 4
positive regulation of chronic inflammatory response -0.61 0.49 -10000 0 -1.3 133 133
natural killer cell activation 0.008 0.008 0.059 6 -10000 0 6
JAK2 0.002 0.028 -10000 0 -0.57 1 1
PIK3R1 0.011 0.037 -10000 0 -0.58 2 2
NFKB1 0.01 0.003 -10000 0 -10000 0 0
RELA 0.01 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.53 0.41 -10000 0 -1.1 113 113
ALOX12B -0.63 0.48 -10000 0 -1.2 160 160
CXCL1 -0.57 0.44 -10000 0 -1.2 118 118
T cell proliferation -0.61 0.49 -10000 0 -1.3 133 133
NFKBIA 0.008 0.036 -10000 0 -0.81 1 1
IL17A -0.28 0.22 -10000 0 -0.62 34 34
PI3K -0.56 0.43 -10000 0 -1.1 133 133
IFNG -0.031 0.045 0.13 5 -0.11 98 103
STAT3 (dimer) -0.53 0.4 -10000 0 -1.1 131 131
IL18R1 0.01 0.044 -10000 0 -0.69 2 2
IL23/IL23R/JAK2/TYK2/SOCS3 -0.32 0.25 -10000 0 -0.81 45 45
IL18/IL18R -0.007 0.12 -10000 0 -0.57 14 14
macrophage activation -0.028 0.015 -10000 0 -0.045 55 55
TNF -0.57 0.44 -10000 0 -1.2 107 107
STAT3/STAT4 -0.57 0.43 -10000 0 -1.1 139 139
STAT4 (dimer) -0.59 0.47 -10000 0 -1.2 133 133
IL18 -0.009 0.11 -10000 0 -0.57 19 19
IL19 -0.67 0.53 -10000 0 -1.3 180 180
STAT5A (dimer) -0.58 0.46 -10000 0 -1.2 130 130
STAT1 -0.033 0.19 -10000 0 -0.79 30 30
SOCS3 0.012 0.026 -10000 0 -0.58 1 1
CXCL9 -0.68 0.47 -10000 0 -1.2 199 199
MPO -0.56 0.44 -10000 0 -1.2 121 121
positive regulation of humoral immune response -0.61 0.49 -10000 0 -1.3 133 133
IL23/IL23R/JAK2/TYK2 -0.64 0.53 -10000 0 -1.4 131 131
IL6 -0.58 0.47 -10000 0 -1.2 124 124
STAT5A 0.014 0 -10000 0 -10000 0 0
IL2 0.007 0.037 -10000 0 -0.8 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.008 0.008 0.059 6 -10000 0 6
CD3E -0.54 0.42 -10000 0 -1.2 103 103
keratinocyte proliferation -0.61 0.49 -10000 0 -1.3 133 133
NOS2 -0.58 0.44 -10000 0 -1.2 128 128
Syndecan-2-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
Syndecan-2/Fibronectin -0.24 0.31 -9999 0 -0.58 232 232
EPHB2 -0.2 0.36 -9999 0 -0.81 138 138
Syndecan-2/TACI -0.061 0.2 -9999 0 -0.54 77 77
LAMA1 -0.35 0.41 -9999 0 -0.8 231 231
Syndecan-2/alpha2 ITGB1 -0.15 0.22 -9999 0 -0.47 162 162
HRAS 0.012 0.036 -9999 0 -0.81 1 1
Syndecan-2/CASK -0.026 0.12 -9999 0 -0.54 25 25
ITGA5 -0.24 0.38 -9999 0 -0.81 164 164
BAX 0.014 0.12 -9999 0 -0.76 2 2
EPB41 0.014 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.023 0.1 -9999 0 -0.49 25 25
LAMA3 -0.21 0.37 -9999 0 -0.8 144 144
EZR 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.01 0.051 -9999 0 -0.65 3 3
Syndecan-2/MMP2 -0.07 0.24 -9999 0 -0.62 77 77
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.004 0.041 -9999 0 -0.47 4 4
dendrite morphogenesis -0.15 0.27 -9999 0 -0.56 154 154
Syndecan-2/GM-CSF -0.3 0.3 -9999 0 -0.56 285 285
determination of left/right symmetry -0.009 0.14 -9999 0 -0.62 25 25
Syndecan-2/PKC delta -0.001 0.12 -9999 0 -0.53 25 25
GNB2L1 0.014 0 -9999 0 -10000 0 0
MAPK3 -0.26 0.28 -9999 0 -0.51 285 285
MAPK1 -0.26 0.28 -9999 0 -0.51 285 285
Syndecan-2/RACK1 -0.023 0.1 -9999 0 -0.46 26 26
NF1 0.014 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.009 0.14 -9999 0 -0.62 25 25
ITGA2 0.01 0.045 -9999 0 -0.58 3 3
MAPK8 0.005 0.13 -9999 0 -0.55 25 25
Syndecan-2/alpha2/beta1 Integrin -0.22 0.26 -9999 0 -0.49 234 234
Syndecan-2/Kininogen -0.035 0.16 -9999 0 -0.56 41 41
ITGB1 0.012 0.036 -9999 0 -0.81 1 1
SRC 0.016 0.1 -9999 0 -0.43 26 26
Syndecan-2/CASK/Protein 4.1 -0.024 0.1 -9999 0 -0.49 25 25
extracellular matrix organization -0.004 0.13 -9999 0 -0.55 27 27
actin cytoskeleton reorganization -0.24 0.31 -9999 0 -0.57 232 232
Syndecan-2/Caveolin-2/Ras -0.026 0.11 -9999 0 -0.49 27 27
Syndecan-2/Laminin alpha3 -0.15 0.27 -9999 0 -0.55 162 162
Syndecan-2/RasGAP -0.023 0.098 -9999 0 -0.44 26 26
alpha5/beta1 Integrin -0.2 0.29 -9999 0 -0.62 165 165
PRKCD 0.014 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.15 0.28 -9999 0 -0.56 154 154
GO:0007205 0.004 0.001 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.022 0.1 -9999 0 -0.42 26 26
RHOA 0.014 0 -9999 0 -10000 0 0
SDCBP 0.014 0 -9999 0 -10000 0 0
TNFRSF13B -0.072 0.25 -9999 0 -0.81 53 53
RASA1 0.011 0.037 -9999 0 -0.58 2 2
alpha2/beta1 Integrin -0.004 0.041 -9999 0 -0.47 4 4
Syndecan-2/Synbindin -0.001 0.12 -9999 0 -0.53 25 25
TGFB1 0.009 0.062 -9999 0 -0.81 3 3
CASP3 0.01 0.11 -9999 0 -0.48 25 25
FN1 -0.35 0.41 -9999 0 -0.81 228 228
Syndecan-2/IL8 -0.11 0.26 -9999 0 -0.56 125 125
SDC2 -0.009 0.14 -9999 0 -0.62 25 25
KNG1 -0.023 0.15 -9999 0 -0.81 18 18
Syndecan-2/Neurofibromin -0.001 0.12 -9999 0 -0.53 25 25
TRAPPC4 0.014 0 -9999 0 -10000 0 0
CSF2 -0.42 0.41 -9999 0 -0.81 277 277
Syndecan-2/TGFB1 -0.004 0.13 -9999 0 -0.55 27 27
Syndecan-2/Syntenin/PI-4-5-P2 -0.024 0.1 -9999 0 -0.49 25 25
Syndecan-2/Ezrin -0.023 0.1 -9999 0 -0.48 25 25
PRKACA 0.01 0.11 -9999 0 -0.48 25 25
angiogenesis -0.11 0.25 -9999 0 -0.55 125 125
MMP2 -0.091 0.27 -9999 0 -0.81 66 66
IL8 -0.15 0.33 -9999 0 -0.8 107 107
calcineurin-NFAT signaling pathway -0.061 0.2 -9999 0 -0.54 77 77
TCGA08_p53

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
CDKN2A -0.26 0.3 -10000 0 -0.59 238 238
TP53 -0.077 0.087 -10000 0 -0.46 4 4
Senescence -0.077 0.087 -10000 0 -0.46 4 4
Apoptosis -0.077 0.087 -10000 0 -0.46 4 4
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.13 0.15 0.29 238 -10000 0 238
MDM4 0.014 0 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.16 0.3 -10000 0 -0.69 62 62
PTK2B 0.012 0.026 -10000 0 -0.58 1 1
mol:Ca2+ -0.041 0.2 -10000 0 -0.68 23 23
EDN1 -0.086 0.21 -10000 0 -0.41 46 46
EDN3 -0.23 0.29 -10000 0 -0.58 211 211
EDN2 -0.088 0.24 -10000 0 -0.66 79 79
HRAS/GDP -0.044 0.17 -10000 0 -0.54 14 14
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.047 0.15 -10000 0 -0.4 27 27
ADCY4 -0.18 0.24 -10000 0 -0.59 82 82
ADCY5 -0.26 0.25 -10000 0 -0.59 134 134
ADCY6 -0.18 0.25 -10000 0 -0.58 92 92
ADCY7 -0.18 0.24 -10000 0 -0.58 87 87
ADCY1 -0.2 0.27 -10000 0 -0.62 98 98
ADCY2 -0.28 0.26 -10000 0 -0.59 160 160
ADCY3 -0.18 0.24 -10000 0 -0.59 82 82
ADCY8 -0.2 0.25 -10000 0 -0.6 96 96
ADCY9 -0.18 0.24 -10000 0 -0.58 88 88
arachidonic acid secretion -0.07 0.21 -10000 0 -0.52 55 55
ETB receptor/Endothelin-1/Gq/GTP -0.049 0.14 -10000 0 -0.44 25 25
GNAO1 0.008 0.067 -10000 0 -0.75 4 4
HRAS 0.011 0.036 -10000 0 -0.81 1 1
ETA receptor/Endothelin-1/G12/GTP -0.076 0.35 0.34 148 -0.66 62 210
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.34 0.32 126 -0.61 91 217
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 -0.39 0.49 -10000 0 -0.83 271 271
EDNRB -0.014 0.062 -10000 0 -0.57 4 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.21 0.38 -10000 0 -0.9 78 78
CYSLTR1 -0.21 0.36 -10000 0 -0.77 97 97
SLC9A1 -0.058 0.16 -10000 0 -0.33 48 48
mol:GDP -0.053 0.18 -10000 0 -0.53 19 19
SLC9A3 -0.17 0.32 -10000 0 -0.7 110 110
RAF1 -0.073 0.19 -10000 0 -0.5 43 43
JUN -0.028 0.17 -10000 0 -0.63 5 5
JAK2 -0.16 0.3 -10000 0 -0.67 66 66
mol:IP3 -0.065 0.16 -10000 0 -0.5 24 24
ETA receptor/Endothelin-1 -0.12 0.42 0.4 153 -0.76 67 220
PLCB1 0.008 0.051 -10000 0 -0.65 3 3
PLCB2 0.007 0.068 -10000 0 -0.76 4 4
ETA receptor/Endothelin-3 -0.22 0.25 -10000 0 -0.48 215 215
FOS -0.12 0.34 -10000 0 -0.94 68 68
Gai/GDP 0.016 0.072 -10000 0 -0.59 2 2
CRK 0.014 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.17 0.28 -10000 0 -0.69 67 67
BCAR1 0.014 0 -10000 0 -10000 0 0
PRKCB1 -0.063 0.16 -10000 0 -0.47 26 26
GNAQ 0.014 0.006 -10000 0 -10000 0 0
GNAZ -0.014 0.14 -10000 0 -0.74 19 19
GNAL -0.061 0.2 -10000 0 -0.58 66 66
Gs family/GDP -0.12 0.15 -10000 0 -0.51 36 36
ETA receptor/Endothelin-1/Gq/GTP -0.067 0.18 -10000 0 -0.45 38 38
MAPK14 -0.025 0.12 -10000 0 -0.71 4 4
TRPC6 -0.043 0.2 -10000 0 -0.71 23 23
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 0.012 0.026 -10000 0 -0.58 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.035 0.12 -10000 0 -0.5 10 10
ETB receptor/Endothelin-2 -0.076 0.19 -10000 0 -0.49 83 83
ETB receptor/Endothelin-3 -0.18 0.21 -10000 0 -0.43 214 214
ETB receptor/Endothelin-1 -0.067 0.18 -10000 0 -0.56 8 8
MAPK3 -0.1 0.29 -10000 0 -0.78 70 70
MAPK1 -0.1 0.29 -10000 0 -0.78 70 70
Rac1/GDP -0.043 0.17 -10000 0 -0.53 14 14
cAMP biosynthetic process -0.23 0.22 -10000 0 -0.56 108 108
MAPK8 -0.045 0.19 -10000 0 -0.6 21 21
SRC 0.014 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.011 0.096 -10000 0 -0.39 9 9
p130Cas/CRK/Src/PYK2 -0.049 0.18 -10000 0 -0.57 17 17
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.046 0.17 -10000 0 -0.53 16 16
COL1A2 -0.28 0.46 -10000 0 -0.84 194 194
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.12 0.23 -10000 0 -0.56 82 82
mol:DAG -0.065 0.16 -10000 0 -0.5 24 24
MAP2K2 -0.083 0.23 -10000 0 -0.62 52 52
MAP2K1 -0.083 0.23 -10000 0 -0.62 52 52
EDNRA -0.079 0.2 -10000 0 -0.41 46 46
positive regulation of muscle contraction -0.13 0.26 -10000 0 -0.65 50 50
Gq family/GDP -0.079 0.15 -10000 0 -0.52 25 25
HRAS/GTP -0.069 0.17 -10000 0 -0.48 33 33
PRKCH -0.056 0.16 -10000 0 -0.48 23 23
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCA -0.057 0.16 -10000 0 -0.48 24 24
PRKCB -0.062 0.17 -10000 0 -0.51 30 30
PRKCE -0.056 0.16 -10000 0 -0.48 23 23
PRKCD -0.056 0.16 -10000 0 -0.48 24 24
PRKCG -0.11 0.21 -10000 0 -0.53 66 66
regulation of vascular smooth muscle contraction -0.14 0.39 -10000 0 -1.1 69 69
PRKCQ -0.063 0.17 -10000 0 -0.49 30 30
PLA2G4A -0.077 0.22 -10000 0 -0.56 55 55
GNA14 -0.071 0.21 -10000 0 -0.58 75 75
GNA15 0.011 0.037 -10000 0 -0.58 2 2
GNA12 0.007 0.072 -10000 0 -0.81 4 4
GNA11 0.009 0.052 -10000 0 -0.58 4 4
Rac1/GTP -0.071 0.35 0.34 152 -0.64 62 214
MMP1 -0.56 0.24 -10000 0 -0.65 460 460
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.016 0.08 -9999 0 -0.42 20 20
Necdin/E2F1 -0.053 0.18 -9999 0 -0.61 45 45
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.11 0.2 -9999 0 -0.47 107 107
NGF (dimer)/p75(NTR)/BEX1 -0.16 0.25 -9999 0 -0.56 134 134
NT-4/5 (dimer)/p75(NTR) -0.029 0.13 -9999 0 -0.57 27 27
IKBKB 0.014 0 -9999 0 -10000 0 0
AKT1 -0.07 0.2 -9999 0 -0.45 104 104
IKBKG 0.014 0 -9999 0 -10000 0 0
BDNF -0.038 0.18 -9999 0 -0.69 38 38
MGDIs/NGR/p75(NTR)/LINGO1 -0.087 0.22 -9999 0 -0.61 69 69
FURIN 0.014 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.068 0.16 -9999 0 -0.55 37 37
LINGO1 -0.054 0.23 -9999 0 -0.81 43 43
Sortilin/TRAF6/NRIF -0.01 0.05 -9999 0 -10000 0 0
proBDNF (dimer) -0.038 0.18 -9999 0 -0.68 38 38
NTRK1 -0.059 0.23 -9999 0 -0.81 46 46
RTN4R -0.02 0.16 -9999 0 -0.81 21 21
neuron apoptosis -0.062 0.18 -9999 0 -0.56 26 26
IRAK1 0.014 0 -9999 0 -10000 0 0
SHC1 -0.097 0.23 -9999 0 -0.54 104 104
ARHGDIA 0.014 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.002 0.028 -9999 0 -0.45 2 2
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.12 0.21 -9999 0 -0.5 107 107
MAGEH1 0.012 0.036 -9999 0 -0.81 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.13 0.22 -9999 0 -0.51 108 108
Mammalian IAPs/DIABLO -0.032 0.14 -9999 0 -0.6 28 28
proNGF (dimer) -0.14 0.31 -9999 0 -0.79 98 98
MAGED1 0.008 0.062 -9999 0 -0.69 4 4
APP 0.012 0.036 -9999 0 -0.81 1 1
NT-4/5 (dimer) 0.009 0.057 -9999 0 -0.73 3 3
ZNF274 0.014 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.077 0.2 -9999 0 -0.46 104 104
NGF -0.14 0.32 -9999 0 -0.79 98 98
cell cycle arrest -0.1 0.22 -9999 0 -0.5 106 106
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.03 0.12 -9999 0 -0.53 1 1
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.025 0.11 -9999 0 -0.57 17 17
NCSTN 0.014 0 -9999 0 -10000 0 0
mol:GTP -0.12 0.22 -9999 0 -0.54 104 104
PSENEN 0.01 0.051 -9999 0 -0.81 2 2
mol:ceramide -0.093 0.22 -9999 0 -0.5 106 106
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.01 0.1 -9999 0 -0.41 1 1
p75(NTR)/beta APP -0.028 0.12 -9999 0 -0.54 27 27
BEX1 -0.044 0.2 -9999 0 -0.81 35 35
mol:GDP -0.11 0.23 -9999 0 -0.51 123 123
NGF (dimer) -0.26 0.29 -9999 0 -0.56 238 238
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.08 0.2 -9999 0 -0.56 69 69
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
RAC1/GTP -0.1 0.19 -9999 0 -0.47 104 104
MYD88 0.014 0 -9999 0 -10000 0 0
CHUK 0.014 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.12 0.22 -9999 0 -0.54 104 104
RHOB 0.014 0 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.046 0.16 -9999 0 -0.62 39 39
NT3 (dimer) -0.16 0.27 -9999 0 -0.58 154 154
TP53 -0.014 0.15 -9999 0 -0.55 5 5
PRDM4 -0.094 0.22 -9999 0 -0.5 106 106
BDNF (dimer) -0.52 0.34 -9999 0 -0.66 404 404
PIK3CA 0.014 0 -9999 0 -10000 0 0
SORT1 -0.009 0.11 -9999 0 -0.58 20 20
activation of caspase activity -0.11 0.2 -9999 0 -0.47 107 107
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.12 0.21 -9999 0 -0.5 106 106
RHOC 0.014 0 -9999 0 -10000 0 0
XIAP 0.014 0 -9999 0 -10000 0 0
MAPK10 -0.061 0.19 -9999 0 -0.52 26 26
DIABLO 0.014 0 -9999 0 -10000 0 0
SMPD2 -0.094 0.22 -9999 0 -0.5 106 106
APH1B 0.014 0 -9999 0 -10000 0 0
APH1A 0.014 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.13 0.23 -9999 0 -0.55 106 106
PSEN1 0.014 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.018 -9999 0 -0.42 1 1
NT3 (dimer)/p75(NTR) -0.15 0.22 -9999 0 -0.45 172 172
MAPK8 -0.052 0.19 -9999 0 -0.54 18 18
MAPK9 -0.049 0.18 -9999 0 -0.53 17 17
APAF1 0.012 0.026 -9999 0 -0.58 1 1
NTF3 -0.16 0.27 -9999 0 -0.58 154 154
NTF4 0.009 0.057 -9999 0 -0.73 3 3
NDN 0.003 0.077 -9999 0 -0.58 9 9
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.094 0.17 -9999 0 -0.42 104 104
p75 CTF/Sortilin/TRAF6/NRIF -0.013 0.062 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.12 0.22 -9999 0 -0.53 104 104
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.056 0.14 -9999 0 -0.47 37 37
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.061 0.15 -9999 0 -0.5 37 37
PRKACB 0.012 0.026 -9999 0 -0.58 1 1
proBDNF (dimer)/p75 ECD -0.039 0.14 -9999 0 -0.51 40 40
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.023 0.17 -9999 0 -0.81 23 23
BIRC2 -0.005 0.12 -9999 0 -0.81 12 12
neuron projection morphogenesis -0.098 0.2 -9999 0 -0.45 104 104
BAD -0.045 0.18 -9999 0 -0.51 17 17
RIPK2 0.014 0 -9999 0 -10000 0 0
NGFR -0.023 0.16 -9999 0 -0.71 26 26
CYCS -0.084 0.22 -9999 0 -0.47 106 106
ADAM17 0.011 0.037 -9999 0 -0.58 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.11 0.2 -9999 0 -0.49 104 104
BCL2L11 -0.045 0.18 -9999 0 -0.51 17 17
BDNF (dimer)/p75(NTR) -0.064 0.17 -9999 0 -0.52 64 64
PI3K -0.11 0.2 -9999 0 -0.49 104 104
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.12 0.21 -9999 0 -0.5 106 106
NDNL2 0.014 0 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
PRKCI 0.014 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.14 0.25 -9999 0 -0.59 123 123
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.12 0.22 -9999 0 -0.51 106 106
TRAF6 0.014 0 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCZ 0.012 0.026 -9999 0 -0.58 1 1
PLG -0.006 0.079 -9999 0 -0.81 5 5
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.099 0.22 -9999 0 -0.59 33 33
SQSTM1 0.014 0 -9999 0 -10000 0 0
NGFRAP1 0.01 0.051 -9999 0 -0.81 2 2
CASP3 -0.039 0.17 -9999 0 -0.47 16 16
E2F1 -0.048 0.22 -9999 0 -0.81 39 39
CASP9 0.014 0 -9999 0 -10000 0 0
IKK complex -0.1 0.17 -9999 0 -0.71 8 8
NGF (dimer)/TRKA -0.17 0.28 -9999 0 -0.63 137 137
MMP7 -0.27 0.39 -9999 0 -0.8 183 183
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.11 0.2 -9999 0 -0.47 106 106
MMP3 -0.53 0.38 -9999 0 -0.8 348 348
APAF-1/Caspase 9 -0.1 0.18 -9999 0 -0.69 19 19
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.24 0.39 -9999 0 -1.1 51 51
PCK1 -0.5 0.62 -9999 0 -1.3 177 177
HNF4A -0.31 0.48 -9999 0 -1.3 61 61
KCNJ11 -0.35 0.52 -9999 0 -1.2 113 113
AKT1 -0.082 0.15 -9999 0 -10000 0 0
response to starvation -0.004 0.023 -9999 0 -10000 0 0
DLK1 -0.44 0.57 -9999 0 -1.2 140 140
NKX2-1 -0.1 0.34 -9999 0 -0.82 57 57
ACADM -0.25 0.4 -9999 0 -1.1 54 54
TAT -0.15 0.24 -9999 0 -0.85 21 21
CEBPB 0.014 0.004 -9999 0 -10000 0 0
CEBPA 0.011 0.045 -9999 0 -0.58 3 3
TTR -0.3 0.33 -9999 0 -0.99 59 59
PKLR -0.29 0.44 -9999 0 -1.1 81 81
APOA1 -0.3 0.46 -9999 0 -1.3 49 49
CPT1C -0.25 0.4 -9999 0 -1.1 54 54
ALAS1 -0.087 0.17 -9999 0 -10000 0 0
TFRC -0.22 0.3 -9999 0 -0.91 35 35
FOXF1 0.019 0.1 -9999 0 -0.72 7 7
NF1 0.021 0 -9999 0 -10000 0 0
HNF1A (dimer) -0.002 0.12 -9999 0 -0.8 10 10
CPT1A -0.24 0.39 -9999 0 -1.1 51 51
HMGCS1 -0.24 0.39 -9999 0 -1.1 53 53
NR3C1 0.019 0.024 -9999 0 -10000 0 0
CPT1B -0.25 0.4 -9999 0 -1.1 52 52
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.012 0.026 -9999 0 -10000 0 0
GCK -0.28 0.42 -9999 0 -1.1 60 60
CREB1 -0.037 0.083 -9999 0 -10000 0 0
IGFBP1 -0.1 0.2 -9999 0 -0.84 17 17
PDX1 -0.12 0.22 -9999 0 -0.79 22 22
UCP2 -0.24 0.39 -9999 0 -1.1 55 55
ALDOB -0.27 0.43 -9999 0 -1.2 60 60
AFP -0.2 0.25 -9999 0 -0.7 62 62
BDH1 -0.24 0.39 -9999 0 -1.1 51 51
HADH -0.25 0.41 -9999 0 -1.1 52 52
F2 -0.32 0.47 -9999 0 -1.3 53 53
HNF1A -0.002 0.12 -9999 0 -0.8 10 10
G6PC -0.061 0.14 -9999 0 -0.68 3 3
SLC2A2 -0.14 0.22 -9999 0 -0.73 8 8
INS -0.012 0.056 -9999 0 -0.83 2 2
FOXA1 -0.21 0.3 -9999 0 -0.59 193 193
FOXA3 -0.15 0.29 -9999 0 -0.91 56 56
FOXA2 -0.3 0.46 -9999 0 -1.2 61 61
ABCC8 -0.26 0.41 -9999 0 -1.1 54 54
ALB -0.23 0.3 -9999 0 -0.82 76 76
Visual signal transduction: Rods

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
mol:K + 0.014 0 -9999 0 -10000 0 0
GNAT1/GTP -0.004 0.047 -9999 0 -0.63 3 3
Metarhodopsin II/Arrestin -0.004 0.048 -9999 0 -0.55 4 4
PDE6G/GNAT1/GTP -0.019 0.1 -9999 0 -0.55 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.002 0.062 -9999 0 -0.81 3 3
GRK1 0 0.05 -9999 0 -0.81 2 2
CNG Channel -0.4 0.28 -9999 0 -0.64 247 247
mol:Na + -0.3 0.26 -9999 0 -0.8 57 57
mol:ADP 0 0.05 -9999 0 -0.81 2 2
RGS9-1/Gbeta5/R9AP -0.018 0.089 -9999 0 -0.53 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.31 0.27 -9999 0 -0.84 57 57
CNGB1 -0.42 0.41 -9999 0 -0.8 273 273
RDH5 0.011 0.044 -9999 0 -0.69 2 2
SAG 0.002 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.27 0.27 -9999 0 -0.77 57 57
Na + (4 Units) -0.28 0.24 -9999 0 -0.74 57 57
RGS9 -0.005 0.12 -9999 0 -0.77 12 12
GNB1/GNGT1 -0.11 0.24 -9999 0 -0.62 94 94
GNAT1/GDP -0.018 0.092 -9999 0 -0.54 11 11
GUCY2D -0.029 0.18 -9999 0 -0.81 27 27
GNGT1 -0.14 0.32 -9999 0 -0.81 94 94
GUCY2F 0 0.05 -9999 0 -0.81 2 2
GNB5 0.014 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.16 0.21 -9999 0 -0.58 53 53
mol:11-cis-retinal 0.011 0.044 -9999 0 -0.69 2 2
mol:cGMP -0.08 0.19 -9999 0 -0.5 81 81
GNB1 0.014 0 -9999 0 -10000 0 0
Rhodopsin -0.007 0.063 -9999 0 -0.59 6 6
SLC24A1 0.014 0 -9999 0 -10000 0 0
CNGA1 -0.028 0.15 -9999 0 -0.58 37 37
Metarhodopsin II -0.006 0.054 -9999 0 -0.5 6 6
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.083 0.2 -9999 0 -0.52 80 80
RGS9BP 0.002 0.081 -9999 0 -0.58 10 10
Metarhodopsin II/Transducin -0.039 0.12 -9999 0 -0.28 100 100
GCAP Family/Ca ++ -0.058 0.16 -9999 0 -0.51 57 57
PDE6A/B -0.22 0.24 -9999 0 -0.46 253 253
mol:Pi -0.018 0.089 -9999 0 -0.53 10 10
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.092 0.19 -9999 0 -0.5 97 97
PDE6B -0.043 0.19 -9999 0 -0.68 42 42
PDE6A -0.25 0.29 -9999 0 -0.58 233 233
PDE6G -0.01 0.14 -9999 0 -0.81 15 15
RHO -0.002 0.071 -9999 0 -0.81 4 4
PDE6 -0.17 0.2 -9999 0 -0.65 39 39
GUCA1A -0.075 0.25 -9999 0 -0.81 56 56
GC2/GCAP Family -0.06 0.17 -9999 0 -0.51 58 58
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.006 0.072 -9999 0 -0.65 6 6
Effects of Botulinum toxin

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
STX1A -0.016 0.13 -9999 0 -0.63 23 23
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.043 0.13 -9999 0 -0.42 53 53
STXBP1 0.014 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.16 0.22 -9999 0 -0.45 186 186
RAB3GAP2/RIMS1/UNC13B -0.036 0.11 -9999 0 -0.53 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.048 0.17 -9999 0 -0.58 50 50
mol:ACh -0.004 0.041 -9999 0 -0.12 59 59
RAB3GAP2 0.014 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.051 0.11 -9999 0 -0.4 27 27
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.16 0.22 -9999 0 -0.44 186 186
UNC13B 0.01 0.045 -9999 0 -0.58 3 3
CHRNA1 -0.22 0.32 -9999 0 -0.65 186 186
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.14 0.25 -9999 0 -0.57 127 127
SNAP25 -0.014 0.079 -9999 0 -0.3 37 37
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.18 0.35 -9999 0 -0.8 127 127
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.006 0.12 -9999 0 -0.54 23 23
STX1A/SNAP25 fragment 1/VAMP2 -0.051 0.11 -9999 0 -0.4 27 27
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.014 0.036 -9999 0 -10000 0 0
NFATC2 -0.061 0.13 -9999 0 -0.4 61 61
NFATC3 -0.014 0.036 -9999 0 -10000 0 0
CD40LG -0.32 0.34 -9999 0 -0.83 112 112
PTGS2 -0.34 0.36 -9999 0 -0.86 127 127
JUNB 0.014 0 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.016 0.016 -9999 0 -10000 0 0
CaM/Ca2+ -0.016 0.016 -9999 0 -10000 0 0
CALM1 0.004 0.011 -9999 0 -10000 0 0
JUN 0.004 0.011 -9999 0 -10000 0 0
mol:Ca2+ -0.017 0.014 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.004 -9999 0 -10000 0 0
FOSL1 -0.005 0.12 -9999 0 -0.79 12 12
CREM 0.013 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.16 0.16 -9999 0 -0.61 21 21
FOS -0.073 0.2 -9999 0 -0.59 67 67
IFNG -0.36 0.38 -9999 0 -0.86 140 140
AP-1/NFAT1-c-4 -0.38 0.37 -9999 0 -1 82 82
FASLG -0.31 0.34 -9999 0 -0.86 91 91
NFAT1-c-4/ICER1 -0.1 0.12 -9999 0 -0.47 17 17
IL2RA -0.32 0.35 -9999 0 -0.87 99 99
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.48 0.42 -9999 0 -0.81 293 293
JunB/Fra1/NFAT1-c-4 -0.1 0.13 -9999 0 -0.58 16 16
IL4 -0.3 0.31 -9999 0 -0.8 81 81
IL2 -0.009 0.034 -9999 0 -0.67 1 1
IL3 -0.028 0.023 -9999 0 -10000 0 0
FKBP1A 0.014 0 -9999 0 -10000 0 0
BATF3 0.007 0.072 -9999 0 -0.81 4 4
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.014 0.002 -9999 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.021 0.097 -10000 0 -0.54 12 12
fibroblast growth factor receptor signaling pathway -0.021 0.097 -10000 0 -0.54 12 12
LAMA1 -0.35 0.41 -10000 0 -0.8 231 231
PRNP 0.012 0.036 -10000 0 -0.81 1 1
GPC1/SLIT2 -0.056 0.14 -10000 0 -0.43 68 68
SMAD2 0.033 0.034 -10000 0 -0.48 1 1
GPC1/PrPc/Cu2+ -0.003 0.037 -10000 0 -0.48 3 3
GPC1/Laminin alpha1 -0.27 0.31 -10000 0 -0.62 231 231
TDGF1 -0.002 0.087 -10000 0 -0.81 6 6
CRIPTO/GPC1 -0.009 0.073 -10000 0 -0.59 8 8
APP/GPC1 -0.003 0.042 -10000 0 -0.55 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.017 0.066 -10000 0 -0.51 8 8
FLT1 0.012 0.036 -10000 0 -0.81 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.003 0.035 -10000 0 -0.53 1 1
SERPINC1 -0.005 0.12 -10000 0 -0.81 11 11
FYN 0.016 0.07 -10000 0 -0.53 8 8
FGR 0.016 0.07 -10000 0 -0.53 8 8
positive regulation of MAPKKK cascade 0.008 0.11 -10000 0 -0.45 11 11
SLIT2 -0.063 0.2 -10000 0 -0.58 67 67
GPC1/NRG -0.097 0.22 -10000 0 -0.6 84 84
NRG1 -0.11 0.3 -10000 0 -0.79 82 82
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.01 0.071 -10000 0 -0.53 9 9
LYN 0.016 0.07 -10000 0 -0.53 8 8
mol:Spermine 0.01 0.034 -10000 0 -0.53 2 2
cell growth -0.021 0.097 -10000 0 -0.54 12 12
BMP signaling pathway -0.011 0.044 0.69 2 -10000 0 2
SRC 0.017 0.066 -10000 0 -0.51 8 8
TGFBR1 0.014 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.37 0.28 -10000 0 -0.58 333 333
GPC1 0.011 0.044 -10000 0 -0.69 2 2
TGFBR1 (dimer) 0.014 0 -10000 0 -10000 0 0
VEGFA 0.002 0.095 -10000 0 -0.81 7 7
BLK -0.061 0.2 -10000 0 -0.54 71 71
HCK 0.013 0.094 -10000 0 -0.64 9 9
FGF2 -0.008 0.12 -10000 0 -0.63 17 17
FGFR1 0.003 0.091 -10000 0 -0.77 7 7
VEGFR1 homodimer 0.012 0.036 -10000 0 -0.81 1 1
TGFBR2 0.011 0.037 -10000 0 -0.58 2 2
cell death -0.003 0.042 -10000 0 -0.55 3 3
ATIII/GPC1 -0.015 0.094 -10000 0 -0.6 13 13
PLA2G2A/GPC1 -0.27 0.2 -10000 0 -0.42 334 334
LCK 0.004 0.11 -10000 0 -0.54 19 19
neuron differentiation -0.097 0.22 -10000 0 -0.6 84 84
PrPc/Cu2+ -0.001 0.027 -10000 0 -0.63 1 1
APP 0.012 0.036 -10000 0 -0.81 1 1
TGFBR2 (dimer) 0.011 0.036 -10000 0 -0.58 2 2
Coregulation of Androgen receptor activity

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
NRIP1 -0.002 0.051 -9999 0 -0.58 3 3
SVIL 0.002 0.035 -9999 0 -0.58 1 1
ZNF318 0.04 0.061 -9999 0 -10000 0 0
JMJD2C 0.007 0.022 -9999 0 -0.1 15 15
T-DHT/AR/Ubc9 -0.12 0.18 -9999 0 -0.4 140 140
CARM1 0.012 0.003 -9999 0 -10000 0 0
PRDX1 0.015 0.004 -9999 0 -10000 0 0
PELP1 0.018 0.01 -9999 0 -10000 0 0
CTNNB1 0.004 0.032 -9999 0 -0.58 1 1
AKT1 0.021 0.017 -9999 0 -10000 0 0
PTK2B 0.005 0.03 -9999 0 -0.58 1 1
MED1 0.02 0.041 -9999 0 -0.81 1 1
MAK 0.027 0.12 -9999 0 -0.71 9 9
response to oxidative stress 0.002 0.004 -9999 0 -10000 0 0
HIP1 0.002 0.035 -9999 0 -0.58 1 1
GSN 0.002 0.026 -9999 0 -10000 0 0
NCOA2 -0.036 0.16 -9999 0 -0.58 42 42
NCOA6 0.002 0.042 -9999 0 -0.81 1 1
DNA-PK 0.031 0.066 -9999 0 -10000 0 0
NCOA4 0.011 0.026 -9999 0 -0.58 1 1
PIAS3 0.005 0.019 -9999 0 -10000 0 0
cell proliferation -0.012 0.1 -9999 0 -0.6 8 8
XRCC5 0.019 0.013 -9999 0 -10000 0 0
UBE3A -0.003 0.038 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.13 0.2 -9999 0 -0.42 154 154
FHL2 -0.018 0.11 -9999 0 -0.95 2 2
RANBP9 0.004 0.023 -9999 0 -10000 0 0
JMJD1A -0.057 0.075 -9999 0 -0.13 250 250
CDK6 0.002 0.098 -9999 0 -0.78 8 8
TGFB1I1 -0.021 0.14 -9999 0 -0.82 15 15
T-DHT/AR/CyclinD1 -0.13 0.2 -9999 0 -0.43 149 149
XRCC6 0.019 0.013 -9999 0 -10000 0 0
T-DHT/AR -0.14 0.2 -9999 0 -0.47 107 107
CTDSP1 0.011 0.005 -9999 0 -10000 0 0
CTDSP2 0.032 0.042 -9999 0 -10000 0 0
BRCA1 0.003 0.024 -9999 0 -10000 0 0
TCF4 0.027 0.03 -9999 0 -10000 0 0
CDKN2A -0.33 0.39 -9999 0 -0.75 238 238
SRF 0.03 0.022 -9999 0 -10000 0 0
NKX3-1 -0.14 0.15 -9999 0 -0.77 9 9
KLK3 -0.22 0.54 -9999 0 -1.4 92 92
TMF1 0.011 0.005 -9999 0 -10000 0 0
HNRNPA1 0.025 0.025 -9999 0 -10000 0 0
AOF2 -0.012 0.027 -9999 0 -0.07 88 88
APPL1 0.041 0.037 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.11 0.18 -9999 0 -0.4 129 129
AR -0.17 0.27 -9999 0 -0.61 140 140
UBA3 0.011 0.005 -9999 0 -10000 0 0
PATZ1 0.025 0.025 -9999 0 -10000 0 0
PAWR 0.011 0.005 -9999 0 -10000 0 0
PRKDC 0.019 0.013 -9999 0 -10000 0 0
PA2G4 0.026 0.027 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.098 0.17 -9999 0 -0.37 129 129
RPS6KA3 0 0.045 -9999 0 -0.58 2 2
T-DHT/AR/ARA70 -0.12 0.18 -9999 0 -0.4 141 141
LATS2 0.023 0.022 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.092 0.17 -9999 0 -0.37 129 129
Cyclin D3/CDK11 p58 0.003 0.007 -9999 0 -10000 0 0
VAV3 -0.036 0.15 -9999 0 -0.59 36 36
KLK2 -0.074 0.14 -9999 0 -0.75 15 15
CASP8 0.017 0.008 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.13 0.19 -9999 0 -0.44 104 104
TMPRSS2 -0.5 0.5 -9999 0 -1 243 243
CCND1 -0.009 0.12 -9999 0 -0.76 13 13
PIAS1 -0.003 0.038 -9999 0 -10000 0 0
mol:T-DHT -0.023 0.035 -9999 0 -0.067 164 164
CDC2L1 0.001 0.002 -9999 0 -10000 0 0
PIAS4 -0.012 0.057 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.12 0.2 -9999 0 -0.42 137 137
CMTM2 -0.008 0.14 -9999 0 -0.8 15 15
SNURF -0.014 0.12 -9999 0 -0.58 23 23
ZMIZ1 -0.005 0.029 -9999 0 -10000 0 0
CCND3 0.014 0.002 -9999 0 -10000 0 0
TGIF1 0.023 0.044 -9999 0 -0.81 1 1
FKBP4 0.004 0.023 -9999 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.27 0.23 -10000 0 -0.94 14 14
IHH -0.054 0.074 -10000 0 -0.76 3 3
SHH Np/Cholesterol/GAS1 -0.043 0.14 -10000 0 -0.48 46 46
LRPAP1 0.014 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.042 0.14 0.48 46 -10000 0 46
SMO/beta Arrestin2 -0.14 0.15 -10000 0 -0.59 25 25
SMO -0.16 0.16 -10000 0 -0.63 25 25
AKT1 -0.059 0.083 -10000 0 -0.6 2 2
ARRB2 0.014 0 -10000 0 -10000 0 0
BOC -0.04 0.17 -10000 0 -0.58 47 47
ADRBK1 0.014 0 -10000 0 -10000 0 0
heart looping -0.15 0.16 -10000 0 -0.62 25 25
STIL -0.13 0.17 -10000 0 -0.63 32 32
DHH N/PTCH2 -0.015 0.087 -10000 0 -0.51 15 15
DHH N/PTCH1 -0.14 0.14 -10000 0 -0.77 9 9
PIK3CA 0.014 0 -10000 0 -10000 0 0
DHH 0.009 0.051 -10000 0 -0.81 2 2
PTHLH -0.45 0.33 -10000 0 -0.65 369 369
determination of left/right symmetry -0.15 0.16 -10000 0 -0.62 25 25
PIK3R1 0.011 0.037 -10000 0 -0.58 2 2
skeletal system development -0.44 0.33 -10000 0 -0.65 369 369
IHH N/Hhip -0.054 0.17 -10000 0 -0.67 34 34
DHH N/Hhip -0.039 0.15 -10000 0 -0.61 33 33
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.15 0.16 -10000 0 -0.62 25 25
pancreas development -0.037 0.19 -10000 0 -0.8 31 31
HHAT 0.014 0 -10000 0 -10000 0 0
PI3K -0.002 0.026 -10000 0 -0.42 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.002 0.091 -10000 0 -0.72 8 8
somite specification -0.15 0.16 -10000 0 -0.62 25 25
SHH Np/Cholesterol/PTCH1 -0.14 0.17 -10000 0 -0.6 44 44
SHH Np/Cholesterol/PTCH2 -0.045 0.15 -10000 0 -0.5 47 47
SHH Np/Cholesterol/Megalin -0.061 0.18 -10000 0 -0.55 58 58
SHH -0.028 0.17 -10000 0 -0.62 38 38
catabolic process -0.16 0.16 -10000 0 -0.73 11 11
SMO/Vitamin D3 -0.15 0.18 -10000 0 -0.64 33 33
SHH Np/Cholesterol/Hhip -0.065 0.18 -10000 0 -0.55 60 60
LRP2 -0.031 0.18 -10000 0 -0.81 27 27
receptor-mediated endocytosis -0.17 0.17 -10000 0 -0.61 47 47
SHH Np/Cholesterol/BOC -0.065 0.15 -10000 0 -0.5 39 39
SHH Np/Cholesterol/CDO -0.044 0.14 -10000 0 -0.49 38 38
mesenchymal cell differentiation 0.064 0.18 0.55 60 -10000 0 60
mol:Vitamin D3 -0.14 0.17 -10000 0 -0.6 44 44
IHH N/PTCH2 -0.025 0.099 -10000 0 -0.56 16 16
CDON -0.001 0.092 -10000 0 -0.58 13 13
IHH N/PTCH1 -0.16 0.16 -10000 0 -0.73 11 11
Megalin/LRPAP1 -0.032 0.14 -10000 0 -0.62 27 27
PTCH2 -0.004 0.11 -10000 0 -0.67 13 13
SHH Np/Cholesterol -0.033 0.13 -10000 0 -0.5 38 38
PTCH1 -0.16 0.16 -10000 0 -0.73 11 11
HHIP -0.038 0.19 -10000 0 -0.8 31 31
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.21 0.26 -9999 0 -0.52 198 198
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.055 0.21 -9999 0 -0.7 49 49
SMAD9 -0.076 0.17 -9999 0 -0.58 45 45
SMAD4 0.012 0.026 -9999 0 -0.58 1 1
SMAD5 -0.051 0.14 -9999 0 -0.48 27 27
BMP7/USAG1 -0.16 0.24 -9999 0 -0.5 161 161
SMAD5/SKI -0.041 0.14 -9999 0 -0.47 21 21
SMAD1 0.041 0.027 -9999 0 -10000 0 0
BMP2 -0.018 0.16 -9999 0 -0.8 20 20
SMAD1/SMAD1/SMAD4 0 0.011 -9999 0 -10000 0 0
BMPR1A 0.011 0.037 -9999 0 -0.58 2 2
BMPR1B -0.062 0.23 -9999 0 -0.75 51 51
BMPR1A-1B/BAMBI -0.063 0.16 -9999 0 -0.48 68 68
AHSG -0.04 0.2 -9999 0 -0.81 32 32
CER1 -0.006 0.087 -9999 0 -0.81 6 6
BMP2-4/CER1 -0.034 0.13 -9999 0 -0.55 26 26
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.093 0.19 -9999 0 -0.54 51 51
BMP2-4 (homodimer) -0.032 0.13 -9999 0 -0.56 30 30
RGMB 0.014 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.05 0.14 -9999 0 -0.49 45 45
RGMA -0.055 0.19 -9999 0 -0.58 60 60
SMURF1 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.093 0.18 -9999 0 -0.5 51 51
BMP2-4/USAG1 -0.13 0.21 -9999 0 -0.57 55 55
SMAD6/SMURF1/SMAD5 -0.041 0.14 -9999 0 -0.46 23 23
SOSTDC1 -0.16 0.29 -9999 0 -0.63 142 142
BMP7/BMPR2/BMPR1A-1B -0.068 0.16 -9999 0 -0.51 42 42
SKI 0.014 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.004 0.084 -9999 0 -0.77 6 6
HFE2 -0.18 0.27 -9999 0 -0.58 162 162
ZFYVE16 0.014 0 -9999 0 -10000 0 0
MAP3K7 0.014 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.044 0.14 -9999 0 -0.55 36 36
SMAD5/SMAD5/SMAD4 -0.042 0.14 -9999 0 -0.47 23 23
MAPK1 0.014 0 -9999 0 -10000 0 0
TAK1/TAB family -0.094 0.13 -9999 0 -0.52 25 25
BMP7 (homodimer) -0.032 0.16 -9999 0 -0.58 40 40
NUP214 0.014 0 -9999 0 -10000 0 0
BMP6/FETUA -0.045 0.16 -9999 0 -0.61 38 38
SMAD1/SKI 0.047 0.026 -9999 0 -10000 0 0
SMAD6 0.014 0 -9999 0 -10000 0 0
CTDSP2 0.014 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.061 0.17 -9999 0 -0.55 52 52
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.34 0.41 -9999 0 -0.81 222 222
BMPR2 (homodimer) 0.014 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.057 0.17 -9999 0 -0.57 52 52
CHRDL1 -0.29 0.29 -9999 0 -0.58 266 266
ENDOFIN/SMAD1 0.047 0.026 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.001 0.004 -9999 0 -10000 0 0
SMAD6/SMURF1 0.014 0 -9999 0 -10000 0 0
BAMBI -0.008 0.12 -9999 0 -0.66 17 17
SMURF2 0.014 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.2 0.21 -9999 0 -0.76 25 25
BMP2-4/GREM1 -0.25 0.29 -9999 0 -0.56 231 231
SMAD7 0.014 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.056 0.17 -9999 0 -0.54 46 46
SMAD1/SMAD6 0.047 0.026 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.032 0.16 -9999 0 -0.58 40 40
BMP6 0.004 0.084 -9999 0 -0.77 6 6
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.075 0.16 -9999 0 -0.43 51 51
PPM1A 0.014 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.047 0.026 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.014 0 -9999 0 -10000 0 0
PPP1CA 0.014 0 -9999 0 -10000 0 0
XIAP 0.014 0 -9999 0 -10000 0 0
CTDSP1 0.014 0 -9999 0 -10000 0 0
PPP1R15A 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.16 0.22 -9999 0 -0.5 110 110
CHRD -0.012 0.14 -9999 0 -0.78 17 17
BMPR2 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.1 0.19 -9999 0 -0.53 51 51
BMP4 0.001 0.088 -9999 0 -0.6 11 11
FST -0.25 0.38 -9999 0 -0.81 169 169
BMP2-4/NOG -0.069 0.18 -9999 0 -0.55 47 47
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.063 0.15 -9999 0 -0.48 42 42
Caspase cascade in apoptosis

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
TOP1 -0.039 0.18 -10000 0 -0.4 88 88
ACTA1 -0.14 0.23 -10000 0 -0.6 90 90
NUMA1 -0.039 0.18 -10000 0 -0.4 88 88
SPTAN1 -0.062 0.23 -10000 0 -0.53 88 88
LIMK1 -0.062 0.23 -10000 0 -0.53 88 88
BIRC3 -0.023 0.17 -10000 0 -0.81 23 23
BIRC2 -0.005 0.12 -10000 0 -0.81 12 12
BAX 0.014 0 -10000 0 -10000 0 0
CASP10 -0.095 0.29 -10000 0 -0.7 91 91
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.014 0 -10000 0 -10000 0 0
PTK2 -0.038 0.18 -10000 0 -0.4 88 88
DIABLO 0.014 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.061 0.22 -10000 0 -0.52 88 88
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.014 0 -10000 0 -10000 0 0
GSN -0.062 0.23 -10000 0 -0.53 88 88
MADD 0.014 0 -10000 0 -10000 0 0
TFAP2A 0.002 0.088 -10000 0 -0.53 7 7
BID -0.028 0.12 -10000 0 -0.28 88 88
MAP3K1 -0.011 0.074 -10000 0 -0.21 31 31
TRADD 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.004 0.02 -10000 0 -0.41 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.062 0.23 -10000 0 -0.53 88 88
CASP9 0.014 0.001 -10000 0 -10000 0 0
DNA repair 0.006 0.063 -10000 0 -0.2 12 12
neuron apoptosis 0.018 0.026 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.054 0.22 -10000 0 -0.52 83 83
APAF1 0.012 0.026 -10000 0 -0.58 1 1
CASP6 -0.002 0.1 -10000 0 -0.46 3 3
TRAF2 0.004 0.088 -10000 0 -0.81 6 6
ICAD/CAD -0.054 0.22 -10000 0 -0.53 83 83
CASP7 0.006 0.064 0.3 19 -10000 0 19
KRT18 0.003 0.065 -10000 0 -0.42 9 9
apoptosis -0.044 0.21 -10000 0 -0.48 84 84
DFFA -0.062 0.23 -10000 0 -0.53 88 88
DFFB -0.064 0.23 -10000 0 -0.54 88 88
PARP1 -0.006 0.063 0.2 12 -10000 0 12
actin filament polymerization 0.049 0.21 0.5 83 -10000 0 83
TNF -0.024 0.17 -10000 0 -0.77 25 25
CYCS -0.018 0.093 -10000 0 -0.27 36 36
SATB1 -0.009 0.12 -10000 0 -0.48 8 8
SLK -0.062 0.23 -10000 0 -0.53 88 88
p15 BID/BAX -0.018 0.11 -10000 0 -0.32 33 33
CASP2 0.033 0.073 -10000 0 -10000 0 0
JNK cascade 0.011 0.074 0.21 31 -10000 0 31
CASP3 -0.074 0.24 -10000 0 -0.57 88 88
LMNB2 0.027 0.06 -10000 0 -0.35 3 3
RIPK1 0.014 0 -10000 0 -10000 0 0
CASP4 0.011 0.037 -10000 0 -0.58 2 2
Mammalian IAPs/DIABLO -0.032 0.14 -10000 0 -0.6 28 28
negative regulation of DNA binding 0.002 0.087 -10000 0 -0.52 7 7
stress fiber formation -0.061 0.22 -10000 0 -0.52 88 88
GZMB -0.12 0.33 -10000 0 -0.79 91 91
CASP1 0.016 0.041 -10000 0 -0.59 2 2
LMNB1 0.027 0.06 -10000 0 -0.35 3 3
APP 0.018 0.027 -10000 0 -10000 0 0
TNFRSF1A 0.014 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.012 0 -10000 0 -10000 0 0
VIM -0.048 0.2 -10000 0 -0.46 87 87
LMNA 0.027 0.06 -10000 0 -0.35 3 3
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.026 0.078 -10000 0 -0.36 10 10
LRDD 0.012 0.036 -10000 0 -0.81 1 1
SREBF1 -0.062 0.23 -10000 0 -0.53 88 88
APAF-1/Caspase 9 0 0.079 0.45 11 -10000 0 11
nuclear fragmentation during apoptosis -0.038 0.17 -10000 0 -0.4 88 88
CFL2 -0.051 0.22 -10000 0 -0.51 83 83
GAS2 -0.1 0.25 -10000 0 -0.57 90 90
positive regulation of apoptosis 0.031 0.06 -10000 0 -0.34 3 3
PRF1 -0.047 0.21 -10000 0 -0.79 39 39
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.11 0.31 -10000 0 -0.91 64 64
NFATC2 -0.041 0.23 -10000 0 -0.72 30 30
NFATC3 -0.008 0.061 -10000 0 -10000 0 0
CD40LG -0.35 0.41 -10000 0 -1 77 77
ITCH 0.018 0.09 -10000 0 -10000 0 0
CBLB 0.018 0.09 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.34 0.45 -10000 0 -1.1 118 118
JUNB 0.014 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.034 0.092 -10000 0 -10000 0 0
T cell anergy -0.006 0.16 -10000 0 -0.53 17 17
TLE4 -0.011 0.17 -10000 0 -0.64 16 16
Jun/NFAT1-c-4/p21SNFT -0.17 0.23 -10000 0 -0.96 20 20
AP-1/NFAT1-c-4 -0.36 0.44 -10000 0 -1.1 81 81
IKZF1 -0.019 0.2 -10000 0 -0.74 22 22
T-helper 2 cell differentiation -0.072 0.23 -10000 0 -0.78 26 26
AP-1/NFAT1 -0.14 0.19 -10000 0 -0.6 45 45
CALM1 0.008 0.059 -10000 0 -10000 0 0
EGR2 -0.063 0.3 -10000 0 -1.4 16 16
EGR3 -0.053 0.26 -10000 0 -1.2 14 14
NFAT1/FOXP3 -0.13 0.33 -10000 0 -0.8 82 82
EGR1 -0.014 0.13 -10000 0 -0.58 25 25
JUN -0.019 0.035 -10000 0 -10000 0 0
EGR4 -0.079 0.26 -10000 0 -0.78 60 60
mol:Ca2+ -0.007 0.063 -10000 0 -10000 0 0
GBP3 -0.026 0.21 -10000 0 -0.7 30 30
FOSL1 -0.005 0.12 -10000 0 -0.79 12 12
NFAT1-c-4/MAF/IRF4 -0.12 0.25 -10000 0 -0.94 24 24
DGKA -0.009 0.17 -10000 0 -0.61 15 15
CREM 0.013 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.22 0.27 -10000 0 -0.95 31 31
CTLA4 -0.16 0.41 -10000 0 -0.89 108 108
NFAT1-c-4 (dimer)/EGR1 -0.11 0.25 -10000 0 -1 21 21
NFAT1-c-4 (dimer)/EGR4 -0.15 0.28 -10000 0 -0.92 32 32
FOS -0.097 0.2 -10000 0 -0.6 67 67
IFNG -0.22 0.34 -10000 0 -0.86 73 73
T cell activation -0.11 0.2 -10000 0 -0.72 11 11
MAF 0.008 0.058 -10000 0 -0.58 5 5
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.038 0.16 0.72 11 -10000 0 11
TNF -0.13 0.31 -10000 0 -0.95 39 39
FASLG -0.12 0.39 -10000 0 -1.3 34 34
TBX21 -0.041 0.19 -10000 0 -0.78 29 29
BATF3 0.007 0.072 -10000 0 -0.81 4 4
PRKCQ 0 0.094 -10000 0 -0.62 11 11
PTPN1 -0.009 0.17 -10000 0 -0.58 19 19
NFAT1-c-4/ICER1 -0.1 0.22 -10000 0 -0.96 17 17
GATA3 -0.016 0.15 -10000 0 -0.77 20 20
T-helper 1 cell differentiation -0.2 0.34 -10000 0 -0.84 73 73
IL2RA -0.3 0.38 -10000 0 -0.96 103 103
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.009 0.17 -10000 0 -0.61 15 15
E2F1 -0.041 0.22 -10000 0 -0.8 39 39
PPARG -0.21 0.29 -10000 0 -0.58 197 197
SLC3A2 -0.009 0.17 -10000 0 -0.61 15 15
IRF4 -0.038 0.19 -10000 0 -0.75 35 35
PTGS2 -0.37 0.44 -10000 0 -1.1 88 88
CSF2 -0.53 0.5 -10000 0 -1 206 206
JunB/Fra1/NFAT1-c-4 -0.1 0.22 -10000 0 -0.93 18 18
IL4 -0.076 0.24 -10000 0 -0.85 23 23
IL5 -0.32 0.37 -10000 0 -1 58 58
IL2 -0.11 0.2 -10000 0 -0.75 10 10
IL3 -0.063 0.051 -10000 0 -10000 0 0
RNF128 -0.034 0.23 -10000 0 -0.65 63 63
NFATC1 -0.038 0.16 -10000 0 -0.72 11 11
CDK4 0.022 0.14 0.65 3 -10000 0 3
PTPRK -0.009 0.17 -10000 0 -0.61 15 15
IL8 -0.39 0.46 -10000 0 -1.1 119 119
POU2F1 0.014 0.002 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.023 0.16 -10000 0 -0.41 26 26
CRKL -0.021 0.15 -10000 0 -0.4 62 62
HRAS -0.012 0.16 -10000 0 -0.58 9 9
mol:PIP3 -0.034 0.14 -10000 0 -0.4 61 61
SPRED1 0.014 0 -10000 0 -10000 0 0
SPRED2 0.011 0.037 -10000 0 -0.58 2 2
GAB1 -0.03 0.16 -10000 0 -0.43 61 61
FOXO3 -0.013 0.14 -10000 0 -0.42 8 8
AKT1 -0.023 0.15 -10000 0 -0.4 61 61
BAD -0.013 0.14 -10000 0 -0.37 55 55
megakaryocyte differentiation -0.04 0.17 -10000 0 -0.43 73 73
GSK3B -0.013 0.14 -10000 0 -0.37 55 55
RAF1 0.002 0.13 -10000 0 -0.46 8 8
SHC1 0.014 0 -10000 0 -10000 0 0
STAT3 -0.03 0.16 -10000 0 -0.43 61 61
STAT1 -0.11 0.37 -10000 0 -1 61 61
HRAS/SPRED1 -0.049 0.1 -10000 0 -0.46 8 8
cell proliferation -0.033 0.16 -10000 0 -0.45 61 61
PIK3CA 0.013 0 -10000 0 -10000 0 0
TEC -0.015 0.13 -10000 0 -0.58 25 25
RPS6KB1 -0.029 0.16 -10000 0 -0.43 62 62
HRAS/SPRED2 -0.05 0.11 -10000 0 -0.46 10 10
LYN/TEC/p62DOK -0.069 0.15 -10000 0 -0.57 14 14
MAPK3 0.017 0.099 -10000 0 -0.33 5 5
STAP1 -0.063 0.19 -10000 0 -0.44 97 97
GRAP2 -0.002 0.1 -10000 0 -0.67 12 12
JAK2 -0.13 0.27 -10000 0 -0.84 61 61
STAT1 (dimer) -0.1 0.36 -10000 0 -1 61 61
mol:Gleevec 0 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.085 0.17 -10000 0 -0.5 24 24
actin filament polymerization -0.031 0.16 -10000 0 -0.43 62 62
LYN 0.012 0.036 -10000 0 -0.81 1 1
STAP1/STAT5A (dimer) -0.071 0.23 -10000 0 -0.59 65 65
PIK3R1 0.011 0.037 -10000 0 -0.58 2 2
CBL/CRKL/GRB2 -0.005 0.14 -10000 0 -0.42 5 5
PI3K -0.016 0.15 -10000 0 -0.41 61 61
PTEN 0.014 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.15 0.44 -10000 0 -1.3 63 63
MAPK8 -0.034 0.17 -10000 0 -0.46 61 61
STAT3 (dimer) -0.029 0.15 -10000 0 -0.42 61 61
positive regulation of transcription 0.019 0.085 -10000 0 -0.28 3 3
mol:GDP -0.071 0.14 -10000 0 -0.62 10 10
PIK3C2B -0.03 0.16 -10000 0 -0.44 61 61
CBL/CRKL -0.012 0.14 -10000 0 -0.38 56 56
FER -0.031 0.16 -10000 0 -0.43 63 63
SH2B3 -0.031 0.16 -10000 0 -0.43 62 62
PDPK1 -0.025 0.13 -10000 0 -0.37 61 61
SNAI2 -0.041 0.17 -10000 0 -0.44 73 73
positive regulation of cell proliferation -0.063 0.26 -10000 0 -0.74 61 61
KITLG 0.011 0.047 -10000 0 -0.6 3 3
cell motility -0.063 0.26 -10000 0 -0.74 61 61
PTPN6 0.008 0.013 -10000 0 -10000 0 0
EPOR -0.004 0.14 -10000 0 -0.67 11 11
STAT5A (dimer) -0.046 0.22 -10000 0 -0.6 61 61
SOCS1 -0.039 0.2 -10000 0 -0.81 33 33
cell migration 0.039 0.17 0.44 69 -10000 0 69
SOS1 0.014 0 -10000 0 -10000 0 0
EPO -0.077 0.26 -10000 0 -0.8 57 57
VAV1 0.003 0.081 -10000 0 -0.6 9 9
GRB10 -0.031 0.16 -10000 0 -0.43 62 62
PTPN11 0.014 0.006 -10000 0 -10000 0 0
SCF/KIT -0.04 0.16 -10000 0 -0.46 63 63
GO:0007205 0.001 0.009 -10000 0 -10000 0 0
MAP2K1 0.013 0.11 -10000 0 -0.37 5 5
CBL 0.014 0 -10000 0 -10000 0 0
KIT -0.12 0.44 -10000 0 -1.3 62 62
MAP2K2 0.013 0.11 -10000 0 -0.37 5 5
SHC/Grb2/SOS1 -0.055 0.13 -10000 0 -0.4 61 61
STAT5A -0.048 0.22 -10000 0 -0.62 61 61
GRB2 0.014 0 -10000 0 -10000 0 0
response to radiation -0.04 0.17 -10000 0 -0.43 73 73
SHC/GRAP2 -0.012 0.076 -10000 0 -0.5 12 12
PTPRO -0.041 0.17 -10000 0 -0.44 73 73
SH2B2 -0.032 0.16 -10000 0 -0.44 62 62
DOK1 0.012 0.036 -10000 0 -0.81 1 1
MATK -0.04 0.17 -10000 0 -0.45 69 69
CREBBP 0.034 0.015 -10000 0 -10000 0 0
BCL2 -0.007 0.18 -10000 0 -1 9 9
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.04 0.056 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.1 0.14 -9999 0 -0.45 38 38
JUN -0.066 0.16 -9999 0 -0.47 39 39
HRAS 0.012 0.036 -9999 0 -0.81 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.17 0.25 -9999 0 -0.61 91 91
RAP1A 0.014 0 -9999 0 -10000 0 0
FRS2 0.007 0.072 -9999 0 -0.81 4 4
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.17 0.24 -9999 0 -0.61 91 91
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.12 0.21 -9999 0 -0.62 48 48
RHOA 0.014 0 -9999 0 -10000 0 0
RAP1A/GTP -0.15 0.22 -9999 0 -0.55 90 90
GRB7 0.004 0.084 -9999 0 -0.71 7 7
RET51/GFRalpha1/GDNF -0.17 0.24 -9999 0 -0.61 90 90
MAPKKK cascade -0.13 0.19 -9999 0 -0.61 37 37
BCAR1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.12 0.2 -9999 0 -0.61 45 45
lamellipodium assembly -0.096 0.13 -9999 0 -0.41 38 38
RET51/GFRalpha1/GDNF/SHC -0.17 0.24 -9999 0 -0.61 90 90
PIK3CA 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.12 0.2 -9999 0 -0.61 44 44
RET9/GFRalpha1/GDNF/Shank3 -0.12 0.2 -9999 0 -0.47 84 84
MAPK3 -0.11 0.22 -9999 0 -0.68 36 36
DOK1 0.012 0.036 -9999 0 -0.81 1 1
DOK6 -0.001 0.1 -9999 0 -0.68 11 11
PXN 0.014 0 -9999 0 -10000 0 0
neurite development -0.092 0.21 -9999 0 -0.62 36 36
DOK5 -0.016 0.13 -9999 0 -0.6 25 25
GFRA1 -0.13 0.25 -9999 0 -0.58 128 128
MAPK8 -0.078 0.17 -9999 0 -0.5 39 39
HRAS/GTP -0.15 0.22 -9999 0 -0.71 37 37
tube development -0.11 0.19 -9999 0 -0.57 44 44
MAPK1 -0.11 0.22 -9999 0 -0.68 36 36
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.064 0.15 -9999 0 -0.53 18 18
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
PDLIM7 0.006 0.08 -9999 0 -0.81 5 5
RET51/GFRalpha1/GDNF/Dok6 -0.16 0.24 -9999 0 -0.57 97 97
SHC1 0.014 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.17 0.24 -9999 0 -0.61 90 90
RET51/GFRalpha1/GDNF/Dok5 -0.18 0.26 -9999 0 -0.62 105 105
PRKCA 0.011 0.044 -9999 0 -0.69 2 2
HRAS/GDP -0.001 0.027 -9999 0 -0.63 1 1
CREB1 -0.078 0.17 -9999 0 -0.49 36 36
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.062 0.15 -9999 0 -0.52 17 17
RET51/GFRalpha1/GDNF/Grb7 -0.17 0.25 -9999 0 -0.62 96 96
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.071 0.25 -9999 0 -0.77 56 56
DOK4 0.014 0 -9999 0 -10000 0 0
JNK cascade -0.065 0.16 -9999 0 -0.46 39 39
RET9/GFRalpha1/GDNF/FRS2 -0.12 0.2 -9999 0 -0.6 48 48
SHANK3 0.014 0 -9999 0 -10000 0 0
RASA1 0.011 0.037 -9999 0 -0.58 2 2
NCK1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.062 0.15 -9999 0 -0.52 17 17
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.088 0.18 -9999 0 -0.52 38 38
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.087 0.17 -9999 0 -0.51 36 36
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.089 0.18 -9999 0 -0.57 36 36
PI3K -0.1 0.24 -9999 0 -0.67 38 38
SOS1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.11 0.19 -9999 0 -0.57 44 44
GRB10 0.012 0.036 -9999 0 -0.81 1 1
activation of MAPKK activity -0.083 0.17 -9999 0 -0.51 38 38
RET51/GFRalpha1/GDNF/FRS2 -0.17 0.25 -9999 0 -0.61 93 93
GAB1 0.014 0 -9999 0 -10000 0 0
IRS1 0.01 0.045 -9999 0 -0.58 3 3
IRS2 0.011 0.037 -9999 0 -0.58 2 2
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.089 0.18 -9999 0 -0.57 36 36
RET51/GFRalpha1/GDNF/PKC alpha -0.17 0.25 -9999 0 -0.61 92 92
GRB2 0.014 0 -9999 0 -10000 0 0
PRKACA 0.014 0 -9999 0 -10000 0 0
GDNF -0.059 0.23 -9999 0 -0.81 44 44
RAC1 0.014 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.25 -9999 0 -0.61 90 90
Rac1/GTP -0.11 0.16 -9999 0 -0.5 38 38
RET9/GFRalpha1/GDNF -0.13 0.22 -9999 0 -0.44 155 155
GFRalpha1/GDNF -0.15 0.25 -9999 0 -0.51 155 155
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.059 0.13 -9999 0 -0.4 15 15
PDGFB-D/PDGFRB/SLAP -0.1 0.23 -9999 0 -0.61 89 89
PDGFB-D/PDGFRB/APS/CBL -0.088 0.2 -9999 0 -0.52 88 88
AKT1 -0.006 0.15 -9999 0 -0.59 3 3
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.028 0.15 -9999 0 -0.42 15 15
PIK3CA 0.014 0 -9999 0 -10000 0 0
FGR -0.065 0.15 -9999 0 -0.39 87 87
mol:Ca2+ -0.025 0.13 -9999 0 -0.35 11 11
MYC 0.007 0.11 -9999 0 -10000 0 0
SHC1 0.014 0 -9999 0 -10000 0 0
HRAS/GDP -0.066 0.16 -9999 0 -0.42 88 88
LRP1/PDGFRB/PDGFB -0.098 0.22 -9999 0 -0.55 92 92
GRB10 0.012 0.036 -9999 0 -0.81 1 1
PTPN11 0.014 0 -9999 0 -10000 0 0
GO:0007205 -0.025 0.13 -9999 0 -0.36 11 11
PTEN 0.014 0 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
GRB7 0.004 0.084 -9999 0 -0.71 7 7
PDGFB-D/PDGFRB/SHP2 -0.097 0.23 -9999 0 -0.61 86 86
PDGFB-D/PDGFRB/GRB10 -0.099 0.23 -9999 0 -0.61 87 87
cell cycle arrest -0.1 0.23 -9999 0 -0.61 89 89
HRAS 0.012 0.036 -9999 0 -0.81 1 1
HIF1A 0.005 0.14 -9999 0 -0.51 3 3
GAB1 -0.025 0.14 -9999 0 -0.38 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.02 0.14 -9999 0 -0.46 2 2
PDGFB-D/PDGFRB -0.083 0.2 -9999 0 -0.53 87 87
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.097 0.23 -9999 0 -0.61 86 86
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.06 0.13 -9999 0 -0.67 2 2
positive regulation of MAPKKK cascade -0.097 0.23 -9999 0 -0.61 86 86
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
mol:IP3 -0.025 0.14 -9999 0 -0.36 11 11
E5 -0.001 0.002 -9999 0 -10000 0 0
CSK 0.014 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.1 0.24 -9999 0 -0.62 90 90
SHB 0.011 0.037 -9999 0 -0.58 2 2
BLK -0.11 0.18 -9999 0 -0.43 97 97
PTPN2 0.012 0.036 -9999 0 -0.8 1 1
PDGFB-D/PDGFRB/SNX15 -0.097 0.23 -9999 0 -0.61 86 86
BCAR1 0.014 0 -9999 0 -10000 0 0
VAV2 -0.022 0.14 -9999 0 -0.42 7 7
CBL 0.014 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.097 0.23 -9999 0 -0.61 86 86
LCK -0.071 0.15 -9999 0 -0.39 87 87
PDGFRB -0.12 0.3 -9999 0 -0.8 86 86
ACP1 0.014 0 -9999 0 -10000 0 0
HCK -0.065 0.15 -9999 0 -0.48 3 3
ABL1 -0.032 0.14 -9999 0 -0.35 86 86
PDGFB-D/PDGFRB/CBL -0.024 0.13 -9999 0 -0.38 11 11
PTPN1 0.013 0.003 -9999 0 -10000 0 0
SNX15 0.014 0 -9999 0 -10000 0 0
STAT3 0.014 0 -9999 0 -10000 0 0
STAT1 -0.033 0.19 -9999 0 -0.79 30 30
cell proliferation 0.009 0.1 -9999 0 -10000 0 0
SLA 0.009 0.062 -9999 0 -0.81 3 3
actin cytoskeleton reorganization -0.022 0.17 -9999 0 -10000 0 0
SRC -0.063 0.15 -9999 0 -0.39 87 87
PI3K -0.066 0.14 -9999 0 -0.67 3 3
PDGFB-D/PDGFRB/GRB7/SHC -0.092 0.2 -9999 0 -0.53 90 90
SH2B2 0.01 0.051 -9999 0 -0.81 2 2
PLCgamma1/SPHK1 -0.029 0.15 -9999 0 -0.43 15 15
LYN -0.064 0.15 -9999 0 -0.39 87 87
LRP1 0.012 0.026 -9999 0 -0.58 1 1
SOS1 0.014 0 -9999 0 -10000 0 0
STAT5B 0.014 0 -9999 0 -10000 0 0
STAT5A 0.014 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.068 0.16 -9999 0 -0.42 12 12
SPHK1 -0.01 0.14 -9999 0 -0.81 15 15
EDG1 0 0.003 -9999 0 -10000 0 0
mol:DAG -0.025 0.14 -9999 0 -0.36 11 11
PLCG1 -0.026 0.14 -9999 0 -0.36 11 11
NHERF/PDGFRB -0.091 0.2 -9999 0 -0.53 87 87
YES1 -0.064 0.15 -9999 0 -0.39 87 87
cell migration -0.09 0.2 -9999 0 -0.53 87 87
SHC/Grb2/SOS1 -0.068 0.16 -9999 0 -0.41 87 87
SLC9A3R2 0.01 0.051 -9999 0 -0.81 2 2
SLC9A3R1 0.009 0.052 -9999 0 -0.58 4 4
NHERF1-2/PDGFRB/PTEN -0.082 0.18 -9999 0 -0.48 87 87
FYN -0.064 0.15 -9999 0 -0.5 4 4
DOK1 -0.05 0.19 -9999 0 -0.47 88 88
HRAS/GTP -0.001 0.027 -9999 0 -0.63 1 1
PDGFB -0.004 0.12 -9999 0 -0.81 11 11
RAC1 -0.008 0.13 -9999 0 -10000 0 0
PRKCD -0.048 0.19 -9999 0 -0.47 87 87
FER -0.05 0.19 -9999 0 -0.48 87 87
MAPKKK cascade -0.067 0.15 -9999 0 -0.41 87 87
RASA1 -0.05 0.19 -9999 0 -0.47 87 87
NCK1 0.014 0 -9999 0 -10000 0 0
NCK2 0.014 0 -9999 0 -10000 0 0
p62DOK/Csk -0.066 0.17 -9999 0 -0.43 88 88
PDGFB-D/PDGFRB/SHB -0.099 0.23 -9999 0 -0.6 88 88
chemotaxis -0.031 0.14 -9999 0 -0.34 86 86
STAT1-3-5/STAT1-3-5 -0.089 0.18 -9999 0 -0.83 6 6
Bovine Papilomavirus E5/PDGFRB -0.093 0.23 -9999 0 -0.62 86 86
PTPRJ 0.014 0 -9999 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.088 0.22 -10000 0 -0.55 59 59
TBX21 -0.14 0.45 -10000 0 -1.2 59 59
B2M 0.012 0.009 -10000 0 -10000 0 0
TYK2 0.016 0.042 -10000 0 -0.83 1 1
IL12RB1 -0.044 0.22 -10000 0 -0.82 39 39
GADD45B -0.056 0.29 -10000 0 -0.8 30 30
IL12RB2 -0.16 0.34 -10000 0 -0.79 114 114
GADD45G -0.066 0.31 -10000 0 -0.87 32 32
natural killer cell activation 0.006 0.024 -10000 0 -10000 0 0
RELB 0.004 0.088 -10000 0 -0.81 6 6
RELA 0.014 0 -10000 0 -10000 0 0
IL18 -0.005 0.11 -10000 0 -0.58 19 19
IL2RA -0.061 0.24 -10000 0 -0.81 47 47
IFNG -0.16 0.33 -10000 0 -0.81 106 106
STAT3 (dimer) -0.077 0.32 -10000 0 -0.79 56 56
HLA-DRB5 -0.012 0.13 -10000 0 -0.71 18 18
FASLG -0.14 0.46 -10000 0 -1.2 64 64
NF kappa B2 p52/RelB -0.2 0.35 -10000 0 -0.95 72 72
CD4 0.01 0.045 -10000 0 -0.7 2 2
SOCS1 -0.039 0.2 -10000 0 -0.81 33 33
EntrezGene:6955 -0.004 0.015 -10000 0 -10000 0 0
CD3D -0.011 0.13 -10000 0 -0.72 16 16
CD3E -0.008 0.12 -10000 0 -0.75 13 13
CD3G -0.028 0.16 -10000 0 -0.67 30 30
IL12Rbeta2/JAK2 -0.11 0.27 -10000 0 -0.6 115 115
CCL3 -0.13 0.43 -10000 0 -1.1 58 58
CCL4 -0.12 0.42 -10000 0 -1.1 58 58
HLA-A 0.003 0.084 -10000 0 -0.77 6 6
IL18/IL18R 0.025 0.13 -10000 0 -0.51 19 19
NOS2 -0.14 0.42 -10000 0 -1 58 58
IL12/IL12R/TYK2/JAK2/SPHK2 -0.069 0.2 -10000 0 -0.52 52 52
IL1R1 -0.11 0.4 -10000 0 -1 55 55
IL4 -0.005 0.024 -10000 0 -10000 0 0
JAK2 0.016 0.034 -10000 0 -0.6 1 1
EntrezGene:6957 -0.004 0.015 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.093 0.33 -10000 0 -0.85 62 62
RAB7A -0.032 0.27 -10000 0 -0.72 20 20
lysosomal transport -0.028 0.26 -10000 0 -0.68 21 21
FOS -0.16 0.48 -10000 0 -1.2 77 77
STAT4 (dimer) -0.079 0.35 -10000 0 -0.86 54 54
STAT5A (dimer) -0.26 0.41 -10000 0 -1 93 93
GZMA -0.15 0.47 -10000 0 -1.2 60 60
GZMB -0.16 0.47 -10000 0 -1.1 78 78
HLX 0.007 0.072 -10000 0 -0.81 4 4
LCK -0.14 0.45 -10000 0 -1.1 66 66
TCR/CD3/MHC II/CD4 -0.032 0.19 -10000 0 -0.58 36 36
IL2/IL2R -0.067 0.19 -10000 0 -0.56 60 60
MAPK14 -0.056 0.31 -10000 0 -0.81 36 36
CCR5 -0.078 0.34 -10000 0 -1.1 27 27
IL1B -0.063 0.24 -10000 0 -0.79 52 52
STAT6 -0.01 0.12 -10000 0 -10000 0 0
STAT4 -0.008 0.13 -10000 0 -0.79 14 14
STAT3 0.014 0 -10000 0 -10000 0 0
STAT1 -0.033 0.19 -10000 0 -0.79 30 30
NFKB1 0.014 0 -10000 0 -10000 0 0
NFKB2 0.014 0 -10000 0 -10000 0 0
IL12B -0.05 0.23 -10000 0 -0.81 44 44
CD8A -0.043 0.2 -10000 0 -0.73 39 39
CD8B -0.066 0.23 -10000 0 -0.73 55 55
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.087 0.22 0.54 59 -10000 0 59
IL2RB 0.001 0.098 -10000 0 -0.78 8 8
proteasomal ubiquitin-dependent protein catabolic process -0.068 0.32 -10000 0 -0.78 53 53
IL2RG -0.012 0.14 -10000 0 -0.78 17 17
IL12 -0.044 0.21 -10000 0 -0.58 63 63
STAT5A 0.014 0 -10000 0 -10000 0 0
CD247 -0.021 0.16 -10000 0 -0.79 21 21
IL2 0.003 0.036 -10000 0 -0.81 1 1
SPHK2 0.014 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.008 0.13 -10000 0 -0.64 20 20
IL12/IL12R/TYK2/JAK2 -0.15 0.49 -10000 0 -1.2 71 71
MAP2K3 -0.056 0.31 -10000 0 -0.79 37 37
RIPK2 0.014 0 -10000 0 -10000 0 0
MAP2K6 -0.067 0.32 -10000 0 -0.81 40 40
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.01 0.045 -10000 0 -0.58 3 3
IL18RAP -0.009 0.14 -10000 0 -0.73 18 18
IL12Rbeta1/TYK2 -0.024 0.18 -10000 0 -0.64 40 40
EOMES -0.078 0.26 -10000 0 -0.67 73 73
STAT1 (dimer) -0.13 0.37 -10000 0 -0.87 73 73
T cell proliferation -0.028 0.26 0.48 1 -0.65 34 35
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.014 0.046 -10000 0 -0.71 2 2
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.14 0.22 -10000 0 -0.73 35 35
ATF2 -0.043 0.29 -10000 0 -0.76 32 32
Visual signal transduction: Cones

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin -0.017 0.085 -9999 0 -0.47 16 16
RGS9BP 0.002 0.081 -9999 0 -0.58 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0.05 -9999 0 -0.81 2 2
mol:Na + -0.092 0.2 -9999 0 -0.54 88 88
mol:ADP -0.053 0.2 -9999 0 -0.62 54 54
GNAT2 0.012 0.005 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.018 0.089 -9999 0 -0.53 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0 0 -9999 0 -10000 0 0
GRK7 -0.07 0.25 -9999 0 -0.81 52 52
CNGB3 -0.13 0.31 -9999 0 -0.81 87 87
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.17 0.28 -9999 0 -0.55 172 172
Cone PDE6 -0.016 0.076 -9999 0 -0.46 10 10
Cone Metarhodopsin II -0.053 0.15 -9999 0 -0.51 54 54
Na + (4 Units) -0.18 0.28 -9999 0 -0.55 172 172
GNAT2/GDP -0.015 0.076 -9999 0 -0.46 10 10
GNB5 0.014 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.01 0.006 -9999 0 -10000 0 0
Cone Transducin -0.018 0.089 -9999 0 -0.49 16 16
SLC24A2 -0.16 0.33 -9999 0 -0.81 106 106
GNB3/GNGT2 -0.022 0.11 -9999 0 -0.58 20 20
GNB3 -0.014 0.15 -9999 0 -0.78 18 18
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 0.007 0.036 -9999 0 -0.81 1 1
ARR3 0.002 0.005 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.092 0.2 -9999 0 -0.55 88 88
mol:Pi -0.018 0.089 -9999 0 -0.53 10 10
Cone CNG Channel -0.077 0.17 -9999 0 -0.45 88 88
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.16 0.33 -9999 0 -0.81 106 106
RGS9 -0.005 0.12 -9999 0 -0.77 12 12
PDE6C 0.002 0.005 -9999 0 -10000 0 0
GNGT2 0.011 0.037 -9999 0 -0.58 2 2
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.002 0.005 -9999 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.013 0.063 -10000 0 -10000 0 0
SMARCC2 0.015 0.006 -10000 0 -10000 0 0
SMARCC1 0.015 0.006 -10000 0 -10000 0 0
TBX21 -0.093 0.23 -10000 0 -0.85 34 34
SUMO2 0.014 0.008 -10000 0 -10000 0 0
STAT1 (dimer) -0.024 0.19 -10000 0 -0.78 30 30
FKBP4 0.014 0 -10000 0 -10000 0 0
FKBP5 0.01 0.051 -10000 0 -0.65 3 3
GR alpha/HSP90/FKBP51/HSP90 0.095 0.098 0.37 9 -0.55 1 10
PRL -0.097 0.17 -10000 0 -0.74 7 7
cortisol/GR alpha (dimer)/TIF2 0.17 0.24 0.58 61 -0.46 1 62
RELA -0.003 0.092 -10000 0 -10000 0 0
FGG 0.1 0.28 0.56 23 -0.65 40 63
GR beta/TIF2 0.062 0.15 0.37 16 -0.39 15 31
IFNG -0.36 0.33 -10000 0 -0.89 118 118
apoptosis 0.024 0.18 0.49 14 -0.63 5 19
CREB1 0.016 0.018 -10000 0 -10000 0 0
histone acetylation 0.005 0.12 0.46 4 -0.46 5 9
BGLAP -0.048 0.14 -10000 0 -0.76 8 8
GR/PKAc 0.095 0.088 0.38 5 -10000 0 5
NF kappa B1 p50/RelA -0.014 0.16 -10000 0 -0.48 8 8
SMARCD1 0.015 0.006 -10000 0 -10000 0 0
MDM2 0.08 0.083 0.31 16 -10000 0 16
GATA3 -0.012 0.15 -10000 0 -0.77 20 20
AKT1 0 0.001 -10000 0 -10000 0 0
CSF2 -0.3 0.28 -10000 0 -0.56 256 256
GSK3B 0.014 0.008 -10000 0 -10000 0 0
NR1I3 0.053 0.17 0.51 9 -0.67 5 14
CSN2 0.12 0.15 0.46 14 -0.53 2 16
BRG1/BAF155/BAF170/BAF60A 0.037 0.025 -10000 0 -10000 0 0
NFATC1 0.015 0.003 -10000 0 -10000 0 0
POU2F1 0.015 0.016 -10000 0 -10000 0 0
CDKN1A 0.031 0.037 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.008 -10000 0 -10000 0 0
SFN 0.008 0.062 -10000 0 -0.69 4 4
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.095 0.098 0.39 4 -0.5 1 5
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.027 0.24 0.49 9 -0.85 25 34
JUN -0.21 0.17 -10000 0 -0.64 37 37
IL4 -0.066 0.12 -10000 0 -0.57 3 3
CDK5R1 0.011 0.051 -10000 0 -0.81 2 2
PRKACA 0.014 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.15 0.31 -10000 0 -0.64 80 80
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.099 0.093 0.38 5 -0.5 1 6
cortisol/GR alpha (monomer) 0.24 0.27 0.68 80 -10000 0 80
NCOA2 -0.034 0.16 -10000 0 -0.58 42 42
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.14 0.2 -10000 0 -0.64 67 67
AP-1/NFAT1-c-4 -0.4 0.26 -10000 0 -0.82 98 98
AFP -0.16 0.2 -10000 0 -0.83 30 30
SUV420H1 0.014 0 -10000 0 -10000 0 0
IRF1 0.11 0.16 0.5 13 -10000 0 13
TP53 0.033 0.052 -10000 0 -0.56 4 4
PPP5C 0.014 0 -10000 0 -10000 0 0
KRT17 -0.39 0.38 -10000 0 -0.94 147 147
KRT14 -0.22 0.37 -10000 0 -1.1 70 70
TBP 0.021 0.023 -10000 0 -10000 0 0
CREBBP 0.073 0.084 0.35 6 -10000 0 6
HDAC1 0.012 0.01 -10000 0 -10000 0 0
HDAC2 0.043 0.031 -10000 0 -10000 0 0
AP-1 -0.41 0.27 -10000 0 -0.83 98 98
MAPK14 0.014 0.008 -10000 0 -10000 0 0
MAPK10 -0.019 0.14 -10000 0 -0.61 28 28
MAPK11 0.014 0.008 -10000 0 -10000 0 0
KRT5 -0.26 0.23 -10000 0 -0.74 50 50
interleukin-1 receptor activity 0.03 0.031 -10000 0 -10000 0 0
NCOA1 0.017 0.001 -10000 0 -10000 0 0
STAT1 -0.024 0.19 -10000 0 -0.78 30 30
CGA -0.061 0.13 -10000 0 -0.7 7 7
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.25 0.2 0.42 263 -10000 0 263
MAPK3 0.014 0.008 -10000 0 -10000 0 0
MAPK1 0.014 0.008 -10000 0 -10000 0 0
ICAM1 -0.13 0.24 -10000 0 -0.7 51 51
NFKB1 -0.003 0.092 -10000 0 -10000 0 0
MAPK8 -0.16 0.16 -10000 0 -0.58 36 36
MAPK9 0.014 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.017 0.18 0.5 13 -0.66 5 18
BAX 0.031 0.037 -10000 0 -10000 0 0
POMC -0.17 0.32 -10000 0 -0.9 60 60
EP300 0.073 0.086 0.36 6 -10000 0 6
cortisol/GR alpha (dimer)/p53 0.22 0.22 0.6 68 -0.53 1 69
proteasomal ubiquitin-dependent protein catabolic process 0.055 0.063 0.28 3 -10000 0 3
SGK1 0.12 0.13 -10000 0 -1.2 2 2
IL13 -0.21 0.19 -10000 0 -0.83 23 23
IL6 -0.18 0.35 -10000 0 -1 65 65
PRKACG 0.003 0.006 -10000 0 -10000 0 0
IL5 -0.19 0.16 -10000 0 -0.76 12 12
IL2 -0.26 0.2 -10000 0 -0.67 50 50
CDK5 0.014 0.005 -10000 0 -10000 0 0
PRKACB 0.012 0.026 -10000 0 -0.58 1 1
HSP90AA1 0.014 0 -10000 0 -10000 0 0
IL8 -0.21 0.34 -10000 0 -0.76 118 118
CDK5R1/CDK5 0.003 0.041 -10000 0 -0.62 2 2
NF kappa B1 p50/RelA/PKAc 0.014 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.21 0.2 0.56 64 -10000 0 64
SMARCA4 0.015 0.006 -10000 0 -10000 0 0
chromatin remodeling 0.15 0.13 0.41 37 -10000 0 37
NF kappa B1 p50/RelA/Cbp 0.073 0.16 0.42 18 -10000 0 18
JUN (dimer) -0.21 0.17 -10000 0 -0.64 37 37
YWHAH 0.014 0 -10000 0 -10000 0 0
VIPR1 -0.082 0.21 -10000 0 -0.88 24 24
NR3C1 0.14 0.16 0.5 40 -10000 0 40
NR4A1 -0.027 0.13 -10000 0 -0.55 15 15
TIF2/SUV420H1 -0.034 0.11 -10000 0 -0.42 42 42
MAPKKK cascade 0.024 0.18 0.49 14 -0.63 5 19
cortisol/GR alpha (dimer)/Src-1 0.22 0.22 0.59 73 -10000 0 73
PBX1 -0.09 0.23 -10000 0 -0.58 92 92
POU1F1 0.003 0.017 -10000 0 -10000 0 0
SELE -0.22 0.4 -10000 0 -1.1 80 80
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.15 0.13 0.42 36 -10000 0 36
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.21 0.2 0.56 64 -10000 0 64
mol:cortisol 0.13 0.16 0.41 78 -10000 0 78
MMP1 -0.64 0.23 -10000 0 -0.71 460 460
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.064 0.16 -10000 0 -0.56 35 35
FYN -0.032 0.23 -10000 0 -0.74 35 35
LAT/GRAP2/SLP76 -0.05 0.19 -10000 0 -0.62 37 37
IKBKB 0.014 0 -10000 0 -10000 0 0
AKT1 -0.008 0.16 -10000 0 -0.48 34 34
B2M 0.013 0.005 -10000 0 -10000 0 0
IKBKG -0.019 0.042 -10000 0 -0.18 3 3
MAP3K8 0.01 0.045 -10000 0 -0.58 3 3
mol:Ca2+ -0.036 0.04 -10000 0 -0.11 38 38
integrin-mediated signaling pathway -0.002 0.027 -10000 0 -0.35 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.03 0.23 -10000 0 -0.69 40 40
TRPV6 -0.27 0.29 -10000 0 -0.59 238 238
CD28 -0.013 0.14 -10000 0 -0.78 17 17
SHC1 -0.036 0.23 -10000 0 -0.68 44 44
receptor internalization -0.037 0.24 -10000 0 -0.69 46 46
PRF1 -0.053 0.28 -10000 0 -0.89 46 46
KRAS 0.01 0.051 -10000 0 -0.81 2 2
GRB2 0.014 0 -10000 0 -10000 0 0
COT/AKT1 0.002 0.13 -10000 0 -0.38 33 33
LAT -0.044 0.25 -10000 0 -0.72 46 46
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.009 0.13 -10000 0 -0.72 16 16
CD3E -0.005 0.12 -10000 0 -0.75 13 13
CD3G -0.026 0.16 -10000 0 -0.67 30 30
RASGRP2 0.007 0.023 -10000 0 -0.12 7 7
RASGRP1 -0.005 0.17 -10000 0 -0.48 37 37
HLA-A 0.005 0.084 -10000 0 -0.76 6 6
RASSF5 0.01 0.045 -10000 0 -0.58 3 3
RAP1A/GTP/RAPL -0.002 0.027 -10000 0 -0.35 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.025 0.056 -10000 0 -0.13 19 19
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.036 0.073 -10000 0 -0.29 11 11
PRKCA -0.011 0.094 -10000 0 -0.31 23 23
GRAP2 -0.002 0.1 -10000 0 -0.67 12 12
mol:IP3 0.037 0.19 0.23 178 -0.48 27 205
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.035 0.22 -10000 0 -0.62 49 49
ORAI1 0.15 0.16 0.32 238 -10000 0 238
CSK -0.04 0.23 -10000 0 -0.71 42 42
B7 family/CD28 -0.16 0.27 -10000 0 -0.8 55 55
CHUK 0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.055 0.27 -10000 0 -0.81 44 44
PTPN6 -0.043 0.23 -10000 0 -0.72 41 41
VAV1 -0.04 0.24 -10000 0 -0.74 39 39
Monovalent TCR/CD3 -0.02 0.17 -10000 0 -0.59 33 33
CBL 0.014 0 -10000 0 -10000 0 0
LCK -0.04 0.24 -10000 0 -0.73 42 42
PAG1 -0.041 0.23 -10000 0 -0.7 44 44
RAP1A 0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.056 0.26 -10000 0 -0.79 45 45
CD80 -0.19 0.35 -10000 0 -0.81 128 128
CD86 0.012 0.036 -10000 0 -0.81 1 1
PDK1/CARD11/BCL10/MALT1 -0.044 0.09 -10000 0 -0.33 20 20
HRAS 0.012 0.036 -10000 0 -0.81 1 1
GO:0035030 -0.086 0.24 -10000 0 -0.64 55 55
CD8A -0.041 0.2 -10000 0 -0.72 39 39
CD8B -0.064 0.23 -10000 0 -0.73 55 55
PTPRC -0.003 0.11 -10000 0 -0.7 12 12
PDK1/PKC theta -0.01 0.19 -10000 0 -0.6 34 34
CSK/PAG1 -0.035 0.22 -10000 0 -0.73 36 36
SOS1 0.014 0 -10000 0 -10000 0 0
peptide-MHC class I 0.012 0.065 -10000 0 -0.58 6 6
GRAP2/SLP76 -0.061 0.21 -10000 0 -0.71 37 37
STIM1 0.075 0.079 -10000 0 -10000 0 0
RAS family/GTP 0.025 0.072 -10000 0 -0.19 6 6
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.042 0.26 -10000 0 -0.75 46 46
mol:DAG -0.013 0.14 -10000 0 -0.43 29 29
RAP1A/GDP 0.013 0.024 -10000 0 -10000 0 0
PLCG1 0.014 0 -10000 0 -10000 0 0
CD247 -0.018 0.16 -10000 0 -0.78 21 21
cytotoxic T cell degranulation -0.049 0.27 -10000 0 -0.83 47 47
RAP1A/GTP -0.002 0.006 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.018 0.19 -10000 0 -0.55 40 40
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.023 0.23 0.26 129 -0.64 29 158
NRAS 0.014 0 -10000 0 -10000 0 0
ZAP70 -0.024 0.17 -10000 0 -0.77 25 25
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.045 0.19 -10000 0 -0.62 35 35
MALT1 0.014 0 -10000 0 -10000 0 0
TRAF6 0.014 0 -10000 0 -10000 0 0
CD8 heterodimer -0.075 0.27 -10000 0 -0.71 69 69
CARD11 -0.037 0.2 -10000 0 -0.79 33 33
PRKCB -0.013 0.1 -10000 0 -0.36 22 22
PRKCE -0.01 0.093 -10000 0 -0.3 22 22
PRKCQ -0.023 0.22 -10000 0 -0.66 39 39
LCP2 0.009 0.062 -10000 0 -0.81 3 3
BCL10 0.014 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.002 0.14 -10000 0 -0.4 33 33
IKK complex 0.033 0.053 -10000 0 -0.13 6 6
RAS family/GDP -0.003 0.009 -10000 0 -0.085 3 3
MAP3K14 0.012 0.1 -10000 0 -0.31 18 18
PDPK1 -0.004 0.15 -10000 0 -0.45 34 34
TCR/CD3/MHC I/CD8/Fyn -0.048 0.26 -10000 0 -0.8 45 45
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.16 0.25 -10000 0 -0.54 152 152
cell-cell adhesion 0.13 0.18 0.69 8 -10000 0 8
Ephrin B/EPHB2/RasGAP -0.14 0.21 -10000 0 -0.47 137 137
ITSN1 0.014 0 -10000 0 -10000 0 0
PIK3CA 0.014 0 -10000 0 -10000 0 0
SHC1 0.014 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.01 0.057 -10000 0 -0.35 14 14
Ephrin B1/EPHB1 -0.028 0.11 -10000 0 -0.48 30 30
HRAS/GDP -0.058 0.11 -10000 0 -0.61 4 4
Ephrin B/EPHB1/GRB7 -0.046 0.13 -10000 0 -0.48 26 26
Endophilin/SYNJ1 -0.1 0.21 -10000 0 -0.43 137 137
KRAS 0.01 0.051 -10000 0 -0.81 2 2
Ephrin B/EPHB1/Src -0.041 0.12 -10000 0 -0.48 22 22
endothelial cell migration -0.002 0.022 -10000 0 -10000 0 0
GRB2 0.014 0 -10000 0 -10000 0 0
GRB7 0.004 0.084 -10000 0 -0.71 7 7
PAK1 -0.12 0.23 -10000 0 -0.7 18 18
HRAS 0.012 0.036 -10000 0 -0.81 1 1
RRAS -0.1 0.22 -10000 0 -0.44 137 137
DNM1 -0.045 0.21 -10000 0 -0.81 37 37
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.003 0.13 -10000 0 -0.46 22 22
lamellipodium assembly -0.13 0.18 -10000 0 -0.69 8 8
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.011 0.091 -10000 0 -0.46 3 3
PIK3R1 0.011 0.037 -10000 0 -0.58 2 2
EPHB2 -0.2 0.36 -10000 0 -0.81 138 138
EPHB3 -0.002 0.096 -10000 0 -0.58 14 14
EPHB1 -0.029 0.18 -10000 0 -0.73 30 30
EPHB4 0.014 0 -10000 0 -10000 0 0
mol:GDP -0.055 0.11 -10000 0 -0.52 6 6
Ephrin B/EPHB2 -0.14 0.21 -10000 0 -0.47 137 137
Ephrin B/EPHB3 -0.026 0.086 -10000 0 -0.52 2 2
JNK cascade -0.11 0.23 -10000 0 -0.45 155 155
Ephrin B/EPHB1 -0.042 0.12 -10000 0 -0.49 22 22
RAP1/GDP -0.045 0.092 -10000 0 -0.53 3 3
EFNB2 0.012 0.026 -10000 0 -0.58 1 1
EFNB3 -0.023 0.14 -10000 0 -0.58 32 32
EFNB1 0.014 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.16 0.23 -10000 0 -0.5 155 155
RAP1B 0.012 0.036 -10000 0 -0.81 1 1
RAP1A 0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.13 0.18 -10000 0 -0.75 8 8
Rap1/GTP -0.13 0.18 -10000 0 -0.75 7 7
axon guidance -0.16 0.25 -10000 0 -0.54 152 152
MAPK3 0.027 0.082 -10000 0 -0.41 3 3
MAPK1 0.027 0.082 -10000 0 -0.41 3 3
Rac1/GDP -0.016 0.12 -10000 0 -0.56 3 3
actin cytoskeleton reorganization -0.1 0.14 -10000 0 -0.54 8 8
CDC42/GDP -0.016 0.12 -10000 0 -0.56 3 3
PI3K -0.002 0.022 -10000 0 -10000 0 0
EFNA5 -0.014 0.12 -10000 0 -0.58 24 24
Ephrin B2/EPHB4 -0.001 0.016 -10000 0 -0.35 1 1
Ephrin B/EPHB2/Intersectin/N-WASP -0.056 0.14 -10000 0 -0.52 5 5
CDC42 0.014 0 -10000 0 -10000 0 0
RAS family/GTP -0.13 0.18 -10000 0 -0.72 8 8
PTK2 0.032 0.047 -10000 0 -10000 0 0
MAP4K4 -0.11 0.23 -10000 0 -0.46 155 155
SRC 0.014 0 -10000 0 -10000 0 0
KALRN -0.038 0.17 -10000 0 -0.58 45 45
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.063 0.18 -10000 0 -0.51 14 14
MAP2K1 0.019 0.086 -10000 0 -0.43 3 3
WASL 0.014 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.15 0.23 -10000 0 -0.49 155 155
cell migration 0.023 0.098 -10000 0 -0.49 3 3
NRAS 0.014 0 -10000 0 -10000 0 0
SYNJ1 -0.1 0.22 -10000 0 -0.44 137 137
PXN 0.014 0 -10000 0 -10000 0 0
TF -0.28 0.25 -10000 0 -0.67 120 120
HRAS/GTP -0.14 0.19 -10000 0 -0.77 9 9
Ephrin B1/EPHB1-2 -0.16 0.23 -10000 0 -0.5 155 155
cell adhesion mediated by integrin 0.014 0.08 0.44 2 -10000 0 2
RAC1 0.014 0 -10000 0 -10000 0 0
mol:GTP -0.15 0.21 -10000 0 -0.85 8 8
RAC1-CDC42/GTP -0.13 0.18 -10000 0 -0.73 9 9
RASA1 0.011 0.037 -10000 0 -0.58 2 2
RAC1-CDC42/GDP -0.045 0.091 -10000 0 -0.53 3 3
ruffle organization -0.085 0.21 -10000 0 -0.75 7 7
NCK1 0.014 0 -10000 0 -10000 0 0
receptor internalization -0.12 0.25 -10000 0 -0.8 23 23
Ephrin B/EPHB2/KALRN -0.16 0.22 -10000 0 -0.48 143 143
ROCK1 0.018 0.055 -10000 0 -10000 0 0
RAS family/GDP -0.1 0.14 -10000 0 -0.54 8 8
Rac1/GTP -0.14 0.19 -10000 0 -0.77 8 8
Ephrin B/EPHB1/Src/Paxillin 0.005 0.097 -10000 0 -0.51 3 3
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.012 0.036 -10000 0 -0.81 1 1
RAS family/GTP/Tiam1 -0.085 0.11 -10000 0 -0.48 5 5
NT3 (dimer)/TRKC -0.22 0.27 -10000 0 -0.5 228 228
NT3 (dimer)/TRKB -0.22 0.26 -10000 0 -0.66 100 100
SHC/Grb2/SOS1/GAB1/PI3K 0.039 0.017 -10000 0 -10000 0 0
RAPGEF1 0.014 0 -10000 0 -10000 0 0
BDNF -0.038 0.18 -10000 0 -0.69 38 38
PIK3CA 0.014 0 -10000 0 -10000 0 0
DYNLT1 0.014 0 -10000 0 -10000 0 0
NTRK1 -0.059 0.23 -10000 0 -0.81 46 46
NTRK2 -0.16 0.29 -10000 0 -0.62 140 140
NTRK3 -0.14 0.26 -10000 0 -0.58 128 128
NT-4/5 (dimer)/TRKB -0.13 0.21 -10000 0 -0.59 48 48
neuron apoptosis 0.11 0.13 0.48 23 -10000 0 23
SHC 2-3/Grb2 -0.12 0.14 -10000 0 -0.52 23 23
SHC1 0.014 0 -10000 0 -10000 0 0
SHC2 -0.11 0.13 0.22 1 -0.41 55 56
SHC3 -0.11 0.14 -10000 0 -0.44 51 51
STAT3 (dimer) 0.013 0.054 -10000 0 -0.34 3 3
NT3 (dimer)/TRKA -0.17 0.23 -10000 0 -0.62 67 67
RIN/GDP -0.047 0.099 -10000 0 -0.28 7 7
GIPC1 0.014 0 -10000 0 -10000 0 0
KRAS 0.01 0.051 -10000 0 -0.81 2 2
DNAJA3 -0.08 0.13 0.25 2 -0.48 8 10
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.014 0.12 -10000 0 -0.73 13 13
MAGED1 0.008 0.062 -10000 0 -0.69 4 4
PTPN11 0.014 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.009 0.057 -10000 0 -0.73 3 3
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.014 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.16 0.26 -10000 0 -0.57 138 138
TRKA/NEDD4-2 -0.055 0.18 -10000 0 -0.62 46 46
ELMO1 0.011 0.044 -10000 0 -0.69 2 2
RhoG/GTP/ELMO1/DOCK1 -0.003 0.036 -10000 0 -0.4 4 4
NGF -0.14 0.32 -10000 0 -0.79 98 98
HRAS 0.012 0.036 -10000 0 -0.81 1 1
DOCK1 0.011 0.037 -10000 0 -0.58 2 2
GAB2 0.01 0.045 -10000 0 -0.58 3 3
RIT2 0.001 0.003 -10000 0 -10000 0 0
RIT1 0.014 0 -10000 0 -10000 0 0
FRS2 0.007 0.072 -10000 0 -0.81 4 4
DNM1 -0.045 0.21 -10000 0 -0.81 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.079 0.12 0.24 2 -0.47 11 13
mol:GDP -0.07 0.14 -10000 0 -0.41 13 13
NGF (dimer) -0.14 0.31 -10000 0 -0.79 98 98
RhoG/GDP -0.002 0.033 -10000 0 -0.53 2 2
RIT1/GDP -0.041 0.1 -10000 0 -0.28 5 5
TIAM1 0.007 0.063 -10000 0 -0.58 6 6
PIK3R1 0.011 0.037 -10000 0 -0.58 2 2
BDNF (dimer)/TRKB -0.13 0.21 -10000 0 -0.59 46 46
KIDINS220/CRKL/C3G -0.001 0.027 -10000 0 -0.62 1 1
SHC/RasGAP -0.002 0.026 -10000 0 -0.42 2 2
FRS2 family/SHP2 -0.004 0.047 -10000 0 -0.53 4 4
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.16 0.27 -10000 0 -0.58 154 154
RAP1/GDP -0.054 0.066 -10000 0 -0.35 1 1
KIDINS220/CRKL 0.012 0.036 -10000 0 -0.81 1 1
BDNF (dimer) -0.038 0.18 -10000 0 -0.68 38 38
ubiquitin-dependent protein catabolic process -0.14 0.25 -10000 0 -0.56 129 129
Schwann cell development -0.049 0.036 -10000 0 -10000 0 0
EHD4 0.014 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.004 0.042 -10000 0 -0.48 4 4
FRS2 family/SHP2/CRK family/C3G/GAB2 0.039 0.03 -10000 0 -10000 0 0
RAP1B 0.012 0.036 -10000 0 -0.81 1 1
RAP1A 0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.25 0.26 -10000 0 -0.62 143 143
ABL1 0.014 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.045 0.07 -10000 0 -0.56 1 1
STAT3 0.013 0.054 -10000 0 -0.34 3 3
axon guidance -0.24 0.25 -10000 0 -0.58 143 143
MAPK3 -0.12 0.25 -10000 0 -0.52 138 138
MAPK1 -0.12 0.25 -10000 0 -0.52 138 138
CDC42/GDP -0.041 0.1 -10000 0 -0.28 5 5
NTF3 -0.16 0.27 -10000 0 -0.58 154 154
NTF4 0.009 0.057 -10000 0 -0.73 3 3
NGF (dimer)/TRKA/FAIM -0.14 0.25 -10000 0 -0.56 129 129
PI3K -0.002 0.026 -10000 0 -0.42 2 2
FRS3 0.014 0 -10000 0 -10000 0 0
FAIM 0.014 0 -10000 0 -10000 0 0
GAB1 0.014 0 -10000 0 -10000 0 0
RASGRF1 -0.17 0.23 0.25 2 -0.55 108 110
SOS1 0.014 0 -10000 0 -10000 0 0
MCF2L -0.19 0.26 -10000 0 -0.45 233 233
RGS19 0.014 0 -10000 0 -10000 0 0
CDC42 0.014 0 -10000 0 -10000 0 0
RAS family/GTP -0.002 0.086 -10000 0 -10000 0 0
Rac1/GDP -0.041 0.1 -10000 0 -0.28 5 5
NGF (dimer)/TRKA/GRIT -0.15 0.25 -10000 0 -0.56 137 137
neuron projection morphogenesis -0.043 0.13 -10000 0 -0.5 3 3
NGF (dimer)/TRKA/NEDD4-2 -0.14 0.25 -10000 0 -0.56 129 129
MAP2K1 0.042 0 -10000 0 -10000 0 0
NGFR -0.023 0.16 -10000 0 -0.71 26 26
NGF (dimer)/TRKA/GIPC/GAIP -0.062 0.16 -10000 0 -0.52 16 16
RAS family/GTP/PI3K 0.03 0.028 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.003 0.039 -10000 0 -0.45 4 4
NRAS 0.014 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.014 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.026 -10000 0 -0.58 1 1
MAPKKK cascade -0.084 0.14 -10000 0 -0.49 18 18
RASA1 0.011 0.037 -10000 0 -0.58 2 2
TRKA/c-Abl -0.055 0.18 -10000 0 -0.62 46 46
SQSTM1 0.014 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.12 0.19 -10000 0 -0.54 46 46
NGF (dimer)/TRKA/p62/Atypical PKCs -0.12 0.21 -10000 0 -0.48 129 129
MATK -0.005 0.12 -10000 0 -0.77 12 12
NEDD4L 0.014 0 -10000 0 -10000 0 0
RAS family/GDP -0.052 0.063 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.086 0.14 0.26 2 -0.38 33 35
Rac1/GTP -0.12 0.13 -10000 0 -0.37 56 56
FRS2 family/SHP2/CRK family -0.004 0.044 -10000 0 -0.45 5 5
LPA4-mediated signaling events

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
ADCY4 0.02 0.016 -9999 0 -0.35 1 1
ADCY5 -0.072 0.17 -9999 0 -0.37 124 124
ADCY6 0.013 0.054 -9999 0 -0.36 11 11
ADCY7 0.02 0.016 -9999 0 -0.35 1 1
ADCY1 -0.005 0.12 -9999 0 -0.54 24 24
ADCY2 -0.11 0.18 -9999 0 -0.36 176 176
ADCY3 0.02 0.016 -9999 0 -0.35 1 1
ADCY8 0 0.085 -9999 0 -0.53 13 13
PRKCE 0.011 0.019 -9999 0 -0.42 1 1
ADCY9 0.019 0.028 -9999 0 -0.36 3 3
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.046 0.096 -9999 0 -0.37 8 8
Thromboxane A2 receptor signaling

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
TGM2 -0.033 0.18 -10000 0 -0.81 28 28
GNB1/GNG2 -0.053 0.076 -10000 0 -0.21 36 36
AKT1 0.001 0.11 -10000 0 -0.26 1 1
EGF -0.1 0.24 -10000 0 -0.58 101 101
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.014 0.12 -10000 0 -0.48 14 14
mol:Ca2+ -0.024 0.16 -10000 0 -0.3 87 87
LYN 0.014 0.12 -10000 0 -0.49 14 14
RhoA/GTP -0.032 0.049 -10000 0 -0.16 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.026 0.18 -10000 0 -0.34 92 92
GNG2 0.014 0 -10000 0 -10000 0 0
ARRB2 0.014 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.007 0.084 -10000 0 -0.52 5 5
G beta5/gamma2 -0.068 0.1 -10000 0 -0.29 35 35
PRKCH -0.031 0.18 -10000 0 -0.38 37 37
DNM1 -0.045 0.21 -10000 0 -0.81 37 37
TXA2/TP beta/beta Arrestin3 -0.023 0.067 -10000 0 -0.32 6 6
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.001 0.095 -10000 0 -0.7 9 9
G12 family/GTP -0.078 0.12 -10000 0 -0.32 42 42
ADRBK1 0.014 0 -10000 0 -10000 0 0
ADRBK2 0.012 0.036 -10000 0 -0.81 1 1
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.12 0.36 27 -10000 0 27
mol:NADP 0.002 0.094 -10000 0 -0.81 7 7
RAB11A 0.014 0 -10000 0 -10000 0 0
PRKG1 -0.024 0.15 -10000 0 -0.64 30 30
mol:IP3 -0.038 0.19 -10000 0 -0.37 91 91
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.064 0.25 -10000 0 -0.5 92 92
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.043 0.18 -10000 0 -0.47 40 40
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.011 0.12 -10000 0 -0.5 15 15
RHOA 0.014 0 -10000 0 -10000 0 0
PTGIR -0.02 0.16 -10000 0 -0.81 21 21
PRKCB1 -0.038 0.19 -10000 0 -0.37 91 91
GNAQ 0.014 0 -10000 0 -10000 0 0
mol:L-citrulline 0.002 0.094 -10000 0 -0.81 7 7
TXA2/TXA2-R family -0.064 0.25 -10000 0 -0.51 99 99
LCK 0.005 0.13 -10000 0 -0.46 20 20
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.04 0.13 -10000 0 -0.51 34 34
TXA2-R family/G12 family/GDP/G beta/gamma 0.021 0.046 -10000 0 -0.38 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.039 0.13 -10000 0 -0.5 34 34
MAPK14 -0.004 0.13 -10000 0 -0.25 11 11
TGM2/GTP -0.049 0.22 -10000 0 -0.48 41 41
MAPK11 -0.004 0.13 -10000 0 -0.25 10 10
ARHGEF1 -0.005 0.099 -10000 0 -0.22 2 2
GNAI2 0.014 0 -10000 0 -10000 0 0
JNK cascade -0.037 0.2 -10000 0 -0.38 94 94
RAB11/GDP 0.013 0.002 -10000 0 -10000 0 0
ICAM1 -0.024 0.16 -10000 0 -0.3 96 96
cAMP biosynthetic process -0.038 0.18 -10000 0 -0.38 42 42
Gq family/GTP/EBP50 -0.006 0.094 -10000 0 -0.39 8 8
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.015 0.12 -10000 0 -0.49 13 13
GNB5 0.014 0 -10000 0 -10000 0 0
GNB1 0.014 0 -10000 0 -10000 0 0
EGF/EGFR -0.004 0.11 -10000 0 -0.34 19 19
VCAM1 -0.032 0.17 -10000 0 -0.33 107 107
TP beta/Gq family/GDP/G beta5/gamma2 0.007 0.084 -10000 0 -0.52 5 5
platelet activation -0.008 0.17 -10000 0 -0.32 33 33
PGI2/IP -0.025 0.12 -10000 0 -0.63 21 21
PRKACA 0.004 0.082 -10000 0 -0.34 24 24
Gq family/GDP/G beta5/gamma2 0.01 0.075 -10000 0 -0.42 5 5
TXA2/TP beta/beta Arrestin2 -0.029 0.092 -10000 0 -0.36 36 36
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.018 0.16 -10000 0 -0.57 34 34
mol:DAG -0.045 0.21 -10000 0 -0.42 91 91
EGFR -0.015 0.15 -10000 0 -0.76 19 19
TXA2/TP alpha -0.058 0.24 -10000 0 -0.52 47 47
Gq family/GTP -0.033 0.089 -10000 0 -0.24 76 76
YES1 0.015 0.12 -10000 0 -0.49 13 13
GNAI2/GTP -0.036 0.12 -10000 0 -0.48 25 25
PGD2/DP -0.009 0.071 -10000 0 -0.54 9 9
SLC9A3R1 0.009 0.052 -10000 0 -0.58 4 4
FYN 0.014 0.12 -10000 0 -0.5 14 14
mol:NO 0.002 0.094 -10000 0 -0.81 7 7
GNA15 0.011 0.037 -10000 0 -0.58 2 2
PGK/cGMP -0.031 0.11 -10000 0 -0.43 37 37
RhoA/GDP 0.013 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.06 0.18 -10000 0 -0.78 20 20
NOS3 0.002 0.095 -10000 0 -0.81 7 7
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCA -0.031 0.18 -10000 0 -0.38 37 37
PRKCB -0.035 0.18 -10000 0 -0.36 85 85
PRKCE -0.031 0.18 -10000 0 -0.35 81 81
PRKCD -0.035 0.19 -10000 0 -0.38 86 86
PRKCG -0.059 0.22 -10000 0 -0.43 101 101
muscle contraction -0.053 0.24 -10000 0 -0.47 99 99
PRKCZ -0.025 0.18 -10000 0 -0.37 33 33
ARR3 0.002 0.005 -10000 0 -10000 0 0
TXA2/TP beta -0.04 0.14 -10000 0 -0.5 35 35
PRKCQ -0.035 0.18 -10000 0 -0.36 86 86
MAPKKK cascade -0.05 0.22 -10000 0 -0.44 93 93
SELE -0.038 0.18 -10000 0 -0.39 86 86
TP beta/GNAI2/GDP/G beta/gamma -0.039 0.13 -10000 0 -0.66 13 13
ROCK1 0.014 0 -10000 0 -10000 0 0
GNA14 -0.072 0.21 -10000 0 -0.58 75 75
chemotaxis -0.078 0.28 -10000 0 -0.6 98 98
GNA12 0.007 0.072 -10000 0 -0.81 4 4
GNA13 0.014 0 -10000 0 -10000 0 0
GNA11 0.009 0.052 -10000 0 -0.58 4 4
Rac1/GTP 0.006 0.006 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.003 0.017 -10000 0 -10000 0 0
AES 0.003 0.014 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.007 0.065 -10000 0 -0.56 7 7
SMAD4 0.012 0.026 -10000 0 -0.58 1 1
DKK2 -0.007 0.12 -10000 0 -0.68 15 15
TLE1 0.003 0.014 -10000 0 -10000 0 0
MACF1 0.014 0.001 -10000 0 -10000 0 0
CTNNB1 0.037 0.11 -10000 0 -0.41 2 2
WIF1 -0.26 0.3 -10000 0 -0.59 233 233
beta catenin/RanBP3 -0.012 0.086 0.37 11 -10000 0 11
KREMEN2 -0.27 0.39 -10000 0 -0.81 180 180
DKK1 -0.29 0.39 -10000 0 -0.79 195 195
beta catenin/beta TrCP1 0.043 0.1 -10000 0 -10000 0 0
FZD1 0.005 0.084 -10000 0 -0.77 6 6
AXIN2 -0.011 0.2 -10000 0 -1.4 11 11
AXIN1 0.014 0.001 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.006 0.024 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.082 0.064 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.006 0.041 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.051 0.076 -10000 0 -10000 0 0
HNF1A -0.013 0.11 -10000 0 -0.81 10 10
CTBP1 0.003 0.015 -10000 0 -10000 0 0
MYC 0.013 0.045 -10000 0 -0.53 1 1
RANBP3 0.013 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.2 0.26 -10000 0 -0.54 187 187
NKD1 -0.017 0.15 -10000 0 -0.77 20 20
TCF4 0.003 0.015 -10000 0 -10000 0 0
TCF3 0.003 0.015 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.012 0.075 -10000 0 -0.48 12 12
Ran/GTP 0.001 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.012 0.089 0.4 21 -10000 0 21
LEF1 -0.004 0.075 -10000 0 -0.75 5 5
DVL1 0.066 0.052 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.091 0.073 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.37 0.35 -10000 0 -0.63 306 306
LRP6 0.013 0.026 -10000 0 -0.58 1 1
CSNK1A1 0.003 0.017 -10000 0 -10000 0 0
NLK 0.014 0.003 -10000 0 -10000 0 0
CCND1 -0.004 0.15 -10000 0 -0.85 13 13
WNT1 0 0.094 -10000 0 -0.81 7 7
GSK3A 0.014 0.001 -10000 0 -10000 0 0
GSK3B 0.014 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
PPP2R5D 0.05 0.067 0.36 20 -10000 0 20
APC 0.028 0.077 -10000 0 -0.45 12 12
WNT1/LRP6/FZD1 0.11 0.12 0.24 230 -10000 0 230
CREBBP 0.003 0.015 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 0.012 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.084 0.14 -10000 0 -0.5 4 4
regulation of S phase of mitotic cell cycle -0.045 0.12 -10000 0 -10000 0 0
GNAO1 0.008 0.067 -10000 0 -0.75 4 4
HRAS 0.012 0.036 -10000 0 -0.81 1 1
SHBG/T-DHT -0.001 0.034 -10000 0 -0.55 2 2
PELP1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.012 0 -10000 0 -10000 0 0
MAP2K1 -0.042 0.14 -10000 0 -0.51 2 2
T-DHT/AR -0.12 0.19 -10000 0 -0.43 140 140
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.007 67 67
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.026 -10000 0 -0.58 1 1
mol:GDP -0.12 0.19 -10000 0 -0.44 140 140
cell proliferation -0.051 0.18 -10000 0 -0.58 19 19
PIK3CA 0.014 0 -10000 0 -10000 0 0
FOS -0.086 0.29 -10000 0 -0.82 67 67
mol:Ca2+ -0.014 0.021 -10000 0 -0.088 10 10
MAPK3 -0.045 0.16 -10000 0 -0.49 19 19
MAPK1 -0.019 0.091 -10000 0 -0.27 19 19
PIK3R1 0.011 0.037 -10000 0 -0.58 2 2
mol:IP3 0 0.002 -10000 0 -0.004 67 67
cAMP biosynthetic process 0.011 0.039 -10000 0 -0.51 2 2
GNG2 0.014 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 67 67
HRAS/GTP -0.08 0.13 -10000 0 -0.46 5 5
actin cytoskeleton reorganization -0.001 0.017 -10000 0 -10000 0 0
SRC 0.013 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 67 67
PI3K -0.001 0.022 -10000 0 -0.35 2 2
apoptosis 0.043 0.17 0.42 67 -10000 0 67
T-DHT/AR/PELP1 -0.097 0.16 -10000 0 -0.36 140 140
HRAS/GDP -0.11 0.18 -10000 0 -0.41 141 141
CREB1 -0.048 0.18 -10000 0 -0.45 67 67
RAC1-CDC42/GTP -0.001 0.017 -10000 0 -10000 0 0
AR -0.15 0.26 -10000 0 -0.58 140 140
GNB1 0.014 0 -10000 0 -10000 0 0
RAF1 -0.05 0.14 -10000 0 -0.45 5 5
RAC1-CDC42/GDP -0.1 0.17 -10000 0 -0.39 140 140
T-DHT/AR/PELP1/Src -0.086 0.14 -10000 0 -0.5 4 4
MAP2K2 -0.042 0.14 -10000 0 -0.51 2 2
T-DHT/AR/PELP1/Src/PI3K -0.045 0.12 -10000 0 -10000 0 0
GNAZ -0.014 0.14 -10000 0 -0.74 19 19
SHBG 0.01 0.051 -10000 0 -0.81 2 2
Gi family/GNB1/GNG2/GDP 0.012 0.068 -10000 0 -0.45 1 1
mol:T-DHT 0 0.001 -10000 0 -0.003 48 48
RAC1 0.014 0 -10000 0 -10000 0 0
GNRH1 -0.015 0.13 -10000 0 -0.62 22 22
Gi family/GTP -0.044 0.079 -10000 0 -0.37 8 8
CDC42 0.014 0 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.014 0.077 -10000 0 -10000 0 0
epithelial cell differentiation -0.071 0.12 -10000 0 -0.57 4 4
ITCH 0.027 0.019 -10000 0 -10000 0 0
WWP1 -0.009 0.071 -10000 0 -10000 0 0
FYN 0.012 0.036 -10000 0 -0.81 1 1
EGFR -0.015 0.15 -10000 0 -0.76 19 19
PRL -0.003 0.079 -10000 0 -0.81 5 5
neuron projection morphogenesis -0.028 0.16 -10000 0 -10000 0 0
PTPRZ1 -0.011 0.12 -10000 0 -0.58 22 22
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.082 0.16 -10000 0 -0.51 27 27
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.08 0.2 -10000 0 -0.52 78 78
ADAM17 0.025 0.042 -10000 0 -0.57 2 2
ErbB4/ErbB4 -0.023 0.092 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.032 0.087 -10000 0 -0.49 5 5
NCOR1 0.014 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.069 0.19 -10000 0 -0.49 78 78
GRIN2B -0.067 0.18 -10000 0 -0.53 28 28
ErbB4/ErbB2/betacellulin -0.098 0.16 -10000 0 -0.62 3 3
STAT1 -0.033 0.19 -10000 0 -0.79 30 30
HBEGF 0.014 0 -10000 0 -10000 0 0
PRLR -0.11 0.24 -10000 0 -0.58 104 104
E4ICDs/ETO2 -0.015 0.078 -10000 0 -10000 0 0
axon guidance -0.015 0.087 -10000 0 -0.4 2 2
NEDD4 0.027 0.019 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.091 0.18 -10000 0 -0.44 107 107
CBFA2T3 0.012 0.026 -10000 0 -0.58 1 1
ErbB4/ErbB2/HBEGF 0.005 0.071 -10000 0 -0.52 3 3
MAPK3 -0.037 0.17 -10000 0 -0.47 27 27
STAT1 (dimer) -0.044 0.15 -10000 0 -0.56 29 29
MAPK1 -0.037 0.17 -10000 0 -0.47 27 27
JAK2 0.012 0.026 -10000 0 -0.58 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.071 0.19 -10000 0 -0.49 80 80
NRG1 -0.07 0.24 -10000 0 -0.6 84 84
NRG3 -0.002 0.08 -10000 0 -0.68 7 7
NRG2 -0.32 0.29 -10000 0 -0.58 296 296
NRG4 -0.028 0.15 -10000 0 -0.6 35 35
heart development -0.015 0.087 -10000 0 -0.4 2 2
neural crest cell migration -0.07 0.19 -10000 0 -0.48 80 80
ERBB2 0.027 0.057 -10000 0 -0.53 5 5
WWOX/E4ICDs -0.014 0.077 -10000 0 -10000 0 0
SHC1 0.014 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.071 0.13 -10000 0 -0.47 35 35
apoptosis 0.066 0.087 0.55 4 -10000 0 4
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.22 0.19 -10000 0 -0.46 100 100
ErbB4/ErbB2/epiregulin -0.085 0.17 -10000 0 -0.6 8 8
ErbB4/ErbB4/betacellulin/betacellulin -0.13 0.18 -10000 0 -0.46 52 52
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.087 0.13 -10000 0 -0.65 4 4
MDM2 -0.011 0.079 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.089 0.17 -10000 0 -0.49 77 77
STAT5A -0.006 0.082 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.085 0.2 -10000 0 -0.5 90 90
DLG4 0.012 0.026 -10000 0 -0.58 1 1
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.037 0.054 -10000 0 -10000 0 0
STAT5A (dimer) -0.075 0.12 -10000 0 -0.62 4 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.007 0.081 -10000 0 -10000 0 0
LRIG1 -0.001 0.092 -10000 0 -0.58 13 13
EREG -0.15 0.27 -10000 0 -0.58 144 144
BTC -0.17 0.27 -10000 0 -0.58 162 162
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.015 0.088 -10000 0 -0.4 2 2
ERBB4 -0.023 0.093 -10000 0 -10000 0 0
STAT5B 0.014 0 -10000 0 -10000 0 0
YAP1 -0.019 0.057 -10000 0 -0.39 10 10
GRB2 0.014 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.019 0.11 -10000 0 -0.5 6 6
glial cell differentiation 0.037 0.053 -10000 0 -10000 0 0
WWOX 0.014 0 -10000 0 -10000 0 0
cell proliferation -0.14 0.22 -10000 0 -0.66 44 44
BCR signaling pathway

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
JUN -0.029 0.15 -9999 0 -0.43 30 30
IKBKB -0.009 0.079 -9999 0 -0.28 3 3
AKT1 -0.027 0.12 -9999 0 -0.29 43 43
IKBKG -0.008 0.082 -9999 0 -0.29 7 7
CALM1 -0.045 0.12 -9999 0 -0.4 33 33
PIK3CA 0.014 0 -9999 0 -10000 0 0
MAP3K1 -0.057 0.21 -9999 0 -0.63 34 34
MAP3K7 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ -0.056 0.13 -9999 0 -0.42 35 35
DOK1 0.012 0.036 -9999 0 -0.81 1 1
AP-1 -0.022 0.097 -9999 0 -0.27 12 12
LYN 0.012 0.036 -9999 0 -0.81 1 1
BLNK -0.043 0.17 -9999 0 -0.58 50 50
SHC1 0.014 0 -9999 0 -10000 0 0
BCR complex -0.14 0.29 -9999 0 -0.65 111 111
CD22 -0.12 0.27 -9999 0 -0.82 56 56
CAMK2G -0.035 0.11 -9999 0 -0.4 17 17
CSNK2A1 0.014 0 -9999 0 -10000 0 0
INPP5D 0.011 0.037 -9999 0 -0.58 2 2
SHC/GRB2/SOS1 -0.11 0.2 -9999 0 -0.66 33 33
GO:0007205 -0.056 0.13 -9999 0 -0.43 35 35
SYK 0.01 0.045 -9999 0 -0.58 3 3
ELK1 -0.047 0.12 -9999 0 -0.41 34 34
NFATC1 -0.067 0.19 -9999 0 -0.48 72 72
B-cell antigen/BCR complex -0.14 0.29 -9999 0 -0.65 111 111
PAG1/CSK -0.002 0.038 -9999 0 -0.62 2 2
NFKBIB 0.008 0.03 -9999 0 -10000 0 0
HRAS -0.049 0.14 -9999 0 -0.44 33 33
NFKBIA 0.008 0.029 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.014 0.025 -9999 0 -10000 0 0
RasGAP/Csk -0.11 0.22 -9999 0 -0.56 84 84
mol:GDP -0.054 0.12 -9999 0 -0.41 35 35
PTEN 0.014 0 -9999 0 -10000 0 0
CD79B -0.025 0.17 -9999 0 -0.73 27 27
NF-kappa-B/RelA/I kappa B alpha 0.014 0.024 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.091 0.23 -9999 0 -0.55 81 81
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
mol:IP3 -0.057 0.13 -9999 0 -0.44 35 35
CSK 0.014 0 -9999 0 -10000 0 0
FOS -0.072 0.16 -9999 0 -0.43 53 53
CHUK -0.008 0.082 -9999 0 -0.29 7 7
IBTK 0.014 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.07 0.13 -9999 0 -0.57 16 16
PTPN6 -0.11 0.25 -9999 0 -0.76 56 56
RELA 0.014 0 -9999 0 -10000 0 0
BCL2A1 0.008 0.038 -9999 0 -0.13 30 30
VAV2 -0.15 0.27 -9999 0 -0.75 75 75
ubiquitin-dependent protein catabolic process 0.012 0.029 -9999 0 -10000 0 0
BTK -0.004 0.031 -9999 0 -10000 0 0
CD19 -0.15 0.3 -9999 0 -0.78 83 83
MAP4K1 -0.007 0.13 -9999 0 -0.76 14 14
CD72 -0.071 0.25 -9999 0 -0.8 54 54
PAG1 0.01 0.051 -9999 0 -0.81 2 2
MAPK14 -0.038 0.18 -9999 0 -0.52 33 33
SH3BP5 0.01 0.045 -9999 0 -0.58 3 3
PIK3AP1 -0.063 0.16 -9999 0 -0.48 49 49
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.083 0.2 -9999 0 -0.58 46 46
RAF1 -0.039 0.13 -9999 0 -0.41 32 32
RasGAP/p62DOK/SHIP -0.1 0.22 -9999 0 -0.79 27 27
CD79A -0.14 0.31 -9999 0 -0.74 106 106
re-entry into mitotic cell cycle -0.022 0.097 -9999 0 -0.27 12 12
RASA1 0.011 0.037 -9999 0 -0.58 2 2
MAPK3 -0.018 0.11 -9999 0 -0.42 3 3
MAPK1 -0.018 0.11 -9999 0 -0.42 3 3
CD72/SHP1 -0.11 0.3 -9999 0 -0.83 57 57
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 -0.042 0.18 -9999 0 -0.51 35 35
actin cytoskeleton organization -0.09 0.24 -9999 0 -0.62 74 74
NF-kappa-B/RelA 0.034 0.047 -9999 0 -10000 0 0
Calcineurin -0.047 0.089 -9999 0 -0.44 3 3
PI3K -0.13 0.22 -9999 0 -0.62 72 72
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.069 0.13 -9999 0 -0.47 36 36
SOS1 0.014 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.062 0.22 -9999 0 -0.73 40 40
DAPP1 -0.091 0.21 -9999 0 -0.73 38 38
cytokine secretion -0.061 0.18 -9999 0 -0.45 72 72
mol:DAG -0.057 0.13 -9999 0 -0.44 35 35
PLCG2 0.012 0.026 -9999 0 -0.58 1 1
MAP2K1 -0.028 0.12 -9999 0 -0.43 6 6
B-cell antigen/BCR complex/FcgammaRIIB -0.12 0.26 -9999 0 -0.66 84 84
mol:PI-3-4-5-P3 -0.088 0.15 -9999 0 -0.41 70 70
ETS1 -0.027 0.11 -9999 0 -0.42 6 6
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.13 0.23 -9999 0 -0.56 93 93
B-cell antigen/BCR complex/LYN -0.093 0.2 -9999 0 -0.73 31 31
MALT1 0.014 0 -9999 0 -10000 0 0
TRAF6 0.014 0 -9999 0 -10000 0 0
RAC1 -0.099 0.26 -9999 0 -0.67 74 74
B-cell antigen/BCR complex/LYN/SYK -0.13 0.27 -9999 0 -0.89 46 46
CARD11 -0.073 0.17 -9999 0 -0.49 58 58
FCGR2B 0.006 0.068 -9999 0 -0.58 7 7
PPP3CA 0.014 0 -9999 0 -10000 0 0
BCL10 0.014 0 -9999 0 -10000 0 0
IKK complex 0.007 0.039 -9999 0 -10000 0 0
PTPRC -0.003 0.11 -9999 0 -0.69 12 12
PDPK1 -0.028 0.12 -9999 0 -0.29 43 43
PPP3CB 0.014 0 -9999 0 -10000 0 0
PPP3CC 0.014 0 -9999 0 -10000 0 0
POU2F2 0.008 0.04 -9999 0 -0.14 31 31
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.062 0.19 0.59 54 -10000 0 54
KIRREL -0.022 0.14 -10000 0 -0.63 25 25
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.062 0.19 -10000 0 -0.59 54 54
PLCG1 0.014 0 -10000 0 -10000 0 0
ARRB2 0.014 0 -10000 0 -10000 0 0
WASL 0.014 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.057 0.17 -10000 0 -0.56 43 43
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.009 0.12 -10000 0 -0.6 10 10
FYN -0.036 0.16 -10000 0 -0.51 44 44
mol:Ca2+ -0.056 0.17 -10000 0 -0.56 43 43
mol:DAG -0.056 0.17 -10000 0 -0.56 43 43
NPHS2 -0.024 0.13 -10000 0 -0.84 13 13
mol:IP3 -0.056 0.17 -10000 0 -0.56 43 43
regulation of endocytosis -0.049 0.15 -10000 0 -0.5 37 37
Nephrin/NEPH1/podocin/Cholesterol -0.058 0.17 -10000 0 -0.57 43 43
establishment of cell polarity -0.062 0.19 -10000 0 -0.59 54 54
Nephrin/NEPH1/podocin/NCK1-2 -0.052 0.16 -10000 0 -0.54 36 36
Nephrin/NEPH1/beta Arrestin2 -0.026 0.16 -10000 0 -0.5 37 37
NPHS1 -0.048 0.2 -10000 0 -0.82 33 33
Nephrin/NEPH1/podocin -0.051 0.16 -10000 0 -0.52 44 44
TJP1 0.014 0 -10000 0 -10000 0 0
NCK1 0.014 0 -10000 0 -10000 0 0
NCK2 0.014 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.057 0.17 -10000 0 -0.56 43 43
CD2AP 0.014 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.057 0.17 -10000 0 -0.56 43 43
GRB2 0.014 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.055 0.2 -10000 0 -0.53 65 65
cytoskeleton organization -0.013 0.15 -10000 0 -0.77 10 10
Nephrin/NEPH1 -0.047 0.14 -10000 0 -0.44 54 54
Nephrin/NEPH1/ZO-1 -0.051 0.15 -10000 0 -0.55 37 37
IL27-mediated signaling events

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
TGFB1 0.012 0.069 -10000 0 -0.8 3 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.063 0.19 0.63 29 -10000 0 29
IL27/IL27R/JAK1 -0.11 0.21 -10000 0 -0.83 21 21
TBX21 -0.11 0.26 -10000 0 -0.73 40 40
IL12B -0.059 0.23 -10000 0 -0.81 44 44
IL12A -0.009 0.095 -10000 0 -0.48 20 20
IL6ST -0.064 0.2 -10000 0 -0.59 65 65
IL27RA/JAK1 -0.014 0.12 -10000 0 -0.59 16 16
IL27 -0.029 0.17 -10000 0 -0.82 23 23
TYK2 0.011 0.037 -10000 0 -0.82 1 1
T-helper cell lineage commitment -0.017 0.12 -10000 0 -0.68 7 7
T-helper 2 cell differentiation 0.063 0.19 0.63 29 -10000 0 29
T cell proliferation during immune response 0.063 0.19 0.63 29 -10000 0 29
MAPKKK cascade -0.063 0.19 -10000 0 -0.63 29 29
STAT3 0.014 0 -10000 0 -10000 0 0
STAT2 0.014 0 -10000 0 -10000 0 0
STAT1 -0.034 0.19 -10000 0 -0.8 30 30
IL12RB1 -0.049 0.21 -10000 0 -0.8 39 39
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.17 0.32 -10000 0 -0.67 128 128
IL27/IL27R/JAK2/TYK2 -0.064 0.19 -10000 0 -0.64 29 29
positive regulation of T cell mediated cytotoxicity -0.063 0.19 -10000 0 -0.63 29 29
STAT1 (dimer) -0.19 0.3 0.52 1 -0.92 44 45
JAK2 0.011 0.027 -10000 0 -0.58 1 1
JAK1 0.013 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.053 0.18 -10000 0 -0.61 28 28
T cell proliferation -0.084 0.21 -10000 0 -0.6 44 44
IL12/IL12R/TYK2/JAK2 -0.058 0.18 -10000 0 -0.64 19 19
IL17A -0.018 0.12 -10000 0 -0.68 7 7
mast cell activation 0.063 0.19 0.63 29 -10000 0 29
IFNG -0.018 0.049 -10000 0 -0.11 107 107
T cell differentiation -0.007 0.009 -10000 0 -0.024 72 72
STAT3 (dimer) -0.053 0.18 -10000 0 -0.62 27 27
STAT5A (dimer) -0.053 0.18 -10000 0 -0.62 27 27
STAT4 (dimer) -0.065 0.2 -10000 0 -0.63 36 36
STAT4 -0.008 0.13 -10000 0 -0.79 14 14
T cell activation -0.006 0.02 0.092 20 -10000 0 20
IL27R/JAK2/TYK2 -0.056 0.17 -10000 0 -0.75 9 9
GATA3 0.002 0.15 -10000 0 -0.68 20 20
IL18 -0.004 0.082 -10000 0 -0.42 19 19
positive regulation of mast cell cytokine production -0.052 0.18 -10000 0 -0.6 27 27
IL27/EBI3 -0.029 0.16 -10000 0 -0.63 32 32
IL27RA -0.023 0.13 -10000 0 -0.63 20 20
IL6 -0.046 0.19 -10000 0 -0.62 51 51
STAT5A 0.014 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 0.018 0.07 -10000 0 -10000 0 0
IL1B -0.051 0.19 -10000 0 -0.61 52 52
EBI3 -0.004 0.1 -10000 0 -0.72 10 10
TNF -0.017 0.13 -10000 0 -0.6 25 25
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.009 0.061 -10000 0 -0.59 4 4
HDAC1 0.01 0.005 -10000 0 -10000 0 0
AES 0.012 0.001 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
DTX1 0.01 0.051 -10000 0 -0.65 3 3
LRP6/FZD1 -0.008 0.065 -10000 0 -0.56 7 7
TLE1 0.013 0.001 -10000 0 -10000 0 0
AP1 -0.024 0.12 -10000 0 -0.29 82 82
NCSTN 0.014 0 -10000 0 -10000 0 0
ADAM10 0.011 0.037 -10000 0 -0.58 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.039 0.046 -10000 0 -10000 0 0
NICD/RBPSUH -0.005 0.053 -10000 0 -0.58 4 4
WIF1 -0.26 0.3 -10000 0 -0.59 233 233
NOTCH1 -0.006 0.056 -10000 0 -0.62 4 4
PSENEN 0.01 0.051 -10000 0 -0.81 2 2
KREMEN2 -0.27 0.39 -10000 0 -0.81 180 180
DKK1 -0.29 0.39 -10000 0 -0.79 195 195
beta catenin/beta TrCP1 0.02 0.045 -10000 0 -0.35 1 1
APH1B 0.014 0 -10000 0 -10000 0 0
APH1A 0.014 0 -10000 0 -10000 0 0
AXIN1 0.001 0.025 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.019 0.044 -10000 0 -10000 0 0
PSEN1 0.014 0 -10000 0 -10000 0 0
FOS -0.063 0.2 -10000 0 -0.58 67 67
JUN 0.014 0 -10000 0 -10000 0 0
MAP3K7 0.012 0.002 -10000 0 -10000 0 0
CTNNB1 0.013 0.048 -10000 0 -0.37 1 1
MAPK3 0.014 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.2 0.26 -10000 0 -0.54 187 187
HNF1A -0.003 0.11 -10000 0 -0.81 10 10
CTBP1 0.012 0.001 -10000 0 -10000 0 0
MYC 0.025 0.013 -10000 0 -10000 0 0
NKD1 -0.017 0.15 -10000 0 -0.77 20 20
FZD1 0.005 0.084 -10000 0 -0.77 6 6
NOTCH1 precursor/Deltex homolog 1 -0.007 0.064 -10000 0 -0.61 5 5
apoptosis -0.023 0.12 -10000 0 -0.29 82 82
Delta 1/NOTCHprecursor -0.009 0.06 -10000 0 -0.58 4 4
DLL1 0.007 0.063 -10000 0 -0.58 6 6
PPARD 0.025 0.013 -10000 0 -10000 0 0
Gamma Secretase -0.002 0.028 -10000 0 -0.45 2 2
APC 0.001 0.031 -10000 0 -0.35 2 2
DVL1 -0.019 0.028 -10000 0 -10000 0 0
CSNK2A1 0.014 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.37 0.35 -10000 0 -0.63 306 306
LRP6 0.012 0.026 -10000 0 -0.58 1 1
CSNK1A1 0.014 0.001 -10000 0 -10000 0 0
NLK 0.014 0.006 -10000 0 -10000 0 0
CCND1 0.006 0.14 -10000 0 -0.82 13 13
WNT1 -0.001 0.094 -10000 0 -0.81 7 7
Axin1/APC/beta catenin 0.025 0.042 -10000 0 -0.4 1 1
DKK2 -0.007 0.12 -10000 0 -0.68 15 15
NOTCH1 precursor/DVL1 -0.01 0.052 -10000 0 -0.58 4 4
GSK3B 0.013 0 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.007 0.064 -10000 0 -0.62 5 5
PPP2R5D 0.002 0.066 0.32 20 -10000 0 20
MAPK1 0.014 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.16 0.17 -10000 0 -0.52 29 29
RBPJ 0.014 0 -10000 0 -10000 0 0
CREBBP 0.017 0.003 -10000 0 -10000 0 0
Ephrin B reverse signaling

Figure S42.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S42.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.012 0.026 -10000 0 -0.58 1 1
EPHB2 -0.2 0.36 -10000 0 -0.8 138 138
EFNB1 -0.023 0.16 -10000 0 -0.62 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.16 0.23 -10000 0 -0.82 21 21
Ephrin B2/EPHB1-2 -0.15 0.23 -10000 0 -0.5 155 155
neuron projection morphogenesis -0.16 0.22 -10000 0 -0.78 21 21
Ephrin B1/EPHB1-2/Tiam1 -0.17 0.26 -10000 0 -0.89 21 21
DNM1 -0.045 0.21 -10000 0 -0.81 37 37
cell-cell signaling 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.007 0.09 -10000 0 -0.6 11 11
YES1 -0.016 0.12 -10000 0 -0.84 11 11
Ephrin B1/EPHB1-2/NCK2 -0.17 0.25 -10000 0 -0.9 19 19
PI3K 0.006 0.096 -10000 0 -0.63 11 11
mol:GDP -0.17 0.25 -10000 0 -0.87 21 21
ITGA2B -0.069 0.25 -10000 0 -0.81 52 52
endothelial cell proliferation -0.001 0.016 -10000 0 -0.35 1 1
FYN -0.016 0.12 -10000 0 -0.84 11 11
MAP3K7 -0.013 0.093 -10000 0 -0.64 11 11
FGR -0.016 0.12 -10000 0 -0.83 11 11
TIAM1 0.007 0.063 -10000 0 -0.58 6 6
PIK3R1 0.011 0.037 -10000 0 -0.58 2 2
RGS3 0.014 0 -10000 0 -10000 0 0
cell adhesion -0.04 0.19 -10000 0 -0.52 54 54
LYN -0.016 0.12 -10000 0 -0.84 11 11
Ephrin B1/EPHB1-2/Src Family Kinases -0.018 0.11 -10000 0 -0.78 11 11
Ephrin B1/EPHB1-2 -0.02 0.1 -10000 0 -0.7 11 11
SRC -0.016 0.12 -10000 0 -0.83 11 11
ITGB3 -0.017 0.15 -10000 0 -0.73 21 21
EPHB1 -0.03 0.18 -10000 0 -0.73 30 30
EPHB4 0.014 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.001 0.016 -10000 0 -0.36 1 1
alphaIIb/beta3 Integrin -0.083 0.22 -10000 0 -0.62 70 70
BLK -0.032 0.12 -10000 0 -0.83 11 11
HCK -0.016 0.12 -10000 0 -0.83 11 11
regulation of stress fiber formation 0.17 0.25 0.88 19 -10000 0 19
MAPK8 0.011 0.1 -10000 0 -0.64 11 11
Ephrin B1/EPHB1-2/RGS3 -0.17 0.25 -10000 0 -0.57 71 71
endothelial cell migration -0.007 0.079 -10000 0 -0.54 11 11
NCK2 0.014 0 -10000 0 -10000 0 0
PTPN13 -0.004 0.1 -10000 0 -0.69 11 11
regulation of focal adhesion formation 0.17 0.25 0.88 19 -10000 0 19
chemotaxis 0.17 0.25 0.49 172 -10000 0 172
PIK3CA 0.014 0 -10000 0 -10000 0 0
Rac1/GTP -0.16 0.23 -10000 0 -0.81 21 21
angiogenesis -0.019 0.1 -10000 0 -0.69 11 11
LCK -0.019 0.12 -10000 0 -0.83 11 11
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.029 0.033 -9999 0 -10000 0 0
SNTA1 0.012 0.036 -9999 0 -0.81 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.024 0.059 -9999 0 -0.53 4 4
MAPK12 -0.007 0.14 -9999 0 -0.55 21 21
CCND1 0 0.086 -9999 0 -0.37 15 15
p38 gamma/SNTA1 0 0.13 -9999 0 -0.51 22 22
MAP2K3 0.012 0.026 -9999 0 -0.58 1 1
PKN1 0.01 0.051 -9999 0 -0.81 2 2
G2/M transition checkpoint -0.006 0.13 -9999 0 -0.55 21 21
MAP2K6 0.006 0.086 -9999 0 -0.35 26 26
MAPT -0.14 0.18 -9999 0 -0.32 241 241
MAPK13 0.021 0.038 -9999 0 -0.42 4 4
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.016 0.029 -9999 0 -0.36 3 3
Regulation of nuclear SMAD2/3 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
EP300 0.007 0.028 -10000 0 -0.58 1 1
HSPA8 0.016 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.035 0.15 -10000 0 -0.52 16 16
AKT1 0 0.033 -10000 0 -10000 0 0
GSC -0.016 0.19 -10000 0 -0.7 32 32
NKX2-5 -0.16 0.31 -10000 0 -0.71 123 123
muscle cell differentiation 0.13 0.21 0.64 52 -10000 0 52
SMAD2-3/SMAD4/SP1 -0.04 0.1 -10000 0 -10000 0 0
SMAD4 0.002 0.043 -10000 0 -0.55 1 1
CBFB 0.014 0 -10000 0 -10000 0 0
SAP18 0.015 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 0 0.063 -10000 0 -0.53 6 6
SMAD3/SMAD4/VDR 0.005 0.039 -10000 0 -10000 0 0
MYC 0.028 0.034 -10000 0 -10000 0 0
CDKN2B -0.25 0.58 -10000 0 -1.4 111 111
AP1 -0.004 0.1 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.056 0.041 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.063 0.16 -10000 0 -0.56 14 14
SP3 0.016 0 -10000 0 -10000 0 0
CREB1 0.014 0 -10000 0 -10000 0 0
FOXH1 -0.1 0.29 -10000 0 -0.8 74 74
SMAD3/SMAD4/GR 0.028 0.063 -10000 0 -10000 0 0
GATA3 -0.015 0.15 -10000 0 -0.76 20 20
SKI/SIN3/HDAC complex/NCoR1 0.055 0.023 -10000 0 -10000 0 0
MEF2C/TIF2 -0.16 0.28 -10000 0 -0.76 54 54
endothelial cell migration 0.36 0.33 0.64 297 -10000 0 297
MAX 0.035 0.02 -10000 0 -10000 0 0
RBBP7 0.015 0.002 -10000 0 -10000 0 0
RBBP4 0.013 0.026 -10000 0 -0.58 1 1
RUNX2 0.01 0.051 -10000 0 -0.65 3 3
RUNX3 0.002 0.095 -10000 0 -0.81 7 7
RUNX1 0.014 0 -10000 0 -10000 0 0
CTBP1 0.014 0 -10000 0 -10000 0 0
NR3C1 0.035 0.02 -10000 0 -10000 0 0
VDR 0.011 0.037 -10000 0 -0.58 2 2
CDKN1A 0.021 0.093 -10000 0 -10000 0 0
KAT2B -0.019 0.13 -10000 0 -0.58 26 26
SMAD2/SMAD2/SMAD4/FOXH1 -0.073 0.2 -10000 0 -0.55 74 74
DCP1A 0.014 0 -10000 0 -10000 0 0
SKI 0.015 0.002 -10000 0 -10000 0 0
SERPINE1 -0.36 0.33 -10000 0 -0.64 297 297
SMAD3/SMAD4/ATF2 0.007 0.046 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.001 0.073 -10000 0 -0.52 5 5
SAP30 0.013 0.036 -10000 0 -0.8 1 1
Cbp/p300/PIAS3 0.004 0.034 -10000 0 -10000 0 0
JUN 0.017 0.11 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 -0.013 0.12 -10000 0 -0.58 16 16
TFE3 0 0.019 -10000 0 -10000 0 0
COL1A2 -0.24 0.34 -10000 0 -0.68 192 192
mesenchymal cell differentiation -0.005 0.056 0.5 2 -10000 0 2
DLX1 -0.31 0.4 -10000 0 -0.8 203 203
TCF3 0.014 0 -10000 0 -10000 0 0
FOS -0.056 0.2 -10000 0 -0.57 67 67
SMAD3/SMAD4/Max 0.028 0.063 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.004 0.021 -10000 0 -10000 0 0
ZBTB17 0.024 0.026 -10000 0 -10000 0 0
LAMC1 0.011 0.043 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.006 0.057 -10000 0 -0.59 2 2
IRF7 -0.015 0.15 -10000 0 -0.8 18 18
ESR1 -0.01 0.16 -10000 0 -0.68 28 28
HNF4A -0.07 0.24 -10000 0 -0.81 51 51
MEF2C -0.13 0.27 -10000 0 -0.62 69 69
SMAD2-3/SMAD4 -0.004 0.058 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.006 0.025 -10000 0 -10000 0 0
IGHV3OR16-13 -0.002 0.012 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.01 0.051 -10000 0 -0.81 2 2
CREBBP 0.008 0.01 -10000 0 -10000 0 0
SKIL 0.012 0.036 -10000 0 -0.81 1 1
HDAC1 0.015 0.002 -10000 0 -10000 0 0
HDAC2 0.015 0.002 -10000 0 -10000 0 0
SNIP1 0.016 0.004 -10000 0 -10000 0 0
GCN5L2 -0.009 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.002 0.045 -10000 0 -10000 0 0
MSG1/HSC70 0.01 0.07 -10000 0 -0.62 6 6
SMAD2 0 0.038 -10000 0 -10000 0 0
SMAD3 0.007 0.04 -10000 0 -0.53 1 1
SMAD3/E2F4-5/DP1/p107/SMAD4 0.02 0.046 -10000 0 -0.45 1 1
SMAD2/SMAD2/SMAD4 -0.023 0.081 -10000 0 -0.35 27 27
NCOR1 0.015 0.002 -10000 0 -10000 0 0
NCOA2 -0.034 0.16 -10000 0 -0.58 42 42
NCOA1 0.014 0 -10000 0 -10000 0 0
MYOD/E2A -0.073 0.16 -10000 0 -0.42 89 89
SMAD2-3/SMAD4/SP1/MIZ-1 -0.031 0.095 -10000 0 -10000 0 0
IFNB1 0.006 0.15 -10000 0 -0.68 16 16
SMAD3/SMAD4/MEF2C -0.13 0.26 -10000 0 -0.69 44 44
CITED1 0.004 0.088 -10000 0 -0.81 6 6
SMAD2-3/SMAD4/ARC105 0.003 0.061 -10000 0 -0.49 2 2
RBL1 0.012 0.026 -10000 0 -0.58 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.067 0.22 -10000 0 -0.49 107 107
RUNX1-3/PEBPB2 -0.007 0.061 -10000 0 -0.53 7 7
SMAD7 -0.022 0.11 -10000 0 -10000 0 0
MYC/MIZ-1 0.034 0.066 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.12 0.16 0.36 4 -0.41 2 6
IL10 0.013 0.15 -10000 0 -0.6 22 22
PIASy/HDAC complex 0.023 0.013 -10000 0 -10000 0 0
PIAS3 0.008 0.008 -10000 0 -10000 0 0
CDK2 0.007 0.01 -10000 0 -10000 0 0
IL5 0.011 0.13 -10000 0 -0.57 14 14
CDK4 0.008 0.011 -10000 0 -10000 0 0
PIAS4 0.023 0.013 -10000 0 -10000 0 0
ATF3 0.003 0.084 -10000 0 -0.66 8 8
SMAD3/SMAD4/SP1 -0.047 0.091 -10000 0 -10000 0 0
FOXG1 -0.11 0.27 -10000 0 -0.73 83 83
FOXO3 0.007 0.044 -10000 0 -10000 0 0
FOXO1 0.007 0.044 -10000 0 -10000 0 0
FOXO4 0.005 0.051 -10000 0 -0.41 2 2
heart looping -0.13 0.26 -10000 0 -0.62 69 69
CEBPB 0.007 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.21 0.28 -10000 0 -0.56 201 201
MYOD1 -0.095 0.22 -10000 0 -0.59 89 89
SMAD3/SMAD4/HNF4 -0.049 0.17 -10000 0 -0.56 51 51
SMAD3/SMAD4/GATA3 -0.014 0.12 -10000 0 -0.56 17 17
SnoN/SIN3/HDAC complex/NCoR1 0.012 0.036 -10000 0 -0.81 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.008 0.067 -10000 0 -0.47 4 4
SMAD3/SMAD4/SP1-3 -0.025 0.082 -10000 0 -10000 0 0
MED15 0.01 0.051 -10000 0 -0.81 2 2
SP1 -0.034 0.073 -10000 0 -10000 0 0
SIN3B 0.015 0.002 -10000 0 -10000 0 0
SIN3A 0.015 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.16 0.27 -10000 0 -0.55 136 136
ITGB5 0.009 0.09 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.053 0.017 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.089 0.17 -10000 0 -0.44 31 31
AR -0.15 0.26 -10000 0 -0.58 140 140
negative regulation of cell growth 0.023 0.054 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.059 0.15 -10000 0 -0.42 37 37
E2F5 0.01 0.045 -10000 0 -0.58 3 3
E2F4 0.014 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.062 0.17 -10000 0 -0.49 42 42
SMAD2-3/SMAD4/FOXO1-3a-4 -0.035 0.15 -10000 0 -10000 0 0
TFDP1 0.012 0.036 -10000 0 -0.81 1 1
SMAD3/SMAD4/AP1 0 0.11 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.005 0.056 -10000 0 -0.5 2 2
TGIF2 0.01 0.051 -10000 0 -0.81 2 2
TGIF1 0.012 0.036 -10000 0 -0.81 1 1
ATF2 0.012 0.026 -10000 0 -0.58 1 1
IL1-mediated signaling events

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
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.012 0.026 -9999 0 -0.58 1 1
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.014 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.023 0.071 -9999 0 -0.52 2 2
IRAK/TOLLIP 0.033 0.004 -9999 0 -10000 0 0
IKBKB 0.014 0 -9999 0 -10000 0 0
IKBKG 0.014 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.24 0.29 -9999 0 -0.56 222 222
IL1A -0.2 0.36 -9999 0 -0.8 134 134
IL1B -0.039 0.19 -9999 0 -0.6 53 53
IRAK/TRAF6/p62/Atypical PKCs 0 0.011 -9999 0 -10000 0 0
IL1R2 -0.11 0.24 -9999 0 -0.59 103 103
IL1R1 0.012 0.026 -9999 0 -0.58 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.023 0.073 -9999 0 -0.73 1 1
TOLLIP 0.014 0 -9999 0 -10000 0 0
TICAM2 0.013 0.001 -9999 0 -10000 0 0
MAP3K3 0.014 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.071 0.005 -9999 0 -10000 0 0
JUN 0.033 0.071 -9999 0 -0.48 2 2
MAP3K7 0.014 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.045 0.13 -9999 0 -0.84 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.12 0.21 -9999 0 -0.49 129 129
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.12 0.2 -9999 0 -0.73 2 2
IL1 beta fragment/IL1R1/IL1RAP -0.05 0.15 -9999 0 -0.49 50 50
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 0.026 0.075 -9999 0 -0.53 2 2
IRAK1 0.027 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.11 0.18 -9999 0 -0.42 132 132
IRAK4 0.012 0.026 -9999 0 -0.58 1 1
PRKCI 0.014 0 -9999 0 -10000 0 0
TRAF6 0.014 0 -9999 0 -10000 0 0
PI3K -0.002 0.026 -9999 0 -0.42 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.014 0.089 -9999 0 -0.83 1 1
CHUK 0.014 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.05 0.15 -9999 0 -0.49 50 50
IL1 beta/IL1R2 -0.12 0.2 -9999 0 -0.56 59 59
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.041 0.12 -9999 0 -0.75 1 1
IRAK3 0.003 0.088 -9999 0 -0.74 7 7
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.045 0.13 -9999 0 -0.84 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.039 0.14 -9999 0 -0.71 2 2
IL1 alpha/IL1R1/IL1RAP -0.14 0.23 -9999 0 -0.54 129 129
RELA 0.014 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.014 0 -9999 0 -10000 0 0
MYD88 0.014 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.04 0.003 -9999 0 -10000 0 0
IL1RAP 0.01 0.051 -9999 0 -0.65 3 3
UBE2N 0.014 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.036 0.11 -9999 0 -0.68 1 1
CASP1 0.012 0.026 -9999 0 -0.58 1 1
IL1RN/IL1R2 -0.18 0.26 -9999 0 -0.5 190 190
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.047 0.14 -9999 0 -0.46 50 50
TMEM189-UBE2V1 0.01 0.006 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.012 0.11 -9999 0 -0.68 2 2
PIK3CA 0.014 0 -9999 0 -10000 0 0
IL1RN -0.14 0.26 -9999 0 -0.58 132 132
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.022 0.066 -9999 0 -10000 0 0
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 -0.002 0.11 -9999 0 -0.81 10 10
Syndecan-3/Src/Cortactin -0.11 0.14 -9999 0 -0.56 11 11
Syndecan-3/Neurocan -0.025 0.1 -9999 0 -0.44 29 29
POMC -0.083 0.26 -9999 0 -0.77 64 64
EGFR -0.015 0.15 -9999 0 -0.76 19 19
Syndecan-3/EGFR -0.017 0.082 -9999 0 -0.44 17 17
AGRP 0.005 0.006 -9999 0 -10000 0 0
NCSTN 0.014 0 -9999 0 -10000 0 0
PSENEN 0.01 0.051 -9999 0 -0.81 2 2
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.014 0 -9999 0 -10000 0 0
APH1A 0.014 0 -9999 0 -10000 0 0
NCAN -0.033 0.18 -9999 0 -0.81 27 27
long-term memory -0.01 0.064 -9999 0 -0.42 11 11
Syndecan-3/IL8 -0.094 0.18 -9999 0 -0.46 105 105
PSEN1 0.014 0 -9999 0 -10000 0 0
Src/Cortactin -0.012 0.085 -9999 0 -0.62 10 10
FYN 0.012 0.036 -9999 0 -0.81 1 1
limb bud formation -0.002 0.023 -9999 0 -0.37 2 2
MC4R 0.005 0.036 -9999 0 -0.81 1 1
SRC 0.014 0 -9999 0 -10000 0 0
PTN -0.21 0.29 -9999 0 -0.58 198 198
FGFR/FGF/Syndecan-3 -0.002 0.023 -9999 0 -0.37 2 2
neuron projection morphogenesis -0.12 0.16 -9999 0 -0.63 14 14
Syndecan-3/AgRP -0.002 0.022 -9999 0 -0.35 2 2
Syndecan-3/AgRP/MC4R -0.002 0.028 -9999 0 -0.43 1 1
Fyn/Cortactin -0.013 0.089 -9999 0 -0.62 11 11
SDC3 -0.002 0.024 -9999 0 -0.37 2 2
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.092 0.18 -9999 0 -0.45 105 105
IL8 -0.15 0.33 -9999 0 -0.8 107 107
Syndecan-3/Fyn/Cortactin -0.011 0.065 -9999 0 -0.43 11 11
Syndecan-3/CASK -0.002 0.022 -9999 0 -0.35 2 2
alpha-MSH/MC4R -0.073 0.2 -9999 0 -0.59 64 64
Gamma Secretase -0.002 0.028 -9999 0 -0.45 2 2
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.01 0.075 -9999 0 -0.57 9 9
alphaV beta3 Integrin -0.036 0.13 -9999 0 -0.55 25 25
PTK2 -0.006 0.15 -9999 0 -0.58 10 10
IGF1R 0.012 0.036 -9999 0 -0.81 1 1
PI4KB 0.014 0 -9999 0 -10000 0 0
MFGE8 0.014 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
CDKN1B -0.037 0.1 -9999 0 -0.4 33 33
VEGFA 0.002 0.095 -9999 0 -0.81 7 7
ILK -0.037 0.1 -9999 0 -0.4 33 33
ROCK1 0.014 0 -9999 0 -10000 0 0
AKT1 0 0.11 -9999 0 -0.49 4 4
PTK2B 0.012 0.12 -9999 0 -0.46 27 27
alphaV/beta3 Integrin/JAM-A -0.06 0.16 -9999 0 -0.49 55 55
CBL 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.027 0.12 -9999 0 -0.54 22 22
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.055 0.12 -9999 0 -0.51 6 6
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.015 0.084 -9999 0 -0.42 4 4
alphaV/beta3 Integrin/Syndecan-1 -0.024 0.11 -9999 0 -0.54 19 19
PI4KA 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.25 0.25 -9999 0 -0.75 50 50
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.31 0.28 -9999 0 -0.55 291 291
RPS6KB1 -0.21 0.26 -9999 0 -0.69 50 50
TLN1 0.01 0.051 -9999 0 -0.81 2 2
MAPK3 -0.11 0.15 -9999 0 -0.59 29 29
GPR124 0.009 0.062 -9999 0 -0.81 3 3
MAPK1 -0.11 0.15 -9999 0 -0.58 31 31
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
alphaV/beta3 Integrin/Tumstatin -0.081 0.2 -9999 0 -0.58 59 59
cell adhesion -0.023 0.096 -9999 0 -0.46 19 19
ANGPTL3 0.001 0.062 -9999 0 -0.81 3 3
VEGFR2 homodimer/VEGFA homodimer/Src -0.008 0.065 -9999 0 -0.49 9 9
IGF-1R heterotetramer 0.012 0.036 -9999 0 -0.81 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.011 0.037 -9999 0 -0.58 2 2
ITGB3 -0.017 0.15 -9999 0 -0.73 21 21
IGF1 -0.086 0.22 -9999 0 -0.59 86 86
RAC1 0.014 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.027 0.12 -9999 0 -0.56 21 21
apoptosis 0.006 0.076 -9999 0 -0.76 5 5
CD47 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.024 0.11 -9999 0 -0.54 19 19
VCL 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.088 0.2 -9999 0 -0.58 60 60
CSF1 0.007 0.063 -9999 0 -0.58 6 6
PIK3C2A -0.037 0.1 -9999 0 -0.4 33 33
PI4 Kinase/Pyk2 -0.055 0.14 -9999 0 -0.74 6 6
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.029 0.11 -9999 0 -0.49 27 27
FAK1/Vinculin 0.005 0.12 -9999 0 -0.48 6 6
alphaV beta3/Integrin/ppsTEM5 -0.027 0.12 -9999 0 -0.56 21 21
RHOA 0.014 0 -9999 0 -10000 0 0
VTN -0.039 0.2 -9999 0 -0.81 33 33
BCAR1 0.014 0 -9999 0 -10000 0 0
FGF2 -0.008 0.12 -9999 0 -0.63 17 17
F11R 0.007 0.09 -9999 0 -0.46 18 18
alphaV/beta3 Integrin/Lactadherin -0.024 0.11 -9999 0 -0.54 19 19
alphaV/beta3 Integrin/TGFBR2 -0.025 0.11 -9999 0 -0.54 19 19
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.008 0.055 -9999 0 -0.48 4 4
HSP90AA1 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.024 0.1 -9999 0 -0.5 21 21
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.35 0.41 -9999 0 -0.81 228 228
alphaV/beta3 Integrin/Pyk2 0.011 0.12 -9999 0 -0.46 27 27
SDC1 0.014 0 -9999 0 -10000 0 0
VAV3 0.012 0.1 -9999 0 -0.5 7 7
PTPN11 0.014 0 -9999 0 -10000 0 0
IRS1 0.01 0.045 -9999 0 -0.58 3 3
FAK1/Paxillin 0.005 0.12 -9999 0 -0.46 7 7
cell migration 0.015 0.12 -9999 0 -0.43 5 5
ITGAV 0.006 0.076 -9999 0 -0.76 5 5
PI3K -0.054 0.14 -9999 0 -0.71 7 7
SPP1 -0.44 0.41 -9999 0 -0.81 285 285
KDR 0.011 0.037 -9999 0 -0.58 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.006 0.076 -9999 0 -0.76 5 5
COL4A3 -0.079 0.25 -9999 0 -0.73 64 64
angiogenesis -0.076 0.17 -9999 0 -0.66 19 19
Rac1/GTP -0.024 0.082 -9999 0 -0.53 3 3
EDIL3 -0.09 0.26 -9999 0 -0.71 75 75
cell proliferation -0.025 0.11 -9999 0 -0.54 19 19
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.15 0.27 -9999 0 -0.6 136 136
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.01 0.051 -9999 0 -0.81 2 2
TCEB1 0.012 0.036 -9999 0 -0.81 1 1
HIF1A/p53 0.024 0.041 -9999 0 -10000 0 0
HIF1A 0.019 0.034 -9999 0 -10000 0 0
COPS5 0.014 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.039 -9999 0 -0.45 4 4
FIH (dimer) 0.014 0 -9999 0 -10000 0 0
CDKN2A -0.34 0.39 -9999 0 -0.76 238 238
ARNT/IPAS -0.11 0.19 -9999 0 -0.43 136 136
HIF1AN 0.014 0 -9999 0 -10000 0 0
GNB2L1 0.014 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.026 0.032 -9999 0 -10000 0 0
CUL2 0.012 0.036 -9999 0 -0.81 1 1
OS9 0.014 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.003 0.04 -9999 0 -0.53 3 3
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.026 0.032 -9999 0 -10000 0 0
PHD1-3/OS9 -0.029 0.11 -9999 0 -0.48 28 28
HIF1A/RACK1/Elongin B/Elongin C -0.007 0.041 -9999 0 -0.55 2 2
VHL 0.014 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.026 0.032 -9999 0 -10000 0 0
EGLN3 -0.036 0.19 -9999 0 -0.77 33 33
EGLN2 0.014 0 -9999 0 -10000 0 0
EGLN1 0.014 0 -9999 0 -10000 0 0
TP53 0.009 0.052 -9999 0 -0.58 4 4
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.037 0.026 -9999 0 -10000 0 0
ARNT 0.014 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.014 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.17 0.22 -9999 0 -0.43 195 195
Wnt 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
Noncanonical Wnts/FZD -0.039 0.16 -9999 0 -0.73 11 11
FZD6 0.009 0.057 -9999 0 -0.73 3 3
WNT6 -0.052 0.22 -9999 0 -0.76 44 44
WNT4 -0.008 0.12 -9999 0 -0.63 17 17
FZD3 0.006 0.068 -9999 0 -0.58 7 7
WNT5A 0.005 0.072 -9999 0 -0.61 7 7
WNT11 -0.075 0.24 -9999 0 -0.74 61 61
LPA receptor mediated events

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.038 0.095 -9999 0 -0.81 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.02 0.054 -9999 0 -10000 0 0
AP1 -0.07 0.13 -9999 0 -0.57 11 11
mol:PIP3 -0.046 0.11 -9999 0 -0.56 6 6
AKT1 0.03 0.083 -9999 0 -0.52 1 1
PTK2B 0.002 0.073 -9999 0 -0.3 5 5
RHOA 0.012 0.055 -9999 0 -0.32 1 1
PIK3CB 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0.012 0.073 -9999 0 -0.46 3 3
MAGI3 0.012 0.026 -9999 0 -0.58 1 1
RELA 0.014 0 -9999 0 -10000 0 0
apoptosis -0.016 0.11 -9999 0 -0.61 4 4
HRAS/GDP -0.001 0.027 -9999 0 -0.63 1 1
positive regulation of microtubule depolymerization -0.12 0.16 -9999 0 -0.42 28 28
NF kappa B1 p50/RelA -0.031 0.086 -9999 0 -0.54 4 4
endothelial cell migration -0.077 0.26 -9999 0 -0.75 66 66
ADCY4 -0.002 0.12 -9999 0 -0.44 15 15
ADCY5 -0.048 0.14 -9999 0 -0.53 17 17
ADCY6 -0.006 0.12 -9999 0 -0.47 16 16
ADCY7 -0.002 0.12 -9999 0 -0.44 15 15
ADCY1 -0.009 0.12 -9999 0 -0.43 16 16
ADCY2 -0.068 0.14 -9999 0 -0.48 22 22
ADCY3 -0.002 0.12 -9999 0 -0.44 15 15
ADCY8 -0.009 0.12 -9999 0 -0.42 19 19
ADCY9 -0.003 0.12 -9999 0 -0.44 15 15
GSK3B 0.01 0.07 -9999 0 -10000 0 0
arachidonic acid secretion 0.005 0.11 -9999 0 -0.42 15 15
GNG2 0.013 0 -9999 0 -10000 0 0
TRIP6 0.019 0.021 -9999 0 -10000 0 0
GNAO1 -0.022 0.13 -9999 0 -0.42 16 16
HRAS 0.012 0.036 -9999 0 -0.81 1 1
NFKBIA 0.017 0.085 -9999 0 -0.43 3 3
GAB1 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.008 0.1 -9999 0 -0.89 7 7
JUN 0.013 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.013 0.046 -9999 0 -0.58 2 2
TIAM1 -0.011 0.12 -9999 0 -1.1 7 7
PIK3R1 0.011 0.036 -9999 0 -0.58 2 2
mol:IP3 0.012 0.074 -9999 0 -0.47 3 3
PLCB3 0.016 0.047 -9999 0 -0.53 2 2
FOS -0.063 0.2 -9999 0 -0.58 67 67
positive regulation of mitosis 0.005 0.11 -9999 0 -0.42 15 15
LPA/LPA1-2-3 -0.046 0.11 -9999 0 -0.65 4 4
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.014 0 -9999 0 -10000 0 0
stress fiber formation 0.007 0.086 -9999 0 -0.39 4 4
GNAZ -0.036 0.15 -9999 0 -0.54 21 21
EGFR/PI3K-beta/Gab1 -0.048 0.11 -9999 0 -0.59 6 6
positive regulation of dendritic cell cytokine production -0.045 0.11 -9999 0 -0.64 4 4
LPA/LPA2/MAGI-3 -0.012 0.032 -9999 0 -0.35 1 1
ARHGEF1 -0.002 0.11 -9999 0 -0.56 5 5
GNAI2 -0.018 0.12 -9999 0 -0.38 12 12
GNAI3 -0.018 0.12 -9999 0 -0.38 12 12
GNAI1 -0.019 0.12 -9999 0 -0.38 13 13
LPA/LPA3 -0.026 0.076 -9999 0 -0.43 13 13
LPA/LPA2 -0.015 0.04 -9999 0 -10000 0 0
LPA/LPA1 -0.053 0.13 -9999 0 -0.36 77 77
HB-EGF/EGFR -0.39 0.26 -9999 0 -0.55 379 379
HBEGF -0.44 0.29 -9999 0 -0.62 374 374
mol:DAG 0.012 0.074 -9999 0 -0.47 3 3
cAMP biosynthetic process -0.015 0.12 -9999 0 -0.46 15 15
NFKB1 0.014 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
LYN 0.017 0.085 -9999 0 -0.49 1 1
GNAQ 0.006 0.059 -9999 0 -0.32 4 4
LPAR2 0.013 0 -9999 0 -10000 0 0
LPAR3 -0.001 0.092 -9999 0 -0.58 13 13
LPAR1 -0.02 0.11 -9999 0 -0.6 12 12
IL8 -0.22 0.18 -9999 0 -0.49 92 92
PTK2 -0.007 0.11 -9999 0 -0.61 4 4
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.016 0.11 -9999 0 -0.62 4 4
EGFR -0.015 0.15 -9999 0 -0.76 19 19
PLCG1 -0.005 0.077 -9999 0 -0.32 13 13
PLD2 -0.007 0.11 -9999 0 -0.61 4 4
G12/G13 -0.042 0.1 -9999 0 -0.6 5 5
PI3K-beta -0.028 0.07 -9999 0 -0.55 2 2
cell migration -0.01 0.046 -9999 0 -0.28 1 1
SLC9A3R2 0.01 0.051 -9999 0 -0.81 2 2
PXN 0.007 0.087 -9999 0 -0.4 4 4
HRAS/GTP 0.005 0.11 -9999 0 -0.44 13 13
RAC1 0.014 0 -9999 0 -10000 0 0
MMP9 -0.58 0.37 -9999 0 -0.81 374 374
PRKCE 0.012 0.026 -9999 0 -0.58 1 1
PRKCD 0.019 0.071 -9999 0 -0.48 2 2
Gi(beta/gamma) 0.002 0.11 -9999 0 -0.53 5 5
mol:LPA -0.021 0.069 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.025 0.084 -9999 0 -0.52 4 4
MAPKKK cascade 0.005 0.11 -9999 0 -0.42 15 15
contractile ring contraction involved in cytokinesis 0.012 0.055 -9999 0 -0.32 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.04 0.12 -9999 0 -0.3 88 88
GNA15 0.005 0.067 -9999 0 -0.33 14 14
GNA12 0.007 0.072 -9999 0 -0.81 4 4
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT -0.12 0.16 -9999 0 -0.43 28 28
GNA11 0.004 0.066 -9999 0 -0.3 17 17
Rac1/GTP -0.009 0.11 -9999 0 -0.95 7 7
MMP2 -0.077 0.26 -9999 0 -0.76 66 66
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.056 0.23 -10000 0 -0.89 21 21
NCK1/PAK1/Dok-R -0.027 0.089 -10000 0 -0.41 21 21
NCK1/Dok-R -0.05 0.22 -10000 0 -1.1 21 21
PIK3CA 0.013 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol -0.006 0.04 0.24 12 -10000 0 12
RELA 0.014 0 -10000 0 -10000 0 0
SHC1 0.014 0.001 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.084 0.26 -10000 0 -0.83 53 53
TNIP2 0.014 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.044 0.2 -10000 0 -1 21 21
FN1 -0.35 0.41 -10000 0 -0.81 228 228
PLD2 0.034 0.25 -10000 0 -1.1 21 21
PTPN11 0.014 0 -10000 0 -10000 0 0
GRB14 -0.045 0.18 -10000 0 -0.61 48 48
ELK1 0.047 0.22 -10000 0 -1 21 21
GRB7 0.004 0.084 -10000 0 -0.71 7 7
PAK1 0.012 0.036 -10000 0 -0.81 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.33 0.35 -10000 0 -0.85 133 133
CDKN1A 0.063 0.19 -10000 0 -0.65 11 11
ITGA5 -0.24 0.38 -10000 0 -0.81 164 164
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.051 0.22 -10000 0 -1.1 21 21
CRK 0.014 0 -10000 0 -10000 0 0
mol:NO 0.062 0.18 -10000 0 -0.65 21 21
PLG 0.022 0.25 -10000 0 -1.1 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.035 0.2 -10000 0 -0.85 21 21
GRB2 0.014 0 -10000 0 -10000 0 0
PIK3R1 0.012 0.037 -10000 0 -0.58 2 2
ANGPT2 0.019 0.19 -10000 0 -0.6 26 26
BMX -0.005 0.28 -10000 0 -1.2 21 21
ANGPT1 0.018 0.23 -10000 0 -1.2 14 14
tube development 0.055 0.2 -10000 0 -0.73 13 13
ANGPT4 0.008 0.007 -10000 0 -10000 0 0
response to hypoxia 0.001 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.002 0.27 -10000 0 -1.2 21 21
alpha5/beta1 Integrin -0.2 0.29 -10000 0 -0.62 165 165
FGF2 -0.008 0.12 -10000 0 -0.63 17 17
STAT5A (dimer) 0.058 0.22 -10000 0 -0.85 11 11
mol:L-citrulline 0.062 0.18 -10000 0 -0.65 21 21
AGTR1 -0.047 0.18 -10000 0 -0.59 51 51
MAPK14 0.036 0.25 -10000 0 -1.1 21 21
Tie2/SHP2 -0.031 0.17 -10000 0 -1.2 11 11
TEK 0.012 0.2 -10000 0 -1.3 11 11
RPS6KB1 0.059 0.21 -10000 0 -0.85 21 21
Angiotensin II/AT1 -0.033 0.13 -10000 0 -0.44 51 51
Tie2/Ang1/GRB2 0.029 0.26 -10000 0 -1.2 21 21
MAPK3 0.042 0.23 -10000 0 -1 21 21
MAPK1 0.042 0.23 -10000 0 -1 21 21
Tie2/Ang1/GRB7 0.024 0.26 -10000 0 -1.2 21 21
NFKB1 0.014 0 -10000 0 -10000 0 0
MAPK8 0.03 0.26 -10000 0 -1.2 21 21
PI3K 0.048 0.25 -10000 0 -1 21 21
FES 0.036 0.25 -10000 0 -1.1 21 21
Crk/Dok-R -0.05 0.22 -10000 0 -1.1 21 21
Tie2/Ang1/ABIN2 0.029 0.26 -10000 0 -1.2 21 21
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.059 0.21 -10000 0 -0.79 21 21
STAT5A 0.014 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.059 0.21 -10000 0 -0.85 21 21
Tie2/Ang2 0.041 0.25 -10000 0 -1 12 12
Tie2/Ang1 0.026 0.27 -10000 0 -1.2 21 21
FOXO1 0.06 0.22 -10000 0 -0.79 21 21
ELF1 0.017 0.055 -10000 0 -0.59 4 4
ELF2 0.03 0.25 -10000 0 -1.1 21 21
mol:Choline 0.036 0.24 -10000 0 -1.1 21 21
cell migration -0.088 0.086 -10000 0 -10000 0 0
FYN 0.052 0.22 -10000 0 -0.84 13 13
DOK2 0.008 0.067 -10000 0 -0.75 4 4
negative regulation of cell cycle 0.064 0.18 -10000 0 -0.59 11 11
ETS1 0.014 0.072 -10000 0 -0.79 3 3
PXN 0.069 0.18 -10000 0 -0.7 21 21
ITGB1 0.012 0.036 -10000 0 -0.81 1 1
NOS3 0.059 0.2 -10000 0 -0.74 21 21
RAC1 0.014 0 -10000 0 -10000 0 0
TNF -0.018 0.17 -10000 0 -0.76 25 25
MAPKKK cascade 0.036 0.24 -10000 0 -1.1 21 21
RASA1 0.011 0.037 -10000 0 -0.58 2 2
Tie2/Ang1/Shc 0.03 0.26 -10000 0 -1.2 21 21
NCK1 0.014 0 -10000 0 -10000 0 0
vasculogenesis 0.063 0.17 -10000 0 -0.58 21 21
mol:Phosphatidic acid 0.036 0.24 -10000 0 -1.1 21 21
mol:Angiotensin II 0 0.007 -10000 0 -10000 0 0
mol:NADP 0.062 0.18 -10000 0 -0.65 21 21
Rac1/GTP -0.046 0.16 -10000 0 -0.79 21 21
MMP2 -0.027 0.29 -10000 0 -1.1 21 21
Arf6 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
CENTA1/KIF3B -0.004 0.038 -9999 0 -0.35 6 6
ARNO/beta Arrestin1-2 -0.02 0.07 -9999 0 -0.51 1 1
EGFR -0.015 0.15 -9999 0 -0.76 19 19
EPHA2 0.006 0.068 -9999 0 -0.58 7 7
USP6 0.012 0.036 -9999 0 -0.81 1 1
IQSEC1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.1 0.19 -9999 0 -0.45 118 118
ARRB2 0.01 0.003 -9999 0 -10000 0 0
mol:GTP 0.018 0.021 -9999 0 -0.16 1 1
ARRB1 0.011 0.037 -9999 0 -0.58 2 2
FBXO8 0.014 0 -9999 0 -10000 0 0
TSHR -0.009 0.13 -9999 0 -0.81 13 13
EGF -0.1 0.24 -9999 0 -0.58 101 101
somatostatin receptor activity 0 0 -9999 0 -0.001 14 14
ARAP2 0.007 0.063 -9999 0 -0.58 6 6
mol:GDP -0.013 0.077 -9999 0 -0.31 14 14
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 7 7
ITGA2B -0.069 0.25 -9999 0 -0.81 52 52
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.005 0.041 -9999 0 -0.48 1 1
ADAP1 0.012 0.026 -9999 0 -0.58 1 1
KIF13B 0.008 0.058 -9999 0 -0.58 5 5
HGF/MET -0.027 0.11 -9999 0 -0.5 28 28
PXN 0.014 0 -9999 0 -10000 0 0
ARF6/GTP -0.025 0.1 -9999 0 -0.31 15 15
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.085 0.16 -9999 0 -0.38 118 118
ADRB2 -0.032 0.16 -9999 0 -0.58 40 40
receptor agonist activity 0 0 -9999 0 0 17 17
actin filament binding 0 0 -9999 0 -0.001 14 14
SRC 0.014 0 -9999 0 -10000 0 0
ITGB3 -0.017 0.15 -9999 0 -0.73 21 21
GNAQ 0.013 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 8 8
ARF6/GDP 0.04 0.066 -9999 0 -0.39 2 2
ARF6/GDP/GULP/ACAP1 -0.1 0.15 -9999 0 -0.44 42 42
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.065 0.17 -9999 0 -0.5 64 64
ACAP1 -0.005 0.12 -9999 0 -0.81 12 12
ACAP2 0.012 0.036 -9999 0 -0.81 1 1
LHCGR/beta Arrestin2 0.002 0.006 -9999 0 -10000 0 0
EFNA1 0.012 0.036 -9999 0 -0.81 1 1
HGF -0.015 0.14 -9999 0 -0.65 22 22
CYTH3 0.012 0 -9999 0 -10000 0 0
CYTH2 0.01 0.002 -9999 0 -10000 0 0
NCK1 0.014 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 10 10
endosomal lumen acidification 0 0 -9999 0 -0.001 15 15
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.16 0.27 -9999 0 -0.58 149 149
GNAQ/ARNO 0.015 0.008 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 1 1
MET 0.005 0.08 -9999 0 -0.73 6 6
GNA14 -0.072 0.21 -9999 0 -0.58 75 75
GNA15 0.011 0.037 -9999 0 -0.58 2 2
GIT1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 10 10
GNA11 0.009 0.052 -9999 0 -0.58 4 4
LHCGR 0.002 0.005 -9999 0 -10000 0 0
AGTR1 -0.048 0.18 -9999 0 -0.59 51 51
desensitization of G-protein coupled receptor protein signaling pathway 0.002 0.006 -9999 0 -10000 0 0
IPCEF1/ARNO -0.049 0.14 -9999 0 -0.44 17 17
alphaIIb/beta3 Integrin -0.083 0.22 -9999 0 -0.62 70 70
Signaling events mediated by PTP1B

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
PDGFRB -0.12 0.3 -10000 0 -0.81 86 86
Jak2/Leptin Receptor -0.065 0.1 -10000 0 -0.43 6 6
PTP1B/AKT1 -0.018 0.081 0.23 1 -0.34 3 4
FYN 0.012 0.036 -10000 0 -0.81 1 1
p210 bcr-abl/PTP1B -0.028 0.09 0.23 2 -0.33 10 12
EGFR -0.017 0.14 -10000 0 -0.76 19 19
EGF/EGFR -0.1 0.15 -10000 0 -0.43 49 49
CSF1 0.007 0.063 -10000 0 -0.58 6 6
AKT1 0.014 0.001 -10000 0 -10000 0 0
INSR 0.012 0.026 -10000 0 -0.58 1 1
PTP1B/N-cadherin -0.082 0.19 0.23 1 -0.52 71 72
Insulin Receptor/Insulin -0.031 0.055 -10000 0 -0.42 2 2
HCK 0.006 0.076 -10000 0 -0.76 5 5
CRK 0.014 0 -10000 0 -10000 0 0
TYK2 -0.019 0.088 0.25 1 -0.37 7 8
EGF -0.1 0.24 -10000 0 -0.58 101 101
YES1 0.014 0 -10000 0 -10000 0 0
CAV1 -0.043 0.11 0.25 1 -0.37 18 19
TXN 0.01 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.013 0.083 -10000 0 -0.36 2 2
cell migration 0.028 0.09 0.33 10 -0.23 2 12
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.11 0.24 -10000 0 -0.58 104 104
ITGA2B -0.069 0.25 -10000 0 -0.81 52 52
CSF1R 0.01 0.045 -10000 0 -0.58 3 3
Prolactin Receptor/Prolactin -0.088 0.18 -10000 0 -0.44 107 107
FGR 0.012 0.036 -10000 0 -0.81 1 1
PTP1B/p130 Cas -0.019 0.085 0.23 1 -0.34 6 7
Crk/p130 Cas -0.011 0.081 -10000 0 -0.36 2 2
DOK1 -0.045 0.13 0.24 1 -0.35 38 39
JAK2 -0.057 0.12 -10000 0 -0.37 25 25
Jak2/Leptin Receptor/Leptin -0.072 0.11 -10000 0 -0.45 6 6
PIK3R1 0.011 0.037 -10000 0 -0.58 2 2
PTPN1 -0.028 0.091 0.23 2 -0.33 10 12
LYN 0.012 0.036 -10000 0 -0.81 1 1
CDH2 -0.096 0.28 -10000 0 -0.78 72 72
SRC 0.006 0.037 -10000 0 -10000 0 0
ITGB3 -0.017 0.15 -10000 0 -0.73 21 21
CAT1/PTP1B -0.11 0.14 0.26 1 -0.43 22 23
CAPN1 0.013 0.002 -10000 0 -10000 0 0
CSK 0.014 0 -10000 0 -10000 0 0
PI3K -0.022 0.054 -10000 0 -0.51 1 1
mol:H2O2 0 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.063 0.1 -10000 0 -0.42 3 3
negative regulation of transcription -0.056 0.12 -10000 0 -0.36 25 25
FCGR2A -0.028 0.18 -10000 0 -0.81 26 26
FER 0.008 0.037 -10000 0 -0.58 2 2
alphaIIb/beta3 Integrin -0.083 0.22 -10000 0 -0.62 70 70
BLK -0.1 0.28 -10000 0 -0.77 75 75
Insulin Receptor/Insulin/Shc -0.003 0.036 -10000 0 -0.53 2 2
RHOA 0.013 0.002 -10000 0 -10000 0 0
LEPR 0.01 0.045 -10000 0 -0.57 3 3
BCAR1 0.014 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.014 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.099 0.14 -10000 0 -0.42 33 33
PRL -0.004 0.079 -10000 0 -0.8 5 5
SOCS3 0.018 0.061 -10000 0 -1.3 1 1
SPRY2 0.003 0.078 -10000 0 -0.58 9 9
Insulin Receptor/Insulin/IRS1 -0.005 0.045 -10000 0 -0.53 2 2
CSF1/CSF1R -0.017 0.092 -10000 0 -0.4 7 7
Ras protein signal transduction 0.025 0.029 -10000 0 -10000 0 0
IRS1 0.01 0.045 -10000 0 -0.58 3 3
INS -0.002 0.05 -10000 0 -0.8 2 2
LEP -0.094 0.25 -10000 0 -0.67 80 80
STAT5B -0.035 0.086 0.2 1 -0.32 11 12
STAT5A -0.035 0.086 0.2 1 -0.32 10 11
GRB2 0.014 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.097 0.22 0.23 1 -0.55 90 91
CSN2 -0.024 0.089 -10000 0 -0.74 2 2
PIK3CA 0.014 0 -10000 0 -10000 0 0
LAT -0.015 0.087 -10000 0 -0.33 19 19
YBX1 0.021 0.002 -10000 0 -10000 0 0
LCK -0.005 0.12 -10000 0 -0.81 12 12
SHC1 0.014 0 -10000 0 -10000 0 0
NOX4 -0.14 0.32 -10000 0 -0.81 96 96
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.002 0.038 -9999 0 -0.62 2 2
VLDLR 0.002 0.081 -9999 0 -0.58 10 10
CRKL 0.012 0.036 -9999 0 -0.81 1 1
LRPAP1 0.014 0 -9999 0 -10000 0 0
FYN 0.012 0.036 -9999 0 -0.81 1 1
ITGA3 -0.016 0.15 -9999 0 -0.8 19 19
RELN/VLDLR/Fyn -0.079 0.15 -9999 0 -0.59 5 5
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.006 0.044 -9999 0 -0.45 2 2
AKT1 -0.032 0.12 -9999 0 -0.51 6 6
MAP2K7 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
DAB1 -0.016 0.14 -9999 0 -0.81 16 16
RELN/LRP8/DAB1 -0.091 0.17 -9999 0 -0.56 28 28
LRPAP1/LRP8 -0.012 0.085 -9999 0 -0.62 10 10
RELN/LRP8/DAB1/Fyn -0.085 0.16 -9999 0 -0.52 29 29
DAB1/alpha3/beta1 Integrin -0.093 0.16 -9999 0 -0.66 10 10
long-term memory -0.15 0.21 -9999 0 -0.68 33 33
DAB1/LIS1 -0.081 0.15 -9999 0 -0.68 9 9
DAB1/CRLK/C3G -0.078 0.15 -9999 0 -0.66 10 10
PIK3CA 0.014 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.082 0.15 -9999 0 -0.66 10 10
ARHGEF2 0.014 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.13 0.28 -9999 0 -0.68 106 106
CDK5R1 0.01 0.051 -9999 0 -0.81 2 2
RELN -0.11 0.24 -9999 0 -0.58 107 107
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
RELN/LRP8/Fyn -0.083 0.16 -9999 0 -0.61 13 13
GRIN2A/RELN/LRP8/DAB1/Fyn -0.16 0.22 -9999 0 -0.55 87 87
MAPK8 0.006 0.068 -9999 0 -0.58 7 7
RELN/VLDLR/DAB1 -0.087 0.16 -9999 0 -0.36 127 127
ITGB1 0.012 0.036 -9999 0 -0.81 1 1
MAP1B -0.067 0.19 -9999 0 -0.55 35 35
RELN/LRP8 -0.082 0.16 -9999 0 -0.61 12 12
GRIN2B/RELN/LRP8/DAB1/Fyn -0.088 0.16 -9999 0 -0.52 33 33
PI3K -0.002 0.026 -9999 0 -0.42 2 2
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.023 0.12 -9999 0 -0.61 20 20
RAP1A -0.029 0.16 -9999 0 -0.61 10 10
PAFAH1B1 0.014 0 -9999 0 -10000 0 0
MAPK8IP1 0.009 0.057 -9999 0 -0.73 3 3
CRLK/C3G -0.001 0.027 -9999 0 -0.62 1 1
GRIN2B -0.004 0.079 -9999 0 -0.81 5 5
NCK2 0.014 0 -9999 0 -10000 0 0
neuron differentiation -0.012 0.1 -9999 0 -0.39 7 7
neuron adhesion -0.03 0.17 -9999 0 -0.6 9 9
LRP8 -0.002 0.11 -9999 0 -0.81 10 10
GSK3B -0.022 0.12 -9999 0 -0.48 6 6
RELN/VLDLR/DAB1/Fyn -0.081 0.15 -9999 0 -0.53 21 21
MAP3K11 0.014 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.043 0.13 -9999 0 -0.54 6 6
CDK5 0.014 0 -9999 0 -10000 0 0
MAPT -0.24 0.27 -9999 0 -0.53 241 241
neuron migration -0.024 0.17 -9999 0 -0.54 10 10
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.012 0.1 -9999 0 -0.39 7 7
RELN/VLDLR -0.079 0.15 -9999 0 -0.57 14 14
ErbB2/ErbB3 signaling events

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
USP8 0.02 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.023 0.11 -9999 0 -0.51 2 2
NFATC4 -0.019 0.12 -9999 0 -0.52 4 4
ERBB2IP 0.014 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.014 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.039 0.14 -9999 0 -0.59 1 1
JUN 0.001 0.082 -9999 0 -0.37 5 5
HRAS 0.011 0.036 -9999 0 -0.81 1 1
DOCK7 -0.031 0.14 -9999 0 -0.56 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.079 0.17 -9999 0 -0.47 80 80
AKT1 0.011 0.003 -9999 0 -10000 0 0
BAD 0.021 0.003 -9999 0 -10000 0 0
MAPK10 -0.038 0.074 -9999 0 -0.31 6 6
mol:GTP -0.002 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.041 0.15 -9999 0 -0.66 1 1
RAF1 -0.022 0.12 -9999 0 -0.5 2 2
ErbB2/ErbB3/neuregulin 2 -0.19 0.17 -9999 0 -0.62 7 7
STAT3 0.001 0.003 -9999 0 -10000 0 0
cell migration 0.007 0.083 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.002 -9999 0 -10000 0 0
cell proliferation -0.17 0.3 -9999 0 -0.59 140 140
FOS -0.12 0.23 -9999 0 -0.47 88 88
NRAS 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.039 0.14 -9999 0 -0.59 1 1
MAPK3 -0.12 0.24 -9999 0 -0.59 24 24
MAPK1 -0.12 0.24 -9999 0 -0.55 33 33
JAK2 -0.032 0.14 -9999 0 -0.56 1 1
NF2 -0.002 0.005 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.026 0.12 -9999 0 -0.29 81 81
NRG1 -0.11 0.3 -9999 0 -0.79 82 82
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.017 0.11 -9999 0 -0.44 2 2
MAPK9 -0.028 0.061 -9999 0 -10000 0 0
ERBB2 -0.004 0.048 -9999 0 -0.63 3 3
ERBB3 0.003 0.073 -9999 0 -0.58 8 8
SHC1 0.013 0.002 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
apoptosis 0.008 0.011 -9999 0 -10000 0 0
STAT3 (dimer) 0.007 0.009 -9999 0 -10000 0 0
RNF41 0.026 0.008 -9999 0 -10000 0 0
FRAP1 0.01 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.04 0.087 -9999 0 -0.37 1 1
ErbB2/ErbB2/HSP90 (dimer) -0.003 0.041 -9999 0 -0.54 3 3
CHRNA1 -0.18 0.32 -9999 0 -0.59 186 186
myelination -0.007 0.12 -9999 0 -0.46 4 4
PPP3CB -0.029 0.13 -9999 0 -0.51 1 1
KRAS 0.01 0.051 -9999 0 -0.81 2 2
RAC1-CDC42/GDP -0.007 0.1 -9999 0 -0.59 1 1
NRG2 -0.32 0.29 -9999 0 -0.58 296 296
mol:GDP -0.025 0.12 -9999 0 -0.28 81 81
SOS1 0.013 0.001 -9999 0 -10000 0 0
MAP2K2 -0.03 0.13 -9999 0 -0.5 1 1
SRC 0.014 0 -9999 0 -10000 0 0
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.032 0.13 -9999 0 -0.56 1 1
MAP2K1 -0.1 0.2 -9999 0 -0.52 25 25
heart morphogenesis -0.039 0.14 -9999 0 -0.59 1 1
RAS family/GDP -0.016 0.11 -9999 0 -0.46 4 4
GRB2 0.013 0.001 -9999 0 -10000 0 0
PRKACA -0.004 0.009 -9999 0 -10000 0 0
CHRNE 0.011 0.029 -9999 0 -0.23 5 5
HSP90AA1 0.014 0 -9999 0 -10000 0 0
activation of caspase activity -0.011 0.003 -9999 0 -10000 0 0
nervous system development -0.039 0.14 -9999 0 -0.59 1 1
CDC42 0.014 0 -9999 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade -0.024 0.096 -9999 0 -0.4 31 31
EFNA5 -0.014 0.12 -9999 0 -0.58 24 24
FYN 0 0.099 -9999 0 -0.56 7 7
neuron projection morphogenesis -0.024 0.096 -9999 0 -0.4 31 31
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.024 0.097 -9999 0 -0.4 31 31
EPHA5 -0.003 0.094 -9999 0 -0.81 7 7
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.014 0 -9999 0 -10000 0 0
VLDLR 0.002 0.081 -9999 0 -0.58 10 10
LRPAP1 0.014 0 -9999 0 -10000 0 0
NUDC 0.014 0 -9999 0 -10000 0 0
RELN/LRP8 -0.082 0.16 -9999 0 -0.61 12 12
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.014 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.045 0.16 -9999 0 -0.56 12 12
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.016 0.14 -9999 0 -0.81 16 16
IQGAP1 0.014 0 -9999 0 -10000 0 0
PLA2G7 -0.31 0.4 -9999 0 -0.81 204 204
CALM1 0.014 0 -9999 0 -10000 0 0
DYNLT1 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.012 0.085 -9999 0 -0.62 10 10
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.011 0.037 -9999 0 -0.58 2 2
CDK5R1 0.01 0.051 -9999 0 -0.81 2 2
LIS1/Poliovirus Protein 3A 0.018 0 -9999 0 -10000 0 0
CDK5R2 -0.11 0.29 -9999 0 -0.81 75 75
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.095 0.18 -9999 0 -0.39 127 127
YWHAE 0.014 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.045 0.16 -9999 0 -0.54 18 18
MAP1B -0.006 0.041 -9999 0 -0.3 10 10
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.025 0.14 -9999 0 -0.69 4 4
RELN -0.11 0.24 -9999 0 -0.58 107 107
PAFAH/LIS1 -0.19 0.27 -9999 0 -0.53 204 204
LIS1/CLIP170 0.027 0.023 -9999 0 -0.34 2 2
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.064 0.1 -9999 0 -0.53 2 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.033 0.13 -9999 0 -0.56 7 7
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.056 0.17 -9999 0 -0.59 18 18
LIS1/IQGAP1 0.028 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.024 0 -9999 0 -10000 0 0
PAFAH1B3 0.009 0.062 -9999 0 -0.81 3 3
PAFAH1B2 0.011 0.037 -9999 0 -0.58 2 2
MAP1B/LIS1/Dynein heavy chain 0.023 0.03 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.08 0.13 -9999 0 -0.6 8 8
LRP8 -0.002 0.11 -9999 0 -0.81 10 10
NDEL1/Katanin 60 -0.045 0.16 -9999 0 -0.54 18 18
P39/CDK5 -0.094 0.22 -9999 0 -0.76 18 18
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0 -9999 0 -10000 0 0
CDK5 -0.033 0.15 -9999 0 -0.52 12 12
PPP2R5D 0.014 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.001 0.018 -9999 0 -0.3 2 2
CSNK2A1 0.014 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.078 0.15 -9999 0 -0.52 20 20
RELN/VLDLR -0.079 0.15 -9999 0 -0.57 14 14
CDC42 0 0 -9999 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.046 0.18 -9999 0 -0.4 95 95
positive regulation of NF-kappaB transcription factor activity 0 0.002 -9999 0 -10000 0 0
CRKL 0.012 0.036 -9999 0 -0.81 1 1
STAT1 (dimer)/Cbp/p300 -0.083 0.18 -9999 0 -0.72 18 18
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.013 0.029 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.07 0.089 -9999 0 -0.33 10 10
CaM/Ca2+ -0.075 0.15 -9999 0 -10000 0 0
RAP1A 0.014 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.06 0.22 -9999 0 -0.69 27 27
AKT1 -0.019 0.16 -9999 0 -10000 0 0
MAP2K1 -0.023 0.16 -9999 0 -10000 0 0
MAP3K11 -0.036 0.17 -9999 0 -10000 0 0
IFNGR1 0.008 0.016 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.2 0.23 -9999 0 -0.62 83 83
Rap1/GTP -0.057 0.11 -9999 0 -10000 0 0
CRKL/C3G -0.001 0.027 -9999 0 -0.62 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.089 0.17 -9999 0 -0.43 96 96
CEBPB 0.015 0.15 -9999 0 -10000 0 0
STAT3 0.014 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.11 0.21 -9999 0 -0.91 11 11
STAT1 -0.059 0.22 -9999 0 -0.69 27 27
CALM1 0.014 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.15 0.33 -9999 0 -0.8 106 106
PIK3CA 0.014 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.048 0.21 -9999 0 -0.76 18 18
CEBPB/PTGES2/Cbp/p300 -0.035 0.067 -9999 0 -10000 0 0
mol:Ca2+ -0.081 0.16 -9999 0 -0.4 95 95
MAPK3 -0.004 0.14 -9999 0 -10000 0 0
STAT1 (dimer) -0.093 0.12 -9999 0 -0.46 10 10
MAPK1 -0.004 0.14 -9999 0 -10000 0 0
JAK2 0.006 0.03 -9999 0 -0.57 1 1
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
JAK1 0.008 0.016 -9999 0 -10000 0 0
CAMK2D 0.014 0 -9999 0 -10000 0 0
DAPK1 0.027 0.12 -9999 0 -0.57 5 5
SMAD7 -0.003 0.073 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.068 0.14 -9999 0 -10000 0 0
PI3K -0.073 0.14 -9999 0 -10000 0 0
IFNG -0.15 0.33 -9999 0 -0.8 106 106
apoptosis 0.01 0.099 -9999 0 -0.45 4 4
CAMK2G 0.014 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.014 0 -9999 0 -10000 0 0
CAMK2A -0.13 0.26 -9999 0 -0.58 125 125
CAMK2B -0.15 0.27 -9999 0 -0.58 146 146
FRAP1 -0.016 0.15 -9999 0 -10000 0 0
PRKCD -0.018 0.16 -9999 0 -10000 0 0
RAP1B 0.012 0.036 -9999 0 -0.81 1 1
negative regulation of cell growth -0.07 0.089 -9999 0 -0.33 10 10
PTPN2 0.012 0.036 -9999 0 -0.81 1 1
EP300 0.013 0.026 -9999 0 -0.57 1 1
IRF1 -0.017 0.18 -9999 0 -0.51 30 30
STAT1 (dimer)/PIASy -0.086 0.19 -9999 0 -0.76 18 18
SOCS1 -0.034 0.16 -9999 0 -0.65 33 33
mol:GDP -0.066 0.13 -9999 0 -10000 0 0
CASP1 -0.003 0.074 -9999 0 -0.34 1 1
PTGES2 0.014 0 -9999 0 -10000 0 0
IRF9 0.038 0.055 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.071 0.14 -9999 0 -10000 0 0
RAP1/GDP -0.058 0.11 -9999 0 -10000 0 0
CBL -0.037 0.17 -9999 0 -10000 0 0
MAP3K1 -0.035 0.17 -9999 0 -10000 0 0
PIAS1 0.014 0 -9999 0 -10000 0 0
PIAS4 0.014 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.07 0.089 -9999 0 -0.33 10 10
PTPN11 -0.047 0.18 -9999 0 -0.4 95 95
CREBBP 0.014 0.001 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.012 0.036 -9999 0 -0.81 1 1
EGFR -0.015 0.15 -9999 0 -0.76 19 19
EGF/EGFR -0.075 0.14 -9999 0 -0.48 25 25
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.07 0.13 -9999 0 -0.48 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.007 0.072 -9999 0 -0.72 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.1 0.24 -9999 0 -0.58 101 101
EGF/EGFR dimer/SHC -0.085 0.16 -9999 0 -0.55 18 18
mol:GDP -0.069 0.13 -9999 0 -0.47 17 17
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.008 0.058 -9999 0 -0.58 5 5
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.064 0.12 -9999 0 -0.43 18 18
SHC1 0.014 0 -9999 0 -10000 0 0
HRAS/GDP -0.065 0.12 -9999 0 -0.56 3 3
FRAP1 -0.036 0.14 -9999 0 -0.45 17 17
EGF/EGFR dimer -0.1 0.19 -9999 0 -0.45 118 118
SOS1 0.014 0 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.009 0.067 -9999 0 -0.48 10 10
Regulation of Androgen receptor activity

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
HDAC1 0.023 0.003 -9999 0 -10000 0 0
SMARCC1 0.01 0.011 -9999 0 -10000 0 0
REL 0.006 0.077 -9999 0 -0.57 9 9
HDAC7 -0.066 0.16 -9999 0 -0.57 20 20
JUN 0.011 0.005 -9999 0 -10000 0 0
EP300 0.012 0.026 -9999 0 -0.58 1 1
KAT2B -0.016 0.13 -9999 0 -0.58 26 26
KAT5 0.014 0.001 -9999 0 -10000 0 0
MAPK14 -0.008 0.1 -9999 0 -0.44 26 26
FOXO1 0.013 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.08 0.17 -9999 0 -0.61 21 21
MAP2K6 -0.022 0.13 -9999 0 -0.59 26 26
BRM/BAF57 -0.001 0.018 -9999 0 -0.42 1 1
MAP2K4 0.008 0.008 -9999 0 -10000 0 0
SMARCA2 0.01 0.026 -9999 0 -0.58 1 1
PDE9A -0.088 0.2 -9999 0 -1.2 15 15
NCOA2 -0.034 0.16 -9999 0 -0.58 42 42
CEBPA 0.011 0.045 -9999 0 -0.58 3 3
EHMT2 0.011 0.005 -9999 0 -10000 0 0
cell proliferation -0.058 0.17 -9999 0 -0.55 11 11
NR0B1 -0.032 0.17 -9999 0 -0.81 24 24
EGR1 -0.017 0.13 -9999 0 -0.58 25 25
RXRs/9cRA -0.042 0.11 -9999 0 -0.48 8 8
AR/RACK1/Src -0.036 0.12 -9999 0 -0.49 13 13
AR/GR -0.064 0.15 -9999 0 -0.53 18 18
GNB2L1 0.014 0.001 -9999 0 -10000 0 0
PKN1 0.01 0.051 -9999 0 -0.81 2 2
RCHY1 0.014 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.008 0.055 -9999 0 -0.44 7 7
T-DHT/AR/TIF2/CARM1 -0.054 0.16 -9999 0 -0.68 10 10
SRC -0.001 0.095 -9999 0 -0.6 2 2
NR3C1 0.014 0 -9999 0 -10000 0 0
KLK3 -0.28 0.45 -9999 0 -1.2 95 95
APPBP2 0.008 0.008 -9999 0 -10000 0 0
TRIM24 0.01 0.026 -9999 0 -0.58 1 1
T-DHT/AR/TIP60 -0.036 0.13 -9999 0 -0.52 18 18
TMPRSS2 -0.51 0.55 -9999 0 -1.1 244 244
RXRG -0.064 0.2 -9999 0 -0.6 64 64
mol:9cRA -0.001 0.003 -9999 0 -10000 0 0
RXRA 0.013 0.001 -9999 0 -10000 0 0
RXRB 0.013 0.001 -9999 0 -10000 0 0
CARM1 0.014 0.002 -9999 0 -10000 0 0
NR2C2 0.005 0.068 -9999 0 -0.58 7 7
KLK2 -0.037 0.16 -9999 0 -0.64 18 18
AR -0.08 0.17 -9999 0 -0.48 32 32
SENP1 0.013 0.001 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
MDM2 0.018 0.012 -9999 0 -10000 0 0
SRY -0.034 0.16 -9999 0 -0.58 39 39
GATA2 0.009 0.057 -9999 0 -0.73 3 3
MYST2 0.013 0.026 -9999 0 -0.58 1 1
HOXB13 -0.31 0.4 -9999 0 -0.82 197 197
T-DHT/AR/RACK1/Src -0.028 0.12 -9999 0 -0.49 18 18
positive regulation of transcription 0.009 0.057 -9999 0 -0.73 3 3
DNAJA1 0.008 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.004 -9999 0 -10000 0 0
NCOA1 0.017 0.008 -9999 0 -10000 0 0
SPDEF -0.15 0.28 -9999 0 -0.61 135 135
T-DHT/AR/TIF2 -0.033 0.15 -9999 0 -0.6 15 15
T-DHT/AR/Hsp90 -0.038 0.13 -9999 0 -0.52 18 18
GSK3B 0.01 0.006 -9999 0 -10000 0 0
NR2C1 0.015 0.002 -9999 0 -10000 0 0
mol:T-DHT -0.012 0.1 -9999 0 -0.65 2 2
SIRT1 0.012 0.026 -9999 0 -0.58 1 1
ZMIZ2 0.018 0.011 -9999 0 -10000 0 0
POU2F1 0.016 0.022 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.075 0.15 -9999 0 -0.54 33 33
CREBBP 0.013 0.001 -9999 0 -10000 0 0
SMARCE1 0.011 0.005 -9999 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.003 0.096 -9999 0 -0.64 11 11
PDGF/PDGFRA/CRKL -0.011 0.072 -9999 0 -0.47 12 12
positive regulation of JUN kinase activity -0.007 0.049 -9999 0 -0.45 3 3
CRKL 0.012 0.036 -9999 0 -0.81 1 1
PDGF/PDGFRA/Caveolin-3 -0.1 0.19 -9999 0 -0.44 121 121
AP1 -0.13 0.32 -9999 0 -0.95 67 67
mol:IP3 0.01 0.075 -9999 0 -0.47 11 11
PLCG1 0.01 0.075 -9999 0 -0.47 11 11
PDGF/PDGFRA/alphaV Integrin -0.015 0.092 -9999 0 -0.53 15 15
RAPGEF1 0.014 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0.01 0.075 -9999 0 -0.47 11 11
CAV3 -0.12 0.24 -9999 0 -0.58 113 113
CAV1 -0.046 0.21 -9999 0 -0.81 38 38
SHC/Grb2/SOS1 -0.007 0.05 -9999 0 -0.46 3 3
PDGF/PDGFRA/Shf -0.017 0.091 -9999 0 -0.48 18 18
FOS -0.084 0.33 -9999 0 -0.94 67 67
JUN -0.008 0.02 -9999 0 -10000 0 0
oligodendrocyte development -0.015 0.091 -9999 0 -0.52 15 15
GRB2 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
mol:DAG 0.01 0.075 -9999 0 -0.47 11 11
PDGF/PDGFRA -0.003 0.096 -9999 0 -0.64 11 11
actin cytoskeleton reorganization -0.011 0.072 -9999 0 -0.45 13 13
SRF 0.025 0.009 -9999 0 -10000 0 0
SHC1 0.014 0 -9999 0 -10000 0 0
PI3K -0.009 0.06 -9999 0 -0.47 4 4
PDGF/PDGFRA/Crk/C3G -0.008 0.056 -9999 0 -0.51 3 3
JAK1 0.013 0.071 -9999 0 -0.46 11 11
ELK1/SRF 0.031 0.059 -9999 0 -0.42 4 4
SHB 0.011 0.037 -9999 0 -0.58 2 2
SHF 0.003 0.077 -9999 0 -0.58 9 9
CSNK2A1 0.008 0.02 -9999 0 -10000 0 0
GO:0007205 0.01 0.076 -9999 0 -0.48 11 11
SOS1 0.014 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.007 0.049 -9999 0 -0.45 3 3
PDGF/PDGFRA/SHB -0.011 0.072 -9999 0 -0.45 13 13
PDGF/PDGFRA/Caveolin-1 -0.056 0.18 -9999 0 -0.59 49 49
ITGAV 0.006 0.076 -9999 0 -0.76 5 5
ELK1 0.013 0.077 -9999 0 -0.43 12 12
PIK3CA 0.014 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.01 0.067 -9999 0 -0.46 11 11
JAK-STAT cascade 0.013 0.07 -9999 0 -0.46 11 11
cell proliferation -0.017 0.091 -9999 0 -0.48 18 18
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.1 0.28 -9999 0 -0.72 77 77
MKNK1 0.014 0 -9999 0 -10000 0 0
MAPK14 -0.043 0.12 -9999 0 -0.4 13 13
ATF2/c-Jun -0.01 0.095 -9999 0 -10000 0 0
MAPK11 -0.043 0.12 -9999 0 -0.4 13 13
MITF -0.051 0.17 -9999 0 -0.57 23 23
MAPKAPK5 -0.037 0.14 -9999 0 -0.48 13 13
KRT8 -0.12 0.23 -9999 0 -0.63 52 52
MAPKAPK3 0.014 0 -9999 0 -10000 0 0
MAPKAPK2 0.014 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.063 0.18 -9999 0 -0.64 13 13
CEBPB -0.037 0.14 -9999 0 -0.48 13 13
SLC9A1 -0.037 0.14 -9999 0 -0.48 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.031 0.14 -9999 0 -0.47 13 13
p38alpha-beta/MNK1 -0.036 0.15 -9999 0 -0.52 13 13
JUN -0.009 0.094 -9999 0 -10000 0 0
PPARGC1A -0.17 0.25 -9999 0 -0.69 66 66
USF1 -0.037 0.14 -9999 0 -0.48 13 13
RAB5/GDP/GDI1 -0.05 0.085 -9999 0 -0.4 2 2
NOS2 -0.11 0.3 -9999 0 -0.73 89 89
DDIT3 -0.047 0.16 -9999 0 -0.52 18 18
RAB5A 0.014 0 -9999 0 -10000 0 0
HSPB1 -0.019 0.12 -9999 0 -0.39 13 13
p38alpha-beta/HBP1 -0.036 0.15 -9999 0 -0.52 13 13
CREB1 -0.033 0.15 -9999 0 -0.47 13 13
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.024 0.13 -9999 0 -0.46 13 13
RPS6KA4 -0.037 0.14 -9999 0 -0.48 13 13
PLA2G4A -0.045 0.16 -9999 0 -0.54 20 20
GDI1 -0.037 0.14 -9999 0 -0.48 13 13
TP53 -0.052 0.18 -9999 0 -0.59 15 15
RPS6KA5 -0.039 0.15 -9999 0 -0.48 13 13
ESR1 -0.057 0.17 -9999 0 -0.55 24 24
HBP1 0.014 0 -9999 0 -10000 0 0
MEF2C -0.045 0.15 -9999 0 -0.5 15 15
MEF2A -0.037 0.14 -9999 0 -0.48 13 13
EIF4EBP1 -0.035 0.15 -9999 0 -0.47 13 13
KRT19 -0.17 0.22 -9999 0 -0.64 47 47
ELK4 -0.037 0.14 -9999 0 -0.48 13 13
ATF6 -0.037 0.14 -9999 0 -0.48 13 13
ATF1 -0.033 0.15 -9999 0 -0.47 13 13
p38alpha-beta/MAPKAPK2 -0.036 0.15 -9999 0 -0.52 13 13
p38alpha-beta/MAPKAPK3 -0.036 0.15 -9999 0 -0.52 13 13
Signaling events mediated by HDAC Class III

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
EP300 0.012 0.026 -10000 0 -0.58 1 1
HDAC4 0.014 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.014 0.14 0.61 29 -10000 0 29
CDKN1A 0.001 0.012 -10000 0 -10000 0 0
KAT2B -0.016 0.13 -10000 0 -0.58 26 26
BAX 0.014 0 -10000 0 -10000 0 0
FOXO3 0.001 0.02 0.44 1 -10000 0 1
FOXO1 0.014 0 -10000 0 -10000 0 0
FOXO4 0.022 0.024 -10000 0 -0.29 3 3
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.014 0 -10000 0 -10000 0 0
TAT -0.002 0.087 -10000 0 -0.81 6 6
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.079 0.19 -10000 0 -0.44 111 111
PPARGC1A -0.19 0.28 -10000 0 -0.58 181 181
FHL2 0.011 0.037 -10000 0 -0.58 2 2
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 -0.001 0.018 -10000 0 -0.42 1 1
HIST2H4A -0.014 0.15 -10000 0 -0.61 29 29
SIRT1/FOXO3a 0 0.02 0.29 1 -0.35 1 2
SIRT1 -0.001 0.025 -10000 0 -0.58 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 -0.001 0.015 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.012 0.053 -10000 0 -10000 0 0
apoptosis 0.001 0.015 -10000 0 -10000 0 0
SIRT1/PGC1A -0.12 0.17 -10000 0 -0.36 181 181
p53/SIRT1 -0.004 0.041 -10000 0 -0.42 5 5
SIRT1/FOXO4 -0.002 0.024 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.002 0.024 -10000 0 -10000 0 0
HIST1H1E 0.009 0.067 -10000 0 -0.28 26 26
SIRT1/p300 -0.002 0.026 -10000 0 -0.42 2 2
muscle cell differentiation 0.078 0.15 0.6 8 -10000 0 8
TP53 -0.004 0.05 -10000 0 -0.58 4 4
KU70/SIRT1/BAX -0.001 0.015 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
MEF2D 0.014 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.008 0.069 -10000 0 -0.59 7 7
ACSS2 0.021 0.019 -10000 0 -0.42 1 1
SIRT1/PCAF/MYOD -0.079 0.15 -10000 0 -0.6 8 8
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0 0.1 -10000 0 -0.78 9 9
positive regulation of NF-kappaB transcription factor activity -0.03 0.13 -10000 0 -0.59 26 26
MAP2K4 0.011 0.096 -10000 0 -10000 0 0
IKBKB 0.014 0 -10000 0 -10000 0 0
TNFRSF10B 0.014 0 -10000 0 -10000 0 0
TNFRSF10A 0.011 0.037 -10000 0 -0.58 2 2
SMPD1 0.016 0.035 -10000 0 -0.25 8 8
IKBKG 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.012 0.14 -10000 0 -0.78 17 17
TRAIL/TRAILR2 -0.01 0.078 -10000 0 -0.6 9 9
TRAIL/TRAILR3 -0.027 0.12 -10000 0 -0.59 24 24
TRAIL/TRAILR1 -0.012 0.082 -10000 0 -0.56 11 11
TRAIL/TRAILR4 -0.03 0.13 -10000 0 -0.59 26 26
TRAIL/TRAILR1/DAP3/GTP -0.009 0.065 -10000 0 -0.49 8 8
IKK complex -0.024 0.06 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0.014 0.081 -10000 0 -0.59 9 9
MAP3K1 0.003 0.1 -10000 0 -10000 0 0
TRAILR4 (trimer) -0.012 0.14 -10000 0 -0.78 17 17
TRADD 0.014 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.011 0.036 -10000 0 -0.58 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.004 0.1 -10000 0 -10000 0 0
CFLAR 0.014 0 -10000 0 -10000 0 0
MAPK1 0.014 0.081 -10000 0 -0.59 9 9
TRAIL/TRAILR1/FADD/TRADD/RIP -0.061 0.15 -10000 0 -0.45 68 68
mol:ceramide 0.016 0.035 -10000 0 -0.25 8 8
FADD -0.081 0.26 -10000 0 -0.81 60 60
MAPK8 0.014 0.1 -10000 0 -0.5 3 3
TRAF2 0.004 0.088 -10000 0 -0.81 6 6
TRAILR3 (trimer) -0.009 0.13 -10000 0 -0.78 15 15
CHUK 0.014 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.072 0.18 -10000 0 -0.53 68 68
DAP3 0.014 0 -10000 0 -10000 0 0
CASP10 -0.05 0.16 0.28 14 -0.44 65 79
JNK cascade -0.03 0.13 -10000 0 -0.59 26 26
TRAIL (trimer) 0 0.1 -10000 0 -0.78 9 9
TNFRSF10C -0.009 0.13 -10000 0 -0.78 15 15
TRAIL/TRAILR1/DAP3/GTP/FADD -0.062 0.16 -10000 0 -0.46 68 68
TRAIL/TRAILR2/FADD -0.07 0.18 -10000 0 -0.53 68 68
cell death 0.016 0.035 -10000 0 -0.25 8 8
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.003 0.1 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.014 0 -10000 0 -10000 0 0
CASP8 -0.001 0.021 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.06 0.15 -10000 0 -0.45 68 68
Regulation of Telomerase

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
Telomerase catalytic core complex -0.14 0.3 -9999 0 -0.7 88 88
RAD9A 0.014 0 -9999 0 -10000 0 0
AP1 -0.039 0.15 -9999 0 -0.42 67 67
IFNAR2 0.012 0.007 -9999 0 -10000 0 0
AKT1 0 0.063 -9999 0 -0.34 2 2
ER alpha/Oestrogen -0.02 0.12 -9999 0 -0.52 28 28
NFX1/SIN3/HDAC complex 0.039 0.027 -9999 0 -10000 0 0
EGF -0.1 0.24 -9999 0 -0.58 101 101
SMG5 0.014 0 -9999 0 -10000 0 0
SMG6 0.014 0 -9999 0 -10000 0 0
SP3/HDAC2 0.018 0.011 -9999 0 -10000 0 0
TERT/c-Abl -0.16 0.26 -9999 0 -0.66 85 85
SAP18 0.012 0.004 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.16 0.33 -9999 0 -0.81 109 109
WRN 0.014 0 -9999 0 -10000 0 0
SP1 0.013 0.007 -9999 0 -10000 0 0
SP3 0.011 0.006 -9999 0 -10000 0 0
TERF2IP 0.014 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.14 0.23 -9999 0 -0.66 38 38
Mad/Max 0.013 0.044 -9999 0 -0.42 5 5
TERT -0.15 0.31 -9999 0 -0.72 88 88
CCND1 -0.13 0.29 -9999 0 -0.73 45 45
MAX 0.011 0.006 -9999 0 -10000 0 0
RBBP7 0.012 0.004 -9999 0 -10000 0 0
RBBP4 0.011 0.026 -9999 0 -0.58 1 1
TERF2 0 0.004 -9999 0 -10000 0 0
PTGES3 0.014 0 -9999 0 -10000 0 0
SIN3A 0.012 0.004 -9999 0 -10000 0 0
Telomerase/911 0.024 0.042 -9999 0 -10000 0 0
CDKN1B -0.078 0.22 -9999 0 -0.52 106 106
RAD1 0.014 0 -9999 0 -10000 0 0
XRCC5 0.014 0 -9999 0 -10000 0 0
XRCC6 0.014 0 -9999 0 -10000 0 0
SAP30 0.01 0.036 -9999 0 -0.81 1 1
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.011 0.006 -9999 0 -10000 0 0
JUN 0.012 0.006 -9999 0 -10000 0 0
E6 -0.002 0.005 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.009 0.006 -9999 0 -10000 0 0
FOS -0.065 0.2 -9999 0 -0.58 67 67
IFN-gamma/IRF1 -0.12 0.24 -9999 0 -0.61 106 106
PARP2 0.014 0 -9999 0 -10000 0 0
BLM 0.01 0.051 -9999 0 -0.81 2 2
Telomerase -0.007 0.1 -9999 0 -0.43 13 13
IRF1 0.015 0.008 -9999 0 -10000 0 0
ESR1 -0.025 0.16 -9999 0 -0.68 28 28
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.016 -9999 0 -0.37 1 1
ubiquitin-dependent protein catabolic process 0.043 0.029 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.044 0.029 -9999 0 -10000 0 0
HDAC1 0.012 0.004 -9999 0 -10000 0 0
HDAC2 0.013 0.007 -9999 0 -10000 0 0
ATM -0.001 0.019 -9999 0 -0.44 1 1
SMAD3 0.021 0.052 -9999 0 -0.56 4 4
ABL1 0.014 0 -9999 0 -10000 0 0
MXD1 0.006 0.058 -9999 0 -0.58 5 5
MRE11A 0.014 0 -9999 0 -10000 0 0
HUS1 0.012 0.036 -9999 0 -0.81 1 1
RPS6KB1 0.014 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.14 0.25 -9999 0 -0.68 45 45
NR2F2 0.015 0.037 -9999 0 -0.79 1 1
MAPK3 0.013 0.029 -9999 0 -0.61 1 1
MAPK1 0.013 0.029 -9999 0 -0.61 1 1
TGFB1/TGF beta receptor Type II 0.01 0.062 -9999 0 -0.8 3 3
NFKB1 0.014 0 -9999 0 -10000 0 0
HNRNPC 0.014 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.019 -9999 0 -0.44 1 1
NBN 0.014 0 -9999 0 -10000 0 0
EGFR -0.016 0.15 -9999 0 -0.76 19 19
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.095 0.2 -9999 0 -0.45 118 118
MYC 0.011 0.006 -9999 0 -10000 0 0
IL2 0.001 0.038 -9999 0 -0.8 1 1
KU 0 0 -9999 0 -10000 0 0
RAD50 0.014 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
TGFB1 0.01 0.062 -9999 0 -0.8 3 3
TRF2/BLM -0.002 0.036 -9999 0 -0.58 2 2
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.15 0.26 -9999 0 -0.68 68 68
SP1/HDAC2 0.019 0.015 -9999 0 -10000 0 0
PINX1 0.014 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.14 0.23 -9999 0 -0.67 36 36
Smad3/Myc 0.026 0.045 -9999 0 -0.48 4 4
911 complex -0.001 0.023 -9999 0 -0.53 1 1
IFNG -0.15 0.33 -9999 0 -0.8 106 106
Telomerase/PinX1 -0.14 0.23 -9999 0 -0.68 32 32
Telomerase/AKT1/mTOR/p70S6K 0 0.075 -9999 0 -10000 0 0
SIN3B 0.012 0.004 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.14 0.23 -9999 0 -0.67 34 34
response to DNA damage stimulus 0.003 0.006 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0.004 -9999 0 -10000 0 0
TRF2/WRN 0 0.004 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.14 0.23 -9999 0 -0.66 38 38
E2F1 -0.05 0.22 -9999 0 -0.82 39 39
ZNFX1 0.012 0.004 -9999 0 -10000 0 0
PIF1 -0.035 0.19 -9999 0 -0.81 31 31
NCL 0.014 0 -9999 0 -10000 0 0
DKC1 0.014 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.056 0.19 -9999 0 -0.58 61 61
GNB1/GNG2 -0.059 0.13 -9999 0 -0.65 11 11
mol:DAG -0.009 0.13 -9999 0 -0.6 10 10
PLCG1 -0.01 0.14 -9999 0 -0.62 10 10
YES1 -0.028 0.15 -9999 0 -0.68 11 11
FZD3 0.006 0.068 -9999 0 -0.58 7 7
FZD6 0.009 0.057 -9999 0 -0.73 3 3
G protein -0.011 0.14 -9999 0 -0.61 11 11
MAP3K7 -0.057 0.16 -9999 0 -0.66 8 8
mol:Ca2+ -0.008 0.13 -9999 0 -0.57 10 10
mol:IP3 -0.009 0.13 -9999 0 -0.6 10 10
NLK -0.003 0.007 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
CAMK2A -0.07 0.18 -9999 0 -0.52 32 32
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.039 0.16 -9999 0 -0.73 11 11
CSNK1A1 0.014 0 -9999 0 -10000 0 0
GNAS -0.028 0.15 -9999 0 -0.68 11 11
GO:0007205 -0.008 0.13 -9999 0 -0.58 10 10
WNT6 -0.052 0.22 -9999 0 -0.76 44 44
WNT4 -0.008 0.12 -9999 0 -0.63 17 17
NFAT1/CK1 alpha -0.081 0.15 -9999 0 -0.57 26 26
GNG2 0.014 0 -9999 0 -10000 0 0
WNT5A 0.005 0.072 -9999 0 -0.61 7 7
WNT11 -0.075 0.24 -9999 0 -0.74 61 61
CDC42 -0.018 0.14 -9999 0 -0.64 11 11
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.012 0.036 -9999 0 -0.81 1 1
LAT2 -0.054 0.14 -9999 0 -0.49 20 20
AP1 -0.091 0.12 -9999 0 -0.53 13 13
mol:PIP3 -0.07 0.19 -9999 0 -0.55 27 27
IKBKB -0.026 0.11 -9999 0 -0.34 6 6
AKT1 -0.054 0.16 -9999 0 -0.64 6 6
IKBKG -0.026 0.11 -9999 0 -0.34 6 6
MS4A2 -0.012 0.12 -9999 0 -0.6 20 20
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.013 0.001 -9999 0 -10000 0 0
MAP3K1 -0.018 0.12 -9999 0 -0.48 5 5
mol:Ca2+ -0.05 0.15 -9999 0 -0.4 27 27
LYN 0.012 0.037 -9999 0 -0.82 1 1
CBLB -0.052 0.14 -9999 0 -0.48 19 19
SHC1 0.014 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.018 0.079 -9999 0 -0.8 1 1
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.011 0.037 -9999 0 -0.58 2 2
PLD2 -0.091 0.18 -9999 0 -0.63 17 17
PTPN13 -0.048 0.14 -9999 0 -0.5 17 17
PTPN11 0.009 0.009 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.023 0.13 -9999 0 -0.42 3 3
SYK 0.01 0.046 -9999 0 -0.59 3 3
GRB2 0.013 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.12 0.16 -9999 0 -0.56 31 31
LAT -0.064 0.16 -9999 0 -0.53 31 31
PAK2 -0.029 0.13 -9999 0 -0.53 6 6
NFATC2 -0.12 0.23 -9999 0 -0.7 61 61
HRAS -0.04 0.14 -9999 0 -0.46 24 24
GAB2 0.01 0.045 -9999 0 -0.58 3 3
PLA2G1B 0.035 0.019 -9999 0 -10000 0 0
Fc epsilon R1 -0.15 0.21 -9999 0 -0.67 25 25
Antigen/IgE/Fc epsilon R1 -0.14 0.19 -9999 0 -0.62 26 26
mol:GDP -0.046 0.14 -9999 0 -0.48 24 24
JUN 0.014 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
FOS -0.063 0.2 -9999 0 -0.58 67 67
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.087 0.13 -9999 0 -0.48 24 24
CHUK -0.026 0.11 -9999 0 -0.34 6 6
KLRG1 -0.06 0.14 -9999 0 -0.47 25 25
VAV1 -0.058 0.14 -9999 0 -0.49 24 24
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.052 0.14 -9999 0 -0.48 19 19
negative regulation of mast cell degranulation -0.049 0.14 -9999 0 -0.5 13 13
BTK -0.05 0.14 -9999 0 -0.48 20 20
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.085 0.18 -9999 0 -0.63 24 24
GAB2/PI3K/SHP2 -0.1 0.15 -9999 0 -0.67 8 8
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.072 0.16 -9999 0 -0.59 19 19
RAF1 0.023 0.023 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.13 0.18 -9999 0 -0.62 23 23
FCER1G -0.007 0.12 -9999 0 -0.81 12 12
FCER1A -0.2 0.29 -9999 0 -0.58 186 186
Antigen/IgE/Fc epsilon R1/Fyn -0.13 0.18 -9999 0 -0.6 25 25
MAPK3 0.034 0.019 -9999 0 -10000 0 0
MAPK1 0.034 0.019 -9999 0 -10000 0 0
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 0 0.088 -9999 0 -0.65 7 7
DUSP1 -0.017 0.13 -9999 0 -0.58 27 27
NF-kappa-B/RelA -0.037 0.048 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.051 0.14 -9999 0 -0.49 16 16
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.071 0.11 -9999 0 -0.54 7 7
FER -0.053 0.14 -9999 0 -0.48 21 21
RELA 0.014 0 -9999 0 -10000 0 0
ITK -0.032 0.077 -9999 0 -0.41 17 17
SOS1 0.014 0 -9999 0 -10000 0 0
PLCG1 -0.046 0.15 -9999 0 -0.48 24 24
cytokine secretion -0.027 0.035 -9999 0 -10000 0 0
SPHK1 -0.065 0.16 -9999 0 -0.52 33 33
PTK2 -0.053 0.14 -9999 0 -0.52 16 16
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.11 0.16 -9999 0 -0.56 24 24
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.062 0.18 -9999 0 -0.52 21 21
MAP2K2 0.03 0.02 -9999 0 -10000 0 0
MAP2K1 0.03 0.02 -9999 0 -10000 0 0
MAP2K7 0.014 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.082 0.12 -9999 0 -0.44 25 25
MAP2K4 0.019 0.009 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.14 0.19 -9999 0 -0.62 30 30
mol:Choline -0.089 0.18 -9999 0 -0.62 17 17
SHC/Grb2/SOS1 -0.07 0.11 -9999 0 -0.45 19 19
FYN 0.012 0.036 -9999 0 -0.81 1 1
DOK1 0.012 0.036 -9999 0 -0.81 1 1
PXN -0.042 0.13 -9999 0 -0.48 15 15
HCLS1 -0.055 0.14 -9999 0 -0.49 23 23
PRKCB -0.049 0.15 -9999 0 -0.41 22 22
FCGR2B 0.006 0.068 -9999 0 -0.58 7 7
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.05 0.14 -9999 0 -0.51 13 13
LCP2 0.008 0.062 -9999 0 -0.81 3 3
PLA2G4A -0.07 0.17 -9999 0 -0.52 36 36
RASA1 0.011 0.037 -9999 0 -0.58 2 2
mol:Phosphatidic acid -0.089 0.18 -9999 0 -0.62 17 17
IKK complex -0.004 0.091 -9999 0 -0.28 2 2
WIPF1 0.007 0.072 -9999 0 -0.81 4 4
S1P1 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
VEGFR2 homodimer/VEGFA homodimer -0.01 0.076 -9999 0 -0.58 9 9
PDGFRB -0.12 0.3 -9999 0 -0.8 86 86
SPHK1 -0.023 0.055 -9999 0 -0.32 15 15
mol:S1P -0.028 0.066 -9999 0 -0.4 9 9
S1P1/S1P/Gi -0.011 0.13 -9999 0 -0.52 9 9
GNAO1 0.006 0.068 -9999 0 -0.76 4 4
PDGFB-D/PDGFRB/PLCgamma1 -0.057 0.19 -9999 0 -0.58 17 17
PLCG1 -0.01 0.13 -9999 0 -0.49 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.12 0.3 -9999 0 -0.8 86 86
GNAI2 0.012 0.005 -9999 0 -10000 0 0
GNAI3 0.012 0.005 -9999 0 -10000 0 0
GNAI1 0.011 0.027 -9999 0 -0.59 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.009 0.069 -9999 0 -0.5 9 9
S1P1/S1P -0.038 0.08 -9999 0 -0.41 14 14
negative regulation of cAMP metabolic process -0.011 0.13 -9999 0 -0.5 9 9
MAPK3 -0.018 0.17 -9999 0 -0.51 23 23
calcium-dependent phospholipase C activity -0.002 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.011 0.037 -9999 0 -0.58 2 2
PLCB2 -0.001 0.096 -9999 0 -0.43 9 9
RAC1 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.032 0.067 -9999 0 -0.36 12 12
receptor internalization -0.037 0.075 -9999 0 -0.39 14 14
PTGS2 -0.047 0.25 -9999 0 -0.61 77 77
Rac1/GTP -0.032 0.067 -9999 0 -0.36 12 12
RHOA 0.014 0 -9999 0 -10000 0 0
VEGFA 0.002 0.095 -9999 0 -0.81 7 7
negative regulation of T cell proliferation -0.011 0.13 -9999 0 -0.5 9 9
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.015 0.14 -9999 0 -0.74 19 19
MAPK1 -0.018 0.17 -9999 0 -0.51 23 23
S1P1/S1P/PDGFB-D/PDGFRB -0.053 0.18 -9999 0 -0.5 22 22
ABCC1 0.006 0.072 -9999 0 -0.81 4 4
Plasma membrane estrogen receptor signaling

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.031 0.11 -10000 0 -0.47 25 25
ER alpha/Gai/GDP/Gbeta gamma 0.021 0.094 -10000 0 -0.46 4 4
AKT1 0.008 0.14 -10000 0 -0.75 15 15
PIK3CA 0.014 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.006 0.14 -10000 0 -0.76 15 15
mol:Ca2+ -0.028 0.16 -10000 0 -0.6 8 8
IGF1R 0.012 0.036 -10000 0 -0.81 1 1
E2/ER alpha (dimer)/Striatin -0.038 0.12 -10000 0 -0.41 48 48
SHC1 0.014 0 -10000 0 -10000 0 0
apoptosis -0.009 0.14 0.72 15 -10000 0 15
RhoA/GTP -0.019 0.079 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.025 0.085 -10000 0 -0.51 3 3
regulation of stress fiber formation -0.033 0.081 0.5 1 -10000 0 1
E2/ERA-ERB (dimer) -0.037 0.13 -10000 0 -0.48 40 40
KRAS 0.01 0.051 -10000 0 -0.81 2 2
G13/GTP -0.022 0.093 -10000 0 -0.4 28 28
pseudopodium formation 0.033 0.081 -10000 0 -0.5 1 1
E2/ER alpha (dimer)/PELP1 -0.024 0.1 -10000 0 -0.44 28 28
GRB2 0.014 0 -10000 0 -10000 0 0
GNG2 0.014 0 -10000 0 -10000 0 0
GNAO1 0.008 0.067 -10000 0 -0.75 4 4
HRAS 0.012 0.036 -10000 0 -0.81 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.021 0.11 -10000 0 -0.47 16 16
E2/ER beta (dimer) -0.015 0.096 -10000 0 -0.61 13 13
mol:GDP -0.03 0.1 -10000 0 -0.38 39 39
mol:NADP 0.021 0.11 -10000 0 -0.47 16 16
PIK3R1 0.011 0.037 -10000 0 -0.58 2 2
mol:IP3 -0.03 0.16 -10000 0 -0.63 8 8
IGF-1R heterotetramer 0.012 0.036 -10000 0 -0.81 1 1
PLCB1 -0.036 0.16 -10000 0 -0.41 77 77
PLCB2 -0.037 0.16 -10000 0 -0.4 79 79
IGF1 -0.086 0.22 -10000 0 -0.59 86 86
mol:L-citrulline 0.021 0.11 -10000 0 -0.47 16 16
RHOA 0.014 0 -10000 0 -10000 0 0
Gai/GDP -0.012 0.057 -10000 0 -0.56 2 2
JNK cascade -0.015 0.095 -10000 0 -0.61 13 13
BCAR1 0.014 0 -10000 0 -10000 0 0
ESR2 -0.007 0.13 -10000 0 -0.79 13 13
GNAQ 0.014 0 -10000 0 -10000 0 0
ESR1 -0.024 0.16 -10000 0 -0.68 28 28
Gq family/GDP/Gbeta gamma 0.001 0.11 -10000 0 -0.62 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.028 0.063 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.025 0.085 -10000 0 -0.51 3 3
GNAZ -0.014 0.14 -10000 0 -0.74 19 19
E2/ER alpha (dimer) -0.028 0.12 -10000 0 -0.52 28 28
STRN -0.01 0.12 -10000 0 -0.58 21 21
GNAL -0.061 0.2 -10000 0 -0.58 66 66
PELP1 0.014 0 -10000 0 -10000 0 0
MAPK11 0.006 0.085 -10000 0 -0.52 13 13
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 0.012 0.026 -10000 0 -0.58 1 1
HBEGF -0.16 0.16 -10000 0 -0.45 82 82
cAMP biosynthetic process -0.065 0.14 -10000 0 -0.48 30 30
SRC 0.028 0.09 -10000 0 -0.47 3 3
PI3K -0.002 0.026 -10000 0 -0.42 2 2
GNB1 0.014 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.027 0.091 -10000 0 -0.7 1 1
SOS1 0.014 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.052 0.11 -10000 0 -0.51 9 9
Gs family/GTP -0.066 0.14 -10000 0 -0.49 30 30
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.003 0.037 -10000 0 -0.49 3 3
vasodilation 0.021 0.11 -10000 0 -0.45 16 16
mol:DAG -0.03 0.16 -10000 0 -0.63 8 8
Gs family/GDP/Gbeta gamma -0.051 0.11 -10000 0 -0.56 7 7
MSN 0.033 0.087 -10000 0 -0.56 1 1
Gq family/GTP -0.073 0.16 -10000 0 -0.43 76 76
mol:PI-3-4-5-P3 0.007 0.14 -10000 0 -0.73 15 15
NRAS 0.014 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.021 0.11 0.45 16 -10000 0 16
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.028 0.097 -10000 0 -0.39 15 15
NOS3 0.02 0.12 -10000 0 -0.5 16 16
GNA11 0.009 0.052 -10000 0 -0.58 4 4
MAPKKK cascade 0.02 0.14 -10000 0 -0.56 16 16
E2/ER alpha (dimer)/PELP1/Src -0.026 0.09 -10000 0 -0.53 3 3
ruffle organization 0.033 0.081 -10000 0 -0.5 1 1
ROCK2 0.026 0.093 -10000 0 -0.63 1 1
GNA14 -0.072 0.21 -10000 0 -0.58 75 75
GNA15 0.011 0.037 -10000 0 -0.58 2 2
GNA13 0.014 0 -10000 0 -10000 0 0
MMP9 -0.29 0.21 -10000 0 -0.57 46 46
MMP2 -0.022 0.17 -10000 0 -0.55 6 6
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.031 0.041 -9999 0 -0.57 2 2
VEGFR1 homodimer/NRP1 0.022 0.033 -9999 0 -0.62 1 1
mol:DAG -0.05 0.2 -9999 0 -0.48 93 93
VEGFR1 homodimer/NRP1/VEGFR 121 -0.008 0.063 -9999 0 -0.5 8 8
CaM/Ca2+ -0.041 0.19 -9999 0 -0.62 2 2
HIF1A 0.02 0.029 -9999 0 -0.56 1 1
GAB1 0.014 0 -9999 0 -10000 0 0
AKT1 -0.016 0.17 -9999 0 -0.75 3 3
PLCG1 -0.051 0.2 -9999 0 -0.48 93 93
NOS3 -0.012 0.17 -9999 0 -0.72 1 1
CBL 0.014 0 -9999 0 -10000 0 0
mol:NO -0.011 0.16 -9999 0 -0.53 3 3
FLT1 0.03 0.038 -9999 0 -0.71 1 1
PGF -0.13 0.31 -9999 0 -0.81 92 92
VEGFR1 homodimer/NRP2/VEGFR121 -0.01 0.068 -9999 0 -0.49 10 10
CALM1 0.014 0 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
eNOS/Hsp90 -0.003 0.16 -9999 0 -0.66 1 1
endothelial cell proliferation -0.027 0.17 -9999 0 -0.71 1 1
mol:Ca2+ -0.05 0.2 -9999 0 -0.47 93 93
MAPK3 -0.03 0.18 -9999 0 -0.57 2 2
MAPK1 -0.03 0.18 -9999 0 -0.57 2 2
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
PLGF homodimer -0.13 0.31 -9999 0 -0.81 92 92
PRKACA 0.014 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.046 0.21 -9999 0 -0.81 38 38
VEGFA homodimer 0.002 0.094 -9999 0 -0.81 7 7
VEGFR1 homodimer/VEGFA homodimer 0.025 0.072 -9999 0 -0.54 8 8
platelet activating factor biosynthetic process -0.021 0.17 -9999 0 -0.64 1 1
PI3K -0.081 0.18 -9999 0 -0.68 4 4
PRKCA -0.04 0.19 -9999 0 -0.61 2 2
PRKCB -0.045 0.19 -9999 0 -0.61 2 2
VEGFR1 homodimer/PLGF homodimer -0.067 0.22 -9999 0 -0.53 93 93
VEGFA 0.002 0.095 -9999 0 -0.81 7 7
VEGFB 0.012 0.036 -9999 0 -0.81 1 1
mol:IP3 -0.05 0.2 -9999 0 -0.48 93 93
RASA1 0.039 0.047 -9999 0 -0.55 3 3
NRP2 0.01 0.051 -9999 0 -0.81 2 2
VEGFR1 homodimer 0.03 0.037 -9999 0 -0.71 1 1
VEGFB homodimer 0.012 0.036 -9999 0 -0.81 1 1
NCK1 0.014 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.035 0.2 -9999 0 -0.73 10 10
PTPN11 0.014 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.08 0.17 -9999 0 -0.67 4 4
mol:L-citrulline -0.011 0.16 -9999 0 -0.53 3 3
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.008 0.057 -9999 0 -0.53 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.008 0.062 -9999 0 -0.49 8 8
CD2AP 0.014 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.076 0.16 -9999 0 -0.65 4 4
PDPK1 -0.032 0.18 -9999 0 -0.77 3 3
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.008 0.062 -9999 0 -0.49 8 8
mol:NADP -0.011 0.16 -9999 0 -0.53 3 3
HSP90AA1 0.014 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.007 0.057 -9999 0 -0.52 1 1
VEGFR1 homodimer/NRP2 0.03 0.048 -9999 0 -0.56 3 3
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.024 0.13 -10000 0 -0.54 3 3
CRKL -0.006 0.15 -10000 0 -0.56 3 3
mol:DAG 0.006 0.14 -10000 0 -0.61 3 3
HRAS 0.024 0.13 -10000 0 -0.59 2 2
MAPK8 -0.029 0.18 -10000 0 -0.47 67 67
RAP1A -0.005 0.15 -10000 0 -0.63 2 2
GAB1 -0.005 0.15 -10000 0 -0.63 2 2
MAPK14 -0.024 0.17 -10000 0 -0.46 67 67
EPO -0.075 0.26 -10000 0 -0.8 57 57
PLCG1 0.005 0.14 -10000 0 -0.63 3 3
EPOR/TRPC2/IP3 Receptors -0.005 0.12 -10000 0 -0.8 11 11
RAPGEF1 0.014 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.064 0.17 -10000 0 -0.51 67 67
GAB1/SHC/GRB2/SOS1 -0.042 0.11 -10000 0 -0.66 1 1
EPO/EPOR (dimer) -0.057 0.22 -10000 0 -0.62 67 67
IRS2 -0.006 0.15 -10000 0 -0.63 2 2
STAT1 -0.009 0.16 -10000 0 -0.65 5 5
STAT5B 0.01 0.14 -10000 0 -0.64 3 3
cell proliferation -0.018 0.17 -10000 0 -0.72 5 5
GAB1/SHIP/PIK3R1/SHP2/SHC -0.042 0.11 -10000 0 -0.63 2 2
TEC -0.019 0.17 -10000 0 -0.68 9 9
SOCS3 0.012 0.026 -10000 0 -0.58 1 1
STAT1 (dimer) -0.008 0.16 -10000 0 -0.63 5 5
JAK2 0.01 0.029 -10000 0 -0.57 1 1
PIK3R1 0.011 0.037 -10000 0 -0.58 2 2
EPO/EPOR (dimer)/JAK2 -0.002 0.16 -10000 0 -0.47 8 8
EPO/EPOR -0.057 0.22 -10000 0 -0.62 67 67
LYN 0.014 0.036 -10000 0 -0.81 1 1
TEC/VAV2 -0.025 0.19 -10000 0 -0.74 13 13
elevation of cytosolic calcium ion concentration -0.005 0.12 -10000 0 -0.8 11 11
SHC1 0.014 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.032 0.19 -10000 0 -0.52 67 67
mol:IP3 0.006 0.14 -10000 0 -0.61 3 3
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.047 0.12 -10000 0 -0.7 2 2
SH2B3 0.009 0.038 -10000 0 -0.8 1 1
NFKB1 -0.024 0.17 -10000 0 -0.46 67 67
EPO/EPOR (dimer)/JAK2/SOCS3 -0.035 0.094 0.27 1 -0.29 58 59
PTPN6 -0.014 0.15 -10000 0 -0.46 8 8
TEC/VAV2/GRB2 -0.018 0.18 -10000 0 -0.71 13 13
EPOR -0.005 0.12 -10000 0 -0.8 11 11
INPP5D 0.011 0.037 -10000 0 -0.58 2 2
mol:GDP -0.043 0.11 -10000 0 -0.68 1 1
SOS1 0.014 0 -10000 0 -10000 0 0
PLCG2 0.012 0.026 -10000 0 -0.58 1 1
CRKL/CBL/C3G 0.01 0.14 -10000 0 -0.72 1 1
VAV2 -0.021 0.17 -10000 0 -0.75 6 6
CBL -0.005 0.15 -10000 0 -0.63 2 2
SHC/Grb2/SOS1 -0.046 0.12 -10000 0 -0.72 1 1
STAT5A 0.01 0.14 -10000 0 -0.64 3 3
GRB2 0.014 0 -10000 0 -10000 0 0
STAT5 (dimer) 0.027 0.14 -10000 0 -0.67 3 3
LYN/PLCgamma2 -0.002 0.033 -10000 0 -0.52 2 2
PTPN11 0.014 0 -10000 0 -10000 0 0
BTK -0.007 0.15 -10000 0 -0.63 2 2
BCL2 0.016 0.16 -10000 0 -0.74 9 9
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.02 0.077 -9999 0 -0.46 12 12
CRKL 0.012 0.036 -9999 0 -0.81 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.011 0.037 -9999 0 -0.58 2 2
ITGA4 -0.004 0.12 -9999 0 -0.81 11 11
alpha4/beta7 Integrin/MAdCAM1 -0.026 0.11 -9999 0 -0.48 27 27
EPO -0.078 0.26 -9999 0 -0.81 57 57
alpha4/beta7 Integrin -0.015 0.092 -9999 0 -0.59 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.014 0.093 -9999 0 -0.62 12 12
EPO/EPOR (dimer) -0.081 0.21 -9999 0 -0.63 67 67
lamellipodium assembly 0 0.022 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
PI3K -0.002 0.026 -9999 0 -0.42 2 2
ARF6 0.014 0 -9999 0 -10000 0 0
JAK2 -0.017 0.13 -9999 0 -0.52 4 4
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
MADCAM1 -0.016 0.14 -9999 0 -0.81 16 16
cell adhesion -0.026 0.11 -9999 0 -0.48 27 27
CRKL/CBL -0.001 0.027 -9999 0 -0.62 1 1
ITGB1 0.012 0.036 -9999 0 -0.81 1 1
SRC -0.024 0.17 -9999 0 -0.5 52 52
ITGB7 0.011 0.037 -9999 0 -0.58 2 2
RAC1 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.061 0.17 -9999 0 -0.52 61 61
p130Cas/Crk/Dock1 0.002 0.15 -9999 0 -0.8 2 2
VCAM1 -0.063 0.23 -9999 0 -0.77 51 51
RHOA 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.011 0.073 -9999 0 -0.48 12 12
BCAR1 -0.013 0.16 -9999 0 -0.46 52 52
EPOR -0.004 0.12 -9999 0 -0.81 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.014 0 -9999 0 -10000 0 0
GIT1 0.014 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.023 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.014 0 -10000 0 -10000 0 0
HDAC3 0.014 0 -10000 0 -10000 0 0
VDR 0.011 0.037 -10000 0 -0.58 2 2
Cbp/p300/PCAF -0.018 0.079 -10000 0 -0.67 1 1
EP300 0.012 0.026 -10000 0 -0.58 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.007 0.1 -10000 0 -0.48 10 10
KAT2B -0.016 0.13 -10000 0 -0.58 26 26
MAPK14 0.014 0 -10000 0 -10000 0 0
AKT1 0.028 0.11 0.22 2 -0.37 4 6
RAR alpha/9cRA/Cyclin H -0.023 0.06 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.001 0.11 -10000 0 -0.43 15 15
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.022 0.081 -10000 0 -0.47 7 7
NCOR2 0.014 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.002 0.026 -10000 0 -0.42 2 2
RXRs/RARs/NRIP1/9cRA -0.002 0.14 -10000 0 -0.6 6 6
NCOA2 -0.034 0.16 -10000 0 -0.58 42 42
NCOA3 0.014 0 -10000 0 -10000 0 0
NCOA1 0.014 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.011 0.036 -10000 0 -0.58 2 2
RARG 0.013 0.026 -10000 0 -0.58 1 1
RAR gamma1/9cRA -0.001 0.016 -10000 0 -0.35 1 1
MAPK3 0.014 0.001 -10000 0 -10000 0 0
MAPK1 0.014 0 -10000 0 -10000 0 0
MAPK8 0.007 0.068 -10000 0 -0.58 7 7
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.048 0.11 -10000 0 -0.45 11 11
RARA -0.003 0.087 -10000 0 -0.27 1 1
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.021 0.16 -10000 0 -0.57 26 26
PRKCA 0.014 0.045 -10000 0 -0.7 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.019 0.15 -10000 0 -0.64 7 7
RXRG -0.061 0.18 -10000 0 -0.38 116 116
RXRA 0.007 0.082 -10000 0 -0.33 1 1
RXRB -0.015 0.12 -10000 0 -0.35 61 61
VDR/Vit D3/DNA -0.002 0.026 -10000 0 -0.42 2 2
RBP1 -0.17 0.34 -10000 0 -0.8 117 117
CRBP1/9-cic-RA -0.14 0.26 -10000 0 -0.62 117 117
RARB -0.036 0.17 -10000 0 -0.58 45 45
PRKCG -0.08 0.26 -10000 0 -0.8 59 59
MNAT1 0.014 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.015 0.15 -10000 0 -0.54 5 5
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.004 0.13 -10000 0 -0.55 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.001 0.11 -10000 0 -0.44 14 14
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.019 0.15 -10000 0 -0.64 7 7
positive regulation of DNA binding -0.022 0.058 -10000 0 -10000 0 0
NRIP1 -0.019 0.16 -10000 0 -1.3 3 3
RXRs/RARs -0.026 0.15 -10000 0 -0.46 20 20
RXRs/RXRs/DNA/9cRA -0.049 0.11 -10000 0 -0.45 10 10
PRKACA 0.014 0 -10000 0 -10000 0 0
CDK7 0.014 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.016 0.041 -10000 0 -10000 0 0
CCNH 0.014 0 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0.011 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.002 0.095 -10000 0 -0.81 7 7
mol:Halofuginone 0.006 0.001 -10000 0 -10000 0 0
ITGA1 -0.1 0.28 -10000 0 -0.81 73 73
CDKN1A 0.029 0.033 -10000 0 -10000 0 0
PRL-3/alpha Tubulin -0.008 0.071 -10000 0 -0.62 7 7
mol:Ca2+ -0.079 0.18 0.37 5 -0.44 99 104
AGT -0.1 0.24 -10000 0 -0.59 99 99
CCNA2 0.029 0.074 -10000 0 -0.74 1 1
TUBA1B 0.014 0 -10000 0 -10000 0 0
EGR1 0.005 0.093 -10000 0 -0.41 25 25
CDK2/Cyclin E1 0.033 0.062 -10000 0 -10000 0 0
MAPK3 0.016 0.074 -10000 0 -0.62 7 7
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.074 -10000 0 -0.62 7 7
PTP4A1 0.023 0.072 -10000 0 -10000 0 0
PTP4A3 0.002 0.095 -10000 0 -0.81 7 7
PTP4A2 0.014 0 -10000 0 -10000 0 0
ITGB1 0.014 0.079 -10000 0 -0.62 8 8
SRC 0.014 0 -10000 0 -10000 0 0
RAC1 0.025 0.044 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.018 0.099 -10000 0 -0.74 1 1
RABGGTA 0.014 0 -10000 0 -10000 0 0
BCAR1 0.005 0.043 0.37 7 -10000 0 7
RHOC 0.025 0.044 -10000 0 -10000 0 0
RHOA 0.025 0.044 -10000 0 -10000 0 0
cell motility 0.029 0.046 -10000 0 -10000 0 0
PRL-1/alpha Tubulin 0.028 0.067 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.095 0.22 -10000 0 -0.62 80 80
ROCK1 0.029 0.046 -10000 0 -10000 0 0
RABGGTB 0.014 0 -10000 0 -10000 0 0
CDK2 0.014 0 -10000 0 -10000 0 0
mitosis 0.023 0.072 -10000 0 -10000 0 0
ATF5 -0.004 0.12 -10000 0 -0.81 11 11
Cellular roles of Anthrax toxin

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
ANTXR1 0.009 0.062 -10000 0 -0.81 3 3
ANTXR2 -0.004 0.12 -10000 0 -0.81 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.016 -10000 0 -0.097 14 14
monocyte activation -0.025 0.11 -10000 0 -0.29 72 72
MAP2K2 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 -0.002 0.013 -10000 0 -10000 0 0
MAP2K7 -0.002 0.013 -10000 0 -10000 0 0
MAP2K6 -0.018 0.069 -10000 0 -0.31 26 26
CYAA 0.003 0.079 -10000 0 -0.47 14 14
MAP2K4 -0.002 0.013 -10000 0 -10000 0 0
IL1B -0.031 0.14 -10000 0 -0.46 52 52
Channel -0.013 0.081 -10000 0 -0.5 14 14
NLRP1 -0.003 0.025 -10000 0 -0.48 1 1
CALM1 0.014 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.016 0.097 14 -10000 0 14
MAPK3 -0.002 0.013 -10000 0 -10000 0 0
MAPK1 -0.002 0.013 -10000 0 -10000 0 0
PGR -0.046 0.11 -10000 0 -0.33 69 69
PA/Cellular Receptors -0.015 0.088 -10000 0 -0.54 14 14
apoptosis -0.003 0.016 -10000 0 -0.097 14 14
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.004 0.076 -10000 0 -0.45 14 14
macrophage activation 0.019 0.015 -10000 0 -10000 0 0
TNF -0.024 0.17 -10000 0 -0.77 25 25
VCAM1 -0.026 0.11 -10000 0 -0.29 72 72
platelet activation -0.003 0.019 -10000 0 -10000 0 0
MAPKKK cascade -0.011 0.024 0.16 1 -10000 0 1
IL18 0.005 0.061 -10000 0 -0.3 19 19
negative regulation of macrophage activation -0.003 0.016 -10000 0 -0.097 14 14
LEF -0.003 0.016 -10000 0 -0.097 14 14
CASP1 -0.003 0.016 -10000 0 -0.22 1 1
mol:cAMP -0.003 0.019 -10000 0 -10000 0 0
necrosis -0.003 0.016 -10000 0 -0.097 14 14
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.004 0.08 -10000 0 -0.48 14 14
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.12 0.3 -9999 0 -0.81 86 86
alphaV beta3 Integrin -0.028 0.12 -9999 0 -0.57 25 25
PTK2 -0.028 0.091 -9999 0 -0.65 3 3
positive regulation of JNK cascade -0.013 0.053 -9999 0 -0.3 13 13
CDC42/GDP 0.037 0.086 -9999 0 -0.4 13 13
Rac1/GDP 0.039 0.085 -9999 0 -0.4 13 13
RAP1B 0.012 0.036 -9999 0 -0.81 1 1
RAP1A 0.014 0 -9999 0 -10000 0 0
CTNNB1 0.012 0.026 -9999 0 -0.58 1 1
CDC42/GTP -0.016 0.064 -9999 0 -0.37 13 13
nectin-3/I-afadin -0.027 0.12 -9999 0 -0.52 27 27
RAPGEF1 0.034 0.093 -9999 0 -0.44 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.027 0.1 -9999 0 -0.51 13 13
PDGFB-D/PDGFRB -0.12 0.3 -9999 0 -0.81 86 86
TLN1 0.021 0.061 -9999 0 -0.46 2 2
Rap1/GTP -0.014 0.056 -9999 0 -0.38 3 3
IQGAP1 0.014 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.001 0.022 -9999 0 -0.49 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.027 0.12 -9999 0 -0.52 27 27
PVR 0.01 0.051 -9999 0 -0.81 2 2
Necl-5(dimer) 0.01 0.051 -9999 0 -0.81 2 2
mol:GDP 0.034 0.1 -9999 0 -0.49 13 13
MLLT4 0.014 0 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
PI3K -0.095 0.18 -9999 0 -0.46 99 99
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.002 0.031 -9999 0 -0.42 3 3
positive regulation of lamellipodium assembly -0.019 0.06 -9999 0 -0.31 13 13
PVRL1 0.01 0.045 -9999 0 -0.58 3 3
PVRL3 -0.023 0.16 -9999 0 -0.7 27 27
PVRL2 0.012 0.036 -9999 0 -0.81 1 1
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
CDH1 0.007 0.063 -9999 0 -0.58 6 6
CLDN1 -0.018 0.14 -9999 0 -0.65 25 25
JAM-A/CLDN1 -0.039 0.12 -9999 0 -0.49 23 23
SRC -0.026 0.1 -9999 0 -0.57 13 13
ITGB3 -0.017 0.15 -9999 0 -0.73 21 21
nectin-1(dimer)/I-afadin/I-afadin -0.002 0.031 -9999 0 -0.42 3 3
FARP2 0.031 0.098 -9999 0 -0.48 13 13
RAC1 0.014 0 -9999 0 -10000 0 0
CTNNA1 0.014 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.025 0.1 -9999 0 -0.53 16 16
nectin-1/I-afadin -0.002 0.031 -9999 0 -0.42 3 3
nectin-2/I-afadin -0.001 0.027 -9999 0 -0.62 1 1
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.025 0.1 -9999 0 -0.53 14 14
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.012 0.026 -9999 0 -0.58 1 1
positive regulation of filopodium formation -0.013 0.053 -9999 0 -0.3 13 13
alphaV/beta3 Integrin/Talin 0.014 0.11 -9999 0 -0.42 24 24
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.001 0.027 -9999 0 -0.62 1 1
nectin-2(dimer)/I-afadin/I-afadin -0.001 0.027 -9999 0 -0.62 1 1
PIP5K1C 0.015 0.056 -9999 0 -0.36 2 2
VAV2 0.021 0.11 -9999 0 -0.49 13 13
RAP1/GDP -0.016 0.065 -9999 0 -0.45 3 3
ITGAV 0.006 0.076 -9999 0 -0.76 5 5
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.024 0.1 -9999 0 -0.53 15 15
nectin-3(dimer)/I-afadin/I-afadin -0.027 0.12 -9999 0 -0.52 27 27
Rac1/GTP -0.022 0.072 -9999 0 -0.38 13 13
PTPRM 0.006 0.062 -9999 0 -0.27 16 16
E-cadherin/beta catenin/alpha catenin -0.006 0.048 -9999 0 -0.51 3 3
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.016 0.21 -9999 0 -0.63 7 7
CRP -0.036 0.24 -9999 0 -0.74 21 21
cell cycle arrest -0.027 0.23 -9999 0 -0.67 14 14
TIMP1 -0.01 0.2 -9999 0 -0.68 11 11
IL6ST -0.058 0.2 -9999 0 -0.57 65 65
Rac1/GDP -0.012 0.16 -9999 0 -0.56 15 15
AP1 0.005 0.13 -9999 0 -0.55 4 4
GAB2 0.011 0.045 -9999 0 -0.58 3 3
TNFSF11 -0.082 0.3 -9999 0 -0.7 47 47
HSP90B1 0.028 0.05 -9999 0 -10000 0 0
GAB1 0.014 0.001 -9999 0 -10000 0 0
MAPK14 -0.016 0.15 -9999 0 -0.55 17 17
AKT1 0.056 0.029 -9999 0 -10000 0 0
FOXO1 0.063 0.027 -9999 0 -10000 0 0
MAP2K6 -0.028 0.16 -9999 0 -0.55 21 21
mol:GTP 0 0.002 -9999 0 -10000 0 0
MAP2K4 -0.003 0.17 -9999 0 -0.58 9 9
MITF -0.028 0.17 -9999 0 -0.54 25 25
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.012 0.036 -9999 0 -0.81 1 1
A2M 0.021 0.03 -9999 0 -0.65 1 1
CEBPB 0.02 0.007 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.013 0.075 -9999 0 -0.43 3 3
STAT3 -0.028 0.24 -9999 0 -0.7 14 14
STAT1 -0.022 0.09 -9999 0 -0.48 8 8
CEBPD -0.016 0.21 -9999 0 -0.63 7 7
PIK3CA 0.015 0 -9999 0 -10000 0 0
PI3K 0.022 0.027 -9999 0 -0.41 2 2
JUN 0.013 0.001 -9999 0 -10000 0 0
PIAS3/MITF -0.019 0.16 -9999 0 -0.51 24 24
MAPK11 -0.016 0.15 -9999 0 -0.55 17 17
STAT3 (dimer)/FOXO1 0.028 0.2 -9999 0 -0.55 2 2
GRB2/SOS1/GAB family -0.048 0.11 -9999 0 -0.53 9 9
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.023 0.15 -9999 0 -0.56 18 18
GRB2 0.014 0.001 -9999 0 -10000 0 0
JAK2 0.012 0.026 -9999 0 -0.58 1 1
LBP -0.11 0.36 -9999 0 -0.9 73 73
PIK3R1 0.013 0.037 -9999 0 -0.58 2 2
JAK1 0.015 0.004 -9999 0 -10000 0 0
MYC -0.016 0.21 -9999 0 -0.63 7 7
FGG -0.052 0.27 -9999 0 -0.75 33 33
macrophage differentiation -0.027 0.23 -9999 0 -0.67 14 14
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.064 0.15 -9999 0 -0.53 25 25
JUNB -0.016 0.21 -9999 0 -0.63 4 4
FOS -0.063 0.2 -9999 0 -0.58 67 67
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.028 0.16 -9999 0 -0.53 21 21
STAT1/PIAS1 -0.025 0.15 -9999 0 -0.53 13 13
GRB2/SOS1/GAB family/SHP2/PI3K 0.039 0.034 -9999 0 -10000 0 0
STAT3 (dimer) -0.027 0.24 -9999 0 -0.69 14 14
PRKCD 0.005 0.18 -9999 0 -0.64 5 5
IL6R 0.006 0.073 -9999 0 -0.58 8 8
SOCS3 -0.011 0.15 -9999 0 -0.69 6 6
gp130 (dimer)/JAK1/JAK1/LMO4 -0.016 0.12 -9999 0 -0.37 2 2
Rac1/GTP -0.017 0.16 -9999 0 -0.56 15 15
HCK 0.006 0.076 -9999 0 -0.76 5 5
MAPKKK cascade 0.029 0.071 -9999 0 -0.57 3 3
bone resorption -0.076 0.29 -9999 0 -0.66 48 48
IRF1 -0.016 0.21 -9999 0 -0.63 7 7
mol:GDP -0.022 0.16 -9999 0 -0.56 19 19
SOS1 0.013 0.004 -9999 0 -10000 0 0
VAV1 -0.022 0.16 -9999 0 -0.57 19 19
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.02 0.15 -9999 0 -0.63 16 16
PTPN11 -0.002 0.016 -9999 0 -10000 0 0
IL6/IL6RA -0.032 0.15 -9999 0 -0.45 58 58
gp130 (dimer)/TYK2/TYK2/LMO4 -0.022 0.13 -9999 0 -0.43 7 7
gp130 (dimer)/JAK2/JAK2/LMO4 -0.021 0.12 -9999 0 -0.46 3 3
IL6 -0.046 0.19 -9999 0 -0.62 51 51
PIAS3 0.014 0 -9999 0 -10000 0 0
PTPRE 0.01 0.012 -9999 0 -10000 0 0
PIAS1 0.014 0 -9999 0 -10000 0 0
RAC1 0.014 0.002 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.038 0.15 -9999 0 -0.51 23 23
LMO4 0.015 0.011 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.11 0.17 -9999 0 -0.67 13 13
MCL1 0.062 0.027 -9999 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.014 0 -9999 0 -10000 0 0
PTK2 0.014 0 -9999 0 -10000 0 0
CRKL -0.026 0.12 -9999 0 -0.41 7 7
GRB2/SOS1/SHC 0 0 -9999 0 -10000 0 0
HRAS 0.012 0.036 -9999 0 -0.81 1 1
IRS1/Crk -0.025 0.12 -9999 0 -0.4 6 6
IGF-1R heterotetramer/IGF1/PTP1B -0.056 0.12 -9999 0 -0.47 6 6
AKT1 0 0.11 -9999 0 -0.47 2 2
BAD 0.009 0.1 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.025 0.12 -9999 0 -0.4 6 6
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.026 0.12 -9999 0 -0.4 6 6
RAF1 0.014 0.099 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.045 0.1 -9999 0 -0.52 1 1
YWHAZ 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.037 0.13 -9999 0 -0.32 87 87
PIK3CA 0.014 0 -9999 0 -10000 0 0
RPS6KB1 0 0.11 -9999 0 -0.47 2 2
GNB2L1 0.014 0 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0.011 0.088 -9999 0 -10000 0 0
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.04 0.09 -9999 0 -0.55 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.042 0.094 -9999 0 -0.38 5 5
IGF-1R heterotetramer 0 0.045 -9999 0 -0.79 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck -0.025 0.12 -9999 0 -0.4 6 6
Crk/p130 Cas/Paxillin -0.042 0.094 -9999 0 -0.49 1 1
IGF1R 0 0.045 -9999 0 -0.8 1 1
IGF1 -0.087 0.23 -9999 0 -0.6 86 86
IRS2/Crk -0.016 0.12 -9999 0 -0.54 2 2
PI3K -0.046 0.1 -9999 0 -0.54 2 2
apoptosis -0.016 0.091 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.027 -9999 0 -0.63 1 1
PRKCD -0.023 0.15 -9999 0 -0.36 82 82
RAF1/14-3-3 E 0.021 0.089 -9999 0 -10000 0 0
BAD/14-3-3 0.016 0.096 -9999 0 -10000 0 0
PRKCZ 0 0.11 -9999 0 -0.47 2 2
Crk/p130 Cas/Paxillin/FAK1 -0.031 0.07 -9999 0 -10000 0 0
PTPN1 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.033 0.16 -9999 0 -0.38 86 86
BCAR1 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.048 0.11 -9999 0 -0.43 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0.014 0 -9999 0 -10000 0 0
IRS1/NCK2 -0.025 0.12 -9999 0 -0.4 6 6
GRB10 0.012 0.036 -9999 0 -0.81 1 1
PTPN11 -0.025 0.12 -9999 0 -0.4 6 6
IRS1 -0.037 0.13 -9999 0 -0.32 87 87
IRS2 -0.026 0.12 -9999 0 -0.43 7 7
IGF-1R heterotetramer/IGF1 -0.074 0.17 -9999 0 -0.44 87 87
GRB2 0.014 0 -9999 0 -10000 0 0
PDPK1 -0.008 0.11 -9999 0 -0.5 2 2
YWHAE 0.014 0 -9999 0 -10000 0 0
PRKD1 -0.027 0.16 -9999 0 -0.38 85 85
SHC1 0.014 0 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.007 0.038 0.25 9 -10000 0 9
RFC1 0.007 0.038 0.25 9 -10000 0 9
PRKDC 0.007 0.038 0.25 9 -10000 0 9
RIPK1 0.014 0.003 -10000 0 -10000 0 0
CASP7 -0.012 0.04 0.23 4 -10000 0 4
FASLG/FAS/FADD/FAF1 -0.05 0.12 -10000 0 -0.43 9 9
MAP2K4 -0.005 0.13 -10000 0 -0.43 12 12
mol:ceramide -0.023 0.14 -10000 0 -0.47 14 14
GSN 0.007 0.038 0.25 9 -10000 0 9
FASLG/FAS/FADD/FAF1/Caspase 8 -0.021 0.12 -10000 0 -0.44 10 10
FAS 0.011 0.037 -10000 0 -0.58 2 2
BID 0.002 0.046 0.3 1 -0.55 2 3
MAP3K1 0.009 0.078 -10000 0 -10000 0 0
MAP3K7 0.013 0.004 -10000 0 -10000 0 0
RB1 0.006 0.044 0.26 4 -0.34 2 6
CFLAR 0.014 0.003 -10000 0 -10000 0 0
HGF/MET -0.03 0.11 -10000 0 -0.56 11 11
ARHGDIB 0.007 0.038 0.25 6 -10000 0 6
FADD -0.081 0.26 -10000 0 -0.81 60 60
actin filament polymerization -0.007 0.038 -10000 0 -0.25 9 9
NFKB1 -0.031 0.063 -10000 0 -0.27 7 7
MAPK8 -0.013 0.16 -10000 0 -0.53 14 14
DFFA 0.007 0.038 0.25 9 -10000 0 9
DNA fragmentation during apoptosis 0.005 0.047 0.25 8 -0.43 2 10
FAS/FADD/MET -0.068 0.18 -10000 0 -0.55 63 63
CFLAR/RIP1 0.001 0.004 -10000 0 -10000 0 0
FAIM3 0 0.1 -10000 0 -0.78 9 9
FAF1 0.014 0.005 -10000 0 -10000 0 0
PARP1 0.007 0.038 0.25 9 -10000 0 9
DFFB 0.005 0.047 0.25 8 -0.43 2 10
CHUK -0.025 0.054 -10000 0 -10000 0 0
FASLG -0.042 0.2 -10000 0 -0.72 39 39
FAS/FADD -0.073 0.2 -10000 0 -0.62 61 61
HGF -0.015 0.14 -10000 0 -0.65 22 22
LMNA 0.006 0.035 -10000 0 -10000 0 0
CASP6 0.007 0.038 0.25 6 -10000 0 6
CASP10 0.013 0.004 -10000 0 -10000 0 0
CASP3 0.008 0.045 0.3 9 -10000 0 9
PTPN13 0.001 0.085 -10000 0 -0.58 11 11
CASP8 0.006 0.049 0.37 9 -10000 0 9
IL6 -0.089 0.36 -10000 0 -1.2 51 51
MET 0.005 0.08 -10000 0 -0.73 6 6
ICAD/CAD 0.005 0.044 -10000 0 -0.48 1 1
FASLG/FAS/FADD/FAF1/Caspase 10 -0.024 0.14 -10000 0 -0.48 14 14
activation of caspase activity by cytochrome c 0.002 0.046 0.3 1 -0.55 2 3
PAK2 0.007 0.038 0.25 6 -10000 0 6
BCL2 0.002 0.092 -10000 0 -0.68 9 9
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.029 0.032 -9999 0 -10000 0 0
epithelial cell differentiation -0.004 0.033 -9999 0 -10000 0 0
CYFIP2 0.011 0.044 -9999 0 -0.69 2 2
ENAH 0.064 0.046 -9999 0 -0.54 1 1
EGFR -0.015 0.15 -9999 0 -0.76 19 19
EPHA2 0.006 0.068 -9999 0 -0.58 7 7
MYO6 0.036 0.035 -9999 0 -10000 0 0
CTNNB1 0.012 0.026 -9999 0 -0.58 1 1
ABI1/Sra1/Nap1 -0.003 0.036 -9999 0 -0.53 2 2
AQP5 -0.3 0.22 -9999 0 -0.45 338 338
CTNND1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.036 0.035 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.002 0.12 -9999 0 -0.43 32 32
EGF -0.1 0.24 -9999 0 -0.58 101 101
NCKAP1 0.012 0.036 -9999 0 -0.81 1 1
AQP3 -0.13 0.21 -9999 0 -0.46 148 148
cortical microtubule organization -0.004 0.033 -9999 0 -10000 0 0
GO:0000145 0.035 0.033 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.004 0.033 -9999 0 -10000 0 0
MLLT4 0.014 0 -9999 0 -10000 0 0
ARF6/GDP -0.006 0.043 -9999 0 -0.46 2 2
ARF6 0.014 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.005 0.041 -9999 0 -0.48 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.048 0.036 -9999 0 -10000 0 0
PVRL2 0.012 0.036 -9999 0 -0.81 1 1
ZYX 0.036 0.035 -9999 0 -10000 0 0
ARF6/GTP -0.005 0.037 -9999 0 -0.44 1 1
CDH1 0.007 0.063 -9999 0 -0.58 6 6
EGFR/EGFR/EGF/EGF -0.067 0.13 -9999 0 -0.45 20 20
RhoA/GDP -0.004 0.03 -9999 0 -10000 0 0
actin cytoskeleton organization 0.043 0.034 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.012 0.036 -9999 0 -0.81 1 1
GIT1 0.014 0 -9999 0 -10000 0 0
IGF1R 0.012 0.036 -9999 0 -0.81 1 1
IGF1 -0.086 0.22 -9999 0 -0.59 86 86
DIAPH1 -0.002 0.031 -9999 0 -0.57 1 1
Wnt receptor signaling pathway 0.004 0.033 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.006 0.043 -9999 0 -0.47 2 2
CTNNA1 0.014 0 -9999 0 -10000 0 0
VCL 0.043 0.035 -9999 0 -10000 0 0
EFNA1 0.012 0.036 -9999 0 -0.81 1 1
LPP 0.042 0.041 -9999 0 -10000 0 0
Ephrin A1/EPHA2 -0.008 0.051 -9999 0 -0.5 3 3
SEC6/SEC8 -0.004 0.03 -9999 0 -10000 0 0
MGAT3 0.002 0.12 -9999 0 -0.44 32 32
HGF/MET -0.021 0.09 -9999 0 -0.52 11 11
HGF -0.015 0.14 -9999 0 -0.65 22 22
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.029 0.032 -9999 0 -10000 0 0
actin cable formation 0.081 0.041 -9999 0 -0.37 1 1
KIAA1543 0.017 0.11 -9999 0 -0.65 7 7
KIFC3 0.036 0.035 -9999 0 -10000 0 0
NCK1 0.014 0 -9999 0 -10000 0 0
EXOC3 0.014 0 -9999 0 -10000 0 0
ACTN1 0.035 0.041 -9999 0 -0.44 1 1
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP -0.004 0.033 -9999 0 -10000 0 0
EXOC4 0.014 0 -9999 0 -10000 0 0
STX4 0.036 0.035 -9999 0 -10000 0 0
PIP5K1C 0.036 0.035 -9999 0 -10000 0 0
LIMA1 0.014 0 -9999 0 -10000 0 0
ABI1 0.014 0 -9999 0 -10000 0 0
ROCK1 -0.006 0.037 -9999 0 -10000 0 0
adherens junction assembly 0.033 0.11 -9999 0 -0.64 7 7
IGF-1R heterotetramer/IGF1 -0.047 0.1 -9999 0 -0.42 5 5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.001 0.027 -9999 0 -0.62 1 1
MET 0.005 0.08 -9999 0 -0.73 6 6
PLEKHA7 0.017 0.089 -9999 0 -0.56 4 4
mol:GTP -0.005 0.041 -9999 0 -0.48 1 1
establishment of epithelial cell apical/basal polarity 0.062 0.037 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.029 0.032 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.043 0.034 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.029 0.032 -9999 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.16 0.32 -9999 0 -1.2 3 3
PLK1 0.083 0.083 -9999 0 -0.69 2 2
BIRC5 0.06 0.16 -9999 0 -0.61 22 22
HSPA1B 0.15 0.32 -9999 0 -1.2 3 3
MAP2K1 0.046 0.037 -9999 0 -10000 0 0
BRCA2 0.15 0.33 -9999 0 -1.3 5 5
FOXM1 0.15 0.36 -9999 0 -1.4 6 6
XRCC1 0.16 0.32 -9999 0 -1.2 3 3
FOXM1B/p19 -0.18 0.26 -9999 0 -1 21 21
Cyclin D1/CDK4 0.1 0.36 -9999 0 -1.1 8 8
CDC2 0.15 0.33 -9999 0 -1.1 6 6
TGFA 0.11 0.36 -9999 0 -1.1 8 8
SKP2 0.16 0.32 -9999 0 -1.2 4 4
CCNE1 0.009 0.095 -9999 0 -0.8 7 7
CKS1B 0.15 0.33 -9999 0 -1.2 6 6
RB1 -0.048 0.11 -9999 0 -0.72 5 5
FOXM1C/SP1 0.15 0.32 -9999 0 -1.3 5 5
AURKB 0.074 0.12 -9999 0 -0.66 10 10
CENPF 0.16 0.32 -9999 0 -1.2 3 3
CDK4 0.024 0.017 -9999 0 -10000 0 0
MYC 0.16 0.29 -9999 0 -1 3 3
CHEK2 0.046 0.037 -9999 0 -10000 0 0
ONECUT1 0.1 0.38 -9999 0 -1.1 13 13
CDKN2A -0.35 0.39 -9999 0 -0.76 238 238
LAMA4 0.14 0.35 -9999 0 -1.1 7 7
FOXM1B/HNF6 0.094 0.42 -9999 0 -1.3 14 14
FOS 0.051 0.5 -9999 0 -1.1 68 68
SP1 0.015 0.001 -9999 0 -10000 0 0
CDC25B 0.14 0.33 -9999 0 -1.1 5 5
response to radiation 0.027 0.035 -9999 0 -10000 0 0
CENPB 0.16 0.32 -9999 0 -1.2 3 3
CENPA 0.15 0.33 -9999 0 -1.2 6 6
NEK2 0.16 0.32 -9999 0 -1.2 4 4
HIST1H2BA 0.15 0.31 -9999 0 -1.2 3 3
CCNA2 0.018 0.038 -9999 0 -0.82 1 1
EP300 0.012 0.026 -9999 0 -0.58 1 1
CCNB1/CDK1 0.15 0.34 -9999 0 -1.4 4 4
CCNB2 0.16 0.32 -9999 0 -1.3 4 4
CCNB1 0.16 0.33 -9999 0 -1.2 4 4
ETV5 0.15 0.32 -9999 0 -1.2 3 3
ESR1 0.12 0.38 -9999 0 -1.1 20 20
CCND1 0.11 0.38 -9999 0 -1 14 14
GSK3A 0.041 0.032 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.044 0.083 -9999 0 -0.53 8 8
CDK2 0.02 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.032 0.039 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.07 0.19 -9999 0 -1.1 7 7
GAS1 0.15 0.34 -9999 0 -1.2 7 7
MMP2 0.11 0.37 -9999 0 -1.1 10 10
RB1/FOXM1C 0.12 0.36 -9999 0 -1.2 6 6
CREBBP 0.014 0 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.041 0.099 -10000 0 -0.63 5 5
UGCG -0.009 0.12 -10000 0 -0.62 19 19
AKT1/mTOR/p70S6K/Hsp90/TERT 0.015 0.13 -10000 0 -0.42 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0 0.12 -10000 0 -0.61 19 19
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.022 0.077 -10000 0 -0.46 9 9
FRAP1 0.053 0.12 -10000 0 -0.5 13 13
FOXO3 0.061 0.1 -10000 0 -0.55 3 3
AKT1 0.055 0.11 -10000 0 -0.47 10 10
GAB2 0.011 0.045 -10000 0 -0.58 3 3
SMPD1 0.014 0.025 -10000 0 -10000 0 0
SGMS1 0.014 0.025 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.022 0.024 -10000 0 -0.36 2 2
CALM1 0.014 0 -10000 0 -10000 0 0
cell proliferation 0.029 0.082 -10000 0 -0.42 5 5
EIF3A 0.014 0 -10000 0 -10000 0 0
PI3K 0.023 0.029 -10000 0 -0.42 2 2
RPS6KB1 0.008 0.066 -10000 0 -10000 0 0
mol:sphingomyelin -0.001 0.003 -10000 0 -10000 0 0
natural killer cell activation 0.001 0.001 -10000 0 -10000 0 0
JAK3 -0.018 0.16 -10000 0 -0.8 22 22
PIK3R1 0.014 0.037 -10000 0 -0.58 2 2
JAK1 0.017 0.002 -10000 0 -10000 0 0
NFKB1 0.014 0 -10000 0 -10000 0 0
MYC 0.061 0.096 -10000 0 -0.49 3 3
MYB -0.097 0.36 -10000 0 -1.2 51 51
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.042 0.12 -10000 0 -0.54 10 10
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.023 0.061 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.042 0.11 -10000 0 -0.52 10 10
Rac1/GDP 0.027 0.023 -10000 0 -10000 0 0
T cell proliferation 0.051 0.11 -10000 0 -0.51 8 8
SHC1 0.014 0.002 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.001 0.021 -10000 0 -0.064 51 51
PRKCZ 0.051 0.11 -10000 0 -0.53 8 8
NF kappa B1 p50/RelA -0.021 0.076 -10000 0 -0.45 9 9
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.034 0.11 -10000 0 -0.52 13 13
HSP90AA1 0.014 0 -10000 0 -10000 0 0
RELA 0.014 0 -10000 0 -10000 0 0
IL2RA -0.06 0.24 -10000 0 -0.81 47 47
IL2RB 0.004 0.098 -10000 0 -0.78 8 8
TERT -0.17 0.34 -10000 0 -0.81 115 115
E2F1 -0.031 0.15 -10000 0 -0.43 51 51
SOS1 0.014 0.002 -10000 0 -10000 0 0
RPS6 0.014 0 -10000 0 -10000 0 0
mol:cAMP 0 0.01 0.031 51 -10000 0 51
PTPN11 0.014 0.002 -10000 0 -10000 0 0
IL2RG -0.009 0.14 -10000 0 -0.78 17 17
actin cytoskeleton organization 0.051 0.11 -10000 0 -0.51 8 8
GRB2 0.014 0.002 -10000 0 -10000 0 0
IL2 0.007 0.036 -10000 0 -0.8 1 1
PIK3CA 0.017 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.034 0.024 -10000 0 -10000 0 0
LCK -0.002 0.12 -10000 0 -0.8 12 12
BCL2 0.053 0.14 -10000 0 -0.75 10 10
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.038 0.098 -10000 0 -10000 0 0
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.001 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0 0 -10000 0 -10000 0 0
GNB1 0.014 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.042 0.11 -10000 0 -0.33 66 66
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.011 0.028 0.085 66 -10000 0 66
GNAL -0.061 0.2 -10000 0 -0.58 66 66
GNG2 0.014 0 -10000 0 -10000 0 0
CRH 0.001 0.004 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.042 -10000 0 -0.36 7 7
MAPK11 0.009 0 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.002 0.16 -9999 0 -0.57 15 15
MAP3K8 0.009 0.045 -9999 0 -0.58 3 3
FOS 0.009 0.12 -9999 0 -0.48 14 14
PRKCA 0.01 0.044 -9999 0 -0.69 2 2
PTPN7 -0.025 0.18 -9999 0 -0.8 25 25
HRAS 0.012 0.036 -9999 0 -0.81 1 1
PRKCB 0.001 0.096 -9999 0 -0.76 8 8
NRAS 0.013 0.001 -9999 0 -10000 0 0
RAS family/GTP -0.003 0.037 -9999 0 -0.49 3 3
MAPK3 0.012 0.082 -9999 0 -0.38 11 11
MAP2K1 0.028 0.07 -9999 0 -0.45 6 6
ELK1 0.01 0.038 -9999 0 -0.84 1 1
BRAF -0.01 0.052 -9999 0 -0.41 6 6
mol:GTP -0.001 0.002 -9999 0 -0.006 67 67
MAPK1 0.012 0.082 -9999 0 -0.36 13 13
RAF1 -0.01 0.052 -9999 0 -0.41 6 6
KRAS 0.01 0.051 -9999 0 -0.81 2 2
Aurora B signaling

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
Condensin I complex 0.031 0.047 -9999 0 -10000 0 0
STMN1 0.011 0.11 -9999 0 -0.69 12 12
Aurora B/RasGAP/Survivin -0.007 0.15 -9999 0 -0.61 27 27
Chromosomal passenger complex/Cul3 protein complex 0.023 0.079 -9999 0 -0.44 10 10
BIRC5 -0.019 0.16 -9999 0 -0.8 22 22
DES -0.32 0.27 -9999 0 -0.55 293 293
Aurora C/Aurora B/INCENP 0.009 0.093 -9999 0 -0.51 15 15
Aurora B/TACC1 0.005 0.079 -9999 0 -0.5 12 12
Aurora B/PP2A 0.007 0.087 -9999 0 -0.61 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.015 0.024 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0 0.002 -9999 0 -10000 0 0
NDC80 0.004 0.12 -9999 0 -0.62 19 19
Cul3 protein complex -0.006 0.045 -9999 0 -10000 0 0
KIF2C 0.019 0.048 -9999 0 -0.35 5 5
PEBP1 0.014 0.002 -9999 0 -10000 0 0
KIF20A 0.013 0.001 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.005 0.095 -9999 0 -0.62 11 11
SEPT1 -0.001 0.11 -9999 0 -0.81 9 9
SMC2 0.014 0 -9999 0 -10000 0 0
SMC4 0.012 0.036 -9999 0 -0.81 1 1
NSUN2/NPM1/Nucleolin 0.025 0.054 -9999 0 -0.38 5 5
PSMA3 0.014 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.003 -9999 0 -10000 0 0
H3F3B 0.014 0.052 -9999 0 -0.36 10 10
AURKB 0.006 0.11 -9999 0 -0.81 10 10
AURKC 0.003 0.088 -9999 0 -0.74 7 7
CDCA8 0.014 0.037 -9999 0 -0.82 1 1
cytokinesis -0.021 0.085 -9999 0 -0.6 6 6
Aurora B/Septin1 0.006 0.11 -9999 0 -0.49 15 15
AURKA -0.006 0.12 -9999 0 -0.81 12 12
INCENP 0.015 0.003 -9999 0 -10000 0 0
KLHL13 0.01 0.045 -9999 0 -0.58 3 3
BUB1 0.013 0.001 -9999 0 -10000 0 0
hSgo1/Aurora B/Survivin -0.004 0.14 -9999 0 -0.56 27 27
EVI5 0.015 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.011 0.054 -9999 0 -0.44 4 4
SGOL1 0.014 0 -9999 0 -10000 0 0
CENPA 0.016 0.087 -9999 0 -0.47 12 12
NCAPG 0.014 0 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.007 0.087 -9999 0 -0.61 10 10
NCAPD2 0.009 0.062 -9999 0 -0.81 3 3
Aurora B/PP1-gamma 0.007 0.087 -9999 0 -0.61 10 10
RHOA 0.014 0 -9999 0 -10000 0 0
NCAPH 0.009 0.062 -9999 0 -0.81 3 3
NPM1 0.005 0.058 -9999 0 -0.4 10 10
RASA1 0.011 0.037 -9999 0 -0.58 2 2
KLHL9 0.007 0.063 -9999 0 -0.58 6 6
mitotic prometaphase 0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.087 -9999 0 -0.6 10 10
PPP1CC 0.014 0 -9999 0 -10000 0 0
Centraspindlin -0.012 0.06 -9999 0 -0.43 8 8
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 0.005 0.058 -9999 0 -0.4 10 10
MYLK 0.008 0.074 -9999 0 -0.38 17 17
KIF23 0.014 0.002 -9999 0 -10000 0 0
VIM 0.011 0.11 -9999 0 -0.65 13 13
RACGAP1 0.014 0.002 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.005 0.058 -9999 0 -0.4 10 10
Chromosomal passenger complex 0.026 0.074 -9999 0 -0.46 8 8
Chromosomal passenger complex/EVI5 0.029 0.14 -9999 0 -0.53 27 27
TACC1 0.011 0.037 -9999 0 -0.58 2 2
PPP2R5D 0.014 0 -9999 0 -10000 0 0
CUL3 0.014 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.036 0.18 -9999 0 -0.84 20 20
MAP4K1 -0.007 0.13 -9999 0 -0.76 14 14
MAP3K8 0.01 0.045 -9999 0 -0.58 3 3
PRKCB 0.002 0.095 -9999 0 -0.75 8 8
DBNL 0.014 0 -9999 0 -10000 0 0
CRKL 0.012 0.036 -9999 0 -0.81 1 1
MAP3K1 0.029 0.099 -9999 0 -0.53 12 12
JUN 0.024 0.095 -9999 0 -0.58 10 10
MAP3K7 0.029 0.099 -9999 0 -0.53 12 12
GRAP2 -0.002 0.1 -9999 0 -0.67 12 12
CRK 0.014 0 -9999 0 -10000 0 0
MAP2K4 0.037 0.098 -9999 0 -0.5 12 12
LAT -0.009 0.13 -9999 0 -0.81 14 14
LCP2 0.009 0.062 -9999 0 -0.81 3 3
MAPK8 0.017 0.1 -9999 0 -0.55 14 14
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.021 0.1 -9999 0 -0.57 12 12
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.034 0.17 -9999 0 -0.79 20 20
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.006 0.055 -9999 0 -0.65 3 3
VDR 0.011 0.037 -9999 0 -0.58 2 2
FAM120B 0.014 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.017 0.11 -9999 0 -0.45 5 5
RXRs/LXRs/DNA/Oxysterols 0.025 0.12 -9999 0 -0.51 5 5
MED1 0.012 0.036 -9999 0 -0.81 1 1
mol:9cRA 0.005 0.011 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.007 0.11 -9999 0 -0.5 3 3
RXRs/NUR77 -0.004 0.13 -9999 0 -0.49 8 8
RXRs/PPAR -0.094 0.16 -9999 0 -0.5 17 17
NCOR2 0.014 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.002 0.026 -9999 0 -0.42 2 2
RARs/VDR/DNA/Vit D3 -0.027 0.087 -9999 0 -0.52 2 2
RARA 0.014 0 -9999 0 -10000 0 0
NCOA1 0.014 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.011 0.036 -9999 0 -0.58 2 2
RARs/RARs/DNA/9cRA -0.026 0.085 -9999 0 -0.46 1 1
RARG 0.012 0.026 -9999 0 -0.58 1 1
RPS6KB1 0.013 0.041 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.007 0.11 -9999 0 -0.5 3 3
THRA 0.014 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.002 0.026 -9999 0 -0.42 2 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.002 0.13 -9999 0 -0.45 11 11
NR1H4 0.003 0.036 -9999 0 -0.81 1 1
RXRs/LXRs/DNA 0.016 0.13 -9999 0 -0.72 1 1
NR1H2 0.019 0.008 -9999 0 -10000 0 0
NR1H3 0.01 0.088 -9999 0 -0.8 6 6
RXRs/VDR/DNA/Vit D3 0 0.12 -9999 0 -0.44 7 7
NR4A1 0.002 0.081 -9999 0 -0.58 10 10
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.004 0.086 -9999 0 -0.32 5 5
RXRG -0.059 0.2 -9999 0 -0.6 64 64
RXR alpha/CCPG 0.024 0.006 -9999 0 -10000 0 0
RXRA 0.019 0.008 -9999 0 -10000 0 0
RXRB 0.019 0.009 -9999 0 -10000 0 0
THRB -0.032 0.16 -9999 0 -0.58 40 40
PPARG -0.21 0.29 -9999 0 -0.58 197 197
PPARD 0.014 0 -9999 0 -10000 0 0
TNF 0.013 0.18 -9999 0 -0.7 25 25
mol:Oxysterols 0.005 0.01 -9999 0 -10000 0 0
cholesterol transport 0.025 0.12 -9999 0 -0.5 5 5
PPARA 0.014 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.038 0.17 -9999 0 -0.58 45 45
RXRs/NUR77/BCL2 -0.009 0.11 -9999 0 -0.59 2 2
SREBF1 0.033 0.11 -9999 0 -0.54 1 1
RXRs/RXRs/DNA/9cRA -0.002 0.13 -9999 0 -0.45 11 11
ABCA1 0.03 0.13 -9999 0 -0.81 4 4
RARs/THRs -0.047 0.11 -9999 0 -0.55 4 4
RXRs/FXR -0.005 0.12 -9999 0 -0.47 8 8
BCL2 0.002 0.092 -9999 0 -0.68 9 9
S1P3 pathway

Figure S88.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S88.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.12 0.3 -9999 0 -0.81 86 86
mol:S1P 0.001 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.023 0.064 -9999 0 -0.42 2 2
GNAO1 0.009 0.069 -9999 0 -0.76 4 4
S1P/S1P3/G12/G13 0.021 0.061 -9999 0 -0.5 5 5
AKT1 -0.044 0.093 -9999 0 -0.37 8 8
AKT3 0.036 0.1 -9999 0 -0.67 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.12 0.3 -9999 0 -0.81 86 86
GNAI2 0.015 0.002 -9999 0 -10000 0 0
GNAI3 0.015 0.002 -9999 0 -10000 0 0
GNAI1 0.014 0.026 -9999 0 -0.58 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.008 0.069 -9999 0 -0.62 6 6
S1PR2 0.014 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.03 0.077 -9999 0 -0.56 4 4
MAPK3 0.037 0.074 -9999 0 -0.53 4 4
MAPK1 0.037 0.074 -9999 0 -0.53 4 4
JAK2 0.033 0.093 -9999 0 -0.5 8 8
CXCR4 0.021 0.12 -9999 0 -0.53 20 20
FLT1 0.015 0.036 -9999 0 -0.8 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.037 0.074 -9999 0 -0.53 4 4
S1P/S1P3/Gi 0.03 0.078 -9999 0 -0.57 4 4
RAC1 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.014 0.06 -9999 0 -0.52 4 4
VEGFA 0.005 0.095 -9999 0 -0.8 7 7
S1P/S1P2/Gi 0.031 0.059 -9999 0 -0.47 2 2
VEGFR1 homodimer/VEGFA homodimer 0.019 0.079 -9999 0 -0.61 8 8
RHOA 0.014 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.014 0.12 -9999 0 -0.53 6 6
GNAQ 0.014 0 -9999 0 -10000 0 0
GNAZ -0.012 0.14 -9999 0 -0.73 19 19
G12/G13 -0.005 0.054 -9999 0 -0.62 4 4
GNA14 -0.072 0.21 -9999 0 -0.58 75 75
GNA15 0.011 0.037 -9999 0 -0.58 2 2
GNA12 0.007 0.072 -9999 0 -0.81 4 4
GNA13 0.014 0 -9999 0 -10000 0 0
GNA11 0.009 0.052 -9999 0 -0.58 4 4
Rac1/GTP -0.014 0.06 -9999 0 -0.52 4 4
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.014 0 -9999 0 -10000 0 0
SPHK1 -0.01 0.14 -9999 0 -0.81 15 15
GNAI2 0.014 0 -9999 0 -10000 0 0
mol:S1P 0.013 0.057 -9999 0 -0.28 19 19
GNAO1 0.008 0.067 -9999 0 -0.75 4 4
mol:Sphinganine-1-P 0.006 0.11 -9999 0 -0.62 15 15
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.01 0.052 -9999 0 -0.45 4 4
GNAI3 0.014 0 -9999 0 -10000 0 0
G12/G13 -0.005 0.054 -9999 0 -0.62 4 4
S1PR3 0.006 0.068 -9999 0 -0.62 6 6
S1PR2 0.014 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.009 0.045 -9999 0 -10000 0 0
S1PR5 0.008 0.062 -9999 0 -0.69 4 4
S1PR4 -0.032 0.19 -9999 0 -0.8 29 29
GNAI1 0.012 0.026 -9999 0 -0.58 1 1
S1P/S1P5/G12 0.018 0.072 -9999 0 -0.48 6 6
S1P/S1P3/Gq -0.01 0.12 -9999 0 -0.5 8 8
S1P/S1P4/Gi 0.015 0.09 -9999 0 -0.46 4 4
GNAQ 0.014 0 -9999 0 -10000 0 0
GNAZ -0.014 0.14 -9999 0 -0.74 19 19
GNA14 -0.072 0.21 -9999 0 -0.58 75 75
GNA15 0.011 0.037 -9999 0 -0.58 2 2
GNA12 0.007 0.072 -9999 0 -0.81 4 4
GNA13 0.014 0 -9999 0 -10000 0 0
GNA11 0.009 0.052 -9999 0 -0.58 4 4
ABCC1 0.007 0.072 -9999 0 -0.81 4 4
Circadian rhythm pathway

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.001 0.004 -9999 0 -10000 0 0
CLOCK 0.01 0.063 -9999 0 -0.57 6 6
TIMELESS/CRY2 0.045 0.013 -9999 0 -10000 0 0
DEC1/BMAL1 -0.1 0.23 -9999 0 -0.62 87 87
ATR 0.014 0 -9999 0 -10000 0 0
NR1D1 0.044 0.015 -9999 0 -10000 0 0
ARNTL 0.017 0 -9999 0 -10000 0 0
TIMELESS 0.044 0.015 -9999 0 -10000 0 0
NPAS2 0.009 0.068 -9999 0 -0.57 7 7
CRY2 0.014 0 -9999 0 -10000 0 0
mol:CO -0.015 0 -9999 0 -10000 0 0
CHEK1 0.014 0 -9999 0 -10000 0 0
mol:HEME 0.015 0 -9999 0 -10000 0 0
PER1 0.012 0.026 -9999 0 -0.58 1 1
BMAL/CLOCK/NPAS2 0.037 0.063 -9999 0 -0.66 1 1
BMAL1/CLOCK 0.01 0.1 -9999 0 -10000 0 0
S phase of mitotic cell cycle -0.001 0.004 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.001 0.004 -9999 0 -10000 0 0
mol:NADPH 0.015 0 -9999 0 -10000 0 0
PER1/TIMELESS 0.045 0.019 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.13 0.3 -9999 0 -0.81 87 87
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.017 0.069 -10000 0 -0.62 6 6
MAP4K4 0.029 0.081 -10000 0 -0.41 9 9
BAG4 0.011 0.037 -10000 0 -0.58 2 2
PKC zeta/ceramide -0.015 0.043 0.21 1 -0.36 1 2
NFKBIA 0.012 0.036 -10000 0 -0.81 1 1
BIRC3 -0.023 0.17 -10000 0 -0.81 23 23
BAX -0.003 0.021 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
AKT1 0.022 0.009 -10000 0 -10000 0 0
BAD -0.013 0.041 0.21 5 -10000 0 5
SMPD1 0.018 0.053 -10000 0 -0.25 4 4
RB1 -0.014 0.046 0.23 1 -0.36 2 3
FADD/Caspase 8 -0.013 0.17 -10000 0 -0.6 8 8
MAP2K4 -0.005 0.039 -10000 0 -10000 0 0
NSMAF 0.014 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.005 0.039 -10000 0 -10000 0 0
EGF -0.1 0.24 -10000 0 -0.58 101 101
mol:ceramide -0.024 0.044 0.22 5 -10000 0 5
MADD 0.014 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.017 0.069 -10000 0 -0.62 6 6
ASAH1 0.014 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.015 0.046 0.22 2 -0.35 2 4
cell proliferation -0.047 0.093 -10000 0 -0.39 4 4
BID 0.02 0.058 -10000 0 -10000 0 0
MAP3K1 -0.013 0.041 0.21 5 -10000 0 5
EIF2A 0 0.05 -10000 0 -0.44 3 3
TRADD 0.014 0 -10000 0 -10000 0 0
CRADD 0.014 0 -10000 0 -10000 0 0
MAPK3 0.007 0.037 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.007 0.037 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.014 0.04 0.21 1 -10000 0 1
FADD -0.027 0.18 -10000 0 -0.45 68 68
KSR1 -0.013 0.041 0.21 5 -10000 0 5
MAPK8 -0.003 0.05 0.22 1 -0.3 3 4
PRKRA -0.013 0.041 0.21 5 -10000 0 5
PDGFA 0.004 0.088 -10000 0 -0.81 6 6
TRAF2 0.004 0.088 -10000 0 -0.81 6 6
IGF1 -0.086 0.22 -10000 0 -0.59 86 86
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.024 0.044 0.22 5 -10000 0 5
CTSD 0.014 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.03 0.11 -10000 0 -0.42 4 4
PRKCD 0.014 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.026 -10000 0 -0.58 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.017 0.069 -10000 0 -0.62 6 6
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.014 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.022 0.085 -10000 0 -0.44 9 9
TNFR1A/BAG4/TNF-alpha -0.025 0.11 -10000 0 -0.53 21 21
mol:Sphingosine-1-phosphate 0.017 0.068 -10000 0 -0.62 6 6
MAP2K1 0.003 0.037 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.014 0 -10000 0 -10000 0 0
CYCS -0.004 0.035 0.32 1 -10000 0 1
TNFRSF1A 0.014 0 -10000 0 -10000 0 0
NFKB1 0.014 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.026 -10000 0 -0.42 2 2
EIF2AK2 -0.008 0.052 -10000 0 -0.46 3 3
TNF-alpha/TNFR1A/FAN -0.024 0.11 -10000 0 -0.53 21 21
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.034 0.048 -10000 0 -10000 0 0
MAP2K2 0.003 0.037 -10000 0 -10000 0 0
SMPD3 0.001 0.1 -10000 0 -0.33 34 34
TNF -0.024 0.17 -10000 0 -0.77 25 25
PKC zeta/PAR4 -0.001 0.018 -10000 0 -0.42 1 1
mol:PHOSPHOCHOLINE 0.032 0.098 0.22 104 -10000 0 104
NF kappa B1/RelA/I kappa B alpha -0.001 0.023 -10000 0 -0.45 1 1
AIFM1 -0.004 0.035 0.2 4 -10000 0 4
BCL2 0.002 0.092 -10000 0 -0.68 9 9
HIV-1 Nef: Negative effector of Fas and TNF-alpha

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.011 0.037 -9999 0 -0.58 2 2
Caspase 8 (4 units) -0.034 0.075 -9999 0 -0.47 4 4
NEF -0.007 0.046 -9999 0 -10000 0 0
NFKBIA 0.01 0.044 -9999 0 -0.8 1 1
BIRC3 0.012 0.16 -9999 0 -0.74 23 23
CYCS 0.007 0.11 -9999 0 -0.48 6 6
RIPK1 0.014 0 -9999 0 -10000 0 0
CD247 -0.027 0.18 -9999 0 -0.88 21 21
MAP2K7 0.01 0.095 -9999 0 -0.44 4 4
protein ubiquitination 0.03 0.098 -9999 0 -0.44 2 2
CRADD 0.014 0 -9999 0 -10000 0 0
DAXX 0.014 0 -9999 0 -10000 0 0
FAS 0.011 0.037 -9999 0 -0.58 2 2
BID -0.001 0.11 -9999 0 -0.5 7 7
NF-kappa-B/RelA/I kappa B alpha -0.015 0.069 -9999 0 -0.52 1 1
TRADD 0.014 0 -9999 0 -10000 0 0
MAP3K5 0.014 0 -9999 0 -10000 0 0
CFLAR 0.014 0 -9999 0 -10000 0 0
FADD -0.081 0.26 -9999 0 -0.81 60 60
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.015 0.07 -9999 0 -0.52 1 1
MAPK8 0.014 0.098 -9999 0 -0.44 5 5
APAF1 0.012 0.026 -9999 0 -0.58 1 1
TRAF1 -0.007 0.13 -9999 0 -0.81 13 13
TRAF2 0.004 0.088 -9999 0 -0.81 6 6
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.008 0.11 -9999 0 -0.5 6 6
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.013 0.12 -9999 0 -0.46 9 9
CHUK 0.029 0.1 -9999 0 -0.48 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.053 0.15 -9999 0 -0.46 60 60
TCRz/NEF -0.048 0.17 -9999 0 -0.52 48 48
TNF -0.024 0.17 -9999 0 -0.77 25 25
FASLG -0.046 0.25 -9999 0 -0.8 47 47
NFKB1 0.012 0.025 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.025 0.11 -9999 0 -0.53 21 21
CASP6 -0.02 0.047 -9999 0 -10000 0 0
CASP7 0.037 0.12 -9999 0 -0.5 4 4
RELA 0.012 0.025 -9999 0 -10000 0 0
CASP2 0.014 0 -9999 0 -10000 0 0
CASP3 0.037 0.12 -9999 0 -0.5 4 4
TNFRSF1A 0.014 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.026 -9999 0 -0.42 2 2
CASP8 0.014 0 -9999 0 -10000 0 0
CASP9 0.014 0 -9999 0 -10000 0 0
MAP3K14 0.022 0.11 -9999 0 -0.49 4 4
APAF-1/Caspase 9 -0.04 0.1 -9999 0 -0.5 5 5
BCL2 0.016 0.11 -9999 0 -0.46 5 5
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0 0 -9999 0 -10000 0 0
TRAF2/ASK1 -0.006 0.058 -9999 0 -0.54 6 6
ATM 0.012 0.026 -9999 0 -0.58 1 1
MAP2K3 0.015 0.049 -9999 0 -0.34 1 1
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.017 0.067 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.003 0.088 -9999 0 -0.69 8 8
TXN 0.009 0 -9999 0 -10000 0 0
CALM1 0.014 0 -9999 0 -10000 0 0
GADD45A 0.012 0.036 -9999 0 -0.81 1 1
GADD45B 0.014 0 -9999 0 -10000 0 0
MAP3K1 0.014 0 -9999 0 -10000 0 0
MAP3K6 0.012 0.026 -9999 0 -0.58 1 1
MAP3K7 0.014 0 -9999 0 -10000 0 0
MAP3K4 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.001 0.018 -9999 0 -0.42 1 1
TAK1/TAB family 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 -0.008 0.061 -9999 0 -0.49 8 8
TRAF2 0.004 0.088 -9999 0 -0.81 6 6
RAC1/OSM/MEKK3/MKK3 -0.012 0.048 -9999 0 -0.42 3 3
TRAF6 0.009 0 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.16 0.27 -9999 0 -0.58 146 146
CCM2 0.001 0.1 -9999 0 -0.81 8 8
CaM/Ca2+/CAMKIIB -0.1 0.16 -9999 0 -0.36 146 146
MAPK11 0.014 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.09 0.14 -9999 0 -0.49 5 5
OSM/MEKK3 -0.01 0.076 -9999 0 -0.62 8 8
TAOK1 0.009 0.057 -9999 0 -0.35 13 13
TAOK2 0.018 0.016 -9999 0 -0.35 1 1
TAOK3 0.018 0.016 -9999 0 -0.35 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.014 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.014 0 -9999 0 -10000 0 0
MAP3K10 0.014 0 -9999 0 -10000 0 0
MAP3K3 0.014 0 -9999 0 -10000 0 0
TRX/ASK1 0.017 0 -9999 0 -10000 0 0
GADD45/MTK1/MTK1 -0.007 0.051 -9999 0 -0.46 5 5
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.012 0.036 -9999 0 -0.81 1 1
ITGB7 0.011 0.037 -9999 0 -0.58 2 2
ITGA4 -0.004 0.12 -9999 0 -0.81 11 11
alpha4/beta7 Integrin -0.015 0.092 -9999 0 -0.59 13 13
alpha4/beta1 Integrin -0.014 0.093 -9999 0 -0.62 12 12
Arf6 downstream pathway

Figure S95.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S95.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.007 0.16 -10000 0 -0.64 29 29
regulation of axonogenesis -0.02 0.037 -10000 0 -10000 0 0
myoblast fusion 0.007 0.085 0.32 29 -10000 0 29
mol:GTP -0.014 0.045 -10000 0 -0.25 3 3
regulation of calcium-dependent cell-cell adhesion -0.018 0.063 0.4 3 -10000 0 3
ARF1/GTP -0.008 0.03 -10000 0 -10000 0 0
mol:GM1 0 0.036 -10000 0 -0.19 3 3
mol:Choline 0.019 0.042 -10000 0 -0.35 3 3
lamellipodium assembly -0.025 0.078 -10000 0 -0.32 29 29
MAPK3 0.013 0.067 -10000 0 -0.3 3 3
ARF6/GTP/NME1/Tiam1 0.019 0.064 -10000 0 -0.4 3 3
ARF1 0.014 0 -10000 0 -10000 0 0
ARF6/GDP -0.008 0.085 -10000 0 -0.32 29 29
ARF1/GDP 0.003 0.079 -10000 0 -0.49 3 3
ARF6 0.005 0.026 -10000 0 -10000 0 0
RAB11A 0.014 0 -10000 0 -10000 0 0
TIAM1 0.008 0.063 -10000 0 -0.57 6 6
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.013 0.067 -10000 0 -0.3 3 3
actin filament bundle formation 0.022 0.07 0.48 3 -10000 0 3
KALRN -0.039 0.1 -10000 0 -0.33 43 43
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.023 0.07 -10000 0 -0.49 3 3
NME1 0.013 0.036 -10000 0 -0.8 1 1
Rac1/GDP -0.023 0.07 -10000 0 -0.49 3 3
substrate adhesion-dependent cell spreading -0.014 0.045 -10000 0 -0.25 3 3
cortical actin cytoskeleton organization -0.025 0.079 -10000 0 -0.32 29 29
RAC1 0.014 0 -10000 0 -10000 0 0
liver development -0.014 0.045 -10000 0 -0.25 3 3
ARF6/GTP -0.014 0.045 -10000 0 -0.25 3 3
RhoA/GTP -0.008 0.03 -10000 0 -10000 0 0
mol:GDP -0.025 0.08 -10000 0 -0.32 29 29
ARF6/GTP/RAB11FIP3/RAB11A -0.005 0.024 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
PLD1 0.009 0.048 -10000 0 -0.4 3 3
RAB11FIP3 0.014 0 -10000 0 -10000 0 0
tube morphogenesis -0.025 0.078 -10000 0 -0.32 29 29
ruffle organization 0.02 0.037 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.014 0.045 -10000 0 -0.25 3 3
PLD2 0.012 0.036 -10000 0 -10000 0 0
PIP5K1A 0.021 0.037 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.019 0.042 -10000 0 -0.35 3 3
Rac1/GTP -0.025 0.079 -10000 0 -0.32 29 29
Paxillin-dependent events mediated by a4b1

Figure S96.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S96.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.012 0.036 -10000 0 -0.81 1 1
Rac1/GDP 0.002 0.01 -10000 0 -10000 0 0
DOCK1 0.011 0.037 -10000 0 -0.58 2 2
ITGA4 -0.004 0.12 -10000 0 -0.81 11 11
RAC1 0.014 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.015 0.092 -10000 0 -0.59 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.012 0.08 -10000 0 -0.53 12 12
alpha4/beta7 Integrin/Paxillin -0.011 0.072 -10000 0 -0.48 11 11
lamellipodium assembly -0.001 0.03 -10000 0 -10000 0 0
PIK3CA 0.014 0 -10000 0 -10000 0 0
PI3K -0.002 0.026 -10000 0 -0.42 2 2
ARF6 0.014 0 -10000 0 -10000 0 0
TLN1 0.01 0.051 -10000 0 -0.81 2 2
PXN 0.024 0 -10000 0 -10000 0 0
PIK3R1 0.011 0.037 -10000 0 -0.58 2 2
ARF6/GTP -0.009 0.062 -10000 0 -0.41 12 12
cell adhesion -0.012 0.072 -10000 0 -0.45 14 14
CRKL/CBL -0.001 0.027 -10000 0 -0.62 1 1
alpha4/beta1 Integrin/Paxillin -0.011 0.073 -10000 0 -0.48 12 12
ITGB1 0.012 0.036 -10000 0 -0.81 1 1
ITGB7 0.011 0.037 -10000 0 -0.58 2 2
ARF6/GDP 0.002 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.052 0.15 -10000 0 -0.47 52 52
p130Cas/Crk/Dock1 -0.001 0.021 -10000 0 -10000 0 0
VCAM1 -0.063 0.23 -10000 0 -0.77 51 51
alpha4/beta1 Integrin/Paxillin/Talin -0.012 0.073 -10000 0 -0.45 14 14
alpha4/beta1 Integrin/Paxillin/GIT1 -0.01 0.068 -10000 0 -0.45 12 12
BCAR1 0.014 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.067 0.45 12 -10000 0 12
CBL 0.014 0 -10000 0 -10000 0 0
PRKACA 0.014 0 -10000 0 -10000 0 0
GIT1 0.014 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.012 0.073 -10000 0 -0.45 14 14
Rac1/GTP -0.001 0.033 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.004 0.084 0.71 7 -10000 0 7
PI3K Class IB/PDE3B 0.004 0.084 -10000 0 -0.71 7 7
PDE3B 0.004 0.084 -10000 0 -0.71 7 7
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.025 0.098 -10000 0 -0.42 31 31
ATM 0.012 0.026 -10000 0 -0.58 1 1
UBE2D3 0.014 0 -10000 0 -10000 0 0
PRKDC 0.014 0 -10000 0 -10000 0 0
ATR 0.014 0 -10000 0 -10000 0 0
UBE2L3 0.014 0 -10000 0 -10000 0 0
FANCD2 0.027 0.016 -10000 0 -0.34 1 1
protein ubiquitination -0.023 0.089 -10000 0 -0.53 7 7
XRCC5 0.014 0 -10000 0 -10000 0 0
XRCC6 0.014 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.014 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.005 0.04 -10000 0 -0.56 1 1
FANCF 0.009 0.052 -10000 0 -0.58 4 4
BRCA1 0.014 0 -10000 0 -10000 0 0
CCNE1 0.002 0.095 -10000 0 -0.81 7 7
CDK2/Cyclin E1 -0.008 0.071 -10000 0 -0.62 7 7
FANCG 0.007 0.072 -10000 0 -0.81 4 4
BRCA1/BACH1/BARD1 -0.025 0.098 -10000 0 -0.42 31 31
FANCE 0.014 0 -10000 0 -10000 0 0
FANCC 0.014 0 -10000 0 -10000 0 0
NBN 0.014 0 -10000 0 -10000 0 0
FANCA 0.01 0.051 -10000 0 -0.81 2 2
DNA repair 0.055 0.094 -10000 0 -0.76 2 2
BRCA1/BARD1/ubiquitin -0.025 0.098 -10000 0 -0.42 31 31
BARD1/DNA-PK -0.018 0.072 -10000 0 -10000 0 0
FANCL 0.012 0.036 -10000 0 -0.81 1 1
mRNA polyadenylation 0.025 0.098 0.41 31 -10000 0 31
BRCA1/BARD1/CTIP/M/R/N Complex 0.026 0.068 -10000 0 -0.4 1 1
BRCA1/BACH1/BARD1/TopBP1 -0.022 0.085 -10000 0 -0.53 1 1
BRCA1/BARD1/P53 -0.021 0.077 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 -0.021 0.082 -10000 0 -10000 0 0
BRCA1/BACH1 0.014 0 -10000 0 -10000 0 0
BARD1 -0.022 0.14 -10000 0 -0.58 31 31
PCNA 0.012 0.036 -10000 0 -0.81 1 1
BRCA1/BARD1/UbcH5C -0.021 0.082 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 -0.021 0.082 -10000 0 -0.34 31 31
BRCA1/BARD1/RAD51/PCNA -0.021 0.091 -10000 0 -0.86 2 2
BARD1/DNA-PK/P53 -0.019 0.07 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.025 0.098 -10000 0 -0.42 31 31
BRCA1/BARD1/CTIP -0.019 0.073 -10000 0 -10000 0 0
FA complex 0.037 0.042 -10000 0 -0.5 1 1
BARD1/EWS -0.025 0.098 -10000 0 -0.42 31 31
RBBP8 0.023 0.019 -10000 0 -0.42 1 1
TP53 0.009 0.052 -10000 0 -0.58 4 4
TOPBP1 0.012 0.036 -10000 0 -0.81 1 1
G1/S transition of mitotic cell cycle 0.02 0.076 -10000 0 -10000 0 0
BRCA1/BARD1 -0.023 0.09 -10000 0 -0.53 7 7
CSTF1 0.014 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.025 0.1 -10000 0 -0.42 31 31
CDK2 0.014 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.01 0.051 -10000 0 -0.81 2 2
RAD50 0.014 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.025 0.098 -10000 0 -0.42 31 31
EWSR1 0.014 0 -10000 0 -10000 0 0
Aurora A signaling

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.02 0.052 -9999 0 -0.53 1 1
BIRC5 -0.021 0.16 -9999 0 -0.81 22 22
NFKBIA 0.024 0.053 -9999 0 -0.53 1 1
CPEB1 -0.074 0.22 -9999 0 -0.62 71 71
AKT1 0.025 0.047 -9999 0 -10000 0 0
NDEL1 0.014 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.005 0.038 -9999 0 -10000 0 0
NDEL1/TACC3 -0.006 0.045 -9999 0 -0.46 2 2
GADD45A 0.012 0.036 -9999 0 -0.81 1 1
GSK3B 0.013 0.004 -9999 0 -10000 0 0
PAK1/Aurora A 0.02 0.052 -9999 0 -0.53 1 1
MDM2 0.014 0 -9999 0 -10000 0 0
JUB 0.012 0.026 -9999 0 -0.58 1 1
TPX2 0.012 0.088 -9999 0 -0.62 10 10
TP53 0.024 0.042 -9999 0 -0.31 4 4
DLG7 0.014 0.046 -9999 0 -0.29 11 11
AURKAIP1 0.012 0.036 -9999 0 -0.81 1 1
ARHGEF7 0.014 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.006 0.048 -9999 0 -0.48 2 2
G2/M transition of mitotic cell cycle -0.005 0.038 -9999 0 -10000 0 0
AURKA 0.017 0.055 -9999 0 -0.34 11 11
AURKB -0.007 0.042 -9999 0 -0.28 10 10
CDC25B 0.012 0.082 -9999 0 -0.34 22 22
G2/M transition checkpoint -0.005 0.044 -9999 0 -0.55 1 1
mRNA polyadenylation -0.052 0.13 -9999 0 -0.36 70 70
Aurora A/CPEB -0.053 0.13 -9999 0 -0.36 70 70
Aurora A/TACC1/TRAP/chTOG -0.005 0.038 -9999 0 -10000 0 0
BRCA1 0.014 0 -9999 0 -10000 0 0
centrosome duplication 0.02 0.052 -9999 0 -0.53 1 1
regulation of centrosome cycle -0.006 0.044 -9999 0 -0.45 2 2
spindle assembly -0.005 0.038 -9999 0 -10000 0 0
TDRD7 0.014 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.024 0.1 -9999 0 -0.49 22 22
CENPA -0.008 0.045 -9999 0 -0.37 6 6
Aurora A/PP2A 0.021 0.046 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.031 0.042 -9999 0 -10000 0 0
negative regulation of DNA binding 0.024 0.042 -9999 0 -0.31 4 4
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.011 0.037 -9999 0 -0.58 2 2
Ajuba/Aurora A -0.005 0.044 -9999 0 -0.55 1 1
mitotic prometaphase 0.001 0.009 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.055 -9999 0 -0.34 11 11
TACC1 0.011 0.037 -9999 0 -0.58 2 2
TACC3 0.01 0.051 -9999 0 -0.81 2 2
Aurora A/Antizyme1 -0.005 0.043 -9999 0 -0.48 1 1
Aurora A/RasGAP 0.019 0.051 -9999 0 -0.35 2 2
OAZ1 0.014 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0.004 -9999 0 -10000 0 0
GIT1 0.014 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.001 0.023 -9999 0 -0.53 1 1
Importin alpha/Importin beta/TPX2 0.012 0.088 -9999 0 -0.62 10 10
PPP2R5D 0.014 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.02 0.087 -9999 0 -0.53 10 10
PAK1 0.012 0.036 -9999 0 -0.81 1 1
CKAP5 0.014 0 -9999 0 -10000 0 0
HIF-2-alpha transcription factor network

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.008 0.096 -10000 0 -0.68 10 10
oxygen homeostasis -0.002 0.017 -10000 0 -10000 0 0
TCEB2 0.01 0.051 -10000 0 -0.81 2 2
TCEB1 0.012 0.036 -10000 0 -0.81 1 1
VHL/Elongin B/Elongin C/HIF2A -0.024 0.081 -10000 0 -0.59 2 2
EPO -0.048 0.28 -10000 0 -0.73 34 34
FIH (dimer) 0.011 0.016 -10000 0 -10000 0 0
APEX1 0.014 0.015 -10000 0 -10000 0 0
SERPINE1 -0.25 0.39 -10000 0 -0.83 52 52
FLT1 0.005 0.044 -10000 0 -10000 0 0
ADORA2A -0.025 0.24 -10000 0 -0.8 8 8
germ cell development -0.044 0.27 -10000 0 -0.82 21 21
SLC11A2 -0.021 0.23 -10000 0 -0.87 5 5
BHLHE40 -0.023 0.24 -10000 0 -0.88 6 6
HIF1AN 0.011 0.016 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.064 0.1 -10000 0 -0.58 2 2
ETS1 0.025 0.063 -10000 0 -0.8 3 3
CITED2 0 0.058 -10000 0 -1.2 1 1
KDR 0.002 0.087 -10000 0 -1.3 2 2
PGK1 -0.021 0.23 -10000 0 -0.87 5 5
SIRT1 0.012 0.026 -10000 0 -0.58 1 1
response to hypoxia -0.001 0.005 -10000 0 -10000 0 0
HIF2A/ARNT -0.033 0.27 -10000 0 -1 7 7
EPAS1 0.005 0.13 -10000 0 -0.44 7 7
SP1 0.022 0.003 -10000 0 -10000 0 0
ABCG2 -0.028 0.25 -10000 0 -0.84 10 10
EFNA1 -0.022 0.24 -10000 0 -0.92 5 5
FXN -0.022 0.23 -10000 0 -0.82 6 6
POU5F1 -0.048 0.28 -10000 0 -0.87 21 21
neuron apoptosis 0.032 0.26 0.96 7 -10000 0 7
EP300 0.012 0.026 -10000 0 -0.58 1 1
EGLN3 -0.039 0.2 -10000 0 -0.78 33 33
EGLN2 0.011 0.016 -10000 0 -10000 0 0
EGLN1 0.011 0.016 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.003 0.04 -10000 0 -0.53 3 3
VHL 0.014 0 -10000 0 -10000 0 0
ARNT 0.014 0.015 -10000 0 -10000 0 0
SLC2A1 -0.031 0.26 -10000 0 -0.86 14 14
TWIST1 -0.034 0.26 -10000 0 -0.85 18 18
ELK1 0.02 0.036 -10000 0 -0.8 1 1
HIF2A/ARNT/Cbp/p300 -0.053 0.096 -10000 0 -0.57 2 2
VEGFA -0.026 0.25 -10000 0 -0.92 10 10
CREBBP 0.014 0 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin -0.028 0.12 -9999 0 -0.57 25 25
AKT1 0.085 0.059 -9999 0 -0.51 2 2
PTK2B 0.031 0.12 -9999 0 -0.65 3 3
VEGFR2 homodimer/Frs2 0.031 0.067 -9999 0 -0.58 6 6
CAV1 -0.046 0.21 -9999 0 -0.81 38 38
CALM1 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.013 0.078 -9999 0 -0.5 13 13
endothelial cell proliferation 0.094 0.064 -9999 0 -0.46 2 2
mol:Ca2+ 0.051 0.069 -9999 0 -0.58 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.008 0.063 -9999 0 -0.6 2 2
RP11-342D11.1 0.042 0.069 -9999 0 -0.58 2 2
CDH5 0.011 0.044 -9999 0 -0.69 2 2
VEGFA homodimer -0.007 0.057 -9999 0 -0.48 7 7
SHC1 0.014 0 -9999 0 -10000 0 0
SHC2 0.004 0.084 -9999 0 -0.71 7 7
HRAS/GDP -0.008 0.054 -9999 0 -10000 0 0
SH2D2A -0.11 0.3 -9999 0 -0.81 81 81
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.008 0.048 -9999 0 -0.47 2 2
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.082 0.19 -9999 0 -0.49 88 88
VEGFR1 homodimer 0.012 0.036 -9999 0 -0.81 1 1
SHC/GRB2/SOS1 -0.008 0.056 -9999 0 -0.54 2 2
GRB10 0.051 0.075 -9999 0 -0.62 3 3
PTPN11 0.014 0 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
PAK1 0.012 0.036 -9999 0 -0.81 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.01 0.064 -9999 0 -0.58 2 2
HRAS 0.012 0.036 -9999 0 -0.81 1 1
VEGF/Rho/ROCK1/Integrin Complex 0.039 0.066 -9999 0 -0.5 2 2
HIF1A 0.012 0.026 -9999 0 -0.58 1 1
FRS2 0.007 0.072 -9999 0 -0.81 4 4
oxygen and reactive oxygen species metabolic process -0.008 0.062 -9999 0 -0.6 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.003 0.091 -9999 0 -0.77 7 7
Nck/Pak -0.001 0.027 -9999 0 -0.62 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.01 0.07 -9999 0 -0.64 2 2
mol:GDP -0.008 0.055 -9999 0 -0.53 2 2
mol:NADP 0.073 0.058 -9999 0 -10000 0 0
eNOS/Hsp90 0.076 0.056 -9999 0 -10000 0 0
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
mol:IP3 0.052 0.07 -9999 0 -0.58 2 2
HIF1A/ARNT -0.001 0.018 -9999 0 -0.42 1 1
SHB 0.011 0.037 -9999 0 -0.58 2 2
VEGFA 0.005 0.094 -9999 0 -0.8 7 7
VEGFC -0.1 0.29 -9999 0 -0.8 74 74
FAK1/Vinculin 0.057 0.09 -9999 0 -0.71 2 2
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.028 0.11 -9999 0 -0.69 3 3
PTPN6 0.014 0 -9999 0 -10000 0 0
EPAS1 0.023 0.023 -9999 0 -10000 0 0
mol:L-citrulline 0.073 0.058 -9999 0 -10000 0 0
ITGAV 0.006 0.076 -9999 0 -0.76 5 5
PIK3CA 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.012 0.073 -9999 0 -0.6 2 2
VEGFR2 homodimer/VEGFA homodimer -0.009 0.067 -9999 0 -0.64 2 2
VEGFR2/3 heterodimer 0.029 0.077 -9999 0 -0.57 8 8
VEGFB 0.012 0.036 -9999 0 -0.81 1 1
MAPK11 0.054 0.07 -9999 0 -0.6 2 2
VEGFR2 homodimer 0.035 0.052 -9999 0 -0.79 2 2
FLT1 0.012 0.036 -9999 0 -0.81 1 1
NEDD4 0.016 0.003 -9999 0 -10000 0 0
MAPK3 0.056 0.068 -9999 0 -0.53 2 2
MAPK1 0.056 0.068 -9999 0 -0.53 2 2
VEGFA145/NRP2 -0.011 0.08 -9999 0 -0.61 9 9
VEGFR1/2 heterodimer 0.035 0.052 -9999 0 -0.64 3 3
KDR 0.035 0.052 -9999 0 -0.8 2 2
VEGFA165/NRP1/VEGFR2 homodimer 0.048 0.074 -9999 0 -0.58 2 2
SRC 0.014 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.058 0.068 -9999 0 -0.54 2 2
PI3K -0.008 0.053 -9999 0 -0.58 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.009 0.067 -9999 0 -0.51 9 9
FES 0.052 0.071 -9999 0 -0.59 2 2
GAB1 -0.008 0.055 -9999 0 -0.6 2 2
VEGFR2 homodimer/VEGFA homodimer/Src -0.009 0.067 -9999 0 -0.51 9 9
CTNNB1 0.012 0.026 -9999 0 -0.58 1 1
SOS1 0.014 0 -9999 0 -10000 0 0
ARNT 0.014 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.047 0.12 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Yes -0.009 0.067 -9999 0 -0.51 9 9
PI3K/GAB1 0.086 0.061 -9999 0 -0.52 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.012 0.071 -9999 0 -0.58 2 2
PRKACA 0.014 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.076 0.18 -9999 0 -0.5 78 78
HSP90AA1 0.014 0 -9999 0 -10000 0 0
CDC42 0.052 0.071 -9999 0 -0.59 2 2
actin cytoskeleton reorganization -0.082 0.18 -9999 0 -0.48 88 88
PTK2 0.052 0.095 -9999 0 -0.77 2 2
EDG1 0.042 0.069 -9999 0 -0.58 2 2
mol:DAG 0.052 0.07 -9999 0 -0.58 2 2
CaM/Ca2+ -0.008 0.056 -9999 0 -0.53 2 2
MAP2K3 0.054 0.077 -9999 0 -0.56 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.05 0.077 -9999 0 -0.64 3 3
PLCG1 0.052 0.071 -9999 0 -0.59 2 2
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.009 0.065 -9999 0 -0.6 2 2
IQGAP1 0.014 0 -9999 0 -10000 0 0
YES1 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.009 0.067 -9999 0 -0.51 9 9
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.009 0.067 -9999 0 -0.51 9 9
cell migration 0.08 0.08 -9999 0 -0.59 2 2
mol:PI-3-4-5-P3 0.072 0.063 -9999 0 -0.54 2 2
FYN 0.012 0.036 -9999 0 -0.81 1 1
VEGFB/NRP1 0.047 0.069 -9999 0 -0.55 2 2
mol:NO 0.073 0.058 -9999 0 -10000 0 0
PXN 0.014 0 -9999 0 -10000 0 0
HRAS/GTP -0.008 0.053 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.051 0.077 -9999 0 -0.64 3 3
VHL 0.014 0 -9999 0 -10000 0 0
ITGB3 -0.017 0.15 -9999 0 -0.73 21 21
NOS3 0.075 0.063 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Sck -0.014 0.083 -9999 0 -0.51 13 13
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCA 0.057 0.07 -9999 0 -0.54 2 2
PRKCB 0.051 0.085 -9999 0 -0.54 2 2
VCL 0.014 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.042 0.07 -9999 0 -0.47 9 9
VEGFR1/2 heterodimer/VEGFA homodimer -0.01 0.07 -9999 0 -0.5 10 10
VEGFA165/NRP2 -0.011 0.08 -9999 0 -0.61 9 9
MAPKKK cascade 0.072 0.069 -9999 0 -0.58 1 1
NRP2 0.01 0.051 -9999 0 -0.81 2 2
VEGFC homodimer -0.1 0.28 -9999 0 -0.8 74 74
NCK1 0.014 0 -9999 0 -10000 0 0
ROCK1 0.014 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.057 0.09 -9999 0 -0.71 2 2
MAP3K13 0.047 0.079 -9999 0 -0.59 2 2
PDPK1 0.077 0.059 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.011 0.045 -9999 0 -0.58 3 3
ELF1 -0.012 0.11 -9999 0 -0.56 4 4
CCNA2 0.012 0.036 -9999 0 -0.81 1 1
PIK3CA 0.014 0 -9999 0 -10000 0 0
JAK3 -0.02 0.16 -9999 0 -0.81 22 22
PIK3R1 0.012 0.037 -9999 0 -0.58 2 2
JAK1 0.014 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.043 0.11 -9999 0 -0.58 8 8
SHC1 0.014 0 -9999 0 -10000 0 0
SP1 0.017 0.043 -9999 0 -10000 0 0
IL2RA -0.036 0.22 -9999 0 -0.71 47 47
IL2RB 0.002 0.098 -9999 0 -0.78 8 8
SOS1 0.014 0 -9999 0 -10000 0 0
IL2RG -0.012 0.14 -9999 0 -0.78 17 17
G1/S transition of mitotic cell cycle 0.032 0.089 -9999 0 -0.61 5 5
PTPN11 0.014 0 -9999 0 -10000 0 0
CCND2 0.021 0.097 -9999 0 -0.76 8 8
LCK -0.005 0.12 -9999 0 -0.81 12 12
GRB2 0.014 0 -9999 0 -10000 0 0
IL2 0.004 0.036 -9999 0 -0.81 1 1
CDK6 0.001 0.098 -9999 0 -0.78 8 8
CCND3 0.051 0.098 -9999 0 -0.59 3 3
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.048 0.11 -9999 0 -0.61 4 4
TC10/GTP -0.043 0.098 -9999 0 -0.68 1 1
Insulin Receptor/Insulin/IRS1/Shp2 -0.004 0.039 -9999 0 -0.45 2 2
HRAS 0.012 0.036 -9999 0 -0.81 1 1
APS homodimer 0.01 0.051 -9999 0 -0.81 2 2
GRB14 -0.045 0.18 -9999 0 -0.61 48 48
FOXO3 -0.007 0.042 -9999 0 -0.64 2 2
AKT1 0.022 0.098 -9999 0 -10000 0 0
INSR 0.014 0.026 -9999 0 -0.57 1 1
Insulin Receptor/Insulin 0.036 0.03 -9999 0 -0.4 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.012 0.036 -9999 0 -0.81 1 1
SORBS1 -0.084 0.22 -9999 0 -0.58 86 86
CRK 0.014 0 -9999 0 -10000 0 0
PTPN1 0.035 0.029 -9999 0 -0.39 2 2
CAV1 -0.012 0.14 -9999 0 -0.47 40 40
CBL/APS/CAP/Crk-II/C3G -0.048 0.11 -9999 0 -0.6 2 2
Insulin Receptor/Insulin/IRS1/NCK2 -0.004 0.039 -9999 0 -0.45 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.037 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.038 0.036 -9999 0 -0.5 1 1
RPS6KB1 0.029 0.092 -9999 0 -10000 0 0
PARD6A 0.011 0.044 -9999 0 -0.69 2 2
CBL 0.014 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.02 -9999 0 -0.44 1 1
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.024 0.072 -9999 0 -10000 0 0
HRAS/GTP -0.005 0.035 -9999 0 -10000 0 0
Insulin Receptor 0.014 0.026 -9999 0 -0.57 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.004 0.036 -9999 0 -10000 0 0
PRKCI -0.007 0.02 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.03 0.089 -9999 0 -0.52 2 2
SHC1 0.014 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade -0.001 0.024 -9999 0 -10000 0 0
PI3K -0.005 0.038 -9999 0 -10000 0 0
NCK2 0.014 0 -9999 0 -10000 0 0
RHOQ 0.014 0 -9999 0 -10000 0 0
mol:H2O2 0 0.003 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.027 -9999 0 -0.63 1 1
AKT2 0.022 0.098 -9999 0 -10000 0 0
PRKCZ -0.008 0.029 -9999 0 -0.48 1 1
SH2B2 0.01 0.051 -9999 0 -0.81 2 2
SHC/SHIP 0.031 0.042 -9999 0 -10000 0 0
F2RL2 -0.2 0.36 -9999 0 -0.8 137 137
TRIP10 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.002 0.031 -9999 0 -0.46 2 2
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.002 0.028 -9999 0 -0.42 2 2
RAPGEF1 0.014 0 -9999 0 -10000 0 0
RASA1 0.011 0.037 -9999 0 -0.58 2 2
NCK1 0.014 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.052 0.12 -9999 0 -0.64 2 2
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.003 0.038 -9999 0 -0.47 3 3
INPP5D 0.024 0.044 -9999 0 -0.42 2 2
SOS1 0.014 0 -9999 0 -10000 0 0
SGK1 -0.005 0.057 -9999 0 -0.91 2 2
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
IRS1 0.01 0.045 -9999 0 -0.58 3 3
p62DOK/RasGAP -0.001 0.025 -9999 0 -10000 0 0
INS 0.001 0.05 -9999 0 -0.8 2 2
mol:PI-3-4-P2 0.024 0.044 -9999 0 -0.42 2 2
GRB2 0.014 0 -9999 0 -10000 0 0
EIF4EBP1 0.022 0.11 -9999 0 -0.61 1 1
PTPRA 0.015 0.003 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.012 0.026 -9999 0 -0.58 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.033 0.03 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.004 0.04 -9999 0 -0.46 2 2
Insulin Receptor/Insulin/IRS3 -0.003 0.042 -9999 0 -0.55 3 3
Par3/Par6 -0.12 0.2 -9999 0 -0.46 136 136
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.008 0.067 -9999 0 -0.75 4 4
CDC42/GTP -0.021 0.069 -9999 0 -0.48 3 3
PLCG1 0.018 0.084 -9999 0 -0.5 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.014 0 -9999 0 -10000 0 0
GNAI3 0.014 0 -9999 0 -10000 0 0
G12/G13 -0.005 0.054 -9999 0 -0.62 4 4
cell migration -0.021 0.068 -9999 0 -0.47 3 3
S1PR5 0.008 0.062 -9999 0 -0.69 4 4
S1PR4 -0.032 0.19 -9999 0 -0.8 29 29
MAPK3 0.018 0.084 -9999 0 -0.5 3 3
MAPK1 0.018 0.084 -9999 0 -0.5 3 3
S1P/S1P5/Gi 0.024 0.059 -9999 0 -0.48 1 1
GNAI1 0.012 0.026 -9999 0 -0.58 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.008 0.062 -9999 0 -0.49 8 8
RHOA 0.003 0.12 -9999 0 -0.46 32 32
S1P/S1P4/Gi 0.009 0.088 -9999 0 -0.53 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.014 0.14 -9999 0 -0.74 19 19
S1P/S1P4/G12/G13 -0.031 0.12 -9999 0 -0.49 32 32
GNA12 0.007 0.072 -9999 0 -0.81 4 4
GNA13 0.014 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 -0.006 0.06 -9999 0 -0.55 6 6
CRKL 0.029 0.059 -9999 0 -0.43 1 1
mol:PIP3 -0.023 0.004 -9999 0 -10000 0 0
AKT1 0 0.014 -9999 0 -10000 0 0
PTK2B 0.012 0.026 -9999 0 -0.58 1 1
RAPGEF1 0.036 0.056 -9999 0 -0.4 1 1
RANBP10 0.014 0 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.023 0.097 -9999 0 -0.53 11 11
MAP3K5 0.04 0.06 -9999 0 -10000 0 0
HGF/MET/CIN85/CBL/ENDOPHILINS -0.022 0.092 -9999 0 -0.48 13 13
AP1 -0.031 0.13 -9999 0 -0.37 67 67
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.014 0 -9999 0 -10000 0 0
apoptosis -0.07 0.24 -9999 0 -0.7 67 67
STAT3 (dimer) 0.029 0.067 -9999 0 -0.48 1 1
GAB1/CRKL/SHP2/PI3K -0.01 0.045 -9999 0 -0.43 1 1
INPP5D 0.011 0.037 -9999 0 -0.58 2 2
CBL/CRK 0.036 0.053 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.014 0 -9999 0 -10000 0 0
PTEN 0.014 0 -9999 0 -10000 0 0
ELK1 -0.001 0.028 -9999 0 -0.26 6 6
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.008 0.032 -9999 0 -10000 0 0
PAK1 0.007 0.025 -9999 0 -0.47 1 1
HGF/MET/RANBP10 -0.023 0.097 -9999 0 -0.53 11 11
HRAS 0.022 0.083 -9999 0 -0.61 2 2
DOCK1 0.034 0.059 -9999 0 -0.4 1 1
GAB1 0.023 0.058 -9999 0 -0.27 3 3
CRK 0.03 0.055 -9999 0 -10000 0 0
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.022 0.094 -9999 0 -0.48 17 17
JUN 0.014 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET 0.004 0.054 -9999 0 -0.22 28 28
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
cell morphogenesis 0.058 0.072 -9999 0 -0.45 1 1
GRB2/SHC 0.02 0.048 -9999 0 -10000 0 0
FOS -0.063 0.2 -9999 0 -0.58 67 67
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.001 0.028 -9999 0 -0.25 6 6
HGF/MET/MUC20 -0.023 0.099 -9999 0 -0.43 28 28
cell migration 0.02 0.047 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
CBL 0.014 0 -9999 0 -10000 0 0
MET/RANBP10 -0.006 0.06 -9999 0 -0.55 6 6
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.023 0.07 -9999 0 -0.52 1 1
MET/MUC20 -0.006 0.061 -9999 0 -0.56 6 6
RAP1B 0.041 0.057 -9999 0 -0.38 2 2
RAP1A 0.042 0.054 -9999 0 -10000 0 0
HGF/MET/RANBP9 -0.023 0.097 -9999 0 -0.53 11 11
RAF1 0.03 0.079 -9999 0 -0.56 2 2
STAT3 0.03 0.067 -9999 0 -0.49 1 1
cell proliferation 0.039 0.083 -9999 0 -0.44 1 1
RPS6KB1 0.01 0.021 -9999 0 -10000 0 0
MAPK3 -0.007 0.026 -9999 0 -0.26 4 4
MAPK1 -0.007 0.026 -9999 0 -0.26 4 4
RANBP9 0.014 0 -9999 0 -10000 0 0
MAPK8 0.05 0.079 -9999 0 -0.46 7 7
SRC 0.03 0.066 -9999 0 -0.48 1 1
PI3K 0.019 0.053 -9999 0 -0.46 1 1
MET/Glomulin 0.007 0.056 -9999 0 -0.5 6 6
SOS1 0.014 0 -9999 0 -10000 0 0
MAP2K1 0.037 0.075 -9999 0 -0.52 2 2
MET 0.005 0.08 -9999 0 -0.73 6 6
MAP4K1 0.033 0.063 -9999 0 -10000 0 0
PTK2 0.014 0 -9999 0 -10000 0 0
MAP2K2 0.037 0.075 -9999 0 -0.52 2 2
BAD 0.007 0.013 -9999 0 -10000 0 0
MAP2K4 0.046 0.057 -9999 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 -0.011 0.048 -9999 0 -10000 0 0
INPPL1 0.014 0 -9999 0 -10000 0 0
PXN 0.014 0 -9999 0 -10000 0 0
SH3KBP1 0.01 0.051 -9999 0 -0.81 2 2
HGS 0.013 0.05 -9999 0 -10000 0 0
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.015 0.14 -9999 0 -0.65 22 22
RASA1 0.011 0.037 -9999 0 -0.58 2 2
NCK1 0.014 0 -9999 0 -10000 0 0
PTPRJ 0.014 0 -9999 0 -10000 0 0
NCK/PLCgamma1 0.021 0.052 -9999 0 -10000 0 0
PDPK1 -0.011 0.015 -9999 0 -0.34 1 1
HGF/MET/SHIP -0.024 0.1 -9999 0 -0.54 12 12
Regulation of p38-alpha and p38-beta

Figure S106.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S106.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.014 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.016 0.13 -9999 0 -0.58 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.014 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.019 0.044 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.014 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.014 0 -9999 0 -10000 0 0
FYN 0.012 0.036 -9999 0 -0.81 1 1
MAP3K12 0.011 0.044 -9999 0 -0.69 2 2
FGR 0.012 0.036 -9999 0 -0.81 1 1
p38 alpha/TAB1 -0.017 0.04 -9999 0 -10000 0 0
PRKG1 -0.024 0.15 -9999 0 -0.64 30 30
DUSP8 0.014 0 -9999 0 -10000 0 0
PGK/cGMP/p38 alpha -0.031 0.078 -9999 0 -0.39 14 14
apoptosis -0.017 0.038 -9999 0 -10000 0 0
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.012 0.036 -9999 0 -0.81 1 1
DUSP1 -0.017 0.13 -9999 0 -0.58 27 27
PAK1 0.012 0.036 -9999 0 -0.81 1 1
SRC 0.014 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.008 0.061 -9999 0 -0.48 8 8
TRAF6 0.014 0 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.001 0.1 -9999 0 -0.81 8 8
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.024 0.092 -9999 0 -0.37 4 4
BLK -0.1 0.28 -9999 0 -0.77 75 75
HCK 0.006 0.076 -9999 0 -0.76 5 5
MAP2K3 0.012 0.026 -9999 0 -0.58 1 1
DUSP16 0.014 0 -9999 0 -10000 0 0
DUSP10 0.012 0.036 -9999 0 -0.81 1 1
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.032 0.066 -9999 0 -10000 0 0
positive regulation of innate immune response 0.032 0.099 -9999 0 -0.4 1 1
LCK -0.005 0.12 -9999 0 -0.81 12 12
p38alpha-beta/MKP7 0.038 0.095 -9999 0 -10000 0 0
p38alpha-beta/MKP5 0.037 0.096 -9999 0 -10000 0 0
PGK/cGMP -0.028 0.11 -9999 0 -0.48 30 30
PAK2 0.014 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.024 0.12 -9999 0 -0.5 4 4
CDC42 0.014 0 -9999 0 -10000 0 0
RALB 0.014 0 -9999 0 -10000 0 0
RALA 0.014 0 -9999 0 -10000 0 0
PAK3 -0.018 0.15 -9999 0 -0.81 18 18
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.014 0.001 -9999 0 -10000 0 0
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.014 0.07 -9999 0 -0.53 1 1
forebrain development -0.023 0.16 -9999 0 -0.51 20 20
GNAO1 0.007 0.067 -9999 0 -0.75 4 4
SMO/beta Arrestin2 0.003 0.089 -9999 0 -0.42 21 21
SMO -0.011 0.12 -9999 0 -0.59 21 21
ARRB2 0.013 0.005 -9999 0 -10000 0 0
GLI3/SPOP 0.055 0.036 -9999 0 -10000 0 0
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0.014 0 -9999 0 -10000 0 0
GNAI2 0.013 0.005 -9999 0 -10000 0 0
SIN3/HDAC complex 0.005 0.026 -9999 0 -0.48 1 1
GNAI1 0.011 0.026 -9999 0 -0.58 1 1
XPO1 0.014 0.006 -9999 0 -10000 0 0
GLI1/Su(fu) -0.061 0.11 -9999 0 -0.52 9 9
SAP30 0.012 0.036 -9999 0 -0.81 1 1
mol:GDP -0.011 0.12 -9999 0 -0.59 21 21
MIM/GLI2A 0.012 0.025 -9999 0 -10000 0 0
IFT88 0.014 0 -9999 0 -10000 0 0
GNAI3 0.013 0.005 -9999 0 -10000 0 0
GLI2 0.023 0.066 -9999 0 -10000 0 0
GLI3 0.05 0.039 -9999 0 -10000 0 0
CSNK1D 0.014 0 -9999 0 -10000 0 0
CSNK1E 0.014 0 -9999 0 -10000 0 0
SAP18 0.014 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.014 0 -9999 0 -10000 0 0
GNG2 0.014 0 -9999 0 -10000 0 0
Gi family/GTP 0.014 0.086 -9999 0 -0.5 5 5
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.056 0.034 -9999 0 -10000 0 0
GLI2/Su(fu) 0.03 0.072 -9999 0 -10000 0 0
FOXA2 -0.094 0.23 -9999 0 -0.66 72 72
neural tube patterning -0.023 0.16 -9999 0 -0.51 20 20
SPOP 0.014 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.022 0.046 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
CSNK1G2 0.014 0 -9999 0 -10000 0 0
CSNK1G3 0.014 0 -9999 0 -10000 0 0
MTSS1 0.012 0.025 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.023 0.16 -9999 0 -0.51 20 20
SUFU 0.018 0.051 -9999 0 -0.41 1 1
LGALS3 0.011 0.037 -9999 0 -0.58 2 2
catabolic process 0.062 0.057 -9999 0 -10000 0 0
GLI3A/CBP -0.024 0.11 -9999 0 -10000 0 0
KIF3A 0.014 0 -9999 0 -10000 0 0
GLI1 -0.024 0.16 -9999 0 -0.52 20 20
RAB23 0.01 0.051 -9999 0 -0.81 2 2
CSNK1A1 0.014 0 -9999 0 -10000 0 0
IFT172 0.014 0 -9999 0 -10000 0 0
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.021 0.053 -9999 0 -0.49 1 1
GNAZ -0.015 0.14 -9999 0 -0.74 19 19
RBBP4 0.012 0.026 -9999 0 -0.57 1 1
CSNK1G1 0.014 0 -9999 0 -10000 0 0
PIAS1 0.014 0 -9999 0 -10000 0 0
PRKACA 0.014 0 -9999 0 -10000 0 0
GLI2/SPOP 0.029 0.062 -9999 0 -10000 0 0
STK36 0.014 0.006 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.022 0.076 -9999 0 -0.43 5 5
PTCH1 -0.019 0.18 -9999 0 -1 7 7
MIM/GLI1 -0.039 0.21 -9999 0 -0.68 20 20
CREBBP -0.024 0.11 -9999 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.05 0.02 -9999 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.014 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.015 0.088 -9999 0 -0.51 15 15
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.004 0.023 -9999 0 -10000 0 0
AURKB -0.002 0.11 -9999 0 -0.81 10 10
AURKC 0.003 0.088 -9999 0 -0.74 7 7
Arf6 trafficking events

Figure S109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.25 0.29 -10000 0 -0.58 233 233
CLTC 0.033 0.014 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.028 0.013 -10000 0 -10000 0 0
Dynamin 2/GTP -0.001 0.022 -10000 0 -0.49 1 1
EXOC4 0.014 0 -10000 0 -10000 0 0
CD59 0.03 0.01 -10000 0 -10000 0 0
CPE 0.013 0.06 -10000 0 -0.54 6 6
CTNNB1 0.012 0.026 -10000 0 -0.58 1 1
membrane fusion 0.027 0.014 -10000 0 -10000 0 0
CTNND1 0.033 0.021 -10000 0 -0.46 1 1
DNM2 0.014 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.034 0.009 -10000 0 -10000 0 0
TSHR 0.004 0.088 -10000 0 -0.54 13 13
INS 0.012 0.017 -10000 0 -0.25 2 2
BIN1 -0.001 0.1 -10000 0 -0.74 10 10
mol:Choline 0.027 0.014 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.025 -10000 0 -0.54 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.021 -10000 0 -0.49 1 1
JUP 0.029 0.019 -10000 0 -0.28 1 1
ASAP2/amphiphysin II -0.008 0.061 -10000 0 -0.49 7 7
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.027 0.028 -10000 0 -0.28 1 1
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.014 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.014 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.046 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.014 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.003 0.025 0.38 1 -10000 0 1
positive regulation of phagocytosis 0.02 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 0.025 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.025 0.015 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.039 0.014 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.014 0 -10000 0 -10000 0 0
exocyst 0.046 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.033 0.021 -10000 0 -0.46 1 1
NME1 0.019 0.025 -10000 0 -0.54 1 1
clathrin coat assembly 0.033 0.014 -10000 0 -10000 0 0
IL2RA 0.008 0.072 -10000 0 -10000 0 0
VAMP3 0.02 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.11 0.12 -10000 0 -0.44 2 2
EXOC6 0.014 0 -10000 0 -10000 0 0
PLD1 -0.002 0.021 -10000 0 -0.28 3 3
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.014 0 -10000 0 -10000 0 0
PIP5K1C 0.034 0.009 -10000 0 -10000 0 0
SDC1 0.03 0.01 -10000 0 -10000 0 0
ARF6/GDP 0.018 0.024 -10000 0 -0.54 1 1
EXOC7 0.014 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.003 0.025 -10000 0 -0.39 1 1
mol:Phosphatidic acid 0.027 0.014 -10000 0 -10000 0 0
endocytosis 0.008 0.061 0.49 7 -10000 0 7
SCAMP2 0.014 0 -10000 0 -10000 0 0
ADRB2 0.017 0.084 -10000 0 -0.54 1 1
EXOC3 0.014 0 -10000 0 -10000 0 0
ASAP2 0.014 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.026 0.023 -10000 0 -0.49 1 1
KLC1 0.014 0 -10000 0 -10000 0 0
AVPR2 0.024 0.068 -10000 0 -10000 0 0
RALA 0.014 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.002 0.023 -10000 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.011 0.007 -10000 0 -10000 0 0
BUB1B 0.021 0.025 -10000 0 -10000 0 0
PLK1 0.017 0.022 -10000 0 -0.16 1 1
PLK1S1 0.015 0.014 -10000 0 -0.17 1 1
KIF2A 0.024 0.019 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.017 0.022 -10000 0 -0.16 1 1
GOLGA2 0.014 0 -10000 0 -10000 0 0
Hec1/SPC24 0.011 0.1 -10000 0 -0.47 21 21
WEE1 0.021 0.027 -10000 0 -10000 0 0
cytokinesis 0.03 0.032 -10000 0 -10000 0 0
PP2A-alpha B56 0.035 0.013 -10000 0 -10000 0 0
AURKA 0.012 0.032 -10000 0 -0.18 12 12
PICH/PLK1 0.023 0.085 -10000 0 -0.38 21 21
CENPE 0.024 0.019 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.024 0.019 -10000 0 -10000 0 0
PPP2CA 0.014 0 -10000 0 -10000 0 0
FZR1 0.014 0 -10000 0 -10000 0 0
TPX2 0.012 0.029 -10000 0 -0.18 10 10
PAK1 0.011 0.036 -10000 0 -0.8 1 1
SPC24 -0.005 0.12 -10000 0 -0.81 12 12
FBXW11 0.014 0 -10000 0 -10000 0 0
CLSPN 0.012 0.032 -10000 0 -0.21 9 9
GORASP1 0.014 0 -10000 0 -10000 0 0
metaphase 0 0.001 -10000 0 -0.015 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.009 0.011 -10000 0 -0.071 1 1
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.013 12 12
STAG2 0.014 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0 0.008 -10000 0 -10000 0 0
spindle elongation 0.017 0.022 -10000 0 -0.16 1 1
ODF2 0.013 0.002 -10000 0 -10000 0 0
BUB1 -0.001 0.01 -10000 0 -10000 0 0
TPT1 0.015 0.011 -10000 0 -10000 0 0
CDC25C 0.009 0.048 -10000 0 -0.25 16 16
CDC25B -0.019 0.16 -10000 0 -0.8 21 21
SGOL1 0.011 0.007 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.017 0.077 -10000 0 -0.39 21 21
CDC14B 0.009 0.034 -10000 0 -0.43 3 3
CDC20 -0.005 0.12 -10000 0 -0.81 12 12
PLK1/PBIP1 -0.004 0.032 -10000 0 -0.48 2 2
mitosis 0.001 0.006 0.04 12 -0.022 4 16
FBXO5 0.021 0.02 -10000 0 -10000 0 0
CDC2 0.001 0.004 -10000 0 -0.017 21 21
NDC80 -0.001 0.11 -10000 0 -0.81 9 9
metaphase plate congression 0.016 0.013 -10000 0 -10000 0 0
ERCC6L -0.015 0.072 -10000 0 -0.37 21 21
NLP/gamma Tubulin 0.014 0.012 -10000 0 -10000 0 0
microtubule cytoskeleton organization 0.015 0.011 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -0.011 4 4
PPP1R12A 0.013 0.001 -10000 0 -10000 0 0
interphase 0 0.001 -10000 0 -0.011 4 4
PLK1/PRC1-2 0.03 0.018 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 -0.001 0.01 -10000 0 -10000 0 0
RAB1A 0.014 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.016 0.048 -10000 0 -0.46 4 4
mitotic prometaphase 0 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.033 -10000 0 -0.38 1 1
microtubule-based process 0.023 0.019 -10000 0 -10000 0 0
Golgi organization 0.017 0.022 -10000 0 -0.16 1 1
Cohesin/SA2 -0.002 0.013 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0.001 -10000 0 -10000 0 0
KIF20A 0.014 0 -10000 0 -10000 0 0
APC/C/CDC20 0.011 0.083 -10000 0 -0.52 12 12
PPP2R1A 0.014 0 -10000 0 -10000 0 0
chromosome segregation -0.004 0.032 -10000 0 -0.48 2 2
PRC1 0.014 0 -10000 0 -10000 0 0
ECT2 0.019 0.053 -10000 0 -0.48 5 5
C13orf34 0.017 0.046 -10000 0 -0.47 4 4
NUDC 0.016 0.013 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.021 0.025 -10000 0 -10000 0 0
spindle assembly 0.017 0.017 -10000 0 -10000 0 0
spindle stabilization 0.015 0.014 -10000 0 -0.17 1 1
APC/C/HCDH1 0.016 0.029 -10000 0 -0.36 3 3
MKLP2/PLK1 0.023 0.019 -10000 0 -10000 0 0
CCNB1 0.014 0.003 -10000 0 -10000 0 0
PPP1CB 0.013 0.001 -10000 0 -10000 0 0
BTRC 0.014 0 -10000 0 -10000 0 0
ROCK2 0.016 0.06 -10000 0 -0.42 9 9
TUBG1 0.015 0.011 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.016 0.076 -10000 0 -0.38 21 21
MLF1IP 0.01 0.04 -10000 0 -0.64 2 2
INCENP 0.013 0.001 -10000 0 -10000 0 0
ceramide signaling pathway

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.035 0.08 -10000 0 -0.41 5 5
BAG4 0.011 0.037 -10000 0 -0.58 2 2
BAD 0.029 0.029 -10000 0 -10000 0 0
NFKBIA 0.012 0.036 -10000 0 -0.81 1 1
BIRC3 -0.023 0.17 -10000 0 -0.81 23 23
BAX 0.029 0.029 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.012 0.022 -10000 0 -0.094 9 9
IKBKB 0.041 0.076 -10000 0 -10000 0 0
MAP2K2 0.041 0.031 -10000 0 -10000 0 0
MAP2K1 0.041 0.031 -10000 0 -10000 0 0
SMPD1 0.018 0.022 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.009 0.16 -10000 0 -0.61 7 7
MAP2K4 0.035 0.029 -10000 0 -10000 0 0
protein ubiquitination 0.043 0.077 -10000 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.046 0.034 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.036 0.031 -10000 0 -10000 0 0
CRADD 0.014 0 -10000 0 -10000 0 0
mol:ceramide 0.021 0.031 -10000 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin -0.001 0.024 -10000 0 -0.54 1 1
MADD 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.029 0.03 -10000 0 -10000 0 0
TRADD 0.014 0 -10000 0 -10000 0 0
RELA/p50 0.014 0 -10000 0 -10000 0 0
MAPK3 0.044 0.031 -10000 0 -10000 0 0
MAPK1 0.044 0.031 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha -0.001 0.027 -10000 0 -0.62 1 1
FADD -0.019 0.17 -10000 0 -0.43 65 65
KSR1 0.029 0.031 -10000 0 -10000 0 0
MAPK8 0.038 0.044 -10000 0 -10000 0 0
TRAF2 0.004 0.088 -10000 0 -0.81 6 6
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.041 0.076 -10000 0 -10000 0 0
TNF R/SODD -0.001 0.026 -10000 0 -0.42 2 2
TNF -0.024 0.17 -10000 0 -0.77 25 25
CYCS 0.031 0.03 0.14 4 -10000 0 4
IKBKG 0.041 0.076 -10000 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.028 0.083 -10000 0 -0.42 9 9
RELA 0.014 0 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
AIFM1 0.031 0.03 0.14 4 -10000 0 4
TNF/TNF R/SODD -0.025 0.11 -10000 0 -0.53 21 21
TNFRSF1A 0.014 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.028 0.022 -10000 0 -10000 0 0
NSMAF 0.035 0.079 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
BCL2 0.002 0.092 -10000 0 -0.68 9 9
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure S112.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S112.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.014 0 -10000 0 -10000 0 0
NFATC1 0.06 0.018 -10000 0 -10000 0 0
NFATC2 0.024 0.063 -10000 0 -0.36 5 5
NFATC3 0.025 0.019 -10000 0 -0.4 1 1
YWHAE 0.014 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.011 0.076 -10000 0 -0.38 4 4
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.036 0.098 -10000 0 -0.56 7 7
BCL2/BAX -0.009 0.067 -10000 0 -0.5 9 9
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.003 -10000 0 -10000 0 0
CaM/Ca2+ 0.012 0.002 -10000 0 -10000 0 0
BAX 0.014 0 -10000 0 -10000 0 0
MAPK14 0.014 0.002 -10000 0 -10000 0 0
BAD 0.014 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.018 0.071 -10000 0 -0.37 2 2
Calcineurin A alpha-beta B1/BCL2 0.002 0.091 -10000 0 -0.68 9 9
FKBP8 0.014 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.018 0.071 0.37 2 -10000 0 2
KPNB1 0.014 0 -10000 0 -10000 0 0
KPNA2 0.014 0 -10000 0 -10000 0 0
XPO1 0.014 0 -10000 0 -10000 0 0
SFN 0.008 0.062 -10000 0 -0.69 4 4
MAP3K8 0.01 0.045 -10000 0 -0.58 3 3
NFAT4/CK1 alpha 0 0.01 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.014 0.053 -10000 0 -10000 0 0
CABIN1 0.011 0.076 -10000 0 -0.38 4 4
CALM1 0.014 0.002 -10000 0 -10000 0 0
RAN 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.014 0 -10000 0 -10000 0 0
CAMK4 -0.025 0.17 -10000 0 -0.76 26 26
mol:Ca2+ 0.001 0.002 -10000 0 -10000 0 0
MAPK3 0.014 0 -10000 0 -10000 0 0
YWHAH 0.014 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.03 0.13 -10000 0 -0.62 25 25
YWHAB 0.014 0 -10000 0 -10000 0 0
MAPK8 0.006 0.068 -10000 0 -0.58 7 7
MAPK9 0.014 0 -10000 0 -10000 0 0
YWHAG 0.014 0 -10000 0 -10000 0 0
FKBP1A 0.014 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.001 0.019 -10000 0 -10000 0 0
PRKCH 0.014 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.001 0.018 -10000 0 -0.41 1 1
CASP3 0.014 0.002 -10000 0 -10000 0 0
PIM1 0.012 0.026 -10000 0 -0.58 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.003 0.022 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.045 0.018 -10000 0 -10000 0 0
PRKCB 0.002 0.095 -10000 0 -0.75 8 8
PRKCE 0.012 0.026 -10000 0 -0.58 1 1
JNK2/NFAT4 0.03 0.017 -10000 0 -0.35 1 1
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.014 0 -10000 0 -10000 0 0
NUP214 0.014 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.026 -10000 0 -0.58 1 1
PRKCA 0.011 0.044 -10000 0 -0.69 2 2
PRKCG -0.083 0.26 -10000 0 -0.81 59 59
PRKCQ 0 0.092 -10000 0 -0.62 11 11
FKBP38/BCL2 -0.009 0.067 -10000 0 -0.5 9 9
EP300 0.013 0.026 -10000 0 -0.58 1 1
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
NFATc/JNK1 0.061 0.038 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.021 0.003 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.025 0.11 -10000 0 -0.5 26 26
NFATc/ERK1 0.065 0.017 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.036 0.098 -10000 0 -0.5 11 11
NR4A1 0.048 0.098 -10000 0 -0.55 10 10
GSK3B 0.014 0.002 -10000 0 -10000 0 0
positive T cell selection 0.025 0.019 -10000 0 -0.39 1 1
NFAT1/CK1 alpha -0.012 0.037 -10000 0 -0.36 2 2
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.014 0 -10000 0 -10000 0 0
PRKACA 0.014 0.002 -10000 0 -10000 0 0
AKAP5 -0.026 0.18 -10000 0 -0.81 25 25
MEF2D 0.014 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.014 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.065 0.019 -10000 0 -10000 0 0
CREBBP 0.014 0.002 -10000 0 -10000 0 0
BCL2 0.002 0.092 -10000 0 -0.68 9 9
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0 0.095 -9999 0 -0.64 11 11
HRAS 0.012 0.036 -9999 0 -0.81 1 1
EGFR -0.015 0.15 -9999 0 -0.76 19 19
AKT 0.037 0.047 -9999 0 -0.41 1 1
FOXO3 0.014 0 -9999 0 -10000 0 0
AKT1 0.014 0 -9999 0 -10000 0 0
FOXO1 0.014 0 -9999 0 -10000 0 0
AKT3 -0.001 0.11 -9999 0 -0.81 9 9
FOXO4 0.011 0.037 -9999 0 -0.58 2 2
MET 0.005 0.08 -9999 0 -0.73 6 6
PIK3CA 0.014 0 -9999 0 -10000 0 0
PIK3CB 0.014 0 -9999 0 -10000 0 0
NRAS 0.014 0 -9999 0 -10000 0 0
PIK3CG -0.021 0.16 -9999 0 -0.76 23 23
PIK3R3 0.012 0.026 -9999 0 -0.58 1 1
PIK3R2 0.014 0 -9999 0 -10000 0 0
NF1 0.014 0 -9999 0 -10000 0 0
RAS 0.016 0.047 -9999 0 -0.34 1 1
ERBB2 0.009 0.062 -9999 0 -0.81 3 3
proliferation/survival/translation -0.031 0.027 -9999 0 -10000 0 0
PI3K 0.023 0.052 -9999 0 -0.26 3 3
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
KRAS 0.01 0.051 -9999 0 -0.81 2 2
FOXO 0.047 0.028 -9999 0 -10000 0 0
AKT2 0.014 0 -9999 0 -10000 0 0
PTEN 0.014 0 -9999 0 -10000 0 0
Class I PI3K signaling events

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.002 0.028 -9999 0 -10000 0 0
DAPP1 0.015 0.088 -9999 0 -0.37 3 3
Src family/SYK family/BLNK-LAT/BTK-ITK 0.002 0.16 -9999 0 -0.64 15 15
mol:DAG 0.029 0.085 -9999 0 -0.3 9 9
HRAS 0.013 0.036 -9999 0 -0.8 1 1
RAP1A 0.014 0.002 -9999 0 -10000 0 0
ARF5/GDP 0.04 0.041 -9999 0 -10000 0 0
PLCG2 0.012 0.026 -9999 0 -0.58 1 1
PLCG1 0.014 0 -9999 0 -10000 0 0
ARF5 0.014 0 -9999 0 -10000 0 0
mol:GTP -0.002 0.03 -9999 0 -10000 0 0
ARF1/GTP -0.002 0.027 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
YES1 0.014 0 -9999 0 -10000 0 0
RAP1A/GTP -0.002 0.03 -9999 0 -10000 0 0
ADAP1 -0.003 0.03 -9999 0 -10000 0 0
ARAP3 -0.002 0.03 -9999 0 -10000 0 0
INPPL1 0.014 0 -9999 0 -10000 0 0
PREX1 0.014 0 -9999 0 -10000 0 0
ARHGEF6 0.007 0.063 -9999 0 -0.58 6 6
ARHGEF7 0.014 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
NRAS 0.014 0.002 -9999 0 -10000 0 0
FYN 0.012 0.036 -9999 0 -0.81 1 1
ARF6 0.014 0 -9999 0 -10000 0 0
FGR 0.012 0.036 -9999 0 -0.81 1 1
mol:Ca2+ 0.027 0.047 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.007 0.063 -9999 0 -0.58 6 6
ZAP70 -0.024 0.17 -9999 0 -0.77 25 25
mol:IP3 0.031 0.062 -9999 0 -10000 0 0
LYN 0.012 0.036 -9999 0 -0.81 1 1
ARF1/GDP 0.04 0.041 -9999 0 -10000 0 0
RhoA/GDP -0.003 0.028 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.015 -9999 0 -10000 0 0
BLNK -0.043 0.17 -9999 0 -0.58 50 50
actin cytoskeleton reorganization 0.062 0.043 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
PLEKHA2 0.03 0.023 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
PTEN 0 0.004 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.028 -9999 0 -10000 0 0
RhoA/GTP -0.002 0.028 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.016 0.17 -9999 0 -0.7 16 16
BLK -0.1 0.28 -9999 0 -0.77 75 75
PDPK1 0.012 0.026 -9999 0 -0.58 1 1
CYTH1 -0.002 0.028 -9999 0 -10000 0 0
HCK 0.006 0.076 -9999 0 -0.76 5 5
CYTH3 -0.002 0.028 -9999 0 -10000 0 0
CYTH2 -0.002 0.028 -9999 0 -10000 0 0
KRAS 0.011 0.051 -9999 0 -0.8 2 2
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.003 0.031 -9999 0 -0.44 2 2
SGK1 -0.003 0.034 -9999 0 -0.48 2 2
INPP5D 0.011 0.037 -9999 0 -0.58 2 2
mol:GDP 0.033 0.043 -9999 0 -0.32 1 1
SOS1 0.014 0 -9999 0 -10000 0 0
SYK 0.01 0.045 -9999 0 -0.58 3 3
ARF6/GDP -0.003 0.028 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.002 0.03 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.002 0.03 -9999 0 -10000 0 0
VAV1 0.003 0.081 -9999 0 -0.6 9 9
mol:PI-3-4-P2 0.023 0.027 -9999 0 -0.42 2 2
RAS family/GTP/PI3K Class I 0.031 0.033 -9999 0 -10000 0 0
PLEKHA1 0.03 0.023 -9999 0 -10000 0 0
Rac1/GDP 0.04 0.041 -9999 0 -10000 0 0
LAT -0.009 0.13 -9999 0 -0.81 14 14
Rac1/GTP 0.034 0.056 -9999 0 -0.35 1 1
ITK -0.013 0.068 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.029 0.11 -9999 0 -0.45 9 9
LCK -0.005 0.12 -9999 0 -0.81 12 12
BTK -0.004 0.038 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation 0.049 0.037 -10000 0 -0.37 2 2
adherens junction organization 0.037 0.058 -10000 0 -0.54 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.04 0.084 -10000 0 -0.6 1 1
FMN1 0.022 0.093 -10000 0 -0.65 3 3
mol:IP3 0.041 0.036 -10000 0 -0.39 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.035 0.05 -10000 0 -0.61 2 2
CTNNB1 0.012 0.026 -10000 0 -0.58 1 1
AKT1 0.047 0.039 -10000 0 -0.42 2 2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.039 0.061 -10000 0 -0.47 7 7
CTNND1 0.015 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.042 0.046 -10000 0 -0.56 2 2
VASP 0.042 0.047 -10000 0 -0.58 2 2
ZYX 0.042 0.047 -10000 0 -0.58 2 2
JUB 0.041 0.049 -10000 0 -0.58 2 2
EGFR(dimer) 0.025 0.097 -10000 0 -0.46 17 17
E-cadherin/beta catenin-gamma catenin -0.005 0.051 -10000 0 -0.64 2 2
mol:PI-3-4-5-P3 -0.004 0.035 -10000 0 -0.45 2 2
PIK3CA 0.014 0.001 -10000 0 -10000 0 0
PI3K -0.004 0.036 -10000 0 -0.46 2 2
FYN 0.046 0.059 -10000 0 -0.57 1 1
mol:Ca2+ 0.04 0.035 -10000 0 -0.38 2 2
JUP 0.011 0.036 -10000 0 -0.57 2 2
PIK3R1 0.012 0.037 -10000 0 -0.58 2 2
mol:DAG 0.041 0.036 -10000 0 -0.39 2 2
CDH1 0.006 0.063 -10000 0 -0.57 6 6
RhoA/GDP 0.04 0.084 -10000 0 -0.6 1 1
establishment of polarity of embryonic epithelium 0.042 0.046 -10000 0 -0.56 2 2
SRC 0.014 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
EGFR -0.015 0.15 -10000 0 -0.76 19 19
CASR 0.038 0.065 -10000 0 -0.4 8 8
RhoA/GTP -0.003 0.027 -10000 0 -10000 0 0
AKT2 0.047 0.039 -10000 0 -0.42 2 2
actin cable formation 0.029 0.09 -10000 0 -0.62 3 3
apoptosis 0.004 0.033 0.41 2 -10000 0 2
CTNNA1 0.015 0.001 -10000 0 -10000 0 0
mol:GDP 0.034 0.089 -10000 0 -0.42 16 16
PIP5K1A 0.042 0.047 -10000 0 -0.58 2 2
PLCG1 -0.004 0.031 -10000 0 -0.4 2 2
Rac1/GTP -0.017 0.079 -10000 0 -0.41 17 17
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.006 0.053 -9999 0 -0.67 2 2
E-cadherin/beta catenin -0.006 0.048 -9999 0 -0.42 7 7
CTNNB1 0.012 0.026 -9999 0 -0.58 1 1
JUP 0.011 0.037 -9999 0 -0.58 2 2
CDH1 0.007 0.063 -9999 0 -0.58 6 6
Canonical NF-kappaB pathway

Figure S117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.017 0.005 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.085 0.033 -9999 0 -10000 0 0
ERC1 0.014 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.005 0.049 -9999 0 -0.5 5 5
NFKBIA 0.048 0.035 -9999 0 -0.75 1 1
BIRC2 -0.005 0.12 -9999 0 -0.81 12 12
IKBKB 0.014 0 -9999 0 -10000 0 0
RIPK2 0.014 0 -9999 0 -10000 0 0
IKBKG -0.006 0.033 -9999 0 -10000 0 0
IKK complex/A20 -0.022 0.085 -9999 0 -0.57 2 2
NEMO/A20/RIP2 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
NEMO/ATM 0.046 0.042 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.005 0.025 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 0.007 0.068 -9999 0 -0.67 5 5
NFKB1 0.017 0.005 -9999 0 -10000 0 0
RELA 0.017 0.005 -9999 0 -10000 0 0
MALT1 0.014 0 -9999 0 -10000 0 0
cIAP1/UbcH5C -0.014 0.093 -9999 0 -0.62 12 12
ATM 0.012 0.026 -9999 0 -0.58 1 1
TNF/TNFR1A -0.028 0.13 -9999 0 -0.58 25 25
TRAF6 0.014 0 -9999 0 -10000 0 0
PRKCA 0.011 0.044 -9999 0 -0.69 2 2
CHUK 0.014 0 -9999 0 -10000 0 0
UBE2D3 0.014 0 -9999 0 -10000 0 0
TNF -0.024 0.17 -9999 0 -0.77 25 25
NF kappa B1 p50/RelA -0.001 0.014 -9999 0 -10000 0 0
BCL10 0.014 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.048 0.034 -9999 0 -0.74 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.017 0.005 -9999 0 -10000 0 0
TNFRSF1A 0.014 0 -9999 0 -10000 0 0
IKK complex 0.053 0.039 -9999 0 -10000 0 0
CYLD 0.014 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.006 0.035 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0 0 -9999 0 -10000 0 0
HDAC3 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 -0.001 0.027 -9999 0 -0.62 1 1
GATA1/HDAC5 -0.001 0.027 -9999 0 -0.62 1 1
GATA2/HDAC5 -0.003 0.042 -9999 0 -0.55 3 3
HDAC5/BCL6/BCoR -0.001 0.015 -9999 0 -10000 0 0
HDAC9 -0.021 0.16 -9999 0 -0.81 22 22
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
GATA2 0.009 0.057 -9999 0 -0.73 3 3
HDAC4/RFXANK -0.001 0.027 -9999 0 -0.62 1 1
BCOR 0.012 0.026 -9999 0 -0.58 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.014 0 -9999 0 -10000 0 0
HDAC5 0.014 0 -9999 0 -10000 0 0
GNB1/GNG2 0 0 -9999 0 -10000 0 0
Histones 0.033 0.049 -9999 0 -10000 0 0
ADRBK1 0.014 0 -9999 0 -10000 0 0
HDAC4 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.014 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.014 0 -9999 0 -10000 0 0
HDAC6 0.014 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.001 0.027 -9999 0 -0.62 1 1
CAMK4 -0.025 0.17 -9999 0 -0.76 26 26
Tubulin/HDAC6 0 0 -9999 0 -10000 0 0
SUMO1 0.014 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.014 0 -9999 0 -10000 0 0
GATA1 0.009 0.036 -9999 0 -0.81 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
NR3C1 0.014 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -10000 0 0
SRF 0.014 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin 0 0 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
RANGAP1 0.014 0 -9999 0 -10000 0 0
BCL6/BCoR -0.001 0.018 -9999 0 -0.42 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.025 0.11 -9999 0 -0.53 21 21
HDAC4/ER alpha -0.027 0.12 -9999 0 -0.51 28 28
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.032 0.049 -9999 0 -10000 0 0
cell motility 0 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.014 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.014 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.024 0.16 -9999 0 -0.68 28 28
HDAC6/HDAC11 -0.001 0.018 -9999 0 -0.42 1 1
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C -0.001 0.1 -9999 0 -0.68 11 11
RAN 0.014 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.008 0.053 -9999 0 -0.45 5 5
GNG2 0.014 0 -9999 0 -10000 0 0
NCOR2 0.014 0 -9999 0 -10000 0 0
TUBB2A 0.014 0 -9999 0 -10000 0 0
HDAC11 0.012 0.026 -9999 0 -0.58 1 1
HSP90AA1 0.014 0 -9999 0 -10000 0 0
RANBP2 0.014 0 -9999 0 -10000 0 0
ANKRA2 0.014 0 -9999 0 -10000 0 0
RFXANK 0.012 0.036 -9999 0 -0.81 1 1
nuclear import -0.031 0 -9999 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.01 0.044 0.42 1 -10000 0 1
GNAI2 0.014 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.008 0.062 -10000 0 -0.49 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.008 0.067 -10000 0 -0.75 4 4
RhoA/GTP -0.01 0.045 -10000 0 -0.43 1 1
negative regulation of cAMP metabolic process 0.024 0.059 -10000 0 -0.47 1 1
GNAZ -0.014 0.14 -10000 0 -0.74 19 19
GNAI3 0.014 0 -10000 0 -10000 0 0
GNA12 0.007 0.072 -10000 0 -0.81 4 4
S1PR5 0.008 0.062 -10000 0 -0.69 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.024 0.059 -10000 0 -0.48 1 1
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
GNAI1 0.012 0.026 -10000 0 -0.58 1 1
E-cadherin signaling in the nascent adherens junction

Figure S120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.029 0.085 -9999 0 -0.43 17 17
KLHL20 -0.011 0.039 -9999 0 -0.3 2 2
CYFIP2 0.011 0.044 -9999 0 -0.69 2 2
Rac1/GDP 0.058 0.041 -9999 0 -10000 0 0
ENAH 0.037 0.063 -9999 0 -0.49 7 7
AP1M1 0.014 0 -9999 0 -10000 0 0
RAP1B 0.012 0.036 -9999 0 -0.81 1 1
RAP1A 0.014 0 -9999 0 -10000 0 0
CTNNB1 0.012 0.026 -9999 0 -0.58 1 1
CDC42/GTP -0.003 0.025 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.028 -9999 0 -0.22 2 2
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.005 0.04 -9999 0 -10000 0 0
RAPGEF1 0.051 0.051 -9999 0 -0.4 1 1
CTNND1 0.014 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.007 0.054 -9999 0 -0.47 7 7
CRK 0.045 0.054 -9999 0 -0.42 7 7
E-cadherin/gamma catenin/alpha catenin -0.005 0.051 -9999 0 -0.67 2 2
alphaE/beta7 Integrin -0.002 0.026 -9999 0 -0.42 2 2
IQGAP1 0.014 0 -9999 0 -10000 0 0
NCKAP1 0.012 0.036 -9999 0 -0.81 1 1
Rap1/GTP/I-afadin -0.001 0.022 -9999 0 -0.49 1 1
DLG1 0.037 0.058 -9999 0 -0.45 7 7
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.019 -9999 0 -10000 0 0
MLLT4 0.014 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.005 0.04 -9999 0 -0.49 1 1
PI3K -0.003 0.024 -9999 0 -10000 0 0
ARF6 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.006 0.06 -9999 0 -0.53 6 6
TIAM1 0.007 0.063 -9999 0 -0.58 6 6
E-cadherin(dimer)/Ca2+ -0.004 0.033 -9999 0 -10000 0 0
AKT1 -0.002 0.014 -9999 0 -10000 0 0
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
CDH1 0.007 0.063 -9999 0 -0.58 6 6
RhoA/GDP 0.058 0.04 -9999 0 -10000 0 0
actin cytoskeleton organization -0.008 0.029 -9999 0 -0.21 2 2
CDC42/GDP 0.058 0.04 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.022 0.042 -9999 0 -0.34 6 6
ITGB7 0.011 0.037 -9999 0 -0.58 2 2
RAC1 0.014 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.004 0.035 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin -0.004 0.034 -9999 0 -0.3 7 7
mol:GDP 0.055 0.045 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.011 0.037 -9999 0 -0.58 2 2
p120 catenin/RhoA/GDP -0.004 0.03 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
CTNNA1 0.014 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.028 0.049 -9999 0 -0.25 13 13
NME1 0.012 0.036 -9999 0 -0.81 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.037 0.058 -9999 0 -0.45 7 7
regulation of cell-cell adhesion -0.003 0.022 -9999 0 -10000 0 0
WASF2 -0.004 0.014 -9999 0 -10000 0 0
Rap1/GTP -0.004 0.029 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.005 0.047 -9999 0 -0.58 2 2
CCND1 0.032 0.06 -9999 0 -0.32 13 13
VAV2 0.039 0.077 -9999 0 -0.46 1 1
RAP1/GDP -0.001 0.031 -9999 0 -10000 0 0
adherens junction assembly 0.038 0.056 -9999 0 -0.44 7 7
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.014 0 -9999 0 -10000 0 0
PIP5K1C 0.014 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.006 0.045 -9999 0 -0.56 2 2
E-cadherin/beta catenin -0.004 0.041 -9999 0 -0.38 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.038 0.058 -9999 0 -0.45 7 7
PIK3CA 0.014 0 -9999 0 -10000 0 0
Rac1/GTP -0.017 0.062 -9999 0 -0.47 3 3
E-cadherin/beta catenin/alpha catenin -0.005 0.04 -9999 0 -0.34 7 7
ITGAE 0.014 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.007 0.056 -9999 0 -0.48 7 7
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0.014 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
CHUK 0.014 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.005 0.048 -9999 0 -0.45 6 6
NFKB1 0.014 0 -9999 0 -10000 0 0
MAP3K14 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.007 0.066 -9999 0 -0.62 6 6
RELB 0.004 0.088 -9999 0 -0.81 6 6
NFKB2 0.014 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB -0.006 0.058 -9999 0 -0.54 6 6
regulation of B cell activation -0.006 0.058 -9999 0 -0.54 6 6
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.012 0.026 -9999 0 -0.58 1 1
SMAD2 0.015 0 -9999 0 -10000 0 0
SMAD3 0.044 0.011 -9999 0 -10000 0 0
SMAD3/SMAD4 0.049 0.012 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy -0.001 0.015 -9999 0 -0.34 1 1
SMAD2/SMAD2/SMAD4 0 0.011 -9999 0 -10000 0 0
PPM1A 0.014 0 -9999 0 -10000 0 0
CALM1 0.014 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.021 0.014 -9999 0 -0.31 1 1
MAP3K1 0.014 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.015 0.078 -9999 0 -0.42 19 19
MAPK3 0.014 0 -9999 0 -10000 0 0
MAPK1 0.014 0 -9999 0 -10000 0 0
NUP214 0.014 0 -9999 0 -10000 0 0
CTDSP1 0.014 0 -9999 0 -10000 0 0
CTDSP2 0.014 0 -9999 0 -10000 0 0
CTDSPL 0.014 0 -9999 0 -10000 0 0
KPNB1 0.014 0 -9999 0 -10000 0 0
TGFBRAP1 -0.007 0.11 -9999 0 -0.58 18 18
UBE2I 0.014 0 -9999 0 -10000 0 0
NUP153 0.014 0 -9999 0 -10000 0 0
KPNA2 0.014 0 -9999 0 -10000 0 0
PIAS4 0.014 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.011 0.037 -9999 0 -0.58 2 2
PLK4 0.014 0 -9999 0 -10000 0 0
regulation of centriole replication 0.023 0.027 -9999 0 -0.42 2 2
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.078 0.087 -10000 0 -0.39 1 1
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.014 0 -10000 0 -10000 0 0
AKT2 0.014 0 -10000 0 -10000 0 0
STXBP4 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.057 0.13 0.3 6 -0.43 1 7
YWHAZ 0.014 0 -10000 0 -10000 0 0
CALM1 0.014 0 -10000 0 -10000 0 0
YWHAQ 0.014 0 -10000 0 -10000 0 0
TBC1D4 0.024 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.014 0 -10000 0 -10000 0 0
YWHAB 0.014 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0.014 0 -10000 0 -10000 0 0
ASIP -0.006 0.11 -10000 0 -0.81 10 10
PRKCI 0.014 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.014 0 -10000 0 -10000 0 0
GYS1 0.034 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.026 -10000 0 -0.58 1 1
TRIP10 0.014 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 0.048 0.02 -10000 0 -10000 0 0
VAMP2 0.014 0 -10000 0 -10000 0 0
SLC2A4 -0.063 0.14 0.3 6 -0.48 1 7
STX4 0.014 0 -10000 0 -10000 0 0
GSK3B 0.027 0 -10000 0 -10000 0 0
SFN 0.008 0.062 -10000 0 -0.69 4 4
LNPEP 0.011 0.037 -10000 0 -0.58 2 2
YWHAE 0.014 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

Figure S125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.019 0.084 -9999 0 -0.4 21 21
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.033 0.075 -9999 0 -10000 0 0
SUMO1 0.014 0 -9999 0 -10000 0 0
ZFPM1 0.014 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
FKBP3 0.014 0 -9999 0 -10000 0 0
Histones -0.008 0.036 -9999 0 -10000 0 0
YY1/LSF 0.019 0.063 -9999 0 -0.6 1 1
SMG5 0.014 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.02 0.073 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.022 0.054 -9999 0 -0.34 1 1
SAP18 0.014 0 -9999 0 -10000 0 0
RELA 0.027 0.062 -9999 0 -10000 0 0
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.014 0 -9999 0 -10000 0 0
HDAC3/TR2 0.023 0.052 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.05 0.009 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.03 0.057 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.009 0.057 -9999 0 -0.73 3 3
GATA1 0.009 0.036 -9999 0 -0.81 1 1
Mad/Max -0.004 0.04 -9999 0 -0.42 5 5
NuRD/MBD3 Complex/GATA1/Fog1 0.061 0.013 -9999 0 -10000 0 0
RBBP7 0.014 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.012 0.026 -9999 0 -0.58 1 1
MAX 0.014 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.014 0 -9999 0 -10000 0 0
NFKBIA 0.017 0.06 -9999 0 -0.38 1 1
KAT2B -0.016 0.13 -9999 0 -0.58 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.045 0.015 -9999 0 -10000 0 0
SIN3 complex -0.001 0.021 -9999 0 -0.48 1 1
SMURF1 0.014 0 -9999 0 -10000 0 0
CHD3 0.014 0 -9999 0 -10000 0 0
SAP30 0.012 0.036 -9999 0 -0.81 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.014 0 -9999 0 -10000 0 0
YY1/HDAC3 0.024 0.071 -9999 0 -0.52 1 1
YY1/HDAC2 0.019 0.063 -9999 0 -0.6 1 1
YY1/HDAC1 0.019 0.063 -9999 0 -0.6 1 1
NuRD/MBD2 Complex (MeCP1) 0.05 0.009 -9999 0 -10000 0 0
PPARG -0.13 0.16 -9999 0 -0.46 21 21
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
TNFRSF1A 0.014 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.023 0.052 -9999 0 -10000 0 0
MBD3L2 -0.002 0.05 -9999 0 -0.81 2 2
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.014 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.053 0.016 -9999 0 -10000 0 0
HDAC1 0.014 0 -9999 0 -10000 0 0
HDAC3 0.018 0.057 -9999 0 -10000 0 0
HDAC2 0.014 0 -9999 0 -10000 0 0
YY1 0.016 0.074 -9999 0 -0.68 1 1
HDAC8 0.014 0 -9999 0 -10000 0 0
SMAD7 0.014 0 -9999 0 -10000 0 0
NCOR2 0.014 0 -9999 0 -10000 0 0
MXD1 0.008 0.058 -9999 0 -0.58 5 5
STAT3 0.027 0.016 -9999 0 -0.34 1 1
NFKB1 0.014 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.014 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.011 0.05 -9999 0 -0.56 1 1
YY1/SAP30/HDAC1 -0.012 0.057 -9999 0 -0.62 2 2
EP300 0.012 0.026 -9999 0 -0.58 1 1
STAT3 (dimer non-phopshorylated) 0.027 0.016 -9999 0 -0.34 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.06 -9999 0 -0.38 1 1
histone deacetylation 0.05 0.009 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.033 0.049 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.014 0 -9999 0 -10000 0 0
GATAD2B 0.014 0 -9999 0 -10000 0 0
GATAD2A 0.014 0 -9999 0 -10000 0 0
GATA2/HDAC3 0.02 0.065 -9999 0 -0.59 2 2
GATA1/HDAC1 -0.001 0.027 -9999 0 -0.62 1 1
GATA1/HDAC3 0.016 0.057 -9999 0 -0.48 1 1
CHD4 0.014 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.028 0.13 -9999 0 -0.58 25 25
SIN3/HDAC complex/Mad/Max 0.048 0.024 -9999 0 -10000 0 0
NuRD Complex 0.059 0.01 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.008 0.036 -9999 0 -10000 0 0
SIN3B 0.014 0 -9999 0 -10000 0 0
MTA2 0.014 0 -9999 0 -10000 0 0
SIN3A 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -10000 0 0
HDAC complex -0.001 0.013 -9999 0 -10000 0 0
GATA1/Fog1 -0.001 0.027 -9999 0 -0.62 1 1
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.024 0.17 -9999 0 -0.77 25 25
negative regulation of cell growth 0.048 0.024 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.05 0.009 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.016 0.068 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.048 0.014 -9999 0 -10000 0 0
TFCP2 0.014 0 -9999 0 -10000 0 0
NR2C1 0.014 0 -9999 0 -10000 0 0
MBD3 0.014 0 -9999 0 -10000 0 0
MBD2 0.014 0 -9999 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.039 0.043 -9999 0 -0.61 2 2
PLK1 0.11 0.11 -9999 0 -0.91 2 2
CDKN1B 0.15 0.051 -9999 0 -10000 0 0
FOXO3 0.11 0.11 -9999 0 -0.89 1 1
KAT2B -0.003 0.13 -9999 0 -0.57 26 26
FOXO1/SIRT1 0.008 0.032 -9999 0 -10000 0 0
CAT 0.11 0.11 -9999 0 -0.98 2 2
CTNNB1 0.012 0.026 -9999 0 -0.58 1 1
AKT1 0.029 0.01 -9999 0 -10000 0 0
FOXO1 0.043 0.023 -9999 0 -10000 0 0
MAPK10 0.026 0.08 -9999 0 -0.45 4 4
mol:GTP 0.002 0 -9999 0 -10000 0 0
FOXO4 0.1 0.05 -9999 0 -10000 0 0
response to oxidative stress 0.017 0.011 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.002 0.075 -9999 0 -0.7 2 2
XPO1 0.014 0 -9999 0 -10000 0 0
EP300 0.014 0.026 -9999 0 -0.58 1 1
BCL2L11 0.042 0.025 -9999 0 -10000 0 0
FOXO1/SKP2 0.043 0.03 -9999 0 -0.46 1 1
mol:GDP 0.017 0.011 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
GADD45A 0.12 0.053 -9999 0 -0.48 1 1
YWHAQ 0.014 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.08 0.016 -9999 0 -10000 0 0
MST1 0.018 0.081 -9999 0 -0.72 6 6
CSNK1D 0.014 0 -9999 0 -10000 0 0
CSNK1E 0.014 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.062 0.025 -9999 0 -10000 0 0
YWHAB 0.014 0 -9999 0 -10000 0 0
MAPK8 0.041 0.038 -9999 0 -10000 0 0
MAPK9 0.045 0.005 -9999 0 -10000 0 0
YWHAG 0.014 0 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
YWHAZ 0.014 0 -9999 0 -10000 0 0
SIRT1 0.005 0.031 -9999 0 -0.57 1 1
SOD2 0.16 0.06 -9999 0 -10000 0 0
RBL2 0.12 0.077 -9999 0 -10000 0 0
RAL/GDP 0.035 0.011 -9999 0 -10000 0 0
CHUK 0.026 0.009 -9999 0 -10000 0 0
Ran/GTP 0.015 0.001 -9999 0 -10000 0 0
CSNK1G2 0.014 0 -9999 0 -10000 0 0
RAL/GTP 0.044 0.008 -9999 0 -10000 0 0
CSNK1G1 0.014 0 -9999 0 -10000 0 0
FASLG -0.025 0.27 -9999 0 -0.92 39 39
SKP2 0.012 0.036 -9999 0 -0.81 1 1
USP7 0.015 0 -9999 0 -10000 0 0
IKBKB 0.026 0.009 -9999 0 -10000 0 0
CCNB1 0.11 0.1 -9999 0 -0.79 1 1
FOXO1-3a-4/beta catenin 0.12 0.098 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.043 0.03 -9999 0 -0.46 1 1
CSNK1A1 0.014 0 -9999 0 -10000 0 0
SGK1 0.024 0.038 -9999 0 -0.56 2 2
CSNK1G3 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0.001 -9999 0 -10000 0 0
ZFAND5 0.1 0.045 -9999 0 -10000 0 0
SFN 0.008 0.062 -9999 0 -0.69 4 4
CDK2 0.014 0.004 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.076 0.034 -9999 0 -10000 0 0
CREBBP 0.014 0.004 -9999 0 -10000 0 0
FBXO32 0.11 0.14 -9999 0 -1.3 3 3
BCL6 0.12 0.077 -9999 0 -10000 0 0
RALB 0.015 0 -9999 0 -10000 0 0
RALA 0.015 0 -9999 0 -10000 0 0
YWHAH 0.014 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

Figure S127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.001 0.018 -9999 0 -0.42 1 1
FBXW11 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.022 0.049 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.04 -9999 0 -0.45 1 1
NFKBIA 0.024 0.045 -9999 0 -0.52 1 1
MAPK14 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.028 0 -9999 0 -10000 0 0
ARRB2 0.018 0 -9999 0 -10000 0 0
REL 0.003 0.077 -9999 0 -0.58 9 9
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.027 0.016 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.028 0 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.021 0 -9999 0 -10000 0 0
PIK3R1 0.011 0.037 -9999 0 -0.58 2 2
NFKB1 0.024 0 -9999 0 -10000 0 0
RELA 0.014 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.032 0.041 -9999 0 -0.41 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.048 0.039 -9999 0 -0.43 1 1
SRC 0.014 0 -9999 0 -10000 0 0
PI3K -0.002 0.026 -9999 0 -0.42 2 2
NF kappa B1 p50/RelA 0.032 0.041 -9999 0 -0.42 1 1
IKBKB 0.014 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
SYK 0.01 0.045 -9999 0 -0.58 3 3
I kappa B alpha/PIK3R1 0.029 0.047 -9999 0 -0.49 1 1
cell death 0.046 0.038 -9999 0 -0.41 1 1
NF kappa B1 p105/c-Rel 0.022 0.049 -9999 0 -10000 0 0
LCK -0.005 0.12 -9999 0 -0.81 12 12
BCL3 0.012 0.026 -9999 0 -0.58 1 1
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.014 0 -10000 0 -10000 0 0
mol:PIP3 -0.003 0.028 -10000 0 -10000 0 0
FRAP1 0.015 0.009 -10000 0 -10000 0 0
AKT1 0.028 0.028 -10000 0 -10000 0 0
INSR 0.012 0.026 -10000 0 -0.58 1 1
Insulin Receptor/Insulin -0.003 0.037 -10000 0 -0.48 3 3
mol:GTP -0.002 0.019 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.006 -10000 0 -10000 0 0
TSC2 0.013 0 -10000 0 -10000 0 0
RHEB/GDP -0.002 0.017 -10000 0 -10000 0 0
TSC1 0.014 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.015 0.031 -10000 0 -0.34 4 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.007 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.014 0 -10000 0 -10000 0 0
RPS6KB1 0.028 0.017 -10000 0 -10000 0 0
MAP3K5 0.011 0 -10000 0 -10000 0 0
PIK3R1 0.011 0.037 -10000 0 -0.58 2 2
apoptosis 0.011 0 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -0.001 3 3
EIF4B 0.034 0.016 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.001 0.011 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0.003 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.023 0.032 -10000 0 -0.3 5 5
mTOR/RHEB/GTP/Raptor/GBL 0.033 0.013 -10000 0 -10000 0 0
FKBP1A 0.014 0 -10000 0 -10000 0 0
RHEB/GTP -0.002 0.016 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 3 3
FKBP12/Rapamycin 0 0 -10000 0 -10000 0 0
PDPK1 -0.003 0.028 -10000 0 -10000 0 0
EIF4E 0.014 0 -10000 0 -10000 0 0
ASK1/PP5C 0.023 0.006 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.002 0.02 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 0.001 3 -10000 0 3
RPS6 0.014 0 -10000 0 -10000 0 0
PPP5C 0.014 0 -10000 0 -10000 0 0
EIF4G1 0.014 0 -10000 0 -10000 0 0
IRS1 0.007 0.029 -10000 0 -0.38 3 3
INS -0.003 0.05 -10000 0 -0.81 2 2
PTEN 0.013 0 -10000 0 -10000 0 0
PDK2 -0.002 0.025 -10000 0 -10000 0 0
EIF4EBP1 0.006 0.051 -10000 0 -0.38 9 9
PIK3CA 0.014 0 -10000 0 -10000 0 0
PPP2R5D 0.022 0.008 -10000 0 -10000 0 0
peptide biosynthetic process 0.016 0.035 -10000 0 -0.49 2 2
RHEB 0.014 0 -10000 0 -10000 0 0
EIF4A1 0.014 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -10000 0 0
EEF2 0.016 0.035 -10000 0 -0.49 2 2
eIF4E/4E-BP1 0.014 0.045 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.024 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -9999 0 -10000 0 0
CDKN1B 0.04 0.006 -9999 0 -10000 0 0
CDKN1A 0.04 0.006 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.014 0 -9999 0 -10000 0 0
FOXO3 0.04 0.006 -9999 0 -10000 0 0
AKT1 0 0.005 -9999 0 -10000 0 0
BAD 0.014 0 -9999 0 -10000 0 0
AKT3 0.011 0.052 -9999 0 -0.36 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.038 0.02 -9999 0 -10000 0 0
AKT1/ASK1 0 0.004 -9999 0 -10000 0 0
BAD/YWHAZ 0 0 -9999 0 -10000 0 0
RICTOR 0.014 0 -9999 0 -10000 0 0
RAF1 0.014 0 -9999 0 -10000 0 0
JNK cascade 0 0.004 -9999 0 -10000 0 0
TSC1 0.04 0.006 -9999 0 -10000 0 0
YWHAZ 0.014 0 -9999 0 -10000 0 0
AKT1/RAF1 0.039 0.006 -9999 0 -10000 0 0
EP300 0.012 0.026 -9999 0 -0.58 1 1
mol:GDP 0.033 0.006 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.04 0.006 -9999 0 -10000 0 0
YWHAQ 0.014 0 -9999 0 -10000 0 0
TBC1D4 0.025 0.014 -9999 0 -10000 0 0
MAP3K5 0.014 0 -9999 0 -10000 0 0
MAPKAP1 0.014 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.046 0.013 -9999 0 -10000 0 0
YWHAH 0.014 0 -9999 0 -10000 0 0
AKT1S1 0.04 0.006 -9999 0 -10000 0 0
CASP9 0.04 0.006 -9999 0 -10000 0 0
YWHAB 0.014 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.046 0.006 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.015 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
AKT2/p21CIP1 0 0.01 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.002 -9999 0 -10000 0 0
CHUK 0.04 0.006 -9999 0 -10000 0 0
BAD/BCL-XL 0.053 0.006 -9999 0 -10000 0 0
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.018 0.016 -9999 0 -0.35 1 1
FOXO1-3a-4/14-3-3 family 0.062 0.017 -9999 0 -10000 0 0
PDPK1 0.012 0.026 -9999 0 -0.58 1 1
MDM2 0.04 0.006 -9999 0 -10000 0 0
MAPKKK cascade -0.039 0.006 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.051 0.014 -9999 0 -10000 0 0
TSC1/TSC2 0.046 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.01 -9999 0 -10000 0 0
glucose import -0.12 0.17 -9999 0 -0.48 1 1
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.034 0.004 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.12 0.17 -9999 0 -0.48 1 1
GSK3A 0.04 0.006 -9999 0 -10000 0 0
FOXO1 0.04 0.006 -9999 0 -10000 0 0
GSK3B 0.04 0.006 -9999 0 -10000 0 0
SFN 0.008 0.062 -9999 0 -0.69 4 4
G1/S transition of mitotic cell cycle 0.046 0.006 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.05 0.019 -9999 0 -10000 0 0
PRKACA 0.014 0 -9999 0 -10000 0 0
KPNA1 0.014 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
YWHAG 0.014 0 -9999 0 -10000 0 0
RHEB 0.014 0 -9999 0 -10000 0 0
CREBBP 0.014 0 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.014 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0.032 0 -9999 0 -9999 0 0
HDAC4 0.014 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.014 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.018 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.03 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.014 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.014 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -9999 0 0
RANGAP1 0.014 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.023 0 -9999 0 -9999 0 0
Ran/GTP 0.028 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.014 0 -9999 0 -9999 0 0
UBE2I 0.014 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 0.014 0 -9999 0 -9999 0 0
PIAS1 0.014 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Arf1 pathway

Figure S131.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S131.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0.008 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.022 0 -9999 0 -10000 0 0
AP2 -0.002 0.038 -9999 0 -0.62 2 2
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0.014 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.027 0.013 -9999 0 -0.26 1 1
CD4 0.011 0.044 -9999 0 -0.69 2 2
CLTA 0.012 0.036 -9999 0 -0.81 1 1
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.029 0.01 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0 -9999 0 -10000 0 0
AP2M1 0.01 0.051 -9999 0 -0.81 2 2
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.018 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0.014 0 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.027 0.011 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0.014 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.029 0.01 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.019 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.036 0.022 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.012 0 -9999 0 -10000 0 0
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.012 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.004 0.043 -9999 0 -0.49 4 4
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 520 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.WA.A7H4 TCGA.WA.A7GZ TCGA.UP.A6WW TCGA.UF.A7JV
109_MAP3K5 0.058 0.058 0.058 0.058
47_PPARGC1A 0.014 0.014 0.014 -0.58
105_BMP4 0.014 0.014 0.014 0.014
105_BMP6 0.014 0.014 0.014 0.014
105_BMP7 0.014 0.014 0.014 0.014
105_BMP2 0.014 0.014 0.014 -0.81
131_RELN/VLDLR 0 0 0 0
30_TGFB1/TGF beta receptor Type II 0.013 0.013 0.017 0.013
84_STAT5B 0.039 0.038 -0.026 -0.022
84_STAT5A 0.039 0.038 -0.026 -0.022
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/HNSC-TP/14527301/HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
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